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Gupta N, Yadav M, Singh G, Chaudhary S, Ghosh C, Rathore JS. Decoding the TAome and computational insights into parDE toxin-antitoxin systems in Pseudomonas aeruginosa. Arch Microbiol 2024; 206:360. [PMID: 39066828 DOI: 10.1007/s00203-024-04085-2] [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: 06/04/2024] [Revised: 07/07/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
Toxin-antitoxin (TA) modules are widely found in the genomes of pathogenic bacteria. They regulate vital cellular functions like transcription, translation, and DNA replication, and are therefore essential to the survival of bacteria under stress. With a focus on the type II parDE modules, this study thoroughly examines TAome in Pseudomonas aeruginosa, a bacterium well-known for its adaptability and antibiotic resistance. We explored the TAome in three P. aeruginosa strains: ATCC 27,853, PAO1, and PA14, and found 15 type II TAs in ATCC 27,853, 12 in PAO1, and 13 in PA14, with significant variation in the associated mobile genetic elements. Five different parDE homologs were found by further TAome analysis in ATCC 27,853, and their relationships were confirmed by sequence alignments and precise genomic positions. After comparing these ParDE modules' sequences to those of other pathogenic bacteria, it was discovered that they were conserved throughout many taxa, especially Proteobacteria. Nucleic acids were predicted as potential ligands for ParD antitoxins, whereas ParE toxins interacted with a wide range of small molecules, indicating a diverse functional repertoire. The interaction interfaces between ParDE TAs were clarified by protein-protein interaction networks and docking studies, which also highlighted important residues involved in binding. This thorough examination improves our understanding of the diversity, evolutionary dynamics, and functional significance of TA systems in P. aeruginosa, providing insights into their roles in bacterial physiology and pathogenicity.
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Affiliation(s)
- Nomita Gupta
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Greater Noida, 201312, Uttar Pradesh, India
| | - Mohit Yadav
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Greater Noida, 201312, Uttar Pradesh, India
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
| | - Garima Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Greater Noida, 201312, Uttar Pradesh, India
| | - Shobhi Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Greater Noida, 201312, Uttar Pradesh, India
| | - Chaitali Ghosh
- Department of Zoology, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India
| | - Jitendra Singh Rathore
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Greater Noida, 201312, Uttar Pradesh, India.
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2
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Tomasch J, Kopejtka K, Shivaramu S, Mujakić I, Koblížek M. On the evolution of chromosomal regions with high gene strand bias in bacteria. mBio 2024; 15:e0060224. [PMID: 38752745 PMCID: PMC11237797 DOI: 10.1128/mbio.00602-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
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3
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Wolf YI, Schurov IV, Makarova KS, Katsnelson MI, Koonin EV. Long range segmentation of prokaryotic genomes by gene age and functionality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591304. [PMID: 38903122 PMCID: PMC11188115 DOI: 10.1101/2024.04.26.591304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Bacterial and archaeal genomes encompass numerous operons that typically consist of two to five genes. On larger scales, however, gene order is poorly conserved through the evolution of prokaryotes. Nevertheless, non-random localization of different classes of genes on prokaryotic chromosomes could reflect important functional and evolutionary constraints. We explored the patterns of genomic localization of evolutionarily conserved (ancient) and variable (young) genes across the diversity of bacteria and archaea. Nearly all bacterial and archaeal chromosomes were found to encompass large segments of 100-300 kilobases that were significantly enriched in either ancient or young genes. Similar clustering of genes with lethal knockout phenotype (essential genes) was observed as well. Mathematical modeling of genome evolution suggests that this long-range gene clustering in prokaryotic chromosomes reflects perpetual genome rearrangement driven by a combination of selective and neutral processes rather than evolutionary conservation.
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Affiliation(s)
- Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Ilya V. Schurov
- Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mikhail I. Katsnelson
- Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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4
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Atre M, Joshi B, Babu J, Sawant S, Sharma S, Sankar TS. Origin, evolution, and maintenance of gene-strand bias in bacteria. Nucleic Acids Res 2024; 52:3493-3509. [PMID: 38442257 DOI: 10.1093/nar/gkae155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Gene-strand bias is a characteristic feature of bacterial genome organization wherein genes are preferentially encoded on the leading strand of replication, promoting co-orientation of replication and transcription. This co-orientation bias has evolved to protect gene essentiality, expression, and genomic stability from the harmful effects of head-on replication-transcription collisions. However, the origin, variation, and maintenance of gene-strand bias remain elusive. Here, we reveal that the frequency of inversions that alter gene orientation exhibits large variation across bacterial populations and negatively correlates with gene-strand bias. The density, distance, and distribution of inverted repeats show a similar negative relationship with gene-strand bias explaining the heterogeneity in inversions. Importantly, these observations are broadly evident across the entire bacterial kingdom uncovering inversions and inverted repeats as primary factors underlying the variation in gene-strand bias and its maintenance. The distinct catalytic subunits of replicative DNA polymerase have co-evolved with gene-strand bias, suggesting a close link between replication and the origin of gene-strand bias. Congruently, inversion frequencies and inverted repeats vary among bacteria with different DNA polymerases. In summary, we propose that the nature of replication determines the fitness cost of replication-transcription collisions, establishing a selection gradient on gene-strand bias by fine-tuning DNA sequence repeats and, thereby, gene inversions.
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Affiliation(s)
- Malhar Atre
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Bharat Joshi
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Jebin Babu
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Shabduli Sawant
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Shreya Sharma
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - T Sabari Sankar
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
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5
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Duarte-Velázquez I, de la Mora J, Ramírez-Prado JH, Aguillón-Bárcenas A, Tornero-Gutiérrez F, Cordero-Loreto E, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Muñoz-Carranza SR, Romero-González OE, Cardoso-Reyes LR, Rodríguez-Ojeda RA, Mora-Montes HM, Vargas-Maya NI, Padilla-Vaca F, Franco B. Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships. PeerJ 2022; 10:e13772. [PMID: 35880217 PMCID: PMC9308461 DOI: 10.7717/peerj.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
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Affiliation(s)
- Isabel Duarte-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, México
| | | | - Alondra Aguillón-Bárcenas
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fátima Tornero-Gutiérrez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Eugenia Cordero-Loreto
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fernando Anaya-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Itzel Páramo-Pérez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Ángeles Rangel-Serrano
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | | | - Luis Rafael Cardoso-Reyes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | - Héctor Manuel Mora-Montes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Naurú Idalia Vargas-Maya
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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6
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Hu XP, Lercher MJ. An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes. PLoS Genet 2021; 17:e1009939. [PMID: 34843465 PMCID: PMC8659690 DOI: 10.1371/journal.pgen.1009939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 12/09/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022] Open
Abstract
The distribution of cellular resources across bacterial proteins has been quantified through phenomenological growth laws. Here, we describe a complementary bacterial growth law for RNA composition, emerging from optimal cellular resource allocation into ribosomes and ternary complexes. The predicted decline of the tRNA/rRNA ratio with growth rate agrees quantitatively with experimental data. Its regulation appears to be implemented in part through chromosomal localization, as rRNA genes are typically closer to the origin of replication than tRNA genes and thus have increasingly higher gene dosage at faster growth. At the highest growth rates in E. coli, the tRNA/rRNA gene dosage ratio based on chromosomal positions is almost identical to the observed and theoretically optimal tRNA/rRNA expression ratio, indicating that the chromosomal arrangement has evolved to favor maximal transcription of both types of genes at this condition. Unlike the proteome composition, RNA composition is often assumed to be independent of growth rate in bacteria, despite experimental evidence for a growth rate dependence in many microbes. In this work, we derived a growth-rate dependent optimal tRNA/rRNA concentration ratio by minimizing the combined costs of ribosome and ternary complex at the required protein production rate. The predicted optimal tRNA/rRNA expression ratio, which is a monotonically decreasing function of growth rate, agrees with experimental data for E. coli and other fast-growing microbes. This indicates the existing of an RNA composition growth law. Due to the presence of partially replicated chromosomes, gene dosage is higher for those genes whose DNA is replicated earlier, an effect that becomes stronger at higher growth rates. Because rRNA genes are located closer to origin of replication than tRNA genes in fast-growing species, the tRNA/rRNA gene dosage ratio scales with growth rate in the same direction as the optimal tRNA/rRNA expression ratio. Thus, it appears that the RNA growth law is–at least in part–implemented simply through the genomic positions of tRNA and rRNA genes. This finding indicates that growth rate-dependent optimal resource allocation can influence the genomic organization in bacteria.
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Affiliation(s)
- Xiao-Pan Hu
- Institute for Computer Science and Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Martin J. Lercher
- Institute for Computer Science and Department of Biology, Heinrich Heine University, Düsseldorf, Germany
- * E-mail:
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7
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Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes. Methods Mol Biol 2021. [PMID: 34709630 DOI: 10.1007/978-1-0716-1720-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Computational tool composites alternative way to identify essential genes and it is low-cost and time-efficient. Based on experimental essentiality sets deposited in the databases DEG and OGEE as reference, we developed an automatically computational tool named Geptop to select essential genes from the set of protein-coding genes in a prokaryotic genome, which utilizes the strategy of reciprocally best hit for homology search and evolutionary distance for weight assigning. The latest version of Geptop is 2.0 ( http://guolab.whu.edu.cn/geptop ), which can predict gene essentiality with the mean AUC 0f 0.84 in prokaryotes and is more stable. The chapter is to briefly introduce the tool and tell how to use it.
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8
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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9
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Auboeuf D. Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces. Life (Basel) 2020; 10:life10020007. [PMID: 31973071 PMCID: PMC7175370 DOI: 10.3390/life10020007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made of complex multicellular organisms and, then, modified to fit a DNA-centric view. In this article, it is argued that based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that (i) natural selection plays a dominant role in evolution and (ii) the probability of mutations is independent of the generated phenotype. It is shown that the adaptation of a phenotype to an environment does not correspond to organism fitness, but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome, but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature, and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype in which the phenotype ensures the stability of its originating genome in a cellular and environmental physicochemical parameter-depending manner.
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Affiliation(s)
- Didier Auboeuf
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie, Site Jacques Monod, F-69007, Lyon, France
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10
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Gao NL, Chen J, Wang T, Lercher MJ, Chen WH. Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR. Front Microbiol 2019; 10:2254. [PMID: 31681190 PMCID: PMC6805729 DOI: 10.3389/fmicb.2019.02254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/17/2019] [Indexed: 12/02/2022] Open
Abstract
Viruses and plasmids can introduce novel DNA into bacterial cells, thereby creating an opportunity for genome expansion; conversely, CRISPR, the prokaryotic adaptive immune system, which targets and eliminates foreign DNAs, may impair genome expansions. Recent studies presented conflicting results over the impact of CRISPR on genome expansion. In this study, we constructed a comprehensive dataset of prokaryotic genomes and identified their associations with viruses and plasmids. We found that genomes associated with viruses and/or plasmids were significantly larger than those without, indicating that both viruses and plasmids contribute to genome expansion. Genomes were increasingly larger with increasing numbers of associated viruses or plasmids. Conversely, genomes with CRISPR systems were significantly smaller than those without, indicating that CRISPR has a negative impact on genome size. These results confirmed that on evolutionary timescales, viruses and plasmids facilitate genome expansion, while CRISPR impairs such a process in prokaryotes. Furthermore, our results also revealed that CRISPR systems show a preference for targeting viruses over plasmids.
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Affiliation(s)
- Na L Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Institute for Computer Science and Department of Biology, Heinrich Heine University, Duesseldorf, Germany
| | - Jingchao Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Teng Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Martin J Lercher
- Institute for Computer Science and Department of Biology, Heinrich Heine University, Duesseldorf, Germany
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,College of Life Science, Henan Normal University, Xinxiang, China.,Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou, China
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11
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Wen QF, Liu S, Dong C, Guo HX, Gao YZ, Guo FB. Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes. Front Microbiol 2019; 10:1236. [PMID: 31214154 PMCID: PMC6558110 DOI: 10.3389/fmicb.2019.01236] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/17/2019] [Indexed: 12/16/2022] Open
Abstract
Geptop has performed effectively in the identification of prokaryotic essential genes since its first release in 2013. It estimates gene essentiality for prokaryotes based on orthology and phylogeny. Genome-scale essentiality data of more prokaryotic species are available, and the information has been collected into public essential gene repositories such as DEG and OGEE. A faster and more accurate toolkit is needed to meet the increasing prokaryotic genome data. We updated Geptop by supplementing more validated essentiality data into reference set (from 19 to 37 species), and introducing multi-process technology to accelerate the computing speed. Compared with Geptop 1.0 and other gene essentiality prediction models, Geptop 2.0 can generate more stable predictions and finish the computation in a shorter time. The software is available both as an online server and a downloadable standalone application. We hope that the improved Geptop 2.0 will facilitate researches in gene essentiality and the development of novel antibacterial drugs. The gene essentiality prediction tool is available at http://cefg.uestc.cn/geptop.
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Affiliation(s)
- Qing-Feng Wen
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Shuo Liu
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Chuan Dong
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hai-Xia Guo
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yi-Zhou Gao
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Feng-Biao Guo
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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12
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Quan CL, Gao F. Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes. FEBS Lett 2019; 593:918-925. [PMID: 30941752 DOI: 10.1002/1873-3468.13374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/28/2019] [Accepted: 03/31/2019] [Indexed: 11/10/2022]
Abstract
Base composition asymmetry and gene orientation bias are two common genomic structures in bacterial genomes. Here, correlation coefficients between nucleotide disparities and coding sequence (CDS) skew have been calculated, which provides insights into their relationship from an individual genome perspective. Consequently, we find GC and RY disparities correlate significantly with CDS skew, since around 60% of the bacterial genomes under study have correlation coefficients > 0.9. Then, we present a model for quantitative assessment of nucleotide disparity and CDS skew in which a numerical index R2 is used for evaluation. We find that skew curves with higher R2 perform better on the prediction of replication origins in bacteria.
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Affiliation(s)
- Chun-Lan Quan
- Department of Physics, School of Science, Tianjin University, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), China
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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