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Pal S, Yuvaraj R, Krishnan H, Venkatraman B, Abraham J, Gopinathan A. Unraveling radiation resistance strategies in two bacterial strains from the high background radiation area of Chavara-Neendakara: A comprehensive whole genome analysis. PLoS One 2024; 19:e0304810. [PMID: 38857267 PMCID: PMC11164402 DOI: 10.1371/journal.pone.0304810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/18/2024] [Indexed: 06/12/2024] Open
Abstract
This paper reports the results of gamma irradiation experiments and whole genome sequencing (WGS) performed on vegetative cells of two radiation resistant bacterial strains, Metabacillus halosaccharovorans (VITHBRA001) and Bacillus paralicheniformis (VITHBRA024) (D10 values 2.32 kGy and 1.42 kGy, respectively), inhabiting the top-ranking high background radiation area (HBRA) of Chavara-Neendakara placer deposit (Kerala, India). The present investigation has been carried out in the context that information on strategies of bacteria having mid-range resistance for gamma radiation is inadequate. WGS, annotation, COG and KEGG analyses and manual curation of genes helped us address the possible pathways involved in the major domains of radiation resistance, involving recombination repair, base excision repair, nucleotide excision repair and mismatch repair, and the antioxidant genes, which the candidate could activate to survive under ionizing radiation. Additionally, with the help of these data, we could compare the candidate strains with that of the extremely radiation resistant model bacterium Deinococccus radiodurans, so as to find the commonalities existing in their strategies of resistance on the one hand, and also the rationale behind the difference in D10, on the other. Genomic analysis of VITHBRA001 and VITHBRA024 has further helped us ascertain the difference in capability of radiation resistance between the two strains. Significantly, the genes such as uvsE (NER), frnE (protein protection), ppk1 and ppx (non-enzymatic metabolite production) and those for carotenoid biosynthesis, are endogenous to VITHBRA001, but absent in VITHBRA024, which could explain the former's better radiation resistance. Further, this is the first-time study performed on any bacterial population inhabiting an HBRA. This study also brings forward the two species whose radiation resistance has not been reported thus far, and add to the knowledge on radiation resistant capabilities of the phylum Firmicutes which are abundantly observed in extreme environment.
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Affiliation(s)
- Sowptika Pal
- Molecular Endocrinology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramani Yuvaraj
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Hari Krishnan
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Balasubramanian Venkatraman
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Jayanthi Abraham
- Microbial Biotechnology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anilkumar Gopinathan
- Molecular Endocrinology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Kishino R, Saito T, Muto S, Tomita Y, Sekine Y. Insertion sequence excision is enhanced by a protein that catalyzes branch migration and promotes microhomology-mediated end joining. Genes Cells 2024; 29:131-149. [PMID: 38098298 DOI: 10.1111/gtc.13090] [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: 11/11/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 02/06/2024]
Abstract
Insertion sequence (IS)-excision enhancer (IEE) promotes the excision of ISs in the genome of enterohemorrhagic Escherichia coli O157. Because IEE-dependent IS excision occurs in the presence of transposase, the process of IS transposition may be involved in IS excision; however, little is understood about the molecular mechanisms of IS excision. Our in vitro analysis revealed that IEE exhibits DNA-dependent ATPase activity, which is activated by branched DNA. IEE also catalyzes the branch migration of fork-structured DNA. These results suggest that IEE remodels branched structures of the IS transposition intermediate. Sequence analysis of recombination sites in IS-excision products suggested that microhomologous sequences near the ends of the IS are involved in IS excision. IEE promoted microhomology-mediated end joining (MMEJ), in which base pairing between 6-nucleotides complementary ends of two 3'-protruding DNAs and subsequent elongation of the paired DNA strand occurred. IS-excision frequencies were significantly decreased in cells producing IEE mutants that had lost either branch migration or MMEJ activity, which suggests that these activities of IEE are required for IS excision. Based on our results, we propose a model for IS excision triggered by IEE and transposase.
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Affiliation(s)
- Ren Kishino
- Department of Life Science, Graduate School of Science, Rikkyo University, Tokyo, Japan
| | - Takashi Saito
- Department of Life Science, Graduate School of Science, Rikkyo University, Tokyo, Japan
| | - Shuntaro Muto
- Department of Life Science, Graduate School of Science, Rikkyo University, Tokyo, Japan
| | - Yuzuka Tomita
- Department of Life Science, Graduate School of Science, Rikkyo University, Tokyo, Japan
| | - Yasuhiko Sekine
- Department of Life Science, Graduate School of Science, Rikkyo University, Tokyo, Japan
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Hu Z, Bai X. Self-repair and resuscitation of viable injured bacteria in chlorinated drinking water: Achromobacter as an example. WATER RESEARCH 2023; 245:120585. [PMID: 37690414 DOI: 10.1016/j.watres.2023.120585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Chlorine disinfection for the treatment of drinking water can cause injury to the membrane and DNA of bacterial cells and may induce the surviving injured bacteria into a viable but non-culturable (VBNC) state. It is difficult to monitor viable injured bacteria by heterotrophic plate counting (HPC), and their presence is also easily miscalculated in flow cytometry intact cell counting (FCM-ICC). Viable injured bacteria have a potential risk of resuscitation in drinking water distribution systems (DWDSs) and pose a threat to public health when drinking from faucets. In this study, bacteria with injured membranes were isolated from chlorinated drinking water by FCM cell sorting. The culture rate of injured bacteria varied from 0.08% to 2.6% on agar plates and 0.39% to 6.5% in 96-well plates. As the dominant genus among the five identified genera, as well as an opportunistic pathogen with multiple antibiotic resistance, Achromobacter was selected and further studied. After treatment with chlorine at a concentration of 1.2 mg/L, Achromobacter entered into the intermediate injured state on the FCM plot, and the injury on the bacterial surface was observed by electron microscopy. However, the CTC respiratory activity assay showed that 75.0% of the bacteria were still physiologically active, and they entered into a VBNC state. The injured VBNC Achromobacter in sterile drinking water were resuscitated after approximately 25 h. The cellular repair behavior of injured bacteria was studied by Fourier transform infrared attenuated total reflectance (FTIR-ATR) and comet assays. It was found that DNA injury rather than membrane injury was repaired first. The expression of Ku and ligD increased significantly during the DNA repair period, indicating that non-homologous end-joining (NHEJ) played an important role in repairing DNA double-strand breaks. This study deepened the understanding of the effect of chlorine disinfection on bacterial viability in drinking water and will provide support for the improvement of the chlorine disinfection process for the treatment of drinking water.
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Affiliation(s)
- Zengyi Hu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Yan F, Wang J, Zhang S, Lu Z, Li S, Ji Z, Song C, Chen G, Xu J, Feng J, Zhou X, Zhou H. CRISPR/FnCas12a-mediated efficient multiplex and iterative genome editing in bacterial plant pathogens without donor DNA templates. PLoS Pathog 2023; 19:e1010961. [PMID: 36626407 PMCID: PMC9870152 DOI: 10.1371/journal.ppat.1010961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/23/2023] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
CRISPR-based genome editing technology is revolutionizing prokaryotic research, but it has been rarely studied in bacterial plant pathogens. Here, we have developed a targeted genome editing method with no requirement of donor templates for convenient and efficient gene knockout in Xanthomonas oryzae pv. oryzae (Xoo), one of the most important bacterial pathogens on rice, by employing the heterologous CRISPR/Cas12a from Francisella novicida and NHEJ proteins from Mycobacterium tuberculosis. FnCas12a nuclease generated both small and large DNA deletions at the target sites as well as it enabled multiplex genome editing, gene cluster deletion, and plasmid curing in the Xoo PXO99A strain. Accordingly, a non-TAL effector-free polymutant strain PXO99AD25E, which lacks all 25 xop genes involved in Xoo pathogenesis, has been engineered through iterative genome editing. Whole-genome sequencing analysis indicated that FnCas12a did not have a noticeable off-target effect. In addition, we revealed that these strategies are also suitable for targeted genome editing in another bacterial plant pathogen Pseudomonas syringae pv. tomato (Pst). We believe that our bacterial genome editing method will greatly expand the CRISPR study on microorganisms and advance our understanding of the physiology and pathogenesis of Xoo.
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Affiliation(s)
- Fang Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingwen Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sujie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Zhenwan Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Congfeng Song
- Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Gongyou Chen
- State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China,* E-mail:
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Sowa DJ, Warner MM, Tetenych A, Koechlin L, Balari P, Rascon Perez JP, Caba C, Andres SN. The Mycobacterium tuberculosis Ku C-terminus is a multi-purpose arm for binding DNA and LigD and stimulating ligation. Nucleic Acids Res 2022; 50:11040-11057. [PMID: 36250639 PMCID: PMC9638933 DOI: 10.1093/nar/gkac906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial non-homologous end joining requires the ligase, LigD and Ku. Ku finds the break site, recruits LigD, and then assists LigD to seal the phosphodiester backbone. Bacterial Ku contains a core domain conserved with eukaryotes but has a unique C-terminus that can be divided into a minimal C-terminal region that is conserved and an extended C-terminal region that varies in sequence and length between species. Here, we examine the role of Mycobacterium tuberculosis Ku C-terminal variants, where we removed either the extended or entire C-terminus to investigate the effects on Ku–DNA binding, rates of Ku-stimulated ligation, and binding affinity of a direct Ku–LigD interaction. We find that the extended C-terminus limits DNA binding and identify key amino acids that contribute to this effect through alanine-scanning mutagenesis. The minimal C-terminus is sufficient to stimulate ligation of double-stranded DNA, but the Ku core domain also contributes to stimulating ligation. We further show that wildtype Ku and the Ku core domain alone directly bind both ligase and polymerase domains of LigD. Our results suggest that Ku-stimulated ligation involves direct interactions between the Ku core domain and the LigD ligase domain, in addition to the extended Ku C-terminus and the LigD polymerase domain.
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Affiliation(s)
- Dana J Sowa
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Monica M Warner
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Andriana Tetenych
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Lucas Koechlin
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Pardis Balari
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Jose Pablo Rascon Perez
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Cody Caba
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Sara N Andres
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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Dong M, Liu J, Liu C, Wang H, Sun W, Liu B. CRISPR/CAS9: A promising approach for the research and treatment of cardiovascular diseases. Pharmacol Res 2022; 185:106480. [PMID: 36191879 DOI: 10.1016/j.phrs.2022.106480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/31/2022]
Abstract
The development of gene-editing technology has been one of the biggest advances in biomedicine over the past two decades. Not only can it be used as a research tool to build a variety of disease models for the exploration of disease pathogenesis at the genetic level, it can also be used for prevention and treatment. This is done by intervening with the expression of target genes and carrying out precise molecular targeted therapy for diseases. The simple and flexible clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene-editing technology overcomes the limitations of zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). For this reason, it has rapidly become a preferred method for gene editing. As a new gene intervention method, CRISPR/Cas9 has been widely used in the clinical treatment of tumours and rare diseases; however, its application in the field of cardiovascular diseases is currently limited. This article reviews the application of the CRISPR/Cas9 editing technology in cardiovascular disease research and treatment, and discusses the limitations and prospects of this technology.
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Affiliation(s)
- Mengying Dong
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Jiangen Liu
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Caixia Liu
- Department of Neurology, The Liaoning Province People's Hospital, 33 Wenyi Road, ShenYang, China, 110016
| | - He Wang
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Wei Sun
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041.
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041.
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