Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

1993 ◽  
Vol 36 (3) ◽  
pp. 270-281 ◽  
Author(s):  
Jun Adachi ◽  
Ying Cao ◽  
Masami Hasegawa
Keyword(s):  
Mitochondrial Dna ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Rapid Evolution ◽  
Amino Acid Sequence Level ◽  
Dna Evolution

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 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 Mitochondrial DNA sequence variation among geographical isolates of Opisthorchis viverrini in Thailand and Lao PDR, and phylogenetic relationships with other trematodes

Parasitology ◽  
2008 ◽  
Vol 135 (12) ◽  
pp. 1479-1486 ◽  
Author(s):  
W. SAIJUNTHA ◽  
P. SITHITHAWORN ◽  
S. WONGKHAM ◽  
T. LAHA ◽  
N. B. CHILTON ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Sequence Variation ◽  
Sequence Data ◽  
Lao Pdr ◽  
Opisthorchis Viverrini ◽  
Nucleotide Sequence Variation ◽  
Geographical Isolates

SUMMARYThe present study compared the genetic variation among 14 different geographical isolates of Opisthorchis viverrini sensu lato from Thailand and Lao PDR using sequence data for 2 mitochondrial DNA genes, the subunit 1 of NADH dehydrogenase gene (nad1) and cytochrome c oxidase gene (cox1). Four different nad1 haplotypes were detected among isolates, all of which were identical at the amino acid sequence level. Nucleotide sequence variation among 14 isolates ranged from 0 to 0·3% for nad1. Two different cox1 haplotypes were detected among isolates. These two haplotypes differed at 2 nucleotide positions, one of which resulted in a change in the amino acid sequence. Nucleotide sequence variation among isolates for cox1 ranged from 0 to 0·5%. Comparison of cox1 sequences of O. viverrini to those of other trematodes revealed nucleotide differences of 13–31%. A phylogenetic analysis of the cox1 sequence data revealed strong statistical support for a clade containing O. viverrini and 2 other species of opisthorchid trematodes; O. felineus and Clonorchis sinsensis.

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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