Cargando…

Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae

BACKGROUND: The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization si...

Descripción completa

Detalles Bibliográficos
Autores principales: Guo, Min, Yang, Ruifu, Huang, Chen, Liao, Qiwen, Fan, Guangyi, Sun, Chenghang, Lee, Simon Ming-Yuen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381049/
https://www.ncbi.nlm.nih.gov/pubmed/28376722
http://dx.doi.org/10.1186/s12866-017-0981-y
_version_ 1782519860086964224
author Guo, Min
Yang, Ruifu
Huang, Chen
Liao, Qiwen
Fan, Guangyi
Sun, Chenghang
Lee, Simon Ming-Yuen
author_facet Guo, Min
Yang, Ruifu
Huang, Chen
Liao, Qiwen
Fan, Guangyi
Sun, Chenghang
Lee, Simon Ming-Yuen
author_sort Guo, Min
collection PubMed
description BACKGROUND: The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. RESULTS: In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. CONCLUSION: The results of this study reveal that Planctomycetaceae separates slightly from the members of non-planctomycete bacteria but still has substantial differences from fungi, based on the NLS-like motifs and NLS-bearing protein analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-017-0981-y) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-5381049
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-53810492017-04-10 Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae Guo, Min Yang, Ruifu Huang, Chen Liao, Qiwen Fan, Guangyi Sun, Chenghang Lee, Simon Ming-Yuen BMC Microbiol Research Article BACKGROUND: The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. RESULTS: In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. CONCLUSION: The results of this study reveal that Planctomycetaceae separates slightly from the members of non-planctomycete bacteria but still has substantial differences from fungi, based on the NLS-like motifs and NLS-bearing protein analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-017-0981-y) contains supplementary material, which is available to authorized users. BioMed Central 2017-04-04 /pmc/articles/PMC5381049/ /pubmed/28376722 http://dx.doi.org/10.1186/s12866-017-0981-y Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Guo, Min
Yang, Ruifu
Huang, Chen
Liao, Qiwen
Fan, Guangyi
Sun, Chenghang
Lee, Simon Ming-Yuen
Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae
title Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae
title_full Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae
title_fullStr Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae
title_full_unstemmed Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae
title_short Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae
title_sort evolutionary gradient of predicted nuclear localization signals (nls)-bearing proteins in genomes of family planctomycetaceae
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381049/
https://www.ncbi.nlm.nih.gov/pubmed/28376722
http://dx.doi.org/10.1186/s12866-017-0981-y
work_keys_str_mv AT guomin evolutionarygradientofpredictednuclearlocalizationsignalsnlsbearingproteinsingenomesoffamilyplanctomycetaceae
AT yangruifu evolutionarygradientofpredictednuclearlocalizationsignalsnlsbearingproteinsingenomesoffamilyplanctomycetaceae
AT huangchen evolutionarygradientofpredictednuclearlocalizationsignalsnlsbearingproteinsingenomesoffamilyplanctomycetaceae
AT liaoqiwen evolutionarygradientofpredictednuclearlocalizationsignalsnlsbearingproteinsingenomesoffamilyplanctomycetaceae
AT fanguangyi evolutionarygradientofpredictednuclearlocalizationsignalsnlsbearingproteinsingenomesoffamilyplanctomycetaceae
AT sunchenghang evolutionarygradientofpredictednuclearlocalizationsignalsnlsbearingproteinsingenomesoffamilyplanctomycetaceae
AT leesimonmingyuen evolutionarygradientofpredictednuclearlocalizationsignalsnlsbearingproteinsingenomesoffamilyplanctomycetaceae