Novel algorithms reveal streptococcal transcriptomes and clues about undefined genes

PLoS Computational Biology

Volumn 3, Issue 7, 2007, Pages 1177-1194

  Ryan, Patricia A ^a   Kirk, Brian W ^a   Euler, Chad W ^a   Schuch, Raymond ^a   Fischetti, Vincent A ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CELL ADHESION; GENE EXPRESSION REGULATION; MICROARRAYS; OLIGONUCLEOTIDES;

CELL ADHERENCE; CLUSTERINGS; DYNAMIC PROCESS; GENE EXPRESSION PROFILES; HOSTS INTERACTIONS; IN-VITRO; MOLECULAR EVENTS; NOVEL ALGORITHM; TRANSCRIPTIONAL RESPONSE; TRANSCRIPTOMES;

GENE EXPRESSION;

DNA; TRANSCRIPTOME;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL COLONIZATION; BACTERIAL GENE; BACTERIUM ADHERENCE; CONTROLLED STUDY; DELETION MUTANT; DNA MICROARRAY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ALGORITHM; HOST PARASITE INTERACTION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHARYNX; STATISTICAL SIGNIFICANCE; STREPTOCOCCUS GROUP A; ALGORITHM; AUTOMATED PATTERN RECOGNITION; CELL ADHESION; CELL LINE; CHROMOSOME MAP; CLUSTER ANALYSIS; CYTOLOGY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; PHYSIOLOGY; STATISTICS; STREPTOCOCCUS PYOGENES;

BACTERIA (MICROORGANISMS); STREPTOCOCCUS SP. 'GROUP A';

ALGORITHMS; CELL ADHESION; CELL LINE; CLUSTER ANALYSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; PHARYNX; PHYSICAL CHROMOSOME MAPPING; SEQUENCE ANALYSIS, DNA; STREPTOCOCCUS PYOGENES;

EID: 34547586264     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030132     Document Type: Article

References (64)

1. Quakenbush J (2003) Microarrays - Guilt by association. Science 302: 240-241.
2. Conway T, Schoolnik GK (2003) Microarray expression profiling: Capturing a genome-wide portrait of the transcriptome. Mol Microbiol 47: 879-889.
3. Quakenbush J (2001) Computational analysis of microarray data. Nat Rev Genet 2: 418-427.
4. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
5. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 96: 2896-2901.
6. Audit B, Ouzounis CA (2003) From genes to genomes: Universal scaleinvariant properties of microbial chromosome organization. J Miol Biol 332: 617-633.
7. Cunningham MW (2000) Pathogenesis of group A streptococcal infections. Clin Microbiol Rev 13: 470-511.
8. Voyich JM, Sturdeyant DE, Braughton KR, Kobayashi SD, Lei B, et al. (2003) Genome-wide protective response used by group A Streptococcus to evade destruction by human polymorphonuclear leukocytes. Proc Natl Acad Sci U S A 100: 1996-2001.
9. Graham MR, Smoot LM, Migliaccio CA, Virtaneva K, Sturdevant DE, et al. (2002) Virulence control in group A Streptococcus by a two-component gene regulatory system: Global expression profiling and in vivo infection modeling. Proc Natl Acad Sci U S A 99: 13855-13860.
10. Virtaneva K, Porcella SF, Graham MR, Ireland RM, Johnson CA, et al. (2005) Longitudinal analysis of the group A Streptococcus transcriptome in experimental pharyngitis in cynomolgus macaques. Proc Natl Acad Sci U S A 102: 9014-9019.
11. Broudy TB, Pancholi V, Fischetti VA (2001) Induction of lysogenic bacteriophage and phage-associated toxin from group A streptococci during coculture with human pharyngeal cells. Infect Immun. 69: 1440-1443.
12. Broudy TB, Pancholi V, Fischetti VA (2002) The in vitro interaction of Streptococcus pyogenes with human pharyngeal cells induces a phage-encoded extracellular DNase. Infect Immun 70: 2805-2811.
13. Banks DJ, Lei B, Musser JM (2003) Prophage induction and expression of prophage-encoded virulence factors in group A Streptococcus serotype M3 strain MGAS315. Infect Immun 71: 7079-7086.
14. Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Savic G, et al. (2001) Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A 98: 4658-4663.
15. Ryan PA, Pancholi V, Fischetti VA (2001) Group A streptococci bind to mucin and human pharyngeal cells through sialic acid-containing receptors. Infect Immun 69: 7402-7412.
16. Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32 (Supplement): 490-495.
17. Yang YH, Speed TP (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3: 579-588.
18. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, et al. (2002) Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30: e15.
19. Dudoit S, Yang YH, Callow MJ, Speed TP (2001) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statist Sincia 12: 111-139.
20. Rousseeuw PJ,, Verboven S (2002) Robust estimation in very small samples. Comp Stat Data Anal 40: 741-758.
21. Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, et al. (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276: 19937-19944.
22. Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509-519.
23. Rajeevan MS, Ranamukhaarachchi DG, Vernon SD, Unger ER (2002) Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies. Nucleic Acids Res 30: e10.
24. Courtney HS, Hasty DL, Dale JB (2002) Molecular mechanisms of adhesion, colonization, and invasion of group A Streptococci. Ann Med 34: 77-87.
25. Sierig G, Cywes C, Wessles MR, Ashbaugh CD (2003) Cytotoxic effects of streptolysin o and streptolysin s enhance the virulence of poorly encapsulated group A streptococci. Infect Immun 71: 446-455.
26. Meehl MA, Caparon MG (2004) Specificity of streptolysin O in cytolysin-mediated translocation. Mol Microbiol 52: 1665-1676.
27. Hakansson A, Bentley CC, Shakhnovic EA, Wessels MR (2005) Cytolysin-dependent evasion of lysosomal killing. Proc Natl Acad Sci U S A 102: 5192-5197.
28. Hytönen J, Haataja S, Gerlach D, Podbielski A, Finne J (2001) The SpeB virulence factor of Streptococcus pyogenes, a multifunctional secreted and cell surface molecule with strepadhesin, laminin-binding and cysteine protease activity. Mol Microbiol 39: 512-519.
29. Lukomski S, Burns EH Jr, Wyde PR, Podbielski A, Rurangirwa J, et al. (1998) Genetic inactivation of an extracellular cysteine protease (SpeB) expressed by Streptococcus pyogenes decreases resistance to phagocytosis and dissemination to organs. Infect Immun 66: 771-776.
30. Kansal RG, Aziz RK, Kotb M (2005) Modulation of expression of superantigens by human transferring and lactoferrrin: A novel mechanism in host-streptococcus interactions. J Infect Dis 191: 2121-2129.
31. Kazmi SU, Kansal R, Aziz RK, Hooshdaran M, Norrby-Teglund A, et al. (2001) Reciprocal, temporal expression of SpeA and SpeB in invasive M1T1 group A streptococcal isolates in vivo. Infect Immun 69: 4988-4995.
32. Rasmussmen M, Björck L (2002) Proteolysis and its regulation at the surface of Streptococcus pyogenes. Mol Microbiol. 43: 537-544.
33. Burns EH Jr, Lukomski S, Rurangirwa J, Podbielski A, Musser JM (1998) Genetic inactivation of the extracellular cysteine protease enhances in vitro internalization of group A streptococci by human epithelial and endothelial cells. Microb Pathog 24: 333-339.
34. Chaussee MS, Cole RL, van Putten JP (2000) Streptococcal erythrogenic toxin B abrogates fibronectin-dependent internalization of Streptococcus pyogenes by cultured mammalian cells. Infect Immun 68: 3226-3232.
35. Nyberg P, Rasmussen M, von Pawel-Rammingen U, Björck L (2004) SpeB modulates fibronectin-dependent internalization of Streptococcus pyogenes by efficient proteolysis of cell-wall-anchored protein F1. Microbiol 150: 1559-1569.
36. Mora M, Bensi G, Capo S, Falugi F, Zingaretti C, et al. (2005) Group A Streptococcus produce pilus-like structures containing protective antigens and Lancefield T antigens. Proc Natl Acad Sci U S A 102: 15641-15646.
37. Aziz RK, Pabst MJ, Jeng A, Kansal R, Low DE, et al. (2004) Invasive M1T1 group A Streptococcus undergoes a phase-shift in vivo to prevent the proteolytic degradation of multiple virulence factors by SpeB. Mol Microbiol 51: 123-134.
38. Proft T, Moffatt SL,, Berkhan CJ, Fraser JD (1999) Identification and characterization of novel superantigens from Streptococcus pyogenes. J Exp Med 18: 89-101.
39. Canchaya C, Desiere F, McShan WM, Ferretti JJ, Parkhill J, et al. (2002) Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370. Virology 302: 245-258.
40. Lacks SA, Greenberg B, Lopez P (1995) A cluster of four genes encoding enzymes for five steps in the folate biosynthetic pathway of Streptococcus pneumoniae. J Bacteriol 177: 66-74.
41. 2+ uptake. Proc Natl Acad Sci U S A 100: 10213-10218.
42. Chaussee MS, Sylva GL, Sturdevant DE, Smoot LM, Graham MR, et al. (2002) Rgg influences the expression of multiple regulatory loci to coregulate virulence factor expression in Streptococcus pyogenes. Infect Immun 70: 762-770.
43. Chausee MS, Watson RO, Smoot JC, Musser JM (2001) Identification of Rgg-regulated exoproteins of Streptococcus pyogenes. Infect Immun 69: 822-831.
44. Datta V, Myskowski SM, Kwinn LA, Chiem DN, Varki N, et al. (2005) Mutational analysis of the group A streptococcal operon encoding streptolysin S and its virulence role in invasive infection. Mol Microbiol 56: 681-695.
45. Steiner K, Malke H (2001) relA-independent amino acid starvation response network of Streptococcus pyogenes. J Bacteriol 183: 7354-7364.
46. Bessen DE, Kalia A (2002) Genomic localization of a T serotype locus to a recombinatorial zone encoding extracellular matrix-binding proteins in Streptococcus pyogenes. Infect Immun 70: 1159-1167.
47. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, et al. (2002) The Pfam protein families database. Nucleic Acids Res 30: 276-280.
48. Mazmanian SK, Liu G, Ton-That H, Schneewind O (1999) Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall. Science 285: 760-763.
49. Pallen MJ, Lam AC, Antonio M, Dunbar K (2001) An embarrassment of sortases - A richness of substrates? Trends Microbiol 9: 97-102.
50. Kreikemeyer B, Nakata M, Oehmcke S, Gschwendtner C, Normann J, et al. (2005) Streptococcus pyogenes collagen type I-binding Cpa surface protein: Expression profile, binding characteristics, biological functions, and potential clinical impact. J Biol Chem 39: 33228-33239.
51. Shazand K, Tucker J, Grunberg-Manago M, Rabinowitz JC, Leighton T (1993) Similar organization of the nusA-infB operon in Bacillus subtilis and Escherichia coli. J Bacteriol 175: 2880-2887.
52. Yu L, Gunasekera AH, Mack J, Olejniczak ET, Chovan LE, et al. (2001) Solution structure and function of a conserved protein SP14.3 encoded by an essential Streptococcus pneumoniae gene. J Mol Biol 311: 593-604.
53. Osipiuk J, Gornicki P, Maj L, Dementieva I, Laskowski R, et al. (2001) Streptococcus pneumoniae YlxR at 1.35 A shows a putative new fold. Acta Crystallogr D Biol Crystallogr 57: 1747-1751.
54. Ermolaeva MD, White O, Salzberg SL (2001) Prediction of operons in microbial genomes. Nucleic Acid Res 29: 1216-1221.
55. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S (2002) Computational identification of operons in microbial genomes. Genome Res 12: 1221-1230.
56. Nizet V, Beall B, Bast DJ, Datta V, Kilburn L, et al. (2000) Genetic locus for streptolysin S production by group A streptococcus. Infect Immun 68: 4245-4254.
57. Ribardo DA, McIver KS (2006) Defining the Mga regulon: Comparative transcriptomes analysis reveals both direct and indirect regulation by Mga in the group A streptococcus. Mol Microbiol 62: 491-508.
58. Kreikemeyer B, McIver KS, Podbielski A (2003) Virulence factor regulation and regulatory networks in Streptococcus pyogenes and their impact on pathogen-host interactions. Trends Microbiol 11: 224-232.
59. Nelson D, Loomis L, Fischetti VA (2001) Prevention and elimination of upper respiratory colonization of mice by group A streptococci by using a bacteriophage lytic enzyme. Proc Natl Acad Sci U S A 98: 4107-4112.
60. Philbrick JB, Diner BA, Zilinskas BA (1991) Construction and characterization of cyanobacterial mutants lacking the manganese-stabilizing polypeptide of photosystem II. J Biol Chem 266: 13370-13376.
61. Klebanov L, Qiu S, Welle S, Yakovlev A (2007) Statistical methods and microarray data. Nat Biotechnol 25: 25-26.
62. Euler CW, Ryan PA, Martin JM, Fischetti VA (2007) M.SpyI, a DNA methyltransferase encoded on a mefA chimeric element, modifies the genome of Streptococcus pyogenes. J Bacteriol 189: 1044-1054.
63. Podbielski A, Spellerberg B, Woischnik M, Pohl B, Lutticken R (1996) Novel series of plasmid vectors for gene inactivation and expression in group A streptococci (GAS). Gene 177: 137-147.
64. Provvedi R, Maggi T, Oggioni MR, Manganelli R, Pozzi G (2005) Selection and characterization of a promoter for expression of single-copy recombinant genes in Gram-positive bacteria. BMC Biotechnol 5: 3.