Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

BMC Genomics

Elizabeth Hong-Geller¹  John M Dunbar¹  Sarah K Buddenborg¹  Yulin Shou¹  Sofiya N Micheva-Viteva¹  Chris J Stubben¹ 

[1] Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA

关键词: Gene expression;    Bacterial adaptation;    Stress conditions;    Microarray;    Burkholderia;    Small RNAs;   

Others  :  1217213
DOI  :  10.1186/1471-2164-15-385

 received in 2013-12-13, accepted in 2014-05-06,  发布年份 2014

【 摘 要 】

Background

Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology.

Results

We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors. In particular, the trans-encoded BTH_s1 and s39 exhibited differential expression profiles dependent on growth phase and cell stimuli, such as antibiotics and serum. Furthermore, knockdown of the highly-expressed BTH_s39 by antisense transcripts reduced B. thailandensis cell growth and attenuated host immune response upon infection, indicating that BTH_s39 functions in bacterial metabolism and adaptation to the host. In addition, expression of cis-encoded BTH_s13 and s19 found in the 5′ untranslated regions of their cognate genes correlated with tight regulation of gene transcript levels. This sRNA-mediated downregulation of gene expression may be a conserved mechanism of post-transcriptional gene dosage control.

Conclusions

These studies provide a broad analysis of differential Burkholderia sRNA expression profiles and illustrate the complexity of bacterial gene regulation in response to different environmental stress conditions.

【 授权许可】

   
2014 Stubben et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

【 参考文献 】

• [1]Waters LS, Storz G: Regulatory RNAs in bacteria. Cell 2009, 136:615-628.
• [2]Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
• [3]Aiba H: Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 2007, 10:134-139.
• [4]Jacques JF, Jang S, Prevost K, Desnoyers G, Desmarais M, Imlay J, Masse E: RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli. Mol Microbiol 2006, 62:1181-1190.
• [5]Wadler CS, Vanderpool CK: Characterization of homologs of the small RNA SgrS reveals diversity in function. Nucleic Acids Res 2009, 37:5477-5485.
• [6]Romby P, Vandenesch F, Wagner EG: The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol 2006, 9:229-236.
• [7]Toledo-Arana A, Repoila F, Cossart P: Small noncoding RNAs controlling pathogenesis. Curr Opin Microbiol 2007, 10:182-188.
• [8]Altuvia S: Identification of bacterial small non-coding RNAs: experimental approaches. Curr Opin Microbiol 2007, 10:257-261.
• [9]Mraheil MA, Billion A, Mohamed W, Mukherjee K, Kuenne C, Pischimarov J, Krawitz C, Retey J, Hartsch T, Chakraborty T, Hain T: The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res 2011, 39:4235-4248.
• [10]Weissenmayer BA, Prendergast JGD, Lohan AJ, Loftus BJ: Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs. PLoS One 2011, 6:e17570.
• [11]Koo JT, Alleyne TM, Schiano CA, Jafari N, Lathem WW: Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc Natl Acad Sci U S A 2011, 108:E709-E717.
• [12]Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JCD, Vogel J: Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator. Hfq PLoS Genet 2008, 4:e1000163.
• [13]Dunbar J, Cohn JD, Wall ME: Consistency of gene starts among Burkholderia genomes. BMC Genomics 2011, 12:125. BioMed Central Full Text
• [14]Guo L, Lim K, Gunn J, Bainbridge B, Darveau R, Hackett M, Miller S: Regulation of lipid a modifications by Salmonella typhimuirum virulence genes phoP-phoQ. Science 1997, 276:250-253.
• [15]Del Tordello E, Vacca I, Ram S, Rappuoli R, Serruto D: Neisseria meningitidis NalP cleaves human complement C3, facilitating degradation of C3b and survival in human serum. Proc Natl Acad Sci 2014, 111:427-432.
• [16]Scheurwater E, Reid C, Clarke A: Lytic transglycosylases: bacterial space-making autolysins. Int J Biochem Cell Biol 2008, 40:586-591.
• [17]Wright P, Richter A, Papenfort K, Mann M, Vogel J, Hess W, Backofen R, Georg J: Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A 2013, 110:E3487-E3496.
• [18]Yoder-Himes D, Chain P, Zhu Y, Wurtzel O, Rubin E, Tiedje J, Sorek R: Mapping the Burkholderia cenocepacia nicke response via high-throughput sequencing. Proc Natl Acad Sci 2009, 106:3976-3981.
• [19]Ooi W, Ong C, Nandi T, Kreisberb J, Chua H, Sun G, Chen Y, Mueller C, Conejero L, Eshaghi M, Ang R, Liu J, Sobral B, Korbsrisate S, Gan Y, Titball R, Bancroft G, Valade E, Tan P: The condition-dependent transcriptional landscape of Burkholderia pseudomallei. PLoS Genet 2013, 9:e1003795.
• [20]Yan Y, Su S, Meng X, Ji X, Qu Y, Liu Z, Wang X, Cui Y, Deng Z, Zhou D, Jiang W, Yang R, Han Y: Determination of sRNA expressions by RNA-Seq in Yersinia pestis grown in vitro and during infection. PLoS One 2013, 8:e74495.
• [21]Nudler E, Mironov A: The riboswitch control of bacterial metabolism. Trends Biochem Sci 2004, 29:11-17.
• [22]Zhang J, Lau M, Ferre-D’Amare A: Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 2010, 49:9123-9131.
• [23]Vercoe R, Chang J, Dy R, Taylor C, Gristwood T, Clulow J, Richter C, RPrzybilski R, Pitman A, Fineran P: Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet 2013, 9:e1003454.
• [24]Jungnitz H, West N, Walker M, Chhatwal G, Guzman C: A second two-component regulatory system of Bordetella bronchiseptica required for bacterial resistance to oxidative stress, production of acid phosphatase, and in vivo persistence. Infect Immun 1998, 66:4640-4650.
• [25]Seaver L, Imlay J: Alkyl hydroperoxide is the primary scavenger of endogenous hydrogen peroxide in E. coli. J Bacteriol 2001, 183:7173.
• [26]Heym B, Stavropoulos E, Honore N, Domenech P, Saint-Joanis B, Wilson T, Collins D, Colston M, Cole S: Effects of overexpression of the alkyl hydroperoxide reductase AhpC on the virulence and isoniazid resistance of Mycobacterium tuberculosis. Infect Immun 1997, 65:1395-1401.
• [27]Deaconescu A, Savery M, Darst S: The bacterial transcription-repair coupling factor. Curr Opin Struct Biol 2007, 17:96-102.
• [28]Garcia-Gomez E, Espinosa N, de la Mora J, Dreyfus G, Gonzalez-Pedrajo B: The muramidase EtgA from enteropathogenic E. coli is required for efficient type III secretion. Microbiol 2011, 157:1145-1160.
• [29]Burtnick M, DeShazer D, Nair V, Gherardini F, Brett P: Burkholderia mallei cluster 1 type VI secretion mutants exhibit growth and actin polymerization defects in RAW264.7 murine macrophages. Infect Immun 2010, 78:88-99.
• [30]Burtnick M, Brett P, Harding S, Ngugi S, Ribot W, Chantratita N, Scorpio A, Milne T, Dean R, Fritz D, Peacock S, Prior J, Atkins T, Deshazer D: The cluster 1 type VI secretion system is a major virulence determinant in Burkholderia pseudomallei. Infect Immun 2011, 79:1512-1525.
• [31]Shalom G, Shaw J, Thomas M: In vivo expression technology identifies a type VI secretion system locus in Burkholderia pseudomallei that is induced upon invation of macrophages. Microbiol 2007, 153:2689-2699.
• [32]Shepherd D, Li N, Micheva-Viteva S, Munsky B, Hong-Geller E, Werner J: Counting small RNA in pathogenic bacteria. Anal Chem 2013, 85:4938-4943.
• [33]Brinkac LM, Davidsen T, Beck E, Ganapathy A, Caler E, Dodson RJ, Durkin AS, Harkins DM, Lorenzi H, Madupu R, Sebastian Y, Shrivastava S, Thiagarajan M, Orvis J, Sundaram J, Crabtree J, Galens K, Zhao Y, Inman J, Montgomery R, Schobel S, Galinsky K, Tanenbaum D, Resnick A, Zafar N, White O, Sutton G: Pathema: a clade-specific bioinformatics resource center for pathogen research. Nucleic Acids Res 2010, 38:D408-D414.
• [34]R Development Core Team: R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2008. http://www.R-project.org webcite
• [35]Wilson CL, Miller CJ: Simpleaffy: a BioConductor package for affymetrix quality control and data analysis. Bioinformatics 2005, 21:3683-3685.
• [36]Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A: Rfam: wikipedia, clans and the “decimal” release. Nucleic Acids Res 2011, 39:D141-D145.
• [37]Livny J, Teonadi H, Livny M, Waldor MK: High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 2008, 3:e3197.
• [38]Ott A, Idali A, Marchais A, Gautheret D: NAPP: the nucleic acid phylogenetic profile database. Nucleic Acids Res 2012, 40:D205-D209.
• [39]Kingsford CL, Ayanbule K, Salzberg SL: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007, 8:R22. BioMed Central Full Text
• [40]Glass MB, Gee JE, Steigerwalt AG, Cavuoti D, Barton T, Hardy RD, Godoy D, Spratt BG, Clark TA, Wilkins PP: Pneumonia and septicemia caused by Burkholderia thailandensis in the United States. J Clin Microbiol 2006, 44:4601-4604.
• [41]Sim BM, Chantratita N, Ooi WF, Nandi T, Tewhey R, Wuthiekanun V, Thaipadungpanit J, Tumapa S, Ariyaratne P, Sung WK, Sem X, Chua H, Ramnarayanan K, Lin C, Liu Y, Feil E, Glass M, Tan G, Peacock S, Tan P: Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates. Genome Biol 2010, 11:R89. BioMed Central Full Text
• [42]Hamad M, Zajdowicz S, Holmes R, Voskuil M: An allelic exchange system for compliant genetic manipulation of the select agents Burkholderia pseudomallei and Burkholderia mallei. Gene 2009, 430:123-131.