{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T08:59:02Z","timestamp":1767171542092,"version":"build-2238731810"},"reference-count":123,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2164-15-362","type":"journal-article","created":{"date-parts":[[2014,5,12]],"date-time":"2014-05-12T13:03:09Z","timestamp":1399899789000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Construction and verification of the transcriptional regulatory response network of Streptococcus mutansupon treatment with the biofilm inhibitor carolacton"],"prefix":"10.1186","volume":"15","author":[{"given":"Padhmanand","family":"Sudhakar","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Reck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng Q","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irene W","family":"Dobler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"An-Ping","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,5,12]]},"reference":[{"key":"6097_CR1","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1146\/annurev.micro.56.012302.160705","volume":"56","author":"P Stoodley","year":"2002","unstructured":"Stoodley P, Sauer K, Davies DG, Costerton JW: Biofilms as complex differentiated communities. Annu Rev Microbiol. 2002, 56: 187-209. 10.1146\/annurev.micro.56.012302.160705.","journal-title":"Annu Rev Microbiol"},{"issue":"1","key":"6097_CR2","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1111\/j.1601-1546.2012.00277.x","volume":"22","author":"D Dufour","year":"2012","unstructured":"Dufour D, Leung V, Levesque CM: Bacterial biofilm: structure, function, and antimicrobial resistance. Endo Topics. 2012, 22 (1): 2-16.","journal-title":"Endo Topics"},{"key":"6097_CR3","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1186\/1471-2180-10-199","volume":"10","author":"B Kunze","year":"2010","unstructured":"Kunze B, Reck M, D\u00f6tsch A, Lemme A, Schummer D, Irschik H, Steinmetz H, Wagner-D\u00f6bler I: Damage of Streptococcus mutans biofilms by carolacton, a secondary metabolite from the myxobacterium Sorangium cellulosum. BMC Microbiol. 2010, 10: 199-10.1186\/1471-2180-10-199.","journal-title":"BMC Microbiol"},{"key":"6097_CR4","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1073\/pnas.90.3.965","volume":"90","author":"S Roychoudhury","year":"1993","unstructured":"Roychoudhury S, Zielinski NA, Ninfa AJ, Allen NE, Jungheim LN, Nicas TI, Chakrabarty AM: Inhibitors of two-component signal transduction systems: inhibition of alginate gene activation in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 1993, 90: 965-969. 10.1073\/pnas.90.3.965.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6097_CR5","doi-asserted-by":"publisher","first-page":"5692","DOI":"10.1128\/JB.05424-11","volume":"193","author":"M Reck","year":"2011","unstructured":"Reck M, Rutz K, Kunze B, Tomasch J, Surapaneni SK, Schulz S, Wagner-D\u00f6bler I: The biofilm inhibitor carolacton disturbs membrane integrity and cell division of Streptococcus mutans through the serine\/threonine protein kinase PknB. J Bacteriol. 2011, 193: 5692-5706. 10.1128\/JB.05424-11.","journal-title":"J Bacteriol"},{"key":"6097_CR6","doi-asserted-by":"publisher","first-page":"2699","DOI":"10.1128\/JB.184.10.2699-2708.2002","volume":"184","author":"Y Li","year":"2002","unstructured":"Li Y, Tang N, Aspiras MB, Lau PCY, Lee JH, Ellen RP, Cvitkovitch DG: A quorum-sensing signaling system essential for genetic competence in Streptococcus mutans is involved in biofilm formation. J Bacteriol. 2002, 184: 2699-2708. 10.1128\/JB.184.10.2699-2708.2002.","journal-title":"J Bacteriol"},{"key":"6097_CR7","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/j.femsle.2005.08.018","volume":"251","author":"F Qi","year":"2005","unstructured":"Qi F, Kreth J, L\u00e9vesque CM, Kay O, Mair RW, Shi W, Cvitkovitch DG, Goodman SD: Peptide pheromone induced cell death of Streptococcus mutans. FEMS Microbiol Lett. 2005, 251: 321-326. 10.1016\/j.femsle.2005.08.018.","journal-title":"FEMS Microbiol Lett"},{"key":"6097_CR8","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1111\/j.1574-6968.2001.tb10952.x","volume":"205","author":"SP Bhagwat","year":"2001","unstructured":"Bhagwat SP, Nary J, Burne RA: Effects of mutating putative two-component systems on biofilm formation by Streptococcus mutans UA159. FEMS Microbiol Lett. 2001, 205: 225-230. 10.1111\/j.1574-6968.2001.tb10952.x.","journal-title":"FEMS Microbiol Lett"},{"key":"6097_CR9","doi-asserted-by":"publisher","first-page":"4168","DOI":"10.1128\/JB.01616-06","volume":"189","author":"L Saskov\u00e1","year":"2007","unstructured":"Saskov\u00e1 L, Nov\u00e1kov\u00e1 L, Basler M, Branny P: Eukaryotic-type serine\/threonine protein kinase StkP is a global regulator of gene expression in Streptococcus pneumoniae. J Bacteriol. 2007, 189: 4168-4179. 10.1128\/JB.01616-06.","journal-title":"J Bacteriol"},{"key":"6097_CR10","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/j.jbiotec.2009.07.013","volume":"144","author":"F He","year":"2009","unstructured":"He F, Balling R, Zeng A: Reverse engineering and verification of gene networks:principles, assumptions, and limitations of present methods and future perspectives. J Biotechnol. 2009, 144: 190-203. 10.1016\/j.jbiotec.2009.07.013.","journal-title":"J Biotechnol"},{"key":"6097_CR11","doi-asserted-by":"publisher","first-page":"2898","DOI":"10.1093\/bioinformatics\/bti440","volume":"21","author":"L Cabusora","year":"2005","unstructured":"Cabusora L, Sutton E, Fulmer A, Forst CV: Differential network expression during drug and stress response. Bioinformatics. 2005, 21: 2898-2905. 10.1093\/bioinformatics\/bti440.","journal-title":"Bioinformatics"},{"key":"6097_CR12","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","volume":"22","author":"M Bansal","year":"2006","unstructured":"Bansal M, Della Gatta G, Di Bernardo D: Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics. 2006, 22: 815-822. 10.1093\/bioinformatics\/btl003.","journal-title":"Bioinformatics"},{"key":"6097_CR13","doi-asserted-by":"publisher","first-page":"e24","DOI":"10.1093\/nar\/gks904","volume":"41","author":"M Aluru","year":"2013","unstructured":"Aluru M, Zola J, Nettleton D, Aluru S: Reverse engineering and analysis of large genome-scale gene networks. Nucleic Acids Res. 2013, 41: e24-10.1093\/nar\/gks904.","journal-title":"Nucleic Acids Res"},{"key":"6097_CR14","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","volume":"5","author":"JJ Faith","year":"2007","unstructured":"Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS: Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007, 5: e8-10.1371\/journal.pbio.0050008.","journal-title":"PLoS Biol"},{"key":"6097_CR15","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1038\/msb.2012.56","volume":"8","author":"F He","year":"2012","unstructured":"He F, Chen H, Probst-Kepper M, Geffers R, Eifes S, Del Sol A, Schughart K, Zeng A, Balling R: PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells. Mol Syst Biol. 2012, 8: 624-","journal-title":"Mol Syst Biol"},{"key":"6097_CR16","volume-title":"Brief Bioinform","author":"JP Faria","year":"2013","unstructured":"Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS: Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Brief Bioinform. 2013, Epub ahead of print. doi: 10.1093\/bib\/bbs071"},{"key":"6097_CR17","doi-asserted-by":"publisher","first-page":"1840","DOI":"10.1039\/b907310h","volume":"5","author":"A Fadda","year":"2009","unstructured":"Fadda A, Fierro AC, Lemmens K, Monsieurs P, Engelen K, Marchal K: Inferring the transcriptional network of Bacillus subtilis. Mol Biosyst. 2009, 5: 1840-1852. 10.1039\/b907310h.","journal-title":"Mol Biosyst"},{"key":"6097_CR18","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1186\/1471-2164-11-578","volume":"11","author":"M Castro-Melchor","year":"2010","unstructured":"Castro-Melchor M, Charaniya S, Karypis G, Takano E, Hu W: Genome-wide inference of regulatory networks in Streptomyces coelicolor. BMC Genomics. 2010, 11: 578-10.1186\/1471-2164-11-578.","journal-title":"BMC Genomics"},{"key":"6097_CR19","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2006-7-5-r36","volume":"7","author":"R Bonneau","year":"2006","unstructured":"Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V: The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 2006, 7: R36-10.1186\/gb-2006-7-5-r36.","journal-title":"Genome Biol"},{"key":"6097_CR20","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1186\/1471-2105-12-233","volume":"12","author":"Y Fu","year":"2011","unstructured":"Fu Y, Jarboe LR, Dickerson JA: Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities. BMC Bioinformatics. 2011, 12: 233-10.1186\/1471-2105-12-233.","journal-title":"BMC Bioinformatics"},{"key":"6097_CR21","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/ng873","volume":"31","author":"N Guelzim","year":"2002","unstructured":"Guelzim N, Bottani S, Bourgine P, K\u00e9p\u00e8s F: Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet. 2002, 31: 60-63. 10.1038\/ng873.","journal-title":"Nat Genet"},{"key":"6097_CR22","doi-asserted-by":"crossref","first-page":"51","DOI":"10.3389\/fmicb.2012.00051","volume":"3","author":"R Altwasser","year":"2012","unstructured":"Altwasser R, Linde J, Buyko E, Hahn U, Guthke R: Genome-Wide Scale-Free Network Inference for Candida albicans. Front Microbiol. 2012, 3: 51-","journal-title":"Front Microbiol"},{"key":"6097_CR23","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1039\/c3ib40180d","volume":"6","author":"FQ He","year":"2014","unstructured":"He FQ, Wang W, Zheng P, Sudhakar P, Sun J, Zeng AP: Essential O2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions. Integr Biol. 2014, 6: 215-223. 10.1039\/c3ib40180d.","journal-title":"Integr Biol"},{"key":"6097_CR24","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1186\/1471-2105-11-355","volume":"11","author":"M Bailly-Bechet","year":"2010","unstructured":"Bailly-Bechet M, Braunstein A, Pagnani A, Weigt M, Zecchina R: Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. BMC Bioinformatics. 2010, 11: 355-10.1186\/1471-2105-11-355.","journal-title":"BMC Bioinformatics"},{"key":"6097_CR25","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/ng1532","volume":"37","author":"K Basso","year":"2005","unstructured":"Basso K, Margolin A, Stolovitzky G, Klein U, Dalla-Favera R, Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet. 2005, 37: 382-390. 10.1038\/ng1532.","journal-title":"Nat Genet"},{"key":"6097_CR26","doi-asserted-by":"publisher","first-page":"1433","DOI":"10.1128\/JB.01161-09","volume":"192","author":"KP O\u2019Rourke","year":"2010","unstructured":"O\u2019Rourke KP, Shaw JD, Pesesky MW, Cook BT, Roberts SM, Bond JP, Spatafora GA: Genome-wide characterization of the SloR metalloregulome in Streptococcus mutans. J Bacteriol. 2010, 192: 1433-1443. 10.1128\/JB.01161-09.","journal-title":"J Bacteriol"},{"key":"6097_CR27","doi-asserted-by":"publisher","first-page":"8519","DOI":"10.1128\/JB.01180-07","volume":"189","author":"S Ahn","year":"2007","unstructured":"Ahn S, Wen ZT, Burne RA: Effects of oxygen on virulence traits of Streptococcus mutans. J Bacteriol. 2007, 189: 8519-8527. 10.1128\/JB.01180-07.","journal-title":"J Bacteriol"},{"key":"6097_CR28","doi-asserted-by":"publisher","first-page":"5049","DOI":"10.1128\/JB.00338-07","volume":"189","author":"D Ajdi\u0107","year":"2007","unstructured":"Ajdi\u0107 D, Pham VTT: Global transcriptional analysis of Streptococcus mutans sugar transporters using microarrays. J Bacteriol. 2007, 189: 5049-5059. 10.1128\/JB.00338-07.","journal-title":"J Bacteriol"},{"key":"6097_CR29","doi-asserted-by":"publisher","first-page":"2433","DOI":"10.1099\/mic.0.048314-0","volume":"157","author":"J Liu","year":"2011","unstructured":"Liu J, Wu C, Huang I, Merritt J, Qi F: Differential response of Streptococcus mutans towards friend and foe in mixed-species cultures. Microbiology. 2011, 157: 2433-2444. 10.1099\/mic.0.048314-0.","journal-title":"Microbiology"},{"key":"6097_CR30","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1111\/j.1472-765X.2007.02203.x","volume":"45","author":"CM L\u00e9vesque","year":"2007","unstructured":"L\u00e9vesque CM, Mair RW, Perry JA, Lau PCY, Li Y, Cvitkovitch DG: Systemic inactivation and phenotypic characterization of two-component systems in expression of Streptococcus mutans virulence properties. Lett Appl Microbiol. 2007, 45: 398-404. 10.1111\/j.1472-765X.2007.02203.x.","journal-title":"Lett Appl Microbiol"},{"key":"6097_CR31","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1111\/j.1472-765X.2008.02455.x","volume":"47","author":"JA Perry","year":"2008","unstructured":"Perry JA, L\u00e9vesque CM, Suntharaligam P, Mair RW, Bu M, Cline RT, Peterson SN, Cvitkovitch DG: Involvement of Streptococcus mutans regulator RR11 in oxidative stress response during biofilm growth and in the development of genetic competence. Lett Appl Microbiol. 2008, 47: 439-444. 10.1111\/j.1472-765X.2008.02455.x.","journal-title":"Lett Appl Microbiol"},{"key":"6097_CR32","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/1471-2105-7-69","volume":"7","author":"F He","year":"2006","unstructured":"He F, Zeng A: In search of functional association from time-series microarray data based on the change trend and level of gene expression. BMC Bioinformatics. 2006, 7: 69-10.1186\/1471-2105-7-69.","journal-title":"BMC Bioinformatics"},{"key":"6097_CR33","doi-asserted-by":"publisher","first-page":"3467","DOI":"10.1021\/cr068309+","volume":"107","author":"DA Rodionov","year":"2007","unstructured":"Rodionov DA: Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev. 2007, 107: 3467-3497. 10.1021\/cr068309+.","journal-title":"Chem Rev"},{"key":"6097_CR34","doi-asserted-by":"publisher","first-page":"2463","DOI":"10.1128\/JB.00140-13","volume":"195","author":"SA Leyn","year":"2013","unstructured":"Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA: Genomic Reconstruction of Transcriptional Regulatory Network in Bacillus subtilis. J Bacteriol. 2013, 195: 2463-2473. 10.1128\/JB.00140-13.","journal-title":"J Bacteriol"},{"key":"6097_CR35","doi-asserted-by":"crossref","first-page":"449","DOI":"10.4137\/EBO.S9205","volume":"8","author":"JP Cornish","year":"2012","unstructured":"Cornish JP, Matthews F, Thomas JR, Erill I: Inference of self-regulated transcriptional networks by comparative genomics. Evol Bioinform Online. 2012, 8: 449-461.","journal-title":"Evol Bioinform Online"},{"key":"6097_CR36","doi-asserted-by":"publisher","first-page":"D111","DOI":"10.1093\/nar\/gkp894","volume":"38","author":"PS Novichkov","year":"2010","unstructured":"Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA: RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010, 38: D111-8. 10.1093\/nar\/gkp894.","journal-title":"Nucleic Acids Res"},{"key":"6097_CR37","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1093\/nar\/gkq710","volume":"39","author":"A Medina-Rivera","year":"2011","unstructured":"Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J: Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res. 2011, 39: 808-824. 10.1093\/nar\/gkq710.","journal-title":"Nucleic Acids Res"},{"key":"6097_CR38","doi-asserted-by":"publisher","first-page":"5291","DOI":"10.1128\/JB.00288-08","volume":"190","author":"JA Lemos","year":"2008","unstructured":"Lemos JA, Nascimento MM, Lin VK, Abranches J, Burne RA: Global regulation by (p)ppGpp and CodY in Streptococcus mutans. J Bacteriol. 2008, 190: 5291-5299. 10.1128\/JB.00288-08.","journal-title":"J Bacteriol"},{"key":"6097_CR39","doi-asserted-by":"publisher","first-page":"840","DOI":"10.1038\/nature06847","volume":"452","author":"M Isalan","year":"2008","unstructured":"Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, Raineri E, Garriga-Canut M, Serrano L: Evolvability and hierarchy in rewired bacterial gene networks. Nature. 2008, 452: 840-845. 10.1038\/nature06847.","journal-title":"Nature"},{"key":"6097_CR40","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1186\/1471-2105-5-199","volume":"5","author":"H Ma","year":"2004","unstructured":"Ma H, Buer J, Zeng A: Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics. 2004, 5: 199-10.1186\/1471-2105-5-199.","journal-title":"BMC Bioinformatics"},{"key":"6097_CR41","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/2042-5783-1-3","volume":"1","author":"E Gal\u00e1n-V\u00e1squez","year":"2011","unstructured":"Gal\u00e1n-V\u00e1squez E, Luna B, Mart\u00ednez-Antonio A: The Regulatory Network of Pseudomonas aeruginosa. Microb Inform Exp. 2011, 1: 3-10.1186\/2042-5783-1-3.","journal-title":"Microb Inform Exp"},{"key":"6097_CR42","doi-asserted-by":"publisher","first-page":"e1001027","DOI":"10.1371\/journal.pgen.1001027","volume":"6","author":"YS Dufour","year":"2010","unstructured":"Dufour YS, Kiley PJ, Donohue TJ: Reconstruction of the core and extended regulons of global transcription factors. PLoS Genet. 2010, 6: e1001027-10.1371\/journal.pgen.1001027.","journal-title":"PLoS Genet"},{"key":"6097_CR43","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1128\/AEM.00952-10","volume":"77","author":"S Chaturongakul","year":"2011","unstructured":"Chaturongakul S, Raengpradub S, Palmer ME, Bergholz TM, Orsi RH, Hu Y, Ollinger J, Wiedmann M, Boor KJ: Transcriptomic and phenotypic analyses identify coregulated, overlapping regulons among PrfA, CtsR, HrcA, and the alternative sigma factors sigmaB, sigmaC, sigmaH, and sigmaL in Listeria monocytogenes. Appl Environ Microbiol. 2011, 77: 187-200. 10.1128\/AEM.00952-10.","journal-title":"Appl Environ Microbiol"},{"key":"6097_CR44","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1002\/prot.22053","volume":"73","author":"AS Konagurthu","year":"2008","unstructured":"Konagurthu AS, Lesk AM: Single and multiple input modules in regulatory networks. Proteins. 2008, 73: 320-324. 10.1002\/prot.22053.","journal-title":"Proteins"},{"key":"6097_CR45","doi-asserted-by":"publisher","first-page":"11980","DOI":"10.1073\/pnas.2133841100","volume":"100","author":"S Mangan","year":"2003","unstructured":"Mangan S, Alon U: Structure and function of the feed-forward loop network motif. Proc Natl Acad. Sci. U.S.A. 2003, 100: 11980-11985. 10.1073\/pnas.2133841100.","journal-title":"Proc Natl Acad. Sci. U.S.A"},{"key":"6097_CR46","doi-asserted-by":"publisher","first-page":"2080","DOI":"10.1126\/science.1058758","volume":"292","author":"S Kalir","year":"2001","unstructured":"Kalir S, McClure J, Pabbaraju K, Southward C, Ronen M, Leibler S, Surette MG, Alon U: Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science. 2001, 292: 2080-2083. 10.1126\/science.1058758.","journal-title":"Science"},{"key":"6097_CR47","doi-asserted-by":"crossref","first-page":"31909","DOI":"10.1103\/PhysRevE.70.031909","volume":"70","author":"N Kashtan","year":"2004","unstructured":"Kashtan N, Itzkovitz S, Milo R, Alon U: Topological generalizations of network motifs. Phys Rev E Stat Nonlin Soft Matter Phys. 2004, 70: 31909-","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"6097_CR48","doi-asserted-by":"publisher","first-page":"6643","DOI":"10.1093\/nar\/gkh1009","volume":"32","author":"H Ma","year":"2004","unstructured":"Ma H, Kumar B, Ditges U, Gunzer F, Buer J, Zeng A: An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res. 2004, 32: 6643-6649. 10.1093\/nar\/gkh1009.","journal-title":"Nucleic Acids Res"},{"key":"6097_CR49","doi-asserted-by":"publisher","first-page":"2478","DOI":"10.1128\/AEM.02622-09","volume":"76","author":"P Chen","year":"2010","unstructured":"Chen P, Chen YM, Yu S, Sher S, Lai C, Chia J: Role of GlnR in acid-mediated repression of genes encoding proteins involved in glutamine and glutamate metabolism in Streptococcus mutans. Appl Environ Microbiol. 2010, 76: 2478-2486. 10.1128\/AEM.02622-09.","journal-title":"Appl Environ Microbiol"},{"key":"6097_CR50","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.01802-09","volume":"54","author":"J Ouyang","year":"2010","unstructured":"Ouyang J, Tian X, Versey J, Wishart A, Li Y: The BceABRS four-component system regulates the bacitracin-induced cell envelope stress response in Streptococcus mutans. Antimicrob Agents Chemother. 2010, 54: 3895-3906. 10.1128\/AAC.01802-09.","journal-title":"Antimicrob Agents Chemother"},{"key":"6097_CR51","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1128\/JB.01237-07","volume":"190","author":"J Abranches","year":"2008","unstructured":"Abranches J, Nascimento MM, Zeng L, Browngardt CM, Wen ZT, Rivera MF, Burne RA: CcpA regulates central metabolism and virulence gene expression in Streptococcus mutans. J Bacteriol. 2008, 190: 2340-2349. 10.1128\/JB.01237-07.","journal-title":"J Bacteriol"},{"key":"6097_CR52","doi-asserted-by":"publisher","first-page":"4760","DOI":"10.1128\/AEM.69.8.4760-4769.2003","volume":"69","author":"J Abranches","year":"2003","unstructured":"Abranches J, Chen YM, Burne RA: Characterization of Streptococcus mutans strains deficient in EIIAB Man of the sugar phosphotransferase system. Appl Environ Microbiol. 2003, 69: 4760-4769. 10.1128\/AEM.69.8.4760-4769.2003.","journal-title":"Appl Environ Microbiol"},{"key":"6097_CR53","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1111\/j.1365-2958.2006.05359.x","volume":"62","author":"L Zeng","year":"2006","unstructured":"Zeng L, Wen ZT, Burne RA: A novel signal transduction system and feedback loop regulate fructan hydrolase gene expression in Streptococcus mutans. Mol Microbiol. 2006, 62: 187-200. 10.1111\/j.1365-2958.2006.05359.x.","journal-title":"Mol Microbiol"},{"key":"6097_CR54","doi-asserted-by":"publisher","first-page":"e17335","DOI":"10.1371\/journal.pone.0017335","volume":"6","author":"L Zeng","year":"2011","unstructured":"Zeng L, Das S, Burne RA: Genetic analysis of the functions and interactions of components of the LevQRST signal transduction complex of Streptococcus mutans. PLoS One. 2011, 6: e17335-10.1371\/journal.pone.0017335.","journal-title":"PLoS One"},{"key":"6097_CR55","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1128\/JB.01509-07","volume":"190","author":"AJ Webb","year":"2008","unstructured":"Webb AJ, Homer KA, Hosie AHF: Two closely related ABC transporters in Streptococcus mutans are involved in disaccharide and\/or oligosaccharide uptake. J Bacteriol. 2008, 190: 168-178. 10.1128\/JB.01509-07.","journal-title":"J Bacteriol"},{"key":"6097_CR56","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1128\/mr.50.4.353-380.1986","volume":"50","author":"WJ Loesche","year":"1986","unstructured":"Loesche WJ: Role of Streptococcus mutans in human dental decay. Microbiol Rev. 1986, 50: 353-380.","journal-title":"Microbiol Rev"},{"key":"6097_CR57","doi-asserted-by":"crossref","first-page":"881S","DOI":"10.1093\/ajcn\/78.4.881S","volume":"78","author":"R Touger-Decker","year":"2003","unstructured":"Touger-Decker R, van Loveren C: Sugars and dental caries. Am J Clin Nutr. 2003, 78: 881S-892S.","journal-title":"Am J Clin Nutr"},{"key":"6097_CR58","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1177\/00220345760550020801","volume":"55","author":"J van Houte","year":"1976","unstructured":"van Houte J, Upeslacis VN, Jordan HV, Skobe Z, Green DB: Role of sucrose in colonization of Streptococcus mutans in conventional Sprague\u2013Dawley rats. J Dent Res. 1976, 55: 202-215. 10.1177\/00220345760550020801.","journal-title":"J Dent Res"},{"key":"6097_CR59","first-page":"101","volume":"12","author":"JA Cury","year":"2001","unstructured":"Cury JA, Francisco SB, Del Bel Cury AA, Tabchoury CP: In situ study of sucrose exposure, mutans streptococci in dental plaque and dental caries. Braz Dent J. 2001, 12: 101-104.","journal-title":"Braz Dent J"},{"key":"6097_CR60","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1159\/000065959","volume":"36","author":"M Nobre dos Santos","year":"2002","unstructured":"Nobre dos Santos M, Melo dos Santos L, Francisco SB, Cury JA: Relationship among dental plaque composition, daily sugar exposure and caries in the primary dentition. Caries Res. 2002, 36: 347-352. 10.1159\/000065959.","journal-title":"Caries Res"},{"key":"6097_CR61","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1128\/JB.01377-09","volume":"192","author":"MR Sadykov","year":"2010","unstructured":"Sadykov MR, Mattes TA, Luong TT, Zhu Y, Day SR, Sifri CD, Lee CY, Somerville GA: Tricarboxylic acid cycle-dependent synthesis of Staphylococcus aureus Type 5 and 8 capsular polysaccharides. J Bacteriol. 2010, 192: 1459-1462. 10.1128\/JB.01377-09.","journal-title":"J Bacteriol"},{"key":"6097_CR62","doi-asserted-by":"publisher","first-page":"e1002359","DOI":"10.1371\/journal.ppat.1002359","volume":"7","author":"BP Howden","year":"2011","unstructured":"Howden BP, McEvoy CRE, Allen DL, Chua K, Gao W, Harrison PF, Bell J, Coombs G, Bennett-Wood V, Porter JL, Robins-Browne R, Davies JK, Seemann T, Stinear TP: Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR. PLoS Pathog. 2011, 7: e1002359-10.1371\/journal.ppat.1002359.","journal-title":"PLoS Pathog"},{"key":"6097_CR63","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1111\/j.1399-302X.1995.tb00140.x","volume":"10","author":"SG Dashper","year":"1995","unstructured":"Dashper SG, Riley PF, Reynolds EC: Characterization of glutamine transport in Streptococcus mutans. Oral Microbiol Immunol. 1995, 10: 183-187. 10.1111\/j.1399-302X.1995.tb00140.x.","journal-title":"Oral Microbiol Immunol"},{"key":"6097_CR64","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1128\/jb.179.3.650-655.1997","volume":"179","author":"DG Cvitkovitch","year":"1997","unstructured":"Cvitkovitch DG, Gutierrez JA, Bleiweis AS: Role of the citrate pathway in glutamate biosynthesis by Streptococcus mutans. J Bacteriol. 1997, 179: 650-655.","journal-title":"J Bacteriol"},{"key":"6097_CR65","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/s00203-007-0228-7","volume":"188","author":"H Yu","year":"2007","unstructured":"Yu H, Yao Y, Liu Y, Jiao R, Jiang W, Zhao G: A complex role of Amycolatopsis mediterranei GlnR in nitrogen metabolism and related antibiotics production. Arch Microbiol. 2007, 188: 89-96. 10.1007\/s00203-007-0228-7.","journal-title":"Arch Microbiol"},{"key":"6097_CR66","doi-asserted-by":"publisher","first-page":"1433","DOI":"10.1128\/JB.01161-09","volume":"192","author":"E Rolerson","year":"2010","unstructured":"Rolerson E, Swick A, Newlon L, Palmer C, Pan Y, Keeshan B, Spatafora G: The SloR\/Dlg metalloregulator modulates Streptococcus mutans virulence gene expression. J Bacteriol. 2010, 192: 1433-1443. 10.1128\/JB.01161-09.","journal-title":"J Bacteriol"},{"key":"6097_CR67","doi-asserted-by":"publisher","first-page":"6605","DOI":"10.1128\/JB.06122-11","volume":"193","author":"P Chattoraj","year":"2011","unstructured":"Chattoraj P, Mohapatra SS, Rao JLUM, Biswas I: Regulation of transcription by SMU.1349, a TetR family regulator, in Streptococcus mutans. J Bacteriol. 2011, 193: 6605-6613. 10.1128\/JB.06122-11.","journal-title":"J Bacteriol"},{"key":"6097_CR68","doi-asserted-by":"publisher","first-page":"1799","DOI":"10.1099\/mic.0.2007\/005975-0","volume":"153","author":"J Kreth","year":"2007","unstructured":"Kreth J, Hung DCI, Merritt J, Perry J, Zhu L, Goodman SD, Cvitkovitch DG, Shi W, Qi F: The response regulator ComE in Streptococcus mutans functions both as a transcription activator of mutacin production and repressor of CSP biosynthesis. Microbiology. 2007, 153: 1799-1807. 10.1099\/mic.0.2007\/005975-0.","journal-title":"Microbiology"},{"key":"6097_CR69","doi-asserted-by":"publisher","first-page":"984","DOI":"10.1128\/JB.01169-09","volume":"192","author":"K Krastel","year":"2010","unstructured":"Krastel K, Senadheera DB, Mair R, Downey JS, Goodman SD, Cvitkovitch DG: Characterization of a glutamate transporter operon, glnQHMP, in Streptococcus mutans and its role in acid tolerance. J Bacteriol. 2010, 192: 984-993. 10.1128\/JB.01169-09.","journal-title":"J Bacteriol"},{"key":"6097_CR70","doi-asserted-by":"publisher","first-page":"403","DOI":"10.2217\/fmb.09.129","volume":"5","author":"R Matsui","year":"2010","unstructured":"Matsui R, Cvitkovitch D: Acid tolerance mechanisms utilized by Streptococcus mutans. Future Microbiol. 2010, 5: 403-417. 10.2217\/fmb.09.129.","journal-title":"Future Microbiol"},{"key":"6097_CR71","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1111\/j.1399-302X.1997.tb00390.x","volume":"12","author":"G Svens\u00e4ter","year":"1997","unstructured":"Svens\u00e4ter G, Larsson UB, Greif EC, Cvitkovitch DG, Hamilton IR: Acid tolerance response and survival by oral bacteria. Oral Microbiol Immunol. 1997, 12: 266-273. 10.1111\/j.1399-302X.1997.tb00390.x.","journal-title":"Oral Microbiol Immunol"},{"key":"6097_CR72","doi-asserted-by":"publisher","first-page":"7363","DOI":"10.1128\/JB.01054-09","volume":"191","author":"Y Liu","year":"2009","unstructured":"Liu Y, Burne RA: Multiple two-component systems of Streptococcus mutans regulate agmatine deiminase gene expression and stress tolerance. J Bacteriol. 2009, 191: 7363-7366. 10.1128\/JB.01054-09.","journal-title":"J Bacteriol"},{"key":"6097_CR73","doi-asserted-by":"publisher","first-page":"3968","DOI":"10.1128\/IAI.72.7.3968-3973.2004","volume":"72","author":"SF Lee","year":"2004","unstructured":"Lee SF, Delaney GD, Elkhateeb M: A two-component covRS regulatory system regulates expression of fructosyltransferase and a novel extracellular carbohydrate in Streptococcus mutans. Infect Immun. 2004, 72: 3968-3973. 10.1128\/IAI.72.7.3968-3973.2004.","journal-title":"Infect Immun"},{"key":"6097_CR74","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1177\/154405910708600705","volume":"86","author":"DM Deng","year":"2007","unstructured":"Deng DM, Liu MJ, Cate JM t, Crielaard W: The VicRK system of Streptococcus mutans responds to oxidative stress. J Dent Res. 2007, 86: 606-610. 10.1177\/154405910708600705.","journal-title":"J Dent Res"},{"key":"6097_CR75","doi-asserted-by":"publisher","first-page":"2856","DOI":"10.1099\/mic.0.028456-0","volume":"155","author":"YDN Tremblay","year":"2009","unstructured":"Tremblay YDN, Lo H, Li Y, Halperin SA, Lee SF: Expression of the Streptococcus mutans essential two-component regulatory system VicRK is pH and growth-phase dependent and controlled by the LiaFSR three-component regulatory system. Microbiology. 2009, 155: 2856-2865. 10.1099\/mic.0.028456-0.","journal-title":"Microbiology"},{"key":"6097_CR76","doi-asserted-by":"publisher","first-page":"4064","DOI":"10.1128\/JB.187.12.4064-4076.2005","volume":"187","author":"MD Senadheera","year":"2005","unstructured":"Senadheera MD, Guggenheim B, Spatafora GA, Huang YC, Choi J, Hung DCI, Treglown JS, Goodman SD, Ellen RP, Cvitkovitch DG: A VicRK signal transduction system in Streptococcus mutans affects gtfBCD, gbpB, and ftf expression, biofilm formation, and genetic competence development. J Bacteriol. 2005, 187: 4064-4076. 10.1128\/JB.187.12.4064-4076.2005.","journal-title":"J Bacteriol"},{"key":"6097_CR77","doi-asserted-by":"publisher","first-page":"6415","DOI":"10.1128\/JB.00793-09","volume":"191","author":"D Senadheera","year":"2009","unstructured":"Senadheera D, Krastel K, Mair R, Persadmehr A, Abranches J, Burne RA, Cvitkovitch DG: Inactivation of VicK affects acid production and acid survival of Streptococcus mutans. J Bacteriol. 2009, 191: 6415-6424. 10.1128\/JB.00793-09.","journal-title":"J Bacteriol"},{"key":"6097_CR78","doi-asserted-by":"publisher","first-page":"3773","DOI":"10.1128\/IAI.73.6.3773-3777.2005","volume":"73","author":"CM L\u00e9vesque","year":"2005","unstructured":"L\u00e9vesque CM, Voronejskaia E, Huang YC, Mair RW, Ellen RP, Cvitkovitch DG: Involvement of sortase anchoring of cell wall proteins in biofilm formation by Streptococcus mutans. Infect Immun. 2005, 73: 3773-3777. 10.1128\/IAI.73.6.3773-3777.2005.","journal-title":"Infect Immun"},{"key":"6097_CR79","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1128\/IAI.00725-10","volume":"79","author":"C Duque","year":"2011","unstructured":"Duque C, Stipp RN, Wang B, Smith DJ, H\u00f6fling JF, Kuramitsu HK, Duncan MJ, Mattos-Graner RO: Downregulation of GbpB, a component of the VicRK regulon, affects biofilm formation and cell surface characteristics of Streptococcus mutans. Infect Immun. 2011, 79: 786-796. 10.1128\/IAI.00725-10.","journal-title":"Infect Immun"},{"key":"6097_CR80","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1128\/JB.06071-11","volume":"194","author":"DB Senadheera","year":"2012","unstructured":"Senadheera DB, Cordova M, Ayala EA, LE de Ch\u00e1vez P, Singh K, Downey JS, Svens\u00e4ter G, Goodman SD, Cvitkovitch DG: Regulation of bacteriocin production and cell death by the VicRK signaling system in Streptococcus mutans. J Bacteriol. 2012, 194: 1307-1316. 10.1128\/JB.06071-11.","journal-title":"J Bacteriol"},{"key":"6097_CR81","doi-asserted-by":"publisher","first-page":"3464","DOI":"10.1128\/JB.00119-10","volume":"192","author":"B Sperandio","year":"2010","unstructured":"Sperandio B, Gautier C, Pons N, Ehrlich DS, Renault P, Gu\u00e9don E: Three paralogous LysR-type transcriptional regulators control sulfur amino acid supply in Streptococcus mutans. J Bacteriol. 2010, 192: 3464-3473. 10.1128\/JB.00119-10.","journal-title":"J Bacteriol"},{"key":"6097_CR82","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1111\/j.1365-2958.2011.07633.x","volume":"80","author":"B Fleuchot","year":"2011","unstructured":"Fleuchot B, Gitton C, Guillot A, Vidic J, Nicolas P, Besset C, Fontaine L, Hols P, Leblond-Bourget N, Monnet V, Gardan R: Rgg proteins associated with internalized small hydrophobic peptides: a new quorum-sensing mechanism in streptococci. Mol Microbiol. 2011, 80: 1102-1119. 10.1111\/j.1365-2958.2011.07633.x.","journal-title":"Mol Microbiol"},{"key":"6097_CR83","doi-asserted-by":"publisher","first-page":"39618","DOI":"10.1074\/jbc.M106425200","volume":"276","author":"SR Filipe","year":"2001","unstructured":"Filipe SR, Severina E, Tomasz A: Functional analysis of Streptococcus pneumoniae MurM reveals the region responsible for its specificity in the synthesis of branched cell wall peptides. J Biol Chem. 2001, 276: 39618-39628. 10.1074\/jbc.M106425200.","journal-title":"J Biol Chem"},{"key":"6097_CR84","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1089\/10766290152773310","volume":"7","author":"SR Filipe","year":"2001","unstructured":"Filipe SR, Severina E, Tomasz A: The role of murMN operon in penicillin resistance and antibiotic tolerance of Streptococcus pneumoniae. Microb Drug Resist. 2001, 7: 303-316. 10.1089\/10766290152773310.","journal-title":"Microb Drug Resist"},{"key":"6097_CR85","doi-asserted-by":"publisher","first-page":"1550","DOI":"10.1073\/pnas.032671699","volume":"99","author":"SR Filipe","year":"2002","unstructured":"Filipe SR, Severina E, Tomasz A: The murMN operon: a functional link between antibiotic resistance and antibiotic tolerance in Streptococcus pneumoniae. Proc Natl Acad Sci U S A. 2002, 99: 1550-1555. 10.1073\/pnas.032671699.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6097_CR86","doi-asserted-by":"publisher","first-page":"4891","DOI":"10.1073\/pnas.080067697","volume":"97","author":"SR Filipe","year":"2000","unstructured":"Filipe SR, Tomasz A: Inhibition of the expression of penicillin resistance in Streptococcus pneumoniae by inactivation of cell wall muropeptide branching genes. Proc Natl Acad Sci U S A. 2000, 97: 4891-4896. 10.1073\/pnas.080067697.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6097_CR87","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nrmicro2677","volume":"10","author":"A Typas","year":"2012","unstructured":"Typas A, Banzhaf M, Gross CA, Vollmer W: From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol. 2012, 10: 123-136.","journal-title":"Nat Rev Microbiol"},{"key":"6097_CR88","doi-asserted-by":"publisher","first-page":"3151","DOI":"10.1128\/AAC.46.10.3151-3155.2002","volume":"46","author":"BLM de Jonge","year":"2002","unstructured":"de Jonge BLM, Gage D, Xu N: The carboxyl terminus of peptidoglycan stem peptides is a determinant for methicillin resistance in Staphylococcus aureus. Antimicrob Agents Chemother. 2002, 46: 3151-3155. 10.1128\/AAC.46.10.3151-3155.2002.","journal-title":"Antimicrob Agents Chemother"},{"key":"6097_CR89","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1128\/jb.170.5.2143-2147.1988","volume":"170","author":"JF Garcia-Bustos","year":"1988","unstructured":"Garcia-Bustos JF, Chait BT, Tomasz A: Altered peptidoglycan structure in a pneumococcal transformant resistant to penicillin. J Bacteriol. 1988, 170: 2143-2147.","journal-title":"J Bacteriol"},{"key":"6097_CR90","doi-asserted-by":"publisher","first-page":"5415","DOI":"10.1073\/pnas.87.14.5415","volume":"87","author":"J Garcia-Bustos","year":"1990","unstructured":"Garcia-Bustos J, Tomasz A: A biological price of antibiotic resistance: major changes in the peptidoglycan structure of penicillin-resistant pneumococci. Proc Natl Acad Sci U S A. 1990, 87: 5415-5419. 10.1073\/pnas.87.14.5415.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6097_CR91","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1136\/ard.62.10.976","volume":"62","author":"E Simelyte","year":"2003","unstructured":"Simelyte E, Rimpil\u00e4inen M, Zhang X, Toivanen P: Role of peptidoglycan subtypes in the pathogenesis of bacterial cell wall arthritis. Ann Rheum Dis. 2003, 62: 976-982. 10.1136\/ard.62.10.976.","journal-title":"Ann Rheum Dis"},{"key":"6097_CR92","doi-asserted-by":"publisher","first-page":"2546","DOI":"10.1128\/JB.00028-10","volume":"192","author":"JK Kajfasz","year":"2010","unstructured":"Kajfasz JK, Rivera-Ramos I, Abranches J, Martinez AR, Rosalen PL, Derr AM, Quivey RG, Lemos JA: Two Spx proteins modulate stress tolerance, survival, and virulence in Streptococcus mutans. J Bacteriol. 2010, 192: 2546-2556. 10.1128\/JB.00028-10.","journal-title":"J Bacteriol"},{"key":"6097_CR93","doi-asserted-by":"publisher","first-page":"7032","DOI":"10.1128\/JB.00703-07","volume":"189","author":"B Sperandio","year":"2007","unstructured":"Sperandio B, Gautier C, McGovern S, Ehrlich DS, Renault P, Martin-Verstraete I, Gu\u00e9don E: Control of methionine synthesis and uptake by MetR and homocysteine in Streptococcus mutans. J Bacteriol. 2007, 189: 7032-7044. 10.1128\/JB.00703-07.","journal-title":"J Bacteriol"},{"key":"6097_CR94","doi-asserted-by":"publisher","first-page":"7863","DOI":"10.1128\/JB.187.22.7863-7865.2005","volume":"187","author":"DM Catt","year":"2005","unstructured":"Catt DM, Gregory RL: Streptococcus mutans murein hydrolase. J Bacteriol. 2005, 187: 7863-7865. 10.1128\/JB.187.22.7863-7865.2005.","journal-title":"J Bacteriol"},{"key":"6097_CR95","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1128\/JB.00926-12","volume":"195","author":"D Dufour","year":"2013","unstructured":"Dufour D, L\u00e9vesque CM: Cell death of Streptococcus mutans induced by a quorum-sensing peptide occurs via a conserved streptococcal autolysin. J Bacteriol. 2013, 195: 105-114. 10.1128\/JB.00926-12.","journal-title":"J Bacteriol"},{"key":"6097_CR96","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1101\/gr.10.8.1204","volume":"10","author":"M Huynen","year":"2000","unstructured":"Huynen M, Snel B, Lathe W, Bork P: Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 2000, 10: 1204-1210. 10.1101\/gr.10.8.1204.","journal-title":"Genome Res"},{"key":"6097_CR97","doi-asserted-by":"publisher","first-page":"2822","DOI":"10.1093\/nar\/gki573","volume":"33","author":"H Wu","year":"2005","unstructured":"Wu H, Su Z, Mao F, Olman V, Xu Y: Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Res. 2005, 33: 2822-2837. 10.1093\/nar\/gki573.","journal-title":"Nucleic Acids Res"},{"key":"6097_CR98","doi-asserted-by":"publisher","first-page":"e7979","DOI":"10.1371\/journal.pone.0007979","volume":"4","author":"K Mavromatis","year":"2009","unstructured":"Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM, Kyrpides NC: Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. PLoS One. 2009, 4: e7979-10.1371\/journal.pone.0007979.","journal-title":"PLoS One"},{"key":"6097_CR99","doi-asserted-by":"publisher","first-page":"1707","DOI":"10.1128\/IAI.00027-12","volume":"80","author":"JP Allen","year":"2012","unstructured":"Allen JP, Neely MN: CpsY influences Streptococcus iniae cell wall adaptations important for neutrophil intracellular survival. Infect Immun. 2012, 80: 1707-1715. 10.1128\/IAI.00027-12.","journal-title":"Infect Immun"},{"key":"6097_CR100","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1111\/mmi.12029","volume":"86","author":"MJ Federle","year":"2012","unstructured":"Federle MJ, Morrison DA: One if by land, two if by sea: signalling to the ranks with CSP and XIP. Mol Microbiol. 2012, 86: 241-245. 10.1111\/mmi.12029.","journal-title":"Mol Microbiol"},{"key":"6097_CR101","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1111\/j.1365-2958.2010.07361.x","volume":"78","author":"L Mashburn-Warren","year":"2010","unstructured":"Mashburn-Warren L, Morrison DA, Federle MJ: A novel double-tryptophan peptide pheromone controls competence in Streptococcus spp. via an Rgg regulator. Mol Microbiol. 2010, 78: 589-606. 10.1111\/j.1365-2958.2010.07361.x.","journal-title":"Mol Microbiol"},{"key":"6097_CR102","doi-asserted-by":"publisher","first-page":"E905","DOI":"10.1073\/pnas.1119172109","volume":"109","author":"K Beilharz","year":"2012","unstructured":"Beilharz K, Nov\u00e1kov\u00e1 L, Fadda D, Branny P, Massidda O, Veening J: Control of cell division in Streptococcus pneumoniae by the conserved Ser\/Thr protein kinase StkP. Proc Natl Acad Sci U S A. 2012, 109: E905-13. 10.1073\/pnas.1119172109.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6097_CR103","doi-asserted-by":"publisher","first-page":"2209","DOI":"10.1128\/IAI.01167-09","volume":"78","author":"LD Banu","year":"2010","unstructured":"Banu LD, Conrads G, Rehrauer H, Hussain H, Allan E, van der Ploeg JR: The Streptococcus mutans serine\/threonine kinase, PknB, regulates competence development, bacteriocin production, and cell wall metabolism. Infect Immun. 2010, 78: 2209-2220. 10.1128\/IAI.01167-09.","journal-title":"Infect Immun"},{"key":"6097_CR104","doi-asserted-by":"publisher","first-page":"1628","DOI":"10.1128\/JB.188.4.1628-1632.2006","volume":"188","author":"H Hussain","year":"2006","unstructured":"Hussain H, Branny P, Allan E: A eukaryotic-type serine\/threonine protein kinase is required for biofilm formation, genetic competence, and acid resistance in Streptococcus mutans. J Bacteriol. 2006, 188: 1628-1632. 10.1128\/JB.188.4.1628-1632.2006.","journal-title":"J Bacteriol"},{"key":"6097_CR105","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1038\/nrmicro2620","volume":"9","author":"M G\u00fcell","year":"2011","unstructured":"G\u00fcell M, Yus E, Lluch-Senar M, Serrano L: Bacterial transcriptomics: what is beyond the RNA horiz-ome?. Nat Rev Microbiol. 2011, 9: 658-669. 10.1038\/nrmicro2620.","journal-title":"Nat Rev Microbiol"},{"key":"6097_CR106","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.tim.2011.01.004","volume":"19","author":"S Bhatt","year":"2011","unstructured":"Bhatt S, Romeo T, Kalman D: Honing the message: post-transcriptional and post-translational control in attaching and effacing pathogens. Trends Microbiol. 2011, 19: 217-224. 10.1016\/j.tim.2011.01.004.","journal-title":"Trends Microbiol"},{"key":"6097_CR107","doi-asserted-by":"publisher","first-page":"e54291","DOI":"10.1371\/journal.pone.0054291","volume":"8","author":"S Koyanagi","year":"2013","unstructured":"Koyanagi S, L\u00e9vesque CM: Characterization of a Streptococcus mutans intergenic region containing a small toxic peptide and its cis-encoded antisense small RNA antitoxin. PLoS One. 2013, 8: e54291-10.1371\/journal.pone.0054291.","journal-title":"PLoS One"},{"key":"6097_CR108","doi-asserted-by":"publisher","first-page":"17466","DOI":"10.1073\/pnas.0508778102","volume":"102","author":"A Hasona","year":"2005","unstructured":"Hasona A, Crowley PJ, Levesque CM, Mair RW, Cvitkovitch DG, Bleiweis AS, Brady LJ: Streptococcal viability and diminished stress tolerance in mutants lacking the signal recognition particle pathway or YidC2. Proc Natl Acad Sci U S A. 2005, 102: 17466-17471. 10.1073\/pnas.0508778102.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6097_CR109","doi-asserted-by":"publisher","first-page":"1219","DOI":"10.1128\/JB.01146-06","volume":"189","author":"A Hasona","year":"2007","unstructured":"Hasona A, Zuobi-Hasona K, Crowley PJ, Abranches J, Ruelf MA, Bleiweis AS, Brady LJ: Membrane composition changes and physiological adaptation by Streptococcus mutans signal recognition particle pathway mutants. J Bacteriol. 2007, 189: 1219-1230. 10.1128\/JB.01146-06.","journal-title":"J Bacteriol"},{"key":"6097_CR110","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1093\/bib\/bbp043","volume":"11","author":"PD Karp","year":"2010","unstructured":"Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R: Pathway Tools version 13.0: integrated software for pathway\/genome informatics and systems biology. Brief Bioinform. 2010, 11: 40-79. 10.1093\/bib\/bbp043.","journal-title":"Brief Bioinform"},{"key":"6097_CR111","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1038\/msb.2011.99","volume":"8","author":"T Ideker","year":"2012","unstructured":"Ideker T, Krogan NJ: Differential network biology. Mol Syst Biol. 2012, 8: 565-","journal-title":"Mol Syst Biol"},{"key":"6097_CR112","doi-asserted-by":"publisher","first-page":"e24702","DOI":"10.1371\/journal.pone.0024702","volume":"6","author":"B Valc\u00e1rcel","year":"2011","unstructured":"Valc\u00e1rcel B, W\u00fcrtz P, al Seich Basatena N, Tukiainen T, Kangas AJ, Soininen P, J\u00e4rvelin M, Ala-Korpela M, Ebbels TM, de Iorio M: A differential network approach to exploring differences between biological states: an application to prediabetes. PLoS One. 2011, 6: e24702-10.1371\/journal.pone.0024702.","journal-title":"PLoS One"},{"key":"6097_CR113","doi-asserted-by":"publisher","first-page":"D93","DOI":"10.1093\/nar\/gkn421","volume":"36","author":"N Sierro","year":"2008","unstructured":"Sierro N, Makita Y, de Hoon M, Nakai K: DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 2008, 36: D93-96. 10.1093\/nar\/gkn421.","journal-title":"Nucleic Acids Res"},{"key":"6097_CR114","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","volume":"13","author":"L Li","year":"2003","unstructured":"Li L, Stoeckert CJ, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13: 2178-2189. 10.1101\/gr.1224503.","journal-title":"Genome Res"},{"key":"6097_CR115","doi-asserted-by":"publisher","first-page":"W119","DOI":"10.1093\/nar\/gkn304","volume":"36","author":"M Thomas-Chollier","year":"2008","unstructured":"Thomas-Chollier M, Sand O, Turatsinze J, Janky R, Defrance M, Vervisch E, Broh\u00e9e S, van Helden J: RSAT: regulatory sequence analysis tools. Nucleic Acids Res. 2008, 36: W119-27. 10.1093\/nar\/gkn304.","journal-title":"Nucleic Acids Res"},{"key":"6097_CR116","doi-asserted-by":"publisher","first-page":"1578","DOI":"10.1038\/nprot.2008.97","volume":"3","author":"J Turatsinze","year":"2008","unstructured":"Turatsinze J, Thomas-Chollier M, Defrance M, van Helden J: Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc. 2008, 3: 1578-1588. 10.1038\/nprot.2008.97.","journal-title":"Nat Protoc"},{"key":"6097_CR117","doi-asserted-by":"publisher","first-page":"4286","DOI":"10.1128\/IAI.00207-11","volume":"79","author":"JJ Gillespie","year":"2011","unstructured":"Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW: PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun. 2011, 79: 4286-4298. 10.1128\/IAI.00207-11.","journal-title":"Infect Immun"},{"key":"6097_CR118","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","volume":"27","author":"ME Smoot","year":"2011","unstructured":"Smoot ME, Ono K, Ruscheinski J, Wang P, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27: 431-432. 10.1093\/bioinformatics\/btq675.","journal-title":"Bioinformatics"},{"key":"6097_CR119","doi-asserted-by":"publisher","first-page":"1746","DOI":"10.1093\/bioinformatics\/bth163","volume":"20","author":"N Kashtan","year":"2004","unstructured":"Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics. 2004, 20: 1746-1758. 10.1093\/bioinformatics\/bth163.","journal-title":"Bioinformatics"},{"key":"6097_CR120","doi-asserted-by":"publisher","first-page":"924","DOI":"10.1038\/nprot.2007.132","volume":"2","author":"KL Heckmann","year":"2007","unstructured":"Heckmann KL, Pease LR: Gene splicing and mutagenesis by PCR-driven overlap extension. Nat Protoc. 2007, 2: 924-932. 10.1038\/nprot.2007.132.","journal-title":"Nat Protoc"},{"key":"6097_CR121","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1128\/JB.183.3.897-908.2001","volume":"183","author":"YH Li","year":"2001","unstructured":"Li YH, Lau PC, Lee JH, Ellen RP, Cvitkovitch DG: Natural genetic transformation of Streptococcus mutans growing in biofilms. J Bacteriol. 2001, 183: 897-908. 10.1128\/JB.183.3.897-908.2001.","journal-title":"J Bacteriol"},{"key":"6097_CR122","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1128\/aem.57.4.1194-1201.1991","volume":"57","author":"GM Dunny","year":"1991","unstructured":"Dunny GM, Lee LN, LeBlanc DJ: Improved electroporation and cloning vector system for gram-positive bacteria. Appl Environ Microbiol. 1991, 57: 1194-1201.","journal-title":"Appl Environ Microbiol"},{"key":"6097_CR123","doi-asserted-by":"publisher","first-page":"1863","DOI":"10.1128\/JB.01363-10","volume":"193","author":"A Lemme","year":"2011","unstructured":"Lemme A, Gr\u00f6be L, Reck M, Tomasch J, Wagner-D\u00f6bler I: Subpopulation-specific transcriptome analysis of competence-stimulating-peptide-induced Streptococcus mutans. J Bacteriol. 2011, 193: 1863-1877. 10.1128\/JB.01363-10.","journal-title":"J Bacteriol"}],"updated-by":[{"DOI":"10.1186\/1471-2164-15-739","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2014,8,29]],"date-time":"2014-08-29T00:00:00Z","timestamp":1409270400000}}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-15-362.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T23:54:18Z","timestamp":1630540458000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-15-362"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,12]]},"references-count":123,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6097"],"URL":"https:\/\/doi.org\/10.1186\/1471-2164-15-362","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,12]]},"assertion":[{"value":"27 November 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 April 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 May 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"362"}}