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Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation

Shen, Mengyu, Zhang, Huidong, Shen, Wei, Zou, Zhenyu, Lu, Shuguang, Li, Gang, He, Xuesong, Agnello, Melissa, Shi, Wenyuan, Hu, Fuquan, Le, Shuai·2018·Nucleic Acids Research
DOI 10.1093/nar/gky160PMC PMC5961081
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Figure 1. Characteristics of deletion mutants selected by phage infection. (A) Brown mutants are selected after phage PaoP5 infection. (B) Phage-resistant mutant frequencies in total occur at 1083 ± 524 × 10−8. The brown mutants were detected with a frequency of 227 ± 87 ×10−8. The data was calculated from five biological replicates. (C) Both the hmgA and galU genes were deleted in the brown mutants, as was detected by PCR. (D) Deletion sites and deleted genes in all the brown mutants. (E) Locations of deletions in the chromosomes of nine brown mutants compared with wild-type PAO1. (F) Close-up of E, indicating the deleted chromosomal regions of the nine brown mutants. The locations of the hmgA and galU genes are indicated.
Figure 1. Characteristics of deletion mutants selected by phage infection. (A) Brown mutants are selected after phage PaoP5 infection. (B) Phage-resistant mutant frequencies in total occur at 1083 ± 524 × 10−8. The brown mutants were detected with a frequency of 227 ± 87 ×10−8. The data was calculated from five biological replicates. (C) Both the hmgA and galU genes were deleted in the brown mutants, as was detected by PCR. (D) Deletion sites and deleted genes in all the brown mutants. (E) Locations of deletions in the chromosomes of nine brown mutants compared with wild-type PAO1. (F) Close-up of E, indicating the deleted chromosomal regions of the nine brown mutants. The locations of the hmgA and galU genes are indicated.CC BY-NC · PubMed Central
Figure 2. MutL is required for large chromosomal deletions in P. aeruginosa. (A) Representative pictures of the phage-resistant mutants of PAO1, ΔmutL, ΔmutL::mutL and PAO1::mutL. Many more white mutants were generated in the ΔmutL background, and most mutants generated from the mutL overexpression strain were brown mutants. (B) The frequency of brown mutants and white mutants for each strain selected by phage. No brown mutants were detected from ΔmutL, while overexpression of mutL significantly increased the frequency of brown mutants to 1468 ± 427 × 10−8. (P < 0.05, calculated by one way ANOVA). (C) Genomic organization of PAO1::sacB. Two copies of sacB were inserted into the PAO1 genome immediately downstream from galU. Thus, PAO1::sacB is sensitive to both phage and 5% sucrose selection. (D) The frequency of brown mutants and white mutants for each strain selected by phage and 5% sucrose. Inserting two copies of the sacB gene significantly decreased the rate of white mutants after selection with both phage and 5% sucrose. More than 108ΔmutL::sacB cells were subjected to selection by phage and sucrose without any brown mutants being detected. Each experiment was repeated five times. The asterisks mark P-value of < 0.05 as calculated by Student's t-test.
Figure 2. MutL is required for large chromosomal deletions in P. aeruginosa. (A) Representative pictures of the phage-resistant mutants of PAO1, ΔmutL, ΔmutL::mutL and PAO1::mutL. Many more white mutants were generated in the ΔmutL background, and most mutants generated from the mutL overexpression strain were brown mutants. (B) The frequency of brown mutants and white mutants for each strain selected by phage. No brown mutants were detected from ΔmutL, while overexpression of mutL significantly increased the frequency of brown mutants to 1468 ± 427 × 10−8. (P < 0.05, calculated by one way ANOVA). (C) Genomic organization of PAO1::sacB. Two copies of sacB were inserted into the PAO1 genome immediately downstream from galU. Thus, PAO1::sacB is sensitive to both phage and 5% sucrose selection. (D) The frequency of brown mutants and white mutants for each strain selected by phage and 5% sucrose. Inserting two copies of the sacB gene significantly decreased the rate of white mutants after selection with both phage and 5% sucrose. More than 108ΔmutL::sacB cells were subjected to selection by phage and sucrose without any brown mutants being detected. Each experiment was repeated five times. The asterisks mark P-value of < 0.05 as calculated by Student's t-test.CC BY-NC · PubMed Central
Figure 3. Nicking activity of PaMutL results in DSB and is essential for chromosomal deletions. (A) Confirmation that the nicking function of PaMutL can results in DSB in vitro. Linear DNA was observed from PaMutL (500nM) digested plasmid DNA, but NTD (500 nM) did not cleave dsDNA. SC, supercoiled; L, linearized; N, nicked. (B) DSB made by PaMutL is not site-specific. After incubation of plasmid pUCP24 with PaMutL (200 nM) or NTD (200 nM), the DNA was linearized with EcoRI. The products were analyzed by gel electrophoresis after ethidium bromide staining. (C) Key residues for PaMutL nicking function. (D) A20V,G97S, N37H, R474A and NTD mutants cannot restore the brown mutants, nor could decrease the frequency of white mutants in mutL::sacB.
Figure 3. Nicking activity of PaMutL results in DSB and is essential for chromosomal deletions. (A) Confirmation that the nicking function of PaMutL can results in DSB in vitro. Linear DNA was observed from PaMutL (500nM) digested plasmid DNA, but NTD (500 nM) did not cleave dsDNA. SC, supercoiled; L, linearized; N, nicked. (B) DSB made by PaMutL is not site-specific. After incubation of plasmid pUCP24 with PaMutL (200 nM) or NTD (200 nM), the DNA was linearized with EcoRI. The products were analyzed by gel electrophoresis after ethidium bromide staining. (C) Key residues for PaMutL nicking function. (D) A20V,G97S, N37H, R474A and NTD mutants cannot restore the brown mutants, nor could decrease the frequency of white mutants in mutL::sacB.CC BY-NC · PubMed Central
Figure 4. NHEJ promotes chromosomal deletions while HR inhibits it. (A) Knockout of LigD and Ku significantly decreased the frequency of brown mutants, while complementation of LigD or Ku increased the deletion frequency to 1947 ± 420 × 10−8 and 558 ± 205 × 10−8, respectively (P < 0.05, calculated by one way ANOVA). (B) Knockout of recA and recB significantly increased the frequency of brown mutants to 11192 ± 9569 × 10−8 and 3823 ± 2898 × 10−8, respectively (P < 0.05, calculated by one way ANOVA).
Figure 4. NHEJ promotes chromosomal deletions while HR inhibits it. (A) Knockout of LigD and Ku significantly decreased the frequency of brown mutants, while complementation of LigD or Ku increased the deletion frequency to 1947 ± 420 × 10−8 and 558 ± 205 × 10−8, respectively (P < 0.05, calculated by one way ANOVA). (B) Knockout of recA and recB significantly increased the frequency of brown mutants to 11192 ± 9569 × 10−8 and 3823 ± 2898 × 10−8, respectively (P < 0.05, calculated by one way ANOVA).CC BY-NC · PubMed Central
Figure 5. Model of the mechanism by which MutL makes DSB and results in a DNA fragment deletion through NHEJ that protects P. aeruginosa from phage infection. PaMutL generates DSB occasionally. The end points of DSB are then joined by Ku and LigD. Brown mutants with a deleted a galU/hmgA region are identified after phage infection.
Figure 5. Model of the mechanism by which MutL makes DSB and results in a DNA fragment deletion through NHEJ that protects P. aeruginosa from phage infection. PaMutL generates DSB occasionally. The end points of DSB are then joined by Ku and LigD. Brown mutants with a deleted a galU/hmgA region are identified after phage infection.CC BY-NC · PubMed Central

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Research works printed but not linked: 57

  1. Koskiniemi, 2012, Selection-driven gene loss in bacteria, PLoS Genet., 8, e1002787
  2. Lee, 2012, Repeated, selection-driven genome reduction of accessory genes in experimental populations, PLoS Genet, 8, e1002651
  3. Moran, 2002, Microbial minimalism: genome reduction in bacterial pathogens, Cell, 108, 583
  4. Tanji, 2008, Spontaneous deletion of a 209-kilobase-pair fragment from the Escherichia coli genome occurs with acquisition of resistance to an assortment of infectious phages, Appl. Environ. Microbiol., 74, 4256
  5. Hocquet, 2016, Pyomelanin-producing Pseudomonas aeruginosa selected during chronic infections have a large chromosomal deletion which confers resistance to pyocins, Environ. Microbiol., 18, 3482
  6. Birch, 1991, Chromosomal deletion and rearrangement in Streptomyces glaucescens, J. Bacteriol., 173, 3531
  7. Le, 2014, Chromosomal DNA deletion confers phage resistance to Pseudomonas aeruginosa, Sci. Rep., 4, 4738
  8. He, 2015, Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle, Proc. Natl. Acad. Sci. U.S.A., 112, 244
  9. Stover, 2000, Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen, Nature, 406, 959
  10. Khaledi, 2016, Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa, Antimicrob. Agents Chemother., 60, 4722
  11. Qin, 2012, Pseudomonas aeruginosa syntrophy in chronically colonized airways of cystic fibrosis patients, Antimicrob. Agents Chemother., 56, 5971
  12. Marvig, 2015, Within-host microevolution of Pseudomonas aeruginosa in Italian cystic fibrosis patients, BMC Microbiol., 15, 218
  13. Marvig, 2015, Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis, Nat. Genet., 47, 57
  14. Winsor, 2016, Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database, Nucleic Acids Res, 44, D646
  15. Didelot, 2016, Within-host evolution of bacterial pathogens, Nat. Rev. Microbiol., 14, 150
  16. Ghequire, 2014, Ribosomally encoded antibacterial proteins and peptides from Pseudomonas, FEMS Microbiol Rev, 38, 523
  17. Smith, 2006, Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients, Proc. Natl. Acad. Sci. U.S.A., 103, 8487
  18. Dingemans, 2014, The deletion of TonB-dependent receptor genes is part of the genome reduction process that occurs during adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung, Pathogens Dis., 71, 26
  19. Grindley, 2006, Mechanisms of site-specific recombination, Annu. Rev. Biochem., 75, 567
  20. Li, 2011, GI-type T4SS-mediated horizontal transfer of the 89K pathogenicity island in epidemic Streptococcus suis serotype 2, Mol. Microbiol., 79, 1670
  21. Nilsson, 2005, Bacterial genome size reduction by experimental evolution, Proc. Natl. Acad. Sci. U.S.A., 102, 12112
  22. Salmond, 2015, A century of the phage: past, present and future, Nat. Rev. Microbiol., 13, 777
  23. Labrie, 2010, Bacteriophage resistance mechanisms, Nat. Rev. Microbiol, 8, 317
  24. Lim, 2016, Small colony variants and single nucleotide variations in Pf1 region of PB1 Phage-Resistant pseudomonas aeruginosa, Front. Microbiol., 7, 282
  25. Priebe, 2004, The galU Gene of Pseudomonas aeruginosa is required for corneal infection and efficient systemic spread following pneumonia but not for infection confined to the lung, Infect. Immun., 72, 4224
  26. Rodriguez-Rojas, 2009, Inactivation of the hmgA gene of Pseudomonas aeruginosa leads to pyomelanin hyperproduction, stress resistance and increased persistence in chronic lung infection, Microbiology-(UK), 155, 1050
  27. Shen, 2016, Characterization and comparative genomic analyses of pseudomonas aeruginosa phage PaoP5: New members assigned to PAK_P1-like viruses, Sci. Rep., 6, 34067
  28. Le, 2013, Mapping the tail fiber as the receptor binding protein responsible for differential host specificity of pseudomonas aeruginosa bacteriophages PaP1 and JG004, PLoS One, 8, e68562
  29. Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114
  30. Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754
  31. Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078
  32. Robinson, 2011, Integrative genomics viewer, Nat. Biotechnol., 29, 24
  33. Jacobs, 2003, Comprehensive transposon mutant library of Pseudomonas aeruginosa, Proc. Natl. Acad. Sci. U.S.A., 100, 14339
  34. Choi, 2006, A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation, J. Microbiol. Methods, 64, 391
  35. Correa, 2011, Some amino acids of the Pseudomonas aeruginosa MutL D(Q/M)HA(X)(2)E(X)(4)E conserved motif are essential for the in vivo function of the protein but not for the in vitro endonuclease activity, DNA Repair, 10, 1106
  36. Bolz, 2012, Residues in the N-terminal domain of MutL required for mismatch repair in Bacillus subtilis, J. Bacteriol., 194, 5361
  37. Cronin, 1999, pUCP-Nco and pUCP-Nde: Escherichia-Pseudomonas shuttle vectors for recombinant protein expression in Pseudomonas, Anal. Biochem., 272, 112
  38. Polosina, 2010, MutL: conducting the cell's response to mismatched and misaligned DNA, Bioessays, 32, 51
  39. Groothuizen, 2015, MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA, eLife, 4, e06744
  40. Guarne, 2015, Insights from a decade of biophysical studies on MutL: Roles in strand discrimination and mismatch removal, Prog. Biophys. Mol. Biol., 117, 149
  41. Correa, 2013, Analysis of DNA structure and sequence requirements for Pseudomonas aeruginosa MutL endonuclease activity, J. Biochem., 154, 505
  42. Stephanou, 2007, Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks, J. Bacteriol., 189, 5237
  43. Deriano, 2013, Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage, Annu. Rev. Genet., 47, 433
  44. Courcelle, 2015, RecBCD is required to complete chromosomal replication: implications for double-strand break frequencies and repair mechanisms, DNA Repair, 32, 86
  45. Jasin, 2016, The democratization of gene editing: Insights from site-specific cleavage and double-strand break repair, DNA Repair, 44, 6
  46. Shen, 2018, LncRNA lnc-RI regulates homologous recombination repair of DNA double-strand breaks by stabilizing RAD51 mRNA as a competitive endogenous RNA, Nucleic Acids Res., 46, 717
  47. Kadyrova, 2016, Endonuclease activities of MutL alpha and its homologs in DNA mismatch repair, DNA Repair, 38, 42
  48. Bhagwat, 2002, Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli, Mol. Microbiol., 44, 1421
  49. Qiu, 2015, MutL traps MutS at a DNA mismatch, Proc. Natl. Acad. Sci. U.S.A., 112, 10914
  50. Lenhart, 2016, Mismatch repair in Gram-positive bacteria, Res. Microbiol., 167, 4
  51. Jacquelin, 2005, Pseudomonas aeruginosa MutL protein functions in Escherichia coli, Biochem. J., 388, 879
  52. Oliver, 2002, The mismatch repair system (mutS, mutL and uvrD genes) in Pseudomonas aeruginosa: molecular characterization of naturally occurring mutants, Mol. Microbiol., 43, 1641
  53. Magdanova, 2013, Heterogeneity as an adaptive trait of microbial populations, Microbiology, 82, 1
  54. Paterson, 2010, Antagonistic coevolution accelerates molecular evolution, Nature, 464, 275
  55. Pal, 2007, Coevolution with viruses drives the evolution of bacterial mutation rates, Nature, 450, 1079
  56. Boscaro, 2017, Parallel genome reduction in symbionts descended from closely related free-living bacteria, Nat. Ecol. Evol., 1, 1160
  57. Baumgartner, 2017, Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment, ISME J., 11, 2258

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Metadata

Authors
Shen, M., Zhang, H., Shen, W., Zou, Z., Lu, S., Li, G., He, X., Agnello, M., Shi, W., Hu, F., & Le, S.
Affiliations
  • Department of Microbiology, Third Military Medical University, Chongqing 400038, China
  • Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
  • Department of Medical Laboratory, Chengdu Military General Hospital, Chengdu 610083, China
  • The Forsyth Institute, 245 First St, Cambridge, MA 02142, USA
  • School of Dentistry, University of California, Los Angeles, CA 90095, USA
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2018-03-05
Volume
46
Issue
9
Pages
4505-4514
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gky160
PMC
PMC5961081
Cited by
76
References
2
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor)
Funders
  • National Natural Science Foundation of China (31501004, 31570173)
  • National Key Research and Development Program (2017YFC1002002)
  • NIH (1R01DE023810, 1R01DE026186)

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CoChat. (2026). Citation check: Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation. https://app.cochat.ai/papers/10.1093/nar/gky160
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Shen, M., Zhang, H., Shen, W., Zou, Z., Lu, S., Li, G., He, X., Agnello, M., Shi, W., Hu, F., & Le, S. (2018). Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation. Nucleic Acids Research. https://doi.org/10.1093/nar/gky160