bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Virus Family, the Rudiviridae: Structure, Virus-Host Interactions and Genome Variability of the Sulfolobus Viruses SIRV1 and SIRV2
Authors: Prangishvili David , Arnold Hans Peter , Götz Dorothee , Ziese Ulrike , Holz Ingelore , Kristjansson Jakob K , Zillig Wolfram 
Published: April 2021

Abstract
The unenveloped, stiff-rod-shaped, linear double-stranded DNA viruses SIRV1 and SIRV2 from Icelandic Sulfolobus isolates form a novel virus family, the Rudiviridae. The sizes of the genomes are 32.3 kbp for SIRV1 and 35.8 kbp for SIRV2. The virions consist of a tube-like superhelix formed by the DNA and a single basic 15.8-kD DNA-binding protein. The tube carries a plug and three tail fibers at each end. One turn of the DNA-protein superhelix measures 4.3 nm and comprises 16.5 turns of B DNA. The linear DNA molecules appear to have covalently closed hairpin ends. The viruses are not lytic and are present in their original hosts in carrier states. Both viruses are quite stable in these carrier states. In several laboratory hosts SIRV2 was invariant, but SIRV1 formed many different variants that completely replaced the wild-type virus. Some of these variants were still variable, whereas others were stable. Up to 10% nucleotide substitution was found between corresponding genome fragments of three variants. Some variants showed deletions. Wild-type SIRV1, but not SIRV2, induces an SOS-like response in Sulfolobus. We propose that wild-type SIRV1 is unable to propagate in some hosts but surmounts this host range barrier by inducing a host response effecting extensive variation of the viral genome.
Genetic Control of Telomere Integrity in Schizosaccharomyces pombe: rad3+ and tel1+ Are Parts of Two Regulatory Networks Independent of the Downstream Protein Kinases chk1+ and cds1+
Authors: Matsuura Akira , Naito Taku , Ishikawa Fuyuki 
Published: April 2021

Abstract
The Schizosaccharomyces pombe checkpoint gene named rad3+ encodes an ATM-homologous protein kinase that shares a highly conserved motif with proteins involved in DNA metabolism. Previous studies have shown that Rad3 fulfills its function via the regulation of the Chk1 and Cds1 protein kinases. Here we describe a novel role for Rad3 in the control of telomere integrity. Mutations in the rad3+ gene alleviated telomeric silencing and produced shortened lengths in the telomere repeat tracts. Genetic analysis revealed that the other checkpoint rad mutations rad1, rad17, and rad26 belong to the same phenotypic class with rad3 with regard to control of the telomere length. Of these mutations, rad3 and rad26 have a drastic effect on telomere shortening. tel1+, another ATM homologue in S. pombe, carries out its telomere maintenance function in parallel with the checkpoint rad genes. Furthermore, either a single or double disruption of cds1+ and chk1+ caused no obvious changes in the telomeric DNA structure. Our results demonstrate a novel role of the S. pombe ATM homologues that is independent of chk1+ and cds1+.
Genetic Interactions in Yeast Between Ypt GTPases and Arf Guanine Nucleotide Exchangers
Authors: Jones Sara , Jedd Gregory , Kahn Richard A , Franzusoff Alex , Bartolini Francesca , Segev Nava 
Published: April 2021

Abstract
Two families of GTPases, Arfs and Ypt/rabs, are key regulators of vesicular transport. While Arf proteins are implicated in vesicle budding from the donor compartment, Ypt/rab proteins are involved in the targeting of vesicles to the acceptor compartment. Recently, we have shown a role for Ypt31/32p in exit from the yeast trans-Golgi, suggesting a possible function for Ypt/rab proteins in vesicle budding as well. Here we report the identification of a new member of the Sec7-domain family, SYT1, as a high-copy suppressor of a ypt31/32 mutation. Several proteins that belong to the Sec7-domain family, including the yeast Gea1p, have recently been shown to stimulate nucleotide exchange by Arf GTPases. Nucleotide exchange by Arf GTPases, the switch from the GDP- to the GTP-bound form, is thought to be crucial for their function. Sec7p itself has an important role in the yeast secretory pathway. However, its mechanism of action is not yet understood. We show that all members of the Sec7-domain family exhibit distinct genetic interactions with the YPT genes. Biochemical assays demonstrate that, although the homology between the members of the Sec7-domain family is relatively low (20-35%) and limited to a small domain, they all can act as guanine nucleotide exchange factors (GEFs) for Arf proteins, but not for Ypt GTPases. The Sec7-domain of Sec7p is sufficient for this activity. Interestingly, the Sec7 domain activity is inhibited by brefeldin A (BFA), a fungal metabolite that inhibits some of the Arf-GEFs, indicating that this domain is a target for BFA. These results demonstrate that the ability to act as Arf-GEFs is a general property of all Sec7-domain proteins in yeast. The genetic interactions observed between Arf GEFs and Ypt GTPases suggest the existence of a Ypt-Arf GTPase cascade in the secretory pathway.
Mitochondrial DNA Polymorphism, Sex Ratio Distorters and Population Genetics in the Isopod Armadillidium vulgare
Authors: Rigaud Thierry , Bouchon Didier , Souty-Grosset Catherine , Raimond Roland 
Published: April 2021

AbstractTwo maternally inherited sex ratio distorters (SRD) impose female-biased sex ratios on the wood louse Armadillidium vulgare by feminizing putative males. These SRD are (i) an intracytoplasmic bacterium of the genus Wolbachia, and (ii) another non-Mendelian element of unknown nature: the f element. Mitochondrial DNA variation was investigated in A. vulgare field populations to trace the evolution of host-SRD relationships and to investigate the effect of SRD on host cytoplasmic polymorphism. The Wolbachia endosymbionts showed no polymorphism in their ITS2 sequence and were associated with two closely related mitochondrial types. This situation probably reflects a single infection event followed by a slight differentiation of mitochondria. There was no association between the f element and a given mitochondrial type, which may confirm the fact that this element can be partially paternally transmitted. The spreading of a maternally inherited SRD in a population should reduce the mitochondrial diversity by a hitchhiking process. In A. vulgare, however, a within-population mtDNA polymorphism was often found, because of the deficient spread of Wolbachia and the partial paternal inheritance of the f element. The analysis of molecular variance indicated that A. vulgare populations are genetically structured, but without isolation by distance.
DNA Variation in the Wild Plant Arabidopsis thaliana Revealed by Amplified Fragment Length Polymorphism Analysis
Authors: Miyashita Naohiko T , Kawabe Akira , Innan Hideki 
Published: April 2021

Abstract
To investigate the level and pattern of DNA variation of Arabidopsis thaliana at the entire genome level, AFLP analysis was conducted for 38 ecotypes distributed throughout the world. Ten pairs of selective primers were used to detect a total of 472 bands, of which 374 (79.2%) were polymorphic. The frequency distribution of polymorphic bands was skewed toward an excess of singleton variation. On the basis of AFLP variation, nucleotide diversity for the entire genome was estimated to be 0.0106, which was within the range reported previously for specific nuclear genes. The frequency distribution of pairwise distance was bimodal because of an ecotype (Fl-3) with a large number of unique bands. Linkage disequilibrium between polymorphic AFLPs was tested. The proportion of significant linkage disequilibria was close to random expectation after neglecting the ecotype Fl-3. This result indicates that the effect of recombination could not be ignored in this selfing species. A neighbor-joining tree was constructed on the basis of the AFLP variation. This tree has a star-like topology and shows no clear association between ecotype and geographic origin, suggesting a recent spread of this plant species and limited migration between its habitats.
Identification of SAS4 and SAS5, Two Genes That Regulate Silencing in Saccharomyces cerevisiae
Authors: Xu Eugenia Y , Kim Susan , Replogle Kirstin , Rine Jasper , Rivier David H 
Published: April 2021

Abstract
In Saccharomyces cerevisiae, chromatin-mediated silencing inactivates transcription of the genes at the HML and HMR cryptic mating-type loci and genes near telomeres. Mutations in the Rap1p and Abf1p binding sites of the HMR-E silencer (HMRa-e**) result in a loss of silencing at HMR. We characterized a collection of 15 mutations that restore the α-mating phenotype to MATα HMRa-e** strains. These mutations defined three complementation groups, two new groups and one group that corresponded to the previously identified SAS2 gene. We cloned the genes that complemented members of the new groups and identified two previously uncharacterized genes, which we named SAS4 and SAS5. Neither SAS4 nor SAS5 was required for viability. Null alleles of SAS4 and SAS5 restored SIR4-dependent silencing at HMR, establishing that each is a regulator of silencing. Null alleles of SAS4 and SAS5 bypassed the role of the Abf1p binding site of the HMR-E silencer but not the role of the ACS or Rap1p binding site. Previous analysis indicated that SAS2 is homologous to a human gene that is a site of recurring translocations involved in acute myeloid leukemia. Similarly, SAS5 is a member of a gene family that included two human genes that are the sites of recurring translocations involved in acute myeloid leukemia.
Soma-to-Germline Interactions During Drosophila Oogenesis Are Influenced by Dose-Sensitive Interactions Between cut and the Genes cappuccino, ovarian tumor and agnostic
Authors: Jackson Stephen M , Berg Celeste A 
Published: April 2021

Abstract
The cut gene of Drosophila melanogaster encodes a homeodomain protein that regulates a soma-to-germline signaling pathway required for proper morphology of germline cells during oogenesis. cut is required solely in somatic follicle cells, and when cut function is disrupted, membranes separating adjacent nurse cells break down and the structural integrity of the actin cytoskeleton is compromised. To understand the mechanism by which cut expression influences germline cell morphology, we determined whether binucleate cells form by defective cytokinesis or by fusion of adjacent cells. Egg chambers produced by cut, cappuccino, and chickadee mutants contained binucleate cells in which ring canal remnants stained with antibodies against Hu-li tai shao and Kelch, two proteins that are added to ring canals after cytokinesis is complete. In addition, defects in egg chamber morphology were observed only in middle to late stages of oogenesis, suggesting that germline cell cytokineses were normal in these mutants. cut exhibited dose-sensitive genetic interactions with cappuccino but not with chickadee or other genes that regulate cytoskeletal function, including armadillo, spaghetti squash, quail, spire, Src64B, and Tec29A. Genomic regions containing genes that cooperate with cut were identified by performing a second-site noncomplementing screen using a collection of chromosomal deficiencies. Sixteen regions that interact with cut during oogenesis and eight regions that interact during the development of other tissues were identified. Genetic interactions between cut and the ovarian tumor gene were identified as a result of the screen. In addition, the gene agnostic was found to be required during oogenesis, and genetic interactions between cut and agnostic were revealed. These results demonstrate that a signaling pathway regulating the morphology of germline cells is sensitive to genetic doses of cut and the genes cappuccino, ovarian tumor, and agnostic. Since these genes regulate cytoskeletal function and cAMP metabolism, the cut-mediated pathway functionally links these elements to preserve the cytoarchitecture of the germline cells.
Bioinvasions of the Medfly Ceratitis capitata: Source Estimation Using DNA Sequences at Multiple Intron Loci
Authors: Davies Neil , Villablanca Francis X , Roderick George K 
Published: April 2021

AbstractThe Mediterranean fruit fly, Ceratitis capitata, is a devastating agricultural pest that threatens to become established in vulnerable areas such as California and Florida. Considerable controversy surrounds the status of Californian medfly infestations: Do they represent repeated introductions or the persistence of a resident population? Attempts to resolve this question using traditional population genetic markers and statistical methods are problematic because the most likely source populations in Latin America were themselves only recently colonized and are genetically very similar. Here, significant population structure among several New World medfly populations is demonstrated through the analysis of DNA sequence variation at four intron loci. Surprisingly, in these newly founded populations, estimates of population structure increase when measures of subdivision take into account the relatedness of alleles as well as their frequency. A nonequilibrium, likelihood-based statistical test that utilizes multilocus genotypes suggests that the sole medfly captured in California during 1996 was introduced from Latin America and was less likely to be a remnant of an ancestral Californian population. Many bioinvasions are hierarchical in nature, consisting of several sequential or overlapping invasion events, the totality of which can be termed a metainvasion. Phylogenetic data from multilocus DNA sequences will be vital to understanding the evolutionary and ecological processes that underlie metainvasions and to resolving their constituent levels.
Meiotic Drive of Chromosomal Knobs Reshaped the Maize Genome
Authors: Buckler Edward S , Phelps-Durr Tara L , Buckler Carlyn S Keith , Dawe R Kelly , Doebley John F , Holtsford Timothy P 
Published: April 2021

Abstract
Meiotic drive is the subversion of meiosis so that particular genes are preferentially transmitted to the progeny. Meiotic drive generally causes the preferential segregation of small regions of the genome; however, in maize we propose that meiotic drive is responsible for the evolution of large repetitive DNA arrays on all chromosomes. A maize meiotic drive locus found on an uncommon form of chromosome 10 [abnormal 10 (Ab10)] may be largely responsible for the evolution of heterochromatic chromosomal knobs, which can confer meiotic drive potential to every maize chromosome. Simulations were used to illustrate the dynamics of this meiotic drive model and suggest knobs might be deleterious in the absence of Ab10. Chromosomal knob data from maize's wild relatives (Zea mays ssp. parviglumis and mexicana) and phylogenetic comparisons demonstrated that the evolution of knob size, frequency, and chromosomal position agreed with the meiotic drive hypothesis. Knob chromosomal position was incompatible with the hypothesis that knob repetitive DNA is neutral or slightly deleterious to the genome. We also show that environmental factors and transposition may play a role in the evolution of knobs. Because knobs occur at multiple locations on all maize chromosomes, the combined effects of meiotic drive and genetic linkage may have reshaped genetic diversity throughout the maize genome in response to the presence of Ab10. Meiotic drive may be a major force of genome evolution, allowing revolutionary changes in genome structure and diversity over short evolutionary periods.
The Conversion Gradient at HIS4 of Saccharomyces cerevisiae. I. Heteroduplex Rejection and Restoration of Mendelian Segregation
Authors: Hillers Kenneth J , Stahl Franklin W 
Published: April 2021

Abstract
In Saccharomyces cerevisiae, some gene loci manifest gradients in the frequency of aberrant segregation in meiosis, with the high end of each gradient corresponding to a hotspot for DNA double-strand breaks (DSBs). The slope of a gradient is reduced when mismatch repair functions fail to act upon heteroduplex DNA—aberrant segregation frequencies at the low end of the gradient are higher in the absence of mismatch repair. Two models for the role of mismatch repair functions in the generation of meiotic “conversion gradients” have been proposed. The heteroduplex rejection model suggests that recognition of mismatches by mismatch repair enzymes limits hybrid DNA flanking the site of a DSB. The restoration-conversion model proposes that mismatch repair does not affect the length of hybrid DNA, but instead increasingly favors restoration of Mendelian segregation over full conversion with increasing distance from the DSB site. In our experiment designed to distinguish between these two models, data for one subset of well repairable mismatches in the HIS4 gene failed to show restoration-type repair but did indicate reduction in the length of hybrid DNA, supporting the heteroduplex rejection model. However, another subset of data manifested restoration-type repair, indicating a relationship between Holliday junction resolution and mismatch repair. We also present evidence for the infrequent formation of symmetric hybrid DNA during meiotic DSB repair.
Mutational Analysis of Yeast TFIIB: A Functional Relationship Between Ssu72 and Sub1/Tsp1 Defined by Allele-Specific Interactions With TFIIB
Authors: Wu Wei-Hua , Pinto Inés , Chen Bo-Shiun , Hampsey Michael 
Published: April 2021

Abstract
TFIIB is an essential component of the RNA polymerase II core transcriptional machinery. Previous studies have defined TFIIB domains required for interaction with other transcription factors and for basal transcription in vitro. In the study reported here we investigated the TFIIB structural requirements for transcription initiation in vivo. A library of sua7 mutations encoding altered forms of yeast TFIIB was generated by error-prone polymerase chain reaction and screened for conditional growth defects. Twenty-two single amino acid replacements in TFIIB were defined and characterized. These replacements are distributed throughout the protein and occur primarily at phylogenetically conserved positions. Most replacements have little or no effect on the steady-state protein levels, implying that each affects TFIIB function rather than synthesis or stability. In contrast to the initial sua7 mutants, all replacements, with one exception, have no effect on start site selection, indicating that specific TFIIB structural defects affect transcriptional accuracy. This collection of sua7 alleles, including the initial sua7 alleles, was used to investigate the allele specificity of interactions between ssu72 and sub1, both of which were initially identified as either suppressors (SUB1 2μ) or enhancers (sub1Δ, ssu72-1) of sua7 mutations. We show that the interactions of ssu72-1 and sub1Δ with sua7 are allele specific; that the allele specificities of ssu72 and sub1 overlap; and that each of the sua7 alleles that interacts with ssu72 and sub1 affects the accuracy of transcription start site selection. These results demonstrate functional interactions among TFIIB, Ssu72, and Sub1 and suggest that these interactions play a role in the mechanism of start site selection by RNA polymerase II.
Transposition of the Retrotransposon MAGGY in Heterologous Species of Filamentous Fungi
Authors: Nakayashiki Hitoshi , Kiyotomi Kanako , Tosa Yukio , Mayama Shigeyuki 
Published: April 2021

Abstract
MAGGY is a gypsy-like LTR retrotransposon isolated from the blast fungus Pyricularia grisea (teleomorph, Magnaporthe grisea). We examined transposition of MAGGY in three P. grisea isolates (wheat, finger millet, and crabgrass pathogen), which did not originally possess a MAGGY element, and in two heterologous species of filamentous fungi, Colletotrichum lagenarium and P. zingiberi. Genomic Southern analysis of MAGGY transformants suggested that transposition of MAGGY occurred in all filamentous fungi tested. In contrast, no transposition was observed in any transformants with a modified MAGGY containing a 513-bp deletion in the reverse transcriptase domain. When a MAGGY derivative carrying an artificial intron was introduced into the wheat isolate of P. grisea and C. lagenarium, loss of the intron was observed. These results showed that MAGGY can undergo autonomous RNA-mediated transposition in heterologous filamentous fungi. The frequency of transposition differed among fungal species. MAGGY transposed actively in the wheat isolate of P. grisea and P. zingiberi, but transposition in C. lagenarium appeared to be rare. This is the first report that demonstrates active transposition of a fungal transposable element in heterologous hosts. Possible usage of MAGGY as a genetic tagging tool in filamentous fungi is discussed.
Aspergillus nidulans Mutants Defective in stc Gene Cluster Regulation
Authors: Butchko Robert A E , Adams Thomas H , Keller Nancy P 
Published: April 2021

Abstract
The genes involved in the biosynthesis of sterigmatocystin (ST), a toxic secondary metabolite produced by Aspergillus nidulans and an aflatoxin (AF) precursor in other Aspergillus spp., are clustered on chromosome IV of A. nidulans. The sterigmatocystin gene cluster (stc gene cluster) is regulated by the pathway-specific transcription factor aflR. The function of aflR appears to be conserved between ST- and AF-producing aspergilli, as are most of the other genes in the cluster. We describe a novel screen for detecting mutants defective in stc gene cluster activity by use of a genetic block early in the ST biosynthetic pathway that results in the accumulation of the first stable intermediate, norsolorinic acid (NOR), an orange-colored compound visible with the unaided eye. We have mutagenized this NOR-accumulating strain and have isolated 176 Nor- mutants, 83 of which appear to be wild type in growth and development. Sixty of these 83 mutations are linked to the stc gene cluster and are likely defects in aflR or known stc biosynthetic genes. Of the 23 mutations not linked to the stc gene cluster, 3 prevent accumulation of NOR due to the loss of aflR expression.
Male Seminal Fluid Proteins Are Essential for Sperm Storage in Drosophila melanogaster
Authors: Tram Uyen , Wolfner Mariana F 
Published: April 2021

Abstract
The seminal fluid that is transferred along with sperm during mating acts in many ways to maximize a male’s reproductive success. Here, we use transgenic Drosophila melanogaster males deficient in the seminal fluid proteins derived from the accessory gland (Acps) to investigate the role of these proteins in the fate of sperm transferred to females during mating. Competitive PCR assays were used to show that while Acps contribute to the efficiency of sperm transfer, they are not essential for the transfer of sperm to the female. In contrast, we found that Acps are essential for storage of sperm by females. Direct counts of stored sperm showed that 10% of normal levels are stored by females whose mates transfer little or no Acps along with sperm.