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| <?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d1 20130915//EN" "JATS-archivearticle1.dtd"><article article-type="research-article" dtd-version="1.1d1" xmlns:xlink="http://www.w3.org/1999/xlink"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="hwp">eLife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">03206</article-id><article-id pub-id-type="doi">10.7554/eLife.03206</article-id><article-categories><subj-group subj-group-type="display-channel"><subject>Research article</subject></subj-group><subj-group subj-group-type="heading"><subject>Biophysics and structural biology</subject></subj-group><subj-group subj-group-type="heading"><subject>Immunology</subject></subj-group></article-categories><title-group><article-title>Serum amyloid A is a retinol binding protein that transports retinol during bacterial infection</article-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes" id="author-2104"><name><surname>Derebe</surname><given-names>Mehabaw G</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="equal-contrib">†</xref><xref ref-type="other" rid="par-4"/><xref ref-type="other" rid="par-5"/><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><contrib contrib-type="author" equal-contrib="yes" id="author-13608"><name><surname>Zlatkov</surname><given-names>Clare M</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="equal-contrib">†</xref><xref ref-type="other" rid="par-7"/><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-13609"><name><surname>Gattu</surname><given-names>Sureka</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-13610"><name><surname>Ruhn</surname><given-names>Kelly A</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-13611"><name><surname>Vaishnava</surname><given-names>Shipra</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="other" rid="par-6"/><xref ref-type="fn" rid="con5"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-13613"><name><surname>Diehl</surname><given-names>Gretchen E</given-names></name><xref ref-type="aff" rid="aff2"/><xref ref-type="fn" rid="con6"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-1806"><name><surname>MacMillan</surname><given-names>John B</given-names></name><xref ref-type="aff" rid="aff3"/><xref ref-type="fn" rid="con7"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-13612"><name><surname>Williams</surname><given-names>Noelle S</given-names></name><xref ref-type="aff" rid="aff3"/><xref ref-type="fn" rid="con8"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-13514"><name><surname>Hooper</surname><given-names>Lora V</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="aff" rid="aff4"/><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="other" rid="par-3"/><xref ref-type="other" rid="par-8"/><xref ref-type="fn" rid="con9"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><aff id="aff1"><institution content-type="dept">Department of Immunology</institution>, <institution>University of Texas Southwestern Medical Center</institution>, <addr-line><named-content content-type="city">Dallas</named-content></addr-line>, <country>United States</country></aff><aff id="aff2"><institution content-type="dept">Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute</institution>, <institution>New York University School of Medicine</institution>, <addr-line><named-content content-type="city">New York</named-content></addr-line>, <country>United States</country></aff><aff id="aff3"><institution content-type="dept">Department of Biochemistry</institution>, <institution>University of Texas Southwestern Medical Center</institution>, <addr-line><named-content content-type="city">Dallas</named-content></addr-line>, <country>United States</country></aff><aff id="aff4"><institution>Howard Hughes Medical Institute, University of Texas Southwestern Medical Center</institution>, <addr-line><named-content content-type="city">Dallas</named-content></addr-line>, <country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Powrie</surname><given-names>Fiona M</given-names></name><role>Reviewing editor</role><aff><institution>Oxford University</institution>, <country>United Kingdom</country></aff></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label>For correspondence: <email>lora.hooper@utsouthwestern.edu</email></corresp><fn fn-type="con" id="equal-contrib"><label>†</label><p>These authors contributed equally to this work</p></fn></author-notes><pub-date date-type="pub" publication-format="electronic"><day>29</day><month>07</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>3</volume><elocation-id>e03206</elocation-id><history><date date-type="received"><day>30</day><month>04</month><year>2014</year></date><date date-type="accepted"><day>28</day><month>07</month><year>2014</year></date></history><permissions><copyright-statement>© 2014, Derebe et al</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Derebe et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife03206.pdf"/><abstract><object-id pub-id-type="doi">10.7554/eLife.03206.001</object-id><p>Retinol plays a vital role in the immune response to infection, yet proteins that mediate retinol transport during infection have not been identified. Serum amyloid A (SAA) proteins are strongly induced in the liver by systemic infection and in the intestine by bacterial colonization, but their exact functions remain unclear. Here we show that mouse and human SAAs are retinol binding proteins. Mouse and human SAAs bound retinol with nanomolar affinity, were associated with retinol in vivo, and limited the bacterial burden in tissues after acute infection. We determined the crystal structure of mouse SAA3 at a resolution of 2 Å, finding that it forms a tetramer with a hydrophobic binding pocket that can accommodate retinol. Our results thus identify SAAs as a family of microbe-inducible retinol binding proteins, reveal a unique protein architecture involved in retinol binding, and suggest how retinol is circulated during infection.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.001">http://dx.doi.org/10.7554/eLife.03206.001</ext-link></p></abstract><abstract abstract-type="executive-summary"><object-id pub-id-type="doi">10.7554/eLife.03206.002</object-id><title>eLife digest</title><p>Vitamins are nutrients that organisms require in order to survive and grow. If an organism is unable to synthesize a vitamin in sufficient quantities, it is essential that it obtain the vitamin through its diet instead.</p><p>Vitamin A is found in foods such as eggs, animal liver and carrots, and a diet that is lacking in this vitamin can cause blindness and an increased risk of microbial infections. Vitamin A is not a single compound, but rather a collection of compounds with similar molecular structures. One of these is retinol, which plays a vital role in the body's response to microbial infection. Retinol must bind to specific proteins to be able to move through the bloodstream and be transported around the body.</p><p>Serum retinol binding protein transports ingested retinol from the intestine to the liver and other tissues. However, during microbial infection—when retinol transport is particularly important—the amount of this protein dramatically decreases; as such it is unclear how retinol is transported when the body is under attack from pathogens.</p><p>It had been suggested that Serum Amyloid A (SAA) proteins, a family of proteins made by some liver and intestinal cells, could be involved in the response to infection, because these proteins' levels increase during infection. However, their exact functions were unknown. Derebe, Zlatkov et al. found that mice fed a diet poor in vitamin A produced fewer SAA proteins in their liver and intestinal cells. However, treating the cells with retinol or the molecule it is broken down into—called retinoic acid—caused more SAAs to be made. Derebe, Zlatkov et al. also discovered that SAAs are associated with retinol in blood samples taken from mice infected with salmonella; and that both mouse and human SAAs bind tightly to retinol. Combined, this evidence suggests that SAAs are the retinol binding proteins that transport retinol during infections.</p><p>Derebe, Zlatkov et al. went on to solve the crystal structure of a mouse SAA protein, and showed that four SAA molecules bind together to form a ‘pocket’ that can hold a retinol molecule. Future work will focus on understanding exactly how the transport of retinol by SAAs affects the development of immunity to infections.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.002">http://dx.doi.org/10.7554/eLife.03206.002</ext-link></p></abstract><kwd-group kwd-group-type="author-keywords"><title>Author keywords</title><kwd>retinol transport</kwd><kwd>serum amyloid A</kwd><kwd>acute phase response</kwd><kwd>crystal structure</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd><italic>E. coli</italic></kwd><kwd>mouse</kwd></kwd-group><funding-group><award-group id="par-1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000928</institution-id><institution>Welch Foundation</institution></institution-wrap></funding-source><award-id>I-1762</award-id><principal-award-recipient><name><surname>Hooper</surname><given-names>Lora V</given-names></name></principal-award-recipient></award-group><award-group id="par-2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000011</institution-id><institution>Howard Hughes Medical Institute</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Hooper</surname><given-names>Lora V</given-names></name></principal-award-recipient></award-group><award-group id="par-3"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health</institution></institution-wrap></funding-source><award-id>R01 DK070855</award-id><principal-award-recipient><name><surname>Hooper</surname><given-names>Lora V</given-names></name></principal-award-recipient></award-group><award-group id="par-4"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000861</institution-id><institution>Burroughs Wellcome Fund</institution></institution-wrap></funding-source><award-id>Minority Enrichment Program</award-id><principal-award-recipient><name><surname>Derebe</surname><given-names>Mehabaw G</given-names></name></principal-award-recipient></award-group><award-group id="par-5"><funding-source><institution-wrap><institution>UNCF/Merck Postdoctoral Fellowship</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Derebe</surname><given-names>Mehabaw G</given-names></name></principal-award-recipient></award-group><award-group id="par-6"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100001063</institution-id><institution>Crohn's and Colitis Foundation of America</institution></institution-wrap></funding-source><award-id>Career Development Award</award-id><principal-award-recipient><name><surname>Vaishnava</surname><given-names>Shipra</given-names></name></principal-award-recipient></award-group><award-group id="par-7"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health</institution></institution-wrap></funding-source><award-id>T32 AI005284</award-id><principal-award-recipient><name><surname>Zlatkov</surname><given-names>Clare M</given-names></name></principal-award-recipient></award-group><award-group id="par-8"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000861</institution-id><institution>Burroughs Wellcome Fund</institution></institution-wrap></funding-source><award-id>Investigators in the Pathogenesis of Infectious Diseases</award-id><principal-award-recipient><name><surname>Hooper</surname><given-names>Lora V</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta><meta-name>elife-xml-version</meta-name><meta-value>2</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>Serum amyloid A proteins bind retinol with nanomolar affinity, and do so by forming oligomers that create a hydrophobic pocket that shields retinol from the aqueous environment.</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>Retinol plays a vital role in the physiological response to microbial challenge. Retinol is derived from dietary vitamin A and can be converted enzymatically to retinoic acid, which complexes with nuclear receptors to regulate gene transcription programs in cells (<xref ref-type="bibr" rid="bib16">Germain et al., 2006</xref>). In this way, retinol promotes the maturation of innate immune cells (<xref ref-type="bibr" rid="bib21">Lawson and Berliner, 1999</xref>; <xref ref-type="bibr" rid="bib36">Stephensen, 2001</xref>; <xref ref-type="bibr" rid="bib35">Spencer et al., 2014</xref>), governs the differentiation of adaptive immune cells (<xref ref-type="bibr" rid="bib27">Mucida et al., 2007</xref>; <xref ref-type="bibr" rid="bib18">Hall et al., 2011</xref>), and facilitates the regeneration of epithelial barriers damaged by infection (<xref ref-type="bibr" rid="bib30">Osanai et al., 2007</xref>). A hallmark of vitamin A deficiency in humans is a markedly increased susceptibility to infection (<xref ref-type="bibr" rid="bib34a">Sommer 2008</xref>, <xref ref-type="bibr" rid="bib40a">Underwood, 2004</xref>), underscoring the broad impact of retinol on immunity.</p><p>As a small lipid-soluble compound, retinol cannot freely circulate but is instead transported among cells and tissues by specialized retinol binding proteins. Serum retinol binding protein (RBP) facilitates transport of retinol among the intestine, which is the site of retinol acquisition, the liver, which is the major site of retinoid storage, and other tissues that require retinol for their physiological functions (<xref ref-type="bibr" rid="bib4">Blaner, 1989</xref>). Despite the increased requirement for retinol, serum RBP is markedly reduced following microbial challenge (<xref ref-type="bibr" rid="bib34">Rosales et al., 1996</xref>), leaving open the question of how retinol is transported among tissues during infection.</p><p>Serum amyloid A (SAA) proteins are a family of proteins that are expressed in the intestinal epithelium (<xref ref-type="bibr" rid="bib13">Eckhardt et al., 2010</xref>; <xref ref-type="bibr" rid="bib32">Reigstad and Bäckhed, 2010</xref>) and liver (<xref ref-type="bibr" rid="bib40">Uhlar and Whitehead, 1999</xref>) and circulate in the serum (<xref ref-type="bibr" rid="bib45">Whitehead et al., 1992</xref>). SAA family members are encoded in the genomes of virtually all vertebrates and are highly conserved among species, suggesting essential biological functions (<xref ref-type="bibr" rid="bib39">Uhlar et al., 1994</xref>). Expression of SAAs is strongly induced by microbial exposure. SAAs are induced in intestinal epithelial cells by the microbiota (<xref ref-type="bibr" rid="bib19">Ivanov et al., 2009</xref>; <xref ref-type="bibr" rid="bib33">Reigstad et al., 2009</xref>; <xref ref-type="bibr" rid="bib13">Eckhardt et al., 2010</xref>; <xref ref-type="bibr" rid="bib32">Reigstad and Bäckhed, 2010</xref>), and have been implicated in promoting Th17 cell development in response to specific microbiota components (<xref ref-type="bibr" rid="bib19">Ivanov et al., 2009</xref>). Similarly, liver and serum SAAs are markedly elevated following systemic bacterial or viral infection (<xref ref-type="bibr" rid="bib26">Meek and Benditt, 1986</xref>; <xref ref-type="bibr" rid="bib7">Chiba et al., 2009</xref>).</p><p>Although it has been proposed that SAAs generally contribute to inflammation and immunity (<xref ref-type="bibr" rid="bib13">Eckhardt et al., 2010</xref>), the exact functions of SAAs remain poorly defined. Interestingly, SAAs have characteristics that suggest they could bind hydrophobic ligands. First, all SAAs are predicted to form amphipathic helices with a hydrophobic face that could interact with non-polar molecules (<xref ref-type="bibr" rid="bib37">Stevens, 2004</xref>). Second, SAAs circulate in the serum associated with high-density lipoprotein (HDL), which transports lipid-bound lipoproteins amongst tissues (<xref ref-type="bibr" rid="bib45">Whitehead et al., 1992</xref>). However, the identity of potential SAA ligand(s) remains unclear.</p><p>Here, we show that mouse and human SAAs are retinol binding proteins. We demonstrate that SAA expression in mice requires dietary vitamin A, that mouse and human SAAs bind tightly to retinol, and that SAA recovered from serum following bacterial infection is associated with retinol. We find that <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice, which harbor deletions of both the <italic>Saa1</italic> and <italic>Saa2</italic> genes, have higher bacterial burdens in spleen and liver following an acute bacterial infection, supporting an essential role for SAAs in the response to microbial challenge. Finally, we provide structural insight into the binding interaction by solving the mouse SAA3 crystal structure, which reveals a tetrameric assembly with a hydrophobic binding pocket that can accommodate retinol. These studies thus identify SAAs as a family of retinol binding proteins and reveal a new protein architecture supporting retinol binding. Our findings suggest that SAAs mediate retinol transport during microbial challenge and thus constitute a key component of the physiological response to infection.</p></sec><sec id="s2" sec-type="results"><title>Results</title><sec id="s2-1"><title>SAA expression requires dietary vitamin A</title><p>Initially we uncovered a relationship between SAA expression and dietary vitamin A status in mice. Microarray analysis disclosed that mice fed a vitamin A-deficient diet exhibited lower abundances of serum amyloid A (<italic>Saa</italic>) 1 and 2 transcripts in the intestine as compared to mice fed a vitamin A-replete diet (<xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>; <xref ref-type="table" rid="tbl1">Table 1</xref>). Real-time quantitative PCR and immunofluorescence analysis verified that expression of small intestinal SAA1, 2, and 3 was reduced in mice fed a vitamin A-deficient diet (<xref ref-type="fig" rid="fig1">Figure 1A,B</xref>; <xref ref-type="table" rid="tbl1">Table 1</xref>). Liver expression of SAA1 and 2 was also reduced in mice fed a vitamin A-deficient diet, although the reduction in expression was less pronounced than in the intestine (<xref ref-type="fig" rid="fig1">Figure 1C,D</xref>). This is likely because dietary vitamin A deficiency does not completely deplete stored retinoids in the liver (<xref ref-type="bibr" rid="bib22">Liu and Gudas, 2005</xref>). We also observed elevated expression of intestinal <italic>Saa1</italic> and <italic>Saa2</italic> following addition of retinol directly to the epithelial surface of small intestinal explants, and of liver <italic>Saa1</italic> and <italic>Saa2</italic> after intraperitoneal supplementation with retinoic acid (<xref ref-type="fig" rid="fig1s2">Figure 1—figure supplement 2</xref>). These findings support the idea that retinoids directly impact <italic>Saa</italic> expression. Addition of retinol or retinoic acid to cultured HepG2 cells (a human liver cell line) enhanced expression of <italic>SAA1</italic> and <italic>2</italic> in the presence of IL-1β and IL-6 (<xref ref-type="fig" rid="fig1">Figure 1E,F</xref>), suggesting that the impact of dietary vitamin A on SAA expression is due to cell-intrinsic effects of retinoids. Collectively, these results show that full expression of SAAs in the intestine and liver requires dietary vitamin A.<table-wrap id="tbl1" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.003</object-id><label>Table 1.</label><caption><p>Primers used in Q-PCR analysis</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.003">http://dx.doi.org/10.7554/eLife.03206.003</ext-link></p></caption><table frame="hsides" rules="groups"><thead><tr><th>Primer name</th><th>Primer sequence</th></tr></thead><tbody><tr><td>mouse SAA1 F</td><td>5ʹ-CATTTGTTCACGAGGCTTTCC</td></tr><tr><td>mouse SAA1 R</td><td>5ʹ-GTTTTTCCAGTTAGCTTCCTTCATGT</td></tr><tr><td>mouse SAA2 F</td><td>5ʹ-TGTGTATCCCACAAGGTTTCAGA</td></tr><tr><td>mouse SAA2 R</td><td>5ʹ-TTATTACCCTCTCCTCCTCAAGCA</td></tr><tr><td>mouse SAA3 F</td><td>5ʹ-CGCAGCACGAGCAGGAT</td></tr><tr><td>mouse SAA3 R</td><td>5ʹ-CCAGGATCAAGATGCAAAGAATG</td></tr><tr><td>human SAA1 F</td><td>5ʹ-GGCATACAGCCATACCATTC</td></tr><tr><td>human SAA1 R</td><td>5ʹ-CCTTTTGGCAGCATCATAGT</td></tr><tr><td>human SAA2 F</td><td>5ʹ-GCTTCCTCTTCACTCTGCTCT</td></tr><tr><td>human SAA2 R</td><td>5ʹ-TGCCATATCTCAGCTTCTCTG</td></tr><tr><td>mouse 18S F</td><td>5ʹ-CATTCGAACGTCTGCCCTATC</td></tr><tr><td>mouse 18S R</td><td>5ʹ-CCTGCTGCCTTCCTTGGA</td></tr><tr><td>mouse Gapdh F</td><td>5ʹ-TGGCAAAGTGGAGATTGTTGCC</td></tr><tr><td>mouse Gapdh R</td><td>5ʹ-AAGATGGTGATGGGCTTCCCG</td></tr><tr><td>human Gapdh F</td><td>5ʹ-CCTGGTCACCAGGGCTGCTTTTAAC</td></tr><tr><td>human Gapdh R</td><td>5ʹ-GTCGTTGAGGGCAATGCCAGCC</td></tr></tbody></table></table-wrap><fig-group><fig id="fig1" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.004</object-id><label>Figure 1.</label><caption><title>SAA expression requires dietary vitamin A.</title><p>(<bold>A</bold>) Mice were maintained on a normal (Vit. A+) diet or a vitamin A-deficient (Vit. A−) diet as in <xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>. Ileal <italic>Saa</italic> expression was quantified by Q-PCR (primer sequences are given in <xref ref-type="table" rid="tbl1">Table 1</xref>). N = 3–5 mice per condition. (<bold>B</bold>) Ileal sections were stained with anti-SAA antibody (‘Materials and methods’) and anti-rabbit IgG-Cy3 (red), and counterstained with DAPI (blue). Scale bar = 50 µm. (<bold>C</bold>) Q-PCR determination of <italic>Saa</italic> expression levels in livers of mice on a normal or vitamin A-deficient diet. N = 5 mice/condition. (<bold>D</bold>) Liver sections were stained with anti-SAA antibody and anti-rabbit IgG-Cy3 (red), and counterstained with DAPI (blue). Scale bars = 50 µm. (<bold>E</bold> and <bold>F</bold>) Analysis of SAA expression in HepG2 cells. Cells were cultured in retinoid-free medium and then treated with IL-1β and IL-6 and/or 1 μM retinol (<bold>E</bold>) or 100 nM retinoic acid (<bold>F</bold>). <italic>SAA</italic> expression was determined by Q-PCR. N = 3 independent experiments. Mean ± SEM is plotted. nd, not detected. *p < 0.05; **p < 0.01; ***p < 0.001. p values were determined by two-tailed Student's <italic>t</italic> test.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.004">http://dx.doi.org/10.7554/eLife.03206.004</ext-link></p></caption><graphic xlink:href="elife03206f001"/></fig><fig id="fig1s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03206.005</object-id><label>Figure 1—figure supplement 1.</label><caption><title>Intestinal <italic>Saa1</italic> and <italic>Saa2</italic> are differentially regulated by dietary vitamin A.</title><p>Affymetrix Mouse Genome 430 2.0 arrays were used to compare transcript abundance in small intestines from germ-free (gf) and conventional (cv) mice, and from mice fed a normal diet vs a vitamin A-deficient diet. Differentially expressed transcripts were identified as outlined in ‘Materials and methods’, revealing 329 differentially-expressed genes between the germ-free and conventional groups, and 138 differentially-expressed genes between the vitamin A+ and vitamin A− groups. A Venn diagram representation of the experimental results is shown at left. 19 genes were differentially expressed in both comparisons and are displayed as a heatmap in which expression level is defined by Z-score (defined in ‘Materials and methods’). <italic>Saa1</italic> and <italic>2</italic> are highlighted in blue. Other vitamin A-sensitive genes identified by this screen include granzymes A and B (gene symbols: GzmA and GzmB). There is a known role for retinoic acid in CD8<sup>+</sup> T cell differentiation (<xref ref-type="bibr" rid="bib2">Allie et al., 2013</xref>), which could explain the lowered abundance of granzyme transcripts in the vitamin A-deficient mice. Additionally, the array data reveal unexpected vitamin A-sensitive expression of three glycosyltransferases–fucosyltransferase 2 (Fut2), β1,6-N acetylglucosaminyltransferase (Gcnt1), and β1,3-galactosyltransferase 5 (B3galt5)–that participate in mucin glycan synthesis (<xref ref-type="bibr" rid="bib38">Thomsson et al., 2002</xref>; <xref ref-type="bibr" rid="bib5">Brockhausen et al., 2009</xref>).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.005">http://dx.doi.org/10.7554/eLife.03206.005</ext-link></p></caption><graphic xlink:href="elife03206fs001"/></fig><fig id="fig1s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03206.006</object-id><label>Figure 1—figure supplement 2.</label><caption><title>Retinoid supplementation stimulates <italic>Saa</italic> expression in intestine and liver.</title><p>(<bold>A</bold>) Five centimeter explants from the distal small intestine (ileum) of vitamin A-replete mice were cultured for 6 hr in the presence of 0.1% DMSO or 1 µM retinol in 0.1% DMSO. <italic>Saa</italic> transcript abundance was determined by Q-PCR. N = 6 mice/condition. (<bold>B</bold>) Vitamin A-depleted mice were treated with retinoic acid administered by intraperitoneal injection daily over the course of three days. <italic>Saa</italic> transcript abundance was determined by Q-PCR. Note that injection of DMSO vehicle alone resulted in increased <italic>Saa</italic> expression. N = 4–17 mice/condition. Mean ± SEM is plotted. *p < 0.05, **p < 0.01. p values were determined by the Mann–Whitney test in (<bold>A</bold>) and two-tailed Student's <italic>t</italic> test in (<bold>B</bold>).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.006">http://dx.doi.org/10.7554/eLife.03206.006</ext-link></p></caption><graphic xlink:href="elife03206fs002"/></fig></fig-group></p></sec><sec id="s2-2"><title>Human and mouse SAAs bind retinol</title><p>Transcriptional control by retinoids is frequently observed in proteins that function in retinoid transport and metabolism (<xref ref-type="bibr" rid="bib29">Noy, 2000</xref>). Because SAAs have predicted hydrophobic binding surfaces (<xref ref-type="bibr" rid="bib37">Stevens, 2004</xref>) and are induced by retinol, we hypothesized that they might be retinol binding proteins. We therefore tested for retinol binding activity of recombinant human SAA1 (hSAA1), mouse SAA1 (mSAA1), and mouse SAA3 (mSAA3) using fluorometric binding assays that exploit the unique spectral properties of retinol. (Note that we were unable to express recombinant mSAA2). Retinol exhibits intrinsic fluorescence that is enhanced upon binding to proteins through energy transfer from tryptophan residues, and this fluorescence change can be used to quantify binding (<xref ref-type="bibr" rid="bib8">Cogan et al., 1976</xref>) (<xref ref-type="fig" rid="fig2">Figure 2A</xref>). We did fluorometric titrations to determine apparent dissociation constants (K<sub>d</sub>s) for the all<italic>-trans</italic> isomer of retinol, and extracted K<sub>d</sub>s of 259, 169, and 145 nM for retinol binding to hSAA1, mSAA1, and mSAA3, respectively (<xref ref-type="fig" rid="fig2">Figure 2B,E</xref>). These values are similar to binding affinities calculated for human serum retinol binding protein (hRBP) (<xref ref-type="bibr" rid="bib8">Cogan et al., 1976</xref>) (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplement 1</xref>). Thus, SAAs bind retinol tightly, with affinities similar to that of a known retinol binding protein.<fig-group><fig id="fig2" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.007</object-id><label>Figure 2.</label><caption><title>Human and mouse SAAs bind retinol.</title><p>(<bold>A</bold>) Retinol exhibits intrinsic fluorescence that is enhanced upon binding to proteins through energy transfer from tryptophan residues. All-<italic>trans</italic>-retinol was titrated into mSAA3 and fluorescence emission was monitored following excitation at 348 nm. The chemical structure of retinol is shown. (<bold>B</bold>) All-<italic>trans</italic>-retinol was titrated into hSAA1, mSAA1, mSAA3, human transferrin (hTfr; negative control), and apolipoprotein A1 (ApoA1; negative control). Binding was quantified by monitoring retinol fluorescence at 460 nm following excitation at 348 nm as in (<bold>A</bold>). Plots are representative of five independent experiments. (<bold>C</bold>) Retinoic acid lacks intrinsic fluorescence, but can quench intrinsic protein fluorescence due to energy transfer from tryptophan residues (<xref ref-type="bibr" rid="bib8">Cogan et al., 1976</xref>). All-<italic>trans</italic>-retinoic acid was titrated into mSAA3 and fluorescence quenching was monitored following excitation at 296 nm. The chemical structure of retinoic acid is shown. (<bold>D</bold>) All-<italic>trans</italic>-retinoic acid was titrated into hSAA1, mSAA1, mSAA3, hTfr, and ApoA1. Fluorescence emission was monitored at 334 nm with excitation at 296 nm as in (<bold>C</bold>). Plots are representative of three independent experiments. (<bold>E</bold>) K<sub>d</sub>s were calculated from the binding assay data plotted in (<bold>B</bold>) and (<bold>D</bold>) and were derived from three independent experiments. nd, not determined. Additional ligand binding measurements are provided in <xref ref-type="fig" rid="fig2s1 fig2s2">Figure 2—figure supplements 1 and 2</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.007">http://dx.doi.org/10.7554/eLife.03206.007</ext-link></p></caption><graphic xlink:href="elife03206f002"/></fig><fig id="fig2s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03206.008</object-id><label>Figure 2—figure supplement 1.</label><caption><title>Retinol and retinoic acid binding to human retinol binding protein 4 (hRBP4).</title><p>For comparison, we calculated binding affinities of retinol and retinoic acid to hRBP4 using the fluorescence binding assays described in <xref ref-type="fig" rid="fig2">Figure 2</xref>. The results are consistent with published values (<xref ref-type="bibr" rid="bib8">Cogan et al., 1976</xref>) and are similar to the binding affinities calculated for human and mouse SAAs in <xref ref-type="fig" rid="fig2">Figure 2</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.008">http://dx.doi.org/10.7554/eLife.03206.008</ext-link></p></caption><graphic xlink:href="elife03206fs003"/></fig><fig id="fig2s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03206.009</object-id><label>Figure 2—figure supplement 2.</label><caption><title>Additional ligand binding studies on human and mouse SAAs.</title><p>(<bold>A</bold>–<bold>C</bold>) Retinyl acetate (<bold>A</bold>), β-carotene (<bold>B</bold>), and retinyl palmitate (<bold>C</bold>) were titrated into hSAA1, mSAA1, mSAA3, hTfr (negative control) and ApoA1 (negative control), and fluorescence quenching was monitored at 334 nm with excitation at 296 nm. Plots are representative of three independent experiments. The K<sub>d</sub>s are averages of the values derived from the three experiments. (<bold>D</bold>) Competitive inhibition of retinol binding by cholesterol was quantified. Saturating concentrations of retinol were added to hSAA1, mSAA1, and mSAA3, and fluorescence quenching was monitored as in (<bold>A</bold>–<bold>C</bold>). 10 μM cholesterol was added into the assay and inhibition of fluorescence quenching by retinol was monitored. Values are the average ± SEM of triplicate experiments.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.009">http://dx.doi.org/10.7554/eLife.03206.009</ext-link></p></caption><graphic xlink:href="elife03206fs004"/></fig></fig-group></p><p>Retinoic acid lacks intrinsic fluorescence but can quench inherent protein fluorescence due to energy transfer from tryptophan residues (<xref ref-type="bibr" rid="bib8">Cogan et al., 1976</xref>). We therefore measured retinoic acid binding using a modified fluorescence assay that monitored quenching of protein fluorescence (<xref ref-type="fig" rid="fig2">Figure 2C</xref>). Titration of all<italic>-trans</italic> retinoic acid yielded K<sub>d</sub>s of 268 and 224 nM for retinoic acid binding to hSAA1 and mSAA3, respectively (<xref ref-type="fig" rid="fig2">Figure 2D,E</xref>), which are similar to binding affinities calculated for human RBP binding to retinoic acid (<xref ref-type="bibr" rid="bib8">Cogan et al., 1976</xref>) (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplement 1</xref>). There was weak binding of retinoic acid to mSAA1 and we were unable to calculate a K<sub>d</sub> for the interaction (<xref ref-type="fig" rid="fig2">Figure 2D,E</xref>). Thus, while hSAA1 and mSAA3 bind both retinol and retinoic acid, mSAA1 selectively binds retinol. mSAA1 also showed weak binding to other retinoids, including β-carotene and retinyl acetate, while hSAA1 bound these compounds with K<sub>d</sub>s of 497 and 347 nM, respectively, and mSAA3 bound β-carotene with a K<sub>d</sub> of 159 nM (<xref ref-type="fig" rid="fig2s2">Figure 2—figure supplement 2A,B</xref>). All SAA isoforms bound weakly to retinyl palmitate (<xref ref-type="fig" rid="fig2s2">Figure 2—figure supplement 2C</xref>). Since long chain retinyl esters (such as retinyl palmitate) are the major form of stored retinoid in the liver (<xref ref-type="bibr" rid="bib42">Vogel et al., 1999</xref>), this suggests that SAAs do not transport retinoids for storage. Although a role for SAAs in cholesterol transport and metabolism has been proposed (<xref ref-type="bibr" rid="bib41">van der Westhuyzen et al., 2005</xref>), we found that cholesterol was unable to competitively inhibit retinol binding to SAAs (<xref ref-type="fig" rid="fig2s2">Figure 2—figure supplement 2D</xref>).</p><p>To test whether SAAs also associate with retinol in vivo, we sought to purify SAAs from mouse tissues and assay for the presence of associated retinol. SAAs were difficult to purify from the mouse intestine due to the presence of large amounts of contaminating protein, even under conditions where expression of SAAs was maximally induced. However, SAAs constitute a high proportion of serum protein during acute systemic infection (<xref ref-type="bibr" rid="bib24">McAdam and Sipe, 1976</xref>; <xref ref-type="bibr" rid="bib48">Zhang et al., 2005</xref>). We were therefore able to use size exclusion chromatography to recover a SAA-enriched fraction from the sera of mice infected intraperitoneally with <italic>Salmonella typhimurium</italic> for 24 hr (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1A–C</xref>). Mass spectrometry revealed that the SAA-enriched protein fraction was devoid of other known retinol binding proteins (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1D</xref>). Liquid chromatography tandem mass spectrometry (LC-MS/MS) indicated the presence of retinol in the SAA-enriched fraction (<xref ref-type="fig" rid="fig3">Figure 3</xref>, <xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2A–C</xref>) in a molar ratio of ∼1 mol retinol/4 mol SAA (<xref ref-type="fig" rid="fig3">Figure 3</xref>, inset). In these analyses, retinoic acid was not detected, and retinol was not detected in the equivalent serum fraction recovered from <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice (<xref ref-type="bibr" rid="bib13">Eckhardt et al., 2010</xref>) (<xref ref-type="fig" rid="fig3">Figure 3</xref>), suggesting that the retinol was preferentially associated with SAA.<fig-group><fig id="fig3" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.010</object-id><label>Figure 3.</label><caption><title>Serum SAA is associated with retinol in vivo.</title><p>Wild-type or <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice were infected intraperitoneally with <italic>S. typhimurium</italic> and serum was collected 24 hr later. The serum was fractionated by size exclusion chromatography and a major SAA-containing fraction from wild-type mice was identified by Western blot (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>). The SAA-containing fraction and the equivalent serum fraction from <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice were hexane-extracted and analyzed by LC-MS/MS against retinol and retinoic acid standards. Additional support for the identification of retinol is provided in <xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref>. The LC-MS/MS chromatograms of daughter ion 93 are shown. mol SAA/mol retinol is shown in the inset. Data are representative of duplicate experiments with triplicate samples in each experiment.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.010">http://dx.doi.org/10.7554/eLife.03206.010</ext-link></p></caption><graphic xlink:href="elife03206f003"/></fig><fig id="fig3s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03206.011</object-id><label>Figure 3—figure supplement 1.</label><caption><title>Size-exclusion chromatography and mass spectrometry analysis of SAA-containing serum fractions.</title><p>(<bold>A</bold>) Wild-type and <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice were challenged intraperitoneally with S. typhimurium and serum was collected 24 hr later. The serum was concentrated and the proteins were fractionated into two major peaks by size exclusion chromatography on a Superdex 75 HiLoad 16/60 column. (<bold>B</bold>) SAA was detected in peak 1 by Western blot. (<bold>C</bold>) SDS-PAGE and Western blot analysis of serum peak 1. SDS-PAGE reveals four major protein bands that correspond to SAA bands as determined by Western blot. (<bold>D</bold>) Mass spectrometry analysis was performed to identify other proteins in serum peak 1. No other retinoid binding proteins were detected in the peak.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.011">http://dx.doi.org/10.7554/eLife.03206.011</ext-link></p></caption><graphic xlink:href="elife03206fs005"/></fig><fig id="fig3s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03206.012</object-id><label>Figure 3—figure supplement 2.</label><caption><title>Mouse SAA is associated with retinol in the serum following infection.</title><p>(<bold>A</bold>–<bold>C</bold>) Wild-type mice were infected by intraperitoneal delivery of <italic>S. typhimurium</italic> and serum was collected and processed for retinoids as described in ‘Materials and methods’. (<bold>A</bold>) LC-MS profiles of retinol standard and the SAA-enriched fraction from wild-type mouse serum, prepared as described in <xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>. The retinol peaks were further analyzed by spectroscopy and display maxima at 325 nm, which is characteristic of retinol. (<bold>B</bold> and <bold>C</bold>) Retinoids were extracted from unprocessed serum (<bold>B</bold>) or from the SAA-enriched serum fraction (<bold>C</bold>) of <italic>S. typhimurium</italic> infected wild-type mice and analyzed by LC-MS/MS. Retinol was detected by analyzing two daughter ions (93, 119). The inset in the top left panel shows the derivation of the daughter ions from the parent retinol. We noted a modest decrease in the elution time of retinol between the experiments shown in (<bold>B</bold>) and (<bold>C</bold>); however, this difference was observed in both the experimental sample and the retinol standard.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.012">http://dx.doi.org/10.7554/eLife.03206.012</ext-link></p></caption><graphic xlink:href="elife03206fs006"/></fig></fig-group></p></sec><sec id="s2-3"><title>Mouse SAA3 forms a tetramer with a hydrophobic central channel</title><p>SAAs lack sequence homology to the two known families of retinol binding proteins: cellular retinol binding proteins (CRBP) and serum retinol binding proteins (RBP) (<xref ref-type="bibr" rid="bib4">Blaner, 1989</xref>; <xref ref-type="bibr" rid="bib29">Noy, 2000</xref>). Thus, the three-dimensional structures of CRBP and RBP proteins (<xref ref-type="bibr" rid="bib28">Newcomer et al., 1984</xref>; <xref ref-type="bibr" rid="bib9">Cowan et al., 1993</xref>) provide no direct insight into the structural basis for retinol binding by SAAs. To understand how SAAs bind retinol, we therefore determined the three-dimensional structure of recombinant mSAA3 by X-ray crystallography. The protein was crystallized in a P6<sub>2</sub> space group with two subunits in the asymmetric unit, and the structure was determined to a resolution of 2 Å by single-wavelength anomalous dispersion (SAD) phasing using a selenomethionyl-derivatived crystal (<xref ref-type="fig" rid="fig4">Figure 4A</xref>; <xref ref-type="table" rid="tbl2">Table 2</xref>). The crystal structure reveals that mSAA3 is highly α-helical (<xref ref-type="fig" rid="fig4">Figure 4A</xref>), as predicted on the basis of its primary sequence (<xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>) (<xref ref-type="bibr" rid="bib37">Stevens, 2004</xref>). The structure is very similar to the recently determined structure of human SAA1.1 (<xref ref-type="bibr" rid="bib23">Lu et al., 2014</xref>), an isoform that has a marked tendency to form pathogenic amyloid fibrils (<xref ref-type="bibr" rid="bib47">Yu et al., 2000</xref>). Like the SAA1.1 structure, the mSAA3 structure consists of four α-helices, designated α1-4 from the N- to the C-termini, forming a cone-shaped four-helix bundle with a comparatively longer α1. The helices form two sets of antiparallel helices, α1-α2 and α3-α4, connected by a very short loop (<xref ref-type="fig" rid="fig4">Figure 4A</xref>). The monomer is stabilized by an extensive network of hydrogen bonding interactions among conserved residues and water molecules in the interior of the monomer. As in the SAA1.1 structure, the C-terminal tail wraps around the helix bundle making a number of hydrogen bonding interactions that add to monomer stability, underscoring the importance of the C-terminal tail.<fig-group><fig id="fig4" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.013</object-id><label>Figure 4.</label><caption><title>Structure of mSAA3 and molecular contacts within the tetrameric unit.</title><p>(<bold>A</bold>) Structure of the mSAA3 monomer (side view), with helices and termini labeled. (<bold>B</bold>) Top view of the tetrameric mSAA3 structure. Chains forming dimer pairs are colored cyan and magenta. In (<bold>C</bold>), helices α1-4 and the N- and C-termini of two monomers are labeled. Residues that make dimer contacts are shown as green sticks while residues involved in tetramer stabilization are shown as yellow sticks. (<bold>D</bold> and <bold>E</bold>) Magnified regions of a dimer interface (<bold>D</bold>) and tetramer interface (<bold>E</bold>) are shown. Views are slightly rotated so that the interactions can be clearly visualized. Crystal structure data collection and refinement statistics are provided in <xref ref-type="table" rid="tbl2">Table 2</xref>; alignments of mouse and human SAAs are shown in <xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>; parameters from the protein Interfaces, Surfaces, and Assemblies (PISA) analysis showing a tetrameric state are provided in <xref ref-type="table" rid="tbl3">Table 3</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.013">http://dx.doi.org/10.7554/eLife.03206.013</ext-link></p></caption><graphic xlink:href="elife03206f004"/></fig><fig id="fig4s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03206.014</object-id><label>Figure 4—figure supplement 1.</label><caption><title>Sequence alignment of mouse and human SAAs.</title><p>Secondary structure is based on the mSAA3 crystal structure and is indicated above the sequence. α-helices are shown as solid red bars while loops and non-helical secondary structure are marked as solid black lines.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.014">http://dx.doi.org/10.7554/eLife.03206.014</ext-link></p></caption><graphic xlink:href="elife03206fs007"/></fig></fig-group><table-wrap id="tbl2" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.015</object-id><label>Table 2.</label><caption><p>Crystal structure data collection and refinement statistics</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.015">http://dx.doi.org/10.7554/eLife.03206.015</ext-link></p></caption><table frame="hsides" rules="groups"><tbody><tr><td colspan="2">Data collection</td></tr><tr><td> Space group</td><td>P6<sub>2</sub></td></tr><tr><td rowspan="2"> Cell dimensions (Å)</td><td>a = b = 78.33, c = 62.32</td></tr><tr><td>α = β = 90<sup>o</sup>, γ = 120<sup>o</sup></td></tr><tr><td> Wavelength (Å)</td><td>0.9794</td></tr><tr><td> R<sub>sym</sub> or R<sub>merge</sub> (%)</td><td>8.4</td></tr><tr><td> Resolution (Å)<xref ref-type="table-fn" rid="tblfn1">*</xref></td><td>50–2.05 (2.09–2.05)</td></tr><tr><td> I/σI</td><td>19.19 (3.23)</td></tr><tr><td> Completeness (%)</td><td>99.8 (97.3)</td></tr><tr><td> Redundancy</td><td>6.2 (5.4)</td></tr><tr><td colspan="2">Refinement</td></tr><tr><td> No. reflections</td><td>12,206</td></tr><tr><td> Resolution (Å)<xref ref-type="table-fn" rid="tblfn1">*</xref></td><td>39.17–2.06 (2.14–2.06)</td></tr><tr><td> R<sub>work</sub>/R<sub>free</sub></td><td>0.17/0.21 (0.16/0.19)</td></tr><tr><td> No. atoms</td><td/></tr><tr><td> Protein</td><td>1608</td></tr><tr><td> Ligand/ion</td><td>3</td></tr><tr><td> Water</td><td>61</td></tr><tr><td> R.m.s. deviations</td><td/></tr><tr><td> Bond lengths (Å)</td><td>0.0077</td></tr><tr><td> Bond angles (°)</td><td>0.932</td></tr></tbody></table><table-wrap-foot><fn id="tblfn1"><label>*</label><p>Highest resolution shell is shown in parenthesis.</p></fn></table-wrap-foot></table-wrap></p><p>Size exclusion chromatography and cross-linking experiments showed that mSAA3 forms a tetramer in solution (<xref ref-type="fig" rid="fig5">Figure 5A,B</xref>). Consistent with these findings, analysis of the mSAA3 crystal structure using the Protein Interfaces, Surfaces and Assemblies (PDBePISA) server (<ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/msd-srv/prot_int/">http://www.ebi.ac.uk/msd-srv/prot_int/</ext-link>) yielded a tetrameric quaternary structure (<xref ref-type="fig" rid="fig4">Figure 4B</xref>; <xref ref-type="table" rid="tbl3">Table 3</xref>). This is in contrast to the hexameric structure derived for SAA1.1 (<xref ref-type="bibr" rid="bib23">Lu et al., 2014</xref>). There are several potential reasons for the discrepancy in the oligomeric structures. First, it has been suggested that different SAAs can adopt different oligomeric states (<xref ref-type="bibr" rid="bib43">Wang et al., 2002</xref>, <xref ref-type="bibr" rid="bib44">2011</xref>). SAA1.1 was also observed to produce a ∼43 kDa species in solution (<xref ref-type="bibr" rid="bib23">Lu et al., 2014</xref>), suggesting that SAA1.1 may in part adopt a tetrameric state. Second, SAA1.1 has a more hydrophobic N-terminus than mSAA3, which is thought to be a determinant of amyloidogenicity (<xref ref-type="bibr" rid="bib47">Yu et al., 2000</xref>; <xref ref-type="bibr" rid="bib23">Lu et al., 2014</xref>). Third, the crystallized SAA1.1 protein retained the hexa-histidine tag (<xref ref-type="bibr" rid="bib23">Lu et al., 2014</xref>), which may have contributed to the difference in oligomeric state.<fig id="fig5" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.016</object-id><label>Figure 5.</label><caption><title>Mouse SAA3 is tetrameric in solution.</title><p>(<bold>A</bold>) Size exclusion chromatography profile of purified mouse SAA3 on a Superdex 75 10/300 GL column. Elution of standards (BioRad) is shown in the top panel and elution of SAA3 is shown in the bottom panel. mSAA3 elutes at a position consistent with a tetramer (monomer is 12.2 kDa). (<bold>B</bold>) Cross-linking analysis of mSAA3. Purified mSAA3 was cross-linked with glutaraldehyde and analyzed by SDS-PAGE.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.016">http://dx.doi.org/10.7554/eLife.03206.016</ext-link></p></caption><graphic xlink:href="elife03206f005"/></fig><table-wrap id="tbl3" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.017</object-id><label>Table 3.</label><caption><p>Parameters from the Protein Interfaces, Surfaces, and Assemblies (PISA) analysis</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.017">http://dx.doi.org/10.7554/eLife.03206.017</ext-link></p></caption><table frame="hsides" rules="groups"><thead><tr><th>Parameter</th><th>Value</th></tr></thead><tbody><tr><td>Multimeric state</td><td>4</td></tr><tr><td>Composition</td><td>A<sub>2</sub>B<sub>2</sub></td></tr><tr><td>Dissociation pattern</td><td>2(AB)</td></tr><tr><td>Surface area, Å<sup>2</sup></td><td>19485.8</td></tr><tr><td>Buried area, Å<sup>2</sup></td><td>6125.7</td></tr><tr><td>ΔG<sub>intrinsic</sub>, kcal/mol</td><td>−79.8</td></tr><tr><td>ΔG<sub>diss</sub>, kcal/mol</td><td>11.1</td></tr><tr><td>TΔS<sub>diss</sub>, kcal/mol</td><td>12.6</td></tr></tbody></table></table-wrap></p><p>The mSAA3 tetramer is formed by two sets of tightly associated dimers (<xref ref-type="fig" rid="fig4">Figure 4B,C</xref>). The dimers pack against each other through an aromatic interface formed by W71, as well as a non-polar interaction involving V75 residues (<xref ref-type="fig" rid="fig4">Figure 4C,E</xref>). The dimer is formed by two identical chains oriented pseudo-anti-parallel to each other, and is held together by two pairs of tight hydrogen bond interactions between K74 and D78 residues on oppositely oriented α3 helices (<xref ref-type="fig" rid="fig4">Figure 4C,D</xref>). The interaction is also supported by a set of aromatic interactions between F99 and W103 of the α4 helices (<xref ref-type="fig" rid="fig4">Figure 4C,D</xref>). These interactions result in tightly held α3 helices composed primarily of non-polar residues, thus forming the inside hollow pocket of the tetramer. The hollow pocket is surrounded by the remaining helices, creating a hydrophobic interior that is protected from the external aqueous environment.</p></sec><sec id="s2-4"><title>The mouse SAA3 central channel is predicted to accommodate retinol</title><p>Retinol is a highly apolar lipid-like molecule consisting of a β-ionone ring, an isoprenoid tail, and a hydroxyl group. Thus, it requires a non-polar environment for transport among tissues and within cells. Structures of known retinol binding proteins, including serum RBP, indicate that these proteins consist mainly of β-sheet secondary structures forming a β-barrel tertiary structure, with the retinol molecule held in an interior non-polar binding pocket (<xref ref-type="bibr" rid="bib28">Newcomer et al., 1984</xref>). In contrast, mSAA3 is α-helical and oligomerizes to form a hollow, largely non-polar interior that could serve as a binding pocket for a non-polar small molecule (<xref ref-type="fig" rid="fig6">Figure 6A</xref>). We were unable to obtain mSAA3 crystals with the bound retinol ligand as retinol is highly unstable (<xref ref-type="bibr" rid="bib3">Barua and Furr, 1998</xref>) and the crystals required several weeks to grow. However, a ligand docking analysis using SwissDock (<xref ref-type="bibr" rid="bib17">Grosdidier et al., 2011</xref>) indicated that retinol can be docked in this hydrophobic pocket with favorable free energy (∼ −7 kcal/mol) and FullFitness values (<xref ref-type="bibr" rid="bib49">Zoete et al., 2010</xref>) (∼ −2400 kcal/mol) (<xref ref-type="fig" rid="fig6">Figure 6B–D</xref>). Consistent with this prediction, introducing a Trp71Ala (W71A) mutation in the mSAA3 hydrophobic core reduced the affinity of mSAA3 for retinol (<xref ref-type="fig" rid="fig6">Figure 6E</xref>). Thus, the mSAA3 structure supports our biochemical data showing a retinol binding function for SAAs and explains how mSAA3 could bind retinol.<fig id="fig6" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.018</object-id><label>Figure 6.</label><caption><title>The mSAA3 tetramer forms a hollow hydrophobic binding pocket that can accommodate retinol.</title><p>(<bold>A</bold>) A surface rendering of the tetramer showing the interior cavity, with the electrostatic potential displayed using a color gradient ranging from negative (red) to neutral (white) to positive (blue). The orientation is similar to that in <xref ref-type="fig" rid="fig4">Figure 4B</xref>. (<bold>B</bold>–<bold>D</bold>) Different views of a retinol molecule docked in the putative ligand-binding pocket. (<bold>B</bold>) A semi-transparent surface representation of the protein in the same orientation as <xref ref-type="fig" rid="fig4">Figure 4B</xref>, with a cartoon trace. Retinol atoms are represented as green spheres. The views in (<bold>C</bold>) and (<bold>D</bold>) are rotated by approximately 90° in the horizontal plane relative to (<bold>A</bold>) and (<bold>B</bold>), and (<bold>B</bold>) is rotated by approximately 90° in the vertical plane relative to (<bold>C</bold>). In (<bold>D</bold>), a surface model of the protein is shown, sliced close to the binding pocket. Retinol atoms are shown as sticks. (<bold>E</bold>) Wild-type or Trp71Ala (W71A) mutant mSAA3 was assayed for retinol binding as described in <xref ref-type="fig" rid="fig2">Figure 2</xref>. Representative plots and K<sub>d</sub>s were calculated from the binding assay data and were derived from five independent experiments.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.018">http://dx.doi.org/10.7554/eLife.03206.018</ext-link></p></caption><graphic xlink:href="elife03206f006"/></fig></p></sec></sec><sec id="s3" sec-type="discussion"><title>Discussion</title><p>Numerous biochemical, physiologic, and epidemiologic studies have shown that vitamin A and its derivative retinol are essential for the development of robust immunity (<xref ref-type="bibr" rid="bib36">Stephensen, 2001</xref>). Retinol and retinoic acid are critical for the development of innate and adaptive immunity (<xref ref-type="bibr" rid="bib21">Lawson and Berliner, 1999</xref>; <xref ref-type="bibr" rid="bib27">Mucida et al., 2007</xref>; <xref ref-type="bibr" rid="bib18">Hall et al., 2011</xref>; <xref ref-type="bibr" rid="bib35">Spencer et al., 2014</xref>), and also promote maintenance and repair of epithelial barriers (<xref ref-type="bibr" rid="bib30">Osanai et al., 2007</xref>). However, a prominent response to acute infection is the marked decline in serum RBP (<xref ref-type="bibr" rid="bib34">Rosales et al., 1996</xref>), which paradoxically occurs at a time of increased demand for retinol to support development of immunity and barrier defense. Thus, it has been unclear how retinol is transported among tissues following an acute microbial challenge.</p><p>We propose that SAAs fulfill this role, supported by several lines of evidence. First, SAAs are strongly induced by microbial exposure at sites of retinol uptake (intestine) and storage (liver), and are present at high levels in the circulation following microbial challenge (<xref ref-type="bibr" rid="bib7">Chiba et al., 2009</xref>; <xref ref-type="bibr" rid="bib19">Ivanov et al., 2009</xref>; <xref ref-type="bibr" rid="bib33">Reigstad et al., 2009</xref>). Second, we have shown that SAAs bind retinol at nanomolar affinity in vitro, and that serum SAAs circulate in association with retinol. Third, the three dimensional structure of mSAA3 exhibits a hollow hydrophobic binding pocket, providing structural insight into how SAAs bind retinol.</p><p>Although the precise tissue targets of circulating retinol-bound SAAs remain under investigation, several observations support the idea that SAAs promote immunity to infection. First, <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice exhibit increased susceptibility to chemically-induced colitis in mice (<xref ref-type="bibr" rid="bib13">Eckhardt et al., 2010</xref>), suggesting that SAAs contribute to intestinal immunity. Second, studies in zebrafish show that commensal microbiota stimulate neutrophil migration through induction of SAA (<xref ref-type="bibr" rid="bib20">Kanther et al., 2013</xref>). Third, we found that intraperitoneal infection of <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice with <italic>S. typhimurium</italic> resulted in higher bacterial loads in liver and spleen as compared to wild-type mice (<xref ref-type="fig" rid="fig7">Figure 7A,B</xref>), suggesting that SAAs also contribute to systemic immunity.<fig id="fig7" position="float"><object-id pub-id-type="doi">10.7554/eLife.03206.019</object-id><label>Figure 7.</label><caption><title><italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice have higher bacterial burdens following <italic>S. typhimurium</italic> infection.</title><p>10 week old wild-type and <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice were inoculated intraperitoneally with 10,000 cfu of S. typhimurium. Livers (<bold>A</bold>) and spleens (<bold>B</bold>) were collected after 24 hr and analyzed for bacterial counts by dilution plating. Combined results from two independent experiments are shown. Each point represents one mouse and geometric means are indicated. Dotted line indicates limit of detection. **p < 0.01 using the Mann–Whitney test.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03206.019">http://dx.doi.org/10.7554/eLife.03206.019</ext-link></p></caption><graphic xlink:href="elife03206f007"/></fig></p><p>SAA4 is an SAA isoform that is expressed in the livers of healthy, non-infected mice and humans (<xref ref-type="bibr" rid="bib10">de Beer et al., 1991</xref>, <xref ref-type="bibr" rid="bib11">1994</xref>, <xref ref-type="bibr" rid="bib12">1995</xref>). SAA4 circulates at concentrations that are markedly lower than those observed for SAA1 and 2 following acute infection (<xref ref-type="bibr" rid="bib12">de Beer et al., 1995</xref>) but are similar to the concentrations of RBP in uninfected individuals (<xref ref-type="bibr" rid="bib46">Willett et al., 1985</xref>; <xref ref-type="bibr" rid="bib15">Friedman et al., 1986</xref>). SAA4 is 54–56% homologous to SAA1, 2, and 3, and retains the hydrophobic amino acids that are predicted to line the hydrophobic binding pocket in SAA3. Further, homology modeling using the mouse SAA3 structure and the mouse SAA4 sequences yields a SAA4 model with a highly similar predicted structure (alignment score of 0.1 and a Global Model Quality Estimate of 0.73). Thus, the possibility that SAA4 is a retinol binding protein that functions to transport retinol in healthy, non-infected animals will be a subject for future investigation.</p><p>SAA1, 2, and 3 are markedly induced in the intestinal epithelium by the microbiota (<xref ref-type="bibr" rid="bib19">Ivanov et al., 2009</xref>; <xref ref-type="bibr" rid="bib13">Eckhardt et al., 2010</xref>; <xref ref-type="bibr" rid="bib32">Reigstad and Bäckhed, 2010</xref>), and thus our findings may provide insight into how the intestinal microbiota regulates host immunity and inflammation. Previous studies have suggested that SAAs promote Th17 cell development in response to specific components of the microbiota, such as segmented filamentous bacteria (<xref ref-type="bibr" rid="bib19">Ivanov et al., 2009</xref>). Consistent with a function for SAAs in retinol binding and transport, retinol/retinoic acid is required to elicit Th17 cell responses to infection and mucosal vaccination (<xref ref-type="bibr" rid="bib18">Hall et al., 2011</xref>). A key question is whether there are tissue-specific effects of intestinal epithelial SAAs, or whether the intestinal SAAs enter the circulation with bound retinol acquired directly from the diet. For example, intestinal epithelial SAAs could be involved in the direct delivery of retinol from epithelial cells to underlying immune cells in the lamina propria, or from epithelial cells to mucosal lymphoid tissues.</p><p>Altogether, our results provide insight into the biological function of SAAs, reveal a new protein architecture that supports retinol binding, and suggest how retinol is transported among cells and tissues during infection. These findings may prove useful in designing new strategies for enhancing resistance to infection and/or controlling inflammation during disease.</p></sec><sec id="s4" sec-type="materials|methods"><title>Materials and methods</title><sec id="s4-1"><title>Animals</title><p>C57BL/6 wild-type mice were maintained in the barrier at the University of Texas Southwestern Medical Center. <italic>Saa1/2</italic><sup><italic>−/−</italic></sup> mice were obtained from Dr Frederick C de Beer (<xref ref-type="bibr" rid="bib13">Eckhardt et al., 2010</xref>) at the University of Kentucky and were maintained in the barrier at the University of Texas Southwestern Medical Center. 6–12 weeks old mice were used for all experiments. Experiments were performed using protocols approved by the Institutional Animal Care and Use Committees of the UT Southwestern Medical Center.</p></sec><sec id="s4-2"><title>Antibodies and reagents</title><p>Recombinant mSAA1 and 3 were expressed and purified as described below. hSAA1 protein was from PeproTech (Rocky Hill, NJ) and resuspended as recommended. The protein is a consensus SAA molecule corresponding to human apo-SAA1α except for the presence of an N-terminal methionine and substitution of asparagine for aspartic acid at position 60 and arginine for histidine at position 71. Anti-SAA antiserum was raised against purified recombinant mSAA1. Retinol, retinoic acid, β-carotene, retinyl acetate, retinyl palmitate, and cholesterol were from Sigma-Aldrich (St. Louis, MO) and were reconstituted into ethanol, DMSO, or dioxane, depending on the experiment. IL-1β and IL-6 were from Invitrogen.</p></sec><sec id="s4-3"><title>Vitamin A depletion</title><p>Vitamin A-deficient (TD.09838) and control (∼20,000 IU vitamin A/kg; TD.09839) diets were purchased from Harlan Laboratories (South Easton, MA). At day 10 of gestation, pregnant females were placed on the standard diet or the vitamin A-deficient diet (<xref ref-type="bibr" rid="bib18">Hall et al., 2011</xref>). Mothers and pups were maintained on the diets until weaning, and pups stayed on the diet for two additional months prior to sacrifice.</p></sec><sec id="s4-4"><title>In vivo retinoic acid reconstitution</title><p>The protocol was adapted from a previously described procedure (<xref ref-type="bibr" rid="bib18">Hall et al., 2011</xref>). A total of 250 μg of all-<italic>trans</italic>-retinoic acid (Sigma-Aldrich) was resuspended in 30 μl of biotechnology performance certified DMSO (Sigma-Aldrich). The suspension was administered daily by intraperitoneal injection to vitamin A-deficient mice over the course of 3 days. 24 hr following the third injection, mice were sacrificed and tissues were harvested. Control mice received an injection of the DMSO vehicle.</p></sec><sec id="s4-5"><title>Intestinal explant culture</title><p>Terminal ileum (5 cm) was collected from mice post-sacrifice and flushed with a solution of phosphate-buffered saline with penicillin (100 units/ml) and streptomycin (100 μg/ml). Ileal segments were cultured on equilibrated cell culture plate inserts (PIHA03050; Millipore) at 37°C and 95% oxygen for 6 hr in Dulbecco's modified Eagle's medium (4 g/l glucose and L-glutamine; Invitrogen, Carlsbad, CA) supplemented with 10% charcoal-stripped heat-inactivated fetal bovine serum (Gibco, Carlsbad, CA), 10% NCTC135 media (Sigma), 25 mM HEPES, 100 units/ml penicillin, 100 μg/ml streptomycin, and either 0.1% DMSO or 1 μM retinol in 0.1% DMSO. After culture for 6 hr, segments were flash-frozen and processed for total RNA extraction.</p></sec><sec id="s4-6"><title>Microarray experiments</title><p>Total RNAs were isolated from mouse ileum using the Qiagen Midi-Prep RNA isolation kit. For each condition, RNA was isolated from two independent groups of five to eight mice. The RNAs in each group were pooled and used to generate biotinylated probes for microarray analysis. Probes were hybridized to Affymetrix Mouse Genome 430 2.0 GeneChips in the University of Texas Southwestern Microarray Core.</p><p>To identify genes that are differentially expressed between germ-free and conventional mice, we performed two-way comparisons between germ-free and conventional groups, with germ-free samples designated as baseline. Raw data were imported into Affymetrix (Santa Clara, CA) GeneChip software for analysis, and previously established criteria were used to identify differentially expressed genes (<xref ref-type="bibr" rid="bib6">Cash et al., 2006</xref>). Briefly, a twofold difference was considered significant if three criteria were met: (1) the GeneChip software returned a difference call of increased or decreased; (2) the mRNA was called present by GeneChip software in either germ-free or conventional samples; and (3) the difference was observed in duplicate microarray experiments. We performed a similar analysis to identify genes that are differentially regulated between mice fed a normal diet vs those fed a vitamin A-deficient diet. Finally, we identified 19 genes that were differentially regulated by colonization status and by dietary vitamin A content. Signal intensity data for this group of 19 genes were converted to Z-scores (z = (x − μ)/σ, where x = signal intensity, μ = mean signal intensity for all samples, and σ = SD across all samples), which were visualized as heatmaps using Java TreeView software.</p></sec><sec id="s4-7"><title>Quantitative PCR</title><p>Total RNA was isolated from homogenized tissues or cells using the Qiagen RNeasy RNA isolation kit. Random primed cDNAs were assayed by SYBR Green-based real-time PCR using <italic>SAA</italic>-specific primers as given in <xref ref-type="table" rid="tbl1">Table 1</xref>. Signals were normalized to 18S rRNA or <italic>Gapdh</italic>.</p></sec><sec id="s4-8"><title>Immunofluorescence analysis</title><p>Zinc-fixed, paraffin embedded tissue sections were stained with anti-SAA antiserum raised against purified recombinant mSAA1 and detected using a goat anti-rabbit IgG Cy3 conjugate (Biomeda). Tissues were counterstained with DAPI and images were captured on a Zeiss AxioImager M1 Microscope.</p></sec><sec id="s4-9"><title>Cell culture</title><p>HepG2 cells were purchased from ATCC. Cells were maintained in 1X DMEM, 10% FBS (or charcoal stripped FBS), 1X Penstrep, 1X glutamax, and 1X sodium pyruvate. Cells were maintained at 5% CO<sub>2</sub>. Prior to addition of retinoids, the cells were grown overnight in DMEM containing 10% charcoal-stripped FBS (to removes retinoids) and were treated with 1 μM retinol or 100 nM retinoic acid, 10 ng/ml of IL-1β, and 10 ng/ml IL-6.</p></sec><sec id="s4-10"><title>Expression and purification of recombinant SAAs</title><p>Genes encoding mouse SAA1 and SAA3 (minus the signal sequence) were cloned into the pET28(a)+ expression vector between <italic>NdeI</italic> and <italic>BamHI</italic> restriction endonuclease sites, with an N-terminal hexa-histidine tag followed by a thrombin cleavage site and a C-terminal stop codon. Proteins were expressed in <italic>Escherichia coli</italic> BL21-CodonPlus (DE3)-RILP cells (Stratagene, La Jolla, CA) by induction with 0.4 mM isopropyl-β-D-galactoside (IPTG) for ∼3 hr at 25°C for mSAA1, and at 37°C for mSAA3. Cells were harvested by centrifugation at 4500×<italic>g</italic> for 25 min at 4°C and re-suspended in lysis buffer (50 mM NaH<sub>2</sub>PO<sub>4</sub>, 500 mM NaCl, 10 mM imidizole for mSAA1 and 500 mM NaCl, 50 mM Tris pH 8.0, 10 mM imidazole, 15 mM β-mercaptoethanol for mSAA3). After sonication, decyl maltopyranoside (DM) (Avanti Polar Lipids, Alabaster, AL) was added to a final concentration of 40 mM and incubated for ∼3 hr at 4°C. The mixture was pelleted by centrifugation at 10,000×<italic>g</italic> for 30 min and the supernatant loaded onto a Ni<sup>2+</sup> metal affinity column (Qiagen, Valencia, CA) pre-equilibriated with 4 mM DM in lysis buffer. Non-specific contaminants were washed away with 25 mM imidazole in DM buffer and the protein was eluted in DM buffer containing 300 mM imidazole. All subsequent buffers do not include detergent in order to completely remove detergent. The eluate was desalted with a HiTrap desalting column (GE Life Sciences, Pittsburgh, PA) into a 200 mM NaCl buffer. Thrombin (Roche, Basel, Switzerland) was then added (∼1 unit/1.2 mg protein) and incubated overnight at 4°C. Undigested protein was removed by passing the overnight digest over Ni<sup>2+</sup> affinity matrix, collecting only the flow through. The eluate was concentrated in a 3 K cutoff Amicon Ultra centrifugal device (Millipore, Billerica, MA) and further purified by size exclusion chromatography on either a HiLoad Superdex 200 or a Superdex 75 (10/30) column (GE Life Sciences, Pittsburgh, PA), in 100 mM NaCl, 20 mM Tris pH 8, 15 mM a β-mercaptoethanol and 5% glycerol. For crystallization, mSAA3 was concentrated to ∼3 mg/ml.</p></sec><sec id="s4-11"><title>Mutagenesis</title><p>The mSAA3-W71A mutant was generated using the QuickChange II site-directed mutagenesis kit (Agilent Technologies, Santa Clara, CA). Protein expression, purification, and retinol binding assays were done as for wild-type mSAA3.</p></sec><sec id="s4-12"><title>Binding assays</title><p>Steady state fluorescence was measured using a QuantaMaster 40 spectrofluorometer (Photon Technology International, Edison, NJ) and FelixGX software program. For retinol titrations, samples were excited at 348 nm and emissions monitored at 460 nm. For retinoic acid and other retinoids, samples were excited at 296 nm and tryptophan quenching was monitored by emission at 334 nm. Experiments on mSAA1 and mSAA3 were done in 25 mM Tris pH 8.0, 100 mM NaCl, and 4 mM decyl maltopyranoside (DM). Experiments with hSAA1, human ApoA1, and human transferrin were conducted in PBS. For cholesterol competition assays, saturating concentrations of retinol were added to hSAA1, mSAA1, and mSAA3, and fluorescence quenching was monitored by emission at 334 nm. 10 μM cholesterol was added to the assay and inhibition of fluorescence quenching by retinol was monitored. All assays were done using a protein concentration of 0.5 μM.</p></sec><sec id="s4-13"><title>S. typhimurium infections</title><p><italic>Salmonella enterica</italic> Serovar Typhimurium (SL1344) was grown overnight in Luria Broth at 37°C. Mice were infected intraperitoneally with 1 × 10<sup>4</sup> organisms per mouse. Mice were sacrificed after 24 hr and tissues and serum were collected for experiments.</p></sec><sec id="s4-14"><title>Size exclusion chromatography of serum SAA</title><p>Serum was pooled from 3–5 mice and 500 μl was separated by size-exclusion chromatography on a Superdex 75 HiLoad 16/60 column (GE Life Sciences). Peak fractions were analyzed by SDS-PAGE and stained with Coomassie Blue. Duplicate samples were analyzed by Western blot with anti-SAA antibody to identify peak fractions containing SAA protein.</p></sec><sec id="s4-15"><title>Mass spectrometry analysis of retinol and retinoic acid</title><p>Retinoid extraction was modified and scaled from a previously described procedure (<xref ref-type="bibr" rid="bib25">McClean et al., 1982</xref>). SAA-containing fractions purified by size exclusion chromatography were pooled, added to an equal volume of 1:1 1-butanol:acetonitrile, and vortexed for 60 s. 20 μl of 20.6 M K<sub>2</sub>HPO<sub>4</sub> was added for each 1 ml of pooled fractions. Samples were then vortexed 30 s and 5 ml of hexane per 1 ml sample was added. Samples were vortexed for another 30 s and centrifuged at 1,000×<italic>g</italic> for 5 min and the top organic phase was dried in a nitrogen evaporator (Organomation Associates, Berlin, MA). Samples were prepared the day before the assay and stored at 80°C. Standard solutions were resuspended in ethanol and prepared fresh for every use. Standard curves were generated by spiking retinol or retinoic acid into 1 ml of 20 mM Tris pH 8.0, 100 mM NaCl and processed as for serum samples. Samples were resuspended in 200 μl of acetonitrile before injection. Compound levels were monitored by LC-MS/MS on an AB/Sciex (Framingham, MA) 4000 Qtrap mass spectrometer coupled to a Shimadzu (Columbia, MD) Prominence LC after a 20 μl injection. The compounds were detected using electrospray ionization (ESI) with the mass spectrometer in MRM (multiple reaction monitoring) mode by following the precursor to fragment ion transition 269.2 → 93.1 and 269.2 → 119 for retinol (pos. mode; [M-H<sub>2</sub>O]<sup>+</sup>) and 301.2 → 123.1 for retinoic acid (pos. mode; M+H<sup>+</sup>). An Agilent (Santa Clara, CA) Eclipse XDB C18 column (150 × 4.6 mm, 5 micron packing) was used for chromatography with the following conditions: mobile phase A: acetonitrile:methanol:H<sub>2</sub>O:formic acid (55:33:12:.01); mobile phase B: acetonitrile:formic acid (100:0.01). Over a total run time of 18 min, the following gradient was applied: 0 to 3 min 50% B; 3 to 10 min gradient to 100% B; 10 to 17 min 100% B; 17 to 18 min gradient to 50% B. Stoichiometries of the SAA-retinol association were determined by quantifying serum retinol and serum SAA. Total serum retinol was calculated based on peak areas from the mass spectrometer analysis in samples compared to a retinol standard curve. Serum SAA was quantified by Western blot analysis with anti-SAA antiserum and densitometry.</p></sec><sec id="s4-16"><title>Determination of the mSAA3 crystal structure</title><p>Crystals were grown by sitting-drop vapor diffusion at 20°C by mixing equal volumes of protein and reservoir. An initial hit was obtained in 30–40% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium acetate pH 4.5 after more than a month. Further refinement yielded better crystals at 75–80% MPD. Crystals were directly flash frozen, the MPD serving as a cryoprotectant. Crystals were of space group P6<sub>2</sub> with cell dimensions <italic>a</italic> = 78.327 Å, <italic>c</italic> = 62.319 Å and two subunit copies in the asymmetric unit. Selenomethionyl-derivatived crystals were grown the same way as the native protein crystals, except the culture media used was defined media with selenomethionine additive (Molecular Dimensions, Altamonte Springs, FL) and purification buffers after the last Ni<sup>2+</sup> column elution contained 10 mM DTT (instead of β-mercaptoethanol) and 0.5 mM EDTA.</p><p>Data were collected at 100 K under a nitrogen gas stream at the Advanced Photon Source (APS) beamlines 19ID or 23IDD of the Argonne National Laboratory. Single-wavelength anomalous dispersion (SAD) data were collected at the selenium K edge (0.9793 Å). Diffraction data were processed with the HKL2000/3000 package (<xref ref-type="bibr" rid="bib31">Otwinowski and Minor, 2013</xref>). Heavy atom substructure as well as initial phases were obtained using the SAD pipeline in the PHENIX crystallographic software package (<xref ref-type="bibr" rid="bib1">Afonine et al., 2012</xref>). This was followed by manual model building in Coot (<xref ref-type="bibr" rid="bib14">Emsley et al., 2010</xref>) interspersed with iterative rounds of rigid body, simulated annealing and individual isotropic B-factor refinement and finally TLS refinement in PHENIX. The structure was determined to a resolution of 2 Å. Data collection and refinement statistics are summarized in <xref ref-type="table" rid="tbl2">Table 2</xref>.</p></sec><sec id="s4-17"><title>mSAA3 cross-linking analysis</title><p>Glutaraldehyde (Sigma) was added to varying final concentrations (0.05%, 0.005%, and 0.0005% wt/vol) to purified mSAA3 (0.5 mg/ml in PBS). The reaction mixtures were incubated for ∼30 min on ice, quenched with 0.1 M Tris pH 8, and analyzed by SDS-PAGE.</p></sec><sec id="s4-18"><title>Statistics</title><p>Statistical differences were calculated by the unpaired two-tailed Student's <italic>t</italic> test or Mann–Whitney test using GraphPad Prism software. Results are expressed as the mean ± standard error of the mean (SEM).</p></sec></sec></body><back><ack id="ack"><title>Acknowledgements</title><p>We thank Cassie Behrendt Boyd, Charmaine Clements, and Tess Leal for assistance with mouse experiments, the staff at 19-ID and 23-IDD of the Advanced Photon Source (APS) for beamline access, Jun Liao, Youxing Jiang and Nam Nguyen for beamline access and discussions, the UT Southwestern Structural Biology Laboratory core for help with data collection and Diana Tomchick for advice on crystallography. This work was supported by NIH R01 DK070855 (LVH), the Welch Foundation (I-1762 to LVH), a Burroughs Wellcome Foundation Investigators in the Pathogenesis of Infectious Diseases Award (LVH), and the Howard Hughes Medical Institute (LVH). MGD was supported by a UNCF/Merck Postdoctoral Fellowship and a Burroughs Wellcome Fund Postdoctoral Enrichment Program Award, CMZ was supported by NIH Grant T32 AI005284, and SV was supported by Crohn's and Colitis Foundation of America Fellowship Award. Results shown in this report are derived from work performed at Argonne National Laboratory, Structural Biology Center at the APS. GM/CA at the APS has been funded in whole or in part with Federal funds from the National Cancer Institute (Y1-CO-1020) and the National Institute of General Medical Sciences (Y1-GM-1104). Argonne is operated by UChicago Argonne, LLC, for the U.S. Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. Coordinates of the crystallographic structure of mSAA3 have been deposited in the PDB with accession code 4Q5G.</p></ack><sec sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="conflict" id="conf1"><p>The authors declare that no competing interests exist.</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>MGD, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con2"><p>CMZ, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con3"><p>SG, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con4"><p>KAR, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con5"><p>SV, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con6"><p>GED, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con7"><p>JBMM, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con8"><p>NSW, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con9"><p>LVH, Conception and design, Analysis and interpretation of data, Drafting or revising the article</p></fn></fn-group><fn-group content-type="ethics-information"><title>Ethics</title><fn fn-type="other"><p>Animal experimentation: Animal subjects research approved by all animal experiments were approved by the Institutional Animal Care and Research Advisory Committee at the University of Texas Southwestern Medical Center, and the approved animal protocol number is 2011-0197. The institutional guidelines for the care and use of laboratory animals were followed.</p></fn></fn-group></sec><sec sec-type="supplementary-material"><title>Additional files</title><sec sec-type="datasets"><title>Major dataset</title><p>The following dataset was generated:</p><p><related-object content-type="generated-dataset" document-id="Dataset ID and/or url" document-id-type="dataset" document-type="data" id="dataro1"><name><surname>Derebe</surname><given-names>MG</given-names></name>, <name><surname>Hooper</surname><given-names>LV</given-names></name>, <year>2014</year><x>, </x><source>Crystal Structure of mouse Serum Amyloid A3</source><x>, </x><object-id pub-id-type="art-access-id">4Q5G</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4Q5G">http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4Q5G</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank (<ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/home/home.do">http://www.rcsb.org/pdb/home/home.do</ext-link>).</comment></related-object></p></sec></sec><ref-list><title>References</title><ref id="bib1"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Afonine</surname><given-names>PV</given-names></name><name><surname>Grosse-Kunstleve</surname><given-names>RW</given-names></name><name><surname>Echols</surname><given-names>N</given-names></name><name><surname>Headd</surname><given-names>JJ</given-names></name><name><surname>Moriarty</surname><given-names>NW</given-names></name><name><surname>Mustyakimov</surname><given-names>M</given-names></name><name><surname>Terwilliger</surname><given-names>TC</given-names></name><name><surname>Urzhumtsev</surname><given-names>A</given-names></name><name><surname>Zwart</surname><given-names>PH</given-names></name><name><surname>Adams</surname><given-names>PD</given-names></name></person-group><year>2012</year><article-title>Towards automated crystallographic structure refinement with phenix.refine</article-title><source>Acta Crystallographica Section D, Biological Crystallography</source><volume>68</volume><fpage>352</fpage><lpage>367</lpage><pub-id pub-id-type="doi">10.1107/S0907444912001308</pub-id></element-citation></ref><ref id="bib2"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Allie</surname><given-names>SR</given-names></name><name><surname>Zhang</surname><given-names>W</given-names></name><name><surname>Tsai</surname><given-names>C-Y</given-names></name><name><surname>Noelle</surname><given-names>RJ</given-names></name><name><surname>Usherwood</surname><given-names>EJ</given-names></name></person-group><year>2013</year><article-title>Critical role for all-trans retinoic acid for optimal effector and effector memory CD8 T cell differentiation</article-title><source>The Journal of Immunology</source><volume>190</volume><fpage>2178</fpage><lpage>2187</lpage><pub-id pub-id-type="doi">10.4049/jimmunol.1201945</pub-id></element-citation></ref><ref id="bib3"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Barua</surname><given-names>AB</given-names></name><name><surname>Furr</surname><given-names>HC</given-names></name></person-group><year>1998</year><article-title>Properties of retinoids. 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An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see <ext-link ext-link-type="uri" xlink:href="http://elifesciences.org/review-process">review process</ext-link>). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.</p></boxed-text><p>Thank you for sending your work entitled "Serum amyloid A is a retinol binding protein that transports retinol during bacterial infection" for consideration at <italic>eLife</italic>. Your article has been favorably evaluated by Richard Losick (Senior editor) and 2 reviewers, one of whom is a member of our Board of Reviewing Editors, and one of whom, Andrew MacPherson, has agreed to reveal his identity.</p><p>The Reviewing editor and the other reviewer discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.</p><p>Derebe et al describe the induction of the family of serum amyloid A proteins by vitamin A and their role in the transport of retinol and its derivatives. This is a novel and interesting study that has important implications for understanding of the multiple functions of vitamin A in infection and immunity. The work has been carefully performed to a very high standard work and is suitable for publication essentially in its present form.</p><p>The starting point of the paper was an Affy transcript abundance analysis that captured the coincidence of ileal gene expression alterations comparing germ-free and colonised mice with alterations depending on whether colonised mice were maintained on a vitamin A-deficient or -sufficient diet. The genes that show consistent expression differences include saa 1 and 2 (please note that I assume that saa 3 should be substituted for one of the saa1 labels, which appear twice in <xref ref-type="fig" rid="fig1s1">Figure 1–figure supplement 1</xref>).</p><p>The interpretation that SAA (1 and 3) are transport proteins for retinol is justified by direct binding studies, by elution from serum using the authentic retinol standard to calibrate LC MS and the use of SAA (1 and 2) deficient mice in a strain-combination setup. There is also a neat demonstration of a non-polar binding pocket in crystallographic analysis of SAA3, which is shown directly to form a tetramer through crosslinking studies.</p><p>The binding and structural studies are strong and represent the major advance of the paper. The link between vit A and SAA expression provides some valuable functional insight but this part is not as well-developed. The final experiment showing that SAA-deficient mice are less able to clear experimental <italic>S. typhimurium</italic> challenge at 24 hours is not directly linked to the earlier results mechanistically, although there is abundant evidence of retinoid shaping of immunity that makes this beyond the scope of the paper.</p><p>Specific comments:</p><p>1) The authors nicely show that intestinal and liver SAA expression is reduced following a vitamin A deficient diet. To support a direct effect, do the authors know if Vitamin A supplementation reverses these changes?</p><p>2) The list of other transcripts in the list presented in <xref ref-type="fig" rid="fig1s1">Figure 1–figure supplement 1</xref> is intriguing and it would be helpful if the authors could comment on this a little more. H-Antigen, dual oxidases, the NHE antiporter and the granzymes all have interesting disease associations.</p><p>3) In <xref ref-type="fig" rid="fig1">Figure 1E</xref> the open bars for IL-1beta + IL-6 without retinol appear to be identical for both SAA1 and SAA2: this may be coincidence, but I wondered whether an error had crept in?</p><p>4) Can the authors add any further information on how retinol/RA induces SAA in HepG2 cells?</p><p>5) Further information on the route of infection is required for <xref ref-type="fig" rid="fig7">Figure 7</xref>. What is the impact of SAA deficiency on the intestinal response to <italic>S. typhimurium</italic>? It would also be better to show the geometric means in view of the log scale.</p><p>6) What role might the constitutive (SAA5) play in the process of retinol transport? Given the role of SAA as an acute phase protein, what are the consequences of induction during non-infectious inflammation (e.g. autoinflammatory syndromes) from retinoid signaling?</p></body></sub-article><sub-article article-type="reply" id="SA2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.03206.021</article-id><title-group><article-title>Author response</article-title></title-group></front-stub><body><p><italic>The starting point of the paper was an Affy transcript abundance analysis that captured the coincidence of ileal gene expression alterations comparing germ-free and colonised mice with alterations depending on whether colonised mice were maintained on a vitamin A-deficient or -sufficient diet. The genes that show consistent expression differences include saa 1 and 2 (please note that I assume that saa 3 should be substituted for one of the saa1 labels, which appear twice in</italic> <xref ref-type="fig" rid="fig1s1"><italic>Figure 1–figure supplement 1</italic></xref><italic>)</italic>.</p><p>The figure is correct as labeled. There are multiple probe sets representing <italic>Saa1</italic> on the Affymetrix arrays and both of these probe sets showed a change in transcript abundance. The change in <italic>Saa3</italic> transcript abundance that was detected by Q-PCR analysis in <xref ref-type="fig" rid="fig1">Figure 1A</xref> was not captured by the microarray for reasons that are unclear.</p><p><italic>Specific comments</italic>:</p><p><italic>1) The authors nicely show that intestinal and liver SAA expression is reduced following a vitamin A deficient diet. To support a direct effect, do the authors know if Vitamin A supplementation reverses these changes</italic>?</p><p>This is a great question, and we have performed additional experiments to address this point. To test whether retinoids directly impact intestinal <italic>Saa</italic> expression we performed experiments with intestinal explants supplemented with retinol directly delivered onto the mucosal surface. We initially tried this experiment with explants from vitamin A-deficient mice but found that the tissue viability was extremely poor. However, we were able to detect increased <italic>Saa1</italic> and <italic>2</italic> expression in small intestinal explants harvested from vitamin A-replete mice that were supplemented with direct mucosal delivery of retinol. (While we can detect <italic>Saa3</italic> in vivo, we were unable to detect it in our explant system, likely due to its substantially lower levels of expression relative to <italic>Saa1</italic> and <italic>2</italic>.) These results are now shown in the new Figure 1–figure supplement 3.</p><p>(Note that oral supplementation of retinoids is problematic as retinoids are notoriously labile and thus readily degraded by the acidic pH of the stomach.)</p><p>To assess liver <italic>Saa</italic> expression in retinoid supplemented mice, we performed in vivo reconstitution experiments where retinoic acid was administered intraperitoneally to vitamin A-deficient mice for 3 days. This treatment resulted in elevated expression of both <italic>Saa1</italic> and <italic>Saa2</italic> in the livers of supplemented mice relative to vitamin A-deficient controls. These data are now included in new Figure 1–figure supplement 3.</p><p>Together, these data complement our cell culture analysis in HepG2 cells (<xref ref-type="fig" rid="fig1">Figure 1E and F</xref>) and support the idea that retinoids directly impact SAA expression</p><p><italic>2) The list of other transcripts in the list presented in</italic> <xref ref-type="fig" rid="fig1s1"><italic>supplementary Figure 1</italic></xref> <italic>is intriguing and it would be helpful if the authors could comment on this a little more. H-Antigen, dual oxidases, the NHE antiporter and the granzymes all have interesting disease associations</italic>.</p><p>Several of the other transcripts identified in the microarray analysis in <xref ref-type="fig" rid="fig1s1">Figure 1–figure supplement 1</xref> are indeed interesting and represent targets for future analysis of how vitamin A impacts mucosal function. There is a known role for retinoic acid in CD8<sup>+</sup> T cell differentiation (Allie et al., J. Immunol<italic>.</italic>, vol. 190, p. 2178-2187), which could explain the lowered abundance of granzyme transcripts (GzmA and GzmB) in the vitamin A-deficient mice. More interestingly, the array unexpectedly revealed that expression of three mucus-modifying glycosyltransferases (Fut2, Gcnt1, and B3galt5) is sensitive to dietary vitamin A, suggesting that vitamin A status could impact mucus glycan structure. The potential significance of the increased abundance of sodium:hydrogen antiporter (Slc9a3) transcripts is less apparent as there are no prior reports of its transcriptional regulation by retinoids. We have now added a comment about these findings to the legend of <xref ref-type="fig" rid="fig1s1">Figure 1–figure supplement 1</xref>.</p><p><italic>3) In</italic> <xref ref-type="fig" rid="fig1"><italic>Figure 1E</italic></xref> <italic>the open bars for IL-1beta + IL-6 without retinol appear to be identical for both SAA1 and SAA2: this may be coincidence, but I wondered whether an error had crept in</italic>?</p><p>We double-checked our data, and this is a coincidence. Further, although the figure shows that the average values are similar, close inspection reveals that the errors are slightly different.</p><p><italic>4) Can the authors add any further information on how retinol/RA induces SAA in HepG2 cells</italic>?</p><p>This is an important question and we have continued to push forward our understanding of the molecular basis for retinoid stimulation of SAA expression. We now have an extensive dataset that includes pharmacologic inhibition studies, siRNA knockdown experiments, and <italic>in vivo</italic> genetic experiments, which point to a specific transcriptional mechanism. Given the amount of data that we have accumulated on this point, we are planning to prepare a separate manuscript that describes this mechanism in detail, and are hoping that the reviewers agree that this lies outside the scope of the current manuscript.</p><p><italic>5) Further information on the route of infection is required for</italic> <xref ref-type="fig" rid="fig7"><italic>Figure 7</italic></xref>.</p><p>Thank you for bringing this to our attention. We have now added this information to the figure legend.</p><p><italic>What is the impact of SAA deficiency on the intestinal response to</italic> S. typhimurium<italic>?</italic></p><p>An important point is that the <italic>Saa1/2</italic><sup><italic>-/-</italic></sup> mice retain expression of SAA3, which is produced in the intestine but not in the liver or bloodstream. This was a key reason for our focus on the response of the <italic>Saa1/2</italic><sup><italic>-/-</italic></sup> mice to systemic rather than oral bacterial challenge. When we challenge the <italic>Saa1/2</italic><sup><italic>-/-</italic></sup> mice orally with <italic>S. typhimurium</italic>, we detect no statistically significant differences in luminal colonization levels or dissemination to mucosal or systemic sites, as might be predicted by the presence of intestinal SAA3 in these mice. Ongoing work is focused on generating mice that lack all SAA isoforms, as these will likely produce better insight into the role of SAAs in immunity to mucosal infections.</p><p><italic>It would also be better to show the geometric means in view of the log scale</italic>.</p><p>We agree, and now show the geometric means in <xref ref-type="fig" rid="fig7">Figure 7</xref>.</p><p><italic>6) What role might the constitutive (SAA5) play in the process of retinol transport</italic>?</p><p>We thank the reviewers for raising this important point. SAA5 (now designated as mouse SAA4, and equivalent to SAA4 in humans) is expressed in the livers of uninfected mice and humans and secreted into the bloodstream at concentrations of ∼50 ug/ml. This is well below the concentrations of >1 mg/ml that are observed for SAA1 and SAA2 after acute infection, but similar to the serum concentrations of retinol binding protein in healthy individuals. SAA4 shows 54-56% homology to SAA1, 2, and 3, so it is more distantly related. However, it retains the hydrophobic amino acids that are predicted to line the hydrophobic binding pocket in SAA3. Further, we performed homology modeling using the mouse SAA3 structure and the mouse SAA4 sequence that yielded a SAA4 model with a highly similar predicted structure. We therefore predict that SAA4 is also a retinol binding protein. If so, it is possible that SAA4 functions in retinol transport in healthy, non-infected animals. We have added additional text discussing this point to the Discussion section.</p><p><italic>Given the role of SAA as an acute phase protein</italic>, <italic>what are the consequences of induction during non-infectious inflammation (e.g. autoinflammatory syndromes) from retinoid signaling?</italic></p><p>Liver SAA expression is upregulated by cytokines such as TNFα, IL-1β, and IL-6, and thus could also be induced during inflammatory states that are independent of infection. Supporting this idea, elevated serum SAA levels have been observed in patients with rheumatoid arthritis (e.g., Arthritis Res 2, 142-144). We speculate that SAAs mediate retinol transport during such inflammatory states just as they do during infection, and plan to investigate this possibility in our future studies.</p></body></sub-article></article> |