Isolation, characterization and chromosomal assignment of a partial cDNA for porcine 6-phosphogluconate dehydrogenase

Comparative Approach of the de novo Fatty Acid Synthesis (Lipogenesis) between Ruminant and Non Ruminant Mammalian Species: From Biochemical Level to the Main Regulatory Lipogenic Genes

Over the second half of 20^th century much research on lipogenesis has been conducted, especially focused on increasing the production efficiency and improving the quality of animal derived products. However, many diferences are observed in the physiology of lipogenesis between species. Recently, many studies have also elucidated the involvement of numerous genes in this procedure, highlighting diferences not only at physiology but also at the molecular level. The main scope of this review is to point out the major differences between ruminant and non ruminant species, that are observed in key regulatory genes involved in lipogenesis. Human is used as a central reference and according to the findinggs, main differences are analysed. These findings could serve not only as basis for understanding the main physiology of lipogenesis and further basic research, but also as a basis for any animal scientist to develop new concepts and methods for use in improving animal production and modern genetic improvement.

Enzymatic and mRNA Transcript Response of Ovine 6-Phosphogluconate Dehydrogenase (6PGD) in Respect to Different Milk Yield

Ovine 6-phosphogluconate dehydrogenase (6PGD) is an enzyme of the pentose phosphate pathway, providing the necessary compounds of NADPH for the synthesis of fatty acids. Much of research has been conducted both on enzymatic level and on molecular level. However, to our knowledge, any correlation between enzymatic activity and 6PGD gene expression pattern related to different physiological stages has not been yet reported. With this report, we tried to highlight if any correlation between enzymatic activity and expression of ovine 6PGD gene exists, in respect to different milk yield. According to the determined enzymatic activities and adipocytes characteristics, ewes with low milk production possessed a greater (P ≤ .001) 6PGD activity and larger adipocytes than the highly productive ewes. Although 6PGD expression pattern was higher in low milk yield ewes than in ewes with high milk production, this difference was not found statistically significant. Thus, 6PGD gene expression pattern was not followed by so rapid and great/sizeable changes as it was observed for its respective enzymatic activity, suggesting that other mechanisms such as post translation regulation may be involved in the regulation of the respective gene.

Enzymatic and mRNA transcript response of ovine 6-phosphogluconate dehydrogenase (6PGD) in respect to different weights from weaning to four months of age

Ovine 6-phosphogluconate dehydrogenase (6PGD), an enzyme of the pentose phosphate pathway, provides the necessary compounds of NADPH for the synthesis of fatty acids. Much of research has been conducted not only on the enzymatic level, but also on molecular level elucidating its cDNA sequence. Herein, we tried to elucidate if any correlation between enzymatic activity and expression of ovine 6PGD gene exists, in respect to two different weights from weaning to 4 months old. 18 male and 16 female lambs of Chios breed were randomly selected after weaning and assigned to two groups based on sex in a different experimental open-plan shed. Two subgroups were defined in each sex and they were slaughtered at 25 kg and 30 kg, respectively. Samples of adipose tissue (tail, perirenal and shoulder site) were collected and 6PGD enzymatic activity, gene expression, and characteristics of adipocytes were determined. According to the determined data, tail subcutaneous adipose tissue matures later than the others examined tissues and has a diminished lipogenic activity. A 6PGD gene expression pattern was not followed by analogous changes of its enzymatic activity, suggesting that other mechanisms such as post transcription or/and post translation regulation may be involved.

Selection at 6-PGD locus in laboratory populations of Bactrocera oleae

We have previously shown that laboratory populations of the olive fruitfly Bactrocera oleae come to equilibrium with allele frequencies at the 6-phosphogluconate dehydrogenase (6-PGD) locus markedly different from those of wild populations. In this study, we present new evidence from perturbation experiments in support of the notion that the locus is under selective pressure under laboratory conditions. Eleven populations were started with frequencies at the 6-PGD locus different from the laboratory equilibrium. Over 12 generations, the populations showed a return to the previous equilibrium, indicating a direct and powerful selection pressure on the naturally occurring allozymes of this locus. That is, a marked increase of the F allele followed by a compensatory decrease of allele I. Populations were set up to minimize the effects of associative overdominance, and we discuss the possible influence of this factor. Nucleotide sequence for the 6-PGD F and I alleles revealed two missense mutations at positions 501 and 730 leading to different amino acids among the two alleles.

The porcine PGD gene is preferentially lost from chromosome 6 in pig x rodent somatic cell hybrids

The 6-phosphogluconate dehydrogenase (PGD) and glucose phosphate isomerase (GPI) genes are both located on chromosome 6 in the pig (Sus scrofa domestica). Nonetheless, the PGD gene was absent in a total of 17 GPI-positive cell lines found in three independently derived panels of pig x rodent somatic cell hybrids. In most of these cell lines we found an apparently normal pig chromosome 6 at cytogenetic analysis. These results suggest instability of the porcine PGD gene region in interspecies hybrid cells.

Functional constraints of 6-phosphogluconate dehydrogenase (6-PGD) based on sequence and structural information

The pentose phosphate cycle is considered as a major source of NADPH and pentose needed for nucleic acid biosynthesis. 6-Phosphogluconate dehydrogenase (6PGD), an enzyme participating in this cycle, catalyzes the oxidative decarboxylation of 6PGD to ribulose 5-phosphate with the subsequent release of CO2 and the reduction of NADP. We have determined the amino acid sequence of 6PGD of Bactrocera oleae and constructed a three-dimensional model based on the homologous known sheep structure. In a comparative study of 6PGD sequences from numerous species, all the conserved and variable regions of the enzyme were analyzed and the regions of functional importance were localized, in an attempt promoted also by the direct involvement of the enzyme in various human diseases. Thus, analysis of amino acid variability of 37 6PGD sequences revealed that all regions important for the catalytic activity, such as those forming the substrate and coenzyme binding sites, are highly conserved in all species examined. Moreover, several amino acid residues responsible for substrate and coenzyme specificity were also found to be identical in all species examined. The higher percentage of protein divergence is observed at two regions that accumulate mutations, located at the distant parts of the two domains of the enzyme with respect to their interface. These peripheral regions of non-functional importance are highly variable and are predicted as antigenic, thus reflecting possible regions for antibody recognition. Furthermore, locating the differences between diptera 6PGD sequences on the three-dimensional model suggests probable positions of different amino acid residues appearing at B. oleae fast, intermediate, and slow allozymic variants.

Localization of the telomeric (TTAGGG)n sequences in chromosomes of some domestic animals by fluorescence in situ hybridization

Fluorescence in situ hybridization analysis was carried out on metaphase preparations of a variety of domestic animal species, viz. pigs, cattle, sheep, river buffaloes, swamp buffaloes, horses, and reindeers, using a PCR generated human telomere repeat probe (TTAGGG)n. Three protocols with different hybridization/washing stringencies were applied. Distinct double spots representing the telomeric sites were observed on either ends of the chromosomes in all the species studied, confirming that one-armed chromosomes are not completely telocentric. In pigs, an interstitial telomeric signal was observed on the 6q22 band of all the individuals examined. Although a random variation in the intensity of signals was observed, it was interesting to note that in one of the five cattle studied, very strong hybridization signals were seen on at least three pairs of chromosomes. In sheep, river buffaloes, and swamp buffaloes, where the biarmed chromosomes are considered to be the result of the fusion of 2-3 one-armed chromosomes of the cattle karyotype, no interstitial telomeric signals were observed.

First international workshop on porcine chromosome 6. Report and abstracts

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.

The PiGMaP consortium linkage map of the pig (Sus scrofa)

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (approximately 16.5 Morgans) than the genetic map of the homogametic sex (female) (approximately 21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be approximately 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.

Linkage maps of porcine chromosomes 3, 6, and 9 based on 31 polymorphic markers

Linkage maps of porcine Chromosomes (Chrs) 3, 6, and 9, based on 31 polymorphic markers, are reported. The markers include 14 microsatellites, 12 RFLPs, three protein polymorphisms, and two blood group loci. The genetic interpretations of 11 RFLPs are documented. The markers were scored in a three-generation Wild Boar/Large White pedigree, and genetic maps were constructed on the basis of two-point and multi-point linkage analysis. Altogether the maps span a genetic distance of 216 cM, and previous physical assignments indicate that the linkage groups cover major parts of the three chromosomes. Significant differences in recombination rates between the sexes were observed for all three chromosomes. The recombination rate on the q arm of Chr 6 was markedly low. Sixteen loci are informative with regard to comparative mapping, that is, they have previously been mapped in the human and/or mouse genomes.

Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism

BACKGROUND

The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction product, ribulose 5-phosphate, to ribose 5-phosphate. Crystallographic study of complexes with coenzyme and substrate explain the NADP dependence which determines the enzyme's metabolic role and support the proposed general base-general acid mechanism.

RESULTS

The refined structures of binary coenzyme/analogue complexes show that Arg33 is ordered by binding the 2'-phosphate, and provides one face of the adenine site. The nicotinamide, while less tightly bound, is more extended when reduced than when oxidized. All substrate binding residues are conserved; the 3-hydroxyl of 6-phosphogluconate is hydrogen bonded to N zeta of Lys183 and the 3-hydrogen points towards the oxidized nicotinamide. The 6-phosphate replaces a tightly bound sulphate in the apo-enzyme.

CONCLUSIONS

NADP specificity is achieved primarily by Arg33 which binds the 2'-phosphate but, in its absence, obscures the adenine pocket. The bound oxidized nicotinamide is syn; hydride transfer from bound substrate to the nicotinamide si- face is achieved with a small movement of the nicotinamide nucleotide. Lys183 may act as general base. A water bound to Gly130 in the coenzyme domain is the most likely acid required in decarboxylation. The dihydronicotinamide ring of NADPH competes for ligands with the 1-carboxyl of 6-phosphogluconate.

Localization of the IGHG, PRKACB, and TNP2 genes in pigs by in situ hybridization

The porcine genes encoding the immunoglobulin gamma heavy chain (IGHG), cAMP-dependent protein kinase catalytic beta subunit (PRKACB), and transition protein 2 (TNP2) were mapped to Chromosomes (Chrs) 7 q25-q26, 6q31-q33, and 3p13-cent, respectively, by in situ hybridization. Localization of the IGHG gene confirms the assignment of linkage group III to Chr 7. Our results show that the IGHG locus in pigs, similar to the situation in other mammalian species, viz. humans, mouse, cattle, and river buffaloes, is located on the terminal region of the chromosome. The assignment of the PRKACB gene extends the homology observed between porcine Chr 6q and human Chr 1p. Mapping of the TNP2 gene provides the first marker assigned to the p arm of Chr 3 in pigs. The present study contributes to the development of the physical gene map in pigs and also bears significance in terms of comparative gene mapping.

Isolation of cDNAs encoding 6-phosphogluconate dehydrogenase and glucose-6-phosphate dehydrogenase from the mediterranean fruit fly Ceratitis capitata: correlating genetic and physical maps of chromosome 5

We have isolated and determined the nucleotide sequences for cDNA clones encoding glucose-6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (6PGD) from the medfly Ceratitis capitata. The derived amino acid sequences for G6PD and 6PGD are presented and compared with G6PDs and 6PGDs from other species. The codon usage of the cDNA clones has little bias with the notable exceptions of arginine, glycine and leucine. The chromosomal location of the genes for 6PGD and G6PD were determined by in situ hybridization to salivary gland polytene chromosomes. This localization orients a genetic map of enzymatic loci and illustrates a remarkable similarity in the intra chromosomal order of homologous genes between Drosophila melanogaster and medfly.

Structure and expression of the Drosophila melanogaster gene encoding 6-phosphogluconate dehydrogenase

We have determined the nucleotide sequence and structure of Pgd+, the Drosophila melanogaster gene that encodes the enzyme, 6-phosphogluconate dehydrogenase (6PGD). The derived 481-amino acid sequence for D. melanogaster 6PGD is presented and compared with 6PGD sequences from other species. To characterize the cis-acting sequences necessary for expression of Pgd+, fragments containing this gene as well as Pgd+ promoter-lacZ fusions were introduced into the D. melanogaster germ line by P-element-mediated transformation. Our results indicate that the large second intron is critical for Pgd+ expression in adults. Only 421 bp of Pgd+ 5'-flanking DNA are necessary to direct expression in imaginal discs, gonads and gut of third-instar larvae. Sequences downstream from the transcription start point are necessary for expression in the larval fat body.

Analysis of the gluconate (gnt) operon of Bacillus subtilis

The gluconate (gnt) operon of Bacillus subtilis includes the gntR, gntK, gntP, and gntZ genes, respectively encoding the transcriptional repressor of the operon, gluconate kinase, the gluconate permease, and an unidentified open reading frame (Fujita and Fujita, 1987). We have compared the proteins encoded by the gnt operon of B.subtilis with published sequences and showed that (i) the gluconate repressor is homologous to several putative regulatory proteins in Escherichia coli, (ii) the gluconate kinase of B. subtilis is homologous to xylulose kinase, glycerol kinase and fucose kinase in E. coli (20-26% identity; 12-59 S.D.), (iii) the gluconate permease exhibits a C-terminal domain which is homologous to a hydrophobic protein encoded by an unidentified open reading frame (dsdAp) which precedes the dsdA gene of E. coli (39% identity; 19 S.D.), and (iv) the gntZ gene product is homologous to 6-phosphogluconate dehydrogenases of other bacteria and of animals (48-56%; 82-178 S.D.), thereby suggesting that the B. subtilis gntZ encodes 6-phosphogluconate dehydrogenase. Several conserved regions of the sequenced 6-phosphogluconate dehydrogenases can serve as signature patterns of this protein. Computer analyses have indicated that the previously reported sequences of the porcine and ovine 6-phosphogluconate dehydrogenases, as well as the hypothetical DsdAp protein, are probably erroneous. The probable reasons for the errors are reported along with the proposed revised sequences.