Studying the co-evolution of protein families with the Mirrortree web server

Ochoa, David; Pazos, Florencio

doi:10.1093/bioinformatics/btq137

Cited by 74 publications

(108 citation statements)

References 14 publications

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“…Phylogenetic trees of the translated proteins were constructed by the RAxML program (30) using the maximum-likelihood method with the following parameters: the Dayhoff model with γ-distributed rates, partial deletion, and bootstrap (1,000 replicates; random seed). L-subunit and RAF1 phylogenetic trees were compared using the Mirrortree server (31). Pairwise nonsynonymous (leading to amino acid substitutions) and synonymous (selectively neutral) sequence distances were calculated using the PAML package (32).…”

Section: Methodsmentioning

confidence: 99%

Improving recombinant Rubisco biogenesis, plant photosynthesis and growth by coexpressing its ancillary RAF1 chaperone

Whitney

Birch

Kelso

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

108

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Enabling improvements to crop yield and resource use by enhancing the catalysis of the photosynthetic CO 2 -fixing enzyme Rubisco has been a longstanding challenge. Efforts toward realization of this goal have been greatly assisted by advances in understanding the complexities of Rubisco's biogenesis in plastids and the development of tailored chloroplast transformation tools. Here we generate transplastomic tobacco genotypes expressing Arabidopsis Rubisco large subunits (AtL), both on their own (producing tob AtL plants) and with a cognate Rubisco accumulation factor 1 (AtRAF1) chaperone (producing tob plants) that has undergone parallel functional coevolution with AtL. We show AtRAF1 assembles as a dimer and is produced in tob and Arabidopsis leaves at 10-15 nmol AtRAF1 monomers per square meter. Consistent with a postchaperonin large (L)-subunit assembly role, the AtRAF1 facilitated two to threefold improvements in the amount and biogenesis rate of hybrid L 8 A S 8 t Rubisco [comprising AtL and tobacco small (S) subunits] in tob AtL-R1 leaves compared with tob AtL , despite >threefold lower steady-state Rubisco mRNA levels in tob . Accompanying twofold increases in photosynthetic CO 2 -assimilation rate and plant growth were measured for tob lines. These findings highlight the importance of ancillary protein complementarity during Rubisco biogenesis in plastids, the possible constraints this has imposed on Rubisco adaptive evolution, and the likely need for such interaction specificity to be considered when optimizing recombinant Rubisco bioengineering in plants.T he increasing global demands for food supply, bioenergy production, and CO 2 -sequestration have placed a high need on improving agriculture yields and resource use (1, 2). It is now widely recognized that yield increases are possible by enhancing the light harvesting and CO 2 -fixation processes of photosynthesis (3-5). A major target for improvement is the enzyme Rubisco [ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase] whose deficiencies in CO 2 -fixing speed and efficiency pose a key limitation to photosynthetic CO 2 capture (6, 7). In plants, the complex, multistep catalytic mechanism of Rubisco to bind its 5-carbon substrate RuBP, orient its C-2 for carboxylation, and then process the 6-carbon product into two 3-phosphoglycerate (3PGA) products, limits its throughput to one to four catalytic cycles per second (8). The mechanism also makes Rubisco prone to competitive inhibition by O 2 that produces only one 3PGA and 2-phosphoglycolate (2PG). Metabolic recycling of 2PG by photorespiration requires energy and results in most plants losing 30% of their fixed CO 2 (5). To compensate for these catalytic limitations, plants like rice and wheat invest up to 50% of the leaf protein into Rubisco, which accounts for ∼25% of their leaf nitrogen (9).Natural diversity in Rubisco catalysis demonstrates that plant Rubisco is not the pinnacle of evolution (6, 7). Better-performing versions in some red algae have the potential to raise the yield of ...

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Section: Methodsmentioning

confidence: 99%

Improving recombinant Rubisco biogenesis, plant photosynthesis and growth by coexpressing its ancillary RAF1 chaperone

Whitney

Birch

Kelso

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

108

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“…The more general problem of predicting if two proteins interact with each other has been studied extensively using a wide variety of approaches (de Juan et al, 2013; Hosur et al, 2012; Zhang et al, 2012; Shoemaker and Panchenko, 2007, Valencia and Pazos, 2002, Ochoa and Pazos, 2010). Amino acid residue coevolution has been used to predict residue–residue interactions across interfaces with local statistical models (Pazos et al, 1997; Halperin et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

Овчинников

Kamisetty

Baker

2014

eLife

622

791

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Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood-based method to covary across protein–protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, provided that the number of aligned sequences is greater than the average length of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter.DOI: http://dx.doi.org/10.7554/eLife.02030.001

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“…We compare our DFT method with the state-of-art MirrorTree method in PPI prediction [2, 25]. The correlation of coevolution of the seven proteins in Ebola virus by the MirrorTree is listed in Table 3.…”

Section: Resultsmentioning

confidence: 99%

“…The GenBank access numbers of the virus genomes are listed in supplementary materials (S2 File). We align each pair proteins among all these virus species by Cluster Omega (http://www.ebi.ac.uk/Tools/msa/) [24], and the aligned sequence files are used as inputs for the MirrorTree server to construct MirrorTree and compute coevolution correlation coefficients (http://csbg.cnb.csic.es/mtserver/) [25]. …”

Section: Methods and Algorithmsmentioning

confidence: 99%

A coevolution analysis for identifying protein-protein interactions by Fourier transform

Yin

Yau

2017

PLoS ONE

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Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI).

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Studying the co-evolution of protein families with the Mirrortree web server

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 74 publications

References 14 publications

Improving recombinant Rubisco biogenesis, plant photosynthesis and growth by coexpressing its ancillary RAF1 chaperone

Improving recombinant Rubisco biogenesis, plant photosynthesis and growth by coexpressing its ancillary RAF1 chaperone

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

A coevolution analysis for identifying protein-protein interactions by Fourier transform

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