scholarly journals Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum

2006 ◽  
Vol 34 (16) ◽  
pp. 4583-4592 ◽  
Author(s):  
Hubert Charles ◽  
Federica Calevro ◽  
José Vinuelas ◽  
Jean-Michel Fayard ◽  
Yvan Rahbe
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Aromatic Amino Acid ◽  
Acyrthosiphon Pisum ◽  
Nutritional Stress ◽  
Buchnera Aphidicola ◽  
Over Expression

scholarly journals Further evidence that mechanisms of host/symbiont integration are dissimilar in the maternal versus embryonic Acyrthosiphon pisum bacteriome

EvoDevo ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Celeste R. Banfill ◽  
Alex C. C. Wilson ◽  
Hsiao-ling Lu
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Acyrthosiphon Pisum ◽  
Essential Amino Acids ◽  
Developmental Time ◽  
Follicular Epithelium ◽  
Future Research ◽  
Buchnera Aphidicola ◽  
Bacterial Endosymbionts ◽  
Asexual Embryogenesis

Abstract Background Host/symbiont integration is a signature of evolutionarily ancient, obligate endosymbioses. However, little is known about the cellular and developmental mechanisms of host/symbiont integration at the molecular level. Many insects possess obligate bacterial endosymbionts that provide essential nutrients. To advance understanding of the developmental and metabolic integration of hosts and endosymbionts, we track the localization of a non-essential amino acid transporter, ApNEAAT1, across asexual embryogenesis in the aphid, Acyrthosiphon pisum. Previous work in adult bacteriomes revealed that ApNEAAT1 functions to exchange non-essential amino acids at the A. pisum/Buchnera aphidicola symbiotic interface. Driven by amino acid concentration gradients, ApNEAAT1 moves proline, serine, and alanine from A. pisum to Buchnera and cysteine from Buchnera to A. pisum. Here, we test the hypothesis that ApNEAAT1 is localized to the symbiotic interface during asexual embryogenesis. Results During A. pisum asexual embryogenesis, ApNEAAT1 does not localize to the symbiotic interface. We observed ApNEAAT1 localization to the maternal follicular epithelium, the germline, and, in late-stage embryos, to anterior neural structures and insect immune cells (hemocytes). We predict that ApNEAAT1 provisions non-essential amino acids to developing oocytes and embryos, as well as to the brain and related neural structures. Additionally, ApNEAAT1 may perform roles related to host immunity. Conclusions Our work provides further evidence that the embryonic and adult bacteriomes of asexual A. pisum are not equivalent. Future research is needed to elucidate the developmental time point at which the bacteriome reaches maturity.

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 Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola

2010 ◽  
Vol 19 ◽  
pp. 249-258 ◽  
Author(s):  
A. C. C. Wilson ◽  
P. D. Ashton ◽  
F. Calevro ◽  
H. Charles ◽  
S. Colella ◽  
...  
Keyword(s):  
Amino Acid ◽  
Acyrthosiphon Pisum ◽  
Symbiotic Bacterium ◽  
Pea Aphid ◽  
Buchnera Aphidicola ◽  
Insight Into

scholarly journals Regulation of Transcription in a Reduced Bacterial Genome: Nutrient-Provisioning Genes of the Obligate Symbiont Buchnera aphidicola

2005 ◽  
Vol 187 (12) ◽  
pp. 4229-4237 ◽  
Author(s):  
Nancy A. Moran ◽  
Helen E. Dunbar ◽  
Jennifer L. Wilcox
Keyword(s):  
Amino Acid ◽  
Acid Content ◽  
Acyrthosiphon Pisum ◽  
Bacterial Genome ◽  
Amino Acid Content ◽  
Transcript Abundance ◽  
Regulation Of Transcription ◽  
Buchnera Aphidicola ◽  
Obligate Symbiont ◽  
Dietary Amino Acid

ABSTRACT Buchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. Most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. Using full-genome microarrays for B. aphidicola of the host Schizaphis graminum, we examined transcriptome responses to changes in dietary amino acid content and then verified behavior of individual transcripts using quantitative reverse transcriptase PCR. The only gene showing a consistent and substantial (>twofold) response was metE, which underlies methionine biosynthesis and which is the only amino acid biosynthetic gene retaining its ancestral regulator (metR). In another aphid host, Acyrthosiphon pisum, B. aphidicola has no functional metR and shows no response in metE transcript levels to changes in amino acid concentrations. Thus, the only substantial transcriptional response involves the one gene for which an ancestral regulator is retained. This result parallels that from a previous study on heat stress, in which only the few genes retaining the global heat shock promoter showed responses in transcript abundance. The irreversible losses of transcriptional regulators constrain ability to alter gene expression in the context of environmental fluctuations affecting the symbiotic partners.

scholarly journals Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂′c) measures

2017 ◽  
Vol 22 (3) ◽  
pp. 277-283 ◽  
Author(s):  
Siddhartha Sankar Satapathy ◽  
Ajit Kumar Sahoo ◽  
Suvendra Kumar Ray ◽  
Tapash Chandra Ghosh
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Degeneracy

scholarly journals Elucidation of Codon Usage Signatures across the Domains of Life

2018 ◽  
Author(s):  
Eva Maria Novoa ◽  
Olivier Jaillon ◽  
Irwin Jungreis ◽  
Manolis Kellis
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Single Amino Acid ◽  
Common Belief ◽  
Domain Specific ◽  
Optimal Codons ◽  
A Genome ◽  
Domains Of Life

AbstractDue to the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being ‘synonymous’, these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is generally attributed to mutational drift, is the major determinant of interspecies codon usage bias. Here we find that in addition to the bias caused by GC content, inter-species codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding, and show that the identified domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain with high accuracy. Considering that species belonging to the same domain share similar tRNA decoding strategies, we then wondered whether the inclusion of codon autocorrelation patterns might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to the common belief. Instead, our results reveal that codon autocorrelation patterns are a consequence of codon optimality throughout a sequence, where highly expressed genes display autocorrelated ‘optimal’ codons, whereas lowly expressed genes display autocorrelated ‘non-optimal’ codons.

scholarly journals Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

2021 ◽  
Vol 11 ◽  
Author(s):  
Yicong Li ◽  
Rui Wang ◽  
Huihui Wang ◽  
Feiyang Pu ◽  
Xili Feng ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Essential Gene ◽  
Synonymous Codon ◽  
Phylogenetic Analyses ◽  
Nucleotide Composition ◽  
Synonymous Codon Usage ◽  
Related Gene ◽  
Codon Positions

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.

scholarly journals Prephenate Dehydratase from the Aphid Endosymbiont (Buchnera) Displays Changes in the Regulatory Domain That Suggest Its Desensitization to Inhibition by Phenylalanine

2000 ◽  
Vol 182 (10) ◽  
pp. 2967-2969 ◽  
Author(s):  
Nuria Jiménez ◽  
Fernando González-Candelas ◽  
Francisco J. Silva
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Acyrthosiphon Pisum ◽  
Constitutive Expression ◽  
Essential Amino Acids ◽  
Chorismate Mutase ◽  
Regulatory Domain ◽  
Buchnera Aphidicola ◽  
Prephenate Dehydratase ◽  
Bacterial Endosymbiont

ABSTRACT Buchnera aphidicola, the prokaryotic endosymbiont of aphids, complements dietary deficiencies with the synthesis and provision of several essential amino acids. We have cloned and sequenced a region of the genome of B. aphidicola isolated from Acyrthosiphon pisum which includes the two-domainaroQ/pheA gene. This gene encodes the bifunctional chorismate mutase-prephenate dehydratase protein, which plays a central role in l-phenylalanine biosynthesis. Two changes involved in the overproduction of this amino acid have been detected. First, the absence of an attenuator region suggests a constitutive expression of this gene. Second, the regulatory domain of the Buchneraprephenate dehydratase shows changes in the ESRP sequence, which is involved in the allosteric binding of phenylalanine and is strongly conserved in prephenate dehydratase proteins from practically all known organisms. These changes suggest the desensitization of the enzyme to inhibition by phenylalanine and would permit the bacterial endosymbiont to overproduce phenylalanine.

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