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Cassandra G Extavour - One of the best experts on this subject based on the ideXlab platform.
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evidence of multifaceted functions of Codon usage in translation within the model beetle tribolium castaneum
DNA Research, 2019Co-Authors: Carrie A. Whittle, Arpita Kulkarni, Cassandra G ExtavourAbstract:Synonymous Codon use is non-random. Codons most used in highly transcribed genes, often called optimal Codons, typically have high gene counts of matching tRNA genes (tRNA abundance) and promote accurate and/or efficient translation. Non-optimal Codons, those least used in highly expressed genes, may also affect translation. In multicellular organisms, Codon optimality may vary among tissues. At present, however, tissue specificity of Codon use remains poorly understood. Here, we studied Codon usage of genes highly transcribed in germ line (testis and ovary) and somatic tissues (gonadectomized males and females) of the beetle Tribolium castaneum. The results demonstrate that: (i) the majority of optimal Codons were organism-wide, the same in all tissues, and had numerous matching tRNA gene copies (Opt-Codon↑tRNAs), consistent with translational selection; (ii) some optimal Codons varied among tissues, suggesting tissue-specific tRNA populations; (iii) wobble tRNA were required for translation of certain optimal Codons (Opt-Codonwobble), possibly allowing precise translation and/or protein folding; and (iv) remarkably, some non-optimal Codons had abundant tRNA genes (Nonopt-Codon↑tRNAs), and genes using those Codons were tightly linked to ribosomal and stress-response functions. Thus, Nonopt-Codon↑tRNAs Codons may regulate translation of specific genes. Together, the evidence suggests that Codon use and tRNA genes regulate multiple translational processes in T. castaneum.
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evidence of multifaceted functions of Codon usage in translation within the model beetle tribolium castaneum
bioRxiv, 2019Co-Authors: Carrie A. Whittle, Arpita Kulkarni, Cassandra G ExtavourAbstract:Synonymous Codon use is non-random. Codons most used in highly transcribed genes, often called optimal Codons, typically have high gene counts of matching tRNA genes (tRNA abundance) and promote accurate and/or efficient translation. Non-optimal Codons, those least used in highly expressed genes, may also affect translation. In multicellular organisms, Codon optimality may vary among tissues. At present however, Codon use remains poorly understood in multicellular organisms. Here, we studied Codon usage of genes highly transcribed in germ line (testis, ovary) and somatic tissues (gonadectomized males and females) of the beetle Tribolium castaneum. The results demonstrate that: 1) the majority of optimal Codons were organism-wide, the same in all tissues, and had numerous matching tRNA gene copies (Opt{uparrow}tRNA), consistent with translational selection; 2) some optimal Codons varied among tissues, suggesting tissue-specific tRNA populations; 3) wobble tRNA were required for translation of certain optimal Codons (Opt-Codonwobble), possibly allowing precise translation and/or protein folding; and 4) remarkably, some non-optimal Codons had abundant tRNA genes (Nonopt-Codon{uparrow}tRNAs), and genes using those Codons were tightly linked to ribosomal and stress-response functions. Thus, Nonopt-Codon{uparrow}tRNAs Codons may regulate translation of specific genes. Together, the evidence suggests that Codon use and tRNA genes regulate multiple translational processes in beetles.
Carrie A. Whittle - One of the best experts on this subject based on the ideXlab platform.
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evidence of multifaceted functions of Codon usage in translation within the model beetle tribolium castaneum
DNA Research, 2019Co-Authors: Carrie A. Whittle, Arpita Kulkarni, Cassandra G ExtavourAbstract:Synonymous Codon use is non-random. Codons most used in highly transcribed genes, often called optimal Codons, typically have high gene counts of matching tRNA genes (tRNA abundance) and promote accurate and/or efficient translation. Non-optimal Codons, those least used in highly expressed genes, may also affect translation. In multicellular organisms, Codon optimality may vary among tissues. At present, however, tissue specificity of Codon use remains poorly understood. Here, we studied Codon usage of genes highly transcribed in germ line (testis and ovary) and somatic tissues (gonadectomized males and females) of the beetle Tribolium castaneum. The results demonstrate that: (i) the majority of optimal Codons were organism-wide, the same in all tissues, and had numerous matching tRNA gene copies (Opt-Codon↑tRNAs), consistent with translational selection; (ii) some optimal Codons varied among tissues, suggesting tissue-specific tRNA populations; (iii) wobble tRNA were required for translation of certain optimal Codons (Opt-Codonwobble), possibly allowing precise translation and/or protein folding; and (iv) remarkably, some non-optimal Codons had abundant tRNA genes (Nonopt-Codon↑tRNAs), and genes using those Codons were tightly linked to ribosomal and stress-response functions. Thus, Nonopt-Codon↑tRNAs Codons may regulate translation of specific genes. Together, the evidence suggests that Codon use and tRNA genes regulate multiple translational processes in T. castaneum.
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evidence of multifaceted functions of Codon usage in translation within the model beetle tribolium castaneum
bioRxiv, 2019Co-Authors: Carrie A. Whittle, Arpita Kulkarni, Cassandra G ExtavourAbstract:Synonymous Codon use is non-random. Codons most used in highly transcribed genes, often called optimal Codons, typically have high gene counts of matching tRNA genes (tRNA abundance) and promote accurate and/or efficient translation. Non-optimal Codons, those least used in highly expressed genes, may also affect translation. In multicellular organisms, Codon optimality may vary among tissues. At present however, Codon use remains poorly understood in multicellular organisms. Here, we studied Codon usage of genes highly transcribed in germ line (testis, ovary) and somatic tissues (gonadectomized males and females) of the beetle Tribolium castaneum. The results demonstrate that: 1) the majority of optimal Codons were organism-wide, the same in all tissues, and had numerous matching tRNA gene copies (Opt{uparrow}tRNA), consistent with translational selection; 2) some optimal Codons varied among tissues, suggesting tissue-specific tRNA populations; 3) wobble tRNA were required for translation of certain optimal Codons (Opt-Codonwobble), possibly allowing precise translation and/or protein folding; and 4) remarkably, some non-optimal Codons had abundant tRNA genes (Nonopt-Codon{uparrow}tRNAs), and genes using those Codons were tightly linked to ribosomal and stress-response functions. Thus, Nonopt-Codon{uparrow}tRNAs Codons may regulate translation of specific genes. Together, the evidence suggests that Codon use and tRNA genes regulate multiple translational processes in beetles.
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Evolution of synonymous Codon usage in Neurospora tetrasperma and Neurospora discreta.
Genome Biology and Evolution, 2011Co-Authors: Carrie A. Whittle, Hanna JohannessonAbstract:Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous Codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous Codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined Codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous Codon usage revealed 24 Codons (and two putative Codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal Codons. Although Codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous Codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal Codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal Codons. Optimal Codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.
Paul M. Sharp - One of the best experts on this subject based on the ideXlab platform.
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Synonymous Codon usage variation among Giardia lamblia genes and isolates.
Molecular Biology and Evolution, 1999Co-Authors: Bénédicte Lafay, Paul M. SharpAbstract:The pattern of Codon usage in the amitochondriate diplomonad Giardia lamblia has been investigated. Very extensive heterogeneity was evident among a sample of 65 genes. A discrete group of genes featured unusual Codon usage due to the amino acid composition of their products: these variant surface proteins (VSPs) are unusually rich in Cys and, to a lesser extent, Gly and Thr. Among the remaining 50 genes, correspondence analysis revealed a single major source of variation in synonymous Codon usage. This trend was related to the extent of use of a particular subset of 21 Codons which are inferred to be those which are optimal for translation; at one end of this trend were genes expected to be expressed at low levels with near random Codon usage, while at the other extreme were genes expressed at high levels in which these optimal Codons are used almost exclusively. These optimal Codons all end in C or G so G + C content at silent sites varies enormously among genes, from values around 40%, expected to reflect the background level of the genome, up to nearly 100%. Although VSP genes are occasionally extremely highly expressed, they do not, in general, have high frequencies of optimal Codons, presumably because their high expression is only intermittent. These results indicate that natural selection has been very effective in shaping Codon usage in G. lamblia. These analyses focused on sequences from strains placed within G. lamblia "assemblage A"; a few sequences from other strains revealed extensive divergence at silent sites, including some divergence in the pattern of Codon usage.
Arpita Kulkarni - One of the best experts on this subject based on the ideXlab platform.
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evidence of multifaceted functions of Codon usage in translation within the model beetle tribolium castaneum
DNA Research, 2019Co-Authors: Carrie A. Whittle, Arpita Kulkarni, Cassandra G ExtavourAbstract:Synonymous Codon use is non-random. Codons most used in highly transcribed genes, often called optimal Codons, typically have high gene counts of matching tRNA genes (tRNA abundance) and promote accurate and/or efficient translation. Non-optimal Codons, those least used in highly expressed genes, may also affect translation. In multicellular organisms, Codon optimality may vary among tissues. At present, however, tissue specificity of Codon use remains poorly understood. Here, we studied Codon usage of genes highly transcribed in germ line (testis and ovary) and somatic tissues (gonadectomized males and females) of the beetle Tribolium castaneum. The results demonstrate that: (i) the majority of optimal Codons were organism-wide, the same in all tissues, and had numerous matching tRNA gene copies (Opt-Codon↑tRNAs), consistent with translational selection; (ii) some optimal Codons varied among tissues, suggesting tissue-specific tRNA populations; (iii) wobble tRNA were required for translation of certain optimal Codons (Opt-Codonwobble), possibly allowing precise translation and/or protein folding; and (iv) remarkably, some non-optimal Codons had abundant tRNA genes (Nonopt-Codon↑tRNAs), and genes using those Codons were tightly linked to ribosomal and stress-response functions. Thus, Nonopt-Codon↑tRNAs Codons may regulate translation of specific genes. Together, the evidence suggests that Codon use and tRNA genes regulate multiple translational processes in T. castaneum.
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evidence of multifaceted functions of Codon usage in translation within the model beetle tribolium castaneum
bioRxiv, 2019Co-Authors: Carrie A. Whittle, Arpita Kulkarni, Cassandra G ExtavourAbstract:Synonymous Codon use is non-random. Codons most used in highly transcribed genes, often called optimal Codons, typically have high gene counts of matching tRNA genes (tRNA abundance) and promote accurate and/or efficient translation. Non-optimal Codons, those least used in highly expressed genes, may also affect translation. In multicellular organisms, Codon optimality may vary among tissues. At present however, Codon use remains poorly understood in multicellular organisms. Here, we studied Codon usage of genes highly transcribed in germ line (testis, ovary) and somatic tissues (gonadectomized males and females) of the beetle Tribolium castaneum. The results demonstrate that: 1) the majority of optimal Codons were organism-wide, the same in all tissues, and had numerous matching tRNA gene copies (Opt{uparrow}tRNA), consistent with translational selection; 2) some optimal Codons varied among tissues, suggesting tissue-specific tRNA populations; 3) wobble tRNA were required for translation of certain optimal Codons (Opt-Codonwobble), possibly allowing precise translation and/or protein folding; and 4) remarkably, some non-optimal Codons had abundant tRNA genes (Nonopt-Codon{uparrow}tRNAs), and genes using those Codons were tightly linked to ribosomal and stress-response functions. Thus, Nonopt-Codon{uparrow}tRNAs Codons may regulate translation of specific genes. Together, the evidence suggests that Codon use and tRNA genes regulate multiple translational processes in beetles.
Bénédicte Lafay - One of the best experts on this subject based on the ideXlab platform.
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Synonymous Codon usage variation among Giardia lamblia genes and isolates.
Molecular Biology and Evolution, 1999Co-Authors: Bénédicte Lafay, Paul M. SharpAbstract:The pattern of Codon usage in the amitochondriate diplomonad Giardia lamblia has been investigated. Very extensive heterogeneity was evident among a sample of 65 genes. A discrete group of genes featured unusual Codon usage due to the amino acid composition of their products: these variant surface proteins (VSPs) are unusually rich in Cys and, to a lesser extent, Gly and Thr. Among the remaining 50 genes, correspondence analysis revealed a single major source of variation in synonymous Codon usage. This trend was related to the extent of use of a particular subset of 21 Codons which are inferred to be those which are optimal for translation; at one end of this trend were genes expected to be expressed at low levels with near random Codon usage, while at the other extreme were genes expressed at high levels in which these optimal Codons are used almost exclusively. These optimal Codons all end in C or G so G + C content at silent sites varies enormously among genes, from values around 40%, expected to reflect the background level of the genome, up to nearly 100%. Although VSP genes are occasionally extremely highly expressed, they do not, in general, have high frequencies of optimal Codons, presumably because their high expression is only intermittent. These results indicate that natural selection has been very effective in shaping Codon usage in G. lamblia. These analyses focused on sequences from strains placed within G. lamblia "assemblage A"; a few sequences from other strains revealed extensive divergence at silent sites, including some divergence in the pattern of Codon usage.
