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Buckle AM, Buckle M. Ribosome Evolution and Structural Capacitance. Front Mol Biosci 2019; 6:123. [PMID: 31803754 PMCID: PMC6872460 DOI: 10.3389/fmolb.2019.00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/24/2019] [Indexed: 11/13/2022] Open
Abstract
In addition to the canonical loss-of-function mutations, mutations in proteins may additionally result in gain-of-function through the binary activation of cryptic "structural capacitance elements." Our previous bioinformatic analysis allowed us to propose a new mechanism of protein evolution - structural capacitance - that arises via the generation of new elements of microstructure upon mutations that cause a disorder-to-order (D→O) transition in previously disordered regions of proteins. Here we propose that the D→O transition is a necessary follow-on from expected early codon-anticodon and tRNA acceptor stem-amino acid usage, via the accumulation of structural capacitance elements - reservoirs of disorder in proteins. We develop this argument further to posit that structural capacitance is an inherent consequence of the evolution of the genetic code.
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Affiliation(s)
- Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Malcolm Buckle
- LBPA, ENS Paris-Saclay, CNRS, Université Paris-Saclay, Cachan, France
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Li C, Clark LVT, Zhang R, Porebski BT, McCoey JM, Borg NA, Webb GI, Kass I, Buckle M, Song J, Woolfson A, Buckle AM. Structural Capacitance in Protein Evolution and Human Diseases. J Mol Biol 2018; 430:3200-3217. [PMID: 30111491 DOI: 10.1016/j.jmb.2018.06.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/18/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
Canonical mechanisms of protein evolution include the duplication and diversification of pre-existing folds through genetic alterations that include point mutations, insertions, deletions, and copy number amplifications, as well as post-translational modifications that modify processes such as folding efficiency and cellular localization. Following a survey of the human mutation database, we have identified an additional mechanism that we term "structural capacitance," which results in the de novo generation of microstructure in previously disordered regions. We suggest that the potential for structural capacitance confers select proteins with the capacity to evolve over rapid timescales, facilitating saltatory evolution as opposed to gradualistic canonical Darwinian mechanisms. Our results implicate the elements of protein microstructure generated by this distinct mechanism in the pathogenesis of a wide variety of human diseases. The benefits of rapidly furnishing the potential for evolutionary change conferred by structural capacitance are consequently counterbalanced by this accompanying risk. The phenomenon of structural capacitance has implications ranging from the ancestral diversification of protein folds to the engineering of synthetic proteins with enhanced evolvability.
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Affiliation(s)
- Chen Li
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Liah V T Clark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rory Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julia M McCoey
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Geoffrey I Webb
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Amai Proteins, Prof. A. D. Bergman 2B, Suite 212, Rehovot 7670504, Israel
| | - Malcolm Buckle
- LBPA, ENS Cachan, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
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Ding D, Li L, Shu C, Sun X. K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer. Front Microbiol 2016; 7:530. [PMID: 27148219 PMCID: PMC4837345 DOI: 10.3389/fmicb.2016.00530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/31/2016] [Indexed: 01/17/2023] Open
Abstract
Shewanella oneidensis MR-1 is capable of extracellular electron transfer (EET) and hence has attracted considerable attention. The EET pathways mainly consist of c-type cytochromes, along with some other proteins involved in electron transfer processes. By whole genome study and protein interactions inquisition, we constructed a large-scale electron transfer network containing 2276 interactions among 454 electron transfer related proteins in S. oneidensis MR-1. Using the k-shell decomposition method, we identified and analyzed distinct parts of the electron transfer network. We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network. Furthermore, proteins in the top three shells of the network are mainly located in the cytoplasm and inner membrane; these proteins can be responsible for transfer of electrons into the quinone pool in a wide variety of environmental conditions. In most of the other shells, proteins are broadly located throughout the five cellular compartments (cytoplasm, inner membrane, periplasm, outer membrane, and extracellular), which ensures the important EET ability of S. oneidensis MR-1. Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET. Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.
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Affiliation(s)
- Dewu Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China; Department of Mathematics and Computer Science, Chizhou CollegeChizhou, China
| | - Ling Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing, China
| | - Chuanjun Shu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing, China
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