Dataset Information

Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species.

ABSTRACT: The native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e., the fraction of its proteome in each of seven major cellular compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes: Homo sapiens (human), Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Mus musculus (mouse), Rattus norvegicus (rat), Drosophila melanogaster (fruit/vinegar fly), Anopheles gambiae (African malaria mosquito), Caenorhabitis elegans (nematode), Saccharomyces cerevisiae (baker's yeast), and Schizosaccharomyces pombe (fission yeast). The two largest classes were predicted to be the nucleus and the cytoplasm together accounting for 47-62% of all proteins, while 7-21% of the proteins were predicted in the plasma membrane and 4-15% to be secreted. Overall, the predicted location spectra were largely similar. However, in detail, the differences sufficed to plot trees (UPGMA) and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states (location classes). The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons. Most interestingly, known phylogenetic relations were reproduced better by paralog-only than by ortholog-only trees.

SUBMITTER: Marot-Lassauzaie V

PROVIDER: S-EPMC8379119 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:A novel, non-terminal surgical procedure to remove a single placentome from the pregnant ewe for gene expression and histological analyses was recently developed in our laboratory. This technique allows for evaluation of nutritional insults on placental development at more than one stage of gestation using a single animal. Early attempts to develop a similar technique in cattle were met with complications due to inaccessibility of the gravid uterine horn because of its location and mass. One alternative is to collect a placentome from the contralateral uterine horn; however, the question remains as to whether gene expression varies among placentomes based on location relative to the fetus. Pregnant heifers were maintained on forage during early gestation and later moved into pens with a Calan gate system (American Calan, Northwood, NH). On gestational day (GD) 158, five heifers were assigned to receive a hay-based diet formulated to meet 100% of NRC requirements, and five heifers were fed 70% of NRC requirements until necropsy on GD244. At necropsy, a single representative placentome was selected for analysis from the antimesometrial side: (1) of the gravid uterine horn central to the amnion, (2) over the allantois immediately adjacent to the amnion, (3) in the tip of the gravid uterine horn, and (4) in the tip of the contralateral uterine horn. Mean placentome weight was greater (P < 0.05) for locations central to the amnion and allantois compared to locations within the tips of the ipsilateral and contralateral horns, respectively. Gene expression for angiogenic factors (FGF2, ODC1, VEGFA, and FLT1), nutrient transporters (SLC7A1 and SLC2A1), and factors associated with hormone action (ESR1, IGF1, IGFBP3, CSH1, and PAG1) were unaffected (P > 0.05) by dietary treatment or location of the placentome. Results indicate that location of the placentome in relation to the fetus does not impact gene expression, enhancing the efficacy of nonterminal methodologies for sampling gene expression in placentomes.

Dataset Information

Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets