Journal ArticleDOI
A universal trend of amino acid gain and loss in protein evolution
I. King Jordan,Fyodor A. Kondrashov,Ivan Adzhubei,Yuri I. Wolf,Eugena V. Koonin,Alexey S. Kondrashov,Shasnil Sunyaev +6 more
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TLDR
Comparison of sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life and phylogenies to polarize amino acid substitutions shows expansion of initially under-represented amino acids apparently continues to this day.Abstract:
A comparison of corresponding sets of proteins encoded by closely related genes from organisms representing all three domains of life (Bacteria, Archaea and Eukaryota) suggests that the order in which the genetic code was assembled over 3.5 billion years ago continues to influence the evolution of proteins today. Across these diverse genomes, evolving proteins have accumulated Cys, Met, His, Ser and Phe, and lost many of their Pro, Ala, Glu and Gly residues. The same nine amino acids are currently accrued or lost in human proteins as shown by analysis of nucleotide polymorphisms. The amino acids with declining frequencies were probably among the first incorporated into the genetic code, and most of those with increasing frequencies were probably recruited late. Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G + C)-rich (or (A + T)-rich) genomes contain more (or fewer) amino acids encoded by (G + C)-rich codons1,2,3,4. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late5,6,7. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago8,9, apparently continues to this day.read more
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Posttranslational Chemical Mutagenesis: To Reveal the Role of Noncatalytic Cysteine Residues in Pathogenic Bacterial Phosphatases.
Jean B. Bertoldo,Jean B. Bertoldo,Hernán Terenzi,Stefan Hüttelmaier,Gonçalo J. L. Bernardes,Gonçalo J. L. Bernardes +5 more
TL;DR: This Perspective provides detailed insight into an alternative use of site-selective protein chemistry to probe the role(s) of unpaired Cys residues in the structure and function of disease relevant proteins and reveals structural information about binding pockets and regulatory roles of the modified residues, which can be further validated by conventional site-directed mutagenesis.
Journal ArticleDOI
Concentration of Specific Amino Acids at the Catalytic/Active Centers of Highly-Conserved “Housekeeping” Enzymes of Central Metabolism in Archaea, Bacteria and Eukaryota: Is There a Widely Conserved Chemical Signal of Prebiotic Assembly?
TL;DR: The data support the view that in the most-conserved environment immediately surrounding the C/AC of taxonomically distant and highly conserved essential enzymes of central metabolism there are amino acids whose identity and degree of occupancy is similar to a proposed amino acid set and frequency associated with prebiotic evolution.
Journal ArticleDOI
The very early evolution of protein translocation across membranes.
Aj Harris,Aaron David Goldman +1 more
TL;DR: In this paper, the authors used a computational approach to investigate the early evolutionary history of a system of proteins that, together, embed and translocate other proteins across cell membranes, including the signal recognition particle (SRP) system and the Sec translocation channel.
Journal ArticleDOI
Evolution of protein lipograms: A bioinformatics problem
Harold B. White,Prasad Dhurjati +1 more
TL;DR: The point of the problem described here is that a deficiency or absence of a particular amino acid in a protein may be more than a chance occurrence and may be driven by natural selection.
Journal ArticleDOI
Free amino acid quantification in cloud water at the Puy de Dôme station (France)
P. Renard,Maxence Brissy,Florent Rossi,Martin Leremboure,Saly Jaber,Jean-Luc Baray,Angelica Bianco,Anne-Marie Delort,Laurent Deguillaume +8 more
TL;DR: In this paper , the authors quantified free amino acids (FAAs) in cloud water sampled at the Puy de Dôme station (PUY) during 13 cloud events.
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