1
|
Gao W, Chen X, He J, Sha A, Luo Y, Xiao W, Xiong Z, Li Q. Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains. BMC Genomics 2024; 25:456. [PMID: 38730418 PMCID: PMC11084086 DOI: 10.1186/s12864-024-10374-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are from the same species. The results revealed that the codons of all Pleurotus strains had a preference for ending in A/T. Furthermore, the correlation between codon base compositions and codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) indices was also detected, implying the influence of base composition on codon bias. The two P. ostreatus species were found to have differences in various base bias indicators. The average effective number of codons (ENC) of mitochondrial core PCGs of Pleurotus was found to be less than 35, indicating strong codon preference of mitochondrial core PCGs of Pleurotus. The neutrality plot analysis and PR2-Bias plot analysis further suggested that natural selection plays an important role in Pleurotus codon bias. Additionally, six to ten optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified in eight Pleurotus strains, with UGU and ACU being the most widely used optimal codons in Pleurotus. Finally, based on the combined mitochondrial sequence and RSCU value, the genetic relationship between different Pleurotus strains was deduced, showing large variations between them. This research has improved our understanding of synonymous codon usage characteristics and evolution of this important fungal group.
Collapse
Affiliation(s)
- Wei Gao
- Clinical Medical College & Affiliated Hospital of Chengdu University, Chengdu University, Chengdu, Sichuan, China
| | - Xiaodie Chen
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Jing He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ajia Sha
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yingyong Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Longquanyi District, Chengdu, Sichuan, 610106, China.
| |
Collapse
|
2
|
S. Celina S, Černý J. Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts. PLoS One 2024; 19:e0302224. [PMID: 38662658 PMCID: PMC11045102 DOI: 10.1371/journal.pone.0302224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Crimean-Congo haemorrhagic fever orthonairovirus (CCHFV) is a negative-sense, single-stranded RNA virus with a segmented genome and the causative agent of a severe Crimean-Congo haemorrhagic fever (CCHF) disease. The virus is transmitted mainly by tick species in Hyalomma genus but other ticks such as representatives of genera Dermacentor and Rhipicephalus may also be involved in virus life cycle. To improve our understanding of CCHFV adaptation to its tick species, we compared nucleotide composition and codon usage patterns among the all CCHFV strains i) which sequences and other metadata as locality of collection and date of isolation are available in GenBank and ii) which were isolated from in-field collected tick species. These criteria fulfilled 70 sequences (24 coding for S, 23 for M, and 23 for L segment) of virus isolates originating from different representatives of Hyalomma and Rhipicephalus genera. Phylogenetic analyses confirmed that Hyalomma- and Rhipicephalus-originating CCHFV isolates belong to phylogenetically distinct CCHFV clades. Analyses of nucleotide composition among the Hyalomma- and Rhipicephalus-originating CCHFV isolates also showed significant differences, mainly in nucleotides located at the 3rd codon positions indicating changes in codon usage among these lineages. Analyses of codon adaptation index (CAI), effective number of codons (ENC), and other codon usage statistics revealed significant differences between Hyalomma- and Rhipicephalus-isolated CCHFV strains. Despite both sets of strains displayed a higher adaptation to use codons that are preferred by Hyalomma ticks than Rhipicephalus ticks, there were distinct codon usage preferences observed between the two tick species. These findings suggest that over the course of its long co-evolution with tick vectors, CCHFV has optimized its codon usage to efficiently utilize translational resources of Hyalomma species.
Collapse
Affiliation(s)
- Seyma S. Celina
- Faculty of Tropical AgriSciences, Center for Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jiří Černý
- Faculty of Tropical AgriSciences, Center for Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
| |
Collapse
|
3
|
Weibel CA, Wheeler AL, James JE, Willis SM, McShea H, Masel J. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.02.530449. [PMID: 38712167 PMCID: PMC11071303 DOI: 10.1101/2023.03.02.530449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an "effective population size" is often estimated from the amount of putatively neutral genetic diversity and is assumed to also capture a species' effectiveness of selection. A potentially more direct measure of the effectiveness of selection is the degree to which selection maintains preferred codons. However, past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here we propose a new Codon Adaptation Index of Species (CAIS), based on Kullback-Leibler divergence, that corrects for both confounders. We demonstrate the use of CAIS correlations, as well as the Effective Number of Codons, to show that the protein domains of more highly adapted vertebrate species evolve higher intrinsic structural disorder.
Collapse
Affiliation(s)
- Catherine A. Weibel
- Department of Mathematics, University of Arizona, Tucson, Arizona 85721, USA
- Department of Physics, University of Arizona, Tucson, Arizona 85721, USA
- present address: Department of Applied Physics, Stanford University, California, USA
| | - Andrew L. Wheeler
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona 85721, USA
| | - Jennifer E. James
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
- present address: Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Sweden
| | - Sara M. Willis
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
- present address: University Information Technology Services, University of Arizona, Tucson, Arizona 85721, USA
| | - Hanon McShea
- Department of Earth System Science, Stanford University
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| |
Collapse
|
4
|
Xiong B, Wang T, Huang S, Liao L, Wang X, Deng H, Zhang M, He J, Sun G, He S, Wang Z. Analysis of Codon Usage Bias in Xyloglucan Endotransglycosylase (XET) Genes. Int J Mol Sci 2023; 24:ijms24076108. [PMID: 37047091 PMCID: PMC10094191 DOI: 10.3390/ijms24076108] [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: 12/28/2022] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Xyloglucan endotransglycosylase (XET) genes are widely distributed in most plants, but the codon usage bias of XET genes has remained uncharacterized. Thus, we analyzed the codon usage bias using 4500 codons of 20 XET genes to elucidate the genetic and evolutionary patterns. Phylogenetic and hierarchical cluster analyses revealed that the 20 XET genes belonged to two groups. The closer the genetic distance, the more similar the codon usage preference. The codon usage bias of most XET genes was weak, but there was also some codon usage bias. AGA, AGG, AUC, and GUG were the top four codons (RSCU > 1.5) in the 20 XET genes. CitXET had a stronger codon usage bias, and there were eight optimal codons of CitXET (i.e., AGA, AUU, UCU, CUU, CCA, GCU, GUU, and AAA). The RSCU values underwent a correspondence analysis. The two main factors affecting codon usage bias (i.e., Axes 1 and 2) accounted for 54.8% and 17.6% of the total variation, respectively. Multiple correspondence analysis revealed that XET genes were widely distributed, with Group 1 genes being closer to Axis 1 than Group 2 genes, which were closer to Axis 2. Codons with A/U at the third codon position were distributed closer to Axis 1 than codons with G/C at the third codon position. PgXET, ZmXET, VlXET, VrXET, and PcXET were biased toward codons ending with G/C. In contrast, CitXET, DpXET, and BrpXET were strongly biased toward codons ending with A/U, indicating that these XET genes have a strong codon usage bias. Translational selection and base composition (especially A and U at the third codon position), followed by mutation pressure and natural selection, may be the most important factors affecting codon usage of 20 XET genes. These results may be useful in clarifying the codon usage bias of XET genes and the relevant evolutionary characteristics.
Collapse
Affiliation(s)
- Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Tie Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengjia Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Honghong Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingfei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxian He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Guochao Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Siya He
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
5
|
Kim H, Cho M, Son HS. Comparative analysis of codon usage patterns in Rift Valley fever virus. Genet Mol Biol 2020; 43:e20190240. [PMID: 32422647 PMCID: PMC7323899 DOI: 10.1590/1678-4685-gmb-2019-0240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/16/2020] [Indexed: 11/24/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a vector-borne pathogen and is the most widely
known virus in the genus Phlebovirus. Since it was first
reported, RVFV has spread to western Africa, Egypt and Madagascar from its
traditional endemic region, and infections continue to occur in new areas. In
this study, we analyzed genomic patterns according to the infection properties
of RVFV. Among the four segments of RVFV, the nucleotide composition, overall GC
content and the difference of GC composition in the third position of the codons
(%GC3) between groups were the largest in the S (NP) segment, showing that more
diverse codons were used than in other segments. Furthermore, the results of CAI
analysis of the S (NP) segment showed that viruses isolated from regions where
no previous infections had been reported had the highest values, indicating
greater adaptability to human hosts compared with other viruses. This result
suggests that mutations in the S (NP) segment co-evolve with the infected hosts
and may lead to expansion of the geographic range. The distinctive codon usage
patterns observed in specific genomic regions of a group with similar infection
properties may be related to the increasing likelihood of RVFV infections in new
areas.
Collapse
Affiliation(s)
- Hayeon Kim
- Department of Biomedical Laboratory Science, Kyungdong University, Wonju, Gangwondo, Korea
| | - Myeongji Cho
- Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Hyeon S Son
- Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Korea.,SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, Seoul, Korea
| |
Collapse
|
6
|
Puustusmaa M, Abroi A. cRegions-a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences. PeerJ 2019; 6:e6176. [PMID: 30647994 PMCID: PMC6330207 DOI: 10.7717/peerj.6176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/27/2018] [Indexed: 12/31/2022] Open
Abstract
Identifying cis-acting elements and understanding regulatory mechanisms of a gene is crucial to fully understand the molecular biology of an organism. In general, it is difficult to identify previously uncharacterised cis-acting elements with an unknown consensus sequence. The task is especially problematic with viruses containing regions of limited or no similarity to other previously characterised sequences. Fortunately, the fast increase in the number of sequenced genomes allows us to detect some of these elusive cis-elements. In this work, we introduce a web-based tool called cRegions. It was developed to identify regions within a protein-coding sequence where the conservation in the amino acid sequence is caused by the conservation in the nucleotide sequence. The cRegion can be the first step in discovering novel cis-acting sequences from diverged protein-coding genes. The results can be used as a basis for future experimental analysis. We applied cRegions on the non-structural and structural polyproteins of alphaviruses as an example and successfully detected all known cis-acting elements. In this publication and in previous work, we have shown that cRegions is able to detect a wide variety of functional elements in DNA and RNA viruses. These functional elements include splice sites, stem-loops, overlapping reading frames, internal promoters, ribosome frameshifting signals and other embedded elements with yet unknown function. The cRegions web tool is available at http://bioinfo.ut.ee/cRegions/.
Collapse
Affiliation(s)
- Mikk Puustusmaa
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Aare Abroi
- Institute of Technology, University of Tartu, Tartu, Estonia
| |
Collapse
|
7
|
Wang H, Liu S, Zhang B, Wei W. Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts. PLoS One 2016; 11:e0166260. [PMID: 27893824 PMCID: PMC5125587 DOI: 10.1371/journal.pone.0166260] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/25/2016] [Indexed: 11/19/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.
Collapse
Affiliation(s)
- Hongju Wang
- Medical School of Henan University, Kaifeng, China
| | - Siqing Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wenqiang Wei
- Medical School of Henan University, Kaifeng, China
| |
Collapse
|
8
|
Chi PB, Liberles DA. Selection on protein structure, interaction, and sequence. Protein Sci 2016; 25:1168-78. [PMID: 26808055 PMCID: PMC4918422 DOI: 10.1002/pro.2886] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/10/2022]
Abstract
Characterizing the probabilities of observing amino acid substitutions at specific sites in a protein over evolutionary time is a major goal in the field of molecular evolution. While purely statistical approaches at different levels of complexity exist, approaches rooted in underlying biological processes are necessary to characterize both the context-dependence of sequence changes (epistasis) and to extrapolate to sequences not observed in biological databases. To develop such approaches, an understanding of the different selective forces that act on amino acid substitution is necessary. Here, an overview of selection on and corresponding modeling of folding stability, folding specificity, binding affinity and specificity for ligands, the evolution of new binding sites on protein surfaces, protein dynamics, intrinsic disorder, and protein aggregation as well as the interplay with protein expression level (concentration) and biased mutational processes are presented.
Collapse
Affiliation(s)
- Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
- Department of Mathematics and Computer Science, Ursinus College, Collegeville, Pennsylvania, 19426
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
| |
Collapse
|
9
|
Camiolo S, Melito S, Porceddu A. New insights into the interplay between codon bias determinants in plants. DNA Res 2015; 22:461-70. [PMID: 26546225 PMCID: PMC4675714 DOI: 10.1093/dnares/dsv027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/01/2015] [Indexed: 12/28/2022] Open
Abstract
Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.
Collapse
Affiliation(s)
- S Camiolo
- Dipartimento di Agraria, SACEG, Università degli Studi di Sassari, Sassari, Italy
| | - S Melito
- Dipartimento di Agraria, SACEG, Università degli Studi di Sassari, Sassari, Italy
| | - A Porceddu
- Dipartimento di Agraria, SACEG, Università degli Studi di Sassari, Sassari, Italy
| |
Collapse
|
10
|
Siegal ML, Leu JY. On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2014; 45:496-517. [PMID: 26034410 PMCID: PMC4448758 DOI: 10.1146/annurev-ecolsys-120213-091705] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.
Collapse
Affiliation(s)
- Mark L Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003;
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 11529;
| |
Collapse
|
11
|
Xu C, Dong J, Tong C, Gong X, Wen Q, Zhuge Q. Analysis of synonymous codon usage patterns in seven different citrus species. Evol Bioinform Online 2013; 9:215-28. [PMID: 23761955 PMCID: PMC3667683 DOI: 10.4137/ebo.s11930] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
We used large samples of expressed sequence tags to characterize the patterns of codon usage bias (CUB) in seven different Citrus species and to analyze their evolutionary effect on selection and base composition. We found that A- and T-ending codons are predominant in Citrus species. Next, we identified 21 codons for 18 different amino acids that were considered preferred codons in all seven species. We then performed correspondence analysis and constructed plots for the effective number of codons (ENCs) to analyze synonymous codon usage. Multiple regression analysis showed that gene expression in each species had a constant influence on the frequency of optional codons (FOP). Base composition differences between the proportions were large. Finally, positive selection was detected during the evolutionary process of the different Citrus species. Overall, our results suggest that codon usages were the result of positive selection. Codon usage variation among Citrus genes is influenced by translational selection, mutational bias, and gene length. CUB is strongly affected by selection pressure at the translational level, and gene length plays only a minor role. One possible explanation for this is that the selection-mediated codon bias is consistently strong in Citrus, which is one of the most widely cultivated fruit trees.
Collapse
Affiliation(s)
- Chen Xu
- The Key Lab of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, China. ; Biology Department, Nanjing Xiaozhuang University, Nanjing, China
| | | | | | | | | | | |
Collapse
|
12
|
Abstract
The codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both regionally and transcriptionally associated mutational biases were associated significantly with codon bias, they could not explain the observed differences fully. Similarly, given that transcript abundances did not account for the differences in codon usage, it is unlikely that selection for translational efficiency can account exclusively for the observed codon bias. Thus, we considered the possible evolution of codon bias as an adaptive response to the different abundances of tRNAs in different tissues. Our analysis demonstrated that in some cases, codon usage in genes that were expressed in a broad range of tissues was influenced primarily by the tissue in which the gene was expressed maximally. On the basis of this finding we propose that genes that are expressed in certain tissues might show a tissue-specific compositional signature in relation to codon usage. These findings might have implications for the design of transgenes in relation to optimizing their expression.
Collapse
|
13
|
O'Connell MJ, Doyle AM, Juenger TE, Donoghue MTA, Keshavaiah C, Tuteja R, Spillane C. In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure. BMC Res Notes 2012; 5:359. [PMID: 22805311 PMCID: PMC3502101 DOI: 10.1186/1756-0500-5-359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational biases and selective pressures. RESULTS We have performed synonymous codon usage and codon volatility analyses for all genes in the A. thaliana genome. In contrast to reports for species from other kingdoms, we find that neither codon usage nor volatility are correlated with selection pressure (as measured by dN/dS), nor with gene expression levels on a genome wide level. Our results show that codon volatility and usage are not synonymous, rather that they are correlated with the abundance of G and C at the third codon position (GC3). CONCLUSIONS Our results indicate that while the A. thaliana genome shows evidence for synonymous codon usage bias, this is not related to the expression levels of its constituent genes. Neither codon volatility nor codon usage are correlated with expression levels or selective pressures but, because they are directly related to the composition of G and C at the third codon position, they are the result of mutational bias. Therefore, in A. thaliana codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection.
Collapse
Affiliation(s)
- Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology,Dublin City University, Dublin 9, Ireland
| | | | | | | | | | | | | |
Collapse
|
14
|
Yang Y, Chen K. Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae. Genet Mol Biol 2012; 35:448-54. [PMID: 22888294 PMCID: PMC3389533 DOI: 10.1590/s1415-47572012005000020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 11/09/2011] [Indexed: 11/21/2022] Open
Abstract
We surveyed the substitution patterns in the ent-kaurenoic acid oxidase (KAO) gene in 11 species of Oryzeae with an outgroup in the Ehrhartoidaea. The synonymous and non-synonymous substitution rates showed a high positive correlation with each other, but were negatively correlated with codon usage bias and GC content at third codon positions. The substitution rate was heterogenous among lineages. Likelihood-ratio tests showed that the non-synonymous/synonymous rate ratio changed significantly among lineages. Site-specific models provided no evidence for positive selection of particular amino acid sites in any codon of the KAO gene. This finding suggested that the significant rate heterogeneity among some lineages may have been caused by variability in the relaxation of the selective constraint among lineages or by neutral processes.
Collapse
Affiliation(s)
- Yanhua Yang
- Jiangsu University, China; Chinese Academy of Sciences, China
| | | |
Collapse
|
15
|
Zhu E, Sambath S. Characterization of Synonymous Codon Usage in the Newly Identified Duck Plague Virus UL16 Gene. ADVANCES IN INTELLIGENT AND SOFT COMPUTING 2012. [PMCID: PMC7122970 DOI: 10.1007/978-3-642-27537-1_89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A comparative analysis of the codon usage bias in the newly identified UL16 gene(GenBank accession no.EU195095) of DPV and the UL16 gene of 22 reference herpesviruses was performed. In this study, the synonymous codon usage bias of UL16 gene in the 23 herpesviruses have been analyzed and the results showed obvious differences by the CAI, RSCU, ENC and GC3s. The results revealed that the synonymous codons with A and T at the third codon positon have widely usage in the codon of UL16 gene of DPV. The ENC-GC3s plot revealed that the genetic heterogeneity in UL16 gene of herpesviruses was constrained by G+C content at the third codon position. The phylogenetic analysis suggested that DPV was evolutionarily closer to herpesviruses which further clustered into Alphaherpesvirinae. Furthermore the ORF of DPV UL16 gene has sequential rare codons. There were 21 codons showing distinct usage differences between DPV with Escherichia coli, 19 codons showing distinct usage differences between DPV with yeast, and 20 between DPV and Human. Therefore the Escherichia coli, Yeast and Human expression system were suitable for the expression of DPV UL16 gene if some codons could be optimized.
Collapse
Affiliation(s)
- Egui Zhu
- South China Normal University, Guangzhou, 510631 China, People's Republic
| | - Sabo Sambath
- South China Normal University, Guangzhou, 510631 China, People's Republic
| |
Collapse
|
16
|
Abstract
In this paper, the comprehensive analysis of codon usage bias of Duck enteritis virus (DEV) UL21 gene was performed by using CAI, CHIPS and CUSP program of EMBOSS. Our study showed that codon usage bias of DEV UL21 had strong bias towards the A-ended or T-ended codons, and GC3s contents of the codon usage bias in DEV UL21 gene were significantly varied compared with those of other 27 reference herpesviruses. The CAI, ENC value of DEV CHv strain UL21 gene is 0.615 and 55.167, respectively, indicating that the codon usage bias of this gene is weak and lowly expressed. The plot of ENC versus GC3S content revealed that DEV UL21 gene is subject to GC compositional constraints. The phylogentic analysis about amino acids codon usage bias of DEV UL21 and the27 reference herpesviruses showed that DEV was evolutionarily closer to herpesviruses Mardivirus. In addition, the codon usage bias of DEV UL21 gene was compared with those of E. coli, yeast and humans. There are 42, 45, 39 same codons usage bias between the DEV UL21 to E.coli, Yeast, H.sapiens, respectively, indicaiting that UL21 gene of DEV may be more efficiently expressed in the yeast system.
Collapse
|
17
|
Aoi MC, Rourke BC. Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes. J Mol Evol 2011; 73:74-93. [PMID: 21915654 DOI: 10.1007/s00239-011-9457-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 08/19/2011] [Indexed: 01/13/2023]
Abstract
Synonymous codon usage bias is a broadly observed phenomenon in bacteria, plants, and invertebrates and may result from selection. However, the role of selective pressures in shaping codon bias is still controversial in vertebrates, particularly for mammals. The myosin heavy-chain (MyHC) gene family comprises multiple isoforms of the major force-producing contractile protein in cardiac and skeletal muscles. Slow and fast genes are tandemly arrayed on separate chromosomes, and have distinct patterns of functionality and expression in muscle. We analyze both full-length MyHC genes (~5400 bp) and a larger collection of partial sequences at the 3' end (~500 bp). The MyHC isoforms are an interesting system in which to study codon usage bias because of their length, expression, and critical importance to organismal mobility. Codon bias and GC content differs among MyHC genes with regards to functional type, isoform, and position within the gene. Codon bias even varies by isoform within a species. We find evidence in favor of both chromosomal influences on nucleotide composition and selection against nonsense errors (SANE) acting on codon usage in MyHC genes. Intragenic variation in codon bias and elongation rate is significant, with a strong trend for increasing codon bias and elongation rate towards the 3' end of the gene, although the trend is dependent upon the degeneracy class of the codons. Therefore, patterns of codon usage in MyHC genes are consistent with models supporting SANE as a major force shaping codon usage.
Collapse
Affiliation(s)
- Mikio C Aoi
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | | |
Collapse
|
18
|
Fraser HB. Genome-wide approaches to the study of adaptive gene expression evolution: systematic studies of evolutionary adaptations involving gene expression will allow many fundamental questions in evolutionary biology to be addressed. Bioessays 2011; 33:469-77. [PMID: 21538412 DOI: 10.1002/bies.201000094] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The role of gene expression in evolutionary adaptation has been a subject of debate for over 40 years. cis-regulation of transcription has been proposed to be the primary source of morphological novelty in evolution, though this is based on only a handful of examples. Recently the first genome-wide studies of gene expression adaptation have been published, giving us an initial global view of this process. Systematic studies such as these will allow a number of key questions currently facing the field of gene expression evolution to be addressed.
Collapse
Affiliation(s)
- Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
19
|
Epistasis increases the rate of conditionally neutral substitution in an adapting population. Genetics 2011; 187:1139-52. [PMID: 21288876 DOI: 10.1534/genetics.110.125997] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Kimura observed that the rate of neutral substitution should equal the neutral mutation rate. This classic result is central to our understanding of molecular evolution, and it continues to influence phylogenetics, genomics, and the interpretation of evolution experiments. By demonstrating that neutral mutations substitute at a rate independent of population size and selection at linked sites, Kimura provided an influential justification for the idea of a molecular clock and emphasized the importance of genetic drift in shaping molecular evolution. But when epistasis among sites is common, as numerous empirical studies suggest, do neutral mutations substitute according to Kimura's expectation? Here we study simulated, asexual populations of RNA molecules, and we observe that conditionally neutral mutations--i.e., mutations that do not alter the fitness of the individual in which they arise, but that may alter the fitness effects of subsequent mutations--substitute much more often than expected while a population is adapting. We quantify these effects using a simple population-genetic model that elucidates how the substitution rate at conditionally neutral sites depends on the population size, mutation rate, strength of selection, and prevalence of epistasis. We discuss the implications of these results for our understanding of the molecular clock, and for the interpretation of molecular variation in laboratory and natural populations.
Collapse
|
20
|
Francischetti IMB, Calvo E, Andersen JF, Pham VM, Favreau AJ, Barbian KD, Romero A, Valenzuela JG, Ribeiro JMC. Insight into the Sialome of the Bed Bug, Cimex lectularius. J Proteome Res 2010; 9:3820-31. [PMID: 20441151 DOI: 10.1021/pr1000169] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The evolution of insects to a blood diet leads to the development of a saliva that antagonizes their hosts' hemostasis and inflammation. Hemostasis and inflammation are redundant processes, and thus a complex salivary potion composed of dozens or near 100 different polypeptides is commonly found by transcriptome or proteome analysis of these organisms. Several insect orders or families evolved independently to hematophagy, creating unique salivary potions in the form of novel pharmacological use of endogenous substances and in the form of unique proteins not matching other known proteins, these probably arriving by fast evolution of salivary proteins as they evade their hosts' immune response. In this work we present a preliminary description of the sialome (from the Greek Sialo = saliva) of the common bed bug Cimex lectularius, the first such work from a member of the Cimicidae family. This manuscript is a guide for the supplemental database files http://exon.niaid.nih.gov/transcriptome/C_lectularius/S1/Cimex-S1.zip and http://exon.niaid.nih.gov/transcriptome/C_lectularius/S2/Cimex-S2.xls.
Collapse
Affiliation(s)
- Ivo M B Francischetti
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, Maryland 20852, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
CALVO ERIC, SANCHEZ-VARGAS IRMA, KOTSYFAKIS MICHALIS, FAVREAU AMANDAJ, BARBIAN KENTD, PHAM VANM, OLSON KENNETHE, RIBEIRO JOSÉMC. The salivary gland transcriptome of the eastern tree hole mosquito, Ochlerotatus triseriatus. JOURNAL OF MEDICAL ENTOMOLOGY 2010; 47:376-86. [PMID: 20496585 PMCID: PMC3394432 DOI: 10.1603/me09226] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Saliva of blood-sucking arthropods contains a complex mixture of peptides that affect their host's hemostasis, inflammation, and immunity. These activities can also modify the site of pathogen delivery and increase disease transmission. Saliva also induces hosts to mount an antisaliva immune response that can lead to skin allergies or even anaphylaxis. Accordingly, knowledge of the salivary repertoire, or sialome, of a mosquito is useful to provide a knowledge platform to mine for novel pharmacological activities, to develop novel vaccine targets for vector-borne diseases, and to develop epidemiological markers of vector exposure and candidate desensitization vaccines. The mosquito Ochlerotatus triseriatus is a vector of La Crosse virus and produces allergy in humans. In this work, a total of 1,575 clones randomly selected from an adult female O. triseriatus salivary gland cDNA library was sequenced and used to assemble a database that yielded 731 clusters of related sequences, 560 of which were singletons. Primer extension experiments were performed in selected clones to further extend sequence coverage, allowing for the identification of 159 protein sequences, 66 of which code for putative secreted proteins. Supplemental spreadsheets containing these data are available at http://exon.niaid.nih.gov/transcriptome/Ochlerotatus_triseriatus/S1/Ot-S1.xls and http://exon.niaid. nih.gov/transcriptome/Ochlerotatus_triseriatus/S2/Ot-S2.xls.
Collapse
Affiliation(s)
- ERIC CALVO
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - IRMA SANCHEZ-VARGAS
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - MICHALIS KOTSYFAKIS
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - AMANDA J. FAVREAU
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, Hamilton, MT 59840
| | - KENT D. BARBIAN
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, Hamilton, MT 59840
| | - VAN M. PHAM
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - KENNETH E. OLSON
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - JOSÉ M. C. RIBEIRO
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| |
Collapse
|
22
|
Calvo E, Sanchez-Vargas I, Favreau AJ, Barbian KD, Pham VM, Olson KE, Ribeiro JM. An insight into the sialotranscriptome of the West Nile mosquito vector, Culex tarsalis. BMC Genomics 2010; 11:51. [PMID: 20089177 PMCID: PMC2823692 DOI: 10.1186/1471-2164-11-51] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 01/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saliva of adult female mosquitoes help sugar and blood feeding by providing enzymes and polypeptides that help sugar digestion, control microbial growth and counteract their vertebrate host hemostasis and inflammation. Mosquito saliva also potentiates the transmission of vector borne pathogens, including arboviruses. Culex tarsalis is a bird feeding mosquito vector of West Nile Virus closely related to C. quinquefasciatus, a mosquito relatively recently adapted to feed on humans, and the only mosquito of the genus Culex to have its sialotranscriptome so far described. RESULTS A total of 1,753 clones randomly selected from an adult female C. tarsalis salivary glands (SG) cDNA library were sequenced and used to assemble a database that yielded 809 clusters of related sequences, 675 of which were singletons. Primer extension experiments were performed in selected clones to further extend sequence coverage, allowing for the identification of 283 protein sequences, 80 of which code for putative secreted proteins. CONCLUSION Comparison of the C. tarsalis sialotranscriptome with that of C. quinquefasciatus reveals accelerated evolution of salivary proteins as compared to housekeeping proteins. The average amino acid identity among salivary proteins is 70.1%, while that for housekeeping proteins is 91.2% (P < 0.05), and the codon volatility of secreted proteins is significantly higher than those of housekeeping proteins. Several protein families previously found exclusive of mosquitoes, including only in the Aedes genus have been identified in C. tarsalis. Interestingly, a protein family so far unique to C. quinquefasciatus, with 30 genes, is also found in C. tarsalis, indicating it was not a specific C. quinquefasciatus acquisition in its evolution to optimize mammal blood feeding.
Collapse
Affiliation(s)
- Eric Calvo
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | | | | | | | | | | |
Collapse
|
23
|
Archetti M. Genetic robustness at the codon level as a measure of selection. Gene 2009; 443:64-9. [PMID: 19477246 DOI: 10.1016/j.gene.2009.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 05/15/2009] [Accepted: 05/19/2009] [Indexed: 10/20/2022]
Abstract
Selection at the DNA level is usually detected by analysing substitution rates from multiple-species comparisons. It has been suggested that measures of genetic robustness at the codon level, which can be measured by analysing a single coding sequence, can be used to estimate selection, but the validity of these measures has been questioned. Here I test the efficiency of different measures of genetic robustness at the codon level to estimate the level of selection acting on a gene. I find that volatility and other measures of robustness are correlated with dN/dS, and that this is not simply the effect of a preference for translationally optimal codons. I discuss the possible implications and the possible problems of these methods based on single-sequence codon usage analysis.
Collapse
|
24
|
Auewarakul P, Chatsurachai S, Kongchanagul A, Kanrai P, Upala S, Suriyaphol P, Puthavathana P. Codon volatility of hemagglutinin genes of H5N1 avian influenza viruses from different clades. Virus Genes 2009; 38:404-7. [DOI: 10.1007/s11262-009-0349-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 03/12/2009] [Indexed: 10/21/2022]
|
25
|
Cambray G, Mazel D. Synonymous genes explore different evolutionary landscapes. PLoS Genet 2008; 4:e1000256. [PMID: 19008944 PMCID: PMC2575237 DOI: 10.1371/journal.pgen.1000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 10/07/2008] [Indexed: 11/18/2022] Open
Abstract
The evolutionary potential of a gene is constrained not only by the amino acid sequence of its product, but by its DNA sequence as well. The topology of the genetic code is such that half of the amino acids exhibit synonymous codons that can reach different subsets of amino acids from each other through single mutation. Thus, synonymous DNA sequences should access different regions of the protein sequence space through a limited number of mutations, and this may deeply influence the evolution of natural proteins. Here, we demonstrate that this feature can be of value for manipulating protein evolvability. We designed an algorithm that, starting from an input gene, constructs a synonymous sequence that systematically includes the codons with the most different evolutionary perspectives; i.e., codons that maximize accessibility to amino acids previously unreachable from the template by point mutation. A synonymous version of a bacterial antibiotic resistance gene was computed and synthesized. When concurrently submitted to identical directed evolution protocols, both the wild type and the recoded sequence led to the isolation of specific, advantageous phenotypic variants. Simulations based on a mutation isolated only from the synthetic gene libraries were conducted to assess the impact of sub-functional selective constraints, such as codon usage, on natural adaptation. Our data demonstrate that rational design of synonymous synthetic genes stands as an affordable improvement to any directed evolution protocol. We show that using two synonymous DNA sequences improves the overall yield of the procedure by increasing the diversity of mutants generated. These results provide conclusive evidence that synonymous coding sequences do experience different areas of the corresponding protein adaptive landscape, and that a sequence's codon usage effectively constrains the evolution of the encoded protein.
Collapse
Affiliation(s)
- Guillaume Cambray
- Unité Plasticité du Génome Bactérien, Institut Pasteur, CNRS URA 2171, Paris, France
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, Institut Pasteur, CNRS URA 2171, Paris, France
- * E-mail:
| |
Collapse
|
26
|
Zhao S, Zhang Q, Chen Z, Zhong J. The factors dictating the codon usage variation among the genes in the genome of Burkholderia pseudomallei. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-007-9652-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
|
27
|
Bloom JD, Lu Z, Chen D, Raval A, Venturelli OS, Arnold FH. Evolution favors protein mutational robustness in sufficiently large populations. BMC Biol 2007; 5:29. [PMID: 17640347 PMCID: PMC1995189 DOI: 10.1186/1741-7007-5-29] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 07/17/2007] [Indexed: 11/26/2022] Open
Abstract
Background An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to evolve new functions, but it has remained unclear whether any of these differences might be due to evolutionary selection for these properties. Results Here, we use laboratory experiments to demonstrate that evolution favors protein mutational robustness if the evolving population is sufficiently large. We neutrally evolve cytochrome P450 proteins under identical selection pressures and mutation rates in populations of different sizes, and show that proteins from the larger and thus more polymorphic population tend towards higher mutational robustness. Proteins from the larger population also evolve greater stability, a biophysical property that is known to enhance both mutational robustness and evolvability. The excess mutational robustness and stability is well described by mathematical theory, and can be quantitatively related to the way that the proteins occupy their neutral network. Conclusion Our work is the first experimental demonstration of the general tendency of evolution to favor mutational robustness and protein stability in highly polymorphic populations. We suggest that this phenomenon could contribute to the mutational robustness and evolvability of viruses and bacteria that exist in large populations.
Collapse
Affiliation(s)
- Jesse D Bloom
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Zhongyi Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - David Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Alpan Raval
- Keck Graduate Institute of Applied Life Sciences and School of Mathematical Sciences, Claremont Graduate University, Claremont, CA 91711, USA
| | - Ophelia S Venturelli
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|