scholarly journals Co-adaption of tRNA Gene Copy Number and Amino Acid Usage Influences Translation Rates in Three Life Domains

2017 ◽  
Author(s):  
Meng-Ze Du ◽  
Wen Wei ◽  
Lei Qin ◽  
Shuo Liu ◽  
An-Ying Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Copy Number ◽  
Trna Gene ◽  
Fluorescent Protein ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Translation Rate ◽  
Translation Speed ◽  
Fast Growing

AbstractThe cellular translation process should obey the principle of maximizing efficiency and minimizing resource and energy costs. Here, we validated this principle by focusing on the basic translation components of tRNAs and amino acids. To most efficiently utilize these components, we reasoned that the quantities of the 20 tRNAs and their corresponding amino acids would be consistent in an organism. The two values should match at both the organismal and protein scales. For the former, they co-vary to meet the need to translate more proteins in fast-growing or larger cells. For the latter, they are consistent to different extents for various proteins in an organism to comply with different needs of translation speed. In this work, 310 out of 410 genomes in three domains had significant co-adaptions between the tRNA gene copy number and amino acid composition, and thus validating the principle at the organism scale. Furthermore, fast-growing bacteria co-adapt better than slow-growing ones. Highly expressed proteins and those connected to acute responses have better co-adaption, illustrating the principle at the individual protein scale. Experimentally, manipulating the tRNA gene copy number to optimize co-adaption between enhanced green fluorescent protein (EGFP) and tRNA gene set of Escherichia coli indeed lifted the translation rate (speed). Our results also contribute to revealing a translation rate-associated factor with universal and global effects. From a practical perspective, our findings suggest a strategy to increase the expression of target proteins and have implications for designing chassis cells in the field of synthetic biology field.

scholarly journals Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains

DNA Research ◽  
2017 ◽  
Vol 24 (6) ◽  
pp. 623-633 ◽  
Author(s):  
Meng-Ze Du ◽  
Wen Wei ◽  
Lei Qin ◽  
Shuo Liu ◽  
An-Ying Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Copy Number ◽  
Trna Gene ◽  
Gene Copy Number ◽  
Amino Acid Usage ◽  
Gene Copy ◽  
Life Domains

scholarly journals Synthesis of recombinant human procollagen II in a stably transfected tumour cell line (HT1080)

1994 ◽  
Vol 298 (1) ◽  
pp. 31-37 ◽  
Author(s):  
A Fertala ◽  
A L Sieron ◽  
A Ganguly ◽  
S W Li ◽  
L Ala-Kokko ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Line ◽  
Tumour Cell ◽  
Copy Number ◽  
Gene Copy Number ◽  
Basement Membranes ◽  
Gene Copy ◽  
Nucleotide Sequencing ◽  
Tumour Cell Line ◽  
Col2a1 Gene

Apparently because the biosynthetic pathways involve eight or more highly specific post-translational enzymes, it has been difficult to obtain expression of genes for fibrillar collagens in recombinant systems. Here two constructs of the human gene for procollagen II (COL2A1) were prepared, one with about 0.5 kb of a promoter for a procollagen I gene (COL1A1) and the other with about 4 kb of the promoter for the procollagen II gene. The constructs, together with a neomycin-resistant gene, were transfected into a human tumour cell line (HT1080) that synthesizes the collagen IV found in basement membranes, but does not synthesize any fibrillar collagen. About two per 100 clones resistant to the neomycin analogue G418 synthesized and secreted human procollagen II. Milligram quantities of the recombinant procollagen II were readily isolated from the cultured medium. The recombinant procollagen II had the expected amino acid sequence as defined by nucleotide sequencing of mRNA-derived cDNA and the expected amino acid composition as defined by analysis of procollagen II that was converted into collagen II by digestion with procollagen N- and C-proteinases. Also, analysis of the carbohydrate content indicated that there was glycosylation of some of the hydroxylysine residues but no evidence of post-translational overmodification of the residues. In addition, the protein was shown to have a native conformation as assayed by a series of protease digestions. No essential differences were found between clones transfected with the COL2A1 gene construct containing the COL1A1 promoter and the similar construct containing the COL2A1 promoter in terms of number of clones synthesizing recombinant procollagen II and the levels of expression. With both constructs, the expression of the COL2A1 gene was closely related to copy number. The results demonstrated therefore that it is not essential to use a promoter for a gene normally expressed in a host cell in order to obtain gene copy-number-dependent expression of an exogenous collagen gene in stably transfected cells.

scholarly journals Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

2020 ◽  
Author(s):  
Carrie A. Whittle ◽  
Arpita Kulkarni ◽  
Nina Chung ◽  
Cassandra G. Extavour
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Trna Gene ◽  
Synonymous Codon ◽  
Gene Copy ◽  
Female Gonad ◽  
Optimal Codons ◽  
Gene Copies ◽  
Highly Expressed Genes ◽  
Codon Use

AbstractBackgroundFor multicellular organisms, much remains unknown about the dynamics of synonymous codon and amino acid use in highly expressed genes, including whether their use varies with expression in different tissue types and sexes. Moreover, specific codons and amino acids may have translational functions in highly transcribed genes, that largely depend on their relationships to tRNA gene copies in the genome. However, these relationships and putative functions are poorly understood, particularly in multicellular systems.ResultsHere, we rigorously studied codon and amino acid use in highly expressed genes from reproductive and nervous system tissues (male and female gonad, somatic reproductive system, brain, ventral nerve cord, and male accessory glands) in the cricket Gryllus bimaculatus. We report an optimal codon, defined as the codon preferentially used in highly expressed genes, for each of the 18 amino acids with synonymous codons in this organism. The optimal codons were largely shaped by selection, and their identities were mostly shared among tissue types and both sexes. However, the frequency of optimal codons was highest in gonadal genes. Concordant with translational selection, a majority of the optimal codons had abundant matching tRNA gene copies in the genome, but sometimes obligately required wobble tRNAs. We suggest the latter may comprise a mechanism for slowing translation of abundant transcripts, particularly for cell-cycle genes. Non-optimal codons, defined as those least commonly used in highly transcribed genes, intriguingly often had abundant tRNAs, and had elevated use in a subset of genes with specialized functions (gametic and apoptosis genes), suggesting their use promotes the upregulation of particular mRNAs. In terms of amino acids, we found evidence suggesting that amino acid frequency, tRNA gene copy number, and amino acid biosynthetic costs (size/complexity) had all interdependently evolved in this insect model, potentially for translational optimization.ConclusionsCollectively, the results strongly suggest that codon use in highly expressed genes, including optimal, wobble, and non-optimal codons, and their tRNAs abundances, as well as amino acid use, have been adapted for various functional roles in translation within this cricket. The effects of expression in different tissue types and the two sexes are discussed.

scholarly journals tRNA gene copy number variation in humans

Gene ◽  
2014 ◽  
Vol 536 (2) ◽  
pp. 376-384 ◽  
Author(s):  
James R. Iben ◽  
Richard J. Maraia
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Trna Gene ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Gene Copy Number Variation ◽  
Number Variation

Cytochrome P450 2B diversity in a dietary specialist—the red tree vole (Arborimus longicaudus)

2018 ◽  
Vol 99 (3) ◽  
pp. 578-585 ◽  
Author(s):  
Smiljka Kitanovic ◽  
Chad A Marks-Fife ◽  
Quincy A Parkes ◽  
P Ross Wilderman ◽  
James R Halpert ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Amino Acid ◽  
Copy Number ◽  
Plant Secondary Metabolites ◽  
Gene Copy Number ◽  
Douglas Fir ◽  
Amino Acid Sequences ◽  
Gene Copy ◽  
Amino Acid Residues ◽  
Herbivorous Species

Abstract Although herbivores rely on liver enzymes to biotransform plant secondary metabolites ingested in plant-based diets, only a few enzymes from a handful of species have been characterized at the genomic level. In this study, we examined cytochrome P450 2B (CYP2B) sequence diversity and gene copy number in a conifer specialist, the red tree vole (Arborimus longicaudus). We fed captive individuals exclusively Douglas-fir (Pseudotsuga menziesii) foliage, cloned and sequenced their liver CYP2B cDNA, and estimated CYP2B gene copy number. We identified 21 unique CYP2B nucleotide sequences, and 20 unique CYP2B amino acid sequences. Gene copy number of CYP2B was estimated at 7.7 copies per haploid genome. We compared red tree vole CYP2B with CYP2B sequences of a generalist, the prairie vole (Microtus ochrogaster), found in GenBank. Our study revealed that the CYP2B enzymes of red tree voles possess unique sequences compared to CYP2B enzymes of other herbivorous species. The unique combination of amino acid residues at key substrate recognition sites of CYP2B enzymes may underlie the ability of the red tree vole to specialize on a highly toxic diet of Douglas-fir.

scholarly journals The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Michael J. McDonald ◽  
Chih-Hung Chou ◽  
Krishna BS Swamy ◽  
Hsien-Da Huang ◽  
Jun-Yi Leu
Keyword(s):  
Copy Number ◽  
Evolutionary Dynamics ◽  
Trna Gene ◽  
Gene Copy Number ◽  
Gene Copy ◽  
E Coli ◽  
Codon Use

scholarly journals Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Carrie A. Whittle ◽  
Arpita Kulkarni ◽  
Nina Chung ◽  
Cassandra G. Extavour
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Trna Gene ◽  
Synonymous Codon ◽  
Gene Copy ◽  
Female Gonad ◽  
Optimal Codons ◽  
Gene Copies ◽  
Highly Expressed Genes ◽  
Codon Use

Abstract Background For multicellular organisms, much remains unknown about the dynamics of synonymous codon and amino acid use in highly expressed genes, including whether their use varies with expression in different tissue types and sexes. Moreover, specific codons and amino acids may have translational functions in highly transcribed genes, that largely depend on their relationships to tRNA gene copies in the genome. However, these relationships and putative functions are poorly understood, particularly in multicellular systems. Results Here, we studied codon and amino acid use in highly expressed genes from reproductive and nervous system tissues (male and female gonad, somatic reproductive system, brain and ventral nerve cord, and male accessory glands) in the cricket Gryllus bimaculatus. We report an optimal codon, defined as the codon preferentially used in highly expressed genes, for each of the 18 amino acids with synonymous codons in this organism. The optimal codons were mostly shared among tissue types and both sexes. However, the frequency of optimal codons was highest in gonadal genes. Concordant with translational selection, a majority of the optimal codons had abundant matching tRNA gene copies in the genome, but sometimes obligately required wobble tRNAs. We suggest the latter may comprise a mechanism for slowing translation of abundant transcripts, particularly for cell-cycle genes. Non-optimal codons, defined as those least commonly used in highly transcribed genes, intriguingly often had abundant tRNAs, and had elevated use in a subset of genes with specialized functions (gametic and apoptosis genes), suggesting their use promotes the translational upregulation of particular mRNAs. In terms of amino acids, we found evidence suggesting that amino acid frequency, tRNA gene copy number, and amino acid biosynthetic costs (size/complexity) had all interdependently evolved in this insect model, potentially for translational optimization. Conclusions Collectively, the results suggest a model whereby codon use in highly expressed genes, including optimal, wobble, and non-optimal codons, and their tRNA abundances, as well as amino acid use, have been influenced by adaptation for various functional roles in translation within this cricket. The effects of expression in different tissue types and the two sexes are discussed.

Sign in / Sign up

Export Citation Format

Share Document