Nutrilyzer: A Tool for Deciphering Atomic Stoichiometry of Differentially Expressed Paralogous Proteins
Organisms try to maintain homeostasis by balanced uptake of nutrients from their envi-ronment From an atomic perspective this means that, for example, carbon:nitrogen:sulfur ratios are kept within given limits. Upon limitation of, for example, sulfur, its acquisition is triggered. For yeast it was shown that transporters and enzymes involved in sulfur up-take are encoded as paralogous genes that express different isoforms. Sulfur deprivation leads to upregulation of isoforms (hat are poor in sulfurcontaining amino acids, that is, methinone and cysteine. Accordingly, sulfur-rich isoforms are downregulated. We developed a web-based software, doped Nutrilyzer, that extracts paralogous protein coding sequences from an annotated genome sequence and evaluates their atomic compo-sition. When fed with gene-expression data for nutrient limited and normal conditions, Nutrilyzer provides a list of genes that are significantly differently expressed and simultaneously contain significantly different amounts of the limited nutrient in their atomic composition. Its intended use is in the field of ecological stoichiometry. Nutrilyzer is available at http: //nutrilyzer .hs-mittweida. de. Here we describe the work flow and results with an example from a whole-genome Ara-bidopsis thaliana gene-expression analysis upon oxygen deprivation. 43 paralogs dis-tributed over 37 homology clusters were found to be significantly differently expressed while containing significantly different amounts of oxygen.
Katrin Lotz Falk Schreiber Robbe Wiinschiers
SunGene GmbH, Corrensstr. 3, D-06466 Gatersleben, Germany Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben,Corrensstr. 3, D-06466 University of Applied Sciences Mittweida, Technikumplatz 17,09648 Mittweida, Germany
国际会议
杭州
英文
119-125
2012-04-02（万方平台首次上网日期，不代表论文的发表时间）