1
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Mikucki A, Kahler CM. Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis. Microorganisms 2023; 11:3005. [PMID: 38138149 PMCID: PMC10745880 DOI: 10.3390/microorganisms11123005] [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: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
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2
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Sanders BE, Umaña A, Nguyen TTD, Williams KJ, Yoo CC, Casasanta MA, Wozniak B, Slade DJ. Type IV pili facilitated natural competence in Fusobacterium nucleatum. Anaerobe 2023; 82:102760. [PMID: 37451427 DOI: 10.1016/j.anaerobe.2023.102760] [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: 06/10/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
OBJECTIVES Many bacterial species naturally take up DNA from their surroundings and recombine it into their chromosome through homologous gene transfer (HGT) to aid in survival and gain advantageous functions. Herein we present the first characterization of Type IV pili facilitated natural competence in Fusobacterium nucleatum, which is a Gram-negative, anaerobic bacterium that participates in a range of infections and diseases including periodontitis, preterm birth, and cancer. METHODS Here we used bioinformatics on multiple Fusobacterium species, as well as molecular genetics to characterize natural competence in strain F. nucleatum subsp. nucleatum ATCC 23726. RESULTS We bioinformatically identified components of the Type IV conjugal pilus machinery and show this is a conserved system within the Fusobacterium genus. We next validate Type IV pili in natural competence in F. nucleatum ATCC 23726 and show that gene deletions in key components of pilus deployment (pilQ) and cytoplasmic DNA import (comEC) abolish DNA uptake and chromosomal incorporation. We next show that natural competence may require native F. nucleatum DNA methylation to bypass restriction modification systems and allow subsequent genomic homologous recombination. CONCLUSIONS In summary, this proof of principle study provides the first characterization of natural competence in Fusobacterium nucleatum and highlights the potential to exploit this DNA import mechanism as a genetic tool to characterize virulence mechanisms of an opportunistic oral pathogen.
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Affiliation(s)
- Blake E Sanders
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA
| | - Ariana Umaña
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA
| | - Tam T D Nguyen
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA
| | - Kevin J Williams
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA
| | - Christopher C Yoo
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA
| | - Michael A Casasanta
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA
| | - Bryce Wozniak
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA
| | - Daniel J Slade
- Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg, VA, USA.
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3
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Najafpour B, Pinto PIS, Sanz EC, Martinez-Blanch JF, Canario AVM, Moutou KA, Power DM. Core microbiome profiles and their modification by environmental, biological, and rearing factors in aquaculture hatcheries. MARINE POLLUTION BULLETIN 2023; 193:115218. [PMID: 37441915 DOI: 10.1016/j.marpolbul.2023.115218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
16S rRNA gene sequencing and bacteria- and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalteromonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.
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Affiliation(s)
- Babak Najafpour
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Patricia I S Pinto
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Eric Climent Sanz
- ADM Biopolis, Parc Cientific Universidad De Valencia, Paterna, Spain
| | | | - Adelino V M Canario
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China
| | - Katerina A Moutou
- Department of Biochemistry & Biotechnology, University of Thessaly, Ploutonos 26, Larissa, Greece
| | - Deborah M Power
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China.
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4
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Castillo AI, Almeida RPP. The Multifaceted Role of Homologous Recombination in a Fastidious Bacterial Plant Pathogen. Appl Environ Microbiol 2023; 89:e0043923. [PMID: 37154680 PMCID: PMC10231230 DOI: 10.1128/aem.00439-23] [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: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023] Open
Abstract
Homologous recombination plays a key function in the evolution of bacterial genomes. Within Xylella fastidiosa, an emerging plant pathogen with increasing host and geographic ranges, it has been suggested that homologous recombination facilitates host switching, speciation, and the development of virulence. We used 340 whole-genome sequences to study the relationship between inter- and intrasubspecific homologous recombination, random mutation, and natural selection across individual X. fastidiosa genes. Individual gene orthologs were identified and aligned, and a maximum likelihood (ML) gene tree was generated. Each gene alignment and tree pair were then used to calculate gene-wide and branch-specific r/m values (relative effect of recombination to mutation), gene-wide and branch-site nonsynonymous over synonymous substitution rates (dN/dS values; episodic selection), and branch length (as a proxy for mutation rate). The relationships between these variables were evaluated at the global level (i.e., for all genes among and within a subspecies), among specific functional classes (i.e., COGs), and between pangenome components (i.e., accessory versus core genes). Our analysis showed that r/m varied widely among genes as well as across X. fastidiosa subspecies. While r/m and dN/dS values were positively correlated in some instances (e.g., core genes in X. fastidiosa subsp. fastidiosa and both core and accessory genes in X. fastidiosa subsp. multiplex), low correlation coefficients suggested no clear biological significance. Overall, our results indicate that, in addition to its adaptive role in certain genes, homologous recombination acts as a homogenizing and a neutral force across phylogenetic clades, gene functional groups, and pangenome components. IMPORTANCE There is ample evidence that homologous recombination occurs frequently in the economically important plant pathogen Xylella fastidiosa. Homologous recombination has been known to occur among sympatric subspecies and is associated with host-switching events and virulence-linked genes. As a consequence, is it generally assumed that recombinant events in X. fastidiosa are adaptive. This mindset influences expectations of how homologous recombination acts as an evolutionary force as well as how management strategies for X. fastidiosa diseases are determined. Yet, homologous recombination plays roles beyond that of a source for diversification and adaptation. Homologous recombination can act as a DNA repair mechanism, as a means to facilitate nucleotide compositional change, as a homogenization mechanism within populations, or even as a neutral force. Here, we provide a first assessment of long-held beliefs regarding the general role of recombination in adaptation for X. fastidiosa. We evaluate gene-specific variations in homologous recombination rate across three X. fastidiosa subspecies and its relationship to other evolutionary forces (e.g., natural selection, mutation, etc.). These data were used to assess the role of homologous recombination in X. fastidiosa evolution.
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Affiliation(s)
- Andreina I. Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Rodrigo P. P. Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
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5
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Castro LA, Leitner T, Romero-Severson E. Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies. Virus Evol 2023; 9:vead032. [PMID: 37397911 PMCID: PMC10313349 DOI: 10.1093/ve/vead032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/07/2023] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
Within-host Human immunodeficiency virus (HIV) evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is reactivation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in a bifurcating tree. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an ancestral recombination graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time signals or population bottlenecks. Furthermore, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an approximate Bayesian computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.
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Affiliation(s)
| | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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6
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Ailloud F, Estibariz I, Suerbaum S. Evolved to vary: genome and epigenome variation in the human pathogen Helicobacter pylori. FEMS Microbiol Rev 2021; 45:5900976. [PMID: 32880636 DOI: 10.1093/femsre/fuaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative, spiral shaped bacterium that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori's lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori's diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
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Affiliation(s)
- Florent Ailloud
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Iratxe Estibariz
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany.,DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Pettenkoferstr. 9a, 80336 München, Germany.,National Reference Center for Helicobacter pylori, Pettenkoferstr. 9a, 80336 München, Germany
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7
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Zhang T, Lv K, Lu Q, Wang L, Liu X. Removal of antibiotic-resistant genes during drinking water treatment: A review. J Environ Sci (China) 2021; 104:415-429. [PMID: 33985744 DOI: 10.1016/j.jes.2020.12.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Once contaminate the drinking water source, antibiotic resistance genes (ARGs) will propagate in drinking water systems and pose a serious risk to human health. Therefore, the drinking water treatment processes (DWTPs) are critical to manage the risks posed by ARGs. This study summarizes the prevalence of ARGs in raw water sources and treated drinking water worldwide. In addition, the removal efficiency of ARGs and related mechanisms by different DWTPs are reviewed. Abiotic and biotic factors that affect ARGs elimination are also discussed. The data on presence of ARGs in drinking water help come to the conclusion that ARGs pollution is prevalent and deserves a high priority. Generally, DWTPs indeed achieve ARGs removal, but some biological treatment processes such as biological activated carbon filtration may promote antibiotic resistance due to the enrichment of ARGs in the biofilm. The finding that disinfection and membrane filtration are superior to other DWTPs adds weight to the advice that DWTPs should adopt multiple disinfection barriers, as well as keep sufficient chlorine residuals to inhibit re-growth of ARGs during subsequent distribution. Mechanistically, DWTPs obtain direct and inderect ARGs reduction through DNA damage and interception of host bacterias of ARGs. Thus, escaping of intracellular ARGs to extracellular environment, induced by DWTPs, should be advoided. This review provides the theoretical support for developping efficient reduction technologies of ARGs. Future study should focus on ARGs controlling in terms of transmissibility or persistence through DWTPs due to their biological related nature and ubiquitous presence of biofilm in the treatment unit.
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Affiliation(s)
- Tuqiao Zhang
- Zhejiang Key Laboratory of Drinking Water Safety and Distribution Technology, Zhejiang University, Hangzhou 310058, China
| | - Kunyuan Lv
- Zhejiang Key Laboratory of Drinking Water Safety and Distribution Technology, Zhejiang University, Hangzhou 310058, China
| | - Qingxiao Lu
- Ocean College, Zhejiang University, Hangzhou 310058, China
| | - Lili Wang
- Environmental Engineering, Jiyang College of Zhejiang A & F University, Zhuji 311800, China
| | - Xiaowei Liu
- Zhejiang Key Laboratory of Drinking Water Safety and Distribution Technology, Zhejiang University, Hangzhou 310058, China; Ocean College, Zhejiang University, Hangzhou 310058, China.
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8
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Ren Z, Zhang Y, Wu T, Xue Q, Wang S. Simple and sensitive detection of deoxyribonucleic acid using a RecA-GFP fusion protein-DNA filament as probe. LUMINESCENCE 2021; 36:1272-1276. [PMID: 33837604 DOI: 10.1002/bio.4053] [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: 10/23/2020] [Revised: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 11/06/2022]
Abstract
A simple, rapid and highly sensitive method for detection of double-stranded DNA (dsDNA) was developed using a novel fluorescence probe composed of a RecA-GFP fusion protein that had specific recognition of ssDNA complexes (RecA-GFP-DNA filament). The RecA-GFP fusion protein not only had strong fluorescence, but could also occur by homologous recombination. In the presence of the target dsDNA, the complementary ssDNA of the RecA-GFP-DNA filaments invaded one end of the dsDNA chain. In addition, the other end of the ssDNA dissociated the RecA-GFP filaments. An assay of the probe showed a linear relationship with dsDNA concentration in the range 1-11 nM, with a correlation coefficient of 0.9923. The limit of detection for dsDNA was determined experimentally to be 0.3 nM (3δ). Compared with conventional methods, this method has the advantages of simple operation, high specificity, and high sensitivity.
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Affiliation(s)
- Zijing Ren
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Yuanfu Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Tao Wu
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Qingwang Xue
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Shuhao Wang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
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9
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Huang L, Liu M, Zhu D, Xie L, Huang M, Xiang C, Biville F, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Wang M, Cheng A. Natural Transformation of Riemerella columbina and Its Determinants. Front Microbiol 2021; 12:634895. [PMID: 33746928 PMCID: PMC7965970 DOI: 10.3389/fmicb.2021.634895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
In a previous study, it was shown that Riemerella anatipestifer, a member of Flavobacteriaceae, is naturally competent. However, whether natural competence is universal in Flavobacteriaceae remains unknown. In this study, it was shown for the first time that Riemerella columbina was naturally competent in the laboratory condition; however, Flavobacterium johnsoniae was not naturally competent under the same conditions. The competence of R. columbina was maintained throughout the growth phases, and the transformation frequency was highest during the logarithmic phase. A competition assay revealed that R. columbina preferentially took up its own genomic DNA over heterologous DNA. The natural transformation frequency of R. columbina was significantly increased in GCB medium without peptone or phosphate. Furthermore, natural transformation of R. columbina was inhibited by 0.5 mM EDTA, but could be restored by the addition of CaCl2, MgCl2, ZnCl2, and MnCl2, suggesting that these divalent cations promote the natural transformation of R. columbina. Overall, this study revealed that natural competence is not universal in Flavobacteriaceae members and triggering of competence differs from species to species.
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Affiliation(s)
- Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Li Xie
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Chen Xiang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Francis Biville
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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10
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Wan X, Li X, Liu D, Gao X, Chen Y, Chen Z, Fu C, Lin L, Liu B, Zhao C. Physicochemical characterization and antioxidant effects of green microalga Chlorella pyrenoidosa polysaccharide by regulation of microRNAs and gut microbiota in Caenorhabditis elegans. Int J Biol Macromol 2020; 168:152-162. [PMID: 33301848 DOI: 10.1016/j.ijbiomac.2020.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/22/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022]
Abstract
A novel polysaccharide from Chlorella pyrenoidosa (CPP) was separated and purified with the average molecular weight 15.8 kDa. It was composed of seven monosaccharides including mannose, rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, and arabinose. FT-IR and NMR spectra analysis further revealed that CPP was an acidic polysaccharide consisting of β-L-Arap-(1→, →2)-α-L-Rhap-(1→, β-D-GlcpA-(1→, →4)-α-D-GalpA-(1→, →6)-β-D-Glcp-(1→, →3)-β-D-Manp-(1→, and →3, 6)-β-D-Galp-(1→. The CPP treatment could effectively prolong lifespan of Caenorhabditis elegans under the oxidative stress conditions and inhibit the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) as well as enhancing the level of superoxide dismutase (SOD). It could up-regulate the expressions of Daf-16 and Skn-1 genes via declining miR-48-3p, miR-48-5p, and miR-51-5p translocation. Moreover, 16S rRNA sequencing revealed that the CPP-enriched Faecalibacterium, Haemophilus, Vibrio, and Shewanella were strongly correlated with SOD, MDA, apoptosis, and ROS. These results indicated that CPP may be considered as a desired ingredient on regulating the aging and oxidative diseases.
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Affiliation(s)
- Xuzhi Wan
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoqing Li
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dan Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxiang Gao
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yihan Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengxin Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Caili Fu
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Luan Lin
- Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou Normal University, Quanzhou 362000, China
| | - Bin Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Engineering Research Center of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou 350002, China
| | - Chao Zhao
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Engineering Research Center of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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11
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Zhang G, Li W, Chen S, Zhou W, Chen J. Problems of conventional disinfection and new sterilization methods for antibiotic resistance control. CHEMOSPHERE 2020; 254:126831. [PMID: 32957272 DOI: 10.1016/j.chemosphere.2020.126831] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 05/20/2023]
Abstract
The problem of bacterial antibiotic resistance has attracted considerable research attention, and the effects of water treatment on antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are being increasingly investigated. As an indispensable part of the water treatment process, disinfection plays an important role in controlling antibiotic resistance. At present, there were many studies on the effects of conventional and new sterilization methods on ARB and ARGs. However, there is a lack of literature relating to the limitations of conventional methods and analysis of new techniques. Therefore, this review focuses on analyzing the deficiencies of conventional disinfection and the development of new methods for antibiotic resistance control to guide future research. Firstly, we analyzed the effects and drawbacks of conventional disinfection methods, such as chlorine (Cl), ultraviolet (UV) and ozone on antibiotic resistance control. Secondly, we discuss the research progress and shortcomings of new sterilization methods in antibiotic resistance. Finally, we propose suggestions for future research directions. There is an urgent need for new effective and low-cost sterilization methods. Disinfection via UV and chlorine in combination, UV/chlorine showed greater potential for controlling ARGs.
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Affiliation(s)
- Guosheng Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
| | - Weiying Li
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China.
| | - Sheng Chen
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
| | - Wei Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
| | - Jiping Chen
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
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12
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Spankie TJ, Haywood AL, Dottorini T, Barrow PA, Hirst JD. Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid. J Mol Graph Model 2020; 101:107723. [PMID: 32927271 DOI: 10.1016/j.jmgm.2020.107723] [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: 06/22/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 10/23/2022]
Abstract
One promising strategy to combat antimicrobial resistance is to use bacteriophages that attach to the sex pili produced by transmissible antimicrobial resistance (AMR) plasmids, infect AMR bacteria and select for loss of the AMR plasmids, prolonging the life of existing antimicrobials. The maturation protein of the bacteriophage MS2 attaches to the pili produced by Incompatibility group F plasmid-containing bacteria. This interaction initiates delivery of the viral genetic material into the bacteria. Using protein-protein docking we constructed a model of the F pilus comprising a trimer of subunits binding to the maturation protein. Interactions between the maturation protein and the F pilus were investigated using molecular dynamics simulations. In silico alanine scanning and in silico single-point mutations were explored, with the longer term aim of increasing the affinity of the maturation protein to other Incompatibility group pili, without reducing the strength of binding to F pilin. We report our computational findings on which residues are required for the maturation protein and F pilin to interact, those which had no effect on the interaction and the mutations which led to a stronger interaction.
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Affiliation(s)
- Timothy J Spankie
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Alexe L Haywood
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE125RD, UK
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE125RD, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK.
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13
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Potnis N, Kandel PP, Merfa MV, Retchless AC, Parker JK, Stenger DC, Almeida RPP, Bergsma-Vlami M, Westenberg M, Cobine PA, De La Fuente L. Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa. THE ISME JOURNAL 2019; 13:2319-2333. [PMID: 31110262 PMCID: PMC6776109 DOI: 10.1038/s41396-019-0423-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/09/2022]
Abstract
High rates of homologous recombination (HR) in the bacterial plant pathogen Xylella fastidiosa have been previously detected. This study aimed to determine the extent and explore the ecological significance of HR in the genomes of recombinants experimentally generated by natural transformation and wild-type isolates. Both sets of strains displayed widespread HR and similar average size of recombined fragments consisting of random events (2-10 kb) of inter- and intrasubspecific recombination. A significantly higher proportion and greater lengths (>10 kb, maximum 31.5 kb) of recombined fragments were observed in subsp. morus and in strains isolated in Europe from intercepted coffee plants shipped from the Americas. Such highly recombinant strains pose a serious risk of emergence of novel variants, as genetically distinct and formerly geographically isolated genotypes are brought in close proximity by global trade. Recently recombined regions in wild-type strains included genes involved in regulation and signaling, host colonization, nutrient acquisition, and host evasion, all fundamental traits for X. fastidiosa ecology. Identification of four recombinant loci shared between wild-type and experimentally generated recombinants suggests potential hotspots of recombination in this naturally competent pathogen. These findings provide insights into evolutionary forces possibly affecting the adaptive potential to colonize the host environments of X. fastidiosa.
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Affiliation(s)
- Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
| | - Prem P Kandel
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Marcus V Merfa
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
| | - Adam C Retchless
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer K Parker
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Drake C Stenger
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Maria Bergsma-Vlami
- Dutch National Plant Protection Organization (NPPO-NL), P.O. Box. 9102, Wageningen, 6700 HC, The Netherlands
| | - Marcel Westenberg
- Dutch National Plant Protection Organization (NPPO-NL), P.O. Box. 9102, Wageningen, 6700 HC, The Netherlands
| | - Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA.
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14
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Hou J, Chen Z, Gao J, Xie Y, Li L, Qin S, Wang Q, Mao D, Luo Y. Simultaneous removal of antibiotics and antibiotic resistance genes from pharmaceutical wastewater using the combinations of up-flow anaerobic sludge bed, anoxic-oxic tank, and advanced oxidation technologies. WATER RESEARCH 2019; 159:511-520. [PMID: 31129481 DOI: 10.1016/j.watres.2019.05.034] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/24/2019] [Accepted: 05/11/2019] [Indexed: 06/09/2023]
Abstract
Pharmaceutical wastewater often contains high levels of antibiotic residues and serves as an important reservoir for antibiotic resistance genes (ARGs). However, the current pharmaceutical wastewater treatment plants (PWWTPs) were not sufficiently effective in removing antibiotics and ARGs. Here, we designed a lab-scale simulation reactor, including up-flow anaerobic sludge bed (UASB), anoxic-oxic tank (A/O), and four separate advanced oxidation processes (AOPs) i.e., UV, Ozonation, Fenton, and Fenton/UV, to simultaneously remove 18 antibiotics and 10 ARGs from a real pharmaceutical wastewater. The results showed that all antibiotics were fully eliminated through the reactor during 180 d-operation. Among all treatment units, UASB provided the greatest contribution (85.8 ± 16.1%) for the removal of 18 antibiotics. The mass balance results manifested that degradation was a predominant mechanism for the removal of tetracyclines, sulfamethoxazole, and ampicillin (62.5-80.9%), while sorption to sludge (73.9%) was predominant for enrofloxacin removal in UASB. Meanwhile, the substantial decrease of ARG absolute abundance (log reduction by 0.1-3.1 fold) through the whole reactor was observed although the existence of the partial enrichment (1.2-3.8 log units) from the influent to the A/O unit. Fenton/UV combination was the most effective AOP for the removal of ARGs. Finally, the optimum operating conditions for the removal of ARGs using Fenton was also proposed considering the relatively lower cost and high ARG elimination. Overall, this study provides feasible suggestions for the design of real PWWTPs for simultaneous removal of antibiotics and ARGs.
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Affiliation(s)
- Jie Hou
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Zeyou Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Ju Gao
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Yonglei Xie
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin, 300384, China
| | - Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Songyan Qin
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin, 300384, China
| | - Qing Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, 300071, China.
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China.
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15
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Berry ASF, Salazar-Sánchez R, Castillo-Neyra R, Borrini-Mayorí K, Chipana-Ramos C, Vargas-Maquera M, Ancca-Juarez J, Náquira-Velarde C, Levy MZ, Brisson D. Sexual reproduction in a natural Trypanosoma cruzi population. PLoS Negl Trop Dis 2019; 13:e0007392. [PMID: 31107905 PMCID: PMC6544315 DOI: 10.1371/journal.pntd.0007392] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/31/2019] [Accepted: 04/15/2019] [Indexed: 12/21/2022] Open
Abstract
Background Sexual reproduction provides an evolutionary advantageous mechanism that combines favorable mutations that have arisen in separate lineages into the same individual. This advantage is especially pronounced in microparasites as allelic reassortment among individuals caused by sexual reproduction promotes allelic diversity at immune evasion genes within individuals which is often essential to evade host immune systems. Despite these advantages, many eukaryotic microparasites exhibit highly-clonal population structures suggesting that genetic exchange through sexual reproduction is rare. Evidence supporting clonality is particularly convincing in the causative agent of Chagas disease, Trypanosoma cruzi, despite equally convincing evidence of the capacity to engage in sexual reproduction. Methodology/ Principle Findings In the present study, we investigated two hypotheses that can reconcile the apparent contradiction between the observed clonal population structure and the capacity to engage in sexual reproduction by analyzing the genome sequences of 123 T. cruzi isolates from a natural population in Arequipa, Peru. The distribution of polymorphic markers within and among isolates provides clear evidence of the occurrence of sexual reproduction. Large genetic segments are rearranged among chromosomes due to crossing over during meiosis leading to a decay in the genetic linkage among polymorphic markers compared to the expectations from a purely asexually-reproducing population. Nevertheless, the population structure appears clonal due to a high level of inbreeding during sexual reproduction which increases homozygosity, and thus reduces diversity, within each inbreeding lineage. Conclusions/ Significance These results effectively reconcile the apparent contradiction by demonstrating that the clonal population structure is derived not from infrequent sex in natural populations but from high levels of inbreeding. We discuss epidemiological consequences of this reproductive strategy on genome evolution, population structure, and phenotypic diversity of this medically important parasite. The rearrangement of alleles among individuals in a population during sexual reproduction maintains high allelic diversity within individuals in a population at polymorphic genes. Allelic diversity within individuals can be particularly important for parasites as it enhances their ability to evade host immune systems. Despite the potential benefits of sexual reproduction for parasites, natural populations of the protozoan parasite—and causative agent of human Chagas disease—Trypanosoma cruzi, exhibit clonal population structures indicative of asexual reproduction. This is particularly surprising as T. cruzi has the capacity for sexual reproduction. Here, we resolve this apparent contradiction by sequencing whole genomes of 123 T. cruzi isolates from a natural population in Arequipa, Peru. Evidence of past sexual reproduction and allelic rearrangements are common in this T. cruzi population. However, the majority of sexual reproduction events occur between close relatives resulting in an apparent clonal population structure. Sexual reproduction with distant relatives in areas with greater strain diversity has the potential to affect public health by increasing diversity in immune evasion genes within individuals and enhancing within-host survival, rapidly diversifying antigens that could affect the sensitivity of serological diagnostics, and by generating diversity in pathogenicity or drug resistance.
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Affiliation(s)
- Alexander S. F. Berry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Renzo Salazar-Sánchez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Ricardo Castillo-Neyra
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katty Borrini-Mayorí
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Claudia Chipana-Ramos
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Melina Vargas-Maquera
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Jenny Ancca-Juarez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - César Náquira-Velarde
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Michael Z. Levy
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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16
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Jia X, Zhang Y, Zhang Q, Zhao Q, Traw MB, Wang L, Tian D, Wang C, Yang S. High-resolution insight into recombination events at the SD1 locus in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:683-692. [PMID: 30417595 DOI: 10.1111/tpj.14154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/28/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
Recombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non-reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semi-dwarf phenotype of rice in the 'Green Revolution' of the 1960s. Here, physical separation of two defects allows recombination to generate the wild-type SD1 gene, for which plant height can then be used as a reporter. By screening 18 000 F2 progeny from a cross between two semi-dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of ~3.3 × 10-4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single-nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotype-related functional genes, which are abundant in other plant genomes.
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Affiliation(s)
- Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qijun Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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17
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Abstract
Microbial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a representative set of microorganisms. Our results uncovered important trends. First, microbes with different lifestyles are differentially impacted, with endosymbionts and obligate pathogens being those less prone to undergo this process. Second, certain genetic elements such as restriction-modification systems seem to be associated with higher rates of recombination. Most importantly, recombined genomes show the footprints of natural selection in which recombined regions preferentially contain genes that can be related to specific ecological adaptations. Taken together, our results clarify the relative contributions of factors modulating homologous recombination and show evidence for a clear a role of this process in shaping microbial genomes and driving ecological adaptations. Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes.
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18
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Hörandl E, Speijer D. How oxygen gave rise to eukaryotic sex. Proc Biol Sci 2019; 285:rspb.2017.2706. [PMID: 29436502 PMCID: PMC5829205 DOI: 10.1098/rspb.2017.2706] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
How did full meiotic eukaryotic sex evolve and what was the immediate advantage allowing it to develop? We propose that the crucial determinant can be found in internal reactive oxygen species (ROS) formation at the start of eukaryotic evolution approximately 2 × 109 years ago. The large amount of ROS coming from a bacterial endosymbiont gave rise to DNA damage and vast increases in host genome mutation rates. Eukaryogenesis and chromosome evolution represent adaptations to oxidative stress. The host, an archaeon, most probably already had repair mechanisms based on DNA pairing and recombination, and possibly some kind of primitive cell fusion mechanism. The detrimental effects of internal ROS formation on host genome integrity set the stage allowing evolution of meiotic sex from these humble beginnings. Basic meiotic mechanisms thus probably evolved in response to endogenous ROS production by the ‘pre-mitochondrion’. This alternative to mitosis is crucial under novel, ROS-producing stress situations, like extensive motility or phagotrophy in heterotrophs and endosymbiontic photosynthesis in autotrophs. In multicellular eukaryotes with a germline–soma differentiation, meiotic sex with diploid–haploid cycles improved efficient purging of deleterious mutations. Constant pressure of endogenous ROS explains the ubiquitous maintenance of meiotic sex in practically all eukaryotic kingdoms. Here, we discuss the relevant observations underpinning this model.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Goettingen, Göttingen, Germany
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
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19
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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20
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Wallen RM, Perlin MH. An Overview of the Function and Maintenance of Sexual Reproduction in Dikaryotic Fungi. Front Microbiol 2018; 9:503. [PMID: 29619017 PMCID: PMC5871698 DOI: 10.3389/fmicb.2018.00503] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Sexual reproduction likely evolved as protection from environmental stresses, specifically, to repair DNA damage, often via homologous recombination. In higher eukaryotes, meiosis and the production of gametes with allelic combinations different from parental type provides the side effect of increased genetic variation. In fungi it appears that while the maintenance of meiosis is paramount for success, outcrossing is not a driving force. In the subkingdom Dikarya, fungal members are characterized by existence of a dikaryon for extended stages within the life cycle. Such fungi possess functional or, in some cases, relictual, loci that govern sexual reproduction between members of their own species. All mating systems identified so far in the Dikarya employ a pheromone/receptor system for haploid organisms to recognize a compatible mating partner, although the paradigm in the Ascomycota, e.g., Saccharomyces cerevisiae, is that genes for the pheromone precursor and receptor are not found in the mating-type locus but rather are regulated by its products. Similarly, the mating systems in the Ascomycota are bipolar, with two non-allelic idiomorphs expressed in cells of opposite mating type. In contrast, for the Basidiomycota, both bipolar and tetrapolar mating systems have been well characterized; further, at least one locus directly encodes the pheromone precursor and the receptor for the pheromone of a different mating type, while a separate locus encodes proteins that may regulate the first locus and/or additional genes required for downstream events. Heterozygosity at both of two unlinked loci is required for cells to productively mate in tetrapolar systems, whereas in bipolar systems the two loci are tightly linked. Finally, a trade-off exists in wild fungal populations between sexual reproduction and the associated costs, with adverse conditions leading to mating. For fungal mammal pathogens, the products of sexual reproduction can be targets for the host immune system. The opposite appears true for phytopathogenic fungi, where mating and pathogenicity are inextricably linked. Here, we explore, compare, and contrast different strategies used among the Dikarya, both saprophytic and pathogenic fungi, and highlight differences between pathogens of mammals and pathogens of plants, providing context for selective pressures acting on this interesting group of fungi.
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Affiliation(s)
| | - Michael H. Perlin
- Department of Biology, University of Louisville, Louisville, KY, United States
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21
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Hauck S, Maiden MCJ. Clonally Evolving Pathogenic Bacteria. MOLECULAR MECHANISMS OF MICROBIAL EVOLUTION 2018. [DOI: 10.1007/978-3-319-69078-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Bernstein H, Bernstein C, Michod RE. Sex in microbial pathogens. INFECTION GENETICS AND EVOLUTION 2018; 57:8-25. [DOI: 10.1016/j.meegid.2017.10.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
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Ambur OH, Engelstädter J, Johnsen PJ, Miller EL, Rozen DE. Steady at the wheel: conservative sex and the benefits of bacterial transformation. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0528. [PMID: 27619692 PMCID: PMC5031613 DOI: 10.1098/rstb.2015.0528] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 12/25/2022] Open
Abstract
Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Ole Herman Ambur
- Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, 1478 Oslo, Norway
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pål J Johnsen
- Faculty of Health Sciences, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Eric L Miller
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Daniel E Rozen
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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Chu HY, Sprouffske K, Wagner A. The role of recombination in evolutionary adaptation of Escherichia coli to a novel nutrient. J Evol Biol 2017; 30:1692-1711. [PMID: 28612351 DOI: 10.1111/jeb.13132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/11/2017] [Accepted: 06/05/2017] [Indexed: 12/11/2022]
Abstract
The benefits and detriments of recombination for adaptive evolution have been studied both theoretically and experimentally, with conflicting predictions and observations. Most pertinent experiments examine recombination's effects in an unchanging environment and do not study its genomewide effects. Here, we evolved six replicate populations of either highly recombining R+ or lowly recombining R- E. coli strains in a changing environment, by introducing the novel nutrients L-arabinose or indole into the environment. The experiment's ancestral strains are not viable on these nutrients, but 130 generations of adaptive evolution were sufficient to render them viable. Recombination conferred a more pronounced advantage to populations adapting to indole. To study the genomic changes associated with this advantage, we sequenced the genomes of 384 clones isolated from selected replicates at the end of the experiment. These genomes harbour complex changes that range from point mutations to large-scale DNA amplifications. Among several candidate adaptive mutations, those in the tryptophanase regulator tnaC stand out, because the tna operon in which it resides has a known role in indole metabolism. One of the highly recombining populations also shows a significant excess of large-scale segmental DNA amplifications that include the tna operon. This lineage also shows a unique and potentially adaptive combination of point mutations and DNA amplifications that may have originated independently from one another, to be joined later by recombination. Our data illustrate that the advantages of recombination for adaptive evolution strongly depend on the environment and that they can be associated with complex genomic changes.
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Affiliation(s)
- H-Y Chu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - K Sprouffske
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - A Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, NM, USA
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David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG, Parkhill J. Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLoS Genet 2017. [PMID: 28650958 PMCID: PMC5507463 DOI: 10.1371/journal.pgen.1006855] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires' disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) of diversity within several major disease-associated sequence types (STs) of L. pneumophila. This suggests that recombination represents a potentially important force shaping adaptation and virulence. Despite this, little is known about the biological effects of recombination in L. pneumophila, particularly with regards to homologous recombination (whereby genes are replaced with alternative allelic variants). Using newly available population genomic data, we have disentangled events arising from homologous and non-homologous recombination in six major disease-associated STs of L. pneumophila (subsp. pneumophila), and subsequently performed a detailed characterisation of the dynamics and impact of homologous recombination. We identified genomic "hotspots" of homologous recombination that include regions containing outer membrane proteins, the lipopolysaccharide (LPS) region and Dot/Icm effectors, which provide interesting clues to the selection pressures faced by L. pneumophila. Inference of the origin of the recombined regions showed that isolates have most frequently imported DNA from isolates belonging to their own clade, but also occasionally from other major clades of the same subspecies. This supports the hypothesis that the possibility for horizontal exchange of new adaptations between major clades of the subspecies may have been a critical factor in the recent emergence of several clinically important STs from diverse genomic backgrounds. However, acquisition of recombined regions from another subspecies, L. pneumophila subsp. fraseri, was rarely observed, suggesting the existence of a recombination barrier and/or the possibility of ongoing speciation between the two subspecies. Finally, we suggest that multi-fragment recombination may occur in L. pneumophila, whereby multiple non-contiguous segments that originate from the same molecule of donor DNA are imported into a recipient genome during a single episode of recombination.
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Affiliation(s)
- Sophia David
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, London, United Kingdom
| | - Leonor Sánchez-Busó
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Simon R. Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Pekka Marttinen
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Aalto, Espoo, Finland
| | - Christophe Rusniok
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France
- CNRS UMR 3525, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France
- CNRS UMR 3525, Paris, France
| | - Timothy G. Harrison
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, London, United Kingdom
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- * E-mail:
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Yu Y, Chang D, Xu H, Zhang X, Pan L, Xu C, Huang B, Zhou H, Li J, Guo J, Liu C. The virulence of Streptococcus pneumoniae partially depends on dprA. Braz J Microbiol 2016; 48:225-231. [PMID: 28011228 PMCID: PMC5470456 DOI: 10.1016/j.bjm.2016.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 11/29/2022] Open
Abstract
Streptococcus pneumoniae is one of the most frequent opportunistic pathogens worldwide. DNA processing protein A (DprA) is an important factor involved in bacterial uptake and DNA integration into bacterial genome, but its role in S. pneumoniae virulence remains unclear. The aim of this study was to characterize the effects of the pneumococcal dprA gene on the pathogenesis of S. pneumoniae. To construct a dprA-deficient pneumococcal strain, the dprA gene of the S. pneumoniae strain D39 was inactivated. The virulence of this dprA-deficient strain, designated ΔD39, was compared with that of the wild-type strain by evaluating their respective capabilities to adhere to human pulmonary epithelial cells (PEC-A549) and by analyzing their choline-binding protein expression levels. In addition, the expression profiles of genes associated with virulence and host survival assays were also conducted with the mutant and the wild-type strain. Our results indicate that the capability of ΔD39 to adhere to the PEC-A549 airway cells was significantly lower (p < 0.01) compared with D39. Additionally, the 100-KD choline-binding protein was not detected in ΔD39. The addition of competence-stimulating peptide (CSP) lead to a significantly reduction of psaA mRNA expression in the dprA-deficient mutant and an increased level of psaA transcripts in the wild-type strain (p < 0.01). The median survival time of mice intraperitoneally infected with ΔD39 was significantly higher (p < 0.01) than that of mice infected with D39. The results of this study suggest that DprA has a significant effect on virulence characteristics of S. pneumoniae by influencing the expression of choline-binding protein and PsaA.
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Affiliation(s)
- Yi Yu
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - De Chang
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China; General Hospital of Chinese People's Armed Police Forces, Department of Respiratory Medicine, Beijing, China
| | - Huiwen Xu
- National Institute for Food and Drug Control, Institute for Medical Device Standardization Administration, Beijing, China
| | - Xuelin Zhang
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - Lei Pan
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - Chou Xu
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - Bing Huang
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - Hong Zhou
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - Jia Li
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - Jun Guo
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China
| | - Changting Liu
- Chinese PLA General Hospital, Nanlou Respiratory Diseases Department, Beijing, China.
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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Mirzaghaderi G, Hörandl E. The evolution of meiotic sex and its alternatives. Proc Biol Sci 2016; 283:20161221. [PMID: 27605505 PMCID: PMC5031655 DOI: 10.1098/rspb.2016.1221] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022] Open
Abstract
Meiosis is an ancestral, highly conserved process in eukaryotic life cycles, and for all eukaryotes the shared component of sexual reproduction. The benefits and functions of meiosis, however, are still under discussion, especially considering the costs of meiotic sex. To get a novel view on this old problem, we filter out the most conserved elements of meiosis itself by reviewing the various modifications and alterations of modes of reproduction. Our rationale is that the indispensable steps of meiosis for viability of offspring would be maintained by strong selection, while dispensable steps would be variable. We review evolutionary origin and processes in normal meiosis, restitutional meiosis, polyploidization and the alterations of meiosis in forms of uniparental reproduction (apomixis, apomictic parthenogenesis, automixis, selfing) with a focus on plants and animals. This overview suggests that homologue pairing, double-strand break formation and homologous recombinational repair at prophase I are the least dispensable elements, and they are more likely optimized for repair of oxidative DNA damage rather than for recombination. Segregation, ploidy reduction and also a biparental genome contribution can be skipped for many generations. The evidence supports the theory that the primary function of meiosis is DNA restoration rather than recombination.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, Georg-August-University of Göttingen, Göttingen, Germany
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Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil. PLoS Negl Trop Dis 2016; 10:e0004885. [PMID: 27529479 PMCID: PMC4986980 DOI: 10.1371/journal.pntd.0004885] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/08/2016] [Indexed: 02/04/2023] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are responsible globally for almost one million cryptococcosis cases yearly, mostly in immunocompromised patients, such as those living with HIV. Infections due to C. gattii have mainly been described in tropical and subtropical regions, but its adaptation to temperate regions was crucial in the species evolution and highlighted the importance of this pathogenic yeast in the context of disease. Cryptococcus gattii molecular type VGII has come to the forefront in connection with an on-going emergence in the Pacific North West of North America. Taking into account that previous work pointed towards South America as an origin of this species, the present work aimed to assess the genetic diversity within the Brazilian C. gattii VGII population in order to gain new insights into its origin and global dispersal from the South American continent using the ISHAM consensus MLST typing scheme. Our results corroborate the finding that the Brazilian C. gattii VGII population is highly diverse. The diversity is likely due to recombination generated from sexual reproduction, as evidenced by the presence of both mating types in clinical and environmental samples. The data presented herein strongly supports the emergence of highly virulent strains from ancestors in the Northern regions of Brazil, Amazonia and the Northeast. Numerous genotypes represent a link between Brazil and other parts of the world reinforcing South America as the most likely origin of the C. gattii VGII subtypes and their subsequent global spread, including their dispersal into North America, where they caused a major emergence. Cryptococcus neoformans and Cryptococcus gattii are fungal agents responsible globally for almost one million cryptococcosis cases yearly, mostly in immunocompromised patients, such as those living with HIV. Cryptococcosis is a life-threatening mycosis, frequently causing meningoencephalitis. Infections due to C. gattii were originally described in tropical and subtropical regions, but its adaptation to temperate regions was highlighted by the emergence in the Pacific North West of North America by C. gattii molecular type VGII. The present work aimed to assess the genetic diversity within the Brazilian C. gattii VGII population to gain new insights into its origin and global dispersal from the South American continent using the ISHAM MLST consensus typing scheme. Our results corroborate that the Brazilian C. gattii VGII population is highly diverse, and strongly supports the emergence of highly virulent strains from ancestors in the Northern regions of Brazil. Numerous genotypes represent a link between Brazil and other parts of the world, and the isolates from the transitional ecological area in Northeast Brazil are the most likely ancestor lineages, translocating from caatinga/cerrado by adapting progressively throughout Amazonia in South America, and spread to the North American Pacific Northwest region and other parts of the world on multiple occasions.
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Abstract
The diversification of prokaryotes is accelerated by their ability to acquire DNA from other genomes. However, the underlying processes also facilitate genome infection by costly mobile genetic elements. The discovery that cells can uptake DNA by natural transformation was instrumental to the birth of molecular biology nearly a century ago. Surprisingly, a new study shows that this mechanism could efficiently cure the genome of mobile elements acquired through previous sexual exchanges. Natural transformation was thought to provide new genetic information to bacteria. Instead, a new study suggests it cures the genome of deleterious mobile elements.
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Affiliation(s)
- Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique (CNRS), UMR3525, Paris, France
- * E-mail:
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Sanborn KB, Somasundaran M, Luzuriaga K, Leitner T. Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission. Retrovirology 2015; 12:96. [PMID: 26573574 PMCID: PMC4647327 DOI: 10.1186/s12977-015-0222-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies have demonstrated that single HIV-1 genotypes are commonly transmitted from mother to child, but such analyses primarily used single samples from mother and child. It is possible that in a single sample, obtained early after infection, only the most replication competent virus is detected even when other forms may have been transmitted. Such forms may have advantages later in infection, and may thus be detected in follow-up samples. Because HIV-1 frequently recombines, phylogenetic analyses that ignore recombination may miss transmission of multiple forms if they recombine after transmission. Moreover, recombination may facilitate adaptation, thus providing an advantage in establishing infection. The effect of recombination on viral evolution in HIV-1 infected children has not been well defined. RESULTS We analyzed full-length env sequences after single genome amplification from the plasma of four subtype B HIV-1 infected women (11-67 env clones from 1 time point within a month prior to delivery) and their non-breastfed, intrapartum-infected children (3-6 longitudinal time points per child starting at the time of HIV-1 diagnosis). To address the potential beneficial or detrimental effects of recombination, we used a recently developed hierarchical recombination detection method based on the pairwise homoplasy index (PHI)-test. Recombination was observed in 9-67% of the maternal sequences and in 25-60% of the child sequences. In the child, recombination only occurred between variants that had evolved after transmission; taking recombination into account, we identified transmission of only 1 or 2 phylogenetic lineages from mother to child. Effective HIV-1 evolutionary rates of HIV-1 were initially high in the child and slowed over time (after 1000 days). Recombination was associated with elevated evolutionary rates. CONCLUSIONS Our results confirm that 1-2 variants are typically transmitted from mothers to their newborns. They also demonstrate that early abundant recombination elevates the effective evolutionary rate, suggesting that recombination increases the rate of adaptation in HIV-1 evolution.
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Affiliation(s)
- Keri B Sanborn
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, MA, USA.
| | - Mohan Somasundaran
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, MA, USA.
| | - Katherine Luzuriaga
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, MA, USA.
| | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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Abstract
The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the "semiclonal model" or of "epidemic clonality," demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates linkage disequilibrium in the short term. In the long run, however, the effects of clonality are countered by recombination. We show that many data are at odds with this proposal and that N. meningitidis fits the criteria that we have proposed for predominant clonal evolution (PCE). We point out that (i) the proposed way to distinguish epidemic clonality from PCE may be faulty and (ii) the evidence of deep phylogenies by microarrays and whole-genome sequencing is at odds with the predictions of the semiclonal model. Last, we revisit the species status of N. meningitidis, N. gonorrheae, and N. lactamica in the light of the PCE model.
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Jassim SAA, Limoges RG. Natural solution to antibiotic resistance: bacteriophages 'The Living Drugs'. World J Microbiol Biotechnol 2014; 30:2153-70. [PMID: 24781265 PMCID: PMC4072922 DOI: 10.1007/s11274-014-1655-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/18/2014] [Indexed: 12/13/2022]
Abstract
Antibiotics have been a panacea in animal husbandry as well as in human therapy for decades. The huge amount of antibiotics used to induce the growth and protect the health of farm animals has lead to the evolution of bacteria that are resistant to the drug's effects. Today, many researchers are working with bacteriophages (phages) as an alternative to antibiotics in the control of pathogens for human therapy as well as prevention, biocontrol, and therapy in animal agriculture. Phage therapy and biocontrol have yet to fulfill their promise or potential, largely due to several key obstacles to their performance. Several suggestions are shared in order to point a direction for overcoming common obstacles in applied phage technology. The key to successful use of phages in modern scientific, farm, food processing and clinical applications is to understand the common obstacles as well as best practices and to develop answers that work in harmony with nature.
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Affiliation(s)
- Sabah A. A. Jassim
- Applied Bio Research Inc., 455 Pelissier St., Windsor, ON N9A 6Z9 Canada
| | - Richard G. Limoges
- Applied Bio Research Inc., 455 Pelissier St., Windsor, ON N9A 6Z9 Canada
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35
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Moradigaravand D, Engelstädter J. The impact of natural transformation on adaptation in spatially structured bacterial populations. BMC Evol Biol 2014; 14:141. [PMID: 24951188 PMCID: PMC4080760 DOI: 10.1186/1471-2148-14-141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/08/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. RESULTS In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. CONCLUSION Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.
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Affiliation(s)
- Danesh Moradigaravand
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland.
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Johnston C, Martin B, Fichant G, Polard P, Claverys JP. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat Rev Microbiol 2014; 12:181-96. [DOI: 10.1038/nrmicro3199] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Abstract
Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.
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38
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Yucel EB, Eraslan S, Ulgen KO. The impact of medium acidity on the chronological life span ofSaccharomyces cerevisiae - lipids, signaling cascades, mitochondrial and vacuolar functions. FEBS J 2014; 281:1281-303. [DOI: 10.1111/febs.12705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Esra B. Yucel
- Department of Chemical Engineering; Boğaziçi University; Istanbul Turkey
| | - Serpil Eraslan
- Department of Chemical Engineering; Boğaziçi University; Istanbul Turkey
| | - Kutlu O. Ulgen
- Department of Chemical Engineering; Boğaziçi University; Istanbul Turkey
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Engelstädter J, Moradigaravand D. Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation. Proc Biol Sci 2013; 281:20132609. [PMID: 24285199 DOI: 10.1098/rspb.2013.2609] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Natural transformation is a process whereby bacteria actively take up DNA from the surrounding environment and incorporate it into their genome. Natural transformation is widespread in bacteria, but its evolutionary significance is still debated. Here, we hypothesize that transformation may confer a fitness advantage in changing environments through a process we term 'genetic time travel': by taking up old genes that were retained in the environment, the bacteria may revert to a past genotypic state that proves advantageous in the present or a future environment. We scrutinize our hypothesis by means of a mathematical model involving two bacterial types (transforming and non-transforming), a single locus under natural selection and a free DNA pool. The two bacterial types were competed in environments with changing selection regimes. We demonstrate that for a wide range of parameter values for the DNA turnover rate, the transformation rate and the frequency of environmental change, the transforming type outcompetes the non-transforming type. We discuss the empirical plausibility of our hypothesis, as well as its relationship to other hypotheses for the evolution of transformation in bacteria and sex more generally, speculating that 'genetic time travel' may also be relevant in eukaryotes that undergo horizontal gene transfer.
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Affiliation(s)
- Jan Engelstädter
- School of Biological Sciences, The University of Queensland, , Brisbane, Queensland 4072, Australia, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, , Zurich 8092, Switzerland
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Engelmoer DJP, Donaldson I, Rozen DE. Conservative sex and the benefits of transformation in Streptococcus pneumoniae. PLoS Pathog 2013; 9:e1003758. [PMID: 24244172 PMCID: PMC3828180 DOI: 10.1371/journal.ppat.1003758] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/26/2013] [Indexed: 12/03/2022] Open
Abstract
Natural transformation has significant effects on bacterial genome evolution, but the evolutionary factors maintaining this mode of bacterial sex remain uncertain. Transformation is hypothesized to have both positive and negative evolutionary effects on bacteria. It can facilitate adaptation by combining beneficial mutations into a single individual, or reduce the mutational load by exposing deleterious alleles to natural selection. Alternatively, it may expose transformed cells to damaged or otherwise mutated environmental DNA and is energetically expensive. Here, we examine the long-term effects of transformation in the naturally competent species Streptococcus pneumoniae by evolving populations of wild-type and competence-deficient strains in chemostats for 1000 generations. Half of these populations were exposed to periodic mild stress to examine context-dependent benefits of transformation. We find that competence reduces fitness gain under benign conditions; however, these costs are reduced in the presence of periodic stress. Using whole genome re-sequencing, we show that competent populations fix fewer new mutations and that competence prevents the emergence of mutators. Our results show that during evolution in benign conditions competence helps maintain genome stability but is evolutionary costly; however, during periods of stress this same conservativism enables cells to retain fitness in the face of new mutations, showing for the first time that the benefits of transformation are context dependent. Transformation of environmental DNA can provide bacteria with a means to adapt quickly to a changing environment. While this can benefit microbes by facilitating the spread of antibiotic resistance, it can also be harmful if it causes the loss of beneficial alleles from a population. Therefore, it is unclear what evolutionary factors enable transformation to persist in bacterial populations. We used the naturally transformable opportunistic pathogen Streptococcus pneumoniae to investigate the long-term benefits of transformation. We compared the fitness of laboratory populations of S. pneumoniae after 1000 generations of evolution. Half of these populations were naturally transformable (competent) while the other half was deficient for this function. At the same time, half of the evolving populations were periodically exposed to short periods of mild stress. We find that competence reduces the average fitness gain of evolving populations, but this cost is mitigated in populations facing mild stress. Using whole genome sequencing, we discovered that functional competence reduces the total number of fixed mutations and prevents hyper-mutable cells from increasing in frequency. Our results suggest that competence in S. pneumoniae is a conservative process acting to preserve alleles, rather than an innovative one that persists because it recombines beneficial mutations.
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Affiliation(s)
- Daniel J. P. Engelmoer
- Faculty of Life Science, University of Manchester, Manchester, United Kingdom
- Department of Animal Ecology, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- * E-mail: (DJPE); (DER)
| | - Ian Donaldson
- Faculty of Life Science, University of Manchester, Manchester, United Kingdom
| | - Daniel E. Rozen
- Faculty of Life Science, University of Manchester, Manchester, United Kingdom
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- * E-mail: (DJPE); (DER)
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Forsdyke DR. Implications of HIV RNA structure for recombination, speciation, and the neutralism-selectionism controversy. Microbes Infect 2013; 16:96-103. [PMID: 24211872 DOI: 10.1016/j.micinf.2013.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/24/2013] [Accepted: 10/24/2013] [Indexed: 11/29/2022]
Abstract
The conflict between the needs to encode both a protein (impaired by non-synonymous mutation), and nucleic acid structure (impaired by synonymous or non-synonymous mutation), can sometimes be resolved in favour of the nucleic acid because its structure is critical for a selectively advantageous genome-wide activity--recombination. However, above a sequence difference threshold, recombination is impaired. It may then be advantageous for new species to arise. Building on the work of Grantham and others critical of the neutralist viewpoint, heuristic support for this hypothesis emerged from studies of the base composition and structure of retroviral genomes. The extreme enrichment in the purine A of the RNA of human immunodeficiency virus (HIV-1), parallels the mild purine-loading of the RNAs of most organisms, for which there is an adaptive explanation--immune evasion. However, human T cell leukaemia virus (HTLV-1), with the potential to invade the same host cell, shows extreme enrichment in the pyrimidine C. Assuming the low GC% HIV and the high GC% HTLV-1 to share a common ancestor, it was postulated that differences in GC% had arisen to prevent homologous recombination between these emerging lentiviral species. Sympatrically isolated by this intracellular reproductive barrier, prototypic HIV-1 seized the AU-rich (low GC%) high ground (thus committing to purine A rather than purine G). Prototypic HTLV-1 forwent this advantage and evolved an independent evolutionary strategy--similar to that of the GC%-rich Epstein-Barr virus--profound latency maintained by transcription of one purine-rich mRNA. The evidence supporting these interpretations is reviewed.
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Affiliation(s)
- Donald R Forsdyke
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L3N6, Canada.
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Generalism and the evolution of parasite virulence. Trends Ecol Evol 2013; 28:592-6. [DOI: 10.1016/j.tree.2013.07.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 12/24/2022]
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Moradigaravand D, Engelstädter J. The evolution of natural competence: disentangling costs and benefits of sex in bacteria. Am Nat 2013; 182:E112-26. [PMID: 24021408 DOI: 10.1086/671909] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
One of the most challenging questions in evolutionary biology is how sex has evolved in the face of substantial fitness costs. In this study, we focus on the evolution of bacterial sex in the form of natural transformation, where cells take up exogenous DNA and integrate it into the genome. Besides the physiological cost of producing a DNA uptake system, transformation can potentially impose a genetic cost as a result of an overrepresentation of deleterious mutations in the extracellular DNA pool. On the other hand, the uptake of DNA can be beneficial not only because of genetic effects but also because of the immediate nutritional value of the DNA. To disentangle these fitness costs and benefits, we developed a mathematical model and competed three bacterial types during adaptation to a new environment: competent cells capable of DNA import and digestion; competent cells capable of DNA import, digestion, and recombination; and noncompetent cells. Our results indicate a complex interplay between several physiological and ecological factors, including the rate at which DNA is taken up, the rate of DNA decay in the medium, and the nutritional value of DNA. In finite populations, the recombining type is often favored through the Fisher-Muller effect.
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Affiliation(s)
- Danesh Moradigaravand
- Institute of Biogeochemistry and Pollutant Dynamics, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
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Gene copy number is differentially regulated in a multipartite virus. Nat Commun 2013; 4:2248. [DOI: 10.1038/ncomms3248] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 07/05/2013] [Indexed: 12/14/2022] Open
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Tibayrenc M, Ayala FJ. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci U S A 2012; 109:E3305-13. [PMID: 22949662 PMCID: PMC3511763 DOI: 10.1073/pnas.1212452109] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering ("near-clading"). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes ("clonality/sexuality machinery") to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, Institut de Rercherche pour le Développement 224, Centre National de la Recherche Scientifique 5290, Universités Montpellier 1 and 2, 34394 Montpellier Cedex 5, France; and
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
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Kidane D, Ayora S, Sweasy JB, Graumann PL, Alonso JC. The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery. Crit Rev Biochem Mol Biol 2012; 47:531-55. [PMID: 23046409 DOI: 10.3109/10409238.2012.729562] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.
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Affiliation(s)
- Dawit Kidane
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, CT, USA
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Seitz P, Blokesch M. Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria. FEMS Microbiol Rev 2012; 37:336-63. [PMID: 22928673 DOI: 10.1111/j.1574-6976.2012.00353.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/27/2012] [Accepted: 08/21/2012] [Indexed: 12/23/2022] Open
Abstract
Bacterial genomics is flourishing, as whole-genome sequencing has become affordable, readily available and rapid. As a result, it has become clear how frequently horizontal gene transfer (HGT) occurs in bacteria. The potential implications are highly significant because HGT contributes to several processes, including the spread of antibiotic-resistance cassettes, the distribution of toxin-encoding phages and the transfer of pathogenicity islands. Three modes of HGT are recognized in bacteria: conjugation, transduction and natural transformation. In contrast to the first two mechanisms, natural competence for transformation does not rely on mobile genetic elements but is driven solely by a developmental programme in the acceptor bacterium. Once the bacterium becomes competent, it is able to take up DNA from the environment and to incorporate the newly acquired DNA into its own chromosome. The initiation and duration of competence differ significantly among bacteria. In this review, we outline the latest data on representative naturally transformable Gram-negative bacteria and how their competence windows differ. We also summarize how environmental cues contribute to the initiation of competence in a subset of naturally transformable Gram-negative bacteria and how the complexity of the niche might dictate the fine-tuning of the competence window.
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Affiliation(s)
- Patrick Seitz
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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de Buitléir A, Russell M, Daly M. Wains: a pattern-seeking artificial life species. ARTIFICIAL LIFE 2012; 18:399-423. [PMID: 22938560 DOI: 10.1162/artl_a_00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We describe the initial phase of a research project to develop an artificial life framework designed to extract knowledge from large data sets with minimal preparation or ramp-up time. In this phase, we evolved an artificial life population with a new brain architecture. The agents have sufficient intelligence to discover patterns in data and to make survival decisions based on those patterns. The species uses diploid reproduction, Hebbian learning, and Kohonen self-organizing maps, in combination with novel techniques such as using pattern-rich data as the environment and framing the data analysis as a survival problem for artificial life. The first generation of agents mastered the pattern discovery task well enough to thrive. Evolution further adapted the agents to their environment by making them a little more pessimistic, and also by making their brains more efficient.
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Ambur OH, Frye SA, Nilsen M, Hovland E, Tønjum T. Restriction and sequence alterations affect DNA uptake sequence-dependent transformation in Neisseria meningitidis. PLoS One 2012; 7:e39742. [PMID: 22768309 PMCID: PMC3388099 DOI: 10.1371/journal.pone.0039742] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/26/2012] [Indexed: 12/17/2022] Open
Abstract
Transformation is a complex process that involves several interactions from the binding and uptake of naked DNA to homologous recombination. Some actions affect transformation favourably whereas others act to limit it. Here, meticulous manipulation of a single type of transforming DNA allowed for quantifying the impact of three different mediators of meningococcal transformation: NlaIV restriction, homologous recombination and the DNA Uptake Sequence (DUS). In the wildtype, an inverse relationship between the transformation frequency and the number of NlaIV restriction sites in DNA was observed when the transforming DNA harboured a heterologous region for selection (ermC) but not when the transforming DNA was homologous with only a single nucleotide heterology. The influence of homologous sequence in transforming DNA was further studied using plasmids with a small interruption or larger deletions in the recombinogenic region and these alterations were found to impair transformation frequency. In contrast, a particularly potent positive driver of DNA uptake in Neisseria sp. are short DUS in the transforming DNA. However, the molecular mechanism(s) responsible for DUS specificity remains unknown. Increasing the number of DUS in the transforming DNA was here shown to exert a positive effect on transformation. Furthermore, an influence of variable placement of DUS relative to the homologous region in the donor DNA was documented for the first time. No effect of altering the orientation of DUS was observed. These observations suggest that DUS is important at an early stage in the recognition of DNA, but does not exclude the existence of more than one level of DUS specificity in the sequence of events that constitute transformation. New knowledge on the positive and negative drivers of transformation may in a larger perspective illuminate both the mechanisms and the evolutionary role(s) of one of the most conserved mechanisms in nature: homologous recombination.
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Kalkanci A, Kadioglu A, Wilson D, Jacobsen MD. Gene expression in fungi. IMA Fungus 2012; 2:29-32. [PMID: 22679585 PMCID: PMC3317368 DOI: 10.5598/imafungus.2011.02.01.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 05/06/2011] [Indexed: 10/24/2022] Open
Abstract
This contribution is based on the four presentations made at the Special Interest Group (SIG) meeting titled Gene Expression in Fungi held during IMC9 in Edinburgh. This overview is independent from other articles published or that will be published by each speaker. In the SIG meeting, basic principles of in vivo animal models for virulence studies were discussed. Infection associated genes of Candida albicans and fungal adaptation to the host was summarized. Azole susceptibility was evaluated as a combined result of several changes in expression of pertinent genes. Gene transfer in fungi, resulting in fungal evolution and gene adaptation to environmental factors, was reported.
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Affiliation(s)
- Ayse Kalkanci
- Gazi University Faculty of Medicine, Department of Medical Microbiology, Ankara, 06500 Turkey
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