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Seixas AF, Quendera AP, Sousa JP, Silva AFQ, Arraiano CM, Andrade JM. Bacterial Response to Oxidative Stress and RNA Oxidation. Front Genet 2022; 12:821535. [PMID: 35082839 PMCID: PMC8784731 DOI: 10.3389/fgene.2021.821535] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/21/2021] [Indexed: 01/03/2023] Open
Abstract
Bacteria have to cope with oxidative stress caused by distinct Reactive Oxygen Species (ROS), derived not only from normal aerobic metabolism but also from oxidants present in their environments. The major ROS include superoxide O2−, hydrogen peroxide H2O2 and radical hydroxide HO•. To protect cells under oxidative stress, bacteria induce the expression of several genes, namely the SoxRS, OxyR and PerR regulons. Cells are able to tolerate a certain number of free radicals, but high levels of ROS result in the oxidation of several biomolecules. Strikingly, RNA is particularly susceptible to this common chemical damage. Oxidation of RNA causes the formation of strand breaks, elimination of bases or insertion of mutagenic lesions in the nucleobases. The most common modification is 8-hydroxyguanosine (8-oxo-G), an oxidized form of guanosine. The structure and function of virtually all RNA species (mRNA, rRNA, tRNA, sRNA) can be affected by RNA oxidation, leading to translational defects with harmful consequences for cell survival. However, bacteria have evolved RNA quality control pathways to eliminate oxidized RNA, involving RNA-binding proteins like the members of the MutT/Nudix family and the ribonuclease PNPase. Here we summarize the current knowledge on the bacterial stress response to RNA oxidation, namely we present the different ROS responsible for this chemical damage and describe the main strategies employed by bacteria to fight oxidative stress and control RNA damage.
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Affiliation(s)
- André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - João P Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alda F Q Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Ali HH, Sridhar BBM, Rosenzweig JA. Klebsiella spp. isolates from Houston bayous exhibit increased resistance to lead exposure and possess enhanced virulence potential. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147818. [PMID: 34058587 DOI: 10.1016/j.scitotenv.2021.147818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Houston watersheds are susceptible to microbial contamination as well as chemical contaminations from bordering industrial facilities. Bacterial loads in various Houston bayous were determined, and pathogenic Gram-negative bacteria were isolated for characterization. Isolates included Klebsiella aerogenes and Klebsiella pneumoniae. To determine whether environmental exposures to lead (Pb), measured in our Houston bayou samples, resulted in bacterial adaptations, we compared growth kinetics, biofilm production, oxidative stress resistance, and eukaryotic co-culture growth of environmentally isolated K. aerogenes and K. pneumoniae to their respective commercially acquired reference strains. Interestingly, the K. aerogenes environmental isolate displayed significantly better growth than the reference strain in the presence of 50 ppb of Pb. Unexpectedly, we did not observe any differences in biofilm production of the aforementioned strains when challenged with a range of Pb (0.5-50 ppb). However, when comparing our K. pneumoniae environmental isolate to its reference strain, there were significantly higher levels of biofilm produced by the environmental isolate when challenged with Pb concentrations of 10 and 50 ppb. When grown in eukaryotic cell co-culture with either BAES 2B lung cells or CCD 841 colon epithelial cells in the presence of 20 ppb Pb, the environmental isolates of K. aerogenes and K. pneumoniae had a significantly higher fold-increase over 6 h than their respective reference strains. Taken together, the environmentally isolated Klebsiella spp. appeared to be more Pb-tolerant than their respective reference strains, a possible environmental adaptation. Such enhanced tolerance can promote environmental persistence and increase the possibility of causing human disease.
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Affiliation(s)
- Hanan H Ali
- Department of Environmental and Interdisciplinary Sciences, Texas Southern University Houston, TX, United States of America
| | | | - Jason A Rosenzweig
- Department of Biology, Texas Southern University Houston, TX, United States of America.
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3
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Pseudomonas aeruginosa Polynucleotide Phosphorylase Controls Tolerance to Aminoglycoside Antibiotics by Regulating the MexXY Multidrug Efflux Pump. Antimicrob Agents Chemother 2021; 65:AAC.01846-20. [PMID: 33257447 DOI: 10.1128/aac.01846-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/18/2020] [Indexed: 01/01/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that shows high intrinsic resistance to a variety of antibiotics. The MexX-MexY-OprM efflux pump plays an important role in bacterial resistance to aminoglycoside antibiotics. Polynucleotide phosphorylase (PNPase) is a highly conserved exonuclease that plays important roles in RNA processing and the bacterial response to environmental stresses. Previously, we demonstrated that PNPase controls the tolerance to fluoroquinolone antibiotics by influencing the production of pyocin in P. aeruginosa In this study, we found that mutation of the PNPase-encoding gene (pnp) in P. aeruginosa increases bacterial tolerance to aminoglycoside antibiotics. We further demonstrate that the upregulation of the mexXY genes is responsible for the increased tolerance of the pnp mutant. Furthermore, our experimental results revealed that PNPase controls the translation of the armZ mRNA through its 5' untranslated region (UTR). ArmZ had previously been shown to positively regulate the expression of mexXY Therefore, our results revealed a novel role of PNPase in the regulation of armZ and subsequently the MexXY efflux pump.
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4
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Fan Z, Chen H, Li M, Pan X, Fu W, Ren H, Chen R, Bai F, Jin Y, Cheng Z, Jin S, Wu W. Pseudomonas aeruginosa Polynucleotide Phosphorylase Contributes to Ciprofloxacin Resistance by Regulating PrtR. Front Microbiol 2019; 10:1762. [PMID: 31417536 PMCID: PMC6682600 DOI: 10.3389/fmicb.2019.01762] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that causes various acute and chronic infections. It is intrinsically resistant to a variety of antibiotics. However, production of pyocins during SOS response sensitizes P. aeruginosa to quinolone antibiotics by inducing cell lysis. The polynucleotide phosphorylase (PNPase) is a conserved phosphate-dependent 3′–5′ exonuclease that plays an important role in bacterial response to environmental stresses and pathogenesis by influencing mRNA and small RNA stabilities. Previously, we demonstrated that PNPase controls the type III and type VI secretion systems in P. aeruginosa. In this study, we found that mutation of the PNPase coding gene (pnp) increases the bacterial resistance to ciprofloxacin. Gene expression analyses revealed that the expression of pyocin biosynthesis genes is decreased in the pnp mutant. PrtR, a negative regulator of pyocin biosynthesis genes, is upregulated in the pnp mutant. We further demonstrated that PNPase represses the expression of PrtR on the post-transcriptional level. A fragment containing 43 nucleotides of the 5′ untranslated region was found to be involved in the PNPase mediated regulation of PrtR. Overall, our results reveled a novel layer of regulation on the pyocin biosynthesis by the PNPase in P. aeruginosa.
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Affiliation(s)
- Zheng Fan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Hao Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Mei Li
- Meishan Product Quality Supervision and Inspection Institute and National Pickle Quality Inspection Center, Meishan, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Weixin Fu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huan Ren
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ronghao Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Shouguang Jin
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
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Role of DEAD-box RNA helicase genes in the growth of Yersinia pseudotuberculosis IP32953 under cold, pH, osmotic, ethanol and oxidative stresses. PLoS One 2019; 14:e0219422. [PMID: 31287844 PMCID: PMC6615604 DOI: 10.1371/journal.pone.0219422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Yersinia pseudotuberculosis is an important foodborne pathogen threatening modern food safety due to its ability to survive and grow at low temperatures. DEAD-box RNA helicase CsdA has been shown to play an important role in the low-temperature growth of psychrotrophic Y. pseudotuberculosis. A total of five DEAD-box RNA helicase genes (rhlB, csdA, rhlE, dbpA, srmB) have been identified in Y. pseudotuberculosis IP32953. However, their role in various stress conditions used in food production is unclear. We studied the involvement of the DEAD-box RNA helicase-encoding genes in the cold tolerance of Y. pseudotuberculosis IP32953 using quantitative real-time reverse transcription (RT-qPCR) and mutational analysis. Quantitative RT-PCR revealed that mRNA transcriptional levels of csdA, rhlE, dbpA and srmB were significantly higher after cold shock at 3°C compared to non-shocked culture at 28°C, suggesting the involvement of these four genes in cold shock response at the transcriptional level. The deletion of csdA ceased growth, while the deletion of dbpA or srmB significantly impaired growth at 3°C, suggesting the requirement of these three genes in Y. pseudotuberculosis at low temperatures. Growth of each DEAD-box RNA helicase mutant was also investigated under pH, osmotic, ethanol and oxidative stress conditions. The five helicase-encoding genes did not play major roles in the growth of Y. pseudotuberculosis IP32953 under pH, osmotic, ethanol or oxidative stress.
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Knittel V, Vollmer I, Volk M, Dersch P. Discovering RNA-Based Regulatory Systems for Yersinia Virulence. Front Cell Infect Microbiol 2018; 8:378. [PMID: 30460205 PMCID: PMC6232918 DOI: 10.3389/fcimb.2018.00378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 12/26/2022] Open
Abstract
The genus Yersinia includes three human pathogenic species, Yersinia pestis, the causative agent of the bubonic and pneumonic plague, and enteric pathogens Y. enterocolitica and Y. pseudotuberculosis that cause a number of gut-associated diseases. Over the past years a large repertoire of RNA-based regulatory systems has been discovered in these pathogens using different RNA-seq based approaches. Among them are several conserved or species-specific RNA-binding proteins, regulatory and sensory RNAs as well as various RNA-degrading enzymes. Many of them were shown to control the expression of important virulence-relevant factors and have a very strong impact on Yersinia virulence. The precise targets, the molecular mechanism and their role for Yersinia pathogenicity is only known for a small subset of identified genus- or species-specific RNA-based control elements. However, the ongoing development of new RNA-seq based methods and data analysis methods to investigate the synthesis, composition, translation, decay, and modification of RNAs in the bacterial cell will help us to generate a more comprehensive view of Yersinia RNA biology in the near future.
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Affiliation(s)
- Vanessa Knittel
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ines Vollmer
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marcel Volk
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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7
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Cameron TA, Matz LM, De Lay NR. Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator. PLoS Genet 2018; 14:e1007654. [PMID: 30307990 PMCID: PMC6181284 DOI: 10.1371/journal.pgen.1007654] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Almost 60 years ago, Severo Ochoa was awarded the Nobel Prize in Physiology or Medicine for his discovery of the enzymatic synthesis of RNA by polynucleotide phosphorylase (PNPase). Although this discovery provided an important tool for deciphering the genetic code, subsequent work revealed that the predominant function of PNPase in bacteria and eukaryotes is catalyzing the reverse reaction, i.e., the release of ribonucleotides from RNA. PNPase has a crucial role in RNA metabolism in bacteria and eukaryotes mainly through its roles in processing and degrading RNAs, but additional functions in RNA metabolism have recently been reported for this enzyme. Here, we discuss these established and noncanonical functions for PNPase and the possibility that the major impact of PNPase on cell physiology is through its unorthodox roles.
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Affiliation(s)
- Todd A. Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lisa M. Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Nicholas R. De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas, United States of America
- * E-mail:
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8
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Abstract
RNA molecules have the tendency to fold into complex structures or to associate with complementary RNAs that exoribonucleases have difficulties processing or degrading. Therefore, degradosomes in bacteria and organelles as well as exosomes in eukaryotes have teamed-up with RNA helicases. Whereas bacterial degradosomes are associated with RNA helicases from the DEAD-box family, the exosomes and mitochondrial degradosome use the help of Ski2-like and Suv3 RNA helicases.
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9
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Nuss AM, Heroven AK, Dersch P. RNA Regulators: Formidable Modulators of Yersinia Virulence. Trends Microbiol 2016; 25:19-34. [PMID: 27651123 DOI: 10.1016/j.tim.2016.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/08/2016] [Accepted: 08/24/2016] [Indexed: 10/21/2022]
Abstract
A large repertoire of RNA-based regulatory mechanisms, including a plethora of cis- and trans-acting noncoding RNAs (ncRNAs), sensory RNA elements, regulatory RNA-binding proteins, and RNA-degrading enzymes have been uncovered lately as key players in the regulation of metabolism, stress responses, and virulence of the genus Yersinia. Many of them are strictly controlled in response to fluctuating environmental conditions sensed during the course of the infection, and certain riboregulators have already been shown to be crucial for virulence. Some of them are highly conserved among the family Enterobacteriaceae, while others are genus-, species-, or strain-specific and could contribute to the difference in Yersinia pathogenicity. Importantly, the analysis of Yersinia riboregulators has not only uncovered crucial elements and regulatory mechanisms governing host-pathogen interactions, it also revealed exciting new venues for the design of novel anti-infectives.
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Affiliation(s)
- Aaron M Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ann Kathrin Heroven
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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10
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Neisseria meningitidis Polynucleotide Phosphorylase Affects Aggregation, Adhesion, and Virulence. Infect Immun 2016; 84:1501-1513. [PMID: 26930706 DOI: 10.1128/iai.01463-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/24/2016] [Indexed: 12/16/2022] Open
Abstract
Neisseria meningitidis autoaggregation is an important step during attachment to human cells. Aggregation is mediated by type IV pili and can be modulated by accessory pilus proteins, such as PilX, and posttranslational modifications of the major pilus subunit PilE. The mechanisms underlying the regulation of aggregation remain poorly characterized. Polynucleotide phosphorylase (PNPase) is a 3'-5' exonuclease that is involved in RNA turnover and the regulation of small RNAs. In this study, we biochemically confirm that NMC0710 is the N. meningitidis PNPase, and we characterize its role in N. meningitidis pathogenesis. We show that deletion of the gene encoding PNPase leads to hyperaggregation and increased adhesion to epithelial cells. The aggregation induced was found to be dependent on pili and to be mediated by excessive pilus bundling. PNPase expression was induced following bacterial attachment to human cells. Deletion of PNPase led to global transcriptional changes and the differential regulation of 469 genes. We also demonstrate that PNPase is required for full virulence in an in vivo model of N. meningitidis infection. The present study shows that PNPase negatively affects aggregation, adhesion, and virulence in N. meningitidis.
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Tseng YT, Chiou NT, Gogiraju R, Lin-Chao S. The Protein Interaction of RNA Helicase B (RhlB) and Polynucleotide Phosphorylase (PNPase) Contributes to the Homeostatic Control of Cysteine in Escherichia coli. J Biol Chem 2015; 290:29953-63. [PMID: 26494621 PMCID: PMC4705995 DOI: 10.1074/jbc.m115.691881] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/12/2022] Open
Abstract
PNPase, one of the major enzymes with 3′ to 5′ single-stranded RNA degradation and processing activities, can interact with the RNA helicase RhlB independently of RNA degradosome formation in Escherichia coli. Here, we report that loss of interaction between RhlB and PNPase impacts cysteine homeostasis in E. coli. By random mutagenesis, we identified a mutant RhlBP238L that loses 75% of its ability to interact with PNPase but retains normal interaction with RNase E and RNA, in addition to exhibiting normal helicase activity. Applying microarray analyses to an E. coli strain with impaired RNA degradosome formation, we investigated the biological consequences of a weakened interaction between RhlB and PNPase. We found significant increases in 11 of 14 genes involved in cysteine biosynthesis. Subsequent Northern blot analyses showed that the up-regulated transcripts were the result of stabilization of the cysB transcript encoding a transcriptional activator for the cys operons. Furthermore, Northern blots of PNPase or RhlB mutants showed that RhlB-PNPase plays both a catalytic and structural role in regulating cysB degradation. Cells expressing the RhlBP238L mutant exhibited an increase in intracellular cysteine and an enhanced anti-oxidative response. Collectively, this study suggests a mechanism by which bacteria use the PNPase-RhlB exosome-like complex to combat oxidative stress by modulating cysB mRNA degradation.
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Affiliation(s)
- Yi-Ting Tseng
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, the Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Ni-Ting Chiou
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, the Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | | | - Sue Lin-Chao
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan,
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12
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Redder P, Hausmann S, Khemici V, Yasrebi H, Linder P. Bacterial versatility requires DEAD-box RNA helicases. FEMS Microbiol Rev 2015; 39:392-412. [PMID: 25907111 DOI: 10.1093/femsre/fuv011] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 11/13/2022] Open
Abstract
RNA helicases of the DEAD-box and DEAH-box families are important players in many processes involving RNA molecules. These proteins can modify RNA secondary structures or intermolecular RNA interactions and modulate RNA-protein complexes. In bacteria, they are known to be involved in ribosome biogenesis, RNA turnover and translation initiation. They thereby play an important role in the adaptation of bacteria to changing environments and to respond to stress conditions.
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Affiliation(s)
- Peter Redder
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Stéphane Hausmann
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Vanessa Khemici
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Haleh Yasrebi
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
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Li Z, Malla S, Shin B, Li JM. Battle against RNA oxidation: molecular mechanisms for reducing oxidized RNA to protect cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:335-46. [PMID: 24375979 DOI: 10.1002/wrna.1214] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/08/2023]
Abstract
Oxidation is probably the most common type of damage that occurs in cellular RNA. Oxidized RNA may be dysfunctional and is implicated in the pathogenesis of age-related human diseases. Cellular mechanisms controlling oxidized RNA have begun to be revealed. Currently, a number of ribonucleases and RNA-binding proteins have been shown to reduce oxidized RNA and to protect cells under oxidative stress. Although information about how these factors work is still very limited, we suggest several mechanisms that can be used to minimize oxidized RNA in various organisms.
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Affiliation(s)
- Zhongwei Li
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, USA
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14
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Rosenzweig JA, Chopra AK. The exoribonuclease Polynucleotide Phosphorylase influences the virulence and stress responses of yersiniae and many other pathogens. Front Cell Infect Microbiol 2013; 3:81. [PMID: 24312901 PMCID: PMC3832800 DOI: 10.3389/fcimb.2013.00081] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022] Open
Abstract
Microbes are incessantly challenged by both biotic and abiotic stressors threatening their existence. Therefore, bacterial pathogens must possess mechanisms to successfully subvert host immune defenses as well as overcome the stress associated with host-cell encounters. To achieve this, bacterial pathogens typically experience a genetic re-programming whereby anti-host/stress factors become expressed and eventually translated into effector proteins. In that vein, the bacterial host-cell induced stress-response is similar to any other abiotic stress to which bacteria respond by up-regulating specific stress-responsive genes. Following the stress encounter, bacteria must degrade unnecessary stress responsive transcripts through RNA decay mechanisms. The three pathogenic yersiniae (Yersinia pestis, Y. pseudo-tuberculosis, and Y. enterocolitica) are all psychrotropic bacteria capable of growth at 4°C; however, cold growth is dependent on the presence of an exoribonuclease, polynucleotide phosphorylase (PNPase). PNPase has also been implicated as a virulence factor in several notable pathogens including the salmonellae, Helicobacter pylori, and the yersiniae [where it typically influences the type three secretion system (TTSS)]. Further, PNPase has been shown to associate with ribonuclease E (endoribonuclease), RhlB (RNA helicase), and enolase (glycolytic enzyme) in several Gram-negative bacteria forming a large, multi-protein complex known as the RNA degradosome. This review will highlight studies demonstrating the influence of PNPase on the virulence potentials and stress responses of various bacterial pathogens as well as focusing on the degradosome-dependent and -independent roles played by PNPase in yersiniae stress responses.
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Affiliation(s)
- Jason A Rosenzweig
- Department of Biology, Center for Bionanotechnology and Environmental Research, Texas Southern University Houston, TX, USA ; Department of Environmental and Interdisciplinary Sciences, Texas Southern University Houston, TX, USA
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15
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Lawal A, Kirtley ML, van Lier CJ, Erova TE, Kozlova EV, Sha J, Chopra AK, Rosenzweig JA. The effects of modeled microgravity on growth kinetics, antibiotic susceptibility, cold growth, and the virulence potential of a Yersinia pestis ymoA-deficient mutant and its isogenic parental strain. ASTROBIOLOGY 2013; 13:821-32. [PMID: 23988036 PMCID: PMC3779001 DOI: 10.1089/ast.2013.0968] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 06/09/2013] [Indexed: 06/02/2023]
Abstract
Previously, we reported that there was no enhancement in the virulence potential (as measured by cell culture infections) of the bacterial pathogen Yersinia pestis (YP) following modeled microgravity/clinorotation growth. We have now further characterized the effects of clinorotation (CR) on YP growth kinetics, antibiotic sensitivity, cold growth, and YP's virulence potential in a murine model of infection. Surprisingly, none of the aforementioned phenotypes were altered. To better understand why CR did not enhance YP's virulence potential as it did for other bacterial pathogens, a YP ΔymoA isogenic mutant in the KIM/D27 background strain that is unable to produce the histone-like YmoA protein and influences DNA topography was used in both cell culture and murine models of infection. YmoA represses type three secretion system (T3SS) virulence gene expression in the yersiniae. Similar to our CR-grown parental YP strain data, the CR-grown ΔymoA mutant induced reduced HeLa cell cytotoxicity with concomitantly decreased Yersinia outer protein E (YopE) and low calcium response V (LcrV) antigen production and secretion. Important, however, were our findings that, although no significant differences were observed in survival of mice infected intraperitoneally with either normal gravity (NG)- or CR-grown parental YP, the ΔymoA mutant induced significantly more mortality in infected mice than did the parental strain following CR growth. Taken together, our data demonstrate that CR did enhance the virulence potential of the YP ΔymoA mutant in a murine infection model (relative to the CR-grown parental strain), despite inducing less HeLa cell rounding in our cell culture infection assay due to reduced T3SS activity. Therefore, CR, which induces a unique type of bacterial stress, might be enhancing YP's virulence potential in vivo through a T3SS-independent mechanism when the histone-like YmoA protein is absent.
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Affiliation(s)
- Abidat Lawal
- Department of Biology, Department of Environmental and Interdisciplinary Sciences, Center for Bionanotechnology and Environmental Research (CBER), Texas Southern University, Houston, Texas
| | - Michelle L. Kirtley
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, Institute of Human Infections and Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas
| | - Christina J. van Lier
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, Institute of Human Infections and Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas
| | - Tatiana E. Erova
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, Institute of Human Infections and Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas
| | - Elena V. Kozlova
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, Institute of Human Infections and Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas
| | - Jian Sha
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, Institute of Human Infections and Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas
| | - Ashok K. Chopra
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, Institute of Human Infections and Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas
| | - Jason A. Rosenzweig
- Department of Biology, Department of Environmental and Interdisciplinary Sciences, Center for Bionanotechnology and Environmental Research (CBER), Texas Southern University, Houston, Texas
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Bacterial helicases in post-transcriptional control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:878-83. [PMID: 23291566 DOI: 10.1016/j.bbagrm.2012.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 12/25/2022]
Abstract
Among the five superfamilies of helicases involved in RNA and DNA metabolism, superfamily 2 and superfamily 5 include bacterial RNA-helicases. These enzymes have been shown to be involved in ribosome biogenesis and post-transcriptional gene regulation. Here, we focus on bacterial regulatory mechanisms that are mediated by RNA helicases belonging to superfamily 2, which includes DEAD-box and DEAH-box helicases. Some of these helicases are part of bacterial degradosomes and were shown to unwind RNA duplexes. We will review examples where these enzymes have been implicated in translatability and metabolic stability of bacterial transcripts. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.
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