Cargando…
Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit
BACKGROUND: Na,K-ATPase is a key protein in maintaining membrane potential that has numerous additional cellular functions. Its catalytic subunit (α), found in a wide range of organisms from prokaryotes to complex eukaryote. Several studies have been done to identify the functions as well as determi...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9609216/ https://www.ncbi.nlm.nih.gov/pubmed/36289471 http://dx.doi.org/10.1186/s12862-022-02071-0 |
_version_ | 1784818964438712320 |
---|---|
author | Shahnazari, Marzieh Zakipour, Zahra Razi, Hooman Moghadam, Ali Alemzadeh, Abbas |
author_facet | Shahnazari, Marzieh Zakipour, Zahra Razi, Hooman Moghadam, Ali Alemzadeh, Abbas |
author_sort | Shahnazari, Marzieh |
collection | PubMed |
description | BACKGROUND: Na,K-ATPase is a key protein in maintaining membrane potential that has numerous additional cellular functions. Its catalytic subunit (α), found in a wide range of organisms from prokaryotes to complex eukaryote. Several studies have been done to identify the functions as well as determining the evolutionary relationships of the α-subunit. However, a survey of a larger collection of protein sequences according to sequences similarity and their attributes is very important in revealing deeper evolutionary relationships and identifying specific amino acid differences among evolutionary groups that may have a functional role. RESULTS: In this study, 753 protein sequences using phylogenetic tree classification resulted in four groups: prokaryotes (I), fungi and various kinds of Protista and some invertebrates (II), the main group of invertebrates (III), and vertebrates (IV) that was consisted with species tree. The percent of sequences that acquired a specific motif for the α/β subunit assembly increased from group I to group IV. The vertebrate sequences were divided into four groups according to isoforms with each group conforming to the evolutionary path of vertebrates from fish to tetrapods. Data mining was used to identify the most effective attributes in classification of sequences. Using 1252 attributes extracted from the sequences, the decision tree classified them in five groups: Protista, prokaryotes, fungi, invertebrates and vertebrates. Also, vertebrates were divided into four subgroups (isoforms). Generally, the count of different dipeptides and amino acid ratios were the most significant attributes for grouping. Using alignment of sequences identified the effective position of the respective dipeptides in the separation of the groups. So that (208)GC is apparently involved in the separation of vertebrates from the four other organism groups, and (41)DH, (431)FK, and (451)KC were involved in separation vertebrate isoform types. CONCLUSION: The application of phylogenetic and decision tree analysis for Na,K-ATPase, provides a better understanding of the evolutionary changes according to the amino acid sequence and its related properties that could lead to the identification of effective attributes in the separation of sequences in different groups of phylogenetic tree. In this study, key evolution-related dipeptides are identified which can guide future experimental studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-022-02071-0. |
format | Online Article Text |
id | pubmed-9609216 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-96092162022-10-28 Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit Shahnazari, Marzieh Zakipour, Zahra Razi, Hooman Moghadam, Ali Alemzadeh, Abbas BMC Ecol Evol Research BACKGROUND: Na,K-ATPase is a key protein in maintaining membrane potential that has numerous additional cellular functions. Its catalytic subunit (α), found in a wide range of organisms from prokaryotes to complex eukaryote. Several studies have been done to identify the functions as well as determining the evolutionary relationships of the α-subunit. However, a survey of a larger collection of protein sequences according to sequences similarity and their attributes is very important in revealing deeper evolutionary relationships and identifying specific amino acid differences among evolutionary groups that may have a functional role. RESULTS: In this study, 753 protein sequences using phylogenetic tree classification resulted in four groups: prokaryotes (I), fungi and various kinds of Protista and some invertebrates (II), the main group of invertebrates (III), and vertebrates (IV) that was consisted with species tree. The percent of sequences that acquired a specific motif for the α/β subunit assembly increased from group I to group IV. The vertebrate sequences were divided into four groups according to isoforms with each group conforming to the evolutionary path of vertebrates from fish to tetrapods. Data mining was used to identify the most effective attributes in classification of sequences. Using 1252 attributes extracted from the sequences, the decision tree classified them in five groups: Protista, prokaryotes, fungi, invertebrates and vertebrates. Also, vertebrates were divided into four subgroups (isoforms). Generally, the count of different dipeptides and amino acid ratios were the most significant attributes for grouping. Using alignment of sequences identified the effective position of the respective dipeptides in the separation of the groups. So that (208)GC is apparently involved in the separation of vertebrates from the four other organism groups, and (41)DH, (431)FK, and (451)KC were involved in separation vertebrate isoform types. CONCLUSION: The application of phylogenetic and decision tree analysis for Na,K-ATPase, provides a better understanding of the evolutionary changes according to the amino acid sequence and its related properties that could lead to the identification of effective attributes in the separation of sequences in different groups of phylogenetic tree. In this study, key evolution-related dipeptides are identified which can guide future experimental studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-022-02071-0. BioMed Central 2022-10-26 /pmc/articles/PMC9609216/ /pubmed/36289471 http://dx.doi.org/10.1186/s12862-022-02071-0 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/ Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Shahnazari, Marzieh Zakipour, Zahra Razi, Hooman Moghadam, Ali Alemzadeh, Abbas Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit |
title | Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit |
title_full | Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit |
title_fullStr | Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit |
title_full_unstemmed | Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit |
title_short | Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit |
title_sort | bioinformatics approaches for classification and investigation of the evolution of the na/k-atpase alpha-subunit |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9609216/ https://www.ncbi.nlm.nih.gov/pubmed/36289471 http://dx.doi.org/10.1186/s12862-022-02071-0 |
work_keys_str_mv | AT shahnazarimarzieh bioinformaticsapproachesforclassificationandinvestigationoftheevolutionofthenakatpasealphasubunit AT zakipourzahra bioinformaticsapproachesforclassificationandinvestigationoftheevolutionofthenakatpasealphasubunit AT razihooman bioinformaticsapproachesforclassificationandinvestigationoftheevolutionofthenakatpasealphasubunit AT moghadamali bioinformaticsapproachesforclassificationandinvestigationoftheevolutionofthenakatpasealphasubunit AT alemzadehabbas bioinformaticsapproachesforclassificationandinvestigationoftheevolutionofthenakatpasealphasubunit |