Structural and evolutionary relationships among RuBisCOs inferred from their large and small subunits

Fu Xiang; Yuanping Fang; Jun Xiang

doi:10.7287/peerj.preprints.1525v1

Structural and evolutionary relationships among RuBisCOs inferred from their large and small subunits

Fu Xiang ^1,2, Yuanping Fang^1,2, Jun Xiang^1,2

1 Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal Univeristy, Huanggang, Hubei, China

2 Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, Hubei, China

DOI: 10.7287/peerj.preprints.1525v1

Published: 2015-11-24
Accepted: 2015-11-24

Subject Areas: Computational Biology, Evolutionary Studies
Keywords: protein domain, structural dendrogram, RuBisCO, nonredundant set, structural variation

Copyright: © 2015 Xiang et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Cite this article: Xiang F, Fang Y, Xiang J. 2015. Structural and evolutionary relationships among RuBisCOs inferred from their large and small subunits. PeerJ PrePrints 3:e1525v1 https://doi.org/10.7287/peerj.preprints.1525v1

Abstract

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme to assimilate CO₂ into the biosphere. The structural and evolutionary relationships among RuBisCOs were discussed at the domain level. The nonredundant sets for three superfamilies of RuBisCO, i.e. large subunit C-terminal domain (LSC), large subunit N-terminal domain (LSN) and small subunit domain (SS) were defined using QR factorization based on the structural alignment of the RuBisCO domains with QH as the similarity measure, respectively. The results suggest: (1) the core structures of LSC, LSN and SS are well conserved and homologies; (2) the LSC could have occurred naturally in both bacteria and Achaean kingdoms, and the carboxyl-terminal structure evolves increasingly complicated in both bacteria and Eukaryotae kingdoms; (3) the structural variations, such as coil structures at 67-82 positions of LSN and the βA-βB-loop of SS, could make attribution to the CO₂/O₂ specificity of RuBisCO from different species. Such findings provide insights on RuBisCO improvement.