Research progress in Shigella in the postgenomic era

Science China Life Sciences

Volumn 53, Issue 11, 2010, Pages 1284-1290

  Peng, Jun Ping ^a   Yang, Jian ^a   Jin, Qi ^a  

^a INSTITUTE OF PATHOGEN BIOLOGY   (China)

Author keywords

genomics; proteomics; Shigella; structural biology; transcriptomics

Indexed keywords

BACTERIAL PROTEIN;

ANIMAL; BACTERIAL GENOME; CHEMISTRY; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METABOLISM; MICROBIOLOGY; MORTALITY; PROTEOMICS; REVIEW; SHIGELLA; SHIGELLOSIS;

ANIMALS; BACTERIAL PROTEINS; COMPARATIVE GENOMIC HYBRIDIZATION; DYSENTERY, BACILLARY; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; HUMANS; PROTEOMICS; SHIGELLA;

NEGIBACTERIA; SHIGELLA; SHIGELLA BOYDII; SHIGELLA DYSENTERIAE; SHIGELLA FLEXNERI; SHIGELLA SONNEI;

EID: 78249251496     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-010-4089-y     Document Type: Review

References (80)

1. Kotloff K L, Winickoff J P, Ivanoff B, et al. Global burden of Shigella infections: Implications for vaccine development and implementation of control strategies. Bull World Health Organ, 1999, 77: 651-666.
2. von Seidlein L, Kim D R, Ali M, et al. A multicentre study of Shigella diarrhoea in six Asian countries: Disease burden, clinical manifestations, and microbiology. PLoS Med, 2006, 3: e353.
3. Ashkenazi S, Levy I, Kazaronovski V, et al. Growing antimicrobial resistance of Shigella isolates. J Antimicrob Chemoth, 2003, 51: 427-429.
4. Sansonetti P J. Shigellosis: An old disease in new clothes? PLoS Med, 2006, 3: e354.
5. Pupo G M, Lan R, Reeves P R. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci USA, 2000, 97: 10567-10572.
6. Pupo G M, Karaolis D K, Lan R, et al. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect Immun, 1997, 65: 2685-2692.
7. Peng J, Zhang X, Yang J, et al. The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella. BMC Genomics, 2006, 7: 218.
8. Yang F, Yang J, Zhang X, et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res, 2005, 33: 6445-6458.
9. Jin Q, Yuan Z, Xu J, et al. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res, 2002, 30: 4432-4441.
10. Wirth T, Falush D, Lan R, et al. Sex and virulence in Escherichia coli: An evolutionary perspective. Mol Microbiol, 2006, 60: 1136-1151.
11. Buchrieser C, Glaser P, Rusniok C, et al. The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol Microbiol, 2000, 38: 760-771.
12. Wei J, Goldberg M B, Burland V, et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun, 2003, 71: 2775-2786.
13. Nie H, Yang F, Zhang X, et al. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics, 2006, 7: 173.
14. Jiang Y, Yang F, Zhang X, et al. The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei. Plasmid, 2005, 54: 149-159.
15. Venkatesan M M, Goldberg M B, Rose D J, et al. Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect Immun, 2001, 69: 3271-3285.
16. Jennison A V, Verma N K. Shigella flexneri infection: Pathogenesis and vaccine development. FEMS Microbiol Rev, 2004, 28: 43-58.
17. Lan R, Reeves P R. Escherichia coli in disguise: Molecular origins of Shigella. Microbes Infect, 2002, 4: 1125-1132.
18. Sansonetti P J. Rupture, invasion and inflammatory destruction of the intestinal barrier by Shigella, making sense of prokaryote-eukaryote cross-talks. FEMS Microbiol Rev, 2001, 25: 3-14.
19. Schroeder G N, Hilbi H. Molecular pathogenesis of Shigella spp.: Controlling host cell signaling, invasion, and death by type III secretion. Clin Microbiol Rev, 2008, 21: 134-156.
20. Parsot C. Shigella type III secretion effectors: How, where, when, for what purposes? Curr Opin Microbiol, 2009, 12: 110-116.
21. Peng J, Yang J, Jin Q. The molecular evolutionary history of Shigella spp. and enteroinvasive Escherichia coli. Infect Genet Evol, 2009, 9: 147-152.
22. Ray K, Marteyn B, Sansonetti P J, et al. Life on the inside: The intracellular lifestyle of cytosolic bacteria. Nat Rev Microbiol, 2009, 7: 333-340.
23. Galluzzi L, Kroemer G. Shigella targets the mitochondrial checkpoint of programmed necrosis. Cell Host Microbe, 2009, 5: 107-109.
24. Dobrindt U, Agerer F, Michaelis K, et al. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacteriol, 2003, 185: 1831-1840.
25. Ogura Y, Ooka T, Asadulghani, et al. Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes. Genome Biol, 2007, 8: R138.
26. Chan K, Baker S, Kim C C, et al. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. J Bacteriol, 2003, 185: 553-563.
27. Porwollik S, Wong R M, McClelland M. Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis. Proc Natl Acad Sci USA, 2002, 99: 8956-8961.
28. Salama N, Guillemin K, McDaniel T K, et al. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci USA, 2000, 97: 14668-14673.
29. Dorrell N, Mangan J A, Laing K G, et al. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res, 2001, 11: 1706-1715.
30. Taboada E N, Acedillo R R, Carrillo C D, et al. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J Clin Microbiol, 2004, 42: 4566-4576.
31. Behr M A, Wilson M A, Gill W P, et al. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science, 1999, 284: 1520-1523.
32. Peng J, Yang L, Yang F, et al. Characterization of ST-4821 complex, a unique Neisseria meningitidis clone. Genomics, 2008, 91: 78-87.
33. Peng J, Zhang X, Shao Z, et al. Characterization of a new Neisseria meningitidis serogroup C clone from China. Scan J Infect Dis, 2008, 40: 63-66.
34. Fukiya S, Mizoguchi H, Tobe T, et al. Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J Bacteriol, 2004, 186: 3911-3921.
35. Yang J, Nie H, Chen L, et al. Revisiting the molecular evolutionary history of Shigella spp. J Mol Evol, 2007, 64: 71-79.
36. Lucchini S, Liu H, Jin Q, et al. Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: Insights into the strategies of a cytosolic bacterial pathogen. Infect Immun, 2005, 73: 88-102.
37. Eriksson S, Bjorkman J, Borg S, et al. Salmonella typhimurium mutants that downregulate phagocyte nitric oxide production. Cell Microbiol, 2000, 2: 239-250.
38. Dahan S, Knutton S, Shaw R K, et al. Transcriptome of enterohemorrhagic Escherichia coli O157 adhering to eukaryotic plasma membranes. Infect Immun, 2004, 72: 5452-5459.
39. Le Gall T, Mavris M, Martino M C, et al. Analysis of virulence plasmid gene expression defines three classes of effectors in the type III secretion system of Shigella flexneri. Microbiology, 2005, 151: 951-962.
40. Fu H, Leng W, Wang J, et al. Transcriptional profile induced by furazolidone treatment of Shigella flexneri. Appl Microbiol Biotechnol, 2007, 77: 657-667.
41. Cheng F, Wang J, Peng J, et al. Gene expression profiling of the pH response in Shigella flexneri 2a. FEMS Microbiol Lett, 2007, 270: 12-20.
42. Bin W, Liu M, Peng J, et al. Construction, detection and microarray analysis on Shigella dysenteriae a1 IroN, ShuA single, double mutants. Sci China Ser C-Life Sci, 2006, 49: 251-258.
43. Liu M, Liu H, Sun L, et al. Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant. Sci China Ser C-Life Sci, 2005, 48: 228-240.
44. Oglesby A G, Murphy E R, Iyer V R, et al. Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP. Mol Microbiol, 2005, 58: 1354-1367.
45. Ingersoll M A, Zychlinsky A. ShiA abrogates the innate T-cell response to Shigella flexneri infection. Infect Immun, 2006, 74: 2317-2327.
46. Murphy E R, Payne S M. RyhB, an iron-responsive small RNA molecule, regulates Shigella dysenteriae virulence. Infect Immun, 2007, 75: 3470-3477.
47. Le Gall T, Darlu P, Escobar-Paramo P, et al. Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species. Genome Res, 2005, 15: 260-268.
48. Wei C, Yang J, Zhu J, et al. Comprehensive proteomic analysis of Shigella flexneri 2a membrane proteins. J Proteome Res, 2006, 5: 1860-1865.
49. Wei C, Peng J, Xiong Z, et al. Subproteomic tools to increase genome annotation complexity. Proteomics, 2008, 8: 4209-4213.
50. Peng X, Ye X, Wang S. Identification of novel immunogenic proteins of Shigella flexneri 2a by proteomic methodologies. Vaccine, 2004, 22: 2750-2756.
51. Ying T Y, Wang J J, Wang H L, et al. Immunoproteomics of membrane proteins of Shigella flexneri 2a 2457T. World J Gastroentero, 2005, 11: 6880-6883.
52. Ying T, Wang H, Li M, et al. Immunoproteomics of outer membrane proteins and extracellular proteins of Shigella flexneri 2a 2457T. Proteomics, 2005, 5: 4777-4793.
53. Jennison A V, Raqib R, Verma N K. Immunoproteome analysis of soluble and membrane proteins of Shigella flexneri 2457T. World J Gastroentero, 2006, 12: 6683-6688.
54. Pieper R, Zhang Q, Parmar P P, et al. The Shigella dysenteriae serotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins. Proteomics, 2009, 9: 5029-5045.
55. Lario P I, Pfuetzner R A, Frey E A, et al. Structure and biochemical analysis of a secretin pilot protein. EMBO J, 2005, 24: 1111-1121.
56. Deane J E, Roversi P, Cordes F S, et al. Molecular model of a type III secretion system needle: Implications for host-cell sensing. Proc Natl Acad Sci USA, 2006, 103: 12529-12533.
57. Okon M, Moraes T F, Lario P I, et al. Structural characterization of the type-III pilot-secretin complex from Shigella flexneri. Structure, 2008, 16: 1544-1554.
58. Deane J E, Roversi P, King C, et al. Structures of the Shigella flexneri type 3 secretion system protein MxiC reveal conformational variability amongst homologues. J Mol Biol, 2008, 377: 985-992.
59. Davis J, Wang J, Tropea J E, et al. Novel fold of VirA, a type III secretion system effector protein from Shigella flexneri. Protein Sci, 2008, 17: 2167-2173.
60. Germane K L, Ohi R, Goldberg M B, et al. Structural and functional studies indicate that Shigella VirA is not a protease and does not directly destabilize microtubules. Biochemistry, 2008, 47: 10241-10243.
61. Johnson S, Roversi P, Espina M, et al. Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD. J Biol Chem, 2007, 282: 4035-4044.
62. Singer A U, Rohde J R, Lam R, et al. Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases. Nat Struct Mol Biol, 2008, 15: 1293-1301.
63. Zhu Y, Li H, Hu L, et al. Structure of a Shigella effector reveals a new class of ubiquitin ligases. Nat Struct Mol Biol, 2008, 15: 1302-1308.
64. Lunelli M, Lokareddy R K, Zychlinsky A, et al. IpaB-IpgC interaction defines binding motif for type III secretion translocator. Proc Natl Acad Sci USA, 2009, 106: 9661-9666.
65. van Eerde A, Hamiaux C, Perez J, et al. Structure of Spa15, a type III secretion chaperone from Shigella flexneri with broad specificity. EMBO Rep, 2004, 5: 477-483.
66. Deane J E, Graham S C, Mitchell E P, et al. Crystal structure of Spa40, the specificity switch for the Shigella flexneri type III secretion system. Mol Microbiol, 2008, 69: 267-276.
67. Paxman J J, Borg N A, Horne J, et al. The structure of the bacterial oxidoreductase enzyme DsbA in complex with a peptide reveals a basis for substrate specificity in the catalytic cycle of DsbA enzymes. J Biol Chem, 2009, 284: 17835-17845.
68. Ritschel T, Atmanene C, Reuter K, et al. An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and X-ray crystallography to decipher Tgt protein-protein and protein-RNA interaction. J Mol Biol, 2009, 393: 833-847.
69. Hu Y, Fan C P, Fu G, et al. Crystal structure of a glutamate/aspartate binding protein complexed with a glutamate molecule: Structural basis of ligand specificity at atomic resolution. J Mol Biol, 2008, 382: 99-111.
70. Vulliez-Le Normand B, Saul F A, Phalipon A, et al. Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody. Proc Natl Acad Sci USA, 2008, 105: 9976-9981.
71. Zhu D Y, Zhu Y Q, Huang R H, et al. Crystal structure of the copper homeostasis protein (CutCm) from Shigella flexneri at 1. 7 Å resolution: The first structure of a new sequence family of TIM barrels. Proteins, 2005, 58: 764-768.
72. Wang Q H, Hu W X, Gao W, et al. Crystal structure of the diadenosine tetraphosphate hydrolase from Shigella flexneri 2a. Proteins, 2006, 65: 1032-1035.
73. Kim Y, Maltseva N, Dementieva I, et al. Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 Å resolution. Proteins, 2006, 63: 1097-1101.
74. Aranda K R, Fagundes-Neto U, Scaletsky I C. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. J Clin Microbiol, 2004, 42: 5849-5853.
75. Brandal L T, Lindstedt B A, Aas L, et al. Octaplex PCR and fluorescence-based capillary electrophoresis for identification of human diarrheagenic Escherichia coli and Shigella spp. J Microbiol Meth, 2007, 68: 331-341.
76. Yang Y G, Song M K, Park S J, et al. Direct detection of Shigella flexneri and Salmonella typhimurium in human feces by real-time PCR. J Microbiol Biotechnol, 2007, 17: 1616-1621.
77. Li Y, Liu D, Cao B, et al. Development of a serotype-specific DNA microarray for identification of some Shigella and pathogenic Escherichia coli strains. J Clin Microbiol, 2006, 44: 4376-4383.
78. Jin D, Qi H, Chen S, et al. Simultaneous detection of six human diarrheal pathogens by using DNA microarray combined with tyramide signal amplification. J Microbiol Meth, 2008, 75: 365-368.
79. Li Y, Cao B, Liu B, et al. Molecular detection of all 34 distinct O-antigen forms of Shigella. J Med Microbiol, 2009, 58: 69-81.
80. Keasey S L, Schmid K E, Lee M S, et al. Extensive antibody cross-reactivity among infectious gram-negative bacteria revealed by proteome microarray analysis. Mol Cell Proteomics, 2009, 8: 924-935.