Coevolutionary Analysis Research Articles

Coevolutionary Analysis Enabled Rational Deregulation of Allosteric Enzyme Inhibition in Corynebacterium glutamicum for Lysine Production

Product feedback inhibition of allosteric enzymes is an essential issue for the development of highly efficient microbial strains for bioproduction. Here we used aspartokinase from Corynebacterium glutamicum (CgAK), a key enzyme controlling the biosynthesis of industrially important aspartate family amino acids, as a model to demonstrate a fast and efficient approach to the deregulation of allostery. In the last 50 years many researchers and companies have made considerable efforts to deregulate this enzyme from allosteric inhibition by lysine and threonine. However, only a limited number of positive mutants have been identified so far, almost exclusively by random mutation and selection. In this study, we used statistical coupling analysis of protein sequences, a method based on coevolutionary analysis, to systematically clarify the interaction network within the regulatory domain of CgAK that is essential for allosteric inhibition. A cluster of interconnected residues linking different inhibitors' binding sites as well as other regions of the protein have been identified, including most of the previously reported positions of successful mutations. Beyond these mutation positions, we have created another 14 mutants that can partially or completely desensitize CgAK from allosteric inhibition, as shown by enzyme activity assays. The introduction of only one of the inhibition-insensitive CgAK mutations (here Q298G) into a wild-type C. glutamicum strain by homologous recombination resulted in an accumulation of 58 g/liter L-lysine within 30 h of fed-batch fermentation in a bioreactor.

Within-host co-evolution of Gag P453L and protease D30N/N88D demonstrates virological advantage in a highly protease inhibitor-exposed HIV-1 case

To better understand the mechanism of HIV group-specific antigen (Gag) and protease (PR) co-evolution in drug-resistance acquisition, we analyzed a drug-resistance case by both bioinformatics and virological methods. We especially considered the quality of sequence data and analytical accuracy by introducing single-genome sequencing (SGS) and Spidermonkey/Bayesian graphical models (BGM) analysis, respectively. We analyzed 129 HIV-1 Gag–PR linkage sequences obtained from 8 time points, and the resulting sequences were applied to the Spidermonkey co-evolution analysis program, which identified ten mutation pairs as significantly co-evolving. Among these, we focused on associations between Gag-P453L, the P5′ position of the p1/p6 cleavage-site mutation, and PR-D30N/N88D nelfinavir-resistant mutations, and attempted to clarify their virological significance in vitro by constructing recombinant clones. The results showed that P453L Gag has the potential to improve replication capacity and the Gag processing efficiency of viruses with D30N PR/N88D PR but has little effect on nelfinavir susceptibility. Homology modeling analysis suggested that hydrogen bonds between the 30th PR residue and the R452 Gag are disturbed by the D30N PR mutation, but the impaired interaction is compensated by P453L Gag generating new hydrophobic interactions. Furthermore, database analysis indicated that the P453L Gag/D30N PR/N88D PR association was not specific only to our clinical case, but was common among AIDS patients.

Phylogeny and coevolutionary associations of makialgine mites (Acari, Psoroptidae, Makialginae) provide insight into evolutionary history of their hosts, strepsirrhine primates

Phylogeny of the mite subfamily Makialginae, permanent and highly specialized ectoparasites of strepsirrhine primates distributed in Madagascar and tropical Africa, was inferred based on morphology under maximum parsimony: Galagalges (Cheirogalalges (Makialges (Daubentonialges (Lemuralges, Gaudalges)))). Historical associations were reconstructed by fitting the mite tree onto alternative host topologies. Results of coevolutionary analyses highlight the disparity between morphological and molecular hypotheses on the host evolutionary history. Although phylogenetic relationships of strepsirrhine primates based on the morphological hypothesis returned significant fits to our parasite tree, the most recent molecular hypothesis of host phylogeny resulted in no coevolutionary scenario being different from random. Based on the former reconstructions, we hypothesize that present associations of Daubentoniidae, the earliest derivative extant family of Malagasy primates, acquired the present mite species via extinction of their original parasites and subsequent re-colonization by parasites from derived lemuriform families. Our data suggest that extant associations between Malagasy lemurs and their mites resulted from a single ancient codispersal to Madagascar from Africa. However, because of the host switch in Daubentoniidae, alternative, but less parsimonious, scenarios are possible. Our analyses indirectly support the hypothesis of the monophyletic origin of the infraorder Lemuriformes, the superfamily Lemuroidea, and the sister-group relationships between the families Lemuridae and Indriidae.

Studies on Correlated Pairs at the NBD-NBD and NBD-TMD Interfaces in CFTR

CFTR is an ATP-binding cassette (ABC)-protein, which contains two Nucleotide Binding Domains (NBDs) and two Transmembrane Domains (TMDs), but is unique among these proteins in that ATP binding, formation of a tight NBD-dimer (sandwiching two ATPs at two composite sites) and hydrolysis of one nucleotide drives opening/closure of a transmembrane chloride channel pore. We investigated interactions between residues at the NBD1-NBD2 interface of the catalytically inactive site 1, and the NBD-TMD boundary. Target pairs suggested by coevolution analysis were tested experimentally using mutant cycles. At the NBD1-NBD2 interface we studied pairs T460 (NBD1 Walker A)-H1348 (NBD2 signature sequence), and T460-H1375 (NBD2 D-loop). Mutation T460S decreased burst duration (τb) and open probability (Po), mutation H1348A markedly prolonged τb and increased Po. Mutation H1375A lengthened τb while slightly reducing Po. But mutant cycles built on τb, maximal opening rates, as well as Po and closing rates in non-hydrolytic (K1250R) background have so far not revealed significant changes in coupling between either positions 460-1348 or positions 460-1375 during various steps of the gating cycle. Hence we conclude that site 1 does not move markedly during the gating cycle, consistent with only partial NBD-dimer separation after ATP hydrolysis.At the NBD-TMD interface we studied positions M961 (site of CF-mutation in coupling helix 3) and A1256 (NBD2). Although single mutations M961L and A1256V decreased apparent ATP-affinities, these effects were additive, indicating no change in coupling between these positions upon ATP binding to closed channels. Po and τb were unaffected by these mutations. He et al. (JBC 283:26383) showed that L1260 and L1261 are in close contact with M961, and chemical crosslinking of L1261C with M961C lowers Po. Gating of mutants L1260A and L1261A paired with mutation M961L is under investigation.

Functional Side Chain Interactions in ABCC Transporters Inferred by Improved Coevolution Analysis

Members of the ABCC sub-family of ABC transport proteins underlie insulin secretion, multidrug resistance in some cancers, and cystic fibrosis disease; unlike most other ABC proteins, they are characterized by two markedly dissimilar ATP binding sites. Recent X-ray structures illuminate numerous inter-residue interactions but it remains largely unknown which interactions are crucial for the signal transduction events that mediate conformational changes during transport. We have inferred such interactions by detecting coevolving pairs of amino-acid positions from aligned ABCC protein sequences using several current methods, which vary in their correction for phylogenetic relatedness, and their assumptions about how amino-acid substitutions occur. We evaluated the performance of these methods by testing their ability to predict side-chain contacts given a 3D structural model. Since the heterogeneity of amino-acid substitution rates generates correlations between positions and thus undermines accurate detection of coevolving pairs, we partitioned pairs into classes based on the rate of amino-acid substitutions at both positions of each pair. We then optimized the performance of the methods in three sequential steps: removal of the most redundant sequences from the alignment to correct for phylogenetic artifacts, logical combination of methods in proportion to their individual performances, and adjustment of the coevolution score of each pair according to the performance associated with that pair's substitution rate class. We verified that performance was improved by these procedures, in comparison to results obtained with each method separately and without partitioning pairs by substitution rate. As expected, many of the detected coevolving pairs bridge consecutive turns in alpha-helices in the structural model. Others, however, link distinct structural elements or domains, and so might transduce signals during the protein's conformational cycle. Intriguingly, some of the positions identified have been implicated in cystic fibrosis.[NIH-DK51767]

The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions.

Failure to cospeciate: an unsorted tale of millipedes and mites

Mites form symbiotic relationships with many animal taxa, including fish, amphibians, reptiles, birds, mammals, mollusks and arthropods. They are often found living on millipedes and it has often been speculated that these two groups of arthropods have, in some cases, undergone coevolution. However, this hypothesis has never been formally tested. Millipedes of the family Xystodesmidae Cook 1895 (Diplopoda: Polydesmida) and their symbiotic mites of the genus Stylochyrus Canestrini & Canestrini 1882 were collected in broadleaf forests of the eastern USA. The DNA from two mitochondrial regions (16S/12S and cox1) was sequenced for all collected millipede and mite specimens. Phylogenetic trees were reconstructed for both millipede and mite taxa using Bayesian inference. Pairwise distance data were used in distance-based coevolutionary analyses and reconstructed phylogenies were used in tree-based coevolutionary analyses. The phylogenetic analyses indicate Stylochyrus and xystodesmid millipede evolutionary history is incongruent. Moreover, the evolutionary relationships among mite individuals and populations have very low support values and indicate little to no geographic structuring. The coevolutionary analyses likewise detected no pattern of coevolution among these millipede and mite lineages. Unlike many arthropod species, Stylochyrus mites appear to be highly vagile. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 272–287.

The emergence of hybrid-electric cars: Innovation path creation through co-evolution of supply and demand

Hybrid-electric vehicles have experienced a significant rate of growth in the last 10 years. This is remarkable, since the automotive sector is typically averse to the more radical technological change of engines. The internal combustion engine has been around for more than 100 years after all. In this paper we describe and explain the emergence of electric engines in the automobile market after 1990. We explicate the role of techno-economic mechanisms alongside social and regulatory mechanisms (including the social meaning of an engine). The co-evolutionary analysis is novel in the integrated conception of actor perspectives, feedback effects and competition between products. We find three sources of lock-in through path dependency: from demand, supply as well as the regulatory side. We conclude that automotive engines were significantly locked into a trajectory of internal combustion technology due to techno-economic mechanisms, which produced inertia despite social pressures. The creation of an alternative path, on the other hand, initially stalled. Various stakeholders were unsuccessful in marketing their electric or hybrid-electric vehicles in the 1990s, such as Peugeot/Citroen with various electric models, or Audi with their Duo in 1997. However, after 2000 we find that sustaining efforts of California's Air Resources Board and Toyota were triggering creation of a new innovation path of hybrid-electric engines.

Base Pairing Constraints Drive Structural Epistasis in Ribosomal RNA Sequences

It has long been accepted that the structural constraints stemming from the 3D structure of ribosomal RNA (rRNA) lead to coevolution through compensating mutations between interacting sites. State-of-the-art methods for detecting coevolving sites, however, while reaching high levels of specificity and sensitivity for Watson-Crick (WC) pairs of the helices defining the secondary structure, only scarcely reveal tertiary interactions occurring at the level of the 3D structure. In order to understand the relative failure of coevolutionary methods to detect such interactions, we analyze 2,682 interacting sites derived from high-resolution structures, which include a comprehensive data set of rRNA sequences from Archaea and Bacteria. We report a striking difference in the amount of coevolution between WC and non-WC pairs. In order to understand this pattern, we derive fitness landscapes from the geometry of base pairing interactions and construct neutral networks of substitutions for each type of interaction. These networks show that coevolution is a property of WC pairs because, unlike non-WC pairs, their landscapes exhibit fitness valleys, a single mutation in a WC pair resulting in a fitness drop. Second, we used the inferred neutral networks to estimate the level of constraint acting on each type of base pair and show that it correlates negatively with the observed rate of substitutions for all non-WC pairs. WC pairs appear as outliers, fixing more substitutions than expected according to their level of constraint. We here propose that the rate of substitution in WC pairs is due to coevolution resulting from constraints acting at intermediate levels of organization, namely the one of the helical stem with its forming WC pairs. In agreement with this hypothesis, we report a significant excess of intrahelical, inter-WC pairs coevolution compared with interhelices pairs. Altogether, these results show that detailed biochemical knowledge is required and has to be incorporated into evolutionary reasoning in order to understand the fine patterns of variation at the molecular level. They also demonstrate that coevolutionary analysis provides almost exclusively 2D information and only little 3D signal.

Co-creating games: a co-evolutionary analysis

The phenomenon of consumer co-creation is often framed in terms of whether either economic market forces or socio-cultural non-market forces ultimately dominate. We propose an alternate model of consumer co-creation in terms of co-evolution between markets and non-markets. Our model is based on a recent ethnographic study of a massively multiplayer online game through its development, release and ultimate failure, and is cast in terms of two explanatory models: multiple games and social network markets.We conclude that consumer co-creation is indeed complex, but in ways that relate to both emergent market expectations and the evolution of markets, not to the transcendence of markets.

Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products

Macrophages are involved in many aspects of development, host defense, pathology, and homeostasis. Their normal differentiation, proliferation, and survival are controlled by CSF-1 via the activation of the CSF1R. A recently discovered cytokine, IL-34, was shown to bind the same receptor in humans. Chicken is a widely used model organism in developmental biology, but the factors that control avian myelopoiesis have not been identified previously. The CSF-1, IL-34, and CSF1R genes in chicken and zebra finch were identified from respective genomic/cDNA sequence resources. Comparative analysis of the avian CSF1R loci revealed likely orthologs of mammalian macrophage-specific promoters and enhancers, and the CSF1R gene is expressed in the developing chick embryo in a pattern consistent with macrophage-specific expression. Chicken CSF-1 and IL-34 were expressed in HEK293 cells and shown to elicit macrophage growth from chicken BM cells in culture. Comparative sequence and co-evolution analysis across all vertebrates suggests that the two ligands interact with distinct regions of the CSF1R. These studies demonstrate that there are two separate ligands for a functional CSF1R across all vertebrates.

An evolutionary approach to understanding international business activity: The co-evolution of MNEs and the institutional environment

This paper examines the co-evolution of MNE activities and institutions external and internal to the firm. We develop a theoretical framework for this analysis that draws on the more recent writings of Douglass North on institutions as a response to complex forms of uncertainty associated with the rise in global economic interconnectedness, and of Richard Nelson on the co-evolution of technology and institutions. We link historical changes in the character of MNE activities to changes in the institutional environment, and highlight the scope for firm-level creativity and institutional entrepreneurship that may lead to co-evolution with the environment. We argue that the main drivers for institutional entrepreneurship are now found in the increasing autonomy of MNE subsidiaries. Thus MNE agency derives from more decentralized forms of experimentation in international corporate networks, which competence-creating nodes of new initiatives can co-evolve with local institutions. Unlike most other streams of related literature, our approach connects patterns of institutional change in wider business systems with more micro processes of variety generation and experimentation within and across individual firms. This form of co-evolutionary analysis is increasingly important to understanding the interrelationships between MNE activities and public policy.

IDENTIFYING COEVOLUTIONARY PATTERNS IN HUMAN LEUKOCYTE ANTIGEN (HLA) MOLECULES

The antigenic peptide, major histocompatibility complex molecule (MHC; also called human leukocyte antigen, HLA), coreceptor CD8, or CD4 and T-cell receptor (TCR) function as a complex to initiate effectors' mechanisms of the immune system. The tight functional and physical interaction among these molecules may have involved strong coevolution links among domains within and between proteins. Despite the importance of unraveling such dependencies to understand the arms race of host-pathogen interaction, no previous studies have aimed at achieving such an objective. Here, we perform an exhaustive coevolution analysis and show that indeed such dependencies are strongly shaping the evolution and probably the function of these molecules. We identify intramolecular coevolution in HLA class I and II at domains important for their immune activity. Most of the amino acid sites identified to be coevolving in HLAI have been also detected to undergo positive Darwinian selection highlighting therefore their adaptive value. We also identify coevolution among antigen-binding pockets (P1-P9) and among these and TCR-binding sites. Conversely to HLAI, coevolution is weaker in HLAII. Our results support that such coevolutionary patterns are due to selective pressures of host-pathogen coevolution and cooperative binding of TCRs, antigenic peptides, and CD8/CD4 to HLAI and HLAII.

Estimating sufficient statistics in co-evolutionary analysis by mutual information

Mutual information (MI) is a standard measure in information theory to observe and quantify correlated signals and events in both, empirical data sets and theoretical models. In the field of computational biology the MI turned out to be particularly useful in studies on co-evolutionary signals of sites within biomolecules. A key issue in the applicability of the MI is, however, a correct reference system or null model to understand finite-size effects in the underlying, finite data set. Although some bioinformatics studies exist with rigorous results for theoretical, well-designed random distributions, data from real-world proteins was never used to quantify the effect of finite-size samples. The impact of real-world statistics is, however, most relevant for researchers in all fields concerned with detecting evolutionary signals within biological sequences. We present results on such effects in finite-sized biological data sets and point to future research directions. We are most of all concerned with bacterial, ribosomal proteins as a prototypical example in molecular evolution. We compare to previous published suggestions, give an empirical formula, and propose a protocol to guide future research projects.

A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process

BackgroundThe E1 protein of Hepatitis C Virus (HCV) can be dissected into two distinct hydrophobic regions: a central domain containing an hypothetical fusion peptide (FP), and a C-terminal domain (CT) comprising two segments, a pre-anchor and a trans-membrane (TM) region. In the currently accepted model of the viral fusion process, the FP and the TM regions are considered to be closely juxtaposed in the post-fusion structure and their physical interaction cannot be excluded. In the present study, we took advantage of the natural sequence variability present among HCV strains to test, by purely sequence-based computational tools, the hypothesis that in this virus the fusion process involves the physical interaction of the FP and CT regions of E1.ResultsTwo computational approaches were applied. The first one is based on the co-evolution paradigm of interacting peptides and consequently on the correlation between the distance matrices generated by the sequence alignment method applied to FP and CT primary structures, respectively. In spite of the relatively low random genetic drift between genotypes, co-evolution analysis of sequences from five HCV genotypes revealed a greater correlation between the FP and CT domains than respect to a control HCV sequence from Core protein, so giving a clear, albeit still inconclusive, support to the physical interaction hypothesis.The second approach relies upon a non-linear signal analysis method widely used in protein science called Recurrence Quantification Analysis (RQA). This method allows for a direct comparison of domains for the presence of common hydrophobicity patterns, on which the physical interaction is based upon. RQA greatly strengthened the reliability of the hypothesis by the scoring of a lot of cross-recurrences between FP and CT peptides hydrophobicity patterning largely outnumbering chance expectations and pointing to putative interaction sites. Intriguingly, mutations in the CT region of E1, reducing the fusion process in vitro, strongly reduced the amount of cross-recurrence further supporting interaction between this region and FP.ConclusionOur results support a fusion model for HCV in which the FP and the C-terminal region of E1 are juxtaposed and interact in the post-fusion structure. These findings have general implications for viruses, as any visualization of the post-fusion FP-TM complex has been precluded by the impossibility to obtain crystallised viral fusion proteins containing the trans-membrane region. This limitation gives to sequence based modelling efforts a crucial role in the sketching of a molecular interpretation of the fusion process. Moreover, our data also have a more general relevance for cell biology as the mechanism of intracellular fusion showed remarkable similarities with viral fusion

The evolution of social learning rules: Payoff-biased and frequency-dependent biased transmission

Humans and other animals do not use social learning indiscriminately, rather, natural selection has favoured the evolution of social learning rules that make selective use of social learning to acquire relevant information in a changing environment. We present a gene-culture coevolutionary analysis of a small selection of such rules (unbiased social learning, payoff-biased social learning and frequency-dependent biased social learning, including conformism and anti-conformism) in a population of asocial learners where the environment is subject to a constant probability of change to a novel state. We define conditions under which each rule evolves to a genetically polymorphic equilibrium. We find that payoff-biased social learning may evolve under high levels of environmental variation if the fitness benefit associated with the acquired behaviour is either high or low but not of intermediate value. In contrast, both conformist and anti-conformist biases can become fixed when environment variation is low, whereupon the mean fitness in the population is higher than for a population of asocial learners. Our examination of the population dynamics reveals stable limit cycles under conformist and anti-conformist biases and some highly complex dynamics including chaos. Anti-conformists can out-compete conformists when conditions favour a low equilibrium frequency of the learned behaviour. We conclude that evolution, punctuated by the repeated successful invasion of different social learning rules, should continuously favour a reduction in the equilibrium frequency of asocial learning, and propose that, among competing social learning rules, the dominant rule will be the one that can persist with the lowest frequency of asocial learning.

1SA1-02 バルナーゼとバルスターの相互作用の共進化解析(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)

1SA1-02 バルナーゼとバルスターの相互作用の共進化解析(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)

1SA1-04 BPTI変異体の熱安定性とタンパク質間相互作用の共進化的視点からの解析(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)

1SA1-04 BPTI変異体の熱安定性とタンパク質間相互作用の共進化的視点からの解析(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)

1SA1-01 タンパク質共進化と分子進化速度の共変動(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)

1SA1-01 タンパク質共進化と分子進化速度の共変動(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)

1SA1-03 共進化情報によるタンパク質間相互作用予測(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)

1SA1-03 共進化情報によるタンパク質間相互作用予測(1SA1 タンパク質間相互作用研究の手法としての共進化解析,第47回日本生物物理学会年会)