Transcriptional cross-activation between toxin-antitoxin systems of Escherichia coli

BMC Microbiology

Niilo Kaldalu¹  Tanel Tenson¹  Toomas Mets¹  Villu Kasari¹ 

[1] Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia

关键词: Persisters;    mRNA stability;    Regulatory network;    Transcriptional regulation;    Toxin-antitoxin systems;   

Others  :  1144309
DOI  :  10.1186/1471-2180-13-45

 received in 2012-12-13, accepted in 2013-02-18,  发布年份 2013

【 摘 要 】

Background

Bacterial toxin-antitoxin (TA) systems are formed by potent regulatory or suicide factors (toxins) and their short-lived inhibitors (antitoxins). Antitoxins are DNA-binding proteins and auto-repress transcription of TA operons. Transcription of multiple TA operons is activated in temporarily non-growing persister cells that can resist killing by antibiotics. Consequently, the antitoxin levels of persisters must have been dropped and toxins are released of inhibition.

Results

Here, we describe transcriptional cross-activation between different TA systems of Escherichia coli. We find that the chromosomal relBEF operon is activated in response to production of the toxins MazF, MqsR, HicA, and HipA. Expression of the RelE toxin in turn induces transcription of several TA operons. We show that induction of mazEF during amino acid starvation depends on relBE and does not occur in a relBEF deletion mutant. Induction of TA operons has been previously shown to depend on Lon protease which is activated by polyphospate accumulation. We show that transcriptional cross-activation occurs also in strains deficient for Lon, ClpP, and HslV proteases and polyphosphate kinase. Furthermore, we find that toxins cleave the TA mRNA in vivo, which is followed by degradation of the antitoxin-encoding fragments and selective accumulation of the toxin-encoding regions. We show that these accumulating fragments can be translated to produce more toxin.

Conclusion

Transcriptional activation followed by cleavage of the mRNA and disproportionate production of the toxin constitutes a possible positive feedback loop, which can fire other TA systems and cause bistable growth heterogeneity. Cross-interacting TA systems have a potential to form a complex network of mutually activating regulators in bacteria.

【 授权许可】

   
2013 Kasari et al; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Yamaguchi Y, Inouye M: Regulation of growth and death in Escherichia coli by toxin-antitoxin systems. Nat Rev Microbiol 2011, 9(11):779-790.
• [2]Yamaguchi Y, Park JH, Inouye M: Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet 2011, 45:61-79.
• [3]Shao Y, Harrison EM, Bi D, Tai C, He X, Ou HY, Rajakumar K, Deng Z: TADB: a web-based resource for type 2 toxin-antitoxin loci in bacteria and archaea. Nucleic Acids Res 2011, 39(Database issue):D606-611.
• [4]Pandey DP, Gerdes K: Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 2005, 33(3):966-976.
• [5]Makarova KS, Wolf YI, Koonin EV: Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct 2009, 4:19. BioMed Central Full Text
• [6]Leplae R, Geeraerts D, Hallez R, Guglielmini J, Dreze P, Van Melderen L: Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res 2011, 39(13):5513-5525.
• [7]Magnuson RD: Hypothetical functions of toxin-antitoxin systems. J Bacteriol 2007, 189(17):6089-6092.
• [8]Van Melderen L, Saavedra De Bast M: Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet 2009, 5(3):e1000437.
• [9]Tsilibaris V, Maenhaut-Michel G, Mine N, Van Melderen L: What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome? J Bacteriol 2007, 189(17):6101-6108.
• [10]Yarmolinsky MB: Programmed cell death in bacterial populations. Science 1995, 267(5199):836-837.
• [11]Sayeed S, Brendler T, Davis M, Reaves L, Austin S: Surprising dependence on postsegregational killing of host cells for maintenance of the large virulence plasmid of Shigella flexneri. J Bacteriol 2005, 187(8):2768-2773.
• [12]Masuda Y, Miyakawa K, Nishimura Y, Ohtsubo E: chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100. J Bacteriol 1993, 175(21):6850-6856.
• [13]Gotfredsen M, Gerdes K: The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family. Mol Microbiol 1998, 29(4):1065-1076.
• [14]Christensen SK, Mikkelsen M, Pedersen K, Gerdes K: RelE, a global inhibitor of translation, is activated during nutritional stress. Proc Natl Acad Sci USA 2001, 98(25):14328-14333.
• [15]Aizenman E, Engelberg-Kulka H, Glaser G: An Escherichia coli chromosomal “addiction module” regulated by guanosine [corrected] 3′,5′-bispyrophosphate: a model for programmed bacterial cell death. Proc Natl Acad Sci USA 1996, 93(12):6059-6063.
• [16]Yamaguchi Y, Park JH, Inouye M: MqsR, a crucial regulator for quorum sensing and biofilm formation, is a GCU-specific mRNA interferase in Escherichia coli. J Biol Chem 2009, 284(42):28746-28753.
• [17]Christensen SK, Pedersen K, Hansen FG, Gerdes K: Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA. J Mol Biol 2003, 332(4):809-819.
• [18]Christensen-Dalsgaard M, Gerdes K: Two higBA loci in the Vibrio cholerae superintegron encode mRNA cleaving enzymes and can stabilize plasmids. Mol Microbiol 2006, 62(2):397-411.
• [19]Jorgensen MG, Pandey DP, Jaskolska M, Gerdes K: HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea. J Bacteriol 2009, 191(4):1191-1199.
• [20]Pedersen K, Zavialov AV, Pavlov MY, Elf J, Gerdes K, Ehrenberg M: The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal a site. Cell 2003, 112(1):131-140.
• [21]Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA: Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Mol Microbiol 2009, 71(5):1071-1087.
• [22]Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I: Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell 2011, 147(1):147-157.
• [23]Winther KS, Gerdes K: Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proc Natl Acad Sci USA 2011, 108(18):7403-7407.
• [24]Bernard P, Couturier M: Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J Mol Biol 1992, 226(3):735-745.
• [25]Jiang Y, Pogliano J, Helinski DR, Konieczny I: ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase. Mol Microbiol 2002, 44(4):971-979.
• [26]Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K, Brennan RG: Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science 2009, 323(5912):396-401.
• [27]Correia FF, D’Onofrio A, Rejtar T, Li L, Karger BL, Makarova K, Koonin EV, Lewis K: Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol 2006, 188(24):8360-8367.
• [28]Mutschler H, Gebhardt M, Shoeman RL, Meinhart A: A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis. PLoS Biol 2011, 9(3):e1001033.
• [29]Pedersen K, Christensen SK, Gerdes K: Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol Microbiol 2002, 45(2):501-510.
• [30]Amitai S, Yassin Y, Engelberg-Kulka H: MazF-mediated cell death in Escherichia coli: a point of no return. J Bacteriol 2004, 186(24):8295-8300.
• [31]Hazan R, Sat B, Engelberg-Kulka H: Escherichia coli mazEF-mediated cell death is triggered by various stressful conditions. J Bacteriol 2004, 186(11):3663-3669.
• [32]Nariya H, Inouye M: MazF, an mRNA interferase, mediates programmed cell death during multicellular Myxococcus development. Cell 2008, 132(1):55-66.
• [33]Gerdes K, Christensen SK, Lobner-Olesen A: Prokaryotic toxin-antitoxin stress response loci. Nat Rev Microbiol 2005, 3(5):371-382.
• [34]Cataudella I, Trusina A, Sneppen K, Gerdes K, Mitarai N: Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res 2012, 40(14):6424-6434.
• [35]Overgaard M, Borch J, Jorgensen MG, Gerdes K: Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Mol Microbiol 2008, 69(4):841-857.
• [36]Boggild A, Sofos N, Andersen KR, Feddersen A, Easter AD, Passmore LA, Brodersen DE: The crystal structure of the intact E. coli RelBE toxin-antitoxin complex provides the structural basis for conditional cooperativity. Structure 2012, 20(10):1641-1648.
• [37]Winther KS, Gerdes K: Regulation of enteric vapBC transcription: induction by VapC toxin dimer-breaking. Nucleic Acids Res 2012, 40(10):4347-4357.
• [38]Keren I, Shah D, Spoering A, Kaldalu N, Lewis K: Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 2004, 186(24):8172-8180.
• [39]Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K: Persisters: a distinct physiological state of E. coli. BMC Microbiol 2006, 6:53. BioMed Central Full Text
• [40]Lewis K: Persister cells. Annu Rev Microbiol 2010, 64:357-372.
• [41]Hong SH, Wang X, O’Connor HF, Benedik MJ, Wood TK: Bacterial persistence increases as environmental fitness decreases. Microb Biotechnol 2012, 5(4):509-522.
• [42]Moyed HS, Bertrand KP: HipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 1983, 155(2):768-775.
• [43]Harrison JJ, Wade WD, Akierman S, Vacchi-Suzzi C, Stremick CA, Turner RJ, Ceri H: The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm. Antimicrob Agents Chemother 2009, 53(6):2253-2258.
• [44]Maisonneuve E, Shakespeare LJ, Jorgensen MG, Gerdes K: Bacterial persistence by RNA endonucleases. Proc Natl Acad Sci USA 2011, 108(32):13206-13211.
• [45]Bech FW, Jorgensen ST, Diderichsen B, Karlstrom OH: Sequence of the relB transcription unit from Escherichia coli and identification of the relB gene. EMBO J 1985, 4(4):1059-1066.
• [46]Gerdes K, Bech FW, Jorgensen ST, Lobner-Olesen A, Rasmussen PB, Atlung T, Boe L, Karlstrom O, Molin S, von Meyenburg K: Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J 1986, 5(8):2023-2029.
• [47]Reiss S, Pane-Farre J, Fuchs S, Francois P, Liebeke M, Schrenzel J, Lindequist U, Lalk M, Wolz C, Hecker M: Global analysis of the Staphylococcus aureus response to mupirocin. Antimicrob Agents Chemother 2012, 56(2):787-804.
• [48]Sangurdekar DP, Srienc F, Khodursky AB: A classification based framework for quantitative description of large-scale microarray data. Genome Biol 2006, 7(4):R32. BioMed Central Full Text
• [49]Zurawski G, Zurawski SM: Structure of the Escherichia coli S10 ribosomal protein operon. Nucleic Acids Res 1985, 13(12):4521-4526.
• [50]Kuroda A, Nomura K, Ohtomo R, Kato J, Ikeda T, Takiguchi N, Ohtake H, Kornberg A: Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli. Science 2001, 293(5530):705-708.
• [51]Zhang Y, Zhang J, Hara H, Kato I, Inouye M: Insights into the mRNA cleavage mechanism by MazF, an mRNA interferase. J Biol Chem 2005, 280(5):3143-3150.
• [52]Zhang Y, Zhu L, Zhang J, Inouye M: Characterization of ChpBK, an mRNA interferase from Escherichia coli. J Biol Chem 2005, 280(28):26080-26088.
• [53]Dubnau D, Losick R: Bistability in bacteria. Mol Microbiol 2006, 61(3):564-572.
• [54]Rotem E, Loinger A, Ronin I, Levin-Reisman I, Gabay C, Shoresh N, Biham O, Balaban NQ: Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc Natl Acad Sci USA 2010, 107(28):12541-12546.
• [55]Li GY, Zhang Y, Inouye M, Ikura M: Inhibitory mechanism of Escherichia coli RelE-RelB toxin-antitoxin module involves a helix displacement near an mRNA interferase active site. J Biol Chem 2009, 284(21):14628-14636.
• [56]Ruiz-Echevarria MJ, de la Cueva G, Diaz-Orejas R: Translational coupling and limited degradation of a polycistronic messenger modulate differential gene expression in the parD stability system of plasmid R1. Mol Gen Genet 1995, 248(5):599-609.
• [57]Vazquez-Laslop N, Lee H, Neyfakh AA: Increased persistence in Escherichia coli caused by controlled expression of toxins or other unrelated proteins. J Bacteriol 2006, 188(10):3494-3497.
• [58]Roostalu J, Joers A, Luidalepp H, Kaldalu N, Tenson T: Cell division in Escherichia coli cultures monitored at single cell resolution. BMC Microbiol 2008, 8:68. BioMed Central Full Text
• [59]Kasari V, Kurg K, Margus T, Tenson T, Kaldalu N: The Escherichia coli mqsR and ygiT genes encode a new toxin-antitoxin pair. J Bacteriol 2010, 192(11):2908-2919.
• [60]Kim Y, Wang X, Zhang XS, Grigoriu S, Page R, Peti W, Wood TK: Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ Microbiol 2010, 12(5):1105-1121.
• [61]Winther KS, Gerdes K: Ectopic production of VapCs from enterobacteria inhibits translation and trans-activates YoeB mRNA interferase. Mol Microbiol 2009, 72(4):918-930.
• [62]Garcia-Pino A, Christensen-Dalsgaard M, Wyns L, Yarmolinsky M, Magnuson RD, Gerdes K, Loris R: Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation. J Biol Chem 2008, 283(45):30821-30827.
• [63]Santos Sierra S, Giraldo R, Diaz Orejas R: Functional interactions between chpB and parD, two homologous conditional killer systems found in the Escherichia coli chromosome and in plasmid R1. FEMS Microbiol Lett 1998, 168(1):51-58.
• [64]Santos-Sierra S, Giraldo R, Diaz-Orejas R: Functional interactions between homologous conditional killer systems of plasmid and chromosomal origin. FEMS Microbiol Lett 1997, 152(1):51-56.
• [65]Wilbaux M, Mine N, Guerout AM, Mazel D, Van Melderen L: Functional interactions between coexisting toxin-antitoxin systems of the ccd family in Escherichia coli O157:H7. J Bacteriol 2007, 189(7):2712-2719.
• [66]Grady R, Hayes F: Axe-Txe, a broad-spectrum proteic toxin-antitoxin system specified by a multidrug-resistant, clinical isolate of enterococcus faecium. Mol Microbiol 2003, 47(5):1419-1432.
• [67]Zhu L, Sharp JD, Kobayashi H, Woychik NA, Inouye M: Noncognate Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact. J Biol Chem 2010, 285(51):39732-39738.
• [68]Smith AB, Lopez-Villarejo J, Diago-Navarro E, Mitchenall LA, Barendregt A, Heck AJ, Lemonnier M, Maxwell A, Diaz-Orejas R: A common origin for the bacterial toxin-antitoxin systems parD and ccd, suggested by analyses of toxin/target and toxin/antitoxin interactions. PLoS One 2012, 7(9):e46499.
• [69]Ramage HR, Connolly LE, Cox JS: Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS Genet 2009, 5(12):e1000767.
• [70]Fiebig A, Castro Rojas CM, Siegal-Gaskins D, Crosson S: Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems. Mol Microbiol 2010, 77(1):236-251.
• [71]Lee SK, Chou HH, Pfleger BF, Newman JD, Yoshikuni Y, Keasling JD: Directed evolution of AraC for improved compatibility of arabinose- and lactose-inducible promoters. Appl Environ Microbiol 2007, 73(18):5711-5715.
• [72]Amitai S, Kolodkin-Gal I, Hananya-Meltabashi M, Sacher A, Engelberg-Kulka H: Escherichia coli MazF leads to the simultaneous selective synthesis of both “death proteins” and “survival proteins”. PLoS Genet 2009, 5(3):e1000390.
• [73]Sambrook J, Russell DW: Molecular cloning. A laboratory manual. Cold Spring Harbor, N. Y: Cold Spring Harbor Laboratory Press; 2001.
• [74]Schagger H: Tricine-SDS-PAGE. Nat Protoc 2006, 1(1):16-22.