2016
DOI: 10.1186/s13059-016-1087-9
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Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

Abstract: BackgroundGenomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism’s environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood.ResultsHere we show that differential nitrogen availability, due… Show more

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Cited by 62 publications
(68 citation statements)
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“…In addition, dietary shifts are associated with metabolic adaptation in animals, which manifests in genetic variations of both mitochondrial DNA and nuclear genomes (Ballard & Youngson, 2015;Seward & Kelly, 2016). Species sampling covered all three types of coccinellid diets, but the number of sequenced taxa was still quite limited compared to the richness of species within Coccinellidae.…”
Section: Evolution Of Mitochondrial Protein-coding Genes In Coccinementioning
confidence: 99%
“…In addition, dietary shifts are associated with metabolic adaptation in animals, which manifests in genetic variations of both mitochondrial DNA and nuclear genomes (Ballard & Youngson, 2015;Seward & Kelly, 2016). Species sampling covered all three types of coccinellid diets, but the number of sequenced taxa was still quite limited compared to the richness of species within Coccinellidae.…”
Section: Evolution Of Mitochondrial Protein-coding Genes In Coccinementioning
confidence: 99%
“…Various factors related to CUB are G+C% composition, GC skew, protein hydropathy, transcriptional selection (McInerney, ), gene length (Lawrence & Ochman, ), expression level (Gouy & Gautier, ; Sharp & Li, ), protein structure (D'Onofrio, Ghosh, & Bernardi, ), and dietary nitrogen (Seward & Kelly, ). However the influence of these factors in codon usage is still debated (Zhou, Weems, & Wilke, ).…”
Section: Introductionmentioning
confidence: 99%
“…A comparative genomics approach on a set of animal and plant model organisms has shown N-conservation in the transcriptomes of wild plant taxa relative to both crop plants, which have a history of fertilizer application, and animals, which harvest N in organic form from other organisms (Acquisti et al, 2009a,b). Similarly, bias toward lower numbers of N atoms is reported in the highly expressed proteins of bacteria and yeast (Li et al, 2009), and in bacterial and eukaryotic parasites with low-N diets (Seward and Kelly, 2016).…”
Section: Future Research Prioritiesmentioning
confidence: 99%
“…At the genomic level, environmental nutrient limitation may constrain cellular processes (e.g., photosynthesis, transcriptomes) and over time may result in divergence of genes and the proteins they encode (Acquisti et al, 2009a,b;Elser et al, 2011;Seward and Kelly, 2016; Figure 1).…”
Section: Introductionmentioning
confidence: 99%