Genetics

Multiple Functional Domains of the Yeast 1,3-{beta}-Glucan Synthase Subunit Fks1p Revealed by Quantitative Phenotypic Analysis of Temperature-Sensitive Mutants.

Publication Date: 2010 Feb 1 PMID: 20124029
Authors: Okada, H. - Abe, M. - Asakawa-Minemura, M. - Hirata, A. - Qadota, H. - Morishita, K. - Ohnuki, S. - Nogami, S. - Ohya, Y.
Journal: Genetics

The main filamentous structural component of the cell wall of the yeast Saccharomyces cerevisiae is 1,3-beta-glucan, which is synthesized by a plasma membrane-localized enzyme called 1,3-beta-glucan synthase (GS). Here we analyzed the quantitative cell morphology and biochemical properties of ten different temperature-sensitive (ts) mutants of FKS1, a putative catalytic subunit of GS. To untangle their pleiotropic phenotypes, the mutants were classified into three functional groups. In the first group, mutants fail to synthesize 1,3-beta-glucan at the proper subcellular location, although GS activity is normal in vitro. In the second group, mutants have normal 1,3-beta-glucan content but are defective in polarized growth and endocytosis. In the third group, mutations in the putative catalytic domain of Fks1p result in a loss of the catalytic activity of GS. The differences between the three groups suggest that Fks1p consists of multiple domains which are required for cell wall construction and cellular morphogenesis.

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Drosophila Rab23 is Involved in the Regulation of the Number and Planar Polarization of the Adult Cuticular Hairs.

Publication Date: 2010 Feb 1 PMID: 20124028
Authors: Pataki, C. - Matusek, T. - Kurucz, E. - Ando, I. - Jenny, A. - Mihaly, J.
Journal: Genetics

The planar coordination of cellular polarization is an important, yet not well understood aspect of animal development. In a screen for genes regulating planar cell polarization in Drosophila, we identified Rab23, encoding a putative vesicular trafficking protein. Mutations in the Drosophila Rab23 orthologue result in abnormal trichome orientation and the formation of multiple hairs on the wing, leg and abdomen. We show that Rab23 impairs hexagonal packing of the wing cells, and that it plays a role in cortical polarization of the polarity proteins. We found that Rab23 is able to associate with the proximally accumulated Prickle protein, although Rab23 itself does not appear to display a polarized subcellular distribution in wing cells. The absence of Rab23 leads to increased actin accumulation in the sub-apical region of the pupal wing cells that fail to restrict prehair initiation to a single site. Rab23 acts as a dominant enhancer of the weak multiple hair phenotype exhibited by the core polarity mutations, whereas the Rab23 homozygous mutant phenotype is sensitive to the gene dose of the planar polarity effector genes. Together, our data suggest that Rab23 contributes to the mechanism that inhibits hair formation at positions outside of the distal vertex by activating the planar polarity effector system.

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The Effect of Recombination on the Reconstruction of Ancestral Sequences.

Publication Date: 2010 Feb 1 PMID: 20124027
Authors: Arenas Busto, M. - Posada, D.
Journal: Genetics

While a variety of methods exist to reconstruct ancestral sequences, all of them assume that single phylogeny underlies all the positions in the alignment, and therefore that recombination has not taken place. Using computer simulations we show that recombination can severely bias ancestral sequence reconstruction (ASR), and quantify this effect. If recombination is ignored, the ancestral sequences recovered can be quite distinct from the grand most recent common ancestor of the sample (GMRCA) and better resemble the concatenate of partial most recent common ancestors (MRCAs) at each recombination fragment. When independent phylogenetic trees are assumed for the different recombinant segments, the estimation of the fragment MRCAs improves significantly. Importantly, we show that recombination can change the biological predictions derived from ASRs carried out with real data. Given that recombination is widespread on nuclear genes and in particular in RNA viruses and some bacteria, the reconstruction of ancestral sequences in these cases should consider the potential impact of recombination and ideally be carried out using approaches that accommodate recombination.

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Patterns of Neutral Genetic Variation on Recombining Sex Chromosomes.

Publication Date: 2010 Feb 1 PMID: 20124026
Authors: Kirkpatrick, M. - Guerrero, R. F. - Scarpino, S. V.
Journal: Genetics

Many animals and plants have sex chromosomes that recombine over much of their length. Here we develop coalescent models for neutral sites on these chromosomes. The emphasis is on expected coalescence times (proportional to the expected amount of neutral genetic polymorphism), but we also derive some results for linkage disequilibria between neutral sites. We analyze the standard neutral model, a model with polymorphic Y chromosomes under balancing selection, and the invasion of a neo-Y chromosome. The results may be useful for testing hypotheses regarding how new sex chromosomes originate and how selection acts upon them.

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DMR1 (CCM1/YGR150C) of Saccharomyces cerevisiae Encodes an RNA-Binding Protein from the Pentatricopeptide Repeat Family Required for the Maintenance of the Mitochondrial 15S Ribosomal RNA.

Publication Date: 2010 Feb 1 PMID: 20124025
Authors: Puchta, O. - Lubas, M. - Lipinski, K. A. - Piatkowski, J. - Malecki, M. - Golik, P.
Journal: Genetics

Pentatricopeptide repeat (PPR) proteins form the largest known RNA-binding protein family and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly in mitochondria and chloroplasts, where they modulate organellar genome expression on the posttranscriptional level. The Saccharomyces cerevisiae DMR1 (CCM1, YGR150C) encodes a PPR protein that localizes to mitochondria. Deletion of DMR1 results in a complete and irreversible loss of respiratory capacity and loss of wild-type mtDNA by conversion to rho(-)/rho(0) petites, regardless of the presence of introns in mtDNA. The phenotype of the dmr1Delta mitochondria is characterized by fragmentation of the small subunit mitochondrial rRNA (15S rRNA), that can be reversed by wild-type Dmr1p. Other mitochondrial transcripts, including the large subunit mitochondrial rRNA (21S rRNA), are not affected by the lack of Dmr1p. The purified Dmr1 protein specifically binds to different regions of 15S rRNA in vitro, consistent with the deletion phenotype. Dmr1p is therefore the first yeast PPR protein, which has an rRNA target, and is probably involved in the biogenesis of mitochondrial ribosomes and translation.

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The impact of whole genome sequencing on model system genetics: get ready for the ride.

Publication Date: 2010 Feb PMID: 20103786
Authors: Hobert, O.
Journal: Genetics

Much of our understanding of how organisms develop and function is derived from the extraordinarily powerful, classic approach of screening for mutant organisms in which a specific biological process is disrupted. Reaping the fruits of such forward genetic screens in metazoan model systems like Drosophila, Caenorhabditis elegans, or zebrafish traditionally involves time-consuming positional cloning strategies that result in the identification of the mutant locus. Whole genome sequencing (WGS) has begun to provide an effective alternative to this approach through direct pinpointing of the molecular lesion in a mutated strain isolated from a genetic screen. Apart from significantly altering the pace and costs of genetic analysis, WGS also provides new perspectives on solving genetic problems that are difficult to tackle with conventional approaches, such as identifying the molecular basis of multigenic and complex traits.

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Epigenetic Contribution to Covariance Between Relatives.

Publication Date: 2010 Jan 25 PMID: 20100941
Authors: Tal, O. - Kisdi, E. - Jablonka, E.
Journal: Genetics

Recent research has pointed to the ubiquity and abundance of between-generation epigenetic inheritance. This research has implications for assessing disease risk and the responses to ecological stresses, and also for understanding evolutionary dynamics. An important step towards a general evaluation of these implications is the identification and estimation of the amount of heritable, epigenetic variation in populations. While methods for modeling the phenotypic heritable variance contributed by culture have already been developed, there are no comparable methods for non-behavioral epigenetic inheritance systems. By introducing a model that takes epigenetic transmissibility (the probability of transmission of ancestral phenotypes) and environmental induction into account, we provide novel expressions for covariances between relatives. We have combined classical quantitative genetics approach with information about the number of opportunities for epigenetic reset between generations and assumptions about environmental induction to estimate the heritable epigenetic variance and epigenetic transmissibility for both asexual and sexual populations. This assists in the identification of phenotypes and populations in which epigenetic transmission occurs, and enables a preliminary quantification of their transmissibility, which could then be followed by genomewide association and QTL studies.

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A Genome-wide RNAi Screen for Modifiers of Aggregates Formation by Mutant Huntingtin in Drosophila.

Publication Date: 2010 Jan 25 PMID: 20100940
Authors: Zhang, S. - Binari, R. - Zhou, R. - Perrimon, N.
Journal: Genetics

Protein aggregates are a common pathological feature of most neurodegenerative diseases (NDs). Understanding their formation and regulation will help clarify their controversial roles in disease pathogeneses. To date there has been few systematic study of aggregates formation in Drosophila, a model organism that has been applied extensively in modelling NDs and screening for toxicity modifiers. We generated transgenic flies lines that express eGFP-tagged mutant Huntingtin (Htt) fragments with different length of polyglutamine (polyQ) tract, and showed that these Htt mutants develop protein aggregates in a polyQ-length and age-dependent manner in Drosophila. To identify central regulators of protein aggregation, we further generated stable Drosophila cell lines expressing these Htt mutants and also established a cell-based quantitative assay that allows automated measurement of aggregates within cells. We then performed a genome-wide RNA interference (RNAi) screen for regulators of mutant Htt aggregation and isolated 126 genes involved in diverse cellular processes. Interestingly, although our screen focused only on mutant Htt aggregation, several of the identified candidates were known previously as toxicity modifiers of NDs. Moreover, modulating the in vivo activity of hsp110 (CG6603) or tra1, two hits from the screen, affect neurodegeneration in a dose-dependent manner in a Drosophila model of Huntington's disease (HD). Thus, other aggregates regulators isolated in our screen may identify additional genes involved in protein folding pathway and neurotoxicity.

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An Interspecific Plant Hybrid Shows Novel Changes in Parental Splice Forms of Genes for Splicing Factors.

Publication Date: 2010 Jan 25 PMID: 20100939
Authors: Scascitelli, M. - Cognet, M. - Adams, K. L.
Journal: Genetics

Interspecific hybridization plays an important role in plant adaptive evolution and speciation, and the process often results in phenotypic novelty. Hybrids can show changes in genome structure and gene expression compared with their parents including chromosomal rearrangments, changes in cytosine methylation, up- and down-regulation of gene expression, and gene silencing. Alternative splicing is a fundamental aspect of the expression of many genes. However alternative splicing patterns have not been examined in multiple genes in an interspecific plant hybrid compared with its parents. Here we studied alternative splicing patterns in an interspecific Populus hybrid and its parents by assaying 40 genes using reverse transcription PCR. Most of the genes showed identical alternative splicing patterns between the parents and the hybrid. We found new alternative splicing variants present in the hybrid in two SR genes, involved in the regulation of splicing and alternative splicing. The novel alternative splicing patterns included changes in donor and acceptor sites to create a new exon in one allele of PtRSZ22 in the hybrid, and retention of an intron in both alleles of PtSR34a.1 in the hybrid, with effects on the function of the corresponding truncated proteins, if present. Our results suggest that novel alternative splicing patterns are present in a small percentage of genes in hybrids, but they could make a considerable impact on the expression of some genes. Changes in alternative splicing are likely to be an important component of the genetic changes that occur upon interspecific hybridization.

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Exact Results for the Evolution of Stochastic Switching in Variable Asymmetric Environments.

Publication Date: 2010 Jan 25 PMID: 20100938
Authors: Gaal, B. - Pitchford, J. W. - Wood, A. J.
Journal: Genetics

The ability of bacteria to spontaneously switch their expressed phenotype from an identical underlying genotype is now widely acknowledged. Mechanisms behind these switches have been shown to be evolvable. Important questions thus arise: in a fluctuating environment, under what conditions can stochastic switching evolve and how is the evolutionarily optimal switching rate related to the environmental changes? Here we derive exact analytical results for the long term exponential population growth rate in a two-state periodically changing environment, where the environmental states vary in both their duration and in their impact on the fitness of each phenotype. Using methods from statistical physics we derive conditions under which non-switching is evolutionarily optimal, and we furthermore demonstrate that the transition between the non-switching and switching regimes is discontinuous (a first-order phase transition). Our general analytical method allows the evolutionary effects of asymmetries in selection pressures and environmental growth rates to be quantified. The evolutionary implications of our findings are discussed in relation to their to real-world applications in the light of recent experimental evidence.

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Evolutionary and Functional Properties of a Two-Locus {beta}-Globin Polymorphism in Indian House Mice.

Publication Date: 2010 Jan 25 PMID: 20100937
Authors: Runck, A. M. - Weber, R. E. - Fago, A. - Storz, J. F.
Journal: Genetics

Electrophoretic surveys of hemoglobin (Hb) polymorphism in house mice from South Asia and the Middle East have revealed that two alternative beta-globin haplotypes, Hbb(d) and Hbb(p), are often present at intermediate frequencies in geographically disparate populations. Both haplotypes harbor two functionally distinct beta-globin paralogs, HBB-T1 (which encodes the beta-chain subunits of the major Hb isoform) and HBB-T2 (which encodes the beta-chains of the minor Hb isoform). The Hbb(d) and Hbb(p) haplotypes share identical HBB-T1 alleles, but products of the alternative HBB-T2 alleles (dminor and pminor) are distinguished by two amino acid substitutions. To investigate the possible adaptive significance of the Hbb(d)/Hbb(p) polymorphism we conducted a population genetic analysis of the duplicated beta-globin genes of Indian house mice (Mus castaneus) in conjunction with experimental studies of Hb function in inbred strains of mice that carry the alternative Hbb(d) and Hbb(p) haplotypes. The main objectives of this study were (i) to characterize patterns of nucleotide polymorphism and linkage disequilibrium in the duplicated beta-globin genes of M. castaneus; (ii) to test the hypothesis that the Hbb(d) and Hbb(p) haplotypes are maintained as a balanced polymorphism; and (iii) to assess whether allelic differences in the alternative minor Hb isoforms (dminor and pminor) are associated with different O2-binding properties. A multilocus analysis of polymorphism and divergence revealed that levels of diversity at the HBB-T2 gene exceeded neutral expectations, and reconstructed haplotype networks for both beta-globin paralogs revealed extensive allele sharing with several other closely related species of Mus. However, despite this suggestive evidence for balancing selection, O2-equilibrium curves revealed no discernable functional differences between red cell lysates containing the dminor and pminor Hb isoforms. If the dminor and pminor alleles are maintained as a balanced polymorphism, our results indicate that the associated fitness variance is not directly related to respiratory functions of Hb.

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Cyclin Y is a Novel Conserved Cyclin Essential for Development in Drosophila.

Publication Date: 2010 Jan 25 PMID: 20100936
Authors: Liu, D. - Finley Jr, R. L.
Journal: Genetics

The Drosophila gene CG14939 encodes a member of a highly conserved family of cyclins, the Y type cyclins, which have not been functionally characterized in any organism. Here we report the generation and phenotypic characterization of a null mutant of CG14939, which we rename Cyclin Y (CycY). We show that the null mutant, CycY(E8), is homozygous lethal with most mutant animals arresting during pupal developmet. The mutant exhibits delayed larval growth and major developmental defects during metamorphosis, including impaired gas bubble translocation, head eversion, leg elongation, and adult tissue growth. Heat shock-induced expression of CycY at different times during development resulted in variable levels of rescue, the timing of which suggests a key function for zygotic CycY during the transition from third instar larvae to prepupae. CycY also plays an essential role during embryogenesis since zygotic null embryos from null mothers fail to hatch into first instar larvae. We provide evidence that the CycY protein (CycY) interacts with Eip63E, a Cyclin-dependent kinase (Cdk) for which no cyclin partner had previously been identified. Like CycY, the Eip63E gene has essential functions during embryogenesis, larval development, and metamorphosis. Our data suggest that CycY/Eip63E form a cyclin/Cdk complex that is essential for several developmental processes.

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Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination.

Publication Date: 2010 Jan 18 PMID: 20083614
Authors: Reams, A. B. - Kofoid, E. - Savageau, M. - Roth, J. R.
Journal: Genetics

Tandem duplications are among the most common mutation events. The high loss rate of duplication suggested that the frequency of duplications in a bacterial population (1/1000) might reflect a steady state dictated by relative rates of formation (kF) and loss (kL). This possibility was tested for three genetic loci. Without homologous recombination (RecA), duplication loss rate dropped essentially to zero, but formation rate decreased only slightly and a steady state was still reached rapidly. Under all conditions, steady state was reached faster than predicted by formation and loss rates alone. A major factor in determining steady state proved to be the fitness cost, which can exceed 40% for some genomic regions. Depending on the region tested, duplications reached 40% to 98% of the steady-state frequency within 30 generations-approximately the growth required for a single cell to produce a saturated overnight culture or form a large colony on solid medium (10(9) cells). Long-term bacterial populations are stably polymorphic for duplications of every region of their genome. These polymorphisms contribute to rapid genetic adaptation by providing frequent pre-existing beneficial mutations whenever imposed selection favors increases in some gene activity. While the reported results were obtained with the bacterium S. enterica, the genetic implications seem likely to be of broader biological relevance.

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Deleterious Mutations and Selection for Sex in Finite Diploid Populations.

Publication Date: 2010 Jan 18 PMID: 20083613
Authors: Roze, D. - Michod, R. E.
Journal: Genetics

In diploid populations, indirect benefits of sex may stem from segregation and recombination. Although it has been recognized that finite population size is an important component of selection for recombination, its effects on selection for segregation have been somewhat less studied. In this paper, we develop analytical two and three-locus model to study the effect of recurrent deleterious mutations on a modifier gene increasing sex, in a finite diploid population. The model also incorporates effects of mitotic recombination, causing loss of heterozygosity (LOH). Predictions are tested using multilocus simulations representing deleterious mutations occurring at a large number of loci. The model and simulations show that excess of heterozygosity generated by finite population size is an important component of selection for sex, favoring segregation when deleterious alleles are nearly additive to dominant. Furthermore, sex tends to break correlations in homozygosity among selected loci, which disfavors sex when deleterious alleles are either recessive or dominant. As a result, we find that it is difficult to maintain costly sex when deleterious alleles are recessive. LOH tends to favor sex when deleterious mutations are recessive, but the effect is relatively weak for rates of LOH corresponding to current estimates (of the order 10(-4) to 10(-5)).

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Regulation of Bacterial Conjugation in Microaerobiosis by Host-encoded Functions ArcAB and SdhABCD.

Publication Date: 2010 Jan 18 PMID: 20083612
Authors: Serna, A. - Espinosa, E. - Camacho, E. M. - Casadesus, J.
Journal: Genetics

The virulence plasmid of Salmonella enterica (pSLT) is an F-like conjugative plasmid. High rates pf pSLT transfer occur in the mammalian gut, a microaerobic environment. In this study, we describe genetic screens for host-encoded activators and repressors of the transfer operon (tra) of pSLT. We show that the transcription factor ArcA is an activator of conjugation, especially under microaerobiosis. In turn, SdhABCD (succinate dehydrogenase) is a repressor of mating in aerobiosis. ArcA binds upstream the main tra promoter (ptraY) and activates tra transcription, as previously described in F, R1 and R100. In the absence of ArcA, transfer of pSLT decreased 7 fold in aerobiosis, and >100 fold in microaerobiosis. In aerobiosis, ArcA activates the traY promoter in an ArcB-independent manner, as described in other F-like plasmids. In microaerobiosis, however, the ArcB sensor is necessary for activation of ptraY. Lack of succinate dehydrogenase (Sdh) causes a >20 fold increase in pSLT transfer in aerobiosis, but has little effect under microaerobiosis. Sdh inhibits conjugal transfer by reducing traJ transcription, probably in an indirect manner. In turn, the sdhCDAB operon is repressed by the ArcAB system under microaerobiosis. Hence, the ArcAB two-component system of S. enterica stimulates pSLT transfer under microaerobiosis by two concerted actions: activation of the tra operon and repression of the sdhCDAB operon.

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Flavonoid Phytoalexin Dependent Resistance to Anthracnose Leaf Blight Requires a Functional yellow seed1 in Sorghum bicolor.

Publication Date: 2010 Jan 18 PMID: 20083611
Authors: Ibraheem, F. - Gaffoor, I. - Chopra, S.
Journal: Genetics

In Sorghum bicolor, a group of phytoalexins are induced at the site of infection by Colletotrichum sublineolum, the anthracnose fungus. These compounds, classified as 3-deoxyanthocyanidins, have structural similarities to the precursors of phlobaphenes. Sorghum yellow seed1 (y1) encodes a MYB transcription factor that regulates phlobaphene biosynthesis. Using the candystripe1 transposon mutagenesis system in sorghum, we have isolated functional revertants as well as loss of function alleles of y1. These near isogenic lines of sorghum show that compared to functionally revertant alleles, loss of y1 lines do not accumulate phlobaphenes. Molecular characterization of two null y1 alleles shows a partial internal deletion in the y1 sequence. These null alleles designated as y1-ww1 and y1-ww4, do not accumulate 3-deoxyanthocyanidins when challenged with a non-pathogenic fungus Cochliobolus heterostrophus. Further, as compared to the wild type allele, both y1-ww1 and y1-ww4 show greater susceptibility to the pathogenic fungus C. sublineolum. In fungal inoculated wild type seedlings, y1 and its target flavonoid structural genes are coordinately expressed. However, in y1-ww1 and y1-ww4 seedlings where y1 is not expressed, steady state transcripts of its target genes could not be detected. Co-segregation analysis showed that the functional y1 gene is genetically linked with resistance to C. sublineolum. Overall results demonstrate that the accumulation of sorghum 3-deoxyanthocyanidin phytoalexins and resistance to C. sublineolum in sorghum require a functional y1 gene.

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EOR-2 is an Obligate Binding Partner of the BTB-zinc Finger Protein EOR-1 in Caenorhabditis elegans.

Publication Date: 2010 Jan 11 PMID: 20065070
Authors: Howell, K. L. - Arur, S. - Schedl, T. - Sundaram, M. V.
Journal: Genetics

BTB-zinc finger transcription factors play many important roles in metazoan development. In these proteins, the BTB domain is critical for dimerization and for recruiting cofactors to target genes. Identification of these cofactors is important for understanding how BTB-zinc finger proteins influence transcription. Here we show that the novel but conserved protein EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans. EOR-1 and EOR-2 function together to promote multiple Ras/ERK-dependent cell fates during development, and we show that EOR-1 is a robust substrate of ERK in vitro. A point mutation (L81F) in the EOR-1 BTB domain reduces both ERK phosphorylation and EOR-2 binding and eliminates all detectable biological function without affecting EOR-1 expression levels, localization, or dimerization. This point mutation lies near the predicted charged pocket region of the EOR-1 BTB dimer, a region that, in other BTB-zinc finger proteins, has been proposed to interact with corepressors or coactivators. We also show that a conserved zinc finger-like motif in EOR-2 is required for binding to EOR-1, that the interaction between EOR-1 and EOR-2 is direct, and that EOR-2 can bind to the human BTB-zinc finger protein PLZF. We propose that EOR-2 defines a new family of cofactors for BTB-zinc finger transcription factors that may have conserved roles in other organisms.

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The Fission Yeast Rad32(Mre11)-Rad50-Nbs1 Complex Acts Both Upstream and Downstream of Checkpoint Signaling in the S-Phase DNA Damage Checkpoint.

Publication Date: 2010 Jan 11 PMID: 20065069
Authors: Willis, N. - Rhind, N.
Journal: Genetics

The Mre11-Rad50-Nbs1 (MRN) heterotrimer plays various and complex roles in DNA damage repair and checkpoint signaling. Its role in activating Ataxia-Telangiectasia Mutated (ATM), the central checkpoint kinase in the metazoan double-strand break response, has been well studied. However, its function in the checkpoint independent of ATM activation, as well as functions that are completely checkpoint independent, are less well understood. In fission yeast, DNA damage checkpoint signaling requires Rad3, the homolog of the ATR (ATM and Rad3 Related) kinase, not Tel1, the ATM homolog, allowing us to dissect MRN's ATM-independent S-phase DNA damage checkpoint roles from its role in ATM activation. We find that MRN is involved in Rad3 (ATR) dependent checkpoint signaling in S phase, but not G2, suggesting that MRN is involved in ATR activation through its role in replication fork metabolism. In addition, we define a role for MRN in the S-phase DNA damage checkpoint dependent slowing of replication that is independent of its role in checkpoint signaling. Genetic interactions between MRN and Rhp51, the fission yeast Rad51 homolog, lead us to suggest that MRN participates in checkpoint-dependent replication slowing through negative regulation of recombination.

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Convergently Recruited Nuclear Transport Retrogenes are Male Biased in Expression and Evolving Under Positive Selection in Drosophila.

Publication Date: 2010 Jan 11 PMID: 20065068
Authors: Tracy, C. - Rio, J. - Motiwale, M. - Christensen, S. M. - Betran, E.
Journal: Genetics

The analyses of gene duplications by retroposition have revealed an excess of male-biased duplicates generated from X chromosome to autosomes in flies and mammals. Investigating these genes is of primary importance in understanding sexual dimorphism and genome evolution. In a particular instance, X-linked nuclear transport genes (Ntf-2 and ran) have given rise to autosomal retroposed copies three independent times in Drosophila (along the lineages leading to D. melanogaster, D. ananassae and D. grimshawi). Here we explore in further detail the expression and the mode of evolution of these Drosophila Ntf-2 and ran derived retrogenes. Five out of the six retrogenes show male-biased expression. The ran-like gene of D. melanogaster and D. simulans has undergone recurrent positive selection. Similarly, in D. ananassae and D. atripex, the Ntf-2 and ran retrogenes show evidence of past positive selection. The data suggest that strong selection is acting on the origin and evolution of these retrogenes. Avoiding male meiotic X inactivation, increasing level of expression of X-linked genes in male testes, and/or sexual antagonism might explain the recurrent duplication of retrogenes from X to autosomes. Interestingly, the ran-like in D. yakuba has mostly pseudogenized alleles. Disablement of the ran-like gene in D. yakuba indicates turnover of these duplicates. We discuss the possibility that Dntf-2r and ran-like might be involved in genomic conflicts during spermatogenesis.

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Improved Activities of CBP, hnRNPs and Proteasome Following Down Regulation of Noncoding hsr{omega} Transcripts Help Suppress polyQ Pathogenesis in Fly Models.

Publication Date: 2010 Jan 11 PMID: 20065067
Authors: Mallik, M. - Lakhotia, S. C.
Journal: Genetics

Following earlier reports on modulation of polyQ toxicity in Drosophila by the developmentally active and stress-inducible noncoding hsromega gene, we investigated possible mediators of this modulation. RNAi-mediated down regulation of the large nuclear hsromega-n transcript, which organizes the nucleoplasmic omega speckles, suppressed the enhancement of polyQ toxicity brought about by reduced availability of the hnRNP Hrb87F or of the transcriptional regulator, CREB Binding Protein (CBP). Levels of CBP RNA and protein were reciprocally affected by hsromega transcript levels in eye disc cells. Our data suggest that CBP and hnRNPs like Hrb57A and Hrb87F physically interact with each other. In addition, down regulation of hsromega transcripts partially rescued eye damage following compromised proteasome activity, while over-expression of hsromega and/or polyQ proteins disrupted the proteasomal activity. Rescue of polyQ toxicity by hsromega-RNAi required normal proteasomal function. We suggest that hsromega-RNAi suppresses polyQ toxicity by elevating cellular levels of CBP, by enhancing proteasome-mediated clearance of the pathogenic polyQ aggregates and by inhibiting induced apoptosis. The direct and indirect interactions of the hsromega transcripts with a variety of regulatory proteins like hnRNPs, CBP, proteasome, DIAP1 etc, reinforce the view that the noncoding hsromega RNA functions as a "hub" in cellular networks to maintain homeostasis by regulating the functional availability of crucial cellular regulatory proteins.

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Gene genealogies strongly distorted by weakly interfering mutations in constant environments.

Publication Date: 2010 Feb PMID: 19966069
Authors: Seger, J. - Smith, W. A. - Perry, J. J. - Hunn, J. - Kaliszewska, Z. A. - Sala, L. L. - Pozzi, L. - Rowntree, V. J. - Adler, F. R.
Journal: Genetics

Neutral nucleotide diversity does not scale with population size as expected, and this "paradox of variation" is especially severe for animal mitochondria. Adaptive selective sweeps are often proposed as a major cause, but a plausible alternative is selection against large numbers of weakly deleterious mutations subject to Hill-Robertson interference. The mitochondrial genealogies of several species of whale lice (Amphipoda: Cyamus) are consistently too short relative to neutral-theory expectations, and they are also distorted in shape (branch-length proportions) and topology (relative sister-clade sizes). This pattern is not easily explained by adaptive sweeps or demographic history, but it can be reproduced in models of interference among forward and back mutations at large numbers of sites on a nonrecombining chromosome. A coalescent simulation algorithm was used to study this model over a wide range of parameter values. The genealogical distortions are all maximized when the selection coefficients are of critical intermediate sizes, such that Muller's ratchet begins to turn. In this regime, linked neutral nucleotide diversity becomes nearly insensitive to N. Mutations of this size dominate the dynamics even if there are also large numbers of more strongly and more weakly selected sites in the genome. A genealogical perspective on Hill-Robertson interference leads directly to a generalized background-selection model in which the effective population size is progressively reduced going back in time from the present.

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A comprehensive linkage map of the dog genome.

Publication Date: 2010 Feb PMID: 19966068
Authors: Wong, A. K. - Ruhe, A. L. - Dumont, B. L. - Robertson, K. R. - Guerrero, G. - Shull, S. M. - Ziegle, J. S. - Millon, L. V. - Broman, K. W. - Payseur, B. A. - Neff, M. W.
Journal: Genetics

We have leveraged the reference sequence of a boxer to construct the first complete linkage map for the domestic dog. The new map improves access to the dog's unique biology, from human disease counterparts to fascinating evolutionary adaptations. The map was constructed with approximately 3000 microsatellite markers developed from the reference sequence. Familial resources afforded 450 mostly phase-known meioses for map assembly. The genotype data supported a framework map with approximately 1500 loci. An additional approximately 1500 markers served as map validators, contributing modestly to estimates of recombination rate but supporting the framework content. Data from approximately 22,000 SNPs informing on a subset of meioses supported map integrity. The sex-averaged map extended 21 M and revealed marked region- and sex-specific differences in recombination rate. The map will enable empiric coverage estimates and multipoint linkage analysis. Knowledge of the variation in recombination rate will also inform on genomewide patterns of linkage disequilibrium (LD), and thus benefit association, selective sweep, and phylogenetic mapping approaches. The computational and wet-bench strategies can be applied to the reference genome of any nonmodel organism to assemble a de novo linkage map.

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Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes.

Publication Date: 2010 Feb PMID: 19966067
Authors: Eng, K. H. - Kvitek, D. J. - Keles, S. - Gasch, A. P.
Journal: Genetics

Understanding complex genotype-by-environment interactions (GEIs) is crucial for understanding phenotypic variation. An important factor often overlooked in GEI studies is time. We measured the contribution of GEIs to expression variation in four nonlaboratory Saccharomyces cerevisiae strains responding dynamically to a 25 degrees -37 degrees heat shock. GEI was a major force explaining expression variation, affecting 55% of the genes analyzed. Importantly, almost half of these expression patterns showed GEI influence only during the transition between environments, but not in acclimated cells. This class reveals a genotype-by-environment-by-time interaction that affected expression of a large fraction of yeast genes. Strikingly, although transcripts subject to persistent GEI effects were enriched for nonessential genes with upstream TATA elements, those displaying transient GEIs were enriched for essential genes regardless of TATA regulation. Genes subject to persistent GEI influences showed relaxed constraint on acclimated gene expression compared to the average yeast gene, whereas genes restricted to transient GEIs did not. We propose that transient GEI during the transition between environments provides a previously unappreciated source of expression variation, particularly for essential genes.

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Signatures of recent directional selection under different models of population expansion during colonization of new selective environments.

Publication Date: 2010 Feb PMID: 19966066
Authors: Kim, Y. - Gulisija, D.
Journal: Genetics

A major problem in population genetics is understanding how the genomic pattern of polymorphism is shaped by natural selection and the demographic history of populations. Complex population dynamics confounds patterns of variation and poses serious challenges for identifying genomic imprints of selection. We examine patterns of polymorphism using computer simulations and provide analytical predictions for hitchhiking effects under two models of adaptive niche expansion. The population split (PS) model assumes the separation of a founding population followed by directional selection in the new environment. Here, the new population undergoes a bottleneck and later expands in size. This model has been used in previous studies to account for demographic effects when testing for signatures of selection under colonization or domestication. The genotype-dependent colonization and introgression (GDCI) model is proposed in this study and assumes that a small number of migrants carrying adaptive genotype found a new population, which then grows logistically. The GDCI model also allows for constant migration between the parental and the new population. Both models predict reduction in variation and excess of high frequency of derived alleles relative to neutral expectations, with and without hitchhiking. Under comparable conditions, the GDCI model results in greater reduction in expected heterozygosity and more skew of the site frequency spectrum than the PS model. We also find that soft selective sweeps (fixation of multiple copies of a beneficial mutation) occurs less often in the GDCI model than in the PS model. This result demonstrates the importance of correctly modeling the ecological process in inferring adaptive evolution using DNA sequence polymorphism.

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The genetic signature of conditional expression.

Publication Date: 2010 Feb PMID: 19966065
Authors: Van Dyken, J. D. - Wade, M. J.
Journal: Genetics

Conditionally expressed genes have the property that every individual in a population carries and transmits the gene, but only a fraction, , expresses the gene and exposes it to natural selection. We show that a consequence of this pattern of inheritance and expression is a weakening of the strength of natural selection, allowing deleterious mutations to accumulate within and between species and inhibiting the spread of beneficial mutations. We extend previous theory to show that conditional expression in space and time have approximately equivalent effects on relaxing the strength of selection and that the effect holds in a spatially heterogeneous environment even with low migration rates among patches. We support our analytical approximations with computer simulations and delineate the parameter range under which the approximations fail. We model the effects of conditional expression on sequence polymorphism at mutation-selection-drift equilibrium, allowing for neutral sites, and show that sequence variation within and between species is inflated by conditional expression, with the effect being strongest in populations with large effective size. As decreases, more sites are recruited into neutrality, leading to pseudogenization and increased drift load. Mutation accumulation diminishes the degree of adaptation of conditionally expressed genes to rare environments, and the mutational cost of phenotypic plasticity, which we quantify as the plasticity load, is greater for more rarely expressed genes. Our theory connects gene-level relative polymorphism and divergence with the spatial and temporal frequency of environments inducing gene expression. Our theory suggests that null hypotheses for levels of standing genetic variation and sequence divergence must be corrected to account for the frequency of expression of the genes under study.

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The evolution of control and distribution of adaptive mutations in a metabolic pathway.

Publication Date: 2010 Feb PMID: 19966064
Authors: Wright, K. M. - Rausher, M. D.
Journal: Genetics

In an attempt to understand whether it should be expected that some genes tend to be used disproportionately often by natural selection, we investigated two related phenomena: the evolution of flux control among enzymes in a metabolic pathway and properties of adaptive substitutions in pathway enzymes. These two phenomena are related by the principle that adaptive substitutions should occur more frequently in enzymes with greater flux control. Predicting which enzymes will be preferentially involved in adaptive evolution thus requires an evolutionary theory of flux control. We investigated the evolution of enzyme control in metabolic pathways with two models of enzyme kinetics: metabolic control theory (MCT) and Michaelis-Menten saturation kinetics (SK). Our models generate two main predictions for pathways in which reactions are moderately to highly irreversible: (1) flux control will evolve to be highly unequal among enzymes in a pathway and (2) upstream enzymes evolve a greater control coefficient then those downstream. This results in upstream enzymes fixing the majority of beneficial mutations during adaptive evolution. Once the population has reached high fitness, the trend is reversed, with the majority of neutral/slightly deleterious mutations occurring in downstream enzymes. These patterns are the result of three factors (the first of these is unique to the MCT simulations while the other two seem to be general properties of the metabolic pathways): (1) the majority of randomly selected, starting combinations of enzyme kinetic rates generate pathways that possess greater control for the upstream enzymes compared to downstream enzymes; (2) selection against large pools of intermediate substrates tends to prevent majority control by downstream enzymes; and (3) equivalent mutations in enzyme kinetic rates have the greatest effect on flux for enzymes with high levels of flux control, and these enzymes will accumulate adaptive substitutions, strengthening their control. Prediction 1 is well supported by available data on control coefficients. Data for evaluating prediction 2 are sparse but not inconsistent with this prediction.

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Experimentally increased codon bias in the Drosophila adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity.

Publication Date: 2010 Feb PMID: 19966063
Authors: Hense, W. - Anderson, N. - Hutter, S. - Stephan, W. - Parsch, J. - Carlini, D. B.
Journal: Genetics

Although most amino acids can be encoded by more than one codon, the synonymous codons are not used with equal frequency. This phenomenon is known as codon bias and appears to be a universal feature of genomes. The translational selection hypothesis posits that the use of optimal codons, which match the most abundant species of isoaccepting tRNAs, results in increased translational efficiency and accuracy. Previous work demonstrated that the experimental reduction of codon bias in the Drosophila alcohol dehydrogenase (Adh) gene led to a significant decrease in ADH protein expression. In this study we performed the converse experiment: we replaced seven suboptimal leucine codons that occur naturally in the Drosophila melanogaster Adh gene with the optimal codon. We then compared the in vivo ADH activities imparted by the wild-type and mutant alleles. The introduction of optimal leucine codons led to an increase in ADH activity in third-instar larvae. In adult flies, however, the introduction of optimal codons led to a decrease in ADH activity. There is no evidence that other selectively constrained features of the Adh gene, or its rate of transcription, were altered by the synonymous replacements. These results are consistent with translational selection for codon bias being stronger in the larval stage and suggest that there may be a selective conflict over optimal codon usage between different developmental stages.

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Rate of adaptation in large sexual populations.

Publication Date: 2010 Feb PMID: 19948891
Authors: Neher, R. A. - Shraiman, B. I. - Fisher, D. S.
Journal: Genetics

Adaptation often involves the acquisition of a large number of genomic changes that arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for populations in which genetic information is exchanged, beneficial mutations can arise in different individuals and be combined later. In large populations, when the product of the population size N and the total beneficial mutation rate U(b) is large, many new beneficial alleles can be segregating in the population simultaneously. We calculate the rate of adaptation, v, in several models of such sexual populations and show that v is linear in NU(b) only in sufficiently small populations. In large populations, v increases much more slowly as log NU(b). The prefactor of this logarithm, however, increases as the square of the recombination rate. This acceleration of adaptation by recombination implies a strong evolutionary advantage of sex.

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Regulation of epithelial stem cell replacement and follicle formation in the Drosophila ovary.

Publication Date: 2010 Feb PMID: 19948890
Authors: Nystul, T. - Spradling, A.
Journal: Genetics

Though much has been learned about the process of ovarian follicle maturation through studies of oogenesis in both vertebrate and invertebrate systems, less is known about how follicles form initially. In Drosophila, two somatic follicle stem cells (FSCs) in each ovariole give rise to all polar cells, stalk cells, and main body cells needed to form each follicle. We show that one daughter from each FSC founds most follicles but that cell type specification is independent of cell lineage, in contrast to previous claims of an early polar/stalk lineage restriction. Instead, key intercellular signals begin early and guide cell behavior. An initial Notch signal from germ cells is required for FSC daughters to migrate across the ovariole and on occasion to replace the opposite stem cell. Both anterior and posterior polar cells arise in region 2b at a time when approximately 16 cells surround the cyst. Later, during budding, stalk cells and additional polar cells are specified in a process that frequently transfers posterior follicle cells onto the anterior surface of the next older follicle. These studies provide new insight into the mechanisms that underlie stem cell replacement and follicle formation during Drosophila oogenesis.

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The power of the methods for detecting interlocus gene conversion.

Publication Date: 2010 Feb PMID: 19948889
Authors: Mansai, S. P. - Innan, H.
Journal: Genetics

Interlocus gene conversion can homogenize DNA sequences of duplicated regions with high homology. Such nonvertical events sometimes cause a misleading evolutionary interpretation of data when the effect of gene conversion is ignored. To avoid this problem, it is crucial to test the data for the presence of gene conversion. Here, we performed extensive simulations to compare four major methods to detect gene conversion. One might expect that the power increases with increase of the gene conversion rate. However, we found this is true for only two methods. For the other two, limited power is expected when gene conversion is too frequent. We suggest using multiple methods to minimize the chance of missing the footprint of gene conversion.

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FRQ-interacting RNA helicase mediates negative and positive feedback in the neurospora circadian clock.

Publication Date: 2010 Feb PMID: 19948888
Authors: Shi, M. - Collett, M. - Loros, J. J. - Dunlap, J. C.
Journal: Genetics

The Neurospora circadian oscillator comprises FREQUENCY (FRQ) and its transcription activator, the White Collar Complex (WCC). Repression of WCC's transcriptional activity by FRQ via negative feedback is indispensable for clock function. An unbiased genetic screen that targeted mutants with defects in negative feedback regulation yielded a fully viable arrhythmic strain bearing a novel allele of FRQ-interacting RNA helicase (frh), an essential gene that encodes a putative exosome component protein. In the allele, frh(R806H), clock function is completely disturbed, while roles of FRQ-interacting RNA helicase (FRH) essential for viability are left intact. FRH(R806H) still interacts with FRQ, but interaction between the FRQ-FRH(R806H) complex (FFC) and WCC is severely affected. Phosphorylation of WC-1 is reduced in the mutant leading to constantly elevated WCC activity, which breaks the negative feedback loop. WCC levels are considerably reduced in the mutant, especially those of WC-1, consistent both with loss of positive feedback (FRQ-dependent WC-1 stabilization) and with a reduced level of the FRQ-mediated WCC phosphorylation that leads to high WCC activity accompanied by rapid transcription-associated turnover. FRH overexpression promotes WC-1 accumulation, confirming that FRH together with FRQ plays a role in WC-1 stabilization. Identification of a viable allele of frh, displaying virtually complete loss of both negative and positive circadian feedback, positions FRH as a core component of the central oscillator that is permissive for rhythmicity but appears not to modulate periodicity. Moreover, the results suggest that there are clock-specific roles for FRH that are distinct from the predicted essential exosome-associated functions for the protein.

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Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4-Spt5 in Transcription.

Publication Date: 2010 Feb PMID: 19948887
Authors: Quan, T. K. - Hartzog, G. A.
Journal: Genetics

Spt4-Spt5, a general transcription elongation factor for RNA polymerase II, also has roles in chromatin regulation. However, the relationships between these functions are not clear. Previously, we isolated suppressors of a Saccharomyces cerevisiae spt5 mutation in genes encoding members of the Paf1 complex, which regulates several cotranscriptional histone modifications, and Chd1, a chromatin remodeling enzyme. Here, we show that this suppression of spt5 can result from loss of histone H3 lysines 4 or 36 methylation, or reduced recruitment of Chd1 or the Rpd3S complex. These spt5 suppressors also rescue the synthetic growth defects observed in spt5 mutants that also lack elongation factor TFIIS. Using a FLO8 reporter gene, we found that a chd1 mutation caused cryptic initiation of transcription. We further observed enhancement of cryptic initiation in chd1 isw1 mutants and increased histone acetylation in a chd1 mutant. We suggest that, as previously proposed for H3 lysine 36 methylation and the Rpd3S complex, H3 lysine 4 methylation and Chd1 function to maintain normal chromatin structures over transcribed genes, and that one function of Spt4-Spt5 is to help RNA polymerase II overcome the repressive effects of these histone modifications and chromatin regulators on transcription.

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The nuclear component of a cytonuclear hybrid incompatibility in mimulus maps to a cluster of pentatricopeptide repeat genes.

Publication Date: 2010 Feb PMID: 19933877
Authors: Barr, C. M. - Fishman, L.
Journal: Genetics

Characterizing the genetic and molecular basis of hybrid incompatibilities is a first step toward understanding their evolutionary origins. We fine mapped the nuclear restorer (Rf) of cytoplasm-dependent anther sterility in Mimulus hybrids by identifying and targeting regions of the Mimulus guttatus genome containing large numbers of candidate pentatricopeptide repeat genes (PPRs). The single Mendelian locus Rf was first isolated to a 1.3-cM region on linkage group 7 that spans the genome's largest cluster of PPRs, then split into two tightly linked loci (Rf1 and Rf2) by <10 recombination events in a large (N = 6153) fine-mapping population. Progeny testing of fertile recombinants demonstrated that a dominant M. guttatus allele at each Rf locus was sufficient to restore fertility. Each Rf locus spans a physical region containing numerous PPRs with high homology to each other, suggesting recent tandem duplication or transposition. Furthermore, these PPRs have higher homology to restorers in distantly related taxa (petunia and rice) than to PPRs elsewhere in the Mimulus genome. These results suggest that the cytoplasmic male sterility (CMS)-PPR interaction is highly conserved across flowering plants. In addition, given our theoretical understanding of cytonuclear coevolution, the finding that hybrid CMS results from interactions between a chimeric mitochondrial transcript that is modified by Rf loci identified as PPRs is consistent with a history of selfish mitochondrial evolution and compensatory nuclear coevolution within M. guttatus.

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Coalescent simulation of intracodon recombination.

Publication Date: 2010 Feb PMID: 19933876
Authors: Arenas, M. - Posada, D.
Journal: Genetics

The coalescent with recombination is a very useful tool in molecular population genetics. Under this framework, genealogies often represent the evolution of the substitution unit, and because of this, the few coalescent algorithms implemented for the simulation of coding sequences force recombination to occur only between codons. However, it is clear that recombination is expected to occur most often within codons. Here we have developed an algorithm that can evolve coding sequences under an ancestral recombination graph that represents the genealogies at each nucleotide site, thereby allowing for intracodon recombination. The algorithm is a modification of Hudson's coalescent in which, in addition to keeping track of events occurring in the ancestral material that reaches the sample, we need to keep track of events occurring in ancestral material that does not reach the sample but that is produced by intracodon recombination. We are able to show that at typical substitution rates the number of nonsynonymous changes induced by intracodon recombination is small and that intracodon recombination does not generally result in inflated estimates of the overall nonsynonymous/synonymous substitution ratio (omega). On the other hand, recombination can bias the estimation of omega at particular codons, resulting in apparent rate variation among sites and in the spurious identification of positively selected sites. Importantly, in this case, allowing for variable synonymous rates across sites greatly reduces the false-positive rate and recovers statistical power. Finally, coalescent simulations with intracodon recombination could be used to better represent the evolution of nuclear coding genes or fast-evolving pathogens such as HIV-1.We have implemented this algorithm in a computer program called NetRecodon, freely available at http://darwin.uvigo.es.

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Ploidy and the evolution of endosperm of flowering plants.

Publication Date: 2010 Feb PMID: 19933875
Authors: Cailleau, A. - Cheptou, P. O. - Lenormand, T.
Journal: Genetics

In angiosperms, spermatozoa go by pair in each pollen grain and fertilize, in addition to the egg cell, one of its sister cells, called the central cell. This "double fertilization" leads to the embryo on the one hand and to its nutritive tissue, the endosperm, on the other hand. In addition, in most flowering plants, the endosperm is triploid because of a doubled maternal genetic contribution in the central cell. Most of the hypotheses trying to explain these eccentricities rest on the assumption of a male/female conflict over seed resource allocation. We investigate an alternative hypothesis on the basis of the masking of deleterious alleles. Using analytical methods, we show that a doubled maternal contribution and double fertilization tend to be favored in a wide range of conditions when deleterious mutations alter the function of the endosperm. Furthermore, we show that these conditions vary depending on whether these traits are under male or female control, which allows us to describe a new type of male/female conflict.

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Erect panicle2 encodes a novel protein that regulates panicle erectness in indica rice.

Publication Date: 2010 Feb PMID: 19933874
Authors: Zhu, K. - Tang, D. - Yan, C. - Chi, Z. - Yu, H. - Chen, J. - Liang, J. - Gu, M. - Cheng, Z.
Journal: Genetics

Rice (Oryza sativa L.) inflorescence (panicle) architecture is an important agronomic trait for rice breeding. A number of high-yielding japonica rice strains, characterized by an erect panicle (EP) of their architecture, have been released as commercial varieties in China. But no EP-type indica varieties are released so far. Here, we identified two allelic erect-panicle mutants in indica rice, erect panicle2-1 (ep2-1) and erect panicle2-2 (ep2-2), exhibiting the characteristic erect panicle phenotype. Both mutants were derived from spontaneous mutation. We cloned the EP2 gene by way of a map-based cloning strategy, and a transgenic complementation test rescued the phenotype of ep2-1. Anatomical investigations revealed that the ep2 mutants have more vascular bundles and a thicker stem than that of wild-type plants, explaining the panicle erectness phenotype in ep2 mutants. It was shown that EP2 was specifically expressed in the vascular bundles of internodes by GUS staining and RT-PCR. EP2 encodes a novel plant-specific protein, which localizes to the endoplasmic reticulum with unknown biochemical function. In addition, EP2 also regulates other panicle characteristics, such as panicle length and grain size, but grain number per panicle shows little change, indicating that the mutation of the ep2 gene could be applied in EP-type indica rice breeding.

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Proteasomal degradation of Rpn4 in saccharomyces cerevisiae is critical for cell viability under stressed conditions.

Publication Date: 2010 Feb PMID: 19933873
Authors: Wang, X. - Xu, H. - Ha, S. W. - Ju, D. - Xie, Y.
Journal: Genetics

The proteasome homeostasis in Saccharomyces cerevisiae is regulated by a negative feedback loop in which the transcription factor Rpn4 induces the proteasome genes and is rapidly degraded by the assembled proteasome. In addition to the proteasome genes, Rpn4 regulates numerous other genes involved in a wide range of cellular pathways. Therefore, the Rpn4-proteasome negative feedback circuit not only controls proteasome abundance, but also gauges the expression of other Rpn4 target genes. Our previous work has shown that Rpn4-induced gene expression is critical for cell viability under stressed conditions. Here we investigate whether proteasomal degradation of Rpn4 is also important for cell survival in response to stress. To this end, we generate a stabilized Rpn4 mutant (Rpn4*) that retains its transcription activity. We find that expression of Rpn4* severely reduces cell viability in response to various genotoxic and proteotoxic agents. This detrimental effect can be eliminated by a point mutation that abolishes the transcription activity of Rpn4*, suggesting that overexpression of some Rpn4 target genes weakens the cell's ability to cope with stress. Moreover, we demonstrate that inhibition of Rpn4 degradation causes synthetic growth defects when combined with proteasome impairment resulting from mutation of a proteasome gene or accumulation of misfolded endoplasmic reticulum membrane proteins. Rpn4 thus represents an important stress-responsive mediator whose degradation as well as availability are critical for cell survival under stressed conditions.

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Molecular and genetic analyses of four nonfunctional S haplotype variants derived from a common ancestral S haplotype identified in sour cherry (Prunus cerasus L.).

Publication Date: 2010 Feb PMID: 19917768
Authors: Tsukamoto, T. - Hauck, N. R. - Tao, R. - Jiang, N. - Iezzoni, A. F.
Journal: Genetics

Tetraploid sour cherry (Prunus cerasus) has an S-RNase-based gametophytic self-incompatibility (GSI) system; however, individuals can be either self-incompatible (SI) or self-compatible (SC). Unlike the situation in the Solanaceae, where self-compatibility accompanying polyploidization is often due to the compatibility of heteroallelic pollen, the genotype-dependent loss of SI in sour cherry is due to the compatibility of pollen containing two nonfunctional S haplotypes. Sour cherry individuals with the S(4)S(6)S(36a)S(36b) genotype are predicted to be SC, as only pollen containing both nonfunctional S(36a) and S(36b) haplotypes would be SC. However, we previously found that individuals of this genotype were SI. Here we describe four nonfunctional S(36) variants. Our molecular analyses identified a mutation that would confer loss of stylar S function for one of the variants, and two alterations that might cause loss of pollen S function for all four variants. Genetic crosses showed that individuals possessing two nonfunctional S(36) haplotypes and two functional S haplotypes have reduced self-fertilization due to a very low frequency of transmission of the one pollen type that would be SC. Our finding that the underlying mechanism limiting successful transmission of genetically compatible gametes does not involve GSI is consistent with our previous genetic model for Prunus in which heteroallelic pollen is incompatible. This provides a unique case in which breakdown of SI does not occur despite the potential to generate SC pollen genotypes.

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Mating-system variation, demographic history and patterns of nucleotide diversity in the Tristylous plant Eichhornia paniculata.

Publication Date: 2010 Feb PMID: 19917767
Authors: Ness, R. W. - Wright, S. I. - Barrett, S. C.
Journal: Genetics

Inbreeding in highly selfing populations reduces effective size and, combined with demographic conditions associated with selfing, this can erode genetic diversity and increase population differentiation. Here we investigate the role that variation in mating patterns and demographic history play in shaping the distribution of nucleotide variation within and among populations of the annual neotropical colonizing plant Eichhornia paniculata, a species with wide variation in selfing rates. We sequenced 10 EST-derived nuclear loci in 225 individuals from 25 populations sampled from much of the geographic range and used coalescent simulations to investigate demographic history. Highly selfing populations exhibited moderate reductions in diversity but there was no significant difference in variation between outcrossing and mixed mating populations. Population size interacted strongly with mating system and explained more of the variation in diversity within populations. Bayesian structure analysis revealed strong regional clustering and selfing populations were highly differentiated on the basis of an analysis of F(st). There was no evidence for a significant loss of within-locus linkage disequilibrium within populations, but regional samples revealed greater breakdown in Brazil than in selfing populations from the Caribbean. Coalescent simulations indicate a moderate bottleneck associated with colonization of the Caribbean from Brazil approximately 125,000 years before the present. Our results suggest that the recent multiple origins of selfing in E. paniculata from diverse outcrossing populations result in higher diversity than expected under long-term equilibrium.

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The spontaneous appearance rate of the yeast prion [PSI+] and its implications for the evolution of the evolvability properties of the [PSI+] system.

Publication Date: 2010 Feb PMID: 19917766
Authors: Lancaster, A. K. - Bardill, J. P. - True, H. L. - Masel, J.
Journal: Genetics

Epigenetically inherited aggregates of the yeast prion [PSI+] cause genomewide readthrough translation that sometimes increases evolvability in certain harsh environments. The effects of natural selection on modifiers of [PSI+] appearance have been the subject of much debate. It seems likely that [PSI+] would be at least mildly deleterious in most environments, but this may be counteracted by its evolvability properties on rare occasions. Indirect selection on modifiers of [PSI+] is predicted to depend primarily on the spontaneous [PSI+] appearance rate, but this critical parameter has not previously been adequately measured. Here we measure this epimutation rate accurately and precisely as 5.8 x 10(-7) per generation, using a fluctuation test. We also determine that genetic "mimics" of [PSI+] account for up to 80% of all phenotypes involving general nonsense suppression. Using previously developed mathematical models, we can now infer that even in the absence of opportunities for adaptation, modifiers of [PSI+] are only weakly deleterious relative to genetic drift. If we assume that the spontaneous [PSI+] appearance rate is at its evolutionary optimum, then opportunities for adaptation are inferred to be rare, such that the [PSI+] system is favored only very weakly overall. But when we account for the observed increase in the [PSI+] appearance rate in response to stress, we infer much higher overall selection in favor of [PSI+] modifiers, suggesting that [PSI+]-forming ability may be a consequence of selection for evolvability.

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Estimating divergence parameters with small samples from a large number of Loci.

Publication Date: 2010 Feb PMID: 19917765
Authors: Wang, Y. - Hey, J.
Journal: Genetics

Most methods for studying divergence with gene flow rely upon data from many individuals at few loci. Such data can be useful for inferring recent population history but they are unlikely to contain sufficient information about older events. However, the growing availability of genome sequences suggests a different kind of sampling scheme, one that may be more suited to studying relatively ancient divergence. Data sets extracted from whole-genome alignments may represent very few individuals but contain a very large number of loci. To take advantage of such data we developed a new maximum-likelihood method for genomic data under the isolation-with-migration model. Unlike many coalescent-based likelihood methods, our method does not rely on Monte Carlo sampling of genealogies, but rather provides a precise calculation of the likelihood by numerical integration over all genealogies. We demonstrate that the method works well on simulated data sets. We also consider two models for accommodating mutation rate variation among loci and find that the model that treats mutation rates as random variables leads to better estimates. We applied the method to the divergence of Drosophila melanogaster and D. simulans and detected a low, but statistically significant, signal of gene flow from D. simulans to D. melanogaster.

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The genetics of postmating, prezygotic reproductive isolation between Drosophila virilis and D. americana.

Publication Date: 2010 Feb PMID: 19917764
Authors: Sweigart, A. L.
Journal: Genetics

Many studies have demonstrated the rapid diversification of reproductive genes that function after mating but before fertilization. This process might lead to the evolution of postmating, prezygotic barriers between species. Here, I investigate the phenotypic and genetic basis of postmating, prezygotic isolation between two closely related species of Drosophila, Drosophila virilis and D. americana. I show that a strong barrier to interspecific fertilization results in a 99% reduction in progeny production. A genetic interaction among maternal and paternal alleles at only a few loci prevents the fertilization of D. virilis females by D. americana males. These loci are autosomal and isolation acts recessively; the fertilization incompatibility is caused by at least two loci in the maternal D. virilis parent in combination with at least three loci in the paternal D. americana parent. These findings, together with results from classical experiments, suggest that male-female coevolution within D. americana may have driven postmating, prezygotic isolation between species.

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