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Yu X, Feng Y, Zhang J. Characterization of the Complete Mitochondrial Genome of Wintersweet ( Chimonanthus praecox) and Comparative Analysis within Magnoliids. Life (Basel) 2024; 14:182. [PMID: 38398691 PMCID: PMC10890521 DOI: 10.3390/life14020182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as "La Mei" in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (-0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T's and G's in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution.
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Affiliation(s)
- Xianxian Yu
- College of Urban and Environmental Sciences, Xuchang University, Xuchang 461000, China;
| | - Yanlei Feng
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China;
| | - Jie Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
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Yella VR, Vanaja A. Computational analysis on the dissemination of non-B DNA structural motifs in promoter regions of 1180 cellular genomes. Biochimie 2023; 214:101-111. [PMID: 37311475 DOI: 10.1016/j.biochi.2023.06.002] [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: 12/29/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
The promoter regions of gene regulation are under evolutionary constraints and earlier studies uncovered that they are characterized by enrichment of functional non-B DNA structural signatures like curved DNA, cruciform DNA, G-quadruplex, triple-helical DNA, slipped DNA structures, and Z-DNA. However, these studies are restricted to a few model organisms, single non-B DNA motif types, or whole genomic sequences, and their comparative accumulation in promoter regions of different domains of life has not been reported comprehensively. In this study, for the first time, we investigated the preponderance of non-B DNA-prone motifs in promoter regions in 1180 genomes belonging to 28 taxonomic groups using the non-B DNA Motif Search Tool (nBMST). The trends suggest that they are predominant in promoters compared to the upstream and downstream regions of all three domains of life and variably linked to taxonomic groups. Cruciform DNA motif is the most abundant form of non-B DNA, spanning from archaea to lower eukaryotes. Curved DNA motifs are prominent in host-associated bacteria, and suppressed in mammals. Triplex-DNA and slipped DNA structure repeats are discretely dispersed in all lineages. G-quadruplex motifs are significantly enriched in mammals. We also observed that the unique enrichment of non-B DNA in promoters is strongly linked to genome GC, size, evolutionary time divergence, and ecological adaptations. Overall, our work systematically reports the unique non-B DNA structural landscape of cellular organisms from the perspective of the cis-regulatory code of genomes.
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Affiliation(s)
- Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India.
| | - Akkinepally Vanaja
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India; KL College of Pharmacy, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India
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3
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Porubiaková O, Havlík J, Indu, Šedý M, Přepechalová V, Bartas M, Bidula S, Šťastný J, Fojta M, Brázda V. Variability of Inverted Repeats in All Available Genomes of Bacteria. Microbiol Spectr 2023; 11:e0164823. [PMID: 37358458 PMCID: PMC10434271 DOI: 10.1128/spectrum.01648-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023] Open
Abstract
Noncanonical secondary structures in nucleic acids have been studied intensively in recent years. Important biological roles of cruciform structures formed by inverted repeats (IRs) have been demonstrated in diverse organisms, including humans. Using Palindrome analyser, we analyzed IRs in all accessible bacterial genome sequences to determine their frequencies, lengths, and localizations. IR sequences were identified in all species, but their frequencies differed significantly across various evolutionary groups. We detected 242,373,717 IRs in all 1,565 bacterial genomes. The highest mean IR frequency was detected in the Tenericutes (61.89 IRs/kbp) and the lowest mean frequency was found in the Alphaproteobacteria (27.08 IRs/kbp). IRs were abundant near genes and around regulatory, tRNA, transfer-messenger RNA (tmRNA), and rRNA regions, pointing to the importance of IRs in such basic cellular processes as genome maintenance, DNA replication, and transcription. Moreover, we found that organisms with high IR frequencies were more likely to be endosymbiotic, antibiotic producing, or pathogenic. On the other hand, those with low IR frequencies were far more likely to be thermophilic. This first comprehensive analysis of IRs in all available bacterial genomes demonstrates their genomic ubiquity, nonrandom distribution, and enrichment in genomic regulatory regions. IMPORTANCE Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence and localization of these important regulatory sequences in bacterial genomes. This work revealed a strong abundance of these sequences in regulatory regions and provides researchers with a valuable tool for their manipulation.
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Affiliation(s)
- Otília Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Havlík
- Mendel University in Brno, Brno, Czech Republic
| | - Indu
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Šedý
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Veronika Přepechalová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Stefan Bidula
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jiří Šťastný
- Mendel University in Brno, Brno, Czech Republic
- Brno University of Technology, Faculty of Mechanical Engineering, Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
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Yang W, Zou J, Wang J, Li N, Luo X, Jiang X, Li S. Variation in Rice Plastid Genomes in Wide Crossing Reveals Dynamic Nucleo-Cytoplasmic Interaction. Genes (Basel) 2023; 14:1411. [PMID: 37510315 PMCID: PMC10379430 DOI: 10.3390/genes14071411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Plastid genomes (plastomes) of angiosperms are well known for their relative stability in size, structure, and gene content. However, little is known about their heredity and variations in wide crossing. To such an end, the plastomes of five representative rice backcross inbred lines (BILs) developed from crosses of O. glaberrima/O. sativa were analyzed. We found that the size of all plastomes was about 134,580 bp, with a quadripartite structure that included a pair of inverted repeat (IR) regions, a small single-copy (SSC) region and a large single-copy (LSC) region. They contained 76 protein genes, 4 rRNA genes, and 30 tRNA genes. Although their size, structure, and gene content were stable, repeat-mediated recombination, gene expression, and RNA editing were extensively changed between the maternal line and the BILs. These novel discoveries demonstrate that wide crossing causes not only nuclear genomic recombination, but also plastome variation in plants, and that the plastome plays a critical role in coordinating the nuclear-cytoplasmic interaction.
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Affiliation(s)
- Weilong Yang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518036, China
| | - Jianing Zou
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Jiajia Wang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Nengwu Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Xiaoyun Luo
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Xiaofen Jiang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
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Gastineau R, Otis C, Boyle B, Lemieux C, Turmel M, St-Cyr J, Koken M. The mitochondrial genome of the bioluminescent fish Malacosteus niger Ayres, 1848 (Stomiidae, Actinopterygii) is large and complex, and contains an inverted-repeat structure. Zookeys 2023; 1157:177-191. [DOI: 10.3897/zookeys.1157.97921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/17/2023] [Indexed: 04/08/2023] Open
Abstract
We determined the complete mitogenome sequence of the bioluminescent fish Malacosteus niger using long-read sequencing technologies. The 21,263 bp mitogenome features a complex structure with two copies of a 1198-bp inverted-repeat and a region of 2616-bp containing alternating copies of 16 and 26 bp repeat elements. Whole mitogenome phylogenies inferred from both nucleotide and amino-acid datasets place M. niger among Melanostomiinae. The need for additional complete mitogenome sequences from the subfamily Malacosteinae is discussed.
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6
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Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [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] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
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Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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7
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Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
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8
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Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022; 13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-91-444-16-85
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
- The European Mink Centre, 71-415 Szczecin, Poland
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9
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Bohálová N, Dobrovolná M, Brázda V, Bidula S. Conservation and over-representation of G-quadruplex sequences in regulatory regions of mitochondrial DNA across distinct taxonomic sub-groups. Biochimie 2021; 194:28-34. [PMID: 34942301 DOI: 10.1016/j.biochi.2021.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/22/2021] [Accepted: 12/14/2021] [Indexed: 11/02/2022]
Abstract
G-quadruplexes have important regulatory roles in the nuclear genome but their distribution and potential roles in mitochondrial DNA (mtDNA) are poorly understood. We analysed 11883 mtDNA sequences from 18 taxonomic sub-groups and identified their frequency and location within mtDNA. Large differences in both the frequency and number of putative quadruplex-forming sequences (PQS) were observed amongst all the organisms and PQS frequency was negatively correlated with an increase in evolutionary age. PQS were over-represented in the 3'UTRs, D-loops, replication origins, and stem loops, indicating regulatory roles for quadruplexes in mtDNA. Variations of the G-quadruplex-forming sequence in the conserved sequence block II (CSBII) region of the human D-loop were conserved amongst other mammals, amphibians, birds, reptiles, and fishes. This D-loop PQS was conserved in the duplicated control regions of some birds and reptiles, indicating its importance to mitochondrial function. The guanine tracts in these PQS also displayed significant length heterogeneity and the length of these guanine tracts were generally longest in bird mtDNA. This information provides further insights into how G4s may contribute to the regulation and function of mtDNA and acts as a database of information for future studies investigating mitochondrial G4s in organisms other than humans.
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Affiliation(s)
- Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic; Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic; Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200, Brno, Czech Republic
| | - Stefan Bidula
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events. J Theor Biol 2021; 530:110885. [PMID: 34478743 PMCID: PMC8406619 DOI: 10.1016/j.jtbi.2021.110885] [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: 06/07/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022]
Abstract
The world faces a great unforeseen challenge through the COVID-19 pandemic caused by coronavirus SARS-CoV-2. The virus genome structure and evolution are positioned front and center for further understanding insights on vaccine development, monitoring of transmission trajectories, and prevention of zoonotic infections of new coronaviruses. Of particular interest are genomic elements Inverse Repeats (IRs), which maintain genome stability, regulate gene expressions, and are the targets of mutations. However, little research attention is given to the IR content analysis in the SARS-CoV-2 genome. In this study, we propose a geometric analysis method and using the method to investigate the distributions of IRs in SARS-CoV-2 and its related coronavirus genomes. The method represents each genomic IR sequence pair as a single point and constructs the geometric shape of the genome using the IRs. Thus, the IR shape can be considered as the signature of the genome. The genomes of different coronaviruses are then compared using the constructed IR shapes. The results demonstrate that SARS-CoV-2 genome, specifically, has an abundance of IRs, and the IRs in coronavirus genomes show an increase during evolution events.
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11
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Yang W, Zou J, Yu Y, Long W, Li S. Repeats in mitochondrial and chloroplast genomes characterize the ecotypes of the Oryza. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:7. [PMID: 37309528 PMCID: PMC10236085 DOI: 10.1007/s11032-020-01198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/28/2020] [Indexed: 06/14/2023]
Abstract
Mitochondria and chloroplast are very important organelles for organism, participating in basic life activity. Their genomes contain many repeats which can lead to a variation of genome structure. Oryza is an important genus for human beings' nutrition. Several mitochondrial and chloroplast genomes of Oryza have been sequenced, which help us to insight the distribution and evolution of the repeats in Oryza species. In this paper, we compared six mitochondrial and 13 chloroplast genomes of Oryza and found that the structures of mitochondrial genomes were more diverse than chloroplast genomes. Since repeats can change the structure of the genome, resulting in the structural diversity of the genome, we analyzed all repeats and found 31 repeats in mitochondrial and 13 repeats in chloroplast genomes. Further, we developed 21 pairs of MRS molecular markers and 12 pairs of CRS molecular markers based on mitochondrial repeats and chloroplast repeats, respectively. These molecular markers can be used to detect the repeat-mediated recombination in Oryza mitochondrial and chloroplast genomes by PCR or fluorescence quantification. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-020-01198-6.
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Affiliation(s)
- Weilong Yang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Jianing Zou
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Yajie Yu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Weixiong Long
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
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12
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Smith DR. Can Green Algal Plastid Genome Size Be Explained by DNA Repair Mechanisms? Genome Biol Evol 2020; 12:3797-3802. [PMID: 31971558 PMCID: PMC7043297 DOI: 10.1093/gbe/evaa012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/19/2022] Open
Abstract
A major finding in organelle biology over the past decade is that land plant mitochondrial genomes, which are the largest among eukaryotes, can have a “Jekyll and Hyde” mutational pattern: low for synonymous sites, high for intergenic ones. This has led to the theory that double-strand breaks (DSBs) in the intergenic DNA of plant mitogenomes are repaired by inaccurate mechanisms, such as break-induced replication, which can result in large insertions and, thus, could explain why these genomes are so prone to expansion. But how universal is this theory? Can it apply to other giant organelle DNAs, such as the massive plastid DNAs (ptDNAs) of chlamydomonadalean green algae? Indeed, it can. Analysis of the expanded plastomes from two distinct isolates of the unicellular chlamydomonadalean Chlorosarcinopsis eremi uncovered exceptionally low rates of synonymous substitution in the coding regions but high substitution rates, including frequent indels, in the noncoding ptDNA, mirroring the trend from land plant mitogenomes. Remarkably, nearly all of the substitutions and indels identified in the noncoding ptDNA of C. eremi occur adjacent to or within short inverted palindromic repeats, suggesting that these elements are mutational hotspots. Building upon earlier studies, I propose that these palindromic repeats are predisposed to DSBs and that error-prone repair of these breaks is contributing to genomic expansion. Short palindromic repeats are a common theme among bloated plastomes, including the largest one on record, meaning that these data could have wide-reaching implications for our understanding of ptDNA expansion.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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13
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Miyazawa H, Osigus HJ, Rolfes S, Kamm K, Schierwater B, Nakano H. Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions. Genome Biol Evol 2020; 13:5919586. [PMID: 33031489 PMCID: PMC7813641 DOI: 10.1093/gbe/evaa213] [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] [Accepted: 09/30/2020] [Indexed: 12/16/2022] Open
Abstract
Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32–43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon–intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.
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Affiliation(s)
- Hideyuki Miyazawa
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan.,Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Hans-Jürgen Osigus
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Sarah Rolfes
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Kai Kamm
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Bernd Schierwater
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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14
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Brázda V, Luo Y, Bartas M, Kaura P, Porubiaková O, Šťastný J, Pečinka P, Verga D, Da Cunha V, Takahashi TS, Forterre P, Myllykallio H, Fojta M, Mergny JL. G-Quadruplexes in the Archaea Domain. Biomolecules 2020; 10:biom10091349. [PMID: 32967357 PMCID: PMC7565180 DOI: 10.3390/biom10091349] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/26/2022] Open
Abstract
The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Yu Luo
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
| | - Otilia Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 612 00 Brno, Czech Republic
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
- Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Daniela Verga
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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15
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Liu X, Wu X, Tan H, Xie B, Deng Y. Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita. Comput Struct Biotechnol J 2020; 18:2424-2437. [PMID: 33005305 PMCID: PMC7508693 DOI: 10.1016/j.csbj.2020.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022] Open
Abstract
Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 contained two genotypes, both of which were quadripartite architecture consisting of two identical inverted repeats, separated by a small single-copy region and a large single-copy region. The only difference was opposite directions of the small single-copy region. The mtDNAs ranged from 116,329 bp to 134,035 bp, harboring two large identical inverted repeats. Genes of plasmid-origin were present in regions flanked by inverted repeat ID2. Most of the core genes evolved at a relatively low rate, whereas five tRNA genes located in corresponding regions of Ag0002:1-14000 and Ag0002:50001-61000 showed higher diversity. A long fragment inversion (10 Kb) was suggested to have occurred during the differentiation of two main clades, leading to two different gene orders. The number and distribution of the introns varied greatly among the A. aegerita mtDNAs. Fast invasion of short insertions likely resulted in the diversity of introns as well as other non-coding regions, increasing the variation of the mtDNAs. We raised a model about the evolution of the large repeats to explain the unusual features of A. aegerita mtDNAs. This study constructed quadripartite architecture of A. aegerita mtDNAs analogous to chloroplast DNA, proposed an interconversion model of the divergent mitochondrial genotypes with large inverted repeats. The findings could increase our knowledge of fungal evolution.
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Affiliation(s)
- Xinrui Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaoping Wu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Hao Tan
- Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
- School of Bioengineering, Jiangnan University, Wuxi 214062, China
| | - Baogui Xie
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Youjin Deng
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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16
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Global analysis of inverted repeat sequences in human gene promoters reveals their non-random distribution and association with specific biological pathways. Genomics 2020; 112:2772-2777. [DOI: 10.1016/j.ygeno.2020.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/02/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022]
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17
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Structures and stability of simple DNA repeats from bacteria. Biochem J 2020; 477:325-339. [PMID: 31967649 PMCID: PMC7015867 DOI: 10.1042/bcj20190703] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 01/12/2023]
Abstract
DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.
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18
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Cabañas N, Becerra A, Romero D, Govezensky T, Espinosa-Aguirre JJ, Camacho-Carranza R. Repetitive DNA profile of the amphibian mitogenome. BMC Bioinformatics 2020; 21:197. [PMID: 32429835 PMCID: PMC7236288 DOI: 10.1186/s12859-020-3532-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Background Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians. Results This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry. Conclusions Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.
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Affiliation(s)
- Noel Cabañas
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Tzipe Govezensky
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Jesús Javier Espinosa-Aguirre
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Rafael Camacho-Carranza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico. .,Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico.
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19
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Smith DR. Common Repeat Elements in the Mitochondrial and Plastid Genomes of Green Algae. Front Genet 2020; 11:465. [PMID: 32477407 PMCID: PMC7235400 DOI: 10.3389/fgene.2020.00465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/15/2020] [Indexed: 12/31/2022] Open
Abstract
Despite both originating from endosymbiotic bacteria, one does not typically expect mitochondrial DNA (mtDNA) to show strong sequence identity to plastid DNA (ptDNA). Nevertheless, a recent analysis of Haematococcus lacustris revealed exactly that. A common repeat element has proliferated throughout the mtDNA and ptDNA of this chlamydomonadalean green alga, resulting in the unprecedented situation whereby these two distinct organelle genomes are largely made up of nearly identical sequences. In this short update to the work on H. lacustris, I highlight another chlamydomonadalean species (Stephanosphaera pluvialis) for which matching repeats have spread throughout its organelle genomes (but to a lesser degree than in H. lacustris). What's more, the organelle repeats from S. pluvialis are similar to those from H. lacustris, suggesting that they have a shared origin, and perhaps existed in the mtDNA and ptDNA of the most recent common ancestor of these two species. However, my examination of organelle genomes from other close relatives of H. lacustris and S. pluvialis did not uncover further compelling examples of common organelle repeat elements, meaning that the evolutionary history of these repeats might be more complicated than initially thought.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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20
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Zhang R, Ge F, Li H, Chen Y, Zhao Y, Gao Y, Liu Z, Yang L. PCIR: a database of Plant Chloroplast Inverted Repeats. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5611292. [PMID: 31696928 PMCID: PMC6835207 DOI: 10.1093/database/baz127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/26/2019] [Accepted: 10/07/2019] [Indexed: 01/06/2023]
Abstract
Inverted repeats (IRs) serve as potential biomarkers for genomic instability, DNA replication and other genetic processes. However, little information can be found in databases to help researchers recognize potential IR nucleotides, explore junction sites and annotate related functional genes. Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables detection, searching and visualization of large-scale detailed information on IRs. PCIR contains many datasets, including 21 433 IRs, 113 plants chloroplast genomes, 16 948 functional genes and 21 659 visual maps. This database offers an online prediction tool for detecting IRs based on DNA sequences. PCIR can also analyze phylogenetic relationships using IR information among different species and provide users with high-quality marker maps. This database will be a valuable resource for IR distribution patterns, related genes and architectural features.
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Affiliation(s)
- Rui Zhang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Fangfang Ge
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Huayang Li
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Yudong Chen
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Zhao
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Gao
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Zhiguo Liu
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Long Yang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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21
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Čutová M, Manta J, Porubiaková O, Kaura P, Šťastný J, Jagelská EB, Goswami P, Bartas M, Brázda V. Divergent distributions of inverted repeats and G-quadruplex forming sequences in Saccharomyces cerevisiae. Genomics 2019; 112:1897-1901. [PMID: 31706022 DOI: 10.1016/j.ygeno.2019.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/13/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022]
Abstract
The importance of DNA structure in the regulation of basic cellular processes is an emerging field of research. Among local non-B DNA structures, inverted repeat (IR) sequences that form cruciforms and G-rich sequences that form G-quadruplexes (G4) are found in all prokaryotic and eukaryotic organisms and are targets for regulatory proteins. We analyzed IRs and G4 sequences in the genome of the most important biotechnology microorganism, S. cerevisiae. IR and G4-prone sequences are enriched in specific genomic locations and differ markedly between mitochondrial and nuclear DNA. While G4s are overrepresented in telomeres and regions surrounding tRNAs, IRs are most enriched in centromeres, rDNA, replication origins and surrounding tRNAs. Mitochondrial DNA is enriched in both IR and G4-prone sequences relative to the nuclear genome. This extensive analysis of local DNA structures adds to the emerging picture of their importance in genome maintenance, DNA replication and transcription of subsets of genes.
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Affiliation(s)
- Michaela Čutová
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Jacinta Manta
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Otília Porubiaková
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Patrik Kaura
- Brno University of Technology, Faculty of Mechanical Engineering, Technická 2896/2, 616 69 Brno, Czech Republic
| | - Jiří Šťastný
- Brno University of Technology, Faculty of Mechanical Engineering, Technická 2896/2, 616 69 Brno, Czech Republic; Mendel University in Brno, Zemědělská 1665/1, 61300 Brno, Czech Republic
| | - Eva B Jagelská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pratik Goswami
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Václav Brázda
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
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22
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Shamanskiy VA, Timonina VN, Popadin KY, Gunbin KV. ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation. BMC Genomics 2019; 20:295. [PMID: 31284879 PMCID: PMC6614062 DOI: 10.1186/s12864-019-5536-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA. RESULTS We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats. CONCLUSIONS ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/ . It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research.
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Affiliation(s)
- Viktor A Shamanskiy
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Valeria N Timonina
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Konstantin Yu Popadin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Konstantin V Gunbin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia. .,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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23
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Bartas M, Čutová M, Brázda V, Kaura P, Šťastný J, Kolomazník J, Coufal J, Goswami P, Červeň J, Pečinka P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. Molecules 2019; 24:molecules24091711. [PMID: 31052562 PMCID: PMC6539912 DOI: 10.3390/molecules24091711] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/09/2023] Open
Abstract
The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Michaela Čutová
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
| | - Václav Brázda
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Kolomazník
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Pratik Goswami
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jiří Červeň
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
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Bartas M, Bažantová P, Brázda V, Liao JC, Červeň J, Pečinka P. Identification of Distinct Amino Acid Composition of Human Cruciform Binding Proteins. Mol Biol 2019. [DOI: 10.1134/s0026893319010023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1097018. [PMID: 30140690 PMCID: PMC6081594 DOI: 10.1155/2018/1097018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/19/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023]
Abstract
Chloroplasts are key organelles in the management of oxygen in algae and plants and are therefore crucial for all living beings that consume oxygen. Chloroplasts typically contain a circular DNA molecule with nucleus-independent replication and heredity. Using "palindrome analyser" we performed complete analyses of short inverted repeats (S-IRs) in all chloroplast DNAs (cpDNAs) available from the NCBI genome database. Our results provide basic parameters of cpDNAs including comparative information on localization, frequency, and differences in S-IR presence. In a total of 2,565 cpDNA sequences available, the average frequency of S-IRs in cpDNA genomes is 45 S-IRs/per kbp, significantly higher than that found in mitochondrial DNA sequences. The frequency of S-IRs in cpDNAs generally decreased with S-IR length, but not for S-IRs 15, 22, 24, or 27 bp long, which are significantly more abundant than S-IRs with other lengths. These results point to the importance of specific S-IRs in cpDNA genomes. Moreover, comparison by Levenshtein distance of S-IR similarities showed that a limited number of S-IR sequences are shared in the majority of cpDNAs. S-IRs are not located randomly in cpDNAs, but are length-dependently enriched in specific locations, including the repeat region, stem, introns, and tRNA regions. The highest enrichment was found for 12 bp and longer S-IRs in the stem-loop region followed by 12 bp and longer S-IRs located before the repeat region. On the other hand, S-IRs are relatively rare in rRNA sequences and around introns. These data show nonrandom and conserved arrangements of S-IRs in chloroplast genomes.
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Čechová J, Coufal J, Jagelská EB, Fojta M, Brázda V. p73, like its p53 homolog, shows preference for inverted repeats forming cruciforms. PLoS One 2018; 13:e0195835. [PMID: 29668749 PMCID: PMC5905954 DOI: 10.1371/journal.pone.0195835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/01/2018] [Indexed: 12/12/2022] Open
Abstract
p73 is a member of the p53 protein family and has essential functions in several signaling pathways involved in development, differentiation, DNA damage responses and cancer. As a transcription factor, p73 achieves these functions by binding to consensus DNA sequences and p73 shares at least partial target DNA binding sequence specificity with p53. Transcriptional activation by p73 has been demonstrated for more than fifty p53 targets in yeast and/or human cancer cell lines. It has also been shown previously that p53 binding to DNA is strongly dependent on DNA topology and the presence of inverted repeats that can form DNA cruciforms, but whether p73 transcriptional activity has similar dependence has not been investigated. Therefore, we evaluated p73 binding to a set of p53-response elements with identical theoretical binding affinity in their linear state, but different probabilities to form extra helical structures. We show by a yeast-based assay that transactivation in vivo correlated more with the relative propensity of a response element to form cruciforms than to its expected in vitro DNA binding affinity. Structural features of p73 target sites are therefore likely to be an important determinant of its transactivation function.
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Affiliation(s)
- Jana Čechová
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlarska, Brno, Czech Republic
| | - Jan Coufal
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Eva B. Jagelská
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Miroslav Fojta
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Václav Brázda
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- * E-mail:
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