0
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Evolution of a biological thermocouple by adaptation of cytochrome c oxidase in a subterrestrial metazoan

      Preprint
      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          In this study we report a naturally evolved temperature-sensing electrical regulator in the cytochrome c oxidase of the Devil Worm, Halicephalobus mephisto. This extremophile metazoan was isolated 1.3 km underground in a South African goldmine, where it adapted to heat and potentially to hypoxia, making its mitochondrial sequence a likely target of adaptational change. We obtained the full mitochondrial genome sequence of this organism, and show through dN/dS analysis statistically robust evidence of positive selection in H. mephisto cytochrome c oxidase subunits. Seventeen of these positively-selected amino acid substitutions were localized in proximity to the H- and K-pathway proton channels of the complex. Surprisingly, the H. mephisto cytochrome c oxidase proton pump completely shuts down at low temperatures (20°C) leading to approximately a 4.8-fold reduction in the transmembrane proton gradient voltage (ΔΨ m) compared to optimal temperature (37°C). Direct measurement of oxygen consumption found a corresponding 4.7-fold drop at 20°C compared to 37°C. Correspondingly, the lifecycle of H. mephisto takes four-fold longer at the low temperature compared to higher. This elegant evolutionary adaptation creates a finely-tuned mitochondrial temperature sensor, allowing this ectothermic organism to maximize its reproductive success in varying environmental temperatures. Our study shows that evolutionary innovation may remodel core metabolism to make it more accurately map onto environmental variation.

          Related collections

          Most cited references47

          • Record: found
          • Abstract: found
          • Article: not found

          PAML 4: phylogenetic analysis by maximum likelihood.

          PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

            This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Population size does not influence mitochondrial genetic diversity in animals.

              Within-species genetic diversity is thought to reflect population size, history, ecology, and ability to adapt. Using a comprehensive collection of polymorphism data sets covering approximately 3000 animal species, we show that the widely used mitochondrial DNA (mtDNA) marker does not reflect species abundance or ecology: mtDNA diversity is not higher in invertebrates than in vertebrates, in marine than in terrestrial species, or in small than in large organisms. Nuclear loci, in contrast, fit these intuitive expectations. The unexpected mitochondrial diversity distribution is explained by recurrent adaptive evolution, challenging the neutral theory of molecular evolution and questioning the relevance of mtDNA in biodiversity and conservation studies.
                Bookmark

                Author and article information

                Journal
                bioRxiv
                BIORXIV
                bioRxiv
                Cold Spring Harbor Laboratory
                07 December 2023
                : 2023.12.05.570156
                Affiliations
                [1 ]American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
                [2 ]American University Mathematics and Statistics Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
                [3 ]New York University, Center for Genomics and Systems Biology, New York, NY 10003
                Author notes

                Author contributions:

                Guerin, Megan performed formal analysis, visualization, and writing-original draft

                Ellis, TreVaughn performed formal analysis, visualization, and investigation

                Ware, Mark performed formal analysis and visualization

                Chung, George performed investigation (the D. pachys mitochondrial genome)

                Gunsalus, Kristin performed conceptualization

                Bracht, John performed conceptualization, visualization, formal analysis, investigation, funding acquisition, supervision, project administration, and writing-review and editing

                [*]

                these authors contributed equally to the work

                Author information
                http://orcid.org/0000-0001-9769-4624
                http://orcid.org/0000-0001-8042-7685
                Article
                10.1101/2023.12.05.570156
                10723328
                38106155
                c8df85a1-42a0-4f60-8e69-5b231d67fc9e

                This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.

                History
                Funding
                This work was supported by National Institutes of Health grant 1R15GM146207 (J.R.B)
                Categories
                Article

                Comments

                Comment on this article