Antisense suppression of the putative ribosomal protein S3A gene disrupts ovarian development in Drosophila melanogaster

The Drosophila melanogaster homologue of the Anopheles gambiae C3 cDNA has been isolated and characterized by sequence analysis. The encoded protein was localized by immunochemical and immunocytochemical methods. The Drosophila C3 protein is highly similar to homologues of disputed function, which have previously been identified in fungi, plants and animals. The protein is ubiquitous and localized in the cytoplasm. Cell fractionation followed by detection with a specific antibody preparation shows that the protein is associated with the 40S ribosomal subunit. The C3 gene is located in section 101F of chromosome 4. Antisense transgenic analysis shows that this gene is essential for oogenesis. The most prominent phenotype resulting from antisense depletion of C3 RNA is disappearance of the follicular cells of the ovary (where the concentration of C3 protein is normally high) and abnormalities of the associated germline derivatives, leading to failure of egg production.     

IAP insertion in the murine LamB3 gene results in junctional epidermolysis bullosa

The laminin-5 molecule functions in the attachment of various epithelia to basement membranes. Mutations in the laminin-5-coding genes have been associated with Herlitz junctional epidermolysis bullosa (HJEB), a severe and often lethal blistering disease of humans. Here we report the characterization of a spontaneous mouse mutant with an autosomal recessive blistering disease. These mice exhibit sub-epithelial blisters of the skin and mucosal surfaces and abnormal hemidesmosomes lacking sub-basal dense plates. By linkage analysis the genetic defect was localized to a 2-cM region on distal Chromosome (Chr) 1 where a laminin-5 subunit gene, LamB3, was previously localized. LamB3 mRNA and laminin-5 protein were undetectable by Northern blot analysis and immunohistochemical methods, respectively. DNA sequence analysis indicated that the LamB3 genetic defect resulted from disruption of the coding sequence by insertion of an intracisternal-A particle (IAP) at an exon/intron junction. These findings suggest a role for laminin-5 in hemidesmosome formation and indicate that the LamB3 ^IAP mutant is a useful mouse model for HJEB. Received: 27 March 1997 / Accepted: 14 May 1997     

Genetic mapping of the mouse Rab7 gene and pseudogene and of the human RAB7 homolog

Rab proteins are small GTP-ases localized to distinct membrane compartments in eukaryotic cells and regulating specific steps of intracellular vesicular membrane traffic. The Rab7 protein is localized to the late endosomal compartment and controls late steps of endocytosis. We have isolated, by library screening, the 5′ region, including the promoter, of the mouse Rab7 gene and a Rab7 pseudogene. We have mapped, by genetic linkage analysis, the mouse Rab7 gene on Chromosome (Chr) 6 and the Rab7-ps1 pseudogene on Chr 9, where the Rab7 gene has been previously reported to map. By radiation hybrid mapping, we have located the human RAB7 gene on Chr 3, in a region homologous to the mouse Chr 6, where the Rab7 gene maps. Received: 27 October 1997 / Accepted: 1 January 1998     

Human and murine PTX1/Ptx1 gene maps to the region for Treacher Collins Syndrome

Ptx1 belongs to an expanding family of bicoid-related vertebrate homeobox genes. These genes, like their Drosophila homolog, seem to play a role in the development of anterior structures and, in particular, the brain and facies. We report the chromosomal localization of mouse Ptx1, and the cloning, sequencing, and chromosomal localization of the human homolog PTX1. The putative encoded proteins share 100% homology in the homeodomain and are 88% and 97% conserved in the N- and C-termini respectively. Intron/exon boundaries are also conserved. Murine Ptx1 was localized, by interspecific backcrossing, to Chr 13 within 2.6 cM of Caml. The gene resides centrally on Chromosome (Chr) 13 in a region syntenic with human Chr 5q. Subsequent analysis by fluorescent in situ hybridization places the human gene, PTX1, on 5q31, a region associated with Treacher Collins Franceschetti Syndrome. Taken together with the craniofacial expression pattern of Ptx1 during early development, the localization of the gene in this chromosomal area is consistent with an involvement in Treacher Collins Franceschetti Syndrome. Received: 3 May 1997 / Accepted: 1 July 1997     

Angiotensin-converting enzyme (ACE) gene polymorphisms in patients characterised by coronary angiography

The angiotensin converting enzyme (ACE) gene is implicated as a risk factor for coronary artery disease and myocardial infarction (MI). An insertion/deletion (I/D) polymorphism is believed to be in linkage disequilibrium with a functional site elsewhere. Ten polymorphisms have recently been identified in the ACE gene. We screened patients undergoing coronary angiography (n = 258) for six of these polymorphisms (T-5491C, T-93C, A-240T, T1237C, D/I and 4656(CT)_2/3), and identified a further two rare polymorphisms. ACE levels were associated with genotype for all polymorphisms analysed individually by one way ANOVA (P < 0.0005). The polymorphisms occurring in the 5′ region were in negative linkage disequilibrium with the exonic and 3′ region polymorphisms. The A-240T polymorphism had the greatest association with ACE levels (R² = 14%); none of the others were significantly associated with levels when adjustment was made for A-240T. None of the polymorphisms were associated with the extent of coronary atheroma. Two of the promoter polymorphisms (A-240T and T-93C) were weakly related to the occurrence of MI (P = 0.03 and P = 0.05, respectively, by χ² analysis). The TT genotype of A-240T appeared to be protective against MI with an odds ratio of 0.31 (95% confidence interval, 0.12, 0.83). These findings indicate that polymorphisms in the ACE gene promoter region may have a stronger association with disease than the I/D polymorphism. Received: 16 February 1997 / Accepted: 13 May 1997     

Comparative mapping of human Chromosome 2 identifies segments of conserved synteny near the bovine mh locus

The ``double-muscling' (mh) locus has been localized to an interval between the centromere and the microsatellite marker TGLA44 on bovine Chromosome (Chr) 2 (BTA2). We identified segments of conserved synteny that correspond to this region of BTA2 by assigning large genomic clones containing bovine homologs of seven genes from the long arm of human Chr 2 (HSA2q). Polymorphic markers developed from these clones integrated the physical and linkage maps of BTA2 from 2q12 to 2q44 and extended genetic coverage towards the centromere. This comparative analysis suggests the mh locus resides on HSA2q near both the protein C and collagen type III alpha-1 genes. Overall, our data reveal a complex rearrangement of gene order between BTA2q12-44 and HSA2q14-37 that underscores the need to establish boundaries of conserved synteny when applying comparative mapping information to identify genes or traits of interest. Received: 3 March 1997 / Accepted: 12 May 1997     

The Drosophila melanogaster homologue of the hsp60 gene is encoded by the essential locus l(1)10Ac and is differentially expressed during fly development

 The hsp60 (heat-shock protein 60) gene family of molecular chaperones has been a subject of study in numerous systems due to its important role in the correct folding of non-native proteins in development as well as after heat-shock treatment. Here we present the characterization of the first Drosophila hsp60 homologue. Drosophila HSP60 is most closely related (72% identity across the entire protein sequence) to the mouse mitochondrial HSP60. Western blot experiments indicate that Drosophila HSP60 is enriched in the mitochondrial fraction. The distribution of HSP60 protein is dynamic during fly embryogenesis, suggesting that various cell types might have different HSP60 requirements. The molecular analysis of a P-element-induced mutation that affects the l(1)10Ac locus shows that the transposon is inserted in a 3-kb intron present in the hsp60 gene. By genetic rescue experiments we prove that Drosophila HSP60 is encoded by the essential locus l(1)10Ac opening the possibility for detailed genetic analysis of HSP60 functions in the fly. Received: 24 March 1997 / Accepted: 16 June 1997     

Characterization, chromosomal localization, and genetic variation of the porcine heart fatty acid-binding protein gene

The purpose of this study was to detect genetic variation in the porcine H-FABP gene, a candidate gene for meat quality traits in pigs. Lambda phages containing the porcine H-FABP gene were isolated by plaque hybridization with human H-FABP cDNA. The coding and flanking intronic sequences of the porcine H-FABP gene were determined as well as 1.6 kb of the 5′ upstream region. The various potential regulatory sequences in this region are in accordance with the function and expression of the protein in muscle and mammary tissue. Furthermore, comparison with the homolog region of the mouse identified a highly conserved 13-bp element (CTTCCT [A/C] TTTCGG) that may be involved in regulation of expression. The porcine H-FABP gene was localized on Chromosome (Chr) 6 by porcine sequence-specific PCR on DNA from a pig/rodent cell hybrid panel. In addition, part of the H-FABP gene was screened for genetic variation by PCR-RFLP analysis. Three PCR-RFLPs were detected, one in the upstream region (HinfI) and two in the second intron (HaeIII and MspI). In most pig breeds the corresponding alleles have a variable distribution, possibly a consequence of selective breeding. This genetic variation will enable us to investigate the role of the H-FABP locus in porcine production and meat quality traits. Received: 22 August 1996 / Accepted: 3 January 1997     

Immunochemically distinct NADP-linked isocitrate dehydrogenase isozymes in mitochondria and peroxisomes of Candida tropicalis

Although peroxisomal localization of NADP-linked isocitrate dehydrogenase (Idp) was first demonstrated in Candida tropicalis, the mitochondrial isozyme has not been found in this yeast. Here we report that the presence of mitochondrial Idp in the yeast was demonstrated by screening for its gene with a DNA probe containing conserved sequences of Idps from various organisms. The nucleotide sequence of the gene (CtIDP1) revealed a 1,290-bp open reading frame corresponding to a 430-amino-acid protein with a high similarity to previously reported Idps. Overexpression of CtIDP1 in Saccharomyces cerevisiae gave a high intracellular Idp activity, and the purified recombinant Idp was shown to be a homodimer with a subunit molecular mass of approximately 44 kDa, different from that of peroxisomal Idp (45 kDa) previously purified from C. tropicalis. Western blot analysis of the subcellular fractions from acetate-grown C. tropicalis with polyclonal antibodies raised against the recombinant CtIdp1 showed that the CtIdp1 in C. tropicalis was localized in mitochondria but not in peroxisomes. Similar levels of CtIDP1 mRNA and its protein product were detected in cells grown on glucose, acetate, and n-alkane, although a slight decrease was observed in n-alkane-grown cells. From these results, CtIdp1 was demonstrated to be mitochondrial Idp. The properties of mitochondrial Idp and peroxisomal Idp isozymes were proven to be similar, but they were immunochemically distinct, suggesting the presence of another gene responsible for peroxisomal Idp in C. tropicalis. Received: 11 March 1997 / Accepted: 24 June 1997     

A human homologue of the Drosophila melanogaster sluggish-A (proline oxidase) gene maps to 22q11.2, and is a candidate gene for type-I hyperprolinaemia

We have cloned the complete coding region for a human homologue of the Drosophila melanogaster sluggish-A and yeast PUT1 genes, previously shown to encode proline oxidase activity in these organisms. The predicted 516-residue human protein shows strong homology (51% amino acid sequence identity) to the D. melanogaster protein, indicating that this new human gene may encode proline oxidase. Northern analysis shows that the gene is expressed in human lung, skeletal muscle and brain, to a lesser extent in heart and kidney, and weakly in liver, placenta and pancreas. The gene was mapped by fluorescence in situ hybridization and by in situ hybridization with a [³H]-labelled DNA probe to chromosome 22q11.2, a region previously implicated in type-I hyperprolinaemia in a case of CATCH 22 syndrome, a contiguous gene deletion syndrome involving 22q11. Taken together, the evidence indicates that this new human gene is a good candidate gene for type-I hyperprolinaemia. In view of the neurological phenotype of the D. melanogaster sluggish-A mutant, it is of interest that schizophrenia and bipolar disorder susceptibility genes also map in this region. Received: 14 April 1997 / Accepted: 17 June 1997     

Over-production of stereoselective nitrile hydratase from Pseudomonas putida 5B in Escherichia coli : activity requires a novel downstream protein

The stereoselective nitrile hydratase (NHase) from Pseudomonas putida 5B has been over-produced in Escherichia coli. Maximal enzyme activity requires the co-expression of a novel downstream gene encoding a protein (P14K) of 127 amino acids, which shows no significant homology to any sequences in the protein database. Nitrile hydratase produced in transformed E. coli showed activity as high as 472 units/mg dry cell (sixfold higher than 5B), and retained the stereoselectivity observed in the native organism. Separated from the end of the β subunit by only 51 bp, P14K appears to be part of an operon that includes the α and β structural genes of nitrile hydratase, and other potential coding sequences. Received: 13 May 1997 / Received revision: 22 August 1997 / Accepted: 15 September 1997     

Exclusion of PPEF as the gene causing X-linked juvenile retinoschisis

X-linked juvenile retinoschisis (RS) is a progressive vitreoretinal degeneration localised in Xp22.1-p22.2. A human homologue of the retinal degeneration gene C (rdgC), a gene that in Drosophila melanogaster prevents light-induced retinal degeneration, was localised in the RS obligate gene region. We have tested the gene, designated PPEF in humans, as a candidate gene in RS patients using RT-PCR and the protein truncation test on RNA and SSCP on DNA. No mutations were identified, making it highly unlikely that PPEF is the gene implicated in RS. The data presented facilitate mutation analysis of the PPEF gene in other diseases which have been or will be localised to this region. Received: 20 May 1997 / Accepted: 30 July 1997     

Purification and characterization of a fix ABCX-linked 2[4Fe-4S] ferredoxin from Azotobacter vinelandii

 Ferredoxins that contain 2[4Fe-4S]^2+/+ clusters can be divided into two classes. The "clostridial-type" ferredoxins have two CysXXCysXXCysXXXCysPro motifs. The "photosynthetic bacterial and nif-related" ferredoxins have one motif of that type and one more unusual CysXXCysX_7–9CysXXXCysPro motif. In Azotobacter vinelandii three gene sequences have been reported that contain the latter motif, but until now none of the gene products has been purified. Here we report the purification of a small anionic [Fe-S] protein with yields of ∼3 mg per 500 g cell paste. NH₂-terminal sequence analysis shows that this protein is the product of a previously sequenced A. vinelandii gene that is found upstream of fixA and is cotranscribed with fixABCX. That gene was originally named fixP, but since that gene designation is now commonly used for a very different cb-type cytochrome oxidase we have renamed the gene fixFd and its product Fix Fd. Its sequence places Fix Fd in the class of "photosynthetic bacterial and nif-related" 2[4Fe-4S]^2+/1+ ferredoxins that includes Chromatium vinosum ferredoxin. Studies of the purified protein by Fe analysis, absorption, CD and EPR spectroscopies and electrochemistry confirm this characterization; the reduction potentials of the two clusters are –440 mV vs SHE. The fact that A. vinelandii synthesizes three different proteins with the same sequence motif, each of which is likely to have a different function, shows that although sequence motifs may be used reliably to classify ferredoxins by cluster type they cannot yet be used reliably for classifying ferredoxins by function. Received: 31 January 1997 / Accepted: 9 June 1997     

Cloning and comparative mapping of a gene from the commonly deleted region of DiGeorge and Velocardiofacial syndromes conserved in C. elegans

We have identified and cloned a gene, ES2, encoding a putative 476 amino acid protein with a predicted M _r of 52,568. The gene is localized within the DiGeorge/Velocardiofacial syndrome locus on 22q11.2 and is deleted in all the patients in which a deletion within 22q11 could be demonstrated, with the exception of one patient. ES2 is expressed in all the tissues studied. Sequence comparison showed identity with five ESTs and at the amino acid level the sequence was highly similar to, and collinear with, a hypothetical C. elegans protein of unknown function. Mutation analysis was performed in 16 patients without deletion, but no mutation has been found. The cDNA sequence is conserved in mouse and is localized on MMU16B1-B3, known to contain a syntenic group in common with HSA 22q11.2. Received: 25 March 1996 / Accepted: 15 May 1996     

Cloning and characterization of the mouse Interleukin Enhancer Binding Factor 3 (Ilf3) homolog in a screen for RNA binding proteins

In a screen for RNA-binding proteins expressed during murine spermatogenesis, we have identified a cDNA that encodes a protein of 911 amino acids that contains two copies of the double-stranded RNA-binding motif and has 80% identity with human Interleukin Enhancer Binding Factor 3 (ILF3). Linkage and cytogenetic analyses localized the Ilf3 cDNA to a portion of mouse Chr 9, which shows conserved synteny with a region of human Chr 19 where the human ILF3 gene had been previously localized, supporting that we had cloned the murine homolog of ILF3. Northern analysis indicated the Ilf3 gene is ubiquitously expressed in mouse adult tissues with high levels of expression in the brain, thymus, testis, and ovary. Polyclonal antibodies detected multiple protein species in a subset of the tissues expressing Ilf3 RNA. Immunoreactive species are present at high levels in the thymus, testis, ovary, and the spleen to a lesser extent. The high degree of sequence similarity between the mouse ILF3 protein and other dsRNA binding motif-containing proteins suggests a role in RNA metabolism, while the differential expression indicates the mouse ILF3 protein predominantly functions in tissues containing developing lymphocyte and germ cells. Received: 21 October 1998 / Accepted: 15 January 1999     

AtBUD13 affects pre‐mRNA splicing and is essential for embryo development in Arabidopsis

Pre‐mRNA splicing is an important step for gene expression regulation. Yeast Bud13p (bud‐site selection protein 13) regulates the budding pattern and pre‐mRNA splicing in yeast cells; however, no Bud13p homologs have been identified in plants. Here, we isolated two mutants that carry T‐DNA insertions at the At1g31870 locus and shows early embryo lethality and seed abortion. At1g31870 encodes an Arabidopsis homolog of yeast Bud13p, AtBUD13. Although AtBUD13 homologs are widely distributed in eukaryotic organisms, phylogenetic analysis revealed that their protein domain organization is more complex in multicellular species. AtBUD13 is expressed throughout plant development including embryogenesis and AtBUD13 proteins is localized in the nucleus in Arabidopsis. RNA‐seq analysis revealed that AtBUD13 mutation predominantly results in the intron retention, especially for shorter introns (≤100 bases). Within this group of genes, we identified 52 genes involved in embryogenesis, out of which 22 are involved in nucleic acid metabolism. Our results demonstrate that AtBUD13 plays critical roles in early embryo development by effecting pre‐mRNA splicing.     

Localization of the active gene of aldolase on chromosome 16, and two aldolase A pseudogenes on chromosomes 3 and 10

Summary Southern blot analysis of human genomic DNA hybridized with a coding region aldolase A cDNA probe (600 bases) revealed four restriction fragments with EcoRI restriction enzyme: 7.8 kb, 13 kb, 17 kb and >30 kb. By human-hamster hybrid analysis (Southern technique) the principal fragments, 7.8 kb, 13 kb, >30 kb, were localized to chromosomes 10, 16 and 3 respectively. The 17-kb fragment was very weak in intensity; it co-segregated with the >30-kb fragment and is probably localized on chromosome 3 with the >30-kb fragment. Analysis of a second aldolase A labelled probe protected against S1 nuclease digestion by RNAs from different hybrid cells, indicated the presence of aldolase A mRNAs in hybrid cells containing only chromosome 16. Under the stringency conditions used, the EcoRI sequences detected by the coding region aldolase A cDNA probe did not correspond to aldolase B or C. The 7.8-kb and >30-kb EcoRI sequences, localized respectively on chromosomes 10 and 3, correspond to aldolase A pseudogenes, the 13-kb EcoRI sequence localized on chromosome 16 corresponds to the aldolase active gene. The fact that the aldolase A gene and pseudogenes are located on three different chromosomes supports the hypothesis that the pseudogenes originated from aldolase A mRNAs, copied into DNA and integrated in unrelated chromosomal loci.