scholarly journals Tetrahymena Glutathione Peroxidase Family: A Comparative Analysis of These Antioxidant Enzymes and Differential Gene Expression to Metals and Oxidizing Agents

2020 ◽  
Vol 8 (7) ◽  
pp. 1008
Author(s):  
Liliana L. Cubas-Gaona ◽  
Patricia de Francisco ◽  
Ana Martín-González ◽  
Juan Carlos Gutiérrez
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Insertion Sequence ◽  
Amino Acid Sequences ◽  
Gene Duplications ◽  
Catalytic Center ◽  
Oxidizing Agents ◽  
Glutathione Peroxidases ◽  
Phospholipid Hydroperoxide ◽  
Differential Gene

In the present work, an extensive analysis of the putative glutathione peroxidases (GPx) of the eukaryotic microorganism model Tetrahymena thermophila is carried out. A comparative analysis with GPx present in other Tetrahymena species and other very taxonomically diverse ciliates is also performed. A majority of ciliate GPx have replaced the selenocysteine (Sec) by Cys in its catalytic center, so they can be considered as phospholipid hydroperoxide glutathione peroxidases (PHGPx). Selenocysteine insertion sequence (SECIS) elements have been detected in several ciliate GPx that do not incorporate Sec in their amino acid sequences, and conversely, in other ciliate GPx with Sec, no SECIS elements are detected. These anomalies are analyzed and discussed. From the phylogenetic analysis using the ciliate GPx amino acid sequences, the existence of extensive intra- and interspecific gene duplications that produced multiple GPx isoforms in each species is inferred. The ancestral character of the selenoproteins is also corroborated. The analysis by qRT-PCR of six selected T. thermophila GPx genes has shown a quantitative differential expression between them, depending on the stressor (oxidizing agents, apoptotic inducer or metals) and the time of exposure.

scholarly journals Comparative Analysis of the Putative Amino Acid Sequences of Chlamydial Heat Shock Protein 60 and Escherichia coli GroEL.

2000 ◽  
Vol 62 (9) ◽  
pp. 941-945 ◽  
Author(s):  
Yoshitsugu OCHIAI ◽  
Hideto FUKUSHI ◽  
Cai YAN ◽  
Tsuyoshi YAMAGUCHI ◽  
Katsuya HIRAI
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Amino Acid ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Amino Acid Sequences ◽  
Heat Shock Protein 60

scholarly journals Diversity of radA Genes from Cultured and UnculturedArchaea: Comparative Analysis of Putative RadA Proteins and Their Use as a Phylogenetic Marker

1999 ◽  
Vol 181 (3) ◽  
pp. 907-915 ◽  
Author(s):  
Steven J. Sandler ◽  
Philip Hugenholtz ◽  
Christa Schleper ◽  
Edward F. DeLong ◽  
Norman R. Pace ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Tissue Sample ◽  
Reca Protein ◽  
Amino Acid Sequences ◽  
Sponge Tissue ◽  
Amino Acid Deletion ◽  
Archaeal Species ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species ofCrenarcheota. The two most deeply branching archaealradA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members.

Development of a screening system for inteins active in protein splicing based on intein insertion into the LacZα-peptide

2017 ◽  
Vol 398 (1) ◽  
pp. 57-67 ◽  
Author(s):  
Maximilian Neugebauer ◽  
Jana K. Böcker ◽  
Julian C.J. Matern ◽  
Shmuel Pietrokovski ◽  
Henning D. Mootz
Keyword(s):  
Amino Acid ◽  
Biochemical Characterization ◽  
Amino Acid Sequences ◽  
Side Reactions ◽  
Protein Chemistry ◽  
Protein Splicing ◽  
Catalytic Center ◽  
Host System ◽  
Identify Amino Acid ◽  
Wide Range

Abstract Protein splicing by inteins has found diverse applications in biotechnology, protein chemistry and chemical biology. Inteins display a wide range of efficiencies and rates unpredictable from their amino acid sequences. Here, we identified positions T22S and S35 in the LacZα peptide as intein insertion sites that strictly require protein splicing, in contrast to cleavage side-reactions, to allow for complementation of β-galactosidase activity. Both the cis-variant of the M86 mutant of the Ssp DnaB intein and a split form undergoing protein trans-splicing gave rise to formation of blue colonies in the β-galactosidase read-out. Furthermore, we report the two novel, naturally split VidaL T4Lh-1 and VidaL UvsX-2 inteins whose N-terminal fragments consist of only 15 and 16 amino acids, respectively. Initial biochemical characterization with the LacZα host system of these inteins further underlines its utility. Finally, we used the LacZα host system to rapidly identify amino acid substitutions from a small randomized library at the structurally conserved intein position 2 next to the catalytic center, that are tolerated for protein splicing activity of the M86 intein. These findings demonstrate the potential of the system for initial testing and directed evolution of inteins.

A new insertion sequence, IS14999, from Corynebacterium glutamicum

Microbiology ◽  
2005 ◽  
Vol 151 (2) ◽  
pp. 501-508 ◽  
Author(s):  
Yota Tsuge ◽  
Kana Ninomiya ◽  
Nobuaki Suzuki ◽  
Masayuki Inui ◽  
Hideaki Yukawa
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Corynebacterium Glutamicum ◽  
Insertion Sequence ◽  
Genetic Manipulation ◽  
Insertion Site ◽  
Amino Acid Sequences ◽  
Transfer Event ◽  
Reading Frame ◽  
Partial Homology

A new insertion sequence from Corynebacterium glutamicum ATCC 14999 was isolated and characterized. This IS element, designated IS14999, comprised a 1149 bp nucleotide sequence with 22 bp imperfect terminal inverted repeats. IS14999 carries a single open reading frame of 345 amino acids encoding a putative transposase that appears to have partial homology to IS642, an IS630/Tc1 superfamily element, at the C-terminal region in the amino acid sequence. This indicated that IS14999 belonged to the IS630/Tc1 superfamily, which was first identified in C. glutamicum. IS14999 has a unique distance of 38 amino acid residues between the second and third amino acids in the DDE motif, which is well known as the catalytic centre of transposase. This suggested that IS14999 constituted a new subfamily of the IS630/Tc1 superfamily. A phylogenetic tree constructed on the basis of amino acid sequences of transposases revealed that this new transposable element was more similar to eukaryotic Tc1/mariner family elements than to prokaryotic IS630 family elements. Added to the fact that IS14999 was present in only a few C. glutamicum strains, this implies that IS14999 was probably acquired by a recent lateral transfer event from eukaryotic cells. Analysis of the insertion site in C. glutamicum R revealed that IS14999 appeared to transpose at random and always caused a target duplication of a 5′-TA-3′ dinucleotide upon insertion, like the other IS630/Tc1 family elements. These findings indicated that IS14999 could be a powerful tool for genetic manipulation of corynebacteria and related species.

scholarly journals Unique and Universal Proteins in Human Genome

2020 ◽  
Vol 16 (11) ◽  
pp. 45
Author(s):  
Essam Al-Daoud ◽  
Ghadeer Albesani
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Human Genome ◽  
Reference Genome ◽  
Amino Acid Sequences ◽  
The Other ◽  
Entire Genome ◽  
Whole Genomes ◽  
The Common ◽  
Similar Amino Acid

<span>One of the major troubles with a comparative analysis between human and other species is that only similar amino acid sequences are selected for analysis. To find the connection among the species and find out the unique, the common and the universal proteins, the entire genome of 40 species are compared with the human genome which is utilized as reference genome. More than 11 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 330 unique proteins in human genome and have insignificant hits in all tested genomes, the number of universal proteins in human genome and conserved in all tested species is 82, and there are 180 proteins common in vertebrates genomes, but have insignificant hits in the other tested species. In contrary to the previous studies which use selected set of the genes and do not consider the whole genomes, this study proves that the similarity between human and chimpanzee is only 94.8.</span>

scholarly journals Interaction of human cytokeratins with isatin analogues

2010 ◽  
Vol 56 (1) ◽  
pp. 138-145 ◽  
Author(s):  
O.A. Buneeva ◽  
O.V. Gnedenko ◽  
V.I. Fedchenko ◽  
A.S. Ivanov ◽  
A.E. Medvedev
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Specific Binding ◽  
Optical Biosensor ◽  
Amino Acid Sequences ◽  
Chip Surface ◽  
High Affinity ◽  
Terminal Domain ◽  
Carboxymethyl Dextran

Using an optical biosensor Biacore 3000 the interaction of human recombinant cytokeratins (CK) with isatin analogues (5-aminocaproyl-isatin and 5-aminoisatin) immobilized on the CM-5 chip has been investigated. CK-14 effectively interacted with 5-aminocaproyl-isatin immobilized on the carboxymethyl dextran chip surface, but not with a "shorter" analogue (5-aminoisatin). In contrast to CK14 CK8 effectively interacted only with 5-aminoisatin. In both cases cytokeratin binding with the immobilized isatin analogues was characterized by rather high affinity (Kd of 0.7 μM for the pair CK14/immobilized 5-aminocaproylisatin and 1.7 μM for the pair CK8/immobilized 5-aminoisatin). CK20 did not interact with both immobilized isatin analogues. Taking into consideration non-specific binding of mouse CK14 and rat CK8 with 5-aminocaproyl-Sepharose we have performed comparative analysis of amino acid sequences of human, mouse, and rat CK8 and CK14. The data obtained suggest that in the case of human, mouse, and rat CK14 the N-terminal domain is the most variable amoung these species, whereas the major differences between amino acid sequences of human, mouse, and rat CK8 have been found both in N-terminal and C-terminal regions.

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