Enzyme promiscuity shapes adaptation to novel growth substrates
Guzmán, Gabriela I. ; Sandberg, Troy E. ; LaCroix, Ryan A. ; Nyerges, Ákos ; Papp, Henrietta ; Raad, Markus de; King, Zachary A. ; Hefner, Ying ; Northen, Trent R. ; Notebaart, Richard A. ; Pál, Csaba ; Palsson, Bernhard O. ; Papp, Balázs ; Feist, Adam M. - \ 2019
Molecular Systems Biology 15 (2019)4. - ISSN 1744-4292 - p. e8462 - e8462.
adaptive evolution - enzyme promiscuity - genome‐scale modeling - systems biology
Evidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates in Escherichia coli K-12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non-native substrates-D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high-efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity.
Evolutionary engineering to enhance starter culture performance in food fermentations
Bachmann, H. ; Pronk, J.T. ; Kleerebezem, M. ; Teusink, B. - \ 2015
Current Opinion in Biotechnology 32 (2015). - ISSN 0958-1669 - p. 1 - 7.
yeast saccharomyces-cerevisiae - adaptive evolution - lactococcus-lactis - hyperosmotic conditions - selection - growth - population - strategies - phenotypes - stability
Microbial starter cultures are essential for consistent product quality and functional properties such as flavor, texture, pH or the alcohol content of various fermented foods. Strain improvement programs to achieve desired properties in starter cultures are diverse, but developments in next-generation sequencing lead to an increased interest in evolutionary engineering of desired phenotypes. We here discuss recent developments of strain selection protocols and how computational approaches can assist such experimental design. Furthermore the analysis of evolved phenotypes and possibilities with complex consortia are highlighted. Studies carried out with mainly yeast and lactic acid bacteria demonstrate the power of evolutionary engineering to deliver strains with novel phenotypes as well as insight into underlying mechanisms.
Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network
Espinosa-Soto, C. ; Immink, R.G.H. ; Angenent, G.C. ; Alvarez-Buylla, E.R. ; Folter, de, S. - \ 2014
BMC Systems Biology 8 (2014). - ISSN 1752-0509 - 17 p.
box transcription factors - floral organ identity - flower development - gene duplication - adaptive evolution - homeotic proteins - factor family - in-vitro - dna - complexes
Background: MADS domain proteins are transcription factors that coordinate several important developmental processes in plants. These proteins interact with other MADS domain proteins to form dimers, and it has been proposed that they are able to associate as tetrameric complexes that regulate transcription of target genes. Whether the formation of functional tetramers is a widespread property of plant MADS domain proteins, or it is specific to few of these transcriptional regulators remains unclear. Results: We analyzed the structure of the network of physical interactions among MADS domain proteins in Arabidopsis thaliana. We determined the abundance of subgraphs that represent the connection pattern expected for a MADS domain protein heterotetramer. These subgraphs were significantly more abundant in the MADS domain protein interaction network than in randomized analogous networks. Importantly, these subgraphs are not significantly frequent in a protein interaction network of TCP plant transcription factors, when compared to expectation by chance. In addition, we found that MADS domain proteins in tetramer-like subgraphs are more likely to be expressed jointly than proteins in other subgraphs. This effect is mainly due to proteins in the monophyletic MIKC clade, as there is no association between tetramer-like subgraphs and co-expression for proteins outside this clade. Conclusions: Our results support that the tendency to form functional tetramers is widespread in the MADS domain protein-protein interaction network. Our observations also suggest that this trend is prevalent, or perhaps exclusive, for proteins in the MIKC clade. Because it is possible to retrodict several experimental results from our analyses, our work can be an important aid to make new predictions and facilitates experimental research on plant MADS domain proteins.
Birth, death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification of Fusarium
Proctor, R.H. ; Hove, F. van; Susca, A. ; Stea, G. ; Busman, M. ; Lee, T.A.J. van der; Waalwijk, C. ; Moretti, A. ; Ward, T.J. - \ 2013
Molecular Microbiology 90 (2013)2. - ISSN 0950-382X - p. 290 - 306.
fujikuroi species complex - maximum-likelihood - gibberella-moniliformis - aspergillus-parasiticus - secondary metabolism - comparative genomics - adaptive evolution - multigene family - section liseola - mixed models
Fumonisins are a family of carcinogenic secondary metabolites produced by members of the Fusarium fujikuroi species complex (FFSC) and rare strains of Fusarium oxysporum. In Fusarium, fumonisin biosynthetic genes (FUM) are clustered, and the cluster is uniform in gene organization. Here, sequence analyses indicated that the cluster exists in five different genomic contexts, defining five cluster types. In FUM gene genealogies, evolutionary relationships between fusaria with different cluster types were largely incongruent with species relationships inferred from primary-metabolism (PM) gene genealogies, and FUM cluster types are not trans-specific. In addition, synonymous site divergence analyses indicated that three FUM cluster types predate diversification of FFSC. The data are not consistent with balancing selection or interspecific hybridization, but they are consistent with two competing hypotheses: (i) multiple horizontal transfers of the cluster from unknown donors to FFSC recipients and (ii) cluster duplication and loss (birth and death). Furthermore, low levels of FUM gene divergence in F.¿bulbicola, an FFSC species, and F.¿oxysporum provide evidence for horizontal transfer of the cluster from the former, or a closely related species, to the latter. Thus, uniform gene organization within the FUM cluster belies a complex evolutionary history that has not always paralleled the evolution of Fusarium
Natural selection promotes antigenic evolvability
Graves, C.J. ; Ros, V.I.D. ; Stevenson, B. ; Sniegowski, P.D. ; Brisson, D. - \ 2013
PLoS Pathogens 9 (2013)11. - ISSN 1553-7366
lyme-disease spirochete - strand-break repair - borrelia-burgdorferi - gene conversion - concerted evolution - parasite virulence - adaptive evolution - surface-proteins - tandem repeats - sequence
The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed ‘cassettes’ that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.
Promoter propagation in prokaryotes
Matus-Garcia, M. ; Nijveen, H. ; Passel, M.W.J. van - \ 2012
Nucleic acids research 40 (2012)20. - ISSN 0305-1048 - p. 10032 - 10040.
horizontal gene-transfer - escherichia-coli - adaptive evolution - lactococcus-lactis - sequences - genomes - networks - identification - mutations - families
Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. In many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large impact on rapid adaptation of novel or cryptic functions. Querying all publicly available prokaryotic genomes (1362) uncovered >4000 families of highly conserved PMPs (50 to 100 long with =80% nt identity) in 1043 genomes from 424 different genera. The genomes with the largest number of PMP families are Anabaena variabilis (28 families), Geobacter uraniireducens (27 families) and Cyanothece PCC7424 (25 families). Family size varied from 2 to 93 homologous promoters (in Desulfurivibrio alkaliphilus). Some PMPs are present in particular species, but some are conserved across distant genera. The identified PMPs represent a conservative dataset of very recent or conserved events of mobilization of non-coding DNA and thus they constitute evidence of an extensive reservoir of recyclable regulatory sequences for rapid transcriptional rewiring
Plant ‘evo-devo’ goes genomic: from candidate genes to regulatory networks
Bruijn, S.A. de; Angenent, G.C. ; Kaufmann, K. - \ 2012
Trends in Plant Science 17 (2012)8. - ISSN 1360-1385 - p. 441 - 447.
transcription factor-binding - arabidopsis-thaliana - heterotopic expression - morphological novelty - evolutionary dynamics - molecular-mechanisms - corolla monosymmetry - symmetry evolution - adaptive evolution - leaf form
Plant development gives rise to a staggering complexity of morphological structures with different shapes, colors, and functions. Understanding the evolution of control mechanisms that underlie developmental processes provides insights into causes of morphological diversity and, therefore, is of great interest to biologists. New genomic resources and techniques enable biologists to assess for the first time the evolution of developmental regulatory networks at a global scale. Here, we address the question of how comparative regulatory genomics can be used to reveal the evolutionary dynamics of control networks linked to morphological evolution in plants.
Changed gene expression for candidate ageing genes in long-lived Bicyclus anynana butterflies
Pijpe, J. ; Pul, N. ; Duijn, S. van; Brakefield, P.M. ; Zwaan, B.J. - \ 2011
Experimental Gerontology 46 (2011)6. - ISSN 0531-5565 - p. 426 - 434.
quantitative trait loci - extend life-span - drosophila-melanogaster - oxidative damage - caenorhabditis-elegans - starvation resistance - adaptive evolution - stress resistance - natural variation - longevity
Candidate genes for the regulation of lifespan have emerged from studies that use mutants and genetically manipulated model organisms. However, it is rarely addressed whether these genes contribute to lifespan variation in populations of these species that capture natural standing genetic variation. Here, we explore expression variation in three candidate ageing genes, Indy, sod2, and catalase, in Bicyclus anynana, a butterfly with well understood ecology. We used lines established from natural populations and artificially selected for increased adult starvation resistance. They show a considerable increase in adult lifespan under both starvation and optimal food conditions. We measured adult butterflies of various ages, under a range of optimal and starvation diets, from two selected populations and one unselected control population. In all lines, Indy and catalase are up-regulated in response to starvation while this is not evident for sod2. Under starvation, Indy and catalase are up-regulated in, while this is not evident for sod2. Under optimal food conditions, Indy is down-regulated at a later age, with Indy expression showing relatively high inter-individual variation. We find differences between the selected lines and the unselected line. Under starvation conditions, expression is higher for catalase in one, and for sod2 in both selected lines. Importantly, sod2 expression is also higher in the selected populations under optimal food conditions. We conclude that sod2, but not Indy, is involved in the response to artificial selection for increased starvation resistance. The role of catalase is less clear because of the differences between the two selected lines. Moreover, sod2 appears to be a candidate gene that underpins the genetic correlation between starvation resistance and longevity. Our study indicates that some, but not all, genes identified through mutant screens in other organisms may underpin standing genetic variation for ageing-related traits in stocks of Bicyclus butterflies established from natural populations. Clearly, this needs to be investigated in other organisms as well, especially in the organisms to which mutants screens were applied. This information will narrow down the list of genes that underpin variation in lifespan and ageing in extant populations of organisms, and which may serve as candidate genes in humans
Population admixture, biological invasions and the balance between local adaptation and inbreeding depression
Verhoeven, K.J.F. ; Macel, M. ; Wolfe, L.M. ; Biere, A. - \ 2011
Proceedings of the Royal Society. B: Biological Sciences 278 (2011)1702. - ISSN 0962-8452 - p. 2 - 8.
silene-latifolia caryophyllaceae - genetic differentiation - intraspecific hybridization - multiple introductions - reproductive isolation - divergent selection - adaptive evolution - quantitative trait - plant - success
When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important role in biological invasions. In contrast, populations in their native range often remain differentiated and frequently suffer from inbreeding depression owing to isolation. While the advantages of admixture are evident for introduced populations that experienced recent bottlenecks or that face novel selection pressures, it is less obvious why native range populations do not similarly benefit from admixture. Here we argue that a temporary loss of local adaptation in recent invaders fundamentally alters the fitness consequences of admixture. In native populations, selection against dilution of the locally adapted gene pool inhibits unconstrained admixture and reinforces population isolation, with some level of inbreeding depression as an expected consequence. We show that admixture is selected against despite significant inbreeding depression because the benefits of local adaptation are greater than the cost of inbreeding. In contrast, introduced populations that have not yet established a pattern of local adaptation can freely reap the benefits of admixture. There can be strong selection for admixture because it instantly lifts the inbreeding depression that had built up in isolated parental populations. Recent work in Silene suggests that reduced inbreeding depression associated with post-introduction admixture may contribute to enhanced fitness of invasive populations. We hypothesize that in locally adapted populations, the benefits of local adaptation are balanced against an inbreeding cost that could develop in part owing to the isolating effect of local adaptation itself. The inbreeding cost can be revealed in admixing populations during recent invasions
Adaptation to the cost of resistance in a haploid clonally reproducing organism: The role of mutation, migration and selection
Jeger, M.J. ; Wijngaarden, P.J. ; Hoekstra, R.F. - \ 2008
Journal of Theoretical Biology 252 (2008). - ISSN 0022-5193 - p. 621 - 632.
fungicide spray heterogeneity - compensatory mutations - pesticide resistance - adaptive evolution - antibiotic-resistance - aspergillus-nidulans - relative fitness - drug-resistance - disease-control - sensitivity
A model of compensatory evolution with respect to fungicide resistance in a haploid clonally reproducing fungus is developed in which compensatory mutations mitigate fitness costs associated with resistance. The role of mutation, migration and selection in invasion of rare genotypes when the environment changes from unsprayed to sprayed and from sprayed to unsprayed is analysed in detail. In some circumstances (ignoring back mutations) stable internal steady-state values for multiple genotypes can be obtained. In these cases a threshold value (f*) for the fraction of the population exposed to the fungicide can be derived for the transition between different steady-state conditions. Conditions are derived for invasion-when-rare of resistant genotypes at boundary equilibria established sometime after the onset of spraying and conversely of sensitive genotypes sometime after the cessation of spraying are derived. In these cases conditions are presented for (a) the invasion of a resistant genotype with a compensatory mutation (resistant-compensated) into a sensitive-uncompensated population that has re-equilibrated following the onset of spraying and (b) the invasion of a susceptible-uncompensated genotype into a resistant-compensated population that has re-equilibrated following the cessation of spraying, provided certain conditions are met. A resistant-compensated genotype may be fixed (or at near-fixation) in the population following a period of spraying, provided the mean intrinsic growth rate of the resistant-compensated genotype in a sprayed environment (over exposed and non-exposed parts of the population) is greater than that of the susceptible-uncompensated genotype. The fraction of the population exposed (the efficiency of spraying) is critical in this respect. However, it is possible for a sensitive-uncompensated genotype to invade provided there is no fitness gain associated with the resistant-compensated genotype, introduction by migration occurs following equilibration of the population to the new environment, and competitive effects are re-imposed when spraying ceases. We further derive a threshold level for the resident resistant-compensated population to reduce to following the cessation of spraying, such that the introduced susceptible-uncompensated genotype will invade. These results will be of use in determining the long-term persistence of resistance in a pathogen population once a fungicide is no longer effective and removed from use
Spatial structure inhibits the rate of invasion of beneficial mutations in asexual populations
Habets, M.G.J.L. ; Czaran, T.L. ; Hoekstra, R.F. ; Visser, J.A.G.M. de - \ 2007
Proceedings of the Royal Society. B: Biological Sciences 274 (2007)1622. - ISSN 0962-8452 - p. 2139 - 2143.
promotes biodiversity - adaptive evolution - periodic selection - escherichia-coli - dynamics - coexistence - radiation - resource
Populations in spatially structured environments may be divided into a number of (semi-) isolated subpopulations due to limited offspring dispersal. Limited dispersal and, as a consequence, local competition could slow down the invasion of fitter mutants, allowing the short-term coexistence of ancestral genotypes and mutants. We determined the rate of invasion of beneficial mutants of Escherichia coli, dispersed to different degrees in a spatially structured environment during 40 generations, experimentally and theoretically. Simulations as well as experimental data show a decrease in the rate of invasion with increasingly constrained dispersal. When a beneficial mutant invades from a single spot, competition with the ancestral genotype takes place only along the edges of the growing colony patch. As the colony grows, the fitness of the mutant will decrease due to a decrease in the mutant's fraction that effectively competes with the surrounding ancestor. Despite its inherently higher competitive ability, increased intragenotype competition prevents the beneficial mutant from rapidly taking over, causing short-term coexistence of superior and inferior genotypes.
Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
Teusink, B. ; Wiersma, A. ; Molenaar, D. ; Francke, C. ; Vos, W.M. de; Siezen, R.J. ; Smid, E.J. - \ 2006
Journal of Biological Chemistry 281 (2006)52. - ISSN 0021-9258 - p. 40041 - 40048.
lactic-acid bacteria - bacillus-subtilis metabolism - escherichia-coli - lactococcus-lactis - saccharomyces-cerevisiae - adaptive evolution - flux analysis - network - pathways - balance
A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for interpretation of complex fermentation data, as L. plantarum is adapted to nutrient-rich environments and only grows in media supplemented with vitamins and amino acids. (i) Based on experimental input and output fluxes, maximal ATP production was estimated and related to growth rate. (ii) Optimization of ATP production further identified amino acid catabolic pathways that were not previously associated with free-energy metabolism. (iii) Genome-scale elementary flux mode analysis identified 28 potential futile cycles. (iv) Flux variability analysis supplemented the elementary mode analysis in identifying parallel pathways, e.g. pathways with identical end products but different co-factor usage. Strongly increased flexibility in the metabolic network was observed when strict coupling between catabolic ATP production and anabolic consumption was relaxed. These results illustrate how a genome-scale metabolic model and associated constraint-based modeling techniques can be used to analyze the physiology of growth on a complex medium rather than a minimal salts medium. However, optimization of biomass formation using the Flux Balance Analysis approach, reported to successfully predict growth rate and by product formation in Escherichia coli and Saccharomyces cerevisiae, predicted too high biomass yields that were incompatible with the observed lactate production. The reason is that this approach assumes optimal efficiency of substrate to biomass conversion, and can therefore not predict the metabolically inefficient lactate formation
Insertion-Sequence-Mediated Mutations Isolated During Adaptation to Growth and Starvation in Lactococcus lactis.
Visser, J.A.G.M. de; Akkermans, A.D.L. ; Hoekstra, R.F. ; Vos, W.M. de - \ 2004
Genetics 168 (2004)3. - ISSN 0016-6731 - p. 1145 - 1157.
term experimental evolution - escherichia-coli - transposable elements - beneficial mutations - adaptive evolution - stationary-phase - populations - rearrangements - generations - diversity
We studied the activity of three multicopy insertion sequence (IS) elements in 12 populations of Lactococcus lactis IL1403 that evolved in the laboratory for 1000 generations under various environmental conditions (growth or starvation and shaken or stationary). Using RFLP analysis of single-clone representatives of each population, nine IS-mediated Mutations were detected across all environmental conditions and all involving IS981. When it was assumed that these mutations were neutral, their frequency was higher tinder shaken than under stationary conditions, possibly due to oxygen stress. We characterized seven of the nine mutations at the molecular level and studied their population dynamics where possible. Two were simple insertions into new positions and the other five were recombinational deletions (of 0 kb) among existing and new copies of IS981; in all but one case these mutations disrupted gene functions. The best candidate beneficial mutations were two deletions of which similar versions were detected in two populations each. One of these two parallel deletions, affecting a gene involved in bacteriophage resistance, showed intermediate rearrangements and may also have resulted from increased local transposition rates.
The fate of microbial mutators
Visser, J.A.G.M. de - \ 2002
Microbiology 148 (2002). - ISSN 1350-0872 - p. 1247 - 1252.
high mutation-rates - pathogenic escherichia-coli - adaptive evolution - horizontal transfer - saccharomyces-cerevisiae - populations - bacteria - fitness - selection - survival
Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.
Belkum, A. van; Struelens, M. ; Visser, J.A.G.M. de; Verburgh, H. ; Tibayrenc., M. - \ 2001
Clinical Microbiology Reviews 14 (2001)3. - ISSN 0893-8512 - p. 547 - 560.
resistant staphylococcus-aureus - field gel-electrophoresis - escherichia-coli k-12 - commercial software packages - term experimental evolution - adaptive evolution - molecular evolution - hemorrhagic colitis - infectious-disease - mycobacterium-tuberculosis
Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made