Genetics

doi: 10.1093/genetics/185.4.nppmid: N/A

Population structure with localized haplotype clusters, pp. 1337–1344 Sharon R. Browning and Bruce S. Weir FST is a useful measure of population divergence that measures variation between populations versus the variation within populations. This article presents a new multi-locus version of FST based on localized haplotype clusters that has the appealing property of providing estimates of population structure expected from existing models of human population origins. In particular, it shows African populations to have the lowest divergence from the ancestral population, East Asian populations to have highest divergence, with other populations (European, Indian, and Mexican) having intermediate levels of divergence. Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. miranda, pp. 1381–1396 Penelope R. Haddrill, Laurence Loewe and Brian Charlesworth Two outstanding issues in evolutionary genetics concern the strength of natural selection against new deleterious mutations that cause changes in the amino-acid sequence of a protein, and the proportion of amino-acid sequence differences between related species that have been fixed by selection favoring new advantageous mutations. These investigators compare several different methods for estimating these parameters in two closely related species of Drosophila. They find that, on average, deleterious mutations segregating in the populations are subject to only very weak negative selection, but the majority of new amino-acid mutations are under such strong negative selection that they are extremely unlikely to become fixed in the population. In addition, they find that a large fraction of amino acid sequence differences between species results from positive selection. The consequences of regulation of desat1 expression for pheromone emission and detection in Drosophila melanogaster, pp. 1297–1309 Benjamin Houot, François Bousquet and Jean-François Ferveur Mate recognition requires exchange of sensory signals and precise matching between the transmission and the perception of those signals. desat1 determines both of these aspects of mate recognition since it controls the production and discrimination of sex pheromones in Drosophila. This gene produces different transcripts, each yielding a unique protein. These authors find that they can separately affect signal transmission and perception by selectively manipulating different regulatory regions of desat1. Thus, the dual roles of desat1 on pheromonal communication depends on regulation of its transcriptional activity. Meiotic regulators Ndt80 and Ime2 have different roles in Saccharomyces and Neurospora, pp. 1271–1282 Elizabeth A. Hutchison and N. Louise Glass While meiosis is a highly conserved process, the manner in which the steps of meiosis are controlled is not conserved, even among fungi. These authors find that homologs of regulators of meiosis in yeast regulate other aspects of sexual development in the filamentous fungus Neurospora crassa. Although interactions between these regulators may be conserved, the biological program they control can evolve rapidly. Phantom, a new subclass of Mutator DNA transposons found in insect viruses and widely distributed in animals, pp. 1507–1517 Claudia P. Marquez and Ellen J. Pritham Mutator transposons, which play a critical role in the evolution of plant genomes, are rare in other eukaryotes. This article describes a previously uncharacterized group of DNA transposons, designated Phantom, found in the genomes of a wide range of eukaryotes, and provides evidence that they are Mutator transposons. Interestingly, Phantom proteins were identified in two insect viruses, and they seem to move horizontally from insect to virus, providing a new line of evidence for the role of viruses in the horizontal transfer of DNA transposons in animals. The antidepressant sertraline targets intracellular vesiculogenic membranes in yeast, pp. 1221–1233 Meredith M. Rainey, Daniel Korostyshevsky, Sean Lee and Ethan O. Perlstein Can a unicellular model organism like yeast, which lacks neurons and neurotransmitters, teach us anything about mechanisms of action of psychoactive drugs in people? This article addresses this question by exploiting the cytotoxicity of the selective serotonin reuptake inhibitor sertraline (Zoloft) in a simple drug-resistance selection. The results demonstrate that sertraline targets intracellular membranes of the vesicle transport system. The two pathways that shape drug response in yeast are conserved throughout evolution and play important roles in the function of synapses in multicellular organisms. Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: Selection vs. retroprocessing as the driving force, pp. 1369–1380 Daniel B. Sloan, Alice H. MacQueen, Andrew J. Alverson, Jeffrey D. Palmer and Douglas R. Taylor The evolutionary origin and maintenance of RNA editing have been proposed to determine the frequency of editing. These authors sequenced whole mitochondrial genomes of closely related angiosperm species with highly divergent mutation rates, and found that recent mutational accelerations are associated with rapid loss of editing sites. Based on the pattern of editing site loss, the authors develop a model of gene conversion and RNA editing evolution that may apply throughout the angiosperms. © Genetics 2010 This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Falk, Raphael

doi: 10.1534/genetics.110.120469pmid: 20713742

Morgan's three students (Muller, Sturtevant, and Bridges) introduced reductionist empirical methods to the study of the chromosomal theory of heredity. Herman J. Muller concentrated on mutations, namely changes in the heterocatalytic properties of genes, without losing their autocatalytic (self-replication) properties. Experimental induction of mutations allowed quantitative analyses of genes' parameters, but hopes to deduce their chemicophysical character were never fulfilled. Once the model for DNA structure was proposed, the reductionist notions of mutation analysis were successfully applied to the molecular genes. However, it was soon realized that the concept of the particulate gene was inadequate. The more the molecular analysis of the genome advanced, the clearer it became that the entities of heredity must be conceived within systems' perspectives, for which special tools for handling large number of variables were developed. Analytic mutagenesis, however, continues to be a major strategy for the study of the cellular and chromosomal mechanisms that control mutation inductions.

She, Wenjing; Lin, Weiqiang; Zhu, Yubin; Chen, Yong; Jin, Weiyuan; Yang, Yanjun; Han, Ning; Bian, Hongwu; Zhu, Muyuan; Wang, Junhui

doi: 10.1534/genetics.110.117960pmid: 20516496

Apger, Jennifer; Reubens, Michael; Henderson, Laura; Gouge, Catherine A; Ilic, Nina; Zhou, Helen H; Christensen, Tim W

doi: 10.1534/genetics.110.117234pmid: 20498296

DNA replication and the correct packaging of DNA into different states of chromatin are both essential processes in all eukaryotic cells. High-fidelity replication of DNA is essential for the transmission of genetic material to cells. Likewise the maintenance of the epigenetic chromatin states is essential to the faithful reproduction of the transcriptional state of the cell. It is becoming more apparent that these two processes are linked through interactions between DNA replication proteins and chromatin-associated proteins. In addition, more proteins are being discovered that have dual roles in both DNA replication and the maintenance of epigenetic states. We present an analysis of two Drosophila mutants in the conserved DNA replication protein Mcm10. A hypomorphic mutant demonstrates that Mcm10 has a role in heterochromatic silencing and chromosome condensation, while the analysis of a novel C-terminal truncation allele of Mcm10 suggests that an interaction with Mcm2 is not required for chromosome condensation and heterochromatic silencing but is important for DNA replication.

Nishimura, Yoshiki; Stern, David B

doi: 10.1534/genetics.110.118265pmid: 20519744

Two mechanisms for chloroplast DNA replication have been revealed through the study of an unusual heteroplasmic strain of the green alga Chlamydomonas reinhardtii. Heteroplasmy is a state in which more than one genome type occurs in a mitochondrion or chloroplast. The Chlamydomonas strain spa19 bears two distinct chloroplast genomes, termed PS+ and PS−. PS+ genomes predominate and are stably maintained in vegetative cells, despite their lack of known replication origins. In sexual crosses with spa19 as the mating type plus parent, however, PS+ genomes are transmitted in only ∼25% of tetrads, whereas the PS− genomes are faithfully inherited in all progeny. In this research, we have explored the mechanism underlying this biased uniparental inheritance. We show that the relative reduction and dilution of PS+ vs. PS− genomes takes place during gametogenesis. Bromodeoxyuridine labeling, followed by immunoprecipitation and PCR, was used to compare replication activities of PS+ and PS− genomes. We found that the replication of PS+ genomes is specifically suppressed during gametogenesis and germination of zygospores, a phenomenon that also was observed when spa19 cells were treated with rifampicin, an inhibitor of the chloroplast RNA polymerase. Furthermore, when bromodeoxyuridine incorporation was compared at 11 sites within the chloroplast genome between vegetative cells, gametes, and rifampicin-treated cells by quantitative PCR, we found that incorporation was often reduced at the same sites in gametes that were also sensitive to rifampicin treatment. We conclude that a transcription-mediated form of DNA replication priming, which may be downregulated during gametogenesis, is indispensable for robust maintenance of PS+ genomes. These results highlight the potential for chloroplast genome copy number regulation through alternative replication strategies.

Deng, Huai; Cai, Weili; Wang, Chao; Lerach, Stephanie; Delattre, Marion; Girton, Jack; Johansen, Jørgen; Johansen, Kristen M

doi: 10.1534/genetics.110.117150pmid: 20457875

The essential JIL-1 histone H3S10 kinase is a key regulator of chromatin structure that functions to maintain euchromatic domains while counteracting heterochromatization and gene silencing. In the absence of the JIL-1 kinase, two of the major heterochromatin markers H3K9me2 and HP1a spread in tandem to ectopic locations on the chromosome arms. Here we address the role of the third major heterochromatin component, the zinc-finger protein Su(var)3-7. We show that the lethality but not the chromosome morphology defects associated with the null JIL-1 phenotype to a large degree can be rescued by reducing the dose of the Su(var)3-7 gene and that Su(var)3-7 and JIL-1 loss-of-function mutations have an antagonistic and counterbalancing effect on position-effect variegation (PEV). Furthermore, we show that in the absence of JIL-1 kinase activity, Su(var)3-7 gets redistributed and upregulated on the chromosome arms. Reducing the dose of the Su(var)3-7 gene dramatically decreases this redistribution; however, the spreading of H3K9me2 to the chromosome arms was unaffected, strongly indicating that ectopic Su(var)3-9 activity is not a direct cause of lethality. These observations suggest a model where Su(var)3-7 functions as an effector downstream of Su(var)3-9 and H3K9 dimethylation in heterochromatic spreading and gene silencing that is normally counteracted by JIL-1 kinase activity.

Dakshinamurthy, Arun; Nyswaner, Katherine M; Farabaugh, Philip J; Garfinkel, David J

doi: 10.1534/genetics.110.119115pmid: 20498295

A variety of cellular factors affect the movement of the retrovirus-like transposon Ty1. To identify genes involved in Ty1 virus-like particle (VLP) function, the level of the major capsid protein (Gag-p45) and its proteolytic precursor (Gag-p49p) was monitored in a subset of Ty1 cofactor mutants. Twenty-nine of 87 mutants contained alterations in the level of Gag; however, only bud22Δ showed a striking defect in Gag processing. BUD22 affected the +1 translational frameshifting event required to express the Pol proteins protease, integrase, and reverse transcriptase. Therefore, it is possible that the bud22Δ mutant may not produce enough functional Ty1 protease to completely process Gag-p49 to p45. Furthermore, BUD22 is required for 18S rRNA processing and 40S subunit biogenesis and influences polysome density. Together our results suggest that BUD22 is involved in a step in ribosome biogenesis that not only affects general translation, but also may alter the frameshifting efficiency of ribosomes, an event central to Ty1 retrotransposition.

Kim, Min Su; Ko, Young-Joon; Maeng, Shinae; Floyd, Anna; Heitman, Joseph; Bahn, Yong-Sun

doi: 10.1534/genetics.110.118315pmid: 20516494

Carbon dioxide (CO2) sensing and metabolism via carbonic anhydrases (CAs) play pivotal roles in survival and proliferation of pathogenic fungi infecting human hosts from natural environments due to the drastic difference in CO2 levels. In Cryptococcus neoformans, which causes fatal fungal meningoencephalitis, the Can2 CA plays essential roles during both cellular growth in air and sexual differentiation of the pathogen. However the signaling networks downstream of Can2 are largely unknown. To address this question, the present study employed comparative transcriptome DNA microarray analysis of a C. neoformans strain in which CAN2 expression is artificially controlled by the CTR4 (copper transporter) promoter. The PCTR4∷CAN2 strain showed growth defects in a CO2-dependent manner when CAN2 was repressed but resumed normal growth when CAN2 was overexpressed. The Can2-dependent genes identified by the transcriptome analysis include FAS1 (fatty acid synthase 1) and GPB1 (G-protein β subunit), supporting the roles of Can2 in fatty acid biosynthesis and sexual differentiation. Cas3, a capsular structure designer protein, was also discovered to be Can2-dependent and yet was not involved in CO2-mediated capsule induction. Most notably, a majority of Can2-dependent genes were environmental stress-regulated (ESR) genes. Supporting this, the CAN2 overexpression strain was hypersensitive to oxidative and genotoxic stress as well as antifungal drugs, such as polyene and azole drugs, potentially due to defective membrane integrity. Finally, an oxidative stress-responsive Atf1 transcription factor was also found to be Can2-dependent. Atf1 not only plays an important role in diverse stress responses, including thermotolerance and antifungal drug resistance, but also represses melanin and capsule production in C. neoformans. In conclusion, this study provides insights into the comprehensive signaling networks orchestrated by CA/CO2-sensing pathways in pathogenic fungi.

Rainey, Meredith M; Korostyshevsky, Daniel; Lee, Sean; Perlstein, Ethan O

doi: 10.1534/genetics.110.117846pmid: 20457874

Numerous studies have shown that the clinical antidepressant sertraline (Zoloft) is biologically active in model systems, including fungi, which do not express its putative protein target, the serotonin/5-HT transporter, thus demonstrating the existence of one or more secondary targets. Here we show that in the absence of its putative protein target, sertraline targets phospholipid membranes that comprise the acidic organelles of the intracellular vesicle transport system by a mechanism consistent with the bilayer couple hypothesis. On the basis of a combination of drug-resistance selection and chemical-genomic screening, we hypothesize that loss of vacuolar ATPase activity reduces uptake of sertraline into cells, whereas dysregulation of clathrin function reduces the affinity of membranes for sertraline. Remarkably, sublethal doses of sertraline stimulate growth of mutants with impaired clathrin function. Ultrastructural studies of sertraline-treated cells revealed a phenotype that resembles phospholipidosis induced by cationic amphiphilic drugs in mammalian cells. Using reconstituted enzyme assays, we also demonstrated that sertraline inhibits phospholipase A1 and phospholipase D, exhibits mixed effects on phospholipase C, and activates phospholipase A2. Overall, our study identifies two evolutionarily conserved membrane-active processes—vacuolar acidification and clathrin-coat formation—as modulators of sertraline's action at membranes.

Kim, Sunhong; Johnson, Wade; Chen, Changchun; Sewell, Aileen K; Byström, Anders S; Han, Min

doi: 10.1534/genetics.110.118406pmid: 20479142

The elongator (ELP) complex consisting of Elp1-6p has been indicated to play roles in multiple cellular processes. In yeast, the ELP complex has been shown to genetically interact with Uba4p/Urm1p and Kti11-13p for a function in tRNA modification. Through a Caenorhabditis elegans genetic suppressor screen and positional cloning, we discovered that loss-of-function mutations of moc-3 and dph-3, orthologs of the yeast UBA4 and KTI11, respectively, effectively suppress the Multivulva (Muv) phenotype of the lin-1(e1275, R175Opal) mutation. These mutations do not suppress the Muv phenotype caused by other lin-1 alleles or by gain-of-function alleles of ras or raf that act upstream of lin-1. The suppression can also be reverted by RNA interference of lin-1. Furthermore, we showed that dph-3(lf) also suppressed the defect of lin-1(e1275) in promoting the expression of a downstream target (egl-17). These results indicate that suppression by the moc-3 and dph-3 mutations is due to the elevated activity of lin-1(e1275) itself rather than the altered activity of a factor downstream of lin-1. We further showed that loss-of-function mutations of urm-1 and elpc-1-4, the worm counterparts of URM1 and ELP complex components in yeast, also suppressed lin-1(e1275). We also confirmed that moc-3(lf) and dph-3(lf) have defects in tRNA modifications as do the mutants of their yeast orthologs. These results, together with the observation of a likely readthrough product from a lin-1(e1275)∷gfp fusion transgene indicate that the aberrant tRNA modification led to failed recognition of a premature stop codon in lin-1(e1275). Our genetic data suggest that the functional interaction of moc-3/urm-1 and dph-3 with the ELP complex is an evolutionarily conserved mechanism involved in tRNA functions that are important for accurate translation.