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Iyengar BR, Grandchamp A, Bornberg-Bauer E. How antisense transcripts can evolve to encode novel proteins. Nat Commun 2024; 15:6187. [PMID: 39043684 PMCID: PMC11266595 DOI: 10.1038/s41467-024-50550-3] [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: 08/30/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
Protein coding features can emerge de novo in non coding transcripts, resulting in emergence of new protein coding genes. Studies across many species show that a large fraction of evolutionarily novel non-coding RNAs have an antisense overlap with protein coding genes. The open reading frames (ORFs) in these antisense RNAs could also overlap with existing ORFs. In this study, we investigate how the evolution an ORF could be constrained by its overlap with an existing ORF in three different reading frames. Using a combination of mathematical modeling and genome/transcriptome data analysis in two different model organisms, we show that antisense overlap can increase the likelihood of ORF emergence and reduce the likelihood of ORF loss, especially in one of the three reading frames. In addition to rationalising the repeatedly reported prevalence of de novo emerged genes in antisense transcripts, our work also provides a generic modeling and an analytical framework that can be used to understand evolution of antisense genes.
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Affiliation(s)
- Bharat Ravi Iyengar
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, Germany.
| | - Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, Germany
- Aix-Marseille Université, INSERM, TAGC, Marseille, France
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen, Germany
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2
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Lebherz MK, Iyengar BR, Bornberg-Bauer E. Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution. Genome Biol Evol 2024; 16:evae129. [PMID: 38879874 DOI: 10.1093/gbe/evae129] [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] [Accepted: 06/06/2024] [Indexed: 07/06/2024] Open
Abstract
For protein coding genes to emerge de novo from a non-genic DNA, the DNA sequence must gain an open reading frame (ORF) and the ability to be transcribed. The newborn de novo gene can further evolve to accumulate changes in its sequence. Consequently, it can also elongate or shrink with time. Existing literature shows that older de novo genes have longer ORF, but it is not clear if they elongated with time or remained of the same length since their inception. To address this question we developed a mathematical model of ORF elongation as a Markov-jump process, and show that ORFs tend to keep their length in short evolutionary timescales. We also show that if change occurs it is likely to be a truncation. Our genomics and transcriptomics data analyses of seven Drosophila melanogaster populations are also in agreement with the model's prediction. We conclude that selection could facilitate ORF length extension that may explain why longer ORFs were observed in old de novo genes in studies analysing longer evolutionary time scales. Alternatively, shorter ORFs may be purged because they may be less likely to yield functional proteins.
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Affiliation(s)
- Marie Kristin Lebherz
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster 48149, Germany
| | - Bharat Ravi Iyengar
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster 48149, Germany
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen 72076, Germany
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3
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Gifford DR, Bhattacharyya A, Geim A, Marshall E, Krašovec R, Knight CG. Environmental and genetic influence on the rate and spectrum of spontaneous mutations in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001452. [PMID: 38687010 PMCID: PMC11084559 DOI: 10.1099/mic.0.001452] [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] [Received: 06/26/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024]
Abstract
Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests, we characterized the spectrum of spontaneous mutations in Escherichia coli grown in low and high glucose environments. These conditions are known to affect the rate of spontaneous mutation in wild-type MG1655, but not in a ΔluxS deletant strain - a gene with roles in both quorum sensing and the recycling of methylation products used in E. coli's DNA repair process. We find an increase in AT>GC transitions in the low glucose environment, suggesting that processes relating to the production or repair of this mutation could drive the response of overall mutation rate to glucose concentration. Interestingly, this increase in AT>GC transitions is maintained by the glucose non-responsive ΔluxS deletant. Instead, an elevated rate of GC>TA transversions, more common in a high glucose environment, leads to a net non-responsiveness of overall mutation rate for this strain. Our results show how relatively subtle changes, such as the concentration of a carbon substrate or loss of a regulatory gene, can substantially influence the amount and nature of genetic variation available to selection.
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Affiliation(s)
- Danna R. Gifford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Anish Bhattacharyya
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Alexandra Geim
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Pembroke College, University of Cambridge, Cambridge, UK
| | - Eleanor Marshall
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Rok Krašovec
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Christopher G. Knight
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
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4
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Reichert F, Brinkwirth S, Pfennigwerth N, Haller S, Fritsch LS, Eckmanns T, Werner G, Gatermann S, Hans JB. Prolonged carriage of OXA-244-carbapenemase-producing Escherichia coli complicates epidemiological investigations. Int J Med Microbiol 2024; 314:151595. [PMID: 38159514 DOI: 10.1016/j.ijmm.2023.151595] [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: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
The rapid increase of OXA-244-producing Escherichia coli, predominantly driven by genetically clustered isolates of sequence type (ST)38, has been observed in at least nine European countries, including Germany. However, the reasons for the spread of OXA-244-producing E. coli remain unclear. Here, we aim to evaluate the possibility of prolonged carriage. We identified a total of six different patients with repeated detection of OXA-244-producing E. coli isolates, which were subjected to both short and long-read whole-genome sequencing (WGS). Besides allelic differences using core genome multilocus sequence typing (cgMLST) analyses, we obtained numbers of single-nucleotide polymorphisms (SNPs) to calculate individual base-pair substitution (BPS) rates. To assess possible re-exposure and risk factors for prolonged carriage, case interviews were conducted. The time between detections ranged from eleven months to more than three years. Initial isolates originated in three+ out of six cases from clinical samples, whereas remaining samples were from screening, mostly in the inpatient setting. As expected, cgMLST analyses showed low numbers of allelic differences between isolates of each case ranging from 1 to 4, whereas numbers of SNPs were between 2 and 99 (mean = 36), thus clearly highlighting the discrepancy between these different bacterial typing approaches. For five out of six cases, observed BPS rates suggest that patients can be colonized with OXA-244-producing E. coli, including ST38 cluster isolates, for extensively long times. Thus, we may have previously missed the epidemiological link between cases because exposure to OXA-244-producing E. coli could have occurred in a time frame, which has not been evaluated in previous investigations. Our results may help to guide future epidemiological investigations as well as to support the interpretation of genetic diversity of OXA-244-producing E. coli, particularly among ST38 cluster isolates.
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Affiliation(s)
- Felix Reichert
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany
| | - Simon Brinkwirth
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany; Postgraduate Training for Applied Epidemiology (PAE), Robert Koch-Institute, Berlin, Germany; ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Niels Pfennigwerth
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Sebastian Haller
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany
| | - Lena Sophie Fritsch
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Tim Eckmanns
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany
| | - Guido Werner
- Robert Koch Institute, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode Branch, Germany
| | - Sören Gatermann
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Jörg B Hans
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany.
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5
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Tian R, Rehm FBH, Czernecki D, Gu Y, Zürcher JF, Liu KC, Chin JW. Establishing a synthetic orthogonal replication system enables accelerated evolution in E. coli. Science 2024; 383:421-426. [PMID: 38271510 DOI: 10.1126/science.adk1281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024]
Abstract
The evolution of new function in living organisms is slow and fundamentally limited by their critical mutation rate. Here, we established a stable orthogonal replication system in Escherichia coli. The orthogonal replicon can carry diverse cargos of at least 16.5 kilobases and is not copied by host polymerases but is selectively copied by an orthogonal DNA polymerase (O-DNAP), which does not copy the genome. We designed mutant O-DNAPs that selectively increase the mutation rate of the orthogonal replicon by two to four orders of magnitude. We demonstrate the utility of our system for accelerated continuous evolution by evolving a 150-fold increase in resistance to tigecycline in 12 days. And, starting from a GFP variant, we evolved a 1000-fold increase in cellular fluorescence in 5 days.
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Affiliation(s)
- Rongzhen Tian
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Dariusz Czernecki
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Yangqi Gu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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6
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Zein-Eddine R, Hak F, Le Meur A, Genestet C, Dumitrescu O, Guyeux C, Senelle G, Sola C, Refrégier G. The paradoxes of Mycobacterium tuberculosis molecular evolution and consequences for the inference of tuberculosis emergence date. Tuberculosis (Edinb) 2023; 143S:102378. [PMID: 38012921 DOI: 10.1016/j.tube.2023.102378] [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: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 11/29/2023]
Abstract
The date of Mycobacterium tuberculosis complex emergence has been the subject of long debates. New studies joining archaeological efforts with sequencing methods raise high hopes for solving whether this emergence is closer to 70,000 or to 6000 years before present. Inferring the date of emergence of this pathogen based on sequence data requires a molecular clock. Several clocks inferred from different types of loci and/or different samples, using both sound reasoning and reliable data, are actually very different, which we refer to as the paradoxes of M. tuberculosis molecular evolution. After having presented these paradoxes, we will remind the limits of the molecular clocks used in the different studies such as the assumption of homogeneous substitution rate. We will then review recent results that shed new light on the characteristics of M. tuberculosis molecular evolution: traces of diverse selection pressures, the impact of host dynamics, etc. We provide some ideas on what to do next to get nearer to a reliable dating of Mycobacterium tuberculosis complex emergence. Among them, the collection of additional remains from ancient tuberculosis seems still essential.
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Affiliation(s)
- R Zein-Eddine
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Institut National de la Santé et de la Recherche Médicale: U1182, Centre National de la Recherche Scientifique: UMR7645, France
| | - F Hak
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
| | - A Le Meur
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
| | - C Genestet
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - O Dumitrescu
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - C Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | - G Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | - C Sola
- Université de Paris, IAME, UMR1137, INSERM, Paris, France; AP-HP, GHU Nord, Service de mycobactériologie spécialisée et de référence, Paris, France; Université Paris-Saclay, Saint-Aubin, France
| | - G Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France.
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7
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Fang K, Yang AL, Li YX, Zeng ZY, Wang RF, Li T, Zhao ZW, Zhang HB. Native plants change the endophyte assembly and growth of an invasive plant in response to climatic factors. Appl Environ Microbiol 2023; 89:e0109323. [PMID: 37815356 PMCID: PMC10617555 DOI: 10.1128/aem.01093-23] [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: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 10/11/2023] Open
Abstract
Climate change, microbial endophytes, and local plants can affect the establishment and expansion of invasive species, yet no study has been performed to assess these interactions. Using a growth chamber, we integrated the belowground (rhizosphere soils) and aboveground (mixture of mature leaf and leaf litter) microbiota into an experimental framework to evaluate the impacts of four native plants acting as microbial inoculation sources on endophyte assembly and growth of the invasive plant Ageratina adenophora in response to drought stress and temperature change. We found that fungal and bacterial enrichment in the leaves and roots of A. adenophora exhibited distinct patterns in response to climatic factors. Many fungi were enriched in roots in response to high temperature and drought stress; in contrast, many bacteria were enriched in leaves in response to low temperature and drought stress. Inoculation of microbiota from phylogenetically close native plant species (i.e., Asteraceae Artemisia atrovirens) causes the recipient plant A. adenophora (Asteraceae) to enrich dominant microbial species from inoculation sources, which commonly results in a lower dissimilar endophytic microbiota and thus produces more negative growth effects when compared to non-Asteraceae inoculations. Drought, microbial inoculation source, and temperature directly impacted the growth of A. adenophora. Both drought and inoculation also indirectly impacted the growth of A. adenophora by changing the root endophytic fungal assembly. Our data indicate that native plant identity can greatly impact the endophyte assembly and host growth of invasive plants, which is regulated by drought and temperature.IMPORTANCEThere has been increasing interest in the interactions between global changes and plant invasions; however, it remains to quantify the role of microbial endophytes in plant invasion with a consideration of their variation in the root vs leaf of hosts, as well as the linkages between microbial inoculations, such as native plant species, and climatic factors, such as temperature and drought. Our study found that local plants acting as microbial inoculants can impact fungal and bacterial enrichment in the leaves and roots of the invasive plant Ageratina adenophora and thus produce distinct growth effects in response to climatic factors; endophyte-mediated invasion of A. adenophora is expected to operate more effectively under favorable moisture. Our study is important for understanding the interactions between climate change, microbial endophytes, and local plant identity in the establishment and expansion of invasive species.
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Affiliation(s)
- Kai Fang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ai-Ling Yang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yu-Xuan Li
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Zhao-Ying Zeng
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Rui-Fang Wang
- College of Agriculture and Forestry, Puer University, Puer, Yunnan, China
| | - Tao Li
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Zhi-Wei Zhao
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
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8
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Qin C, Yang Y, Wu X, Chen L, Liu Z, Tang L, Lyu L, Huang D, Wang D, Zhang C, Yuan X, Liu W, Wang H. Twistedly hydrophobic basis with suitable aromatic metrics in covalent organic networks govern micropollutant decontamination. Nat Commun 2023; 14:6740. [PMID: 37875482 PMCID: PMC10597987 DOI: 10.1038/s41467-023-42513-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
The pre-designable structure and unique architectures of covalent organic frameworks (COFs) render them attractive as active and porous medium for water crisis. However, the effect of functional basis with different metrics on the regulation of interfacial behavior in advanced oxidation decontamination remains a significant challenge. In this study, we pre-design and fabricate different molecular interfaces by creating ordered π skeletons, incorporating different pore sizes, and engineering hydrophilic or hydrophobic channels. These synergically break through the adsorption energy barrier and promote inner-surface renewal, achieving a high removal rate for typical antibiotic contaminants (like levofloxacin) by BTT-DATP-COF, compared with BTT-DADP-COF and BTT-DAB-COF. The experimental and theoretical calculations reveal that such functional basis engineering enable the hole-driven levofloxacin oxidation at the interface of BTT fragments to occur, accompanying with electron-mediated oxygen reduction on terphenyl motif to active radicals, endowing it facilitate the balanced extraction of holes and electrons.
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Affiliation(s)
- Chencheng Qin
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China
| | - Yi Yang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China
| | - Xiaodong Wu
- College of Materials Science and Engineering, Nanjing Tech University, 210009, Nanjing, China
| | - Long Chen
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Zhaoli Liu
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Lin Tang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China
| | - Lai Lyu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Danlian Huang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China
| | - Dongbo Wang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China
| | - Chang Zhang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China
| | - Xingzhong Yuan
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China
| | - Wen Liu
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China.
| | - Hou Wang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, 410082, Changsha, China.
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9
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Yang KB, Cameranesi M, Gowder M, Martinez C, Shamovsky Y, Epshtein V, Hao Z, Nguyen T, Nirenstein E, Shamovsky I, Rasouly A, Nudler E. High-resolution landscape of an antibiotic binding site. Nature 2023; 622:180-187. [PMID: 37648864 PMCID: PMC10550828 DOI: 10.1038/s41586-023-06495-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations; however, their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single-residue mutants encompassing the entire rifampicin binding site of Escherichia coli RNA polymerase (RNAP). By genetically mapping drug-enzyme interactions, we identify an alpha helix where mutations considerably enhance or disrupt rifampicin binding. We find mutations in this region that prolong antibiotic binding, converting rifampicin from a bacteriostatic to bactericidal drug by inducing lethal DNA breaks. The latter are replication dependent, indicating that rifampicin kills by causing detrimental transcription-replication conflicts at promoters. We also identify additional binding site mutations that greatly increase the speed of RNAP.Fast RNAP depletes the cell of nucleotides, alters cell sensitivity to different antibiotics and provides a cold growth advantage. Finally, by mapping natural rpoB sequence diversity, we discover that functional rifampicin binding site mutations that alter RNAP properties or confer drug resistance occur frequently in nature.
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Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Maria Cameranesi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yosef Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Vitaliy Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Nirenstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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10
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Campbell RP, Whittington AC, Zorio DAR, Miller BG. Recruitment of a Middling Promiscuous Enzyme Drives Adaptive Metabolic Evolution in Escherichia coli. Mol Biol Evol 2023; 40:msad202. [PMID: 37708398 PMCID: PMC10519446 DOI: 10.1093/molbev/msad202] [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: 04/18/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
A key step in metabolic pathway evolution is the recruitment of promiscuous enzymes to perform new functions. Despite the recognition that promiscuity is widespread in biology, factors dictating the preferential recruitment of one promiscuous enzyme over other candidates are unknown. Escherichia coli contains four sugar kinases that are candidates for recruitment when the native glucokinase machinery is deleted-allokinase (AlsK), manno(fructo)kinase (Mak), N-acetylmannosamine kinase (NanK), and N-acetylglucosamine kinase (NagK). The catalytic efficiencies of these enzymes are 103- to 105-fold lower than native glucokinases, ranging from 2,400 M-1 s-1 for the most active candidate, NagK, to 15 M-1 s-1 for the least active candidate, AlsK. To investigate the relationship between catalytic activities of promiscuous enzymes and their recruitment, we performed adaptive evolution of a glucokinase-deficient E. coli strain to restore glycolytic metabolism. We observed preferential recruitment of NanK via a trajectory involving early mutations that facilitate glucose uptake and amplify nanK transcription, followed by nonsynonymous substitutions in NanK that enhance the enzyme's promiscuous glucokinase activity. These substitutions reduced the native activity of NanK and reduced organismal fitness during growth on an N-acetylated carbon source, indicating that enzyme recruitment comes at a cost for growth on other substrates. Notably, the two most active candidates, NagK and Mak, were not recruited, suggesting that catalytic activity alone does not dictate evolutionary outcomes. The results highlight our lack of knowledge regarding biological drivers of enzyme recruitment and emphasize the need for a systems-wide approach to identify factors facilitating or constraining this important adaptive process.
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Affiliation(s)
- Ryan P Campbell
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Diego A R Zorio
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
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11
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Lobinska G, Pilpel Y, Ram Y. Phenotype switching of the mutation rate facilitates adaptive evolution. Genetics 2023; 225:iyad111. [PMID: 37293818 PMCID: PMC10471227 DOI: 10.1093/genetics/iyad111] [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: 02/05/2023] [Revised: 02/05/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The mutation rate plays an important role in adaptive evolution. It can be modified by mutator and anti-mutator alleles. Recent empirical evidence hints that the mutation rate may vary among genetically identical individuals: evidence from bacteria suggests that the mutation rate can be affected by expression noise of a DNA repair protein and potentially also by translation errors in various proteins. Importantly, this non-genetic variation may be heritable via a transgenerational epigenetic mode of inheritance, giving rise to a mutator phenotype that is independent from mutator alleles. Here, we investigate mathematically how the rate of adaptive evolution is affected by the rate of mutation rate phenotype switching. We model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. We find that switching rates that correspond to so-far empirically described non-genetic systems of inheritance of the mutation rate lead to higher rates of adaptation on both artificial and natural fitness landscapes. These switching rates can maintain within the same individuals both a mutator phenotype and intermediary mutations, a combination that facilitates adaptation. Moreover, non-genetic inheritance increases the proportion of mutators in the population, which in turn increases the probability of hitchhiking of the mutator phenotype with adaptive mutations. This in turns facilitates the acquisition of additional adaptive mutations. Our results rationalize recently observed noise in the expression of proteins that affect the mutation rate and suggest that non-genetic inheritance of this phenotype may facilitate evolutionary adaptive processes.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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12
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Becker L, Sturm J, Eiden F, Holtmann D. Analyzing and understanding the robustness of bioprocesses. Trends Biotechnol 2023; 41:1013-1026. [PMID: 36959084 DOI: 10.1016/j.tibtech.2023.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/25/2023]
Abstract
The robustness of bioprocesses is becoming increasingly important. The main driving forces of this development are, in particular, increasing demands on product purities as well as economic aspects. In general, bioprocesses exhibit extremely high complexity and variability. Biological systems often have a much higher intrinsic variability compared with chemical processes, which makes the development and characterization of robust processes tedious task. To predict and control robustness, a clear understanding of interactions between input and output variables is necessary. Robust bioprocesses can be realized, for example, by using advanced control strategies for the different unit operations. In this review, we discuss the different biological, technical, and mathematical tools for the analysis and control of bioprocess robustness.
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Affiliation(s)
- Lucas Becker
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany
| | - Jonathan Sturm
- Bioprozesstechnik Group, Westfälische Hochschule, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany; iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Frank Eiden
- Bioprozesstechnik Group, Westfälische Hochschule, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Dirk Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany.
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13
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Ren J, Gu B, Chaisson MJP. vamos: variable-number tandem repeats annotation using efficient motif sets. Genome Biol 2023; 24:175. [PMID: 37501141 PMCID: PMC10373352 DOI: 10.1186/s13059-023-03010-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoints do not capture their full diversity. Here we present a method vamos: VNTR Annotation using efficient Motif Sets that instead annotates VNTR using repeat composition under different levels of motif diversity. Using vamos we estimate 7.4-16.7 alleles per locus when applied to 74 haplotype-resolved human assemblies, compared to breakpoint-based approaches that estimate 4.0-5.5 alleles per locus.
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Affiliation(s)
- Jingwen Ren
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, US
| | - Bida Gu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, US
| | - Mark J. P. Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, US
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14
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Insight into molecular diagnosis for antimalarial drug resistance of Plasmodium falciparum parasites: A review. Acta Trop 2023; 241:106870. [PMID: 36849091 DOI: 10.1016/j.actatropica.2023.106870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Malaria is an infectious disease transmitted by the female Anopheles mosquito and poses a severe threat to human health. At present, antimalarial drugs are the primary treatment for malaria. The widespread use of artemisinin-based combination therapies (ACTs) has dramatically reduced the number of malaria-related deaths; however, the emergence of resistance has the potential to reverse this progress. Accurate and timely diagnosis of drug-resistant strains of Plasmodium parasites via detecting molecular markers (such as Pfnhe1, Pfmrp, Pfcrt, Pfmdr1, Pfdhps, Pfdhfr, and Pfk13) is essential for malaria control and elimination. Here, we review the current techniques which commonly used for molecular diagnosis of antimalarial resistance in P. falciparum and discuss their sensitivities and specificities for different drug resistance-associated molecular markers, with the aim of providing insights into possible directions for future precise point-of-care testing (POCT) of antimalarial drug resistance of malaria parasites.
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Abstract
The rise of antibiotic-resistant bacterial infections poses a global threat. Antibiotic resistance development is generally studied in batch cultures which conceals the heterogeneity in cellular responses. Using single-cell imaging, we studied the growth response of Escherichia coli to sub-inhibitory and inhibitory concentrations of nine antibiotics. We found that the heterogeneity in growth increases more than what is expected from growth rate reduction for three out of the nine antibiotics tested. For two antibiotics (rifampicin and nitrofurantoin), we found that sub-populations were able to maintain growth at lethal antibiotic concentrations for up to 10 generations. This perseverance of growth increased the population size and led to an up to 40-fold increase in the frequency of antibiotic resistance mutations in gram-negative and gram-positive species. We conclude that antibiotic perseverance is a common phenomenon that has the potential to impact antibiotic resistance development across pathogenic bacteria.
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16
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Genome stability during serial subculturing in hyperepidemic multidrug-resistant Klebsiella pneumoniae and Escherichia coli. J Glob Antimicrob Resist 2022; 31:152-161. [PMID: 36049731 DOI: 10.1016/j.jgar.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Core-genome single nucleotide variant (cgSNV) analysis represents a powerful tool for epidemiological investigations of multidrug-resistant (MDR) bacteria. However, cgSNV thresholds to confirm whether isolates are the same clone are not formally defined. METHODS We implemented hybrid whole-genome sequencing to study the genomic changes of four MDR isolates belonging to hyperepidemic sequence types (STs) during 20 propagation steps (T20) on MacConkey and CHROMID(R) ESBL plates. The following strains were analyzed: Klebsiella pneumoniae AE-2247421 (OXA-48/NDM-1-producing, ST101), K. pneumoniae MCL-2017-2 (CTX-M-15-producing, ST307), Escherichia coli Ec-042 (OXA-181-producing, ST410), and E. coli Ec-050 (NDM-5-producing, ST167). The genome assembly at T5 and T20 was compared to that at time point zero (T0) and to two reference genomes. RESULTS At T20, AE-2247421 lost the IncL blaOXA-48-carrying plasmid when grown on CHROMID(R) ESBL plates, while a large fragment encompassing blaNDM-1 was lost from its IncC plasmid when grown on both plates. In contrast, no structural changes were noted for the other three strains. Regarding the cgSNVs, the following results were obtained at T5 and T20 (ranges considering the different agar plates and reference genomes): AE-2247421 (1-8 and 2-12 cgSNVs), MCL-2017-2 (both 1-2 cgSNVs), Ec-042 (both 0 cgSNVs), and Ec-050 (0-6 and 0-9 cgSNVs). CONCLUSION We showed that structural changes and accumulation of cgSNVs can occur in few propagation steps under laboratory conditions. These changes might also arise in the clinical context in a short time, especially under antibiotics treatment. This phenomenon should be carefully considered because it might affect the final interpretation of epidemiological genomic analyses.
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17
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Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022; 31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
Abstract
How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.
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Affiliation(s)
- Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Saacnicteh Toledo‐Patiño
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Lianet Noda‐García
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentHebrew University of JerusalemRehovotIsrael
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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18
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Patlán-Vázquez AG, Ayala-García VM, Vallin C, Cortés J, Vásquez-Morales SG, Robleto EA, Nudler E, Pedraza-Reyes M. Dynamics of Mismatch and Alternative Excision-Dependent Repair in Replicating Bacillus subtilis DNA Examined Under Conditions of Neutral Selection. Front Microbiol 2022; 13:866089. [PMID: 35847079 PMCID: PMC9280176 DOI: 10.3389/fmicb.2022.866089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous DNA deamination is a potential source of transition mutations. In Bacillus subtilis, EndoV, a component of the alternative excision repair pathway (AER), counteracts the mutagenicity of base deamination-induced mispairs. Here, we report that the mismatch repair (MMR) system, MutSL, prevents the harmful effects of HNO2, a deaminating agent of Cytosine (C), Adenine (A), and Guanine (G). Using Maximum Depth Sequencing (MDS), which measures mutagenesis under conditions of neutral selection, in B. subtilis strains proficient or deficient in MutSL and/or EndoV, revealed asymmetric and heterogeneous patterns of mutations in both DNA template strands. While the lagging template strand showed a higher frequency of C → T substitutions; G → A mutations, occurred more frequently in the leading template strand in different genetic backgrounds. In summary, our results unveiled a role for MutSL in preventing the deleterious effects of base deamination and uncovered differential patterns of base deamination processing by the AER and MMR systems that are influenced by the sequence context and the replicating DNA strand.
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Affiliation(s)
- Adriana G. Patlán-Vázquez
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
| | | | - Carmen Vallin
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jonathan Cortés
- Biological Research Center, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Suria G. Vásquez-Morales
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
| | - Eduardo A. Robleto
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Evgeny Nudler
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, United States
| | - Mario Pedraza-Reyes
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
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19
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Thomas C, Wurzer L, Malle E, Ristow M, Madreiter-Sokolowski CT. Modulation of Reactive Oxygen Species Homeostasis as a Pleiotropic Effect of Commonly Used Drugs. FRONTIERS IN AGING 2022; 3:905261. [PMID: 35821802 PMCID: PMC9261327 DOI: 10.3389/fragi.2022.905261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/18/2022] [Indexed: 01/17/2023]
Abstract
Age-associated diseases represent a growing burden for global health systems in our aging society. Consequently, we urgently need innovative strategies to counteract these pathological disturbances. Overwhelming generation of reactive oxygen species (ROS) is associated with age-related damage, leading to cellular dysfunction and, ultimately, diseases. However, low-dose ROS act as crucial signaling molecules and inducers of a vaccination-like response to boost antioxidant defense mechanisms, known as mitohormesis. Consequently, modulation of ROS homeostasis by nutrition, exercise, or pharmacological interventions is critical in aging. Numerous nutrients and approved drugs exhibit pleiotropic effects on ROS homeostasis. In the current review, we provide an overview of drugs affecting ROS generation and ROS detoxification and evaluate the potential of these effects to counteract the development and progression of age-related diseases. In case of inflammation-related dysfunctions, cardiovascular- and neurodegenerative diseases, it might be essential to strengthen antioxidant defense mechanisms in advance by low ROS level rises to boost the individual ROS defense mechanisms. In contrast, induction of overwhelming ROS production might be helpful to fight pathogens and kill cancer cells. While we outline the potential of ROS manipulation to counteract age-related dysfunction and diseases, we also raise the question about the proper intervention time and dosage.
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Affiliation(s)
- Carolin Thomas
- Laboratory of Energy Metabolism Institute of Translational Medicine Department of Health Sciences and Technology ETH Zurich, Schwerzenbach, Switzerland
| | - Lia Wurzer
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Ernst Malle
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Michael Ristow
- Laboratory of Energy Metabolism Institute of Translational Medicine Department of Health Sciences and Technology ETH Zurich, Schwerzenbach, Switzerland
| | - Corina T. Madreiter-Sokolowski
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- *Correspondence: Corina T. Madreiter-Sokolowski,
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20
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Maximum depth sequencing reveals an ON/OFF replication slippage switch and apparent in vivo selection for bifidobacterial pilus expression. Sci Rep 2022; 12:9576. [PMID: 35688912 PMCID: PMC9187656 DOI: 10.1038/s41598-022-13668-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
The human gut microbiome, of which the genus Bifidobacterium is a prevalent and abundant member, is thought to sustain and enhance human health. Several surface-exposed structures, including so-called sortase-dependent pili, represent important bifidobacterial gut colonization factors. Here we show that expression of two sortase-dependent pilus clusters of the prototype Bifidobacterium breve UCC2003 depends on replication slippage at an intragenic G-tract, equivalents of which are present in various members of the Bifidobacterium genus. The nature and extent of this slippage is modulated by the host environment. Involvement of such sortase-dependent pilus clusters in microbe-host interactions, including bacterial attachment to the gut epithelial cells, has been shown previously and is corroborated here for one case. Using a Maximum Depth Sequencing strategy aimed at excluding PCR and sequencing errors introduced by DNA polymerase reagents, specific G-tract sequences in B. breve UCC2003 reveal a range of G-tract lengths whose plasticity within the population is functionally utilized. Interestingly, replication slippage is shown to be modulated under in vivo conditions in a murine model. This in vivo modulation causes an enrichment of a G-tract length which appears to allow biosynthesis of these sortase-dependent pili. This work provides the first example of productive replication slippage influenced by in vivo conditions. It highlights the potential for microdiversity generation in “beneficial” gut commensals.
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21
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Li S, Counter CM. An ultra-sensitive method to detect mutations in human RAS templates. Small GTPases 2022; 13:287-295. [PMID: 35658790 PMCID: PMC9584555 DOI: 10.1080/21541248.2022.2083895] [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] [Indexed: 11/04/2022] Open
Abstract
The RAS family of small GTPases is mutated in roughly a fifth of human cancers. Hotspot point mutations at codons G12, G13, and Q61 account for 95% of all these mutations, which are well established to render the encoded proteins oncogenic. In humans, this family comprises three genes: HRAS, NRAS, and KRAS. Accumulating evidence argues that oncogenic RAS point mutations may be initiating, as they are often truncal in human tumours and capable of inducing tumorigenesis in mice. As such, there is great interest in detecting oncogenic mutation in the RAS genes to understand the origins of cancer, as well as for early detection purposes. To this end, we previously adapted the microbial ultra-sensitive Maximum Depth Sequencing (MDS) assay for the murine Kras gene, which was capable of detecting oncogenic mutations in the tissues of mice days after carcinogen exposure, essentially capturing the very first step in tumour initiation. Given this, we report here the adaption and details of this assay to detect mutations in a human KRAS sequence at an analytic sensitivity of one mutation in a million independently barcoded templates. This humanized version of MDS can thus be exploited to detect oncogenic mutations in KRAS at an incredible sensitivity and modified for the same purpose for the other RAS genes.
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Affiliation(s)
- Siqi Li
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher M Counter
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC, USA
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22
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Non-canonical genomic driver mutations of urethane carcinogenesis. PLoS One 2022; 17:e0267147. [PMID: 35482806 PMCID: PMC9049545 DOI: 10.1371/journal.pone.0267147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/03/2022] [Indexed: 11/19/2022] Open
Abstract
The carcinogen urethane induces pulmonary tumors in mice initiated by an incredibly specific Q61L/R oncogenic mutation in the proto-oncogene Kras. Previous Whole-Exome Sequencing of urethane-induced tumors revealed a bias towards A➙T/G and G➙A substitutions. Subsequent ultra-sensitive Maximum-Depth Sequencing of Kras shortly after urethane exposure suggest a further refinement to CA➙CT/G substitutions. As C182AA➙C182T/GA substitutions in Kras result in Q61L/R mutations, the extreme bias of urethane towards these genomic driver mutations can be ascribed to the specificity of the carcinogen for CA➙CT/G substitutions. However, we previously found that changing rare codons to common in the Kras gene to increase protein expression shifted mutations in urethane-induced tumors away from Kras, or when detected in Kras, to G12D mutations that are usually rarely detected in such tumors. Moreover, the loss of p53 partially reversed this effect, generating tumors with either Q61L/R or G12D oncogenic Kras mutations, or no Kras mutations, presumably due to other genomic driver mutations. Determining the origin of these G12D and other unknown non-canonical genomic driver mutations would provide critical insight into the extreme bias of carcinogens for specific genomic driver mutations. We thus compared the types of Single Nucleotide Variations detected by previously performed Maximum-Depth Sequencing immediately after urethane exposure to the mutation signatures derived from Whole Exome Sequencing of urethane-induced tumors. This identified two types of non-canonical mutations. First, a V637E oncogenic mutation in the proto-oncogene Braf that conforms to the mutation signature of urethane, suggesting that the mutational bias of the carcinogen may account for this non-canonical mutation, similar to that for canonical Q61L/R mutations in Kras. Second, G12D and Q61H mutations in Kras that did not fit this mutation signature, and instead shared similarity with Single Nucleotide Variations detected by Maximum-Depth Sequencing from normal cells, suggesting that perhaps these mutations were pre-existing. We thus posit that when canonical Kras mutations are selected against that the carcinogen may instead promote the expansion of pre-existing genomic driver mutations, although admittedly we cannot rule out other mechanisms. Interrogating the mutation signatures of human lung cancers similarly identified KRAS genomic driver mutations that failed to match the mutation signature of the tumor. Thus, we also speculate that the selection for non-canonical genomic driver mutations during urethane carcinogenesis may reflect the process by which discordance between genomic driver mutations and mutational signatures arises in human cancers.
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23
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Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:433-451. [PMID: 35094339 DOI: 10.1007/978-1-0716-1811-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The use of next-generation sequencing (NGS) to profile genomic variation of individual cancer species is revolutionizing the practice of clinical oncology. In liquid biopsy of cancer, sequencing of circulating-free DNA (cfDNA) is gradually applied to all stages of cancer diagnosis and treatment, serving as complement or replacement of tissue biopsies. However, analysis of cfDNA obtained from blood draws still faces technical obstacles due in part to an excess of wild-type DNA originating from normal tissues and hematopoietic cells. The resulting low-level mutation abundance often falls below routine NGS detection sensitivity and limits reliable mutation identification that meets clinical sensitivity and specificity standards. Despite sample preparation advances that reduce sequencing error rates via use of unique molecular identifiers (molecular barcodes) and error-suppression algorithms, excessive amounts of sequencing are still required to detect mutations at allelic frequency levels below 1%. This requirement reduces throughput and increases cost.In this chapter, we describe a sensitive multiplex mutation detection method that enriches mutation-containing DNA during sample preparation, prior to sequencing, thereby increasing signal-to-noise ratios and providing low-level mutation detection without excessive sequencing depth. We couple targeted next-generation sequencing with wild-type DNA removal using Nuclease-assisted Minor-allele Enrichment using Probe Overlap, NaME-PrO, a recently developed method to eliminate wild-type sequences from multiple targets simultaneously. A step by step guide to library preparation and data analysis are provided as well as some precautions during the sample handling.
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24
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Ribeiro-Dos-Santos AM, Hogan MS, Luther RD, Brosh R, Maurano MT. Genomic context sensitivity of insulator function. Genome Res 2022; 32:425-436. [PMID: 35082140 PMCID: PMC8896466 DOI: 10.1101/gr.276449.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022]
Abstract
The specificity of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites genome-wide function as insulator elements, depending on cellular and genomic context. To dissect the influence of genomic context on enhancer blocker activity, we integrated reporter constructs with promoter-only, promoter and enhancer, and enhancer blocker configurations at hundreds of thousands of genomic sites using the Sleeping Beauty transposase. Deconvolution of reporter activity by genomic position reveals distinct expression patterns subject to genomic context, including a compartment of enhancer blocker reporter integrations with robust expression. The high density of integration sites permits quantitative delineation of characteristic genomic context sensitivity profiles and their decomposition into sensitivity to both local and distant DNase I hypersensitive sites. Furthermore, using a single-cell expression approach to test the effect of integrated reporters for differential expression of nearby endogenous genes reveals that CTCF insulator elements do not completely abrogate reporter effects on endogenous gene expression. Collectively, our results lend new insight into genomic regulatory compartmentalization and its influence on the determinants of promoter–enhancer specificity.
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Affiliation(s)
| | - Megan S Hogan
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Raven D Luther
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Ran Brosh
- Institute for Systems Genetics, NYU Grossman School of Medicine
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25
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Melamed D, Nov Y, Malik A, Yakass MB, Bolotin E, Shemer R, Hiadzi EK, Skorecki KL, Livnat A. De novo mutation rates at the single-mutation resolution in a human HBB gene-region associated with adaptation and genetic disease. Genome Res 2022; 32:488-498. [PMID: 35031571 PMCID: PMC8896469 DOI: 10.1101/gr.276103.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022]
Abstract
Although it is known that the mutation rate varies across the genome, previous estimates were based on averaging across various numbers of positions. Here, we describe a method to measure the origination rates of target mutations at target base positions and apply it to a 6-bp region in the human hemoglobin subunit beta (HBB) gene and to the identical, paralogous hemoglobin subunit delta (HBD) region in sperm cells from both African and European donors. The HBB region of interest (ROI) includes the site of the hemoglobin S (HbS) mutation, which protects against malaria, is common in Africa, and has served as a classic example of adaptation by random mutation and natural selection. We found a significant correspondence between de novo mutation rates and past observations of alleles in carriers, showing that mutation rates vary substantially in a mutation-specific manner that contributes to the site frequency spectrum. We also found that the overall point mutation rate is significantly higher in Africans than in Europeans in the HBB region studied. Finally, the rate of the 20A→T mutation, called the “HbS mutation” when it appears in HBB, is significantly higher than expected from the genome-wide average for this mutation type. Nine instances were observed in the African HBB ROI, where it is of adaptive significance, representing at least three independent originations; no instances were observed elsewhere. Further studies will be needed to examine mutation rates at the single-mutation resolution across these and other loci and organisms and to uncover the molecular mechanisms responsible.
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Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C, Frost SDW, Corander J, Croucher NJ, Turner P, Bentley SD. Pneumococcal within-host diversity during colonization, transmission and treatment. Nat Microbiol 2022; 7:1791-1804. [PMID: 36216891 PMCID: PMC9613479 DOI: 10.1038/s41564-022-01238-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]
Abstract
Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child's life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.
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Affiliation(s)
- Gerry Tonkin-Hill
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway
| | - Clare Ling
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chrispin Chaguza
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.47100.320000000419368710Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Susannah J. Salter
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pattaraporn Hinfonthong
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Elissavet Nikolaou
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK ,grid.1058.c0000 0000 9442 535XInfection and Immunity, Murdoch Children’s Research Institute, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria Australia
| | - Natalie Tate
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Claudia Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Claire Chewapreecha
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.10223.320000 0004 1937 0490Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Simon D. W. Frost
- grid.419815.00000 0001 2181 3404Microsoft Research, Redmond, WA USA ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Nicholas J. Croucher
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Paul Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Stephen D. Bentley
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
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DNA Replication-Transcription Conflicts Do Not Significantly Contribute to Spontaneous Mutations Due to Replication Errors in Escherichia coli. mBio 2021; 12:e0250321. [PMID: 34634932 PMCID: PMC8510543 DOI: 10.1128/mbio.02503-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Encounters between DNA replication and transcription can cause genomic disruption, particularly when the two meet head-on. Whether these conflicts produce point mutations is debated. This paper presents detailed analyses of a large collection of mutations generated during mutation accumulation experiments with mismatch repair (MMR)-defective Escherichia coli. With MMR absent, mutations are primarily due to DNA replication errors. Overall, there were no differences in the frequencies of base pair substitutions or small indels (i.e., insertion and deletions of ≤4 bp) in the coding sequences or promoters of genes oriented codirectionally versus head-on to replication. Among a subset of highly expressed genes, there was a 2- to 3-fold bias for indels in genes oriented head-on to replication, but this difference was almost entirely due to the asymmetrical genomic locations of tRNA genes containing mononucleotide runs, which are hot spots for indels. No additional orientation bias in mutation frequencies occurred when MMR− strains were also defective for transcription-coupled repair (TCR). However, in contrast to other reports, loss of TCR slightly increased the overall mutation rate, meaning that TCR is antimutagenic. There was no orientation bias in mutation frequencies among the stress response genes that are regulated by RpoS or induced by DNA damage. Thus, biases in the locations of mutational targets can account for most, if not all, apparent biases in mutation frequencies between genes oriented head-on versus codirectional to replication. In addition, the data revealed a strong correlation of the frequency of base pair substitutions with gene length but no correlation with gene expression levels.
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28
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Domingo E, García-Crespo C, Perales C. Historical Perspective on the Discovery of the Quasispecies Concept. Annu Rev Virol 2021; 8:51-72. [PMID: 34586874 DOI: 10.1146/annurev-virology-091919-105900] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral quasispecies are dynamic distributions of nonidentical but closely related mutant and recombinant viral genomes subjected to a continuous process of genetic variation, competition, and selection that may act as a unit of selection. The quasispecies concept owes its theoretical origins to a model for the origin of life as a collection of mutant RNA replicators. Independently, experimental evidence for the quasispecies concept was obtained from sampling of bacteriophage clones, which revealed that the viral populations consisted of many mutant genomes whose frequency varied with time of replication. Similar findings were made in animal and plant RNA viruses. Quasispecies became a theoretical framework to understand viral population dynamics and adaptability. The evidence came at a time when mutations were considered rare events in genetics, a perception that was to change dramatically in subsequent decades. Indeed, viral quasispecies was the conceptual forefront of a remarkable degree of biological diversity, now evident for cell populations and organisms, not only for viruses. Quasispecies dynamics unveiled complexities in the behavior of viral populations,with consequences for disease mechanisms and control strategies. This review addresses the origin of the quasispecies concept, its major implications on both viral evolution and antiviral strategies, and current and future prospects.
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Affiliation(s)
- Esteban Domingo
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos García-Crespo
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
| | - Celia Perales
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain.,Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
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29
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Liu D, Loh YHE, Hsieh CL, Lieber MR. Mechanistic basis for chromosomal translocations at the E2A gene and its broader relevance to human B cell malignancies. Cell Rep 2021; 36:109387. [PMID: 34260910 PMCID: PMC8327686 DOI: 10.1016/j.celrep.2021.109387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
Analysis of translocation breakpoints in human B cell malignancies reveals that DNA double-strand breaks at oncogenes most frequently occur at CpG sites located within 20-600 bp fragile zones and depend on activation-induced deaminase (AID). AID requires single-stranded DNA (ssDNA) to act, but it has been unclear why or how this region transiently acquires a ssDNA state. Here, we demonstrate the ssDNA state in the 23 bp E2A fragile zone using several methods, including native bisulfite DNA structural analysis in live human pre-B cells. AID deamination within the E2A fragile zone does not require but is increased upon transcription. High C-string density, nascent RNA tails, and direct DNA sequence repeats prolong the ssDNA state of the E2A fragile zone and increase AID deamination at overlapping AID hotspots that contain the CpG sites at which breaks occur in patients. These features provide key insights into lymphoid fragile zones generally.
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Affiliation(s)
- Di Liu
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Yong-Hwee Eddie Loh
- USC Libraries Bioinformatics Services, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Chih-Lin Hsieh
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Michael R Lieber
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA.
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30
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Meissner ME, Julik EJ, Badalamenti JP, Arndt WG, Mills LJ, Mansky LM. Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing. Viruses 2021; 13:v13071338. [PMID: 34372543 PMCID: PMC8310143 DOI: 10.3390/v13071338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/23/2023] Open
Abstract
Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.
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Affiliation(s)
- Morgan E. Meissner
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
| | - Emily J. Julik
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan P. Badalamenti
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA;
| | - William G. Arndt
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lauren J. Mills
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (L.J.M.); (L.M.M.)
| | - Louis M. Mansky
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (L.J.M.); (L.M.M.)
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31
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Maddamsetti R, Grant NA. Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli. Genome Biol Evol 2021; 12:1591-1603. [PMID: 32853353 PMCID: PMC7523724 DOI: 10.1093/gbe/evaa178] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2020] [Indexed: 12/20/2022] Open
Abstract
All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. 2017. The dynamics of molecular evolution over 60,000 generations. Nature 551(7678):45–50.), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB—loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.
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Affiliation(s)
| | - Nkrumah A Grant
- BEACON Center for the Study of Evolution in Action, Michigan State University.,Department of Microbiology and Molecular Genetics, Michigan State University.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University
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32
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Li S, Counter CM. Signaling levels mold the RAS mutation tropism of urethane. eLife 2021; 10:67172. [PMID: 33998997 PMCID: PMC8128437 DOI: 10.7554/elife.67172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/01/2021] [Indexed: 12/29/2022] Open
Abstract
RAS genes are commonly mutated in human cancer. Despite many possible mutations, individual cancer types often have a 'tropism' towards a specific subset of RAS mutations. As driver mutations, these patterns ostensibly originate from normal cells. High oncogenic RAS activity causes oncogenic stress and different oncogenic mutations can impart different levels of activity, suggesting a relationship between oncoprotein activity and RAS mutation tropism. Here, we show that changing rare codons to common in the murine Kras gene to increase protein expression shifts tumors induced by the carcinogen urethane from arising from canonical Q61 to biochemically less active G12 Kras driver mutations, despite the carcinogen still being biased towards generating Q61 mutations. Conversely, inactivating the tumor suppressor p53 to blunt oncogenic stress partially reversed this effect, restoring Q61 mutations. One interpretation of these findings is that the RAS mutation tropism of urethane arises from selection in normal cells for specific mutations that impart a narrow window of signaling that promotes proliferation without causing oncogenic stress.
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Affiliation(s)
- Siqi Li
- Pharmacology and Cancer Biology, Duke University, Durham, United States
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33
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Schubert MG, Goodman DB, Wannier TM, Kaur D, Farzadfard F, Lu TK, Shipman SL, Church GM. High-throughput functional variant screens via in vivo production of single-stranded DNA. Proc Natl Acad Sci U S A 2021; 118:e2018181118. [PMID: 33906944 PMCID: PMC8106316 DOI: 10.1073/pnas.2018181118] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Creating and characterizing individual genetic variants remains limited in scale, compared to the tremendous variation both existing in nature and envisioned by genome engineers. Here we introduce retron library recombineering (RLR), a methodology for high-throughput functional screens that surpasses the scale and specificity of CRISPR-Cas methods. We use the targeted reverse-transcription activity of retrons to produce single-stranded DNA (ssDNA) in vivo, incorporating edits at >90% efficiency and enabling multiplexed applications. RLR simultaneously introduces many genomic variants, producing pooled and barcoded variant libraries addressable by targeted deep sequencing. We use RLR for pooled phenotyping of synthesized antibiotic resistance alleles, demonstrating quantitative measurement of relative growth rates. We also perform RLR using the sheared genomic DNA of an evolved bacterium, experimentally querying millions of sequences for causal variants, demonstrating that RLR is uniquely suited to utilize large pools of natural variation. Using ssDNA produced in vivo for pooled experiments presents avenues for exploring variation across the genome.
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Affiliation(s)
- Max G Schubert
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Daniel B Goodman
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143
| | | | - Divjot Kaur
- Department of Zoology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Fahim Farzadfard
- Research Laboratory of Electronics, Massachussetts Institute of Technology, Cambridge, MA 02139
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachussetts Institute of Technology, Cambridge, MA 02139
| | - Seth L Shipman
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Research Laboratory of Electronics, Massachussetts Institute of Technology, Cambridge, MA 02139
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34
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Gelbart M, Harari S, Ben-Ari Y, Kustin T, Wolf D, Mandelboim M, Mor O, Pennings PS, Stern A. Drivers of within-host genetic diversity in acute infections of viruses. PLoS Pathog 2020; 16:e1009029. [PMID: 33147296 PMCID: PMC7668575 DOI: 10.1371/journal.ppat.1009029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/16/2020] [Accepted: 10/04/2020] [Indexed: 12/01/2022] Open
Abstract
Genetic diversity is the fuel of evolution and facilitates adaptation to novel environments. However, our understanding of what drives differences in the genetic diversity during the early stages of viral infection is somewhat limited. Here, we use ultra-deep sequencing to interrogate 43 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV. Hundreds to thousands of virus templates were sequenced per sample, allowing us to reveal dramatic differences in within-host genetic diversity among virus populations. We found that increased diversity was mostly driven by presence of multiple divergent genotypes in HIV and CMV samples, which we suggest reflect multiple transmitted/founder viruses. Conversely, we detected an abundance of low frequency hyper-edited genomes in RSV samples, presumably reflecting defective virus genomes (DVGs). We suggest that RSV is characterized by higher levels of cellular co-infection, which allow for complementation and hence elevated levels of DVGs. The few days or weeks following infection with a virus, termed acute infection, are critical for virus establishment. Here we sought to characterize what leads to differences in the genetic diversity of different viruses sampled during acute infection. We performed ultra-deep sequencing of hundreds to thousands viral genomes from forty-three samples spanning three pathogenic human viruses: HIV, RSV and CMV. We found major differences in the genetic diversity of these different viruses, and in different patients infected with the same virus. We investigated the factors responsible for these differences. We found that the DNA virus CMV was less diverse, most likely since it has a lower mutation rate than the RNA viruses HIV and RSV. We also found that the samples with the highest genetic diversity, which included one CMV sample and two HIV samples, bore evidence for multiple genotype infection. In other words, patients from whom these samples were taken were infected with two different “strains” of the virus. Finally, we also found evidence that viral genomes of HIV, and in particular RSV, are edited by the innate immune system of the host, leading to the presence of defective virus genomes.
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Affiliation(s)
- Maoz Gelbart
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ya’ara Ben-Ari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dana Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Lautenberg Center for General and Tumor Immunology, IMRIC, the Faculty of Medicine, the Hebrew University, Jerusalem, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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35
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Arbeithuber B, Hester J, Cremona MA, Stoler N, Zaidi A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues. PLoS Biol 2020; 18:e3000745. [PMID: 32667908 PMCID: PMC7363077 DOI: 10.1371/journal.pbio.3000745] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
Mutations create genetic variation for other evolutionary forces to operate on and cause numerous genetic diseases. Nevertheless, how de novo mutations arise remains poorly understood. Progress in the area is hindered by the fact that error rates of conventional sequencing technologies (1 in 100 or 1,000 base pairs) are several orders of magnitude higher than de novo mutation rates (1 in 10,000,000 or 100,000,000 base pairs per generation). Moreover, previous analyses of germline de novo mutations examined pedigrees (and not germ cells) and thus were likely affected by selection. Here, we applied highly accurate duplex sequencing to detect low-frequency, de novo mutations in mitochondrial DNA (mtDNA) directly from oocytes and from somatic tissues (brain and muscle) of 36 mice from two independent pedigrees. We found mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo. Mutation frequencies and patterns differed between germline and somatic tissues and among mtDNA regions, suggestive of distinct mutagenesis mechanisms. Additionally, we discovered a more pronounced genetic drift of mitochondrial genetic variants in the germline of older versus younger mice, arguing for mtDNA turnover during oocyte meiotic arrest. Our study deciphered for the first time the intricacies of germline de novo mutagenesis using duplex sequencing directly in oocytes, which provided unprecedented resolution and minimized selection effects present in pedigree studies. Moreover, our work provides important information about the origins and accumulation of mutations with aging/maturation and has implications for delayed reproduction in modern human societies. Furthermore, the duplex sequencing method we optimized for single cells opens avenues for investigating low-frequency mutations in other studies.
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Affiliation(s)
- Barbara Arbeithuber
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - James Hester
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Marzia A. Cremona
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Nicholas Stoler
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Arslan Zaidi
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Bonnie Higgins
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kate Anthony
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Francesca Chiaromonte
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America
- EMbeDS, Sant’Anna School of Advanced Studies, Pisa, Italy
| | - Francisco J. Diaz
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kateryna D. Makova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
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36
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Berdejo D, Merino N, Pagán E, García-Gonzalo D, Pagán R. Genetic Variants and Phenotypic Characteristics of Salmonella Typhimurium-Resistant Mutants after Exposure to Carvacrol. Microorganisms 2020; 8:microorganisms8060937. [PMID: 32580471 PMCID: PMC7356045 DOI: 10.3390/microorganisms8060937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
The emergence of antimicrobial resistance has raised questions about the safety of essential oils and their individual constituents as food preservatives and as disinfection agents. Further research is required to understand how and under what conditions stable genotypic resistance might occur in food pathogens. Evolution experiments on Salmonella Typhimurium cyclically exposed to sublethal and lethal doses of carvacrol permitted the isolation of SeSCar and SeLCar strains, respectively. Both evolved strains showed a significant increase in carvacrol resistance, assessed by minimum inhibitory and bactericidal concentrations, the study of growth kinetics in the presence of carvacrol, and the evaluation of survival under lethal conditions. Moreover, antibiotic susceptibility tests revealed a development of SeLCar resistance to a wide range of antibiotics. Whole genome sequencing allowed the identification of single nucleotide variations in transcriptional regulators of oxidative stress-response: yfhP in SeSCar and soxR in SeLCar, which could be responsible for the increased resistance by improving the response to carvacrol and preventing its accumulation inside the cell. This study demonstrates the emergence of S. Typhimurium-resistant mutants against carvacrol, which might pose a risk to food safety and should therefore be considered in the design of food preservation strategies, or of cleaning and disinfection treatments.
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37
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Pham P, Malik S, Mak C, Calabrese PC, Roeder RG, Goodman MF. AID-RNA polymerase II transcription-dependent deamination of IgV DNA. Nucleic Acids Res 2020; 47:10815-10829. [PMID: 31566237 PMCID: PMC6846656 DOI: 10.1093/nar/gkz821] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022] Open
Abstract
Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) in immunoglobulin variable (IgV) genes to produce high-affinity antibodies. SHM requires IgV transcription by RNA polymerase II (Pol II). A eukaryotic transcription system including AID has not been reported previously. Here, we reconstitute AID-catalyzed deamination during Pol II transcription elongation in conjunction with DSIF transcription factor. C→T mutations occur at similar frequencies on non-transcribed strand (NTS) and transcribed strand (TS) DNA. In contrast, bacteriophage T7 Pol generates NTS mutations predominantly. AID-Pol II mutations are strongly favored in WRC and WGCW overlapping hot motifs (W = A or T, R = A or G) on both DNA strands. Single mutations occur on 70% of transcribed DNA clones. Mutations are correlated over a 15 nt distance in multiply mutated clones, suggesting that deaminations are catalyzed processively within a stalled or backtracked transcription bubble. Site-by-site comparisons for biochemical and human memory B-cell mutational spectra in an IGHV3-23*01 target show strongly favored deaminations occurring in the antigen-binding complementarity determining regions (CDR) compared to the framework regions (FW). By exhibiting consistency with B-cell SHM, our in vitro data suggest that biochemically defined reconstituted Pol II transcription systems can be used to investigate how, when and where AID is targeted.
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Affiliation(s)
- Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Chiho Mak
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter C Calabrese
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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38
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Li S, MacAlpine DM, Counter CM. Capturing the primordial Kras mutation initiating urethane carcinogenesis. Nat Commun 2020; 11:1800. [PMID: 32286309 PMCID: PMC7156420 DOI: 10.1038/s41467-020-15660-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
The environmental carcinogen urethane exhibits a profound specificity for pulmonary tumors driven by an oncogenic Q61L/R mutation in the gene Kras. Similarly, the frequency, isoform, position, and substitution of oncogenic RAS mutations are often unique to human cancers. To elucidate the principles underlying this RAS mutation tropism of urethane, we adapted an error-corrected, high-throughput sequencing approach to detect mutations in murine Ras genes at great sensitivity. This analysis not only captured the initiating Kras mutation days after urethane exposure, but revealed that the sequence specificity of urethane mutagenesis, coupled with transcription and isoform locus, to be major influences on the extreme tropism of this carcinogen. Why the carcinogen urethane causes only lung tumours driven by a specific oncogenic mutation in just one Ras gene in mice is unclear. Here, the authors capture mutations immediately after urethane exposure and show that the sequence specificity of mutagenesis, transcriptional status, and Ras genetic loci may all contribute to this specificity.
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Affiliation(s)
- Siqi Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Christopher M Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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39
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Mei H, Arbeithuber B, Cremona MA, DeGiorgio M, Nekrutenko A. A High-Resolution View of Adaptive Event Dynamics in a Plasmid. Genome Biol Evol 2020; 11:3022-3034. [PMID: 31539047 PMCID: PMC6827461 DOI: 10.1093/gbe/evz197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2019] [Indexed: 11/30/2022] Open
Abstract
Coadaptation between bacterial hosts and plasmids frequently results in adaptive changes restricted exclusively to host genome leaving plasmids unchanged. To better understand this remarkable stability, we transformed naïve Escherichia coli cells with a plasmid carrying an antibiotic-resistance gene and forced them to adapt in a turbidostat environment. We then drew population samples at regular intervals and subjected them to duplex sequencing—a technique specifically designed for identification of low-frequency mutations. Variants at ten sites implicated in plasmid copy number control emerged almost immediately, tracked consistently across the experiment’s time points, and faded below detectable frequencies toward the end. This variation crash coincided with the emergence of mutations on the host chromosome. Mathematical modeling of trajectories for adaptive changes affecting plasmid copy number showed that such mutations cannot readily fix or even reach appreciable frequencies. We conclude that there is a strong selection against alterations of copy number even if it can provide a degree of growth advantage. This incentive is likely rooted in the complex interplay between mutated and wild-type plasmids constrained within a single cell and underscores the importance of understanding of intracellular plasmid variability.
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Affiliation(s)
- Han Mei
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University
| | | | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University.,Department of Operations and Decision Systems, Université Laval
| | - Michael DeGiorgio
- Department of Biology, The Pennsylvania State University.,Department of Statistics, The Pennsylvania State University.,Institute for CyberScience, The Pennsylvania State University
| | - Anton Nekrutenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University
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40
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Weaver RJ. Hypothesized Evolutionary Consequences of the Alternative Oxidase (AOX) in Animal Mitochondria. Integr Comp Biol 2020; 59:994-1004. [PMID: 30912813 DOI: 10.1093/icb/icz015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The environment in which eukaryotes first evolved was drastically different from what they experience today, and one of the key limiting factors was the availability of oxygen for mitochondrial respiration. During the transition to a fully oxygenated Earth, other compounds such as sulfide posed a considerable constraint on using mitochondrial aerobic respiration for energy production. The ancestors of animals, and those that first evolved from the simpler eukaryotes have mitochondrial respiratory components that are absent from later-evolving animals. Specifically, mitochondria of most basal metazoans have a sulfide-resistant alternative oxidase (AOX), which provides a secondary oxidative pathway to the classical cytochrome pathway. In this essay, I argue that because of its resistance to sulfide, AOX respiration was critical to the evolution of animals by enabling oxidative metabolism under otherwise inhibitory conditions. I hypothesize that AOX allowed for metabolic flexibility during the stochastic oxygen environment of early Earth which shaped the evolution of basal metazoans. I briefly describe the known functions of AOX, with a particular focus on the decreased production of reactive oxygen species (ROS) during stress conditions. Then, I propose three evolutionary consequences of AOX-mediated protection from ROS observed in basal metazoans: 1) adaptation to stressful environments, 2) the persistence of facultative sexual reproduction, and 3) decreased mitochondrial DNA mutation rates. Recognizing the diversity of mitochondrial respiratory systems present in animals may help resolve the mechanisms involved in major evolutionary processes such as adaptation and speciation.
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Affiliation(s)
- Ryan J Weaver
- Department of Biological Sciences, Auburn University, 331 Funchess Hall, Auburn, AL 36849, USA
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41
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Matic I. Mutation Rate Heterogeneity Increases Odds of Survival in Unpredictable Environments. Mol Cell 2020; 75:421-425. [PMID: 31398322 DOI: 10.1016/j.molcel.2019.06.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/14/2019] [Accepted: 06/19/2019] [Indexed: 11/24/2022]
Abstract
Mutation rates affect both a population's present fitness and its capacity to adapt to future environmental changes. When the available genetic variability limits adaptation to environmental change, natural selection favors high mutations rates. However, constitutively high mutation rates compromise the fitness of a population in stable environments. This problem may be resolved if an increase in mutation rates is limited to times of stress, restricted to some genomic regions, and occurs only in a subpopulation of cells. Such within-population heterogeneity of mutation rates can result from genetic, environmental, and stochastic effects. The presence of subpopulations of transient mutator cells does not jeopardize the overall fitness of a population under stable environmental conditions. However, they can increase the odds of survival in changing environments because they represent reservoirs of increased genetic variability. This article presents evidence that such heterogeneity of mutation rates is more the norm than the exception.
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Affiliation(s)
- Ivan Matic
- Department of Infection, Immunity, and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, 75014 Paris, France.
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42
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Vial-Pradel S, Hasegawa Y, Nakagawa A, Miyaki S, Machida Y, Kojima S, Machida C, Takahashi H. SIMON: Simple methods for analyzing DNA methylation by targeted bisulfite next-generation sequencing. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:213-222. [PMID: 31983875 PMCID: PMC6978500 DOI: 10.5511/plantbiotechnology.19.0822a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
DNA methylation in higher organisms has become an expanding field of study as it often involves the regulation of gene expression. Although Whole Genome Bisulfite Sequencing (WG-BS) based on next-generation sequencing (NGS) is the most versatile method, this is a costly technique that lacks in-depth analytic power. There are no conventional methods based on NGS that enable researchers to easily compare the level of DNA methylation from the practical number of samples handled in the laboratory. Although the targeted BS method based on Sanger sequencing is generally used in this case, it lacks in-depth analytic power. Therefore, we propose a new method that combines the high throughput analytic power of NGS and bioinformatics with the specificity and focus offered by PCR-amplification-based bisulfite sequencing methods. We use in silico size sieving of DNA-fragments and primer matchings instead of whole-fragment alignment in our bioinformatics analyses, and named our method SIMON (Simple Inference for Methylome based On NGS). The results of our targeted BS method based on NGS (SIMON method) show that small variations in DNA methylation patterns can be precisely and efficiently measured at a single nucleotide resolution. SIMON method combines pre-existing techniques to provide a cost-effective technique for in-depth studies that focus on pre-identified loci. It offers significant improvements with regard to workflow and the quality of the acquired DNA methylation information. Because of the high accuracy of the analysis, small variations of DNA methylation levels can be precisely determined even with large numbers of samples and loci.
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Affiliation(s)
- Simon Vial-Pradel
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Yoshinori Hasegawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Shido Miyaki
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 271-8510, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 271-8510, Japan
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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43
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Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome. eLife 2019; 8:53535. [PMID: 31815667 PMCID: PMC6941894 DOI: 10.7554/elife.53535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
New enzymes often evolve by gene amplification and divergence. Previous experimental studies have followed the evolutionary trajectory of an amplified gene, but have not considered mutations elsewhere in the genome when fitness is limited by an evolving gene. We have evolved a strain of Escherichia coli in which a secondary promiscuous activity has been recruited to serve an essential function. The gene encoding the ‘weak-link’ enzyme amplified in all eight populations, but mutations improving the newly needed activity occurred in only one. Most adaptive mutations occurred elsewhere in the genome. Some mutations increase expression of the enzyme upstream of the weak-link enzyme, pushing material through the dysfunctional metabolic pathway. Others enhance production of a co-substrate for a downstream enzyme, thereby pulling material through the pathway. Most of these latter mutations are detrimental in wild-type E. coli, and thus would require reversion or compensation once a sufficient new activity has evolved.
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Affiliation(s)
- Andrew B Morgenthaler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
| | - Wallis R Kinney
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
| | - Christopher C Ebmeier
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Corinne M Walsh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, United States
| | - Daniel J Snyder
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Vaughn S Cooper
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - William M Old
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Shelley D Copley
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
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44
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Xie X, Lv R, Yang C, Song Y, Yan Y, Cui Y, Yang R. Soft sweep development of resistance in Escherichia coli under fluoroquinolone stress. J Microbiol 2019; 57:1056-1064. [PMID: 31555989 DOI: 10.1007/s12275-019-9177-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Abstract
We employed a stepwise selection model for investigating the dynamics of antibiotic-resistant variants in Escherichia coli K-12 treated with increasing concentrations of ciprofloxacin (CIP). Firstly, we used Sanger sequencing to screen the variations in the fluoquinolone target genes, then, employed Illumina NGS sequencing for amplicons targeted regions with variations. The results demonstrated that variations G81C in gyrA and K276N and K277L in parC are standing resistance variations (SRVs), while S83A and S83L in gyrA and G78C in parC were emerging resistance variations (ERVs). The variants containing SRVs and/or ERVs were selected successively based on their sensitivities to CIP. Variant strain 1, containing substitution G81C in gyrA, was immediately selected following ciprofloxacin exposure, with obvious increases in the parC SRV, and parC and gyrA ERV allele frequencies. Variant strain 2, containing the SRVs, then dominated the population following a 20× increase in ciprofloxacin concentration, with other associated allele frequencies also elevated. Variant strains 3 and 4, containing ERVs in gyrA and parC, respectively, were then selected at 40× and 160× antibiotic concentrations. Two variants, strains 5 and 6, generated in the selection procedure, were lost because of higher fitness costs or a lower level of resistance compared with variants 3 and 4. For the second induction, all variations/indels were already present as SRVs and selected out step by step at different passages. Whatever the first induction or second induction, our results confirmed the soft selective sweep hypothesis and provided critical information for guiding clinical treatment of pathogens containing SRVs.
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Affiliation(s)
- Xianxing Xie
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.,Huadong Research Institute for Medicine and Biotechnics, Nanjing, P. R. China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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45
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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46
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Kumar V, Rosenbaum J, Wang Z, Forcier T, Ronemus M, Wigler M, Levy D. Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res 2019; 46:e10. [PMID: 29161423 PMCID: PMC5778454 DOI: 10.1093/nar/gkx1054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/18/2017] [Indexed: 11/15/2022] Open
Abstract
We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone.
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Affiliation(s)
- Vijay Kumar
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Julie Rosenbaum
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Talitha Forcier
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
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47
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Hood WR, Williams AS, Hill GE. An Ecologist’s Guide to Mitochondrial DNA Mutations and Senescence. Integr Comp Biol 2019; 59:970-982. [DOI: 10.1093/icb/icz097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Longevity plays a key role in the fitness of organisms, so understanding the processes that underlie variance in senescence has long been a focus of ecologists and evolutionary biologists. For decades, the performance and ultimate decline of mitochondria have been implicated in the demise of somatic tissue, but exactly why mitochondrial function declines as individual’s age has remained elusive. A possible source of decline that has been of intense debate is mutations to the mitochondrial DNA. There are two primary sources of such mutations: oxidative damage, which is widely discussed by ecologists interested in aging, and mitochondrial replication error, which is less familiar to most ecologists. The goal of this review is to introduce ecologists and evolutionary biologists to the concept of mitochondrial replication error and to review the current status of research on the relative importance of replication error in senescence. We conclude by detailing some of the gaps in our knowledge that currently make it difficult to deduce the relative importance of replication error in wild populations and encourage organismal biologists to consider this variable both when interpreting their results and as viable measure to include in their studies.
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Affiliation(s)
- Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ashley S Williams
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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Ecological and Evolutionary Processes Shaping Viral Genetic Diversity. Viruses 2019; 11:v11030220. [PMID: 30841497 PMCID: PMC6466605 DOI: 10.3390/v11030220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023] Open
Abstract
The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.
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Guan Z, Lan H, Sun D, Wang X, Jin K. A potential novel therapy for FGFR1-amplified pancreatic cancer with bone metastasis, screened by next-generation sequencing and a patient-derived xenograft model. Oncol Lett 2018; 17:2303-2307. [PMID: 30719110 PMCID: PMC6350188 DOI: 10.3892/ol.2018.9876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 11/12/2018] [Indexed: 12/26/2022] Open
Abstract
Effective therapies are limited for pancreatic cancer, particularly for those with distant tumour metastases. Therefore, more individualised drug screening is urgently required. Next-generation sequencing (NGS) is a powerful tool to investigate the genomic landscape of patients and the mechanism of drug response, which may provide a broader vision for potential clinical drug screening. Patient-derived xenograft (PDX) models may have a significant advantage in predicting clinical treatment response. In our previous study, a PDX of pancreatic cancer bone metastasis was established, and NGS was conducted to investigate the molecular information. In the present study, these data were further analysed and fibroblast growth factor receptor 1 (FGFR1) amplification was identified in a panel of 416 cancer-associated genes. Thus, AZD4547, an inhibitor against FGFR, was selected as a potential therapy, and was evaluated using the PDX model. AZD4547 was shown to exhibit antitumor activity by reducing the expression of FGFR1 and its targets. The present study also demonstrated the high potential of the novel NGS/PDX-based drug screening platform to improve individualised cancer treatment.
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Affiliation(s)
- Zhonghai Guan
- Department of Colorectal Surgery, Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, P.R. China.,Department of Pediatric Surgical Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Huanrong Lan
- Department of Breast and Thyroid Surgery, Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, P.R. China
| | - Dan Sun
- Zhejiang Center of Medical Academic Exchange, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Xuanwei Wang
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Ketao Jin
- Department of Colorectal Surgery, Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, P.R. China
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Gregori J, Soria ME, Gallego I, Guerrero-Murillo M, Esteban JI, Quer J, Perales C, Domingo E. Rare haplotype load as marker for lethal mutagenesis. PLoS One 2018; 13:e0204877. [PMID: 30281674 PMCID: PMC6169937 DOI: 10.1371/journal.pone.0204877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/19/2018] [Indexed: 12/23/2022] Open
Abstract
RNA viruses replicate with a template-copying fidelity, which lies close to an extinction threshold. Increases of mutation rate by nucleotide analogues can drive viruses towards extinction. This transition is the basis of an antiviral strategy termed lethal mutagenesis. We have introduced a new diversity index, the rare haplotype load (RHL), to describe NS5B (polymerase) mutant spectra of hepatitis C virus (HCV) populations passaged in absence or presence of the mutagenic agents favipiravir or ribavirin. The increase in RHL is more prominent in mutant spectra whose expansions were due to nucleotide analogues than to multiple passages in absence of mutagens. Statistical tests for paired mutagenized versus non-mutagenized samples with 14 diversity indices show that RHL provides consistently the highest standardized effect of mutagenic treatment difference for ribavirin and favipiravir. The results indicate that the enrichment of viral quasispecies in very low frequency minority genomes can serve as a robust marker for lethal mutagenesis. The diagnostic value of RHL from deep sequencing data is relevant to experimental studies on enhanced mutagenesis of viruses, and to pharmacological evaluations of inhibitors suspected to have a mutagenic activity.
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Affiliation(s)
- Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics, S.L., Sant Cugat del Vallés, Barcelona, Spain
| | - María Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
| | - Isabel Gallego
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Mercedes Guerrero-Murillo
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
- * E-mail: (CP); (JQ)
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- * E-mail: (CP); (JQ)
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
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