Protein length in eukaryotic and prokaryotic proteomes

By L. Brocchieri, S. Karlin. 2005

408 citations recorded by the source corpus.

We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. The magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended multi-functional and multi-domain proteins. Comparing Bacteria and Archaea, we determined that the small but significant length difference observed between their proteins results from a combination of three factors: (i) bacterial proteomes include a greater proportion than archaeal proteomes of longer proteins involved in metabolism or cellular processes, (ii) within most functional classes, protein families unique to Bacteria are generally longer than protein families unique to Archaea and (iii) within the same protein family, homologs from Bacteria tend to be longer than the corresponding homologs from Archaea. These differences are interpreted with respect to evolutionary trends and prevailing environmental conditions within the two prokaryotic groups.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Extraction of Protein from Common Plant Leaves for Use as Human Food (2010, background): “The current estimate for the average protein length is 300 residues (Brocchieri and Karlin, 2005).”
Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures (2021, background): “Moreover, since protein sizes range from less than one hundred to tens of thousands of amino acids (Brocchieri & Karlin, 2005), we propose protein-speciﬁc pooling operations that allow hierarchical grouping of such a wide range of sizes, enabling the detection of features at different scales (Sec.”
Assembly of long error-prone reads using de Bruijn graphs (2016, background): “Note that while the average length of a protein-coding gene in most bacterial genomes exceeds 800 [11], the average ORF length in a randomly generated string of nucleotide is only 64.”
Measuring the activity of protein variants on a large scale using deep mutational scanning (2014, background): “In fact, the average human protein, ~350 amino acids in length, can yield 7,000 single mutations and over 22 million double mutations 3 .”