1
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Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov FA, Kondrashov AS, Bazykin GA, Valle L. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. Eur J Hum Genet 2024:10.1038/s41431-024-01598-8. [PMID: 38658779 DOI: 10.1038/s41431-024-01598-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/16/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.
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Affiliation(s)
- Maria A Andrianova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Vladimir B Seplyarskiy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Beatriz Sánchez-Heras
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Elche Health Department, Elche, Spain
- Medical Oncology Department, Cancer Genetic Counseling Unit. Elche University Hospital, Elche, Spain
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Health of Catalonia, Catalan Cancer Plan, Barcelona, Spain
| | - José Luis Soto
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Elche Health Department, Elche, Spain
- Molecular Genetics Unit, Elche University Hospital, Elche, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Emma Borràs
- Molecular Genetics Unit, Consorci Sanitari de Terrassa, Terrassa, Spain
| | - Fyodor A Kondrashov
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Evolutionary and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Alexey S Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Georgii A Bazykin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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2
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Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Somermeyer LG, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov FA, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. A hybrid pathway for self-sustained luminescence. Sci Adv 2024; 10:eadk1992. [PMID: 38457503 PMCID: PMC10923510 DOI: 10.1126/sciadv.adk1992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis-a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.
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Affiliation(s)
- Kseniia A. Palkina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana A. Karataeva
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maxim M. Perfilov
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Liliia I. Fakhranurova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nadezhda M. Markina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena Garcia-Perez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Marta Rodriguez-Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Victor Vazquez-Vilriales
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Ekaterina S. Shakhova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana Mitiouchkina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna Alekberova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alena K. Malyshevskaia
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena B. Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Anastasia Balakireva
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nikita Sytov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Daria I. Boldyreva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vladislav V. Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Fyodor A. Kondrashov
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0412, Japan
| | - Vladimir V. Choob
- Botanical Garden of Lomonosov Moscow State University, Vorobievy Gory 1 b.12, Moscow 119234 Russia
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Ilia V. Yampolsky
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
- Light Bio Inc., Ketchum, ID, USA
| | - Alexander S. Mishin
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Karen S. Sarkisyan
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Light Bio Inc., Ketchum, ID, USA
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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3
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Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova ES, Kondrashov FA, Ivankov DN. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS One 2023; 18:e0282689. [PMID: 36928239 PMCID: PMC10019719 DOI: 10.1371/journal.pone.0282689] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is "solved". However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and <pLDDT> metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding.
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Affiliation(s)
- Marina A. Pak
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Mariia S. Novikova
- Armand Hammer United World College of the American West, Montezuma, New Mexico, United Stated of America
| | - Dmitry S. Petrov
- Specialized Educational and Scientific Center of UrFU (SUNC UrFU), Ekaterinburg, Russia
| | - Ilya S. Vorobyev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Fyodor A. Kondrashov
- Institute of Science and Technology Austria, Maria Gugging, Austria
- Evolutionary and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Dmitry N. Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- * E-mail:
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4
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Saona R, Kondrashov FA, Khudiakova KA. Correction to: Relation Between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions. Bull Math Biol 2023; 85:17. [PMID: 36680604 PMCID: PMC9867669 DOI: 10.1007/s11538-022-01118-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Raimundo Saona
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Lower Austria Austria
| | - Fyodor A. Kondrashov
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Lower Austria Austria
| | - Ksenia A. Khudiakova
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Lower Austria Austria
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5
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Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol ME, Putintseva EV, Sarkisyan KS, Kondrashov FA. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife 2022; 11:75842. [PMID: 35510622 PMCID: PMC9119679 DOI: 10.7554/elife.75842] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/25/2022] [Indexed: 11/24/2022] Open
Abstract
Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design - instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.
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Affiliation(s)
| | - Aubin Fleiss
- Synthetic Biology Group, MRC London Institute of Medical SciencesLondonUnited Kingdom,Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College LondonLondonUnited Kingdom
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
| | - Nina G Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
| | - Anna A Igolkina
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States,Institute for Drug Discovery, Medical School, Leipzig UniversityLeipzigGermany
| | - Maria-Elisenda Alaball Pujol
- Synthetic Biology Group, MRC London Institute of Medical SciencesLondonUnited Kingdom,Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College LondonLondonUnited Kingdom
| | | | - Karen S Sarkisyan
- Synthetic Biology Group, MRC London Institute of Medical SciencesLondonUnited Kingdom,Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College LondonLondonUnited Kingdom,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
| | - Fyodor A Kondrashov
- Institute of Science and Technology AustriaKlosterneuburgAustria,Evolutionary and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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6
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Rella SA, Kulikova YA, Dermitzakis ET, Kondrashov FA. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Sci Rep 2021; 11:15729. [PMID: 34330988 PMCID: PMC8324827 DOI: 10.1038/s41598-021-95025-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 12/21/2022] Open
Abstract
Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period.
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Affiliation(s)
- Simon A Rella
- Institute of Science and Technology Austria, 1 Am Campus, 3400, Klosterneuburg, Austria
| | | | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
| | - Fyodor A Kondrashov
- Institute of Science and Technology Austria, 1 Am Campus, 3400, Klosterneuburg, Austria.
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7
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Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov FA, Aulchenko YS. The limits of normal approximation for adult height. Eur J Hum Genet 2021; 29:1082-1091. [PMID: 33664501 PMCID: PMC8298501 DOI: 10.1038/s41431-021-00836-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/05/2021] [Accepted: 02/11/2021] [Indexed: 11/14/2022] Open
Abstract
Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait.
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Affiliation(s)
- Sergei A Slavskii
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Novosibirsk State University, Novosibirsk, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | | | - Tatiana I Shashkova
- Novosibirsk State University, Novosibirsk, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Tatiana I Axenovich
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | - Yurii S Aulchenko
- Novosibirsk State University, Novosibirsk, Russia.
- Moscow Institute of Physics and Technology, Moscow, Russia.
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- PolyOmica, 's-Hertogenbosch, PA, The Netherlands.
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8
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Mitiouchkina T, Mishin AS, Somermeyer LG, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov FA, Yampolsky IV, Sarkisyan KS. Plants with genetically encoded autoluminescence. Nat Biotechnol 2020; 38:944-946. [PMID: 32341562 PMCID: PMC7610436 DOI: 10.1038/s41587-020-0500-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 03/26/2020] [Indexed: 12/01/2022]
Abstract
Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.
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Affiliation(s)
- Tatiana Mitiouchkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Mishin
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Nadezhda M Markina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Chepurnyh
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Elena B Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana A Karataeva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kseniia A Palkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina S Shakhova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Liliia I Fakhranurova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Aleksandra S Tsarkova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia
| | | | | | | | | | - Dmitry Shlykov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olesya A Melnik
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Victoria O Shipunova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey M Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey I Bubyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Pushin
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V Choob
- Botanical Garden of Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V Dolgov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Ilia V Yampolsky
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Pirogov Russian National Research Medical University, Moscow, Russia.
| | - Karen S Sarkisyan
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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9
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Mitiouchkina T, Mishin AS, Somermeyer LG, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov FA, Yampolsky IV, Sarkisyan KS. Author Correction: Plants with genetically encoded autoluminescence. Nat Biotechnol 2020; 38:1001. [PMID: 32499610 DOI: 10.1038/s41587-020-0578-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Tatiana Mitiouchkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Mishin
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Nadezhda M Markina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Chepurnyh
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Elena B Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana A Karataeva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kseniia A Palkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina S Shakhova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Liliia I Fakhranurova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Aleksandra S Tsarkova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia
| | | | | | | | | | - Dmitry Shlykov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olesya A Melnik
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Victoria O Shipunova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey M Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey I Bubyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Pushin
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V Choob
- Botanical Garden of Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V Dolgov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Ilia V Yampolsky
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Pirogov Russian National Research Medical University, Moscow, Russia.
| | - Karen S Sarkisyan
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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10
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Uroshlev LA, Abdullaev ET, Umarova IR, Il'icheva IA, Panchenko LA, Polozov RV, Kondrashov FA, Nechipurenko YD, Grokhovsky SL. A Method for Identification of the Methylation Level of CpG Islands From NGS Data. Sci Rep 2020; 10:8635. [PMID: 32451390 PMCID: PMC7248081 DOI: 10.1038/s41598-020-65406-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 05/04/2020] [Indexed: 01/01/2023] Open
Abstract
In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data.
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Affiliation(s)
- Leonid A Uroshlev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
| | | | - Iren R Umarova
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Moscow, Russia
| | - Irina A Il'icheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Larisa A Panchenko
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Moscow, Russia
| | - Robert V Polozov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Puschino, Russia
| | | | - Yury D Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Sergei L Grokhovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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11
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Esteban L, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov FA, Ivankov DN. HypercubeME: two hundred million combinatorially complete datasets from a single experiment. Bioinformatics 2019; 36:btz841. [PMID: 31742320 PMCID: PMC7703787 DOI: 10.1093/bioinformatics/btz841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 11/17/2022] Open
Abstract
MOTIVATION Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a "combinatorially complete dataset". So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. RESULTS We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199,847,053 unique combinatorially complete genotype combinations of dimensionality ranging from two to twelve. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data. AVAILABILITY https://github.com/ivankovlab/HypercubeME.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Lyubov R Lonishin
- Faculty of Medical Physics, Institute of Biomedical System and Technologies, Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Daniil M Bobrovskiy
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119234, Russia
| | - Gregory Leleytner
- Department of Innovation and High Technology, Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Natalya S Bogatyreva
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Bioinformatics and Genomics Programme, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, Moscow 142290, Russia
| | | | - Dmitry N Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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12
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Pokusaeva VO, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan KS, Mishin AS, Bogatyreva NS, Ivankov DN, Akopyan AV, Avvakumov SY, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov FA. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genet 2019; 15:e1008079. [PMID: 30969963 PMCID: PMC6476524 DOI: 10.1371/journal.pgen.1008079] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 04/22/2019] [Accepted: 03/11/2019] [Indexed: 11/18/2022] Open
Abstract
Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible. An intuitive understanding of protein evolution dictates that, with the exception of adaptive substitutions, amino acid states should be freely exchangeable between the same gene from different species. However, the extent to which this assertion holds true has not been tested in a controlled experiment. Here, we show that whether an amino acid state can be exchanged between orthologues depends on other amino acid states in the same protein. Furthermore, we show that the mode of interaction of amino acid states is multidimensional. Assuming that amino acid replacements influence the protein in several independent ways substantially improves our ability to predict the effect of an amino acid state in a protein sequence that has not been observed in nature.
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Affiliation(s)
| | - Dinara R. Usmanova
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | | | - Lorena Espinar
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Karen S. Sarkisyan
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Medical Research Council London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | | | - Natalya S. Bogatyreva
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Dmitry N. Ivankov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Arseniy V. Akopyan
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Sergey Ya. Avvakumov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Inna S. Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Guillaume J. Filion
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lucas B. Carey
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Center for Quantitative Biology and Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail: (LBC); (FAK)
| | - Fyodor A. Kondrashov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
- * E-mail: (LBC); (FAK)
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13
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Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov FA, Ivankov DN. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics 2018; 34:3653-3658. [PMID: 29722803 PMCID: PMC6198859 DOI: 10.1093/bioinformatics/bty340] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 03/15/2018] [Accepted: 04/30/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations. Results Here we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here. Availability and implementation All calculations were implemented by in-house PERL scripts. Supplementary information Supplementary data are available at Bioinformatics online. Note The article 10.1093/bioinformatics/bty348, published alongside this paper, also addresses the problem of biases in protein stability change predictions.
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Affiliation(s)
- Dinara R Usmanova
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Natalya S Bogatyreva
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Joan Ariño Bernad
- Centre de Formació Interdisciplinària Superior, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Aleksandra A Eremina
- School of Biological Sciences, College of Science and Engineering, University of Edinburgh, Edinburgh, UK
| | | | - German M Kanevskiy
- Higher Chemical College of the Russian Academy of Sciences, Moscow, Russia
| | - Lyubov R Lonishin
- Faculty of Technical Physics, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great Saint-Petersburg Polytechnic University, Saint-Petersburg, Russia
| | | | - Alisa G Yakupova
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Dmitry N Ivankov
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Science and Technology, Klosterneuburg, Austria
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14
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Zapata L, Pich O, Serrano L, Kondrashov FA, Ossowski S, Schaefer MH. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biol 2018; 19:67. [PMID: 29855388 PMCID: PMC5984361 DOI: 10.1186/s13059-018-1434-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/20/2018] [Indexed: 01/08/2023] Open
Abstract
Background Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments. Electronic supplementary material The online version of this article (10.1186/s13059-018-1434-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis Zapata
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Oriol Pich
- Evolutionary Genomics Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Luis Serrano
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010, Barcelona, Spain
| | - Fyodor A Kondrashov
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Stephan Ossowski
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
| | - Martin H Schaefer
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
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15
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Saint-Léger A, Bello C, Dans PD, Torres AG, Novoa EM, Camacho N, Orozco M, Kondrashov FA, Ribas de Pouplana L. Saturation of recognition elements blocks evolution of new tRNA identities. Sci Adv 2016; 2:e1501860. [PMID: 27386510 PMCID: PMC4928997 DOI: 10.1126/sciadv.1501860] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/31/2016] [Indexed: 06/01/2023]
Abstract
Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure.
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Affiliation(s)
- Adélaïde Saint-Léger
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Carla Bello
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 88 Dr. Aiguader, 08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Pablo D. Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Joint BSC-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Eva Maria Novoa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02139, USA
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Joint BSC-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, 08028 Barcelona, Catalonia, Spain
| | - Fyodor A. Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 88 Dr. Aiguader, 08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain
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16
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17
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Usmanova DR, Ferretti L, Povolotskaya IS, Vlasov PK, Kondrashov FA. A model of substitution trajectories in sequence space and long-term protein evolution. Mol Biol Evol 2014; 32:542-54. [PMID: 25415964 DOI: 10.1093/molbev/msu318] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.
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Affiliation(s)
- Dinara R Usmanova
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, g.Dolgoprudny, Russia Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luca Ferretti
- Systématique, Adaptation et Evolution (UMR 7138), UPMC University Paris 06, CNRS, MNHN, IRD, Paris, France CIRB, Collège de France, Paris, France
| | - Inna S Povolotskaya
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Peter K Vlasov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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18
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Pougach K, Voet A, Kondrashov FA, Voordeckers K, Christiaens JF, Baying B, Benes V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen KJ. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nat Commun 2014; 5:4868. [PMID: 25204769 PMCID: PMC4172970 DOI: 10.1038/ncomms5868] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022] Open
Abstract
The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.
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Affiliation(s)
- Ksenia Pougach
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Arnout Voet
- Structural Bioinformatics, Center for Life Science Technologies (CLST), RIKEN, 230-0045 Yokohama, Japan
| | - Fyodor A. Kondrashov
- Laboratory of Evolutionary Genomics, Centre for genomic regulation (CRG), 08003 Barcelona, Spain
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Joaquin F. Christiaens
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Bianka Baying
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg (EMBL), 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg (EMBL), 69117 Heidelberg, Germany
| | - Ryo Sakai
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, B-3001 Leuven, Belgium
- iMinds Medical Information Technologies Department, KU Leuven, B-3001 Leuven, Belgium
| | - Jan Aerts
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, B-3001 Leuven, Belgium
- iMinds Medical Information Technologies Department, KU Leuven, B-3001 Leuven, Belgium
| | - Bo Zhu
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Patrick Van Dijck
- Molecular Microbiology and Biotechnology Section, KU Leuven, B-3001 Leuven, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
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Seplyarskiy VB, Logacheva MD, Penin AA, Baranova MA, Leushkin EV, Demidenko NV, Klepikova AV, Kondrashov FA, Kondrashov AS, James TY. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Mol Biol Evol 2014; 31:3016-25. [PMID: 25135947 PMCID: PMC4209137 DOI: 10.1093/molbev/msu242] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0–99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.
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Affiliation(s)
- Vladimir B Seplyarskiy
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksey A Penin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Maria A Baranova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny V Leushkin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Natalia V Demidenko
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Anna V Klepikova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, Barcelona, Spain
| | - Alexey S Kondrashov
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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20
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Abstract
Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolution must end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in the mammalian lineage. We find that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications. We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event.
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Affiliation(s)
- Oriol Pich I Roselló
- Facultat de Medicina, Universitat de Barcelona (UB), SpainBioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, SpainUniversitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, SpainUniversitat Pompeu Fabra (UPF), Barcelona, SpainInstitució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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21
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Ivankov DN, Finkelstein AV, Kondrashov FA. A structural perspective of compensatory evolution. Curr Opin Struct Biol 2014; 26:104-12. [PMID: 24981969 PMCID: PMC4141909 DOI: 10.1016/j.sbi.2014.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/11/2014] [Accepted: 05/16/2014] [Indexed: 11/25/2022]
Abstract
The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution.
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Affiliation(s)
- Dmitry N Ivankov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russia
| | - Alexei V Finkelstein
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russia
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, 08010 Barcelona, Spain.
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22
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Koval AV, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov FA, Katanaev VL. Anti-leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochem Pharmacol 2013; 87:571-8. [PMID: 24355563 DOI: 10.1016/j.bcp.2013.12.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 11/26/2022]
Abstract
Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers.
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Affiliation(s)
- A V Koval
- Department of Pharmacology and Toxicology, Faculty of Biology and Medicine, University of Lausanne, Rue du Bugnon 27, Lausanne 1005, Switzerland
| | - P Vlasov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) 88 Dr. Aiguader, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - P Shichkova
- Moscow Institute of Physics and Technology (State University), Moscow, Russia
| | - S Khunderyakova
- Municipal budget institution of general education gymnasium "Pushchino", Pushchino, Russia
| | - Y Markov
- National Research University Higher School of Economics, Moscow, Russia
| | - J Panchenko
- Moscow Institute of Physics and Technology (State University), Moscow, Russia
| | | | - F A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) 88 Dr. Aiguader, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, 08010 Barcelona, Spain
| | - V L Katanaev
- Department of Pharmacology and Toxicology, Faculty of Biology and Medicine, University of Lausanne, Rue du Bugnon 27, Lausanne 1005, Switzerland; Institute of Protein Research, Russian Academy of Science, Instituskaya 4, Moscow Region, Pushchino 142290, Russia.
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23
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Derelle R, Kondrashov FA, Arkhipov VY, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R). BMC Res Notes 2013; 6:310. [PMID: 23915680 PMCID: PMC3750627 DOI: 10.1186/1756-0500-6-310] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/22/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. FINDINGS We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. CONCLUSIONS Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.
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Abstract
Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this question has
not been comprehensively addressed at the molecular level. Here, we use data from 221
human genes with known pathogenic mutations to estimate the rate of irreversibility in
protein evolution. For these genes, we reconstruct ancestral amino acid sequences along
the mammalian phylogeny and identify ancestral amino acid states that match known
pathogenic mutations. Such cases represent inherent evolutionary irreversibility because,
at the present moment, reversals to these ancestral amino acid states are impossible for
the human lineage. We estimate that approximately 10% of all amino acid
substitutions along the mammalian phylogeny are irreversible, such that a return to the
ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes
with high rates of irreversibility, as much as 40% of all amino acid evolution was
estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral
phenotypes, the molecular nature of the high rate of irreversibility in proteins is best
explained by evolution with a high prevalence of compensatory, epistatic interactions
between amino acid sites. Under such mode of protein evolution, once an amino acid
substitution is fixed, the probability of its reversal declines as the protein sequence
accumulates changes that affect the phenotypic manifestation of the ancestral state. The
prevalence of epistasis in evolution indicates that the observed high rate of
irreversibility in protein evolution is an inherent property of protein structure and
function.
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Affiliation(s)
- Onuralp Soylemez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
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26
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Abstract
A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.
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Affiliation(s)
- Fyodor A Kondrashov
- Institució Catalana de Recerca i Estudis Avançats, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, 88 Dr Aiguader, Barcelona 08003, Spain.
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27
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Povolotskaya IS, Kondrashov FA, Ledda A, Vlasov PK. Stop codons in bacteria are not selectively equivalent. Biol Direct 2012; 7:30. [PMID: 22974057 PMCID: PMC3549826 DOI: 10.1186/1745-6150-7-30] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 08/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes. RESULTS We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG. CONCLUSIONS Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.
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Affiliation(s)
- Inna S Povolotskaya
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, 88 Dr, Aiguader, Barcelona 08003, Spain
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28
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Koblik EA, Red'kin YA, Meer MS, Derelle R, Golenkina SA, Kondrashov FA, Arkhipov VY. Acrocephalus orinus: a case of mistaken identity. PLoS One 2011; 6:e17716. [PMID: 21526114 PMCID: PMC3081296 DOI: 10.1371/journal.pone.0017716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 02/11/2011] [Indexed: 11/19/2022] Open
Abstract
Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered.
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Affiliation(s)
- Evgeny A. Koblik
- Zoological Museum of the Moscow State University, Moscow, Russia
| | | | - Margarita S. Meer
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
| | - Romain Derelle
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
| | - Sofia A. Golenkina
- Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Fyodor A. Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
| | - Vladimir Yu. Arkhipov
- Institute of Theoretical & Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- * E-mail:
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29
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Abstract
Background Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome. Results We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes. Conclusions Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently. Reviewers This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).
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30
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Povolotskaya IS, Kondrashov FA. Sequence space and the ongoing expansion of the protein universe. Nature 2010; 465:922-6. [PMID: 20485343 DOI: 10.1038/nature09105] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 04/19/2010] [Indexed: 11/09/2022]
Abstract
The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: approximately 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, approximately 3.5 x 10(9) yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.
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Affiliation(s)
- Inna S Povolotskaya
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Calle Dr Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Spain
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31
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Abstract
The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.
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Affiliation(s)
- Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, , C/Dr. Aiguader 88, Barcelona Biomedical Research Park Building 08003, Barcelona, Spain.
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32
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Meer MV, Kondrashov AS, Artzy-Randrup Y, Kondrashov FA. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature 2010; 464:279-82. [PMID: 20182427 DOI: 10.1038/nature08691] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 11/16/2009] [Indexed: 12/25/2022]
Abstract
A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10(-3) or even about 10(-2), with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.
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Affiliation(s)
- Margarita V Meer
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, C/Dr Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Spain
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Kondrashov AS, Povolotskaya IS, Ivankov DN, Kondrashov FA. Rate of sequence divergence under constant selection. Biol Direct 2010; 5:5. [PMID: 20092641 PMCID: PMC2835663 DOI: 10.1186/1745-6150-5-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 01/21/2010] [Indexed: 12/02/2022] Open
Abstract
Background Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated. Results Strong selection that favors only one allele can make E arbitrarily small and r arbitrarily large. In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality. Conclusions Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection. Reviewers This article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin.
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Affiliation(s)
- Alexey S Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, C/Dr Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Spain
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Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov FA, Gundllapalli S, Frolova L, Söll D, Kisselev L. Translation termination in pyrrolysine-utilizing archaea. FEBS Lett 2009; 583:3455-60. [PMID: 19796638 DOI: 10.1016/j.febslet.2009.09.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 09/24/2009] [Indexed: 10/20/2022]
Abstract
Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.
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Affiliation(s)
- Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
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Schmidt S, Gerasimova A, Kondrashov FA, Adzuhbei IA, Kondrashov AS, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genet 2008; 4:e1000281. [PMID: 19043566 PMCID: PMC2583910 DOI: 10.1371/journal.pgen.1000281] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Accepted: 10/27/2008] [Indexed: 12/04/2022] Open
Abstract
Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human–chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites. Mutations occur in some sites in the genome more frequently than in others. Similarly, mutations in some sites have greater consequences than in others. The effect of mutations might not be independent of the frequency with which mutations occur. Indeed, sites where mutations happen frequently will be preserved if the effects of these mutations are severe or will otherwise be allowed to mutate if there are no consequences for the organism. We compared both human–chimpanzee differences and sequence variation among humans in protein coding genes. We found that highly mutable nucleotide sites, such as the dinucleotide CpG, are on average more important and more frequently preserved by natural selection. Using this information, together with other features such as sequence conservation, opens a new perspective to predict the effect of human mutations, including their potential involvement in diseases.
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Affiliation(s)
- Steffen Schmidt
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anna Gerasimova
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Fyodor A. Kondrashov
- Section on Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ivan A. Adzuhbei
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexey S. Kondrashov
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (ASK); (SS)
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ASK); (SS)
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Assis R, Kondrashov AS, Koonin EV, Kondrashov FA. Nested genes and increasing organizational complexity of metazoan genomes. Trends Genet 2008; 24:475-8. [PMID: 18774620 DOI: 10.1016/j.tig.2008.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 07/24/2008] [Accepted: 08/01/2008] [Indexed: 10/21/2022]
Abstract
The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.
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Affiliation(s)
- Raquel Assis
- Center for Computational Medicine and Biology and the Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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Donaldson ZR, Kondrashov FA, Putnam A, Bai Y, Stoinski TL, Hammock EAD, Young LJ. Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene. BMC Evol Biol 2008; 8:180. [PMID: 18573213 PMCID: PMC2483724 DOI: 10.1186/1471-2148-8-180] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 06/23/2008] [Indexed: 11/29/2022] Open
Abstract
Background The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5' flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5' flanking region of AVPR1A contains a tandem duplication of two ~350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT)25 microsatellite; the second block, DupB, has a complex (CT)4-(TT)-(CT)8-(GT)24 polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior.
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Popadin KY, Mamirova LA, Kondrashov FA. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics 2007; 8:441. [PMID: 17999775 PMCID: PMC2206058 DOI: 10.1186/1471-2105-8-441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 11/14/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. DESCRIPTION We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. CONCLUSION We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.
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Affiliation(s)
- Konstantin Yu Popadin
- Institute for Information Transmission Problems RAS, Bolshoi Karetny pereulok 19, Moscow.
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Abstract
BACKGROUND Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only a small number of possible states. RESULTS We characterize parallelism in evolution of coding sequences in three four-species sets of genomes of mammals, Drosophila, and yeasts. Each such set contains two independent evolutionary paths, which we call paths I and II. An amino acid replacement which occurred along path I also occurs along path II with the probability 50-80% of that expected under selective neutrality. Thus, the per site rate of parallel evolution of proteins is several times higher than their average rate of evolution, but still lower than the rate of evolution of neutral sequences. This deficit may be caused by changes in the fitness landscape, leading to a replacement being possible along path I but not along path II. However, constant, weak selection assumed by the nearly neutral model of evolution appears to be a more likely explanation. Then, the average coefficient of selection associated with an amino acid replacement, in the units of the effective population size, must exceed approximately 0.4, and the fraction of effectively neutral replacements must be below approximately 30%. At a majority of evolvable amino acid sites, only a relatively small number of different amino acids is permitted. CONCLUSION High, but below-neutral, rates of parallel amino acid replacements suggest that a majority of amino acid replacements that occur in evolution are subject to weak, but non-trivial, selection, as predicted by Ohta's nearly-neutral theory.
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Affiliation(s)
- Georgii A Bazykin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetny pereulok 19, Moscow, 127994, Russia
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Fyodor A Kondrashov
- Section on Ecology, Behavior and Evolution, University of California at San Diego, La Jolla, CA 92093, USA
| | - Michael Brudno
- Department of Computer Science and Banting & Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3J4, Canada
| | - Alexander Poliakov
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Inna Dubchak
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Alexey S Kondrashov
- Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA
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Plotnikova OV, Kondrashov FA, Vlasov PK, Grigorenko AP, Ginter EK, Rogaev EI. Conversion and compensatory evolution of the gamma-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. Am J Hum Genet 2007; 81:32-43. [PMID: 17564961 PMCID: PMC1950927 DOI: 10.1086/518616] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 03/30/2007] [Indexed: 11/03/2022] Open
Abstract
We identified a mutation in the CRYGD gene (P23S) of the gamma-crystallin gene cluster that is associated with a polymorphic congenital cataract that occurs with frequency of approximately 0.3% in a human population. To gain insight into the molecular mechanism of the pathogenesis of gamma-crystallin isoforms, we undertook an evolutionary analysis of the available mammalian and newly obtained primate sequences of the gamma-crystallin genes. The cataract-associated serine at site 23 corresponds to the ancestral state, since it was found in CRYGD of a lower primate and all the surveyed nonprimate mammals. Crystallin proteins include two structurally similar domains, and substitutions in mammalian CRYGD protein at site 23 of the first domain were always associated with substitutions in the structurally reciprocal sites 109 and 136 of the second domain. These data suggest that the cataractogenic effect of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly by amino acid changes in a distal domain. We also found that gene conversion was a factor in the evolution of the gamma-crystallin gene cluster throughout different mammalian clades. The high rate of gene conversion observed between the functional CRYGD gene and two primate gamma-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled with a surprising finding of apparent negative selection in primate pseudogenes suggest a deleterious impact of recently derived pseudogenes involved in gene conversion in the gamma-crystallin gene cluster.
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Affiliation(s)
- Olga V Plotnikova
- Laboratory of Molecular Brain Genetics, Research Center of Mental Health, Russian Academy of Medical Sciences, and Lomonosov Moscow State University, Moscow, Russia
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Kondrashov FA, Gurbich TA, Vlasov PK. Selection for functional uniformity of tuf duplicates in gamma-proteobacteria. Trends Genet 2007; 23:215-8. [PMID: 17383049 DOI: 10.1016/j.tig.2007.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 02/14/2007] [Accepted: 03/07/2007] [Indexed: 10/23/2022]
Abstract
Having an extra copy of a gene is thought to provide some functional redundancy, which results in a higher rate of evolution in duplicated genes. In this article, we estimate the impact of gene duplication on the selection of tuf paralogs, and we find that in the absence of gene conversion, tuf paralogs have evolved significantly slower than when gene conversion has been a factor in their evolution. Thus, tuf gene copies evolve under a selective pressure that ensures their functional uniformity, and gene conversion reduces selection against amino acid substitutions that affect the function of the encoded protein, EF-Tu.
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Affiliation(s)
- Fyodor A Kondrashov
- Section on Ecology, Behavior and Evolution, Division of Biological Sciences, University of California at San Diego, 2218 Muir Biology Building, La Jolla, CA 92093, USA.
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Kondrashov FA, Koonin EV, Morgunov IG, Finogenova TV, Kondrashova MN. Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct 2006; 1:31. [PMID: 17059607 PMCID: PMC1630690 DOI: 10.1186/1745-6150-1-31] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 10/23/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. RESULTS Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. CONCLUSION The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.
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Affiliation(s)
- Fyodor A Kondrashov
- Section on Ecology, Behavior and Evolution, Division of Biological Sciences, University of California at San Diego, 2218 Muir Biology Building, La Jolla, CA 92093, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Igor G Morgunov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russian Federation
| | - Tatiana V Finogenova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russian Federation
| | - Marie N Kondrashova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation
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Babenko VN, Basu MK, Kondrashov FA, Rogozin IB, Koonin EV. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer 2006; 6:36. [PMID: 16469093 PMCID: PMC1431556 DOI: 10.1186/1471-2407-6-36] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2005] [Accepted: 02/09/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. METHODS A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues. RESULTS We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. CONCLUSION The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during tumorigenic somatic evolution.
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Affiliation(s)
- Vladimir N Babenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
| | - Malay K Basu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
| | - Fyodor A Kondrashov
- Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
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Rogaev EI, Moliaka YK, Malyarchuk BA, Kondrashov FA, Derenko MV, Chumakov I, Grigorenko AP. Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol 2006; 4:e73. [PMID: 16448217 PMCID: PMC1360101 DOI: 10.1371/journal.pbio.0040073] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 01/10/2006] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.
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Affiliation(s)
- Evgeny I Rogaev
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
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Kondrashov FA, Ogurtsov AY, Kondrashov AS. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. J Theor Biol 2005; 240:616-26. [PMID: 16343547 DOI: 10.1016/j.jtbi.2005.10.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 10/26/2005] [Accepted: 10/27/2005] [Indexed: 11/24/2022]
Abstract
The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is approximately 10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is approximately 30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s approximately 0.25/Ne approximately 10(-5), where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries approximately 10(7) suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.
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Affiliation(s)
- Fyodor A Kondrashov
- Section of Ecology, Behavior and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0346, USA.
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Abstract
New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10(-9)-10(-10) per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.
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Affiliation(s)
- Fyodor A Kondrashov
- Rybka Research Institute, 25138 Woodfield School Rd., Gaithersburg, MD 20882, USA
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Yampolsky LY, Kondrashov FA, Kondrashov AS. Distribution of the strength of selection against amino acid replacements in human proteins. Hum Mol Genet 2005; 14:3191-201. [PMID: 16174645 DOI: 10.1093/hmg/ddi350] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The impact of an amino acid replacement on the organism's fitness can vary from lethal to selectively neutral and even, in rare cases, beneficial. Substantial data are available on either pathogenic or acceptable replacements. However, the whole distribution of coefficients of selection against individual replacements is not known for any organism. To ascertain this distribution for human proteins, we combined data on pathogenic missense mutations, on human non-synonymous SNPs and on human-chimpanzee divergence of orthologous proteins. Fractions of amino acid replacements which reduce fitness by >10(-2), 10(-2)-10(-4), 10(-4)-10(-5) and <10(-5) are 25, 49, 14 and 12%, respectively. On average, the strength of selection against a replacement is substantially higher when chemically dissimilar amino acids are involved, and the Grantham's index of a replacement explains 35% of variance in the average logarithm of selection coefficients associated with different replacements. Still, the impact of a replacement depends on its context within the protein more than on its own nature. Reciprocal replacements are often associated with rather different selection coefficients, in particular, replacements of non-polar amino acids with polar ones are typically much more deleterious than replacements in the opposite direction. However, differences between evolutionary fluxes of reciprocal replacements are only weakly correlated with the differences between the corresponding selection coefficients.
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Affiliation(s)
- Lev Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37614-1710, USA
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Abstract
Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify approximately 90% of all known pathogenic mutations as deleterious together with only approximately 30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least approximately 30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively.
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Affiliation(s)
- Fyodor A Kondrashov
- Section on Ecology, Behavior and Evolution, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA.
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Kondrashov FA. [The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus]. Biofizika 2005; 50:396-403. [PMID: 15977827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The case of the convergent loss of the D-hairpin in mitochondrial cysteine tRNA of the nine-banded armadillo Dasypus novemcinctus is described. This evolutionary event sheds light on the molecular structure-function relationship and on the effect of this relationship on the processes of evolution of biopolymers and macromolecules.
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