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 protei...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.展开更多
Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean science.Microbial oceanography integrates the principles of marine microbiol...Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean science.Microbial oceanography integrates the principles of marine microbiology,microbial ecology and oceanography to study the role of microorganisms in the biogeochemical dynamics of natural marine ecosystems.The application of genomics tools to study marine microbes is resulting in rapid advancements in microbial oceanography that has important implications in global carbon cycle,climate change,and ecosystem function.Here we review the application of genomics and metagenomics in microbial oceanography and suggest future directions in microbial oceanography research.展开更多
基金supported by basic grants from CONACYT–Mexico to AT and LDa scholarship to ORS(Grant No.347589/237183)
文摘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.
文摘Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean science.Microbial oceanography integrates the principles of marine microbiology,microbial ecology and oceanography to study the role of microorganisms in the biogeochemical dynamics of natural marine ecosystems.The application of genomics tools to study marine microbes is resulting in rapid advancements in microbial oceanography that has important implications in global carbon cycle,climate change,and ecosystem function.Here we review the application of genomics and metagenomics in microbial oceanography and suggest future directions in microbial oceanography research.
