scholarly journals Virus-host coexistence in phytoplankton through the genomic lens

2020 ◽  
Vol 6 (14) ◽  
pp. eaay2587 ◽  
Author(s):  
Sheree Yau ◽  
Marc Krasovec ◽  
L. Felipe Benites ◽  
Stephane Rombauts ◽  
Mathieu Groussin ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Large Deletion ◽  
Genomic Rearrangements ◽  
Dsdna Virus ◽  
Viral Production ◽  
Boom And Bust ◽  
Microbe Interactions ◽  
Clonal Lines ◽  
Virus Interactions ◽  
Parallel Growth

Virus-microbe interactions in the ocean are commonly described by “boom and bust” dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.

scholarly journals Virus-host coexistence in phytoplankton through the genomic lens

2019 ◽  
Author(s):  
Yau Sheree ◽  
Marc Krasovec ◽  
Stephane Rombauts ◽  
Mathieu Groussin ◽  
L. Felipe Benites ◽  
...  
Keyword(s):  
Single Cell ◽  
Orthologous Genes ◽  
Hedging Strategy ◽  
Continuous Growth ◽  
Phase Switching ◽  
Host Interactions ◽  
Boom And Bust ◽  
Nw Mediterranean ◽  
Nw Mediterranean Sea ◽  
Virus Interactions

AbstractPhytoplankton-virus interactions are major determinants of geochemical cycles in the oceans. Viruses are responsible for the redirection of carbon and nutrients away from larger organisms back towards microorganisms via the lysis of microalgae in a process coined the ‘viral shunt’. Virus-host interactions are generally expected to follow ‘boom and bust’ dynamics, whereby a numerically dominant strain is lysed and replaced by a virus resistant strain. Here, we isolated a microalga and its infective nucleo-cytoplasmic large DNA virus (NCLDV) concomitantly from the environment in the surface NW Mediterranean Sea, Ostreococcus mediterraneus, and show continuous growth in culture of both the microalga and the virus. Evolution experiments through single cell bottlenecks demonstrate that, in the absence of the virus, susceptible cells evolve from one ancestral resistant single cell, and vice–versa; that is that resistant cells evolve from one ancestral susceptible cell. This provides evidence that the observed sustained viral production is the consequence of a minority of virus-susceptible cells. The emergence of these cells is explained by low-level phase switching between virus-resistant and virus-susceptible phenotypes, akin to a bet hedging strategy. Whole genome sequencing and analysis of the ~14 Mb microalga and the ~200 kb virus points towards ancient speciation of the microalga within the Ostreococcus species complex and frequent gene exchanges between prasinoviruses infecting Ostreococcus species. Re-sequencing of one susceptible strain demonstrated that the phase switch involved a large 60 Kb deletion of one chromosome. This chromosome is an outlier chromosome compared to the streamlined, gene dense, GC-rich standard chromosomes, as it contains many repeats and few orthologous genes. While this chromosome has been described in three different genera, its size increments have been previously associated to antiviral immunity and resistance in another species from the same genus. Mathematical modelling of this mechanism predicts microalga–virus population dynamics consistent with the observation of continuous growth of both virus and microalga. Altogether, our results suggest a previously overlooked strategy in phytoplankton–virus interactions.

scholarly journals Experimental evolution of the megaplasmid pMPPla107 in Pseudomonas stutzeri enables identification of genes contributing to sensitivity to an inhibitory agent

2021 ◽  
Vol 377 (1842) ◽  
Author(s):  
Brian A. Smith ◽  
Kevin Dougherty ◽  
Meara Clark ◽  
David A. Baltrus
Keyword(s):  
Pseudomonas Syringae ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Pseudomonas Stutzeri ◽  
Large Deletion ◽  
Host Cells ◽  
Single Amino Acid ◽  
Fitness Costs ◽  
Nonsynonymous Change ◽  
Single Amino Acid Change

Horizontally transferred elements, such as plasmids, can burden host cells with various metabolic and fitness costs and may lead to other potentially detrimental phenotypic effects. Acquisition of the Pseudomonas syringae megaplasmid pMPPla107 by various Pseudomonads causes sensitivity to a growth-inhibiting substance that is produced in cultures by Pseudomonads during growth under standard laboratory conditions. After approximately 500 generations of laboratory passage of Pseudomonas stutzeri populations containing pMPPla107, strains from two out of six independent passage lines displayed resistance to this inhibitory agent. Resistance was transferable and is, therefore, associated with mutations occurring on pMPPla107. Resequencing experiments demonstrated that resistance is likely due to a large deletion on the megaplasmid in one line, and to a nonsynonymous change in an uncharacterized megaplasmid locus in the other strain. We further used allele exchange experiments to confirm that resistance is due to this single amino acid change in a previously uncharacterized megaplasmid protein, which we name SkaA. These results provide further evidence that costs and phenotypic changes associated with horizontal gene transfer can be compensated through single mutational events and emphasize the power of experimental evolution and resequencing to better understand the genetic basis of evolved phenotypes. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

scholarly journals Rapid evolution of bacterial mutualism in the plant rhizosphere

2020 ◽  
Author(s):  
Erqin Li ◽  
Ronnie de Jonge ◽  
Chen Liu ◽  
Henan Jiang ◽  
Ville-Petri Friman ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Direct Evidence ◽  
Rapid Evolution ◽  
Evolutionary Transition ◽  
Transcription Factor Gene ◽  
Growth Cycles ◽  
Factor Gene ◽  
Two Component ◽  
Microbe Interactions ◽  
Fitness Benefits

SummaryEven though beneficial plant-microbe interactions are commonly observed in nature, direct evidence for the evolution of bacterial mutualism in the rhizosphere remains elusive. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacterium evolves into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition was accompanied with increased mutualist fitness via two mechanisms: i) improved competitiveness for root exudates and ii) enhanced capacity for activating the root-specific transcription factor gene MYB72, which triggers the production of plant-secreted scopoletin antimicrobial for which the mutualists evolved relatively higher tolerance to. Genetically, mutualism was predominantly associated with different mutations in the GacS/GacA two-component regulator system, which conferred high fitness benefits only in the presence of plants. Together, our results show that bacteria can rapidly evolve along the parasitism-mutualism continuum in the plant rhizosphere at an agriculturally relevant evolutionary timescale.

scholarly journals Identification of mutations in the Bruton's tyrosine kinase gene, including a novel genomic rearrangements resulting in large deletion, in Korean X-linked agammaglobulinemia patients

2003 ◽  
Vol 48 (6) ◽  
pp. 322-326 ◽  
Author(s):  
Eun-Kyeong Jo ◽  
Yue Wang ◽  
Hirokazu Kanegane ◽  
Takeshi Futatani ◽  
Chang-Hwa Song ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Large Deletion ◽  
Genomic Rearrangements ◽  
Bruton’S Tyrosine Kinase ◽  
Kinase Gene ◽  
Bruton's Tyrosine Kinase ◽  
Tyrosine Kinase Gene

scholarly journals Rapid evolution of bacterial mutualism in the plant rhizosphere

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Erqin Li ◽  
Ronnie de Jonge ◽  
Chen Liu ◽  
Henan Jiang ◽  
Ville-Petri Friman ◽  
...  
Keyword(s):  
Plant Growth ◽  
Experimental Evolution ◽  
Direct Evidence ◽  
Rapid Evolution ◽  
Evolutionary Transition ◽  
Growth Cycles ◽  
Two Component ◽  
Microbe Interactions ◽  
Fitness Benefits ◽  
Positive Effect

AbstractWhile beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.

scholarly journals Experimental Evolution of the Megaplasmid pMPPla107 in Pseudomonas stutzeri Enables Identification of Genes Contributing to Sensitivity to an Inhibitory Agent

2019 ◽  
Author(s):  
Brian A. Smith ◽  
Kevin Dougherty ◽  
Meara Clark ◽  
David A. Baltrus
Keyword(s):  
Pseudomonas Syringae ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Pseudomonas Stutzeri ◽  
Large Deletion ◽  
Host Cells ◽  
Standard Laboratory ◽  
Fitness Costs ◽  
Killing Activity ◽  
Compensatory Mutations

ABSTRACTHorizontally transferred elements such as plasmids can, at times, burden host cells with various metabolic and fitness costs. Our previous work demonstrated that acquisition of the Pseudomonas syringae megaplasmid pMPPla107 causes sensitivity to a growth inhibiting substance that is produced in cultures during growth under standard laboratory conditions. After 500 generations of laboratory passage of P. stutzeri lines containing pMPPla107, two out of six independent lines displayed resistance to this inhibitory agent. We therefore sequenced the genomes of isolates from each independent evolutionary line to identify the genetic basis of this resistance phenotype through comparative genomics. Our analysis demonstrates that two different compensatory mutations on the megaplasmid ameliorate the sensitivity phenotype: 1) a large deletion of approximately 368kb in pMPPla107 and 2) a SNP in the gene we name skaA for Supernatant Killing Activity. These results provide further evidence that costs associated with horizontal gene transfer can be compensated through single mutational events and emphasize the power of experimental evolution and resequencing to better understand the genetic basis of evolved phenotypes.

scholarly journals Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatiana Maroilley ◽  
Xiao Li ◽  
Matthew Oldach ◽  
Francesca Jean ◽  
Susan J. Stasiuk ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Chromosomal Rearrangements ◽  
Large Deletion ◽  
Genomic Rearrangements ◽  
Model Organisms ◽  
Whole Genome ◽  
Short Read ◽  
C Elegans ◽  
Long Read

AbstractGenomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.

scholarly journals Experimental evolution of independent genetic pathways for resistance to Pseudomonas aeruginosa pathogenicity within the nematode Caenorhabditis remanei

2018 ◽  
Author(s):  
Heather Archer ◽  
Patrick C. Phillips
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Opportunistic Pathogen ◽  
Nematode Resistance ◽  
Genetic Pathways ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Caenorhabditis Remanei ◽  
Pathogenic Effects

ABSTRACTPathogenic host-microbe interactions can result from continuous evolution of a host’s ability to resist infection and a pathogen’s ability to survive and replicate. Pseudomonas aeruginosa is a versatile and opportunistic pathogen, ubiquitous in the environment, and capable of damaging plants, vertebrates, and invertebrates. Previous studies in nematodes suggest that the pathogenic effects of P. aeruginosa can result from multiple distinct pathways: a toxin-based effect that kills within a few hours and a generalized virulence that kills over the course of multiple days. Using experimental evolution in the highly polymorphic nematode Caenorhabditis remanei, we show that nematode resistance to the two modes of pathogenesis in P. aeruginosa evolves through genetically independent pathways. These results demonstrate that multiple virulence patterns in a pathogen can result in multiple responses in the host, and the genetic lines established here create resources for further exploration of the genetic basis for resistance to P. aeruginosa.

Experimental evolution of a fungal pathogen into a gut symbiont

Science ◽  
2018 ◽  
Vol 362 (6414) ◽  
pp. 589-595 ◽  
Author(s):  
Gloria Hoi Wan Tso ◽  
Jose Antonio Reales-Calderon ◽  
Alrina Shin Min Tan ◽  
XiaoHui Sem ◽  
Giang Thi Thu Le ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Fungal Pathogen ◽  
Experimental System ◽  
New Host ◽  
Evolutionary Forces ◽  
Cytokine Responses ◽  
Microbe Interactions ◽  
New Hosts ◽  
Opportunistic Fungal Pathogen ◽  
Systemic Infections

Gut microbes live in symbiosis with their hosts, but how mutualistic animal-microbe interactions emerge is not understood. By adaptively evolving the opportunistic fungal pathogenCandida albicansin the mouse gastrointestinal tract, we selected strains that not only had lost their main virulence program but also protected their new hosts against a variety of systemic infections. This protection was independent of adaptive immunity, arose as early as a single day postpriming, was dependent on increased innate cytokine responses, and was thus reminiscent of “trained immunity.” Because both the microbe and its new host gain some advantages from their interaction, this experimental system might allow direct study of the evolutionary forces that govern the emergence of mutualism between a mammal and a fungus.

scholarly journals Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal–Microbe Interactions

2016 ◽  
Vol 07 ◽  
Author(s):  
Kim L. Hoang ◽  
Levi T. Morran ◽  
Nicole M. Gerardo
Keyword(s):  
Experimental Evolution ◽  
Microbe Interactions
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