Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins  

作　　者：Obed Ramirez-Sachez Paulino Perez-Rodriguez Luis Delaye Axel Tiessen 

机构地区：[1]Genetic Engineering Department,CINVESTAV Unidad Irapuato,Irapuato,CP 36821,Mexico [2]Colegio de Postgraduados,Campus Montecillo,Texcoco,CP 56230,Mexico

出　　处：《Genomics, Proteomics & Bioinformatics》2016年第6期357-370,共14页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by basic grants from CONACYT–Mexico to AT and LD;a scholarship to ORS(Grant No.347589/237183)

摘　　要：Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylo- genetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues （aa）, average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are -81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by -10 exons of small size [-176 nucleotides （nt）]. Streptophyta have on average only -5.7 exons of medium size （-230 nt）. Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons （ 〉 400 nt）. Among subcellular compartments, membrane proteins are the largest （-520 aa）, whereas the smallest proteins correspond to the gene ontology group of ribosome （-240 aa）. Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have -34% more but -20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylo- genetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues （aa）, average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are -81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by -10 exons of small size [-176 nucleotides （nt）]. Streptophyta have on average only -5.7 exons of medium size （-230 nt）. Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons （ 〉 400 nt）. Among subcellular compartments, membrane proteins are the largest （-520 aa）, whereas the smallest proteins correspond to the gene ontology group of ribosome （-240 aa）. Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have -34% more but -20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.

关 键 词：Digital proteome EUKARYA Evolution Viridiplantae Polypeptide length 

分 类 号：Q[生物学]