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Lamolle G, Iriarte A, Musto H. Codon usage in the flatworm Schistosoma mansoni is shaped by the mutational bias towards A+T and translational selection, which increases GC-ending codons in highly expressed genes. Mol Biochem Parasitol 2021; 247:111445. [PMID: 34942292 DOI: 10.1016/j.molbiopara.2021.111445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 11/30/2022]
Abstract
Schistosoma mansoni is a trematode flatworm that parasitizes humans and produces a disease called bilharzia. At the genomic level, it is characterized by a low genomic GC content and an "isochore-like" structure, where GC-richest regions, mainly placed at the extremes of the chromosomes, are interspersed with low GC-regions. Furthermore, the GC-richest regions are at the same time the gene-richest, and where the most heavily expressed genes are placed. Taking these features into account, we decided to reanalyze the codon usage of this flatworm. Our results show that a) when all genes are considered together, the strong mutational bias towards A + T leads to a predominance of A/T-ending codons, b) a multivariate analysis discriminates between highly and lowly expressed genes, c) the sequences expressed at highest levels display a significant increase in G/C-ending codons, d) when comparing the molecular distances with a closely related species the synonymous distance in highly expressed genes is significantly lower than in lowly expressed sequences. Therefore, we conclude that despite previous results, which were performed with a small sample of genes, codon usage in S. mansoni is the result of two forces that operate in opposite directions: while mutational bias leads to a predominance of A/T codons, translational selection, working at the level of speed, increment G/C ending triplets.
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Affiliation(s)
- Guillermo Lamolle
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Avenida A. Navarro 3051, 11600 Montevideo, Uruguay.
| | - Héctor Musto
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Lamolle G, Fontenla S, Rijo G, Tort JF, Smircich P. Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes. Front Genet 2019; 10:771. [PMID: 31543897 PMCID: PMC6739440 DOI: 10.3389/fgene.2019.00771] [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] [Received: 05/24/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
In the present work, we performed a comparative genome-wide analysis of 22 species representative of the main clades and lifestyles of the phylum Platyhelminthes. We selected a set of 700 orthologous genes conserved in all species, measuring changes in GC content, codon, and amino acid usage in orthologous positions. Values of 3rd codon position GC spanned over a wide range, allowing to discriminate two distinctive clusters within freshwater turbellarians, Cestodes and Trematodes respectively. Furthermore, a hierarchical clustering of codon usage data differs remarkably from the phylogenetic tree. Additionally, we detected a synonymous codon usage bias that was more dramatic in extreme GC-poor or GC-rich genomes, i.e., GC-poor Schistosomes preferred to use AT-rich terminated synonymous codons, while GC-rich M. lignano showed the opposite behavior. Interestingly, these biases impacted the amino acidic usage, with preferred amino acids encoded by codons following the GC content trend. These are associated with non-synonymous substitutions at orthologous positions. The detailed analysis of the synonymous and non-synonymous changes provides evidence for a two-hit mechanism where both mutation and selection forces drive the diverse coding strategies of flatworms.
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Affiliation(s)
- Guillermo Lamolle
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Gastón Rijo
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, IIBCE, MEC, Montevideo, Uruguay.,Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la Republica, UDELAR, Montevideo, Uruguay
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Maldonado LL, Stegmayer G, Milone DH, Oliveira G, Rosenzvit M, Kamenetzky L. Whole genome analysis of codon usage in Echinococcus. Mol Biochem Parasitol 2018; 225:54-66. [DOI: 10.1016/j.molbiopara.2018.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/20/2018] [Accepted: 08/01/2018] [Indexed: 01/15/2023]
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Lamolle G, Protasio AV, Iriarte A, Jara E, Simón D, Musto H. An Isochore-Like Structure in the Genome of the Flatworm Schistosoma mansoni. Genome Biol Evol 2016; 8:2312-8. [PMID: 27435793 PMCID: PMC5010904 DOI: 10.1093/gbe/evw170] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic genomes are compositionally heterogeneous, that is, composed by regions that differ in guanine-cytosine (GC) content (isochores). The most well documented case is that of vertebrates (mainly mammals) although it has been also noted among unicellular eukaryotes and invertebrates. In the human genome, regarded as a typical mammal, this heterogeneity is associated with several features. Specifically, genes located in GC-richest regions are the GC3-richest, display CpG islands and have shorter introns. Furthermore, these genes are more heavily expressed and tend to be located at the extremes of the chromosomes. Although the compositional heterogeneity seems to be widespread among eukaryotes, the associated properties noted in the human genome and other mammals have not been investigated in depth in other taxa Here we provide evidence that the genome of the parasitic flatworm Schistosoma mansoni is compositionally heterogeneous and exhibits an isochore-like structure, displaying some features associated, until now, only with the human and other vertebrate genomes, with the exception of gene concentration.
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Affiliation(s)
- Guillermo Lamolle
- Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, Udelar, Montevideo, Uruguay
| | - Anna V Protasio
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Andrés Iriarte
- Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, Udelar, Montevideo, Uruguay Dpto. de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Udelar, Montevideo, Uruguay
| | - Eugenio Jara
- Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, Udelar, Montevideo, Uruguay
| | - Diego Simón
- Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, Udelar, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, Udelar, Montevideo, Uruguay
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Tourova TP, Nazina TN, Mikhailova EM, Rodionova TA, Ekimov AN, Mashukova AV, Poltaraus AB. alkB homologs in thermophilic bacteria of the genus Geobacillus. Mol Biol 2008. [DOI: 10.1134/s0026893308020076] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tang Y, Cho PY, Kim TI, Hong SJ. Clonorchis sinensis: codon usage in nuclear genes. Exp Parasitol 2006; 115:187-91. [PMID: 17027003 DOI: 10.1016/j.exppara.2006.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 06/22/2006] [Accepted: 08/02/2006] [Indexed: 10/24/2022]
Abstract
Codon usage in Clonorchis sinensis was analyzed using 12,515 codons from 38 coding sequences. Total GC content was 49.83%, and GC1, GC2 and GC3 contents were 56.32%, 43.15% and 50.00%, respectively. The effective number of codons converged at 51-53 codons. When plotted against total GC content or GC3, codon usage was distributed in relation to GC3 biases. Relative synonymous codon usage for each codon revealed a single major trend, which was highly correlated with GC content at the third position when codons began with A or U at the first two positions. In codons beginning with G or C base at the first two positions, the G or C base rarely occurred at the third position. These results suggest that codon usage is shaped by a bias towards G or C at the third base, and that this is affected by the first and second bases.
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Affiliation(s)
- Yi Tang
- Department of Parasitology, Chung-Ang University College of Medicine, Tongjak-gu, Seoul 156-756, Republic of Korea
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Sorokin DY, Tourova TP, Kolganova TV, Spiridonova EM, Berg IA, Muyzer G. Thiomicrospira halophila sp. nov., a moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium from hypersaline lakes. Int J Syst Evol Microbiol 2006; 56:2375-2380. [PMID: 17012565 DOI: 10.1099/ijs.0.64445-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enrichments at 2 M NaCl and pH 7.5–8, with thiosulfate or sulfide as electron donor, inoculated with sediments from hypersaline chloride–sulfate lakes of the Kulunda Steppe (Altai, Russia) resulted in the domination of two different groups of moderately halophilic, chemolithoautotrophic, sulfur-oxidizing bacteria. Under fully aerobic conditions with thiosulfate, bacteria belonging to the genus Halothiobacillus dominated while, under microaerophilic conditions, a highly motile, short vibrio-shaped phenotype outcompeted the halothiobacilli. Three genetically and phenotypically highly similar vibrio-shaped isolates were obtained in pure culture and one of them, strain HL 5T, was identified as a member of the Thiomicrospira crunogena cluster by 16S rRNA gene sequencing. The new isolates were able to grow with thiosulfate as electron donor within a broad salinity range from 0.5 to 3.5 M NaCl with an optimum at 1.5 M and within a pH range from 6.5 to 8.5 with an optimum at pH 7.5–7.8. Comparative analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene sequences demonstrated that strain HL 5T possessed two genes, cbbL-1 and cbbL-2, of the form I RuBisCO and a cbbM gene of the form II RuBisCO, similar to the other members of the Thiomicrospira crunogena cluster. On the basis of phenotypic and genetic comparison, the new halophilic isolates are proposed to be placed into a novel species, Thiomicrospira halophila sp. nov. (type strain HL 5T=DSM 15072T=UNIQEM U 221T).
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Affiliation(s)
- Dimitry Yu Sorokin
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia
| | - Tatjana P Tourova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia
| | | | | | - Ivan A Berg
- Department of Microbiology, Faculty of Biology, Moscow State University, Moscow, Russia
| | - Gerard Muyzer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Tourova TP, Spiridonova EM, Berg IA, Kuznetsov BB, Sorokin DY. Occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium. MICROBIOLOGY-SGM 2006; 152:2159-2169. [PMID: 16804189 DOI: 10.1099/mic.0.28699-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The occurrence of the different genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the key enzyme of the Calvin-Benson-Bassham cycle of autotrophic CO(2) fixation, was investigated in the members of the genus Thiomicrospira and the relative genus Thioalkalimicrobium, all obligately chemolithoautotrophic sulfur-oxidizing Gammaproteobacteria. The cbbL gene encoding the 'green-like' form I RubisCO large subunit was found in all analysed species, while the cbbM gene encoding form II RubisCO was present only in Thiomicrospira species. Furthermore, species belonging to the Thiomicrospira crunogena 16S rRNA-based phylogenetic cluster also possessed two genes of green-like form I RubisCO, cbbL-1 and cbbL-2. Both 16S-rRNA- and cbbL-based phylogenies of the Thiomicrospira-Thioalkalimicrobium-Hydrogenovibrio group were congruent, thus supporting its monophyletic origin. On the other hand, it also supports the necessity for taxonomy reorganization of this group into a new family with four genera.
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Affiliation(s)
- Tatjana P Tourova
- Institute of Microbiology, Russian Academy of Sciences, p-t 60-letiya Oktyabrya, 7/2, Moscow, Russia
| | | | - Ivan A Berg
- Department of Microbiology, Moscow State University, Moscow, Russia
| | | | - Dimitry Yu Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Institute of Microbiology, Russian Academy of Sciences, p-t 60-letiya Oktyabrya, 7/2, Moscow, Russia
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Gupta SK, Banerjee T, Basak S, Sahu K, Sau S, Ghosh TC. Studies on codon usage inThermoplasma acidophilum and its possible implications on the occurrences of lateral gene transfer. J Basic Microbiol 2005; 45:344-54. [PMID: 16187257 DOI: 10.1002/jobm.200510576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Codon usage studies have been carried out on the coding sequences of Thermoplasma acidophilum, which is an archaeon and grows at very low pH and high temperature. Overall codon usage data analysis indicates that all the four bases are almost equifrequent at the third position of codons, which is expected (since genomic GC % of this genome is about 46%). However, multivariate statistical analysis indicates that there are two major trends in the codon usage variation among the genes in this organism. In the first major trend it is observed that genes having G and C ending codons are clustered at one end while, A and T ending ones are clustered at the other end. We have also found a significant positive correlation between the expressivities of genes and GC contents at the synonymous third codon positions. In the second major trend, it is seen that the genes are clustered into three distinct parts. A comparative analyses of codon usage data of T. acidophilum and Sulfolobus solfataricus reveals that one of the three clusters of genes of T. acidophilum is very similar to a considerable number of S. solfataricus genes, suggesting possible occurrences of lateral gene transfer between these two microorganisms as reported by earlier workers.
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Affiliation(s)
- S K Gupta
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme, VII M Calcutta 700 054. India
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Fadiel A, Lithwick S, Naftolin F. The influence of environmental adaptation on bacterial genome structure. Lett Appl Microbiol 2005; 40:12-8. [PMID: 15612996 DOI: 10.1111/j.1472-765x.2004.01619.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Researchers have long been puzzled by the diversity of life. Now that the complete genomic sequence of many organisms has been determined, it is possible to evaluate the impact of organismal variation on sequence structure or vice versa. The aim of this investigation was to explore genomic changes mandated by organismal adaptation to its ecological niches. METHODS AND RESULTS Coding sequences from three phylogenetically related bacterial species namely Mycoplasma genitalium, M. pneumoniae and Ureaplasma urealyticum were subject to in depth sequence analyses. M. genitalium and M. pneumoniae both belong to the genus Mycoplasma while U. urealyticum is a member of the genus Ureaplasma. However, M. genitalium and U. urealyticum are urogenital pathogens while M. pneumoniae is a respiratory pathogen. Complete transcriptomes were downloaded from NCBI for each species, and were subject to in silico investigation using in-house software, and public sequence analysis tools. Clear similarities in transcriptome structure were identified among the functionally similar species M. genitalium and U. urealyticum while no such relationship was identified among the phylogenetically related species M. genitalium and M. pneumoniae. CONCLUSIONS It is plausible to conclude that, in these bacterial species, environmental stimuli might be more influential in shaping sequence signatures than phylogenetic relationships. SIGNIFICANCE AND IMPACT OF THE STUDY This study suggests that molecular signatures within the transcriptomes of the species examined are likely to be a product of evolutionary adaptation to diverse environmental ecological stimuli, and not a result of common phylogeny.
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Affiliation(s)
- A Fadiel
- The Bioinformatics Supercomputing Centre, The Hospital for Sick Children, Toronto, ON, Canada.
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Mittleider D, Green LC, Mann VH, Michael SF, Didier ES, Brindley PJ. Sequence survey of the genome of the opportunistic microsporidian pathogen, Vittaforma corneae. J Eukaryot Microbiol 2002; 49:393-401. [PMID: 12425527 DOI: 10.1111/j.1550-7408.2002.tb00218.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The microsporidian Vittaforma corneae has been reported as a pathogen of the human stratum corneum, where it can cause keratitis, and is associated with systemic infections. In addition to this direct role as an infectious, etiologic agent of human disease, V. corneae has been used as a model organism for another microsporidian, Enterocytozoon bieneusi, a frequent and problematic pathogen of HIV-infected patients that, unlike V. corneae, is difficult to maintain and to study in vitro. Unfortunately, few molecular sequences are available for V. corneae. In this study, seventy-four genome survey sequences (GSS) were obtained from genomic DNA of spores of laboratory-cultured V. corneae. Approximately, 41 discontinuous kilobases of V. corneae were cloned and sequenced to generate these GSS. Putative identities were assigned to 44 of the V. corneae GSS based on BLASTX searches, representing 21 discrete proteins. Of these 21 deduced V. corneae proteins, only two had been reported previously from other microsporidia (until the recent report of the Encephalitozoon cuniculi genome). Two of the V. corneae proteins were of particular interest, reverse transcriptase and topoisomerase IV (parC). Since the existence of transposable elements in microsporidia is controversial, the presence of reverse transcriptase in V. corneae will contribute to resolution of this debate. The presence of topoisomerase IV was remarkable because this enzyme previously had been identified only from prokaryotes. The 74 GSS included 26.7 kilobases of unique sequences from which two statistics were generated: GC content and codon usage. The GC content of the unique GSS was 42%, lower than that of another microsporidian, E. cuniculi (48% for protein-encoding regions), and substantially higher than that predicted for a third microsporidian, Spraguea lophii (28%). A comparison using the Pearson correlation coefficient showed that codon usage in V. corneae was similar to that in the yeasts, Saccharomyces cerevisiae (r = 0.79) and Shizosaccharomyces pombe (r = 0.70), but was markedly dissimilar to E. cuniculi (r = 0.19).
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Affiliation(s)
- Derek Mittleider
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, USA
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Morton BR, Sorhannus U, Fox M. Codon adaptation and synonymous substitution rate in diatom plastid genes. Mol Phylogenet Evol 2002; 24:1-9. [PMID: 12128023 DOI: 10.1016/s1055-7903(02)00263-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Diatom plastid genes are examined with respect to codon adaptation and rates of silent substitution (Ks). It is shown that diatom genes follow the same pattern of codon usage as other plastid genes studied previously. Highly expressed diatom genes display codon adaptation, or a bias toward specific major codons, and these major codons are the same as those in red algae, green algae, and land plants. It is also found that there is a strong correlation between Ks and variation in codon adaptation across diatom genes, providing the first evidence for such a relationship in the algae. It is argued that this finding supports the notion that the correlation arises from selective constraints, not from variation in mutation rate among genes. Finally, the diatom genes are examined with respect to variation in Ks among different synonymous groups. Diatom genes with strong codon adaptation do not show the same variation in synonymous substitution rate among codon groups as the flowering plant psbA gene which, previous studies have shown, has strong codon adaptation but unusually high rates of silent change in certain synonymous groups. The lack of a similar finding in diatoms supports the suggestion that the feature is unique to the flowering plant psbA due to recent relaxations in selective pressure in that lineage.
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Affiliation(s)
- Brian R Morton
- Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA.
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Gupta SK, Ghosh TC. Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene 2001; 273:63-70. [PMID: 11483361 DOI: 10.1016/s0378-1119(01)00576-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Codon usage biases of all DNA sequences (length greater than or equal to 300 bp) from the complete genome of Pseudomonas aeruginosa have been analyzed. As P. aeruginosa is a GC-rich organism, G and/or C are expected to predominate in their codons. Overall codon usage data analysis indicates that indeed codons ending in G and/or C are predominant in this organism. But multivariate statistical analysis indicates that there is a single major trend in the codon usage variation among the genes in this organism, which has a strong negative correlation with the expressivities of the genes. The majority of the lowly expressed genes are scattered towards the positive end of the major axis whereas the highly expressed genes are clustered towards the negative end. This is the first report where the prokaryotic organism having highly skewed base composition is dictated mainly by translational selection, though some other factors such as the lengths of the genes as well as the hydrophobicity of genes also influence the codon usage variation among the genes in this organism in a minor way.
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Affiliation(s)
- S K Gupta
- Distributed Information Centre, Bose Institute, P 1/12, C.I.T. Scheme, VII M, Calcutta 700 054, India
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Fadiel A, Lithwick S, Wanas MQ, Cuticchia AJ. Influence of intercodon and base frequencies on codon usage in filarial parasites. Genomics 2001; 74:197-210. [PMID: 11386756 DOI: 10.1006/geno.2001.6531] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Base frequency, codon usage, and intercodon identity were analyzed in five filarial parasite species representing five Onchocercidae genera. Wucheria bancrofti, Brugia malayi, Onchocerca volvulus, Acanthocheilonema viteae, and Dirofilaria immitis gene sequences were downloaded from NCBI, and analysis was performed using locally designed computer programs and other freely available applications. A clear sequence bias was observed among the nematode species examined. At the nucleotide level, AT basepairs were present in gene sequences at higher frequencies than GC. In addition, codons ending in A or T were used proportionately more than those with G or C in the third-codon position. In addition, the amino acids used most often corresponded to codons ending in AT basepairs. Intercodon base proportion was biased in that A was found most often at N4, second only to T in certain specific cases. Since all of these sequence biases were observed in a relatively consistent fashion among all of the organisms studied, we conclude that sequence bias is a genetic characteristic, which is associated with multiple filarial genera.
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Affiliation(s)
- A Fadiel
- Bioinformatics Supercomputing Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1Z8, Canada.
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Grocock RJ, Sharp PM. Synonymous codon usage in Cryptosporidium parvum: identification of two distinct trends among genes. Int J Parasitol 2001; 31:402-12. [PMID: 11306119 DOI: 10.1016/s0020-7519(01)00129-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The usage of alternative synonymous codons in the apicomplexan Cryptosporidium parvum has been investigated. A data set of 54 genes was analysed. Overall, A- and U-ending codons predominate, as expected in an A+T-rich genome. Two trends of codon usage variation among genes were identified using correspondence analysis. The primary trend is in the extent of usage of a subset of presumably translationally optimal codons, that are used at significantly higher frequencies in genes expected to be expressed at high levels. Fifteen of the 18 codons identified as optimal are more G+C-rich than the otherwise common codons, so that codon selection associated with translation opposes the general mutation bias. Among 40 genes with lower frequencies of these optimal codons, a secondary trend in G+C content was identified. In these genes, G+C content at synonymously variable third positions of codons is correlated with that in 5' and 3' flanking sequences, indicative of regional variation in G+C content, perhaps reflecting regional variation in mutational biases.
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Affiliation(s)
- R J Grocock
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK
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Abstract
Codon usage bias of Entamoeba histolytica, a protozoan parasite, was investigated using the available DNA sequence data. Entamoeba histolytica having AT rich genome, is expected to have A and/or T at the third position of codons. Overall codon usage data analysis indicates that A and/or T ending codons are strongly biased in the coding region of this organism. However, multivariate statistical analysis suggests that there is a single major trend in codon usage variation among the genes. The genes which are supposed to be highly expressed are clustered at one end, while the majority of the putatively lowly expressed genes are clustered at the other end. The codon usage pattern is distinctly different in these two sets of genes. C ending codons are significantly higher in the putatively highly expressed genes suggesting that C ending codons are translationally optimal in this organism. In the putatively lowly expressed genes A and/or T ending codons are predominant, which suggests that compositional constraints are playing the major role in shaping codon usage variation among the lowly expressed genes. These results suggest that both mutational bias and translational selection are operational in the codon usage variation in this organism.
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Affiliation(s)
- T C Ghosh
- Distributed Information Centre, Bose Institute, P 1/12, C.I.T. Scheme, VII M, 700 054, Calcutta, India.
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McEwan NR, Gatherer D, Eschenlauer SC, McIntosh FM, Calza RE, John Wallace R, Jamie Newbold C. An Unusual Codon Usage Pattern in the Ciliate Family Ophryoscolecidae and its Implications for Determining the Source of Cloned DNA. Anaerobe 2000. [DOI: 10.1006/anae.1999.0310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Romero H, Zavala A, Musto H. Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica. Gene 2000; 242:307-11. [PMID: 10721724 DOI: 10.1016/s0378-1119(99)00491-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is widely accepted that the compositional pressure is the only factor shaping codon usage in unicellular species displaying extremely biased genomic compositions. This seems to be the case in the prokaryotes Mycoplasma capricolum, Rickettsia prowasekii and Borrelia burgdorferi (GC-poor), and in Micrococcus luteus (GC-rich). However, in the GC-poor unicellular eukaryotes Dictyostelium discoideum and Plasmodium falciparum, there is evidence that selection, acting at the level of translation, influences codon choices. This is a twofold intriguing finding, since (1) the genomic GC levels of the above mentioned eukaryotes are lower than the GC% of any studied bacteria, and (2) bacteria usually have larger effective population sizes than eukaryotes, and hence natural selection is expected to overcome more efficiently the randomizing effects of genetic drift among prokaryotes than among eukaryotes. In order to gain a new insight about this problem, we analysed the patterns of codon preferences of the nuclear genes of Entamoeba histolytica, a unicellular eukaryote characterised by an extremely AT-rich genome (GC = 25%). The overall codon usage is strongly biased towards A and T in the third codon positions, and among the presumed highly expressed sequences, there is an increased relative usage of a subset of codons, many of which are C-ending. Since an increase in C in third codon positions is 'against' the compositional bias, we conclude that codon usage in E. histolytica, as happens in D. discoideum and P. falciparum, is the result of an equilibrium between compositional pressure and selection. These findings raise the question of why strongly compositionally biased eukaryotic cells may be more sensitive to the (presumed) slight differences among synonymous codons than compositionally biased bacteria.
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Affiliation(s)
- H Romero
- Laboratorio de Organización y Evolución del Genoma, Sección Bioquímica, Facultad de Ciencias, Montevideo, Uruguay
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