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
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
Citations
More filters
Proceedings Article
Hydrophobic-Hydrophilic Forces and their Effects on Protein Structural Similarity
TL;DR: This paper looked into the sub-conformations' hydrophobic-hydrophilic nature by incorporating a HP approach and proposed a way of evaluating how these type of forces affect the protein folding process.
Journal ArticleDOI
Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias
TL;DR: This study conducted genome-wide analyses of amino acids usage and genetic codons structure in 7270 species across three domains of life and indicated that the amino acids A, D, E, G, L, P, R, S, T and V might be the first recruited into the last universal common ancestry proteins.
Journal ArticleDOI
Compactness of Protein Folds Alters Disulfide-Bond Reducibility by Three Orders of Magnitude: A Comprehensive Kinetic Case Study on the Reduction of Differently Sized Tryptophan Cage Model Proteins
Dániel Horváth,Nóra Taricska,Ernő Keszei,Pál Stráner,Viktor Farkas,Gábor Tóth,András Perczel +6 more
TL;DR: It is found that structural, steric, and electrostatic factors influence the reduction rate, resulting in orders of magnitude differences in reduction half‐lives even for structurally similar, well‐folded derivatives of a small model protein.
Journal ArticleDOI
Aminosäuren und die Entstehung des Lebens. Spuren aus dem Weltraum
TL;DR: The European Rosetta mission as mentioned in this paper will verify the outlined hypotheses on modern theories on the origin of life on Earth by analyzing cometary ice samples in situ using a lander on a cometary surface.
Posted ContentDOI
Universal and taxon-specific trends in protein sequences as a function of age
TL;DR: The authors performed integrated phylostratigraphy across 435 fully sequenced and dated eukaryotic species, using sensitive HMM methods to detect homology of protein domains and applying a variety of quality filters.
References
More filters
Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI
A Simple Sequentially Rejective Multiple Test Procedure
TL;DR: In this paper, a simple and widely accepted multiple test procedure of the sequentially rejective type is presented, i.e. hypotheses are rejected one at a time until no further rejections can be done.
Journal ArticleDOI
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
Steven J. Clough,Andrew F. Bent +1 more
TL;DR: The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement.
Journal ArticleDOI
A genomic perspective on protein families
TL;DR: Comparison of proteins encoded in seven complete genomes from five major phylogenetic lineages and elucidation of consistent patterns of sequence similarities allowed the delineation of 720 clusters of orthologous groups (COGs), which comprise a framework for functional and evolutionary genome analysis.
Journal ArticleDOI
Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA.
TL;DR: A large number of morphologically normal, fertile, transgenic rice plants were obtained by co-cultivation of rice tissues with Agrobacterium tumefaciens, and sequence analysis revealed that the boundaries of the T-DNA in transgenic Rice plants were essentially identical to those intransgenic dicotyledons.