1
|
Li Z, Zhou X, Liao D, Liu R, Zhao X, Wang J, Zhong Q, Zeng Z, Peng Y, Tan Y, Yang Z. Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials. Front Cell Infect Microbiol 2023; 13:1180194. [PMID: 37662009 PMCID: PMC10471985 DOI: 10.3389/fcimb.2023.1180194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations. Methods This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted. Results General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies. Disucssion This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.
Collapse
Affiliation(s)
- Zijiao Li
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xiang Zhou
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Danxi Liao
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Ruolan Liu
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xia Zhao
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Jing Wang
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zhuo Zeng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yizhi Peng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yinling Tan
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zichen Yang
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| |
Collapse
|
2
|
Vo MT, Ko K, Ramsay B. Carbon-limited fed-batch production of medium-chain-length polyhydroxyalkanoates by a phaZ-knockout strain of Pseudomonas putida KT2440. J Ind Microbiol Biotechnol 2015; 42:637-46. [PMID: 25563970 DOI: 10.1007/s10295-014-1574-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
A medium-chain-length poly-3-hydroxyalkanote (MCL-PHA) depolymerase knockout mutant of Pseudomonas putida KT2440 was produced by double homologous recombination. A carbon-limited shake-flask study confirmed that depolymerase activity was eliminated. Lysis of both mutant and wild-type strains occurred under these conditions. In carbon-limited, fed-batch culture, the yield of unsaturated monomers from unsaturated substrate averaged only 0.62 mol mol(-1) for the phaZ minus strain compared to 0.72 mol mol(-1) for the wild type. The mutant strain also produced more CO2 and less residual biomass from the same amount of carbon substrate. However, most results indicated that elimination of PHA depolymerase activity had little impact on the overall yield of biomass and PHA.
Collapse
Affiliation(s)
- Minh Tri Vo
- Chemical Engineering, Queen's University, Kingston, ON, K7L 3N6, Canada
| | | | | |
Collapse
|
3
|
Ciesielski S, Górniak D, Możejko J, Świątecki A, Grzesiak J, Zdanowski M. The diversity of bacteria isolated from antarctic freshwater reservoirs possessing the ability to produce polyhydroxyalkanoates. Curr Microbiol 2014; 69:594-603. [PMID: 24939384 PMCID: PMC4201758 DOI: 10.1007/s00284-014-0629-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/30/2014] [Indexed: 11/30/2022]
Abstract
The diversity of polyhydroxyalkanoates-producing bacteria in freshwater reservoirs in the Ecology Glacier foreland, Antarctica, was examined by a cultivation-dependent method. Isolated strains were analyzed phylogenetically by 16S rRNA gene sequencing, and classified as members of Alpha-, Beta-, or Gammaproteobacteria classes. Polymerase chain reaction was used to detect PHA synthase genes. Potential polyhydroxyalkanoates (PHAs) producers belonging mainly to Pseudomonas sp., and Janthinobacterium sp. were isolated from all five sampling sites, suggesting that PHA synthesis is a common bacterial feature at pioneer sites. All Pseudomonas strains had the genetic potential to synthesize medium-chain-length PHAs, whereas some isolated Janthinobacterium strains might produce short-chain-length PHAs or medium-chain-length PHAs. It is the first report revealing that Janthinobacterium species could have the potential to produce medium-chain-length PHAs.
Collapse
Affiliation(s)
- Slawomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Sloneczna 45G, 10-718, Olsztyn, Poland,
| | | | | | | | | | | |
Collapse
|
4
|
Gutierrez M, Choi MH, Tian B, Xu J, Rho JK, Kim MO, Cho YH, Yoon SC. Simultaneous inhibition of rhamnolipid and polyhydroxyalkanoic acid synthesis and biofilm formation in Pseudomonas aeruginosa by 2-bromoalkanoic acids: effect of inhibitor alkyl-chain-length. PLoS One 2013; 8:e73986. [PMID: 24023921 PMCID: PMC3762805 DOI: 10.1371/journal.pone.0073986] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 07/25/2013] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa, an opportunistic human pathogen is known to synthesize rhamnolipid and polyhydroxyalkanoic acid (PHA) of which the acyl-group precursors (e.g., (R)-3-hydroxydecanoic acid) are provided through RhlA and PhaG enzyme, respectively, which have 57% gene sequence homology. The inhibitory effect of three 2-bromo-fatty acids of 2-bromohexanoic acid (2-BrHA), 2-bromooctanoic acid (2-BrOA) and 2-bromodecanoic acid (2-BrDA) was compared to get an insight into the biochemical nature of their probable dual inhibition against the two enzymes. The 2-bromo-compounds were found to inhibit rhamnolipid and PHA synthesis simultaneously in alkyl-chain-length dependent manner at several millimolar concentrations. The separate and dual inhibition of the RhlA and PhaG pathway by the 2-bromo-compounds in the wild-type cells was verified by investigating their inhibitory effects on the rhamnolipid and PHA synthesis in P. aeruginosa ΔphaG and ΔrhlA mutants. Unexpectedly, the order of inhibition strength was found 2-BrHA (≥90% at 2 mM) > 2-BrOA > 2-BrDA, equally for all of the rhamnolipids and PHA synthesis, swarming motility and biofilm formation. We suggest that the novel strongest inhibitor 2-BrHA could be potentially exploited to control the rhamnolipid-associated group behaviors of this pathogen as well as for its utilization as a lead compound in screening for antimicrobial agents based on new antimicrobial targets.
Collapse
Affiliation(s)
- Merced Gutierrez
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Graduate School, Gyeongsang National University, Jinju, Republic of Korea
- National Research Foundation Funded Pioneer Research Center for Alzheimer Disease Control, Gyeongsang National University, Jinju, Republic of Korea
| | - Mun Hwan Choi
- National Research Foundation Funded Pioneer Research Center for Alzheimer Disease Control, Gyeongsang National University, Jinju, Republic of Korea
| | - Baoxia Tian
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Graduate School, Gyeongsang National University, Jinju, Republic of Korea
- National Research Foundation Funded Pioneer Research Center for Alzheimer Disease Control, Gyeongsang National University, Jinju, Republic of Korea
| | - Ju Xu
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Graduate School, Gyeongsang National University, Jinju, Republic of Korea
| | - Jong Kook Rho
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Graduate School, Gyeongsang National University, Jinju, Republic of Korea
| | - Myeong Ok Kim
- National Research Foundation Funded Pioneer Research Center for Alzheimer Disease Control, Gyeongsang National University, Jinju, Republic of Korea
- Neurobiology Laboratory, Division of Applied Life Sciences, Graduate School, Gyeongsang National University, Jinju, Republic of Korea
| | - You-Hee Cho
- Laboratory of Antiinfective Agents and Phage Therapy, College of Pharmacy, CHA University, Gyeonggi-do, Republic of Korea
| | - Sung Chul Yoon
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Graduate School, Gyeongsang National University, Jinju, Republic of Korea
- National Research Foundation Funded Pioneer Research Center for Alzheimer Disease Control, Gyeongsang National University, Jinju, Republic of Korea
- * E-mail:
| |
Collapse
|