Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Veeranagouda, Yaligara ^a,b   Husain, Fasahath ^a   Tenorio, Elizabeth L ^c   Wexler, Hannah M ^a,b  

^a GLAVAHCS   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c TUFTS MEDICAL CENTER   (United States)

Author keywords

Bacteroides fragilis; COG; DEG; Essential genes; Massively parallel sequencing; Transposon mutants

Indexed keywords

TRANSCRIPTOME; CULTURE MEDIUM; TRANSPOSON;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL SURVIVAL; BACTERIUM CONJUGATION; BACTERIUM MUTANT; BACTEROIDES FRAGILIS; BACTEROIDES THETAIOTAOMICRON; CLASSIFICATION; ESSENTIAL GENE; GENE DISRUPTION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE INSERTION; GENE LIBRARY; GENE PATHWAY; GENETIC ANALYSIS; GENETIC COMPLEMENTATION; MOLECULAR GENETICS; NONHUMAN; ORTHOLOGY; PORPHYROMONAS GINGIVALIS; RNA SEQUENCE; SATURATED TRANSPOSON MUTANT LIBRARY; SEQUENCE ANALYSIS; SPECIES COMPARISON; STRAIN DIFFERENCE; TRANSPOSON; BACTERIAL GENE; CHEMISTRY; CULTURE MEDIUM; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; PHYSIOLOGY;

BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES FRAGILIS; NEGIBACTERIA; POSIBACTERIA;

BACTEROIDES FRAGILIS; CULTURE MEDIA; DNA TRANSPOSABLE ELEMENTS; GENE LIBRARY; GENES, BACTERIAL; GENES, ESSENTIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MUTATION;

EID: 84904721645     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-429     Document Type: Article

References (35)

1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007, 449:804-810. 10.1038/nature06244, 3709439, 17943116.
2. Wareham DW, Wilks M, Ahmed D, Brazier JS, Millar M. Anaerobic sepsis due to multidrug-resistant Bacteroides fragilis: microbiological cure and clinical response with linezolid therapy. Clin Inf Dis 2005, 40:e67-e68.
3. Brook I. The role of anaerobic bacteria in bacteremia. Anaerobe 2010, 16:183-189. 10.1016/j.anaerobe.2009.12.001, 20025984.
4. Wexler HM. Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev 2007, 20:593-621. 10.1128/CMR.00008-07, 2176045, 17934076.
5. Troy EB, Kasper DL. Beneficial effects of Bacteroides fragilis polysaccharides on the immune system. Frontiers bioscience (Landmark edition) 2010, 15:25-34.
6. Baughn AD, Malamy MH. The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen. Nature 2004, 427:441-444. 10.1038/nature02285, 14749831.
7. Houston S, Blakely G, McDowell A, Martin L, Patrick S. Binding and degradation of fibrinogen by Bacteroides fragilis and characterization of a 54 kDa fibrinogen-binding protein. Microbiol 2010, 156:2516-2526.
8. Connolly JC, McLean C, Tabaqchali S. The effect of capsular polysaccharide and lipopolysaccharide of Bacteroides fragilis on polymorph function and serum killing. J Med Microbiol 1984, 17:259-271. 10.1099/00222615-17-3-259, 6374150.
9. Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeño-Tárraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J. Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis. Microbiol 2010, 156:3255-3269.
10. Coyne MJ, Tzianabos AO, Mallory BC, Carey VJ, Kasper DL, Comstock LE. Polysaccharide Biosynthesis Locus Required for Virulence of Bacteroides fragilis Polysaccharide Biosynthesis Locus Required for Virulence of Bacteroides fragilis. Infect Immun 2001, 69:4342-4350. 10.1128/IAI.69.7.4342-4350.2001, 98505, 11401972.
11. Sherwood JE, Fraser S, Citron DM, Wexler H, Blakely G, Jobling K, Patrick S. Multi-drug resistant Bacteroides fragilis recovered from blood and severe leg wounds caused by an improvised explosive device (IED) in Afghanistan. Anaerobe 2011, 17:152-155. 10.1016/j.anaerobe.2011.02.007, 21376821.
12. Husain F, Veeranagouda Y, Hsi J, Meggersee R, Abratt V, Wexler HM. Two multidrug-resistant clinical isolates of Bacteroides fragilis carry a novel metronidazole resistance nim gene (nimJ). Antimicrob Agents Chemother 2013, 57:3767-3774. 10.1128/AAC.00386-13, 3719759, 23716049.
13. Baugh L, Gallagher L, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC. Combining functional and structural genomics to sample the essential Burkholderia structome. PLoS One 2013, 8:e53851. 10.1371/journal.pone.0053851, 3561365, 23382856.
14. Goodman AL, Wu M, Gordon JI. Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nat Protoc 2011, 6:1969-1980. 10.1038/nprot.2011.417, 3310428, 22094732.
15. Loman NJ, Constantinidou C, Chan JZM, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 2012, 10:599-606. 10.1038/nrmicro2850, 22864262.
16. Griffin JE, Gawronski JD, Dejesus MA, Ioerger TR, Akerley BJ, Sassetti CM. High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog 2011, 7:e1002251. 10.1371/journal.ppat.1002251, 3182942, 21980284.
17. Khatiwara A, Jiang T, Sung SS, Dawoud T, Kim JN, Bhattacharya D, Kim HB, Ricke SC, Kwon YM. Genome scanning for conditionally essential genes in Salmonella enterica Serotype Typhimurium. Appl Environ Microbiol 2012, 78:3098-3107. 10.1128/AEM.06865-11, 3346488, 22367088.
18. Salama NR, Shepherd B, Falkow S. Global Transposon Mutagenesis and Essential Gene Analysis of Helicobacter pylori. J Bacteriol 2004, 186:7926-7935. 10.1128/JB.186.23.7926-7935.2004, 529078, 15547264.
19. Liberati NT, Urbach JM, Miyata S, Lee DG, Drenkard E, Wu G, Villanueva J, Wei T, Ausubel FM. An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc Natl Acad Sci U S A 2006, 103:2833-2838. 10.1073/pnas.0511100103, 1413827, 16477005.
20. Luo H, Lin Y, Gao F, Zhang CT, Zhang R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res 2013, 42:D574-D580. 3965060, 24243843.
21. Klein B, Tenorio EL, Lazinski DW, Camilli A, Duncan MJ, Hu LT. Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis. BMC Genomics 2012, 13:578. 10.1186/1471-2164-13-578, 3547785, 23114059.
22. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko K, Tomita M, Wanner BL, Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2:1-11.
23. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 200, 100:4678-4683.
24. Cerdeno Tarraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B, Quail MA, Barron A, Clark L, Corton C, Doggett J, Holden MT, Larke N, Line A, Lord A, Norbertczak H, Ormond D, Price C, Rabbinowitsch E, Woodward J, Barrell B, Parkhill J. Extensive DNA inversions in the B. fragilis genome control variable gene expression: Supplemental online material. Science 2005, 307:1463-1465. 10.1126/science.1107008, 15746427.
25. Veeranagouda Y, Husain F, Wexler H. Transposon mutagenesis of Bacteroides fragilis using a mariner transposon vector. Anaerobe 2013, 22:126-129.
26. Rasmussen BA, Kovacs E. Cloning and identification of a two-component signal-transducing regulatory system from Bacteroides fragilis. Mol Microbiol 1993, 7:765-776. 10.1111/j.1365-2958.1993.tb01167.x, 8469117.
27. Krishnan K, Duncan M. Role of sodium in the RprY-dependent stress response in Porphyromonas gingivalis. PLoS One 2013, 8:e63180. 10.1371/journal.pone.0063180, 3646045, 23671672.
28. Kuwahara T, Yamashita A, Hirakawa H, Nakayama H, Toh H, Okada N, Kuhara S, Hattori M, Hayashi T, Ohnishi Y. Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc Natl Acad Sci U S A 2004, 101:14919-14924. 10.1073/pnas.0404172101, 522005, 15466707.
29. Chaudhuri R, Allen A, Owen P, Shalom G, Stone K, Harrison M, Burgis T, Lockyer M, Garcia-Lara J, Foster S, Pleasance S, Peters S, Maskell D, Charles I. Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH). BMC Genomics 2009, 10:291. 10.1186/1471-2164-10-291, 2721850, 19570206.
30. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
31. Wexler H, Tenorio E, Pumbwe L. Characteristics of Bacteroides fragilis lacking the major outer membrane protein, OmpA. Microbiol 2009, 155:2694-2706.
32. Wexler H. Pump it up: occurrence and regulation of multi-drug efflux pumps in Bacteroides fragilis. Anaerobe 2012, 18:200-208. 10.1016/j.anaerobe.2011.12.017, 22266580.
33. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res 2012, 40:D115-D122. 10.1093/nar/gkr1044, 3245086, 22194640.
34. Alikhan NF, Petty N, Ben Zakour N, Beatson S. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011, 12:402. 10.1186/1471-2164-12-402, 3163573, 21824423.
35. Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 2009, 4:363-371. 10.1038/nprot.2009.2, 19247286.