51
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Starr TN, Picton LK, Thornton JW. Alternative evolutionary histories in the sequence space of an ancient protein. Nature 2017; 549:409-413. [PMID: 28902834 PMCID: PMC6214350 DOI: 10.1038/nature23902] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/08/2017] [Indexed: 12/28/2022]
Abstract
To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents an optimal state driven by natural selection or the contingent product of historical chance events; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution. Here we combine ancestral protein reconstruction with deep mutational scanning to characterize alternative histories in the sequence space around an ancient transcription factor, which evolved a novel biological function through well-characterized mechanisms. We find hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome. These alternatives all require prior permissive substitutions that do not enhance the derived function, but not all require the same permissive changes that occurred during history. We find that if evolution had begun from a different starting point within the network of sequences encoding the ancestral function, outcomes with different genetic and biochemical forms would probably have resulted; this contingency arises from the distribution of functional variants in sequence space and epistasis between residues. Our results illuminate the topology of the vast space of possibilities from which history sampled one path, highlighting how the outcome of evolution depends on a serial chain of compounding chance events.
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Affiliation(s)
- Tyler N Starr
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Lora K Picton
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
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52
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Zachar I, Szathmáry E. Breath-giving cooperation: critical review of origin of mitochondria hypotheses : Major unanswered questions point to the importance of early ecology. Biol Direct 2017; 12:19. [PMID: 28806979 PMCID: PMC5557255 DOI: 10.1186/s13062-017-0190-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/20/2017] [Indexed: 02/08/2023] Open
Abstract
The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria. REVIEWERS This article was reviewed by Michael W. Gray, William F. Martin and Purificación López-García.
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Affiliation(s)
- István Zachar
- Eötvös Loránd University, Department of Plant Systematics, Ecology and Theoretical Biology, Pázmány P. sétány 1/C, Budapest, 1117, Hungary.
- Evolutionary Systems Research Group, MTA, Centre for Ecological Research, Hungarian Academy of Sciences, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary.
| | - Eörs Szathmáry
- Eötvös Loránd University, Department of Plant Systematics, Ecology and Theoretical Biology, Pázmány P. sétány 1/C, Budapest, 1117, Hungary
- Evolutionary Systems Research Group, MTA, Centre for Ecological Research, Hungarian Academy of Sciences, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary
- Parmenides Foundation, Kirchplatz 1, 82049 Pullach/Munich, Munich, Germany
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53
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Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nat Commun 2017; 8:216. [PMID: 28790313 PMCID: PMC5548793 DOI: 10.1038/s41467-017-00238-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.
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Affiliation(s)
- Tamar Friedlander
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.,The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Roshan Prizak
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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54
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Luna JM, Barajas JM, Teng KY, Sun HL, Moore MJ, Rice CM, Darnell RB, Ghoshal K. Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer. Mol Cell 2017; 67:400-410.e7. [PMID: 28735896 PMCID: PMC5603316 DOI: 10.1016/j.molcel.2017.06.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/11/2017] [Accepted: 06/20/2017] [Indexed: 12/13/2022]
Abstract
MicroRNA-122, an abundant and conserved liver-specific miRNA, regulates hepatic metabolism and functions as a tumor suppressor, yet systematic and direct biochemical elucidation of the miR-122 target network remains incomplete. To this end, we performed Argonaute crosslinking immunoprecipitation (Argonaute [Ago]-CLIP) sequencing in miR-122 knockout and control mouse livers, as well as in matched human hepatocellular carcinoma (HCC) and benign liver tissue to identify miRNA target sites transcriptome-wide in two species. We observed a majority of miR-122 binding on 3' UTRs and coding exons followed by extensive binding to other genic and non-genic sites. Motif analysis of miR-122-dependent binding revealed a G-bulged motif in addition to canonical motifs. A large number of miR-122 targets were found to be species specific. Upregulation of several common mouse and human targets, most notably BCL9, predicted survival in HCC patients. These results broadly define the molecular consequences of miR-122 downregulation in hepatocellular carcinoma.
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Affiliation(s)
- Joseph M Luna
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Juan M Barajas
- Department of Pathology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Kun-Yu Teng
- Department of Pathology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Hui-Lung Sun
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Michael J Moore
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Kalpana Ghoshal
- Department of Pathology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
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55
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Pál C, Papp B. Evolution of complex adaptations in molecular systems. Nat Ecol Evol 2017; 1:1084-1092. [PMID: 28782044 PMCID: PMC5540182 DOI: 10.1038/s41559-017-0228-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/02/2017] [Indexed: 12/31/2022]
Abstract
A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume multiple neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in changing environment. Finally, we argue that molecular 'springboards', such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths.
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Affiliation(s)
- Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary.
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary
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56
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The SPOR Domain, a Widely Conserved Peptidoglycan Binding Domain That Targets Proteins to the Site of Cell Division. J Bacteriol 2017; 199:JB.00118-17. [PMID: 28396350 DOI: 10.1128/jb.00118-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Sporulation-related repeat (SPOR) domains are small peptidoglycan (PG) binding domains found in thousands of bacterial proteins. The name "SPOR domain" stems from the fact that several early examples came from proteins involved in sporulation, but SPOR domain proteins are quite diverse and contribute to a variety of processes that involve remodeling of the PG sacculus, especially with respect to cell division. SPOR domains target proteins to the division site by binding to regions of PG devoid of stem peptides ("denuded" glycans), which in turn are enriched in septal PG by the intense, localized activity of cell wall amidases involved in daughter cell separation. This targeting mechanism sets SPOR domain proteins apart from most other septal ring proteins, which localize via protein-protein interactions. In addition to SPOR domains, bacteria contain several other PG-binding domains that can exploit features of the cell wall to target proteins to specific subcellular sites.
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57
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Lynch M, Ackerman MS, Gout JF, Long H, Sung W, Thomas WK, Foster PL. Genetic drift, selection and the evolution of the mutation rate. Nat Rev Genet 2017; 17:704-714. [PMID: 27739533 DOI: 10.1038/nrg.2016.104] [Citation(s) in RCA: 452] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Matthew S Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Hongan Long
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
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58
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Martin H, Touzet P, Dufay M, Godé C, Schmitt E, Lahiani E, Delph LF, Van Rossum F. Lineages of Silene nutans developed rapid, strong, asymmetric postzygotic reproductive isolation in allopatry. Evolution 2017; 71:1519-1531. [PMID: 28384386 DOI: 10.1111/evo.13245] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 03/18/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
Abstract
Reproductive isolation can rise either as a consequence of genomic divergence in allopatry or as a byproduct of divergent selection in parapatry. To determine whether reproductive isolation in gynodioecious Silene nutans results from allopatric divergence or from ecological adaptation following secondary contact, we investigated the pattern of postzygotic reproductive isolation and hybridization in natural populations using two phylogeographic lineages, western (W1) and eastern (E1). Experimental crosses between the lineages identified strong, asymmetric postzygotic isolation between the W1 and the E1 lineages, independent of geographic overlap. The proportion of ovules fertilized, seeds aborted, and seeds germinated revealed relatively little effect on the fitness of hybrids. In contrast, hybrid mortality was high and asymmetric: while half of the hybrid seedlings with western lineage mothers died, nearly all hybrid seedlings with E1 mothers died. This asymmetric mortality mirrored the proportion of chlorotic seedlings, and is congruent with cytonuclear incompatibility. We found no evidence of hybridization between the lineages in regions of co-occurrence using nuclear and plastid markers. Together, our results are consistent with the hypothesis that strong postzygotic reproductive isolation involving cytonuclear incompatibilities arose in allopatry. We argue that the dynamics of cytonuclear gynodioecy could facilitate the evolution of reproductive isolation.
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Affiliation(s)
- Hélène Martin
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Pascal Touzet
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Mathilde Dufay
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Cécile Godé
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Eric Schmitt
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Emna Lahiani
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Lynda F Delph
- Department of Biology, Indiana University, Bloomington, Indiana, 47405
| | - Fabienne Van Rossum
- Meise Botanic Garden (formerly National Botanic Garden of Belgium), Nieuwelaan 38, BE-1860, Meise, Belgium.,Écologie végétale et Biogéochimie, Université Libre de Bruxelles, CP244, Boulevard du Triomphe, BE-1050, Brussels, Belgium.,Fédération Wallonie-Bruxelles, rue A. Lavallée 1, BE-1080, Brussels, Belgium
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59
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Einav T, Phillips R. Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants. J Phys Chem B 2017; 121:3813-3824. [PMID: 28134524 DOI: 10.1021/acs.jpcb.6b12672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a framework for computing the gating properties of ligand-gated ion channel mutants using the Monod-Wyman-Changeux (MWC) model of allostery. We derive simple analytic formulas for key functional properties such as the leakiness, dynamic range, half-maximal effective concentration ([EC50]), and effective Hill coefficient, and explore the full spectrum of phenotypes that are accessible through mutations. Specifically, we consider mutations in the channel pore of nicotinic acetylcholine receptor (nAChR) and the ligand binding domain of a cyclic nucleotide-gated (CNG) ion channel, demonstrating how each mutation can be characterized as only affecting a subset of the biophysical parameters. In addition, we show how the unifying perspective offered by the MWC model allows us, perhaps surprisingly, to collapse the plethora of dose-response data from different classes of ion channels into a universal family of curves.
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Affiliation(s)
- Tal Einav
- Department of Physics, California Institute of Technology , Pasadena, California 91125, United States
| | - Rob Phillips
- Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
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60
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A thousand empirical adaptive landscapes and their navigability. Nat Ecol Evol 2017; 1:45. [PMID: 28812623 DOI: 10.1038/s41559-016-0045] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/05/2016] [Indexed: 01/22/2023]
Abstract
The adaptive landscape is an iconic metaphor that pervades evolutionary biology. It was mostly applied in theoretical models until recent years, when empirical data began to allow partial landscape reconstructions. Here, we exhaustively analyse 1,137 complete landscapes from 129 eukaryotic species, each describing the binding affinity of a transcription factor to all possible short DNA sequences. We find that the navigability of these landscapes through single mutations is intermediate to that of additive and shuffled null models, suggesting that binding affinity-and thereby gene expression-is readily fine-tuned via mutations in transcription factor binding sites. The landscapes have few peaks that vary in their accessibility and in the number of sequences they contain. Binding sites in the mouse genome are enriched in sequences found in the peaks of especially navigable landscapes and the genetic diversity of binding sites in yeast increases with the number of sequences in a peak. Our findings suggest that landscape navigability may have contributed to the enormous success of transcriptional regulation as a source of evolutionary adaptations and innovations.
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61
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Barton NH. How does epistasis influence the response to selection? Heredity (Edinb) 2017; 118:96-109. [PMID: 27901509 PMCID: PMC5176114 DOI: 10.1038/hdy.2016.109] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/19/2016] [Accepted: 09/19/2016] [Indexed: 11/08/2022] Open
Abstract
Much of quantitative genetics is based on the 'infinitesimal model', under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the 'drift load', and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.
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Affiliation(s)
- N H Barton
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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62
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Pugh C, Kolaczkowski O, Manny A, Korithoski B, Kolaczkowski B. Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference. BMC Evol Biol 2016; 16:241. [PMID: 27825296 PMCID: PMC5101713 DOI: 10.1186/s12862-016-0818-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/28/2016] [Indexed: 02/07/2023] Open
Abstract
Background Although resurrecting ancestral proteins is a powerful tool for understanding the molecular-functional evolution of gene families, nearly all studies have examined proteins functioning in relatively stable biological processes. The extent to which more dynamic systems obey the same ‘rules’ governing stable processes is unclear. Here we present the first detailed investigation of the functional evolution of the RIG-like receptors (RLRs), a family of innate immune receptors that detect viral RNA in the cytoplasm. Results Using kinetic binding assays and molecular dynamics simulations of ancestral proteins, we demonstrate how a small number of adaptive protein-coding changes repeatedly shifted the RNA preference of RLRs throughout animal evolution by reorganizing the shape and electrostatic distribution across the RNA binding pocket, altering the hydrogen bond network between the RLR and its RNA target. In contrast to observations of proteins involved in metabolism and development, we find that RLR-RNA preference ‘flip flopped’ between two functional states, and shifts in RNA preference were not always coupled to gene duplications or speciation events. We demonstrate at least one reversion of RLR-RNA preference from a derived to an ancestral function through a novel structural mechanism, indicating multiple structural implementations of similar functions. Conclusions Our results suggest a model in which frequent shifts in selection pressures imposed by an evolutionary arms race preclude the long-term functional optimization observed in stable biological systems. As a result, the evolutionary dynamics of immune receptors may be less constrained by structural epistasis and historical contingency. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0818-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charles Pugh
- Department of Microbiology & Cell Science and Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Oralia Kolaczkowski
- Department of Microbiology & Cell Science and Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Austin Manny
- Department of Microbiology & Cell Science and Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Bryan Korithoski
- Department of Microbiology & Cell Science and Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Bryan Kolaczkowski
- Department of Microbiology & Cell Science and Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA. .,Genetics Institute, University of Florida, Gainesville, USA.
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63
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Intrinsic limits to gene regulation by global crosstalk. Nat Commun 2016; 7:12307. [PMID: 27489144 PMCID: PMC4976215 DOI: 10.1038/ncomms12307] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/21/2016] [Indexed: 01/21/2023] Open
Abstract
Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements. Limited specificity of transcription factor-DNA interactions leads to crosstalk in gene regulation. Here the authors consider global crosstalk in regulatory networks of growing size and complexity, and show that it imposes constraints on gene regulation and on the evolution of regulatory networks.
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64
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Orlenko A, Teufel AI, Chi PB, Liberles DA. Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biol Direct 2016; 11:31. [PMID: 27393343 PMCID: PMC4938953 DOI: 10.1186/s13062-016-0133-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/02/2016] [Indexed: 11/15/2022] Open
Abstract
Background While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily stable rate limiting (flux controlling) steps. Results A set of evolutionary simulations using a kinetic model of a metabolic pathway was performed under different conditions to evaluate the evolutionary stability of rate limiting steps. Simulations used combinations of selection for steady state flux, selection against the cost of molecular biosynthesis, and selection against the accumulation of high concentrations of a deleterious intermediate. Two mutational regimes were used, one with mutations that on average were neutral to molecular phenotype and a second with a preponderance of activity-destroying mutations. The evolutionary stability of rate limiting steps was low in all simulations with non-neutral mutational processes. Clustering of parameter co-evolution showed divergent inter-molecular evolutionary patterns under different evolutionary regimes. Conclusions This study provides a null model for pathway evolution when compensatory processes dominate with potential applications to predicting pathway functional change. This result also suggests a possible mechanism in which studies in statistical genetics that aim to associate a genotype to a phenotype assuming independent action of variants may be mis-specified through a mis-characterization of the link between individual gene function and pathway function. A better understanding of the genotype-phenotype map has potential applications in differentiating between compensatory changes and directional selection on pathways as well as detecting SNPs and fixed differences that might have phenotypic effects. Reviewers This article was reviewed by Arne Elofsson, David Ardell, and Shamil Sunyaev. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0133-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alena Orlenko
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Ashley I Teufel
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Peter B Chi
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, 19426, USA
| | - David A Liberles
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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65
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Silveira CB, Rohwer FL. Piggyback-the-Winner in host-associated microbial communities. NPJ Biofilms Microbiomes 2016; 2:16010. [PMID: 28721247 PMCID: PMC5515262 DOI: 10.1038/npjbiofilms.2016.10] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 01/02/2023] Open
Abstract
Phages can exploit their bacterial hosts by lytic infection, when many viral particles are released at cell lysis, or by lysogeny, when phages integrate into the host's genome. We recently proposed a new dynamic model of bacteria-phage interactions in which lysogeny predominates at high microbial abundance and growth rates. This model, named Piggyback-the-Winner (PtW), contrasts to current accepted models on the frequency of lysis and lysogeny and predicts that phages integrate into their hosts' genomes as prophages when microbial abundances and growth rates are high. According to PtW, switching to the temperate life cycle reduces phage predation control on bacterial abundance and confers superinfection exclusion, preventing that a closely-related phage infects the same bacterial cell. Here we examine how PtW is important for metazoans. Specifically, we postulate that PtW and the recently described bacteriophage adherence to mucus (BAM) model are strongly interrelated and have an important role in the development of the microbiome. In BAM, phage produced by the microbiome attach to mucins and protect underlying epithelial cells from invading bacteria. Spatial structuring of the mucus creates a gradient of phage replication strategies consistent with PtW. We predict that lysogeny is favored at the top mucosal layer and lytic predation predominates in the bacteria-sparse intermediary layers. The lysogeny confers competitive advantage to commensals against niche invasion and the lytic infection eliminates potential pathogens from deeper mucus layers.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Forest L Rohwer
- Department of Biology, San Diego State University, San Diego, California, USA
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66
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Sousa FL, Neukirchen S, Allen JF, Lane N, Martin WF. Lokiarchaeon is hydrogen dependent. Nat Microbiol 2016; 1:16034. [PMID: 27572645 DOI: 10.1038/nmicrobiol.2016.34] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/23/2016] [Indexed: 01/25/2023]
Abstract
The nature of the host that acquired the mitochondrion at the eukaryote origin is an important microbial evolutionary issue. Modern phylogenetics indicates that the host was an archaeon. The metagenome sequence of Candidatus Lokiarchaeon has identified it as being the closest relative of the host yet known. Here, we report comparative genomic evidence indicating that Lokiarchaeon is hydrogen dependent, as one theory for the eukaryote origin-the hydrogen hypothesis-predicts for the host lineage.
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Affiliation(s)
- Filipa L Sousa
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Sinje Neukirchen
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
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67
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Tuğrul M, Paixão T, Barton NH, Tkačik G. Dynamics of Transcription Factor Binding Site Evolution. PLoS Genet 2015; 11:e1005639. [PMID: 26545200 PMCID: PMC4636380 DOI: 10.1371/journal.pgen.1005639] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/09/2015] [Indexed: 11/19/2022] Open
Abstract
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics. Evolution has produced a remarkable diversity of living forms that manifests in qualitative differences as well as quantitative traits. An essential factor that underlies this variability is transcription factor binding sites, short pieces of DNA that control gene expression levels. Nevertheless, we lack a thorough theoretical understanding of the evolutionary times required for the appearance and disappearance of these sites. By combining a biophysically realistic model for how cells read out information in transcription factor binding sites with model for DNA sequence evolution, we explore these timescales and ask what factors crucially affect them. We find that the emergence of binding sites from a random sequence is generically slow under point and insertion/deletion mutational mechanisms. Strong selection, sufficient genomic sequence in which the sites can evolve, the existence of partially decayed old binding sites in the sequence, as well as certain biophysical mechanisms such as cooperativity, can accelerate the binding site gain times and make them consistent with the timescales suggested by comparative analyses of genomic data.
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Affiliation(s)
- Murat Tuğrul
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- * E-mail:
| | - Tiago Paixão
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Gašper Tkačik
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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68
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Azmak O, Bayer H, Caplin A, Chun M, Glimcher P, Koonin S, Patrinos A. Using Big Data to Understand the Human Condition: The Kavli HUMAN Project. BIG DATA 2015; 3:173-188. [PMID: 26487987 PMCID: PMC4605457 DOI: 10.1089/big.2015.0012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Until now, most large-scale studies of humans have either focused on very specific domains of inquiry or have relied on between-subjects approaches. While these previous studies have been invaluable for revealing important biological factors in cardiac health or social factors in retirement choices, no single repository contains anything like a complete record of the health, education, genetics, environmental, and lifestyle profiles of a large group of individuals at the within-subject level. This seems critical today because emerging evidence about the dynamic interplay between biology, behavior, and the environment point to a pressing need for just the kind of large-scale, long-term synoptic dataset that does not yet exist at the within-subject level. At the same time that the need for such a dataset is becoming clear, there is also growing evidence that just such a synoptic dataset may now be obtainable-at least at moderate scale-using contemporary big data approaches. To this end, we introduce the Kavli HUMAN Project (KHP), an effort to aggregate data from 2,500 New York City households in all five boroughs (roughly 10,000 individuals) whose biology and behavior will be measured using an unprecedented array of modalities over 20 years. It will also richly measure environmental conditions and events that KHP members experience using a geographic information system database of unparalleled scale, currently under construction in New York. In this manner, KHP will offer both synoptic and granular views of how human health and behavior coevolve over the life cycle and why they evolve differently for different people. In turn, we argue that this will allow for new discovery-based scientific approaches, rooted in big data analytics, to improving the health and quality of human life, particularly in urban contexts.
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69
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Lindtke D, Buerkle CA. The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact. Evolution 2015; 69:1987-2004. [DOI: 10.1111/evo.12725] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 07/08/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Dorothea Lindtke
- Department of Botany and Program in Ecology; University of Wyoming; Laramie Wyoming 82071
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN United Kingdom
| | - C. Alex Buerkle
- Department of Botany and Program in Ecology; University of Wyoming; Laramie Wyoming 82071
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70
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Anderson DW, McKeown AN, Thornton JW. Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites. eLife 2015; 4:e07864. [PMID: 26076233 PMCID: PMC4500092 DOI: 10.7554/elife.07864] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/13/2015] [Indexed: 02/07/2023] Open
Abstract
Complexes of specifically interacting molecules, such as transcription factor proteins (TFs) and the DNA response elements (REs) they recognize, control most biological processes, but little is known concerning the functional and evolutionary effects of epistatic interactions across molecular interfaces. We experimentally characterized all combinations of genotypes in the joint protein-DNA sequence space defined by an historical transition in TF-RE specificity that occurred some 500 million years ago in the DNA-binding domain of an ancient steroid hormone receptor. We found that rampant epistasis within and between the two molecules was essential to specific TF-RE recognition and to the evolution of a novel TF-RE complex with unique derived specificity. Permissive and restrictive epistatic mutations across the TF-RE interface opened and closed potential evolutionary paths accessible by the other, making the evolution of each molecule contingent on its partner's history and allowing a molecular complex with novel specificity to evolve.
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Affiliation(s)
- Dave W Anderson
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Alesia N McKeown
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, United States
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