scholarly journals In‐depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

2021 ◽  
Author(s):  
Tatyana S. Tikhomirova ◽  
Maxim A. Matyunin ◽  
Michail Yu. Lobanov ◽  
Oxana V. Galzitskaya
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequences ◽  
Depth Analysis

scholarly journals In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

2021 ◽  
Author(s):  
Tatyana Tikhomirova ◽  
Maxim Matyunin ◽  
Mikhail Lobanov ◽  
Oxana Galzitskaya
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Dominant Role ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Mutational Pressure ◽  
Depth Analysis

Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. In turn, their amino acid composition remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage.

scholarly journals High-Throughput Sequencing of Phage Display Libraries Reveals Parasitic Enrichment of Indel Mutants Caused by Amplification Bias

2021 ◽  
Vol 22 (11) ◽  
pp. 5513
Author(s):  
Sander Plessers ◽  
Vincent Van Deuren ◽  
Rob Lavigne ◽  
Johan Robben
Keyword(s):  
Amino Acid ◽  
Phage Display ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Selection ◽  
Acid Modification ◽  
Phage Display Technology ◽  
Amplification Bias ◽  
Large Deletions ◽  
Depth Analysis

The combination of phage display technology with high-throughput sequencing enables in-depth analysis of library diversity and selection-driven dynamics. We applied short-read sequencing of the mutagenized region on focused display libraries of two homologous nucleic acid modification eraser proteins—AlkB and FTO—biopanned against methylated DNA. This revealed enriched genotypes with small indels and concomitant doubtful amino acid motifs within the FTO library. Nanopore sequencing of the entire display vector showed additional enrichment of large deletions overlooked by region-specific sequencing, and further impacted the interpretation of the obtained amino acid motifs. We could attribute enrichment of these corrupted clones to amplification bias due to arduous FTO display slowing down host cell growth as well as phage production. This amplification bias appeared to be stronger than affinity-based target selection. Recommendations are provided for proper sequence analysis of phage display data, which can improve motive discovery in libraries of proteins that are difficult to display.

scholarly journals Expression of Ubiquitin Gene in Microsporum canis and Trichophyton mentagrophytes Cultured with Fluconazole

2001 ◽  
Vol 45 (9) ◽  
pp. 2559-2562 ◽  
Author(s):  
Rui Kano ◽  
Ken Okabayashi ◽  
Yuka Nakamura ◽  
Shinichi Watanabe ◽  
Atsuhiko Hasegawa
Keyword(s):  
Amino Acid ◽  
Antifungal Activity ◽  
Proteasome Inhibitor ◽  
Trichophyton Mentagrophytes ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Antifungal Drug ◽  
Microsporum Canis

ABSTRACT The expression of the ubiquitin (Ub) gene in dermatophytes was examined for its relation to resistance against the antifungal drug fluconazole. The nucleotide sequences and the deduced amino acid sequences of the Ub gene in Microsporum canis were proven to be 99% similar to those of the Ub gene in Trichophyton mentagrophytes. Expression of mRNA of Ub in M. canisand T. mentagrophytes was enhanced when the fungi were cultured with fluconazole. The antifungal activity of fluconazole against these dermatophytes was increased in the presence of Ub proteasome inhibitor.

scholarly journals Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil

2015 ◽  
Vol 45 (12) ◽  
pp. 2197-2200 ◽  
Author(s):  
Thor Vinícius Martins Fajardo ◽  
Monique Bezerra Nascimento ◽  
Marcelo Eiras ◽  
Osmar Nickel ◽  
Gilvan Pio-Ribeiro
Keyword(s):  
Amino Acid ◽  
Molecular Characterization ◽  
Molecular Analysis ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Causal Agent ◽  
Ringspot Virus ◽  
Prunus Necrotic Ringspot Virus ◽  
First Time

ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV), except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP) and coat (CP) protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of the MP and CP nucleotide sequences of a Brazilian PNRSV isolate from rose and others from this same host showed highest identities of 96.7% and 98.6%, respectively, and Rose-Br isolate was classified in PV32 group.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

Amino acid and nucleotide sequences of human peroxisomal enoyl-CoA hydratase : 3-hydroxyacyl-CoA dehydrogenase cDNA

1998 ◽  
Vol 21 (1) ◽  
pp. 23-28 ◽  
Author(s):  
S. Fukuda ◽  
Y. Suzuki ◽  
N. Shimozawa ◽  
Z. Zhang ◽  
T. Orii ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequences ◽  
Hydroxyacyl Coa Dehydrogenase ◽  
Enoyl Coa Hydratase

scholarly journals WEB-server for search of a periodicity in amino acid and nucleotide sequences

2017 ◽  
Vol 937 ◽  
pp. 012013
Author(s):  
F E Frenkel ◽  
K G Skryabin ◽  
E V Korotkov
Keyword(s):  
Amino Acid ◽  
Web Server ◽  
Nucleotide Sequences
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