1
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Jain PM, Nellikka A, Kammara R. Understanding bacteriocin heterologous expression: A review. Int J Biol Macromol 2024; 277:133916. [PMID: 39033897 DOI: 10.1016/j.ijbiomac.2024.133916] [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: 11/29/2023] [Revised: 07/12/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024]
Abstract
Bacteriocins are a diverse group of ribosomally synthesised antimicrobial peptides/proteins that play an important role in self-defence. They are widely used as bio-preservatives and effective substitutes for disease eradication. They can be used in conjunction with or as an alternative to antibiotics to minimize the risk of resistance development. There are remarkably few reports indicating resistance to bacteriocins. Although there are many research reports that emphasise heterologous expression of bacteriocin, there are no convincing reports on the significant role that intrinsic and extrinsic factors play in overexpression. A coordinated and cooperative expression system works in concert with multiple genetic elements encoding native proteins, immunoproteins, exporters, transporters and enzymes involved in the post-translational modification of bacteriocins. The simplest way could be to utilise the existing E. coli expression system, which is conventional, widely used for heterologous expression and has been further extended for bacteriocin expression. In this article, we will review the intrinsic and extrinsic factors, advantages, disadvantages and major problems associated with bacteriocin overexpression in E. coli. Finally, we recommend the most effective strategies as well as numerous bacteriocin expression systems from E. coli, Lactococcus, Kluveromyces lactis, Saccharomyces cerevisiae and Pichia pastoris for their suitability for successful overexpression.
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Affiliation(s)
- Priyanshi M Jain
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Anagha Nellikka
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Rajagopal Kammara
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India.
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2
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Hashemzaei M, Ghoshoon MB, Jamshidi M, Moradbeygi F, Hashemzehi A. A Review on Romiplostim Mechanism of Action and the Expressive Approach in E. coli. Recent Pat Biotechnol 2024; 18:95-109. [PMID: 38282441 DOI: 10.2174/1872208317666230503094451] [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: 11/01/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 01/30/2024]
Abstract
Immune thrombocytopenic purpura (ITP) is an autoimmune disorder determined by immune-mediated platelet demolition and reduction of platelet production. Romiplostim is a new thrombopoiesis motivating peptibody that binds and stimulates the human thrombopoietin receptor the patent of which was registered in 2008. It is used to treat thrombocytopenia in patients with chronic immune thrombocytopenic purpura. Romiplostim is a 60 kDa peptibody designed to inhibit cross-reacting immune responses. It consists of four high-affinity TPO-receptor binding domains for the Mpl receptor and one human IgG1 Fc domain. Escherichia coli is a good host for the fabrication of recombinant proteins such as romiplostim. The expression of a gene intended in E. coli is dependent on many factors such as a protein's inherent ability to fold, mRNA's secondary structure, its solubility, its toxicity preferential codon use, and its need for post-translational modification (PTM). This review focuses on the structure, function, mechanism of action, and expressive approach to romiplostim in E. coli.
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Affiliation(s)
- Masoud Hashemzaei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mehrnaz Jamshidi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Moradbeygi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Hashemzehi
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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3
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Bertels F, Rainey PB. Ancient Darwinian replicators nested within eubacterial genomes. Bioessays 2023; 45:e2200085. [PMID: 36456469 DOI: 10.1002/bies.202200085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception - a class of MGE termed REPIN. REPINs are non-autonomous MGEs whose duplication depends on non-jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.
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Affiliation(s)
- Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
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4
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Rashad S, Byrne SR, Saigusa D, Xiang J, Zhou Y, Zhang L, Begley TJ, Tominaga T, Niizuma K. Codon Usage and mRNA Stability are Translational Determinants of Cellular Response to Canonical Ferroptosis Inducers. Neuroscience 2022; 501:103-130. [PMID: 35987429 PMCID: PMC10023133 DOI: 10.1016/j.neuroscience.2022.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022]
Abstract
Ferroptosis is a non-apoptotic cell death mechanism characterized by the generation of lipid peroxides. While many effectors in the ferroptosis pathway have been mapped, its epitranscriptional regulation is not yet fully understood. Ferroptosis can be induced via system xCT inhibition (Class I) or GPX4 inhibition (Class II). Previous works have revealed important differences in cellular response to different ferroptosis inducers. Importantly, blocking mRNA transcription or translation appears to protect cells against Class I ferroptosis inducing agents but not Class II. In this work, we examined the impact of blocking transcription (via Actinomycin D) or translation (via Cycloheximide) on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. Blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. Cycloheximide led to increased levels of GSH alone or when co-treated with Erastin via the activation of the reverse transsulfuration pathway. RNA sequencing analysis revealed early activation of a strong alternative splice program before observed changes in transcription. mRNA stability analysis revealed divergent mRNA stability changes in cellular response to Erastin or RSL3. Importantly, codon optimality biases were drastically different in either condition. Our data also implicated translation repression and rate as an important determinant of the cellular response to ferroptosis inducers. Given that mRNA stability and codon usage can be influenced via the tRNA epitranscriptome, we evaluated the role of a tRNA modifying enzyme in ferroptosis stress response. Alkbh1, a tRNA demethylase, led to translation repression and increased the resistance to Erastin but made cells more sensitive to RSL3.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan; Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Shane R Byrne
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan; Department of Integrative Genomics, Tohoku University Medical Megabank Organization, Sendai, Japan
| | - Jingdong Xiang
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yuan Zhou
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Liyin Zhang
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Thomas J Begley
- The RNA Institute, University at Albany, Albany, NY, USA; Department of Biological Sciences, University at Albany, Albany, NY, USA; RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY, USA
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan; Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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5
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Prashar A, Kinkar OU, Hadapad AB, Makde RD, Hire RS. Purification, characterization and toxicity assessment of PirAB toxins from Photorhabdus akhurstii subsp. akhurstii K-1. J Invertebr Pathol 2022; 194:107829. [PMID: 36167186 DOI: 10.1016/j.jip.2022.107829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022]
Abstract
Photorhabdus insect related proteins A & B (PirA, PirB) from Photorhabdus and Xenorhabdus bacteria exhibit both oral and injectable toxicity against lepidopteran and dipteran insect pest. The pirA, pirAt (encoding 6 N-terminal truncated PirA), pirB genes, pirA-pirB (with ERIC sequences), pirA-pirB-mERIC (modified pirA-pirB with mutated ERIC sequences) and polycistronic-pirAB were cloned and expressed in Escherichia coli. However, PirA protein was expressed in insoluble form and therefore the pirA gene was modified to produce PirAt. Moreover, pirA-pirB-mERIC, polycistronic-pirAB and co-transformed pirA/pirB genes were not expressed in the studied prokaryotic expression systems. None of the single purified proteins or mixtures of the individually expressed and purified proteins were toxic to mosquito larvae of Aedes aegypti and Culex quinquefasciatus. However, PirA-PirB protein mixtures purified from pirA-pirB operon plasmid were toxic to A. aegypti and C. quinquefasciatus larvae with LC50 values of 991 and 614 ng/ml, respectively. The presence of ERIC sequences between the two orfs of the pirA-pirB operon could help to obtain the proteins in biologically active form. Further, results confirm that PirA-PirB proteins of P. akhurstii subsp. akhurstii K-1 are binary insecticidal toxins and ERIC sequences could play an important role in expression of Pir proteins. Reports of biophysical characterization of individually purified PirAt, PirB and expressed PirA-PirB toxin mixture could provide the structural insight into these proteins.
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Affiliation(s)
- Arpit Prashar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Omkar U Kinkar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India.
| | - Ashok B Hadapad
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India.
| | - Ramesh S Hire
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India.
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6
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Abstract
Detailed studies of the Gram-negative model bacterium, Escherichia coli, have demonstrated that post-transcriptional events exert important and possibly greater control over gene regulation than transcription initiation or effective translation. Thus, over the past 30 years, considerable effort has been invested in understanding the pathways of mRNA turnover in E. coli. Although it is assumed that most of the ribonucleases and accessory proteins involved in mRNA decay have been identified, our understanding of the regulation of mRNA decay is still incomplete. Furthermore, the vast majority of the studies on mRNA decay have been conducted on exponentially growing cells. Thus, the mechanism of mRNA decay as currently outlined may not accurately reflect what happens when cells find themselves under a variety of stress conditions, such as, nutrient starvation, changes in pH and temperature, as well as a host of others. While the cellular machinery for degradation is relatively constant over a wide range of conditions, intracellular levels of specific ribonucleases can vary depending on the growth conditions. Substrate competition will also modulate ribonucleolytic activity. Post-transcriptional modifications of transcripts by polyadenylating enzymes may favor a specific ribonuclease activity. Interactions with small regulatory RNAs and RNA binding proteins add additional complexities to mRNA functionality and stability. Since many of the ribonucleases are found at the inner membrane, the physical location of a transcript may help determine its half-life. Here we discuss the properties and role of the enzymes involved in mRNA decay as well as the multiple factors that may affect mRNA decay under various in vivo conditions.
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Affiliation(s)
| | - Sidney R. Kushner
- Department of Genetics, University of Georgia, Athens GA 30602,Department of Microbiology, University of Georgia, Athens GA 30602,To whom correspondence should be addressed:
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7
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Jeon HJ, Lee Y, N MPA, Wang X, Chattoraj DK, Lim HM. sRNA-mediated regulation of gal mRNA in E. coli: Involvement of transcript cleavage by RNase E together with Rho-dependent transcription termination. PLoS Genet 2021; 17:e1009878. [PMID: 34710092 PMCID: PMC8577784 DOI: 10.1371/journal.pgen.1009878] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/09/2021] [Accepted: 10/14/2021] [Indexed: 11/18/2022] Open
Abstract
In bacteria, small non-coding RNAs (sRNAs) bind to target mRNAs and regulate their translation and/or stability. In the polycistronic galETKM operon of Escherichia coli, binding of the Spot 42 sRNA to the operon transcript leads to the generation of galET mRNA. The mechanism of this regulation has remained unclear. We show that sRNA-mRNA base pairing at the beginning of the galK gene leads to both transcription termination and transcript cleavage within galK, and generates galET mRNAs with two different 3'-OH ends. Transcription termination requires Rho, and transcript cleavage requires the endonuclease RNase E. The sRNA-mRNA base-paired segments required for generating the two galET species are different, indicating different sequence requirements for the two events. The use of two targets in an mRNA, each of which causes a different outcome, appears to be a novel mode of action for a sRNA. Considering the prevalence of potential sRNA targets at cistron junctions, the generation of new mRNA species by the mechanisms reported here might be a widespread mode of bacterial gene regulation.
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Affiliation(s)
- Heung Jin Jeon
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
- Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Yonho Lee
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Monford Paul Abishek N
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Xun Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Dhruba K. Chattoraj
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Heon M. Lim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
- * E-mail:
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8
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Park HJ, Gokhale CS, Bertels F. How sequence populations persist inside bacterial genomes. Genetics 2021; 217:6151697. [PMID: 33724360 PMCID: PMC8049555 DOI: 10.1093/genetics/iyab027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/04/2021] [Indexed: 01/04/2023] Open
Abstract
Compared to their eukaryotic counterparts, bacterial genomes are small and contain extremely tightly packed genes. Repetitive sequences are rare but not completely absent. One of the most common repeat families is REPINs. REPINs can replicate in the host genome and form populations that persist for millions of years. Here, we model the interactions of these intragenomic sequence populations with the bacterial host. We first confirm well-established results, in the presence and absence of horizontal gene transfer (hgt) sequence populations either expand until they drive the host to extinction or the sequence population gets purged from the genome. We then show that a sequence population can be stably maintained, when each individual sequence provides a benefit that decreases with increasing sequence population size. Maintaining a sequence population of stable size also requires the replication of the sequence population to be costly to the host, otherwise the sequence population size will increase indefinitely. Surprisingly, in regimes with high hgt rates, the benefit conferred by the sequence population does not have to exceed the damage it causes to its host. Our analyses provide a plausible scenario for the persistence of sequence populations in bacterial genomes. We also hypothesize a limited biologically relevant parameter range for the provided benefit, which can be tested in future experiments.
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Affiliation(s)
- Hye Jin Park
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.,Asia Pacific Center for Theoretical Physics, Pohang, 37673, Korea.,Department of Physics, POSTECH, Pohang, 37673, Korea
| | - Chaitanya S Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Frederic Bertels
- Research Group for Microbial Molecular Evolution, Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
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9
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The evolution and history of gene editing technologies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:1-62. [PMID: 33685594 DOI: 10.1016/bs.pmbts.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Scientific enquiry must be the driving force of research. This sentiment is manifested as the profound impact gene editing technologies are having in our current world. There exist three main gene editing technologies today: Zinc Finger Nucleases, TALENs and the CRISPR-Cas system. When these systems were being uncovered, none of the scientists set out to design tools to engineer genomes. They were simply trying to understand the mechanisms existing in nature. If it was not for this simple sense of wonder, we probably would not have these breakthrough technologies. In this chapter, we will discuss the history, applications and ethical issues surrounding these technologies, focusing on the now predominant CRISPR-Cas technology. Gene editing technologies, as we know them now, are poised to have an overwhelming impact on our world. However, it is impossible to predict the route they will take in the future or to comprehend the full impact of its repercussions.
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10
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Vargas-Blanco DA, Shell SS. Regulation of mRNA Stability During Bacterial Stress Responses. Front Microbiol 2020; 11:2111. [PMID: 33013770 PMCID: PMC7509114 DOI: 10.3389/fmicb.2020.02111] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5' ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.
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Affiliation(s)
- Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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11
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Kondo T, Yumura S. Strategies for enhancing gene expression in Escherichia coli. Appl Microbiol Biotechnol 2020; 104:3825-3834. [PMID: 32125482 DOI: 10.1007/s00253-020-10430-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023]
Abstract
Regulation of gene expression is fundamental for cellular function. Upon manipulation of the mechanism of gene expression in Escherichia coli, various bioproducts have been developed that are valuable industrially and medically in the last four decades. To efficiently produce bioproducts, numerous molecular tools are used for enhancing expression at the transcriptional and translational levels. Our recent discovery identified a new approach that enhances the gene expression in E. coli using the gene sequence of the eukaryote, Dictyostelium discoideum. In this review, we highlight the current molecular strategies used for high-level gene expression techniques commonly utilized in basic and applied microbiology.
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Affiliation(s)
- Tomo Kondo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan.
| | - Shigehiko Yumura
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan
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12
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Dar D, Sorek R. High-resolution RNA 3'-ends mapping of bacterial Rho-dependent transcripts. Nucleic Acids Res 2019; 46:6797-6805. [PMID: 29669055 PMCID: PMC6061677 DOI: 10.1093/nar/gky274] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/04/2018] [Indexed: 01/20/2023] Open
Abstract
Transcription termination in bacteria can occur either via Rho-dependent or independent (intrinsic) mechanisms. Intrinsic terminators are composed of a stem-loop RNA structure followed by a uridine stretch and are known to terminate in a precise manner. In contrast, Rho-dependent terminators have more loosely defined characteristics and are thought to terminate in a diffuse manner. While transcripts ending in an intrinsic terminator are protected from 3′-5′ exonuclease digestion due to the stem-loop structure of the terminator, it remains unclear what protects Rho-dependent transcripts from being degraded. In this study, we mapped the exact steady-state RNA 3′ ends of hundreds of Escherichia coli genes terminated either by Rho-dependent or independent mechanisms. We found that transcripts generated from Rho-dependent termination have precise 3′-ends at steady state. These termini were localized immediately downstream of energetically stable stem-loop structures, which were not followed by uridine rich sequences. We provide evidence that these structures protect Rho-dependent transcripts from 3′-5′ exonucleases such as PNPase and RNase II, and present data localizing the Rho-utilization (rut) sites immediately downstream of these protective structures. This study represents the first extensive in-vivo map of exact RNA 3′-ends of Rho-dependent transcripts in E. coli.
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Affiliation(s)
- Daniel Dar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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13
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Hajnsdorf E, Kaberdin VR. RNA polyadenylation and its consequences in prokaryotes. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0166. [PMID: 30397102 DOI: 10.1098/rstb.2018.0166] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2018] [Indexed: 11/12/2022] Open
Abstract
Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in Escherichia coli more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that E. coli poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin-antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Eliane Hajnsdorf
- CNRS UMR8261 associated with University Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain .,IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain.,Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620 Plentzia, Spain
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14
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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15
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Ishino Y, Krupovic M, Forterre P. History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology. J Bacteriol 2018; 200:e00580-17. [PMID: 29358495 PMCID: PMC5847661 DOI: 10.1128/jb.00580-17] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in the Escherichia coli genome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparative genomics, structural biology, and advanced biochemistry could then work hand in hand, not only culminating in the explosion of genome editing tools based on CRISPR-Cas9 and other class II CRISPR-Cas systems but also providing insights into the origin and evolution of this system from mobile genetic elements denoted casposons. To celebrate the 30th anniversary of the discovery of CRISPR, this minireview briefly discusses the fascinating history of CRISPR-Cas systems, from the original observation of an enigmatic sequence in E. coli to genome editing in humans.
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Affiliation(s)
- Yoshizumi Ishino
- Unité de Biologie Moléculaire du Gène Chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Mart Krupovic
- Unité de Biologie Moléculaire du Gène Chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Patrick Forterre
- Unité de Biologie Moléculaire du Gène Chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
- Institute of Integrative Cellular Biology, Université Paris Sud, Orsay, France
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Regulatory Elements Located in the Upstream Region of the Rhizobium leguminosarum rosR Global Regulator Are Essential for Its Transcription and mRNA Stability. Genes (Basel) 2017; 8:genes8120388. [PMID: 29244767 PMCID: PMC5748706 DOI: 10.3390/genes8120388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/24/2017] [Accepted: 12/07/2017] [Indexed: 11/16/2022] Open
Abstract
Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a symbiotic relationship with clover (Trifolium spp.). Previously, the rosR gene, encoding a global regulatory protein involved in motility, synthesis of cell-surface components, and other cellular processes was identified and characterized in this bacterium. This gene possesses a long upstream region that contains several regulatory motifs, including inverted repeats (IRs) of different lengths. So far, the role of these motifs in the regulation of rosR transcription has not been elucidated in detail. In this study, we performed a functional analysis of these motifs using a set of transcriptional rosR-lacZ fusions that contain mutations in these regions. The levels of rosR transcription for different mutant variants were evaluated in R. leguminosarum using both quantitative real-time PCR and β-galactosidase activity assays. Moreover, the stability of wild type rosR transcripts and those with mutations in the regulatory motifs was determined using an RNA decay assay and plasmids with mutations in different IRs located in the 5′-untranslated region of the gene. The results show that transcription of rosR undergoes complex regulation, in which several regulatory elements located in the upstream region and some regulatory proteins are engaged. These include an upstream regulatory element, an extension of the -10 element containing three nucleotides TGn (TGn-extended -10 element), several IRs, and PraR repressor related to quorum sensing.
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17
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Bertels F, Gallie J, Rainey PB. Identification and Characterization of Domesticated Bacterial Transposases. Genome Biol Evol 2017; 9:2110-2121. [PMID: 28910967 PMCID: PMC5581495 DOI: 10.1093/gbe/evx146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2017] [Indexed: 12/26/2022] Open
Abstract
Selfish genetic elements, such as insertion sequences and transposons are found in most genomes. Transposons are usually identifiable by their high copy number within genomes. In contrast, REP-associated tyrosine transposases (RAYTs), a recently described class of bacterial transposase, are typically present at just one copy per genome. This suggests that RAYTs no longer copy themselves and thus they no longer function as a typical transposase. Motivated by this possibility we interrogated thousands of fully sequenced bacterial genomes in order to determine patterns of RAYT diversity, their distribution across chromosomes and accessory elements, and rate of duplication. RAYTs encompass exceptional diversity and are divisible into at least five distinct groups. They possess features more similar to housekeeping genes than insertion sequences, are predominantly vertically transmitted and have persisted through evolutionary time to the point where they are now found in 24% of all species for which at least one fully sequenced genome is available. Overall, the genomic distribution of RAYTs suggests that they have been coopted by host genomes to perform a function that benefits the host cell.
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Affiliation(s)
- Frederic Bertels
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jenna Gallie
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Laboratoire de Génétique de l'Evolution, Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), PSL Research University, Paris, France
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18
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Gupta A, Venkataraman B, Vasudevan M, Gopinath Bankar K. Co-expression network analysis of toxin-antitoxin loci in Mycobacterium tuberculosis reveals key modulators of cellular stress. Sci Rep 2017; 7:5868. [PMID: 28724903 PMCID: PMC5517426 DOI: 10.1038/s41598-017-06003-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 06/07/2017] [Indexed: 11/09/2022] Open
Abstract
Research on toxin-antitoxin loci (TA loci) is gaining impetus due to their ubiquitous presence in bacterial genomes and their observed roles in stress survival, persistence and drug tolerance. The present study investigates the expression profile of all the seventy-nine TA loci found in Mycobacterium tuberculosis. The bacterium was subjected to multiple stress conditions to identify key players of cellular stress response and elucidate a TA-coexpression network. This study provides direct experimental evidence for transcriptional activation of each of the seventy-nine TA loci following mycobacterial exposure to growth-limiting environments clearly establishing TA loci as stress-responsive modules in M. tuberculosis. TA locus activation was found to be stress-specific with multiple loci activated in a duration-based response to a particular stress. Conditions resulting in arrest of cellular translation led to greater up-regulation of TA genes suggesting that TA loci have a primary role in arresting translation in the cell. Our study identifed higBA2 and vapBC46 as key loci that were activated in all the conditions tested. Besides, relBE1, higBA3, vapBC35, vapBC22 and higBA1 were also upregulated in multpile stresses. Certain TA modules exhibited co-activation across multiple conditions suggestive of a common regulatory mechanism.
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Affiliation(s)
- Amita Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,Department of Biochemistry and Centre for Innovation in Infectious Diseases Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, 110021, India.
| | - Balaji Venkataraman
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
| | - Kiran Gopinath Bankar
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
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19
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Transcriptional and post-transcriptional regulation of pst2 operon expression in Vibrio cholerae O1. INFECTION GENETICS AND EVOLUTION 2017; 51:10-16. [DOI: 10.1016/j.meegid.2017.02.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 11/23/2022]
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Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics. Appl Environ Microbiol 2017; 83:AEM.00289-17. [PMID: 28363966 DOI: 10.1128/aem.00289-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/24/2017] [Indexed: 02/05/2023] Open
Abstract
Increasing the resistance of plant-fermenting bacteria to lignocellulosic inhibitors is useful to understand microbial adaptation and to develop candidate strains for consolidated bioprocessing. Here, we study and improve inhibitor resistance in Clostridium phytofermentans (also called Lachnoclostridium phytofermentans), a model anaerobe that ferments lignocellulosic biomass. We survey the resistance of this bacterium to a panel of biomass inhibitors and then evolve strains that grow in increasing concentrations of the lignin phenolic, ferulic acid, by automated, long-term growth selection in an anaerobic GM3 automat. Ultimately, strains resist multiple inhibitors and grow robustly at the solubility limit of ferulate while retaining the ability to ferment cellulose. We analyze genome-wide transcription patterns during ferulate stress and genomic variants that arose along the ferulate growth selection, revealing how cells adapt to inhibitors through changes in gene dosage and regulation, membrane fatty acid structure, and the surface layer. Collectively, this study demonstrates an automated framework for in vivo directed evolution of anaerobes and gives insight into the genetic mechanisms by which bacteria survive exposure to chemical inhibitors.IMPORTANCE Fermentation of plant biomass is a key part of carbon cycling in diverse ecosystems. Further, industrial biomass fermentation may provide a renewable alternative to fossil fuels. Plants are primarily composed of lignocellulose, a matrix of polysaccharides and polyphenolic lignin. Thus, when microorganisms degrade lignocellulose to access sugars, they also release phenolic and acidic inhibitors. Here, we study how the plant-fermenting bacterium Clostridium phytofermentans resists plant inhibitors using the lignin phenolic, ferulic acid. We examine how the cell responds to abrupt ferulate stress by measuring changes in gene expression. We evolve increasingly resistant strains by automated, long-term cultivation at progressively higher ferulate concentrations and sequence their genomes to identify mutations associated with acquired ferulate resistance. Our study develops an inhibitor-resistant bacterium that ferments cellulose and provides insights into genomic evolution to resist chemical inhibitors.
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21
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Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TBK, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Front Microbiol 2017; 8:195. [PMID: 28265262 PMCID: PMC5317091 DOI: 10.3389/fmicb.2017.00195] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 01/26/2017] [Indexed: 11/13/2022] Open
Abstract
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.
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Affiliation(s)
- Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Olga M Sigalova
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD, Australia
| | - Olga Kovaleva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Nikolai A Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | | | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Oleg N Reva
- Center for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria Pretoria, South Africa
| | - Margarita L Miroshnichenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, USA; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
| | - Mikhail S Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State UniversityMoscow, Russia; Skolkovo Institute of Science and TechnologyMoscow, Russia; Faculty of Computer Science, National Research University - Higher School of EconomicsMoscow, Russia
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22
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3'-UTR engineering to improve soluble expression and fine-tuning of activity of cascade enzymes in Escherichia coli. Sci Rep 2016; 6:29406. [PMID: 27406241 PMCID: PMC4942690 DOI: 10.1038/srep29406] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/20/2016] [Indexed: 02/06/2023] Open
Abstract
3′-Untranslated region (3′UTR) engineering was investigated to improve solubility of heterologous proteins (e.g., Baeyer-Villiger monooxygenases (BVMOs)) in Escherichia coli. Insertion of gene fragments containing putative RNase E recognition sites into the 3′UTR of the BVMO genes led to the reduction of mRNA levels in E. coli. Importantly, the amounts of soluble BVMOs were remarkably enhanced resulting in a proportional increase of in vivo catalytic activities. Notably, this increase in biocatalytic activity correlated to the number of putative RNase E endonucleolytic cleavage sites in the 3′UTR. For instance, the biotransformation activity of the BVMO BmoF1 (from Pseudomonas fluorescens DSM50106) in E. coli was linear to the number of RNase E cleavage sites in the 3′UTR. In summary, 3′UTR engineering can be used to improve the soluble expression of heterologous enzymes, thereby fine-tuning the enzyme activity in microbial cells.
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23
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Abstract
Gram-negative and gram-positive bacteria use a variety of enzymatic pathways to degrade mRNAs. Although several recent reviews have outlined these pathways, much less attention has been paid to the regulation of mRNA decay. The functional half-life of a particular mRNA, which affects how much protein is synthesized from it, is determined by a combination of multiple factors. These include, but are not necessarily limited to, (a) stability elements at either the 5' or the 3' terminus, (b) posttranscriptional modifications, (c) ribosome density on individual mRNAs, (d) small regulatory RNA (sRNA) interactions with mRNAs, (e) regulatory proteins that alter ribonuclease binding affinities, (f) the presence or absence of endonucleolytic cleavage sites, (g) control of intracellular ribonuclease levels, and (h) physical location within the cell. Changes in physiological conditions associated with environmental alterations can significantly alter the impact of these factors in the decay of a particular mRNA.
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Affiliation(s)
- Bijoy K Mohanty
- Department of Genetics, University of Georgia, Athens, Georgia 30602;
| | - Sidney R Kushner
- Department of Genetics, University of Georgia, Athens, Georgia 30602;
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24
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Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network. Appl Environ Microbiol 2015; 81:5477-85. [PMID: 26048924 DOI: 10.1128/aem.01365-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/28/2015] [Indexed: 01/16/2023] Open
Abstract
Thermotoga maritima is a hyperthermophilic anaerobe that utilizes a vast network of ABC transporters to efficiently metabolize a variety of carbon sources to produce hydrogen. For unknown reasons, this organism does not metabolize glucose as readily as it does glucose di- and polysaccharides. The leading hypothesis implicates the thermolability of glucose at the physiological temperatures at which T. maritima lives. After a 25-day laboratory evolution, phenotypes were observed with growth rates up to 1.4 times higher than and glucose utilization rates exceeding 50% those of the wild type. Genome resequencing revealed mutations in evolved cultures related to glucose-responsive ABC transporters. The native glucose ABC transporter, GluEFK, has more abundant transcripts either as a result of gene duplication-amplification or through mutations to the operator sequence regulating this operon. Conversely, BglEFGKL, a transporter of beta-glucosides, is substantially downregulated due to a nonsense mutation to the solute binding protein or due to a deletion of the upstream promoter. Analysis of the ABC2 uptake porter families for carbohydrate and peptide transport revealed that the solute binding protein, often among the transcripts detected at the highest levels, is predominantly downregulated in the evolved cultures, while the membrane-spanning domain and nucleotide binding components are less varied. Similar trends were observed in evolved strains grown on glycerol, a substrate that is not dependent on ABC transporters. Therefore, improved growth on glucose is achieved through mutations favoring GluEFK expression over BglEFGKL, and in lieu of carbon catabolite repression, the ABC transporter network is modulated to achieve improved growth fitness.
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25
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Borirak O, Rolfe MD, de Koning LJ, Hoefsloot HCJ, Bekker M, Dekker HL, Roseboom W, Green J, de Koster CG, Hellingwerf KJ. Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1269-79. [PMID: 26049081 DOI: 10.1016/j.bbapap.2015.05.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/12/2015] [Accepted: 05/28/2015] [Indexed: 10/23/2022]
Abstract
Time-series transcript- and protein-profiles were measured upon initiation of carbon catabolite repression in Escherichia coli, in order to investigate the extent of post-transcriptional control in this prototypical response. A glucose-limited chemostat culture was used as the CCR-free reference condition. Stopping the pump and simultaneously adding a pulse of glucose, that saturated the cells for at least 1h, was used to initiate the glucose response. Samples were collected and subjected to quantitative time-series analysis of both the transcriptome (using microarray analysis) and the proteome (through a combination of 15N-metabolic labeling and mass spectrometry). Changes in the transcriptome and corresponding proteome were analyzed using statistical procedures designed specifically for time-series data. By comparison of the two sets of data, a total of 96 genes were identified that are post-transcriptionally regulated. This gene list provides candidates for future in-depth investigation of the molecular mechanisms involved in post-transcriptional regulation during carbon catabolite repression in E. coli, like the involvement of small RNAs.
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Affiliation(s)
- Orawan Borirak
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Matthew D Rolfe
- Krebs Institute, Molecular Biology and Biotechnology, University of Sheffield, United Kingdom
| | - Leo J de Koning
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Huub C J Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Martijn Bekker
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Henk L Dekker
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Winfried Roseboom
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Jeffrey Green
- Krebs Institute, Molecular Biology and Biotechnology, University of Sheffield, United Kingdom
| | - Chris G de Koster
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
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RNA Degradation in Staphylococcus aureus: Diversity of Ribonucleases and Their Impact. Int J Genomics 2015; 2015:395753. [PMID: 25977913 PMCID: PMC4419217 DOI: 10.1155/2015/395753] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
The regulation of RNA decay is now widely recognized as having a central role in bacterial adaption to environmental stress. Here we present an overview on the diversity of ribonucleases (RNases) and their impact at the posttranscriptional level in the human pathogen Staphylococcus aureus. RNases in prokaryotes have been mainly studied in the two model organisms Escherichia coli and Bacillus subtilis. Based on identified RNases in these two models, putative orthologs have been identified in S. aureus. The main staphylococcal RNases involved in the processing and degradation of the bulk RNA are (i) endonucleases RNase III and RNase Y and (ii) exonucleases RNase J1/J2 and PNPase, having 5' to 3' and 3' to 5' activities, respectively. The diversity and potential roles of each RNase and of Hfq and RppH are discussed in the context of recent studies, some of which are based on next-generation sequencing technology.
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27
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Goulas T, Cuppari A, Garcia-Castellanos R, Snipas S, Glockshuber R, Arolas JL, Gomis-Rüth FX. The pCri System: a vector collection for recombinant protein expression and purification. PLoS One 2014; 9:e112643. [PMID: 25386923 PMCID: PMC4227841 DOI: 10.1371/journal.pone.0112643] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/09/2014] [Indexed: 12/11/2022] Open
Abstract
A major bottleneck in structural, biochemical and biophysical studies of proteins is the need for large amounts of pure homogenous material, which is generally obtained by recombinant overexpression. Here we introduce a vector collection, the pCri System, for cytoplasmic and periplasmic/extracellular expression of heterologous proteins that allows the simultaneous assessment of prokaryotic and eukaryotic host cells (Escherichia coli, Bacillus subtilis, and Pichia pastoris). By using a single polymerase chain reaction product, genes of interest can be directionally cloned in all vectors within four different rare restriction sites at the 5'end and multiple cloning sites at the 3'end. In this way, a number of different fusion tags but also signal peptides can be incorporated at the N- and C-terminus of proteins, facilitating their expression, solubility and subsequent detection and purification. Fusion tags can be efficiently removed by treatment with site-specific peptidases, such as tobacco etch virus proteinase, thrombin, or sentrin specific peptidase 1, which leave only a few extra residues at the N-terminus of the protein. The combination of different expression systems in concert with the cloning approach in vectors that can fuse various tags makes the pCri System a valuable tool for high throughput studies.
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Affiliation(s)
- Theodoros Goulas
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
- * E-mail: (TG); (FXGR)
| | - Anna Cuppari
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
| | - Raquel Garcia-Castellanos
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
| | - Scott Snipas
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Department of Biology, Zurich, Switzerland
| | - Joan L. Arolas
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
| | - F. Xavier Gomis-Rüth
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
- * E-mail: (TG); (FXGR)
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28
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Abstract
mRNA degradation is an important mechanism for controlling gene expression in bacterial cells. This process involves the orderly action of a battery of cellular endonucleases and exonucleases, some universal and others present only in certain species. These ribonucleases function with the assistance of ancillary enzymes that covalently modify the 5' or 3' end of RNA or unwind base-paired regions. Triggered by initiating events at either the 5' terminus or an internal site, mRNA decay occurs at diverse rates that are transcript specific and governed by RNA sequence and structure, translating ribosomes, and bound sRNAs or proteins. In response to environmental cues, bacteria are able to orchestrate widespread changes in mRNA lifetimes by modulating the concentration or specific activity of cellular ribonucleases or by unmasking the mRNA-degrading activity of cellular toxins.
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Affiliation(s)
- Monica P Hui
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016;
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29
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Communication between binding sites is required for YqjI regulation of target promoters within the yqjH-yqjI intergenic region. J Bacteriol 2014; 196:3199-207. [PMID: 24982304 DOI: 10.1128/jb.01835-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The nickel-responsive transcription factor YqjI represses its own transcription and transcription of the divergent yqjH gene, which encodes a novel ferric siderophore reductase. The intergenic region between the two promoters is complex, with multiple sequence features that may impact YqjI-dependent regulation of its two target promoters. We utilized mutagenesis and DNase I footprinting to characterize YqjI regulation of the yqjH-yqjI intergenic region. The results show that YqjI binding results in an extended footprint at the yqjI promoter (site II) compared to the yqjH promoter (site I). Mutagenesis of in vivo gene reporter constructs revealed that the two YqjI binding sites, while separated by nearly 200 bp, appear to communicate in order to provide full YqjI-dependent regulation at the two target promoters. Thus, YqjI binding at both promoters is required for full repression of either promoter, suggesting that the two YqjI binding sites cooperate to control transcription from the divergent promoters. Furthermore, internal deletions that shorten the total length of the intergenic region disrupt the ability of YqjI to regulate the yqjH promoter. Finally, mutagenesis of the repetitive extragenic palindromic (REP) elements within the yqjH-yqjI intergenic region shows that these sequences are not required for YqjI regulation. These studies provide a complex picture of novel YqjI transcriptional regulation within the yqjH-yqjI intergenic region and suggest a possible model for communication between the YqjI binding sites at each target promoter.
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Abstract
Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.
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Arraiano CM. Post-transcriptional control of gene expression: bacterial mRNA degradation. World J Microbiol Biotechnol 2014; 9:421-32. [PMID: 24420109 DOI: 10.1007/bf00328030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/1993] [Indexed: 11/30/2022]
Abstract
Many biological processes cannot be fully understood without detailed knowledge of RNA metabolism. The continuous breakdown and resynthesis of prokaryotic mRNA permit rapid production of new kinds of proteins. In this way, mRNA levels can regulate protein synthesis and cellular growth. Analysing mRNA degradation in prokaryotes has been particularly difficult because most mRNA undergo rapid exponential decay. Prokaryotic mRNAs differ in their susceptibility to degradation by endonucleases and exonucleases, possibly because of variation in their sequencing and structure. In spite of numerous studies, details of mRNA degradation are still largely unknown. This review highlights those aspects of mRNA metabolism which seem most influential in the regulation of gene expression.
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Affiliation(s)
- C M Arraiano
- Instituto de Tecnologia Quimica e Biológica (ITQB), Apt 127, 2780, Oeiras, Portugal
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Identification of critical genes for growth in olive brine by transposon mutagenesis of Lactobacillus pentosus C11. Appl Environ Microbiol 2013; 79:4568-75. [PMID: 23686273 DOI: 10.1128/aem.01159-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Olive brine represents a stressful environment due to the high NaCl concentration, presence of phenolic compounds known as antimicrobials, and low availability of nutrients. Thus, only a few strains of lactic acid bacteria (LAB) are adapted to grow in and ferment table olives. To identify the mechanisms by which these few strains are able to grow in olive brine, Lactobacillus pentosus C11, a particularly resistant strain isolated from naturally fermented table olives, was mutagenized by random transposition using the P(junc)-TpaseIS1223 system (H. Licandro-Seraut, S. Brinster, M. van de Guchte, H. Scornec, E. Maguin, P. Sansonetti, J. F. Cavin, and P. Serror, Appl. Environ. Microbiol. 78:5417-5423, 2012). A library of 6,000 mutants was generated and screened for adaptation and subsequent growth in a medium, named BSM (brine screening medium), which presents the stressful conditions encountered in olive brine. Five transposition mutants impaired in growth on BSM were identified. Transposition occurred in two open reading frames and in three transcription terminators affecting stability of transcripts. Thus, several essential genes for adaptation and growth of L. pentosus C11 in olive brine were identified.
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Rochat T, Bouloc P, Repoila F. Gene expression control by selective RNA processing and stabilization in bacteria. FEMS Microbiol Lett 2013; 344:104-13. [PMID: 23617839 DOI: 10.1111/1574-6968.12162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 11/27/2022] Open
Abstract
RNA maturation is a key event regulating genes at post-transcriptional level. In bacteria, it is employed to adjust the amounts of proteins and functional RNAs, often in response to environmental constraints. During the process of RNA maturation, enzymes and factors that would otherwise promote RNA degradation convert a labile RNA into a stable and biologically functional molecule.
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Affiliation(s)
- Tatiana Rochat
- INRA, UR892, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
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Liu L, Yang H, Shin HD, Chen RR, Li J, Du G, Chen J. How to achieve high-level expression of microbial enzymes: strategies and perspectives. Bioengineered 2013; 4:212-23. [PMID: 23686280 DOI: 10.4161/bioe.24761] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbial enzymes have been used in a large number of fields, such as chemical, agricultural and biopharmaceutical industries. The enzyme production rate and yield are the main factors to consider when choosing the appropriate expression system for the production of recombinant proteins. Recombinant enzymes have been expressed in bacteria (e.g., Escherichia coli, Bacillus and lactic acid bacteria), filamentous fungi (e.g., Aspergillus) and yeasts (e.g., Pichia pastoris). The favorable and very advantageous characteristics of these species have resulted in an increasing number of biotechnological applications. Bacterial hosts (e.g., E. coli) can be used to quickly and easily overexpress recombinant enzymes; however, bacterial systems cannot express very large proteins and proteins that require post-translational modifications. The main bacterial expression hosts, with the exception of lactic acid bacteria and filamentous fungi, can produce several toxins which are not compatible with the expression of recombinant enzymes in food and drugs. However, due to the multiplicity of the physiological impacts arising from high-level expression of genes encoding the enzymes and expression hosts, the goal of overproduction can hardly be achieved, and therefore, the yield of recombinant enzymes is limited. In this review, the recent strategies used for the high-level expression of microbial enzymes in the hosts mentioned above are summarized and the prospects are also discussed. We hope this review will contribute to the development of the enzyme-related research field.
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Affiliation(s)
- Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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Abstract
Escherichia coli contains multiple 3' to 5' RNases, of which two, RNase PH and polynucleotide phosphorylase (PNPase), use inorganic phosphate as a nucleophile to catalyze RNA cleavage. It is known that an absence of these two enzymes causes growth defects, but the basis for these defects has remained undefined. To further an understanding of the function of these enzymes, the degradation pattern of different cellular RNAs was analyzed. It was observed that an absence of both enzymes results in the appearance of novel mRNA degradation fragments. Such fragments were also observed in strains containing mutations in RNase R and PNPase, enzymes whose collective absence is known to cause an accumulation of structured RNA fragments. Additional experiments indicated that the growth defects of strains containing RNase R and PNPase mutations were exacerbated upon RNase PH removal. Taken together, these observations suggested that RNase PH could play a role in structured RNA degradation. Biochemical experiments with RNase PH demonstrated that this enzyme digests through RNA duplexes of moderate stability. In addition, mapping and sequence analysis of an mRNA degradation fragment that accumulates in the absence of the phosphorolytic enzymes revealed the presence of an extended stem-loop motif at the 3' end. Overall, these results indicate that RNase PH plays a novel role in the degradation of structured RNAs and provides a potential explanation for the growth defects caused by an absence of the phosphorolytic RNases.
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From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome. Q Rev Biophys 2011; 45:105-45. [DOI: 10.1017/s003358351100014x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AbstractThe RNA degradosome is a massive multi-enzyme assembly that occupies a nexus in RNA metabolism and post-transcriptional control of gene expression inEscherichia coliand many other bacteria. Powering RNA turnover and quality control, the degradosome serves also as a machine for processing structured RNA precursors during their maturation. The capacity to switch between destructive and processing modes involves cooperation between degradosome components and is analogous to the process of RNA surveillance in other domains of life. Recruitment of components and cellular compartmentalisation of the degradosome are mediated through small recognition domains that punctuate a natively unstructured segment within a scaffolding core. Dynamic in conformation, variable in composition and non-essential under certain laboratory conditions, the degradosome has nonetheless been maintained throughout the evolution of many bacterial species, due most likely to its diverse contributions in global cellular regulation. We describe the role of the degradosome and its components in RNA decay pathways inE. coli, and we broadly compare these pathways in other bacteria as well as archaea and eukaryotes. We discuss the modular architecture and molecular evolution of the degradosome, its roles in RNA degradation, processing and quality control surveillance, and how its activity is regulated by non-coding RNA. Parallels are drawn with analogous machinery in organisms from all life domains. Finally, we conjecture on roles of the degradosome as a regulatory hub for complex cellular processes.
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Iguchi A, Shirai H, Seto K, Ooka T, Ogura Y, Hayashi T, Osawa K, Osawa R. Wide distribution of O157-antigen biosynthesis gene clusters in Escherichia coli. PLoS One 2011; 6:e23250. [PMID: 21876740 PMCID: PMC3158064 DOI: 10.1371/journal.pone.0023250] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/12/2011] [Indexed: 11/20/2022] Open
Abstract
Most Escherichia coli O157-serogroup strains are classified as enterohemorrhagic E. coli (EHEC), which is known as an important food-borne pathogen for humans. They usually produce Shiga toxin (Stx) 1 and/or Stx2, and express H7-flagella antigen (or nonmotile). However, O157 strains that do not produce Stxs and express H antigens different from H7 are sometimes isolated from clinical and other sources. Multilocus sequence analysis revealed that these 21 O157:non-H7 strains tested in this study belong to multiple evolutionary lineages different from that of EHEC O157:H7 strains, suggesting a wide distribution of the gene set encoding the O157-antigen biosynthesis in multiple lineages. To gain insight into the gene organization and the sequence similarity of the O157-antigen biosynthesis gene clusters, we conducted genomic comparisons of the chromosomal regions (about 59 kb in each strain) covering the O-antigen gene cluster and its flanking regions between six O157:H7/non-H7 strains. Gene organization of the O157-antigen gene cluster was identical among O157:H7/non-H7 strains, but was divided into two distinct types at the nucleotide sequence level. Interestingly, distribution of the two types did not clearly follow the evolutionary lineages of the strains, suggesting that horizontal gene transfer of both types of O157-antigen gene clusters has occurred independently among E. coli strains. Additionally, detailed sequence comparison revealed that some positions of the repetitive extragenic palindromic (REP) sequences in the regions flanking the O-antigen gene clusters were coincident with possible recombination points. From these results, we conclude that the horizontal transfer of the O157-antigen gene clusters induced the emergence of multiple O157 lineages within E. coli and speculate that REP sequences may involve one of the driving forces for exchange and evolution of O-antigen loci.
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Affiliation(s)
- Atsushi Iguchi
- Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan.
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Salvail H, Massé E. Regulating iron storage and metabolism with RNA: an overview of posttranscriptional controls of intracellular iron homeostasis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:26-36. [PMID: 21793218 DOI: 10.1002/wrna.102] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Iron (Fe) is a double-edged sword for most living organisms. Although it is essential for the catalytic activity of a large number of enzymes, ferrous iron (Fe(2+) ) becomes cytotoxic in the presence of normal respiratory by-products such as H(2) O(2) . Because of this toxicity, intracellular iron concentrations ought to be regulated by elaborated homeostasis systems that, despite decades of extensive studies, have not yet revealed all of their surprising arrays of mechanistic details. Within the last few years, our understanding of iron metabolism has revealed that posttranscriptional regulation represents a major contribution to iron homeostasis in a host of organisms. While the small RNA RyhB regulates iron homeostasis in bacteria, its functional homolog protein Cth2 performs a similar task in yeasts. Recent advances in the elucidation of the mechanism of action and functions of RyhB have been made in Escherichia coli. In addition, other RyhB-like small RNAs have been identified in several bacterial species, such as Pseudomonas aeruginosa, Salmonella enterica, Vibrio cholerae, Neisseria meningitidis, and Shigella spp. These recent findings have shed light on the complexity of iron homeostasis.
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Affiliation(s)
- Hubert Salvail
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Québec, Canada
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Kristoffersen SM, Tourasse NJ, Kolstø AB, Økstad OA. Interspersed DNA repeats bcr1-bcr18 of Bacillus cereus group bacteria form three distinct groups with different evolutionary and functional patterns. Mol Biol Evol 2010; 28:963-83. [PMID: 20961964 DOI: 10.1093/molbev/msq269] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many short (<400 bp) interspersed sequence repeats exist in bacteria, yet little is known about their origins, mode of generation, or possible function. Here, we present a comprehensive analysis of 18 different previously identified repeated DNA elements, bcr1-bcr18 (Økstad OA, Hegna I, Lindback T, Rishovd AL, Kolstø AB. 1999. Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. Microbiology. 145:621-631.; Tourasse NJ, Helgason E, Økstad OA, Hegna IK, Kolstø AB. 2006. The Bacillus cereus group: novel aspects of population structure and genome dynamics. J Appl Microbiol. 101:579-593.), in 36 sequenced genomes from the Bacillus cereus group of bacteria. This group consists of genetically closely related species with variable pathogenic specificity toward different hosts and includes among others B. anthracis, B. cereus, and B. thuringiensis. The B. cereus group repeat elements could be classified into three categories with different properties: Group A elements (bcr1-bcr3) exhibited highly variable copy numbers ranging from 4 to 116 copies per strain, showed a nonconserved chromosomal distribution pattern between strains, and displayed several features characteristic of mobile elements. Group B repeats (bcr4-bcr6) were present in 0-10 copies per strain and were associated with strain-specific genes and disruptions of genome synteny, implying a possible contribution to genome rearrangements and/or horizontal gene transfer events. bcr5, in particular, was associated with large gene clusters showing resemblance to integrons. In agreement with their potentially mobile nature or involvement in horizontal transfers, the sequences of the repeats from Groups A and B (bcr1-bcr6) followed a phylogeny different from that of the host strains. Conversely, repeats from Group C (bcr7-bcr18) had a conserved chromosomal location and orthologous gene neighbors in the investigated B. cereus group genomes, and their phylogeny matched that of the host chromosome. Several of the group C repeats exhibited a conserved secondary structure or had parts of the structure conserved, possibly indicating functional RNAs. Accordingly, five of the repeats in group C overlapped regions encoding previously characterized riboswitches. Similarly, other group C repeats could represent novel riboswitches, encode small RNAs, and/or constitute other types of regulatory elements with specific biological functions. The current analysis suggests that the multitude of repeat elements identified in the B. cereus group promote genome dynamics and plasticity and could contribute to the flexible and adaptive life style of these bacteria.
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Affiliation(s)
- Simen M Kristoffersen
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Blindern, Oslo, Norway
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Yang TY, Sung YM, Lei GS, Romeo T, Chak KF. Posttranscriptional repression of the cel gene of the ColE7 operon by the RNA-binding protein CsrA of Escherichia coli. Nucleic Acids Res 2010; 38:3936-51. [PMID: 20378712 PMCID: PMC2896534 DOI: 10.1093/nar/gkq177] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Carbon storage regulator (CsrA) is a eubacterial RNA-binding protein that acts as a global regulator of many functionally diverse chromosomal genes. Here, we reveal that CsrA represses expression from an extrachromosomal element of Escherichia coli, the lysis gene (cel) of the ColE7 operon (cea-cei-cel). This operon and colicin expression are activated upon SOS response. Disruption of csrA caused ∼5-fold increase of the lysis protein. Gel mobility shift assays established that both the single-stranded loop of the T1 stem–loop distal to cei, and the putative CsrA binding site overlapping the Shine–Dalgarno sequence (SD) of the cel gene are important for CsrA binding. Substitution mutations at SD relieved CsrA-dependent repression of the cel gene in vivo. Steady-state levels and half-life of the cel mRNA were not affected by CsrA, implying that regulation is mediated at the translational level. Levels of CsrB and CsrC sRNAs, which bind to and antagonize CsrA, were drastically reduced upon induction of the SOS response, while the CsrA protein itself remained unaffected. Thus, CsrA is a trans-acting modulator that downregulates the expression of lysis protein, which may confer a survival advantage on colicinogenic E. coli under environment stress conditions.
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Affiliation(s)
- Tsung-Yeh Yang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
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Wu X, Wu S, Li D, Zhang J, Hou L, Ma J, Liu W, Ren D, Zhu Y, He F. Computational identification of rare codons of Escherichia coli based on codon pairs preference. BMC Bioinformatics 2010; 11:61. [PMID: 20109184 PMCID: PMC2828438 DOI: 10.1186/1471-2105-11-61] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 01/28/2010] [Indexed: 12/04/2022] Open
Abstract
Background Codon bias is believed to play an important role in the control of gene expression. In Escherichia coli, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engineering operations. Previous studies have confirmed the existence of codon pair's preference in many genomes, but the underlying cause of this bias has not been well established. Here we focus on the patterns of rarely-used synonymous codons. A novel method was introduced to identify the rare codons merely by codon pair bias in Escherichia coli. Results In Escherichia coli, we defined the "rare codon pairs" by calculating the frequency of occurrence of all codon pairs in coding sequences. Rare codons which are disliked in genes could make great contributions to forming rare codon pairs. Meanwhile our investigation showed that many of these rare codon pairs contain termination codons and the recognized sites of restriction enzymes. Furthermore, a new index (Frare) was developed. Through comparison with the classical indices we found a significant negative correlation between Frare and the indices which depend on reference datasets. Conclusions Our approach suggests that we can identify rare codons by studying the context in which a codon lies. Also, the frequency of rare codons (Frare) could be a useful index of codon bias regardless of the lack of expression abundance information.
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Affiliation(s)
- Xianming Wu
- School of Biological Science and Technology, Shenyang Agricultural University, Shenyang, PR China
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Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA. EMBO J 2009; 28:1551-61. [PMID: 19407815 DOI: 10.1038/emboj.2009.116] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 03/30/2009] [Indexed: 11/08/2022] Open
Abstract
Most polycistronic genes are expressed in a single transcript, in which each cistron produces a fixed amount of protein. In this report, we show the first example of differential degradation of a polycistronic gene induced by a small regulatory RNA (sRNA). Our data show that the iron-responsive sRNA, RyhB, binds to the second cistron of the polycistronic mRNA, iscRSUA, which encodes the necessary machinery for biosynthesis of Fe-S clusters, and promotes the cleavage of the downstream iscSUA transcript. This cleavage gives rise to the remaining 5'-section of the transcript encoding IscR, a transcriptional regulator responsible for activation and repression of several genes depending on the cellular Fe-S level. Our data indicate that the iscR transcript is stable and that translation is active. The stability of the iscR transcript depends on a 111-nucleotide long non-translated RNA section located between iscR and iscS, which forms a strong repetitive extragenic palindromic secondary structure and may protect against ribonucleases degradation. This novel regulation shows how sRNAs and mRNA structures can work together to modulate the transcriptional response to a specific stress.
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Régnier P, Hajnsdorf E. Poly(A)-assisted RNA decay and modulators of RNA stability. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:137-85. [PMID: 19215772 DOI: 10.1016/s0079-6603(08)00804-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In Escherichia coli, RNA degradation is orchestrated by the degradosome with the assistance of complementary pathways and regulatory cofactors described in this chapter. They control the stability of each transcript and regulate the expression of many genes involved in environmental adaptation. The poly(A)-dependent degradation machinery has diverse functions such as the degradation of decay intermediates generated by endoribonucleases, the control of the stability of regulatory non coding RNAs (ncRNAs) and the quality control of stable RNA. The metabolism of poly(A) and mechanism of poly(A)-assisted degradation are beginning to be understood. Regulatory factors, exemplified by RraA and RraB, control the decay rates of subsets of transcripts by binding to RNase E, in contrast to regulatory ncRNAs which, assisted by Hfq, target RNase E to specific transcripts. Destabilization is often consecutive to the translational inactivation of mRNA. However, there are examples where RNA degradation is the primary regulatory step.
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Affiliation(s)
- Philippe Régnier
- CNRS UPR9073, Institut de Biologie Physico-Chimique, Paris, France
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Sandal I, Seleem MN, Elswaifi SF, Sriranganathan N, Inzana TJ. Construction of a high-efficiency shuttle vector for Histophilus somni. J Microbiol Methods 2008; 74:106-9. [DOI: 10.1016/j.mimet.2008.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Revised: 04/04/2008] [Accepted: 04/07/2008] [Indexed: 11/30/2022]
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Carpousis AJ, Khemici V, Poljak L. Assaying DEAD-box RNA helicases and their role in mRNA degradation in Escherichia coli. Methods Enzymol 2008; 447:183-97. [PMID: 19161844 DOI: 10.1016/s0076-6879(08)02210-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The DEAD-box RNA helicases are a ubiquitous family of enzymes involved in processes that include RNA splicing, ribosome biogenesis, and mRNA degradation. In general, these enzymes help to unwind short stretches of double-stranded RNA in processes that involve the remodeling of RNA structure or of ribonucleoprotein complexes. Here we describe work from our laboratory on the characterization of the RhlB of Escherichia coli, a DEAD-box RNA helicase that is part of a multienzyme complex known as the RNA degradosome. RhlB interacts physically and functionally with RNase E and polynucleotide phosphorylase (PNPase), two other components of the RNA degradosome. We describe enzyme assays that demonstrated that the interaction between RhlB and RNase E is necessary for the ATPase and RNA unwinding activities of RhlB. We also describe an mRNA degradation assay that showed that RhlB facilitates the degradation of structured mRNA by PNPase. These assays are discussed in the context of how they have contributed to our understanding of the function of RhlB in mRNA degradation.
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Affiliation(s)
- Agamemnon J Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique and Université Paul Sabatier, Toulouse, France
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Kime L, Jourdan SS, McDowall KJ. Identifying and characterizing substrates of the RNase E/G family of enzymes. Methods Enzymol 2008; 447:215-41. [PMID: 19161846 DOI: 10.1016/s0076-6879(08)02212-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of RNA decay and processing in Escherichia coli has revealed a central role for RNase E, an endonuclease that is essential for cell viability. This enzyme is required for the normal rapid decay of many transcripts and is involved in the processing of precursors of 16S and 5S ribosomal RNA, transfer RNA, the transfer-messenger RNA, and the RNA component of RNase P. Although there is reasonable knowledge of the repertoire of transcripts cleaved by RNase E in E. coli, a detailed understanding of the molecular recognition events that control the cleavage of RNA by this key enzyme is only starting to emerge. Here we describe methods for identifying sites of endonucleolytic cleavage and determining whether they depend on functional RNase E. This is illustrated with the pyrG eno bicistronic transcript, which is cleaved in the intergenic region primarily by an RNase E-dependent activity and not as previously thought by RNase III. We also describe the use of oligoribonucleotide and in vitro-transcribed substrates to investigate cis-acting factors such as 5'-monophosphorylation, which can significantly enhance the rate of cleavage but is insufficient to ensure processivity. Most of the approaches that we describe can be applied to the study of homologs of E. coli RNase E, which have been found in approximately half of the eubacteria that have been sequenced.
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Affiliation(s)
- Louise Kime
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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Shivachandra SB, Kumar AA, Chaudhuri P. Molecular characterization of Avian strains of Pasteurella multocida serogroup-A:1 based on amplification of repetitive regions by PCR. Comp Immunol Microbiol Infect Dis 2008; 31:47-62. [PMID: 17537513 DOI: 10.1016/j.cimid.2007.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2007] [Indexed: 12/01/2022]
Abstract
Repetitive extragenic palindromic (REP)-PCR (polymerase chain reaction), enterobacterial repetitive intergenic consensus (ERIC)-PCR, and single primer PCR assays were employed to characterize 66 strains of Pasteurella multocida serogroup A:1 isolated from avian species belonging to different regions of India. REP-PCR resulted in amplification of REP sequences from the genome which were in the range of approximately 200 to approximately 3000 bp and accounted for a total of 54 distinguishing profiles (D=0.99). ERIC-PCR analysis also generated amplified products in the range of approximately 200 to approximately 3200 bp categorizing strains into a total of 50 different profiles (D=0.98). Amplification of repetitive regions using a microsatellite primer (GTG)(5), resulted in clear distinctive bands ranging from approximately 200 to approximately 2400 bp. Strains were assigned to 43 profiles (D=0.96). No correlation could be drawn between genotypic profiles and avian hosts with their geographical area of origin. Avian strains of P. multocida serogroup A:1 were found to be highly heterogeneous with diverse profiles. REP-PCR was found to be highly discriminatory and simple method for differentiation of phenotypically similar strains. The present study also indicated that PCR based amplification of repetitive regions of P. multocida is a rapid technique with good discrimination and could be employed directly for routine typing of field isolates from fowl cholera outbreaks.
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Affiliation(s)
- S B Shivachandra
- Division of Bacteriology and Mycology, Indian Veterinary Research Institute, Izatnagar 243122, UP, India.
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48
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Abstract
The RNA degradosome of Escherichia coli is a multiprotein complex involved in the degradation of mRNA. The principal components are RNase E, PNPase, RhlB, and enolase. RNase E is a large multidomain protein with an N-terminal catalytic region and a C-terminal noncatalytic region that is mostly natively unstructured protein. The noncatalytic region contains sites for binding RNA and for protein-protein interactions with other components of the RNA degradosome. Several recent studies suggest that there are alternative forms of the RNA degradosome depending on growth conditions or other factors. These alternative forms appear to modulate RNase E activity in the degradation of mRNA. RNA degradosome-like complexes appear to be conserved throughout the Proteobacteria, but there is a surprising variability in composition that might contribute to the adaptation of these bacteria to the enormously wide variety of niches in which they live.
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Affiliation(s)
- Agamemnon J Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, Unité Mixte de Recherche 5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 31062 Toulouse, France.
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49
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Abstract
This chapter discusses several topics relating to the mechanisms of mRNA decay. These topics include the following: important physical properties of mRNA molecules that can alter their stability; methods for determining mRNA half-lives; the genetics and biochemistry of proteins and enzymes involved in mRNA decay; posttranscriptional modification of mRNAs; the cellular location of the mRNA decay apparatus; regulation of mRNA decay; the relationships among mRNA decay, tRNA maturation, and ribosomal RNA processing; and biochemical models for mRNA decay. Escherichia coli has multiple pathways for ensuring the effective decay of mRNAs and mRNA decay is closely linked to the cell's overall RNA metabolism. Finally, the chapter highlights important unanswered questions regarding both the mechanism and importance of mRNA decay.
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50
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Lewis JP, Plata K, Yu F, Rosato A, Anaya C. Transcriptional organization, regulation and role of the Porphyromonas gingivalis W83 hmu haemin-uptake locus. MICROBIOLOGY-SGM 2007; 152:3367-3382. [PMID: 17074906 DOI: 10.1099/mic.0.29011-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Porphyromonas gingivalis, an oral bacterium associated with periodontal disease, requires haemin for growth. Although several multigenic clusters encoding haemin-uptake systems are present on the genome of P. gingivalis, little is known regarding their transcriptional organization and expression. This study identified a 23 kDa iron-regulated haemin-binding protein encoded by a larger than previously reported variant of hmuY. It was shown that the hmu locus is larger than previously reported and is composed of six genes, hmuYRSTUV, encoding a novel hybrid haemin-uptake system. The locus has an operonic organization and the transcriptional start site is located 292 bp upstream of hmuY. The data indicate that the regulation of the operon is iron-dependent. Interestingly, differential regulation within the operon was demonstrated, resulting in excess of the hmuYR message encoding the outer-membrane proteins when compared to the full-length transcript. In addition, the hmuY transcript is more prevalent than the hmuR transcript. Secondary structure analysis of the hmuYRSTUV mRNA predicted the formation of several potential stem-loops in the 5' ends of hmuR- and hmuS-specific mRNAs, consistent with the differential regulation observed. Finally, it was demonstrated that haemin binding and uptake are elevated in iron-depleted conditions and are reduced 45 % and 70 %, respectively, in an hmu-deficient strain when compared to the parental strain, indicating that the hmu locus plays a major role in haemin acquisition in P. gingivalis. Since homologues of the hmu locus were also found in Bacteroides fragilis, Bacteroides thetaiotaomicron and Prevotella intermedia, these findings may have implications for a better understanding of haemin acquisition in those organisms as well.
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Affiliation(s)
- Janina P Lewis
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Konrad Plata
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Fan Yu
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Adriana Rosato
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Cecilia Anaya
- University of San Luis, San Luis, Argentina
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
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