Intragenomic enzyme complements

Researchers in applied biocatalysis are now reaping the rewards of intensive effort and technological developments in the sequencing of the genomes of microbial and plant species. The genomic resource contains the sequences of millions of new genes with potential application in industrial biotechnology and includes families of enzymes within discrete genomes that potentially catalyze equivalent chemical reactions. One of the key emerging characteristics of these intragenomic complements of enzymes is the impressive breadth of catalytic diversity that is observed within them. This diversity may have been acquired either in order to combat the spectrum of metabolic challenges with which the organism may be presented in its natural environment or as part of the biosynthetic machinery evolved to produce a spectrum of secondary metabolites that will prove to be advantageous in establishing a niche. Attempts have been made to functionally characterize the intragenomic complements of enzyme families catalyzing diverse reactions including carbonyl reduction, ester hydrolysis and Baeyer–Villiger oxidation, in Gram-positive bacteria, yeasts, filamentous fungi and the plant Arabidopsis thaliana. These studies are beginning to describe in detail for the first time the impressive range of catalytic potential within single organisms for attributes such as substrate range, enantioselectivity or thermostability, each of which is of interest from an enzyme discovery perspective.     

Intragenomic politics

The mammalian genome contains multiple genetic factions with distinct interests in the outcomes of interactions among kin. In the context of an offspring's relations with its mother, these factions are proposed to align into two 'parties', one favoring increased demand by offspring and the other favoring reduced demand. A possible alignment has inhibitors of demand located on the X chromosome and enhancers of demand located on autosomes, because X-linked loci are maternally derived two-thirds of the time by contrast to autosomal loci which are maternally derived half of the time.     

Dichogamy,gender variation and bet-hedging inPseudowintera colorata

Summary Temporal patterns of variability in the longevity of the male and female phases of individual flowers and in the gender expression of plants of a dichogamous New Zealand tree,Pseudowintera colorata (Winteraceae), were documented in field studies. Two measures for the duration of phases in a dichogamous flower are distinguished; the nominal phases based on morphological features of the flower, and the effective phases reflecting the duration of their functions. Flower and phase longevity and phenotypic gender varied considerably throughout the season and among individuals. Temporal variability in phenotypic gender was loosely synchronized among the 12 plants sampled. Three effects of an environmental factor (temperature) were noted. First, increased temperatures shortened the duration of the female phase but had no effect on the duration of the male phase. Second, pollination frequency was positively correlated with temperature. These results indirectly suggest that increased pollination may shorten the duration of the female phase. Third, average population maleness, measured as the proportion of open flowers in the population on a given day which were in the male phase, was positively correlated with temperature. It is postulated that temperature indirectly influences temporal patterns of gender expression in the population through its differential effects on the longevity of the male and female phases in individual flowers. A theoretical model of bet-hedging shows that, if the direction of an environmental effect on the proportions of the sexual phases is irreversible, selection favours asynchronous dichogamy and reduces the temporal variability as much as possible. If the direction of the response is reversible, heterodichogamy is favoured.     

Formal Darwinism,the individual-as-maximizing-agent analogy and bet-hedging

The central argument of The origin of species was that mechanical processes (inheritance of features and the differential reproduction they cause) can give rise to the appearance of design. The ''mechanical processes'' are now mathematically represented by the dynamic systems of population genetics, and the appearance of design by optimization and game theory in which the individual plays the part of the maximizing agent. Establishing a precise individual-as-maximizing-agent (IMA) analogy for a population-genetics system justifies optimization approaches, and so provides a modern formal representation of the core of Darwinism. It is a hitherto unnoticed implication of recent population-genetics models that, contrary to a decades-long consensus, an IMA analogy can be found in models with stochastic environments (subject to a convexity assumption), in which individuals maximize expected reproductive value. The key is that the total reproductive value of a species must be considered as constant, so therefore reproductive value should always be calculated in relative terms. This result removes a major obstacle from the theoretical challenge to find a unifying framework which establishes the IMA analogy for all of Darwinian biology, including as special cases inclusive fitness, evolutionarily stable strategies, evolutionary life-history theory, age-structured models and sex ratio theory. This would provide a formal, mathematical justification of fruitful and widespread but ''intentional'' terms in evolutionary biology, such as ''selfish'', ''altruism'' and ''conflict''.     

The evolution of bet-hedging adaptations to rare scenarios

When faced with a variable environment, organisms may switch between different strategies according to some probabilistic rule. In an infinite population, evolution is expected to favor the rule that maximizes geometric mean fitness. If some environments are encountered only rarely, selection may not be strong enough for optimal switching probabilities to evolve. Here we calculate the evolution of switching probabilities in a finite population by analyzing fixation probabilities of alleles specifying switching rules. We calculate the conditions required for the evolution of phenotypic switching as a form of bet-hedging as a function of the population size N, the rate theta at which a rare environment is encountered, and the selective advantage s associated with switching in the rare environment. We consider a simplified model in which environmental switching and phenotypic switching are one-way processes, and mutation is symmetric and rare with respect to the timescale of fixation events. In this case, the approximate requirements for bet-hedging to be favored by a ratio of at least R are that sN>log(R) and thetaN>square root R .     

Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes

More than one copy of rRNA operons, which code for both the small-subunit (SSU) and large-subunit (LSU) rRNA, are often found in prokaryotes. It is generally assumed that all rRNA operons within a single cell are almost identical. A notable exception is the extremely halophilic archaeal genus Haloarcula, most species of which are known to harbor highly divergent rRNA operons that differ at approximately 5% of the nucleotide positions in the SSU gene and at 1 to 2% of the nucleotide positions in the LSU gene. We report that such intragenomic heterogeneity is not unique to Haloarcula, as high levels of intragenomic sequence variation have been observed for the SSU genes of two other genera of extreme halophiles, Halosimplex and Natrinema. To investigate this in detail, the two rRNA operons of Halosimplex carlsbadense and the four operons of Natrinema sp. strain XA3-1 were cloned and completely sequenced. The SSU and LSU genes of H. carlsbadense show the highest levels of intragenomic heterogeneity observed so far in archaea (6.7 and 2.6%). The operons of Natrinema sp. strain XA3-1 have additional unusual characteristics, such as identical internal transcribed spacers, while one of four SSU genes is 5% divergent and all LSU genes differ from each other by 0.9 to 1.9%. The heterogeneity among the Natrinema sp. strain XA3-1 LSU genes is localized in hot spots, and one of these regions is shown to be the result of a recombination event with a distantly related halophile. This is the first example of interspecies recombination between rRNA genes in archaea, and the recombination occurred over one of the largest phylogenetic distances ever reported for such an event. We suggest that intragenomic heterogeneity of rRNA operons is an ancient and stable trait in several lineages of the Halobacteriales. The impact of this phenomenon on the taxonomy of extremely halophilic archaea is discussed.     

Mating portfolios: bet-hedging,sexual selection and female multiple mating

Polyandry (female multiple mating) has profound evolutionary and ecological implications. Despite considerable work devoted to understanding why females mate multiply, we currently lack convincing empirical evidence to explain the adaptive value of polyandry. Here, we provide a direct test of the controversial idea that bet-hedging functions as a risk-spreading strategy that yields multi-generational fitness benefits to polyandrous females. Unfortunately, testing this hypothesis is far from trivial, and the empirical comparison of the across-generations fitness payoffs of a polyandrous (bet hedger) versus a monandrous (non-bet hedger) strategy has never been accomplished because of numerous experimental constraints presented by most ‘model’ species. In this study, we take advantage of the extraordinary tractability and versatility of a marine broadcast spawning invertebrate to overcome these challenges. We are able to simulate multi-generational (geometric mean) fitness among individual females assigned simultaneously to a polyandrous and monandrous mating strategy. Our approaches, which separate and account for the effects of sexual selection and pure bet-hedging scenarios, reveal that bet-hedging, in addition to sexual selection, can enhance evolutionary fitness in multiply mated females. In addition to offering a tractable experimental approach for addressing bet-hedging theory, our study provides key insights into the evolutionary ecology of sexual interactions.     

Egg size variability in trematodes: test of the bet-hedging hypothesis

The hypothesis according to which egg size variability in hermaphroditic parasites results from bet-hedging was investigated in a comparative analysis using trematodes as a model. We hypothesized that the species reproducing mainly by self-fertilization should produce smaller eggs than those species that regularly practice cross-fertilization. Indeed, because self-fertilization is usually associated with inbreeding depression, selection should favor individuals spreading the risk of genetically disturbed development across more but smaller eggs, instead of producing fewer eggs, each possessing a large resource supply, of which many may fail to develop because of genetic deficiencies. On the basis of earlier theoretical and empirical studies, we assumed that the ratio length of testis-length of ovary positively correlates with the mating group size and, hence, with opportunities for cross-fertilization. In accordance with the bet-hedging hypothesis, we found, across trematode species, a positive relationship between this ratio and the mean egg volume produced by adults. This result was, however, observed only for the trematodes infecting birds and not for the species infecting fishes and mammals. In addition, once the influence of trematode phylogeny was taken into account, there was no significant trend, suggesting that phylogenetic legacies played a large role in generating the previous signal. Experimental tests of the bet-hedging hypothesis will be necessary to clarify the matter.     

Intragenomic Spread of Plastid-Targeting Presequences in the Coccolithophore Emiliania huxleyi

Nucleus-encoded plastid-targeted proteins of photosynthetic organisms are generally equipped with an N-terminal presequence required for crossing the plastid membranes. The acquisition of these presequences played a fundamental role in the establishment of plastids. Here, we report a unique case of two non-homologous proteins possessing completely identical presequences consisting of a bipartite plastid-targeting signal in the coccolithophore Emiliania huxleyi. We further show that this presequence is highly conserved in five additional proteins that did not originally function in plastids, representing de novo plastid acquisitions. These are among the most recent cases of presequence spreading from gene to gene and shed light on important evolutionary processes that have been usually erased by the ancient history of plastid evolution. We propose a mechanism of acquisition involving genomic duplications and gene replacement through non-homologous recombination that may have played a more general role for equipping proteins with targeting information.     

Intragenomic variation of fungal ribosomal genes is higher than previously thought

Nuclear ribosomal genes in most eukaryotes are present in multiple copies and often used for taxonomic and phylogenetic analyses. We comprehensively examined intragenomic polymorphism levels of three nuclear ribosomal loci for four important plant pathogenic fungi by polymerase chain reaction amplification and cloning. Here, we show that single nucleotide polymorphisms are present in an unexpectedly high amount. This might have implications for studies of fungal evolution, phylogenetics, and population genetics. Furthermore, our work demonstrates that the majority of all ribosomal sequences obtained from one individual and gene is identical to the majority rule consensus sequence of all detected sequence variants. Due to the large number of polymorphisms found and the fact that the polymorphism level differed markedly even between ribosomal genes of one and the same individual, we assume that nuclear ribosomal genes might not always evolve in a strictly concerted manner.     

Plastic bet-hedging in an amphicarpic annual: an integrated strategy under variable conditions

Amphicarpy is a form of diversified bet-hedging expressed mostly in annual plants, where two types of offspring are produced with two distinct ecological roles: long-range aerial dispersers and highly competitive subterranean, sedentary fruit. Emex spinosa is a semi-arid, amphicarpic annual, inhabiting habitats with different levels of environmental variation. We tested the hypothesis that, in E. spinosa, bet-hedging may be “fine-tuned” by plasticity in the phenotype ratio (aerial/subterranean fruit mass) as a function of environmental conditions. We conducted a greenhouse experiment, manipulating nutrient availability and intraspecific density, to determine the pattern of ratio shifts. In order to determine whether the integrated strategy is an adaptation to variable habitats, a similar common garden experiment was conducted, comparing two natural populations differing in environmental variability. The offspring ratio shifted in response to both nutrient availability and plant density. In pots containing single plants the ratio increased steeply with nutrient availability, while in pots containing eight plants a more moderate increase occurred. These shifts were the result of plasticity in allocation to both achene types, as well as ontogenetic effects on aerial achene production. The degree of response increased with the heterogeneity of the habitat of origin. We found evidence for an adaptive integrated strategy, with bet-hedging “fine-tuned” by phenotypic plasticity. Strenuous conditions tended to shift the offspring ratio towards securing subterranean reproductive success, while favorable conditions resulted in a shift towards dispersible achenes. The authors Asaf Sadeh and Hagai Guterman contributed equally to this study.     

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell–cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing “arms race.” Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic’s effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell–cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated.     

Germ banking: bet-hedging and variable release from egg and seed dormancy

Many species produce eggs or seeds that refrain from hatching despite developmental preparedness and favorable environmental conditions. Instead, these propagules hatch in intervals over long periods. Such variable hatch or germination tactics may represent bet-hedging against future catastrophes. Empiricists have independently recognized these approaches in diverse species. Terms such as seed banking, delayed egg hatching, and embryonic diapause have been used to describe these tactics, but connections between fields of study have been rare. Here we suggest a general term, germ banking, to incorporate all previous terms, unifying many seemingly disparate biological strategies under a single definition. We define the phenomenon of germ banking and use several biological examples to illustrate it. We then discuss the different causes of variation in emergence timing, delineate which constitute germ banking, and distinguish between germ banking and optimal timing of diapause. The wide-ranging consequences of germ banking are discussed, including modification of the age structure of a population, the alteration of microevolutionary dynamics, the migration of alleles from the past, the maintenance of genetic and species diversity, and the promotion of species coexistence. We end by posing questions to direct future research.     

Constitutive but no Triops-induced differences in bet-hedging strategies for hatching in Daphnia

Since cladocerans from the genus Daphnia are known to have evolved several inducible defenses (morphological and life history shifts) against the notostracan predator Triops, we investigated whether hatching was also altered in response to Triops. We tested whether dormant eggs of Daphnia magna are able to detect Triops cancriformis kairomones in the water as a signal of predation pressure and alter their hatching response accordingly to avoid predation. We predicted that, in the presence of Triops kairomones, hatching fractions might be reduced (postponing hatching to a next growing season) and/or that hatching might peak earlier (increasing chances to reproduce before Triops becomes predatory). We also tested whether this response depended on the origin of the population. Ephippia from three D. magna populations, originating from one permanent lake and two temporary pond systems, were exposed to Triops kairomone and control treatments. We observed significant population differences in hatching patterns, both in terms of the fraction of eggs that hatch as well as the timing of hatching, with evidence for within-season bet-hedging through delayed hatching in the populations inhabiting temporary habitats. However, no indication was found that the populations also adjust their hatching pattern to the presence of Triops kairomones.     

An empirical test of bet-hedging polyandry hypothesis in the field cricket Gryllus bimaculatus

Journal of Ethology - Theory shows that polyandry (mating with multiple males within a reproductive season) works as bet-hedging to increase the geometric mean fitness (GMF) of polyandrous genotype...     

Intragenomic conflict over queen determination favours genomic imprinting in eusocial Hymenoptera

Colonies of eusocial Hymenoptera, such as ants, bees and wasps, have long been recognized as candidates for the study of genomic imprinting on the grounds of evolutionary conflicts that arise from close interactions among colony members and relatedness asymmetry owing to haplodiploidy. Although a general kinship theory of genomic imprinting predicts its occurrence under various circumstances of the colony life cycle, new theoretical approaches are required to account for the specifics of real colonies based on recent advances in molecular-level understanding of ants and honeybees. Using a multivariate quantitative genetic model, we examined the potential impact of genomic imprinting on genes that determine the carrier female's propensity to develop into the queen caste. When queen overproduction owing to the increased propensity comes at a colony-level cost, the conflict between maternally and paternally inherited genes in polyandrous (queen multiple mating) colonies favours genomic imprinting. Moreover, we show that the genomic imprinting can occur even under monandry (queen single mating), once incorporating the costs differentially experienced by new males and new queens. Our model predicts the existence of imprinted 'genetic royal cheats' with patriline-specific expression in polyandrous colonies, and seems consistent with the paternal effect on queen determination in monandrous Argentine ants.