bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction Between Ustilago maydis REC2 and RAD51 Genes in DNA Repair and Mitotic Recombination
Authors: Ferguson David O , Rice Michael C , Rendi Mara H , Kotani Hidehito , Kmiect Eric B , Holloman William K
Published: January 2021

A gene encoding a Ustilago maydis Rad51 orthologue has been isolated. rad51-1, a mutant constructed by disrupting the gene, was as sensitive to killing by ultraviolet light and γ radiation as the rec2-1 mutant and slightly more sensitive to killing by methyl methanesulfonate. There was no suppression of killing by ultraviolet light when a rec2-1 strain was transformed with a multicopy plasmid containing RAD51, nor was there suppression when rad51-1 was transformed with a multicopy plasmid containing REC2. Recombination proficiency as measured by a gap repair assay was diminished in both rec2-1 and rad51-1 strains. In rec2-1 the frequency of recombination was decreased, but the spectrum of events was similar to that observed in wild type, while in rad51-1 the frequency as well as the spectrum of recombination events were different. Studies with the rec2-1 rad51-1 double mutant indicated that there was epistasis in the action of REC2 and RAD51 in certain repair and recombination functions, but some measure of independent action in other functions.
Mobilization of a Minos Transposon in Drosophila melanogaster Chromosomes and Chromatid Repair by Heteroduplex Formation
Authors: Arcà Bruno , Zabalou Sophia , Loukeris Thanasis G , Savakis Charalambos
Published: January 2021

Transposase-mediated mobilization of the element Minos has been studied in the Drosophila melanogaster genome. Excision and transposition of a nonautonomous Minos transposon in the presence of a Minos transposase gene was detected with a dominant eye color marker carried by the transposon. Frequencies of excision in somatic tissues and in the germ line were higher in flies heterozygous for the transposon than in homozygotes or hemizygotes. Transposition of a X chromosome-linked insertion of Minos into new autosomal sites occurred in 1-12% of males expressing transposase, suggesting that this system is usable for gene tagging and enhancer trapping in Drosophila. Sequence analysis of PCR-amplified donor sites after excision showed precise restoration of the original target sequence in ∼75% of events in heterozygotes and the presence of footprints or partially deleted elements in the remaining events. Most footprints consisted of the four terminal bases of the transposon, flanked by the TA target duplication. Sequencing of a chromosomal donor site that was directly cloned after excision showed a characteristic two-base mismatch heteroduplex in the center of the 6bp footprint. Circular extrachromosomal forms of the transposon, presumably representing excised Minos elements, could be detected only in the presence of transposase. A model for chromatid repair after Minosexcision is discussed in which staggered cuts are first produced at the ends of the inverted repeats, the broken chromatid ends are joined, and the resulting heteroduplex is subsequently repaired. The model also suggests a simple mechanism for the production of the target site duplication and for regeneration of the transposon ends during reintegration.
“Parahomologous” Gene Targeting in Drosophila Cells: An Efficient, Homology-Dependent Pathway of Illegitimate Recombination Near a Target Site
Authors: Cherbas Lucy , Cherbas Peter
Published: January 2021

Drosophila cells in culture can be transformed by introducing exogenous DNA carrying a selectable marker. Here we report on the fate of plasmids that contain an extended fragment of Drosophila DNA in addition to the selectable marker. A small minority of the resulting transformants appear to arise from homologous recombination at the chromosomal target. However, the majority of the insertions are the products of illegitimate events in the vicinity of the target DNA, and they often cause mutations in the targeted region. The efficiency of this process, its homology dependence, and the clustering of the products define a novel transformation pathway that we call “parahomologous targeting.”
Spectrum of Bmp5 Mutations From Germline Mutagenesis Experiments in Mice
Authors: Marker Paul C , Seung Kwonjune , Bland Adrienne E , Russell Liane B , Kingsley David M
Published: January 2021

Over 40 years of mutagenesis experiments using the mouse specific-locus test have produced a large number of induced germline mutations at seven loci, among them the short ear locus. We have previously shown that the short ear locus encodes bone morphogenetic protein 5 (BMP5), a member of a large family of secreted signaling molecules that play key roles in axis formation, tissue differentiation, mesenchymalepithelial interactions, and skeletal development. Here we examine 24 chemical- and radiation-induced mutations at the short ear locus. Sequence changes in the Bmp5 open reading frame confirm the importance of cysteine residues in the function of TGFβ superfamily members. The spectrum of N-ethyl-N-nitrosourea-induced mutations also provides new information about the basepair, sequence context, and strand specificity of germline mutations in mammals.
Gain-of-Function Mutations in TnsC, an ATP-Dependent Transposition Protein That Activates the Bacterial Transposon Tn7
Authors: Stellwagen Anne E , Craig Nancy L
Published: January 2021

The bacterial transposon Tn7 encodes five genes whose protein products are used in different combinations to direct transposition to different types of target sites. TnsABC+D directs transposition to a specific site in the Escherichia coli chromosome called attTn7, whereas TnsABC+E directs transposition to non-attTn7 sites. These transposition reactions can also recognize and avoid “immune” targets that already contain a copy of Tn7. TnsD and TnsE are required to activate TnsABC as well as to select a target site; no transposition occurs with wild-type TnsABC alone. Here, we describe the isolation of TnsC gain-of-function mutants that activate the TnsA+B transposase in the absence of TnsD or TnsE. Some of these TnsC mutants enable the TnsABC machinery to execute transposition without sacrificing its ability to discriminate between different types of targets. Other TnsC mutants appear to constitutively activate the TnsABC machinery so that it bypasses target signals. We also present experiments that suggest that target selection occurs early in the Tn7 transposition pathway in vivo: favorable attTn7 targets appear to promote the excision of Tn7 from the chromosome, whereas immune targets do not allow transposon excision to occur. This work supports the view that TnsC plays a central role in the evaluation and utilization of target DNAs.
Progression Into the First Meiotic Division Is Sensitive to Histone HN-HZB Dimer Concentration in Saccharomyces cerevisiae
Authors: Tsui Kochung , Simon Lee , Norris David
Published: January 2021

The yeast Saccharomyces cerevisiae contains two genes for histone H2A and two for histone H2B located in two divergently transcribed gene pairs: HTA1-HTB1 and HTA2-HTB2. Diploid strains lacking HTA1-HTB1 (hta1-htb1Δ/hta1-htb1Δ, HTA2-HTB2/HTA2-HTB2) grow vegetatively, but will not sporulate. This sporulation phenotype results from a partial depletion of H2A-H2B dimers. Since the expression patterns of HTA1-HTB1 and HTA2-HTB2 are similar in mitosis and meiosis, the sporulation pathway is therefore more sensitive than the mitotic cycle to depletion of H2A-H2B dimers. After completing premeiotic DNA replication, commitment to meiotic recombination, and chiasma resolution, the hta1-htb1Δ/hta1-htb1Δ, HTA2-HTB2/HTA2-HTB2 mutant arrests before the first meiotic division. The arrest is not due to any obvious disruptions in spindle pole bodies or microtubules. The meiotic block is not bypassed in backgrounds homozygous for spo13, rad50Δ, or rad9Δ mutations, but is bypassed in the presence of hydroxyurea, a drug known to inhibit DNA chain elongation. We hypothesize that the deposition of H2A-H2B dimers in the mutant is unable to keep pace with the replication fork, thereby leading to a disruption in chromosome structure that interferes with the meiotic divisions.
Dissection of Filamentous Growth by Transposon Mutagenesis in Saccharomyces cerevisiae
Authors: Mösch Hans-Ulrich , Fink Gerald R
Published: January 2021

Diploid Saccharomyces cerevisiae strains starved for nitrogen undergo a developmental transition from growth as single yeast form (YF) cells to a multicellular form consisting of filaments of pseudohyphal (PH) cells. Filamentous growth is regulated by an evolutionarily conserved signaling pathway that includes the small GTP-binding proteins Ras2p and Cdc42p, the protein kinases Ste20p, Ste11p and Ste7p, and the transcription factor Ste12p. Here, we designed a genetic screen for mutant strains defective for filamentous growth (dfg) to identify novel targets of the filamentation signaling pathway, and we thereby identified 16 different genes, CDC39, STE12, TEC1, WH13, NAB1, DBR1, CDC55, SRV2, TPM1, SPA2, BNI1, DFG5, DFG9, DFG10, BUD8 and DFG16, mutations that block filamentous growth. Phenotypic analysis of dfg mutant strains genetically dissects filamentous growth into the cellular processes of signal transduction, bud site selection, cell morphogenesis and invasive growth. Epistasis tests between dfg mutant alleles and dominant activated alleles of the RAS2 and STE11 genes, RAS2Val19 and STE11-4, respectively, identify putative targets for the filamentation signaling pathway. Several of the genes described here have homologues in filamentous fungi, where they also regulate fungal development.
oroshigane, a New Segment Polarity Gene of Drosophila melanogaster, Functions in Hedgehog Signal Transduction
Authors: Epps Janet L , Jones Jessa B , Tanda Soichi
Published: January 2021

Here we describe a new segment polarity gene of Drosophila melanogaster, oroshigane (oro). Identified as a dominant enhancer of Bar (B), oro is also recessive embryonic lethal, and homozygous oro embryos show variable substitution of naked cuticle with denticles. These patterns are distinctly similar to those of hedgehog (hh) and wingless (wg) embryos, which indicates that oro functions in determining embryonic segment polarity. Evidence that oro function is involved in Hh signal transduction during embryogenesis is provided by its genetic interactions with the segment polarity genes patched (ptc) and fused (fu). Furthermore, ptcIN is a dominant suppressor of the oro embryonic lethal phenotype, suggesting a close and dose-dependent relationship between oro and ptc in Hh signal transduction. oro function is also required in imaginal development. The oro1 allele significantly reduces decapentaplegic (dpp), but not hh, expression in the eye imaginal disc. Furthermore, oro enhances the fu1 wing phenotype in a dominant manner. Based upon the interactions of oro with hh, ptc, and fu, we propose that the oro gene plays important roles in Hh signal transduction.
Contrasting Patterns of Nucleotide Sequence Variation at the Glucose Dehydrogenase (Gld) Locus in Different Populations of Drosophila melanogaster
Authors: Hamblin Martha T , Aquadro Charles F
Published: January 2021

We have analyzed nucleotide sequence variation at the Glucose dehydrogenase (Gld) locus from four populations of Drosophila melanogaster from four continents. All four population samples show a significant reduction in silent variation compared to the neutral expectation. The levels of silent variation across all four populations are consistent with the predictions of the background selection model; however, Zimbabwe has a remarkably low level of variation. In the face of dramatically reduced silent polymorphism, an amino acid variant, leading to the common allozyme polymorphism at Gld, remains in low to intermediate frequency in all non-African samples. In the Chinese population sample, the ratio of replacement to silent variation is significantly elevated compared to the neutral expectation. The difference in patterns of variation across these population samples suggests that selection on Gld (or the Gld region) has been different in the Chinese population than in the other three.
Impact of Migration and Fitness on the Stability of Lethal t-Haplotype Polymorphism in Mus musculus: A Computer Study
Authors: Durand Dannie , Ardlie Kristin , Buttel Linda , Levins Simon A , Silver Lee M
Published: January 2021

The t-haplotype is a chromosomal region in Mus musculus characterized by meiotic drive such that heterozygous males transmit t-bearing chromosomes to roughly 90% of their offspring. Most naturally occurring t-haplotypes express a recessive embryonic lethality, preventing fixation of the t-haplotype. Surprisingly, the t-haplotype occurs in nature as a persistent, low-frequency polymorphism. Early modeling studies led Lewontin to hypothesize that this low level polymorphism results from a balance between genetic drift in small demes and interdemic migration. Here, we show that while combinations of deme size and migration rate that predict natural t-haplotype frequencies exist, the range of such values is too narrow to be biologically plausible, suggesting that small deme size and interdemic migration alone do not explain the observed t-haplotype frequencies. In response, we tested other factors that might explain the observed t-polymorphism. Two led to biologically plausible models: substantially reduced heterozygous fitness and reduced meiotic drive. This raises the question whether these phenomena occur in nature. Our data suggest an alternative explanation: there is no stable, low-level t-polymorphism. Rather wild populations are in one of two stable states characterized by extinction of the t-haplotype and a high t-haplotype frequency, respectively, or in transition between the two.
Breeding Value and Variance Component Estimation From Data Containing Inbred Individuals: Application to Gynogenetic Families in Common Carp (Cyprinus carpio L.)
Authors: Bijma Piter , Van Arendonk Johan A M , Bovenhuis Henk
Published: January 2021

Under gynogenetic reproduction, offspring receive genes only from their dams and completely homozygous offspring are produced within one generation. When gynogenetic reproduction is applied to fully inbred individuals, homozygous clone lines are produced. A mixed model method was developed for breeding value and variance component estimation in gynogenetic families, which requires the inverse of the numerator relationship matrix. A general method for creating the inverse for a population with unusual relationships between animals is presented, which reduces to simple rules as is illustrated for gynogenetic populations. The presence of clones in gynogenetic populations causes singularity of the numerator relationship matrix. However, clones can be regarded as repeated observations of the same genotype, which can be accommodated by modifying the incidence matrix, and by considering only unique genotypes in the estimation procedure. Optimum gynogenetic sib family sizes for estimating heritabilities and estimates of their accuracy were derived and compared to those for conventional full-sib designs. This was done by means of a deterministic derivation and by stochastic simulation using Gibbs sampling. Optimum family sizes were smallest for gynogenetic families. Only for low heritabilities, there was a small advantage in accuracy under the gynogenetic design.
Roles of Replication Protein-A Subunits 2 and 3 in DNA Replication Fork Movement in Saccharomyces cerevisiae
Authors: Maniar Hina S , Wilson Richa , Brill Steven J
Published: January 2021

Replication Protein-A, the eukaryotic SSB, consists of a large subunit (RPA1) with strong ssDNA binding activity and two smaller subunits (RPA2 and 3) that may cooperate with RPA1 to bind ssDNA in a higher-order mode. To determine the in vivo function of the two smaller subunits and the potential role of higher-order ssDNA binding, we isolated an assortment of heat-lethal mutations in the genes encoding RPA2 and RPA3. At the permissive temperature, the mutants show a range of effects on DNA replication fidelity and sensitivities to UV and MMS. At the nonpermissive temperature, four out of five RPA2 mutants show a fast-stop DNA synthesis phenotype typical of a replication fork block. In contrast, the fifth RPA2 mutant and all RPA3 mutants are able to complete at least one round of DNA replication at the nonpermissive temperature. The effect of these mutations on the stability of the RPA complex was tested using a coprecipitation assay. At the nonpermissive temperature, we find that RPA1 and RPA2 are dissociated in the fast-stop mutants, but not in the slow-stop mutants. Thus, replication fork movement in vivo requires the association of at least two subunits of RPA. This result is consistent with the hypothesis that RPA functions in vivo by binding ssDNA in a higher-order mode.
Mutation of the cys-9 Gene, Which Encodes Thioredoxin Reductase, Affects the Circadian Conidiation Rhythm in Neurospora crassa
Authors: Onai Kiyoshi , Nakashima Hideaki
Published: January 2021

Ten cysteine auxotrophs of Neurospora crassa were examined with regard to the period lengths of their circadian conidiation rhythms. One of the these cysteine auxotrophs, cys-9, showed dramatic changes in the circadian conidiation rhythm. At 10 μm methionine, the cys-9 mutant had a period length that was 5 hr shorter than that of the wild-type strain during the first 3 days after transfer to continuous darkness. At this concentration of methionine, the period length was unstable after the fourth day and varied widely from 11 to 31 hr. In contrast, other cysteine auxotrophs did not show such instability of the period length at any of the concentrations of methionine tested. Furthermore, only the cys-9 mutant exhibited partial loss of the capacity for temperature compensation of the period length. With regard to cold-induced phase-shifting of the circadian conidiation rhythm, the cys-9 mutant was more sensitive than the wild-type strain to low temperature. The cys-9  + gene was cloned and was found to encode NADPH-dependent thioredoxin reductase. These results indicate that mutation of the gene for thioredoxin reductase results in abnormal expression of the circadian conidiation rhythm in N. crassa.
Distinct Requirements for Somatic and Germline Expression of a Generally Expressed Caernorhabditis elegans Gene
Authors: Kelly William G , Xu SiQun , Montgomery Mary K , Fire Andrew
Published: January 2021

In screening for embryonic-lethal mutations in Caernorhabditis elegans, we defined an essential gene (let-858) that encodes a nuclear protein rich in acidic and basic residues. We have named this product nucampholin. Closely homologous sequences in yeast, plants, and mammals demonstrate strong evolutionary conservation in eukaryotes. Nucampholin resides in all nuclei of C. elegans and is essential in early development and in differentiating tissue. Antisense-mediated depletion of LET-858 activity in early embryos causes a lethal phenotype similar to characterized treatments blocking embryonic gene expression. Using transgene-rescue, we demonstrated the additional requirement for let-858 in the larval germline. The broad requirements allowed investigation of soma-germline differences in gene expression. When introduced into standard transgene arrays, let-858 (like many other C. elegans genes) functions well in soma but poorly in germline. We observed incremental silencing of simple let-858 arrays in thefirstfew generations following transformation and hypothesized that silencing might reflect recognition of arrays as repetitive or heterochromatin-like. To give the transgene a more physiological context, we included an excess of random genomic fragments with the injected DNA. The resulting transgenes show robust expression in both germline and soma. Our results suggest the possibility of concerted mechanisms for silencing unwanted germline expression of repetitive sequences.
The Evolution of Bacterial Transformation: Sex With Poor Relations
Authors: Redfield Rosemary J , Schrag Matthew R , Dean Antony M
Published: January 2021

Bacteria are the only organisms known to actively take up DNA and recombine it into their genomes. While such natural transformation systems may provide many of the same benefits that sexual reproduction provides eukaryotes, there are important differences that critically alter the consequences, especially when recombination's main benefit is reducing the mutation load. Here, analytical and numerical methods are used to study the selection of transformation genes in populations undergoing deleterious mutation. Selection for transformability depends on the shape of the fitness function against mutation. If the fitness function is linear, then transformation would be selectively neutral were it not for the possibility that transforming cells may take up DNA that converts them into nontransformable cells. If the selection includes strong positive (synergistic) epistasis, then transformation can be advantageous in spite of this risk. The effect of low quality DNA (from selectively killed cells) on selection is then studied analytically and found to impose an additional cost. The limited data available for real bacterial populations suggest that the conditions necessary for the evolution of transformation are unlikely to be met, and thus that DNA uptake may have some function other than recombination of deleterious mutations.
Polymorphism and Locus-Specific Effects on Polymorphism at Microsatellite Loci in Natural Drosophila melanogaster Populations
Authors: Schlötterer Christian , Vogl Claus , Tautz Diethard
Published: January 2021

We have studied the natural variation at microsatellite loci in two African and five non-African populations of Drosophila melanogaster. Ten dinucleotide simple sequence loci were cloned from chromosomally mapped P1 clones and typed for single individuals from isofemale lines of the respective populations. We find that the African populations harbor the largest degree of diversity, while the non-African populations show a lower diversity. This supports previous results that D. melanogaster originated in Africa and spread across the rest of the world in historic times. Using genetic distance measures, we find also a distinct population subdivision between the non-African populations. Most interestingly, we find for some loci in some populations a strongly reduced variability, which cannot be explained by bottleneck effects. Employing a conservative test based on the variance in repeat number, we find that at least one locus in one population deviates significantly from the expectations of mutation-drift equilibrium. We suggest that this may be due to a recent selective sweep in this chromosomal region that may have been caused by a linked locus that was involved in local adaptation of the population.
The Caenorhabditis elegans spe-5 Gene Is Required for Morphogenesis of a Sperm-Specific Organelle and Is Associated With an Inherent Cold-Sensitive Phenotype
Authors: Machaca Khaled , L'Hernault Steven W
Published: January 2021

The nonrandom segregation of organelles to the appropriate compartment during asymmetric cellular division is observed in many developing systems. Caenorhabditis elegans spermatogenesis is an excellent system to address this issue genetically. The proper progression of spermatogenesis requires specialized intracellular organelles, the fibrous body-membranous organelle complexes (FB-MOs). The FB-MOs play a critical role in cytoplasmic partitioning during the asymmetric cellular division associated with sperm meiosis II. Here we show that spe-5 mutants contain defective, vacuolated FB-MOs and usually arrest spermatogenesis at the spermatocyte stage. Occasionally, spe-5 mutants containing defective FB-MOs will form spermatids that are capable of differentiating into functional spermatozoa. These spe-5 spermatids exhibit an incomplete penetrance for tubulin mis-segregation during the second meiotic division. In addition to morphological and FB-MO segregation defects, all six spe-5 mutants are cold-sensitive, exhibiting a more penetrant sterile phenotype at 16° than 25°. This cold sensitivity could be an inherent property of FB-MO morphogenesis.
Insertions of a Novel Class of Transposable Elements With a Strong Target Site Preference at the r Locus of Maize
Authors: Walker Elsbeth L , Eggleston William B , Demopulos Demetrios , Kermicle Jerry , Dellaporta Stephen L
Published: January 2021

The r locus of maize regulates anthocyanin synthesis in various tissues of maize through the production of helix-loop-helix DNA binding proteins capable of inducing expression of structural genes in the anthocyanin biosynthetic pathway. The complex r variant, R-r:standard (R-r), undergoes frequent mutation through a variety of mechanisms including displaced synapsis and crossing over, and intrachromosomal recombination. Here we report a new mechanism for mutation at the R-r complex: insertion of a novel family of transposable elements. Because the elements were first identified in the R-p gene of the R-r complex, they have been named P Instability Factor (PIF). Two different PIF elements were cloned and found to have identical sequences at their termini but divergent internal sequences. In addition, the PIF elements showed a marked specificity of insertion sites. Six out of seven PIF-containing derivatives examined had an element inserted at an identical location. Two different members of the PIF element family were identified at this position. The seventh PIF-containing derivative examined had the element inserted at a distinct position within r. Even at this location, however, the element inserted into a conserved target sequence. The timing of PIF excision is unusual. Germinal excision rates can range up to several percent of progeny. Yet somatic sectors are rare, even in lines exhibiting high germinal reversion rates.
Conditions for Protected Inversion Polymorphism Under Supergene Selection
Authors: Alvarez Gonzalo , Zapata Carlos
Published: January 2021

Conditions for protected inversion polymorphism under the operation of both karyotype and supergene selection in a viability model have been analytically determined. When supergene selection (the effect of recombination in homokaryotypes lowering the mean fitness of their offspring) is acting on gene arrangements and there is no karyotype selection, it is demonstrated that a polymorphic stable equilibrium is reached by the population, which is a function of only the recombination effects in homokaryotypes. Under both supergene and karyotype selection the degree of dominance (h) of karyotype selection is critical to produce a protected inversion polymorphism. In general, the opportunity for protected polymorphism increases as the degree of dominance decreases. For small s values, the conditions for protected polymorphism are r > 2sh and c > 2s(h – 1), where r and c are the average loss of viability for offspring of ST/ST and IN/IN homokaryotypes, respectively. These findings suggest that supergene selection may be an important balancing mechanism contributing to the maintenance of inversion polymorphism.
Quantitative Trait Loci Differentiating the Outbreeding Mimulus guttatus From the Inbreeding M. platycalyx
Authors: Lin Jing-Zhong , Ritland Kermit
Published: January 2021

Theoretical predictions about the evolution of selfing depend on the genetic architecture of loci controlling selfing (monogenic vs. polygenic determination, large vs. small effect of alleles, dominance vs. recessiveness), and studies of such architecture are lacking. We inferred the genetic basis of mating system differences between the outbreeding Mimulus guttatus and the inbreeding M. platycalyx by quantitative trait locus (QTL) mapping using random amplified polymorphic DNA and isozyme markers. One to three QTL were detected for each of five mating system characters, and each QTL explained 7.6–28.6% of the phenotypic variance. Taken together, QTL accounted for up to 38% of the variation in mating system characters, and a large proportion of variation was unaccounted for. Inferred QTL often affected more than one trait, contributing to the genetic correlation between those traits. These results are consistent with the hypothesis that quantitative variation in plant mating system characters is primarily controlled by loci with small effect.
A Test of Neutrality Based on Interlocus Associations
Authors: Kelly John K
Published: January 2021

The evolutionary processes governing variability within genomic regions of low recombination have been the focus of many studies. Here, I investigate the statistical properties of a measure of intrlocus genetic associations under the assumption that mutations are selectively neutral and sites are completely linked. This measure, denoted ZnS, is based on the squared correlation of allelic identity at pairs of polymorphic sites. Upper bounds for ZnS are determined by simulations. Various deviations from the neutral model, including several different forms of natural selection, will inflate the value of ZnS relative to its neutral theory expectations. Larger than expected values of ZnS are observed in genetic samples from the yellow-ac-scute and Adh regions of Drosophila melanogaster.
Mutations in Saccharomyces cerevisiae That Block Meiotic Prophase Chromosome Metabolism and Confer Cell Cycle Arrest at Pachytene Identify Two New Meiosis-Specific Genes SAE1 and SAE3
Authors: McKee Andrew H Z , Kleckner Nancy
Published: January 2021

Two new meiosis-specific genes, SAE1 and SAE3, have been identified in a screen for mutations that confer an intermediate block in meiotic prophase. Such mutations confer a block to spore formation that is circumvented by addition of a mutation that eliminates meiotic recombination initiation and other aspects of chromosome metabolism, i.e., spo11. We show that sae1-1 and sae3-1 mutations each confer a distinct defect in meiotic recombination. sae1-1 produces recombinants but very slowly and ultimately to less than half the wild-type level; sae3-1 makes persistent hyper-resected meiotic double-strand breaks and has a severe defect in formation of recombinants. Both mutants arrest at the pachytene stage of meiotic prophase, sae1-1 temporarily and sae3-1 permanently. The phenotypes conferred by sae3-1 are similar to those conferred by mutation of the yeast RecA homologue DMC1, suggesting that SAE3 and DMC1 act at the same step(s) of chromosome metabolism. These results provide further evidence that intermediate blocks to prophase chromosome metabolism cause cell-cycle arrest. SAE1 encodes a 208-residue protein homologous to vertebrate mRNA cap-binding protein 20. SAE3 corresponds to a meiosis-specific RNA encoding an unusually short open reading frame of 50 codons.
Phenotypic and Genetic Analysis of “Chameleon,” a Paramecium Mutant With an Enhanced Sensitivity to Magnesium
Authors: Preston Robin R , Hammond Jocelyn A
Published: January 2021

Three mutant strains of Paramecium tetraurelia with an enhanced sensitivity to magnesium have been isolated. These new “Chameleon” mutants result from partial- or codominant mutations at a single locus, Cha. Whereas the wild type responded to 5 mm Mg2+ by swimming backward for 10–15 sec, Cha mutants responded with ∼30 sec backward swimming. Electrophysiological analysis suggested that this behavior may be caused by slowing in the rate at which a Mg2+-specific ion conductance deactivates following membrane excitation. This would be consistent with an observed increase in the sensitivity of Cha mutants to nickel poisoning, since Ni2+ is also able to enter the cell via this pathway. More extensive behavioral analysis showed that Cha cells also overresponded to Na+, but there was no evidence for a defect in intracellular Ca2+ homeostasis that might account for a simultaneous enhancement of both the Mg2+ and Na+ conductances. The possibility that the Cha locus may encode a specific regulator of the Mg2+- and Na+-permeabilities is considered.
Topological Constraints on Transvection Between white Genes Within the Transposing Element TE35B in Drosophila melanogaster
Authors: Gubb David , Roote John , Trenear Jennifer , Coulson Darin , Ashburner Michael
Published: January 2021

The transposable element TE35B carries two copies of the white (w) gene at 35B1.2 on the second chromosome. These w genes are suppressed in a zeste-1 (z1) mutant background in a synapsis-dependent manner. Single-copy derivatives of the original TE35B stock give red eyes when heterozygous, but zeste eyes when homozygous. TE35B derivatives carrying single, double or triple copies of w were crossed to generate flies carrying from two to five ectopic w genes. Within this range, z1-mediated suppression is insensitive to copynumber and does not distinguish between w genes that are in cis or in trans. Suppression does not require the juxtaposition of even numbers of w genes, but is extremely sensitive to chromosomal topology. When arranged in a tight cluster, in triple-copy TE derivatives, w genes are non-suppressible. Breakpoints falling within TE35B and separating two functional w genes act as partial suppressors of z1. Similarly, breakpoints immediately proximal or distal to both w genes give partial suppression. This transvection-dependent downregulation of w genes may result from mis-activation of the X-chromosome dosage compensation mechanism.
Mismatch Repair in Schizosacchromyces pombe Requires the mutL Homologous Gene pms1: Molecular Cloning and Functional Analysis
Authors: Schär Primo , Baur Michel , Schneider Claudine , Kohli Jürg
Published: January 2021

Homologues of the bacterial mutS and mutL genes involved in DNA mismatch repair have been found in organisms from bacteria to humans. Here, we describe the structure and function of a newly identified Schizosaccharomyces pombe gene that encodes a predicted amino acid sequence of 794 residues with a high degree of homology to MutL related proteins. On the basis of its closer relationship to the eukaryotic “PMS” genes than to the “MLH” genes, we have designated the S. pombe homologue pms1. Disruption of the pms1 gene causes a significant increase of spontaneous mutagenesis as documented by reversion rate measurements. Tetrad analyses of crosses homozygous for the pms1 mutation reveal a reduction of spore viability from >92% to 80% associated with a low proportion (∼50%) of meioses producing four viable spores and a significant, allele-dependent increase of the level of post-meiotic segregation of genetic marker allele pairs. The mutant phenotypes are consistent with a general function of pms1 in correction of mismatched base pairs arising as a consequence of DNA polymerase errors during DNA synthesis, or of hybrid DNA formation between homologous but not perfectly complementary DNA strands during meiotic recombination.
Effective Size and F-Statistics of Subdivided Populations. II. Dioecious Species
Authors: Wang Jinliang
Published: January 2021

For a dioecious diploid population subdivided into an arbitrary number of subpopulations, we have derived recurrence equations for the inbreeding coefficient and coancestries between individuals within and among subpopulations and formulas for effective size and F-statistics. Stable population size and structure, discrete generations, autosomal inheritance, and the island migration model are assumed, and arbitrary distributions of the numbers of male and female progeny per family, different numbers and variable migration rates of males and females are incorporated in our derivation. Some published equations for effective size and F-statistics for a subdivided population are shown to be incorrect because several incorrect probabilities are used in the derivation. A more general equation for effective size is obtained by finding eigenvalue solutions to the recurrence equations for inbreeding coefficient and coancestry in this article, which reduces to the simple and familiar expressions derived by previous authors for the special case of a single unsubdivided population. Our general expressions for F-statistics also reduce to the classical results Of Wright's infinite island model and its extensions. It is shown that population structure is important in determining effective size and F-statistics and should be recognized and incorporated into programs for genetic conservation and evolution.
Overlapping Functions for Two G Protein α Subunits in Neurospora crassa
Authors: Baasiri Rudeina A , Lu Xiaohui , Rowley Patricia S , Turner Gloria E , Borkovich Katherine A
Published: January 2021

Heterotrimeric G proteins, consisting of α, β and γ subunits, mediate a variety of signaling pathways in eukaryotes. We have previously identified two genes, gna-1 and gna-2, that encode G protein α subunits in the filamentous fungus Neurospora crassa. Mutation of gna-1 results in female infertility and sensitivity to hyperosmotic media. In this study, we investigate the expression and functions of gna-2. Results from Western analysis and measurements of gna-2 promoter-lacZ fusion activity indicate that gna-2 is expressed during the vegetative and sexual cycle of N. crassa in both A and a mating types. Activating mutations predicted to abolish the GTPase activity of GNA-2 cause subtle defects in aerial hyphae formation and conidial germination. Extensive phenotypic analysis of Δgna-2 strains did not reveal abnormalities during vegetative or sexual development. In contrast, deletion of gna-2 in a Δgna-1 strain accentuates the Δgna-1 phenotypes. Δgna-1 Δgna-2 strains have a slower rate of hyphal apical extension than Δgna-1 strains on hyperosmotic media. Moreover, Δgna-1 Δgna-2 mutants have more pronounced defects in female fertility than Δgna-1 strains. We propose that gna-1 and gna-2 have overlapping functions and may constitute a gene family. This is the first report of G protein α subunits with overlapping functions in eukaryotic microbes.
Evolutionary History of the Sex-Peptide (Acp70A) Gene Region in Drosophila melanogaster
Authors: Cirera Susanna , Aguadé Montserrat
Published: January 2021

In Drosophila the products of the seminal fluid stimulate oviposition and suppress remating in the female. Of all the accessory gland peptides (Acp's) involved in these two responses, the sex-peptide (coded by the Acp70A gene) is among the best characterized at the functional level. A 1.2-kb fragment encompassing the Acp70A gene of nine lines from a natural population of D. melanogaster and one allele of D. sechellia was sequenced to study the forces shaping nucleotide variation within and between species. The coding region of D. simulans and D. mauritiana was also sequenced. A Ser to Ala replacement polymorphism at the last position of the signal peptide was detected in D. melanogaster. The Ser and Ala alleles are at intermediate frequencies. The level of nucleotide variation is lower for the derived Ala allele, which is compatible with a recent origin and an increase in frequency due to positive selection. Variation at the 5′ flanking region is structured in two major highly differentiated haplotypes, whose distribution does not conform to neutral expectations. Selective and/or historical factors could contribute to the observed overall patterning of nucleotide variation at the Acp70A region.
Cytonuclear Theory for Haplodiploid Species and X-Linked Genes. I. Hardy-Weinberg Dynamics and Continent-Island, Hybrid Zone Models
Authors: Goodisman Michael A D , Asmussen Marjorie A
Published: January 2021

We develop models that describe the cytonuclear structure for either a cytoplasmic and nuclear marker in a haplodiploid species or a cytoplasmic and X-linked marker in a diploid species. Sex-specific disequilibrium statistics that summarize nonrandom cytonuclear associations in such systems are defined, and their basic Hardy-Weinberg dynamics and admixture formulae are delimited. We focus on the context of hybrid zones and develop continent-island models whereby individuals from two genetically differentiated source populations migrate into and mate within a single zone of admixture. We examine the effects of differential migration of the sexes, assortative mating by pure type females, and census time (relative to mating and migration), as well as special cases of random mating and migration subsumed under the general models. We show that pure type individuals and nonzero cytonuclear disequilibria can be maintained within a hybrid zone if there is continued migration from both source populations, and that females generally have a greater influence over these cytonuclear variables than males. The resulting theoretical framework can be used to estimate the rates of assortative mating and sex-specific gene flow in hybrid zones and other zones of admixture involving haplodiploid or sex-linked cytonuclear data.
Genetic Interactions Between HOP1, RED1 and MEK1 Suggest That MEK1 Regulates Assembly of Axial Element Components During Meiosis in the Yeast Saccharomyces cerevisiae
Authors: Hollingsworth Nancy M , Ponte Lisa
Published: January 2021

During meiosis, axial elements are generated by the condensation of sister chromatids along a protein core as precursors to the formation of the synaptonemal complex (X). Functional axial elements are essential for wild-type levels of recombination and proper reductional segregation at meiosis I. Genetic and cytological data suggest that three meiosis-specific genes, HOP1, RED1 and MEK1, are involved in axial element formation in the yeast Saccharomyces cerevisiae. HOP1 and RED1 encode structural components of axial elements while MEK1 encodes a putative protein kinase. Using a partially functional allele of MEK1, new genetic interactions have been found between HOP1, RED1 and MEK1. Overexpression of HOP1 partially suppresses the spore inviability and recombination defects of mekl-974; in contrast, overexpression of RED1 exacerbates the mek1-974 spore inviability. Co-overexpression of HOP1 and RED1 in mek1-974 diploids alleviates the negative effect of overexpressing RED1 alone. Red1p/Red1p as well as Hop1p/Red1p interactions have been reconstituted in two hybrid experiments. Our results suggest a model whereby Mekl kinase activity controls axial element assembly by regulating the affinity with which Hoplp and Redlp interact with each other.
“Break Copy” Duplication: A Model for Chromosome Fragment Formation in Saccharomyces cerevisiae
Authors: Morrow Dwight M , Connelly Carla , Hieter Philip
Published: January 2021

Introduction of a chromosome fragmentation vector (CFV) into the budding yeast Saccharomyces cerevisiae results in a targeted homologous recombination event that yields an independently segregating chromosome fragment (CF) and an alteration in the strain's karyotype. Fragmentation with an acentric CFV directed in a centromere-proximal orientation generates a CF that contains all sequences proximal to the targeting segment and results in loss of the endogenous targeted chromosome to yield a 2N-1+CF karyotype. In contrast, fragmentation with a centric CFV directed in a centromere-distal orientation generates a CF that contains all sequences distal to the targeting segment and retention of the endogenous targeted chromosome to yield a 2N+CF karyotype. We have termed this phenomenon “break copy” duplication. Using yeast strains in which the centromere had been transposed to a new location, it was demonstrated that the centromere inhibited break copy duplication. These data suggest that CF formation is the product of an unscheduled DNA replication event initiated by the free end of the CFV and is analogous to a “half” double-strand break gap-repair reaction. We suggest that break copy duplication may have evolved as a mechanism for maintenance of ploidy following DNA breakage.
Essential Functional Interactions of SAGA, a Saccharomyces cerevisiae Complex of Spt, Ada, and Gcn5 Proteins, With the Snf/Swi and Srb/Mediator Complexes
Authors: Roberts Shannon M , Winston Fred
Published: January 2021

The Saccharomyces cerevisiae transcription factor Spt20/Ada5 was originally identified by mutations that suppress Ty insertion alleles and by mutations that suppress the toxicity caused by Gal4-VP16 overexpression. Here we present evidence for physical associations between Spt20/Ada5 and three other Spt proteins, suggesting that they exist in a complex. A related study demonstrates that this complex also contains the histone acetyltransferase, Gcn5, and Ada2. This complex has been named SAGA (Spt/Ada/Gcn5 acetyltransferase). To identify functions that genetically interact with SAGA, we have screened for mutations that cause lethality in an spt20Δ/ada5Δ mutant. Our screen identified mutations in SNF2, SIN4, and GAL11. These mutations affect two known transcription complexes: Snf/Swi, which functions in nucleosome remodeling, and Srb/mediator, which is required for regulated transcription by RNA polymerase II. Systematic analysis has demonstrated that spt20Δ/ada5Δ and spt7Δ mutations cause lethality with every snf/swi and srb/mediator mutation tested. Furthermore, a gcn5Δ mutation causes severe sickness with snf/swi mutations, but not with srb/mediator mutations. These findings suggest that SAGA has multiple activities and plays critical roles in transcription by RNA polymerase II.
DMC1 Functions in a Saccharomyces cerevisiae Meiotic Pathway That Is Largely Independent of the RAD51 Pathway
Authors: Dresser Michael E , Ewing Debra J , Conrad Michael N , Dominguez Ana M , Barstead Robert , Jiang Hua , Kodadek Thomas
Published: January 2021

Meiotic recombinationin the yeast Saccharomyces cerevisiae requires two similar recA-like proteins, Dmc1p and Rad51p. A screen for dominant meiotic mutants provided DMC1-G126D, a dominant allele mutated in the conserved ATP-binding site (specifically, the A-loop motif) that confers a null phenotype. A recessive null allele, dmc1-K69E, was isolated as an intragenic suppressor of DMC1-G126D. Dmc1-K69Ep, unlike Dmc1p, does not interact homotypically in a two-hybrid assay, although it does interact with other fusion proteins identified by two-hybrid screen with Dmc1p. Dmc1p, unlike Rad51p, does not interact in the two-hybrid assay with Rad52p or Rad54p. However, Dmc1p does interact with Tid1p, a Rad54p homologue, with Tid4p, a Rad16p homologue, and with other fusion proteins that do not interact with Rad51p, suggesting that Dmc1p and Rad51p function in separate, though possibly overlapping, recombinational repair complexes. Epistasis analysis suggests that DMC1 and RAD51 function in separate pathways responsible for meiotic recombination. Taken together, our results are consistent with a requirement for DMC1 for meiosis-specific entry of DNA double-strand break ends into chromatin. Interestingly, the pattern on CHEF gels of chromosome fragments that result from meiotic DNA double-strand break formation is different in DMC1 mutant strains from that seen in rad50S strains.
Heterochromatic trans-Inactivation of Drosophila white Transgenes
Authors: Martin-Morris Linda E , Csink Amy K , Darer Douglas R , Talbert Paul B , Henikoff Steven
Published: January 2021

Position effect variegation of most Drosophila melanogaster genes, including the white eye pigment gene, is recessive. We find that this is not always the case for white transgenes. Three examples are described in which a lesion causing variegation is capable of silencing the white transgene on the paired homologue (trans-inactivation). These examples include two different transgene constructs inserted at three distinct genomic locations. The lesions that cause variegation of white minimally disrupt the linear order of genes on the chromosomes, permitting close homologous pairing. At one of these sites, trans-inactivation has also been extended to include a vital gene in the vicinity of the white transgene insertion. These findings suggest that many Drosophila genes, in many positions in the genome, can sense the heterochromatic state of a paired homologue.