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Lu W, Zha B, Lyu J, LingHu C, Chen J, Deng S, Zhang X, Li L, Wang G. Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces. Front Microbiol 2024; 15:1500886. [PMID: 39736996 PMCID: PMC11683593 DOI: 10.3389/fmicb.2024.1500886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 11/25/2024] [Indexed: 01/01/2025] Open
Abstract
Background Numerous studies have demonstrated that Akkermansia is closely associated with human health. These bacteria colonize the mucus layer of the gastrointestinal tract and utilize mucin as their sole source of carbon and nitrogen. Akkermansia spp. exhibit potential as probiotics under specific conditions. However, the gene accumulation curve derived from pan-genome analysis suggests that the genome of Akkermansia strains remains open. Consequently, current genome mining efforts are insufficient to fully capture the intraspecific and interspecific characteristics of Akkermansia, necessitating continuous exploration of the genomic and phenotypic diversity of new isolates. Methods Based on this finding, we sequenced, assembled, and functionally annotated the whole genomes of four new human isolates from our laboratory: AKK-HX001, AKK-HX002, AKK-HX003, and AKK-HX004. Results Phylogenetic analysis revealed that all four isolates belonged to the AmII phylogroup, whereas the type strain DSM 22959 is classified within the AmI phylogroup. Moreover, 2,184 shared homologous genes were identified among the four isolates. Functional annotation using the COG, KEGG, and CAZy databases indicated that the functional genes of the four isolates were primarily associated with metabolism. Two antibiotic resistance genes were identified in AKK-HX001 and AKK-HX002, while three resistance genes were detected in AKK-HX003 and AKK-HX004. Additionally, each of the four isolates possessed two virulence genes and three pathogenicity genes, none of which were associated with pathogenicity. The prediction of mobile genetic elements indicated unequal distributions of GIs among the isolates, and a complete CRISPR system was identified in all isolates except AKK-HX003. Two annotated regions of secondary metabolite biosynthesis genes, both belonging to Terpene, were detected using the antiSMASH online tool. Conclusion These findings indicate that the four Akkermansia isolates, which belong to a phylogroup distinct from the model strain DSM 22959, exhibit lower genetic risk and may serve as potential probiotic resources for future research.
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Affiliation(s)
- Wenjing Lu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Biqing Zha
- Jiujiang Center for Disease Control and Prevention, Jiujiang, China
| | - Jie Lyu
- Microbiome Research and Application Center, BYHEALTH Institute of Nutrition and Health, Guangzhou, China
| | - Chenxi LingHu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jing Chen
- Chengdu East New District Public Health Center, Chengdu, China
| | - Sisi Deng
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Xiangling Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Liang Li
- Microbiome Research and Application Center, BYHEALTH Institute of Nutrition and Health, Guangzhou, China
| | - Guoqing Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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2
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Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Protein interactions in human pathogens revealed through deep learning. Nat Microbiol 2024; 9:2642-2652. [PMID: 39294458 PMCID: PMC11445079 DOI: 10.1038/s41564-024-01791-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/23/2024] [Indexed: 09/20/2024]
Abstract
Identification of bacterial protein-protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
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Affiliation(s)
- Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Minkyung Baek
- Department of Biological Sciences, Seoul National University, Seoul, South Korea.
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Aditya Krishnakumar
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Catherine A Tower
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Blake A Jackson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Thulasi Warrier
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deborah T Hung
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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3
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Sarıgül İ, Žukova A, Alparslan E, Remm S, Pihlak M, Kaldalu N, Tenson T, Maiväli Ü. Involvement of Escherichia coli YbeX/CorC in ribosomal metabolism. Mol Microbiol 2024; 121:984-1001. [PMID: 38494741 DOI: 10.1111/mmi.15248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/19/2024]
Abstract
YbeX of Escherichia coli, a member of the CorC protein family, is encoded in the same operon with ribosome-associated proteins YbeY and YbeZ. Here, we report the involvement of YbeX in ribosomal metabolism. The ΔybeX cells accumulate distinct 16S rRNA degradation intermediates in the 30S particles and the 70S ribosomes. E. coli lacking ybeX has a lengthened lag phase upon outgrowth from the stationary phase. This growth phenotype is heterogeneous at the individual cell level and especially prominent under low extracellular magnesium levels. The ΔybeX strain is sensitive to elevated growth temperatures and to several ribosome-targeting antibiotics that have in common the ability to induce the cold shock response in E. coli. Although generally milder, the phenotypes of the ΔybeX mutant overlap with those caused by ybeY deletion. A genetic screen revealed partial compensation of the ΔybeX growth phenotype by the overexpression of YbeY. These findings indicate an interconnectedness among the ybeZYX operon genes, highlighting their roles in ribosomal assembly and/or degradation.
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Affiliation(s)
- İsmail Sarıgül
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Amata Žukova
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Emel Alparslan
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sille Remm
- Institute of Technology, University of Tartu, Tartu, Estonia
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Margus Pihlak
- Department of Cybernetics, Tallinn University of Technology, Tallinn, Estonia
| | - Niilo Kaldalu
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ülo Maiväli
- Institute of Technology, University of Tartu, Tartu, Estonia
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4
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Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Essential and virulence-related protein interactions of pathogens revealed through deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589144. [PMID: 38645026 PMCID: PMC11030334 DOI: 10.1101/2024.04.12.589144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Identification of bacterial protein-protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning-based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
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5
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Song D, Qi X, Huang Y, Jia A, Liang Y, Man C, Yang X, Jiang Y. Comparative proteomics reveals the antibiotic resistance and virulence of Cronobacter isolated from powdered infant formula and its processing environment. Int J Food Microbiol 2023; 407:110374. [PMID: 37678039 DOI: 10.1016/j.ijfoodmicro.2023.110374] [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: 05/26/2023] [Revised: 07/31/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Cronobacter species are opportunistic foodborne pathogens that can cause neonatal meningitis, sepsis, and necrotizing enterocolitis. In this genus, certain level strains have high mortality to infant (Cronobacter sakazakii and Cronobacter malonaticus) and antibiotic tolerance. Cronobacter has strong environmental tolerance (acid resistance, high temperature resistance, UV resistance, antibiotic resistance, etc.) and can survive in a variety of environments. It has been isolated in various production environments and products in several countries. However, the relationships between Cronobacter antibiotic tolerance and virulence remain unclear, especially at the molecular level. In this study, 96 strains of Cronobacter were isolated from powdered infant formula and its processing environment and screened for antibiotic tolerance, and proteomic maps of the representative strains of Cronobacter with antibiotic tolerance were generated by analyzing proteomics data using multiple techniques to identify protein that are implicated in Cronobacter virulence and antibiotic resistance. The increase in antibiotic tolerance of Cronobacter had a certain increase in the production of enterotoxin and hemolysin. Only triple tolerated Cronobacter sakazakii decreased the utilization of sialic acid. A total of 16,131 intracellular proteins were detected in eight representative strains, and different proteomes were present in strains with different antibiotic tolerance, including 56 virulence-related proteins. Multiple virulence proteins regulated by unknown genes were also found in the eight isolated representative strains.
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Affiliation(s)
- Danliangmin Song
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Xuehe Qi
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China.
| | - Yan Huang
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Ai Jia
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Yaqi Liang
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, Harbin 150030, China.
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, Harbin 150030, China.
| | - Yujun Jiang
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China.
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6
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Complications and Treatments of Pseudomonas aeruginosa Infection After Rhinoplasty With Implants: A Clinical Study. J Craniofac Surg 2023; 34:e104-e108. [PMID: 35882015 DOI: 10.1097/scs.0000000000008774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/06/2022] [Indexed: 10/16/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic pathogen, and because of its specificity, its treatments appear tricky in postrhinoplasty infections with internal implants. This study summarizes the clinical characteristics and treatment of this type of infections to provide some reference for clinical work. METHODS We retrospectively analyzed 10 patients who were diagnosed with a nasal infection of P. aeruginosa after implant nasal augmentation. The results of the bacterial culture and drug sensitivity test of the patients' wound secretions were summarized and analyzed. We summarized the characteristics of the patients' infection and the treatments, and we also summarized the patients' prognosis. RESULTS In these 10 cases, their implants included rib cartilage and ear cartilage alone, as well as their own cartilage combined with expanded polytetrafluoroethylene and silicone. All patients developed wound infections within 1 month after rhinoplasty, with bacterial cultures of P. aeruginosa . Prolonged use of sensitive antibiotics, as well as wound dressing changes, failed to keep the infection well under control. Patients whose implant was removed and thoroughly debrided within 1 week of infection did not experience any serious complications. In patients who were infected for >1 week before surgery to remove the implants, complications such as nasal column necrosis and nasal contracture occurred, and later the nasal repair was performed after multiple surgeries. CONCLUSIONS For bacterial infections in postrhinoplasty wounds with implants, we recommend early bacterial culture. If the infection is clearly P. aeruginosa , the implant should be removed and thoroughly debrided as soon as possible to avoid serious complications. LEVEL OF EVIDENCE Level IV.
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7
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Lee J, Jo I, Kwon AR, Ha NC. Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus. J Microbiol Biotechnol 2023; 33:28-34. [PMID: 36457189 PMCID: PMC9895993 DOI: 10.4014/jmb.2209.09019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
Endoribonuclease YbeY is specific to the single-stranded RNA of ribosomal RNAs and small RNAs. This enzyme is essential for the maturation and quality control of ribosomal RNA in a wide range of bacteria and for virulence in some pathogenic bacteria. In this study, we determined the crystal structure of YbeY from Staphylococcus aureus at a resolution of 1.9 Å in the presence of zinc chloride. The structure showed a zinc ion at the active site and two molecules of tricarboxylic acid citrate, which were also derived from the crystallization conditions. Our structure showed the zinc ion-bound local environment at the molecular level for the first time. Molecular comparisons were performed between the carboxylic moieties of citrate and the phosphate moiety of the RNA backbone, and a model of YbeY in complex with a single strand of RNA was subsequently constructed. Our findings provide molecular insights into how the YbeY enzyme recognizes single-stranded RNA in bacteria.
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Affiliation(s)
- Jinwook Lee
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Inseong Jo
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul 08826, Republic of Korea,Current address: Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Ae-Ran Kwon
- Department of Beauty Care, College of Medical Science, Daegu Haany University, Gyeongsan 38610, Republic of Korea
| | - Nam-Chul Ha
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul 08826, Republic of Korea,Corresponding author Phone: +82-2-880-4853 E-mail:
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8
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Costa VG, Costa SM, Saramago M, Cunha MV, Arraiano CM, Viegas SC, Matos RG. Developing New Tools to Fight Human Pathogens: A Journey through the Advances in RNA Technologies. Microorganisms 2022; 10:2303. [PMID: 36422373 PMCID: PMC9697208 DOI: 10.3390/microorganisms10112303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 09/18/2024] Open
Abstract
A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of the advantages of RNA in terms of its functional performance, have attracted the attention of synthetic biologists to create potent RNA-based tools for biotechnological and medical applications. In this review, we have gathered the knowledge on the connection between RNA metabolism and pathogenesis in Gram-positive and Gram-negative bacteria. We further discuss how RNA techniques have contributed to the building of this knowledge and the development of new tools in synthetic biology for the diagnosis and treatment of diseases caused by pathogenic microorganisms. Infectious diseases are still a world-leading cause of death and morbidity, and RNA-based therapeutics have arisen as an alternative way to achieve success. There are still obstacles to overcome in its application, but much progress has been made in a fast and effective manner, paving the way for the solid establishment of RNA-based therapies in the future.
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Affiliation(s)
| | | | | | | | | | - Sandra C. Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal; (V.G.C.); (S.M.C.); (M.S.); (M.V.C.); (C.M.A.)
| | - Rute G. Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal; (V.G.C.); (S.M.C.); (M.S.); (M.V.C.); (C.M.A.)
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9
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Liu P, Yue C, Liu L, Gao C, Lyu Y, Deng S, Tian H, Jia X. The function of small RNA in Pseudomonas aeruginosa. PeerJ 2022; 10:e13738. [PMID: 35891650 PMCID: PMC9308961 DOI: 10.7717/peerj.13738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/25/2022] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas aeruginosa, the main conditional pathogen causing nosocomial infection, is a gram-negative bacterium with the largest genome among the known bacteria. The main reasons why Pseudomonas aeruginosa is prone to drug-resistant strains in clinic are: the drug-resistant genes in its genome and the drug resistance easily induced by single antibiotic treatment. With the development of high-throughput sequencing technology and bioinformatics, the functions of various small RNAs (sRNA) in Pseudomonas aeruginosa are being revealed. Different sRNAs regulate gene expression by binding to protein or mRNA to play an important role in the complex regulatory network. In this article, first, the importance and biological functions of different sRNAs in Pseudomonas aeruginosa are explored, and then the evidence and possibilities that sRNAs served as drug therapeutic targets are discussed, which may introduce new directions to develop novel disease treatment strategies.
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Affiliation(s)
- Pei Liu
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Changwu Yue
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Lihua Liu
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Can Gao
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Yuhong Lyu
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Shanshan Deng
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Hongying Tian
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Xu Jia
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China,School of Basic Medical Science, Chengdu Medical College, Chengdu, Sichuan, China
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10
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Babu VMP, Sankari S, Ghosal A, Walker GC. A Mutant Era GTPase Suppresses Phenotypes Caused by Loss of Highly Conserved YbeY Protein in Escherichia coli. Front Microbiol 2022; 13:896075. [PMID: 35663862 PMCID: PMC9159920 DOI: 10.3389/fmicb.2022.896075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 12/03/2022] Open
Abstract
Ribosome assembly is a complex fundamental cellular process that involves assembling multiple ribosomal proteins and several ribosomal RNA species in a highly coordinated yet flexible and resilient manner. The highly conserved YbeY protein is a single-strand specific endoribonuclease, important for ribosome assembly, 16S rRNA processing, and ribosome quality control. In Escherichia coli, ybeY deletion results in pleiotropic phenotypes including slow growth, temperature sensitivity, accumulation of precursors of 16S rRNA, and impaired formation of fully assembled 70S subunits. Era, an essential highly conserved GTPase protein, interacts with many ribosomal proteins, and its depletion results in ribosome assembly defects. YbeY has been shown to interact with Era together with ribosomal protein S11. In this study, we have analyzed a suppressor mutation, era(T99I), that can partially suppress a subset of the multiple phenotypes of ybeY deletion. The era(T99I) allele was able to improve 16S rRNA processing and ribosome assembly at 37°C. However, it failed to suppress the temperature sensitivity and did not improve 16S rRNA stability. The era(T99I) allele was also unable to improve the 16S rRNA processing defects caused by the loss of ribosome maturation factors. We also show that era(T99I) increases the GroEL levels in the 30S ribosome fractions independent of YbeY. We propose that the mechanism of suppression is that the changes in Era's structure caused by the era(T99I) mutation affect its GTP/GDP cycle in a way that increases the half-life of RNA binding to Era, thereby facilitating alternative processing of the 16S RNA precursor. Taken together, this study offers insights into the role of Era and YbeY in ribosome assembly and 16S rRNA processing events.
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Affiliation(s)
| | | | | | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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11
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Temporal Transcriptional Responses of a Vibrio alginolyticus Strain to
Podoviridae
Phage HH109 Revealed by RNA-Seq. mSystems 2022; 7:e0010622. [PMID: 35400200 PMCID: PMC9040624 DOI: 10.1128/msystems.00106-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio alginolyticus
is a common opportunistic pathogen that causes mass mortality in cultured marine animals. Phage HH109 lyses pathogenic
V. alginolyticus
strain E110 with high efficiency and thus serves as a useful model to understand the dynamic interplay of a phage and its host.
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12
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Li H, Xia Y, Tian Z, Jin Y, Bai F, Cheng Z, Swietnicki W, Wu W, Pan X. Dihydrolipoamide Acetyltransferase AceF Influences the Type III Secretion System and Resistance to Oxidative Stresses through RsmY/Z in Pseudomonas aeruginosa. Microorganisms 2022; 10:microorganisms10030666. [PMID: 35336241 PMCID: PMC8950878 DOI: 10.3390/microorganisms10030666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 01/27/2023] Open
Abstract
Carbon metabolism plays an important role in bacterial physiology and pathogenesis. The type III secretion system (T3SS) of Pseudomonas aeruginosa is a virulence factor that contributes to acute infections. It has been demonstrated that bacterial metabolism affects the T3SS. Meanwhile, expression of T3SS genes is negatively regulated by the small RNAs RsmY and RsmZ. In this study, we studied the relationship between the dihydrolipoamide acetyltransferase gene aceF and the T3SS. Our results reveal an upregulation of RsmY and RsmZ in the aceF mutant, which represses the expression of the T3SS genes. Meanwhile, the aceF mutant is more tolerant to hydrogen peroxide. We demonstrate that the expression levels of the catalase KatB and the alkyl hydroperoxide reductase AhpB are increased in the aceF mutant. The simultaneous deletion of rsmY and rsmZ in the aceF mutant restored the expression levels of katB and ahpB, as well as bacterial susceptibility to hydrogen peroxide. Thus, we identify a novel role of AceF in the virulence and oxidative response of P. aeruginosa.
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Affiliation(s)
- Haozhou Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
| | - Yushan Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
| | - Zhenyang Tian
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
| | - Wieslaw Swietnicki
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. R. Weigla 12, 53-114 Wroclaw, Poland;
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.L.); (Y.X.); (Z.T.); (Y.J.); (F.B.); (Z.C.); (W.W.)
- Correspondence:
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13
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Zhang J, Hess WR, Zhang C. "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria. MLIFE 2022; 1:21-39. [PMID: 38818322 PMCID: PMC10989914 DOI: 10.1002/mlf2.12015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 06/01/2024]
Abstract
RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes. In bacteria, the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis, but not much is known in other bacteria. Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO2 and solar energy. A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria. Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E. coli and B. subtilis, and only a limited number of them have been experimentally investigated. In this review, we summarize the current knowledge about these RNA-turnover-related proteins in cyanobacteria. Although many of them are biochemically similar to their counterparts in E. coli and B. subtilis, they appear to have distinct cellular functions, suggesting a different mechanism of RNA turnover regulation in cyanobacteria. The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field.
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Affiliation(s)
- Ju‐Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Cheng‐Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
- Institut WUT‐AMUAix‐Marseille University and Wuhan University of TechnologyWuhanChina
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Shan X, Fu J, Li X, Peng X, Chen L. Comparative proteomics and secretomics revealed virulence, and coresistance-related factors in non O1/O139 Vibrio cholerae recovered from 16 species of consumable aquatic animals. J Proteomics 2022; 251:104408. [PMID: 34737110 DOI: 10.1016/j.jprot.2021.104408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/12/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023]
Abstract
Vibrio cholerae can cause pandemic cholera in humans. The bacterium resides in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. In this study, we determined virulence-associated genes, cross-resistance between antibiotics and heavy metals, and genome fingerprinting profiles of non O1/O139 V. cholerae isolates (n = 20) recovered from 16 species of consumable aquatic animals. Secretomes and proteomes of V. cholerae with distinct genotypes and phenotypes were obtained by using two-dimensional gel electrophoresis (2D-GE) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. Comparative secretomic analysis revealed 4 common and 45 differential extracellular proteins among 20 V. cholerae strains, including 13 virulence- and 8 resistance-associated proteins. A total of 21,972 intracellular proteins were identified, and comparative proteomic analysis revealed 215 common and 913 differential intracellular proteins, including 22 virulence- and 8 resistance-associated proteins. Additionally, different secretomes and proteomes were observed between V. cholerae isolates of fish and shellfish origins. A number of novel proteins with unknown function and strain-specific proteins were also discovered in the V. cholerae isolates. SIGNIFICANCE: V. cholerae can cause pandemic cholera in humans. The bacterium is distributed in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. Non-O1/O139 V. cholerae has been reported to cause sporadic cholera-like diarrhea and bacteremia diseases, which indicates virulence factors rather than the major cholera toxin (CT) exist. This study for the first time investigated proteomes and secretomes of non-O1/O139 V. cholerae originating from aquatic animals. This resulted in the identification of a number of virulence and coresistance-related factors, as well as novel proteins and strain-specific proteins in V. cholerae isolates recovered from 16 species of consumable aquatic animals. These results fill gaps for better understanding of pathogenesis and resistance of V. cholerae, and also support the increasing need for novel diagnosis and vaccine targets against the leading waterborne pathogen worldwide.
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Affiliation(s)
- Xinying Shan
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Junfeng Fu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaohui Li
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
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15
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Apura P, Gonçalves LG, Viegas SC, Arraiano CM. The world of ribonucleases from pseudomonads: a short trip through the main features and singularities. Microb Biotechnol 2021; 14:2316-2333. [PMID: 34427985 PMCID: PMC8601179 DOI: 10.1111/1751-7915.13890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/30/2021] [Indexed: 11/27/2022] Open
Abstract
The development of synthetic biology has brought an unprecedented increase in the number molecular tools applicable into a microbial chassis. The exploration of such tools into different bacteria revealed not only the challenges of context dependency of biological functions but also the complexity and diversity of regulatory layers in bacterial cells. Most of the standardized genetic tools and principles/functions have been mostly based on model microorganisms, namely Escherichia coli. In contrast, the non-model pseudomonads lack a deeper understanding of their regulatory layers and have limited molecular tools. They are resistant pathogens and promising alternative bacterial chassis, making them attractive targets for further studies. Ribonucleases (RNases) are key players in the post-transcriptional control of gene expression by degrading or processing the RNA molecules in the cell. These enzymes act according to the cellular requirements and can also be seen as the recyclers of ribonucleotides, allowing a continuous input of these cellular resources. This makes these post-transcriptional regulators perfect candidates to regulate microbial physiology. This review summarizes the current knowledge and unique properties of ribonucleases in the world of pseudomonads, taking into account genomic context analysis, biological function and strategies to use ribonucleases to improve biotechnological processes.
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Affiliation(s)
- Patrícia Apura
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Luis G. Gonçalves
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Sandra C. Viegas
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
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Oxidative Stress Response in Pseudomonas aeruginosa. Pathogens 2021; 10:pathogens10091187. [PMID: 34578219 PMCID: PMC8466533 DOI: 10.3390/pathogens10091187] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative environmental and human opportunistic pathogen highly adapted to many different environmental conditions. It can cause a wide range of serious infections, including wounds, lungs, the urinary tract, and systemic infections. The high versatility and pathogenicity of this bacterium is attributed to its genomic complexity, the expression of several virulence factors, and its intrinsic resistance to various antimicrobials. However, to thrive and establish infection, P. aeruginosa must overcome several barriers. One of these barriers is the presence of oxidizing agents (e.g., hydrogen peroxide, superoxide, and hypochlorous acid) produced by the host immune system or that are commonly used as disinfectants in a variety of different environments including hospitals. These agents damage several cellular molecules and can cause cell death. Therefore, bacteria adapt to these harsh conditions by altering gene expression and eliciting several stress responses to survive under oxidative stress. Here, we used PubMed to evaluate the current knowledge on the oxidative stress responses adopted by P. aeruginosa. We will describe the genes that are often differently expressed under oxidative stress conditions, the pathways and proteins employed to sense and respond to oxidative stress, and how these changes in gene expression influence pathogenicity and the virulence of P. aeruginosa. Understanding these responses and changes in gene expression is critical to controlling bacterial pathogenicity and developing new therapeutic agents.
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Pusic P, Sonnleitner E, Bläsi U. Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:8632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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Affiliation(s)
- Petra Pusic
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, Centre of Molecular Biology, Vienna Biocenter (VBC), University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Elisabeth Sonnleitner
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, Centre of Molecular Biology, Vienna Biocenter (VBC), University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Udo Bläsi
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, Centre of Molecular Biology, Vienna Biocenter (VBC), University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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18
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YbeY, éminence grise of ribosome biogenesis. Biochem Soc Trans 2021; 49:727-745. [PMID: 33929506 DOI: 10.1042/bst20200669] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/30/2022]
Abstract
YbeY is an ultraconserved small protein belonging to the unique heritage shared by most existing bacteria and eukaryotic organelles of bacterial origin, mitochondria and chloroplasts. Studied in more than a dozen of evolutionarily distant species, YbeY is invariably critical for cellular physiology. However, the exact mechanisms by which it exerts such penetrating influence are not completely understood. In this review, we attempt a transversal analysis of the current knowledge about YbeY, based on genetic, structural, and biochemical data from a wide variety of models. We propose that YbeY, in association with the ribosomal protein uS11 and the assembly GTPase Era, plays a critical role in the biogenesis of the small ribosomal subunit, and more specifically its platform region, in diverse genetic systems of bacterial type.
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YbeY controls the type III and type VI secretion systems and biofilm formation through RetS in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:AEM.02171-20. [PMID: 33310711 PMCID: PMC8090875 DOI: 10.1128/aem.02171-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
YbeY is a highly conserved RNase in bacteria and plays essential roles in the maturation of 16S rRNA, regulation of small RNAs (sRNAs) and bacterial responses to environmental stresses. Previously, we verified the role of YbeY in rRNA processing and ribosome maturation in Pseudomonas aeruginosa and demonstrated YbeY-mediated regulation of rpoS through a sRNA ReaL. In this study, we demonstrate that mutation of the ybeY gene results in upregulation of the type III secretion system (T3SS) genes as well as downregulation of the type VI secretion system (T6SS) genes and reduction of biofilm formation. By examining the expression of the known sRNAs in P. aeruginosa, we found that mutation of the ybeY gene leads to downregulation of the small RNAs RsmY/Z that control the T3SS, the T6SS and biofilm formation. Further studies revealed that the reduced levels of RsmY/Z are due to upregulation of retS Taken together, our results reveal the pleiotropic functions of YbeY and provide detailed mechanisms of YbeY-mediated regulation in P. aeruginosa IMPORTANCE Pseudomonas aeruginosa causes a variety of acute and chronic infections in humans. The type III secretion system (T3SS) plays an important role in acute infection and the type VI secretion system (T6SS) and biofilm formation are associated with chronic infections. Understanding of the mechanisms that control the virulence determinants involved in acute and chronic infections will provide clues for the development of effective treatment strategies. Our results reveal a novel RNase mediated regulation on the T3SS, T6SS and biofilm formation in P. aeruginosa.
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