bluuebunny/crossref_metadata_2025 huggingface dataset:
A Screen for Genes Involved in the Anaphase Proteolytic Pathway Identifies tsm1+, a Novel Schizosaccharomyces pombe Gene Important for Microtubule Integrity
Authors: Grishchuk Ekaterina L , Howe James L , McIntosh J Richard
Published: April 2021

The growth of several mitotic mutants of Schizosaccharomyces pombe, including nuc2-663, is inhibited by the protease inhibitor N-Tosyl-L-Phenylalanine Chloromethyl Ketone (TPCK). Because nuc2+ encodes a presumptive component of the Anaphase Promoting Complex, which is required for the ubiquitin-dependent proteolysis of certain proteins during exit from mitosis, we have used sensitivity to TPCK as a criterion by which to search for novel S. pombe mutants defective in the anaphase-promoting pathway. In a genetic screen for temperature-sensitive mitotic mutants that were also sensitive to TPCK at a permissive temperature, we isolated three tsm (TPCK-sensitive mitotic) strains. Two of these are alleles of cut1+, but tsm1-512 maps to a novel genetic location. The tsm1-512 mutation leads to delayed nuclear division at restrictive temperatures, apparently as a result of an impaired ability to form a metaphase spindle. After shift of early G2 cells to 36°, tsm1-512 arrests transiently in the second mitotic division and then exits mitosis, as judged by spindle elongation and septation. The chromosomes, however, often fail to segregate properly. Genetic interactions between tsm1-512 and components of the anaphase proteolytic pathway suggest a functional involvement of the Tsm1 protein in this pathway.
Tip Loci: Six Chlamydomonas Nuclear Suppressors That Permit the Translocation of Proteins with Mutant Thylakoid Signal Sequences
Authors: Bernd Karen K , Kohorn Bruce D
Published: April 2021

Mutations within the signal sequence of cytochrome f (cytf) in Chlamydomonas inhibit thylakoid membrane protein translocation and render cells nonphotosynthetic. Twenty-seven suppressors of the mutant signal sequences were selected for their ability to restore photoautotrophic growth and these describe six nuclear loci named tip1 through 6 for thylakoid insertion protein. The tip mutations restore the translocation of cytf and are not allele specific, as they suppress a number of different cytf signal sequence mutations. Tip5 and 2 may act early in cytf translocation, while Tip1, 3, 4, and 6 are engaged later. The tip mutations have no phenotype in the absence of a signal sequence mutation and there is genetic interaction between tip4, and tip5 suggesting an interaction of their encoded proteins. As there is overlap in the energetic, biochemical and genetic requirements for the translocation of nuclear and chloroplast-encoded thylakoid proteins, the tip mutations likely identify components of a general thylakoid protein translocation apparatus.
A Genetic Screen for Temperature-Sensitive Cell-Division Mutants of Caenorhabditis elegans
Authors: O'Connell Kevin F , Leys Charles M , White John G
Published: April 2021

A novel screen to isolate conditional cell-division mutants in Caenorhabditis elegans has been developed. The screen is based on the phenotypes associated with existing cell-division mutations: some disrupt postembryonic divisions and affect formation of the gonad and ventral nerve cord—resulting in sterile, uncoordinated animals—while others affect embryonic divisions and result in lethality. We obtained 19 conditional mutants that displayed these phenotypes when shifted to the restrictive temperature at the appropriate developmental stage. Eighteen of these mutations have been mapped; 17 proved to be single alleles of newly identified genes, while 1 proved to be an allele of a previously identified gene. Genetic tests on the embryonic lethal phenotypes indicated that for 13 genes, embryogenesis required maternal expression, while for 6, zygotic expression could suffice. In all cases, maternal expression of wild-type activity was found to be largely sufficient for embryogenesis. Cytological analysis revealed that 10 mutants possessed embryonic cell-division defects, including failure to properly segregate DNA, failure to assemble a mitotic spindle, late cytokinesis defects, prolonged cell cycles, and improperly oriented mitotic spindles. We conclude that this approach can be used to identify mutations that affect various aspects of the cell-division cycle.
A New Marker for Mosaic Analysis in Caenorhabditis elegans Indicates a Fusion Between hyp6 and hyp7, Two Major Components of the Hypodermis
Authors: Yochem John , Gu Trent , Han Min
Published: April 2021

A fusion of the sur-5 protein to the green fluorescent protein containing a nuclear localization signal is demonstrated as a marker for genetic mosaic analysis in the nematode Caenorhabditis elegans. Because of an extensive accumulation of bright fluorescence in many nuclei, normal growth plates, each containing hundreds of worms, can be rapidly screened with a dissecting microscope for rare mosaic individuals. As the marker can also be used to detect transgenic worms, the construction of strains for mosaic analyses can be minimized. In the course of examining rare mosaic animals, an unexpected pattern of fluorescence was noticed for hyp6, a syncytial component of the hypodermis, which indicated that the marker may serve as a means of assessing cellular fusions during development. Immunofluorescent staining of adherens junctions confirmed a postembryonic fusion of hyp6 with hyp7, the major syncytium of the hypodermis.
Molecular Evolution of a Sex Determination Protein: FEM-2 (PP2C) in Caenorhabditis
Authors: Hansen Dave , Pilgrim Dave
Published: April 2021

Somatic sex determination in Caenorhabditis elegans involves a signal transduction pathway linking a membrane receptor to a transcription factor. The fem-2 gene is central to this pathway, producing a protein phosphatase (FEM-2) of the type 2C (PP2C). FEM-2 contains a long amino terminus that is absent in canonical PP2C enzymes. The function of this domain is difficult to predict, since it shows no sequence similarity to any other known proteins or motifs. Here we report the cloning of the fem-2 homologue from Caenorhabditis briggsae (Cb-fem-2). The sequence identity is much higher than that observed for other C. briggsae homologues of C. elegans sex determination proteins. However, this level is not uniform across the entire lengths of the proteins; it is much lower in the amino termini. Thus, the two domains of the same protein are evolving at different rates, suggesting that they have different functional constraints. Consistent with this, Cb-FEM-2 is able to replace some, but not all, of the Ce-FEM-2 in vivo function. We show that removal of the amino terminus from Ce-FEM-2 has no effect on its in vitro phosphatase activity, or its ability to replace the in vivo function of a yeast PP2C enzyme, but that it is necessary for proper FEM-2 function in worms. This demonstrates that the amino terminus is not an extended catalytic domain or a direct negative regulator of phosphatase activity.
The Y Chromosomal Fertility Factor Threads in Drosophila hydei Harbors a Functional Gene Encoding an Axonemal Dynein β Heavy Chain Protein
Authors: Kurek Roman , Reugels Alexander M , Glaätzer Karl Heinz , Bünemann Hans
Published: April 2021

To understand the contradiction between megabase-sized lampbrush loops and putative protein encoding genes both associated with the loci of Y chromosomal fertility genes of Drosophila on the molecular level, we used PCR-mediated cloning to identify and isolate the cDNA sequence of the Y chromosomal Drosophila hydei gene DhDhc7(Y). Alignment of the sequences of the putative protein DhDhc7(Y) and the outer arm dynein β heavy chain protein DYH2 of Tripneustes gratilla shows homology over the entire length of the protein chains. Therefore the proteins can be assumed to fulfill orthologous functions within the sperm tail axonemes of both species. Functional dynein β heavy chain molecules, however, are necessary for the assembly and attachment of outer dynein arms within the sperm tail axoneme. Localization of DhDhc7(Y) to the fertility factor Threads, comprising at least 5.1 Mb of transcriptionally active repetitive DNA, results from an infertile Threads− mutant where large clusters of Threads specifically transcribed satellites and parts of DhDhc7(Y) encoding sequences are missing simultaneously. Consequently, the complete lack of the outer dynein arms in Threads− males most probably causes sperm immotility and hence infertility of the fly. Moreover, preliminary sequence analysis and several other features support the hypothesis that DhDhc7(Y) on the lampbrush loops Threads in D. hydei and Dhc-Yh3 on the lampbrush loops kl-5 in Drosophila melanogaster on the heterochromatic Y chromosome of both species might indeed code for orthologous dynein β heavy chain proteins.
hobo Induced Rearrangements in the yellow Locus Influence the Insulation Effect of the gypsy su(Hw)-Binding Region in Drosophila melanogaster
Authors: Gause Maria , Hovhannisyan Hayk , Kan Tatiana , Kuhfittig Steffi , Mogila Vladic , Georgiev Pavel
Published: April 2021

The su(Hw) protein is responsible for the insulation mediated by the su(Hw)-binding region present in the gypsy retrotransposon. In the y2 mutant, su(Hw) protein partially inhibits yellow transcription by repressing the function of transcriptional enhancers located distally from the yellow promoter with respect to gypsy. y2 mutation derivatives have been induced by the insertion of two hobo copies on the both sides of gypsy: into the yellow intron and into the 5′ regulatory region upstream of the wing and body enhancers. The hobo elements have the same structure and orientation, opposite to the direction of yellow transcription. In the sequence context, where two copies of hobo are separated by the su(Hw)-binding region, hobo-dependent rearrangements are frequently associated with duplications of the region between the hobo elements. Duplication of the su(Hw)-binding region strongly inhibits the insulation of the yellow promoter separated from the body and wing enhancers by gypsy. These results provide a better insight into mechanisms by which the su(Hw)-binding region affects the enhancer function.
Loss of Notum Macrochaetae as an Interspecific Hybrid Anomaly Between Drosophila melanogaster and D. simulans
Authors: Takano Toshiyuki S
Published: April 2021

With the aim of revealing genetic variation accumulated among closely related species during the course of evolution, this study focuses on loss of macrochaetae on the notum as one of the developmental anomalies seen in interspecific hybrids between Drosophila melanogaster and its closely related species. Interspecific hybrids between a line of D. melanogaster and D. simulans isofemale lines exhibited a wide range in the number of missing bristles. By contrast, D. mauritiana and D. sechellia lines showed almost no reduction in bristle number in hybrids with D. melanogaster. Genetic analysis showed that the D. simulans X chromosome confers a large effect on hybrid bristle loss, although X-autosome interaction may be involved. This suggests that at least one genetic factor contributing to hybrid anomalies arose recently on a D. simulans X chromosome. Moreover, the results indicate sex dependency: the male hybrids were more susceptible to bristle loss than the female hybrids were. Use of cell type markers suggests that the defect does not lie in cell fate decisions during bristle development, but in the maintenance of neural fate and/or differentiation of the descendants of sensory mother cells.
Quantitative Trait Locus Mapping in Dairy Cattle by Means of Selective Milk DNA Pooling Using Dinucleotide Microsatellite Markers: Analysis of Milk Protein Percentage
Authors: Lipkin Ehud , Mosig Mathias O , Darvasi Ariel , Ezra Ephraim , Shalom A , Friedmann Adam , Soller Morris
Published: April 2021

“Selective DNA pooling” accomplishes quantitative trait locus (QTL) mapping through densitometric estimates of marker allele frequencies in pooled DNA samples of phenotypically extreme individuals. With poly(TG) microsatellites, such estimates are confounded by “shadow” (“stutter”) bands. A correction procedure was developed on the basis of an observed linear regression between shadow band intensity and allele TG repeat number. Using this procedure, a selective DNA pooling study with respect to milk protein percentage was implemented in Israel-Holstein dairy cattle. Pools were prepared from milk samples of high and low daughters of each of seven sires and genotyped with respect to 11 markers. Highly significant associations with milk protein percentage were found for 5 of the markers; 4 of these markers confirmed previous reports. Selective DNA pooling accessed 80.6 and 48.3%, respectively, of the information that would have been available through individual selective genotyping or total population genotyping. In effect, the statistical power of 45,600 individual genotypings was obtained from 328 pool genotypings. This methodology can make genome-wide mapping of QTL accessible to moderately sized breeding organizations.
Characterization of Soymar1, a Mariner Element in Soybean
Authors: Jarvik Tyler , Lark Karl G
Published: April 2021

Mariner elements, a family of DNA-mediated transposable elements with short, inverted terminal repeats, have been reported in a wide variety of arthropods, as well as planarians, nematodes, and humans. No such element has been reported in a plant. Here we report a mariner element in the plant soybean (Glycine max (L.) Merr.). Although this sequence belongs to the mariner family, it is clearly distinct from previously reported mariner-like elements, as well as from the Tc1 transposon family. Novel aspects of its sequence could be useful as a starting point to identify mariner-like elements in new organisms, and it may prove useful in creating a transformation vector for plants.
Demand Theory of Gene Regulation. I. Quantitative Development of the Theory
Authors: Savageau Michael A
Published: April 2021

The study of gene regulation has shown that a variety of molecular mechanisms are capable of performing this essential function. The physiological implications of these various designs and the conditions that might favor their natural selection are far from clear in most instances. Perhaps the most fundamental alternative is that involving negative or positive modes of control. Induction of gene expression can be accomplished either by removing a restraining element, which permits expression from a high-level promoter, or by providing a stimulatory element, which facilitates expression from a low-level promoter. This particular design feature is one of the few that is well understood. According to the demand theory of gene regulation, the negative mode will be selected for the control of a gene whose function is in low demand in the organism's natural environment, whereas the positive mode will be selected for the control of a gene whose function is in high demand. These qualitative predictions are well supported by experimental evidence. Here we develop the quantitative implications of this demand theory. We define two key parameters: the cycle time C, which is the average time for a gene to complete an ON/OFF cycle, and demand D, which is the fraction of the cycle time that the gene is ON. Mathematical analysis involving mutation rates and growth rates in different environments yields equations that characterize the extent and rate of selection. Further analysis of these equations reveals two thresholds in the C vs. D plot that create a well-defined region within which selection of wild-type regulatory mechanisms is realizable. The theory also predicts minimum and maximum values for the demand D, a maximum value for the cycle time C, as well as an inherent asymmetry between the regions for selection of the positive and negative modes of control.
Sro7p, a Saccharomyces cerevisiae Counterpart of the Tumor Suppressor l(2)gl Protein, Is Related to Myosins in Function
Authors: Kagami Mitsuhiro , Toh-e Akio , Matsui Yasushi
Published: April 2021

Yeast SRO7 was identified as a multicopy suppressor of a defect in Rho3p, a small GTPase that maintains cell polarity. Sro7p and Sro77p, a homologue of Sro7p, possess domains homologous to the protein that are encoded by the Drosophila tumor suppressor gene lethal (2) giant larvae [l(2)gl]. sro7Δ sro77Δ mutants showed a partial defect of organization of the polarized actin cytoskeleton and a cold-sensitive growth phenotype. A human counterpart of l(2)gl could suppress the sro7Δ sro77Δ defect. Similar to the l(2)gl protein, Sro7p formed a complex with Myo1p, a type II myosin. These results indicate that Sro7p and Sro77p are the yeast counterparts of the l(2)gl protein. Our genetic analysis revealed that deletion of SRO7 and SRO77 showed reciprocal suppression with deletion of MYO1 (i.e., the sro7Δ sro77Δ defect was suppressed by myo1Δ and vice versa). In addition, SRO7 showed genetic interactions with MYO2, encoding an essential type V myosin: Overexpression of SRO7 suppressed a defect in MYO2 and, conversely, overexpression of MYO2 suppressed the cold-sensitive phenotype of sro7Δ sro77Δ mutants. These results indicate that Sro7 function is closely related to both Myo1p and Myo2p. We propose a model in which Sro7 function is involved in the targeting of the myosin proteins to their intrinsic pathways.
Identification of the Genes Encoding the Cytosolic Translation Release Factors from Podospora anserina and Analysis of Their Role During the Life Cycle
Authors: Gagny Bénédicte , Silar Philippe
Published: April 2021

In an attempt to decipher their role in the life history and senescence process of the filamentous fungus Podospora anserina, we have cloned the su1 and su2 genes, previously identified as implicated in cytosolic translation fidelity. We show that these genes are the equivalents of the SUP35 and SUP45 genes of Saccharomyces cerevisiae, which encode the cytosolic translation termination factors eRF3 and eRF1, respectively. Mutations in these genes that suppress nonsense mutations may lead to drastic mycelium morphology changes and sexual impairment but have little effect on life span. Deletion of su1, coding for the P. anserina eRF3, is lethal. Diminution of its expression leads to a nonsense suppressor phenotype whereas its overexpression leads to an antisuppressor phenotype. P. anserina eRF3 presents an N-terminal region structurally related to the yeast eRF3 one. Deletion of the N-terminal region of P. anserina eRF3 does not cause any vegetative alteration; especially life span is not changed. However, it promotes a reproductive impairment. Contrary to what happens in S. cerevisiae, deletion of the N terminus of the protein promotes a nonsense suppressor phenotype. Genetic analysis suggests that this domain of eRF3 acts in P. anserina as a cis-activator of the C-terminal portion and is required for proper reproduction.
Intragenic Suppressors of Dictyostelium Myosin G680 Mutants Demarcate Discrete Structural Elements: Implications for Conformational States of the Motor
Authors: Patterson Bruce
Published: April 2021

We are using intragenic suppression to generate inferences about currently inaccessible conformations of the molecular motor myosin. We identified 19 unique suppressors of Dictyostelium G680A and G680V mutants and find that they are structurally and chemically restricted, suggestive of specific, compensatory mechanisms of action. Suppressors cluster in two adjacent elements of the myosin structure, one of which is dominated by substitutions that increase the volume of hydrophobic residues. The suppressors outline a general model for the mechanism of suppression of the G680A and G680V alterations. Secondary phenotypes conferred by suppressors independent of the G680 changes demonstrate that they will be useful substrates for biochemical and genetic characterization.
A Pseudoautosomal Random Amplified Polymorphic DNA Marker for the Sex Chromosomes of Silene dioica
Authors: Di Stilio Verónica S , Kesseli Richard V , Mulcahy David L
Published: April 2021

The segregation pattern of an 810-bp random amplified polymorphic DNA (RAPD) band in the F1 and backcross generations of a Silene dioica (L.) Clairv. family provides evidence that this molecular marker is located in the pseudoautosomal region (PAR) of the X and Y chromosomes. The marker was found through a combination of bulked segregant analysis (BSA) and RAPD techniques. Recombination rates between this pseudoautosomal marker and the differentiating portion of the Y chromosome are 15% in both generations. Alternative explanations involving nondisjunction or autosomal inheritance are presented and discussed. Chromosome counts provide evidence against the nondisjunction hypothesis, and probability calculations argue against the possibility of autosomal inheritance. This constitutes the first report of a pseudoautosomal DNA marker for plant sex chromosomes.
Testing Natural Selection vs. Genetic Drift in Phenotypic Evolution Using Quantitative Trait Locus Data
Authors: Orr H Allen
Published: April 2021

Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the “high line” with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed.
The [KIL-d] Cytoplasmic Genetic Element of Yeast Results in Epigenetic Regulation of Viral M Double-Stranded RNA Gene Expression
Authors: Tallóczy Zsolt , Menon Sujoy , Neigeborn Lenore , Leibowitz Michael J
Published: April 2021

[KIL-d] is a cytoplasmically inherited genetic trait that causes killer virus-infected cells of Saccharomyces cerevisiae to express the normal killer phenotypes in a/α cells, but to show variegated defective killer phenotypes in a or α type cells. Mating of [KIL-d] haploids results in “healing” of their phenotypic defects, while meiosis of the resulting diploids results in “resetting” of the variegated, but mitotically stable, defects. We show that [KIL-d] does not reside on the double-stranded RNA genome of killer virus. Thus, the [KIL-d] effect on viral gene expression is epigenetic in nature. Resetting requires nuclear events of meiosis, since [KIL-d] can be cytoplasmically transmitted during cytoduction without causing defects in killer virus expression. Subsequently, mating of these cytoductants followed by meiosis generates spore clones expressing variegated defective phenotypes. Cytoduction of wild-type cytoplasm into a phenotypically defective [KIL-d] haploid fails to heal, nor does simultaneous or sequential expression of both MAT alleles cause healing. Thus, healing is not triggered by the appearance of heterozygosity at the MAT locus, but rather requires the nuclear fusion events which occur during mating. Therefore, [KIL-d] appears to interact with the nucleus in order to exert its effects on gene expression by the killer virus RNA genome.
The Female-Determining Gene F of the Housefly, Musca domestica, Acts Maternally to Regulate Its Own Zygotic Activity
Authors: Dübendorfer Andreas , Hediger Monika
Published: April 2021

In Musca domestica, the common housefly, female development requires the continuous activity of the sex-determining gene F from early embryogenesis until metamorphosis. To activate F in embryogenesis, two conditions must be met: There must be no male-determining M factor in the zygotic genome, and the egg must be preconditioned by F activity in the maternal germ line. This maternal activity can be suppressed by introducing an M factor into the maternal germ line, which causes all offspring, including those that do not carry M, to develop as males. By transplantation of pole cells (germline progenitor cells) we have constructed such females with a genetically male germ line and, simultaneously, males with a genetically female germ line carrying a constitutive allele of F [FDominant (FD)]. Crosses between these animals yielded offspring that, despite the presence of M in the maternal germ line, were of female sex, solely due to zygotic FD brought in via the sperm. This shows that zygotic F function alone is sufficient to promote female development and that in the wild-type situation, maternal F product serves no other function but to activate the zygotic F gene.
Interactions Among Dosage-Dependent Trans-Acting Modifiers of Gene Expression and Position-Effect Variegation in Drosophila
Authors: Bhadra Utpal , Bhadra Manika Pal , Birchler James A
Published: April 2021

We have investigated the effect of dosage-dependent trans-acting regulators of the white eye color gene in combinations to understand their interaction properties. The consequences of the interactions will aid in an understanding of aneuploid syndromes, position-effect variegation (PEV), quantitative traits, and dosage compensation, all of which are affected by dosage-dependent modifiers. Various combinations modulate two functionally related transcripts, white and scarlet, differently. The overall trend is that multiple modifiers are noncumulative or epistatic to each other. In some combinations, developmental transitions from larvae to pupae to adults act as a switch for whether the effect is positive or negative. With position-effect variegation, similar responses were found as with gene expression. The highly multigenic nature of dosage-sensitive modulation of both gene expression and PEV suggests that dosage effects can be progressively transduced through a series of steps in a hierarchical manner.
Molecular Evolution of Two Lineages of L1 (LINE-1) Retrotransposons in the California Mouse, Peromyscus californicus
Authors: Casavant N Carol , Lee Rhonda N , Sherman Amy N , Wichman Holly A
Published: April 2021

The large number of L1 [long interspersed elements (LINE)-1] sequences found in the genome is due to the insertion of copies of the retrotransposon over evolutionary time. The majority of copies appear to be replicates of a few active, or “master” templates. A continual replacement of master templates over time gives rise to lineages distinguishable by their own unique set of shared-sequence variants. A previous analysis of L1 sequences in deer mice, Peromyscus maniculatus and P. leucopus, revealed two active L1 lineages, marked by different rates of evolution, whose most recent common ancestor predates the expansion of the Peromyscus species. Here we exploit lineage-specific, shared-sequence variants to reveal a paucity of Lineage 2 sequences in at least one species, P. californicus. The dearth of Lineage 2 copies in P. californicus suggests that Lineage 2 may have been unproductive until after the most recent common ancestor of P. californicus and P. maniculatus. We also show that Lineage 1 appears to have a higher rate of evolution in P. maniculatus relative to either P. californicus or P. leucopus. As a phylogenetic tool, L1 lineage-specific variants support a close affinity between P. californicus and P. eremicus relative to the other species examined.
The Association of Flowering Time Quantitative Trait Loci with Duplicated Regions and Candidate Loci in Brassica oleracea
Authors: Bohuon E J R , Ramsay L D , Craft J A , Arthur A E , Marshall D F , Lydiate D J , Kearsey M J
Published: April 2021

A population of 150 doubled haploid lines of rapid cycling Brassica oleracea, derived from an F1 from a var. alboglabra × var. italica cross, was scored for flowering time in two trials. Using information on 82 mapped molecular markers, spread evenly across the nine linkage groups, QTL were identified at six locations; one each on linkage groups O2 and O3 and two each on linkage groups O5 and O9. In total, these QTL explained 58 and 93% of the genetical variation in the two trials. Three of these QTL, on linkage groups O2, O3, and O9, were situated in regions showing considerable homology both with each other and with chromosome regions of B. nigra that have been shown to affect flowering time. These same regions are all homologous to a single tract of Arabidopsis chromosome 5, which contains a number of the flowering-related genes, one or more of which may be candidates for the QTL found in Brassica.
Arabidopsis TSO1 Regulates Directional Processes in Cells During Floral Organogenesis
Authors: Hauser Bernard A , Villanueva Jacinto M , Gasser Charles S
Published: April 2021

Flowers of the previously described Arabidopsis tso1-1 mutant had aberrant, highly reduced organs in place of petals, stamens, and carpels. Cells of tso1-1 flowers had division defects, including failure in cytokinesis, partial cell wall formation, and elevated nuclear DNA content. We describe here two new tso1 alleles (tso1-3 and tso1-4), which caused defects in ovule development, but had little effect on gross floral morphology. Early ovule development occurred normally in tso1-3 and tso1-4, but the shapes and alignments of integument cells became increasingly more disordered as development progressed. tso1-3 ovules usually lacked embryo sacs due to a failure to form megaspore mother cells. The cell division defects described for the strong tso1-1 mutant were rarely observed in tso1-3 ovules. The aberrations in tso1-3 mutants primarily resulted from a failure in directional expansion of cells and/or coordination of this process among adjacent cells. Effects of tso1-3 appeared to be independent of effects of other ovule development mutations, with the exception of leunig, which exhibited a synergistic interaction. The data are consistent with TSO1 acting in processes governing directional movement of cellular components, indicating a likely role for TSO1 in cytoskeletal function.
Statistical Analysis of Half-Tetrads
Authors: Zhao Hongyu , Speed Terence P
Published: April 2021

Half-tetrads, where two meiotic products from a single meiosis are recovered together, arise in different forms in a variety of organisms. Closely related to ordered tetrads, half-tetrads yield information on chromatid interference, chiasma interference, and centromere positions. In this article, for different half-tetrad types and different marker configurations, we derive the relations between multilocus half-tetrad probabilities and multilocus ordered tetrad probabilities. These relations are used to obtain equality and inequality constraints among multilocus half-tetrad probabilities that are imposed by the assumption of no chromatid interference. We illustrate how to apply these results to study chiasma interference and to map centromeres using multilocus half-tetrad data.
The Saccharomyces cerevisiae RAD9, RAD17, RAD24 and MEC3 Genes Are Required for Tolerating Irreparable, Ultraviolet-Induced DNA Damage
Authors: Paulovich A G , Armour C D , Hartwell L H
Published: April 2021

In wild-type Saccharomyces cerevisiae, a checkpoint slows the rate of progression of an ongoing S phase in response to exposure to a DNA-alkylating agent. Mutations that eliminate S phase regulation also confer sensitivity to alkylating agents, leading us to suggest that, by regulating the S phase rate, cells are either better able to repair or better able to replicate damaged DNA. In this study, we determine the effects of mutations that impair S phase regulation on the ability of excision repair-defective cells to replicate irreparably UV-damaged DNA. We assay survival after UV irradiation, as well as the genetic consequences of replicating a damaged template, namely mutation and sister chromatid exchange induction. We find that RAD9, RAD17, RAD24, and MEC3 are required for UV-induced (although not spontaneous) mutagenesis, and that RAD9 and RAD17 (but not REV3, RAD24, and MEC3) are required for maximal induction of replication-dependent sister chromatid exchange. Therefore, checkpoint genes not only control cell cycle progression in response to damage, but also play a role in accommodating DNA damage during replication.
Sex and the Evolution of Intrahost Competition in RNA Virus φ6
Authors: Turner Paul E , Chao Lin
Published: April 2021

Sex allows beneficial mutations that occur in separate lineages to be fixed in the same genome. For this reason, the Fisher-Muller model predicts that adaptation to the environment is more rapid in a large sexual population than in an equally large asexual population. Sexual reproduction occurs in populations of the RNA virus φ6 when multiple bacteriophages coinfect the same host cell. Here, we tested the model's predictions by determining whether sex favors more rapid adaptation of φ6 to a bacterial host, Pseudomonas phaseolicola. Replicate populations of φ6 were allowed to evolve in either the presence or absence of sex for 250 generations. All experimental populations showed a significant increase in fitness relative to the ancestor, but sex did not increase the rate of adaptation. Rather, we found that the sexual and asexual treatments also differ because intense intrahost competition between viruses occurs during coinfection. Results showed that the derived sexual viruses were selectively favored only when coinfection is common, indicating that within-host competition detracts from the ability of viruses to exploit the host. Thus, sex was not advantageous because the cost created by intrahost competition was too strong. Our findings indicate that high levels of coinfection exceed an optimum where sex may be beneficial to populations of φ6, and suggest that genetic conflicts can evolve in RNA viruses.
The Schizosaccharomyces pombe cho1+ Gene Encodes a Phospholipid Methyltransferase
Authors: Kanipes Margaret I , Hill John E , Henry Susan A
Published: April 2021

The isolation of mutants of Schizosaccharomyces pombe defective in the synthesis of phosphatidylcholine via the methylation of phosphatidylethanolamine is reported. These mutants are choline auxotrophs and fall into two unlinked complementation groups, cho1 and cho2. We also report the analysis of the cho1+ gene, the first structural gene encoding a phospholipid biosynthetic enzyme from S. pombe to be cloned and characterized. The cho1+ gene disruption mutant (cho1Δ) is viable if choline is supplied and resembles the cho1 mutants isolated after mutagenesis. Sequence analysis of the cho1+ gene indicates that it encodes a protein closely related to phospholipid methyltransferases from Saccharomyces cerevisiae and rat. Phospholipid methyltransferases encoded by a rat liver cDNA and the S. cerevisiae OPI3 gene are both able to complement the choline auxotrophy of the S. pombe cho1 mutants. These results suggest that both the structure and function of the phospholipid N-methyltransferases are broadly conserved among eukaryotic organisms.
Histone Deacetylase Homologs Regulate Epigenetic Inheritance of Transcriptional Silencing and Chromosome Segregation in Fission Yeast
Authors: Grewal Shiv I S , Bonaduce Michael J , Klar Amar J S
Published: April 2021

Position-effect control at the silent mat2-mat3 interval and at centromeres and telomeres in fission yeast is suggested to be mediated through the assembly of heterochromatin-like structures. Therefore, trans-acting genes that affect silencing may encode either chromatin proteins, factors that modify them, or factors that affect chromatin assembly. Here, we report the identification of an essential gene, clr6 (c ryptic loci r egulator), which encodes a putative histone deacetylase that when mutated affects epigenetically maintained repression at the mat2-mat3 region and at centromeres and reduces the fidelity of chromosome segregation. Furthermore, we show that the Clr3 protein, when mutated, alleviates recombination block at mat region as well as silencing at donor loci and at centromeres and telomeres, also shares strong homology to known histone deacetylases. Genetic analyses indicate that silencing might be regulated by at least two overlapping histone deacetylase activities. We also found that transient inhibition of histone deacetylase activity by trichostatin A results in the increased missegregation of chromosomes in subsequent generations and, remarkably, alters the imprint at the mat locus, causing the heritable conversion of the repressed epigenetic state to the expressed state. This work supports the model that the level of histone deacetylation has a role in the assembly of repressive heterochromatin and provides insight into the mechanism of epigenetic inheritance.
Expression and Properties of Wild-Type and Mutant Forms of the Drosophila Sex Comb on Midleg (SCM) Repressor Protein
Authors: Bornemann Douglas , Miller Ellen , Simon Jeffrey
Published: April 2021

The Sex comb on midleg (Scm) gene encodes a transcriptional repressor of the Polycomb group (PcG). Here we show that SCM protein is nuclear and that its expression is widespread during fly development. SCM protein contains a C-terminal domain, termed the SPM domain, which mediates protein-protein interactions. The biochemical function of another domain consisting of two 100-amino-acid-long repeats, termed “mbt” repeats, is unknown. We have determined the molecular lesions of nine Scm mutant alleles, which identify functional requirements for specific domains. The Scm alleles were tested for genetic interactions with mutations in other PcG genes. Intriguingly, three hypomorphic Scm mutations, which map within an mbt repeat, interact with PcG mutations more strongly than do Scm null alleles. The strongest interactions produce partial synthetic lethality that affects doubly heterozygous females more severely than males. We show that mbt repeat alleles produce stable SCM proteins that associate with normal sites in polytene chromosomes. We also analyzed progeny from Scm mutant germline clones to compare the effects of an mbt repeat mutation during embryonic vs. pupal development. We suggest that the mbt repeat alleles produce altered SCM proteins that incorporate into and impair function of PcG protein complexes.
Evidence for 3′ Untranslated Region-Dependent Autoregulation of the Drosophila Gene Encoding the Neuronal Nuclear RNA-Binding Protein ELAV
Authors: Samson Marie-Laure
Published: April 2021

The Drosophila locus embryonic lethal abnormal visual system (elav) encodes a nuclear RNA-binding protein essential for normal neuronal differentiation and maintenance of neurons. ELAV is thought to play its role by binding to RNAs produced by other genes necessary for neuronal differentiation and consequently to affect their metabolism by an as yet unknown mechanism. ELAV structural homologues have been identified in a wide range of organisms, including humans, indicating an important conserved role for the protein. Analysis of elav germline transformants presented here shows that one copy of elav minigenes lacking a complete 3′ untranslated region (3′ UTR) rescues null mutations at elav, but that two copies are lethal. Additional in vivo experiments demonstrate that elav expression is regulated through the 3′ UTR of the gene and indicate that this level of regulation is dependent upon ELAV itself. Because ELAV is an RNA-binding protein, the simplest model to account for these findings is that ELAV binds to the 3′ UTR of its own RNA to autoregulate its expression. I discuss the implications of these results for normal elav function.
Multiple Origins of Cytologically Identical Chromosome Inversions in the Anopheles gambiae Complex
Authors: Caccone Adalgisa , Min Gi-Sik , Powell Jeffrey R
Published: April 2021

For more than 60 years, evolutionary cytogeneticists have been using naturally occurring chromosomal inversions to infer phylogenetic histories, especially in insects with polytene chromosomes. The validity of this method is predicated on the assumption that inversions arise only once in the history of a lineage, so that sharing a particular inversion implies shared common ancestry. This assumption of monophyly has been generally validated by independent data. We present the first clear evidence that naturally occurring inversions, identical at the level of light microscopic examination of polytene chromosomes, may not always be monophyletic. The evidence comes from DNA sequence analyses of regions within or very near the breakpoints of an inversion called the 2La that is found in the Anopheles gambiae complex. Two species, A. merus and A. arabiensis, which are fixed for the “same” inversion, do not cluster with each other in a phylogenetic analysis of the DNA sequences within the 2La. Rather, A. merus 2La is most closely related to strains of A. gambiae homozygous for the 2L+. A. gambiae and A. merus are sister taxa, the immediate ancestor was evidently homozygous 2L+, and A. merus became fixed for an inversion cytologically identical to that in A. arabiensis. A. gambiae is polymorphic for 2La/2L+, and the 2La in this species is nearly identical at the DNA level to that in A. arabiensis, consistent with the growing evidence that introgression has or is occurring between these two most important vectors of malaria in the world. The parallel evolution of the “same” inversion may be promoted by the presence of selectively important genes within the breakpoints.
Genetic Variation and Phylogeography of Central Asian and Other House Mice, Including a Major New Mitochondrial Lineage in Yemen
Authors: Prager Ellen M , Orrego Cristián , Sage Richard D
Published: April 2021

The mitochondrial DNA (mtDNA) control region and flanking tRNAs were sequenced from 76 mice collected at 60 localities extending from Egypt through Turkey, Yemen, Iran, Afghanistan, Pakistan, and Nepal to eastern Asia. Segments of the Y chromosome and of a processed p53 pseudogene (ψp53) were amplified from many of these mice and from others collected elsewhere in Eurasia and North Africa. The 251 mtDNA types, including 54 new ones reported here, now identified from commensal house mice (Mus musculus group) by sequencing this segment can be organized into four major lineages—domesticus, musculus, castaneus, and a new lineage found in Yemen. Evolutionary tree analysis suggested the domesticus mtDNAs as the sister group to the other three commensal mtDNA lineages and the Yemeni mtDNAs as the next oldest lineage. Using this tree and the phylogeographic approach, we derived a new model for the origin and radiation of commensal house mice whose main features are an origin in west-central Asia (within the present-day range of M. domesticus) and the sequential spreading of mice first to the southern Arabian Peninsula, thence eastward and northward into south-central Asia, and later from south-central Asia to north-central Asia (and thence into most of northern Eurasia) and to southeastern Asia. Y chromosomes with and without an 18-bp deletion in the Zfy-2 gene were detected among mice from Iran and Afghanistan, while only undeleted Ys were found in Turkey, Yemen, Pakistan, and Nepal. Polymorphism for the presence of a ψp53 was observed in Georgia, Iran, Turkmenistan, Afghanistan, and Pakistan. Sequencing of a 128-bp ψp53 segment from 79 commensal mice revealed 12 variable sites and implicated ≥14 alleles. The allele that appeared to be phylogenetically ancestral was widespread, and the greatest diversity was observed in Turkey, Afghanistan, Pakistan, and Nepal. Two mice provided evidence for a second ψp53 locus in some commensal populations.
A High-Resolution Linkage Map of the Citrus Tristeza Virus Resistance Gene Region in Poncirus trifoliata (L.) Raf.
Authors: Fang D Q , Federici C T , Roose M L
Published: April 2021

Resistance to citrus tristeza virus (CTV) was evaluated in 554 progeny of 10 populations derived from Poncirus trifoliata. A dominant gene (Ctv) controlled CTV resistance in P. trifoliata. Twenty-one dominant PCR-based DNA markers were identified as linked to Ctv by bulked segregant analysis. Of the 11 closest markers to Ctv, only 2 segregated in all populations. Ten of these markers were cloned and sequenced, and codominant RFLP markers were developed. Seven RFLP markers were then evaluated in 10 populations. Marker orders were consistent in all linkage maps based on data of single populations or on combined data of populations with similar segregation patterns. In a consensus map, the six closest marker loci spanned 5.3 cM of the Ctv region. Z16 cosegregated with Ctv. C19 and AD08 flanked Ctv at distances of 0.5 and 0.8 cM, respectively. These 3 markers were present as single copies in the Poncirus genome, and could be used directly for bacterial artificial chromosome library screening to initiate a walk toward Ctv. BLAST searches of the GenBank database revealed high sequence similarities between 2 markers and known plant disease resistance genes, indicating that a resistance gene cluster exists in the Ctv region in P. trifoliata.
Chromosome Break-Induced DNA Replication Leads to Nonreciprocal Translocations and Telomere Capture
Authors: Bosco Giovanni , Haber James E
Published: April 2021

In yeast, broken chromosomes can be repaired by recombination, resulting in nonreciprocal translocations. In haploid cells suffering an HO endonuclease-induced, double-strand break (DSB), nearly 2% of the broken chromosome ends recombined with a sequence near the opposite chromosome end, which shares only 72 bp of homology with the cut sequence. This produced a repaired chromosome with the same 20-kb sequence at each end. Diploid strains were constructed in which the broken chromosome shared homology with the unbroken chromosome only on the centromere-proximal side of the DSB. More than half of these cells repaired the DSB by copying sequences distal to the break from the unbroken template chromosome. All these events were RAD52 dependent. Pedigree analysis established that DSBs occurring in G1 were repaired by a replicative mechanism, producing two identical daughter cells. We discuss the implications of these data in understanding telomerase-independent replication of telomeres, gene amplification, and the evolution of chromosomal ends.
Mapping a Telomere Using the Translocation eT1(III;V) in Caenorhabditis elegans
Authors: Adames K A , Gawne Jocelyn , Wicky Chantal , Müller Fritz , Rose Ann M
Published: April 2021

In Caenorhabditis elegans, individuals heterozygous for a reciprocal translocation produce reduced numbers of viable progeny. The proposed explanation is that the segregational pattern generates aneuploid progeny. In this article, we have examined the genotype of arrested embryonic classes. Using appropriate primers in PCR amplifications, we identified one class of arrested embryo, which could be readily recognized by its distinctive spot phenotype. The corresponding aneuploid genotype was expected to be lacking the left portion of chromosome V, from the eT1 breakpoint to the left (unc-60) end. The phenotype of the homozygotes lacking this DNA was a stage 2 embryonic arrest with a dark spot coinciding with the location in wild-type embryos of birefringent gut granules. Unlike induced events, this deletion results from meiotic segregation patterns, eliminating complexity associated with unknown material that may have been added to the end of a broken chromosome. We have used the arrested embryos, lacking chromosome V left sequences, to map a telomere probe. Unique sequences adjacent to the telomeric repeats in the clone cTel3 were missing in the arrested spot embryo. The result was confirmed by examining aneuploid segregants from a second translocation, hT1(I;V). Thus, we concluded that the telomere represented by clone cTel3 maps to the left end of chromosome V. In this analysis, we have shown that reciprocal translocations can be used to generate segregational aneuploids. These aneuploids are deleted for terminal sequences at the noncrossover ends of the C. elegans autosomes.