scholarly journals Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level

2009 ◽  
Vol 26 (10) ◽  
pp. 2275-2284 ◽  
Author(s):  
Y. Suzuki ◽  
T. Gojobori ◽  
S. Kumar
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Amino Acid Sequence Level ◽  
Cpg Dinucleotides

Nucleoid-associated proteins in Crenarchaea

2011 ◽  
Vol 39 (1) ◽  
pp. 116-121 ◽  
Author(s):  
Rosalie P.C. Driessen ◽  
Remus Th. Dame
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structural Effect ◽  
Chromatin Organization ◽  
Large Set ◽  
Chromosomal Dna ◽  
Amino Acid Sequence Level ◽  
Generic Level ◽  
Architectural Proteins ◽  
Associated Proteins

Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.

scholarly journals Sequence of the S10 cDNA from 'McIntosh' Apple and a PCR-digestion Identification Method

HortScience ◽  
2002 ◽  
Vol 37 (1) ◽  
pp. 187-190 ◽  
Author(s):  
Kentaro Kitahara ◽  
Shogo Matsumoto
Keyword(s):  
Polymerase Chain Reaction ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Restriction Enzyme ◽  
Chain Reaction ◽  
Specific Primers ◽  
Amino Acid Sequence Level ◽  
Identification Method ◽  
Polymerase Chain

An S-allele cDNA was cloned from pistils of 'McIntosh' apple (Malus ×domestica Borkh.). The allele, designated Si in Japan and S10 in Europe, is an S-RNase that is very similar (94%) to the S3-RNase at the deduced amino acid sequence level. This allele can be detected by amplification using the polymerase chain reaction (PCR) and specific primers, followed by digestion with restriction enzyme EheI. The S10 allele was discovered in 'Empire', 'Maypole', 'Shinano Red', 'Spencer', and 'Vista Bella'. The S-allele cDNAs sequenced to date are listed with their Japanese and European designations.

scholarly journals Comparative Domain-Fold Analysis of the SARS-CoV-2 ORF1ab Polyprotein: Insight into Co-Evolution, Conservation of Folding Patterns, Potential Therapeutic Strategies, and the Possibility of Reemergence

2020 ◽  
Author(s):  
Srijeeb Karmakar ◽  
Sachin Kumar ◽  
Vimal Katiyar
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Rna Viruses ◽  
Small Variation ◽  
Therapeutic Strategies ◽  
Domain Specific ◽  
In Silico Study ◽  
Protein Functions ◽  
Insight Into

The high transmissibility and replication of SARS-CoV-2 have been attributed to enhanced protein functions which are dependent on protein folding. Our in silico study endeavored to scrutinize SARS-CoV-2 ORF1ab by analyzing the conserved folding patterns of its transcribed proteins. Accordingly, the findings indicated that SARS-CoV-2 ORF1ab shares domain-specific fold-fingerprints with a spectrum of unrelated organisms. Closer observation revealed slight changes in folding patterns engendered with small variation in the intrinsic amino acid sequence. By correlating with the evolvability-potential of RNA-viruses and COVID-19 pandemic, we hypothesize that SARS-CoV-2 could undergo fast recombination with the host, SARS-CoV-2 minor variants and other viral species resulting in a reservoir of SARS-CoV-2 quasispecies. It is highly possible that natural selection will cause a future emergence of evolved SARS-CoV-2-descendants. Nonetheless, we hope that this insightful study will assist in elucidating SARS-CoV-2 protein functionalities, development of vaccines, and the possibility and nature of future emergence.

scholarly journals Nucleotide Substitution and Recombination at Orthologous Loci in Staphylococcus aureus

2005 ◽  
Vol 187 (8) ◽  
pp. 2698-2704 ◽  
Author(s):  
Austin L. Hughes ◽  
Robert Friedman
Keyword(s):  
Staphylococcus Aureus ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Ribosomal Proteins ◽  
Nucleotide Substitution ◽  
Binding Protein ◽  
Amino Acid Sequence Level ◽  
Fibrinogen Binding ◽  
Genes Encoding ◽  
Orthologous Loci

ABSTRACT The pattern of nucleotide substitution was examined at 2,129 orthologous loci among five genomes of Staphylococcus aureus, which included two sister pairs of closely related genomes (MW2/MSSA476 and Mu50/N315) and the more distantly related MRSA252. A total of 108 loci were unusual in lacking any synonymous differences among the five genomes; most of these were short genes encoding proteins highly conserved at the amino acid sequence level (including many ribosomal proteins) or unknown predicted genes. In contrast, 45 genes were identified that showed anomalously high divergence at synonymous sites. The latter genes were evidently introduced by homologous recombination from distantly related genomes, and in many cases, the pattern of nucleotide substitution made it possible to reconstruct the most probable recombination event involved. These recombination events introduced genes encoding proteins that differed in amino acid sequence and thus potentially in function. Several of the proteins are known or likely to be involved in pathogenesis (e.g., staphylocoagulase, exotoxin, Ser-Asp fibrinogen-binding bone sialoprotein-binding protein, fibrinogen and keratin-10 binding surface-anchored protein, fibrinogen-binding protein ClfA, and enterotoxin P). Therefore, the results support the hypothesis that exchange of homologous genes among S. aureus genomes can play a role in the evolution of pathogenesis in this species.

scholarly journals A common structural blueprint for plant UDP-sugar-producing pyrophosphorylases

2011 ◽  
Vol 439 (3) ◽  
pp. 375-381 ◽  
Author(s):  
Leszek A. Kleczkowski ◽  
Matt Geisler ◽  
Elisabeth Fitzek ◽  
Malgorzata Wilczynska
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Molecular Mobility ◽  
Regulatory Mechanism ◽  
Catalytic Domain ◽  
Evolutionary Relationships ◽  
Amino Acid Sequence Level ◽  
Significant Homology ◽  
Regulatory Functions

Plant pyrophosphorylases that are capable of producing UDP-sugars, key precursors for glycosylation reactions, include UDP-glucose pyrophosphorylases (A- and B-type), UDP-sugar pyrophosphorylase and UDP-N-acetylglucosamine pyrophosphorylase. Although not sharing significant homology at the amino acid sequence level, the proteins share a common structural blueprint. Their structures are characterized by the presence of the Rossmann fold in the central (catalytic) domain linked to enzyme-specific N-terminal and C-terminal domains, which may play regulatory functions. Molecular mobility between these domains plays an important role in substrate binding and catalysis. Evolutionary relationships and the role of (de)oligomerization as a regulatory mechanism are discussed.

The staining pattern of the tropomyosin sequence is displayed in a new paracrystal

1986 ◽  
Vol 44 ◽  
pp. 150-151
Author(s):  
M.K. Lamvik ◽  
L.L. Klatt
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Staining Pattern ◽  
Banding Patterns ◽  
Mass Thickness ◽  
New Form

Tropomyosin paracrystals have been used extensively as test specimens and magnification standards due to their clear periodic banding patterns. The paracrystal type discovered by Ohtsuki1 has been of particular interest as a test of unstained specimens because of alternating bands that differ by 50% in mass thickness. While producing specimens of this type, we came across a new paracrystal form. Since this new form displays aligned tropomyosin molecules without the overlaps that are characteristic of the Ohtsuki-type paracrystal, it presents a staining pattern that corresponds to the amino acid sequence of the molecule.

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