Transcriptomic characterization of an infection of Mycobacterium smegmatis by the cluster A4 mycobacteriophage kampy

PLoS ONE

Volumn 10, Issue 10, 2015, Pages

  Halleran, Andrew ^a   Clamons, Samuel ^a,b   Saha, Margaret ^a  

^a Dept of Economics and Thomas Jefferson Program in Public Policy at the College of William and Mary   (United States)

^b California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BIOINFORMATICS; DNA METHYLATION; DNA SYNTHESIS; GENE CONTROL; GENE EXPRESSION PROFILING; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; MASS SPECTROMETRY; MYCOBACTERIOPHAGE; MYCOBACTERIOSIS; MYCOBACTERIUM SMEGMATIS; NONHUMAN; RNA SEQUENCE; TRANSCRIPTOMICS; BIOLOGY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; OPEN READING FRAME; VIROLOGY; VIRUS GENE; VIRUS LATENCY;

TRANSCRIPTOME;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, VIRAL; GENES, VIRAL; MYCOBACTERIOPHAGES; MYCOBACTERIUM SMEGMATIS; OPEN READING FRAMES; TRANSCRIPTION, GENETIC; TRANSCRIPTOME; VIRUS LATENCY;

EID: 84949981475     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0141100     Document Type: Article

References (41)

1. Gardner GM, Weiser RS. A bacteriophage for Mycobacterium smegmatis. Proc Soc Exp Biol Med. 1947; 66:205. PMID: 20270730
2. Muzaffar R, Batool S, Aziz F, Naqvi A, Rizvi A. Evaluation of the FASTPlaqueTB assay for direct detection of Mycobacterium tuberculosis in sputum specimens. Int J Tuberc Lung Dis. 2002; 6:635-640. PMID: 12102304
3. Marei AM, El-Behedy EM, Mohtady HA, Afify AF. Evaluation of a rapid bacteriophage-based method for the detection of Mycobacterium tuberculosis in clinical samples. J Med Microbiol. 2003; 52:331-335. PMID: 12676872
4. McNerney R, Kambashi BS, Kinkese J, Tembwe R, Godfrey-Faussett P. Development of a bacteriophage phage replication assay for diagnosis of pulmonary tuberculosis. J Clin Microbiol 2004; 42:2115-2120. PMID: 15131178
5. Stover CK, de la Cruz VF, Fuerst TR, Burlein JE, Benson LA, Bennett LT, et al. New use of BCG for recombinant vaccines. Nature. 1991; 351:456-460. PMID: 1904554
6. Sarkis GJ, Jacobs WR Jr., Hatfull GF. L5 luciferase reporter mycobacteriophages: a sensitive tool for the detection and assay of live mycobacteria. Mol Microbiol. 1995; 15:1055-1067. PMID: 7623662
7. Pearson RE, Jurgensen S, Sarkis GJ, Hatfull GF, Jacobs WR Jr. Construction of D29 shuttle phasmids and luciferase reporter phages for detection of mycobacteria. Gene. 1996; 183:129-136. PMID: 8996097
8. Stella EJ, de la Iglesia AI, Morbidoni HR. Mycobacteriophages as versatile tools for genetic manipulation of mycobacteria and development of simple methods for diagnosis of mycobacterial diseases. Rev Argent Microbiol. 2009; 41:45-55. PMID: 19391526
9. Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, et al. Origins of highly mosaic mycobacteriophage genomes. Cell. 2003; 113:171-182. PMID: 12705866
10. Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, et al. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2006; 2:e92. PMID: 16789831
11. Hatfull Graham F. "Complete genome sequences of 63 mycobacteriophages. Genome Announc. 2013; 1.6:e00847-13. doi: 10.1128/genomeA.00847-13 PMID: 24285655
12. Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, et al. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. MBio. 2014; 5:e01051-01013. doi: 10.1128/mBio.01051-13 PMID: 24496795
13. Lawrence JG, Hatfull GF, Hendrix RW. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol. 2002; 184:4891-4905. PMID: 12169615
14. Pope WH, et al. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife. 2015; 4:e06416. doi: 10.7554/eLife.06416 PMID: 25919952
15. Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, et al. Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J Mol Biol. 2010; 397:119-143. doi: 10.1016/j.jmb.2010.01.011 PMID: 20064525
16. Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC bioinformatics. 2011: 12(1), 395.
17. Pope WH, Anders KR, Baird M, Bowman CA, Boyle MM, Broussard G, et al. Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes. Journal of virology. 2014; 88(5), 2461-2480. doi: 10.1128/JVI.03363-13 PMID: 24335314
18. Cresawn SG, Pope WH, Jacobs-Sera D, Bowman CA, Russell DA, Dedrick RA et al. Comparative genomics of cluster O mycobacteriophages. PLOS ONE. 2015; 10(3).
19. Pope WH, Jacobs-Sera D, Russell DA, Rubin DH, Kajee A, Msibi ZN, et al. F. Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the mycobacterium neighborhood. MBio. 2014; 5(6), e02145-14.
20. Mehla J, Dedrick RM, Caufield JH, Siefring R, Mair M, Johnson A, et al. The protein interactome of mycobacteriophage Giles predicts functions for unknown proteins. Journal of bacteriology. 2015; JB-00164.
21. Seegers JF, Mc Grath S, O'Connell-Motherway M, Arendt EK, van de Guchte M, Creaven M, et al. Molecular and transcriptional analysis of the temperate lactococcal bacteriophage Tuc2009. Virology. 2004; 329:40-52. PMID: 15476873
22. Poranen MM, Ravantti JJ, Grahn AM, Gupta R, Auvinen P, Bamford DH. 2006. Global changes in cellular gene expression during bacteriophage PRD1 infection. J Virol 80:8081-8088. PMID: 16873264
23. Osterhout RE, Figueroa IA, Keasling JD, Arkin AP. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 2007; 7:82. PMID: 17764558
24. Luke K, Radek A, Liu X, Campbell J, Uzan M, Haselkorn R, et al. Microarray analysis of gene expression during bacteriophage T4 infection. Virology. 2002; 299(2), 182-191. PMID: 12202221
25. Ainsworth S, Zomer A, Mahony J, van Sinderen D. Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Appl Environ Microbiol. 2013; 79:4786-4798. doi: 10.1128/AEM.01197-13 PMID: 23728817
26. Lavigne R, Lecoutere E, Wagemans J, Cenens W, Aertsen A, Schoofs L, et al. A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus. Mbio. 2013; 4:e00061-00013. doi: 10. 1128/mBio.00061-13 PMID: 23512961
27. Dedrick RM, Marinelli LJ, Newton GL, Pogliano K, Pogliano J, Hatfull GF. Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles. Mol Microbiol. 2013; 88:577-589. doi: 10.1111/mmi.12210 PMID: 23560716
28. Wang C, et al. "The concordance between RNA-Seq and microarray data depends on chemical treatment and transcript abundance." Nature biotechnology 32.9 (2014): 926-932.
29. Morris P, Marinelli LJ, Jacobs-Sera D, Hendrix RW, Hatfull GF. Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination. J Bacteriol. 2008; 190:2172-2182. doi: 10.1128/JB.01657-07 PMID: 18178732
30. Dotsch A, Eckweiler D, Schniederjans M, Zimmermann A, Jensen V, Scharfe M, et al. The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. PLoS One. 2012; 7:e31092. doi: 10.1371/journal.pone.0031092 PMID: 22319605
31. Xu J, Hendrix RW, Duda RL. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Molecular cell. 2004; 16(1), 11-21. PMID: 15469818
32. Pelleg D, Moore AW. "X-means: Extending K-means with Efficient Estimation of the Number of Clusters." ICML. 2000.
33. SoftBerry. 2013. http://www.softberry.com/berry.phtml
34. Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids research, 33(suppl 2). 2005: W244-W248.
35. Lee MH, et al. "Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guerin." Proceedings of the National Academy of Sciences 88.8. (1991): 3111-3115.
36. Nesbit CE, Levin ME, Donnelly MU, Hatfull GF. Transcriptional regulation of repressor synthesis in mycobacteriophage L5. Molecular microbiology. 1995; 7(6): 1045-1056.
37. Ford ME, et al. "Mycobacteriophage TM4: genome structure and gene expression." Tubercle and Lung Disease 79.2 (1998): 63-73 PMID: 10645443
38. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010; 11: R106. doi: 10.1186/gb-2010-11-10-r106 PMID: 20979621
39. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5:R80. PMID: 15461798
40. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Stat Soc Series B Stat Methodol. 1995; 57:289-300, vol. 57.
41. Wang R, Prince JT, Marcotte EM. Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res 2005; 15:1118-1126. PMID: 16077011