1
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Onodera H, Niwa T, Taguchi H, Chadani Y. Prophage excision switches the primary ribosome rescue pathway and rescue-associated gene regulations in Escherichia coli. Mol Microbiol 2023; 119:44-58. [PMID: 36471624 PMCID: PMC10107115 DOI: 10.1111/mmi.15003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
Escherichia coli has multiple pathways to release nonproductive ribosome complexes stalled at the 3' end of nonstop mRNA: tmRNA (SsrA RNA)-mediated trans-translation and stop codon-independent termination by ArfA/RF2 or ArfB (YaeJ). The arfA mRNA lacks a stop codon and its expression is repressed by trans-translation. Therefore, ArfA is considered to complement the ribosome rescue activity of trans-translation, but the physiological situations in which ArfA is expressed have not been elucidated. Here, we found that the excision of CP4-57 prophage adjacent to E. coli ssrA leads to the inactivation of tmRNA and switches the primary rescue pathway from trans-translation to ArfA/RF2. This "rescue-switching" rearranges not only the proteome landscape in E. coli but also the phenotype such as motility. Furthermore, among the proteins with significantly increased abundance in the ArfA+ cells, we found ZntR, whose mRNA is transcribed together as the upstream part of nonstop arfA mRNA. Repression of ZntR and reconstituted model genes depends on the translation of the downstream nonstop ORFs that trigger the trans-translation-coupled exonucleolytic degradation by polynucleotide phosphorylase (PNPase). Namely, our studies provide a novel example of trans-translation-dependent regulation and re-define the physiological roles of prophage excision.
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Affiliation(s)
- Haruka Onodera
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tatsuya Niwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuhei Chadani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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2
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Moreno S, Muriel-Millán LF, Rodríguez-Martínez K, Ortíz-Vasco C, Bedoya-Pérez LP, Espín G. The ribosome rescue pathways SsrA-SmpB, ArfA, and ArfB mediate tolerance to heat and antibiotic stresses in Azotobacter vinelandii. FEMS Microbiol Lett 2022; 369:6824435. [PMID: 36368695 DOI: 10.1093/femsle/fnac104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/29/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria have a mechanism to rescue stalled ribosomes known as trans-translation consisting of SsrA, a transfer-messenger RNA (tmRNA), and the small protein SmpB. Other alternative rescue mechanisms mediated by ArfA and ArfB proteins are present only in some species. Ribosome rescue mechanisms also play a role in tolerance to antibiotics and various stresses such as heat. This study shows that the genome of the soil bacterium A. vinelandii harbours genes encoding for tmRNA, SmpB, two paralogs of ArfA (arfA1 and arfA2), and ArfB. A number of mutant strains carrying mutations in the ssrA, arfA1, arfA2, and arfB genes were constructed and tested for their growth and susceptibility to heat and the antibiotic tetracycline. We found that the inactivation of both ssrA and one or the two arfA genes was detrimental to growth and caused a higher susceptibility to heat and to the antibiotic tetracycline. Interestingly, the arfB mutant strain was unable to grow after 2 h of incubation at 45°C. Inactivation of arfB in the ssrA-arfA1-arfA2 strain caused a lethal phenotype since the quadruple mutant could not be isolated. Taken together, our data suggest that both arfA1 and arfA2, as well as arfB, are functional as back up mechanisms, and that the ArfB pathway has an essential role that confers A. vinelandii resistance to high temperatures.
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Affiliation(s)
- Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Luis Felipe Muriel-Millán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad Universitaria, CDMX, México
| | - Karen Rodríguez-Martínez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Cristian Ortíz-Vasco
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Leidy Patricia Bedoya-Pérez
- Programa de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
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3
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Greeson EM, Madsen CS, Makela AV, Contag CH. Magnetothermal Control of Temperature-Sensitive Repressors in Superparamagnetic Iron Nanoparticle-Coated Bacillus subtilis. ACS NANO 2022; 16:16699-16712. [PMID: 36200984 DOI: 10.1021/acsnano.2c06239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents in magnetic resonance imaging (MRI) and magnetic particle imaging (MPI), and resulting images can be used to guide magnetothermal heating. Alternating magnetic fields (AMF) cause local temperature increases in regions with SPIONs, and we investigated the ability of magnetic hyperthermia to regulate temperature-sensitive repressors (TSRs) of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium and used here for thermal control of reporter gene expression in Gram-positive, Bacillus subtilis. In vitro heating of B. subtilis with TlpA39 controlling bacterial luciferase expression resulted in a 14.6-fold (12 hours; h) and 1.8-fold (1 h) increase in reporter transcripts with a 10.0-fold (12 h) and 12.1-fold (1 h) increase in bioluminescence. To develop magnetothermal control, B. subtilis cells were coated with three SPION variations. Electron microscopy coupled with energy dispersive X-ray spectroscopy revealed an external association with, and retention of, SPIONs on B. subtilis. Furthermore, using long duration AMF we demonstrated magnetothermal induction of the TSRs in SPION-coated B. subtilis with a maximum of 5.6-fold increases in bioluminescence. After intramuscular injections of SPION-coated B. subtilis, histology revealed that SPIONs remained in the same locations as the bacteria. For in vivo studies, 1 h of AMF is the maximum exposure due to anesthesia constraints. Both in vitro and in vivo, there was no change in bioluminescence after 1 h of AMF treatment. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to transcriptional control that expands options for targeted bacteriotherapies.
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Affiliation(s)
- Emily M Greeson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Cody S Madsen
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ashley V Makela
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Christopher H Contag
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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4
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Jadhav P, Chen Y, Butzin N, Buceta J, Urchueguía A. Bacterial degrons in synthetic circuits. Open Biol 2022; 12:220180. [PMID: 35975648 PMCID: PMC9382460 DOI: 10.1098/rsob.220180] [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] [Indexed: 11/18/2022] Open
Abstract
Bacterial proteases are a promising post-translational regulation strategy in synthetic circuits because they recognize specific amino acid degradation tags (degrons) that can be fine-tuned to modulate the degradation levels of tagged proteins. For this reason, recent efforts have been made in the search for new degrons. Here we review the up-to-date applications of degradation tags for circuit engineering in bacteria. In particular, we pay special attention to the effects of degradation bottlenecks in synthetic oscillators and introduce mathematical approaches to study queueing that enable the quantitative modelling of proteolytic queues.
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Affiliation(s)
- Prajakta Jadhav
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
| | - Arantxa Urchueguía
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
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5
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Xu S, Cao Q, Liu Z, Chen J, Yan P, Li B, Xu Y. Transcriptomic Analysis Reveals the Role of tmRNA on Biofilm Formation in Bacillus subtilis. Microorganisms 2022; 10:microorganisms10071338. [PMID: 35889057 PMCID: PMC9319509 DOI: 10.3390/microorganisms10071338] [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: 06/09/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus strains are widely distributed in terrestrial and marine environments, and some of them are used as biocontrol organisms for their biofilm-formation ability. In Bacillus subtilis, biofilm formation is fine-tuned by a complex network, a clear understanding of which still requires study. In bacteria, tmRNA, encoded by the ssrA gene, catalyzes trans-translation that can rescue ribosomes stalled on mRNA transcripts lacking a functional stop codon. tmRNA also affects physiological bioprocesses in some bacteria. In this study, we constructed a ssrA mutant in B. subtilis and found that the biofilm formation in the ssrA mutant was largely impaired. Moreover, we isolated a biofilm-formation suppressor of ssrA, in which the biofilm formation was restored to a level even stronger than that in the wild type. We further performed RNAseq assays with the wild type, ssrA mutant, and suppressor of ssrA for comparisons of their transcriptomes. By analyzing the transcriptomic data, we predicted the possible functions of some differentially expressed genes (DEGs) in the tmRNA regulation of biofilm formation in B. subtilis. Finally, we found that the overexpression of two DEGs, acoA and yhjR, could restore the biofilm formation in the ssrA mutant, indicating that AcoA and YhjR were immediate regulators involved in the tmRNA regulatory web controlling biofilm formation in B. subtilis. Our data can improve the knowledge about the molecular network involved in Bacillus biofilm formation and provide new targets for manipulation of Bacillus biofilms for future investigation.
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Affiliation(s)
- Shanshan Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Qianqian Cao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Zengzhi Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Junpeng Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Peiguang Yan
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Bingyu Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen 518055, China
- Correspondence: (B.L.); (Y.X.)
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- Correspondence: (B.L.); (Y.X.)
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6
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Muto A, Goto S, Kurita D, Ushida C, Himeno H. Involvement of GcvB small RNA in intrinsic resistance to multiple aminoglycoside antibiotics in Escherichia coli. J Biochem 2021; 169:485-489. [PMID: 33169170 DOI: 10.1093/jb/mvaa122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/23/2020] [Indexed: 11/14/2022] Open
Abstract
Deleting the gene for small RNA GcvB in Escherichia coli was found to increase the sensitivity to several aminoglycoside antibiotics, such as neomycin, streptomycin, kanamycin, kasugamycin and spectinomycin, at low concentrations. GcvB, conserved in gram-negative enteric bacteria, is known to negatively control the expression of many genes for amino acid incorporation systems, especially the periplasmic ABC-transporter proteins. Deletions of several amino acid transporter genes in ΔgcvB cells decreased the antibiotic sensitivity to the wild-type level, suggesting that those genes are involved in uptake of aminoglycosides into the cell. Since GcvB is constitutively synthesized in growing cells, repressing synthesis of amino acid transporters, it contributes to the intrinsic resistance to several aminoglycoside antibiotics.
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Affiliation(s)
- Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Chisato Ushida
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Hyota Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
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7
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Tamilmaran N, Sankaranarayanan R, Selvakumar A S P, Munavar MH. Horizontal transfer of domains in ssrA gene among Enterobacteriaceae. Genes Cells 2021; 26:541-550. [PMID: 33971069 DOI: 10.1111/gtc.12869] [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: 02/13/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 11/29/2022]
Abstract
The tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans-translation. Additionally, regions of the ssrA gene (coding for tmRNA) were reported to serve as integration sites for various bacteriophages. Though variations in ssrA genes were reported, their functional relevance is less studied. In this study, we investigated the horizontal gene transfer (HGT) of ssrA among the members of Enterobacteriaceae. This was done by predicting recombination signals in ssrA gene (belonging to Enterobacteriaceae) using RDP5 (Recombination Detection Program 5). Our results revealed 7 recombination signals in ssrA gene belonging to different species. We further showed that the recombination signals were more in the domains present in the 3' end than 5' end of tmRNA. Of note, the mRNA region was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya and Enterobacter were highly represented in the recombination signals. Sequence analysis revealed the presence of integration sites for different class of bacteriophages in ssrA gene. The locations of phage recognition sites are comparable with recombination signals. Taken together, our results revealed a diverse nature of HGT and recombination which possibly due to transduction mediated by phages.
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Affiliation(s)
- Nagarajan Tamilmaran
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | | | - M Hussain Munavar
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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8
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Liu X, Lin S, Liu T, Zhou Y, Wang W, Yao J, Guo Y, Tang K, Chen R, Benedik MJ, Wang X. Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella. Nucleic Acids Res 2021; 49:3427-3440. [PMID: 33693785 PMCID: PMC8034616 DOI: 10.1093/nar/gkab137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 12/20/2022] Open
Abstract
Lateral gene transfer (LGT) plays a key role in shaping the genome evolution and environmental adaptation of bacteria. Xenogeneic silencing is crucial to ensure the safe acquisition of LGT genes into host pre-existing regulatory networks. We previously found that the host nucleoid structuring protein (H-NS) silences prophage CP4So at warm temperatures yet enables this prophage to excise at cold temperatures in Shewanella oneidensis. However, whether H-NS silences other genes and how bacteria modulate H-NS to regulate the expression of genes have not been fully elucidated. In this study, we discovered that the H-NS silences many LGT genes and the xenogeneic silencing of H-NS relies on a temperature-dependent phosphorylation at warm temperatures in S. oneidensis. Specifically, phosphorylation of H-NS at Ser42 is critical for silencing the cold-inducible genes including the excisionase of CP4So prophage, a cold shock protein, and a stress-related chemosensory system. By contrast, nonphosphorylated H-NS derepresses the promoter activity of these genes/operons to enable their expression at cold temperatures. Taken together, our results reveal that the posttranslational modification of H-NS can function as a regulatory switch to control LGT gene expression in host genomes to enable the host bacterium to react and thrive when environmental temperature changes.
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Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Shituan Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiqing Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
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Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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10
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Filbeck S, Cerullo F, Paternoga H, Tsaprailis G, Joazeiro CAP, Pfeffer S. Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Mol Cell 2020; 81:104-114.e6. [PMID: 33259811 DOI: 10.1016/j.molcel.2020.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved RQC factor, senses the obstruction and recruits tRNAAla(UGC) to modify nascent-chain C termini with a polyalanine degron. However, how RqcH and its eukaryotic homologs (Rqc2 and NEMF), despite their relatively simple architecture, synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained unknown. Here, we present cryoelectron microscopy (cryo-EM) structures of Bacillus subtilis RQC complexes representing different Ala tail synthesis steps. The structures explain how tRNAAla is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNAAla into a hybrid A/P-state associated with peptidyl-transfer. Finally, we provide structural, biochemical, and molecular genetic evidence identifying the Hsp15 homolog (encoded by rqcP) as a novel RQC component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Helge Paternoga
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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11
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Ul Haq I, Müller P, Brantl S. Intermolecular Communication in Bacillus subtilis: RNA-RNA, RNA-Protein and Small Protein-Protein Interactions. Front Mol Biosci 2020; 7:178. [PMID: 32850966 PMCID: PMC7430163 DOI: 10.3389/fmolb.2020.00178] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 11/29/2022] Open
Abstract
In bacterial cells we find a variety of interacting macromolecules, among them RNAs and proteins. Not only small regulatory RNAs (sRNAs), but also small proteins have been increasingly recognized as regulators of bacterial gene expression. An average bacterial genome encodes between 200 and 300 sRNAs, but an unknown number of small proteins. sRNAs can be cis- or trans-encoded. Whereas cis-encoded sRNAs interact only with their single completely complementary mRNA target transcribed from the opposite DNA strand, trans-encoded sRNAs are only partially complementary to their numerous mRNA targets, resulting in huge regulatory networks. In addition to sRNAs, uncharged tRNAs can interact with mRNAs in T-box attenuation mechanisms. For a number of sRNA-mRNA interactions, the stability of sRNAs or translatability of mRNAs, RNA chaperones are required. In Gram-negative bacteria, the well-studied abundant RNA-chaperone Hfq fulfils this role, and recently another chaperone, ProQ, has been discovered and analyzed in this respect. By contrast, evidence for RNA chaperones or their role in Gram-positive bacteria is still scarce, but CsrA might be such a candidate. Other RNA-protein interactions involve tmRNA/SmpB, 6S RNA/RNA polymerase, the dual-function aconitase and protein-bound transcriptional terminators and antiterminators. Furthermore, small proteins, often missed in genome annotations and long ignored as potential regulators, can interact with individual regulatory proteins, large protein complexes, RNA or the membrane. Here, we review recent advances on biological role and regulatory principles of the currently known sRNA-mRNA interactions, sRNA-protein interactions and small protein-protein interactions in the Gram-positive model organism Bacillus subtilis. We do not discuss RNases, ribosomal proteins, RNA helicases or riboswitches.
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Affiliation(s)
| | | | - Sabine Brantl
- Matthias-Schleiden-Institut, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Jena, Germany
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12
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Fritze J, Zhang M, Luo Q, Lu X. An overview of the bacterial SsrA system modulating intracellular protein levels and activities. Appl Microbiol Biotechnol 2020; 104:5229-5241. [PMID: 32342145 DOI: 10.1007/s00253-020-10623-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/07/2020] [Accepted: 04/13/2020] [Indexed: 12/18/2022]
Abstract
In bacteria, the truncated forms of mRNAs, which usually lack a stop codon, are occasionally generated by premature termination of gene transcription and/or endo- or exonucleolytic cleavage events. Ribosomes proceeding on these molecules stall at the 3' end of the chain and are rescued by a widely distributed mechanism known as trans-translation, which includes two essential elements, ssrA RNA (a special RNA) and SmpB (a small protein). Through this mechanism, the polypeptides translated from truncated mRNAs are marked by a short peptide, known as SsrA tag, at their C-termini and directed to the specific endogenous proteases for C-terminal proteolysis. Based on the deep understanding of the SsrA tagging and degradation mechanisms, recently a series of SsrA-based genetic tools have been developed for gene regulation on the level of post-translation. They are successfully applied for controllable regulation of biological circuits in bacteria. In the present article, we systematically summarize the history, structural characteristics, and functional mechanisms of the SsrA tagging and degrading machineries, as well as their technical uses and limitations.Key Points• SsrA system plays an important role in ribosome rescue in bacteria.• SsrA-based genetic tools are useful for controlling protein levels and activities.
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Affiliation(s)
- Jacques Fritze
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,University of Stuttgart, Stuttgart, Germany
| | - Mingyi Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Quan Luo
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China. .,School of Life Sciences, Hubei University, Wuhan, China.
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China. .,Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China. .,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China. .,Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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13
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Peng M, Cao X, Tang Y, Li H, Ma X, Liu Z. Large-scale identification of trans-translation substrates targeted by tmRNA in Aeromonas veronii. Microb Pathog 2020; 145:104226. [PMID: 32353577 DOI: 10.1016/j.micpath.2020.104226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 10/24/2022]
Abstract
Transfer-messenger RNA (tmRNA) is ubiquitous in bacteria, acting as the core component for the trans-translation system that contributes to label the aberrantly synthesized peptides for degradation and to release the stalled ribosomes. Deletion of tmRNA causes a variety of phenotypes related to important physiological processes in bacteria. To illustrate the molecular mechanism of the versatility of tmRNA in aquatic pathogen Aeromonas veronii, we mutated the C-terminal nucleotides of tmRNA (MutmRNA) for encoding a tag containing six histidine residues (His6tag), so as to capture and enrich the trans-translation substrates from the cell lysates through a Ni2+-NTA affinity chromatograph. The results showed that the concentrated substrates were detected as distinct and specific bands in western blotting using anti-His antibody, demonstrating that specific defective mRNAs were frequently and intensively rescued by trans-translation during the translation process in A. veronii. The substrates were analyzed by LC-MS/MS and further identified by searching a theoretically constructed database specific for A. veronii. Total of 24 potential substrates were identified, with various functions involved in metabolism, as well as structure and signal-based cellular events. Among the identified substrates, PspA and AsmA were labeled by Flag, and expressed in the presence of the modified trans-translation system in E. coli. Their labelings with MutmRNA were validated by purification through Ni2+-NTA column followed by western blotting using anti-Flag antibody. This study provided the most abundant set of endogenous targets for tmRNA in A. veronii, and facilitated further investigations about the molecular mechanism and signal pathway of tmRNA-mediated trans-translation.
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Affiliation(s)
- Muzhi Peng
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228, Haikou, China
| | - Xin Cao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228, Haikou, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228, Haikou, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228, Haikou, China
| | - Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228, Haikou, China.
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228, Haikou, China.
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14
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Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. Nat Commun 2019; 10:5397. [PMID: 31776341 PMCID: PMC6881298 DOI: 10.1038/s41467-019-13408-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems. In bacteria, the conserved trans-translation system serves as the primary pathway of ribosome rescue, but many species can also use alternative rescue pathways. Here the authors report that in B. subtilis, the rescue factor BrfA binds to non-stop stalled ribosomes, recruits RF2 but not RF1, and induces transition of the ribosome into an open active conformation.
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15
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Liu X, Tang K, Zhang D, Li Y, Liu Z, Yao J, Wood TK, Wang X. Symbiosis of a P2‐family phage and deep‐sea
Shewanella putrefaciens. Environ Microbiol 2019; 21:4212-4232. [DOI: 10.1111/1462-2920.14781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Dali Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention Guangdong Provincial Institute of Public Health Guangzhou 511430 China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Thomas K. Wood
- Department of Chemical Engineering Pennsylvania State University University Park PA 16802‐4400 USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
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16
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Lytvynenko I, Paternoga H, Thrun A, Balke A, Müller TA, Chiang CH, Nagler K, Tsaprailis G, Anders S, Bischofs I, Maupin-Furlow JA, Spahn CMT, Joazeiro CAP. Alanine Tails Signal Proteolysis in Bacterial Ribosome-Associated Quality Control. Cell 2019; 178:76-90.e22. [PMID: 31155236 DOI: 10.1016/j.cell.2019.05.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/11/2019] [Accepted: 04/30/2019] [Indexed: 11/19/2022]
Abstract
In ribosome-associated quality control (RQC), Rqc2/NEMF closely supports the E3 ligase Ltn1/listerin in promoting ubiquitylation and degradation of aberrant nascent-chains obstructing large (60S) ribosomal subunits-products of ribosome stalling during translation. However, while Ltn1 is eukaryote-specific, Rqc2 homologs are also found in bacteria and archaea; whether prokaryotic Rqc2 has an RQC-related function has remained unknown. Here, we show that, as in eukaryotes, a bacterial Rqc2 homolog (RqcH) recognizes obstructed 50S subunits and promotes nascent-chain proteolysis. Unexpectedly, RqcH marks nascent-chains for degradation in a direct manner, by appending C-terminal poly-alanine tails that act as degrons recognized by the ClpXP protease. Furthermore, RqcH acts redundantly with tmRNA/ssrA and protects cells against translational and environmental stresses. Our results uncover a proteolytic-tagging mechanism with implications toward the function of related modifications in eukaryotes and suggest that RQC was already active in the last universal common ancestor (LUCA) to help cope with incomplete translation.
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Affiliation(s)
- Iryna Lytvynenko
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Helge Paternoga
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Anna Thrun
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Annika Balke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Tina A Müller
- Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Christina H Chiang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Katja Nagler
- BioQuant Center, University of Heidelberg, 69120 Heidelberg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | | | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Ilka Bischofs
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; BioQuant Center, University of Heidelberg, 69120 Heidelberg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
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17
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Expression, purification and characterization of the full-length SmpB protein from Mycobacterium tuberculosis. Protein Expr Purif 2018; 151:9-17. [DOI: 10.1016/j.pep.2018.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/26/2018] [Accepted: 05/28/2018] [Indexed: 11/20/2022]
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18
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Yang J, Liu Y, Liu Z, Meng C, Lin D. Backbone and side-chain resonance assignments for the tmRNA-binding protein, SmpB, from Mycobacterium tuberculosis. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:175-179. [PMID: 28258549 DOI: 10.1007/s12104-017-9742-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/24/2017] [Indexed: 06/06/2023]
Abstract
Small protein B (SmpB) is an essential molecule in trans-translation which is a universal biological pathway for protein synthesis in bacteria. Trans-translation can release stalled ribosomes from defective mRNAs and target tag-protein fragments for degradation, and then restart protein synthesis. The SmpB-tmRNA complex coordinating with other components of the trans-translation system, plays vital roles in Mycobacterium tuberculosis under both stress conditions and non-replicating conditions. Thus, elucidation of molecular details and dynamic properties of the SmpB-tmRNA interaction is a crucial step towards effectively blocking trans-translation process to shorten the duration of tuberculosis treatment. Here, we report resonance assignments for 1H, 13C and 15N of M. tuberculosis SmpB (MtSmpB, spanning residues 4-133) protein determined by a suite of 2D/3D heteronuclear NMR experiments along with predicted the secondary structure.
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Affiliation(s)
- Juanjuan Yang
- Institute of Pharmaceutical Biotechnology and Engineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yindi Liu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhao Liu
- Institute of Pharmaceutical Biotechnology and Engineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Chun Meng
- Institute of Pharmaceutical Biotechnology and Engineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Donghai Lin
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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19
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Elsholz AKW, Birk MS, Charpentier E, Turgay K. Functional Diversity of AAA+ Protease Complexes in Bacillus subtilis. Front Mol Biosci 2017; 4:44. [PMID: 28748186 PMCID: PMC5506225 DOI: 10.3389/fmolb.2017.00044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/15/2017] [Indexed: 12/20/2022] Open
Abstract
Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis. We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics.
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Affiliation(s)
- Alexander K W Elsholz
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany
| | - Marlene S Birk
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany.,The Laboratory for Molecular Infection Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden.,Humboldt UniversityBerlin, Germany
| | - Kürşad Turgay
- Faculty of Natural Sciences, Institute of Microbiology, Leibniz UniversitätHannover, Germany
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20
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Sun Y, Weng Y, Zhang Y, Yan X, Guo L, Wang J, Song X, Yuan Y, Chang FY, Wang CL. Systematic expression profiling analysis mines dys-regulated modules in active tuberculosis based on re-weighted protein-protein interaction network and attract algorithm. Microb Pathog 2017; 107:48-53. [PMID: 28323150 DOI: 10.1016/j.micpath.2017.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/09/2017] [Accepted: 03/16/2017] [Indexed: 02/02/2023]
Abstract
About 90% of tuberculosis (TB) patients latently infected with Mycobacterium tuberculosis (Mtb) show no symptoms, yet have a 10% chance in lifetime to progress active TB. Nevertheless, current diagnosis approaches need improvement in efficiency and sensitivity. The objective of this work was to detect potential signatures for active TB to further improve the understanding of the biological roles of functional modules involved in this disease. First, targeted networks of active TB and control groups were established via re-weighting protein-protein interaction (PPI) networks using Pearson's correlation coefficient (PCC). Candidate modules were detected from the targeted networks, and the modules with Jaccard score >0.7 were defined as attractors. After that, identification of dys-regulated modules was conducted from the attractors using attract method, Subsequently, gene oncology (GO) enrichment analyses were implemented for genes in the dys-regulated modules. We obtained 33 and 65 candidate modules from the targeted networks of control and active TB groups, respectively. Overall, 13 attractors were identified. Using the cut-off criteria of false discovery rate <0.05, there were 4 dys-regulated modules (Module 1, 2, 3, and 4). Based on the GO annotation results, genes in Modules 1, 2 and 4 were only involved in translation. Most genes in Module 1, 2 and 4 were associated with ribosomes. Accordingly, these dys-regulated modules might serve as potential biomarkers of active TB, facilitating the development for a more efficient, and sensitive diagnostic assay for active TB.
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Affiliation(s)
- Ying Sun
- Department of Cadres' Ward, China Meitan General Hospital, Beijing 100028, China
| | - Yan Weng
- Department of Gastroenterology, China Meitan General Hospital, Beijing 100028, China.
| | - Ying Zhang
- Central Supply Service Department, Jilin Hospital of Integrated Traditional Chinese and Western Medicine, Jilin 132400, Jilin Province, China
| | - Xiang Yan
- Department of Anesthesiology, No 65334 Hospital of PLA, Yanji 133000, Jilin Province, China
| | - Lei Guo
- Department of Cadres' Ward, China Meitan General Hospital, Beijing 100028, China
| | - Jia Wang
- Department of Cadres' Ward, China Meitan General Hospital, Beijing 100028, China
| | - Xin Song
- Department of Cadres' Ward, China Meitan General Hospital, Beijing 100028, China
| | - Ying Yuan
- Department of Cadres' Ward, China Meitan General Hospital, Beijing 100028, China
| | - Fu-Ye Chang
- Department of Cadres' Ward, China Meitan General Hospital, Beijing 100028, China
| | - Chun-Ling Wang
- Department of Cadres' Ward, China Meitan General Hospital, Beijing 100028, China
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21
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Brito L, Wilton J, Ferrándiz MJ, Gómez-Sanz A, de la Campa AG, Amblar M. Absence of tmRNA Has a Protective Effect against Fluoroquinolones in Streptococcus pneumoniae. Front Microbiol 2017; 7:2164. [PMID: 28119681 PMCID: PMC5222879 DOI: 10.3389/fmicb.2016.02164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/23/2016] [Indexed: 11/13/2022] Open
Abstract
The transfer messenger RNA (tmRNA), encoded by the ssrA gene, is a small non-coding RNA involved in trans-translation that contributes to the recycling of ribosomes stalled on aberrant mRNAs. In most bacteria, its inactivation has been related to a decreased ability to respond to and recover from a variety of stress conditions. In this report, we investigated the role of tmRNA in stress adaptation in the human pathogen Streptococcus pneumoniae. We constructed a tmRNA deletion mutant and analyzed its response to several lethal stresses. The ΔssrA strain grew slower than the wild type, indicating that, although not essential, tmRNA is important for normal pneumococcal growth. Moreover, deletion of tmRNA increased susceptibility to UV irradiation, to exogenous hydrogen peroxide and to antibiotics that inhibit protein synthesis and transcription. However, the ΔssrA strain was more resistant to fluoroquinolones, showing twofold higher MIC values and up to 1000-fold higher survival rates than the wild type. Deletion of SmpB, the other partner in trans-translation, also reduced survival to levofloxacin in a similar extent. Accumulation of intracellular reactive oxygen species associated to moxifloxacin and levofloxacin treatment was also highly reduced (∼100-fold). Nevertheless, the ΔssrA strain showed higher intracellular accumulation of ethidium bromide and levofloxacin than the wild type, suggesting that tmRNA deficiency protects pneumococcal cells from fluoroquinolone-mediated killing. In fact, analysis of chromosome integrity revealed that deletion of tmRNA prevented the fragmentation of the chromosome associated to levofloxacin treatment. Moreover, such protective effect appears to relay mainly on inhibition of protein synthesis, since a similar effect was observed with antibiotics that inhibit that process. The emergence and spread of drug-resistant pneumococci is a matter of concern and these results contribute to a better comprehension of the mechanisms underlying fluoroquinolones action.
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Affiliation(s)
- Liliana Brito
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Joana Wilton
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - María J Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Alicia Gómez-Sanz
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain; Presidencia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Mónica Amblar
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
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22
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Jones AJ, Venkataramanan KP, Papoutsakis T. Overexpression of two stress-responsive, small, non-coding RNAs, 6S and tmRNA, imparts butanol tolerance in Clostridium acetobutylicum. FEMS Microbiol Lett 2016; 363:fnw063. [PMID: 26989157 DOI: 10.1093/femsle/fnw063] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2016] [Indexed: 12/25/2022] Open
Abstract
While extensively studied in several model organisms, the role of small, non-coding RNAs in the stress response remains largely unexplored in Clostridium organisms. About 100 years after the first industrial Acetone-Butanol-Ethanol fermentation process, based on the Weizmann Clostridium acetobutylicum strain, strain tolerance to butanol remains a crucial factor limiting the economics of the process. Several studies have examined the response of this organism to metabolite stress, and several genes have been engaged to impart enhanced tolerance, but no sRNAs have yet been directly engaged in this task. We show that the two stress-responsive sRNAs, 6S and tmRNA, upon overexpression impart tolerance to butanol as assessed by viability assays under process-relevant conditions. 6S overexpression enhances cell densities as well as butanol titres. We discuss the likely mechanisms that these two sRNAs might engage in this tolerance phenotype. Our data support the continued exploration of sRNAs as a basis for engineering enhanced tolerance and enhanced solvent production, especially because sRNA-based strategies impose a minimal metabolic burden on the cells.
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Affiliation(s)
- Alexander J Jones
- Department of Biological Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Keerthi P Venkataramanan
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Terry Papoutsakis
- Department of Biological Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
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Whitfield MG, Soeters HM, Warren RM, York T, Sampson SL, Streicher EM, van Helden PD, van Rie A. A Global Perspective on Pyrazinamide Resistance: Systematic Review and Meta-Analysis. PLoS One 2015. [PMID: 26218737 PMCID: PMC4517823 DOI: 10.1371/journal.pone.0133869] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Pyrazinamide (PZA) is crucial for tuberculosis (TB) treatment, given its unique ability to eradicate persister bacilli. The worldwide burden of PZA resistance remains poorly described. Methods Systematic PubMed, Science Direct and Scopus searches for articles reporting phenotypic (liquid culture drug susceptibility testing or pyrazinamidase activity assays) and/or genotypic (polymerase chain reaction or DNA sequencing) PZA resistance. Global and regional summary estimates were obtained from random-effects meta-analysis, stratified by presence or risk of multidrug resistant TB (MDR-TB). Regional summary estimates were combined with regional WHO TB incidence estimates to determine the annual burden of PZA resistance. Information on single nucleotide polymorphisms (SNPs) in the pncA gene was aggregated to obtain a global summary. Results Pooled PZA resistance prevalence estimate was 16.2% (95% CI 11.2-21.2) among all TB cases, 41.3% (29.0-53.7) among patients at high MDR-TB risk, and 60.5% (52.3-68.6) among MDR-TB cases. The estimated global burden is 1.4 million new PZA resistant TB cases annually, about 270,000 in MDR-TB patients. Among 1,815 phenotypically resistant isolates, 608 unique SNPs occurred at 397 distinct positions throughout the pncA gene. Interpretation PZA resistance is ubiquitous, with an estimated one in six incident TB cases and more than half of all MDR-TB cases resistant to PZA globally. The diversity of SNPs across the pncA gene complicates the development of rapid molecular diagnostics. These findings caution against relying on PZA in current and future TB drug regimens, especially in MDR-TB patients.
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Affiliation(s)
- Michael G. Whitfield
- SA MRC Centre for TB Research, Stellenbosch University, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
- Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Heidi M. Soeters
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Robin M. Warren
- SA MRC Centre for TB Research, Stellenbosch University, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
- Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
- * E-mail:
| | - Talita York
- SA MRC Centre for TB Research, Stellenbosch University, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
- Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Samantha L. Sampson
- SA MRC Centre for TB Research, Stellenbosch University, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
- Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Elizabeth M. Streicher
- SA MRC Centre for TB Research, Stellenbosch University, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
- Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Paul D. van Helden
- SA MRC Centre for TB Research, Stellenbosch University, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
- Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Annelies van Rie
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- International Health Unit, Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
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Draft Genome Sequences of Two Pyrazinamide-Resistant Clinical Isolates, Mycobacterium tuberculosis 13-4152 and 13-2459. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00758-15. [PMID: 26139726 PMCID: PMC4490854 DOI: 10.1128/genomea.00758-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report draft genome sequences of two pyrazinamide (PZA)-resistant isolates, Mycobacterium tuberculosis 13-4152 and 13-2459. Isolate 13-4152 is PZA resistant, though it lacks mutations in known genes of PZA resistance. The comparative analysis of these genomes with those stored in GenBank revealed unique mutations, which may elucidate new mechanisms of PZA resistance.
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Maslov DA, Zaĭchikova MV, Chernousova LN, Shur KV, Bekker OB, Smirnova TG, Larionova EE, Andreevskaya SN, Zhang Y, Danilenko VN. Resistance to pyrazinamide in Russian Mycobacterium tuberculosis isolates: pncA sequencing versus Bactec MGIT 960. Tuberculosis (Edinb) 2015; 95:608-12. [PMID: 26071666 DOI: 10.1016/j.tube.2015.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/22/2015] [Accepted: 05/24/2015] [Indexed: 11/29/2022]
Abstract
Resistance to pyrazinamide (PZA) may impact clinical outcome of anti-tuberculosis chemotherapy. PZA susceptibility testing using MGIT 960 is not reliable and little information is available on the prevalence of PZA resistance in Russia. A collection of 64 clinical isolates of Mycobacterium tuberculosis, including 35 multidrug resistant and extensively drug-resistant (MDR/XDR), was analyzed for PZA resistance using MGIT 960, Wayne test, and sequencing of PZA resistance genes pncA, rpsA and panD. In addition, we analyzed 519 MDR-TB strains for susceptibility to PZA by MGIT 960. Sequencing of pncA revealed 17 of 25 (68%) MDR strains and all 10 XDR strains harboring pncA mutations. A correlation of φ = 0.81 between MGIT 960 and pncA sequencing was observed. Mutations in rpsA and panD not associated with PZA resistance as defined by MGIT 960 were identified. We found 1 PZA-resistant strain without mutations in known PZA resistance genes. Almost 73% of MDR-TB strains isolated in Moscow, Russia, were PZA-resistant by MGIT 960 testing of 519 MDR-TB clinical isolates. Further studies are needed to determine the role of rpsA and panD mutations in possible low-level PZA resistance and to identify the molecular basis of new PZA resistance in the isolate without known PZA resistance mutations.
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Affiliation(s)
- Dmitry A Maslov
- Laboratory of Bacterial Genetics, Department of Genetics and Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russia
| | - Marina V Zaĭchikova
- Laboratory of Bacterial Genetics, Department of Genetics and Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russia
| | - Larisa N Chernousova
- Department of Microbiology, Central TB Research Institute, Russian Academy of Medical Sciences, 2 Yauzskaya Alleya, 107564 Moscow, Russia
| | - Kirill V Shur
- Laboratory of Bacterial Genetics, Department of Genetics and Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russia
| | - Olga B Bekker
- Laboratory of Bacterial Genetics, Department of Genetics and Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russia
| | - Tatiana G Smirnova
- Department of Microbiology, Central TB Research Institute, Russian Academy of Medical Sciences, 2 Yauzskaya Alleya, 107564 Moscow, Russia
| | - Elena E Larionova
- Department of Microbiology, Central TB Research Institute, Russian Academy of Medical Sciences, 2 Yauzskaya Alleya, 107564 Moscow, Russia
| | - Sofya N Andreevskaya
- Department of Microbiology, Central TB Research Institute, Russian Academy of Medical Sciences, 2 Yauzskaya Alleya, 107564 Moscow, Russia
| | - Ying Zhang
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Valery N Danilenko
- Laboratory of Bacterial Genetics, Department of Genetics and Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russia.
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Domingues S, Moreira RN, Andrade JM, Dos Santos RF, Bárria C, Viegas SC, Arraiano CM. The role of RNase R in trans-translation and ribosomal quality control. Biochimie 2014; 114:113-8. [PMID: 25542646 DOI: 10.1016/j.biochi.2014.12.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/18/2014] [Indexed: 01/11/2023]
Abstract
Gene expression not only depends on the rate of transcription but is also largely controlled at the post-transcriptional level. Translation rate and mRNA decay greatly influence the final protein levels. Surveillance mechanisms are essential to ensure the quality of the RNA and proteins produced. Trans-translation is one of the most important systems in the quality control of bacterial translation. This process guarantees the destruction of abnormal proteins and also leads to degradation of the respective defective RNAs through the action of Ribonuclease R (RNase R). This exoribonuclease hydrolyzes RNAs starting from their 3' end. Besides its involvement in trans-translation, RNase R also participates in the quality control of rRNA molecules involved in ribosomal biogenesis. RNase R is thus emerging as a key factor in ensuring translation accuracy. This review focuses on issues related to the quality control of translation, with special emphasis on the role of RNase R.
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Affiliation(s)
- Susana Domingues
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ricardo N Moreira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cátia Bárria
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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Kurita D, Miller MR, Muto A, Buskirk AR, Himeno H. Rejection of tmRNA·SmpB after GTP hydrolysis by EF-Tu on ribosomes stalled on intact mRNA. RNA (NEW YORK, N.Y.) 2014; 20:1706-1714. [PMID: 25246654 PMCID: PMC4201823 DOI: 10.1261/rna.045773.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 07/18/2014] [Indexed: 06/03/2023]
Abstract
Messenger RNAs lacking a stop codon trap ribosomes at their 3' ends, depleting the pool of ribosomes available for protein synthesis. In bacteria, a remarkable quality control system rescues and recycles stalled ribosomes in a process known as trans-translation. Acting as a tRNA, transfer-messenger RNA (tmRNA) is aminoacylated, delivered by EF-Tu to the ribosomal A site, and accepts the nascent polypeptide. Translation then resumes on a reading frame within tmRNA, encoding a short peptide tag that targets the nascent peptide for degradation by proteases. One unsolved issue in trans-translation is how tmRNA and its protein partner SmpB preferentially recognize stalled ribosomes and not actively translating ones. Here, we examine the effect of the length of the 3' extension of mRNA on each step of trans-translation by pre-steady-state kinetic methods and fluorescence polarization binding assays. Unexpectedly, EF-Tu activation and GTP hydrolysis occur rapidly regardless of the length of the mRNA, although the peptidyl transfer to tmRNA decreases as the mRNA 3' extension increases and the tmRNA·SmpB binds less tightly to the ribosome with an mRNA having a long 3' extension. From these results, we conclude that the tmRNA·SmpB complex dissociates during accommodation due to competition between the downstream mRNA and the C-terminal tail for the mRNA channel. Rejection of the tmRNA·SmpB complex during accommodation is reminiscent of the rejection of near-cognate tRNA from the ribosome in canonical translation.
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Mickey R Miller
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Allen R Buskirk
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages. BMC Genomics 2014; 15:938. [PMID: 25344729 PMCID: PMC4223743 DOI: 10.1186/1471-2164-15-938] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 10/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alteromonas macleodii is a ubiquitous gammaproteobacterium shown to play a biogeochemical role in marine environments. Two A. macleodii strains (AltDE and AltDE1) isolated from the same sample (i.e., the same place at the same time) show considerable genomic differences. In this study, we investigate the transcriptional response of these two strains to varying growth conditions in order to investigate differences in their ability to adapt to varying environmental parameters. RESULTS RNA sequencing revealed transcriptional changes between all growth conditions examined (e.g., temperature and medium) as well as differences between the two A. macleodii strains within a given condition. The main inter-strain differences were more marked in the adaptation to grow on minimal medium with glucose and, even more so, under starvation. These differences suggested that AltDE1 may have an advantage over AltDE when glucose is the major carbon source, and co-culture experiments confirmed this advantage. Additional differences were observed between the two strains in the expression of ncRNAs and phage-related genes, as well as motility. CONCLUSIONS This study shows that the genomic diversity observed in closely related strains of A. macleodii from a single environment result in different transcriptional responses to changing environmental parameters. This data provides additional support for the idea that greater diversity at the strain level of a microbial community could enhance the community's ability to adapt to environmental shifts.
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Abstract
PZA is a unique anti-tuberculosis drug that plays a key role in shortening the TB therapy. PZA kills non-replicating persisters that other TB drugs fail to kill, and thus making it an essential drug for inclusion in any drug combinations for treating drug susceptible and drug-resistant TB such as MDR-TB. PZA acts differently from common antibiotics by inhibiting multiple targets such as energy production, trans-translation and perhaps pantothenate /coenzyme A required for persister survival. Resistance to PZA is mostly caused by mutations in the pncA gene encoding pyrazinamidase involved in conversion of the prodrug PZA to the active form POA. Mutations in the drug target RpsA are also found in some PZA-resistant strains. The recent finding that panD mutations are found in some PZA-resistant strains without pncA or rpsA mutations may suggest a third PZA resistance gene and a potential new target of PZA. Current phenotype based PZA susceptibility testing is not reliable due to false resistance, and sequencing of the pncA gene represents a more rapid, cost-effective and more reliable molecular test for PZA susceptibility testing and should be used for guiding improved treatment of MDR/XDR-TB. Finally, the story of PZA has important implications for not only TB therapy but also chemotherapy in general. PZA serves as a model prototype persister drug and hopefully a 'tipping point' that inspires new efforts at developing a new type of antibiotics or drugs that target non-replicating persisters for improved treatment of not only TB but also other persistent bacterial infections.
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Himeno H, Kurita D, Muto A. tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell. Front Genet 2014; 5:66. [PMID: 24778639 PMCID: PMC3985003 DOI: 10.3389/fgene.2014.00066] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/15/2014] [Indexed: 11/13/2022] Open
Abstract
Transfer messenger RNA (tmRNA; also known as 10Sa RNA or SsrA RNA) is a small RNA molecule that is conserved among bacteria. It has structural and functional similarities to tRNA: it has an upper half of the tRNA-like structure, its 5’ end is processed by RNase P, it has typical tRNA-specific base modifications, it is aminoacylated with alanine, it binds to EF-Tu after aminoacylation and it enters the ribosome with EF-Tu and GTP. However, tmRNA lacks an anticodon, and instead it has a coding sequence for a short peptide called tag-peptide. An elaborate interplay of actions of tmRNA as both tRNA and mRNA with the help of a tmRNA-binding protein, SmpB, facilitates trans-translation, which produces a single polypeptide from two mRNA molecules. Initially alanyl-tmRNA in complex with EF-Tu and SmpB enters the vacant A-site of the stalled ribosome like aminoacyl-tRNA but without a codon–anticodon interaction, and subsequently truncated mRNA is replaced with the tag-encoding region of tmRNA. During these processes, not only tmRNA but also SmpB structurally and functionally mimics both tRNA and mRNA. Thus trans-translation rescues the stalled ribosome, thereby allowing recycling of the ribosome. Since the tag-peptide serves as a target of AAA+ proteases, the trans-translation products are preferentially degraded so that they do not accumulate in the cell. Although alternative rescue systems have recently been revealed, trans-translation is the only system that universally exists in bacteria. Furthermore, it is unique in that it employs a small RNA and that it prevents accumulation of non-functional proteins from truncated mRNA in the cell. It might play the major role in rescuing the stalled translation in the bacterial cell.
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Affiliation(s)
- Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
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Abstract
Problems during gene expression can result in a ribosome that has translated to the 3' end of an mRNA without terminating at a stop codon, forming a nonstop translation complex. The nonstop translation complex contains a ribosome with the mRNA and peptidyl-tRNA engaged, but because there is no codon in the A site, the ribosome cannot elongate or terminate the nascent chain. Recent work has illuminated the importance of resolving these nonstop complexes in bacteria. Transfer-messenger RNA (tmRNA)-SmpB specifically recognizes and resolves nonstop translation complexes in a reaction known as trans-translation. trans-Translation releases the ribosome and promotes degradation of the incomplete nascent polypeptide and problematic mRNA. tmRNA and SmpB have been found in all bacteria and are essential in some species. However, other bacteria can live without trans-translation because they have one of the alternative release factors, ArfA or ArfB. ArfA recruits RF2 to nonstop translation complexes to promote hydrolysis of the peptidyl-tRNAs. ArfB recognizes nonstop translation complexes in a manner similar to tmRNA-SmpB recognition and directly hydrolyzes the peptidyl-tRNAs to release the stalled ribosomes. Genetic studies indicate that most or all species require at least one mechanism to resolve nonstop translation complexes. Consistent with such a requirement, small molecules that inhibit resolution of nonstop translation complexes have broad-spectrum antibacterial activity. These results suggest that resolving nonstop translation complexes is a matter of life or death for bacteria.
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Himeno H, Kurita D, Muto A. Mechanism of trans-translation revealed by in vitro studies. Front Microbiol 2014; 5:65. [PMID: 24600445 PMCID: PMC3929946 DOI: 10.3389/fmicb.2014.00065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/04/2014] [Indexed: 11/28/2022] Open
Abstract
tmRNA is a bacterial small RNA having a structure resembling the upper half of tRNA and its 3′ end accepts alanine followed by binding to EF-Tu like tRNA. Instead of lacking a lower half of the cloverleaf structure including the anticodon, tmRNA has a short coding sequence for tag-peptide that serves as a target of cellular proteases. An elaborate coordination of two functions as tRNA and mRNA facilitates an irregular translation termed trans-translation: a single polypeptide is synthesized from two mRNA molecules. It allows resumption of translation stalled on a truncated mRNA, producing a chimeric polypeptide comprising the C-terminally truncated polypeptide derived from truncated mRNA and the C-terminal tag-peptide encoded by tmRNA. Trans-translation promotes recycling of the stalled ribosomes in the cell, and the resulting C-terminally tagged polypeptide is preferentially degraded by cellular proteases. Biochemical studies using in vitro trans-translation systems together with structural studies have unveiled the molecular mechanism of trans-translation, during which the upper and lower halves of tRNA are mimicked by the tRNA-like structure of tmRNA and a tmRNA-specific binding protein called SmpB, respectively. They mimic not only the tRNA structure but also its behavior perhaps at every step of the trans-translation process in the ribosome. Furthermore, the C-terminal tail of SmpB, which is unstructured in solution, occupies the mRNA path in the ribosome to play a crucial role in trans-translation, addressing how tmRNA·SmpB recognizes the ribosome stalled on a truncated mRNA.
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Affiliation(s)
- Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan ; RNA Research Center, Hirosaki University Hirosaki, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan ; RNA Research Center, Hirosaki University Hirosaki, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
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Kogure H, Handa Y, Nagata M, Kanai N, Güntert P, Kubota K, Nameki N. Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ. Nucleic Acids Res 2013; 42:3152-63. [PMID: 24322300 PMCID: PMC3950681 DOI: 10.1093/nar/gkt1280] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on a non-stop mRNA, and for ribosome-binding efficiency. We focused on residues conserved among bacterial YaeJ proteins. Additionally, we determined the solution structure of the GGQ domain of YaeJ from E. coli using nuclear magnetic resonance spectroscopy. YaeJ and a human homolog, ICT1, had similar levels of PTH activity, despite various differences in sequence and structure. While no YaeJ-specific residues important for PTH activity occur in the structured GGQ domain, Arg118, Leu119, Lys122, Lys129 and Arg132 in the following C-terminal extension were required for PTH activity. All of these residues are completely conserved among bacteria. The equivalent residues were also found in the C-terminal extension of ICT1, allowing an appropriate sequence alignment between YaeJ and ICT1 proteins from various species. Single amino acid substitutions for each of these residues significantly decreased ribosome-binding efficiency. These biochemical findings provide clues to understanding how YaeJ enters the A-site of stalled ribosomes.
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Affiliation(s)
- Hiroyuki Kogure
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University, Frankfurt am Main, Germany and Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
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Personne Y, Parish T. Mycobacterium tuberculosis possesses an unusual tmRNA rescue system. Tuberculosis (Edinb) 2013; 94:34-42. [PMID: 24145139 DOI: 10.1016/j.tube.2013.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 12/31/2022]
Abstract
Trans-translation is a key process in bacteria which recycles stalled ribosomes and tags incomplete nascent proteins for degradation. This ensures the availability of ribosomes for protein synthesis and prevents the accumulation of dysfunctional proteins. The tmRNA, ssrA, is responsible for both recovering stalled ribosomes and encodes the degradation tag; ssrA associates and functions with accessory proteins such as SmpB. Although ssrA and smpB are ubiquitous in bacteria, they are not essential for the viability of many species. The Mycobacterium tuberculosis genome has homologues of both ssrA and smpB. We demonstrated that ssrA is essential in M. tuberculosis, since the chromosomal copy of the gene could only be deleted in the presence of a functional copy integrated elsewhere. However, we were able to delete the proteolytic tagging function by constructing strains carrying a mutant allele (ssrADD). This demonstrates that ribosome rescue by ssrA is the essential function in M. tuberculosis, SmpB was not required for aerobic growth, since we were able to construct a deletion strain. However, the smpBΔ strain was more sensitive to antibiotics targeting the ribosome. Strains with deletion of smpB or mutations in ssrA did not show increased sensitivity (or resistance) to pyrazinamide suggesting that this antibiotic does not directly target these components of the tmRNA tagging system.
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Affiliation(s)
- Yoann Personne
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Tanya Parish
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, UK.
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Additional routes to Staphylococcus aureus daptomycin resistance as revealed by comparative genome sequencing, transcriptional profiling, and phenotypic studies. PLoS One 2013; 8:e58469. [PMID: 23554895 PMCID: PMC3598801 DOI: 10.1371/journal.pone.0058469] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 02/05/2013] [Indexed: 12/17/2022] Open
Abstract
Daptomycin is an extensively used anti-staphylococcal agent due to the rise in methicillin-resistant Staphylococcus aureus, but the mechanism(s) of resistance is poorly understood. Comparative genome sequencing, transcriptomics, ultrastructure, and cell envelope studies were carried out on two relatively higher level (4 and 8 µg/ml−1) laboratory-derived daptomycin-resistant strains (strains CB1541 and CB1540 respectively) compared to their parent strain (CB1118; MW2). Several mutations were found in the strains. Both strains had the same mutations in the two-component system genes walK and agrA. In strain CB1540 mutations were also detected in the ribose phosphate pyrophosphokinase (prs) and polyribonucleotide nucleotidyltransferase genes (pnpA), a hypothetical protein gene, and in an intergenic region. In strain CB1541 there were mutations in clpP, an ATP-dependent protease, and two different hypothetical protein genes. The strain CB1540 transcriptome was characterized by upregulation of cap (capsule) operon genes, genes involved in the accumulation of the compatible solute glycine betaine, ure genes of the urease operon, and mscL encoding a mechanosensitive chanel. Downregulated genes included smpB, femAB and femH involved in the formation of the pentaglycine interpeptide bridge, genes involved in protein synthesis and fermentation, and spa encoding protein A. Genes altered in their expression common to both transcriptomes included some involved in glycine betaine accumulation, mscL, ure genes, femH, spa and smpB. However, the CB1541 transcriptome was further characterized by upregulation of various heat shock chaperone and protease genes, consistent with a mutation in clpP, and lytM and sceD. Both strains showed slow growth, and strongly decreased autolytic activity that appeared to be mainly due to decreased autolysin production. In contrast to previous common findings, we did not find any mutations in phospholipid biosynthesis genes, and it appears there are multiple pathways to and factors in daptomycin resistance.
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Castro TLP, Seyffert N, Ramos RTJ, Barbosa S, Carvalho RDO, Pinto AC, Carneiro AR, Silva WM, Pacheco LGC, Downson C, Schneider MPC, Miyoshi A, Azevedo V, Silva A. Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method. Microb Biotechnol 2013; 6:168-77. [PMID: 23316806 PMCID: PMC3917459 DOI: 10.1111/1751-7915.12020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/13/2012] [Accepted: 11/14/2012] [Indexed: 11/29/2022] Open
Abstract
Corynebacterium pseudotuberculosis equi is a Gram-positive pathogenic bacterium which affects a variety of hosts. Besides the great economic losses it causes to horse-breeders, this organism is also known to be an important infectious agent to cattle and buffaloes. As an outcome of the efforts in characterizing the molecular basis of its virulence, several complete genome sequences were made available in recent years, enabling the large-scale assessment of genes throughout distinct isolates. Meanwhile, the RNA-seq stood out as the technology of choice for comprehensive transcriptome studies, which may bring valuable information regarding active genomic regions, despite of the still impeditive associated costs. In an attempt to increase the use of generated reads per instrument run, by effectively eliminating unwanted rRNAs from total RNA samples without relying on any commercially available kits, we applied denaturing high-performance liquid chromatography (DHPLC) as an alternative method to assess the transcriptional profile of C. pseudotuberculosis. We have found that the DHPLC depletion method, allied to Ion Torrent sequencing, allows mapping of transcripts in a comprehensive way and identifying novel transcripts when a de novo approach is used. These data encourage us to use DHPLC in future transcriptional evaluations in C. pseudotuberculosis.
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Affiliation(s)
- Thiago L P Castro
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Nubia Seyffert
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Rommel T J Ramos
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
| | - Silvanira Barbosa
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
| | - Rodrigo D O Carvalho
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Anne Cybelle Pinto
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | | | - Wanderson Marques Silva
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Universidade Federal da BahiaSalvador, Brazil
| | | | - Maria P C Schneider
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
| | - Anderson Miyoshi
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Artur Silva
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
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Abstract
The soil-dwelling bacterium Bacillus subtilis is widely used as a model organism to study the Gram-positive branch of Bacteria. A variety of different developmental pathways, such as endospore formation, genetic competence, motility, swarming and biofilm formation, have been studied in this organism. These processes are intricately connected and regulated by networks containing e.g. alternative sigma factors, two-component systems and other regulators. Importantly, in some of these regulatory networks the activity of important regulatory factors is controlled by proteases. Furthermore, together with chaperones, the same proteases constitute the cellular protein quality control (PQC) network, which plays a crucial role in protein homeostasis and stress tolerance of this organism. In this review, we will present the current knowledge on regulatory and general proteolysis in B. subtilis and discuss its involvement in developmental pathways and cellular stress management.
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Affiliation(s)
- Noël Molière
- Institut für Mikrobiologie, Leibniz Universität Hannover, Schneiderberg 50, 30167, Hannover, Germany,
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40
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Svetlanov A, Puri N, Mena P, Koller A, Karzai AW. Francisella tularensis tmRNA system mutants are vulnerable to stress, avirulent in mice, and provide effective immune protection. Mol Microbiol 2012; 85:122-41. [PMID: 22571636 PMCID: PMC3395464 DOI: 10.1111/j.1365-2958.2012.08093.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Through targeted inactivation of the ssrA and smpB genes, we establish that the trans-translation process is necessary for normal growth, adaptation to cellular stress and virulence by the bacterial pathogen Francisella tularensis. The mutant bacteria grow slower, have reduced resistance to heat and cold shocks, and are more sensitive to oxidative stress and sublethal concentrations of antibiotics. Modifications of the tmRNA tag and use of higher-resolution mass spectrometry approaches enabled the identification of a large number of native tmRNA substrates. Of particular significance to understanding the mechanism of trans-translation, we report the discovery of an extended tmRNA tag and extensive ladder-like pattern of endogenous protein-tagging events in F. tularensis that are likely to be a universal feature of tmRNA activity in eubacteria. Furthermore, the structural integrity and the proteolytic function of the tmRNA tag are both crucial for normal growth and virulence of F. tularensis. Significantly, trans-translation mutants of F. tularensis are impaired in replication within macrophages and are avirulent in mouse models of tularemia. By exploiting these attenuated phenotypes, we find that the mutant strains provide effective immune protection in mice against lethal intradermal, intraperitoneal and intranasal challenges with the fully virulent parental strain.
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Affiliation(s)
- Anton Svetlanov
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Neha Puri
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Patricio Mena
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Antonius Koller
- The Proteomic Center, Stony Brook University, Stony Brook, New York, 11794
| | - A. Wali Karzai
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
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41
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Kim SR, Kwak JW, Lee SK, Jung SG, Han MS, Kim BS, Kook MS, Oh HK, Park HJ. Expression of ssrA in non-pathogen-induced adaptation in the oral cavity through signal exchange with oral pathogens. J Korean Assoc Oral Maxillofac Surg 2012. [DOI: 10.5125/jkaoms.2012.38.1.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Sung-Ryoul Kim
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Jae-Woo Kwak
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Sung-Ka Lee
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Seung-Gon Jung
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Man-Seung Han
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Bang-Sin Kim
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Min-Suk Kook
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Hee-Kyun Oh
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
| | - Hong-Ju Park
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Science Research Institute, 2nd Stage of Brain Korea 21, Chonnam National University, Gwangju, Korea
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42
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Janssen BD, Hayes CS. The tmRNA ribosome-rescue system. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:151-91. [PMID: 22243584 DOI: 10.1016/b978-0-12-386497-0.00005-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The bacterial tmRNA quality control system monitors protein synthesis and recycles stalled translation complexes in a process termed "ribosome rescue." During rescue, tmRNA acts first as a transfer RNA to bind stalled ribosomes, then as a messenger RNA to add the ssrA peptide tag to the C-terminus of the nascent polypeptide chain. The ssrA peptide targets tagged peptides for proteolysis, ensuring rapid degradation of potentially deleterious truncated polypeptides. Ribosome rescue also facilitates turnover of the damaged messages responsible for translational arrest. Thus, tmRNA increases the fidelity of gene expression by promoting the synthesis of full-length proteins. In addition to serving as a global quality control system, tmRNA also plays important roles in bacterial development, pathogenesis, and environmental stress responses. This review focuses on the mechanism of tmRNA-mediated ribosome rescue and the role of tmRNA in bacterial physiology.
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Affiliation(s)
- Brian D Janssen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
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43
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Shi W, Zhang X, Jiang X, Ruan H, Barry CE, Wang H, Zhang W, Zhang Y. Pyrazinamide inhibits trans-translation in Mycobacterium tuberculosis. Science 2011; 333:1630-2. [PMID: 21835980 PMCID: PMC3502614 DOI: 10.1126/science.1208813] [Citation(s) in RCA: 361] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Pyrazinamide (PZA) is a first-line tuberculosis drug that plays a unique role in shortening the duration of tuberculosis chemotherapy. PZA is hydrolyzed intracellularly to pyrazinoic acid (POA) by pyrazinamidase (PZase, encoded by pncA), an enzyme frequently lost in PZA-resistant strains, but the target of POA in Mycobacterium tuberculosis has remained elusive. Here, we identify a previously unknown target of POA as the ribosomal protein S1 (RpsA), a vital protein involved in protein translation and the ribosome-sparing process of trans-translation. Three PZA-resistant clinical isolates without pncA mutation harbored RpsA mutations. RpsA overexpression conferred increased PZA resistance, and we confirmed that POA bound to RpsA (but not a clinically identified ΔAla mutant) and subsequently inhibited trans-translation rather than canonical translation. Trans-translation is essential for freeing scarce ribosomes in nonreplicating organisms, and its inhibition may explain the ability of PZA to eradicate persisting organisms.
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Affiliation(s)
- Wanliang Shi
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Xuelian Zhang
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Jiang
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Haiming Ruan
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Clifton E. Barry
- Tuberculosis Research Section, NIAID, NIH, Bethesda, MD 20892, USA
| | - Honghai Wang
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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44
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Andini N, Nash KA. Expression of tmRNA in mycobacteria is increased by antimicrobial agents that target the ribosome. FEMS Microbiol Lett 2011; 322:172-9. [PMID: 21718348 DOI: 10.1111/j.1574-6968.2011.02350.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The specialized RNA, tmRNA, is a central component of prokaryote trans-translation; a process that salvages stalled translational complexes. Evidence from other bacteria suggested that exposure to ribosome inhibitors elevated tmRNA levels, although it was unclear whether such changes resulted from increased tmRNA synthesis. Consequently, this study was initiated to determine the effect of ribosome inhibitors on the expression of tmRNA in mycobacteria. Exposure of Mycobacterium smegmatis to ribosome-targeting antimicrobial agents was associated with increased levels of the tmRNA precursor, pre-tmRNA, and mature tmRNA. For example, exposure to 16 μg mL⁻¹ erythromycin for 3 h increased pre-tmRNA and tmRNA by 18- and 6-fold, respectively. Equivalent results were found following exposure of Mycobacterium bovis BCG to streptomycin. Exposure to antimicrobial agents with nonribosome targets did not affect tmRNA levels. The increased tmRNA levels were associated with increased output from the ssrA promoter, which controls tmRNA transcription, without evidence of a change in tmRNA degradation. These results suggest that the upregulation of tmRNA expression was an important response of bacteria to exposure to ribosome-inhibiting antimicrobial agents.
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Affiliation(s)
- Nadya Andini
- Department of Pathology and Laboratory Medicine, Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, CA, USA
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45
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Keiler KC, Ramadoss NS. Bifunctional transfer-messenger RNA. Biochimie 2011; 93:1993-7. [PMID: 21664408 DOI: 10.1016/j.biochi.2011.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 05/25/2011] [Indexed: 01/14/2023]
Abstract
Transfer-messenger RNA (tmRNA) is a bifunctional RNA that has properties of a tRNA and an mRNA. tmRNA uses these two functions to release ribosomes stalled during translation and target the nascent polypeptides for degradation. This concerted reaction, known as trans-translation, contributes to translational quality control and regulation of gene expression in bacteria. tmRNA is conserved throughout bacteria, and is one of the most abundant RNAs in the cell, suggesting that trans-translation is of fundamental importance for bacterial fitness. Mutants lacking tmRNA activity typically have severe phenotypes, including defects in viability, virulence, and responses to environmental stresses.
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Affiliation(s)
- Kenneth C Keiler
- Pennsylvania State University, Department of Biochemistry & Molecular Biology, 401 Althouse Lab, University Park, PA 16802, USA.
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46
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Abstract
Ribosomes are trapped at the 3′ ends of mRNAs that lack a natural stop codon. In bacteria, a reaction called trans-translation recycles ribosomes entrapped at such ‘non-stop’ mRNAs. The main player in trans-translation is tmRNA (SsrA-RNA), a bi-functional RNA that acts as both a tRNA and an mRNA. In the trans-translation reaction, alanine-charged tmRNA loads at the ribosomal A-site and translation shifts to the resume codon in tmRNA. Translation of tmRNA stops at a natural stop codon at the end of the small reading frame of tmRNA. In this way, the reaction simultaneously adds a peptide tag to the end of the nascent, incomplete polypeptide and recycles the stalled ribosomes. The peptide tag is recognized by cellular proteases that rapidly degrade the incomplete, potentially harmful polypeptides. The trans-translation reaction is not essential in most bacteria, raising the possibility that ribosomes stalled at non-stop mRNAs can be rescued by alternative routes. In this issue of Molecular Microbiology, Chadani et al. show that a novel translation factor, ArfA, can recycle a ribosome trapped at the 3′ end of a non-stop mRNA in the absence of trans-translation. AfrA is essential in the absence of tmRNA, showing that the two systems work in parallel to resolve stalled ribosomes.
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Affiliation(s)
- Hyouta Himeno
- Department of Biochemistry and Molecular Biology,Faculty of Agriculture and Life Science, HirosakiUniversity, Hirosaki 036-8561, Japan.
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47
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Handa Y, Inaho N, Nameki N. YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes. Nucleic Acids Res 2010; 39:1739-48. [PMID: 21051357 PMCID: PMC3061065 DOI: 10.1093/nar/gkq1097] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger RNA (tmRNA). In the absence of tmRNA, however, there is evidence that stalled ribosomes are released from non-stop mRNAs. Here, we show a novel ribosome rescue system mediated by a small basic protein, YaeJ, from Escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (RF). In vitro translation experiments using the E. coli-based reconstituted cell-free protein synthesis system revealed that YaeJ can hydrolyze peptidyl-tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs containing rare codon clusters that extend downstream from the P-site and prevent Ala-tmRNA•SmpB from entering the empty A-site. In addition, YaeJ had no effect on translation of a normal mRNA with a stop codon. These results suggested a novel tmRNA-independent rescue system for stalled ribosomes in E. coli. YaeJ was almost exclusively found in the 70S ribosome and polysome fractions after sucrose density gradient sedimentation, but was virtually undetectable in soluble fractions. The C-terminal basic residue-rich extension was also found to be required for ribosome binding. These findings suggest that YaeJ functions as a ribosome-attached rescue device for stalled ribosomes.
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Affiliation(s)
- Yoshihiro Handa
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu-shi, Gunma 376-8515, Japan
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48
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Kurita D, Muto A, Himeno H. Role of the C-terminal tail of SmpB in the early stage of trans-translation. RNA (NEW YORK, N.Y.) 2010; 16:980-990. [PMID: 20348441 PMCID: PMC2856891 DOI: 10.1261/rna.1916610] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Accepted: 02/11/2010] [Indexed: 05/29/2023]
Abstract
Trans-translation relieves a stalled translation on the bacterial ribosome by transfer-messenger RNA (tmRNA) with the help of SmpB, an essential cofactor of tmRNA. Here, we examined the role of the unstructured C-terminal tail of SmpB using an in vitro trans-translation system. It was found that truncation of the C-terminal tail or substitution of tryptophan residue at 147 in the middle of the C-terminal tail affected the activity in the early stage of trans-translation. Our investigations also revealed that the C-terminal tail is not required for the events until GTP is hydrolyzed by EF-Tu in complex with tmRNA-SmpB. A synthetic peptide corresponding to the C-terminal tail of SmpB inhibited peptidyl-transfer of alanyl-tmRNA and A-site binding of SmpB, but not GTP hydrolysis. These results suggest that the C-terminal tail has a role in the step of accommodation of alanyl-tmRNA-SmpB into the A-site. Directed hydroxyl radical probing indicated that tryptophan residue at 147 is located just downstream of the decoding center in the mRNA path when SmpB is in the A-site.
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MESH Headings
- Amino Acid Substitution
- Base Sequence
- Binding Sites/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Guanosine Triphosphate/metabolism
- Kinetics
- Models, Biological
- Models, Molecular
- Mutagenesis, Site-Directed
- Peptide Elongation Factor Tu/metabolism
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/metabolism
- Protein Biosynthesis
- Protein Structure, Tertiary
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribosomes/metabolism
- Sequence Deletion
- Tryptophan/chemistry
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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49
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Examination of post-transcriptional regulations in prokaryotes by integrative biology. C R Biol 2009; 332:958-73. [DOI: 10.1016/j.crvi.2009.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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50
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Hase Y, Yokoyama S, Muto A, Himeno H. Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells. RNA (NEW YORK, N.Y.) 2009; 15:1766-1774. [PMID: 19620234 PMCID: PMC2743055 DOI: 10.1261/rna.1687309] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2009] [Accepted: 06/03/2009] [Indexed: 05/28/2023]
Abstract
RsgA is a unique GTP hydrolytic protein in which GTPase activity is significantly enhanced by the small ribosomal subunit. Deletion of RsgA causes slow cell growth as well as defects in subunit assembly of the ribosome and 16S rRNA processing, suggesting its involvement in maturation of the small subunit. In this study, we found that removal of RsgA or inactivation of its ribosome small subunit-dependent GTPase activity provides Escherichia coli cells with resistance to high salt stress. Salt stress suppressed the defects in subunit assembly of the ribosome and processing of 16S rRNA as well as truncation of the 3' end of 16S rRNA in RsgA-deletion cells. In contrast, salt stress transiently impaired subunit assembly of the ribosome and processing of 16S rRNA and induced 3' truncation of 16S rRNA in wild-type cells. These results suggest that the action of RsgA on the ribosome, which usually facilitates maturation of the small subunit, disturbs it under a salt stress condition. Consistently, there was a drastic but transient decrease in the intracellular amount of RsgA after salt shock. Salt shock would make the pathway of maturation of the ribosome small subunit RsgA independent.
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Affiliation(s)
- Yoichi Hase
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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