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Chauvier A, Walter NG. Regulation of bacterial gene expression by non-coding RNA: It is all about time! Cell Chem Biol 2024; 31:71-85. [PMID: 38211587 DOI: 10.1016/j.chembiol.2023.12.011] [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: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding andapplications of RNAs for therapeutics and drug targets.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Tao S, Zhou D, Chen H, Li N, Zheng L, Fang Y, Xu Y, Jiang Q, Liang W. Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains. Front Microbiol 2023; 14:1177841. [PMID: 37168121 PMCID: PMC10165109 DOI: 10.3389/fmicb.2023.1177841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 05/13/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.
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Affiliation(s)
- Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, China
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Dongdong Zhou
- Department of General Medicine, Ningbo First Hospital, Ningbo, China
| | - Huimin Chen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Na Li
- Bengbu Medical College, Bengbu, China
| | - Lin Zheng
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Yewei Fang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Qi Jiang
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, China
- *Correspondence: Qi Jiang,
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
- Wei Liang,
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Tao S, Chen H, Li N, Fang Y, Xu Y, Liang W. Association of CRISPR-Cas System with the Antibiotic Resistance and Virulence Genes in Nosocomial Isolates of Enterococcus. Infect Drug Resist 2022; 15:6939-6949. [PMID: 36474907 PMCID: PMC9719680 DOI: 10.2147/idr.s388354] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 04/07/2024] Open
Abstract
PURPOSE This study aimed to investigate the prevalence of the CRISPR-Cas system in nosocomial isolates of Enterococcus and their possible association with antibiotic resistance and virulence genes. MATERIALS AND METHODS Identification and antimicrobial susceptibility of the microorganism were performed by the automatized VITEK 2 Compact system (bioMerieux, France). A total of 100 Enterococcus isolates were collected and identified by VITEK 2 Compact automatic microbial identification drug susceptibility analyzer. The prevalence of various CRISPR-Cas systems, antibiotic resistance genes and virulence genes were investigated by polymerase chain reaction (PCR). The prevalence of CRISPR-Cas systems associated with antibiotic resistance and virulence genes was performed by appropriate statistical tests. RESULTS A total of 100 isolates of Enterococcus were identified and there were 62/100(62.0%) Enterococcus faecalis isolates and 38/100(38.0%) Enterococcus faecalis isolates. In total, 46 (46.0%) of 100 isolates had at least one CRISPR-Cas locus. CRISPR elements were more prevalent in Enterococcus faecalis isolates. The results of PCR demonstrated that CRISPR1-Cas, orphan CRISPR2, and CRISPR3-Cas were present in 23 (23.0%), 42 (42.0%) and 5 (5.0%) Enterococcus isolates, respectively. Compared with CRISPR-Casnegative isolates, the CRISPR-Cas positive isolates showed significant lower resistance rates against ampicillin, erythromycin, levofloxacin, tetracycline, vancomycin, gentamicin, streptomycin, and rifampicin. Presumably consistent with drug susceptibility, fewer CRISPR loci were identified in vanA, tetM, ermB, aac6'-aph(2"), aadE, and ant(6) positive isolates. There was a significant negative correlation between the CRISPR-Cas locus and the enterococcal virulence factors enterococcal surface protein (esp) gene. CONCLUSION In conclusion, the results indicated that the absence of the CRISPR-Cas system was negatively associated with some antibiotic resistance in clinical isolates of Enterococcus faecalis and Enterococcus faecium. Also, there was a negative correlation with the carriage of antibiotic resistance genes. Furthermore, CRISPR-Cas may prevent some isolates from acquiring certain virulence factors.
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Affiliation(s)
- Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
| | - Huimin Chen
- School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, People’s Republic of China
| | - Yewei Fang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, People’s Republic of China
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
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Getahun YA, Ali DA, Taye BW, Alemayehu YA. Multidrug-Resistant Microbial Therapy Using Antimicrobial Peptides and the CRISPR/Cas9 System. Vet Med (Auckl) 2022; 13:173-190. [PMID: 35983086 PMCID: PMC9379109 DOI: 10.2147/vmrr.s366533] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/27/2022] [Indexed: 11/24/2022]
Abstract
The emergence and spread of multidrug-resistant microbes become a serious threat to animal and human health globally because of their less responsiveness to conventional antimicrobial therapy. Multidrug-resistant microbial infection poses higher morbidity and mortality rate with significant economic losses. Currently, antimicrobial peptides and the CRISPR/Cas9 system are explored as alternative therapy to circumvent the challenges of multidrug-resistant organisms. Antimicrobial peptides are small molecular weight, cationic peptides extracted from all living organisms. It is a promising drug candidate for the treatment of multidrug-resistant microbes by direct microbial killing or indirectly modulating the innate immune system. The CRISPR/Cas9 system is another novel antimicrobial alternative used to manage multidrug-resistant microbial infection. It is a versatile gene-editing tool that uses engineered single guide RNA for targeted gene recognition and the Cas9 enzyme for the destruction of target nucleic acids. Both the CRISPR/Cas9 system and antimicrobial peptides were used to successfully treat nosocomial infections caused by ESKAPE pathogens, which developed resistance to various antimicrobials. Despite, their valuable roles in multidrug-resistant microbial treatments, both the antimicrobial peptides and the CRISPR/Cas systems have various limitations like toxicity, instability, and incurring high manufacturing costs. Thus, this review paper gives detailed explanations of the roles of the CRISPR/Cas9 system and antimicrobial peptides in circumventing the challenges of multidrug-resistant microbial infections, its limitation and prospects in clinical applications.
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Affiliation(s)
- Yared Abate Getahun
- Livestock and Fishery Research Center, College of Agriculture, Arba Minch University, Arba Minch, Southern Nation Nationalities and Peoples Regional State, Ethiopia
- Correspondence: Yared Abate Getahun, Email
| | - Destaw Asfaw Ali
- Department of Paraclinical Studies, College of Veterinary Medicine, Gondar University, Gondar City, Amhara Regional State, Ethiopia
| | - Bihonegn Wodajnew Taye
- Faculty of Veterinary Medicine, College of Agriculture, Assosa University, Assosa City, Benshangul Gumez Regional State, Ethiopia
| | - Yismaw Alemie Alemayehu
- Department of Animal Science, College of Agriculture, Wollega University, Nekemtie City, Oromia Regional State, Ethiopia
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Guo T, Sun X, Li M, Wang Y, Jiao H, Li G. The Involvement of the csy1 Gene in the Antimicrobial Resistance of Acinetobacter baumannii. Front Med (Lausanne) 2022; 9:797104. [PMID: 35155494 PMCID: PMC8825777 DOI: 10.3389/fmed.2022.797104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/03/2022] [Indexed: 12/26/2022] Open
Abstract
Acinetobacter baumannii is an important, opportunistic nosocomial pathogen that causes a variety of nosocomial infections, and whose drug resistance rate has increased in recent years. The CRISPR-Cas system exists in several bacteria, providing adaptive immunity to foreign nucleic acid invasion. This study explores whether CRISPR-Cas is related to drug resistance. Antibiotics were used to treat strains ATCC19606 and AB43, and the expression of CRISPR-related genes was found to be changed. The Csy proteins (Csy1–4) were previously detected to promote target recognition; however, the potential function of csy1 gene is still unknown. Thus, the RecAb homologous recombination system was utilized to knock out the csy1 gene from A. baumannii AB43, which carries the Type I-Fb CRISPR-Cas system, and to observe the drug resistance changes in wild-type and csy1-deleted strains. The AB43Δcsy1 mutant strain was found to become resistant to antibiotics, while the wild-type strain was sensitive to antibiotics. Moreover, transcriptome analysis revealed that the csy1 gene regulates genes encoding CRISPR-Cas-related proteins, drug-resistant efflux pumps, membrane proteins, and oxidative phosphorylation-related proteins, inhibiting antimicrobial resistance in A. baumannii. The in vitro resistance development assay revealed that the complete CRISPR-Cas system could inhibit the development of bacterial resistance. Our findings expand our understanding of the role of CRISPR-Cas csy1 gene in A. baumannii and link the CRISPR-Cas system to the biogenesis of bacterial drug-resistant structures.
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Affiliation(s)
- Tingting Guo
- Department of Microbiology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, China
| | - Xiaoli Sun
- Department of Microbiology, School of Medicine, Yangzhou University, Yangzhou, China
| | - Mengying Li
- Department of Microbiology, School of Medicine, Yangzhou University, Yangzhou, China.,Department of Pharmacy, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou, China
| | - Yuhang Wang
- Department of Microbiology, School of Medicine, Yangzhou University, Yangzhou, China
| | - Hongmei Jiao
- Department of Microbiology, School of Medicine, Yangzhou University, Yangzhou, China
| | - Guocai Li
- Department of Microbiology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, China
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