1887

Microbiology Society logo

Volume 166, Issue 2

A corepressor participates in LexA-independent regulation of error-prone polymerases in Open Access

Abstract

The DNA damage response of the multidrug-resistant pathogen , which induces mutagenic UmuD′C error-prone polymerases, differs from that of many bacteria. species lack a LexA repressor, but induce gene transcription after DNA damage. One regulator, UmuDAb, binds to and represses the promoters of the multiple ATCC 17978 alleles and the divergently transcribed and genes. is unique to the genus and of unknown function. 5' RACE (rapid amplification of cDNA ends) PCR mapping of the and transcriptional start sites revealed that their −35 promoter elements overlapped the UmuDAb binding site, suggesting that UmuDAb simultaneously repressed expression of both genes by blocking polymerase access. This coordinated control of and suggested that might also regulate DNA damage-inducible gene transcription. RNA-sequencing experiments in 17 978 cells showed that regulated approximately 25 % (=39) of the mitomycin C-induced regulon, with coregulating 17 of these -regulated genes. Eight genes (the polymerases, and ) were de-repressed in the absence of DNA damage, and nine genes were uninduced in the presence of DNA damage, in both and mutant strains. These data suggest has multiple roles, both as a co-repressor and as a positive regulator of DNA damage-inducible gene transcription. Additionally, 57 genes were induced by mitomycin C in the mutant but not in wild-type cells. This regulon contained multiple genes for DNA replication, recombination and repair, transcriptional regulators, RND efflux, and transport. This study uncovered another regulator of the atypical DNA damage response of this genus, to help describe how this pathogen acquires drug resistance through its expression of the error-prone polymerases under DdrR and UmuDAb control.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): DdrR , DNA damage , LexA , repressor , SOS response and UmuDAb
Funding
This study was supported by the:
  • National Institute of General Medical Sciences (Award P30GM106396)
    • Principle Award Recipient: Janelle M Hare
  • Foundation for the National Institutes of Health (Award P20GM103436)
    • Principle Award Recipient: Janelle M Hare
  • National Institute of General Medical Sciences (Award R15GM085722)
    • Principle Award Recipient: Janelle M Hare
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000866
2019-11-05
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/166/2/212.html?itemId=/content/journal/micro/10.1099/mic.0.000866&mimeType=html&fmt=ahah

References

  1. Friedberg EC. DNA Repair and Mutagenesis Washington, DC: ASM Press; 1995
     [Google Scholar]
  2. Battista JR, Donnelly CE, Ohta T, Walker GC. The SOS response and induced mutagenesis. Prog Clin Biol Res 1990; 340A:169–178
     [Google Scholar]
  3. Mount DW, Low KB, Edmiston SJ. Dominant mutations (Lex) in Escherichia coli K-12 which affect radiation sensitivity and frequency of ultraviolet lght-induced mutations. J Bacteriol 1972; 112:886–893
     [Google Scholar]
  4. Little JW, Edmiston SH, Pacelli LZ, Mount DW. Cleavage of the Escherichia coli lexA protein by the recA protease. Proc Natl Acad Sci USA 1980; 77:3225–3229 [View Article]
     [Google Scholar]
  5. Little JW, Mount DW, Yanisch-Perron CR. Purified lexA protein is a repressor of the recA and lexA genes. Proc Natl Acad Sci USA 1981; 78:4199–4203 [View Article]
     [Google Scholar]
  6. Hare JM, Adhikari S, Lambert KV, Hare AE, Grice AN. The Acinetobacter regulatory UmuDAb protein cleaves in response to DNA damage with chimeric LexA/UmuD characteristics. FEMS Microbiol Lett 2012; 334:57–65 [View Article]
     [Google Scholar]
  7. Jara LM, Cortés P, Bou G, Barbé J, Aranda J. Differential roles of antimicrobials in the acquisition of drug resistance through activation of the SOS response in Acinetobacter baumannii . Antimicrob Agents Chemother 2015; 59:4318–4320 [View Article]
     [Google Scholar]
  8. Macguire AE, Ching MC, Diamond BH, Kazakov A, Novichkov P et al. Activation of phenotypic subpopulations in response to ciprofloxacin treatment in Acinetobacter baumannii . Mol Microbiol 2014; 92:138–152 [View Article]
     [Google Scholar]
  9. Hare JM, Bradley JA, Lin CL, Elam TJ. Diverse responses to UV light exposure in Acinetobacter include the capacity for DNA damage-induced mutagenesis in the opportunistic pathogens Acinetobacter baumannii and Acinetobacter ursingii . Microbiology 2012; 158:601–611 [View Article]
     [Google Scholar]
  10. Norton MD, Spilkia AJ, Godoy VG. Antibiotic resistance acquired through a DNA damage-inducible response in Acinetobacter baumannii . J Bacteriol 2013; 195:1335–1345 [View Article]
     [Google Scholar]
  11. Aranda J, López M, Leiva E, Magán A, Adler B et al. Role of Acinetobacter baumannii UmuD homologs in antibiotic resistance acquired through DNA damage-induced mutagenesis. Antimicrob Agents Chemother 2014; 58:1771–1773 [View Article]
     [Google Scholar]
  12. Norton MD, Spilkia AJ, Godoy VG. Antibiotic resistance acquired through a DNA damage-inducible response in Acinetobacter baumannii . J Bacteriol 2013; 195:1335–1345 [View Article]
     [Google Scholar]
  13. Aranda J, Poza M, Shingu-Vázquez M, Cortés P, Boyce JD et al. Identification of a DNA-damage-inducible regulon in Acinetobacter baumannii . J Bacteriol 2013; 195:5577–5582 [View Article]
     [Google Scholar]
  14. Witkowski TA, Grice AN, Stinnett DB, Wells WK, Peterson MA et al. UmuDAb: an error-prone polymerase accessory homolog whose N-terminal domain is required for repression of DNA damage inducible gene expression in Acinetobacter baylyi . PLoS One 2016; 11:e0152013 [View Article]
     [Google Scholar]
  15. Hare JM, Perkins SN, Gregg-Jolly LA, Constitutively Expressed A. A constitutively expressed, truncated umuDC operon regulates the recA-dependent DNA damage induction of a gene in Acinetobacter baylyi strain ADP1. Appl Environ Microbiol 2006; 72:4036–4043 [View Article]
     [Google Scholar]
  16. Kelley WL. Lex marks the spot: the virulent side of SOS and a closer look at the LexA regulon. Mol Microbiol 2006; 62:1228–1238 [View Article]
     [Google Scholar]
  17. Hare JM, Ferrell JC, Witkowski TA, Grice AN. Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of Acinetobacter baumannii and Acinetobacter baylyi . PLoS One 2014; 9:e93861 [View Article]
     [Google Scholar]
  18. Hare JM, Perkins SN, Gregg-Jolly LA. A constitutively expressed, truncated umuDC operon regulates the recA-dependent DNA damage induction of a gene in Acinetobacter baylyi strain ADP1. Appl Env Microbiol 2006; 72:4036–4043 [View Article]
     [Google Scholar]
  19. Centers for Disease Control and Prevention Antibiotic Resistance Threats in the United States Atlanta, GA: CDC; 2013 pp 1–114
     [Google Scholar]
  20. Kokotek W, Lotz W. Construction of a lacZ-kanamycin-resistance cassette, useful for site-directed mutagenesis and as a promoter probe. Gene 1989; 84:467–471 [View Article]
     [Google Scholar]
  21. de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A et al. A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol 2008; 4:174 [View Article]
     [Google Scholar]
  22. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 2013; 31:46–53 [View Article]
     [Google Scholar]
  23. Di Nocera PP, Rocco F, Giannouli M, Triassi M, Zarrilli R. Genome organization of epidemic Acinetobacter baumannii strains. BMC Microbiol 2011; 11:224 [View Article]
     [Google Scholar]
  24. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN et al. New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev 2007; 21:601–614 [View Article]
     [Google Scholar]
  25. Aravind L, Anand S, Iyer LM. Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems. Biol Direct 2013; 8:20 [View Article]
     [Google Scholar]
  26. Schnarr M, Oertel-Buchheit P, Kazmaier M, Granger-Schnarr M. Dna binding properties of the LexA repressor. Biochimie 1991; 73:423–431 [View Article]
     [Google Scholar]
  27. Kamenšek S, Browning DF, Podlesek Z, Busby SJW, Žgur-Bertok D et al. Silencing of DNase colicin E8 gene expression by a complex nucleoprotein assembly ensures timely colicin induction. PLoS Genet 2015; 11:e1005354 [View Article]
     [Google Scholar]
  28. Butala M, Sonjak S, Kamenšek S, Hodošček M, Browning DF et al. Double locking of an Escherichia coli promoter by two repressors prevents premature colicin expression and cell lysis. Mol Microbiol 2012; 86:129–139 [View Article]
     [Google Scholar]
  29. Fornelos N, Butala M, Hodnik V, Anderluh G, Bamford JK et al. Bacteriophage GIL01 gp7 interacts with host LexA repressor to enhance DNA binding and inhibit RecA-mediated auto-cleavage. Nucleic Acids Res 2015; 43:7315–7329 [View Article]
     [Google Scholar]
  30. Quinones M, Kimsey HH, Waldor MK. Lexa cleavage is required for CTX prophage induction. Mol Cell 2005; 17:291–300 [View Article]
     [Google Scholar]
  31. Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res 2009; 37:D479–D482 [View Article]
     [Google Scholar]
  32. Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU. Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 2005; 69:101–123 [View Article]
     [Google Scholar]
  33. Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli . Genetics 2001; 158:41
     [Google Scholar]
  34. Nedialkova LP, Denzler R, Koeppel MB, Diehl M, Ring D et al. Inflammation fuels colicin Ib-dependent competition of Salmonella serovar typhimurium and E. coli in enterobacterial blooms. PLoS Pathog 2014; 10:e1003844 [View Article]
     [Google Scholar]
  35. Price MN, Huang KH, Alm EJ, Arkin AP. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 2005; 33:880–892 [View Article]
     [Google Scholar]
  36. He X, Lu F, Yuan F, Jiang D, Zhao P et al. Biofilm formation caused by clinical Acinetobacter baumannii isolates is associated with overexpression of the AdeFGH efflux pump. Antimicrob Agents Chemother 2015; 59:4817–4825 [View Article]
     [Google Scholar]
  37. Hood MI, Jacobs AC, Sayood K, Dunman PM, Skaar EP. Acinetobacter baumannii increases tolerance to antibiotics in response to monovalent cations. Antimicrob Agents Chemother 2010; 54:10291041 [View Article]
     [Google Scholar]
  38. Hoang TT, Karkhoff-Schweizer RR, Kutchma AJ, Schweizer HP. A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 1998; 212:77–86 [View Article]
     [Google Scholar]
  39. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–D269 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000866
Loading
A corepressor participates in LexA-independent regulation of error-prone polymerases in Acinetobacter
Microbiology 166, 212 (2020); https://doi.org/10.1099/mic.0.000866
/content/journal/micro/10.1099/mic.0.000866
/content/journal/micro/10.1099/mic.0.000866
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error