bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutants affecting processing of DNA in macronuclear development in paramecium.
Authors: Rudman B , Preer L B , Polisky B , Preer J R 
Published: January 2021

Abstract
In Paramecium tetraurelia, stock 51, the A surface protein is coded by the wild type A51 gene, present in micronuclei in two copies and in macronuclei in about 1500 copies. DNA processing, comprised of DNA cleavage, copy number amplification and telomere addition occurs at autogamy and conjugation when old macronuclei degrade and new macronuclei are formed from micronuclei. In this paper we characterize mutants with macronuclear A gene deletions. These mutants are notable in three respects. First, the mutants do not appear to be simple micronuclear deletions. Although genetic analysis shows that the d12 mutant d12(-1300) is homozygous for the allele A-1300 and the mutant d12(+1) for A+1, analysis by the polymerase chain reaction indicates that the micronuclei in these two mutants contain intact, but presumably altered, micronuclear A genes. They undergo deletion during DNA processing when new macronuclei are formed. Second, the position of the deletions in these alleles has been shown to change. The deficiency present in the d12 allele A-1300 was originally determined to extend from position -1300 (relative to the start of translation of the A gene) to the end of the chromosome. Later, a derivative of this strain, homozygous for the d12 allele A+1 was isolated in which the start site of the deletion was found to have moved from -1300 to +1. Third, a surprising interaction occurs in crosses between a line homozygous for the d12 allele and one homozygous for the wild-type A51 allele. Previous work on the non-Mendelian d48 mutant (which has intact A51 genes in its micronucleus, but has truncated A51 genes in its macronucleus) has shown that intact A51 alleles must be present in the old macronucleus in order for A51 alleles to undergo proper processing. We find that d12 alleles act on A51 alleles in heterozygotes such that intact macronuclear A genes are no longer required for proper processing of A51. Thus, in crosses of 51 x d12 (either +1 or -1300) d12 exconjugants, as well as 51 exconjugants, give rise to clones carrying both intact A51 and truncated d12 alleles. Remarkably the d12 alleles, which are themselves deleted during processing, are capable in the heterozygote of fostering normal processing of the A51 allele.
Suppressors of the organ-specific differentiation gene pha-1 of Caenorhabditis elegans.
Authors: Schnabel H , Bauer G , Schnabel R 
Published: January 2021

Abstract
The embryonic lethal gene pha-1 of the nematode Caenorhabditis elegans is required for late differentiation and morphogenesis of the pharynx in the developing embryo. Revertants of two temperature-sensitive alleles of pha-1 were isolated with the aim of obtaining mutations in genes that interact with pha-1. By various methods of mutagenesis, chemical, X-ray, transposon, or by spontaneous reversion, 220 recessive revertants were obtained, defining three complementation groups. The largest, sup-35 on linkage group (LG) III, maps close to but is separable from pha-1. This suppressor can exert its effect either maternally or zygotically to allow survival of pha-1(ts) embryos. The other two, sup-36 and sup-37, are required zygotically and map on LGIV and LGV, respectively. We have not noted a phenotype distinguishing any of the suppressors from wild type except for suppression of pha-1. That suppression is the null phenotype of at least sup-35 is indicated by the high frequency of mutation and by the fact that heterozygotes carrying sup-35 and a deficiency spanning the locus are also able to suppress. Five spontaneous mutations in sup-35 were found to be associated with recombination.
Heteroduplex DNA formation is associated with replication and recombination in poxvirus-infected cells.
Authors: Fisher C , Parks R J , Lauzon M L , Evans D H 
Published: January 2021

Abstract
Poxviruses are large DNA viruses that replicate in the cytoplasm of infected cells and recombine at high frequencies. Calcium phosphate precipitates were used to cotransfect Shope fibroma virus-infected cells with different DNA substrates and the recombinant products assayed by genetic and biochemical methods. We have shown previously that bacteriophage lambda DNAs can be used as substrates in these experiments and recombinants assayed on Escherichia coli following DNA recovery and in vitro packaging. Using this assay it was observed that 2-3% of the phage recovered from crosses between point mutants retained heteroduplex at at least one of the mutant sites. The reliability of this genetic analysis was confirmed using DNA substrates that permitted the direct detection of heteroduplex molecules by denaturant gel electrophoresis and Southern blotting. It was further noted that heteroduplex formation coincided with the onset of both replication and recombination suggesting that poxviruses, like certain bacteriophage, make no clear biochemical distinction between these three processes. The fraction of heteroduplex molecules peaked about 12-hr postinfection then declined later in the infection. This decline was probably due to DNA replication rather than mismatch repair because, while high levels of induced DNA polymerase persisted beyond the time of maximal heteroduplex recovery, we were unable to detect any type of mismatch repair activity in cytoplasmic extracts. These results suggest that, although heteroduplex molecules are formed during the progress of poxviral infection, gene conversion through mismatch repair probably does not produce most of the recombinants. The significance of these observations are discussed considering some of the unique properties of poxviral biology.
Mutations in the bli-4 (I) locus of Caenorhabditis elegans disrupt both adult cuticle and early larval development.
Authors: Peters K , McDowall J , Rose A M 
Published: January 2021

Abstract
The bli-4 (I) gene of Caenorhabditis elegans had been previously defined by a single recessive mutation, e937, which disrupts the structure of adult-stage cuticle causing the formation of fluid-filled separations of the cuticle layers, or blisters. We report the identification of 11 new alleles of bli-4, all early larval lethals, including an allele induced by transposon mutagenesis. Nine of the lethal alleles failed to complement the blistered phenotype of e937; two alleles, s90 and h754, complement e937. The complementing alleles arrested development somewhat later than the noncomplementing alleles, which blocked just prior to hatching. We conclude that bli-4 is a complex locus with an essential function late in embryogenesis. We investigated the blistered phenotype of e937 through interactions with other mutations that alter worm morphology or cuticle structure. Recessive and dominant epistasis of several dumpy mutations over the blistered phenotype was observed. Using two heterochronic mutations that alter the developmental stage at which adult cuticle is expressed, we observed that adult worms that lack an adult-stage cuticle could not express blisters. However, late larval worms that expressed the adult cuticle did not express blisters either. It seems likely that the presence of the adult cuticle is necessary, but not sufficient, for blister expression. Blistering resulting from e937 is more severe in trans to null alleles, indicating that e937 is hypomorphic. We postulate that the adult-specific blistering is due to an altered or reduced function of bli-4 gene product in the adult cuticle.(ABSTRACT TRUNCATED AT 250 WORDS)
Segregation of recombinant chromatids following mitotic crossing over in yeast.
Authors: Chua P , Jinks-Robertson S 
Published: January 2021

Abstract
It has long been assumed that chromatid segregation following mitotic crossing over in yeast is random, with the recombinant chromatids segregating to opposite poles of the cell (x-segregation) or to the same pole of the cell (z-segregation) with equal frequency. X-segregation events can be readily identified because heterozygous markers distal to the point of the exchange are reduced to homozygosity. Z-segregation events yield daughter cells which are identical phenotypically to nonrecombinant cells and thus can only be identified by the altered linkage relationships of genetic markers on opposite sides of the exchange. We have systematically examined the segregation patterns of chromatids with a spontaneous mitotic exchange in the CEN5-CAN1 interval on chromosome V. We find that the number of x-segregation events is equal to the number of z-segregations, thus demonstrating that chromatid segregation is indeed random. In addition, we have found that at least 5% of the cells selected for a recombination event on chromosome V are trisomic for this chromosome, indicating a strong association between mitotic recombination and chromosome nondisjunction.
The homeotic gene Sex combs reduced of Drosophila melanogaster is differentially regulated in the embryonic and imaginal stages of development.
Authors: Pattatucci A M , Kaufman T C 
Published: January 2021

Abstract
The Sex combs reduced (Scr) locus is unique among the genes contained within the Antennapedia complex (ANT-C) of Drosophila melanogaster in that it directs functions that are required for both cephalic and thoracic development in the embryo and the adult. Antibodies raised against protein encoded by Scr were used to follow the distribution of this gene product in embryos and imaginal discs of third instar larvae. Analysis of Scr protein accumulation in embryos hemizygous for breakpoint lesions mapping throughout the locus has allowed us to determine that sequences required for establishment of the Scr embryonic pattern are contained within a region of DNA that overlaps with the identified upstream regulatory region of the segmentation gene fushi tarazu (ftz). Gain-of-function mutations in Scr result in the presence of ectopic sex comb teeth on the first tarsal segment of mesothoracic and metathoracic legs of adult males. Heterozygous combinations of gain-of-function alleles with a wild-type Scr gene exhibit no evidence of ectopic protein localization in the second and third thoracic segments of embryos. However, mesothoracic and metathoracic leg imaginal discs can be shown to accumulate ectopically expressed Scr protein, implying a differential regulation of the Scr gene during these two periods of development. Additionally, we have found that the spatial pattern of Scr gene expression in imaginal tissues involved in the development of the adult thorax is governed in part by synapsis of homologous chromosomes in this region of the ANT-C. However, those imaginal discs that arise anteriorly to the prothorax do not appear to be sensitive to this form of gene regulation. Finally, we have demonstrated that the extent of Scr expression is influenced by mutations at the Polycomb (Pc) locus but not by mutant alleles of the zeste (z) gene. Taken together, our data suggests that Scr gene expression is differentially regulated both temporally and spatially in a manner that is sensitive to the structure of the locus.
The maternally inherited regulation of P elements in Drosophila melanogaster can be elicited by two P copies at cytological site 1A on the X chromosome.
Authors: Ronsseray S , Lehmann M , Anxolabéhère D 
Published: January 2021

Abstract
Two P elements, inserted at the cytological site 1A on an X chromosome from an Drosophila melanogaster natural population (Lerik, USSR), were isolated by genetic methods to determine if they are sufficient to cause the P cytotype, the cellular condition that regulates the P family of transposable element. The resulting "Lerik P(1A)" line (abbreviated "Lk-P(1A)") carries only one P element in situ hybridization site but genomic Southern analysis indicates that this site contains two, probably full length, P copies separated by at least one EcoRI cleavage site. Because the Lk-P(1A) line shows some transposase activity, at least one of these two P elements is autonomous. The Lk-P(1A) line fully represses germline P element activity as judged by the GD sterility and snw hypermutability assays; this result shows that the P cytotype can be elicited by only two P element copies. However, the Lk-P(1A) line does not fully repress delta 2-3(99B) transposase activity in the soma, although it fully represses delta 2-3(99B) transposase activity in the germline (delta 2-3(99B) is an in vitro modified P element that produces a high level of transposase activity in both the germline and the soma). The germline regulatory properties of the Lk-P(1A) line are maternally transmitted, even when the delta 2-3(99B) element is used as the source of transposase. By contrast, the partial regulation of delta 2-3(99B) somatic activity is chromosomally inherited. These results suggest that the regulatory P elements of the Lk-P(1A) line are inserted near a germline-specific enhancer.
A source of small repeats in genomic DNA.
Authors: Fieldhouse D , Golding B 
Published: January 2021

Abstract
The processes of spontaneous mutation are known to be influenced by neighboring DNA. Imperfect nearby repeats in the neighboring DNA have been observed to mutate to form perfect repeats. The repeats may be either direct or inverted. Such a mutational process should create perfect direct and inverted repeats in intergenic DNA. A larger than expected number of direct repeats has generally been observed in a wide range of species in both coding and noncoding DNA. Simulations are carried out to determine how this process might influence the repetitive structure of genomic DNA. These simulations show that small repeats created by this kind of a mutational process can explain the excess number of repeats in intergenic DNA. The simulations suggest that this mechanism may be a common cause of mutations, including single-base changes. The influences of the distance between imperfect repeats and of their degree of similarity are investigated.
Site-directed mutagenesis of a Saccharomyces cerevisiae mitochondrial translation initiation codon.
Authors: Folley L S , Fox T D 
Published: January 2021

Abstract
We have used a generally applicable strategy for gene replacement in yeast mitochondria to mutate the translation initiation codon of the COX3 gene from AUG to AUA. The mutation, cox3-1, substantially reduced, but did not eliminate, translation of cytochrome c oxidase subunit III (coxIII). Strains bearing the mutation exhibited a leaky (partial) nonrespiratory growth phenotype and a reduced incorporation of radiolabeled amino acids into coxIII in vivo in the presence of cycloheximide. Hybridization experiments demonstrated that the mutation had little or no effect on levels of the COX3 mRNA. Residual translation of the cox3-1 mutant mRNA was dependent upon the three nuclearly coded mRNA-specific activators PET494, PET54 and PET122, known from previous studies to work through a site (or sites) upstream of the initiation codon to promote translation of the wild-type mRNA. Furthermore, respiratory growth of cox3-1 mutant strains was sensitive to decreased dosage of genes PET494 and PET122 in heterozygous mutant diploids, unlike the growth of strains carrying wild-type mtDNA. Some residual translation of the cox3-1 mRNA appeared to initiate at the mutant AUA codon, despite the fact that the 610-base 5'-mRNA leader contains numerous AUA triplets. We conclude that, while AUG is an important component of the COX3 translation initiation site, the site probably is also specified by other sequence or structural features.
SUM1-1: a suppressor of silencing defects in Saccharomyces cerevisiae.
Authors: Laurenson P , Rine J 
Published: January 2021

Abstract
The repression of transcription of the silent mating-type locus HMRa in the yeast Saccharomyces cerevisiae requires the four SIR proteins, histone H4 and a flanking site designated HMR-E. The SUM1-1 mutation alleviated the need for many of these components in transcriptional repression. In the absence of each of the SIR proteins, SUM1-1 restored repression in MAT alpha strains; thus, SUM1-1 appeared to bypass the need for the SIR genes in repression of HMRa. Repression was not specific to the genes normally present at HMR, since the TRP1 gene placed at HMR was repressed by SUM1-1 in a sir3 strain. Therefore, like the mechanisms of silencing normally used at HMR, silencing by SUM1-1 was gene-nonspecific. SUM1-1 suppressed point mutations in histone H4, but failed to suppress strongly a deletion mutation in histone H4. Similarly, SUM1-1 suppressed mutations in the three known elements of HMR-E, but was unable to suppress a deletion of HMR-E. These epistasis analyses implied that the functions required for repression at HMR can be ordered, with the SIR genes and silencer elements acting upstream of SUM1-1. SUM1-1 itself may function at the level of chromatin in the assembly of inactive DNA at the silent mating-type loci.
Ac transposition from a T-DNA can generate linked and unlinked clusters of insertions in the tomato genome.
Authors: Osborne B I , Corr C A , Prince J P , Hehl R , Tanksley S D , McCormick S , Baker B 
Published: January 2021

Abstract
We have investigated the distribution of transposed Acs in the tomato genome. Our approach has been to clone the regions flanking the T-DNAs and transposed Acs from two transgenic lines of tomato and place these sequences on the tomato restriction fragment length polymorphism (RFLP) map. The distribution of transposed Acs around the T-DNA and at locations unlinked to the T-DNA indicates that Ac transposes to linked and unlinked sites in tomato as it does in maize. The structure and terminal sequence of these cloned elements shows that Ac remains intact after transposition. We discuss these results and their bearing on gene tagging strategies using Ac and Ds.
Molecular basis for allelic polymorphism of the maize Globulin-1 gene.
Authors: Belanger F C , Kriz A L 
Published: January 2021

Abstract
An abundant protein in maize (Zea mays L.) embryos is a storage globulin encoded by the polymorphic Glb1 gene. Several Glb1 protein size alleles and a null allele have been described. Here we report the isolation and nucleotide sequence analysis of genomic clones corresponding to two Glb1 size alleles (Glb1-L and Glb1-S) and to the Glb1-0 null allele. The Glb1-L and Glb1-0 alleles differ from Glb1-S by the presence of small nucleotide insertions which are imperfect or perfect duplications, respectively, of adjacent sequences. In the case of Glb1-L, the insertion is in-frame and results in a protein larger than that encoded by Glb1-S, whereas in Glb1-0 the insertion causes a translational frameshift which introduces a premature termination codon. Although steady-state levels of Glb1-0 transcripts are extremely low in Glb1-0/0 embryos, nuclear transcription assays indicate that the Glb1-0 gene is transcribed at a level comparable to that of Glb1-L. This suggests that the low amounts of Glb1-0 transcripts in the cytoplasm may be due to mRNA instability.
Extrachromosomal recombination is deranged in the rec2 mutant of Ustilago maydis.
Authors: Fotheringham S , Holloman W K 
Published: January 2021

Abstract
Transformation of a leu1 auxotroph of Ustilago maydis to prototrophy with an autonomously replicating plasmid containing the selectable LEU1 gene was found to be efficient regardless of whether the transforming DNA was circular or linear. When pairs of autonomously replicating plasmids bearing noncomplementing leu1 alleles were used to cotransform strains deleted entirely for the genomic copy of the LEU1 gene, Leu+ transformants were observed to arise by extrachromosomal recombination. The frequency of recombination increased severalfold when one plasmid of the pair was made linear by cleavage at one end of the leu1 gene, but increased 10-100-fold when both plasmids were first made linear. The increase in recombination noted in wild-type and rec1 strains was not apparent in the rec2 mutant unless the members of the pair of plasmids were cut at opposite ends of the leu1 gene to yield linear molecules offset in only one of the two possible configurations. Use of a pair of plasmid substrates designed to measure nonreciprocal and multiple exchange events revealed only a minor fraction of the total events arise through these modes, and further that no stimulation occurred when the plasmid DNA was linear. It is unlikely that the defect in rec2 lies in a mismatch correction step since a high yield of Leu+ recombinants was obtained from the rec2 mutant when it was transformed with heteroduplex DNA constructed from plasmids with the two different leu1 alleles.
Structure and transcription of the singed locus of Drosophila melanogaster.
Authors: Paterson J , O'Hare K 
Published: January 2021

Abstract
Developmental and genetic studies of the singed gene of Drosophila melanogaster indicate that the gene has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. During metamorphosis a single 3.6-kilobase (kb) RNA is made, and this RNA is also present in adults and early embryos. Early embryos and adult females have additional 3.3- and 3.0-kb RNAs. The RNAs differ only in the length of the 3' untranslated region and a single gene product of 57 kilodaltons is predicted. Analysis of RNA from females lacking ovaries suggests that the 3.3- and 3.0-kb RNAs are made only in ovaries. The absence of the 3.3- and 3.0-kb RNAs in pupae and the time course of their appearance in adult females after eclosion suggests that transcription of singed in the ovary is from middle to late stages of oogenesis. Analysis of RNA in embryos from the reciprocal crosses between wild type and singed-3 showed that all three RNAs are maternally inherited with very little zygotic transcription in embryos. The mutation singed-3 appears to separate the two requirements for singed function as it has an extreme effect upon bristle development, but does not obviously affect oogenesis. In singed-3, there is a deletion at the 5' end of the gene, but the coding region is intact. Transcription in singed-3 is from a cryptic promoter in the upstream flanking sequences which is sufficiently active during oogenesis for fertility, but less active than the wild-type promoter during metamorphosis. The role of the single singed gene product may be in the asymmetric organization and/or movement of cytoplasmic components.
Lack of polymorphism on the Drosophila fourth chromosome resulting from selection.
Authors: Berry A J , Ajioka J W , Kreitman M 
Published: January 2021

Abstract
Evolutionary processes can be inferred from comparisons of intraspecific polymorphism and interspecific divergence. We sequenced a 1.1-kb fragment of the cubitus interruptus Dominant (ciD) locus located on the nonrecombining fourth chromosome for ten natural lines of Drosophila melanogaster and nine of Drosophila simulans. We found no polymorphism within D. melanogaster and a single polymorphism within D. simulans; divergence between the species was about 5%. Comparison with the alcohol dehydrogenase gene and its two flanking regions in D. melanogaster, for which comparable data are available, revealed a statistically significant departure from neutrality in all three tests. This lack of polymorphism in the ciD locus may reflect recent positive selective sweeps on the fourth chromosome with extreme hitchhiking generated by the lack of recombination. By simulation, we estimate there to be a 50% chance that the selective sweeps occurred within the past 30,000 years in D. melanogaster and 75,000 in D. simulans.