title: No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes.
abstract: The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans.
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France.
authors.forename: Clémentine M
authors.initials: CM
authors.lastname: Francois
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Duret
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Simon
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France.
authors.forename: Florian
authors.initials: F
authors.lastname: Mermillod-Blondin
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France.
authors.forename: Florian
authors.initials: F
authors.lastname: Malard
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France.
authors.forename: Lara
authors.initials: L
authors.lastname: Konecny-Dupré
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France.
authors.forename: Rémi
authors.initials: R
authors.lastname: Planel
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Penel
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France Institut Universitaire de France, Paris, France.
authors.forename: Christophe J
authors.initials: CJ
authors.lastname: Douady
authors.affiliation: Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France tristan.lefebure@univ-lyon1.fr.
authors.forename: Tristan
authors.initials: T
authors.lastname: Lefébure
mesh_terms: D000596:Amino Acids / Q000235:genetics / Q000378:metabolism; D000818:Animals; D017753:Ecosystem; D033321:Isopoda / Q000235:genetics* / Q000378:metabolism*; D009584:Nitrogen / Q000172:deficiency* / Q000378:metabolism*; D009711:Nucleotides / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D020543:Proteome; D012641:Selection, Genetic; D059467:Transcriptome
chemical_list: D000596:Amino Acids; D009711:Nucleotides; D020543:Proteome; D009584:Nitrogen
keywords: C:N mismatch.; N availability; RNA and protein composition; comparative approach; nitrogen cost; orthologous gene families; stoichiogenomics