scholarly journals Genetic exchange and the origin of adaptations: prokaryotes to primates

2008 ◽  
Vol 363 (1505) ◽  
pp. 2813-2820 ◽  
Author(s):  
Michael L Arnold ◽  
Yuval Sapir ◽  
Noland H Martin
Keyword(s):  
Gene Transfer ◽  
Adaptive Evolution ◽  
Lateral Gene Transfer ◽  
De Novo ◽  
Genetic Material ◽  
Introgressive Hybridization ◽  
Genetic Exchange ◽  
Viral Recombination ◽  
Adaptive Trait

Data supporting the occurrence of adaptive trait transfer (i.e. the transfer of genes and thus the phenotype of an adaptive trait through viral recombination, lateral gene transfer or introgressive hybridization) are provided in this review. Specifically, we discuss examples of lateral gene transfer and introgressive hybridization that have resulted in the transfer or de novo origin of adaptations. The evolutionary clades in which this process has been identified include all types of organisms. However, we restrict our discussion to bacteria, fungi, plants and animals. Each of these examples reflects the same consequence, namely that the transfer of genetic material, through whatever mechanism, may result in adaptive evolution. In particular, each of the events discussed has been inferred to impact adaptations to novel environmental settings in the recipient lineage.

scholarly journals Adaptive Evolution of C4 Photosynthesis through Recurrent Lateral Gene Transfer

2012 ◽  
Vol 22 (5) ◽  
pp. 445-449 ◽  
Author(s):  
Pascal-Antoine Christin ◽  
Erika J. Edwards ◽  
Guillaume Besnard ◽  
Susanna F. Boxall ◽  
Richard Gregory ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Adaptive Evolution ◽  
Lateral Gene Transfer ◽  
C4 Photosynthesis

Bacterial origin of thymidylate and folate metabolism in Asgard Archaea

2021 ◽  
Author(s):  
Jonathan Filee ◽  
Hubert J. Becker ◽  
Lucille Mellottee ◽  
Zhihui LI ◽  
Jean-Christophe Lambry ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Trees ◽  
De Novo ◽  
Horizontal Transmission ◽  
Folate Metabolism ◽  
Ecological Niches ◽  
Sequence Information ◽  
Amino Acid Utilization ◽  
Genome Wide

Little is known about the evolution and biosynthetic function of DNA precursor and the folate metabolism in the Asgard group of archaea. As Asgard occupy a key position in the archaeal and eukaryotic phylogenetic trees, we have exploited very recently emerged genome and metagenome sequence information to investigate these central metabolic pathways. Our genome-wide analyses revealed that the recently cultured Asgard archaeon Candidatus Prometheoarchaeum syntrophicum strain MK-D1 (Psyn) contains a complete folate-dependent network for the biosynthesis of DNA/RNA precursors, amino acids and syntrophic amino acid utilization. Altogether our experimental and computational data suggest that phylogenetic incongruences of functional folate-dependent enzymes from Asgard archaea reflect their persistent horizontal transmission from various bacterial groups, which has rewired the key metabolic reactions in an important and recently identified archaeal phylogenetic group. We also experimentally validated the functionality of the lateral gene transfer of Psyn thymidylate synthase ThyX. This enzyme uses bacterial-like folates efficiently and is inhibited by mycobacterial ThyX inhibitors. Our data raise the possibility that the thymidylate metabolism, required for de novo DNA synthesis, originated in bacteria and has been independently transferred to archaea and eukaryotes. In conclusion, our study has revealed that recent prevalent lateral gene transfer has markedly shaped the evolution of Asgard archaea by allowing them to adapt to specific ecological niches.

scholarly journals Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

mBio ◽  
2017 ◽  
Vol 8 (3) ◽  
Author(s):  
Bradon R. McDonald ◽  
Cameron R. Currie
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Point Mutations ◽  
Time Span ◽  
Genetic Exchange ◽  
Bacterial Evolution ◽  
Phylogenetic Groups ◽  
Modern Biology ◽  
Genus Streptomyces ◽  
Bacterial Genus

ABSTRACT Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces . Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution. IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces , with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.

scholarly journals The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7216 ◽  
Author(s):  
Lucile Vigué ◽  
Adam Eyre-Walker
Keyword(s):  
Population Genetics ◽  
Gene Transfer ◽  
Neisseria Meningitidis ◽  
Population Size ◽  
Effective Population Size ◽  
Adaptive Evolution ◽  
Lateral Gene Transfer ◽  
Pathogenic Bacteria ◽  
Core Genome ◽  
Effective Population

Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.

scholarly journals Genomic Background Governs Opposing Responses to Nalidixic Acid Upon Megaplasmid Acquisition in Pseudomonas

2019 ◽  
Author(s):  
David A. Baltrus ◽  
Caitlin Smith ◽  
MacKenzie Derrick ◽  
Courtney Leligdon ◽  
Zoe Rosenthal ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nalidixic Acid ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Horizontal Gene Transfer Event ◽  
Genetic Material ◽  
Fitness Costs ◽  
Transfer Event ◽  
Phenotypic Changes

AbstractHorizontal gene transfer is a significant driver of evolutionary dynamics across microbial populations. Although the benefits of the acquisition of new genetic material are often quite clear, experiments across systems have demonstrated that gene transfer events can cause significant phenotypic changes and entail fitness costs in a way that is dependent on the genomic and environmental context. Here we test for the generality of one previously identified cost, sensitization of cells to the antibiotic nalidixic acid after acquisition of a ∼1Mb megaplasmid, across Pseudomonas strains and species. Overall, we find that the presence of this megaplasmid sensitizes many different Pseudomonas strains to nalidixic acid, but that this same horizontal gene transfer event increases resistance of Pseudomonas putida KT2440 to nalidixic acid across assays as well as to ciprofloxacin under competitive conditions. These phenotypic results are not easily explained away as secondary consequences of overall fitness effects and appear to occur independently of another cost associated with this megaplasmid, sensitization to higher temperatures. Lastly, we draw parallels between these reported results and the phenomenon of sign epistasis for de novo mutations and explore how context dependence of effects of plasmid acquisition could impact overall evolutionary dynamics and the evolution of antimicrobial resistance.ImportanceNumerous studies have demonstrated that gene transfer events (e.g. plasmid acquisition) can entail a variety of costs that arise as byproducts of the incorporation of foreign DNA into established physiological and genetic systems. These costs can be ameliorated through evolutionary time by the occurrence of compensatory mutations, which stabilize presence of a horizontally transferred region within the genome but which also may skew future adaptive possibilities for these lineages. Here we demonstrate another possible outcome, that phenotypic changes arising as a consequence of the same horizontal gene transfer event are costly to some strains but may actually be beneficial in other genomic backgrounds under the right conditions. These results provide new a new viewpoint for considering conditions that promote plasmid maintenance and highlight the influence of genomic and environmental contexts when considering amelioration of fitness costs after HGT events.

scholarly journals MECHANISMS OF RESISTANCE TRANSFER IN BACTERIA

2010 ◽  
Vol 3 (1) ◽  
pp. 85-92 ◽  
Author(s):  
Maja Velhner ◽  
Jelena Petrović ◽  
Igor Stojanov ◽  
Radomir Ratajac ◽  
Dragica Stojanović
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Genomic Structure ◽  
Genetic Material ◽  
Mobile Genetic Elements ◽  
Mechanisms Of Resistance ◽  
Genetic Elements ◽  
Resistance Transfer ◽  
The Future ◽  
Microbial Infections

Wide application of antimicorbial agents forces bacteria to utilize specific genes and rearrange genomic structure in order to survive in the environment. In this article lateral gene transfer, mobile genetic elements, plasmid mediated resistance and spontaneous mutators in bacteria are briefly described. This resourceful means, by which microorganisms manage to communicate and transfer genetic material in their own kingdom, raises concerns about the possibility to keep microbial infections under control in the future.

scholarly journals Chromosomal Recombination Targets in Chlamydia Interspecies Lateral Gene Transfer

2019 ◽  
Vol 201 (23) ◽  
Author(s):  
Robert J. Suchland ◽  
Steven J. Carrell ◽  
Yibing Wang ◽  
Kevin Hybiske ◽  
Debbie B. Kim ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Genome Sequence ◽  
Genetic Exchange ◽  
Selection Marker ◽  
Hybrid Strain ◽  
Genome Sequence Analysis ◽  
Content Type

ABSTRACT Lateral gene transfer (LGT) among Chlamydia trachomatis strains is common, in both isolates generated in the laboratory and those examined directly from patients. In contrast, there are very few examples of recent acquisition of DNA by any Chlamydia spp. from any other species. Interspecies LGT in this system was analyzed using crosses of tetracycline (Tc)-resistant C. trachomatis L2/434 and chloramphenicol (Cam)-resistant C. muridarum VR-123. Parental C. muridarum strains were created using a plasmid-based Himar transposition system, which led to integration of the Camr marker randomly across the chromosome. Fragments encompassing 79% of the C. muridarum chromosome were introduced into a C. trachomatis background, with the total coverage contained on 142 independent recombinant clones. Genome sequence analysis of progeny strains identified candidate recombination hot spots, a property not consistent with in vitro C. trachomatis × C. trachomatis (intraspecies) crosses. In both interspecies and intraspecies crosses, there were examples of duplications, mosaic recombination endpoints, and recombined sequences that were not linked to the selection marker. Quantitative analysis of the distribution and constitution of inserted sequences indicated that there are different constraints on interspecies LGT than on intraspecies crosses. These constraints may help explain why there is so little evidence of interspecies genetic exchange in this system, which is in contrast to very widespread intraspecies exchange in C. trachomatis. IMPORTANCE Genome sequence analysis has demonstrated that there is widespread lateral gene transfer among strains within the species C. trachomatis and with other closely related Chlamydia species in laboratory experiments. This is in contrast to the complete absence of foreign DNA in the genomes of sequenced clinical C. trachomatis strains. There is no understanding of any mechanisms of genetic transfer in this important group of pathogens. In this report, we demonstrate that interspecies genetic exchange can occur but that the nature of the fragments exchanged is different than those observed in intraspecies crosses. We also generated a large hybrid strain library that can be exploited to examine important aspects of chlamydial disease.

scholarly journals Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. E2: Massive bacterial transfer of genes involved in carbohydrate metabolism

2019 ◽  
Author(s):  
Isabel Duarte ◽  
Martijn A. Huynen
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Large Scale ◽  
Plant Cell Wall ◽  
Phylogenetic Analyses ◽  
Genetic Material ◽  
Wall Material ◽  
Chytrid Fungus ◽  
Evolutionary Mechanisms ◽  
Unicellular Eukaryotes

ABSTRACTLateral gene transfer (also known as Horizontal Gene Transfer) is the transmission of genetic material between phylogenetically unrelated organisms. Previous studies have been showing the importance of this process for the evolution of unicellular eukaryotes, particularly those living in highly competitive niches such as the herbivore gut.Pyromices sp. is an obligate anaerobic chytrid fungus that grows as a commensal organism in the gut of mammalian herbivores, possessing hydrogenosomes instead of mitochondria, producing hydrogen, and playing a key role in the digestion of plant cell wall material. These particular features make its genome particularly valuable for the study of the evolution and adaptation of unicellular eukaryotes to the cellulose-rich and anaerobic environment of the herbivore gut.Here we performed a detailed large-scale lateral gene transfer (LGT) analysis of the genome from the chytrid fungus Piromyces sp. strain E2. For this we set out to elucidate (i) which proteins were likely transferred to its genome, (ii) from which bacterial donor species, and (iii) which functions were laterally acquired. Using sequence comparison and phylogenetic analyses, we have found 704 LGT candidates, representing nearly 5% of the Piromyces sp. orfeome (i.e. the complete set of open reading frames), mostly transferred from Firmicutes, Fibrobacteres, Bacteroidetes and Proteobacteria, closely following the microbial abundance reported for the herbivore gut. With respect to the functional analysis, the LGT candidate set includes proteins from 250 different orthologous groups, with a clear over-representation of genes belonging to the Carbohydrate Transport and Metabolism functional class. Finally, we performed a graph density analysis on the metabolic pathways formed by the LGT candidate proteins, showing that the acquired functions fit cohesively within Piromyces metabolic network, and are not randomly distributed within the global KEGG metabolic map. Overall, our study suggests that Piromyces’ adaptation to living anaerobically and in the a cellulose-rich environment has been undoubtedly fostered by the acquisition of foreign genes from bacterial neighbors, showing the global importance of such evolutionary mechanisms for successful eukaryotic thriving in such competitive environments.

scholarly journals Genome expansion in early eukaryotes drove the transition from lateral gene transfer to meiotic sex

2020 ◽  
Author(s):  
Marco Colnaghi ◽  
Nick Lane ◽  
Andrew Pomiankowski
Keyword(s):  
Gene Transfer ◽  
Genome Size ◽  
Lateral Gene Transfer ◽  
Genetic Material ◽  
Theoretical Models ◽  
Deleterious Mutations ◽  
Strong Constraint ◽  
Muller's Ratchet ◽  
Muller’S Ratchet ◽  
Recombination Length

ABSTRACTProkaryotes generally reproduce clonally but can also acquire new genetic material via lateral gene transfer (LGT). Like sex, LGT can prevent the accumulation of deleterious mutations predicted by Muller’s ratchet for asexual populations. This similarity between sex and LGT raises the question why did eukaryotes abandon LGT in favor of sexual reproduction? Understanding the limitations of LGT provides insight into this evolutionary transition. We model the evolution of a haploid population undergoing LGT at a rate λ and subjected to a mutation rate μ. We take into account recombination length, L, and genome size, g, neglected by previous theoretical models. We confirm that LGT counters Muller’s ratchet by reducing the rate of fixation of deleterious mutations in small genomes. We then demonstrate that this beneficial effect declines rapidly with genome size. Populations with larger genomes are subjected to a faster rate of fixation of deleterious mutations and become more vulnerable to stochastic frequency fluctuations. Muller’s ratchet therefore generates a strong constraint on genome size. Importantly, we show that the degeneration of larger genomes can be resisted by increases in the recombination length, the average number of contiguous genes drawn from the environment for LGT. Large increases in genome size, as in early eukaryotes, are only possible as L reaches the same order of magnitude as g. This requirement for recombination across the whole genome can explain the strong selective pressure towards the evolution of sexual cell fusion and reciprocal recombination during early eukaryotic evolution – the origin of meiotic sex.

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