Gene order and genetic distance of 13 loci spanning murine chromosome 15.

Thirteen genetic loci spanning murine chromosome 15 from 15A2 (Mlvi-2) to 15F2-3 (Gdc-1) have been mapped. The genetic distance extends to 55.4 cM. Among 151 animals, only 1 animal with a double cross-over was found. The linear order is unambiguous, with the exception of the distal end on 15F1-3. Our analysis favors the order cen-Ela-1/Hox-3-Wnt-1-Gdc-1-ter. This ordering makes necessary the introduction of three tightly spaced double recombination events around and within the Hox-3 locus. Alternatively, Hox-3 may be most distal, and several double recombinations at the telomere lead to map expansion. Despite the unequal distribution along chromosome 15 of G-versus R-bands, a comparison of distances determined by physical and genetic mapping does not indicate an overt difference in distance between both mapping techniques.     

Genetic regulation of the cytochrome P-450 system in Drosophila melanogaster. I. Chromosomal determination of some cytochrome P-450-dependent reactions

The genetic regulation of some cytochrome P-450-dependent enzyme activities has been studied in adult Drosophila. Strains having genetically determined high or low enzyme activities were crossed with a marker strain and the metabolism was analyzed in microsomes from hybrids carrying different combinations of chromosomes from the strain under test. High p-nitroanisole (PNA) N-demethylation, biphenyl 3-hydroxylation and an increased amount of a protein with an apparent mol. wt. of 54 000, after SDS-gel electrophoresis of the microsomes in insecticide-resistant Drosophila strains, are inherited as dominant second chromosome traits. A low capacity for benzo[a]pyrene (BP) hydroxylation and 7-ethoxycoumarin O-deethylation in the Hikone R strain is semidominantly inherited in both cases and determined by gene(s) on the third chromosome. A semidominantly inherited high 4-hydroxylation of biphenyl and a high amount of a protein with an apparent mol. wt. of 56 000 in the Oregon R strain are also localized to the second chromosome. The results indicate that several other cytochrome P-450-dependent activities are not regulated by the genes mentioned above. In conclusion, at least three genes regulating the cytochrome P-450 system in Drosophila have been identified.     

Alkali burns of the rabbit cornea. I. A histochemical study of beta-glucuronidase, beta-galactosidase and N-acetyl-beta-D-glucosaminidase.

In alkali burned rabbit corneas activities of beta-glucuronidase, N-acetyl-beta-D-glucosaminidase and acid beta-galactosidase were studied histochemically in various time intervals after the traumatization. The technic with semipermeable membranes was employed. Within four days after the injury enzyme activities in the traumatized area were almost lacking. The corresponding activities in the unaffected part of the cornea were within the norm. On the 7th day enzyme activities were on an increase (but still subnormal) in the traumatized area. This area was surrounded by a zone of keratocytes with high levels of enzyme activities. This was particularly remarkable in keratocytes subjacent to the epithelium. The activation of all enzymes studied was present in the basal layer of the epithelium and in the endothelium as well. On the 14th day enzyme activities in the traumatized area were nearly restored and on the 32nd day they could not be distinguished from the normal cornea. Beta-galactosidase displayed a relatively maximal increase in the activity of all enzymes investigated.     

Genetic and physiological analysis of germination efficiency in maize in relation to nitrogen metabolism reveals the importance of cytosolic glutamine synthetase

We have developed an approach combining physiology and quantitative genetics to enhance our understanding of nitrogen (N) metabolism during kernel germination. The physiological study highlighted the central role of glutamine (Gln) synthetase (GS) and Gln synthesis during this developmental process because a concomitant increase of both the enzyme activity and the amino acid content was observed. This result suggests that Gln is acting either as a sink for ammonium released during both storage protein degradation and amino acid deamination or as a source for amino acid de novo synthesis by transamination. In the two parental lines used for the quantitative genetics approach, we found that the increase in Gln occurred earlier in Io compared with F(2), a result consistent with its faster germinating capacity. The genetic study was carried out on 140 F6 recombinant inbred lines derived from the cross between F(2) and Io. Quantitative trait locus mapping identified three quantitative trait loci (QTLs) related to germination trait (T50, time at which 50% of the kernels germinated) that explain 18.2% of the phenotypic variance; three QTLs related to a trait linked to germination performance, kernel size/weight (thousand kernels weight), that explain 17% of the phenotypic variance; two QTLs related to GS activity at early stages of germination that explain 17.7% of the phenotypic variance; and one QTL related to GS activity at late stages of germination that explains 7.3% of the phenotypic variance. Coincidences of QTL for germination efficiency and its components with genes encoding cytosolic GS (GS1) and the corresponding enzyme activity were detected, confirming the important role of the enzyme during the germination process. A triple colocalization on chromosome 4 between gln3 (a structural gene encoding GS1) and a QTL for GS activity and T50 was found; whereas on chromosome 5, a QTL for GS activity and thousand kernels weight colocalized with gln4, another structural gene encoding GS1. This observation suggests that for each gene, the corresponding enzyme activity is of major importance for germination efficiency either through the size of the grain or through its faster germinating capacity. Consistent with the possible nonoverlapping function of the two GS1 genes, we found that in the parental line Io, the expression of Gln3 was transiently enhanced during the first hours of germination, whereas that of gln4 was constitutive.     

Genetic regulation of the cytochrome P-450 system in Drosophila melanogaster. II. Localization of some genes regulating cytochrome P-450 activity

The localization of some genes determining the capacity for some cytochrome P-450 -dependent reactions have been studied in adult Drosophila. Strains with genetically determined high or low enzyme activities were crossed with strains carrying recessive visible markers on the chromosomes, and enzyme activities were measured in microsomes from recombinant F2 progeny. A dominantly inherited high p-nitroanisole (PNA) demethylation and biphenyl 3-hydroxylation in insecticide-resistant strains were both shown to be located around 65 cM on the second chromosome, regulated by one gene or closely linked genes. This localizes these activities to the same region as the gene responsible for the cross resistance to several classes of insecticides and a high metabolism of vinyl chloride in resistant strains. The occurrence of a regulatory gene mutation as a basis for the insecticide resistance is proposed. Hydroxylation of benzo[a]pyrene (BP) and deethylation of 7-ethoxy-coumarin seems to be determined by two third chromosome genes, at approx. 51 and 58 cM, respectively. The capacity for biphenyl 4-hydroxylation was shown to be determined by two genes on the second chromosome, one at or to the left of the gene black (48 cM) responsible for a low metabolism in strain Berlin K, and one at about 63 cM giving high formation of this metabolite in Oregon R. The latter could not be separated from the gene in insecticide-resistant strains at c:a 65 cM discussed above on the basis of the genetic localization, but observations supporting the occurrence of two closely linked genes regulating these different activities are available. In conclusion, 4-5 genes determining the capacity for several reactions, being a part of the genetic regulation of the cytochrome P-450 system in Drosophila melanogaster were indicated.     

Characterization of the Proteinases Present in Germinating Seeds of Scots Pine, Pinus sylvestris

Methods were developed to determine proteinase activity in germinating seeds of Scots pine. The assays were based on the liberation of TCA-soluble peptides from haemoglobin at pH 3.7 and from casein at pH 5.4 and pH 7.0; the reaction products were determined by the Lowry method. — Endosperms separated from seeds at the time of rapid storage protein mobilization (seedling length between 20 and 50 mm) showed high proteinase activities in all three assays. Experiments with different inhibitors suggested that at least four enzymes were involved. One of the enzymes resembled mammalian and microbial pepsin-like acid proteinases: the pH optimum was 3.7 and the enzyme was inhibited by pepstatin.—The proteinase activities in the endosperms were high enough to account for the mobilization of the reserve proteins during germination. Moreover the activities at pH 3.7.5.4. and 7.0 in the endosperms were 10-, 25-, and 50-fold the corresponding activities in the growing seedlings (a “reference” tissue). Consequently, it seems that both the acid and neutral proteinases take part in the mobilization of storage proteins in the germinating seed.     

Expression of galactose genes in mammalian cells. I. Galactose enzymes in Chinese hamster ovary cell hybrids

Galactokinase and galactose 1-phosphate uridyl transferase activities have been studied in several Chinese hamster ovary clonal lines following hybridization of two glycine-requiring mutants. Initially, the hybrids have about twice the parental activity of both enzymes. However, with time, there is a further increase beyond this activity, especially for the transferase enzyme, followed by a decline and a leveling off. The final average kinase activity in the hybrids is about 1.2 times the parental kinase, while the final average transferase is about 1.9 times the parental amount. The cultures lose about 10% of their chromosomes during the period under study; however, there is no obvious correlation between gross chromosome loss and enzyme activity. Protein calculated on a per chromosome basis (to correct for chromosome loss) behaves in a manner similar to the enzyme activities. One possible interpretation of the results is that, following hybridization, there is a derepression of some activities followed by repression during which time new levels of cellular parameters become established. This investigation was aided in part by U.S. Public Health Service Grant 1RO1 GM18481-01. Paper no. 476 from the Department of Biophysics and Genetics, University of Colorado, Denver, Colorado.     

Modulation of Gene Expression Made Easy

A new approach for modulating gene expression, based on randomization of promoter (spacer) sequences, was developed. The method was applied to chromosomal genes in Lactococcus lactis and shown to generate libraries of clones with broad ranges of expression levels of target genes. In one example, overexpression was achieved by introducing an additional gene copy into a phage attachment site on the chromosome. This resulted in a series of strains with phosphofructokinase activities from 1.4 to 11 times the wild-type activity level. In this example, the pfk gene was cloned upstream of a gusA gene encoding β-glucuronidase, resulting in an operon structure in which both genes are transcribed from a common promoter. We show that there is a linear correlation between the expressions of the two genes, which facilitates screening for mutants with suitable enzyme activities. In a second example, we show that the method can be applied to modulating the expression of native genes on the chromosome. We constructed a series of strains in which the expression of the las operon, containing the genes pfk, pyk, and ldh, was modulated by integrating a truncated copy of the pfk gene. Importantly, the modulation affected the activities of all three enzymes to the same extent, and enzyme activities ranging from 0.5 to 3.5 times the wild-type level were obtained.     

Positive Selection during Niche Adaptation Results in Large-Scale and Irreversible Rearrangement of Chromosomal Gene Order in Bacteria

Analysis of bacterial genomes shows that, whereas diverse species share many genes in common, their linear order on the chromosome is often not conserved. Whereas rearrangements in gene order could occur by genetic drift, an alternative hypothesis is rearrangement driven by positive selection during niche adaptation (SNAP). Here, we provide the first experimental support for the SNAP hypothesis. We evolved Salmonella to adapt to growth on malate as the sole carbon source and followed the evolutionary trajectories. The initial adaptation to growth in the new environment involved the duplication of 1.66 Mb, corresponding to one-third of the Salmonella chromosome. This duplication is selected to increase the copy number of a single gene, dctA, involved in the uptake of malate. Continuing selection led to the rapid loss or mutation of duplicate genes from either copy of the duplicated region. After 2000 generations, only 31% of the originally duplicated genes remained intact and the gene order within the Salmonella chromosome has been significantly and irreversibly altered. These results experientially validate predictions made by the SNAP hypothesis and show that SNAP can be a strong driving force for rearrangements in chromosomal gene order.     

Dosage Compensation in Drosophila: Nadp-Enzyme Activities and Cross-Reacting Material

The relationships between gene dosage, enzyme activities and CRM levels have been determined for G6PD and 6PGD. Enzyme activities and CRM levels were directly proportional and increased in genotypes carrying duplications of the respective structural genes. When a duplication consisting of the distal 45% of the X chromosome was used to duplicate Pgd+, 6PGD activity and CRM increased and G6PD activity decreased. When the proximal 55% of the X chromosome was duplicated, G6PD activity and CRM increased whereas 6PGD activity and CRM levels decreased. These observations support the model of dosage compensation of X-linked genes that invokes an autosomal activator in limited concentrations for which X-linked loci compete. The distal 45% of the X chromosome, when duplicated, caused a significant increase in NADP-malic enzyme activity and CRM levels, as if a structural gene for NADP-ME is sex-linked.     

The cell cycle-coupled expression of topoisomerase IIalpha during S phase is regulated by mRNA stability and is disrupted by heat shock or ionizing radiation.

Topoisomerase II is a multifunctional protein required during DNA replication, chromosome disjunction at mitosis, and other DNA-related activities by virtue of its ability to alter DNA supercoiling. The enzyme is encoded by two similar but nonidentical genes: the topoisomerase IIalpha and IIbeta genes. In HeLa cells synchronized by mitotic shake-off, topoisomeraseII alpha mRNA levels were found to vary as a function of cell cycle position, being 15-fold higher in late S phase (14 to 18 h postmitosis) than during G1 phase. Also detected was a corresponding increase in topoisomerase IIalpha protein synthesis at 14 to 18 h postmitosis which resulted in significantly higher accumulation of the protein during S and G2 phases. Topoisomerase IIalpha expression was not dependent on DNA synthesis during S phase, which could be inhibited without effect on the timing or level of mRNA expression. Mechanistically, topoisomerase IIalpha expression appears to be coupled to cell cycle position mainly through associated changes in mRNA stability. When cells are in S phase and mRNA levels are maximal, the half-life of topoisomerase IIalpha mRNA was determined to be approximately 30 min. A similar decrease in mRNA stability was also induced by two external factors known to delay cell cycle progression. Treatment of S-phase cells, at the time of maximum topoisomerase IIalpha mRNA stability, with either ionizing radiation (5 Gy) or heat shock (45 degrees C for 15 min) caused the accumulated topoisomerase IIalpha mRNA to decay. This finding suggests a potential relationship between stress-induced decreases in topoisomerase IIalpha expression and cell cycle progression delays in late S/G2.     

The development of ribonuclease and acid phosphatase during germination of Pisum arvense

1. Development of ribonuclease activity in the cotyledons of germinating peas is biphasic, the time of appearance of the two phases depending on the conditions of growth. 2. Acid phosphatase exhibits a single phase of development. 3. Cycloheximide inhibits development of ribonuclease activity in phase II but not in phase I. 4. (14)C-labelled amino acids are not incorporated into ribonuclease isolated during phase I. 5. The buoyant density of ribonuclease isolated during phase I is not affected by imbibition of the seed in 80% deuterium oxide. 6. Acid phosphatase was isolated from the supernatant fraction of the cotyledons of germinating peas and partially purified. 7. Development of acid phosphatase activity during germination is inhibited by treatment of the seed with cycloheximide or actinomycin D. 8. Partial purification of acid phosphatase from peas germinated in the presence of (14)C-labelled amino acids suggests that the enzyme is radioactively labelled. 9. Germination of peas in the presence of 80% deuterium oxide results in an increase in the buoyant density of acid phosphatase. 10. The results suggest that increase in ribonuclease activity during the first 4 days of germination does not result from synthesis of protein de novo, but that the corresponding increase in acid phosphatase activity does result from synthesis de novo.     

Comparative architectural aspects of regions of conserved synteny on human chromosome 11p15.3 and mouse chromosome 7 (including genes WEE1 and LMO1)

Human chromosome 11p15.3 is associated with chromosome aberrations in the Beckwith Wiedemann Syndrome and implicated in the pathogenesis of different tumor types including lung cancer and leukemias. To date, only single tumor-relevant genes with linkage to this region (e.g. LMO1) have been found suggesting that this region may harbor additional potential disease associated genes. Although this genomic area has been studied for years, the exact order of genes/chromosome markers between D11S572 and the WEE1 gene locus remained unclear. Using the FISH technique and PAC clones of the flanking markers we determined the order of the genomic markers. Based on these clones we established a PAC contig of the respective region. To analyse the chromosome area in detail the synteny of the orthologous region on distal mouse chromosome 7 was determined and a corresponding mouse clone contig established, proving the conserved order of the genes and markers in both species: "cen-WEE1-D11S2043-ZNF143-RANBP7-CEGF1- ST5-D11S932-LMO1-D11S572-TUB-tel", with inverted order of the murine genes with respect to the telomere/centromere orientation. The region covered by these contigs comprises roughly 1.6 MB in human as well as in mouse. The genomic sequence of the two subregions (around WEE1 and LMO1) in both species was determined using a shotgun sequencing strategy. Comparative sequence analysis techniques demonstrate that the content of repetitive elements seems to decline from centromere to telomere (52.6% to 34.5%) in human and in the corresponding murine region from telomere to centromere (41.87% to 27.82%). Genomic organisation of the regions around WEE1 and LMO1 was conserved, although the length of gene regions varied between the species in an unpredictable ratio. CpG islands were found conserved in putative promoter regions of the known genes but also in regions which so far have not been described as harboring expressed sequences.     

Mutations affecting gyrase in Haemophilus influenzae.

Mutants separately resistant to novobiocin, coumermycin, nalidixic acid, and oxolinic acid contained gyrase activity as measured in vitro that was resistant to the antibiotics, indicating that the mutations represented structural alterations of the enzyme. One Novr mutant contained an altered B subunit of the enzyme, as judged by the ability of a plasmid, pNov1, containing the mutation to complement a temperature-sensitive gyrase B mutation in Escherichia coli and to cause novobiocin resistance in that strain. Three other Novr mutations did not confer antibiotic resistance to the gyrase but appeared to increase the amount of active enzyme in the cell. One of these, novB1, could only act in cis, whereas a new mutation, novC, could act in trans. An RNA polymerase mutation partially substituted for the novB1 mutation, suggesting that novB1 may be a mutation in a promoter region for the B subunit gene. Growth responses of strains containing various combinations of mutations on plasmids or on the chromosome indicated that low-level resistance to novobiocin or coumermycin may have resulted from multiple copies of wild-type genes coding for the gyrase B subunit, whereas high-level resistance required a structural change in the gyrase B gene and was also dependent on alteration in a regulatory region. When there was mismatch at the novB locus, with the novB1 mutation either on a plasmid or the chromosome, and the corresponding wild-type gene present in trans, chromosome to plasmid recombination during transformation was much higher than when the genes matched, probably because plasmid to chromosome recombination, eliminating the plasmid, was inhibited by the mismatch.     

Mapping of genes expressed in Fusarium graminearum-infected heads of wheat cultivar 'Frontana'.

The isolation, physical, and genetic mapping of a group of wheat genes expressed in infected heads of Triticum aestivum 'Frontana' resistant to Fusarium head blight is reported. A cDNA library was built from heads of 'Frontana' through suppressive subtractive hybridization, to enrich for sequences induced by the pathogen Fusarium graminearum during infection. A group of 1794 clones was screened by dot blot hybridization for differential gene expression following infection. Twenty of these clones showed a strong difference in intensity of hybridization between infected and mock-inoculated wheat head samples, suggesting that they corresponded to genes induced during infection. The 20 clones were sequenced and used for mapping analysis. We determined a precise chromosomal location for 14 selected clones by using series of chromosome deletion stocks. It was shown that the 14 clones detected 90 fragments with the use of the restriction enzyme EcoRI; 52 bands were assigned to chromosome bins, whereas 38 fragments could not be assigned. The selected clones were also screened for polymorphisms on a 'Wuhan' x 'Maringa' wheat doubled haploid mapping population. One clone, Ta01_02b03, was related to a quantitative trait locus for type II resistance located on chromosome 2AL, as determined with simple sequence repeat markers on another mapping population, but did not map in the same location on our population. Another clone, Ta01_06f04, was identified by BLAST (basic local alignment search tool) search in public databases to code for a novel beta-1,3-glucanase, homologous to a major pathogenesis-related protein. This clone mapped to chromosomal regions on chromosome 3, including 3BL and 3DL, where B glucanase gene clusters are known to exist. Seven other clones, including 1 coding for an ethylene-response element binding protein and 3 for ribosomal proteins, and 4 clones corresponding to proteins with unknown function, were also mapped.     

Localization and Activity of a Carboxypeptidase in Germinating Seeds of Scots Pine, Pinus sylvestris

Extracts prepared from the endosperm of germinating seeds of Scots pine, Pinus sylvestris L., hydrolysed two typical carboxypeptidase substrates, Z-Phe-Ala and Z-Phe-Phe, with pH optima at 4.2 and 5.0. The activities were completely destroyed by diisopropylfluorophosphate. Identical heat inactivation curves and elution patterns in gel chromatography on Sephadex G-200 suggest that the two activities are due to a single enzyme. In resting seeds very low carboxypeptidase activity was present in both the endosperm and the embryo. During germination on agar gel at 20°C in the dark the activities, expressed as enzyme units per seed, increased in the seedling and particularly in the endosperm up to the stage when the reserves of the endosperm were completely depleted. The time of rapid increase of activity in the endosperm did not coincide with the onset of storage protein mobilization. On the contrary, the major part of the increase occurred after the bulk of endosperm nitrogen had already been transferred to the seedling. The results suggest that the carboxypeptidase does not play a major role in the mobilization of storage proteins in germinating pine seeds. On the other hand, it probably functions in the proteolytic reactions associated with the senescence of the reserve-depleted endosperm.