scholarly journals tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis

Open Biology ◽  
2021 ◽  
Vol 11 (11) ◽  
Author(s):  
Chengzhang Liu ◽  
Jianbo Yuan ◽  
Xiaojun Zhang ◽  
Songjun Jin ◽  
Fuhua Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Stress Responses ◽  
Copy Number ◽  
Sea Cucumber ◽  
Food Resource ◽  
Amino Acid Content ◽  
Translation Efficiency ◽  
Sea Cucumbers ◽  
Saponin Biosynthesis

Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Using the sea cucumber Apostichopus japonicus as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic non-coding RNAs, transfer RNAs (tRNAs) tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence, which might be a compromise between functionality and translation efficiency for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of A. japonicus was positively correlated with amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitates their saponin synthesis and survival using food resources with low nutrient content.

scholarly journals Amino Acid and Fatty Acid Compositions of Sea Cucumber Stichopus Vastus from Salemo Island Waters, Indonesia

2018 ◽  
Vol 13 (1) ◽  
pp. 9
Author(s):  
Abdullah Rasyid
Keyword(s):  
Fatty Acid ◽  
Amino Acid ◽  
Saturated Fatty Acid ◽  
Polyunsaturated Fatty Acid ◽  
Acid Content ◽  
Essential Amino Acid ◽  
Sea Cucumber ◽  
Amino Acid Content ◽  
Monounsaturated Fatty Acid ◽  
Essential Amino Acid Content

Coastal waters of Indonesia have considerable biodiversity of sea cucumbers. In the present study the amino acid and fatty acid contents in sea cucumber Stichopus vastus collected from Salemo Island waters Indonesia were determined. Results showed that all essential and non-essential amino acids were found in S. vastus. The major essential amino acid content was arginine (28651.62 mg/Kg). Whereas the major non-essential amino acid content was glycine (60907.24 mg/Kg). The total fatty acids were determined in which finding suggested that saturated fatty acid was more than polyunsaturated fatty acid and monounsaturated fatty acid. The higher saturated fatty acid, polyunsaturated fatty acid and monounsaturated fatty acid were palmitic acid (0.07%), arachidonic acid (0.13%) and palmitoleic acid (0.03%) respectively.  

scholarly journals Codon usage of highly expressed genes affects proteome-wide translation efficiency

2018 ◽  
Vol 115 (21) ◽  
pp. E4940-E4949 ◽  
Author(s):  
Idan Frumkin ◽  
Marc J. Lajoie ◽  
Christopher J. Gregg ◽  
Gil Hornung ◽  
George M. Church ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Protein Translation ◽  
Translation Efficiency ◽  
Synonymous Codons ◽  
Codon Composition ◽  
Theoretical Predictions ◽  
Highly Expressed Genes

Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed “codon usage bias.” Previous studies have demonstrated that synonymous changes in a coding sequence can exert significantciseffects on the gene’s expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences the cellular economy of translation, we massively converted abundant codons to their rare synonymous counterpart in several highly expressed genes inEscherichia coli. This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions. Interestingly, we could alleviate the observed phenotypes by increasing the supply of the tRNA for the highly demanded codon, thus demonstrating that the codon usage of highly expressed genes was selected in evolution to maintain the efficiency of global protein translation.

scholarly journals Analysis at single-cell resolution identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons

2021 ◽  
Author(s):  
William Gao ◽  
Carlos J Gallardo-Dodd ◽  
Claudia Kutter
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Single Cell ◽  
Adult Mouse ◽  
Trna Gene ◽  
Supply And Demand ◽  
Cell Types ◽  
Ribosome Profiling ◽  
Translation Efficiency ◽  
Gene Usage

The correlation between codon and anticodon pools influences the efficiency of translation, but whether differences exist in these pools across individual cells is unknown. We determined that codon usage and amino acid demand are highly stable across different cell types using single-cell RNA-sequencing atlases of adult mouse and fetal human. After demonstrating the robustness of ATAC-sequencing for analysis of tRNA gene usage, we quantified anticodon usage and amino acid supply in adult mouse and fetal human single-cell ATAC-seq atlases. We found that tRNA gene usage is overall coordinated across cell types, except in neurons which clustered separately from other cell types. Integration of these datasets revealed a strong and statistically significant correlation between amino acid supply and demand across almost all cell types. Neurons have an enhanced translation efficiency over other cell types, driven by an increased supply of Ala-AGC anticodons. This results in faster decoding of the Ala-GCC codon, as determined by cell-type specific ribosome profiling, and a reduction of Ala-AGC anticodon pools may be implicated in neurological pathologies. This study, the first such examination of codon usage, anticodon usage, and translation efficiency at single-cell resolution, identifies conserved features of translation elongation across mammalian cellular diversity and evolution.

scholarly journals Komposisi Kandungan Asam Amino Pada Teripang Emas (Stichoupus horens) di Perairan Pulau Bintan, Kepulauan Riau

2018 ◽  
Vol 6 (2) ◽  
pp. 186-192
Author(s):  
Gianto Gianto ◽  
Made Suhandana ◽  
R. Marwita Sari Putri
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Glutamic Acid ◽  
Sea Cucumber ◽  
Acid Value ◽  
Essential Amino Acids ◽  
Sea Cucumbers ◽  
High Protein Content ◽  
Acid Component ◽  
Amino Acid Component

This study aims to analyze the amino acid component contained in the golden sea cucumber so that it can be used as a basis for consideration, management, especially the development of sea cucumbers. Protein in sea cucumbers have complete amino acids, both essential amino acids and non-essential amino acids. The result of the proximate test of golden sea cucumber has high protein content which is 95,14% and fat 0,20% compared to other sea cucumber type while the protein of sea cucumber is very low that is 1.78% and 1.54% ash. The highest content of dried sea cucumber amino acids in golden sea cucumber meat seen in glutamic acid of 6.6049%, 7.1769% glycine, aspartic acid 3.9227% and proline of 3.4189% while the results of wet sea cucumber amino acids have a low amino acid value with glutamic acid 0.2281%, Glycine 0.2308% and Alanin 0.2169%.

scholarly journals Edaphic controls on genome size and GC content of bacteria in soil microbial communities

2021 ◽  
Author(s):  
Peter Francis Chuckran ◽  
Cody Flagg ◽  
Jeffrey Propster ◽  
William Austin Rutherford ◽  
Ella T. Sieradzki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Genome Size ◽  
Acid Content ◽  
Bacterial Genome ◽  
Soil Microbial Communities ◽  
Gc Content ◽  
Amino Acid Content ◽  
The United States ◽  
Soil Bacterial

Genomic traits, such as genome size, GC content, codon usage, and amino acid content, shed insight into the evolutionary processes of bacteria and selective forces behind microbial community composition. Nutrient limitation has been shown to reduce bacterial genome size and influence nucleotide composition, yet little research has been conducted in the soil environment, and the factors which shape soil bacterial genomic traits remain largely unknown. Here we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across the United States from the National Ecological Observation Network (NEON) and observed the distribution of these traits across numerous environmental gradients. We found that genomic trait averages were most strongly related to pH, which we suggest results in both physiological constraints on growth as well as affects availability of nutrients in soil. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with larger genomes and lower GC-content, potentially a result of increased physiological stress and increased metabolic diversity. Conversely, smaller genomes with high GC content were associated with high pH and low soil carbon to nitrogen ratios, indicating potential resource driven selection against carbon-rich AT base pairs. We found that this relationship of nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms which underpin nucleotide and amino acid selection in soil bacterial communities.

Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons

2021 ◽  
pp. gr.275944.121
Author(s):  
William Gao ◽  
Carlos J Gallardo-Dodd ◽  
Claudia Kutter
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Single Cell ◽  
Trna Gene ◽  
Cell Types ◽  
Ribosome Profiling ◽  
Translation Efficiency ◽  
Cell Type ◽  
Gene Usage ◽  
Cell Type Specific

The correlation between codon and anticodon pools influences the efficiency of translation, but whether differences exist in these pools across individual cells is unknown. We determined that codon usage and amino acid demand are highly stable across different cell types using available mouse and human single-cell RNA sequencing atlases. After demonstrating the robustness of ATAC-seq measurements for the analysis of tRNA gene usage, we quantified anticodon usage and amino acid supply in both mouse and human single-cell ATAC-seq atlases. We found that tRNA gene usage is overall coordinated across cell types, except in neurons, which clustered separately from other cell types. Integration of these datasets revealed a strong and statistically significant correlation between amino acid supply and demand across almost all cell types. Neurons have an enhanced translation efficiency over other cell types, driven by an increased supply of tRNAAla (AGC) anticodons. This results in faster decoding of the Ala-GCC codon, as determined by cell type-specific ribosome profiling, suggesting that the reduction of tRNAAla (AGC) anticodon pools may be implicated in neurological pathologies. This study, the first such examination of codon usage, anticodon usage, and translation efficiency resolved at the cell type level with single-cell information, identifies a conserved landscape of translation elongation across mammalian cellular diversity and evolution.

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