bluuebunny/crossref_metadata_2025 huggingface dataset:
A superfamily of Arabidopsis thaliana retrotransposons.
Authors: Konieczny A , Voytas D F , Cummings M P , Ausubel F M
Published: January 2021

We describe a superfamily of Arabidopsis thaliana retrotransposable elements that consists of at least ten related families designated Ta1-Ta10. The Ta1 family has been described previously. Two genomic clones representing the Ta2 and Ta3 elements were isolated from an A. thaliana (race Landsberg erecta) lambda library using sequences derived from the reverse transcriptase region of Ta1 as hybridization probes. Nucleotide sequence analysis showed that the Ta1, Ta2 and Ta3 families share greater than 75% amino acid identity in pairwise comparisons of their reverse transcriptase and RNase H genes. In addition to Ta1, Ta2 and Ta3, we identified seven other related retrotransposon families in Landsberg erecta, Ta4-Ta10, using degenerate primers and the polymerase chain reaction to amplify a highly conserved region of retrotransposon-encoded reverse transcriptase. One to two copies of elements Ta2-Ta10 are present in the genomes of the A. thaliana races Landsberg erecta and Columbia indicating that the superfamily comprises at least 0.1% of the A. thaliana genome. The nucleotide sequences of the reverse transcriptase regions of the ten element families place them in the category of copia-like retrotransposons and phylogenetic analysis of the amino acid sequences suggests that horizontal transfer may have played a role in their evolution.
Expression of overdominance for specific activity at the phosphoglucomutase-2 locus in the Pacific oyster, Crassostrea gigas.
Authors: Pogson G H
Published: January 2021

Environmental and genetic components of specific activity variation at the phosphoglucomutase-2 locus in the Pacific oyster, Crassostrea gigas, were examined to assess the direct role played by this polymorphism in a heterozygosity/growth relationship. Both environmental variables studied, season and intertidal position, exerted highly significant effects on phosphoglucomutase specific activity but no interactions occurred between these factors and Pgm-2 genotype. Highly significant differences were also detected between Pgm-2 genotypes. The three most common heterozygotes (Pgm-2(92/100), Pgm-2(96/100) and Pgm-2(100/104) consistently expressed greater specific activities than the Pgm-2(92/92), Pgm-2(96/96), Pgm-2(100/100) and Pgm-2(104/104) homozygotes. Overall, the specific activities of heterozygotes for the Pgm-2(100) allele exceeded heterozygotes by 24% and 20% in the mantle and adductor muscle tissues, respectively. Heterozygotes formed between the three less frequent Pgm-2(92), Pgm-2(96) and Pgm-2(104) alleles differed sharply from those possessing the Pgm-2(100) allele in being indistinguishable from homozygotes. The possibility of these patterns arising from the undetected presence of an inactive Pgm-2 allele was examined and found to be inconsistent with all of its predicted effects on the specific activity data. Genuine overdominance was shown to be capable of explaining the specific activities of ten structural locus genotypes, allelic frequency distributions in natural populations, and the maintenance of the enzyme polymorphism in a balanced state. The results provide evidence favoring the overdominance explanation for one locus involved in a heterozygosity/growth relationship and suggest that the reported effects of this locus on adult body weight may have been caused by the greater flux capacities of heterozygotes for the Pgm-2(100) allele.
Heteroduplex chain polarity in recombination of phage lambda by the red, RecBCD, RecBC(D-) and RecF pathways.
Authors: Siddiqi I , Stahl M M , Stahl F W
Published: January 2021

We have examined the chain polarity of heteroduplex DNA in unreplicated, bacteriophage lambda splice recombinants when recombination was by the RecBCD, RecBC(D-), or RecF pathway of Escherichia coli or the Red pathway of lambda. For each of these pathways, recombination is activated by the cutting of cos that accompanies chromosome packaging, and is effected by recombination enzymes acting at the right end created by that cutting. For exchanges occurring near cos, one parent makes a lesser physical and genetic contribution than does the other. For each pathway, when the phage carried standard cos, this minority contribution was predominantly on the r chain, ending 5' at the right end of lambda. When standard cos was replaced by a cloned inverted cos located centrally on the standard lambda genetic map, minority contribution was predominantly on the l chain. In each case, the polarity of the overlap was usually that formed by 3' overhangs of parental information and material. These results are discussed in the context of current models of recombination for the different pathways.
Genetic control of pheromones in Drosophila simulans. I. Ngbo, a locus on the second chromosome.
Authors: Ferveur J F
Published: January 2021

7-Tricosene and 7-pentacosene are predominant hydrocarbons on the cuticle of both sexes in Drosophila simulans. The pheromonal role of 7-tricosene has been clearly established for conspecific males, while a synergistic effect for 7-pentacosene has been postulated. Interstrain variation for the production of both compounds is very marked, but similar for both sexes. The genetic basis of this polymorphism was investigated. A major role was found for the second chromosome, which controls the 7-tricosene:7-pentacosene ratio. The main locus involved in controlling this variation, Ngbo, was mapped to position 65.3 on the second chromosome. The production of 7-pentacosene is directly related to the Ngbo genotype, which is additively expressed with two known alleles, Seychelles and Cameroon. These alleles act codominantly and are, respectively, hypomorphic and hypermorphic with regard to their effect on 7-pentacosene production. The production of 7-tricosene, which is partially inversely related to that of 7-pentacosene, is also affected by secondary interactions with the second chromosome and with the autosomal background.
Evolution of the transposable element mariner in Drosophila species.
Authors: Maruyama K , Hartl D L
Published: January 2021

The distribution of the transposable element mariner was examined in the genus Drosophila. Among the eight species comprising the melanogaster species subgroup, the element is present in D. mauritiana, D. simulans, D. sechellia, D. yakuba and D. teissieri, but it is absent in D. melanogaster, D. erecta and D. orena. Multiple copies of mariner were sequenced from each species in which the element occurs. The inferred phylogeny of the elements and the pattern of divergence were examined in order to evaluate whether horizontal transfer among species or stochastic loss could better account for the discontinuous distribution of the element among the species. The data suggest that the element was present in the ancestral species before the melanogaster subgroup diverged and was lost in the lineage leading to D. melanogaster and the lineage leading to D. erecta and D. orena. This inference is consistent with the finding that mariner also occurs in members of several other species subgroups within the overall melanogaster species group. Within the melanogaster species subgroup, the average divergence of mariner copies between species was lower than the coding region of the alcohol dehydrogenase (Adh) gene. However, the divergence of mariner elements within species was as great as that observed for Adh. We conclude that the relative sequence homogeneity of mariner elements within species is more likely a result of rapid amplification of a few ancestral elements than of concerted evolution. The mariner element may also have had unequal mutation rates in different lineages.
The genetic basis of a species-specific character in the Drosophila virilis species group.
Authors: Spicer G S
Published: January 2021

The genetic basis of the species-specific dorsal abdominal stripe of Drosophila novamexicana was examined. The dorsal stripe is present in D. novamexicana and absent in all other members of the Drosophila virilis species group. Interspecific crosses between D. novamexicana and genetically marked D. virilis revealed that all four of the autosomes (except the tiny dot chromosome, which was not marked) and the sex chromosomes (the X and Y chromosome effects could not be disentangled) showed a significant effect on the width of the dorsal stripe. All the autosomes act approximately additively; only minor interactions were detected among them. No significant maternal effects were found. This means that a minimum of five loci are involved in the character difference between the two species, and this is the maximum number that this technique could discern. These results suggest that, based on the number of factors involved in the character difference, the inheritance of this character should be considered polygenic, but because chromosome 2 (the largest chromosome in the species) contributed over half of the variance toward the character difference, it is best to consider the inheritance oligogenic based on effect. The implications of these findings are discussed in light of the importance of macromutation in speciation and the sex chromosome theory of speciation.
Isolation and characterization of the prune locus of Drosophila melanogaster.
Authors: Teng D H , Bender L B , Engele C M , Tsubota S , Venkatesh T
Published: January 2021

The complementary lethal interaction between the prune (pn) and Killer of prune loci of Drosophila melanogaster is an unusual and highly specific phenomenon. A lesion in pn results in a brownish-purple color of the compound eyes, while the conditional dominant Killer of prune mutation exhibits no phenotype by itself. However, a hemizygous or homozygous pn mutant carrying a copy of the Killer of prune gene dies during the late second to third instar stage of larval development. As a step toward understanding the molecular nature of this lethality and the role of pn in pigment biosynthesis, we have cloned the pn locus by using a transposon tag in the P element-induced allele, pn38. In addition, seven independent revertant lines were generated by the remobilization of transposons in pn38. The pn gene is located in a region that is transcriptionally active, and the isolated cDNAs that correspond to this area fall into three transcription units: I, II and III. Southern analysis shows that the restriction fragment length polymorphisms in five pn alleles are localized within a 1.2-kilobase genomic fragment, of which only transcription unit II is a part. The cDNA of this unit recognizes 1.65- and 1.8-kilobase messages in wild-type Drosophila adult head and body tissues that are absent or extremely reduced in pn mutants. Taken together, the results suggest that transcription unit II defines a part of the pn locus and its cDNA encodes a putative structural gene of pn.
Interaction of the yeast omnipotent suppressors SUP1(SUP45) and SUP2(SUP35) with non-mendelian factors.
Authors: Dagkesamanskaya A R , Ter-Avanesyan M D
Published: January 2021

The SUP1 and SUP2 genes code for protein factors intimately involved in the control of translational accuracy. The disrupted alleles of these genes confer a recessive lethal phenotype in both [psi+] and [psi-] genetic backgrounds, indicating an essential function for the corresponding proteins. In [psi+] diploids, heterozygous for the SUP1 null allele, several dominant phenotypes were evident with slow growth and inability to sporulate. These dominant phenotypes disappear after transformation with the multicopy plasmid carrying the wild-type allele of the SUP1 gene. Such dominant phenotypes were not observed for the SUP2 null allele. The incompatibility of multicopy plasmids carrying the SUP2 gene with guanidine hydrochloride-curable cytoplasmic factor(s) was also demonstrated. The possible mechanisms of interaction of the SUP1 and SUP2 genes with the [psi] determinant are discussed.
Molecular analysis of the Coprinus cinereus mating type A factor demonstrates an unexpectedly complex structure.
Authors: May G , Le Chevanton L , Pukkila P J
Published: January 2021

We report here the molecular cloning of the A43 mating type factor from Coprinus cinereus, a basidiomycetous fungus. Our molecular analyses revealed an unexpected source of variation in the A factor. Though genetic studies have demonstrated that A has two subunits, alpha and beta, we located three nonoverlapping fragments in the A43 region that have A factor function following DNA-mediated transformation. The three fragments demonstrate no similarity to one another as judged by restriction enzyme maps and by hybridization on Southern blots. We conclude that the A43 factor is composed of at least three subunits. When strains carrying different A factors are examined by hybridization to the cloned subunits, extensive polymorphism is seen. Both intensity of hybridization and restriction fragment lengths vary between strains. Some strains fail to show any hybridization to a probe. In contrast, other strains from widely separated geographic locations apparently share very similar subunits. From comparative restriction enzyme mapping of A43 and a mutated A43 factor, we inferred that a 12-kb deletion in the A factor was responsible for the constitutive, dominant phenotype of the mutated A factor. The results of transformation experiments support an activator model for the activity of the A factor in regulating the A pathway.
Three genes which affect founding of aggregations in Polysphondylium pallidum.
Authors: Francis D , Shaffer A , Smoyer K
Published: January 2021

PN6024 is an extraordinary mutant strain of the cellular slime mold Polysphondylium pallidum, characterized by having defects in many unlinked genes. New strains with altered development appeared spontaneously as aberrant clones of PN6024. Genetic crosses using the macrocyst sexual cycle were used to show that PN6030 (a clone like PN6024 in phenotype) carries mutations at two loci, emm and hge, whereas PN6031 (a clone of altered morphology) carries in addition a mutation at a third locus, mgt. hge and possibly mgt are linked to the mating type locus mat. The relatively high frequency of recombination between mat and hge is strong evidence that meiosis precedes macrocyst germination. The mutant genes themselves are of interest. A major effect of the emm-1 mutation is to remove the requirement for light to trigger aggregation. hge-1 greatly reduces the frequency of aggregation, whereas mgt-1 greatly increases it under standard conditions. None of these mutations interrupts later development leading to stalks and spore cells. It is hypothesized that all three genes act on steps immediately preceding the differentiation of the founder cells which initiate aggregation.
Sequence identity in an early chorion multigene family is the result of localized gene conversion.
Authors: Hibner B L , Burke W D , Eickbush T H
Published: January 2021

The multigene families that encode the chorion (eggshell) of the silk moth, Bombyx mori, are closely linked on one chromosome. We report here the isolation and characterization of two segments, totaling 102 kb of genomic DNA, containing the genes expressed during the early period of choriogenesis. Most of these early genes can be divided into two multigene families, ErA and ErB, organized into five divergently transcribed ErA/ErB gene pairs. Nucleotide sequence identity in the major coding regions of the ErA genes was 96%, while nucleotide sequence identity for the ErB major coding regions was only 63%. Selection pressure on the encoded proteins cannot explain this difference in the level of sequence conservation between the ErA and ErB gene families, since when only fourfold redundant codon positions are considered, the divergence within the ErA genes is 8%, while the divergence within the ErB genes (corrected for multiple substitutions at the same site) is 110%. The high sequence identity of the ErA major exons can be explained by sequence exchange events similar to gene conversion localized to the major exon of the ErA genes. These gene conversions are correlated with the presence of clustered copies of the nucleotide sequence GGXGGX, encoding paired glycine residues. This sequence has previously been correlated with gradients of gene conversion that extend throughout the coding and noncoding regions of the High-cysteine (Hc) chorion genes of B. mori. We suggest that the difference in the extent of the conversion tracts in these gene families reflects a tendency for these recombination events to become localized over time to the protein encoding regions of the major exons.
Three-locus linkage analysis using recombinant inbred strains and Bayes' theorem.
Authors: Neumann P E
Published: January 2021

Recombinant inbred (RI) strains are useful in linkage analysis and gene mapping. However, the generally small number of strains in an RI strain set limits the power of RI strains in linkage detection. Several methods for increasing the power of RI strains have been used, including summing data across RI strain sets and excluding linkage to genomic regions. In this paper, Bayesian analysis is applied to three-locus linkage data. This method further increases the power of RI strains to detect linkage and gives estimations of the probability of each of the three possible gene orders if the test locus is linked to the pair of marker loci. Several examples are presented, including reconsideration of the position of the proto-oncogene L-myc on the mouse linkage map.
Genetic analysis of a meiotic recombination hotspot on chromosome III of Saccharomyces cerevisiae.
Authors: Symington L S , Brown A , Oliver S G , Greenwell P , Petes T D
Published: January 2021

In a previous study, we analyzed meiotic recombination events that occurred in the 22-kb region (LEU2 to CEN3) of chromosome III of Saccharomyces cerevisiae. We found one region with an enhanced level of crossovers (a hotspot) and one region with a depressed level of crossovers. In this study, we show that about one-third of the crossovers that occur between LEU2 and CEN3 are initiated in a 1.3-kb region located approximately 6 kb from the centromere. Both crossovers and gene conversion events are initiated at this site. Events initiated at this position can be resolved as crossovers in regions located either centromere-distally or centromere-proximally from the initiation site.
Genetic variance for body size in a natural population of Drosophila buzzatii.
Authors: Ruiz A , Santos M , Barbadilla A , Quezada-Díaz J E , Hasson E , Fontdevila A
Published: January 2021

Previous work has shown thorax length to be under directional selection in the Drosophila buzzatii population of Carboneras. In order to predict the genetic consequences of natural selection, genetic variation for this trait was investigated in two ways. First, narrow sense heritability was estimated in the laboratory F2 generation of a sample of wild flies by means of the offspring-parent regression. A relatively high value, 0.59, was obtained. Because the phenotypic variance of wild flies was 7-9 times that of the flies raised in the laboratory, "natural" heritability may be estimated as one-seventh to one-ninth that value. Second, the contribution of the second and fourth chromosomes, which are polymorphic for paracentric inversions, to the genetic variance of thorax length was estimated in the field and in the laboratory. This was done with the assistance of a simple genetic model which shows that the variance among chromosome arrangements and the variance among karyotypes provide minimum estimates of the chromosome's contribution to the additive and genetic variances of the trait, respectively. In males raised under optimal conditions in the laboratory, the variance among second-chromosome karyotypes accounted for 11.43% of the total phenotypic variance and most of this variance was additive; by contrast, the contribution of the fourth chromosome was nonsignificant. The variance among second-chromosome karyotypes accounted for 1.56-1.78% of the total phenotypic variance in wild males and was nonsignificant in wild females. The variance among fourth chromosome karyotypes accounted for 0.14-3.48% of the total phenotypic variance in wild flies. At both chromosomes, the proportion of additive variance was higher in mating flies than in nonmating flies.
The effect of modifiers of position-effect variegation on the variegation of heterochromatic genes of Drosophila melanogaster.
Authors: Hearn M G , Hedrick A , Grigliatti T A , Wakimoto B T
Published: January 2021

Dominant modifiers of position-effect variegation of Drosophila melanogaster were tested for their effects on the variegation of genes normally located in heterochromatin. These modifiers were previously isolated as strong suppressors of the variegation of euchromatic genes and have been postulated to encode structural components of heterochromatin or other products that influence chromosome condensation. While eight of the modifiers had weak or no detectable effects, six acted as enhancers of light (lt) variegation. The two modifiers with the strongest effects on lt were shown to also enhance the variegation of neighboring heterochromatic genes. These results suggest that the wild-type gene products of some modifiers of position-effect variegation are required for proper expression of genes normally located within or near the heterochromatin of chromosome 2. We conclude that these heterochromatic genes have fundamentally different regulatory requirements compared to those typical of euchromatic genes.
A comprehensive study of genic variation in natural populations of Drosophila melanogaster. IV. Mitochondrial DNA variation and the role of history vs. selection in the genetic structure of geographic populations.
Authors: Hale L R , Singh R S
Published: January 2021

Preliminary studies with restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in natural populations of Drosophila melanogaster revealed considerable variation in terms of nucleotide sequence and overall size. In this report we present data from more isofemale lines and more restriction enzymes, and explore the utility of the data in inferring a colonization history of this species. Size variation in the noncoding A + T-rich region is particularly plentiful, with size variants occurring in all restriction site haplotypes in all populations. We report here classes of small-scale mobility polymorphisms (apparent range of 20 bp) in specific restriction fragments in the coding region. The variation in one such fragment appears to be generated even more rapidly than in the noncoding region. On the basis of the distribution of restriction site haplotypes, the species range can be divided into three major regions along longitudinal lines: Euro-African populations are the most diverse and are taken to be oldest; Far East populations have a complex distribution of haplotypes; Western Hemisphere populations are the least diverse and are interpreted to be the youngest. The history inferred from mtDNA alone is remarkably similar to one based on several nuclear markers. The mtDNA haplotype distribution is also very different from that of allozymes in these same populations. We interpret this as further evidence that natural selection is still the most parsimonious explanation for the parallel latitudinal allozyme clines in this species.
Perturbation-reperturbation test of selection vs. hitchhiking of the two major alleles of Esterase-5 in Drosophila pseudoobscura.
Authors: Arnason E
Published: January 2021

A perturbation-reperturbation tests selective neutrality of 100/100/100/100/100 and 106/100/100/100/100, the two most common alleles at the highly polymorphic X-linked locus Esterase-5 in Drosophila pseudoobscura. A total of 22 replicate populations are set up in cages, 11 start at a high frequency of 76% (U) and 11 at a low frequency of 21% (N) of the 106 allele. Allele frequencies change directionally and decrease in both U and N populations as groups and reach equilibria of 60 and 14%, respectively, after 200-300 days. These changes suggest natural selection. A hypothesis of balancing selection accounts for the pattern and predicts a dynamic equilibrium. A rival neutral hypothesis accounts for the pattern equally well by postulating hitchhiking and breakup of linkage leaving the Est-5 variants to drift at neutral equilibria. A reperturbation of allele frequencies in each population, creating 22 additional reperturbed populations EN and EU, with the original populations as controls, directly addresses the question of balancing selection or hitchhiking and breakup of linkage effects. Allele frequencies do not change directionally among the reperturbed populations as a group. The hypothesis of balancing selection is rejected in favor of the hypothesis of initial hitchhiking and dissipated linkage effects. The power of the experimental design to detect selection is studied by simulation. Within the limits of power set by the design, it is concluded that the 100 and 106 are iso-fitness alleles of Est-5 under the environmental conditions of the laboratory populations. The requirements of a method of perturbation and reperturbation are discussed.
Fine mapping of satellite DNA sequences along the Y chromosome of Drosophila melanogaster: relationships between satellite sequences and fertility factors.
Authors: Bonaccorsi S , Lohe A
Published: January 2021

The entirely heterochromatic Y chromosome of Drosophila melanogaster contains a series of simple sequence satellite DNAs which together account for about 80% of its length. Molecular cloning of the three simple sequence satellite DNAs of D. melanogaster (1.672, 1.686 and 1.705 g/ml) revealed that each satellite comprises several distinct repeat sequences. Together 11 related sequences were identified and 9 of them were shown to be located on the Y chromosome. In the present study we have finely mapped 8 of these sequences along the Y by in situ hybridization on mitotic chromosome preparations. The hybridization experiments were performed on a series of cytologically determined rearrangements involving the Y chromosome. The breakpoints of these rearrangements provided an array of landmarks along the Y which have been used to localize each sequence on the various heterochromatic blocks defined by Hoechst and N-banding techniques. The results of this analysis indicate a good correlation between the N-banded regions and 1.705 repeats and between the Hoechst-bright regions and the 1.672 repeats. However, the molecular basis for banding does not appear to depend exclusively on DNA content, since heterochromatic blocks showing identical banding patterns often contain different combinations of satellite repeats. The distribution of satellite repeats has also been analyzed with respect to the male fertility factors of the Y chromosome. Both loop-forming (kl-5, kl-3 and ks-1) and non-loop-forming (kl-2 and ks-2) fertility genes contain substantial amounts of satellite DNAs. Moreover, each fertility region is characterized by a specific combination of satellite sequences rather than by an homogeneous array of a single type of repeat.(ABSTRACT TRUNCATED AT 250 WORDS)
Evolutionary dynamics of mitochondrial DNA duplications in parthenogenetic geckos, Heteronotia binoei.
Authors: Moritz C
Published: January 2021

Mitochondrial DNA (mtDNA) from triploid parthenogenetic geckos of the Heteronotia binoei complex varies in size from 17.2 to 27.6 kilobases (kb). Comparisons of long vs. short genomes using restriction endonucleases revealed a series of tandem direct duplications ranging in size from 1.2 to 10.4 kb. This interpretation was supported by transfer-hybridization experiments which also demonstrated that coding sequences were involved. Some of the duplications have been modified by deletion and restriction site changes, but no other rearrangements were detected. Analysis of the phylogenetic and geographic distribution of length variation suggests that duplications have arisen repeatedly within the parthenogenetic form of H. binoei. The parthenogens, and thus the duplications, are of recent origin; modifications of the duplicated sequences, particularly by deletion, has therefore been rapid. The absence of duplications from the mtDNA of the diploid sexual populations of H. binoei reinforces the correlation between nuclear polyploidy and duplication of mtDNA sequences reported for other lizards. In comparison to the genomes of sexual H. binoei and of most other animals, the mtDNA of these parthenogenetic geckos is extraordinarily variable in length and organization.
Lewontin and Kojima meet Fisher: linkage in a symmetric model of sex determination.
Authors: Feldman M W , Christiansen F B , Otto S P
Published: January 2021

The effect of linkage and epistasis on the evolution of the sex-ratio is studied in a symmetric two-locus model of autosomal sex determination closely related to the symmetric viability model of R. C. Lewontin and K. Kojima. R. A. Fisher's expectation of an even sex ratio for autosomal sex determination by a single gene governs the dynamics when the loci are tightly linked. However, recombination may preclude optimization of the sex ratio just as occurs in viability selection models. Many of the evolutionary phenomena known for the symmetric viability model also occur here. In addition, we exhibit a series of new phenomena related to the presence of surfaces of even sex ratio.
The Drosophila Broad-Complex encodes a family of related proteins containing zinc fingers.
Authors: DiBello P R , Withers D A , Bayer C A , Fristrom J W , Guild G M
Published: January 2021

The Broad-Complex (BR-C) is essential for metamorphosis in Drosophila melanogaster. This locus is coextensive with the 2B5 ecdysone-responsive early puff and is necessary for puffing and transcription of many subsequently activated late genes in the developing salivary gland. Mapping of 31 cDNA clones indicates that approximately 100 kb of the genome is devoted to the synthesis of many BR-C RNAs. Sequence analyses of these cDNA clones show that the BR-C encodes a family of related proteins characterized by a common core amino-terminal domain fused to alternate carboxy domains each containing a pair of zinc fingers. Most proteins also contain domains rich in distinctive amino acids located between the common core and zinc finger regions. BR-C mutant alleles resulting from chromosomal rearrangements at 2B5 are associated with deletions of 5'-untranslated sequences, separation of the core coding domain from the downstream zinc finger domains, or a P element insertional disruption of a zinc finger coding sequence. We infer that the BR-C directly regulates late gene expression by specifying the synthesis of a family of proteins with DNA binding potential.
Geographic distribution and inheritance of three cytoplasmic incompatibility types in Drosophila simulans.
Authors: Montchamp-Moreau C , Ferveur J F , Jacques M
Published: January 2021

Wolbachia-like microorganisms have been implicated in unidirectional cytoplasmic incompatibility between strains of Drosophila simulans. Reduced egg eclosion occurs when females from uninfected strains (type W) are crossed with males from infected strains (type R). Here we characterize a third incompatibility type (type S) which is also correlated with the presence of Wolbachia-like microorganisms. Despite the fact that the symbionts cannot be morphologically distinguished, we observed complete bidirectional incompatibility between R and S strains. This indicates that the determinants of incompatibility are different in the two infected types. S/W incompatibility is unidirectional and similar to R/W incompatibility. A worldwide survey of D. simulans strains showed that type S incompatibility was found only in insular populations which harbor the mitochondrial type SiI. Both W and R types were found among mainland and island populations harboring the worldwide mitochondrial type SiII. Type S incompatibility could be involved in the reinforcement of the geographical isolation of SiI populations.
The lethal(1)TW-6cs mutation of Drosophila melanogaster is a dominant antimorphic allele of nod and is associated with a single base change in the putative ATP-binding domain.
Authors: Rasooly R S , New C M , Zhang P , Hawley R S , Baker B S
Published: January 2021

The l(1)TW-6cs mutation is a cold-sensitive recessive lethal mutation in Drosophila melanogaster, that affects both meiotic and mitotic chromosome segregation. We report the isolation of three revertants of this mutation. All three revert both the meiotic and mitotic effects as well as the cold sensitivity, demonstrating that all three phenotypes are due to a single lesion. We further show that these revertants fail to complement an amorphic allele of the nod (no distributive disjunction) locus, which encodes a kinesin-like protein. These experiments demonstrate that l(1)TW-6cs is an antimorphic allele of nod, and we rename it nodDTW. Sequencing of the nod locus on a nodDTW-bearing chromosome reveals a single base change in the putative ATP-binding region of the motor domain of nod. Recessive, loss-of-function mutations at the nod locus specifically disrupt the segregation of nonexchange chromosomes in female meiosis. We demonstrate that, at 23.5 degrees, the meiotic defects in nodDTW/+ females are similar to those observed in nod/nod females; that is, the segregation of nonexchange chromosomes is abnormal. However, in nodDTW/nodDTW females, or in nodDTW/+ females at 18 degrees, we observe a more severe meiotic defect that apparently affects the segregation of both exchange and nonexchange chromosomes. In addition, nodDTW homozygotes and hemizygous males have previously been shown to exhibit mitotic defects including somatic chromosome breakage and loss. We propose that the defective protein encoded by the nodDTW allele interferes with proper chromosome movement during both meiosis and mitosis, perhaps by binding irreversibly to microtubules.
Low nucleotide diversity in man.
Authors: Li W H , Sadler L A
Published: January 2021

The nucleotide diversity (pi) in humans is studied by using published cDNA and genomic sequences that have been carefully checked for sequencing accuracy. This measure of genetic variability is defined as the number of nucleotide differences per site between two randomly chosen sequences from a population. A total of more than 75,000 base pairs from 49 loci are compared. The DNA regions studied are the 5' and 3' untranslated regions and the amino acid coding regions. The coding regions are divided into nondegenerate sites (i.e., sites at which all possible changes are nonsynonymous), twofold degenerate sites (i.e., sites at each of which one of the three possible changes is synonymous) and fourfold degenerate sites (i.e., sites at which all three possible changes are synonymous). The pi values estimated are, respectively, 0.03 and 0.04% for the 5' and 3' UT regions, and 0.03, 0.06 and 0.11% for nondegenerate, twofold degenerate and fourfold degenerate sites. Since the highest pi value is only 0.11%, which is about one order of magnitude lower than those in Drosophila populations, the nucleotide diversity in humans is very low. The low diversity is probably due to a relatively small long-term effective population size rather than any severe bottleneck during human evolution.
Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.
Authors: Slatkin M , Hudson R R
Published: January 2021

We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population that has been growing in size exponentially for a long time. We show that, in a population of constant size, the sample distribution of pairwise differences will typically deviate substantially from the geometric distribution expected, because the history of coalescent events in a single sample of genes imposes a substantial correlation on pairwise differences. Consequently, a goodness-of-fit test of observed pairwise differences to the geometric distribution, which assumes that each pairwise comparison is independent, is not a valid test of the hypothesis that the genes were sampled from a panmictic population of constant size. In an exponentially growing population in which the product of the current population size and the growth rate is substantially larger than one, our analytical and simulation results show that most coalescent events occur relatively early and in a restricted range of times. Hence, the "gene tree" will be nearly a "star phylogeny" and the distribution of pairwise differences will be nearly a Poisson distribution. In that case, it is possible to estimate r, the population growth rate, if the mutation rate, mu, and current population size, N0, are assumed known. The estimate of r is the solution to ri/mu = ln(N0r) - gamma, where i is the average pairwise difference and gamma approximately 0.577 is Euler's constant.
Permanent rescue of a non-Mendelian mutation of Paramecium by microinjection of specific DNA sequences.
Authors: Jessop-Murray H , Martin L D , Gilley D , Preer J R , Polisky B
Published: January 2021

The mutant Paramecium tetraurelia cell line d48 is unable to express the serotype A protein on its surface. Although the A gene is intact in the micronuclei of d48, the A gene copies in the macronucleus contain a large deletion eliminating virtually the entire coding sequence. Previous studies showed that microinjection of a plasmid containing the entire A gene into the macronucleus of d48 permanently restored A expression after autogamy. Together with other data, this result suggests that in wild type cells the A gene in the old macronucleus ensures the presence of a cytoplasmic factor that prevents A gene deletions at autogamy. In d48, where there are few, if any copies of the intact A gene in the old macronucleus, deletions occur during macronuclear formation. To elucidate the specific molecular mechanisms involved in this unusual phenomenon, we attempted to define the region(s) of the A gene necessary for rescuing d48. We show that microinjection of a 4.5-kb internal A gene fragment is sufficient for proper processing at autogamy and leads to permanent rescue of d48; i.e., the rescued strain is indistinguishable from wild type. Thus, rescue of d48 does not require upstream transcriptional control sequences, intact A mRNA or A serotype protein. We also show that various fragments of the A gene have the ability to rescue d48 to different extents, some being more efficient than others. We find no evidence to suggest that the A gene gives rise to a small stable RNA that might act as or encode a cytoplasmic factor. Molecular mechanisms that may be involved in the rescue of d48 are discussed.
Genetic analysis of a major segment [LGV(left)] of the genome of Caenorhabditis elegans.
Authors: Johnsen R C , Baillie D L
Published: January 2021

From 10,900 F1 progeny of ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans nematodes, we isolated 194 lethal mutations on the left arm of LGV, a region balanced by the reciprocal translocation of eT1. The analysis of 166 of those mutations resulted in the identification of one deficiency and alleles of 78 genes including 38 new genes, thus increasing the number of identified essential genes to 101. We estimate that there are a minimum of 120 essential genes in this region, which comprises approximately 7% of the recombinational distance, although only about 4.2% of the genes, in C. elegans. We calculate that there are a minimum of 2850 essential genes in the genome. The left arm of LGV has two recombinational gene clusters separated by a high-recombination and/or essential gene-sparse region. One gene in this region, let-330, is the largest EMS target on the left arm of LGV, with twice as many alleles (16) as the next most EMS-mutable genes, let-332 and rol-3. Another gene in the sparse region, lin-40, and the region near lin-40 are major targets for Tc1 mobilization-induced mutagenesis. The analysis of essential genes in large regions should help to define C. elegans in terms of all its genes and aid in the understanding of the relationship of genome structure to genome function.
The genetic structure of natural populations of Drosophila melanogaster. XXII. Comparative study of DNA polymorphisms in northern and southern natural populations.
Authors: Takano T S , Kusakabe S , Mukai T
Published: January 2021

Restriction map variation in four gene regions (Adh, Amy, Pu and Gpdh) was surveyed for 86 second chromosomes from northern (Aomori) and southern (Ogasawara) Japanese populations of Drosophila melanogaster (43 chromosomes from each population). The regions examined cover a total of 62 kilobases. Estimates of nucleotide diversity (pi) were approximately constant across the gene regions and populations examined. The distribution of restriction site polymorphisms was compatible with the expectation from the neutral mutation-random genetic drift hypothesis, but insertion/deletion polymorphisms were not consistent with it. While the two populations shared a majority of restriction site polymorphisms, frequencies of individual restriction site variants were significantly different between the two populations at 7 out of 35 segregating sites. In addition, an insertion in the Amy region was found in 15 chromosomes from the Ogasawara sample but absent in the Aomori sample. A considerable difference was observed in the number of rare insertions and deletions between the two populations. The numbers of aberrations uniquely represented were 16 in the Ogasawara sample and only 3 in the Aomori sample. These findings suggest that the two populations were differentiated from each other to some degree by means of random genetic drift and/or other factors.
The male sterility-associated pcf gene and the normal atp9-1 gene in Petunia are located on different mitochondrial DNA molecules.
Authors: Folkerts O , Hanson M R
Published: January 2021

A mitochondrial DNA (mtDNA) region termed the S-pcf locus has previously been correlated with cytoplasmic male sterility (CMS) in Petunia. In order to understand the relationship of the S-pcf locus to homologous sequences found elsewhere in mtDNAs of both CMS and fertile lines, the structure of the mitochondrial genome of CMS Petunia line 3688 was determined by cosmid walking. The S-pcf locus, which includes the only copies of genes for NADH dehydrogenase subunit 3 (nad3) and small ribosomal subunit protein 12 (rps12) was found to be located on a circular map of 396 kb, while a second almost identical circular map of 407 kb carries the only copies of the genes for 18S and 5S rRNA (rrn18 and rrn5), the only copy of a conserved unidentified gene (orf25), and the only known functional copy of atp9. Three different copies of a recombination repeat were found in six genomic environments, predicting sub-genomic circles of 277, 266 and 130 kb. The ratio of atp9 to S-pcf mtDNA sequences was approximately 1.5 to 1, indicating that sub-genomic molecules carrying these genes differ in abundance. Comparison of the mtDNA organization of the CMS line with that of the master circle of fertile Petunia line 3704 reveals numerous changes in order and orientation of ten different sectors.
Doubling Ty1 element copy number in Saccharomyces cerevisiae: host genome stability and phenotypic effects.
Authors: Boeke J D , Eichinger D J , Natsoulis G
Published: January 2021

Haploid yeast strains bearing approximately double the normal number of Ty1 elements have been constructed using marked GAL/Ty1 fusion plasmids. The strains maintain their high transposon copy number and overall genome structure in the absence of selection. The strains bearing extra Ty1 copies are surprisingly similar phenotypically to the parental strain. The results suggest that the limit to transposon copy number, if any, has not been reached. When these strains are crossed by wild-type strains (i.e., bearing the normal complement of Ty1 elements) or by strains of opposite mating type also bearing excess Ty1 elements, normal to very slightly reduced spore viability is observed, indicating that increasing the extent of transposon homology scattered around the genome does not result in significant increases in frequency of ectopic reciprocal recombination. The results suggest that yeast cells have evolved mechanisms for coping with excess transposon copies in the genome.
Mutant lambda repressors with increased operator affinities reveal new, specific protein-DNA contacts.
Authors: Benson N , Adams C , Youderian P
Published: January 2021

The binding specificities of four mutant lambda cI repressor proteins with increased affinities for operator DNA were examined. Two mutant repressors (Glu34----Lys and Glu83----Lys) have the same specificity of binding as wild-type repressor, whereas two (Gly48----Ser and Gly48----Asn) have new binding specificities. The Gly48----Asn mutant repressor recognizes lambda operators with changes at base pair 3 with a different order of affinity than wild-type repressor, suggesting that the side chain of Asn48 makes additional specific DNA contacts at or near this base pair. When paired with a change that disrupts the specific interaction of the amino-terminal arm of lambda repressor with DNA (Lys4----Gln), one change that increases the affinity of repressor (Gly48----Ser) suppresses the binding defect of the Lys4----Gln repressor, resulting in a double mutant repressor with a new binding specificity different than that of both its parents and of wild type. These results lend strong support to the model of direct recognition of the lambda operator by lambda repressor proposed from the crystal structure of the repressor/operator complex.
The rec102 mutant of yeast is defective in meiotic recombination and chromosome synapsis.
Authors: Bhargava J , Engebrecht J , Roeder G S
Published: January 2021

A mutation at the REC102 locus was identified in a screen for yeast mutants that produce inviable spores. rec102 spore lethality is rescued by a spo13 mutation, which causes cells to bypass the meiosis I division. The rec102 mutation completely eliminates meiotically induced gene conversion and crossing over but has no effect on mitotic recombination frequencies. Cytological studies indicate that the rec102 mutant makes axial elements (precursors to the synaptonemal complex), but homologous chromosomes fail to synapse. In addition, meiotic chromosome segregation is significantly delayed in rec102 strains. Studies of double and triple mutants indicate that the REC102 protein acts before the RAD52 gene product in the meiotic recombination pathway. The REC102 gene was cloned based on complementation of the mutant defect and the gene was mapped to chromosome XII between CDC25 and STE11.
A spontaneous chromosomal amplification of the ADH2 gene in Saccharomyces cerevisiae.
Authors: Paquin C E , Dorsey M , Crable S , Sprinkel K , Sondej M , Williamson V M
Published: January 2021

A spontaneous antimycin A-resistant mutant carrying approximately four extra copies of ADH2 on chromosome XII was isolated from yeast strain 315-1D which lacks a functional copy of ADH1 and thus is antimycin A-sensitive. The additional copies of the normally glucose-repressed ADH2 are expressed during growth on glucose accounting for the antimycin A resistance. These extra copies are inserted into nonadjacent ribosomal DNA sequences (rDNA) near the recombination stimulating sequence HOT1. Each extra copy of the ADH2 gene (1548 bp) replaces most of the 37S transcript (approximately 7400 bp) in one of the approximately 200 copies of the rDNA present in the yeast genome. All four extra copies of ADH2 are lost at a rate of approximately 1 x 10(-5) deletions per cell per generation. One of the joints between the rDNA and ADH2 DNA is located 7 nucleotides downstream from 20 adenine residues in the normal copy of ADH2. This joint occurs at the end of a stretch of 16-29 thymidines in the rDNA which has been expanded to 57-59 thymidines. The other novel joint is located in a short region of sequence similarity between ADH2 and the rDNA. These observations suggest that amplification of ADH2 was a two step process: first the ADH2 gene was inserted into the rDNA, then multiple copies were generated by unequal crossing over or gene conversion within the rDNA.