A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.

Chromatography, Liquid / methods Computational Biology / methods Evolution, Molecular Gene Expression Regulation, Plant Gene Ontology Gene Regulatory Networks Genomics / methods Phylogeny Plant Proteins / genetics Plants / classification Proteome / genetics Proteomics / methods Species Specificity Tandem Mass Spectrometry / methods Transcriptome / genetics

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
11 01 2021
Historique:
accepted: 19 10 2020
revised: 19 09 2020
received: 31 12 2019
pubmed: 22 11 2020
medline: 2 2 2021
entrez: 21 11 2020
Statut: ppublish

Résumé

Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.

Identifiants

DOI: 10.1093/nar/gkaa1041 PMID: 33219668 PMC: PMC7797074
pubmed: 33219668
pii: 5997432
doi: 10.1093/nar/gkaa1041
pmc: PMC7797074
doi:

Substances chimiques

Plant Proteins 0
Proteome 0

Types de publication

Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

e3

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Junha Shin (J)

Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.

Harald Marx (H)

Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Alicia Richards (A)

Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Dries Vaneechoutte (D)

Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium.
VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Ghent, Belgium.

Dhileepkumar Jayaraman (D)

Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.

Junko Maeda (J)

Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.

Sanhita Chakraborty (S)

Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.

Michael Sussman (M)

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Klaas Vandepoele (K)

Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium.
VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Ghent, Belgium.

Jean-Michel Ané (JM)

Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.

Joshua Coon (J)

Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Sushmita Roy (S)

Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA.

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Classifications MeSH

Recherchemedicale.com › Techniques d'investigation › Techniques de chimie analytique › Chromatographie › Chromatographie en phase liquide › A network-based comparative framework to study...
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