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Kim J, Cha IT, Lee KE, Son YK, Yu J, Seol D. Genomic insights and comparative analysis of Flavobacterium bizetiae HJ-32-4 isolated from soil. Antonie Van Leeuwenhoek 2023; 116:975-986. [PMID: 37542623 DOI: 10.1007/s10482-023-01858-5] [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: 09/14/2022] [Accepted: 07/19/2023] [Indexed: 08/07/2023]
Abstract
In the late 1970s, Flavobacterium bizetiae was first isolated from diseased fish in Canada. After four decades of preservation, it was reported as a novel species in 2020. Here, we report the first complete genome sequence of HJ-32-4, a novel strain of F. bizetiae. Interestingly, HJ-32-4 was isolated from soil in Gangwon-do, Republic of Korea, unlike the other two previously reported F. bizetiae strains which were isolated from fish. We generated a single circular chromosome of HJ-32-4, comprising 5,745,280 bp with a GC content of 34.2%. The average nucleotide identity (ANI) value of 96.2% indicated that HJ-32-4 belongs to F. bizetiae CIP 105534T. The virulence factor was not detected in the genome. Comparative genomic analysis of F. bizetiae and major flavobacterial pathogens revealed that F. bizetiae had a larger genome size and the ratio of peptidases (PEP) and glycoside hydrolase (GH) genes of F. bizetiae were lower than those of the rest strains, implying that F. bizetiae exhibits similar characteristics with non-pathogenic strains from a genomic point of view. However, further experimental verification is required to ensure these in silico predictions. This study will provide insight into the overall characteristics of HJ-32-4 compared to other strains.
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Affiliation(s)
- Jisu Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - In-Tae Cha
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Youn Kyoung Son
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea.
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
- Department of Surgery, Seoul National University Bundang Hospital, 172 Dolma-ro, Bundang-gu, Seongnam, 13605, Republic of Korea.
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2
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Lamolle G, Iriarte A, Simón D, Musto H. Amino acid usage and protein expression levels in the flatworm Schistosoma mansoni. Mol Biochem Parasitol 2023; 255:111581. [PMID: 37478919 DOI: 10.1016/j.molbiopara.2023.111581] [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: 03/06/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
Schistosoma mansoni is a parasitic flatworm that causes a human disease called schistosomiasis, or bilharzia. At the genomic level, S. mansoni is AT-rich, but has some compositional heterogeneity. Indeed, some regions of its genome are GC-rich, mainly in the regions located near the extreme ends of the chromosomes. Recently, we showed that, despite the strong bias towards A/T ending codons, highly expressed genes tend to use GC-rich codons. Here, we address the following question: are highly expressed sequences biased in their amino acid frequencies? Our analyses show that these sequences in S. mansoni, as in species ranging from bacteria to human, are strongly biased in nucleotide composition. Highly expressed genes tend to use GC-rich codons (in the first and second codon positions), which code the energetically cheapest amino acids. Therefore, we conclude that amino acid usage, at least in highly expressed genes, is strongly shaped by natural selection to avoid energetically expensive residues. Whether this is an adaptation to the parasitic way of life of S. mansoni, is unclear since the same pattern occurs in free-living species.
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Affiliation(s)
- Guillermo Lamolle
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Andrés Iriarte
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Avenida A. Navarro 3051, 11600 Montevideo, Uruguay
| | - Diego Simón
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay; Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Héctor Musto
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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3
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Fu Y, Liang F, Li C, Warren A, Shin MK, Li L. Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa. Microorganisms 2023; 11:1833. [PMID: 37513005 PMCID: PMC10384029 DOI: 10.3390/microorganisms11071833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.
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Affiliation(s)
- Yu Fu
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Fasheng Liang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Congjun Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Mann Kyoon Shin
- Department of Biology, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
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4
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Muselmani W, Kashif-Khan N, Bagnéris C, Santangelo R, Williams MA, Savva R. A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase. Viruses 2023; 15:1348. [PMID: 37376646 DOI: 10.3390/v15061348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
DNA-mimicking proteins encoded by viruses can modulate processes such as innate cellular immunity. An example is Ung-family uracil-DNA glycosylase inhibition, which prevents Ung-mediated degradation via the stoichiometric protein blockade of the Ung DNA-binding cleft. This is significant where uracil-DNA is a key determinant in the replication and distribution of virus genomes. Unrelated protein folds support a common physicochemical spatial strategy for Ung inhibition, characterised by pronounced sequence plasticity within the diverse fold families. That, and the fact that relatively few template sequences are biochemically verified to encode Ung inhibitor proteins, presents a barrier to the straightforward identification of Ung inhibitors in genomic sequences. In this study, distant homologs of known Ung inhibitors were characterised via structural biology and structure prediction methods. A recombinant cellular survival assay and in vitro biochemical assay were used to screen distant variants and mutants to further explore tolerated sequence plasticity in motifs supporting Ung inhibition. The resulting validated sequence repertoire defines an expanded set of heuristic sequence and biophysical signatures shared by known Ung inhibitor proteins. A computational search of genome database sequences and the results of recombinant tests of selected output sequences obtained are presented here.
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Affiliation(s)
- Wael Muselmani
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Naail Kashif-Khan
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Claire Bagnéris
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Rosalia Santangelo
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Mark A Williams
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Renos Savva
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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How Many Factors Influence Genomic GC Content Among Prokaryotes? J Mol Evol 2023; 91:6-9. [PMID: 36370165 DOI: 10.1007/s00239-022-10077-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 11/14/2022]
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6
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Khrustalev VV, Khrustaleva TA, Popinako AV. Germline mutations directions are different between introns of the same gene: case study of the gene coding for amyloid-beta precursor protein. Genetica 2023; 151:61-73. [PMID: 36129589 DOI: 10.1007/s10709-022-00166-6] [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: 07/23/2022] [Accepted: 09/08/2022] [Indexed: 02/01/2023]
Abstract
Amyloid-beta precursor protein (APP) is highly conserved in mammals. This feature allowed us to compare nucleotide usage biases in fourfold degenerated sites along the length of its coding region for 146 species of mammals and birds in search of fragments with significant deviations. Even though cytosine usage has the highest value in fourfold degenerated sites in APP coding region from all tested placental mammals, in contrast to marsupial mammals with the bias toward thymine usage, the most frequent germline and somatic mutations in human APP coding region are C to T and G to A transitions. The same mutational AT-pressure is characteristic for germline mutations in introns of human APP gene. However, surprisingly, there are several exceptional introns with deviations in germline mutations rates. The most of those introns surround exons with exceptional biases in nucleotide usage in fourfold degenerated sites. Existence of such fragments in exons 4 and 5, as well as in exon 14, can be connected with the presence of lncRNA genes in complementary strand of DNA. Exceptional nucleotide usage bias in exons 16 and 17 that contain a sequence encoding amyloid-beta peptides can be explained either by the presence of yet unmapped lncRNA(s), or by the autonomous expression of a short mRNA that encodes just C-terminal part of the APP providing an alternative source of amyloid-beta peptides. This hypothesis is supported by the increased rate of T to C transitions in introns 16-17 and 17-18 of Human APP gene relatively to other introns.
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Affiliation(s)
| | | | - Anna Vladimirovna Popinako
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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7
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Lu C, Huang X, Deng J. Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance. BMC Genomics 2023; 24:37. [PMID: 36670383 PMCID: PMC9863192 DOI: 10.1186/s12864-023-09131-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial genomes (mitogenomes) have been widely used in species identification and phylogenetic research. However, only three complete mitogenomes, and very few mitochondrial genes of scale insects (Hemiptera: Coccoidea) can be searched in GenBank. Mitogenome comparisons between scale insects or between scale insects and other hemipteran species have not yet been reported. RESULTS In this study, detailed annotation of three new mitogenomes and comparative analysis of scale insects were completed, as well as comparative analysis of the gene composition, gene arrangement, codon usage and evolutionary forces between scale insects and 488 other hemipteran species for the first time. We found that high A + T content, gene rearrangement and truncated tRNAs are common phenomena in soft scales. The average A + T content and codon usage bias of scale insects are higher and stronger than those of other hemipteran insects, respectively. The atp8 gene of Hemiptera and nine other protein-coding genes of scale insects are under positive selection with higher evolutionary rates. CONCLUSIONS The study revealed the particularity of the scale insect mitogenomes, which will provide a good reference for future research on insect phylogenetic relationships, insect pest control, biogeography and identification.
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Affiliation(s)
- Congcong Lu
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaolei Huang
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jun Deng
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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8
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Musto H. In Memoriam of Giorgio Bernardi and Noboru Sueoka: A Personal View. J Mol Evol 2022; 90:325-327. [PMID: 35838772 DOI: 10.1007/s00239-022-10066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Héctor Musto
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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9
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Wang Y, Yao L, Fan J, Zhao X, Zhang Q, Chen Y, Guo C. The Codon Usage Bias Analysis of Free-Living Ciliates' Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction of Stylonychia lemnae. Front Microbiol 2022; 13:785889. [PMID: 35308388 PMCID: PMC8927777 DOI: 10.3389/fmicb.2022.785889] [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: 09/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Ciliates represent higher unicellular animals, and several species are also important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome in ciliates can not only promote a better understanding of the genetic mode and evolution history of these organisms but also help optimize codons to improve the gene editing efficiency of model ciliates. In this study, macronuclear genome sequences of nine free-living ciliates were analyzed with CodonW software to calculate the following indices: the guanine-cytosine content (GC); the frequency of the nucleotides U, C, A, and G at the third position of codons (U3s, C3s, A3s, G3s); the effective number of codons (ENC); the correlation between GC at the first and second positions (GC12); the frequency of the nucleotides G + C at the third position of synonymous codons (GC3s); the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, neutrality plot analysis, and correlation analysis were performed to explore the factors that influence codon preference. The results showed that the GC contents in nine ciliates' MAC genomes were lower than 50% and appeared AT-rich. The base compositions of GC12 and GC3s are markedly distinct and the codon usage pattern and evolution of ciliates are affected by genetic mutation and natural selection. According to the synonymous codon analysis, the codons of most ciliates ended with A or U and eight codons were the general optimal codons of nine ciliates. A clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) expression vector of Stylonychia lemnae was constructed by optimizing the macronuclear genome codon and was successfully used to knock out the Adss gene. This is the first such extensive investigation of the MAC genome CUB of ciliates and the initial successful application of the CRISPR/Cas9 technique in free-living ciliates.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China
| | - Lin Yao
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China.,Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, Harbin, China
| | - Jinfeng Fan
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China
| | - Qing Zhang
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China
| | - Ying Chen
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China.,School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, Harbin, China
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10
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Luchetti A, Forni G, Martelossi J, Savojardo C, Martelli PL, Casadio R, Skaist AM, Wheelan SJ, Mantovani B. Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis. Genomics 2021; 113:4163-4172. [PMID: 34748900 DOI: 10.1016/j.ygeno.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 12/21/2022]
Abstract
This analysis presents five genome assemblies of four Notostraca taxa. Notostraca origin dates to the Permian/Upper Devonian and the extant forms show a striking morphological similarity to fossil taxa. The comparison of sequenced genomes with other Branchiopoda genomes shows that, despite the morphological stasis, Notostraca share a dynamic genome evolution with high turnover for gene families' expansion/contraction and a transposable elements content comparable to other branchiopods. While Notostraca substitutions rate appears similar or lower in comparison to other branchiopods, a subset of genes shows a faster evolutionary pace, highlighting the difficulty of generalizing about genomic stasis versus dynamism. Moreover, we found that the variation of Triops cancriformis transposable elements content appeared linked to reproductive strategies, in line with theoretical expectations. Overall, besides providing new genomic resources for the study of these organisms, which appear relevant for their ecology and evolution, we also confirmed the decoupling of morphological and molecular evolution.
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Affiliation(s)
- Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy.
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Jacopo Martelossi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Alyza M Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarah J Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
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11
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Khrustalev VV, Khrustaleva TA, Stojarov AN, Sharma N, Bhaskar B, Giri R. The history of mutational pressure changes during the evolution of adeno-associated viruses: A message to gene therapy and DNA-vaccine vectors designers. INFECTION GENETICS AND EVOLUTION 2019; 77:104100. [PMID: 31678645 DOI: 10.1016/j.meegid.2019.104100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/25/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
The use of virus-associated vectors for gene therapy and vaccination have emerged as safe and effective delivery system. Like all other genetic materials, these vehicles are also prone to spontaneous mutations. To understand what types of nucleotide mutations are expected in the vector, one needs to know distinct characteristics of mutational process in the corresponding virus. In this study we analyzed mutational pressure directions along the length of the genomes of all types of primate adeno-associated viruses (AAV) that are frequently used in gene therapy or DNA-vaccines. We observed clear evidences of transcription-associated mutational pressure in AAV: nucleotide usage biases are changing drastically after each of the three promoters: the higher the rate of transcription, the stronger the bias towards GC to AT mutations. Moreover, the usage of G decreased at the lower transcription rate (after P19 promoter) than the usage of C (after P40 promoter). Since nucleotide usage biases are retrospective indices, we created a scenario of changes in transcriptional map during the AAV evolution. Current mutational pressure directions are different for AAV types, while all of them demonstrate high rates of T to C transitions in the second long ORF. Since transcription rate and cell tropism are the main factors determining the preferable direction of nucleotide mutations in AAV, mutational pressure should be checked experimentally in DNA vectors before their final design with the aim to make the transferred gene more stable against those mutations.
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Affiliation(s)
| | - Tatyana Aleksandrovna Khrustaleva
- Biochemical Group of Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Nitin Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Bhaskar Bhaskar
- School of Basic Sciences, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India; BioX Centre, Indian Institute of Technology Mandi, VPO Kamand, 175005, India
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12
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Johri P, Marinov GK, Doak TG, Lynch M. Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. Genome Biol Evol 2019; 11:1398-1416. [PMID: 30980669 PMCID: PMC6505448 DOI: 10.1093/gbe/evz081] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
The evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across 13 highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ∼20% to ∼40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.
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Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington
| | - Georgi K Marinov
- Department of Biology, Indiana University, Bloomington.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington.,National Center for Genome Analysis Support, Indiana University, Bloomington
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington.,Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe
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13
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Luchetti A, Forni G, Skaist AM, Wheelan SJ, Mantovani B. Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea). ZOOLOGICAL LETTERS 2019; 5:15. [PMID: 31149346 PMCID: PMC6537178 DOI: 10.1186/s40851-019-0131-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/19/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The crustacean class Branchiopoda includes fairy shrimps, clam shrimps, tadpole shrimps, and water fleas. Branchiopods, which are well known for their great variety of reproductive strategies, date back to the Cambrian and extant taxa can be mainly found in freshwater habitats, also including ephemeral ponds. Mitochondrial genomes of the notostracan taxa Lepidurus apus lubbocki (Italy), L. arcticus (Iceland) and Triops cancriformis (an Italian and a Spanish population) are here characterized for the first time and analyzed together with available branchiopod mitogenomes. RESULTS Overall, branchiopod mitogenomes share the basic structure congruent with the ancestral Pancrustacea model. On the other hand, rearrangements involving tRNAs and the control region are observed among analyzed taxa. Remarkably, an unassigned region in the L. apus lubbocki mitogenome showed a chimeric structure, likely resulting from a non-homologous recombination event between the two flanking trnC and trnY genes. Notably, Anostraca and Onychocaudata mitogenomes showed increased GC content compared to both Notostraca and the common ancestor, and a significantly higher substitution rate, which does not correlate with selective pressures, as suggested by dN/dS values. CONCLUSIONS Branchiopod mitogenomes appear rather well-conserved, although gene rearrangements have occurred. For the first time, it is reported a putative non-homologous recombination event involving a mitogenome, which produced a pseudogenic tRNA sequence. In addition, in line with data in the literature, we explain the higher substitution rate of Anostraca and Onychocaudata with the inferred GC substitution bias that occurred during their evolution.
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Affiliation(s)
- Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
| | - Alyza M. Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sarah J. Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
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Cao Y, Cao R, Huang Y, Zhou H, Liu Y, Li X, Zhong W, Hao P. A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza a viruses. BMC Genomics 2018; 19:925. [PMID: 29363430 PMCID: PMC5780764 DOI: 10.1186/s12864-017-4330-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA editing in animals. The roles of RNA editing events have been implicated in important biological pathways. Cellular RNA editing activity in response to influenza A virus infection has not been fully characterized in human and avian hosts. This study was designed as a big data analysis to investigate the role and response of RNA editing in epithelial cells during the course of infection with various subtypes of influenza A viruses. Results Using a bioinformatics pipeline modified from our previous study, we characterized the profiles of A-to-I and C-to-U RNA editing events in human epithelial cells during the course of influenza A virus infection. Our results revealed a striking diversity of A-to-I RNA editing activities in human epithelial cells in responses to different subtypes of influenza A viruses. The infection of H1N1 and H3N2 significantly up-regulated normalized A-to-I RNA editing levels in human epithelial cells, whereas that of H5N1 did not change it and H7N9 infection significantly down-regulated normalized A-to-I editing level in A549 cells. Next, the expression levels of ADAR and APOBEC enzymes responsible for A-to-I and C-to-U RNA editing during the course of virus infection were examined. The increase of A-to-I RNA editing activities in infections with some influenza A viruses (H1N1 and H3N2) is linked to the up-regulation of ADAR1 but not ADAR2. Further, the pattern recognition receptors of human epithelial cells infected with H1N1, H3N2, H5N1 and H7N9 were examined. Variable responsive changes in gene expression were observed with RIG-I like receptors and Toll like receptors. Finally, the effect of influenza A virus infection on cellular RNA editing activity was also analyzed in avian hosts. Conclusion This work represents the first comprehensive study of cellular RNA editing activity in response to different influenza A virus infections in human and avian hosts, highlighting the critical role of RNA editing in innate immune response and the pathogenicity of different subtypes of influenza A viruses. Electronic supplementary material The online version of this article (10.1186/s12864-017-4330-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Cao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Ruiyuan Cao
- National Engineering Research Center For the Emergence Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Yaowei Huang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Hongxia Zhou
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China
| | - Yuanhua Liu
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Wu Zhong
- National Engineering Research Center For the Emergence Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China.
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Khrustalev VV, Khrustaleva TA, Sharma N, Giri R. Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication. Front Cell Infect Microbiol 2017; 7:44. [PMID: 28275585 PMCID: PMC5319961 DOI: 10.3389/fcimb.2017.00044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/07/2017] [Indexed: 12/21/2022] Open
Abstract
Zika virus (ZIKV) spread led to the recent medical health emergency of international concern. Understanding the variations in virus system is of utmost need. Using available complete sequences of ZIKV we estimated directions of mutational pressure along the length of consensus sequences of three lineages of the virus. Results showed that guanine usage is growing in ZIKV RNA plus strand due to adenine to guanine transitions, while adenine usage is growing due to cytosine to adenine transversions. Especially high levels of guanine have been found in two-fold degenerated sites of certain areas of RNA plus strand with high amount of secondary structure. The usage of cytosine in two-fold degenerated sites shows direct dependence on the amount of secondary structure in 52% (consensus sequence of East African ZIKV lineage)—32% (consensus sequence of epidemic strains) of the length of RNA minus strand. These facts are the evidences of ADAR-editing of both strands of ZIKV genome during pauses in replication. RNA plus strand can also be edited by ADAR during pauses in translation caused by the appearance of groups of rare codons. According to our results, RNA minus strand of epidemic ZIKV strain has lower number of points in which polymerase can be stalled (allowing ADAR-editing) compared to other strains. The data on preferable directions of mutational pressure in epidemic ZIKV strain is useful for future vaccine development and understanding the evolution of new strains.
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Affiliation(s)
| | - Tatyana A Khrustaleva
- Laboratory of Cellular Technologies, Institute of Physiology of the National Academy of Sciences of Belarus Minsk, Belarus
| | - Nitin Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi Mandi, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi Mandi, India
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Samchenko AA, Kiselev SS, Kabanov AV, Kondratjev MS, Komarov VM. On the nature of the domination of oligomeric (dA:dT) n tracts in the structure of eukaryotic genomes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916060233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Agashe D, Shankar N. The evolution of bacterial DNA base composition. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:517-28. [DOI: 10.1002/jez.b.22565] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/22/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Deepa Agashe
- National Center for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
| | - Nachiket Shankar
- National Center for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
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Oota S, Kawamura K, Kawai Y, Saitou N. A new framework for studying the isochore evolution: estimation of the equilibrium GC content based on the temporal mutation rate model. Genome Biol Evol 2010; 2:558-71. [PMID: 20675617 PMCID: PMC2997559 DOI: 10.1093/gbe/evq041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Isochore is the genome-wide mosaic structure in guanine-cytosine (GC) content. The origin of isochores is thought to have emerged in the ancestral amniote genome, and the GC-rich isochore is eroded in the mammalian lineages. However, there are many enigmas in the isochore evolution: 1) although all the mammalians, birds, and even reptiles, which are clearly polyphyletic, have isochore, opossum and platypus lack GC-rich and GC-poor isochore classes; 2) although the isochore is predicted to vanish according to a fairly robust theory, a completely opposite conclusion was led in some mammalian lineages; and 3) the major three hypotheses on the isochore evolution cannot explain observed evidences without flaws. So far compositional evolution has been studied under the assumption that per base pair rate of GC→AT (u) and AT→GC (v) mutations are temporally constant (the constant model). With this model alone, however, it is difficult to explain the isochore evolution. We propose a simple model for compositional evolution based on the temporal per base pair rate of mutations (the variable model). In this model, rates u and v vary depending on temporal GC contents. Mathematically, the variable model is an expansion of the constant model. By using high-density human single nucleotide polymorphism data, we compared the variable model with the constant model. Although the variable model gave consistent results with the constant model, it can potentially describe the complicated isochore evolution, which the constant model cannot explain. The versatile characteristics of the variable model may shed new light on the mysterious isochore evolution.
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Affiliation(s)
- Satoshi Oota
- Department of Biological Systems, RIKEN BioResource Center, Tsukuba, 305-0074 Japan.
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Lorén JG, Farfán M, Miñana-Galbis D, Fusté MC. Prediction of whole-genome DNA G+C content within the genus Aeromonas based on housekeeping gene sequences. Syst Appl Microbiol 2010; 33:237-42. [DOI: 10.1016/j.syapm.2010.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 10/19/2022]
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20
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Becq J, Churlaud C, Deschavanne P. A benchmark of parametric methods for horizontal transfers detection. PLoS One 2010; 5:e9989. [PMID: 20376325 PMCID: PMC2848678 DOI: 10.1371/journal.pone.0009989] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 03/10/2010] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity.
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Affiliation(s)
- Jennifer Becq
- Dynamique des Structures et Interactions des Macromolécules Biologiques, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR-S 665, Université Paris Diderot, Institut National de la Transfusion Sanguine, Paris, France
| | - Cécile Churlaud
- Molécules Thérapeutiques in silico, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR-S 973, Université Paris Diderot, Paris, France
| | - Patrick Deschavanne
- Molécules Thérapeutiques in silico, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR-S 973, Université Paris Diderot, Paris, France
- * E-mail:
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21
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Bahl MI, Hansen LH, Goesmann A, Sørensen SJ. The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established α, β and δ sub-groups. Plasmid 2007; 58:31-43. [PMID: 17306874 DOI: 10.1016/j.plasmid.2006.11.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 11/07/2006] [Accepted: 11/29/2006] [Indexed: 10/23/2022]
Abstract
The 54,383bp plasmid pKJK5 was recovered from a soil environment by exogenous plasmid isolation and conveys resistance towards tetracycline and trimethoprim. Sequencing and annotation revealed a high level of structural similarity of the backbone genes to other IncP-1 plasmids containing a Tra1 and Tra2 region, a central control module and a replication initiation module. A considerable degree of divergence was associated with the backbone genes of pKJK5 as compared to homologous genes in the alpha, beta and delta subgroups, which indicates that pKJK5 may belong to a novel subgroup of IncP-1 plasmids, which may also accommodate the partially sequenced non-subgroup classified plasmid pEMT3. Individual backbone genes in pKJK5 have a GC-content, which is consistently lower (average 6.3%) than the homologous genes from the archetype IncP-1beta plasmid R751 indicating homogenous amelioration of IncP-1 plasmid backbone genes. Two discrete accessory elements of 2145bp (load 1) and 11678bp (load 2) respectively are situated between the Tra1 and Tra2 regions of pKJK5, both bounded by inverted repeats and direct flanking repeats indicative of transposon-mediated insertion. Load 1 consists of an insertion sequence ISPa17 and load 2 is a Tn402-derivative containing a class 1 integron, IS1326 and a fragment identical to a region of plasmid pTB11 harboring a tetracycline resistance determinant and part of an IncP-1alphaoriV region.
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Affiliation(s)
- Martin Iain Bahl
- Department of Microbiology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen K, Denmark
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22
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Abu Seadah AA, El Shikh ME. RAPD typing of Aspergillus chevalieri, Aspergillus nidulans, Aspergillus tetrazonus (quadrilineatus) and their teleomorphs using 5'-d[AACGCGCAAC]-3' and 5'-d[CCCGTCAGCA]-3' primers. Mol Biol Rep 2007; 35:89-95. [PMID: 17268891 DOI: 10.1007/s11033-007-9057-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Accepted: 01/10/2007] [Indexed: 10/23/2022]
Abstract
Sexuality in fungi has long been a matter of concerns and debates that always necessitated extensive analysis of the relationship between organisms assumed to represent different developmental forms of the same organism. Moreover, mating-virulence correlation and the growing worry of opportunistic fungal infections in immunocompromised states associated with AIDS, cancer chemotherapy and organ transplantation protocols have been critically addressed nowadays. In view of that, we genetically characterized Aspergillus chevalieri, Aspergillus nidulans, Aspergillus tetrazonus (quadrilineatus) and their teleomorphs with RAPD analysis using 5'-d[AACGCGCAAC]-3' and 5'-d[CCCGTCAGCA]-3' primers. The reported similarities between the sexual and the asexual forms of the tested species, using Dice coefficient, ranged between 40% and 70% which holds pretty much with the current systematics of the genus. The study presents a rapid consistent method for identification of A. chevalieri, A. nidulans, A. tetrazonus (quadrilineatus) and their teleomorphs based on the banding pattern of RAPD-generated fragments that can be reliably used ahead of further applications on these species.
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Abstract
The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change.
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Affiliation(s)
- Arlin Stoltzfus
- Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA.
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24
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Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol 2005; 6:R67. [PMID: 16086849 PMCID: PMC1273634 DOI: 10.1186/gb-2005-6-8-r67] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Revised: 04/25/2005] [Accepted: 06/29/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Introns comprise a large fraction of eukaryotic genomes, yet little is known about their functional significance. Regulatory elements have been mapped to some introns, though these are believed to account for only a small fraction of genome wide intronic DNA. No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns. RESULTS We examine the relationship between intron length and levels of evolutionary constraint by analyzing inter-specific divergence at 225 intron fragments in Drosophila melanogaster and Drosophila simulans, sampled from a broad distribution of intron lengths. We document a strongly negative correlation between intron length and divergence. Interestingly, we also find that divergence in introns is negatively correlated with GC content. This relationship does not account for the correlation between intron length and divergence, however, and may simply reflect local variation in mutational rates or biases. CONCLUSION Short introns make up only a small fraction of total intronic DNA in the genome. Our finding that long introns evolve more slowly than average implies that, while the majority of introns in the Drosophila genome may experience little or no selective constraint, most intronic DNA in the genome is likely to be evolving under considerable constraint. Our results suggest that functional elements may be ubiquitous within longer introns and that these introns may have a more general role in regulating gene expression than previously appreciated. Our finding that GC content and divergence are negatively correlated in introns has important implications for the interpretation of the correlation between divergence and levels of codon bias observed in Drosophila.
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Affiliation(s)
- Penelope R Haddrill
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Daniel L Halligan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Peter Andolfatto
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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Wernegreen JJ, Funk DJ. Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome. J Mol Evol 2005; 59:849-58. [PMID: 15599516 DOI: 10.1007/s00239-003-0192-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 06/29/2004] [Indexed: 10/26/2022]
Abstract
The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (AT-->GC vs. GC-->AT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 AT-->GC:GC-->AT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of AT-->GC and GC-->AT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N(e) in the molecular evolution of bacterial endosymbionts.
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Affiliation(s)
- Jennifer J Wernegreen
- Josephine Bay Paul Center for Comparative Molecular Biology & Evolution, The Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
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Auewarakul P. Composition bias and genome polarity of RNA viruses. Virus Res 2004; 109:33-7. [PMID: 15826910 PMCID: PMC7114242 DOI: 10.1016/j.virusres.2004.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Revised: 09/13/2004] [Accepted: 10/06/2004] [Indexed: 11/15/2022]
Abstract
I have observed a relationship between GC content in coding sequences of RNA viruses and their genome polarity. Positive-stranded RNA viruses have significantly higher GC contents than negative-stranded RNA viruses. Coding sequences of all negative-stranded RNA viruses are biased toward high A in coding strands (high T in genomes), while two distinct patterns were observed among positive-stranded RNA genomes. This finding suggests that RNA viruses with different genome polarity are under different mutational pressure, which may be a consequence of the difference in the strategies of viral genome expression and replication. The GC content directly affects the viral codon adaptation index using highly expressed human genes as the reference set, which may theoretically predict the efficiency of viral gene expression in human cells.
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Affiliation(s)
- Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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Kern AD, Begun DJ. Patterns of Polymorphism and Divergence from Noncoding Sequences of Drosophila melanogaster and D. simulans: Evidence for Nonequilibrium Processes. Mol Biol Evol 2004; 22:51-62. [PMID: 15456897 DOI: 10.1093/molbev/msh269] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite the fact that D. melanogaster and D. simulans have been the central model system for molecular population genetics, few data are available for noncoding regions. Here, we present an analysis of population genetic data from intergenic regions and comparisons of these data to previously collected data from introns and exons. Polymorphisms and fixations were categorized as A/T to G/C or G/C to A/T changes and were polarized by inferring the ancestral state using both parsimony and maximum likelihood. Noncoding fixations in both D. melanogaster and D. simulans were consistent with equilibrium base-composition evolution. However, polarized noncoding polymorphisms, revealed a different pattern. Although A/T to G/C and G/C to A/T polymorphisms in D. simulans were consistent with equilibrium, we observed a highly significant dearth of A/T to G/C polymorphisms in D. melanogaster introns but not in intergenic sequences. Such data could be explained by recent evolution of mutational biases associated with transcription or by lineage-specific selection on base composition. These data reveal the complexity of evolutionary processes acting even on noncoding DNA in Drosophila.
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Affiliation(s)
- Andrew D Kern
- Center for Population Biology, University of California, Davis, USA.
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Abstract
Guanine plus cytosine (GC) content ranges broadly among bacterial genomes. In this study, we explore the use of a Brownian-motion model for the evolution of GC content over time. This model assumes that GC content varies over time in a continuous and homogeneous manner. Using this model and a maximum-likelihood approach, we analyzed the evolution of GC content across several bacterial phylogenies. Using three independent tests, we found that the observed divergence in GC content was consistent with a homogeneous Brownian-motion model. For example, similar rates of GC content evolution were inferred in several different bacterial subclades, indicating that there is relatively little rate heterogeneity in GC content evolution over broad evolutionary time scales. We thus argue that the homogeneous Brownian-motion model provides a good working model for GC content evolution. We then use this model to determine the overall rate of GC content evolution among eubacteria. We also determine the time frame over which GC content remains similar in related taxa, using a flexible definition for "similarity" in GC content so that, depending on the context, more or less stringent criteria may be applied. Our results have implications for models of sequence evolution, including those used for phylogenetic reconstruction and for inferring unusual changes in GC content.
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Affiliation(s)
- Eric Haywood-Farmer
- Department of Zoology, University of British Columbia, Vancouver V6T 1Z4, Canada
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Abstract
The genes from the genome of the AT-rich bacterium Campylobacter jejuni were analysed and characterised with respect to usage and amino acid usage. Codon usage is generally biased for all amino acids having synonymous codons, so that AT-rich synonyms are most frequently used. Markov chain analysis showed that codon bias and over- or underrepresentation of the corresponding tri-letter words are not related. Predicted secondary structure, lipophilicity, codon position within the gene, strand, and position on the (+)-strand were all shown to be determinants of codon usage, and these effects were in part directly explained by compositional phenomena. Codon context and the GC-content at the wobble position of the fourfold degenerate sites exert indirect effects on codon usage. The factors that affect codon usage seem to affect all amino acids, rather than selected amino acids. The usage of amino acids correlates well with the GC-content of genes, i.e. usage of amino acids encoded by GC-rich codons increases with GC-content and vice versa.
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Affiliation(s)
- Anders Fuglsang
- Royal Danish School of Pharmacy, Institute of Pharmacology, Copenhagen, Denmark.
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30
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31
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Abstract
The GC content of bacterial genomes varies from 25 to 75%, but the reason for this variation is unclear. Here, we show that genomes of bacteria that rely on their host for survival (obligatory pathogens or symbionts) tend to be AT rich. Furthermore, we have analysed bacterial phages, plasmids and insertion sequences, which might also be regarded as 'intracellular pathogens', and show that they too are significantly richer in AT than their hosts. We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences.
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Affiliation(s)
- Eduardo P C Rocha
- Atelier de BioInformatique, Université Pierre et Marie Curie, 12, rue Cuvier, 75005 Paris, France.
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32
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Barker FK, Barrowclough GF, Groth JG. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc Biol Sci 2002; 269:295-308. [PMID: 11839199 PMCID: PMC1690884 DOI: 10.1098/rspb.2001.1883] [Citation(s) in RCA: 289] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Passerine birds comprise over half of avian diversity, but have proved difficult to classify. Despite a long history of work on this group, no comprehensive hypothesis of passerine family-level relationships was available until recent analyses of DNA-DNA hybridization data. Unfortunately, given the value of such a hypothesis in comparative studies of passerine ecology and behaviour, the DNA-hybridization results have not been well tested using independent data and analytical approaches. Therefore, we analysed nucleotide sequence variation at the nuclear RAG-1 and c-mos genes from 69 passerine taxa, including representatives of most currently recognized families. In contradiction to previous DNA-hybridization studies, our analyses suggest paraphyly of suboscine passerines because the suboscine New Zealand wren Acanthisitta was found to be sister to all other passerines. Additionally, we reconstructed the parvorder Corvida as a basal paraphyletic grade within the oscine passerines. Finally, we found strong evidence that several family-level taxa are misplaced in the hybridization results, including the Alaudidae, Irenidae, and Melanocharitidae. The hypothesis of relationships we present here suggests that the oscine passerines arose on the Australian continental plate while it was isolated by oceanic barriers and that a major northern radiation of oscines (i.e. the parvorder Passerida) originated subsequent to dispersal from the south.
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Affiliation(s)
- F Keith Barker
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
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33
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Takano-Shimizu T. Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. Mol Biol Evol 2001; 18:606-19. [PMID: 11264413 DOI: 10.1093/oxfordjournals.molbev.a003841] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
I present here evidence of remarkable local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. The substitution pattern at 10 loci in the telomeric region of the X chromosome was studied for four species of the Drosophila melanogaster species subgroup. Drosophila orena and Drosophila erecta are clearly the most closely related species pair (the erecta complex) among the four species studied; however, the overall data at the 10 loci revealed a clear dichotomy in the silent substitution patterns between the AT-biased- substitution melanogaster and erecta lineages and the GC-biased-substitution yakuba and orena lineages, suggesting two or more independent changes in GC/AT substitution biases. More importantly, the results indicated a between- loci heterogeneity in GC/AT substitution bias in this small region independently in the yakuba and orena lineages. Indeed, silent substitutions in the orena lineage were significantly biased toward G and C at the consecutive yellow, lethal of scute, and asense loci, but they were significantly biased toward A and T at sta. The substitution bias toward G and C was centered in different areas in yakuba (significantly biased at EG:165H7.3, EG:171D11.2, and suppressor of sable). The similar silent substitution patterns in coding and noncoding regions, furthermore, suggested mutational biases as a cause of the substitution biases. On the other hand, previous study reveals that Drosophila yakuba has about 20-fold higher crossover frequencies in the telomeric region of the X chromosome than does D. melanogaster; this study revealed that the total genetic map length of the yakuba X chromosome was only about 1.5 times as large as that of melanogaster and that the map length of the X-telomeric y-sta region did not differ between Drosophila yakuba and D. erecta. Taken together, the data strongly suggested that an approximately 20- fold reduction in the X-telomeric crossover frequencies occurred in the ancestral population of D. melanogaster after the melanogaster-yakuba divergence but before the melanogaster-simulans divergence.
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Affiliation(s)
- T Takano-Shimizu
- Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan.
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34
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Abstract
The human genome, as in other eukaryotes, has a wide heterogeneity in the DNA base composition. The evolutionary basis for this heterogeneity has been unknown. A previous study of the human genome (846 genes analyzed) has shown that, in the major range of the G+C content in the third codon position (0.25-0.75), biases from the Parity Rule 2 (PR2) among the synonymous codons of the four-codon amino acids are similar except in the highest G+C range (Sueoka, N., 1999. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58.). PR2 is an intra-strand rule where A=T and G=C are expected when there are no biases between the two complementary strands of DNA in mutation and selection rates (substitution rates). In this study, 14,026 human genes were analyzed. In addition, the third codon positions of two-codon amino acids were analyzed. New results show the following: (a) The G+C contents of the third codon position of human genes are scattered in the G+C range of 0.22-0.96 in the third codon position. (b) The PR2 biases are similar in the range of 0.25-0.75, whereas, in the high G+C range (0.75-0.96; 13% of the genes), the PR2-bias fingerprints are different from those of the major range. (c) Unlike the PR2 biases, the G+C contents of the third codon position for both four-codon and two-codon amino acids are all correlated almost perfectly with the G+C content of the third codon position over the total G+C ranges. These results support the notion that the directional mutation pressure, rather than the directional selection pressure, is mainly responsible for the heterogeneity of the G+C content of the third codon position.
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Affiliation(s)
- N Sueoka
- University of Colorado, Department of Molecular, Cellular, and Developmental Biology, Boulder, CO 80309-0347, USA.
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35
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Picardeau M, Lobry JR, Hinnebusch BJ. Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. Genome Res 2000; 10:1594-604. [PMID: 11042157 PMCID: PMC310945 DOI: 10.1101/gr.124000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Lyme disease agent Borrelia burgdorferi has a genome composed of a linear chromosome and a series of linear and circular plasmids. We previously mapped the oriC of the linear chromosome to the center of the molecule, where a pronounced switch in CG skew occurs. In this study, we analyzed B. burgdorferi plasmid sequences for AT and CG skew in an effort to similarly identify plasmid replication origins. Cumulative skew diagrams of the plasmids suggested that they, like the linear chromosome, replicate bidirectionally from an internal origin. The B. burgdorferi linear chromosome contains homologs to partitioning protein genes soj and spoOJ, which are closely linked to oriC at the minimum cumulative skew point of the 1-Mb molecule. A soj/parA homolog also maps to cumulative skew minima of the B. burgdorferi linear and circular plasmids, further suggesting that these regions contain the replication origin. The heterogeneity in these genes and in the nucleotide sequences of the putative origin regions could account for the mutual compatibility of the multiple DNA elements in B. burgdorferi.
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Affiliation(s)
- M Picardeau
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Laboratory of Human Bacterial Pathogenesis, Hamilton, Montana 59840, USA
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36
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Casjens S, Palmer N, van Vugt R, Huang WM, Stevenson B, Rosa P, Lathigra R, Sutton G, Peterson J, Dodson RJ, Haft D, Hickey E, Gwinn M, White O, Fraser CM. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol Microbiol 2000; 35:490-516. [PMID: 10672174 DOI: 10.1046/j.1365-2958.2000.01698.x] [Citation(s) in RCA: 598] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have determined that Borrelia burgdorferi strain B31 MI carries 21 extrachromosomal DNA elements, the largest number known for any bacterium. Among these are 12 linear and nine circular plasmids, whose sequences total 610 694 bp. We report here the nucleotide sequence of three linear and seven circular plasmids (comprising 290 546 bp) in this infectious isolate. This completes the genome sequencing project for this organism; its genome size is 1 521 419 bp (plus about 2000 bp of undetermined telomeric sequences). Analysis of the sequence implies that there has been extensive and sometimes rather recent DNA rearrangement among a number of the linear plasmids. Many of these events appear to have been mediated by recombinational processes that formed duplications. These many regions of similarity are reflected in the fact that most plasmid genes are members of one of the genome's 161 paralogous gene families; 107 of these gene families, which vary in size from two to 41 members, contain at least one plasmid gene. These rearrangements appear to have contributed to a surprisingly large number of apparently non-functional pseudogenes, a very unusual feature for a prokaryotic genome. The presence of these damaged genes suggests that some of the plasmids may be in a period of rapid evolution. The sequence predicts 535 plasmid genes >/=300 bp in length that may be intact and 167 apparently mutationally damaged and/or unexpressed genes (pseudogenes). The large majority, over 90%, of genes on these plasmids have no convincing similarity to genes outside Borrelia, suggesting that they perform specialized functions.
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Affiliation(s)
- S Casjens
- Division of Molecular Biology and Genetics, Department of Oncological Sciences, University of Utah Medical School, Salt Lake City, UT 84132, USA
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37
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Wan H, Wootton JC. A global compositional complexity measure for biological sequences: AT-rich and GC-rich genomes encode less complex proteins. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0097-8485(00)80008-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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38
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Abstract
I studied the cause of the significant difference in the synonymous-substitution pattern found in the achaete-scute complex genes in two Drosophila lineages, higher codon bias in Drosophila yakuba, and lower bias in D. melanogaster. Besides these genes, the functionally unrelated yellow gene showed the same substitution pattern, suggesting a region-dependent phenomenon in the X-chromosome telomere. Because the numbers of A/T --> G/C substitutions were not significantly different from those of G/C --> A/T in the yellow noncoding regions of these species, a AT/GC mutational bias could not completely account for the synonymous-substitution biases. In contrast, we did find an approximately 14-fold difference in recombination rates in the X-chromosome telomere regions between the two species, suggesting that the reduction of recombination rates in this region resulted in the reduction of the efficacy of selection in D. melanogaster. In addition, the D. orena yellow showed a 5% increase in the G + C content at silent sites in the coding and noncoding regions since the divergence from D. erecta. This pattern was significantly different from those at the orena Adh and Amy loci. These results suggest that local changes in recombination rates and mutational pressures are contributing to the irregular synonymous-substitution patterns in Drosophila.
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Affiliation(s)
- T Takano-Shimizu
- Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan.
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39
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Rodríguez-Trelles F, Tarrío R, Ayala FJ. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group. Genetics 1999; 153:339-50. [PMID: 10471717 PMCID: PMC1460741 DOI: 10.1093/genetics/153.1.339] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigated the nucleotide composition of five genes, Xdh, Adh, Sod, Per, and 28SrRNA, in nine species of Drosophila (subgenus Sophophora) and one of Scaptodrosophila. The six species of the Drosophila saltans group markedly differ from the others in GC content and codon use bias. The GC content in the third codon position, and to a lesser extent in the first position and the introns, is higher in the D. melanogaster and D. obscura groups than in the D. saltans group (in Scaptodrosophila it is intermediate but closer to the melanogaster and obscura species). Differences are greater for Xdh than for Adh, Sod, Per, and 28SrRNA, which are functionally more constrained. We infer that rapid evolution of GC content in the saltans lineage is largely due to a shift in mutation pressure, which may have been associated with diminished natural selection due to smaller effective population numbers rather than reduced recombination rates. The rate of GC content evolution impacts the rate of protein evolution and may distort phylogenetic inferences. Previous observations suggesting that GC content evolution is very limited in Drosophila may have been distorted due to the restricted number of genes and species (mostly D. melanogaster) investigated.
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Affiliation(s)
- F Rodríguez-Trelles
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525, USA.
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40
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Picardeau M, Lobry JR, Hinnebusch BJ. Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome. Mol Microbiol 1999; 32:437-45. [PMID: 10231498 DOI: 10.1046/j.1365-2958.1999.01368.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Borrelia burgdorferi chromosome is linear, with telomeres characterized by terminal inverted repeats and covalently closed single-stranded hairpin loops. The replication mechanism of these unusual molecules is unknown. Previous analyses of bacterial chromosomes for which the complete sequence has been determined, including that of B. burgdorferi, revealed an abrupt switch in polarity of CG skew at known or putative origins of replication. We used nascent DNA strand analysis to physically map the B. burgdorferi origin to within a 2 kb region at the centre of the linear chromosome, and to show that replication proceeds bidirectionally from this origin. The results are consistent with replication models in which termination occurs at the telomeres after bidirectional, symmetrical elongation from the central origin. Sequences typical of origins of other bacterial chromosomes were not found at the origin of this spirochete. The most likely location of the replication origin of the linear chromosome is the 240 bp sequence between dnaA and dnaN where the switch in CG skew occurs.
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Affiliation(s)
- M Picardeau
- NIH, NIAID, Rocky Mountain Laboratories, Laboratory of Microbial Structure and Function, 903 S. 4th St., Hamilton, MT 59840, USA
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41
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Abstract
In a recent analysis J.G. Lawrence and H. Ochman [Proc Natl Acad Sci USA 1998;95:9413-9417 (Reference 1)] surmised that about 10% of the current E. coli genome consists of genes that were acquired in over 200 events of lateral gene transfer, which occurred subsequent to the divergence of E. coli and Salmonella some 100 million years ago. Overall, the data suggest that no less than 18% of E. coli's genes might be relatively recent foreign acquisitions, and that the average rate of acquisition may be close to about 16 kb per million years. These quantitative estimates of comparatively recent genome flux have profound impact on evolutionary genome comparisons. They tend to suggest that a search should be on to identify principles that might ultimately govern gene distribution patterns across prokaryotic genomes.
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Affiliation(s)
- W Martin
- Institut für Genetik, Technische Universität Braunschweig, Federal Republic of Germany.
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42
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Abstract
The availability of the complete sequence of Escherichia coli strain MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial genomes. We found that 755 of 4,288 ORFs (547.8 kb) have been introduced into the E. coli genome in at least 234 lateral transfer events since this species diverged from the Salmonella lineage 100 million years (Myr) ago. The average age of introduced genes was 14.4 Myr, yielding a rate of transfer 16 kb/Myr/lineage since divergence. Although most of the acquired genes subsequently were deleted, the sequences that have persisted ( approximately 18% of the current chromosome) have conferred properties permitting E. coli to explore otherwise unreachable ecological niches.
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Affiliation(s)
- J G Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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43
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Maeshiro T, Kimura M. The role of robustness and changeability on the origin and evolution of genetic codes. Proc Natl Acad Sci U S A 1998; 95:5088-93. [PMID: 9560233 PMCID: PMC20218 DOI: 10.1073/pnas.95.9.5088] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We propose that an essential factor on the origin of genetic codes is a balanced accomplishment of robustness and changeability, two antithetical, but fundamental, properties for the survival and evolution of organisms. These measures are defined as the intrinsic properties of genetic codes. An evaluation of these properties explains the structural regularity of genetic codes, estimates the order of codon reassignment in deviant codes, and predicts the most probable deviant codes that exist. The enumeration of genetic codes that could have evolved from the standard genetic code under the selection pressure on robustness and changeability strongly limits the freedom of codon reassignments. The codon reassignments of all currently known deviant genetic codes belong to this predicted evolutionary path, and they generally give the highest improvements on robustness and changeability.
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Affiliation(s)
- T Maeshiro
- Department 6, ATR Human Information Processing Research Laboratories, 2-2 Hikaridai, Seika, Soraku, Kyoto, 619-0237 Japan
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44
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Bashford JD, Tsohantjis I, Jarvis PD. A supersymmetric model for the evolution of the genetic code. Proc Natl Acad Sci U S A 1998; 95:987-92. [PMID: 9448272 PMCID: PMC18647 DOI: 10.1073/pnas.95.3.987] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A model is presented for the structure and evolution of the eukaryotic and vertebrate mitochondrial genetic codes, based on the representation theory of the Lie superalgebra A(5,0) approximately sl(6/1). A key role is played by pyrimidine and purine exchange symmetries in codon quartets.
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Affiliation(s)
- J D Bashford
- Department of Physics and Mathematical Physics, University of Adelaide Adelaide, S. A. 5005, Australia
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45
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Bernardi G, Hughes S, Mouchiroud D. The major compositional transitions in the vertebrate genome. J Mol Evol 1997; 44 Suppl 1:S44-51. [PMID: 9071011 DOI: 10.1007/pl00000051] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The vertebrate genome underwent two major compositional transitions, between therapsids and mammals and between dinosaurs and birds. These transitions concerned a sizable part (roughly one-third) of the genome, the gene-richest part of it, and consisted in an increase in GC levels (GC is the molar fraction of guanine + cytosine in DNA) which affected both coding sequences (especially third codon positions) and noncoding sequences. These major transitions were studied here by comparing GC3 levels (GC3 is the GC of third codon positions) of orthologous genes from Xenopus, chicken, calf, and man.
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Affiliation(s)
- G Bernardi
- Laboratoire de Genetique Moleculaire, Institut Jacques Monod, Paris, France
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46
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Abstract
To explain now-numerous cases of codon reassignment (departure from the "universal" code), we suggest a pathway in which the transformed codon is temporarily ambiguous. All the unusual tRNA activities required have been demonstrated. In addition, the repetitive use of certain reassignments, the phylogenetic distribution of reassignments, and the properties of present-day reassinged tRNAs are each consistent with evolution of the code via an ambiguous translational intermediate.
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47
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Abstract
Under the hypothesis of no-strand-bias conditions, the Watson and Crick base-pairing rule decreases the complexity of models of DNA evolution by reducing to six the maximum number of substitution rates. It was shown that intrastrand equimolarity between A and T (A*=T*) and between G and C (G*=C*) [corrected] is a general asymptotic property of this class of models. This statistical prediction was observed on 60 long genomic fragments (> 50 kbp) from various kingdoms, even when the effect of the two opposite orientations for coding sequences is removed. The practical consequence of the model for estimating the expected number of substitutions per site between two homologous DNA sequences is discussed.
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Affiliation(s)
- J R Lobry
- Laboratoire de Biométrie, CNRS URA 243, Université Claude Bernard, Villeurbanne, France
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