scholarly journals Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals

Mobile DNA ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Bo Gao ◽  
Wencheng Zong ◽  
Csaba Miskey ◽  
Numan Ullah ◽  
Mohamed Diaby ◽  
...  
Keyword(s):  
Horizontal Transfer ◽  
Amino Acid Residues ◽  
Animal Kingdom ◽  
Transposase Gene ◽  
High Identity ◽  
Sequence Identity ◽  
Natural Isolates ◽  
Average Sequence Identity ◽  
Catalytic Amino Acid ◽  
Sibling Family

Abstract Background A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown. Results Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5–1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86–95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates. Conclusions We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the “cat” genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.

scholarly journals Liftoff: accurate mapping of gene annotations

2020 ◽  
Author(s):  
Alaina Shumate ◽  
Steven L Salzberg
Keyword(s):  
Reference Genome ◽  
Supplementary Information ◽  
Closely Related Species ◽  
Protein Coding ◽  
Human Reference Genome ◽  
Sequence Identity ◽  
Gene Annotations ◽  
Genome Assemblies ◽  
Average Sequence Identity ◽  
High Quality Genome

Abstract Motivation Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however for most species, only the reference genome is well-annotated. Results One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously-annotated reference genome. Here we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely-related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript, and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity &gt;99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity. Availability and Implementation Liftoff can be installed via bioconda and PyPI. Additionally, the source code for Liftoff is available at https://github.com/agshumate/Liftoff Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Partial Sequencing of IS1216V Transposase Gene of Staphylococcus Aureus Isolated from Food Samples

2019 ◽  
Vol 14 (2) ◽  
pp. 24-27
Author(s):  
Ibtesam G. Auda
Keyword(s):  
Staphylococcus Aureus ◽  
Insertion Sequence ◽  
Enzymatic Reaction ◽  
Food Samples ◽  
Animal Origin ◽  
Local Foods ◽  
Transposase Gene ◽  
High Identity ◽  
Food Of Animal Origin ◽  
Total Food

Background:  Insertion sequence is a short DNA sequence encode for proteins implicated in the transposition activity. Transposase  catalyzes the enzymatic reaction allowing the insertion sequence  to +9*lo2 move. ;qqa;. Objective: To study the sequencing of transposase gene, tnp, IS1216V of S. aureus isolated from food and then compared with that documented in National Center for Biotechnology Information (NCBI). Methods: Food samples of animal and plant origin were collected, and screened for presence of S. aureus, IS1216V was identified in the Tn1546-like elements in the genomes of all Staphylococcus aureus isolates. Results: About 75% of total food samples were positive to S. aureus especially in the food of animal origin. tnp amplification showed that, 85% of isolates gave positive result.   Sequencing of amplified part of  IS1216V tnp of S. aureus isolates showed that,  tnp gene had high identity (78-79%) with the reference strains of NCBI. Conclusion: High percentage of  local food samples were contaminated with S. aureus especially of animal origin. Most of the S. aureus isolates showed the presence of transposase gene (tnp) of IS1216V. Sequencing showed some dissimilarity between the sequence of transposase gene (tnp) of IS1216V  S. aureus isolated from local foods and strains  recorded in database of  NCBI.

Identification of Catalytic Amino Acid Residues by Chemical Modification in Dextranase

2016 ◽  
Vol 26 (5) ◽  
pp. 837-845 ◽  
Author(s):  
Jin-A Ko ◽  
Seung-Hee Nam ◽  
Doman Kim ◽  
Jun-Ho Lee ◽  
Young-Min Kim
Keyword(s):  
Amino Acid ◽  
Chemical Modification ◽  
Amino Acid Residues ◽  
Catalytic Amino Acid

scholarly journals cDNA cloning and amino acid sequence of human mitochondrial Δ3Δ2-enoyl-CoA isomerase: comparison of the human enzyme with its rat counterpart, mitochondrial short-chain isomerase

1994 ◽  
Vol 300 (1) ◽  
pp. 1-5 ◽  
Author(s):  
J M Kilponen ◽  
H M Häyrinen ◽  
M Rehn ◽  
J K Hiltunen
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Basic Amino Acid ◽  
Peptide Sequencing ◽  
Amino Acid Residues ◽  
Mature Protein ◽  
Nucleotide Level ◽  
Sequence Identity ◽  
Human Enzyme

We report the isolation of a cDNA encoding a mature human monofunctional delta 3 delta 2-enoyl-CoA isomerase and the determination of its nucleotide sequence. The purified uncleaved protein, as well as several internal tryptic and CNBr fragments, were subjected to N-terminal peptide sequencing. The deduced amino acid sequence of the mature protein consists of 260 amino acids with a predicted M(r) of 28735. The human mitochondrial isomerase exhibits a 74% (78%) sequence identity with the corresponding rat counterpart at amino acid (nucleotide) level(s). Many basic amino acid residues in rat isomerase have been changed to acidic or neutral residues in human enzyme, explaining the differences observed between these proteins.

A comparative study of the effects of the Hofmeister series anions of the ionic salts and ionic liquids on the stability of α-chymotrypsin

2015 ◽  
Vol 39 (2) ◽  
pp. 938-952 ◽  
Author(s):  
Awanish Kumar ◽  
Anjeeta Rani ◽  
Pannuru Venkatesu
Keyword(s):  
Ionic Liquids ◽  
Amino Acid ◽  
Comparative Study ◽  
Hofmeister Series ◽  
Amino Acid Residues ◽  
Ionic Salts ◽  
The Stability ◽  
Catalytic Amino Acid

Direct interactions between the anion and the catalytic amino acid residues lead to denaturation of CT.

scholarly journals Homology Modeling and Prediction of Catalytic Amino Acid in the Neurotoxin from Indian Cobra (Naja naja)

2008 ◽  
Vol 2 (1) ◽  
pp. 97-102 ◽  
Author(s):  
Pallavi Somvanshi ◽  
Vijai Singh
Keyword(s):  
Amino Acid ◽  
Homology Modeling ◽  
Active Site ◽  
3D Structure ◽  
Nerve Impulse ◽  
Amino Acid Residues ◽  
Small Peptide ◽  
Naja Naja ◽  
Modeling And Prediction ◽  
Catalytic Amino Acid

The neurotoxin secreted by Indian cobra (Naja naja) binds to acetylcholine receptor of nerve cells, which leads to a lump in the nerve impulse, ceases breathing, thereby causing the death of a person due to suffocation. These neurotoxins are small peptide with approximately 7 kDa. Homology modeling was performed to generate the 3D structure of neurotoxins (A, B, C and D) of N. naja, using the known protein template crystal structure (PDB: 2CTX). The validation of 3D structure was done using PROCHECK. Furthermore, the prediction of catalytic amino acid residues in the active site domain of the 3-D structure of neurotoxin was identified. The 3-D structures of neurotoxin and catalytic amino acid residue may be used to target and design the antivenom drugs against the Indian cobra.

scholarly journals Why do unrelated insertion sequences occur together in the genome of Escherichia coli?

Genetics ◽  
1988 ◽  
Vol 118 (3) ◽  
pp. 537-541
Author(s):  
D L Hartl ◽  
S A Sawyer
Keyword(s):  
Escherichia Coli ◽  
Horizontal Transfer ◽  
Process Model ◽  
Insertion Sequence ◽  
Branching Process ◽  
Insertion Sequences ◽  
Reference Collection ◽  
Natural Isolates ◽  
Positive Correlations

Abstract Natural isolates of Escherichia coli are polymorphic for the presence or absence of insertion sequences. Among the ECOR reference collection of 71 natural isolates studied for the number of copies of the insertion sequences IS1, IS2, IS3, IS4, IS5 and IS30, the number of strains containing no copies of the insertion sequences were 11, 28, 23, 43, 46 and 36, respectively. Significant correlations occur in the ECOR strains in the presence or absence of unrelated insertion sequences in the chromosome and plasmid complements. Strains containing any insertion sequence are more likely to contain additional, unrelated insertion sequences than would be expected by chance. We suggest that the positive correlations result from horizontal transfer mediated by plasmids. A branching-process model for the plasmid-mediated transmission of insertion sequences among hosts yields such a correlation, even in the absence of interactions affecting transposition or fitness. The predictions of the model are quantitatively in agreement with the observed correlations among insertion sequences.

α-Amylase from germinating soybean (Glycine max) seeds – Purification, characterization and sequential similarity of conserved and catalytic amino acid residues

2010 ◽  
Vol 71 (14-15) ◽  
pp. 1657-1666 ◽  
Author(s):  
Arpana Kumari ◽  
Vinay Kumar Singh ◽  
Jörg Fitter ◽  
Tino Polen ◽  
Arvind M. Kayastha
Keyword(s):  
Glycine Max ◽  
Amino Acid ◽  
Amino Acid Residues ◽  
Catalytic Amino Acid

scholarly journals Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 980 ◽  
Author(s):  
Susanna K. P. Lau ◽  
Hayes K. H. Luk ◽  
Antonio C. P. Wong ◽  
Rachel Y. Y. Fan ◽  
Carol S. F. Lam ◽  
...  
Keyword(s):  
Novel Species ◽  
Structural Proteins ◽  
Interspecies Transmission ◽  
Cleavage Sites ◽  
Amino Acid Residues ◽  
Dipeptidyl Peptidase 4 ◽  
Sequence Identity ◽  
Animal Source ◽  
Novel Coronavirus ◽  
African Bats

While dromedaries are the immediate animal source of Middle East Respiratory Syndrome (MERS) epidemic, viruses related to MERS coronavirus (MERS-CoV) have also been found in bats as well as hedgehogs. To elucidate the evolution of MERS-CoV-related viruses and their interspecies transmission pathway, samples were collected from different mammals in China. A novel coronavirus related to MERS-CoV, Erinaceus amurensis hedgehog coronavirus HKU31 (Ea-HedCoV HKU31), was identified from two Amur hedgehogs. Genome analysis supported that Ea-HedCoV HKU31 represents a novel species under Merbecovirus, being most closely related to Erinaceus CoV from European hedgehogs in Germany, with 79.6% genome sequence identity. Compared to other members of Merbecovirus, Ea-HedCoV HKU31 possessed unique non-structural proteins and putative cleavage sites at ORF1ab. Phylogenetic analysis showed that Ea-HedCoV HKU31 and BetaCoV Erinaceus/VMC/DEU/2012 were closely related to NeoCoV and BatCoV PREDICT from African bats in the spike region, suggesting that the latter bat viruses have arisen from recombination between CoVs from hedgehogs and bats. The predicted HKU31 receptor-binding domain (RBD) possessed only one out of 12 critical amino acid residues for binding to human dipeptidyl peptidase 4 (hDPP4), the MERS-CoV receptor. The structural modeling of the HKU31-RBD-hDPP4 binding interphase compared to that of MERS-CoV and Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) suggested that HKU31-RBD is unlikely to bind to hDPP4. Our findings support that hedgehogs are an important reservoir of Merbecovirus, with evidence of recombination with viruses from bats. Further investigations in bats, hedgehogs and related animals are warranted to understand the evolution of MERS-CoV-related viruses.

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