How genomic and developmental dynamics affect evolutionary processes

Evolutionary genetics is concerned with natural selection and neutral drift, to the virtual exclusion of almost everything else. In its current focus on DNA variation, it reduces phenotypes to symbols. Varying phenotypes, however, are the units of evolution, and, if we want a comprehensive theory of evolution, we need to consider both the internal and external evolutionary forces that shape the development of phenotypes. Genetic systems are redundant, modular and subject to a variety of genomic mechanisms of "turnover" (transposition, gene conversion, unequal crossingover, slippage and so on). As such the construction and spread of novel combinations of modules by turnover, in particular within gene promoters, contributes significantly to the evolution of phenotypes. Furthermore, redundancy, turnover and modularity lead to ever more complex networks of genetic interactions and ever more functions for a given module. The significant interaction between genomic turnover and natural selection leads to a molecular coevolution between interacting modules and hence facilitates the establishment of biological novelties.     

Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis

Gene duplication provides a window of opportunity for biological variants to persist under the protection of a co-expressed copy with similar or redundant function. Duplication catalyzes innovation (neofunctionalization), subfunction degeneration (subfunctionalization), and genetic buffering (redundancy), and the genetic survival of each paralog is triggered by mechanisms that add, compromise, or do not alter protein function. We tested the applicability of three types of mechanisms for promoting the retained expression of duplicated genes in 290 expressed paralogs of the tetraploid clawed frog, Xenopus laevis. Tests were based on explicit expectations concerning the ka/ks ratio, and the number and location of nonsynonymous substitutions after duplication. Functional constraints on the majority of paralogs are not significantly different from a singleton ortholog. However, we recover strong support that some of them have an asymmetric rate of nonsynonymous substitution: 6% match predictions of the neofunctionalization hypothesis in that (1) each paralog accumulated nonsynonymous substitutions at a significantly different rate and (2) the one that evolves faster has a higher ka/ks ratio than the other paralog and than a singleton ortholog. Fewer paralogs (3%) exhibit a complementary pattern of substitution at the protein level that is predicted by enhancement or degradation of different functional domains, and the remaining 13% have a higher average ka/ks ratio in both paralogs that is consistent with altered functional constraints, diversifying selection, or activity-reducing mutations after duplication. We estimate that these paralogs have been retained since they originated by genome duplication between 21 and 41 million years ago. Multiple mechanisms operate to promote the retained expression of duplicates in the same genome, in genes in the same functional class, over the same period of time following duplication, and sometimes in the same pair of paralogs. None of these paralogs are superfluous; degradation or enhancement of different protein subfunctions and neofunctionalization are plausible hypotheses for the retained expression of some of them. Evolution of most X. laevis paralogs, however, is consistent with retained expression via mechanisms that do not radically alter functional constraints, such as selection to preserve post-duplication stoichiometry or temporal, quantitative, or spatial subfunctionalization.     

The cellular robustness by genetic redundancy in budding yeast

The frequent dispensability of duplicated genes in budding yeast is heralded as a hallmark of genetic robustness contributed by genetic redundancy. However, theoretical predictions suggest such backup by redundancy is evolutionarily unstable, and the extent of genetic robustness contributed from redundancy remains controversial. It is anticipated that, to achieve mutual buffering, the duplicated paralogs must at least share some functional overlap. However, counter-intuitively, several recent studies reported little functional redundancy between these buffering duplicates. The large yeast genetic interactions released recently allowed us to address these issues on a genome-wide scale. We herein characterized the synthetic genetic interactions for ～500 pairs of yeast duplicated genes originated from either whole-genome duplication (WGD) or small-scale duplication (SSD) events. We established that functional redundancy between duplicates is a pre-requisite and thus is highly predictive of their backup capacity. This observation was particularly pronounced with the use of a newly introduced metric in scoring functional overlap between paralogs on the basis of gene ontology annotations. Even though mutual buffering was observed to be prevalent among duplicated genes, we showed that the observed backup capacity is largely an evolutionarily transient state. The loss of backup capacity generally follows a neutral mode, with the buffering strength decreasing in proportion to divergence time, and the vast majority of the paralogs have already lost their backup capacity. These observations validated previous theoretic predictions about instability of genetic redundancy. However, departing from the general neutral mode, intriguingly, our analysis revealed the presence of natural selection in stabilizing functional overlap between SSD pairs. These selected pairs, both WGD and SSD, tend to have decelerated functional evolution, have higher propensities of co-clustering into the same protein complexes, and share common interacting partners. Our study revealed the general principles for the long-term retention of genetic redundancy.     

Regulation of the Calvin cycle for CO2 fixation as an example for general control mechanisms in metabolic cycles.

The theory of a metabolic cycle with the main portion of its intermediates remaining inside the cycle during one turnover has been developed. On this basis, the regulation of the Calvin cycle is analyzed. It is demonstrated that not only the reactions of non-equilibrium enzymes, as the carboxylation of ribulose 1,5-bisphosphate, but reactions that operate close to a thermodynamic equilibrium, especially the reduction of 3-phosphoglycerate and the transketolase reaction can significantly influence the total turnover period in the Calvin cycle. The role of compensating mechanisms in the maintenance of the photosynthesis rate upon changes of environmental conditions and of enzyme contents is analyzed for the Calvin cycle. It is shown that the change of the total quantity of the metabolites is one of the main self-regulated mechanisms in the Calvin cycle. A change of the ATP/ADP ratio can be used by the cell to maintain the CO2 assimilation rate, when the total quantity of the metabolites is changed. The developed analysis permits to explain some experimental data obtained with transgenic plants with restricted efflux of carbon from the chloroplasts.     

Mammary cancer susceptibility: human genes and rodent models

Breast cancer is a complex disease, showing a strong genetic component. Several human susceptibility genes have been identified, especially in the last few months. Most of these genes are low-penetrance genes and it is clear that numerous other susceptibility genes remain to be identified. The function of several susceptibility genes indicates that one critical biological pathway is the DNA damage response. However, other pathways certainly play a significant role in breast cancer susceptibility. Rodent models of breast cancer are useful models in two respects. They can help identify new mammary susceptibility genes by taking advantage of the very divergent susceptibilities exhibited by different mouse or rat strains and carrying out relevant genetic analyses. They also provide investigators with experimental systems that can help decipher the mechanism(s) of resistance to mammary cancer. Recent genetic and biological results obtained with mouse and especially with rat strains indicate that (1) numerous quantitative trait loci control mammary cancer susceptibility or resistance, with distinct loci acting in different strains, and (2) distinct resistance mechanisms operate in different rat resistant strains, precocious mammary differentiation being one of these mechanisms.     

Photoreceptor membrane turnover in the crayfish Cherax destructor: electron microscopy and anti-rhodopsin electron-microscopic immunocytochemistry

Summary Examination of the ultrastructure of retinula cells of the Australian crayfish Cherax destructor at different times over a 24-hour cycle, together with patterns of anti-rhodopsin antigenicity, has lead to the formulation of a model of photoreceptor membrane turnover in these animals. Its main features are: (a) the existence of two bursts of rhabdomeral membrane breakdown; one, light-sensitive and synchronous, occurring at dawn, the other, constituting the first part of the membrane replacement phase itself, occurring during the afternoon and night, (b) the desynchronisation of the replacement phase of turnover between animals and to a lesser extent between cells of the same retina, (c) confinement of ultrastructurally detectable signs of photoreceptor membrane processing to the retinula cells themselves, and (d) replacement of a substantial part if not all of the rhabdomeral membrane daily. This model is compatible with many of the observations reported on the American crayfish Procambarus, and utilises the same basic mechanisms that are believed to operate in photoreceptor membrane turnover in many other arthropod compound eyes.     

Balance between noise and adaptation in competition models of perceptual bistability

Perceptual bistability occurs when a physical stimulus gives rise to two distinct interpretations that alternate irregularly. Noise and adaptation processes are two possible mechanisms for switching in neuronal competition models that describe the alternating behaviors. Either of these processes, if strong enough, could alone cause the alternations in dominance. We examined their relative role in producing alternations by studying models where by smoothly varying the parameters, one can change the rhythmogenesis mechanism from being adaptation-driven to noise-driven. In consideration of the experimental constraints on the statistics of the alternations (mean and shape of the dominance duration distribution and correlations between successive durations) we ask whether we can rule out one of the mechanisms. We conclude that in order to comply with the observed mean of the dominance durations and their coefficient of variation, the models must operate within a balance between the noise and adaptation strength—both mechanisms are involved in producing alternations, in such a way that the system operates near the boundary between being adaptation-driven and noise-driven.     

High sequence turnover in the regulatory regions of the developmental gene hunchback in insects

Extensive sequence analysis of the developmental gene hunchback and its 5' and 3' regulatory regions in Drosophila melanogaster, Drosophila virilis, Musca domestica, and Tribolium castaneum, using a variety of computer algorithms, reveals regions of high sequence simplicity probably generated by slippage-like mechanisms of turnover. No regions are entirely refractory to the action of slippage, although the density and composition of simple sequence motifs varies from region to region. Interestingly, the 5' and 3' flanking regions share short repetitive motifs despite their separation by the gene itself, and the motifs are different in composition from those in the exons and introns. Furthermore, there are high levels of conservation of motifs in equivalent orthologous regions. Detailed sequence analysis of the P2 promoter and DNA footprinting assays reveal that the number, orientation, sequence, spacing, and protein-binding affinities of the BICOID-binding sites varies between species and that the 'P2' promoter, the nanos response element in the 3' untranslated region, and several conserved boxes of sequence in the gene (e.g., the two zinc-finger regions) are surrounded by cryptically-simple-sequence DNA. We argue that high sequence turnover and genetic redundancy permit both the general maintenance of promoter functions through the establishment of coevolutionary (compensatory) changes in cis- and trans-acting genetic elements and, at the same time, the possibility of subtle changes in the regulation of hunchback in the different species.     

Mechanisms of genetic robustness in RNA viruses

Two key features of RNA viruses are their compacted genomes and their high mutation rate. Accordingly, deleterious mutations are common and have an enormous impact on viral fitness. In their multicellular hosts, robustness can be achieved by genomic redundancy, including gene duplication, diploidy, alternative metabolic pathways and biochemical buffering mechanisms. However, here we review evidence suggesting that during RNA virus evolution, alternative robustness mechanisms may have been selected. After briefly describing how genetic robustness can be quantified, we discuss mechanisms of intrinsic robustness arising as consequences of RNA-genome architecture, replication peculiarities and quasi-species population dynamics. These intrinsic robustness mechanisms operate efficiently at the population level, despite the mutational sensitivity shown by individual genomes. Finally, we discuss the possibility that viruses might exploit cellular buffering mechanisms for their own benefit, producing a sort of extrinsic robustness.     

Ingénierie génétique et spermatogenèse

The knowledge of mammal spermatogenesis takes great advantage of the powerful method of functional analysis by genetic engineering. This method allows to study the factors implicated in meiosis depending on the sex and their possible relationships with tumorigenesis and apoptosis. It can be distinguished the factors possibly involved in sterilities and those that can be compensated by genetic redundancy. The mechanisms of spermiogenesis can be dissected, as can be those of the heat shock response and the hemato-testicular barrier. Data extent to the biology of reproduction at various levels in both sexes and to the question of sterility-associated diseases. Knock-out mice also show the importance of the male germ cell genotype/phenotype dissociation in hemizygous. As an experimental approach, the method knows some limitations such as the differences between species in the function and expression of homologous genes. The unexpected failures of spermatogenesis found in many cases supports the notion that spermatogenesis is very sensitive to genetic damages and show that many genes have to be investigated.     

SoxB1 downregulation in vegetal lineages of sea urchin embryos is achieved by both transcriptional repression and selective protein turnover

Patterning of cell fates along the sea urchin animal-vegetal embryonic axis requires the opposing functions of nuclear beta-catenin/TCF-Lef, which activates the endomesoderm gene regulatory network, and SoxB1, which antagonizes beta-catenin and limits its range of function. A crucial aspect of this interaction is the temporally controlled downregulation of SoxB1, first in micromeres and then in macromere progeny. We show that SoxB1 is regulated at the level of protein turnover in these lineages. This mechanism is dependent on nuclear beta-catenin function. It can be activated by Pmar1, but not by Krl, both of which function downstream of beta-catenin/TCF-Lef. At least partially distinct, lineage-specific mechanisms operate, as turnover in the macromeres depends on entry of SoxB1 into nuclei, and on redundant destruction signals, neither of which is required in micromeres. Neither of these turnover mechanisms operates in mesomere progeny, which give rise to ectoderm. However, in mesomeres, SoxB1 appears to be subject to negative autoregulation that helps to maintain tight regulation of SoxB1 mRNA levels in presumptive ectoderm. Between the seventh and tenth cleavage stages, beta-catenin not only promotes degradation of SoxB1, but also suppresses accumulation of its message in macromere-derived blastomeres. Collectively, these different mechanisms work to regulate precisely the levels of SoxB1 in the progeny of different tiers of blastomeres arrayed along the animal-vegetal axis.     

Neurodegenerative disease: a different view of diagnosis

Neurodegenerative diseases have traditionally been defined as clinicopathological entities. Although this has been a productive paradigm in terms of the development of treatment strategies, molecular genetic approaches have revealed that there is overlap between different entities in pathogenic mechanisms. In this article, it is argued that neurodegenerative disease should also be thought of as the consequences of sequential biochemical processes, and that some parts of these processes appear to operate in more than one disease entity. Defining these pathways and, in particular, developing an appreciation of the commonalities between different diseases, should aid in the development of therapies that are effective in several diseases.     

Competitive and positional cues in the patterning of nerve connections

The visual system of lower vertebrates has served as an important testing ground for the mechanisms that generate topographic neuronal connections. During both the outgrowth and the regeneration of the optic nerve, a smoothly ordered map of the retina is formed on its major target, the optic tectum (the retinotectal projection). Experiments performed on this projection have offered support for a variety of mechanisms, including the matching of positional cues in the retina and tectum, the guidance of nerve fibers by interactions between fibers, competition for synaptic space, and the refinement of connections based on neuronal activity. Unfortunately, individual experiments that support any one of these mechanisms have been taken at times as evidence against the involvement of any other mechanism; for example, experiments demonstrating the importance of positional cues have been thought mistakenly to indicate that activity-based interactions are unimportant. Computer simulations, in which multiple, somewhat opposed, mechanisms are allowed to operate in concert demonstrate that such a hybrid model is able to generate a full range of experimental results. More importantly, the elimination of any one of the mechanisms renders the model unable to fit entire classes of findings. Thus, the patterning of the retinotectal projection is best viewed as a process in which the optic nerve terminals attempt to satisfy multiple constraints in selecting their target sites.     

Phylogenetic viewpoints on regulation of light harvesting and electron transport in eukaryotic photosynthetic organisms

The comparative study of photosynthetic regulation in the thylakoid membrane of different phylogenetic groups can yield valuable insights into mechanisms, genetic requirements and redundancy of regulatory processes. This review offers a brief summary on the current understanding of light harvesting and photosynthetic electron transport regulation in different photosynthetic eukaryotes, with a special focus on the comparison between higher plants and unicellular algae of secondary endosymbiotic origin. The foundations of thylakoid structure, light harvesting, reversible protein phosphorylation and PSI-mediated cyclic electron transport are traced not only from green algae to vascular plants but also at the branching point between the “green” and the “red” lineage of photosynthetic organisms. This approach was particularly valuable in revealing processes that (1) are highly conserved between phylogenetic groups, (2) serve a common physiological role but nevertheless originate in divergent genetic backgrounds or (3) are missing in one phylogenetic branch despite their unequivocal importance in another, necessitating a search for alternative regulatory mechanisms and interactions.     

The two faces of mutation: extinction and adaptation in RNA viruses

From a population standpoint, two main features characterize the replication of RNA viruses and viruses that use RNA as a replicative intermediate: high genetic variability, and enormous fluctuations in population size. Their genetic variability mainly reflects a lack of the proof-reading and post-replicative error correction mechanisms that operate during cellular DNA replication, but recombination and segment exchange can also play an important role. Viral population size can change tremendously as a consequence of transmission between hosts or between different tissues within an infected host. A new infection can be initiated with very few particles that subsequently expand many trillion-fold. Repeated bottleneck events can lead to drastic fitness losses or even to viral extinction, whereas continuously large population sizes result in fitness gains and adaptation. Here we review experimental evidence for the effects of mutation, selection, and genetic drift on the adaptation and extinction of RNA viruses.     

Decoding mechanisms by which silent codon changes influence protein biogenesis and function

ScopeSynonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health.PurposeThis synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics.Physiological and medical relevanceUnderstanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies.     

Heritability, correlations and in silico mapping of locomotor behavior and neurochemistry in inbred strains of mice

The midbrain dopamine system mediates normal and pathologic behaviors related to motor activity, attention, motivation/reward and cognition. These are complex, quantitative traits whose variation among individuals is modulated by genetic, epigenetic and environmental factors. Conventional genetic methods have identified several genes important to this system, but the majority of factors contributing to the variation remain unknown. To understand these genetic and environmental factors, we initiated a study measuring 21 behavioral and neurochemical traits in 15 common inbred mouse strains. We report trait data, heritabilities and genetic and non-genetic correlations between pheno-types. In general, the behavioral traits were more heritable than neurochemical traits, and both genetic and non-genetic correlations within these trait sets were high. Surprisingly, there were few significant correlations between the behavioral and the individual neurochemical traits. However, striatal serotonin and one measure of dopamine turnover (DOPAC/DA) were highly correlated with most behavioral measures. The variable accounting for the most variation in behavior was mouse strain and not a specific neurochemical measure, suggesting that additional genetic factors remain to be determined to account for these behavioral differences. We also report the prospective use of the in silico method of quantitative trait loci (QTL) analysis and demonstrate difficulties in the use of this method, which failed to detect significant QTLs for the majority of these traits. These data serve as a framework for further studies of correlations between different midbrain dopamine traits and as a guide for experimental cross designs to identify QTLs and genes that contribute to these traits.