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Bohlin J. A simple stochastic model describing the evolution of genomic GC content in asexually reproducing organisms. Sci Rep 2022; 12:18569. [PMID: 36329129 PMCID: PMC9631610 DOI: 10.1038/s41598-022-21709-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
A genome's nucleotide composition can usually be summarized with (G)uanine + (C)ytosine (GC) or (A)denine + (T)hymine (AT) frequencies as GC% = 100% - AT%. Genomic AT/GC content has been linked to environment and selective processes in asexually reproducing organisms. A model is presented relating the evolution of genomic GC content over time to AT [Formula: see text] GC and GC [Formula: see text] AT mutation rates. By employing Itô calculus it is shown that if mutation rates are subject to random perturbations, that can vary over time, several implications follow. In particular, an extra Brownian motion term appears influencing genomic nucleotide variability; the greater the random perturbations the more genomic nucleotide variability. This can have several interpretations depending on the context. For instance, reducing the influence of the random perturbations on the AT/GC mutation rates and thus genomic nucleotide variability, to limit fitness decreasing and deleterious mutations, will likely suggest channeling of resources. On the other hand, increased genomic nucleotide diversity may be beneficial in variable environments. In asexually reproducing organisms, the Brownian motion term can be considered to be inversely reflective of the selective pressures an organism is subjected to at the molecular level. The presented model is a generalization of a previous model, limited to microbial symbionts, to all asexually reproducing, non-recombining organisms. Last, a connection between the presented model and the classical Luria-Delbrück mutation model is presented in an Itô calculus setting.
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Affiliation(s)
- Jon Bohlin
- grid.418193.60000 0001 1541 4204Division of Infection Control, Department of Methods Development and Analysis, Norwegian Institute of Public Health, Oslo, Norway ,grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. Box 4404, Lovisenberggata 8, 0403 Oslo, Norway
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2
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Oldrieve GR, Malacart B, López-Vidal J, Matthews KR. The genomic basis of host and vector specificity in non-pathogenic trypanosomatids. Biol Open 2022; 11:bio059237. [PMID: 35373253 PMCID: PMC9099014 DOI: 10.1242/bio.059237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/25/2022] [Indexed: 11/20/2022] Open
Abstract
Trypanosoma theileri, a non-pathogenic parasite of bovines, has a predicted surface protein architecture that likely aids survival in its mammalian host. Their surface proteins are encoded by genes which account for ∼10% of their genome. A non-pathogenic parasite of sheep, Trypanosoma melophagium, is transmitted by the sheep ked and is closely related to T. theileri. To explore host and vector specificity between these species, we sequenced the T. melophagium genome and transcriptome and an annotated draft genome was assembled. T. melophagium was compared to 43 kinetoplastid genomes, including T. theileri. T. melophagium and T. theileri have an AT biased genome, the greatest bias of publicly available trypanosomatids. This trend may result from selection acting to decrease the genomic nucleotide cost. The T. melophagium genome is 6.3Mb smaller than T. theileri and large families of proteins, characteristic of the predicted surface of T. theileri, were found to be absent or greatly reduced in T. melophagium. Instead, T. melophagium has modestly expanded protein families associated with the avoidance of complement-mediated lysis. We propose that the contrasting genomic features of these species is linked to their mode of transmission from their insect vector to their mammalian host. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Guy R. Oldrieve
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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3
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Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals. J Mol Evol 2022; 90:139-148. [DOI: 10.1007/s00239-022-10047-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
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4
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Clark DR, McKew BA, Binley A, Heppell CM, Whitby C, Trimmer M. Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers. ISME COMMUNICATIONS 2022; 2:5. [PMID: 37938696 PMCID: PMC9723640 DOI: 10.1038/s43705-022-00087-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2023]
Abstract
Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these communities is strongly determined by the local physico-chemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of the different microbial functional groups that cycle N and C across nine UK rivers, spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). Furthermore, the GC-content (percentage of guanine-cytosine bases in a DNA sequence) and codon-usage bias of ammonia monooxygenase DNA sequences, and the hydrophobicity and net-charge of the corresponding amino acid sequences, were all strongly correlated with BFI, likely reflecting physiological adaptations to different riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the "paradox of scales" that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.
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Affiliation(s)
- Dave R Clark
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK.
- Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK.
| | - Boyd A McKew
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Andrew Binley
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Catherine M Heppell
- School of Geography, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Corinne Whitby
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Mark Trimmer
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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5
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Begum NS, Chakraborty S. Influencing elements of codon usage bias in Birnaviridae and its evolutionary analysis. Virus Res 2022; 310:198672. [PMID: 34986367 DOI: 10.1016/j.virusres.2021.198672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022]
Abstract
Birnaviridae is a family of double stranded (ds) RNA virus with non-enveloped virions and 2-segmented genomes. These viruses are known to cause diseases in many hosts. Virus of this family has affected the fish and poultry economy in a wide sector. Unevenness in the use of synonymous codons for a particular amino acid in the coding strand of DNA is known as codon usage bias (CUB). Codons that code the same amino acid are used with variable frequency in a variety of life forms. To understand the pattern of CUB in Birnaviridae, we carried out bioinformatics study to understand the properties of coding sequences of proteins. ENC value of Birnaviridae suggested low CUB. Nucleotide analysis revealed high GC content. Parameters such as RSCU values, nucleotide skewness, translational selection, parity plot and neutrality plot were studied to investigate the pattern of codon use and it was clear that both mutational pressure and natural selection contributed to the designing of CUB in Birnaviridae family. The neutrality plot revealed natural selection to dominate the structuring of CUB and hence remained the major CUB determinant in Birnaviridae. Outcome of our study exemplified the pattern of codon use in the Birnaviridae genomes and contributed the basic primary data for fundamental evolutionary research on them.
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Affiliation(s)
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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6
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Tikhomirova TS, Matyunin MA, Lobanov MY, Galzitskaya OV. In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein? Proteins 2021; 90:1119-1141. [PMID: 34964171 DOI: 10.1002/prot.26294] [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: 09/10/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022]
Abstract
Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.
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Affiliation(s)
- Tatyana S Tikhomirova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Maxim A Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Michail Yu Lobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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7
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Ferreira M, Ventorim R, Almeida E, Silveira S, Silveira W. Protein Abundance Prediction Through Machine Learning Methods. J Mol Biol 2021; 433:167267. [PMID: 34563548 DOI: 10.1016/j.jmb.2021.167267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing the protein pool. Protein abundance is impacted by translation kinetics, which rely on features of codons. In this study, we evaluated the effect of codon usage bias of genes on protein abundance. Notably, we observed differences regarding codon usage patterns between genes coding for highly abundant proteins and genes coding for less abundant proteins. Analysis of synonymous codon usage and evolutionary selection showed a clear split between the two groups. Our machine learning models predicted protein abundances from codon usage metrics with remarkable accuracy, achieving strong correlation with experimental data. Upon integration of the predicted protein abundance in enzyme-constrained genome-scale metabolic models, the simulated phenotypes closely matched experimental data, which demonstrates that our predictive models are valuable tools for systems metabolic engineering approaches.
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Affiliation(s)
- Mauricio Ferreira
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@mauriciomyces
| | - Rafaela Ventorim
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
| | - Eduardo Almeida
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@elm_almeida
| | - Sabrina Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@sabrina_as
| | - Wendel Silveira
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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8
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Zhang Y, Jin X, Wang H, Miao Y, Yang X, Jiang W, Yin B. Compelling Evidence Suggesting the Codon Usage of SARS-CoV-2 Adapts to Human After the Split From RaTG13. Evol Bioinform Online 2021; 17:11769343211052013. [PMID: 34646060 PMCID: PMC8504689 DOI: 10.1177/11769343211052013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 needs to efficiently make use of the resources from hosts in order to survive and propagate. Among the multiple layers of regulatory network, mRNA translation is the rate-limiting step in gene expression. Synonymous codon usage usually conforms with tRNA concentration to allow fast decoding during translation. It is acknowledged that SARS-CoV-2 has adapted to the codon usage of human lungs so that the virus could rapidly proliferate in the lung environment. While this notion seems to nicely explain the adaptation of SARS-CoV-2 to lungs, it is unable to tell why other viruses do not have this advantage. In this study, we retrieve the GTEx RNA-seq data for 30 tissues (belonging to over 17 000 individuals). We calculate the RSCU (relative synonymous codon usage) weighted by gene expression in each human sample, and investigate the correlation of RSCU between the human tissues and SARS-CoV-2 or RaTG13 (the closest coronavirus to SARS-CoV-2). Lung has the highest correlation of RSCU to SARS-CoV-2 among all tissues, suggesting that the lung environment is generally suitable for SARS-CoV-2. Interestingly, for most tissues, SARS-CoV-2 has higher correlations with the human samples compared with the RaTG13-human correlation. This difference is most significant for lungs. In conclusion, the codon usage of SARS-CoV-2 has adapted to human lungs to allow fast decoding and translation. This adaptation probably took place after SARS-CoV-2 split from RaTG13 because RaTG13 is less perfectly correlated with human. This finding depicts the trajectory of adaptive evolution from ancestral sequence to SARS-CoV-2, and also well explains why SARS-CoV-2 rather than other viruses could perfectly adapt to human lung environment.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaojie Jin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Haiyan Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yaoyao Miao
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
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9
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Zhang B, Havird JC, Wang E, Lv J, Xu X. Massive gene rearrangement in mitogenomes of phytoseiid mites. Int J Biol Macromol 2021; 186:33-39. [PMID: 34237359 DOI: 10.1016/j.ijbiomac.2021.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 01/14/2023]
Abstract
Mitochondrial (mt) gene sequences have been widely used to infer phylogeny in animals. The relative order of mt genes in the mitogenome can also be a useful marker for evolution, but the propensity of mt gene rearrangements vary tremendously among taxa. Ticks and mites in Acari exemplify this trend as some families retain the ancestral arthropod gene order, while others show highly divergent gene orders. Mites in Phytoseiidae, many of which are effective biological control agents, show some of the most divergent gene orders. However, the diversity of mitogenome order within this family is little known. We thus sequenced three mt genomes of phytoseiid mites from two of the most speciose genera: Amblyseius swirskii (Athias-Henriot), Amblyseius tsugawai (Ehara) and Neoseiulus womersleyi (Schicha). We find differences in mt GC skew and nucleotide composition, especially between N. womersleyi and the two Amblyseius species. Each species within Phytoseiidae (including three previously available sequences) present a unique gene order. Phytoseiid mitogenomes show some of the highest numbers of breakpoints when compared to the ancestral arthropod order (up to 33), as well as high numbers of breakpoints within the family (14-30). This suggests a history of massive, ongoing mitogenome rearrangements in the family. Phylogenetic analyses of mt sequences confirm that the degree of gene rearrangements follows phylogenetic relatedness. We discuss possible causes for the high degree of mt gene rearrangement within phytoseiid mites as well as selection in the mt and nuclear genome tied to the independent evolution of many diverse feeding strategies in the family. Finally, we suggest N. womersleyi should be used instead of the synonym Amblyseius pseudolongispinosus.
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Affiliation(s)
- Bo Zhang
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Endong Wang
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jiale Lv
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xuenong Xu
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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10
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Majda S, Beisser D, Boenigk J. Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates. Commun Biol 2021; 4:328. [PMID: 33712682 PMCID: PMC7954800 DOI: 10.1038/s42003-021-01781-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation. We sequenced the genomes of 16 chrysophyte strains and compared them in terms of size, function, and sequence characteristics in relation to photo-, mixo- and heterotrophic nutrition. All strains were sequenced with Illumina and partly with PacBio. Heterotrophic taxa have reduced genomes and a higher GC content of up to 59% as compared to phototrophic taxa. Heterotrophs have a large pan genome, but a small core genome, indicating a differential specialization of the distinct lineages. The pan genome of mixotrophs and heterotrophs taken together but not the pan genome of the mixotrophs alone covers the complete functionality of the phototrophic strains indicating a random reduction of genes. The observed ploidy ranges from di- to tetraploidy and was found to be independent of taxonomy or trophic mode. Our results substantiate an evolution driven by nutrient and carbon limitation.
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Affiliation(s)
- Stephan Majda
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany.
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
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11
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Zhao S, Song S, Qi Q, Lei W. Cost-efficiency tradeoff is optimized in various cancer types revealed by genome-wide analysis. Mol Genet Genomics 2021; 296:369-378. [PMID: 33449159 DOI: 10.1007/s00438-020-01747-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023]
Abstract
The tradeoff between cost and efficiency is omnipresent in organisms. Specifically, how the evolutionary force shapes the tradeoff between biosynthetic cost and translation efficiency remains unclear. In the cancer community, whether the adjustment of cost-efficiency tradeoff acts as a strategy to facilitate tumor proliferation and contributes to oncogenesis is uninvestigated. To address this issue, we retrieved the gene expression profile in various cancer types and the matched normal samples from The Cancer Genome Atlas (TCGA). We found that the highly expressed genes in cancers generally have higher tAI/nitro ratios than those in normal samples. This is possibly caused by the higher tAI/nitro ratios observed in oncogenes than tumor suppressor genes (TSG). Furthermore, in the cancer samples, derived mutations in oncogenes usually lead to higher tAI/nitro ratios, while those mutations in TSG lead to lower tAI/nitro. For a special case of kidney cancer, we investigated several crucial genes in tumor samples versus normal samples, and discovered that the changes in tAI/nitro ratios are correlated with the changes in translation level. Our study for the first time revealed the optimization of cost-efficiency tradeoff in cancers. The cost-efficiency dilemma is optimized by the tumor cells, and is possibly beneficial for the translation and production of oncogenes, and eventually contributes to proliferation and oncogenesis. Our findings could provide novel perspectives in depicting the cancer genomes and might help unravel the cancer evolution.
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Affiliation(s)
- Shufen Zhao
- Department of Oncological Radiotherapy, Affiliated Hospital of Medical College Qingdao University, Shandong, China
| | - Shanai Song
- Department of Oncological Radiotherapy, Affiliated Hospital of Medical College Qingdao University, Shandong, China
| | - Qi Qi
- Department of Oncological Radiotherapy, Affiliated Hospital of Medical College Qingdao University, Shandong, China
| | - Wei Lei
- Department of Oncological Radiotherapy, Affiliated Hospital of Medical College Qingdao University, Shandong, China.
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12
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Xu Q, Chen H, Sun W, Zhu D, Zhang Y, Chen JL, Chen Y. Genome-wide analysis of the synonymous codon usage pattern of Streptococcus suis. Microb Pathog 2021; 150:104732. [PMID: 33429052 DOI: 10.1016/j.micpath.2021.104732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 01/21/2023]
Abstract
Streptococcus suis (S. suis) is a gram-positive coccus that causes disease in humans and animals. The codon usage pattern of bacteria reveals a range of evolutionary changes that assist them to enhance tolerance to environments. To better understand the genetic features during the evolution of S. suis, we performed codon usage analysis. Nine pathogenic strains of different serotypes and different geographical distribution were analyzed to better understand the differences in their evolutionary process. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A/T-ending codons are dominant in S. suis. Neutrality analysis, correspondence analysis and ENC-plot results revealed that natural selection is the predominant element prompting codon usage. Cluster analysis based on RSCU was roughly consistent with the dendrogram rooted genomic BLAST analysis. Comparison of synonymous codon usage pattern between S. suis and susceptible hosts (H. sapiens and S. scrofa) revealed that the codon usage of S. suis is separated from the synonymous codon usage of susceptible hosts. The CAI values implied that S. suis includes a series of predicted highly expressed coding sequences contained in metabolism and transcriptional regulation, revealing the necessity of this pathogen to deal with various environmental conditions. The study of codon usage in S. suis may provide evidence involving the molecular evolution of bacteria and a better understanding of evolutionary relationships between S. suis and its corresponding hosts.
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Affiliation(s)
- Quanming Xu
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen Sun
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dewen Zhu
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongyi Zhang
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ye Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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13
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Kay C, Williams TA, Gibson W. Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution. BMC Evol Biol 2020; 20:161. [PMID: 33297939 PMCID: PMC7724854 DOI: 10.1186/s12862-020-01701-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
Background Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA. African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of the maxicircle, a component of trypanosome mitochondrial DNA to study the evolutionary history of trypanosomes. Results We used long-read sequencing to completely assemble maxicircle mitochondrial DNA from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome maxicircle gene coding regions from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of pre-edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. The gene coding regions of maxicircle mitochondrial DNAs were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense. Conclusions Our data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum, major human and animal pathogens.
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Affiliation(s)
- C Kay
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - T A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - W Gibson
- School of Biological Sciences, University of Bristol, Bristol, UK
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14
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Barbhuiya PA, Uddin A, Chakraborty S. Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia. J Cell Physiol 2020; 236:2850-2868. [PMID: 32960450 DOI: 10.1002/jcp.30050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/07/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022]
Abstract
In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.
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Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi, Assam, India
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15
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Vettor R. The right nutrition for the nutrition related diseases. Rev Endocr Metab Disord 2020; 21:293-296. [PMID: 32779061 DOI: 10.1007/s11154-020-09582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Roberto Vettor
- Department of Medicine, Endocrine-Metabolic Unit, Padova University, Padova, Italy.
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16
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Ge Z, Li X, Cao X, Wang R, Hu W, Gen L, Han S, Shang Y, Liu Y, Zhou JH. Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias. Genomics 2020; 112:4657-4665. [PMID: 32818632 DOI: 10.1016/j.ygeno.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/09/2022]
Abstract
Given the high therapeutic value of the staphylococcal phage, the genome co-evolution of the phage and the host has gained great attention. Though the genome-wide AT richness in staphylococcal phages has been well-studied with nucleotide usage bias, here we proved that host factor, lifestyle and taxonomy are also important factors in understanding the phage nucleotide usages bias using information entropy formula. Such correlation is especially prominent when it comes to the synonymous codon usages of staphylococcal phages, despite the overall scattered codon usage pattern represented by principal component analysis. This strong relationship is explained by nucleotide skew which testified that the usage biases of nucleotide at different codon positions are acting on synonymous codons. Therefore, our study reveals a hidden relationship of genome evolution with host limitation and phagic phenotype, providing new insight into phage genome evolution at genetic level.
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Affiliation(s)
- Zhiyi Ge
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Xuerui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, United States of America
| | - Wen Hu
- Gansu Police Vocational College, Lanzhou 730046, Gansu, PR China
| | - Ling Gen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Shengyi Han
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China; The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, Gansu Province, PR China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Jian-Hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China.
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17
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Preuss M, Verbruggen H, Zuccarello GC. The Organelle Genomes in the Photosynthetic Red Algal Parasite Pterocladiophila hemisphaerica (Florideophyceae, Rhodophyta) Have Elevated Substitution Rates and Extreme Gene Loss in the Plastid Genome. JOURNAL OF PHYCOLOGY 2020; 56:1006-1018. [PMID: 32215918 DOI: 10.1111/jpy.12996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Comparative organelle genome studies of parasites can highlight genetic changes that occur during the transition from a free-living to a parasitic state. Our study focuses on a poorly studied group of red algal parasites, which are often closely related to their red algal hosts and from which they presumably evolved. Most of these parasites are pigmented and some show photosynthetic capacity. Here, we assembled and annotated the complete organelle genomes of the photosynthetic red algal parasite, Pterocladiophila hemisphaerica. The plastid genome is the smallest known red algal plastid genome at 68,701 bp. The plastid genome has many genes missing, including all photosynthesis-related genes. In contrast, the mitochondrial genome is similar in architecture to that of other free-living red algae. Both organelle genomes show elevated mutation rates and significant changes in patterns of selection, measured as dN/dS ratios. This caused phylogenetic analyses, even of multiple aligned proteins, to be unresolved or give contradictory relationships. Full plastid datasets interfered by selected best gene evolution models showed the supported relationship of P. hemisphaerica within the Ceramiales, but the parasite was grouped with support as sister to the Gracilariales when interfered under the GHOST model. Nuclear rDNA showed a supported grouping of the parasite within a clade containing several red algal orders including the Gelidiales. This photosynthetic parasite, which is unable to photosynthesize with its own plastid due to the total loss of all photosynthesis genes, raises intriguing questions on parasite-host organelle genome capabilities and interactions.
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Affiliation(s)
- Maren Preuss
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
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18
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Bohlin J, Rose B, Brynildsrud O, Birgitte Freiesleben De Blasio. A simple stochastic model describing genomic evolution over time of GC content in microbial symbionts. J Theor Biol 2020; 503:110389. [PMID: 32634385 DOI: 10.1016/j.jtbi.2020.110389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
An organism's genomic base composition is usually summarized by its AT or GC content due to Chargaff's parity laws. Variation in prokaryotic GC content can be substantial between taxa but is generally small within microbial genomes. This variation has been found to correlate with both phylogeny and environmental factors. Since novel single-nucleotide polymorphisms (SNPs) within genomes are at least partially linked to the environment through natural selection, SNP GC content can be considered a compound measure of an organism's environmental influences, lifestyle, phylogeny as well as other more or less random processes. While there are several models describing genomic GC content few, if any, consider AT/GC mutation rates subjected to random perturbations. We present a mathematical model that describes how GC content in microbial genomes evolves over time as a function of the AT → GC and GC → AT mutation rates with Gaussian white noise disturbances. The model, which is suited specifically to non-recombining vertically transmitted prokaryotic symbionts, suggests that small differences in the AT/GC mutation rates can lead to profound differences in outcome due to the ensuing stochastic process. In other words, the model indicates that time to extinction could be a consequence of the mutation rate trajectory on which the symbiont embarked early on in its evolutionary history.
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Affiliation(s)
- Jon Bohlin
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Brittany Rose
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ola Brynildsrud
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Birgitte Freiesleben De Blasio
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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19
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Zhou JH, Li H, Li X, Gao J, Xu L, Han S, Liu Y, Shang Y, Cao X. Tracing Brucella evolutionary dynamics in expanding host ranges through nucleotide, codon and amino acid usages in genomes. J Biomol Struct Dyn 2020; 39:3986-3995. [PMID: 32448095 DOI: 10.1080/07391102.2020.1773313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The host range of Brucella organisms has expanded from terrestrial and marine mammals to fish and amphibians. The high homology genomes of different Brucella organisms promote us to investigate evolutionary patterns for nucleotide, codon and amino acid usage patterns at gene levels among Brucella species. Although the similar patterns for nucleotide and synonymous codon usages exist in gene population, GC composition at the first codon position has significant correlations to that of the second and third codon positions, respectively, suggesting that nucleotide usages surrounding one codon influence synonymous codon usage patterns. Evolutionary patterns represented by synonymous codon and amino acid usages reflect host factor impacting Brucella speciation. As for genetic variations of important virulent factors involved with different biological functions, genes encoding lipoplysaccharides (LPSs) display more distinctive codon adaptation to Brucella than those of the BvrR/BvrS system and type IV secretion system. By Bayesian analysis, the polygenetic constructions for these genes of virulent factors shared by Brucella species display the purifying/positive selections and partially host factor in mediating genetic variations of these genes. The systemic analyses for nucleotide, synonymous codon and amino acid usages at gene level and genetic variations of important virulent factor genes display that host limitation influences either genetic characterizations at gene level or a particular gene involved in virulent factors of Brucella.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jian-Hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Hua Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,China Agricultural Vet Biology and Technology limited liability company, Lanzhou, Gansu, P.R. China
| | - Xuerui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Jing Gao
- Gansu Center for Animal Disease Prevention and Control, Lanzhou, Gansu, P.R. China
| | - Long- Xu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, P.R. China
| | - Shengyi Han
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, P.R. China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
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20
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. RESULTS We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. CONCLUSIONS These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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21
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Pavlovic Djuranovic S, Erath J, Andrews RJ, Bayguinov PO, Chung JJ, Chalker DL, Fitzpatrick JAJ, Moss WN, Szczesny P, Djuranovic S. Plasmodium falciparum translational machinery condones polyadenosine repeats. eLife 2020; 9:e57799. [PMID: 32469313 PMCID: PMC7295572 DOI: 10.7554/elife.57799] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/28/2020] [Indexed: 01/04/2023] Open
Abstract
Plasmodium falciparum is a causative agent of human malaria. Sixty percent of mRNAs from its extremely AT-rich (81%) genome harbor long polyadenosine (polyA) runs within their ORFs, distinguishing the parasite from its hosts and other sequenced organisms. Recent studies indicate polyA runs cause ribosome stalling and frameshifting, triggering mRNA surveillance pathways and attenuating protein synthesis. Here, we show that P. falciparum is an exception to this rule. We demonstrate that both endogenous genes and reporter sequences containing long polyA runs are efficiently and accurately translated in P. falciparum cells. We show that polyA runs do not elicit any response from No Go Decay (NGD) or result in the production of frameshifted proteins. This is in stark contrast to what we observe in human cells or T. thermophila, an organism with similar AT-content. Finally, using stalling reporters we show that Plasmodium cells evolved not to have a fully functional NGD pathway.
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Affiliation(s)
| | - Jessey Erath
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
| | - Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of MedicineSt. LouisUnited States
| | - Joyce J Chung
- Department of Biology, Washington UniversitySt LouisUnited States
| | | | - James AJ Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
- Washington University Center for Cellular Imaging, Washington University School of MedicineSt. LouisUnited States
- Department of Neuroscience, Washington University School of MedicineSt. LouisUnited States
- Department of Biomedical Engineering, Washington UniversitySt LouisUnited States
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Pawel Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Department of BioinformaticsWarsawPoland
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
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22
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Auboeuf D. Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces. Life (Basel) 2020; 10:life10020007. [PMID: 31973071 PMCID: PMC7175370 DOI: 10.3390/life10020007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made of complex multicellular organisms and, then, modified to fit a DNA-centric view. In this article, it is argued that based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that (i) natural selection plays a dominant role in evolution and (ii) the probability of mutations is independent of the generated phenotype. It is shown that the adaptation of a phenotype to an environment does not correspond to organism fitness, but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome, but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature, and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype in which the phenotype ensures the stability of its originating genome in a cellular and environmental physicochemical parameter-depending manner.
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Affiliation(s)
- Didier Auboeuf
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie, Site Jacques Monod, F-69007, Lyon, France
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Yuan M, Zhang L, Zhang Q, Zhang L, Li M, Wang X, Feng R, Tang P. Mitogenome evolution in ladybirds: Potential association with dietary adaptation. Ecol Evol 2020; 10:1042-1053. [PMID: 32015863 PMCID: PMC6988538 DOI: 10.1002/ece3.5971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022] Open
Abstract
Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein-coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits.
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Affiliation(s)
- Ming‐Long Yuan
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Li‐Jun Zhang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Qi‐Lin Zhang
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunmingChina
| | - Li Zhang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Min Li
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Xiao‐Tong Wang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Run‐Qiu Feng
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Pei‐An Tang
- Collaborative Innovation Center for Modern Grain Circulation and SafetyCollege of Food Science and EngineeringNanjing University of Finance and EconomicsNanjingChina
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24
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Erath J, Djuranovic S, Djuranovic SP. Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle. Front Microbiol 2019; 10:2823. [PMID: 31866984 PMCID: PMC6908487 DOI: 10.3389/fmicb.2019.02823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is caused by unicellular apicomplexan parasites of the genus Plasmodium, which includes the major human parasite Plasmodium falciparum. The complex cycle of the malaria parasite in both mosquito and human hosts has been studied extensively. There is tight control of gene expression in each developmental stage, and at every level of gene synthesis: from RNA transcription, to its subsequent translation, and finally post-translational modifications of the resulting protein. Whole-genome sequencing of P. falciparum has laid the foundation for significant biological advances by revealing surprising genomic information. The P. falciparum genome is extremely AT-rich (∼80%), with a substantial portion of genes encoding intragenic polyadenosine (polyA) tracks being expressed throughout the entire parasite life cycle. In most eukaryotes, intragenic polyA runs act as negative regulators of gene expression. Recent studies have shown that translation of mRNAs containing 12 or more consecutive adenosines results in ribosomal stalling and frameshifting; activating mRNA surveillance mechanisms. In contrast, P. falciparum translational machinery can efficiently and accurately translate polyA tracks without activating mRNA surveillance pathways. This unique feature of P. falciparum raises interesting questions: (1) How is P. falciparum able to efficiently and correctly translate polyA track transcripts, and (2) What are the specifics of the translational machinery and mRNA surveillance mechanisms that separate P. falciparum from other organisms? In this review, we analyze possible evolutionary shifts in P. falciparum protein synthesis machinery that allow efficient translation of an AU rich-transcriptome. We focus on physiological and structural differences of P. falciparum stage specific ribosomes, ribosome-associated proteins, and changes in mRNA surveillance mechanisms throughout the complete parasite life cycle, with an emphasis on the mosquito and liver stages.
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Affiliation(s)
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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25
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Yin Y, Li B, Mou K, Khan MT, Kaushik AC, Wei D, Zhang YJ. Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in glioma. BMC Med Genomics 2019; 12:125. [PMID: 31464612 PMCID: PMC6716898 DOI: 10.1186/s12920-019-0571-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background The five-year survival rate and therapeutic effect of malignant glioma is low. Identification of key/associated proteins and pathways in glioma is necessary for developing effective diagnosis and targeted therapy of glioma. In addition, Glioma involves hypoxia-specific microenvironment, whether hypoxia restriction influences the stoichioproteomic characteristics of expressed proteins is unknown. Methods In this study, we analyzed the most comprehensive immunohistochemical data from 12 human glioma samples and 4 normal cell types of cerebral cortex, identified differentially expressed proteins (DEPs), and researched the oxygen contents of DEPs, highly and lowly expressed proteins. Further we located key genes on human genome to determine their locations and enriched them for key functional pathways. Results Our results showed that although no difference was detected on whole proteome, the average oxygen content of highly expressed proteins is 6.65% higher than that of lowly expressed proteins in glioma. A total of 1480 differentially expressed proteins were identified in glioma, including 226 up regulated proteins and 1254 down regulated proteins. The average oxygen content of up regulated proteins is 2.56% higher than that of down regulated proteins in glioma. The localization of differentially expressed genes on human genome showed that most genes were on chromosome 1 and least on Y. The up regulated proteins were significantly enriched in pathways including cell cycle, pathways in cancer, oocyte meiosis, DNA replication etc. Functional dissection of the up regulated proteins with high oxygen contents showed that 51.28% of the proteins were involved in cell cycle and cyclins. Conclusions Element signature of oxygen limitation could not be detected in glioma, just as what happened in plants and microbes. Unsaved use of oxygen by the highly expressed proteins and DEPs were adapted to the fast division of glioma cells. This study can help to reveal the molecular mechanism of glioma, and provide a new approach for studies of cancer-related biomacromolecules. In addition, this study lays a foundation for application of stoichioproteomics in precision medicine. Electronic supplementary material The online version of this article (10.1186/s12920-019-0571-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongqin Yin
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331, People's Republic of China
| | - Bo Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331, People's Republic of China
| | - Kejie Mou
- Department of Neurosurgery, Bishan Hospital, Bishan, Chongqing, 402760, China
| | - Muhammad T Khan
- Shanghai Jiao Tong University, Shanghai, China.,Capital University of Science & Technology, Islamabad, Pakistan
| | | | - Dongqing Wei
- Shanghai Jiao Tong University, Shanghai, China. .,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, China.
| | - Yu-Juan Zhang
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331, People's Republic of China.
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26
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Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs. mSystems 2019; 4:4/4/e00342-19. [PMID: 31337658 PMCID: PMC6650546 DOI: 10.1128/msystems.00342-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence. Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.
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Barbhuiya PA, Uddin A, Chakraborty S. Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus
Bombina. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:99-112. [DOI: 10.1002/jez.b.22852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/10/2019] [Accepted: 03/20/2019] [Indexed: 01/16/2023]
Affiliation(s)
| | - Arif Uddin
- Department of ZoologyMoinul Hoque Choudhury Memorial Science CollegeHailakandi Assam India
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28
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Bohlin J, Pettersson JHO. Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals. Comput Struct Biotechnol J 2019; 17:362-370. [PMID: 30949307 PMCID: PMC6429543 DOI: 10.1016/j.csbj.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/07/2023] Open
Abstract
Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.
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Affiliation(s)
- Jon Bohlin
- Norwegian Institute of Public Health, Division of Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Lovisenberggata 8, 0456 Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, PO-Box 222 Skøyen, N-0213 Oslo, Norway.,Norwegian University of Life Sciences, Faculty of Veterinary Sciences, Production Animal Clinical Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - John H-O Pettersson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School the University of Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
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29
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Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proc Natl Acad Sci U S A 2019; 116:934-943. [PMID: 30598433 PMCID: PMC6338844 DOI: 10.1073/pnas.1816822116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.
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Affiliation(s)
- Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, 100 Taipei, Taiwan
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202
| | - Samuel S Jones
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
| | - Julia Naumann
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | | | - Eric K Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, 106 Taipei, Taiwan
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Claude W dePamphilis
- Department of Biology, Pennsylvania State University, University Park, PA 16802;
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
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30
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Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int J Mol Sci 2018; 19:ijms19124010. [PMID: 30545112 PMCID: PMC6321445 DOI: 10.3390/ijms19124010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.
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31
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Bohlin J, Eldholm V, Brynildsrud O, Petterson JHO, Alfsnes K. Modeling of the GC content of the substituted bases in bacterial core genomes. BMC Genomics 2018; 19:589. [PMID: 30081825 PMCID: PMC6080486 DOI: 10.1186/s12864-018-4984-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
Background The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strains. We also wanted to explore whether sbGC for each strain was associated with the corresponding species’ core genome GC content (cgGC). We present a simple mathematical model that estimates sbGC from cgGC. The model assumes only that the estimated sbGC is a function of cgGC proportional to fixed AT→GC (α) and GC → AT (β) mutation rates. Non-linear regression was used to estimate parameters α and β from the empirical data described above. Results We found that sbGC for each strain showed a non-linear association with the corresponding cgGC with a bias towards higher GC content for most core genomes (66.3% of the strains), assuming as a null-hypothesis that sbGC should be approximately equal to cgGC. The most GC rich core genomes (i.e. approximately %GC > 60), on the other hand, exhibited slightly less GC-biased sbGC than expected. The best fitted regression model indicates that GC → AT mutation rates β = (1.91 ± 0.13) p < 0.001 are approximately (1.91/0.79) = 2.42 times as high, on average, as AT→GC α = (− 0.79 ± 0.25) p < 0.001 mutation rates. Whether the observed sbGC GC-bias for all but the most GC-rich prokaryotic species is due to selection, compensating for the GC → AT mutation bias, and/or selective neutral processes is currently debated. Residual standard error was found to be σ = 0.076 indicating estimated errors of sbGC to be approximately within ±15.2% GC (95% confidence interval) for the strains of all species in the study. Conclusion Not only did our mathematical model give reasonable estimates of sbGC it also provides further support to previous observations that mutation rates in prokaryotes exhibit a universal GC → AT bias that appears to be remarkably consistent between taxa. Electronic supplementary material The online version of this article (10.1186/s12864-018-4984-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jon Bohlin
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway.
| | - Vegard Eldholm
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Ola Brynildsrud
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - John H-O Petterson
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Kristian Alfsnes
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
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32
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Seward EA, Kelly S. Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria. Genome Biol 2018; 19:102. [PMID: 30064467 PMCID: PMC6066932 DOI: 10.1186/s13059-018-1480-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/11/2018] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Most amino acids are encoded by multiple synonymous codons. However, synonymous codons are not used equally, and this biased codon use varies between different organisms. It has previously been shown that both selection acting to increase codon translational efficiency and selection acting to decrease codon biosynthetic cost contribute to differences in codon bias. However, it is unknown how these two factors interact or how they affect molecular sequence evolution. RESULTS Through analysis of 1320 bacterial genomes, we show that bacterial genes are subject to multi-objective selection-driven optimization of codon use. Here, selection acts to simultaneously decrease transcript biosynthetic cost and increase transcript translational efficiency, with highly expressed genes under the greatest selection. This optimization is not simply a consequence of the more translationally efficient codons being less expensive to synthesize. Instead, we show that transfer RNA gene copy number alters the cost-efficiency trade-off of synonymous codons such that, for many species, selection acting on transcript biosynthetic cost and translational efficiency act in opposition. Finally, we show that genes highly optimized to reduce cost and increase efficiency show reduced rates of synonymous and non-synonymous mutation. CONCLUSIONS This analysis provides a simple mechanistic explanation for variation in evolutionary rate between genes that depends on selection-driven cost-efficiency optimization of the transcript. These findings reveal how optimization of resource allocation to messenger RNA synthesis is a critical factor that determines both the evolution and composition of genes.
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Affiliation(s)
- Emily A Seward
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Abstract
Genome and transcript sequences are composed of long strings of nucleotide monomers (A, C, G, and T/U) that require different quantities of nitrogen atoms for biosynthesis. Here, it is shown that the strength of selection acting on transcript nitrogen content is influenced by the amount of nitrogen plants require to conduct photosynthesis. Specifically, plants that require more nitrogen to conduct photosynthesis experience stronger selection on transcript sequences to use synonymous codons that cost less nitrogen to biosynthesize. It is further shown that the strength of selection acting on transcript nitrogen cost constrains molecular sequence evolution such that genes experiencing stronger selection evolve at a slower rate. Together these findings reveal that the plant molecular clock is set by photosynthetic efficiency, and provide a mechanistic explanation for changes in plant speciation rates that occur concomitant with improvements in photosynthetic efficiency and changes in the environment such as light, temperature, and atmospheric CO2 concentration.
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Affiliation(s)
- Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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34
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Zhang YJ, Zhu C, Ding Y, Yan ZW, Li GH, Lan Y, Wen JF, Chen B. Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton. BMC Genomics 2018; 19:469. [PMID: 29914356 PMCID: PMC6006717 DOI: 10.1186/s12864-018-4845-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/31/2018] [Indexed: 01/24/2023] Open
Abstract
Background Eukaryotic cells contain a huge variety of internally specialized subcellular compartments. Stoichiogenomics aims to reveal patterns of elements usage in biological macromolecules. However, the stoichiogenomic characteristics and how they adapt to various subcellular microenvironments are still unknown. Results Here we first updated the definition of stoichiogenomics. Then we applied it to subcellular research, and detected distinctive nitrogen content of nuclear and hydrogen, sulfur content of extracellular proteomes. Specially, we found that acidic amino acids (AAs) content of cytoskeletal proteins is the highest. The increased charged AAs are mainly caused by the eukaryotic originated cytoskeletal proteins. Functional subdivision of the cytoskeleton showed that activation, binding/association, and complexes are the three largest functional categories. Electrostatic interaction analysis showed an increased electrostatic interaction between both primary sequences and PPI interfaces of 3D structures, in the cytoskeleton. Conclusions This study creates a blueprint of subcellular stoichiogenomic characteristics, and explains that charged AAs of the cytoskeleton increased greatly in evolution, which offer material basis for the eukaryotic cytoskeletal proteins to act in two ways of electrostatic interactions, and further perform their activation, binding/association and complex formation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4845-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Juan Zhang
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China
| | - Chengxu Zhu
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Yiran Ding
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Zheng-Wen Yan
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China
| | - Yang Lan
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China.
| | - Bin Chen
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China.
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35
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de Freitas Nascimento J, Kelly S, Sunter J, Carrington M. Codon choice directs constitutive mRNA levels in trypanosomes. eLife 2018; 7:e32467. [PMID: 29543152 PMCID: PMC5896880 DOI: 10.7554/elife.32467] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs. Third, translation was necessary for the accelerated mRNA turnover resulting from codon choice. Thus, in trypanosomes, the information determining the levels of most mRNAs resides in the open reading frame and translation is required to access this information.
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Affiliation(s)
| | - Steven Kelly
- Department of Plant SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Jack Sunter
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Mark Carrington
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
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36
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Wang YN, Ji WH, Li XR, Liu YS, Zhou JH. Unique features of nucleotide and codon usage patterns in mycoplasmas revealed by information entropy. Biosystems 2017; 165:1-7. [PMID: 29274363 DOI: 10.1016/j.biosystems.2017.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/11/2017] [Accepted: 12/15/2017] [Indexed: 11/25/2022]
Abstract
Currently, the comparison between GC usage pattern at the 3rd codon position and codon usage index is commonly used to estimate the roles of evolutionary forces in shaping synonymous codon usages, however, this kind of analysis often losses the information about the role of A/T usage bias in shaping synonymous codon usage bias. To overcome this limitation and better understand the interplay between nucleotide and codon usages for the evolution of bacteria at gene levels, in this study, we employed the information entropy method with some modification to estimate roles of nucleotide compositions in the overall codon usage bias for 18 mycoplasma species in combination with Davies-Bouldin index. At gene levels, the overall nucleotide usage bias represents A content as the highest, followed by T, G and C for mycoplasmas, resulting in a low GC content. This feature is universal across these species derived from different hosts, suggesting that the hosts have the limited impact on nucleotide usage bias of mycoplasmas. Information entropy and Davies-Bouldin index can better reveal that the nucleotide usage bias at the 3rd codon position is essential in shaping the overall nucleotide bias for all given mycoplasmas except M. pneumoniae M129. Davies-Bouldin index revealed that the 1st and 2nd codon position play more important role in synonymous codon usage bias than that of the 3rd position at gene levels. To our knowledge, this is the first comprehensive investigation into cooperation between nucleotide and codon usages for mycoplasma and extends our knowledge of the mechanisms that contribute to codon usage and evolution of this microorganism.
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Affiliation(s)
- Yi-Ning Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Wen-Heng Ji
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Xue-Rui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Yong-Sheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Jian-Hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China.
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37
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Chowdhury K, Kumar S, Sharma T, Sharma A, Bhagat M, Kamai A, Ford BM, Asthana S, Mandal CC. Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides. Gene 2017; 639:85-95. [PMID: 28986316 DOI: 10.1016/j.gene.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 08/07/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022]
Abstract
Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing cancer cells.
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Affiliation(s)
- Kaushik Chowdhury
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Suresh Kumar
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Tanu Sharma
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Ankit Sharma
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Meenakshi Bhagat
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Asangla Kamai
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Bridget M Ford
- Department of Biology, University of the Incarnate Word, San Antonio 78209, TX, USA
| | - Shailendra Asthana
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India.
| | - Chandi C Mandal
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India.
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38
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Guignard MS, Leitch AR, Acquisti C, Eizaguirre C, Elser JJ, Hessen DO, Jeyasingh PD, Neiman M, Richardson AE, Soltis PS, Soltis DE, Stevens CJ, Trimmer M, Weider LJ, Woodward G, Leitch IJ. Impacts of Nitrogen and Phosphorus: From Genomes to Natural Ecosystems and Agriculture. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00070] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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39
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Bohlin J, Eldholm V, Pettersson JHO, Brynildsrud O, Snipen L. The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes. BMC Genomics 2017; 18:151. [PMID: 28187704 PMCID: PMC5303225 DOI: 10.1186/s12864-017-3543-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/02/2017] [Indexed: 12/02/2022] Open
Abstract
Background The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding accessory genomes in 36 species, represented by the genomes of 731 bacterial strains, to assess the impact of selective forces on base composition in microbes. We also explore, in turn, how these results compare with findings for whole genome intragenic regions. Results We found that GC content in coding regions is significantly higher in core genomes than accessory genomes and whole genomes. Likewise, GC content variation within coding regions was significantly lower in core genomes than in accessory genomes and whole genomes. Relative entropy in coding regions, measured as the difference between observed and expected trinucleotide frequencies estimated from mononucleotide frequencies, was significantly higher in the core genomes than in accessory and whole genomes. Relative entropy was positively associated with coding region GC content within the accessory genomes, but not within the corresponding coding regions of core or whole genomes. Conclusion The higher intragenic GC content and relative entropy, as well as the lower GC content variation, observed in the core genomes is most likely associated with selective constraints. It is unclear whether the positive association between GC content and relative entropy in the more mobile accessory genomes constitutes signatures of selection or selective neutral processes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3543-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jon Bohlin
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway.
| | - Vegard Eldholm
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - John H O Pettersson
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Ola Brynildsrud
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1430, Ås, Norway
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