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Nickerson CA, McLean RJC, Barrila J, Yang J, Thornhill SG, Banken LL, Porterfield DM, Poste G, Pellis NR, Ott CM. Microbiology of human spaceflight: microbial responses to mechanical forces that impact health and habitat sustainability. Microbiol Mol Biol Rev 2024; 88:e0014423. [PMID: 39158275 PMCID: PMC11426028 DOI: 10.1128/mmbr.00144-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
SUMMARYUnderstanding the dynamic adaptive plasticity of microorganisms has been advanced by studying their responses to extreme environments. Spaceflight research platforms provide a unique opportunity to study microbial characteristics in new extreme adaptational modes, including sustained exposure to reduced forces of gravity and associated low fluid shear force conditions. Under these conditions, unexpected microbial responses occur, including alterations in virulence, antibiotic and stress resistance, biofilm formation, metabolism, motility, and gene expression, which are not observed using conventional experimental approaches. Here, we review biological and physical mechanisms that regulate microbial responses to spaceflight and spaceflight analog environments from both the microbe and host-microbe perspective that are relevant to human health and habitat sustainability. We highlight instrumentation and technology used in spaceflight microbiology experiments, their limitations, and advances necessary to enable next-generation research. As spaceflight experiments are relatively rare, we discuss ground-based analogs that mimic aspects of microbial responses to reduced gravity in spaceflight, including those that reduce mechanical forces of fluid flow over cell surfaces which also simulate conditions encountered by microorganisms during their terrestrial lifecycles. As spaceflight mission durations increase with traditional astronauts and commercial space programs send civilian crews with underlying health conditions, microorganisms will continue to play increasingly critical roles in health and habitat sustainability, thus defining a new dimension of occupational health. The ability of microorganisms to adapt, survive, and evolve in the spaceflight environment is important for future human space endeavors and provides opportunities for innovative biological and technological advances to benefit life on Earth.
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Affiliation(s)
- Cheryl A. Nickerson
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | | | - Jennifer Barrila
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | - Jiseon Yang
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | | | - Laura L. Banken
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | - D. Marshall Porterfield
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - George Poste
- Complex Adaptive Systems Initiative, Arizona State University, Tempe, Arizona, USA
| | | | - C. Mark Ott
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, Texas, USA
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2
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Humphrey ED, Sukhodolets MV. Isolation and Partial Characterization of Novel, Structurally Uniform (Hfq 6) n≥8 Assemblies Carrying Accessory Transcription and Translation Factors. Biochemistry 2024; 63:1647-1662. [PMID: 38869079 DOI: 10.1021/acs.biochem.3c00728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In growing E. coli cells, the transcription-translation complexes (TTCs) form characteristic foci; however, the exact molecular composition of these superstructures is not known with certainty. Herein, we report that, during our recently developed "fast" procedures for purification of E. coli RNA polymerase (RP), a fraction of the RP's α/RpoA subunits is displaced from the core RP complexes and copurifies with multiprotein superstructures carrying the nucleic acid-binding protein Hfq and the ribosomal protein S6. We show that the main components of these large multiprotein assemblies are fixed protein copy-number (Hfq6)n≥8 complexes; these complexes have a high level of structural uniformity and are distinctly unlike the previously described (Hfq6)n "head-to-tail" polymers. We describe purification of these novel, structurally uniform (Hfq6)n≥8 complexes to near homogeneity and show that they also contain small nonprotein molecules and accessory S6. We demonstrate that Hfq, S6, and RP have similar solubility profiles and present evidence pointing to a role of the Hfq C-termini in superstructure formation. Taken together, our data offer new insights into the composition of the macromolecular assemblies likely acting as scaffolds for transcription complexes and ribosomes during bacterial cells' active growth.
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Affiliation(s)
- Elijah D Humphrey
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
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3
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Ponath F, Zhu Y, Vogel J. Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σ E-dependent small RNA with unusual mRNA activation activity. mBio 2024; 15:e0353623. [PMID: 38436569 PMCID: PMC11005410 DOI: 10.1128/mbio.03536-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/05/2024] Open
Abstract
The oral commensal Fusobacterium nucleatum can spread to extra-oral sites, where it is associated with diverse pathologies, including pre-term birth and cancer. Due to the evolutionary distance of F. nucleatum to other model bacteria, we lack a deeper understanding of the RNA regulatory networks that allow this bacterium to adapt to its various niches. As a first step in that direction, we recently showed that F. nucleatum harbors a global stress response governed by the extracytoplasmic function sigma factor, σE, which displays a striking functional conservation with Proteobacteria and includes a noncoding arm in the form of a regulatory small RNA (sRNA), FoxI. To search for putative additional σE-dependent sRNAs, we comprehensively mapped the 5' and 3' ends of transcripts in the model strain ATCC 23726. This enabled the discovery of FoxJ, a ~156-nucleotide sRNA previously misannotated as the 5' untranslated region (UTR) of ylmH. FoxJ is tightly controlled by σE and activated by the same stress conditions as is FoxI. Both sRNAs act as mRNA repressors of the abundant porin FomA, but FoxJ also regulates genes that are distinct from the target suite of FoxI. Moreover, FoxJ differs from other σE-dependent sRNAs in that it also positively regulates genes at the post-transcriptional level. We provide preliminary evidence for a new mode of sRNA-mediated mRNA activation, which involves the targeting of intra-operonic terminators. Overall, our study provides an important resource through the comprehensive annotation of 5' and 3' UTRs in F. nucleatum and expands our understanding of the σE response in this evolutionarily distant bacterium.IMPORTANCEThe oral microbe Fusobacterium nucleatum can colonize secondary sites, including cancer tissue, and likely deploys complex regulatory systems to adapt to these new environments. These systems are largely unknown, partly due to the phylogenetic distance of F. nucleatum to other model organisms. Previously, we identified a global stress response mediated by σE that displays functional conservation with the envelope stress response in Proteobacteria, comprising a coding and noncoding regulatory arm. Through global identification of transcriptional start and stop sites, we uncovered the small RNA (sRNA) FoxJ as a novel component of the noncoding arm of the σE response in F. nucleatum. Together with its companion sRNA FoxI, FoxJ post-transcriptionally modulates the synthesis of envelope proteins, revealing a conserved function for σE-dependent sRNAs between Fusobacteriota and Proteobacteria. Moreover, FoxJ activates the gene expression for several targets, which is a mode of regulation previously unseen in the noncoding arm of the σE response.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
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4
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Cao D, Subhadra B, Lee YJ, Thoresen M, Cornejo S, Olivier A, Woolums A, Inzana TJ. Contribution of Hfq to gene regulation and virulence in Histophilus somni. Infect Immun 2024; 92:e0003824. [PMID: 38391206 PMCID: PMC10929436 DOI: 10.1128/iai.00038-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Histophilus somni is one of the predominant bacterial pathogens responsible for bovine respiratory and systemic diseases in cattle. Despite the identification of numerous H. somni virulence factors, little is known about the regulation of such factors. The post-transcriptional regulatory protein Hfq may play a crucial role in regulation of components that affect bacterial virulence. The contribution of Hfq to H. somni phenotype and virulence was investigated following creation of an hfq deletion mutant of H. somni strain 2336 (designated H. somni 2336Δhfq). A comparative analysis of the mutant to the wild-type strain was carried out by examining protein and carbohydrate phenotype, RNA sequence, intracellular survival in bovine monocytes, serum susceptibility, and virulence studies in mouse and calf models. H. somni 2336Δhfq exhibited a truncated lipooligosaccharide (LOS) structure, with loss of sialylation. The mutant demonstrated increased susceptibility to intracellular and serum-mediated killing compared to the wild-type strain. Transcriptomic analysis displayed significant differential expression of 832 upregulated genes and 809 downregulated genes in H. somni 2336Δhfq compared to H. somni strain 2336, including significant downregulation of lsgB and licA, which contribute to LOS oligosaccharide synthesis and sialylation. A substantial number of differentially expressed genes were associated with polysaccharide synthesis and other proteins that could influence virulence. The H. somni 2336Δhfq mutant strain was attenuated in a mouse septicemia model and somewhat attenuated in a calf intrabronchial challenge model. H. somni was recovered less frequently from nasopharyngeal swabs, endotracheal aspirates, and lung tissues of calves challenged with H. somni 2336Δhfq compared to the wild-type strain, and the percentage of abnormal lung tissue in calves challenged with H. somni 2336Δhfq was lower than in calves challenged with the wild-type strain. In conclusion, our results support that Hfq accounts for the regulation of H. somni virulence factors.
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Affiliation(s)
- Dianjun Cao
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, New York, USA
| | - Bindu Subhadra
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, New York, USA
| | - Yue-Jia Lee
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, New York, USA
| | - Merrilee Thoresen
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Santiago Cornejo
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Alicia Olivier
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Amelia Woolums
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Thomas J. Inzana
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, New York, USA
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Turbant F, Machiels Q, Waeytens J, Wien F, Arluison V. The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific. Int J Mol Sci 2024; 25:1434. [PMID: 38338713 PMCID: PMC10855545 DOI: 10.3390/ijms25031434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes and are usually useful for the cell. For this reason, they are classified as "functional amyloids". In this work, we focus our analysis on a bacterial functional amyloid called Hfq. Hfq is a pleiotropic regulator that mediates several aspects of genetic expression, mainly via the use of small noncoding RNAs. Our previous work showed that Hfq amyloid-fibrils interact with membranes. This interaction influences Hfq amyloid structure formation and stability, but the specifics of the lipid on the dynamics of this process is unknown. Here, we show, using spectroscopic methods, how lipids specifically drive and modulate Hfq amyloid assembly or, conversely, its disassembly. The reported effects are discussed in light of the consequences for bacterial cell life.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Quentin Machiels
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- SDV Department, Université Paris Cité, 75006 Paris, France
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6
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Spiteri D, Griffin S, Karatzas KA, Scerri C, Valdramidis VP. Escherichia coli K-12 Transcriptomics for Assessing the Mechanism of Action of High-Power Ultrasound. Microorganisms 2023; 11:2768. [PMID: 38004779 PMCID: PMC10673019 DOI: 10.3390/microorganisms11112768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
An investigation into the mechanisms of action on bacteria involving exposure to stress factors was conducted in this study. The effects of ultrasound on Escherichia coli K-12 MG1655 and its isogenic mutant, ∆gadW, under high power ultrasound treatments (26 kHz) were screened and identified by analysing their transcriptome differences between primary and secondary sequential treatments using RNA-Seq. This also helped to assess any developed protection for cells between different generations. According to our results, 1825 genes of all tested conditions were expressed, playing different roles in the cell. The expression of these genes is associated with DNA damage, cell membrane integrity, and also metabolic effects. The studied strains also showed different differential expressed genes (DEGs), with some genes being directly responsible for defence mechanisms, while others play an indirect effect due to cell damage. A gradual decrease in the expression of the genes, as we moved from just one cycle of ultrasound treatment to sequential treatment, was evident from a heat map analysis of the results. Overall, E. coli K-12 builds a self-protection mechanism by increasing the expression of genes involved in the respiration for increased growth, and production of flagellum and pili. It can be concluded that high power ultrasound is a technology that triggers several different defence mechanisms which directly link to E. coli.
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Affiliation(s)
- David Spiteri
- Department of Food Science and Nutrition, University of Malta, MSD 2080 Msida, Malta; (D.S.); (S.G.)
- Centre for Molecular Medicine and Biobanking, University of Malta, MSD 2080 Msida, Malta;
| | - Sholeem Griffin
- Department of Food Science and Nutrition, University of Malta, MSD 2080 Msida, Malta; (D.S.); (S.G.)
- Centre for Molecular Medicine and Biobanking, University of Malta, MSD 2080 Msida, Malta;
| | | | - Christian Scerri
- Centre for Molecular Medicine and Biobanking, University of Malta, MSD 2080 Msida, Malta;
- Department of Physiology and Biochemistry, University of Malta, MSD 2080 Msida, Malta
| | - Vasilis P. Valdramidis
- Department of Food Science and Nutrition, University of Malta, MSD 2080 Msida, Malta; (D.S.); (S.G.)
- Department of Chemistry, National and Kapodistrian University of Athens, 34400 Psachna, Greece
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7
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Bhatia RP, Kirit HA, Lewis CM, Sankaranarayanan K, Bollback JP. Evolutionary barriers to horizontal gene transfer in macrophage-associated Salmonella. Evol Lett 2023; 7:227-239. [PMID: 37475746 PMCID: PMC10355182 DOI: 10.1093/evlett/qrad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 07/22/2023] Open
Abstract
Horizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental data supporting these predictions. Here, we address this gap by measuring the relative fitness of 44 genes horizontally transferred from Escherichia coli to Salmonella enterica in infection-relevant environments. We estimated the distribution of fitness effects in each environment and identified that dosage-dependent effects across different environments are a significant barrier to HGT. The majority of genes were found to be deleterious. We also found longer genes had stronger negative fitness consequences than shorter ones, showing that gene length was negatively associated with HGT. Furthermore, fitness effects of transferred genes were found to be environmentally dependent. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment acting as evolutionary barriers to HGT.
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Affiliation(s)
- Rama P Bhatia
- Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Hande Acar Kirit
- Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
- Department of Anthropology, University of Oklahoma, Norman, OK, United States
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jonathan P Bollback
- Corresponding author: Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom.
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Jeje O, Ewunkem AJ, Jeffers-Francis LK, Graves JL. Serving Two Masters: Effect of Escherichia coli Dual Resistance on Antibiotic Susceptibility. Antibiotics (Basel) 2023; 12:antibiotics12030603. [PMID: 36978471 PMCID: PMC10044975 DOI: 10.3390/antibiotics12030603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The prevalence of multidrug-resistant bacteria and their increased pathogenicity has led to a growing interest in metallic antimicrobial materials and bacteriophages as potential alternatives to conventional antibiotics. This study examines how resistance to excess iron (III) influences the evolution of bacteriophage resistance in the bacterium Escherichia coli. We utilized experimental evolution in E. coli to test the effect of the evolution of phage T7 resistance on populations resistant to excess iron (III) and populations without excess iron resistance. Phage resistance evolved rapidly in both groups. Dual-resistant (iron (III)/phage) populations were compared to their controls (excess iron (III)-resistant, phage-resistant, no resistance to either) for their performance against each stressor, excess iron (III) and phage; and correlated resistances to excess iron (II), gallium (III), silver (I) and conventional antibiotics. Excess iron (III)/phage-resistant populations demonstrated superior 24 h growth compared to all other populations when exposed to increasing concentrations of iron (II, III), gallium (III), ampicillin, and tetracycline. No differences in 24 h growth were shown between excess iron (III)/phage-resistant and excess iron (III)-resistant populations in chloramphenicol, sulfonamide, and silver (I). The genomic analysis identified selective sweeps in the iron (III) resistant (rpoB, rpoC, yegB, yeaG), phage-resistant (clpX →/→ lon, uvaB, yeaG, fliR, gatT, ypjF, waaC, rpoC, pgi, and yjbH) and iron (III)/phage resistant populations (rcsA, hldE, rpoB, and waaC). E. coli selected for resistance to both excess iron (III) and T7 phage showed some evidence of a synergistic effect on various components of fitness. Dual selection resulted in correlated resistances to ionic metals {iron (II), gallium (III), and silver (I)} and several conventional antibiotics. There is a likelihood that this sort of combination antimicrobial treatment may result in bacterial variants with multiple resistances.
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Affiliation(s)
- Olusola Jeje
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
| | - Akamu J Ewunkem
- Department of Biological Sciences, Winston Salem State University, 601 S Martin Luther King Jr Drive, Winston Salem, NC 27110, USA
| | - Liesl K Jeffers-Francis
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
| | - Joseph L Graves
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
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9
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Kwon SJ, Lee J, Lee HS. Metabolic changes of the acetogen Clostridium sp. AWRP through adaptation to acetate challenge. Front Microbiol 2022; 13:982442. [PMID: 36569090 PMCID: PMC9768041 DOI: 10.3389/fmicb.2022.982442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution (ALE) under the acetate challenge. Acetate-adapted strain 46 T-a displayed acetate tolerance to acetate up to 10 g L-1 and increased ethanol production in small-scale cultures. The adapted strain showed a higher cell density than AWRP even without exogenous acetate supplementation. 46 T-a was shown to have reduced gas consumption rate and metabolite production. It was intriguing to note that 46 T-a, unlike AWRP, continued to consume H2 at low CO2 levels. Genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase (Hyt) crucial for autotrophic growth in CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed that most genes involved in the CO2-fixation Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated in 46 T-a. Several metabolic pathways involved in dissimilation of nucleosides and carbohydrates were significantly up-regulated in 46 T-a, indicating that 46 T-a evolved to utilize organic substrates rather than CO2 + H2. Further investigation into degeneration in carbon fixation of the acetate-adapted strain will provide practical implications for CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation.
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Affiliation(s)
- Soo Jae Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea
- Department of Marine Biotechnology, University of Science and Technology, Daejeon, South Korea
| | - Joungmin Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea
- Department of Marine Biotechnology, University of Science and Technology, Daejeon, South Korea
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10
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Ponath F, Zhu Y, Cosi V, Vogel J. Expanding the genetic toolkit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum. Proc Natl Acad Sci U S A 2022; 119:e2201460119. [PMID: 36161895 PMCID: PMC9546586 DOI: 10.1073/pnas.2201460119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
Fusobacterium nucleatum, long known as a common oral microbe, has recently garnered attention for its ability to colonize tissues and tumors elsewhere in the human body. Clinical and epidemiological research has now firmly established F. nucleatum as an oncomicrobe associated with several major cancer types. However, with the current research focus on host associations, little is known about gene regulation in F. nucleatum itself, including global stress-response pathways that typically ensure the survival of bacteria outside their primary niche. This is due to the phylogenetic distance of Fusobacteriota to most model bacteria, their limited genetic tractability, and paucity of known gene functions. Here, we characterize a global transcriptional stress-response network governed by the extracytoplasmic function sigma factor, σE. To this aim, we developed several genetic tools for this anaerobic bacterium, including four different fluorescent marker proteins, inducible gene expression, scarless gene deletion, and transcriptional and translational reporter systems. Using these tools, we identified a σE response partly reminiscent of phylogenetically distant Proteobacteria but induced by exposure to oxygen. Although F. nucleatum lacks canonical RNA chaperones, such as Hfq, we uncovered conservation of the noncoding arm of the σE response in form of the noncoding RNA FoxI. This regulatory small RNA acts as an mRNA repressor of several membrane proteins, thereby supporting the function of σE. In addition to the characterization of a global stress response in F. nucleatum, the genetic tools developed here will enable further discoveries and dissection of regulatory networks in this early-branching bacterium.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, D-97080 Germany
| | - Yan Zhu
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, D-97080 Germany
| | - Valentina Cosi
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, D-97080 Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, D-97080 Germany
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, D-97080 Germany
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11
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Barrila J, Yang J, Franco Meléndez KP, Yang S, Buss K, Davis TJ, Aronow BJ, Bean HD, Davis RR, Forsyth RJ, Ott CM, Gangaraju S, Kang BY, Hanratty B, Nydam SD, Nauman EA, Kong W, Steel J, Nickerson CA. Spaceflight Analogue Culture Enhances the Host-Pathogen Interaction Between Salmonella and a 3-D Biomimetic Intestinal Co-Culture Model. Front Cell Infect Microbiol 2022; 12:705647. [PMID: 35711662 PMCID: PMC9195300 DOI: 10.3389/fcimb.2022.705647] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Physical forces associated with spaceflight and spaceflight analogue culture regulate a wide range of physiological responses by both bacterial and mammalian cells that can impact infection. However, our mechanistic understanding of how these environments regulate host-pathogen interactions in humans is poorly understood. Using a spaceflight analogue low fluid shear culture system, we investigated the effect of Low Shear Modeled Microgravity (LSMMG) culture on the colonization of Salmonella Typhimurium in a 3-D biomimetic model of human colonic epithelium containing macrophages. RNA-seq profiling of stationary phase wild type and Δhfq mutant bacteria alone indicated that LSMMG culture induced global changes in gene expression in both strains and that the RNA binding protein Hfq played a significant role in regulating the transcriptional response of the pathogen to LSMMG culture. However, a core set of genes important for adhesion, invasion, and motility were commonly induced in both strains. LSMMG culture enhanced the colonization (adherence, invasion and intracellular survival) of Salmonella in this advanced model of intestinal epithelium using a mechanism that was independent of Hfq. Although S. Typhimurium Δhfq mutants are normally defective for invasion when grown as conventional shaking cultures, LSMMG conditions unexpectedly enabled high levels of colonization by an isogenic Δhfq mutant. In response to infection with either the wild type or mutant, host cells upregulated transcripts involved in inflammation, tissue remodeling, and wound healing during intracellular survival. Interestingly, infection by the Δhfq mutant led to fewer transcriptional differences between LSMMG- and control-infected host cells relative to infection with the wild type strain. This is the first study to investigate the effect of LSMMG culture on the interaction between S. Typhimurium and a 3-D model of human intestinal tissue. These findings advance our understanding of how physical forces can impact the early stages of human enteric salmonellosis.
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Affiliation(s)
- Jennifer Barrila
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- *Correspondence: Jennifer Barrila, ; Cheryl A. Nickerson,
| | - Jiseon Yang
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Karla P. Franco Meléndez
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Gainesville, FL, United States
| | - Shanshan Yang
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Kristina Buss
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Trenton J. Davis
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Heather D. Bean
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Richard R. Davis
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Rebecca J. Forsyth
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - C. Mark Ott
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX, United States
| | - Sandhya Gangaraju
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Bianca Y. Kang
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Brian Hanratty
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Seth D. Nydam
- Department of Animal Care & Technologies, Arizona State University, Tempe, AZ, United States
| | - Eric A. Nauman
- School of Mechanical Engineering, Weldon School of Biomedical Engineering and Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, United States
| | - Wei Kong
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, United States
| | - Jason Steel
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Cheryl A. Nickerson
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- *Correspondence: Jennifer Barrila, ; Cheryl A. Nickerson,
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12
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Martorana AM, Moura ECCM, Sperandeo P, Di Vincenzo F, Liang X, Toone E, Zhou P, Polissi A. Degradation of Components of the Lpt Transenvelope Machinery Reveals LPS-Dependent Lpt Complex Stability in Escherichia coli. Front Mol Biosci 2022; 8:758228. [PMID: 35004843 PMCID: PMC8727689 DOI: 10.3389/fmolb.2021.758228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Lipopolysaccharide (LPS) is a peculiar component of the outer membrane (OM) of many Gram-negative bacteria that renders these bacteria highly impermeable to many toxic molecules, including antibiotics. LPS is assembled at the OM by a dedicated intermembrane transport system, the Lpt (LPS transport) machinery, composed of seven essential proteins located in the inner membrane (IM) (LptB2CFG), periplasm (LptA), and OM (LptDE). Defects in LPS transport compromise LPS insertion and assembly at the OM and result in an overall modification of the cell envelope and its permeability barrier properties. LptA is a key component of the Lpt machine. It connects the IM and OM sub-complexes by interacting with the IM protein LptC and the OM protein LptD, thus enabling the LPS transport across the periplasm. Defects in Lpt system assembly result in LptA degradation whose stability can be considered a marker of an improperly assembled Lpt system. Indeed, LptA recruitment by its IM and OM docking sites requires correct maturation of the LptB2CFG and LptDE sub-complexes, respectively. These quality control checkpoints are crucial to avoid LPS mistargeting. To further dissect the requirements for the complete Lpt transenvelope bridge assembly, we explored the importance of LPS presence by blocking its synthesis using an inhibitor compound. Here, we found that the interruption of LPS synthesis results in the degradation of both LptA and LptD, suggesting that, in the absence of the LPS substrate, the stability of the Lpt complex is compromised. Under these conditions, DegP, a major chaperone–protease in Escherichia coli, is responsible for LptD but not LptA degradation. Importantly, LptD and LptA stability is not affected by stressors disturbing the integrity of LPS or peptidoglycan layers, further supporting the notion that the LPS substrate is fundamental to keeping the Lpt transenvelope complex assembled and that LptA and LptD play a major role in the stability of the Lpt system.
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Affiliation(s)
- Alessandra M Martorana
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Elisabete C C M Moura
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Flavia Di Vincenzo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Xiaofei Liang
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Eric Toone
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Pei Zhou
- Department of Chemistry, Duke University, Durham, NC, United States.,Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
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13
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Troung SF, Sukhodolets MV. The bacterial protein Hfq: Stable modifications and growth phase-dependent changes in SPAM profiles. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1183:122958. [PMID: 34628185 DOI: 10.1016/j.jchromb.2021.122958] [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: 07/06/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022]
Abstract
In bacteria transcription is coupled to translation, and while it is broadly accepted that transcription-translation complexes (TTCs) are formed in growing bacterial cells, the exact spatial organization of these macromolecular assemblies is not known with certainty. Recent studies indicated the formation of orderly cytosolic superstructures in growing E. coli cells. The bacterial nucleic acid (NA)-binding protein Hfq has been shown to function at the interface of RNA synthesis-degradation machinery; multiple, independent studies link Hfq to orderly cytosolic assemblies. In this work, using fast cell lysis/2D-PAGE and in vitro reconstitution analyses we studied the Hfq modifications and small protein-associated molecules (SPAM). We demonstrate that native Hfq carries stable modifications and simulate 2D patterns of native Hfq-SPAM complexes in reconstitution experiments with purified Hfq and synthetic NA probes. We also demonstrate that genetically engineered Hfq lacking the conserved arginine residues positioned near the rim of the disc formed by the subunits' N-terminal domains binds DNA with a reduced affinity in comparison with wild-type Hfq. These results are consistent with the proposed Hfq-mediated DNA remodeling and point to the involvement of this patch of conserved arginines in interactions with DNA.
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Affiliation(s)
- Stanley F Troung
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, TX 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, TX 77710, United States.
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14
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Deletion of Yersinia pestis ail causes temperature sensitive pleiotropic effects including cell lysis that are suppressed by carbon source, cations, or loss of phospholipase A activity. J Bacteriol 2021; 203:e0036121. [PMID: 34398663 PMCID: PMC8508112 DOI: 10.1128/jb.00361-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Maintenance of phospholipid (PL) and lipopoly- or lipooligo-saccharide (LPS or LOS) asymmetry in the outer membrane (OM) of Gram-negative bacteria is essential but poorly understood. The Yersinia pestis OM Ail protein was required to maintain lipid homeostasis and cell integrity at elevated temperature (37° C). Loss of this protein had pleiotropic effects. A Y. pestis Δail mutant and KIM6+ wild- type were systematically compared for (i) growth requirements at 37° C, (ii) cell structure, (iii) antibiotic and detergent sensitivity, (iv) proteins released into supernates, (v) induction of the heat shock response, and (vi) physiological and genetic suppressors that restored the wild- type phenotype. The Δail mutant grew normally at 28° C but lysed at 37° C when it entered stationary phase as shown by cell count, SDS-PAGE of cell supernatants, and electron microscopy. Immuno-fluorescent microscopy showed that the Δail mutant did not assemble Caf1 capsule. Expression of heat shock promoters rpoE or rpoH fused to a lux operon reporter were not induced when the Δail mutant was shifted from the 28° C to 37° C (p<0.001 and p<0.01 respectively). Mutant lysis was suppressed by addition of 11 mM glucose, 22 or 44 mM glycerol, 2.5 mM Ca2+, or 2.5 mM Mg2+ to the growth medium, or by a mutation in the phospholipase A gene (pldA::miniTn5, ΔpldA, or PldAS164A). A model, accounting for the temperature-sensitive lysis of the Δail mutant and the Ail-dependent stabilization of the OM tetraacylated LOS at 37°C is presented. IMPORTANCE The Gram-negative pathogen, Yersinia pestis, transitions between a flea vector (ambient temperature) and a mammalian host (37° C). In response to 37° C, Y. pestis modifies its outer membrane (OM) by reducing the fatty acid content in lipid A, changing the outer leaflet from being predominantly hexaacylated to being predominantly tetraacylated. It also increases the Ail concentration, so it becomes the most prominent OM protein. Both measures are needed for Y. pestis to evade the host innate immune response. Deletion of ail destabilizes the OM at 37° C causing the cells to lyse. These results show that a protein is essential for maintaining lipid asymmetry and lipid homeostasis in the bacterial OM.
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15
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Djapgne L, Oglesby AG. Impacts of Small RNAs and Their Chaperones on Bacterial Pathogenicity. Front Cell Infect Microbiol 2021; 11:604511. [PMID: 34322396 PMCID: PMC8311930 DOI: 10.3389/fcimb.2021.604511] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/07/2021] [Indexed: 12/25/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are critical post-transcriptional regulators that exert broad effects on cell physiology. One class of sRNAs, referred to as trans-acting sRNAs, base-pairs with mRNAs to cause changes in their stability or translation. Another class of sRNAs sequesters RNA-binding proteins that in turn modulate mRNA expression. RNA chaperones play key roles in these regulatory events by promoting base-pairing of sRNAs to mRNAs, increasing the stability of sRNAs, inducing conformational changes on mRNA targets upon binding, or by titrating sRNAs away from their primary targets. In pathogenic bacteria, sRNAs and their chaperones exert broad impacts on both cell physiology and virulence, highlighting the central role of these systems in pathogenesis. This review provides an overview of the growing number and roles of these chaperone proteins in sRNA regulation, highlighting how these proteins contribute to bacterial pathogenesis.
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Affiliation(s)
- Louise Djapgne
- Department of Chemistry, Georgetown College, Washington, DC, United States
| | - Amanda G Oglesby
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States.,Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD, United States
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16
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Ponath F, Tawk C, Zhu Y, Barquist L, Faber F, Vogel J. RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum. Nat Microbiol 2021; 6:1007-1020. [PMID: 34239075 DOI: 10.1038/s41564-021-00927-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 05/24/2021] [Indexed: 12/14/2022]
Abstract
Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered renewed attention for its association with several different human cancers. The growing interest in this emerging cancer-associated bacterium contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. As fusobacteria lack all established small RNA-associated proteins, post-transcriptional networks in these bacteria are also unknown. In the present study, using differential RNA-sequencing, we generate high-resolution global RNA maps for five clinically relevant fusobacterial strains-F. nucleatum subspecies nucleatum, animalis, polymorphum and vincentii, as well as F. periodonticum-for early, mid-exponential growth and early stationary phase. These data are made available in an online browser, and we use these to uncover fundamental aspects of fusobacterial gene expression architecture and a suite of non-coding RNAs. Developing a vector for functional analysis of fusobacterial genes, we discover a conserved fusobacterial oxygen-induced small RNA, FoxI, which serves as a post-transcriptional repressor of the major outer membrane porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum adaptation to different environments, which may elucidate how these bacteria colonize different compartments of the human body.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Caroline Tawk
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Yan Zhu
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Franziska Faber
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany. .,Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany. .,Faculty of Medicine, University of Würzburg, Würzburg, Germany.
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17
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Yang X, Dong M, Zhou Z, Deng L, Deng C, Liu H, Zhong Z, Fu H, Ren Z, Hu Y, Shen L, Geng Y, Peng G. RNA-binding protein Hfq plays a vital role in cellulose decomposition throughout affecting cellulase gene expression. Biotechnol Lett 2021; 43:1779-1785. [PMID: 34129180 DOI: 10.1007/s10529-021-03145-7] [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: 01/11/2021] [Accepted: 05/04/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To study the function of the RNA-binding protein Hfq in Bacillus subtilis cellulose decomposition. RESULTS In the medium with sodium carboxymethylcellulose (Na-CMC) as the sole carbon source, the knockout of Hfq resulted in a 38.0% ± 2.1% and 76.6% ± 7.1% decrease in cellulose hydrolysis ability and cellulase activity, respectively. The results of real-time quantitative PCR revealed that several cellulase genes (eglS, bglA, and bglC) were significantly downregulated in the Hfq knockout strain. The isogenic Δhfq complemented strain recovered the cellulose hydrolysis ability, cellulase activity, and expression level of cellulase genes. In addition, the survival of Hfq mutant in stationary phase was significantly affected. CONCLUSION RNA-binding protein Hfq is involved in the regulation of cellulose hydrolysis ability, cellulase activity, cellulase gene expression, and stationary phase survival.
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Affiliation(s)
- Xingtao Yang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Mengyao Dong
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Ziyao Zhou
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Lei Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Cao Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Haifeng Liu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Zhijun Zhong
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Hualin Fu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Zhihua Ren
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Yanchun Hu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Liuhong Shen
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Yi Geng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Guangneng Peng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
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18
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Kinnersley M, Schwartz K, Yang DD, Sherlock G, Rosenzweig F. Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment. BMC Biol 2021; 19:20. [PMID: 33541358 PMCID: PMC7863352 DOI: 10.1186/s12915-021-00954-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/08/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Microbial evolution experiments can be used to study the tempo and dynamics of evolutionary change in asexual populations, founded from single clones and growing into large populations with multiple clonal lineages. High-throughput sequencing can be used to catalog de novo mutations as potential targets of selection, determine in which lineages they arise, and track the fates of those lineages. Here, we describe a long-term experimental evolution study to identify targets of selection and to determine when, where, and how often those targets are hit. RESULTS We experimentally evolved replicate Escherichia coli populations that originated from a mutator/nonsense suppressor ancestor under glucose limitation for between 300 and 500 generations. Whole-genome, whole-population sequencing enabled us to catalog 3346 de novo mutations that reached > 1% frequency. We sequenced the genomes of 96 clones from each population when allelic diversity was greatest in order to establish whether mutations were in the same or different lineages and to depict lineage dynamics. Operon-specific mutations that enhance glucose uptake were the first to rise to high frequency, followed by global regulatory mutations. Mutations related to energy conservation, membrane biogenesis, and mitigating the impact of nonsense mutations, both ancestral and derived, arose later. New alleles were confined to relatively few loci, with many instances of identical mutations arising independently in multiple lineages, among and within replicate populations. However, most never exceeded 10% in frequency and were at a lower frequency at the end of the experiment than at their maxima, indicating clonal interference. Many alleles mapped to key structures within the proteins that they mutated, providing insight into their functional consequences. CONCLUSIONS Overall, we find that when mutational input is increased by an ancestral defect in DNA repair, the spectrum of high-frequency beneficial mutations in a simple, constant resource-limited environment is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever go to fixation.
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Affiliation(s)
- Margie Kinnersley
- Division of Biological Sciences, The University of Montana, Missoula, MT, 59812, USA
| | - Katja Schwartz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA
| | - Dong-Dong Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.
| | - Frank Rosenzweig
- Division of Biological Sciences, The University of Montana, Missoula, MT, 59812, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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19
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Bustamante V, González IA, Dreyse P, Palavecino CE. The mode of action of the PSIR-3 photosensitizer in the photodynamic inactivation of Klebsiella pneumoniae is by the production of type II ROS which activate RpoE-regulated extracytoplasmic factors. Photodiagnosis Photodyn Ther 2020; 32:102020. [PMID: 32977066 DOI: 10.1016/j.pdpdt.2020.102020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/30/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Due to increased bacterial multi-drug resistance (MDR), there is an antibiotic depletion to treat infectious diseases. Consequently, other promising options have emerged, such as the antimicrobial photodynamic inactivation therapy (aPDI) based on photosensitizer (PS) compounds to produce light-activated local oxidative stress (photooxidative stress). However, there are scarce studies regarding the mode of action of PS compounds to induce photooxidative stress on pathogenic γ-proteobacteria such as MDR-Klebsiella pneumoniae. METHODOLOGY The mode of action exerted by the cationic Ir(III)-based PS (PSIR-3) to inhibit the growth of K. pneumoniae was analyzed. RT-qPCR determined the transcriptional response induced by PSIR-3 on bacteria treated with aPDI. The expression levels of genes associated with a bacterial oxidative response, such as oxyR and sodA, and the extracytoplasmic, regulators rpoE and hfq were determined. Also, were determined the transcriptional response of the extracytoplasmic factors mrkD, acrB, magA, and rmpA. RESULTS At 17 μW/cm2 photon flux and 4 μg/mL of the PSIR-3 compound, the K. pneumoniae growth was inhibited in 3 log10. Compared with untreated bacteria, the transcriptional response induced by PSIR-3 occurs via the extracytoplasmic sigma factor rpoE and hfq. In contrast, no participation in the oxyR pathway or induction of the sodA gene was observed. This response was accompanied by the upregulation of the extracytoplasmic virulence factors mrkD, magA, and rmpA. CONCLUSIONS PDI aPDI produced by PSIR-3 kills K. pneumoniae and may induce damage to the bacterial envelope. The bacterium tries to avoid this injury by activation of extracytoplasmic factors mediated through the rpoE regulon.
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Affiliation(s)
- Vanessa Bustamante
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Post Cod: 8330546, Santiago, Chile.
| | - Iván A González
- Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile.
| | - Paulina Dreyse
- Departamento de Química, Universidad Técnica Federico Santa María, Av. España 1680, Casilla 2390123, Valparaíso, Chile.
| | - Christian Erick Palavecino
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Post Cod: 8330546, Santiago, Chile.
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20
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Hör J, Matera G, Vogel J, Gottesman S, Storz G. Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0030-2019. [PMID: 32213244 PMCID: PMC7112153 DOI: 10.1128/ecosalplus.esp-0030-2019] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Indexed: 12/20/2022]
Abstract
The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Gianluca Matera
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892
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Efthimiou G, Tsiamis G, Typas MA, Pappas KM. Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions. Front Microbiol 2019; 10:2393. [PMID: 31681245 PMCID: PMC6813237 DOI: 10.3389/fmicb.2019.02393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/02/2019] [Indexed: 01/13/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) strains are important human pathogens and a significant health hazard for hospitals and the food industry. They are resistant to β-lactam antibiotics including methicillin and extremely difficult to treat. In this study, we show that the Staphylococcus aureus COL (MRSA) strain, with a known complete genome, can easily survive and grow under acidic and alkaline conditions (pH5 and pH9, respectively), both planktonically and as a biofilm. A microarray-based analysis of both planktonic and biofilm cells was performed under acidic and alkaline conditions showing that several genes are up- or down-regulated under different environmental conditions and growth modes. These genes were coding for transcription regulators, ion transporters, cell wall biosynthetic enzymes, autolytic enzymes, adhesion proteins and antibiotic resistance factors, most of which are associated with biofilm formation. These results will facilitate a better understanding of the physiological adjustments occurring in biofilm-associated S. aureus COL cells growing in acidic or alkaline environments, which will enable the development of new efficient treatment or disinfection strategies.
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Affiliation(s)
- Georgios Efthimiou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - George Tsiamis
- Department of Environmental Engineering, University of Patras, Agrinio, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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22
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Valenzuela-Valderrama M, González IA, Palavecino CE. Photodynamic treatment for multidrug-resistant Gram-negative bacteria: Perspectives for the treatment of Klebsiella pneumoniae infections. Photodiagnosis Photodyn Ther 2019; 28:256-264. [PMID: 31505296 DOI: 10.1016/j.pdpdt.2019.08.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/09/2019] [Indexed: 12/25/2022]
Abstract
The emergence of multi-drug resistance for pathogenic bacteria is one of the most pressing global threats to human health in the 21st century. Hence, the availability of new treatment becomes indispensable to prevent morbidity and mortality caused by infectious agents. This article reviews the antimicrobial properties of photodynamic therapy (PDT), which is based on the use of photosensitizers compounds (PSs). The PSs are non-toxic small molecules, which induce oxidative stress only under excitation with light. Then, the PDT has the advantage to be locally activated using phototherapy devices. We focus on PDT for the Klebsiella pneumoniae, as an example of Gram-negative bacteria, due to its relevance as an agent of health-associated infections (HAI) and a multi-drug resistant bacteria. K. pneumoniae is a fermentative bacillus, member of the Enterobacteriaceae family, which is most commonly associated with producing infection of the urinary tract (UTI) and pneumonia. K. pneumoniae infections may occur in deep organs such as bladder or lungs tissues; therefore, activating light must get access or penetrate tissues with sufficient power to produce effective PDT. Consequently, the rationale for selecting the most appropriate PSs, as well as photodynamic devices and photon fluence doses, were reviewed. Also, the mechanisms by which PDT activates the immune system and its importance to eradicate the infection successfully, are discussed.
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Affiliation(s)
- Manuel Valenzuela-Valderrama
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile; Centro de Estudios Avanzados en Enfermedades Crónicas (ACCDiS), Independencia, Santiago 8380000, Chile.
| | - Iván Alonzo González
- Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile.
| | - Christian Erick Palavecino
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile.
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23
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Hews CL, Cho T, Rowley G, Raivio TL. Maintaining Integrity Under Stress: Envelope Stress Response Regulation of Pathogenesis in Gram-Negative Bacteria. Front Cell Infect Microbiol 2019; 9:313. [PMID: 31552196 PMCID: PMC6737893 DOI: 10.3389/fcimb.2019.00313] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/19/2019] [Indexed: 12/20/2022] Open
Abstract
The Gram-negative bacterial envelope is an essential interface between the intracellular and harsh extracellular environment. Envelope stress responses (ESRs) are crucial to the maintenance of this barrier and function to detect and respond to perturbations in the envelope, caused by environmental stresses. Pathogenic bacteria are exposed to an array of challenging and stressful conditions during their lifecycle and, in particular, during infection of a host. As such, maintenance of envelope homeostasis is essential to their ability to successfully cause infection. This review will discuss our current understanding of the σE- and Cpx-regulated ESRs, with a specific focus on their role in the virulence of a number of model pathogens.
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Affiliation(s)
- Claire L Hews
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Timothy Cho
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tracy L Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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24
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Kelly CL, Harris AWK, Steel H, Hancock EJ, Heap JT, Papachristodoulou A. Synthetic negative feedback circuits using engineered small RNAs. Nucleic Acids Res 2019; 46:9875-9889. [PMID: 30212900 PMCID: PMC6182179 DOI: 10.1093/nar/gky828] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
Negative feedback is known to enable biological and man-made systems to perform reliably in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have primarily relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA molecules that can inhibit translation of target messenger RNAs (mRNAs). In this work, we modelled, built and validated two synthetic negative feedback circuits that use rationally-designed sRNAs for the first time. The first circuit builds upon the well characterised tet-based autorepressor, incorporating an externally-inducible sRNA to tune the effective feedback strength. This allows more precise fine-tuning of the circuit output in contrast to the sigmoidal, steep input–output response of the autorepressor alone. In the second circuit, the output is a transcription factor that induces expression of an sRNA, which inhibits translation of the mRNA encoding the output, creating direct, closed-loop, negative feedback. Analysis of the noise profiles of both circuits showed that the use of sRNAs did not result in large increases in noise. Stochastic and deterministic modelling of both circuits agreed well with experimental data. Finally, simulations using fitted parameters allowed dynamic attributes of each circuit such as response time and disturbance rejection to be investigated.
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Affiliation(s)
- Ciarán L Kelly
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK.,Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Andreas W K Harris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Edward J Hancock
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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25
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Abstract
The ability of bacteria to thrive in diverse habitats and to adapt to ever-changing environmental conditions relies on the rapid and stringent modulation of gene expression. It has become evident in the past decade that small regulatory RNAs (sRNAs) are central components of networks controlling the bacterial responses to stress. Functioning at the posttranscriptional level, sRNAs base-pair with cognate mRNAs to alter translation, stability, or both to either repress or activate the targeted transcripts; the RNA chaperone Hfq participates in stabilizing sRNAs and in promoting pairing between target and sRNA. In particular, sRNAs act at the heart of crucial stress responses, including those dedicated to overcoming membrane damage and oxidative stress, discussed here. The bacterial cell envelope is the outermost protective barrier against the environment and thus is constantly monitored and remodeled. Here, we review the integration of sRNAs into the complex networks of several major envelope stress responses of Gram-negative bacteria, including the RpoE (σE), Cpx, and Rcs regulons. Oxidative stress, caused by bacterial respiratory activity or induced by toxic molecules, can lead to significant damage of cellular components. In Escherichia coli and related bacteria, sRNAs also contribute significantly to the function of the RpoS (σS)-dependent general stress response as well as the specific OxyR- and SoxR/S-mediated responses to oxidative damage. Their activities in gene regulation and crosstalk to other stress-induced regulons are highlighted.
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26
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The nonsense-mediated mRNA decay (NMD) pathway differentially regulates COX17, COX19 and COX23 mRNAs. Curr Genet 2018; 65:507-521. [PMID: 30317392 PMCID: PMC6420912 DOI: 10.1007/s00294-018-0892-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/12/2023]
Abstract
The differential regulation of COX17, COX19 and COX23 mRNAs by the nonsense-mediated mRNA decay (NMD) pathway was investigated. The NMD pathway regulates mRNAs that aberrantly terminate translation. This includes mRNAs harboring premature translation termination codons and natural mRNAs. Most natural mRNAs regulated by NMD encode fully functional proteins involved in various cellular processes. However, the cause and targeting of most of these mRNAs by the pathway is not understood. Analysis of a set of mRNAs involved in copper homeostasis showed that a subset of these mRNAs function in mitochondrial copper homeostasis. Here, we examined the regulation of COX17, COX19 and COX23 mRNAs by NMD. These mRNAs encode homologous mitochondrial proteins involved in metallation of cytochrome c oxidase. We found that COX17, COX19 and COX23 mRNAs are differentially regulated by NMD depending on environmental copper levels. A long 3'-UTR contributes to the direct regulation of COX19 mRNA by the pathway. Alternatively, COX23 mRNA contains a long 3'-UTR, but is indirectly regulated by the pathway under two conditions tested here. Analysis of the functionality of the NMD targeting features in COX23 mRNA showed that the COX23 3'-UTR is sufficient to trigger NMD. The regulation of mRNAs involved in mitochondrial copper metabolism by NMD is physiologically significant because excess copper enhances growth of NMD mutants on a non-fermentable carbon source. These findings suggest that regulation of mRNAs encoding homologous proteins by NMD can be differential depending on environmental copper levels. Furthermore, these findings suggest copper ion homeostatic mechanisms in the mitochondria occur at the mRNA level via the NMD pathway.
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27
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Jameelah M, Dewanti-Hariyadi R, Nurjanah S. Expression of rpoS, ompA and hfq genes of Cronobacter sakazakii strain Yrt2a during stress and viable but nonculturable state. Food Sci Biotechnol 2018; 27:915-920. [PMID: 30263819 PMCID: PMC6049694 DOI: 10.1007/s10068-018-0313-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/03/2018] [Accepted: 01/07/2018] [Indexed: 11/24/2022] Open
Abstract
Cronobacter spp. in powdered infant formula has been etiologically linked to meningitis and necrotizing enterocolitis in certain groups of infants. This study aimed to determine whether C. sakazakii Yrt2a strain experiencing desiccation stress could enter viable but nonculturable (VBNC) state as well as to examine the expression of genes associated with stress and virulence during the above states. Stress and VBNC conditions were determined based on viability and culturability assays. Expression of genes related to stress (rpoS) and virulence (hfq and ompA) was evaluated by real-time PCR. The results showed that C. sakazakii Yrt2a entered VBNC 24 days post exposure to 2 h of desiccation treatment. The expression of rpoS, hfq and ompA genes was up-regulated during stress conditions, suggesting that Cronobacter successfully managed stress to maintain its culturability while maintaining its virulence. The expression of the target genes decreased at VBNC state but remained higher than that of a normal state. These findings reinforce the assumption that C. sakazakii undergoing VBNC state maintains its pathogenicity.
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Affiliation(s)
- Maryam Jameelah
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, Bogor Agricultural University, IPB Dramaga, Bogor, 16680 Indonesia
| | - Ratih Dewanti-Hariyadi
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, Bogor Agricultural University, IPB Dramaga, Bogor, 16680 Indonesia
- Southeast Asian Food and Agricultural Science and Technology Center, Bogor Agricultural University, Jl. Puspa Lingkar Kampus IPB Dramaga, Bogor, 16680 Indonesia
| | - Siti Nurjanah
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, Bogor Agricultural University, IPB Dramaga, Bogor, 16680 Indonesia
- Southeast Asian Food and Agricultural Science and Technology Center, Bogor Agricultural University, Jl. Puspa Lingkar Kampus IPB Dramaga, Bogor, 16680 Indonesia
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28
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Cho SH, Haning K, Shen W, Blome C, Li R, Yang S, Contreras LM. Identification and Characterization of 5' Untranslated Regions (5'UTRs) in Zymomonas mobilis as Regulatory Biological Parts. Front Microbiol 2017; 8:2432. [PMID: 29375488 PMCID: PMC5770649 DOI: 10.3389/fmicb.2017.02432] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/23/2017] [Indexed: 01/03/2023] Open
Abstract
Regulatory RNA regions within a transcript, particularly in the 5' untranslated region (5'UTR), have been shown in a variety of organisms to control the expression levels of these mRNAs in response to various metabolites or environmental conditions. Considering the unique tolerance of Zymomonas mobilis to ethanol and the growing interest in engineering microbial strains with enhanced tolerance to industrial inhibitors, we searched natural cis-regulatory regions in this microorganism using transcriptomic data and bioinformatics analysis. Potential regulatory 5'UTRs were identified and filtered based on length, gene function, relative gene counts, and conservation in other organisms. An in vivo fluorescence-based screening system was developed to confirm the responsiveness of 36 5'UTR candidates to ethanol, acetate, and xylose stresses. UTR_ZMO0347 (5'UTR of gene ZMO0347 encoding the RNA binding protein Hfq) was found to down-regulate downstream gene expression under ethanol stress. Genomic deletion of UTR_ZMO0347 led to a general decrease of hfq expression at the transcript level and increased sensitivity for observed changes in Hfq expression at the protein level. The role of UTR_ZMO0347 and other 5'UTRs gives us insight into the regulatory network of Z. mobilis in response to stress and unlocks new strategies for engineering robust industrial strains as well as for harvesting novel responsive regulatory biological parts for controllable gene expression platforms in this organism.
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Affiliation(s)
- Seung Hee Cho
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, United States
| | - Katie Haning
- Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States
| | - Wei Shen
- Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Cameron Blome
- Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States
| | - Runxia Li
- Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, United States.,Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States
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29
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Ellis MJ, Carfrae LA, Macnair CR, Trussler RS, Brown ED, Haniford DB. Silent but deadly: IS200 promotes pathogenicity in Salmonella Typhimurium. RNA Biol 2017; 15:176-181. [PMID: 29120256 DOI: 10.1080/15476286.2017.1403001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA). This sRNA represses expression of genes encoded within Salmonella Pathogenicity Island 1 (SPI-1), and accordingly limits invasion into non-phagocytic cells in vitro. We present new data here that shows IS200 elements are important for colonization of the mouse gastrointestinal tract. We discuss our previous and current findings in the context of transposon biology and suggest that otherwise 'silent' transposons may in fact play an important role in controlling host gene expression.
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Affiliation(s)
- Michael J Ellis
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
| | - Lindsey A Carfrae
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - Craig R Macnair
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - Ryan S Trussler
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
| | - Eric D Brown
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - David B Haniford
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
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Abstract
Bacteria have robust responses to a variety of stresses. In particular, bacteria like Escherichia coli have multiple cell envelope stress responses, and generally we evaluate what these responses are doing by the repair systems they induce. However, probably at least as important in interpreting what is being sensed as stress are the genes that these stress systems downregulate, directly or indirectly. This is discussed here for the Cpx and sigma E systems of E. coli.
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, NCI, Center for Cancer Research, Bethesda, Maryland, USA
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31
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Ishihama A. Building a complete image of genome regulation in the model organism Escherichia coli. J GEN APPL MICROBIOL 2017; 63:311-324. [PMID: 28904250 DOI: 10.2323/jgam.2017.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The model organism, Escherichia coli, contains a total of more than 4,500 genes, but the total number of RNA polymerase (RNAP) core enzyme or the transcriptase is only about 2,000 molecules per genome. The regulatory targets of RNAP are, however, modulated by changing its promoter selectivity through two-steps of protein-protein interplay with 7 species of the sigma factor in the first step, and then 300 species of the transcription factor (TF) in the second step. Scientists working in the field of prokaryotic transcription in Japan have made considerable contributions to the elucidation of genetic frameworks and regulatory modes of the genome transcription in E. coli K-12. This review summarizes the findings by this group, first focusing on three sigma factors, the stationary-phase sigma RpoS, the heat-shock sigma RpoH, and the flagellar-chemotaxis sigma RpoF, as examples. It also presents an overview of the current state of the systematic research being carried out to identify the regulatory functions of all TFs from a single and the same bacterium E. coli K-12, using the genomic SELEX and PS-TF screening systems. All these studies have been undertaken with the aim of understanding the genome regulation in E. coli K-12 as a whole.
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Affiliation(s)
- Akira Ishihama
- Research Institute of Micro-Nano Technology, Hosei University
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32
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Chen J, Gottesman S. Hfq links translation repression to stress-induced mutagenesis in E. coli. Genes Dev 2017; 31:1382-1395. [PMID: 28794186 PMCID: PMC5580658 DOI: 10.1101/gad.302547.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Here, Chen et al. show an example of Hfq repressing translation in the absence of sRNAs via major remodeling of the mRNA. They demonstrate that, by interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis. Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA–RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis. Here we report that Hfq deploys dual mechanisms to control mutS expression. First, Hfq binds directly to an (AAN)3 motif within the mutS 5′ untranslated region (UTR), repressing translation in the absence of sRNA partners both in vivo and in vitro. Second, Hfq acts in a canonical pathway, promoting base-pairing of ArcZ sRNA with the mutS leader to inhibit translation. Most importantly, using pathway-specific mutS chromosomal alleles that specifically abrogate either regulatory pathway or both, we demonstrate that tight control of MutS levels in stationary phase contributes to stress-induced mutagenesis. By interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis.
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Affiliation(s)
- Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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33
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Mitobe J, Sinha R, Mitra S, Nag D, Saito N, Shimuta K, Koizumi N, Koley H. An attenuated Shigella mutant lacking the RNA-binding protein Hfq provides cross-protection against Shigella strains of broad serotype. PLoS Negl Trop Dis 2017; 11:e0005728. [PMID: 28727722 PMCID: PMC5544247 DOI: 10.1371/journal.pntd.0005728] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 08/04/2017] [Accepted: 06/19/2017] [Indexed: 11/19/2022] Open
Abstract
Few live attenuated vaccines protect against multiple serotypes of bacterial pathogen because host serotype-specific immune responses are limited to the serotype present in the vaccine strain. Here, immunization with a mutant of Shigella flexneri 2a protected guinea pigs against subsequent infection by S. dysenteriae type 1 and S. sonnei strains. This deletion mutant lacked the RNA-binding protein Hfq leading to increased expression of the type III secretion system via loss of regulation, resulting in attenuation of cell viability through repression of stress response sigma factors. Such increased antigen production and simultaneous attenuation were expected to elicit protective immunity against Shigella strains of heterologous serotypes. Thus, the vaccine potential of this mutant was tested in two guinea pig models of shigellosis. Animals vaccinated in the left eye showed fewer symptoms upon subsequent challenge via the right eye, and even survived subsequent intestinal challenge. In addition, oral vaccination effectively induced production of immunoglobulins without severe side effects, again protecting all animals against subsequent intestinal challenge with S. dysenteriae type 1 or S. sonnei strains. Antibodies against common virulence proteins and the O-antigen of S. flexneri 2a were detected by immunofluorescence microscopy. Reaction of antibodies with various strains, including enteroinvasive Escherichia coli, suggested that common virulence proteins induced protective immunity against a range of serotypes. Therefore, vaccination is expected to cover not only the most prevalent serotypes of S. sonnei and S. flexneri 2a, but also various Shigella strains, including S. dysenteriae type 1, which produces Shiga toxin.
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Affiliation(s)
- Jiro Mitobe
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
- * E-mail:
| | - Ritam Sinha
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Soma Mitra
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Dhrubajyoti Nag
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Noriko Saito
- Laboratory of Electron Microscopy, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Hemanta Koley
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
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Leskinen K, Pajunen MI, Varjosalo M, Fernández-Carrasco H, Bengoechea JA, Skurnik M. Several Hfq-dependent alterations in physiology of Yersinia enterocolitica O:3 are mediated by derepression of the transcriptional regulator RovM. Mol Microbiol 2017; 103:1065-1091. [PMID: 28010054 DOI: 10.1111/mmi.13610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2016] [Indexed: 12/27/2022]
Abstract
In bacteria, the RNA chaperone Hfq enables pairing of small regulatory RNAs with their target mRNAs and therefore is a key player of post-transcriptional regulation network. As a global regulator, Hfq is engaged in the adaptation to external environment, regulation of metabolism and bacterial virulence. In this study we used RNA-sequencing and quantitative proteomics (LC-MS/MS) to elucidate the role of this chaperone in the physiology and virulence of Yersinia enterocolitica serotype O:3. This global approach revealed the profound impact of Hfq on gene and protein expression. Furthermore, the role of Hfq in the cell morphology, metabolism, cell wall integrity, resistance to external stresses and pathogenicity was evaluated. Importantly, our results revealed that several alterations typical for the hfq-negative phenotype were due to derepression of the transcriptional factor RovM. The overexpression of RovM caused by the loss of Hfq chaperone resulted in extended growth defect, alterations in the lipid A structure, motility and biofilm formation defects, as well as changes in mannitol utilization. Furthermore, in Y. enterocolitica RovM only in the presence of Hfq affected the abundance of RpoS. Finally, the impact of hfq and rovM mutations on the virulence was assessed in the mouse infection model.
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Affiliation(s)
- Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology, University of Helsinki, Finland
| | - Maria I Pajunen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology, University of Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki.,Biocentrum Helsinki, Finland: Finnish Institute of Molecular Medicine, Finland
| | | | - José A Bengoechea
- Centre for Experimental Medicine, Queens University Belfast, Belfast, UK
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology, University of Helsinki, Finland.,Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
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35
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Colameco S, Elliot MA. Non-coding RNAs as antibiotic targets. Biochem Pharmacol 2016; 133:29-42. [PMID: 28012959 DOI: 10.1016/j.bcp.2016.12.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
Antibiotics inhibit a wide range of essential processes in the bacterial cell, including replication, transcription, translation and cell wall synthesis. In many instances, these antibiotics exert their effects through association with non-coding RNAs. This review highlights many classical antibiotic targets (e.g. rRNAs and the ribosome), explores a number of emerging targets (e.g. tRNAs, RNase P, riboswitches and small RNAs), and discusses the future directions and challenges associated with non-coding RNAs as antibiotic targets.
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Affiliation(s)
- Savannah Colameco
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Marie A Elliot
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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36
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The Small RNA GcvB Promotes Mutagenic Break Repair by Opposing the Membrane Stress Response. J Bacteriol 2016; 198:3296-3308. [PMID: 27698081 PMCID: PMC5116933 DOI: 10.1128/jb.00555-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/22/2016] [Indexed: 12/19/2022] Open
Abstract
Microbes and human cells possess mechanisms of mutagenesis activated by stress responses. Stress-inducible mutagenesis mechanisms may provide important models for mutagenesis that drives host-pathogen interactions, antibiotic resistance, and possibly much of evolution generally. In Escherichia coli, repair of DNA double-strand breaks is switched to a mutagenic mode, using error-prone DNA polymerases, via the SOS DNA damage and general (σS) stress responses. We investigated small RNA (sRNA) clients of Hfq, an RNA chaperone that promotes mutagenic break repair (MBR), and found that GcvB promotes MBR by allowing a robust σS response, achieved via opposing the membrane stress (σE) response. Cells that lack gcvB were MBR deficient and displayed reduced σS-dependent transcription but not reduced σS protein levels. The defects in MBR and σS-dependent transcription in ΔgcvB cells were alleviated by artificially increasing σS levels, implying that GcvB promotes mutagenesis by allowing a normal σS response. ΔgcvB cells were highly induced for the σE response, and blocking σE response induction restored both mutagenesis and σS-promoted transcription. We suggest that GcvB may promote the σS response and mutagenesis indirectly, by promoting membrane integrity, which keeps σE levels lower. At high levels, σE might outcompete σS for binding RNA polymerase and so reduce the σS response and mutagenesis. The data show the delicate balance of stress response modulation of mutagenesis. IMPORTANCE Mutagenesis mechanisms upregulated by stress responses promote de novo antibiotic resistance and cross-resistance in bacteria, antifungal drug resistance in yeasts, and genome instability in cancer cells under hypoxic stress. This paper describes the role of a small RNA (sRNA) in promoting a stress-inducible-mutagenesis mechanism, mutagenic DNA break repair in Escherichia coli The roles of many sRNAs in E. coli remain unknown. This study shows that ΔgcvB cells, which lack the GcvB sRNA, display a hyperactivated membrane stress response and reduced general stress response, possibly because of sigma factor competition for RNA polymerase. This results in a mutagenic break repair defect. The data illuminate a function of GcvB sRNA in opposing the membrane stress response, and thus indirectly upregulating mutagenesis.
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Fröhlich KS, Haneke K, Papenfort K, Vogel J. The target spectrum of SdsR small RNA in Salmonella. Nucleic Acids Res 2016; 44:10406-10422. [PMID: 27407104 PMCID: PMC5137417 DOI: 10.1093/nar/gkw632] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/11/2016] [Accepted: 06/29/2016] [Indexed: 12/28/2022] Open
Abstract
Model enteric bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some sRNAs are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. One of these ‘core sRNAs’ of largely unknown function is the abundant ∼100-nucleotide SdsR sRNA which is transcribed by the general stress σ-factor, σS and accumulates in stationary phase. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, sdsR genes are present in almost all enterobacterial genomes, suggesting that additional, conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 20 previously unknown candidate targets of SdsR which include mRNAs coding for physiologically important regulators such as the carbon utilization regulator, CRP, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. Processing of SdsR by RNase E results in two cellular SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the new SdsR targets present valuable leads to determine sRNA functions in resting bacteria.
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Affiliation(s)
- Kathrin S Fröhlich
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany
| | - Katharina Haneke
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
| | - Kai Papenfort
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
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38
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Fu Y, Chen L, Zhang W. Regulatory mechanisms related to biofuel tolerance in producing microbes. J Appl Microbiol 2016; 121:320-32. [PMID: 27123568 DOI: 10.1111/jam.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/20/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Y. Fu
- Laboratory of Synthetic Microbiology; School of Chemical Engineering & Technology; Tianjin University; Tianjin China
- Key Laboratory of Systems Bioengineering (Ministry of Education); Tianjin University; Tianjin China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - L. Chen
- Laboratory of Synthetic Microbiology; School of Chemical Engineering & Technology; Tianjin University; Tianjin China
- Key Laboratory of Systems Bioengineering (Ministry of Education); Tianjin University; Tianjin China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - W. Zhang
- Laboratory of Synthetic Microbiology; School of Chemical Engineering & Technology; Tianjin University; Tianjin China
- Key Laboratory of Systems Bioengineering (Ministry of Education); Tianjin University; Tianjin China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
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39
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Peccarelli M, Scott TD, Steele M, Kebaara BW. mRNAs involved in copper homeostasis are regulated by the nonsense-mediated mRNA decay pathway depending on environmental conditions. Fungal Genet Biol 2016; 86:81-90. [DOI: 10.1016/j.fgb.2015.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 12/20/2022]
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40
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Feliciano JR, Grilo AM, Guerreiro SI, Sousa SA, Leitão JH. Hfq: a multifaceted RNA chaperone involved in virulence. Future Microbiol 2015; 11:137-51. [PMID: 26685037 DOI: 10.2217/fmb.15.128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hfq has emerged in recent years as a master regulator of gene expression in bacteria, mainly due to its ability to mediate the interaction of small noncoding RNAs with their mRNA targets, including those related to virulence in Gram-negative bacteria. In this work, we review current knowledge on the involvement of Hfq in the regulation of virulence traits related to secretion systems, alternative sigma factors, outer membrane proteins, polysaccharides and iron metabolism. Recent data from transcriptomics and proteomics studies performed for major pathogens are included. We also summarize and correlate current knowledge on how Hfq protein impacts pathogenicity of bacterial pathogens.
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Affiliation(s)
- Joana R Feliciano
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | | | - Soraia I Guerreiro
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sílvia A Sousa
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Jorge H Leitão
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal.,Departamento de Bioengenharia, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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41
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Arce-Rodríguez A, Calles B, Nikel PI, de Lorenzo V. The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype ofPseudomonas putida. Environ Microbiol 2015; 18:3309-3326. [DOI: 10.1111/1462-2920.13052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Alejandro Arce-Rodríguez
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Belén Calles
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Pablo I. Nikel
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
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42
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van Nues RW, Castro-Roa D, Yuzenkova Y, Zenkin N. Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate. Nucleic Acids Res 2015; 44:2577-92. [PMID: 26609136 PMCID: PMC4824073 DOI: 10.1093/nar/gkv1302] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/08/2015] [Indexed: 11/23/2022] Open
Abstract
Coupled transcription and translation in bacteria are tightly regulated. Some small RNAs (sRNAs) control aspects of this coupling by modifying ribosome access or inducing degradation of the message. Here, we show that sRNA IsrA (IS61 or McaS) specifically associates with core enzyme of RNAP in vivo and in vitro, independently of σ factor and away from the main nucleic-acids-binding channel of RNAP. We also show that, in the cells, IsrA exists as ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase. Our findings suggest that IsrA might be directly involved in transcription or can participate in regulation of gene expression by delivering proteins associated with it to target mRNAs through its interactions with transcribing RNAP and through regions of sequence-complementarity with the target. In this eukaryotic-like model only in the context of a complex with its target, IsrA and its associated proteins become active. In this manner, in the form of sRNPs, bacterial sRNAs could regulate a number of targets with various outcomes, depending on the set of associated proteins.
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Affiliation(s)
- Rob W van Nues
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Daniel Castro-Roa
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
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43
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Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing. J Bacteriol 2015; 198:427-35. [PMID: 26553849 DOI: 10.1128/jb.00711-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Recent breakthroughs in next-generation sequencing technologies have led to the identification of small noncoding RNAs (sRNAs) as a new important class of regulatory molecules. In prokaryotes, sRNAs are often bound to the chaperone protein Hfq, which allows them to interact with their partner mRNA(s). We screened the genome of the zoonotic and human pathogen Brucella suis 1330 for the presence of this class of RNAs. We designed a coimmunoprecipitation strategy that relies on the use of Hfq as a bait to enrich the sample with sRNAs and eventually their target mRNAs. By deep sequencing analysis of the Hfq-bound transcripts, we identified a number of mRNAs and 33 sRNA candidates associated with Hfq. The expression of 10 sRNAs in the early stationary growth phase was experimentally confirmed by Northern blotting and/or reverse transcriptase PCR. IMPORTANCE Brucella organisms are facultative intracellular pathogens that use stealth strategies to avoid host defenses. Adaptation to the host environment requires tight control of gene expression. Recently, small noncoding RNAs (sRNAs) and the sRNA chaperone Hfq have been shown to play a role in the fine-tuning of gene expression. Here we have used RNA sequencing to identify RNAs associated with the B. suis Hfq protein. We have identified a novel list of 33 sRNAs and 62 Hfq-associated mRNAs for future studies aiming to understand the intracellular lifestyle of this pathogen.
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44
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Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs. BIOMED RESEARCH INTERNATIONAL 2015; 2015:153561. [PMID: 26618164 PMCID: PMC4651636 DOI: 10.1155/2015/153561] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 01/31/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is asymmetric due to the presence of lipopolysaccharide (LPS) facing the outer leaflet of the OM and phospholipids facing the periplasmic side. LPS is essential for bacterial viability, since it provides a permeability barrier and is a major virulence determinant in pathogenic bacteria. In Escherichia coli, several steps of LPS biosynthesis and assembly are regulated by the RpoE sigma factor and stress responsive two-component systems as well as dedicated small RNAs. LPS composition is highly heterogeneous and dynamically altered upon stress and other challenges in the environment because of the transcriptional activation of RpoE regulon members and posttranslational control by RpoE-regulated Hfq-dependent RybB and MicA sRNAs. The PhoP/Q two-component system further regulates Kdo2-lipid A modification via MgrR sRNA. Some of these structural alterations are critical for antibiotic resistance, OM integrity, virulence, survival in host, and adaptation to specific environmental niches. The heterogeneity arises following the incorporation of nonstoichiometric modifications in the lipid A part and alterations in the composition of inner and outer core of LPS. The biosynthesis of LPS and phospholipids is tightly coupled. This requires the availability of metabolic precursors, whose accumulation is controlled by sRNAs like SlrA, GlmZ, and GlmY.
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45
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Mechanism to control the cell lysis and the cell survival strategy in stationary phase under heat stress. SPRINGERPLUS 2015; 4:599. [PMID: 26543734 PMCID: PMC4627973 DOI: 10.1186/s40064-015-1415-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 10/07/2015] [Indexed: 11/10/2022]
Abstract
An array of stress signals triggering the bacterial cellular stress response is well known in Escherichia coli and other bacteria. Heat stress is usually sensed through the misfolded outer membrane porin (OMP) precursors in the periplasm, resulting in the activation of σ(E) (encoded by rpoE), which binds to RNA polymerase to start the transcription of genes required for responding against the heat stress signal. At the elevated temperatures, σ(E) also serves as the transcription factor for σ(H) (the main heat shock sigma factor, encoded by rpoH), which is involved in the expression of several genes whose products deal with the cytoplasmic unfolded proteins. Besides, oxidative stress in form of the reactive oxygen species (ROS) that accumulate due to heat stress, has been found to give rise to viable but non-culturable (VBNC) cells at the early stationary phase, which is in turn lysed by the σ(E)-dependent process. Such lysis of the defective cells may generate nutrients for the remaining population to survive with the capacity of formation of colony forming units (CFUs). σ(H) is also known to regulate the transcription of the major heat shock proteins (HSPs) required for heat shock response (HSR) resulting in cellular survival. Present review concentrated on the cellular survival against heat stress employing the harmonized impact of σ(E) and σ(H) regulons and the HSPs as well as their inter connectivity towards the maintenance of cellular survival.
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46
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Abstract
DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB), and III (dnaQ/mutD); Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG), and X (exoX); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.
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47
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Matilla MA, Leeper FJ, Salmond GPC. Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 2015; 17:2993-3008. [PMID: 25753587 PMCID: PMC4552970 DOI: 10.1111/1462-2920.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 02/02/2023]
Abstract
Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.
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Affiliation(s)
- Miguel A Matilla
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Finian J Leeper
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW, UK
| | - George P C Salmond
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK,*For correspondence. E-mail ; Tel. +44 (0)1223 333650; Fax +44 (0)1223 766108
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48
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Vakulskas CA, Potts AH, Babitzke P, Ahmer BMM, Romeo T. Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol Mol Biol Rev 2015; 79:193-224. [PMID: 25833324 PMCID: PMC4394879 DOI: 10.1128/mmbr.00052-14] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. This ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. It is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. Studies over the past 2 decades have established that the CsrA/RsmA proteins, global regulators of posttranscriptional gene expression, play important roles in the expression of virulence factors of numerous proteobacterial pathogens. To accomplish these tasks, CsrA binds to the 5' untranslated and/or early coding regions of mRNAs and alters translation, mRNA turnover, and/or transcript elongation. CsrA activity is regulated by noncoding small RNAs (sRNAs) that contain multiple CsrA binding sites, which permit them to sequester multiple CsrA homodimers away from mRNA targets. Environmental cues sensed by two-component signal transduction systems and other regulatory factors govern the expression of the CsrA-binding sRNAs and, ultimately, the effects of CsrA on secretion systems, surface molecules and biofilm formation, quorum sensing, motility, pigmentation, siderophore production, and phagocytic avoidance. This review presents the workings of the Csr system, the paradigm shift that it generated for understanding posttranscriptional regulation, and its roles in virulence networks of animal and plant pathogens.
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Affiliation(s)
- Christopher A Vakulskas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Anastasia H Potts
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Tony Romeo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
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49
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Papenfort K, Vanderpool CK. Target activation by regulatory RNAs in bacteria. FEMS Microbiol Rev 2015; 39:362-78. [PMID: 25934124 DOI: 10.1093/femsre/fuv016] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5(') untranslated region (UTR), the coding sequence or the 3(') UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA Department of Biology I, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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50
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Rochat T, Delumeau O, Figueroa-Bossi N, Noirot P, Bossi L, Dervyn E, Bouloc P. Tracking the Elusive Function of Bacillus subtilis Hfq. PLoS One 2015; 10:e0124977. [PMID: 25915524 PMCID: PMC4410918 DOI: 10.1371/journal.pone.0124977] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/20/2015] [Indexed: 11/25/2022] Open
Abstract
RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species including Escherichia coli, Salmonella enterica and Vibrio cholera. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive and somewhat controversial. In the present study, we have further addressed this point by comparing growth phenotypes and transcription profiles between wild-type and an hfq deletion mutant of the model Gram-positive bacterium, Bacillus subtilis. The absence of Hfq had no significant consequences on growth rates under nearly two thousand metabolic conditions and chemical treatments. The only phenotypic difference was a survival defect of B. subtilis hfq mutant in rich medium in stationary phase. Transcriptomic analysis correlated this phenotype with a change in the levels of nearly one hundred transcripts. Albeit a significant fraction of these RNAs (36%) encoded sporulation-related functions, analyses in a strain unable to sporulate ruled out sporulation per se as the basis of the hfq mutant’s stationary phase fitness defect. When expressed in Salmonella, B. subtilis hfq complemented the sharp loss of viability of a degP hfq double mutant, attenuating the chronic σE-activated phenotype of this strain. However, B. subtilis hfq did not complement other regulatory deficiencies resulting from loss of Hfq-dependent small RNA activity in Salmonella indicating a limited functional overlap between Salmonella and B. subtilis Hfqs. Overall, this study confirmed that, despite structural similarities with other Hfq proteins, B. subtilis Hfq does not play a central role in post-transcriptional regulation but might have a more specialized function connected with stationary phase physiology. This would account for the high degree of conservation of Hfq proteins in all 17 B. subtilis strains whose genomes have been sequenced.
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Affiliation(s)
- Tatiana Rochat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91405, Orsay, France; INRA, UR892, Virologie et Immunologie Moléculaires, F-78352, Jouy-en-Josas, France
| | - Olivier Delumeau
- INRA, UMR1319 Micalis, F-78350, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350, Jouy-en-Josas, France
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91190, Gif-sur-Yvette, France
| | - Philippe Noirot
- INRA, UMR1319 Micalis, F-78350, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350, Jouy-en-Josas, France
| | - Lionello Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91190, Gif-sur-Yvette, France
| | - Etienne Dervyn
- INRA, UMR1319 Micalis, F-78350, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350, Jouy-en-Josas, France
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91405, Orsay, France
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