Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation

Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Details about the molecular mechanism...

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Autores principales:	Jun-Xiao Ma, Yi Yang, Guang Li, Bin-Guang Ma
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	rhizobia protein-protein interaction network analysis multiomics data integration symbiosis Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/ff37d3d9ad7b45f6b417cf376ab600d5
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spelling	oai:doaj.org-article:ff37d3d9ad7b45f6b417cf376ab600d52021-11-11T17:19:15ZComputationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation10.3390/ijms2221119071422-00671661-6596https://doaj.org/article/ff37d3d9ad7b45f6b417cf376ab600d52021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11907https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Details about the molecular mechanisms of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand for new studies integrating multiomics information. Here, we present a comprehensive computational framework integrating the reconstructed protein interactome of <i>B. diazoefficiens</i> USDA110 with its transcriptome and proteome data to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome of <i>B. diazoefficiens</i> USDA110 by computational approaches. Based on the comparison of interactomes between <i>B. diazoefficiens</i> USDA110 and other rhizobia, we inferred that the slow growth of <i>B. diazoefficiens</i> USDA110 may be due to the requirement of more protein modifications, and we further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and nine novel functional modules and eleven key protein hubs playing key roles in symbiosis were identified. The reconstructed interactome of <i>B. diazoefficiens</i> USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.Jun-Xiao MaYi YangGuang LiBin-Guang MaMDPI AGarticlerhizobiaprotein-protein interactionnetwork analysismultiomicsdata integrationsymbiosisBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11907, p 11907 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	rhizobia protein-protein interaction network analysis multiomics data integration symbiosis Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	rhizobia protein-protein interaction network analysis multiomics data integration symbiosis Biology (General) QH301-705.5 Chemistry QD1-999 Jun-Xiao Ma Yi Yang Guang Li Bin-Guang Ma Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation
description	Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Details about the molecular mechanisms of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand for new studies integrating multiomics information. Here, we present a comprehensive computational framework integrating the reconstructed protein interactome of <i>B. diazoefficiens</i> USDA110 with its transcriptome and proteome data to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome of <i>B. diazoefficiens</i> USDA110 by computational approaches. Based on the comparison of interactomes between <i>B. diazoefficiens</i> USDA110 and other rhizobia, we inferred that the slow growth of <i>B. diazoefficiens</i> USDA110 may be due to the requirement of more protein modifications, and we further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and nine novel functional modules and eleven key protein hubs playing key roles in symbiosis were identified. The reconstructed interactome of <i>B. diazoefficiens</i> USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.
format	article
author	Jun-Xiao Ma Yi Yang Guang Li Bin-Guang Ma
author_facet	Jun-Xiao Ma Yi Yang Guang Li Bin-Guang Ma
author_sort	Jun-Xiao Ma
title	Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation
title_short	Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation
title_full	Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation
title_fullStr	Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation
title_full_unstemmed	Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation
title_sort	computationally reconstructed interactome of <i>bradyrhizobium diazoefficiens</i> usda110 reveals novel functional modules and protein hubs for symbiotic nitrogen fixation
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/ff37d3d9ad7b45f6b417cf376ab600d5
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Computationally Reconstructed Interactome of <i>Bradyrhizobium diazoefficiens</i> USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation

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