scholarly journals Experimental evolution makes microbes more cooperative with their local host genotype

Science ◽  
2020 ◽  
Vol 370 (6515) ◽  
pp. 476-478 ◽  
Author(s):  
Rebecca T. Batstone ◽  
Anna M. O’Brien ◽  
Tia L. Harrison ◽  
Megan E. Frederickson
Keyword(s):  
Experimental Evolution ◽  
Evolutionary History ◽  
Host Choice ◽  
Bacterial Symbionts ◽  
Inoculation Experiment ◽  
Host Genotype ◽  
Ensifer Meliloti ◽  
Evolution Experiment ◽  
Local Host ◽  
Microbial Strains

Advances in microbiome science require a better understanding of how beneficial microbes adapt to hosts. We tested whether hosts select for more-cooperative microbial strains with a year-long evolution experiment and a cross-inoculation experiment designed to explore how nitrogen-fixing bacteria (rhizobia) adapt to legumes. We paired the bacterium Ensifer meliloti with one of five Medicago truncatula genotypes that vary in how strongly they “choose” bacterial symbionts. Independent of host choice, E. meliloti rapidly adapted to its local host genotype, and derived microbes were more beneficial when they shared evolutionary history with their host. This local adaptation was mostly limited to the symbiosis plasmids, with mutations in putative signaling genes. Thus, cooperation depends on the match between partner genotypes and increases as bacteria adapt to their local host.

scholarly journals Experimental Evolution Reveals a Genetic Basis for Membrane-Associated Virus Release

2020 ◽  
Author(s):  
Juan-Vicente Bou ◽  
Rafael Sanjuán
Keyword(s):  
Experimental Evolution ◽  
Genetic Basis ◽  
Close Association ◽  
Site Directed Mutagenesis ◽  
Full Genome ◽  
Virus Release ◽  
Viral Shedding ◽  
Free Virion ◽  
Viral Particles ◽  
Evolution Experiment

Abstract Many animal viruses replicate and are released from cells in close association to membranes. However, whether this is a passive process or is controlled by the virus remains poorly understood. Importantly, the genetic basis and evolvability of membrane-associated viral shedding have not been investigated. To address this, we performed a directed evolution experiment using coxsackievirus B3, a model enterovirus, in which we repeatedly selected the free-virion or the fast-sedimenting membrane-associated viral subpopulations. The virus responded to this selection regime by reproducibly fixing a series of mutations that altered the extent of membrane-associated viral shedding, as revealed by full-genome ultra-deep sequencing. Specifically, using site-directed mutagenesis, we showed that substitution N63H in the viral capsid protein VP3 reduced the ratio of membrane-associated to free viral particles by 2 orders of magnitude. These findings open new avenues for understanding the mechanisms and implications of membrane-associated viral transmission.

scholarly journals Gene-level quantitative trait mapping in an expandedC. elegansmultiparent experimental evolution panel

2019 ◽  
Author(s):  
Luke M. Noble ◽  
Matthew V. Rockman ◽  
Henrique Teotónio
Keyword(s):  
Experimental Evolution ◽  
Recombinant Inbred Lines ◽  
Single Gene ◽  
Ancestral Population ◽  
C Elegans ◽  
Quantitative Trait Mapping ◽  
Trait Variance ◽  
Gene Level ◽  
Evolution Experiment

ABSTRACTTheCaenorhabditis elegansmultiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the genetic basis and evolution of quantitative traits. We have expanded the resource with new lines and new populations, and here report updated additive and epistatic mapping simulations and the genetic and haplotypic composition of CeMEE version 2. Additive QTL explaining 3% of trait variance are detected with >80% power, and the median detection interval is around the length of a single gene on the highly recombinant chromosome arms. Although CeMEE populations are derived from a long-term evolution experiment, genetic structure is dominated by variation present in the ancestral population and is not obviously associated with phenotypic differentiation.C. elegansprovides exceptional experimental advantages for the study of phenotypic evolution.

scholarly journals Selection maintains protein interactome resilience in the long-term evolution experiment with Escherichia coli

2021 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Experimental Evolution ◽  
Long Term Evolution ◽  
Rate Of Change ◽  
Network Resilience ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Term Evolution ◽  
Protein Interactome ◽  
Evolution Experiment

AbstractMost cellular functions are carried out by a dynamic network of interacting proteins. An open question is whether the network properties of protein interactomes represent phenotypes under natural selection. One proposal is that protein interactomes have evolved to be resilient, such that they tend to maintain connectivity when proteins are removed from the network. This hypothesis predicts that interactome resilience should be maintained during long-term experimental evolution. I tested this prediction by modeling the evolution of protein-protein interaction (PPI) networks in Lenski’s long-term evolution experiment with Escherichia coli (LTEE). In this test, I removed proteins affected by nonsense, insertion, deletion, and transposon mutations in evolved LTEE strains, and measured the resilience of the resulting networks. I compared the rate of change of network resilience in each LTEE population to the rate of change of network resilience for corresponding randomized networks. The evolved PPI networks are significantly more resilient than networks in which random proteins have been deleted. Moreover, the evolved networks are generally more resilient than networks in which the random deletion of proteins was restricted to those disrupted in LTEE. These results suggest that evolution in the LTEE has favored PPI networks that are, on average, more resilient than expected from the genetic variation across the evolved populations. My findings therefore support the hypothesis that selection maintains protein interactome resilience over evolutionary time.Significance StatementUnderstanding how protein-protein interaction (PPI) networks evolve is a central goal of evolutionary systems biology. One property that has been hypothesized to be important for PPI network evolution is resilience, which means that networks tend to maintain connectivity even after many nodes (proteins in this case) have been removed. This hypothesis predicts that PPI network resilience should be maintained during long-term experimental evolution. Consistent with this prediction, I found that the PPI networks that evolved over 50,000 generations of Lenski’s long-term evolution experiment with E. coli are more resilient than expected by chance.

scholarly journals Experimental Evolution ofEscherichia coliK-12 in the Presence of Proton Motive Force (PMF) Uncoupler Carbonyl Cyanidem-Chlorophenylhydrazone Selects for Mutations Affecting PMF-Driven Drug Efflux Pumps

2018 ◽  
Vol 85 (5) ◽  
Author(s):  
Jessie M. Griffith ◽  
Preston J. Basting ◽  
Katarina M. Bischof ◽  
Erintrude P. Wrona ◽  
Karina S. Kunka ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Point Mutations ◽  
Proton Motive Force ◽  
Motive Force ◽  
Multidrug Efflux ◽  
Content Type ◽  
Fitness Advantage ◽  
Evolution Experiment ◽  
Drug Efflux Pumps ◽  
K 12

ABSTRACTExperimental evolution ofEscherichia coliK-12 with benzoate, a partial uncoupler of the proton motive force (PMF), selects for mutations that decrease antibiotic resistance. We conducted experimental evolution in the presence of carbonyl cyanidem-chlorophenylhydrazone (CCCP), a strong uncoupler. Cultures were serially diluted daily 1:100 in LBK medium containing 20 to 150 µM CCCP buffered at pH 6.5 or at pH 8.0. After 1,000 generations, the populations tolerated up to 150 µM CCCP. Sequenced isolates had mutations inmprA(emrR), which downregulates the EmrAB-TolC pump that exports CCCP. AmprA::kanRdeletion conferred growth at 60 μM CCCP, though not at the higher levels resisted by evolved strains (150 µM). SomemprAmutant strains also had point mutations affectingemrA, but deletion ofemrAabolished the CCCP resistance. Thus, CCCP-evolved isolates contained additional adaptations. One isolate lackedemrAormprAmutations but had mutations incecR(ybiH), whose product upregulates drug pumps YbhG and YbhFSR, and ingadE, which upregulates the multidrug pump MdtEF. AcecR::kanRdeletion conferred partial resistance to CCCP. Other multidrug efflux genes that had mutations includedybhRandacrAB. TheacrBisolate was sensitive to the AcrAB substrates chloramphenicol and tetracycline. Other mutant genes in CCCP-evolved strains includerng(RNase G) andcyaA(adenylate cyclase). Overall, experimental evolution revealed a CCCP-dependent fitness advantage for mutations increasing CCCP efflux via EmrA and for mutations that may deactivate proton-driven pumps for drugs not present (cecR,gadE,acrAB, andybhR). These results are consistent with our previous report of drug sensitivity associated with evolved benzoate tolerance.IMPORTANCEThe genetic responses of bacteria to depletion of proton motive force (PMF), and their effects on drug resistance, are poorly understood. PMF drives export of many antibiotics, but the energy cost may decrease fitness when antibiotics are absent. Our evolution experiment reveals genetic mechanisms of adaptation to the PMF uncoupler CCCP, including selection for increased CCCP efflux but also against the expression of PMF-driven pumps for drugs not present. The results have implications for our understanding of the gut microbiome, which experiences high levels of organic acids that decrease PMF.

scholarly journals Shaping Bacterial Symbiosis With Legumes by Experimental Evolution

2014 ◽  
Vol 27 (9) ◽  
pp. 956-964 ◽  
Author(s):  
Marta Marchetti ◽  
Alain Jauneau ◽  
Delphine Capela ◽  
Philippe Remigi ◽  
Carine Gris ◽  
...  
Keyword(s):  
Immune Responses ◽  
Experimental Evolution ◽  
Plant Immunity ◽  
Parallel Evolution ◽  
In Planta ◽  
Plant Selection ◽  
Bacterial Symbiosis ◽  
Symbiotic Plasmid ◽  
Nodulation Competitiveness ◽  
Evolution Experiment

Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta–in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.

scholarly journals Bacterial symbionts in insects or the story of communities affecting communities

2011 ◽  
Vol 366 (1569) ◽  
pp. 1389-1400 ◽  
Author(s):  
Julia Ferrari ◽  
Fabrice Vavre
Keyword(s):  
Bacterial Communities ◽  
Horizontal Transmission ◽  
Model Systems ◽  
Community Genetics ◽  
Bacterial Symbionts ◽  
Ideal Model ◽  
Host Genotype ◽  
Or Gene ◽  
Dynamic Communities ◽  
The Cost

Bacterial symbionts are widespread in insects and other animals. Most of them are predominantly vertically transmitted, along with their hosts' genes, and thus extend the heritable genetic variation present in one species. These passengers have a variety of repercussions on the host's phenotypes: besides the cost imposed on the host for maintaining the symbiont population, they can provide fitness advantages to the host or manipulate the host's reproduction. We argue that insect symbioses are ideal model systems for community genetics. First, bacterial symbionts directly or indirectly affect the interactions with other species within a community. Examples include their involvement in modifying the use of host plants by phytophagous insects, in providing resistance to natural enemies, but also in reducing the global genetic diversity or gene flow between populations within some species. Second, one emerging picture in insect symbioses is that many species are simultaneously infected with more than one symbiont, which permits studying the factors that shape bacterial communities; for example, horizontal transmission, interactions between host genotype, symbiont genotype and the environment and interactions among symbionts. One conclusion is that insects' symbiotic complements are dynamic communities that affect and are affected by the communities in which they are embedded.

Long-Term Experimental Evolution in Escherichia coli. IX. Characterization of Insertion Sequence-Mediated Mutations and Rearrangements

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 477-488
Author(s):  
Dominique Schneider ◽  
Esther Duperchy ◽  
Evelyne Coursange ◽  
Richard E Lenski ◽  
Michel Blot
Keyword(s):  
Escherichia Coli ◽  
Experimental Evolution ◽  
Insertion Sequence ◽  
Term Evolution ◽  
Molecular Events ◽  
Evolution Experiment ◽  
Two Populations ◽  
Escherichia Coli B

Abstract As part of a long-term evolution experiment, two populations of Escherichia coli B adapted to a glucose minimal medium for 10,000 generations. In both populations, multiple IS-associated mutations arose that then went to fixation. We identify the affected genetic loci and characterize the molecular events that produced nine of these mutations. All nine were IS-mediated events, including simple insertions as well as recombination between homologous elements that generated inversions and deletions. Sequencing DNA adjacent to the insertions indicates that the affected genes are involved in central metabolism (knockouts of pykF and nadR), cell wall synthesis (adjacent to the promoter of pbpA-rodA), and ill-defined functions (knockouts of hokB-sokB and yfcU). These genes are candidates for manipulation and competition experiments to determine whether the mutations were beneficial or merely hitchhiked to fixation.

scholarly journals Phylogenetic Relationship Between the Endosymbiont “candidatus Riesia Pediculicola” and Its Human Lice Host

2021 ◽  
Author(s):  
alissa hammoud ◽  
Meriem Louni ◽  
Dorothée Missé ◽  
Florence Fenollar ◽  
Oleg Mediannikov
Keyword(s):  
Evolutionary History ◽  
Housekeeping Genes ◽  
Mitochondrial Genes ◽  
Bacterial Symbionts ◽  
Pediculus Humanus ◽  
Molecular Approaches ◽  
Endosymbiotic Bacteria ◽  
Insect Phylogeny ◽  
The World ◽  
Unbalanced Diet

Abstract Background: The human louse is one of the most ancient haematophagous ectoparasites that is related intimately to its host and has been of great concern to public health throughout human history. Previously, Pediculus humanus was classified within six divergent mitochondrial clades (A, D, B, F, C and E). Like all haematophagous lice, P. humanus directly depends on the presence of bacterial symbionts, known as “Candidatus Riesia pediculicola”, to complement their unbalanced diet. In this study, we evaluated the coevolution of human lice around the world and their endosymbiotic bacteria. Using molecular approaches, we targeted lice mitochondrial genes from the six diverged clades and Candidatus R. pediculicola housekeeping genes. Methods: A total of 126 lice were selected for molecular analysis of the cytb gene for lice clade determination. In parallel, four PCR primer pairs were developed targeting three housekeeping genes of Candidatus R. pediculicola: ftsZ, groEL and two regions of the rpoB gene (rpoB-1 and rpoB-2).Results: The endosymbiont phylogeny perfectly mirrored the host insect phylogeny, using the ftsZ and rpoB-2 genes, suggesting a strict vertical transmission and a host-symbiont co-speciation following the evolutionary course of the human louse. Conclusion: Our results unequivocally indicate that lice endosymbiont have experienced a similar co-evolutionary history, and that the human louse clade can be determined by their endosymbiotic bacteria.

Bacterial symbiont and salivary peptide evolution in the context of leech phylogeny

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1815-1827 ◽  
Author(s):  
MARK E. SIDDALL ◽  
GI-SIK MIN ◽  
FRANK M. FONTANELLA ◽  
ANNA J. PHILLIPS ◽  
SARA C. WATSON
Keyword(s):  
Bioactive Compounds ◽  
Evolutionary History ◽  
Blood Feeding ◽  
Medicinal Leech ◽  
Gene Products ◽  
Bacterial Symbionts ◽  
Evolutionary Selection ◽  
Salivary Peptide ◽  
History Of ◽  
And Function

SUMMARYThe evolutionary history of leeches is employed as a general framework for understanding more than merely the systematics of this charismatic group of annelid worms, and serves as a basis for understanding blood-feeding related correlates ranging from the specifics of gut-associated bacterial symbionts to salivary anticoagulant peptides. A variety of medicinal leech families were examined for intraluminal crop bacterial symbionts. Species ofAeromonasand Bacteroidetes were characterized with DNA gyrase B and 16S rDNA. Bacteroidetes isolates were found to be much more phylogenetically diverse and suggested stronger evidence of phylogenetic correlation than the gammaproteobacteria. Patterns that look like co-speciation with limited taxon sampling do not in the full context of phylogeny. Bioactive compounds that are expressed as gene products, like those in leech salivary glands, have ‘passed the test’ of evolutionary selection. We produced and bioinformatically mined salivary gland EST libraries across medicinal leech lineages to experimentally and statistically evaluate whether evolutionary selection on peptides can identify structure-function activities of known therapeutically relevant bioactive compounds like antithrombin, hirudin and antistasin. The combined information content of a well corroborated leech phylogeny and broad taxonomic coverage of expressed proteins leads to a rich understanding of evolution and function in leech history.

scholarly journals The Pine Bark Adelgid, Pineus strobi, Contains Two Novel Bacteriocyte-Associated Gammaproteobacterial Symbionts

2013 ◽  
Vol 80 (3) ◽  
pp. 878-885 ◽  
Author(s):  
Elena R. Toenshoff ◽  
Gitta Szabó ◽  
Daniela Gruber ◽  
Matthias Horn
Keyword(s):  
Evolutionary History ◽  
Adelges Tsugae ◽  
Pine Bark ◽  
23S Rrna ◽  
Bacterial Symbionts ◽  
Content Type ◽  
Transmission Electron ◽  
History Of ◽  
Bacterial Endosymbionts

ABSTRACTBacterial endosymbionts of the pine bark adelgid,Pineus strobi(Insecta: Hemiptera: Adelgidae), were investigated using transmission electron microscopy, 16S and 23S rRNA-based phylogeny, and fluorescencein situhybridization. Two morphologically different symbionts affiliated with theGammaproteobacteriawere present in distinct bacteriocytes. One of them (“CandidatusAnnandia pinicola”) is most closely related to an endosymbiont ofAdelges tsugae, suggesting that they originate from a lineage already present in ancient adelgids before the hosts diversified into the two major clades,AdelgesandPineus. The otherP. strobisymbiont (“CandidatusHartigia pinicola”) represents a novel symbiont lineage in members of the Adelgidae. Our findings lend further support for a complex evolutionary history of the association of adelgids with a phylogenetically diverse set of bacterial symbionts.

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