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Mukherjee S, Kuang Z, Ghosh S, Detroja R, Carmi G, Tripathy S, Barash D, Frenkel-Morgenstern M, Nevo E, Li K. Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis. BIOLOGY 2022; 11:biology11081110. [PMID: 35892966 PMCID: PMC9331176 DOI: 10.3390/biology11081110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary The microevolutionary dynamics of soil bacteria under microclimatic differences are largely unexplored in contrast to our improving knowledge of their vast diversity. In this study, we performed a comparative metagenomic analysis of two sharply divergent rocks and soil types at the Evolution Plateau (EP) in eastern Upper Galilee, Israel. We have identified the significant differences in bacterial taxonomic diversity, functions, and patterns of RNA-based gene regulation between the bacteria from two different soil types. Furthermore, we have identified several species with a significant genetic divergence of the same species between the two soil types, highlighting the soil bacteria’s incipient sympatric speciation. Abstract Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.
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Affiliation(s)
- Sumit Mukherjee
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
- Correspondence: (S.M.); (K.L.)
| | - Zhuoran Kuang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
| | - Samrat Ghosh
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Gon Carmi
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
| | - Kexin Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Correspondence: (S.M.); (K.L.)
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Wu Y, Zhang D, Duan A, Ao Y, Li S. The application of riboswitch sequencing for human gut bacterial classification and identification. Mol Phylogenet Evol 2022; 169:107409. [PMID: 35063674 DOI: 10.1016/j.ympev.2022.107409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022]
Abstract
Bacteria, especially gut bacteria play important roles in human health and diseases. The classification of many bacterial genera by the 16S ribosomal RNA (rRNA) has failed due to its low inter-species resolution. Given the wide distribution of riboswitches in bacteria, they may help 16S rRNA differentiate closely related species. We found that among 28 groups of species that could not be distinguished by 16S rRNA, eight of them could be separated by the TPP riboswitch and other riboswitches. Moreover, the species in the 16S rRNA database and these riboswitch databases overlap, therefore, using riboswitch databases can help 16S rRNA better identify species. In addition, we used Klenow DNA polymerase and a pair of short primers to facilitate the library construction of TPP riboswitches for sequencing. The sequencing results showed that the TPP riboswitch could detect the major phyla similar to those detected by 16S rRNA. Therefore, the TPP riboswitch and other riboswitch classes could potentially be applied to gut bacteria classification.
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Affiliation(s)
- Yaoyao Wu
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Deying Zhang
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510627, P. R. China(2)
| | - Anqi Duan
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Yaqi Ao
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Sanshu Li
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China.
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3
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Mukherjee S, Detroja R, Balamurali D, Matveishina E, Medvedeva Y, Valencia A, Gorohovski A, Frenkel-Morgenstern M. Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells. NAR Genom Bioinform 2021; 3:lqab074. [PMID: 34458728 PMCID: PMC8386243 DOI: 10.1093/nargab/lqab074] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/02/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Many human genes are transcribed from both strands and produce sense-antisense gene pairs. Sense-antisense (SAS) chimeric transcripts are produced upon the coalescing of exons/introns from both sense and antisense transcripts of the same gene. SAS chimera was first reported in prostate cancer cells. Subsequently, numerous SAS chimeras have been reported in the ChiTaRS-2.1 database. However, the landscape of their expression in human cells and functional aspects are still unknown. We found that longer palindromic sequences are a unique feature of SAS chimeras. Structural analysis indicates that a long hairpin-like structure formed by many consecutive Watson-Crick base pairs appears because of these long palindromic sequences, which possibly play a similar role as double-stranded RNA (dsRNA), interfering with gene expression. RNA-RNA interaction analysis suggested that SAS chimeras could significantly interact with their parental mRNAs, indicating their potential regulatory features. Here, 267 SAS chimeras were mapped in RNA-seq data from 16 healthy human tissues, revealing their expression in normal cells. Evolutionary analysis suggested the positive selection favoring sense-antisense fusions that significantly impacted the evolution of their function and structure. Overall, our study provides detailed insight into the expression landscape of SAS chimeras in human cells and identifies potential regulatory features.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Deepak Balamurali
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Elena Matveishina
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russian Federation
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russian Federation
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russian Federation
- Department of Biomedical Physics, Moscow Institute of Technology, Dolgoprudny 141701, Russian Federation
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), C/ Jordi Girona 29, 08034, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Alessandro Gorohovski
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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Psomopoulos FE, van Helden J, Médigue C, Chasapi A, Ouzounis CA. Ancestral state reconstruction of metabolic pathways across pangenome ensembles. Microb Genom 2021; 6. [PMID: 32924924 PMCID: PMC7725326 DOI: 10.1099/mgen.0.000429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As genome sequencing efforts are unveiling the genetic diversity of the biosphere with an unprecedented speed, there is a need to accurately describe the structural and functional properties of groups of extant species whose genomes have been sequenced, as well as their inferred ancestors, at any given taxonomic level of their phylogeny. Elaborate approaches for the reconstruction of ancestral states at the sequence level have been developed, subsequently augmented by methods based on gene content. While these approaches of sequence or gene-content reconstruction have been successfully deployed, there has been less progress on the explicit inference of functional properties of ancestral genomes, in terms of metabolic pathways and other cellular processes. Herein, we describe PathTrace, an efficient algorithm for parsimony-based reconstructions of the evolutionary history of individual metabolic pathways, pivotal representations of key functional modules of cellular function. The algorithm is implemented as a five-step process through which pathways are represented as fuzzy vectors, where each enzyme is associated with a taxonomic conservation value derived from the phylogenetic profile of its protein sequence. The method is evaluated with a selected benchmark set of pathways against collections of genome sequences from key data resources. By deploying a pangenome-driven approach for pathway sets, we demonstrate that the inferred patterns are largely insensitive to noise, as opposed to gene-content reconstruction methods. In addition, the resulting reconstructions are closely correlated with the evolutionary distance of the taxa under study, suggesting that a diligent selection of target pangenomes is essential for maintaining cohesiveness of the method and consistency of the inference, serving as an internal control for an arbitrary selection of queries. The PathTrace method is a first step towards the large-scale analysis of metabolic pathway evolution and our deeper understanding of functional relationships reflected in emerging pangenome collections.
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Affiliation(s)
- Fotis E Psomopoulos
- Institute of Applied Biosciences (INAB), Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece
| | - Jacques van Helden
- Lab. Technological Advances for Genomics & Clinics (TAGC), Université d'Aix-Marseille (AMU), INSERM Unit U1090, 163, Avenue de Luminy, 13288 Marseille cedex 09, France
| | - Claudine Médigue
- UMR 8030, CNRS, Université Evry-Val-d'Essonne, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Evry, France
| | - Anastasia Chasapi
- Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece
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5
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The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy. Viruses 2021; 13:v13040656. [PMID: 33920240 PMCID: PMC8069663 DOI: 10.3390/v13040656] [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: 12/08/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.
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6
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McCluskey K, Boudreault J, St-Pierre P, Perez-Gonzalez C, Chauvier A, Rizzi A, Beauregard PB, Lafontaine DA, Penedo JC. Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2. Nucleic Acids Res 2020; 47:6478-6487. [PMID: 31045204 PMCID: PMC6614840 DOI: 10.1093/nar/gkz316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Riboswitches are cis-acting regulatory RNA biosensors that rival the efficiency of those found in proteins. At the heart of their regulatory function is the formation of a highly specific aptamer–ligand complex. Understanding how these RNAs recognize the ligand to regulate gene expression at physiological concentrations of Mg2+ ions and ligand is critical given their broad impact on bacterial gene expression and their potential as antibiotic targets. In this work, we used single-molecule FRET and biochemical techniques to demonstrate that Mg2+ ions act as fine-tuning elements of the amino acid-sensing lysC aptamer's ligand-free structure in the mesophile Bacillus subtilis. Mg2+ interactions with the aptamer produce encounter complexes with strikingly different sensitivities to the ligand in different, yet equally accessible, physiological ionic conditions. Our results demonstrate that the aptamer adapts its structure and folding landscape on a Mg2+-tunable scale to efficiently respond to changes in intracellular lysine of more than two orders of magnitude. The remarkable tunability of the lysC aptamer by sub-millimolar variations in the physiological concentration of Mg2+ ions suggests that some single-aptamer riboswitches have exploited the coupling of cellular levels of ligand and divalent metal ions to tightly control gene expression.
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Affiliation(s)
- Kaley McCluskey
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK
| | - Julien Boudreault
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Patrick St-Pierre
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Cibran Perez-Gonzalez
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK.,Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Adrien Chauvier
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Adrien Rizzi
- Département de Chimie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Pascale B Beauregard
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | | | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK.,Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, Scotland KY16 9ST, UK
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Ramos-Silva P, Serrano M, Henriques AO. From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile. Mol Biol Evol 2020; 36:2714-2736. [PMID: 31350897 PMCID: PMC6878958 DOI: 10.1093/molbev/msz175] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.
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Affiliation(s)
- Paula Ramos-Silva
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Mukherjee S, Das Mandal S, Gupta N, Drory-Retwitzer M, Barash D, Sengupta S. RiboD: a comprehensive database for prokaryotic riboswitches. Bioinformatics 2019; 35:3541-3543. [DOI: 10.1093/bioinformatics/btz093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/24/2019] [Accepted: 02/05/2019] [Indexed: 01/05/2023] Open
Abstract
Abstract
Summary
Riboswitches are cis-regulatory non-coding genomic segments that control the expression of downstream genes by undergoing conformational change upon ligand binding. We present a comprehensive database of prokaryotic riboswitches that allows the user to search for riboswitches using multiple criteria, extract information about riboswitch location and gene/operon it regulates. RiboD provides a very useful resource that can be utilized for the better understanding of riboswitch-based gene regulation in bacteria and archaea.
Availability and implementation
RiboD can be freely accessed on the web at http://ribod.iiserkol.ac.in/.
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Affiliation(s)
- Sumit Mukherjee
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
| | - Sukhen Das Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
| | - Nikita Gupta
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU) Varanasi, Varanasi, India
| | | | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
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Sinumvayo JP, Zhao C, Tuyishime P. Recent advances and future trends of riboswitches: attractive regulatory tools. World J Microbiol Biotechnol 2018; 34:171. [PMID: 30413889 DOI: 10.1007/s11274-018-2554-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/02/2018] [Indexed: 01/06/2023]
Abstract
Bacterial genomes contain a huge amount of different genes. These genes are spatiotemporally expressed to accomplish some required functions within the organism. Inside the cell, any step of gene expression may be modulated at four possible places such as transcription initiation, translation regulation, mRNA stability and protein stability. To achieve this, there is a necessity of strong regulators either natural or synthetic which can fine-tune gene expression regarding the required function. In recent years, riboswitches as metabolite responsive control elements residing in the untranslated regions of certain messenger RNAs, have been known to control gene expression at transcription or translation level. Importantly, these control elements do not prescribe the involvement of protein factors for metabolite binding. However, they own their particular properties to sense intramolecular metabolites (ligands). Herein, we highlighted current important bacterial riboswitches, their applications to support genetic control, ligand-binding domain mechanisms and current progress in synthetic riboswitches.
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Affiliation(s)
- Jean Paul Sinumvayo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Philibert Tuyishime
- University of Chinese Academy of Sciences, Beijing, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi. Sci Rep 2018; 8:5563. [PMID: 29615754 PMCID: PMC5882874 DOI: 10.1038/s41598-018-23900-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/20/2018] [Indexed: 01/01/2023] Open
Abstract
Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi where their presence has been experimentally validated in a few instances. We analyzed all the available complete fungal and related genomes and identified TPP riboswitch-based regulation systems in 138 fungi and 15 oomycetes. We find that TPP riboswitches are most abundant in Ascomycota and Basidiomycota where they regulate TPP biosynthesis and/or transporter genes. Many of these transporter genes were found to contain conserved domains consistent with nucleoside, urea and amino acid transporter gene families. The genomic location of TPP riboswitches when correlated with the intron structure of the regulated genes enabled prediction of the precise regulation mechanism employed by each riboswitch. Our comprehensive analysis of TPP riboswitches in fungi provides insights about the phylogenomic distribution, regulatory patterns and functioning mechanisms of TPP riboswitches across diverse fungal species and provides a useful resource that will enhance the understanding of RNA-based gene regulation in eukaryotes.
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