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Ajay A, Begum T, Arya A, Kumar K, Ahmad S. Global and local genomic features together modulate the spontaneous single nucleotide mutation rate. Comput Biol Chem 2024; 112:108107. [PMID: 38875896 DOI: 10.1016/j.compbiolchem.2024.108107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 04/23/2024] [Accepted: 05/17/2024] [Indexed: 06/16/2024]
Abstract
Spontaneous mutations are evolutionary engines as they generate variants for the evolutionary downstream processes that give rise to speciation and adaptation. Single nucleotide mutations (SNM) are the most abundant type of mutations among them. Here, we perform a meta-analysis to quantify the influence of selected global genomic parameters (genome size, genomic GC content, genomic repeat fraction, number of coding genes, gene count, and strand bias in prokaryotes) and local genomic features (local GC content, repeat content, CpG content and the number of SNM at CpG islands) on spontaneous SNM rates across the tree of life (prokaryotes, unicellular eukaryotes, multicellular eukaryotes) using wild-type sequence data in two different taxon classification systems. We find that the spontaneous SNM rates in our data are correlated with many genomic features in prokaryotes and unicellular eukaryotes irrespective of their sample sizes. On the other hand, only the number of coding genes was correlated with the spontaneous SNM rates in multicellular eukaryotes primarily contributed by vertebrates data. Considering local features, we notice that local GC content and CpG content significantly were correlated with the spontaneous SNM rates in the unicellular eukaryotes, while local repeat fraction is an important feature in prokaryotes and certain specific uni- and multi-cellular eukaryotes. Such predictive features of the spontaneous SNM rates often support non-linear models as the best fit compared to the linear model. We also observe that the strand asymmetry in prokaryotes plays an important role in determining the spontaneous SNM rates but the SNM spectrum does not.
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Affiliation(s)
- Akash Ajay
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Tina Begum
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Ajay Arya
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Krishan Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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2
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Maghrebi M, Marín-Sanz M, Miras Moreno MB, Quagliata G, Caldo F, Gatti N, Mannino G, Pesenti M, D'Alessandro S, Nocito FF, Lucini L, Sestili F, Astolfi S, Barro F, Vigani G. The drought-induced plasticity of mineral nutrients contributes to drought tolerance discrimination in durum wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109077. [PMID: 39213946 DOI: 10.1016/j.plaphy.2024.109077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/06/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Drought is a major challenge for the cultivation of durum wheat, a crucial crop for global food security. Plants respond to drought by adjusting their mineral nutrient profiles to cope with water scarcity, showing the importance of nutrient plasticity for plant acclimation and adaptation to diverse environments. Therefore, it is essential to understand the genetic basis of mineral nutrient profile plasticity in durum wheat under drought stress to select drought-tolerant varieties. The research study investigated the responses of different durum wheat genotypes to severe drought stress at the seedling stage. The study employed an ionomic, molecular, biochemical and physiological approach to shed light on distinct behaviors among different genotypes. The drought tolerance of SVEMS16, SVEVO, and BULEL was related to their capacity of maintaining or increasing nutrient's accumulation, while the limited nutrient acquisition capability of CRESO and S.CAP likely resulted in their susceptibility to drought. The study highlighted the importance of macronutrients such as SO42-, NO3-, PO43-, and K+ in stress resilience and identified variant-containing genes potentially influencing nutritional variations under drought. These findings provide valuable insights for further field studies to assess the drought tolerance of durum wheat genotypes across various growth stages, ultimately ensuring food security and sustainable production in the face of changing environmental conditions.
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Affiliation(s)
- Moez Maghrebi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Centro dell'Innovazione, Università degli studi di Torino, Turin, Italy
| | - Miriam Marín-Sanz
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, 14004-Córdoba, Spain
| | - Maria Begona Miras Moreno
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, 14004-Córdoba, Spain
| | - Giulia Quagliata
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Francesco Caldo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Centro dell'Innovazione, Università degli studi di Torino, Turin, Italy
| | - Noemi Gatti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Centro dell'Innovazione, Università degli studi di Torino, Turin, Italy
| | - Giuseppe Mannino
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Centro dell'Innovazione, Università degli studi di Torino, Turin, Italy
| | - Michele Pesenti
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, 20133 Milano, Italy
| | - Stefano D'Alessandro
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Centro dell'Innovazione, Università degli studi di Torino, Turin, Italy
| | - Fabio Francesco Nocito
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, 20133 Milano, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Universita Cattolica del Sacro Cuore, I-29122, Piacenza, Italy
| | - Francesco Sestili
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Stefania Astolfi
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Francisco Barro
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, 14004-Córdoba, Spain
| | - Gianpiero Vigani
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Centro dell'Innovazione, Università degli studi di Torino, Turin, Italy.
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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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Ostroverkhova D, Tyryshkin K, Beach AK, Moore EA, Masoudi-Sobhanzadeh Y, Barbari SR, Rogozin IB, Shaitan KV, Panchenko AR, Shcherbakova PV. DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors. Cell Rep 2024; 43:113655. [PMID: 38219146 PMCID: PMC10830898 DOI: 10.1016/j.celrep.2023.113655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/07/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
Alterations in the exonuclease domain of DNA polymerase ε cause ultramutated cancers. These cancers accumulate AGA>ATA transversions; however, their genomic features beyond the trinucleotide motifs are obscure. We analyze the extended DNA context of ultramutation using whole-exome sequencing data from 524 endometrial and 395 colorectal tumors. We find that G>T transversions in POLE-mutant tumors predominantly affect sequences containing at least six consecutive purines, with a striking preference for certain positions within polypurine tracts. Using this signature, we develop a machine-learning classifier to identify tumors with hitherto unknown POLE drivers and validate two drivers, POLE-E978G and POLE-S461L, by functional assays in yeast. Unlike other pathogenic variants, the E978G substitution affects the polymerase domain of Pol ε. We further show that tumors with POLD1 drivers share the extended signature of POLE ultramutation. These findings expand the understanding of ultramutation mechanisms and highlight peculiar mutagenic properties of polypurine tracts in the human genome.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Annette K Beach
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yosef Masoudi-Sobhanzadeh
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada.
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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Xiao Y, Xiao Z, Liu L, Ma Y, Zhao H, Wu Y, Huang J, Xu P, Liu J, Li J. Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfish Oplegnathus fasciatus. Gigascience 2024; 13:giae045. [PMID: 39028586 PMCID: PMC11258905 DOI: 10.1093/gigascience/giae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/21/2024] [Accepted: 06/22/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND The use of sex-specific molecular markers has become a prominent method in enhancing fish production and economic value, as well as providing a foundation for understanding the complex molecular mechanisms involved in fish sex determination. Over the past decades, research on male and female sex identification has predominantly employed molecular biology methodologies such as restriction fragment length polymorphism, random amplification of polymorphic DNA, simple sequence repeat, and amplified fragment length polymorphism. The emergence of high-throughput sequencing technologies, particularly Illumina, has led to the utilization of single nucleotide polymorphism and insertion/deletion variants as significant molecular markers for investigating sex identification in fish. The advancement of sex-controlled breeding encounters numerous challenges, including the inefficiency of current methods, intricate experimental protocols, high costs of development, elevated rates of false positives, marker instability, and cumbersome field-testing procedures. Nevertheless, the emergence and swift progress of PacBio high-throughput sequencing technology, characterized by its long-read output capabilities, offers novel opportunities to overcome these obstacles. FINDINGS Utilizing male/female assembled genome information in conjunction with short-read sequencing data survey and long-read PacBio sequencing data, a catalog of large-segment (>100 bp) insertion/deletion genetic variants was generated through a genome-wide variant site-scanning approach with bidirectional comparisons. The sequence tagging sites were ranked based on the long-read depth of the insertion/deletion site, with markers exhibiting lower long-read depth being considered more effective for large-segment deletion variants. Subsequently, a catalog of bulk primers and simulated PCR for the male/female variant loci was developed, incorporating primer design for the target region and electronic PCR (e-PCR) technology. The Japanese parrotfish (Oplegnathus fasciatus), belonging to the Oplegnathidae family within the Centrarchiformes order, holds significant economic value as a rocky reef fish indigenous to East Asia. The criteria for rapid identification of male and female differences in Japanese parrotfish were established through agarose gel electrophoresis, which revealed 2 amplified bands for males and 1 amplified band for females. A high-throughput identification catalog of sex-specific markers was then constructed using this method, resulting in the identification of 3,639 (2,786 INS/853 DEL, ♀ as reference) and 3,672 (2,876 INS/833 DEL, ♂ as reference) markers in conjunction with 1,021 and 894 high-quality genetic sex identification markers, respectively. Sixteen differential loci were randomly chosen from the catalog for validation, with 11 of them meeting the criteria for male/female distinctions. The implementation of cost-effective and efficient technological processes would facilitate the rapid advancement of genetic breeding through expediting the high-throughput development of sex genetic markers for various species. CONCLUSIONS Our study utilized assembled genome information from male and female individuals obtained from PacBio, in addition to data from short-read sequencing data survey and long-read PacBio sequencing data. We extensively employed genome-wide variant site scanning and identification, high-throughput primer design of target regions, and e-PCR batch amplification, along with statistical analysis and ranking of the long-read depth of the variant sites. Through this integrated approach, we successfully compiled a catalog of large insertion/deletion sites (>100 bp) in both male and female Japanese parrotfish.
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Affiliation(s)
- Yongshuang Xiao
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhizhong Xiao
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Weihai Hao Huigan Marine Biotechnology Co., Weihai, 26449, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd, East Lake High-Tech Zone, Wuhan, 430073, China
| | - Yuting Ma
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Haixia Zhao
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yanduo Wu
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jinwei Huang
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Pingrui Xu
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jing Liu
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jun Li
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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Horton JS, Taylor TB. Mutation bias and adaptation in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37943288 DOI: 10.1099/mic.0.001404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Genetic mutation, which provides the raw material for evolutionary adaptation, is largely a stochastic force. However, there is ample evidence showing that mutations can also exhibit strong biases, with some mutation types and certain genomic positions mutating more often than others. It is becoming increasingly clear that mutational bias can play a role in determining adaptive outcomes in bacteria in both the laboratory and the clinic. As such, understanding the causes and consequences of mutation bias can help microbiologists to anticipate and predict adaptive outcomes. In this review, we provide an overview of the mechanisms and features of the bacterial genome that cause mutational biases to occur. We then describe the environmental triggers that drive these mechanisms to be more potent and outline the adaptive scenarios where mutation bias can synergize with natural selection to define evolutionary outcomes. We conclude by describing how understanding mutagenic genomic features can help microbiologists predict areas sensitive to mutational bias, and finish by outlining future work that will help us achieve more accurate evolutionary forecasts.
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Affiliation(s)
- James S Horton
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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Yu G, Liu Y, Li Z, Deng S, Wu Z, Zhang X, Chen W, Yang J, Chen X, Yang JR. Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect. Nat Commun 2023; 14:5853. [PMID: 37730811 PMCID: PMC10511511 DOI: 10.1038/s41467-023-41550-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
The transcriptional intermediates of RNAs fold into secondary structures with multiple regulatory roles, yet the details of such cotranscriptional RNA folding are largely unresolved in eukaryotes. Here, we present eSPET-seq (Structural Probing of Elongating Transcripts in eukaryotes), a method to assess the cotranscriptional RNA folding in Saccharomyces cerevisiae. Our study reveals pervasive structural transitions during cotranscriptional folding and overall structural similarities between nascent and mature RNAs. Furthermore, a combined analysis with genome-wide R-loop and mutation rate approximations provides quantitative evidence for the antimutator effect of nascent RNA folding through competitive inhibition of the R-loops, known to facilitate transcription-associated mutagenesis. Taken together, we present an experimental evaluation of cotranscriptional folding in eukaryotes and demonstrate the antimutator effect of nascent RNA folding. These results suggest genome-wide coupling between the processing and transmission of genetic information through RNA folding.
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Affiliation(s)
- Gongwang Yu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yao Liu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zizhang Li
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuyun Deng
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhuoxing Wu
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaoyu Zhang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wenbo Chen
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Junnan Yang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaoshu Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
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9
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Carvajal-Garcia J, Samadpour AN, Hernandez Viera AJ, Merrikh H. Oxidative stress drives mutagenesis through transcription-coupled repair in bacteria. Proc Natl Acad Sci U S A 2023; 120:e2300761120. [PMID: 37364106 PMCID: PMC10318952 DOI: 10.1073/pnas.2300761120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
In bacteria, mutations lead to the evolution of antibiotic resistance, which is one of the main public health problems of the twenty-first century. Therefore, determining which cellular processes most frequently contribute to mutagenesis, especially in cells that have not been exposed to exogenous DNA damage, is critical. Here, we show that endogenous oxidative stress is a key driver of mutagenesis and the subsequent development of antibiotic resistance. This is the case for all classes of antibiotics and highly divergent species tested, including patient-derived strains. We show that the transcription-coupled repair pathway, which uses the nucleotide excision repair proteins (TC-NER), is responsible for endogenous oxidative stress-dependent mutagenesis and subsequent evolution. This suggests that a majority of mutations arise through transcription-associated processes rather than the replication fork. In addition to determining that the NER proteins play a critical role in mutagenesis and evolution, we also identify the DNA polymerases responsible for this process. Our data strongly suggest that cooperation between three different mutagenic DNA polymerases, likely at the last step of TC-NER, is responsible for mutagenesis and evolution. Overall, our work identifies a highly conserved pathway that drives mutagenesis due to endogenous oxidative stress, which has broad implications for all diseases of evolution, including antibiotic resistance development.
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Affiliation(s)
- Juan Carvajal-Garcia
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232
| | | | | | - Houra Merrikh
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232
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10
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Schlosser G. Rebuilding ships while at sea-Character individuality, homology, and evolutionary innovation. J Morphol 2023; 284:e21522. [PMID: 36282954 PMCID: PMC10100095 DOI: 10.1002/jmor.21522] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/15/2022] [Accepted: 10/15/2022] [Indexed: 11/05/2022]
Abstract
How novel traits originate in evolution is still one of the most perplexing questions in Evolutionary Biology. Building on a previous account of evolutionary innovation, I here propose that evolutionary novelties are those individualized characters that are not homologous to any characters in the ancestor. To clarify this definition, I here provide a detailed analysis of the concepts of "character individuality" and "homology" first, before addressing their role for our understanding of evolutionary innovation. I will argue (1) that functional as well as structural considerations are important for character individualization; and (2) that compositional (structural) and positional homology need to be clearly distinguished to properly describe the evolutionary transformations of hierarchically structured characters. My account will therefore integrate functional and structural perspectives and put forward a new multi-level view of character identity and transformation.
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Affiliation(s)
- Gerhard Schlosser
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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11
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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12
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Kiyama T, Chen CK, Zhang A, Mao CA. Differential Susceptibility of Retinal Neurons to the Loss of Mitochondrial Biogenesis Factor Nrf1. Cells 2022; 11:cells11142203. [PMID: 35883647 PMCID: PMC9321222 DOI: 10.3390/cells11142203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The retina, the accessible part of the central nervous system, has served as a model system to study the relationship between energy utilization and metabolite supply. When the metabolite supply cannot match the energy demand, retinal neurons are at risk of death. As the powerhouse of eukaryotic cells, mitochondria play a pivotal role in generating ATP, produce precursors for macromolecules, maintain the redox homeostasis, and function as waste management centers for various types of metabolic intermediates. Mitochondrial dysfunction has been implicated in the pathologies of a number of degenerative retinal diseases. It is well known that photoreceptors are particularly vulnerable to mutations affecting mitochondrial function due to their high energy demand and susceptibility to oxidative stress. However, it is unclear how defective mitochondria affect other retinal neurons. Nuclear respiratory factor 1 (Nrf1) is the major transcriptional regulator of mitochondrial biogenesis, and loss of Nrf1 leads to defective mitochondria biogenesis and eventually cell death. Here, we investigated how different retinal neurons respond to the loss of Nrf1. We provide in vivo evidence that the disruption of Nrf1-mediated mitochondrial biogenesis results in a slow, progressive degeneration of all retinal cell types examined, although they present different sensitivity to the deletion of Nrf1, which implicates differential energy demand and utilization, as well as tolerance to mitochondria defects in different neuronal cells. Furthermore, transcriptome analysis on rod-specific Nrf1 deletion uncovered a previously unknown role of Nrf1 in maintaining genome stability.
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Affiliation(s)
- Takae Kiyama
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
| | - Ching-Kang Chen
- Department of Ophthalmology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Annie Zhang
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
| | - Chai-An Mao
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
- The MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Correspondence:
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13
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Shoemaker WR, Polezhaeva E, Givens KB, Lennon JT. Seed banks alter the molecular evolutionary dynamics of Bacillus subtilis. Genetics 2022; 221:iyac071. [PMID: 35511143 PMCID: PMC9157070 DOI: 10.1093/genetics/iyac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/23/2022] [Indexed: 11/14/2022] Open
Abstract
Fluctuations in the availability of resources constrain the growth and reproduction of individuals, which subsequently affects the evolution of their respective populations. Many organisms contend with such fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e. a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. The ability of these bacteria to enter a dormant state increased the accumulation of genetic diversity over time and altered the trajectory of mutations, findings that were recapitulated using simulations based on a mathematical model of evolutionary dynamics. While the ability to form a seed bank did not alter the degree of negative selection, we found that it consistently altered the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank can affect the direction and rate of molecular evolution over an extended evolutionary timescale.
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Affiliation(s)
- William R Shoemaker
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA 90095, USA
| | | | - Kenzie B Givens
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA 90095, USA
- Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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14
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Ji YW, Ahn H, Shin KJ, Kim TI, Seo KY, Stulting RD, Kim EK. De Novo L509P Mutation of the TGFBI Gene Associated with Slit-Lamp Findings of Lattice Corneal Dystrophy Type IIIA. J Clin Med 2022; 11:jcm11113055. [PMID: 35683443 PMCID: PMC9181583 DOI: 10.3390/jcm11113055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Mutations of the transforming growth factor-β-induced (TGFBI) gene produce various types of corneal dystrophy. Here, we report a novel de novo L509P mutation not located in a known hot spot of the transforming growth factor-β-induced (TGFBI) gene and its clinical phenotype, which resembles that of lattice corneal dystrophy type IIIA (LCD IIIA). Case presentation: A 36-year-old man (proband) visited our clinic due to decreased visual acuity with intermittent ocular irritation in conjunction with painful recurrent erosions in both eyes for 10 years. Molecular genetic analyses revealed a TGFBI L509P mutation (c.1526T>C) in the proband and one of his sons. Interestingly, neither TGFBI mutations nor corneal abnormalities were detected in either of the proband’s biological parents, indicating the occurrence of a de novo L509P mutation. Clinical examinations, including slit-lamp retro-illumination and Fourier-domain anterior segment optical coherence tomography (FD-OCT), revealed gray deposits in the anterior stroma and deeper refractile lines extending from limbus to limbus in both corneas of the proband, consistent with a diagnosis of LCD IIIA. Superficial diffuse haze and surface irregularity were observed in conjunction with corneal erosions and visual impairment, necessitating phototherapeutic keratectomy (PTK). A 60 μm PTK of the Bowman layer and anterior stroma of the proband’s left eye was performed following the removal of the epithelium in order to remove superficial corneal opacities. His BCVA improved from 20/400 to 20/50 at postoperative week 8 and was maintained for 45 months. Pinhole-corrected VA was 20/20 at the last visit, and corneal opacities had not recurred. Conclusions: An inheritable de novo mutation of L509P in the TGFBI gene can produce severe LCD IIIA, which can be successfully treated with OCT-guided PRK.
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Affiliation(s)
- Yong Woo Ji
- Department of Ophthalmology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin 16995, Korea;
| | - Hyunmin Ahn
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (H.A.); (T.-i.K.); (K.Y.S.)
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Tae-im Kim
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (H.A.); (T.-i.K.); (K.Y.S.)
- Corneal Dystrophy Research Institute, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyoung Yul Seo
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (H.A.); (T.-i.K.); (K.Y.S.)
| | | | - Eung Kweon Kim
- Corneal Dystrophy Research Institute, Yonsei University College of Medicine, Seoul 03722, Korea
- Saevit Eye Hospital, Goyang 10447, Korea
- Correspondence:
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15
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Lin RR, Li XY, Weng QH, Zhou XX, Zheng FY, Cai JP. A study on UHPLC-MS/MS analyses of DNA and RNA oxidative damage metabolites in patients with cervical carcinoma: 8-oxoG in urine as a potential biomarker of cervical carcinoma. Heliyon 2022; 8:e09321. [PMID: 35520626 PMCID: PMC9061785 DOI: 10.1016/j.heliyon.2022.e09321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/05/2022] [Accepted: 04/20/2022] [Indexed: 11/25/2022] Open
Abstract
Objective Methods Results Conclusions
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16
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Jiang H, Yan B, Meng Z, Zhang L, Lei H, Luo J. The MDM2 Single-Nucleotide Polymorphism T309G Is Associated With the Development of Epimacular Membranes. Front Cell Dev Biol 2022; 10:841660. [PMID: 35359434 PMCID: PMC8963840 DOI: 10.3389/fcell.2022.841660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: To investigate the role of the mouse double minute 2 (MDM2) gene single-nucleotide polymorphism (SNP) T309G in the development of epimacular membranes (EMMs) by analyzing the genotype distribution and consistency of the polymorphism in paired membrane-blood samples. Methods: This was a cross–sectional genetic association study of patients with proliferative vitreoretinopathy (PVR) or EMMs. PVR membranes (PVRMs), internal limiting membranes (ILMs) (PVR-ILMs) and blood samples (PVR-blood) from patients with PVR, and EMMs, EMM-ILMs and EMM-blood from patients with EMMs were collected. The genotype of all samples was determined by Sanger sequencing. Sex composition, mean age, the genotype distribution of MDM2 T309G, the allelic frequency of the MDM2 SNP309 G allele (% G) and the somatic mutation rate at the MDM2 T309G locus (% M) were analyzed and compared. The PVR and healthy Chinese donor groups were used as controls for different comparisons. Results: The EMM group of 62 patients was older than the PVR group of 61 patients by an average of 8.87 years (p < 0.0001), but the two groups were statistically similar in the sex composition (p = 0.1754). Importantly, G allele carriers were at a higher risk of developing EMMs than non-G allele carriers (p = 0.0479; OR = 2.047). Moreover, EMM-blood exhibited a significantly higher % G than blood samples from healthy Chinese donors (EMM-blood: 56.78%, donors: 45.61%; p = 0.0256; OR = 1.567). Regarding membrane-blood consistency, % M was significantly different between PVRMs and EMMs (PVRMs: 2.63%, EMMs: 21.57%; p = 0.0097; OR = 10.18) but not between different types of ILMs (PVR-ILMs: 18.18%, EMM-ILMs: 29.17%; p = 0.6855). Furthermore, EMMs (p = 0.0053; OR = 8.250) and EMM-ILMs (p = 0.0233; OR = 14.40) from patients with preoperative macular holes were more predisposed toward somatic mutations at the MDM2 T309G locus than those from patients without preoperative macular holes. Conclusions:MDM2 T309G is associated with the development of EMMs. Herein, the MDM2 SNP309 G allele is first reported as an associated factor of EMMs in a Chinese population. In addition, EMMs and ILMs are genetically unstable at the MDM2 T309G locus, especially when complicated with preoperative macular holes.
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Affiliation(s)
- Heng Jiang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Bin Yan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhishang Meng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lusi Zhang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hetian Lei
- Shenzhen Eye Institute, Shenzhen Eye Hospital, Jinan University, Shenzhen, China
- *Correspondence: Hetian Lei, , Jing Luo,
| | - Jing Luo
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Hetian Lei, , Jing Luo,
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17
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OUP accepted manuscript. FEMS Yeast Res 2022; 22:6574410. [DOI: 10.1093/femsyr/foac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
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18
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Pu Y, Yin H, Dong C, Xiang H, Wu W, Zhou B, Du D, Chen Y, Xu H. Sono-Controllable and ROS-Sensitive CRISPR-Cas9 Genome Editing for Augmented/Synergistic Ultrasound Tumor Nanotherapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2104641. [PMID: 34536041 DOI: 10.1002/adma.202104641] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/10/2021] [Indexed: 12/17/2022]
Abstract
The potential of the cluster regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9)-based therapeutic genome editing is severely hampered by the difficulties in precise regulation of the in vivo activity of the CRISPR-Cas9 system. Herein, sono-controllable and reactive oxygen species (ROS)-sensitive sonosensitizer-integrated metal-organic frameworks (MOFs), denoted as P/M@CasMTH1, are developed for augmented sonodynamic therapy (SDT) efficacy using the genome-editing technology. P/M@CasMTH1 nanoparticles comprise singlet oxygen (1 O2 )-generating MOF structures anchored with CRISPR-Cas9 systems via 1 O2 -cleavable linkers, which serve not only as a delivery vector of CRISPR-Cas9 targeting MTH1, but also as a sonoregulator to spatiotemporally activate the genome editing. P/M@CasMTH1 escapes from the lysosomes, harvests the ultrasound (US) energy and converts it into abundant 1 O2 to induce SDT. The generated ROS subsequently trigger cleavage of ROS-responsive thioether bonds, thus inducing controllable release of the CRISPR-Cas9 system and initiation of genome editing. The genomic disruption of MTH1 conspicuously augments the therapeutic efficacy of SDT by destroying the self-defense system in tumor cells, thereby causing cellular apoptosis and tumor suppression. This therapeutic strategy for synergistic MTH1 disruption and abundant 1 O2 generation provides a paradigm for augmenting SDT efficacy based on the emerging nanomedicine-enabled genome-editing technology.
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Affiliation(s)
- Yinying Pu
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai Engineering Research Center of Ultrasound Diagnosis and Treatment, National Clinical Research Center for Interventional Medicine, Shanghai, 200072, China
| | - Haohao Yin
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai Engineering Research Center of Ultrasound Diagnosis and Treatment, National Clinical Research Center for Interventional Medicine, Shanghai, 200072, China
| | - Caihong Dong
- Department of Ultrasound, Zhongshan Hospital, Fudan University, and Shanghai Institute of Medical Imaging, Shanghai, 200032, P. R. China
| | - Huijing Xiang
- Shanghai Engineering Research Center of Organ Repair, Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Wencheng Wu
- State Key Lab of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, 200050, P. R. China
| | - Bangguo Zhou
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai Engineering Research Center of Ultrasound Diagnosis and Treatment, National Clinical Research Center for Interventional Medicine, Shanghai, 200072, China
| | - Dou Du
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai Engineering Research Center of Ultrasound Diagnosis and Treatment, National Clinical Research Center for Interventional Medicine, Shanghai, 200072, China
| | - Yu Chen
- Shanghai Engineering Research Center of Organ Repair, Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Huixiong Xu
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai Engineering Research Center of Ultrasound Diagnosis and Treatment, National Clinical Research Center for Interventional Medicine, Shanghai, 200072, China
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19
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Schlingmann KP, Jouret F, Shen K, Nigam A, Arjona FJ, Dafinger C, Houillier P, Jones DP, Kleinerüschkamp F, Oh J, Godefroid N, Eltan M, Güran T, Burtey S, Parotte MC, König J, Braun A, Bos C, Ibars Serra M, Rehmann H, Zwartkruis FJ, Renkema KY, Klingel K, Schulze-Bahr E, Schermer B, Bergmann C, Altmüller J, Thiele H, Beck BB, Dahan K, Sabatini D, Liebau MC, Vargas-Poussou R, Knoers NV, Konrad M, de Baaij JH. mTOR-Activating Mutations in RRAGD Are Causative for Kidney Tubulopathy and Cardiomyopathy. J Am Soc Nephrol 2021; 32:2885-2899. [PMID: 34607910 PMCID: PMC8806087 DOI: 10.1681/asn.2021030333] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/07/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Over the last decade, advances in genetic techniques have resulted in the identification of rare hereditary disorders of renal magnesium and salt handling. Nevertheless, approximately 20% of all patients with tubulopathy lack a genetic diagnosis. METHODS We performed whole-exome and -genome sequencing of a patient cohort with a novel, inherited, salt-losing tubulopathy; hypomagnesemia; and dilated cardiomyopathy. We also conducted subsequent in vitro functional analyses of identified variants of RRAGD, a gene that encodes a small Rag guanosine triphosphatase (GTPase). RESULTS In eight children from unrelated families with a tubulopathy characterized by hypomagnesemia, hypokalemia, salt wasting, and nephrocalcinosis, we identified heterozygous missense variants in RRAGD that mostly occurred de novo. Six of these patients also had dilated cardiomyopathy and three underwent heart transplantation. We identified a heterozygous variant in RRAGD that segregated with the phenotype in eight members of a large family with similar kidney manifestations. The GTPase RagD, encoded by RRAGD, plays a role in mediating amino acid signaling to the mechanistic target of rapamycin complex 1 (mTORC1). RagD expression along the mammalian nephron included the thick ascending limb and the distal convoluted tubule. The identified RRAGD variants were shown to induce a constitutive activation of mTOR signaling in vitro. CONCLUSIONS Our findings establish a novel disease, which we call autosomal dominant kidney hypomagnesemia (ADKH-RRAGD), that combines an electrolyte-losing tubulopathy and dilated cardiomyopathy. The condition is caused by variants in the RRAGD gene, which encodes Rag GTPase D; these variants lead to an activation of mTOR signaling, suggesting a critical role of Rag GTPase D for renal electrolyte handling and cardiac function.
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Affiliation(s)
- Karl P. Schlingmann
- Department of General Pediatrics, University Children’s Hospital, Münster, Germany
| | - François Jouret
- Division of Nephrology, Department of Internal Medicine, University of Liège Hospital, Liège, Belgium,Interdisciplinary Group of Applied Genoproteomics, Cardiovascular Sciences, University of Liège, Liège, Belgium
| | - Kuang Shen
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Anukrati Nigam
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Francisco J. Arjona
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claudia Dafinger
- Department of Pediatrics and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany,Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Pascal Houillier
- Cordeliers Research Center, Centre National de la Recherche Scientifique (CNRS), ERL8228, Institut National de la Santé et de la Recherche Médicale (INSERM), Sorbonne University, University of Paris, Paris, France,Department of Physiology, Assistance Publique-Hôpitaux de Paris (AP-HP), European Hospital Georges Pompidou, Paris, France,Reference Center for Hereditary Renal Diseases in Children and Adults (MARHEA), Paris, France
| | - Deborah P. Jones
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Felix Kleinerüschkamp
- Department of Pediatric Cardiology, University Children’s Hospital, Münster, Germany
| | - Jun Oh
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nathalie Godefroid
- Division of Pediatric Nephrology, Saint-Luc University Clinics, Catholic University of Louvain, Brussels, Belgium
| | - Mehmet Eltan
- Department of Pediatric Endocrinology and Diabetes, School of Medicine, Marmara University, Istanbul, Turkey
| | - Tülay Güran
- Department of Pediatric Endocrinology and Diabetes, School of Medicine, Marmara University, Istanbul, Turkey
| | - Stéphane Burtey
- Center for Nephrology and Renal Transplantation, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille University, Marseille, France
| | - Marie-Christine Parotte
- Division of Nephrology-Dialysis, Department of Internal Medicine, CHR Verviers East Belgium, Verviers, Belgium
| | - Jens König
- Department of General Pediatrics, University Children’s Hospital, Münster, Germany
| | - Alina Braun
- Department of Pediatrics and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany,Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Caro Bos
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Ibars Serra
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Holger Rehmann
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Fried J.T. Zwartkruis
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kirsten Y. Renkema
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Eric Schulze-Bahr
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, Münster, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany,CECAD, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Carsten Bergmann
- Limbach Genetics, Medizinische Genetik Mainz, Mainz, Germany,Division of Nephrology, Department of Medicine, University Hospital Freiburg, Breisgau, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Bodo B. Beck
- Institute of Human Genetics, University Hospital Cologne and University of Cologne, Faculty of Medicine, Cologne, Germany,Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany,Center for Rare Diseases, Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Karin Dahan
- Center of Human Genetics, Gosselies, Belgium,Division of Nephrology, Saint-Luc University Clinics, Catholic University of Louvain, Brussels, Belgium
| | - David Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Max C. Liebau
- Department of Pediatrics and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany,Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany,Center for Rare Diseases, Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Rosa Vargas-Poussou
- Department of Genetics, AP-HP, European Hospital Georges Pompidou, Paris, France
| | - Nine V.A.M. Knoers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martin Konrad
- Department of General Pediatrics, University Children’s Hospital, Münster, Germany
| | - Jeroen H.F. de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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20
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Lin J, Liu X, Lu Z, Huang S, Wu S, Yu W, Liu Y, Zheng X, Huang X, Sun Q, Qiao Y, Liu Z. Modeling a cataract disorder in mice with prime editing. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:494-501. [PMID: 34589272 PMCID: PMC8463286 DOI: 10.1016/j.omtn.2021.06.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/25/2021] [Indexed: 11/19/2022]
Abstract
Prime editing enables efficient introduction of targeted transversions, insertions, and deletions in mammalian cells and several organisms. However, genetic disease models with base deletions by prime editing have not yet been reported in mice. Here, we successfully generate a mouse model with a cataract disorder through microinjection of prime editor 3 (PE3) plasmids to efficiently induce targeted single-base deletion. Notably, a generated mouse with a high G-deletion rate (38.2%) displays a nuclear cataract phenotype; the PE3-induced deletions in mutant mice achieve high rates of germline transmission to their progenies, with phenotypic inheritance of cataract. Our data propose that modeling a genetic disease with a single nucleotide deletion in mice can be achieved with prime genome editing in vivo.
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Affiliation(s)
- Jianxiang Lin
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xingchen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongyang Lu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Susu Wu
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Wenxia Yu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoguo Zheng
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunbo Qiao
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
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21
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Lennon JT, den Hollander F, Wilke-Berenguer M, Blath J. Principles of seed banks and the emergence of complexity from dormancy. Nat Commun 2021; 12:4807. [PMID: 34376641 PMCID: PMC8355185 DOI: 10.1038/s41467-021-24733-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/02/2021] [Indexed: 02/07/2023] Open
Abstract
Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.
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Affiliation(s)
- Jay T. Lennon
- grid.411377.70000 0001 0790 959XIndiana University, Department of Biology, Bloomington, USA
| | - Frank den Hollander
- grid.5132.50000 0001 2312 1970Universiteit Leiden, Mathematical Institute, Leiden, Netherlands
| | - Maite Wilke-Berenguer
- grid.7468.d0000 0001 2248 7639Humboldt-Universität zu Berlin, Institute of Mathematics, Berlin, Germany
| | - Jochen Blath
- grid.6734.60000 0001 2292 8254Technische Universität Berlin, Institute of Mathematics, Berlin, Germany
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22
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The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life (Basel) 2021; 11:life11080773. [PMID: 34440517 PMCID: PMC8398314 DOI: 10.3390/life11080773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
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23
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Orłowska R, Zimny J, Bednarek PT. Copper Ions Induce DNA Sequence Variation in Zygotic Embryo Culture-Derived Barley Regenerants. FRONTIERS IN PLANT SCIENCE 2021; 11:614837. [PMID: 33613587 PMCID: PMC7889974 DOI: 10.3389/fpls.2020.614837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/22/2020] [Indexed: 05/18/2023]
Abstract
In vitro tissue culture could be exploited to study cellular mechanisms that induce sequence variation. Altering the metal ion composition of tissue culture medium affects biochemical pathways involved in tissue culture-induced variation. Copper ions are involved in the mitochondrial respiratory chain and Yang cycle. Copper ions may participate in oxidative mutations, which may contribute to DNA sequence variation. Silver ions compete with copper ions to bind to the complex IV subunit of the respiratory chain, thus affecting the Yang cycle and DNA methylation. The mechanisms underlying somaclonal variation are unknown. In this study, we evaluated embryo-derived barley regenerants obtained from a single double-haploid plant via embryo culture under varying copper and silver ion concentrations and different durations of in vitro culture. Morphological variation among regenerants and the donor plant was not evaluated. Methylation-sensitive Amplified Fragment Length Polymorphism analysis of DNA samples showed DNA methylation pattern variation in CG and CHG (H = A, C, or T) sequence contexts. Furthermore, modification of in vitro culture conditions explained DNA sequence variation, demethylation, and de novo methylation in the CHG context, as indicated by analysis of variance. Linear regression indicated that DNA sequence variation was related to de novo DNA methylation in the CHG context. Mediation analysis showed the role of copper ions as a mediator of sequence variation in the CHG context. No other contexts showed a significant sequence variation in mediation analysis. Silver ions did not act as a mediator between any methylation contexts and sequence variation. Thus, incorporating copper ions in the induction medium should be treated with caution.
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Affiliation(s)
- Renata Orłowska
- Plant Breeding and Acclimatization Institute–National Research Institute, Błonie, Poland
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24
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Tagel M, Ilves H, Leppik M, Jürgenstein K, Remme J, Kivisaar M. Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp. Microorganisms 2020; 9:microorganisms9010025. [PMID: 33374637 PMCID: PMC7822408 DOI: 10.3390/microorganisms9010025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudouridines are known to be important for optimal translation. In this study we demonstrate an unexpected link between pseudouridylation of tRNA and mutation frequency in Pseudomonas species. We observed that the lack of pseudouridylation activity of pseudouridine synthases TruA or RluA elevates the mutation frequency in Pseudomonas putida 3 to 5-fold. The absence of TruA but not RluA elevates mutation frequency also in Pseudomonas aeruginosa. Based on the results of genetic studies and analysis of proteome data, the mutagenic effect of the pseudouridylation deficiency cannot be ascribed to the involvement of error-prone DNA polymerases or malfunctioning of DNA repair pathways. In addition, although the deficiency in TruA-dependent pseudouridylation made P. putida cells more sensitive to antimicrobial compounds that may cause oxidative stress and DNA damage, cultivation of bacteria in the presence of reactive oxygen species (ROS)-scavenging compounds did not eliminate the mutator phenotype. Thus, the elevated mutation frequency in the absence of tRNA pseudouridylation could be the result of a more specific response or, alternatively, of a cumulative effect of several small effects disturbing distinct cellular functions, which remain undetected when studied independently. This work suggests that pseudouridines link the translation machinery to mutation frequency.
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Affiliation(s)
- Mari Tagel
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | | | | | | | - Jaanus Remme
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | - Maia Kivisaar
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
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25
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Bednarek PT, Zebrowski J, Orłowska R. Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture. Int J Mol Sci 2020; 21:E5770. [PMID: 32796744 PMCID: PMC7461140 DOI: 10.3390/ijms21165770] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Tissue culture is an essential tool for the regeneration of uniform plant material. However, tissue culture conditions can be a source of abiotic stress for plants, leading to changes in the DNA sequence and methylation patterns. Despite the growing evidence on biochemical processes affected by abiotic stresses, how these altered biochemical processes affect DNA sequence and methylation patterns remains largely unknown. In this study, the methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach was used to investigate de novo methylation, demethylation, and sequence variation in barley regenerants derived by anther culture. Additionally, we used Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy to identify the spectral features of regenerants, which were then analyzed by mediation analysis. The infrared spectrum ranges (710-690 and 1010-940 cm-1) identified as significant in the mediation analysis were most likely related to β-glucans, cellulose, and S-adenosyl-L-methionine (SAM). Additionally, the identified compounds participated as predictors in moderated mediation analysis, explaining the role of demethylation of CHG sites (CHG_DMV) in in vitro tissue culture-induced sequence variation, depending on the duration of tissue culture. The data demonstrate that ATR-FTIR spectroscopy is a useful tool for studying the biochemical compounds that may affect DNA methylation patterns and sequence variation, if combined with quantitative characteristics determined using metAFLP molecular markers and mediation analysis. The role of β-glucans, cellulose, and SAM in DNA methylation, and in cell wall, mitochondria, and signaling, are discussed to highlight the putative cellular mechanisms involved in sequence variation.
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Affiliation(s)
- Piotr T. Bednarek
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland;
| | - Jacek Zebrowski
- Institute of Biology and Biotechnology, University of Rzeszow, Al. Rejtana 16c A, 35-959 Rzeszow, Poland;
| | - Renata Orłowska
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland;
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26
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Le LAT, Chang PY, Ando S, Conrad TM, Nunose S, Sakai A, Uefune H, Furukohri A, Akiyama MT, Maki H. Nutritional conditions and oxygen concentration affect spontaneous occurrence of homologous recombination events but not spontaneous mutagenesis in Escherichia coli. Genes Genet Syst 2020; 95:85-93. [PMID: 32389919 DOI: 10.1266/ggs.19-00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Effects of environmental factors for growth of Escherichia coli on spontaneous mutagenesis and homologous recombination events are described. By analyzing rifampicin-resistant (Rifr) mutation frequencies in an E. coli strain lacking MutM and MutY repair enzymes, which suppress base substitution mutations caused by 8-oxoguanine (7,8 dihydro-8-oxoguanine; 8-oxoG) in DNA, we examined levels of oxidative DNA damage produced in normally growing cells. The level of 8-oxoG DNA damage was about 9- and 63-fold higher in cells grown in M9-glucose and M9-glycerol media, respectively, than in those grown in LB medium. We also found that about 14-fold more 8-oxoG DNA damage was produced in cells grown in about 0.1% oxygen than in those grown in the normal atmosphere. However, Rifr mutation frequency in wild-type cells was unchanged in such different growth conditions, suggesting that the capacity of repair mechanisms is sufficient to suppress mutations caused by 8-oxoG even at very high levels in cells growing in the particular conditions. On the other hand, the frequency of spontaneous homologous recombination events in wild-type E. coli cells varied with different growth conditions. When cells were grown in M9-glucose and M9-glycerol media, the spontaneous recombination frequency increased to about 4.3- and 7.3-fold, respectively, higher than that in LB medium. Likewise, the spontaneous recombination frequency was about 3.5-fold higher in cells growing in the hypoxic condition than in cells growing in the atmosphere. When cells were grown in anaerobic conditions, the recombination frequency decreased to half of that in the atmosphere. These data indicated that spontaneous homologous recombination is highly responsive to environmental factors such as nutrition and oxygen concentration.
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Affiliation(s)
- Lan Anh Thi Le
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Phooi Yee Chang
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Sayaka Ando
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Thomas M Conrad
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Shohei Nunose
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Akiko Sakai
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Haruka Uefune
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Asako Furukohri
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Masahiro Tatsumi Akiyama
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Hisaji Maki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
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Abstract
Frameshifts in protein coding sequences are widely perceived as resulting in either nonfunctional or even deleterious protein products. Indeed, frameshifts typically lead to markedly altered protein sequences and premature stop codons. By analyzing complete proteomes from all three domains of life, we demonstrate that, in contrast, several key physicochemical properties of protein sequences exhibit significant robustness against +1 and -1 frameshifts. In particular, we show that hydrophobicity profiles of many protein sequences remain largely invariant upon frameshifting. For example, over 2,900 human proteins exhibit a Pearson's correlation coefficient R between the hydrophobicity profiles of the original and the +1-frameshifted variants greater than 0.7, despite an average sequence identity between the two of only 6.5% in this group. We observe a similar effect for protein sequence profiles of affinity for certain nucleobases as well as protein sequence profiles of intrinsic disorder. Finally, analysis of significance and optimality demonstrates that frameshift stability is embedded in the structure of the universal genetic code and may have contributed to shaping it. Our results suggest that frameshifting may be a powerful evolutionary mechanism for creating new proteins with vastly different sequences, yet similar physicochemical properties to the proteins from which they originate.
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28
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Kivisaar M. Mutation and Recombination Rates Vary Across Bacterial Chromosome. Microorganisms 2019; 8:microorganisms8010025. [PMID: 31877811 PMCID: PMC7023495 DOI: 10.3390/microorganisms8010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure which is established by binding of the nucleoid-associated proteins (NAPs) and other proteins. This review gives an overview of recent findings indicating that the mutagenic and recombination processes in bacteria vary at different chromosomal positions. Involvement of NAPs and other possible mechanisms in these regional differences are discussed. Variations in mutation and recombination rates across the bacterial chromosome may have implications in the evolution of bacteria.
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Affiliation(s)
- Maia Kivisaar
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
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29
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Hu JJ, Chen Y, Li ZH, Peng SY, Sun Y, Zhang XZ. Augment of Oxidative Damage with Enhanced Photodynamic Process and MTH1 Inhibition for Tumor Therapy. NANO LETTERS 2019; 19:5568-5576. [PMID: 31262183 DOI: 10.1021/acs.nanolett.9b02112] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Tumor cells adapt to reactive oxygen species (ROS) attacking by launching DNA damage repairing mechanisms such as nucleotide pool sanitizing enzyme mutt homologue 1 (MTH1) to mitigate the oxidatively induced DNA lesions, which could greatly limit the therapeutic efficiency of current oxidation therapy. Here, an amplified oxidative damage strategy for tumor therapy was proposed that was focused not only on the enhancement of ROS generation but also the inhibition of subsequent MTH1 enzyme activity simultaneously. In our formulation, mesoporous silica-coated Prussian blue nanoplatforms (PB@MSN) with excellent catalase-like activity and drug loading capability were employed to encapsulate MTH1 inhibitor TH287, followed by the modification of tetraphenylporphrin zinc (Zn-Por) via metallo-supramolecular coordination (PMPT), where Zn-Por behaved as photodynamic and fluorescence imaging agents, as well as acid-responsive gatekeepers. The intelligent PMPT nanosystems could induce the decomposition of H2O2 to relieve the hypoxic tumor environment, thus elevating the generation of singlet oxygen for improved oxidative damage. In the meantime, controllable-released TH287 from pores could hinder MTH1-mediated damage repairing process and aggravate oxidative damage, thereby resulting in cellular toxicity as well as tumor growth inhibition.
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Affiliation(s)
- Jing-Jing Hu
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Ying Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Zi-Hao Li
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Si-Yuan Peng
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Yunxia Sun
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
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30
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Bando M, Kinugawa T, Manabe Y, Masugi M, Nakajima H, Suzuki K, Tsunoyama Y, Wada T, Toki H. Study of mutation from DNA to biological evolution. Int J Radiat Biol 2019; 95:1390-1403. [DOI: 10.1080/09553002.2019.1606957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Masako Bando
- Research Center for Nuclear Physics, Osaka University, Osaka, Japan
| | - Tetsuhiro Kinugawa
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Yuichiro Manabe
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Miwako Masugi
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Hiroo Nakajima
- Institute for Radiation Sciences, Osaka University, Suita, Japan
| | - Kazuyo Suzuki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Tsunoyama
- Radioisotope Research Center, Agency for Health, Safety and Environment Kyoto University, Kyoto, Japan
| | - Takahiro Wada
- Department of Pure and Applied Physics, Faculty of Engineering Science, Kansai University, Suita, Japan
| | - Hiroshi Toki
- Research Center for Nuclear Physics, Osaka University, Osaka, Japan
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31
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Oka S, Hayashi M, Taguchi K, Hidaka M, Tsuzuki T, Sekiguchi M. ROS control in human iPS cells reveals early events in spontaneous carcinogenesis. Carcinogenesis 2019; 41:36-43. [DOI: 10.1093/carcin/bgz081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/03/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sugako Oka
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Michio Hayashi
- Section of Biochemistry, Fukuoka Dental College, Fukuoka, Japan
| | - Kenichi Taguchi
- Cancer Pathology Laboratory, Department of Cancer Biology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Masumi Hidaka
- Department of Physiological Science and Molecular Biology, Fukuoka Dental College, Fukuoka, Japan
| | - Teruhisa Tsuzuki
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Mutsuo Sekiguchi
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
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32
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Kamolsukyeunyong W, Ruengphayak S, Chumwong P, Kusumawati L, Chaichoompu E, Jamboonsri W, Saensuk C, Phoonsiri K, Toojinda T, Vanavichit A. Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population. RICE (NEW YORK, N.Y.) 2019; 12:16. [PMID: 30888525 PMCID: PMC6424995 DOI: 10.1186/s12284-019-0274-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/25/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal. RESULTS We used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78-7.78 Mb (QBPH4.1) and 15.22-17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations. CONCLUSION On the one hand, HPs of OsLekRK2-3, OsSTPS2, and BPH32 determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population, BPH9 together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.
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Affiliation(s)
- Wintai Kamolsukyeunyong
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Siriphat Ruengphayak
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Pantharika Chumwong
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Lucia Kusumawati
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Ekawat Chaichoompu
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
- Interdisciplinary Graduate Program in Genetic Engineering and Bioinformatics, Kasetsart University, Chatuchak, Bangkok Thailand
| | - Watchareewan Jamboonsri
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Chatree Saensuk
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Kunyakarn Phoonsiri
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Theerayut Toojinda
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
- Integrative Crop Biotechnology and Management Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Apichart Vanavichit
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
- Agronomy Department, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom Thailand
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Article Effect and Mechanism of Ganoderma lucidum Polysaccharides on Human Fibroblasts and Skin Wound Healing in Mice. Chin J Integr Med 2018; 25:203-209. [DOI: 10.1007/s11655-018-3060-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2018] [Indexed: 10/27/2022]
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Wang M, Ji Y, Feng S, Liu C, Xiao Z, Wang X, Wang Y, Xia G. The non-random patterns of genetic variation induced by asymmetric somatic hybridization in wheat. BMC PLANT BIOLOGY 2018; 18:244. [PMID: 30332989 PMCID: PMC6192298 DOI: 10.1186/s12870-018-1474-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Asymmetric somatic hybridization is an efficient crop breeding approach by introducing several exogenous chromatin fragments, which leads to genomic shock and therefore induces genome-wide genetic variation. However, the fundamental question concerning the genetic variation such as whether it occurs randomly and suffers from selection pressure remains unknown. RESULTS Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Both nucleotide substitutions and indels (insertions and deletions) had lower frequencies in coding sequences than in un-translated regions. The frequencies of nucleotide substitutions and indels were both comparable between chromosomes with and without introgressed fragments. Nucleotide substitutions distributed unevenly and were preferential to indel-flanking sequences, and the frequency of nucleotide substitutions at 5'-flanking sequences of indels was obviously higher in chromosomes with introgressed fragments than in those without exogenous fragment. Nucleotide substitutions and indels both had various frequencies among seven groups of allelic chromosomes, and the frequencies of nucleotide substitutions were strongly negatively correlative to those of indels. Among three sets of genomes, the frequencies of nucleotide substitutions and indels were both heterogeneous, and the frequencies of nucleotide substitutions exhibited drastically positive correlation to those of indels. CONCLUSIONS Our work demonstrates that the genetic variation induced by asymmetric somatic hybridization is attributed to both whole genomic shock and local chromosomal shock, which is a predetermined and non-random genetic event being closely associated with selection pressure. Asymmetric somatic hybrids provide a worthwhile model to further investigate the nature of genomic shock induced genetic variation.
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Affiliation(s)
- Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Yujie Ji
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shiting Feng
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Chun Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Zhen Xiao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Xiaoping Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050041 China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
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35
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Duan C, Huan Q, Chen X, Wu S, Carey LB, He X, Qian W. Reduced intrinsic DNA curvature leads to increased mutation rate. Genome Biol 2018; 19:132. [PMID: 30217230 PMCID: PMC6138893 DOI: 10.1186/s13059-018-1525-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis. RESULTS Here, we use a combination of synthetic genes and sequences of thousands of isolated yeast colonies to show that intrinsic DNA curvature is a major cis determinant of mutation rate. Mutation rate negatively correlates with DNA curvature within genes, and a 10% decrease in curvature results in a 70% increase in mutation rate. Consistently, both yeast and humans accumulate mutations in regions with small curvature. We further show that this effect is due to differences in the intrinsic mutation rate, likely due to differences in mutagen sensitivity and not due to differences in the local activity of DNA repair. CONCLUSIONS Our study establishes a framework for understanding the cis properties of DNA sequence in modulating the local mutation rate and identifies a novel causal source of non-uniform mutation rates across the genome.
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Affiliation(s)
- Chaorui Duan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoshu Chen
- Human Genome Research Institute and Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shaohuan Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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36
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GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2018; 115:E7109-E7118. [PMID: 29987035 PMCID: PMC6064992 DOI: 10.1073/pnas.1807334115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The chromosomes of many eukaryotes have regions of high GC content interspersed with regions of low GC content. In the yeast Saccharomyces cerevisiae, high-GC regions are often associated with high levels of meiotic recombination. In this study, we constructed URA3 genes that differ substantially in their base composition [URA3-AT (31% GC), URA3-WT (43% GC), and URA3-GC (63% GC)] but encode proteins with the same amino acid sequence. The strain with URA3-GC had an approximately sevenfold elevated rate of ura3 mutations compared with the strains with URA3-WT or URA3-AT About half of these mutations were single-base substitutions and were dependent on the error-prone DNA polymerase ζ. About 30% were deletions or duplications between short (5-10 base) direct repeats resulting from DNA polymerase slippage. The URA3-GC gene also had elevated rates of meiotic and mitotic recombination relative to the URA3-AT or URA3-WT genes. Thus, base composition has a substantial effect on the basic parameters of genome stability and evolution.
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37
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Benedetti D, Lopes Alderete B, de Souza CT, Ferraz Dias J, Niekraszewicz L, Cappetta M, Martínez-López W, Da Silva J. DNA damage and epigenetic alteration in soybean farmers exposed to complex mixture of pesticides. Mutagenesis 2018; 33:87-95. [PMID: 29244183 DOI: 10.1093/mutage/gex035] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Exposure to pesticides can trigger genotoxic and mutagenic processes through different pathways. However, epidemiological studies are scarce, and further work is needed to find biomarkers sensitive to the health of exposed populations. Considering that there are few evaluations of soybean farmers, the aim of this study was to assess the effects of human exposure to complex mixtures of pesticides. The alkaline comet assay modified with restriction enzyme (hOGG1: human 8-oxoguanine DNA glycosylase) was used to detect oxidised guanine, and compared with the buccal micronucleus cytome assay, global methylation, haematological parameters, biochemical analyses (serum glutamic oxaloacetic transaminase, serum glutamic pyruvic transaminase, gamma-glutamyl-transferase and butyrylcholinesterase), and particle-induced X-ray emission (PIXE) for the analysis of inorganic elements. Farm workers (n = 137) exposed to different types of pesticides were compared with a non-exposed reference group (control; n = 83). Results of the enzyme-modified comet assay suggest oxidation of guanine in DNA generated by pesticides exposure. It was observed that DNA damage (comet assay and micronucleus test) was significantly increased in exposed individuals compared to the unexposed group. The micronucleus test demonstrated elimination of nuclear material by budding, defective cytokinesis and dead cells. Occupationally exposed individuals also showed genomic hypermethylation of DNA, which correlated with micronucleus frequency. No differences were detected regarding the haematological and biochemical parameters. Finally, significantly higher concentrations of Al and P were observed in the urine of the soybean farmers. DNA damage could be a consequence of the ability of the complex mixture, including Al and P, to cause oxidative damage. These data indicate that persistent genetic instability associated with hypermethylation of DNA in soybean workers after long-term exposure to a low-level to pesticides mixtures may be critical for the development of adverse health effects such as cancer.
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Affiliation(s)
- Danieli Benedetti
- Laboratory of Genetic Toxicology, PPGBioSaúde and PPGGTA, Lutheran University of Brazil (ULBRA), Av. Farroupilha, Prédio, Canoas, RS, Brazil
| | - Barbara Lopes Alderete
- Laboratory of Genetic Toxicology, PPGBioSaúde and PPGGTA, Lutheran University of Brazil (ULBRA), Av. Farroupilha, Prédio, Canoas, RS, Brazil
| | - Claudia Telles de Souza
- Laboratory of Environmental Chemistry and Oleochemistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Johnny Ferraz Dias
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Liana Niekraszewicz
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Mónica Cappetta
- Laboratory of Genetic Epidemiology, Genetics Department, Medicine School, Universidad de la República, Montevideo, Uruguay
| | - Wilner Martínez-López
- Department of Genetic Toxicology and Chromosome Pathology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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Huizinga J, Stanley KO, Clune J. The Emergence of Canalization and Evolvability in an Open-Ended, Interactive Evolutionary System. ARTIFICIAL LIFE 2018; 24:157-181. [PMID: 30485140 DOI: 10.1162/artl_a_00263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Many believe that an essential component for the discovery of the tremendous diversity in natural organisms was the evolution of evolvability, whereby evolution speeds up its ability to innovate by generating a more adaptive pool of offspring. One hypothesized mechanism for evolvability is developmental canalization, wherein certain dimensions of variation become more likely to be traversed and others are prevented from being explored (e.g., offspring tend to have similar-size legs, and mutations affect the length of both legs, not each leg individually). While ubiquitous in nature, canalization is rarely reported in computational simulations of evolution, which deprives us of in silico examples of canalization to study and raises the question of which conditions give rise to this form of evolvability. Answering this question would shed light on why such evolvability emerged naturally, and it could accelerate engineering efforts to harness evolution to solve important engineering challenges. In this article, we reveal a unique system in which canalization did emerge in computational evolution. We document that genomes entrench certain dimensions of variation that were frequently explored during their evolutionary history. The genetic representation of these organisms also evolved to be more modular and hierarchical than expected by chance, and we show that these organizational properties correlate with increased fitness. Interestingly, the type of computational evolutionary experiment that produced this evolvability was very different from traditional digital evolution in that there was no objective, suggesting that open-ended, divergent evolutionary processes may be necessary for the evolution of evolvability.
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Affiliation(s)
- Joost Huizinga
- University of Wyoming, Department of Computer Science, Evolving AI Lab.
- Uber, Uber AI Labs.
| | - Kenneth O Stanley
- University of Central Florida, Department of Computer Science, EPLex.
- Uber, Uber AI Labs.
| | - Jeff Clune
- University of Wyoming, Department of Computer Science, Evolving AI Lab.
- Uber, Uber AI Labs.
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39
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Krašovec R, Richards H, Gifford DR, Hatcher C, Faulkner KJ, Belavkin RV, Channon A, Aston E, McBain AJ, Knight CG. Spontaneous mutation rate is a plastic trait associated with population density across domains of life. PLoS Biol 2017; 15:e2002731. [PMID: 28837573 PMCID: PMC5570273 DOI: 10.1371/journal.pbio.2002731] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/21/2017] [Indexed: 12/21/2022] Open
Abstract
Rates of random, spontaneous mutation can vary plastically, dependent upon the environment. Such plasticity affects evolutionary trajectories and may be adaptive. We recently identified an inverse plastic association between mutation rate and population density at 1 locus in 1 species of bacterium. It is unknown how widespread this association is, whether it varies among organisms, and what molecular mechanisms of mutagenesis or repair are required for this mutation-rate plasticity. Here, we address all 3 questions. We identify a strong negative association between mutation rate and population density across 70 years of published literature, comprising hundreds of mutation rates estimated using phenotypic markers of mutation (fluctuation tests) from all domains of life and viruses. We test this relationship experimentally, determining that there is indeed density-associated mutation-rate plasticity (DAMP) at multiple loci in both eukaryotes and bacteria, with up to 23-fold lower mutation rates at higher population densities. We find that the degree of plasticity varies, even among closely related organisms. Nonetheless, in each domain tested, DAMP requires proteins scavenging the mutagenic oxidised nucleotide 8-oxo-dGTP. This implies that phenotypic markers give a more precise view of mutation rate than previously believed: having accounted for other known factors affecting mutation rate, controlling for population density can reduce variation in mutation-rate estimates by 93%. Widespread DAMP, which we manipulate genetically in disparate organisms, also provides a novel trait to use in the fight against the evolution of antimicrobial resistance. Such a prevalent environmental association and conserved mechanism suggest that mutation has varied plastically with population density since the early origins of life.
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Affiliation(s)
- Rok Krašovec
- Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
| | - Huw Richards
- Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
| | - Danna R. Gifford
- Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
| | - Charlie Hatcher
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Katy J. Faulkner
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Roman V. Belavkin
- School of Engineering and Information Sciences, Middlesex University, London, United Kingdom
| | - Alastair Channon
- School of Computing and Mathematics, Keele University, Keele, United Kingdom
| | - Elizabeth Aston
- School of Computing and Mathematics, Keele University, Keele, United Kingdom
| | - Andrew J. McBain
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Christopher G. Knight
- Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
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40
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Finn TJ, Shewaramani S, Leahy SC, Janssen PH, Moon CD. Dynamics and genetic diversification of Escherichia coli during experimental adaptation to an anaerobic environment. PeerJ 2017; 5:e3244. [PMID: 28480139 PMCID: PMC5419217 DOI: 10.7717/peerj.3244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/29/2017] [Indexed: 01/25/2023] Open
Abstract
Background Many bacteria are facultative anaerobes, and can proliferate in both anoxic and oxic environments. Under anaerobic conditions, fermentation is the primary means of energy generation in contrast to respiration. Furthermore, the rates and spectra of spontaneous mutations that arise during anaerobic growth differ to those under aerobic growth. A long-term selection experiment was undertaken to investigate the genetic changes that underpin how the facultative anaerobe, Escherichia coli, adapts to anaerobic environments. Methods Twenty-one populations of E. coli REL4536, an aerobically evolved 10,000th generation descendent of the E. coli B strain, REL606, were established from a clonal ancestral culture. These were serially sub-cultured for 2,000 generations in a defined minimal glucose medium in strict aerobic and strict anaerobic environments, as well as in a treatment that fluctuated between the two environments. The competitive fitness of the evolving lineages was assessed at approximately 0, 1,000 and 2,000 generations, in both the environment of selection and the alternative environment. Whole genome re-sequencing was performed on random colonies from all lineages after 2,000-generations. Mutations were identified relative to the ancestral genome, and based on the extent of parallelism, traits that were likely to have contributed towards adaptation were inferred. Results There were increases in fitness relative to the ancestor among anaerobically evolved lineages when tested in the anaerobic environment, but no increases were found in the aerobic environment. For lineages that had evolved under the fluctuating regime, relative fitness increased significantly in the anaerobic environment, but did not increase in the aerobic environment. The aerobically-evolved lineages did not increase in fitness when tested in either the aerobic or anaerobic environments. The strictly anaerobic lineages adapted more rapidly to the anaerobic environment than did the fluctuating lineages. Two main strategies appeared to predominate during adaptation to the anaerobic environment: modification of energy generation pathways, and inactivation of non-essential functions. Fermentation pathways appeared to alter through selection for mutations in genes such as nadR, adhE, dcuS/R, and pflB. Mutations were frequently identified in genes for presumably dispensable functions such as toxin-antitoxin systems, prophages, virulence and amino acid transport. Adaptation of the fluctuating lineages to the anaerobic environments involved mutations affecting traits similar to those observed in the anaerobically evolved lineages. Discussion There appeared to be strong selective pressure for activities that conferred cell yield advantages during anaerobic growth, which include restoring activities that had previously been inactivated under long-term continuous aerobic evolution of the ancestor.
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Affiliation(s)
- Thomas J Finn
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand.,New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sonal Shewaramani
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand.,New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States of America
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Christina D Moon
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
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41
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Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol 2016; 17:241. [PMID: 27894357 PMCID: PMC5125044 DOI: 10.1186/s13059-016-1110-1] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.
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Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Alexander Hoischen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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42
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Gao Z, Wyman MJ, Sella G, Przeworski M. Interpreting the Dependence of Mutation Rates on Age and Time. PLoS Biol 2016; 14:e1002355. [PMID: 26761240 PMCID: PMC4711947 DOI: 10.1371/journal.pbio.1002355] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/11/2015] [Indexed: 01/06/2023] Open
Abstract
Mutations can originate from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that arise between replication cycles and are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell divisions, providing a framework for understanding how mutation rates depend on sex, age, and cell division rate. We show that the accrual of mutations should track cell divisions not only when mutations are replicative in origin but also when they are non-replicative and repaired efficiently. One implication is that observations from diverse fields that to date have been interpreted as pointing to a replicative origin of most mutations could instead reflect the accumulation of mutations arising from endogenous reactions or exogenous mutagens. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, unless life history traits co-vary, the phylogenetic “molecular clock” should not be expected to run steadily across species. Modeling how the source of mutations relates to their rate of accumulation with age, sex, and number of cell divisions helps to explain perplexing observations about germline and somatic mutations. We relate how mutations arise to how they accumulate in different sexes, with age and with cell division. This model provides a single framework within which to interpret emerging results from evolutionary biology, human genetics, and cancer genetics. We show that the accrual of mutations should track cell divisions not only when mutations originate during DNA replication but also when they arise through non-replicative mechanisms and are repaired efficiently. This realization means that previous observations of correlations between mutation and cell division rates actually provide little support to the commonly held belief that most germline and somatic mutations arise from replication errors. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, without covariation in life history traits, the phylogenetic “molecular clock” should not be expected to run at constant rates across species.
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Affiliation(s)
- Ziyue Gao
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (ZG); (MP)
| | - Minyoung J. Wyman
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail: (ZG); (MP)
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43
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Brovarets' OO, Hovorun DM. Proton tunneling in the A∙T Watson-Crick DNA base pair: myth or reality? J Biomol Struct Dyn 2015; 33:2716-20. [PMID: 26362836 DOI: 10.1080/07391102.2015.1092886] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The results and conclusions reached by Godbeer et al. in their recent work, that proton tunneling in the A∙T(WC) Watson-Crick (WC) DNA base pair occurs according to the Löwdin's (L) model, but with a small (~10(-9)) probability were critically analyzed. Here, it was shown that this finding overestimates the possibility of the proton tunneling at the A∙T(WC)↔A*∙T*(L) tautomerization, because this process cannot be implemented as a chemical reaction. Furthermore, it was outlined those biologically important nucleobase mispairs (A∙A*↔A*∙A, G∙G*↔G*∙G, T∙T*↔T*∙T, C∙C*↔C*∙C, H∙H*↔H*∙H (H - hypoxanthine)) - the players in the field of the spontaneous point mutagenesis - where the tunneling of protons is expected and for which the application of the model proposed by Godbeer et al. can be productive.
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Affiliation(s)
- Ol'ha O Brovarets'
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., 03680 Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., 03022 Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., 03680 Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., 03022 Kyiv , Ukraine
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44
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Lian K, Leiros HKS, Moe E. MutT from the fish pathogen Aliivibrio salmonicida is a cold-active nucleotide-pool sanitization enzyme with unexpectedly high thermostability. FEBS Open Bio 2015; 5:107-16. [PMID: 25737836 PMCID: PMC4338371 DOI: 10.1016/j.fob.2015.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/27/2015] [Indexed: 02/08/2023] Open
Abstract
Upon infection by pathogenic bacteria, production of reactive oxygen species (ROS) is part of the host organism's first line of defence. ROS damage a number of macromolecules, and in order to withstand such a harsh environment, the bacteria need to have well-functioning ROS scavenging and repair systems. Herein, MutT is an important nucleotide-pool sanitization enzyme, which degrades 8-oxo-dGTP and thus prevents it from being incorporated into DNA. In this context, we have performed a comparative biochemical and structural analysis of MutT from the fish pathogen Aliivibrio salmonicida (AsMutT) and the human pathogen Vibrio cholerae (VcMutT), in order to analyse their function as nucleotide sanitization enzymes and also determine possible cold-adapted properties of AsMutT. The biochemical characterisation revealed that both enzymes possess activity towards the 8-oxo-dGTP substrate, and that AsMutT has a higher catalytic efficiency than VcMutT at all temperatures studied. Calculations based on the biochemical data also revealed a lower activation energy (E a) for AsMutT compared to VcMutT, and differential scanning calorimetry experiments showed that AsMutT displayed an unexpected higher melting temperature (T m) value than VcMutT. A comparative analysis of the crystal structure of VcMutT, determined to 2.42 Å resolution, and homology models of AsMutT indicate that three unique Gly residues in loops of VcMutT, and additional long range ion-pairs in AsMutT could explain the difference in temperature stability of the two enzymes. We conclude that AsMutT is a stable, cold-active enzyme with high catalytic efficiency and reduced E a, compared to the mesophilic VcMutT.
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Affiliation(s)
- Kjersti Lian
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Elin Moe
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, The Arctic University of Norway, 9037 Tromsø, Norway ; Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. da República - EAN, 2780-157 Oeiras, Portugal
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Lewis DL, Notey JS, Chandrayan SK, Loder AJ, Lipscomb GL, Adams MWW, Kelly RM. A mutant ('lab strain') of the hyperthermophilic archaeon Pyrococcus furiosus, lacking flagella, has unusual growth physiology. Extremophiles 2014; 19:269-81. [PMID: 25472011 DOI: 10.1007/s00792-014-0712-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
A mutant ('lab strain') of the hyperthermophilic archaeon Pyrococcus furiosus DSM3638 exhibited an extended exponential phase and atypical cell aggregation behavior. Genomic DNA from the mutant culture was sequenced and compared to wild-type (WT) DSM3638, revealing 145 genes with one or more insertions, deletions, or substitutions (12 silent, 33 amino acid substitutions, and 100 frame shifts). Approximately, half of the mutated genes were transposases or hypothetical proteins. The WT transcriptome revealed numerous changes in amino acid and pyrimidine biosynthesis pathways coincidental with growth phase transitions, unlike the mutant whose transcriptome reflected the observed prolonged exponential phase. Targeted gene deletions, based on frame-shifted ORFs in the mutant genome, in a genetically tractable strain of P. furiosus (COM1) could not generate the extended exponential phase behavior observed for the mutant. For example, a putative radical SAM family protein (PF2064) was the most highly up-regulated ORF (>25-fold) in the WT between exponential and stationary phase, although this ORF was unresponsive in the mutant; deletion of this gene in P. furiosus COM1 resulted in no apparent phenotype. On the other hand, frame-shifting mutations in the mutant genome negatively impacted transcription of a flagellar biosynthesis operon (PF0329-PF0338).Consequently, cells in the mutant culture lacked flagella and, unlike the WT, showed minimal evidence of exopolysaccharide-based cell aggregation in post-exponential phase. Electron microscopy of PF0331-PF0337 deletions in P. furiosus COM1 showed that absence of flagella impacted normal cell aggregation behavior and, furthermore, indicated that flagella play a key role, beyond motility, in the growth physiology of P. furiosus.
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Affiliation(s)
- Derrick L Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, EB-1,911 Partners Way, Raleigh, NC, 27695-7905, US
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Ferenci T, Maharjan R. Mutational heterogeneity: A key ingredient of bet-hedging and evolutionary divergence? Bioessays 2014; 37:123-30. [DOI: 10.1002/bies.201400153] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Thomas Ferenci
- School of Molecular Bioscience; University of Sydney; NSW Australia
| | - Ram Maharjan
- School of Molecular Bioscience; University of Sydney; NSW Australia
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Shin HJ, Lim WK. Comparative evaluation of an electrochemical bioreporter for detecting phenolic compounds. Prep Biochem Biotechnol 2014; 46:71-7. [DOI: 10.1080/10826068.2014.979207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Oka S, Leon J, Tsuchimoto D, Sakumi K, Nakabeppu Y. MUTYH, an adenine DNA glycosylase, mediates p53 tumor suppression via PARP-dependent cell death. Oncogenesis 2014; 3:e121. [PMID: 25310643 PMCID: PMC4216901 DOI: 10.1038/oncsis.2014.35] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/15/2014] [Accepted: 08/25/2014] [Indexed: 12/12/2022] Open
Abstract
p53-regulated caspase-independent cell death has been implicated in suppression of tumorigenesis, however, the regulating mechanisms are poorly understood. We previously reported that 8-oxoguanine (8-oxoG) accumulation in nuclear DNA (nDNA) and mitochondrial DNA triggers two distinct caspase-independent cell death through buildup of single-strand DNA breaks by MutY homolog (MUTYH), an adenine DNA glycosylase. One pathway depends on poly-ADP-ribose polymerase (PARP) and the other depends on calpains. Deficiency of MUTYH causes MUTYH-associated familial adenomatous polyposis. MUTYH thereby suppresses tumorigenesis not only by avoiding mutagenesis, but also by inducing cell death. Here, we identified the functional p53-binding site in the human MUTYH gene and demonstrated that MUTYH is transcriptionally regulated by p53, especially in the p53/DNA mismatch repair enzyme, MLH1-proficient colorectal cancer-derived HCT116+Chr3 cells. MUTYH-small interfering RNA, an inhibitor for p53 or PARP suppressed cell death without an additive effect, thus revealing that MUTYH is a potential mediator of p53 tumor suppression, which is known to be upregulated by MLH1. Moreover, we found that the p53-proficient, mismatch repair protein, MLH1-proficient colorectal cancer cell line express substantial levels of MUTYH in nuclei but not in mitochondria, suggesting that 8-oxoG accumulation in nDNA triggers MLH1/PARP-dependent cell death. These results provide new insights on the molecular mechanism of tumorigenesis and potential new strategies for cancer therapies.
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Affiliation(s)
- S Oka
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - J Leon
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - D Tsuchimoto
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - K Sakumi
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - Y Nakabeppu
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
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Nakabeppu Y. Cellular levels of 8-oxoguanine in either DNA or the nucleotide pool play pivotal roles in carcinogenesis and survival of cancer cells. Int J Mol Sci 2014; 15:12543-57. [PMID: 25029543 PMCID: PMC4139859 DOI: 10.3390/ijms150712543] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/23/2014] [Accepted: 07/08/2014] [Indexed: 01/06/2023] Open
Abstract
8-Oxoguanine, a major oxidized base lesion formed by reactive oxygen species, causes G to T transversion mutations or leads to cell death in mammals if it accumulates in DNA. 8-Oxoguanine can originate as 8-oxo-dGTP, formed in the nucleotide pool, or by direct oxidation of the DNA guanine base. MTH1, also known as NUDT1, with 8-oxo-dGTP hydrolyzing activity, 8-oxoguanine DNA glycosylase (OGG1) an 8-oxoG DNA glycosylase, and MutY homolog (MUTYH) with adenine DNA glycosylase activity, minimize the accumulation of 8-oxoG in DNA; deficiencies in these enzymes increase spontaneous and induced tumorigenesis susceptibility. However, different tissue types have different tumorigenesis susceptibilities. These can be reversed by combined deficiencies in the defense systems, because cell death induced by accumulation of 8-oxoG in DNA is dependent on MUTYH, which can be suppressed by MTH1 and OGG1. In cancer cells encountering high oxidative stress levels, a high level of 8-oxo-dGTP accumulates in the nucleotide pool, and cells therefore express increased levels of MTH1 in order to eliminate 8-oxo-dGTP. Suppression of MTH1 may be an efficient strategy for killing cancer cells; however, because MTH1 and OGG1 protect normal tissues from oxidative-stress-induced cell death, it is important that MTH1 inhibition does not increase the risk of healthy tissue degeneration.
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Affiliation(s)
- Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, and Research Center for Nucleotide Pool, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan.
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Renda BA, Hammerling MJ, Barrick JE. Engineering reduced evolutionary potential for synthetic biology. MOLECULAR BIOSYSTEMS 2014; 10:1668-78. [PMID: 24556867 DOI: 10.1039/c3mb70606k] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of synthetic biology seeks to engineer reliable and predictable behaviors in organisms from collections of standardized genetic parts. However, unlike other types of machines, genetically encoded biological systems are prone to changes in their designed sequences due to mutations in their DNA sequences after these devices are constructed and deployed. Thus, biological engineering efforts can be confounded by undesired evolution that rapidly breaks the functions of parts and systems, particularly when they are costly to the host cell to maintain. Here, we explain the fundamental properties that determine the evolvability of biological systems. Then, we use this framework to review current efforts to engineer the DNA sequences that encode synthetic biology devices and the genomes of their microbial hosts to reduce their ability to evolve and therefore increase their genetic reliability so that they maintain their intended functions over longer timescales.
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Affiliation(s)
- Brian A Renda
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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