Abstract
Staphylococcus aureus is the most important Gram-positive colonizer of human skin and nasal passage, causing high morbidity and mortality. SD-repeat containing protein D (SdrD), an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules) family surface protein, plays an important role in S. aureus adhesion and pathogenesis, while its binding target and molecular mechanism remain largely unknown. Here we solved the crystal structures of SdrD N2-N3 domain and N2-N3-B1 domain. Through structural analysis and comparisons, we characterized the ligand binding site of SdrD, and proposed a featured sequence motif of its potential ligands. In addition, the structures revealed for the first time the interactions between B1 domain and N2-N3 domain among B domain-containing MSCRAMMs. Our results may help in understanding the roles SdrD plays in S. aureus adhesion and shed light on the development of novel antibiotics.
Keywords: SdrD, adhesin, MSCRAMM, Staphylococcus aureus
References
- Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, Mc-Coy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. Sect. D-Biol. Crystallogr. 2002;58:1948–1954. doi: 10.1107/S0907444902016657. [DOI] [PubMed] [Google Scholar]
- Barbu EM, Ganesh VK, Gurusiddappa S, Mackenzie RC, Foster TJ, Sudhof TC, Hook M. beta-Neurexin is a ligand for the Staphylococcus aureus MSCRAMM SdrC. PLoS Pathog. 2010;6:11. doi: 10.1371/journal.ppat.1000726. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: A common cause of persistent infections. Science. 1999;284:1318–1322. doi: 10.1126/science.284.5418.1318. [DOI] [PubMed] [Google Scholar]
- Deivanayagam CCS, Rich RL, Carson M, Owens RT, Danthuluri S, Bice T, Hook M, Narayana SVL. Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein. Struct Fold Des. 2000;8:67–78. doi: 10.1016/S0969-2126(00)00081-2. [DOI] [PubMed] [Google Scholar]
- Deivanayagam CCS, Wann ER, Chen W, Carson M, Rajashankar KR, Hook M, Narayana SVL. A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A. EMBO J. 2002;21:6660–6672. doi: 10.1093/emboj/cdf619. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Diekema DJ, Pfaller MA, Schmitz FJ, Smayevsky J, Bell J, Jones RN, Beach M, Grp SP. Survey of infections due to Staphylococcus species: Frequency of occurrence and antimicrobial susceptibility of isolates collected in the United States, Canada, Latin America, Europe, and the Western Pacific region for the SENTRY Antimicrobial Surveillance Program, 1997–1999. Clin Infect Dis. 2001;32:S114–132. doi: 10.1086/320184. [DOI] [PubMed] [Google Scholar]
- Downer R, Roche F, Park PW, Mecham RP, Foster TJ. The elastin-binding protein of Staphylococcus aureus (EbpS) is expressed at the cell surface as an integral membrane protein and not as a cell wall-associated protein. J Biol Chem. 2002;277:243–250. doi: 10.1074/jbc.M107621200. [DOI] [PubMed] [Google Scholar]
- Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D-Biol Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. [DOI] [PubMed] [Google Scholar]
- Foster TJ, Hook M. Surface protein adhesins of Staphylococcus aureus. Trends Microbiol. 1998;6:484–488. doi: 10.1016/S0966-842X(98)01400-0. [DOI] [PubMed] [Google Scholar]
- Ganesh VK, Barbu EM, Deivanayagam CCS, Le B, Anderson AS, Matsuka YV, Lin SL, Foster TJ, Narayana SVL, Hook M. Structural and biochemical characterization of Staphylococcus aureus clumping factor B/ligand interactions. J Biol Chem. 2011;286:25963–25972. doi: 10.1074/jbc.M110.217414. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ganesh VK, Rivera JJ, Smeds E, Ko YP, Bowden MG, Wann ER, Gurusiddappa S, Fitzgerald JR, Hook M. A structural model of the Staphylococcus aureus ClfA-fibrinogen interaction opens new avenues for the design of anti-Staphylococcal therapeutics. PLoS Pathog. 2008;4:10. doi: 10.1371/journal.ppat.1000226. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gordon RJ, Lowy FD. Pathogenesis of methicillinresistant Staphylococcus aureus infection. Clin Infect Dis. 2008;46:S350–359. doi: 10.1086/533591. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hartford OM, Wann ER, Hook M, Foster TJ. Identification of residues in the Staphylococcus aureus fibrinogen-binding MSCRAMM clumping factor A (ClfA) that are important for ligand binding. J. Biol. Chem. 2001;276:2466–2473. doi: 10.1074/jbc.M007979200. [DOI] [PubMed] [Google Scholar]
- Jancarik J, Scott WG, Milligan DL, Koshland DE, Kim SH. Crystallization and preliminary-x-ray diffraction study of the ligand-binding domain of the bacterial chemotaxis-mediating aspartate receptor of salmonella-typhimurium. J Mol Biol. 1991;221:31–34. doi: 10.1016/0022-2836(91)80198-4. [DOI] [PubMed] [Google Scholar]
- Josefsson E, O’Connell D, Foster TJ, Durussel I, Cox JA. The binding of calcium to the B-repeat segment of SdrD, a cell surface protein of Staphylococcus aureus. J Biol Chem. 1998;273:31145–31152. doi: 10.1074/jbc.273.47.31145. [DOI] [PubMed] [Google Scholar]
- Kluytmans J, van Belkum A, Verbrugh H. Nasal carriage of Staphylococcus aureus: Epidemiology, underlying mechanisms, and associated risks. Clin Microbiol Rev. 1997;10:505–520. doi: 10.1128/cmr.10.3.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lowy FD. Antimicrobial resistance: the example of Staphylococcus aureus. J Clin Invest. 2003;111:1265–1273. doi: 10.1172/JCI18535. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maltezou HC, Giamarellou H. Community-acquired methicillin-resistant Staphylococcus aureus infections. Int J Antimicrob Agents. 2006;27:87–96. doi: 10.1016/j.ijantimicag.2005.11.004. [DOI] [PubMed] [Google Scholar]
- McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr. 2007;40:658–674. doi: 10.1107/S0021889807021206. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McCrea KW, Hartford O, Davis S, Eidhin DN, Lina G, Speziale P, Foster TJ, Hook M. The serine-aspartate repeat (Sdr) protein family in Staphylococcus epidermidis. Microbiology (UK) 2000;146:1535–1546. doi: 10.1099/00221287-146-7-1535. [DOI] [PubMed] [Google Scholar]
- Mongkolrattanothai K, Boyle S, Kahana MD, Daum RS. Severe Staphylococcus aureus infections caused by clonally related community-acquired methicillin-susceptible and methicillin-resistant isolates. Clin Infect Dis. 2003;37:1050–1058. doi: 10.1086/378277. [DOI] [PubMed] [Google Scholar]
- Moran GJ, Krishnadasan A, Gorwitz RJ, Fosheim GE, McDougal LK, Carey RB, Talan DA, Grp EMINS. Methicillin-resistant S-aureus infections among patients in the emergency department. N Engl J Med. 2006;355:666–674. doi: 10.1056/NEJMoa055356. [DOI] [PubMed] [Google Scholar]
- O’Riordan K, Lee JC. Staphylococcus aureus capsular polysaccharides. Clin Microbiol Rev. 2004;17:218–234. doi: 10.1128/CMR.17.1.218-234.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–326. doi: 10.1016/S0076-6879(97)76066-X. [DOI] [PubMed] [Google Scholar]
- Patti JM, Hook M. Microbial adhesins recognizing extracellular-matrix macromolecules. Curr Opin Cell Biol. 1994;6:752–758. doi: 10.1016/0955-0674(94)90104-X. [DOI] [PubMed] [Google Scholar]
- Ponnuraj K, Bowden MG, Davis S, Gurusiddappa S, Moore D, Choe D, Xu Y, Hook M, Narayana SVL. A “dock, lock, and latch” structural model for a staphylococcal adhesin binding to fibrinogen. Cell. 2003;115:217–228. doi: 10.1016/S0092-8674(03)00809-2. [DOI] [PubMed] [Google Scholar]
- Schito GC. The importance of the development of antibiotic resistance in Staphylococcus aureus. Clin Microbiol Infect. 2006;12:3–8. doi: 10.1111/j.1469-0691.2006.01343.x. [DOI] [PubMed] [Google Scholar]
- Schneider TR, Sheldrick GM. Substructure solution with SHELXD. Acta Crystallogr Sect D-Biol Crystallogr. 2002;58:1772–1779. doi: 10.1107/S0907444902011678. [DOI] [PubMed] [Google Scholar]
- Trad S, Allignet J, Frangeul L, Davi M, Vergassola M, Couve E, Morvan A, Kechrid A, Buchrieser C, Glaser P, et al. DNA macroarray for identification and typing of Staphylococcus aureus isolates. J Clin Microbiol. 2004;42:2054–2064. doi: 10.1128/JCM.42.5.2054-2064.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tung HS, Guss B, Hellman U, Persson L, Rubin K, Ryden C. A bone sialoprotein-binding protein from Staphylococcus aureus: a member of the staphylococcal Sdr family. Biochem J. 2000;345:611–619. doi: 10.1042/bj3450611. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weber JT. Community-associated methicillin-resistant Staphylococcus aureus. Clin Infect Dis. 2005;41:S269–272. doi: 10.1086/430788. [DOI] [PubMed] [Google Scholar]
- Xiang H, Feng Y, Wang JW, Liu B, Chen YG, Liu L, Deng XM, Yang MJ. Crystal structures reveal the multi-ligand binding mechanism of Staphylococcus aureus ClfB. Plos Pathogens. 2012;8:2751–2751. doi: 10.1371/journal.ppat.1002751. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhang LQ, Xiang H, Gao JL, Hu J, Miao SY, Wang LF, Deng XM, Li ST. Purification, characterization, and crystallization of the adhesive domain of SdrD from Staphylococcus aureus. Protein Expr Purif. 2010;69:204–208. doi: 10.1016/j.pep.2009.09.007. [DOI] [PubMed] [Google Scholar]