Showing papers in "Journal of Genetics in 1999"

Conserved nucleotide sequences in highly expressed genes in plants

Abstract: Genes that code for proteins expressed at high and low levels in plants were classified into separate data sets. The two data sets were analysed to identify the conserved nucleotide sequences that may characterize genes with contrasting levels of expression. The AUG context that characterized the highly expressed genes is (A/C)N2AAN3(A/T)T(A/C) AACAATGGCTNCC(T/A)CNA(C/T)(A/C). The data set of highly expressed genes shows overrepresentation of codons for alanine at the second position and serine at the third and fourth positions after the translation initiation codon. The characteristic transcription initiation site in the highly expressed genes is CAN(A/C)(A/C)(C/A)C(C/A)N2A(C/A). The promoter region is characterized by two tandemly repeated TATA elements, sometimes with one and rarely with two point mutations in the highly expressed genes. Besides the two tandemly repeated TATA elements, the promoter context in the highly expressed genes is overrepresented by C, C and G at the -3, -1 and+9 positions respectively. The characteristic TATA motif in the highly expressed plant genes is (T/C)(T/A)N2TCACTATATATAG. Most of these features are not present in the genes ubiquitously expressed at low levels in plants.

Inefficient mismatch repair: genetic defects and down regulation

Abstract: The mismatch repair system is involved in the maintenance of genomic integrity by editing DNA replication and recombination. However, although most mutations are neutral or deleterious, a mutator phenotype due to an inefficient mismatch repair may generate advantageous variants and may therefore be selected for. We review the evidence for inefficient mismatch repair due either to genetic defects in mismatch repair genes or to physiological conditions. Among natural isolates ofEscherichia coli andSalmonella enterica, about 1% are mutator bacteria, mostly deficient in mismatch repair (most of them defective in themutS gene). Characterization of mutators derived from laboratory strains led also to the isolation of mismatch repair mutants in which the most frequently found defects are inmutL andmutS. The correlation of the size of the antimutator genes with the frequency of their defective alleles amongE. coli andSalmonella strains reveals thatmutU mutants are underrepresented. Analysis of the progeny of a defined M13 phage heteroduplex DNA transfected intoE. coli cells shows that mismatch repair efficiency progressively decreases from the end of the exponential growth in K-12 and is variable among natural isolates. Implications of this defective mismatch repair activity for evolution and tumorigenesis will be discussed.

Genetic variation at twentythree microsatellite loci in sixteen human populations

Abstract: We have analysed genetic variation at 23 microsatellite loci in a global sample of 16 ethnically and geographically diverse human populations. On the basis of their ancestral heritage and geographic locations, the studied populations can be divided into five major groups, viz. African, Caucasian, Asian Mongoloid, American Indian and Pacific Islander. With respect to the distribution of alleles at the 23 loci, large variability exists among the examined populations. However, with the exception of the American Indians and the Pacific Islanders, populations within a continental group show a greater degree of similarity. Phylogenetic analyses based on allele frequencies at the examined loci show that the first split of the present-day human populations had occurred between the Africans and all of the non-African populations, lending support to an African origin of modern human populations. Gene diversity analyses show that the coefficient of gene diversity estimated from the 23 loci is, in general, larger for populations that have remained isolated and probably of smaller effective sizes, such as the American Indians and the Pacific Islanders. These analyses also demonstrate that the component of total gene diversity, which is attributed to variation between groups of populations, is significantly larger than that among populations within each group. The empirical data presented in this work and their analyses reaffirm that evolutionary histories and the extent of genetic variation among human populations can be studied using microsatellite loci.

Drosophila melanogaster chemosensory and muscle development: identification and properties of a novel allele of scalloped and of a new locus, SG18.1, in a Gal4 enhancer trap screen

Abstract: Our primary interest is to probe into the genetic and molecular mechanisms underlying the development of the chemosensory and neuromuscular systems inDrosophila melanogaster. We have generated and characterized 40 Gal4 enhancer trap lines with P-Gal4 insertion as an attempt to identify genes with a likely role in the development and differentiation of chemosensory and neuromuscular tissues, and at the same time to obtain Gal4 drivers that would facilitate targeted ectopic expression of genes in these tissues. Insertion strain SG18.1 has reporter gene activity in major olfactory components of the adult fly and in their presumptive areas in the imaginal discs. SG29.1 has an insertion in thescalloped gene and has been useful in understanding genetic interactions that pattern the wing and in defining the role ofscalloped in muscle development in flies.

Ecological strategies and fitness tradeoffs inEscherichia coli mutants adapted to prolonged starvation

Abstract: Many bacteria in nature are nutritionally deprived, and there has been heightened interest during the past decade in the properties of these bacteria. We subjected five populations ofEscherichia coli to prolonged starvation in a minimal salts medium, during which time the density of viable cells declined by several orders of magnitude. From each one, we isolated a surviving clone that showed some heritable difference in colony morphology. We then characterized these mutants in two ecologically relevant respects. First, we determined the nature of their selective advantage, if any, during prolonged starvation. (i) Three of the five mutants had significantly lower net death rate when progenitor and mutant clones were starved separately. (ii) Three mutants showed a significant reduction in death rate in mixed culture that was frequency dependent and manifest when the mutant clone was initially rare. This pattern suggests that these mutants fed on some byproduct of progenitor cells (living or dead). (iii) Two mutants caused the death rate of their progenitors to increase significantly relative to the rate measured in the absence of the mutant. This pattern suggests that these mutants had become allelopathic to their progenitors. Thus, three distinct ecological adaptations to prolonged starvation are evident. No advantage was detected for one mutant, whereas two mutants exhibited multiple advantages. Second, we asked whether the starvation-selected mutants were as fit in growth-supporting conditions as their progenitors. All five mutants were inferior to their progenitor during competition in fresh medium. Evidently, there is an evolutionary tradeoff between performance under growth and starvation conditions.

Analysis of variations in RAPD profiles among accessions ofProsopis

Abstract: The genetic variability among accessions ofProsopis was determined using randomly amplified polymorphic DNA (RAPD) profiles. Similarities of profiles were determined using the algorithm of Jaccard, and UPGMA and neighbour joining trees were generated from the similarity data. The average similarity was highest among the accessions ofP. glandulosa (0.52 ± 0.18) and least in the accessions ofP. juliflora (0.37 ± 0.15), indicating that the latter species has greater diversity among accessions. Our observations suggest that RAPD analysis could help in identifying genetic variations among different accessions ofProsopis.

Chromosome polymorphisms and natural selection inLeptysma argentina (Orthoptera): external phenotype affected by a centric fusion predicts adult survival

Abstract: The relationship between fitness variation associated with a quantitative trait and a Mendelian factor affecting that trait was examined in a natural population of the South American grasshopperLeptysma argentina. Previous studies have shown that a centric fusion between chromosomes 3 and 6 (fusion 3/6) increases adult survival and body size in this grasshopper. Here we examined the possible relationships among fusion 3/6, a size-related trait (prothorax height) and adult survival in a natural population. The study was based on two generations, comparing samples taken at the beginning and at the end of the adult life span. All individuals were karyotyped and scored for prothorax height (PH). A nonparametric regression analysis revealed that adult survival monotonically increased with PH in both generations. Moreover, fusion 3/6 was found to have an additive effect on this trait. Within generations, fusion frequency increased with adult survival in males (but not significantly so), as expected if phenotypic selection on PH influences the fusion polymorphism. Using regression analyses, we show that the correlation between PH and adult survival is not a purely environmental correlation genetically independent from the fusion polymorphism. A simple model is proposed for testing similar hypotheses in studies of selection on a trait influenced by a known genetic polymorphism.

Overexpression of the gene for Rpb7 subunit of yeast RNA polymerase II rescues the phenotypes associated with absence of the largest, nonessential subunit Rpb4

Abstract: The easily dissociable subcomplex of Rpb4 and Rpb7 subunits of yeast RNA polymerase II has been considered, for long, to play a role in stabilizing Pol II under stress. On the basis of previous genetic and biochemical observations, it was proposed that within the subcomplex one of the functions of Rpb4p is to stabilize the interaction between Rpb7p and the rest of Pol II. We took a direct approach to test the latter possibility by overexpression and mutagenesis ofRPB7 in absence of Rpb4p. We report here the results, which support the latter hypothesis. While it has been previously reported that absence of Rpb4p results in reduction in overall transcription by Pol II, our comparative analysis of RNAs fromRPB4 andrpb4δ cells suggests that there are indeed several genes differentially expressed between the two cells. We propose that the qualitative differences in overall transcription in presence and absence of Rpb4p imply a more active role for Rpb4p in transcription of at least a subset of genes.

Comparison of spontaneous and adaptive mutation spectra in yeast

Abstract: Adaptive mutations occur in nongrowing populations of cells to overcome strong, nonlethal selection conditions. Several models have been proposed for the molecular mechanism(s) for this phenomenon inEscherichia coli, but the mechanisms involved in adaptive mutagenesis in the yeastSaccharomyces cerevisiae are largely unknown. We present here a comparison of the mutational spectra of spontaneous and adaptive frameshift reversion events in yeast. In contrast to results fromE. coli, we find that the mutational spectrum of adaptive mutations inS. cerevisiae is not similar to that seen in mismatch repair defective cells, but rather resembles the spontaneous mutational events that occur during normal growth.

Hypermutation in stationary-phaseE. coli: tales from thelac operon

Abstract: Escherichia coli cells are capable of complex regulatory responses to environmental conditions and stresses. In some circumstances, the response includes an increase in the mutation rate, effectively mutagenizing the genome. The classic example is the SOS response to DNA damage. Recent work indicates that other environmental stresses can also result in mutation of the genome. Modulation of mutation rate may be a more prevalent stress response than previously thought. In this review we focus on genome-wide mutation inE. coli cells subjected to a nonlethal genetic selection for reversion of alac frameshift allele. Reversion of thelac frameshift allele occurs via a novel mechanism that requires homologous recombination functions, and is enhanced by transiently diminished postsynthesis mismatch repair. A model for recombination-dependent stationary-phase mutation will be presented and its relevance for genome-wide mutation discussed.

Allozymic variation in four Indian species of genus Mus :a comparative analysis

Abstract: The present study focusses on allozyme variation in the commensal house mouseMus musculus, the pygmy field miceM. booduga andM. terricolor, and the spiny mouseM. platythrix. Genetic heterozygosity was estimated using a set of 24 polymorphic biochemical genetic markers. The extent of variability present inM. booduga, M. terricolor andM. platythrix has been compared with that in theM. musculus complex. Levels of allozyme variation at species level indicate thatM. musculus has the maximum heterogeneity, followed byM. booduga andM. terricolor, whileM. platythrix shows comparatively homogeneous genetic make-up. Gene frequency data have been used to trace phylogenetic relationships among these four species.

Evolution of a recent neo-Y sex chromosome in a laboratory population of Drosophila

Abstract: In many species of animals, one of the sexes has a chromosome that is structurally and functionally different from its socalled homologue. Conventionally, it is called Y chromosome or W chromosome depending on whether it is present in males or females respectively. The corresponding homologous chromosomes are called X and Z chromosomes. The dimorphic sex chromosomes are believed to have originated from undifferentiated autosomes. In extant species it is difficult to envisage the changes that have occurred in the evolution of dimorphic sex chromosomes. In our laboratory, interracial hybridization between twoDrosophila chromosomal races has resulted in the evolution of a novel race, which we have called Cytorace 1. Here we record that in the genome of Cytorace 1 one of the autosomes of its parents is inherited in a manner similar to that of a classical Y chromosome. Thus this unique Cytorace 1 has the youngest neo-Y sex chromosome (5000 days old; about 300 generations) and it can serve as a ‘window’ for following the transition of an autosome to a Y sex chromosome.

About the special section

Abstract: This issue includes a set of eight papers on stationaryphase mutations in microorganisms. These invited papers were edited by Franklin W. Stahl, J. Gowrishankar, S. Mahadevan and Durgadas P. Kasbekar. Their editorial follows this note. This issue is special also because it honours P. Meera Khan, who was associated with this journal for many years, and served on its editorial board from 1992 until his untimely death last year. Meera, as he was known to his friends, made significant contributions to somatic cell genetics and cancer genetics. He will be remembered for the range and depth of his contributions to these and other areas. All of us who knew Meera remember his courtesy and the quiet dignity of his ways. To me he was a trusted friend for over 40 years. He leaves behind his wife Prabha, two sons and four grandchildren. The profile that appears in this issue was prepared by H. E A. Vasen, who was associated with Meera Khan for over 20 years in research in cancer genetics.

A novel mutation 5’ to the HMG box of theSRY gene in a case of Swyer syndrome

Abstract: We describe a novel mutation in the coding region of theSRY gene in a 46, XY female with Swyer syndrome. Analysis ofSRY was carried out by direct sequencing of a 780-bp PCR product that included theSRY open reading frame (ORF). This revealed the presence of a point mutation, ins 108A, in the coding region 5’ to the HMG box which results in a frame shift and premature termination of the encoded protein. No other mutation was found in theSRY ORF. We infer that sex reversal in this individual is a result of this insertion. In none of the 13 other 46, XY females that were studied was a mutation detected inSRY, confirming earlier findings that most cases of XY femaleness are due to causes other than mutation inSRY. These observations and those of others are discussed in relation to the aetiology of XY sex reversal.

Genetics of mosquitoes

Abstract: Beginning in the mid-1950s, much progress has been made in studying various aspects of the genetics of mosquitoes, particularly involving several species of three principal genera,Aedes, Culex andAnopheles, that transmit important human diseases. Here I discuss selected areas of research involving formal genetics; genome structure, organization and evolution at the interspecific and intraspecific level; and evolutionary genetics of theAedes scutellaris group. Information and insights gained from in-depth analyses of these areas, particularly transmission genetics, cytogenetics and genetics of chromosomal rearrangements, and of mutagen-induced sexual sterility, have proved invaluable for the development of the theory and evaluation of feasibility of genetic control of natural populations. As a result, mosquitoes represent some of the best studied taxa at various levels of genetic organization. Recent developments in molecular genetics offer exciting possibilities for extension of these concepts.

Adaptive mutation inEscherichia coli strain FC40

Abstract: Mutations can arise in static populations of cells that are subjected to nonlethal selective pressure, a phenomenon that has been called ‘adaptive mutation’. This phenomenon has been extensively studied in FC40, a strain ofEscherichia coli that cannot metabolize lactose (Lac−) but that reverts to lactose utilization (Lac+) when lactose is its sole energy and carbon source. The adaptive Lac+ mutations arise by two mutational processes: a recombination-dependent process that is highly active on the episome carrying the Lac− allele, and an unknown process that affects the whole genome. Most of the Lac+ mutations are due to the first process, which also produces nonselected mutations on the F′ episome. However, about 10% of the Lac+ mutations arise in a subpopulation of cells that experience a period of transient hypermutation. Although minor contributors to any one type of mutation, the hypermutators account for nearly all cases of multiple mutations. The evolutionary implications of these results are: (i) DNA synthesis associated with recombination may be an important source of spontaneous mutation, particularly in cells that are not actively growing; (ii) the efficient mutational mechanism that occurs on the episome could result in the horizontal transfer of new alleles among species that carry and exchange conjugal plasmids; and (iii) a subpopulation of transient hypermutators could be a source of multiple mutations that would allow for rapid adaptive evolution under adverse conditions.

Emergence of a mutagenic ochre suppressor mutation under lactose selection in appm mutant ofEscherichia coli harbouring the F′lacZU118 episome

Abstract: WhenEscherichia coli harbouring theppm (earlier calledadi) mutation and the F′lacZU118 episome is subjected to lactose selection in the presence of suboptimal concentrations of glycerol, Lac+ colonies emerge after 5–6 days. They are shown to harbour an ochre suppressor mutation at 15.15 min. Inactivation ofrecA results in approximately four-fold reduction in the response. In theppm — ochre suppressor double mutant background the leakiness of thelacZ allele carried by F′ CC105 is enhanced, suggesting misreading of a valine codon (GUG) as glutamic acid codon (GAG). This is accompanied by reversion of thelacZ mutation tolacZ + (GTG → GAG). In LB medium both the leakiness and reversion are inhibited by streptomycin. Inactivation ofrecA did not affect leakiness but abolished reversion. These data are discussed in relation to the importance of allele leakiness and restricted growth in stationary-phase (adaptive) mutagenesis.

Adaptive mutability in bacteria

Abstract: Reactive oxygen species (ROS) are a common source of damage to cellular DNA, and have been implicated in mutagenesis and carcinogenesis. In bacteria, their mutagenicity appears to be mediated in part by the mutagenic SOS system and in part by SOS-independent mechanisms. Since acrobically growing log-phase cells (which by definition are well adapted to their environment) would not be especially well served by the near-continuous induction of their potentially mutagenic SOS systems, it may be that several mechanisms are required to ensure that this does not become a major problem. In addition to some well-documented ROS-scavenging and antioxidant defence systems, it is suggested that ROS-mediated cleavage of the LexA repressor may only be able to activate transcription of the mutagenically important SOS genes (e.g. theumuDC genes) ofEscherichia coli if the cells concerned also contain substantial quantities of a transcription activator known as the cAMP/CRP complex. This may be why aerobically incubated stationary-phase bacteria (which ought to contain increased levels of cAMP/CRP as a consequence of their nutritionally deprived status) often turn out to be significantly more mutable than their log-phase counterparts. Thus when bacteria are being selected for some new characteristic under nutritional duress, it may be their spontaneous mutation-generation systems that are responding adaptively, not the mutations that they produce.

Requirement of flex (female lethal on X) in the development of the female germ line of Drosophila melanogaster

Abstract: Drosophila melanogaster females homozygous for flex, an X- linked recessive mutation, do not survive. Hemizygous males are unaffected. Homozygous embryos appear to lack SXL, the product of the Sex-lethal (Sxl) gene, apparently as a result of disruption of Sxl splicing. It is known that both Sxl and its somatic splicing regulators [snf and fl(2)d] also function in the development of the female germ line. For this reason, we investigated the role of flex in the germ line by generating flex/flex clones in flex/+ females. Females carrying such clones in their germ lines do not lay eggs whereas females carrying flex eggs lay viable eggs. Additionally, DAPI staining of ovarioles showed that diploid germ cells that are homozygous mutant for flex do not complete oogenesis. These results indicate that the flex(+) gene product may be required for the development of the female germ line.

Some puzzling observations on heat-induced transversion mutagenesis in bacteriophage T4

Abstract: A question of some interest in the early decades of genetics was whether the nondividing gene could mutate spontaneously. This question was sidelined when attention switched to the induction of mutations, first by ionizing irradiation, then by ultraviolet irradiation, and finally by chemical agents. The matter was revived by Schr6dinger's (1944) unfortunate attribution of an almost mystical stability to the gene. The first convincing experimental attack on the question was mounted by Lotte Auerbach (1959), who demonstrated that dry Neurospora crassa spores accumulate mutations during storage. The issue then fell silent again for several years until a moment in the middle 1960s when one of us (J. W. D.) decided to take a shortcut and perform some reversion experiments using stocks of bacteriophage T4 rll mutants that had been stored for a few years in the refrigerator. T4 stocks can be very stable, and quick-and-dirty experiments are quite feasible using stocks several years old. In this instance, however, J. W. D. noticed that revertant frequencies in some of the stocks had risen substantially. Subsequent work established several genetic and kinetic parameters of this mutation process. First, only G:C base pairs mutate spontaneously in extracellular T4 particles (Drake 1966). Second, both transitions and transversions occur (Drake and McGuire 1967). The transitions are produced by the deamination of the 5-hydroxymethylcytosine residues that comprise 'C' in T4 DNA (Baltz et al. 1976). The transversions arise by a spontaneous chemical event targeting G residues (Bingham et al. 1976) and seem to consist exclusively of G:C---* T:A (Kricker and Drake 1990). The premutagenic lesion generating transversions seems to mispair only infrequently (less than 10% per replication) (Ripley 1988, describing heat-mutagenesis experiments performed some years earlier at the University of Illinois, Urbana-Champaign). Oxygen-mediated mutagenesis can occur via the production of 8-oxoguanine, which can pair correctly with C or incorrectly with A to produce the transversion G:C--* T:A and which is subject to diverse repair processes and frequent

P. Meera Khan (1935–1998)

Abstract: Following a short hospitalization for liver cancer, Prof. Meera Khan, member of the editorial board of this journal, passed away on 1 April last year. He left behind his wife Prabha, two sons and four grandchildren. Prof. Meera Khan, known to his friends and colleagues as Meera, was born in Ambajipeta, Andhra Pradesh state, India, in 1935 and graduated from Andhra Medical College, Visakhapatnam, in 1959. During this period he had the