Genomic Phage Clones Research Articles

The β-conglycinin deficiency in wild soybean is associated with the tail-to-tail inverted repeat of the α-subunit genes

β-conglycinin, a major seed protein in soybean, is composed of α, α', and β subunits sharing a high homology among them. Despite its many health benefits, β-conglycinin has a lower amino acid score and lower functional gelling properties compared to glycinin, another major soybean seed protein. In addition, the α, α', and β subunits also contain major allergens. A wild soybean (Glycine soja Sieb et Zucc.) line, 'QT2', lacks all of the β-conglycinin subunits, and the deficiency is controlled by a single dominant gene, Scg-1 (Suppressor of β-conglycinin). This gene was characterized using a soybean cultivar 'Fukuyutaka', 'QY7-25', (its near-isogenic line carrying the Scg-1 gene), and the F₂ population derived from them. The physical map of the Scg-1 region covered by lambda phage genomic clones revealed that the two α-subunit genes, a β-subunit gene, and a pseudo α-subunit gene were closely organized. The two α-subunit genes were arranged in a tail-to-tail orientation, and the genes were separated by 197 bp in Scg-1 compared to 3.3 kb in the normal allele (scg-1). In addition, small RNA was detected in immature seeds of the mutants by northern blot analysis using an RNA probe of the α subunit. These results strongly suggest that β-conglycinin deficiency in QT2 is controlled by post-transcriptional gene silencing through the inverted repeat of the α subunits.

Identification and initial characterization of a putative Mycoplasma gallinarum leucine aminopeptidase gene.

Aminopeptidases (APN) may play a role in host colonization of M. gallinarum. Characterization of endogenous APN activity suggests that the leucine APN (LAP) of M. gallinarum is a metallo-aminopeptidase activated by Mn2+ and is present in the cytosol and possibly associated with the inner leaflet of the membrane. A 1.36-kb open reading frame (ORF) identified from overlapping genomic phage clones showed 68% nucleotide identity and 51% amino acid identity with the M. salivarium LAP gene. This ORF is expressed as a 1.5-kb monocistronic transcript and is present as a single copy in M. gallinarum. This gene sequence was modified to account for codon usage, and expression in E. coli produced a 51-kDa protein, which compares well with the product predicted from the ORF. This ORF is a strong candidate for contributing the LAP activity of M. gallinarum protein extracts.

Importance of TRF1 for Functional Telomere Structure

Telomeres are comprised of telomeric DNA sequences and associated binding molecules. Their structure functions to protect the ends of linear chromosomes and ensure chromosomal stability. One of the mammalian telomere-binding factors, TRF1, localizes telomeres by binding to double-stranded telomeric DNA arrays. Because the overexpression of wild-type and dominant-negative TRF1 induces progressive telomere shortening and elongation in human cells, respectively, a proposed major role of TRF1 is that of a negative regulator of telomere length. Here we report another crucial function of TRF1 in telomeres. In conditional mouse TRF1 null mutant embryonic stem cells, TRF1 deletion induced growth defect and chromosomal instability. Although no clear telomere shortening or elongation was observed in short term cultured TRF1-deficient cells, abnormal telomere signals were observed, and TRF1-interacting telomere-binding factor, TIN2, lost telomeric association. Furthermore, another double-stranded telomeric DNA-binding factor, TRF2, also showed decreased telomeric association. Importantly, end-to-end fusions with detectable telomere signals at fusion points accumulated in TRF1-deficient cells. These results strongly suggest that TRF1 interacts with other telomere-binding molecules and integrates into the functional telomere structure.

Genomic and molecular characterization of CL-43 and its proximal promoter

Collectins are part of the innate immune system as they bind nonself glycoconjugates on the surface of microorganisms and inhibit infection by direct neutralization, agglutination or opsonization of the invaders. Conglutinin and CL-43 are serum proteins that have only been found and characterized in Bovidae. We have studied molecular and genomic characteristics of CL-43 to identify polymorphisms that might be associated with disease-susceptible phenotypes or other traits in cattle, and to elucidate how the Bovidae may benefit from possessing additional collectins. Screening a bovine cDNA library resulted in the isolation of two plasmid clones that encoded the entire translated sequence of CL-43. The 5′-untranslated end and start point of transcription were identified by 5′-RACE and showed that the mRNA transcript comprises either 1326 or 1241 nucleotides because of alternative splicing. Both transcripts encode a protein of 321 amino acids including a signal peptide of 20 residues. Characterization of two overlapping genomic lambda phage clones showed that the gene comprised seven exons spanning 8.5 kbp. The CL-43 gene, like the conglutinin gene, was mapped to Bos taurus chromosome 28 at q1.8. The CL-43 promoter has 96% identity with the conglutinin promoter recently described by us, and the assignment of potential cis-regulatory elements shows that several hepatic transcription factors may regulate transcription in the acute phase response and in response to metabolic changes.

Structures of two major histocompatibility complex class I genes of the rainbow trout (Oncorhynchus mykiss).

Here we describe two rainbow trout major histocompatibility complex (MHC) class I genes characterized from lambda phage genomic clones prepared from a single fish. Clone GC71 contains all exons except a leader peptide-encoding exon. An open reading frame is maintained, and thus the gene MhcOnmy-U71 could be expressed in this individual. The class I gene found on clone GC41 lacks exons encoding the leader peptide and cytoplasmic domain. This gene, MhcOnmy-U41p, is a pseudogene due to a deletion in the alpha(2) domain-encoding exon causing premature termination. Both the Onmy-U71 and Onmy-U41p genes are distinguished by long introns between the exons encoding the alpha(1) and alpha(2) domains. Clone GC41 also contains the 3' exons of the LMP7/ PSMB8 gene encoding the gamma-interferon-induced proteosome subunit of rainbow trout.

Novel characterisation of the gene encoding conglutinin reveals that previously characterised promoter corresponds to the CL-43 promoter

Conglutinin, a collectin found in bovine serum, is an opsonin that binds to glycoconjugates on the surface of microorganisms or on deposited iC3b, and acts in concert with phagocytes to establish a first-line of immune defense. We have isolated a genomic conglutinin phage clone and found that the 5′-flanking region shows 95.8% identity with the sequence previously published, which on the other hand shows 99.7% identity with the CL-43 promoter. We conclude that the previously published promoter corresponds to the CL-43 promoter and that the functional studies performed on it apply to transcription of CL-43. Comparison of potential cis-regulatory elements in relation to the functional studies indicates that the two genes are regulated by different mechanisms.

A Novel MS7 Repeat Specific for Heterochromatin of Sex Chromosomes in Voles of Genus Microtus, Group arvalis: Genomic Organization and Chromosomal Localization

The tandemly arranged MS4 repeat with monomeric units of 4.1 kb is species-specifically distributed in heterochromatin of sex chromosomes of four common vole species of genus Microtus, group arvalis. In this work, we studied the genomic organization of the MS4 homolog in euchromatin of the X chromosome of M. arvalis. It has been shown by analyzing the phage genomic clones that one MS4 copy makes a part of a monomeric unit exceeding 8.5 kb that also includes a new MS7 repeat and, possibly, LINE fragments. MS7 is located together with MS4 in heterochromatin of common vole sex chromosomes, but in a substantially lesser amount. Probably, as a result of an evolutionary transition of an original repeat from euchromatin of the X chromosome to heterochromatin of the Y chromosome, MS4 underwent multiple amplification, and MS7 spread throughout heterochromatin, being surrounded by the MS4 tandem arrays.

Characterization and genomic sequence of the murine 60 kD Ro gene.

Autoantibodies binding 60 kD Ro (or SS-A) are commonly found in patients with systemic lupus erythematosus and Sjögren's syndrome. While many studies have examined the autoimmune response directed against this RNA-protein, its function is still uncertain. As part of a broad effort to better understand animal models of anti-Ro autoimmunity we have characterized the murine 60 kD Ro gene. Southern blot analysis of mouse genomic DNA suggests that the 60 kD Ro gene is a single copy gene. The complete sequence of the gene was determined from three overlapping genomic lambda phage clones (GenBank accession number AF065398). The murine 60 kD Ro gene spans approximately 23 kb and consists of 8 or 9 exons. DNA sequence analysis revealed the presence of multiple B1 repetitive units. It maps in synteny with the human 60 kD Ro gene. Therefore, the isolation and characterization of the 60 kD Ro gene will be instrumental for future studies on protein function and the role this protein plays in the development of autoimmune responses.

The human secretin receptor gene: genomic organization and promoter characterization

Secretin is the most potent regulator of pancreatic bicarbonate, electrolyte and volume secretion. In this report, the organization of the human secretin receptor (hSR) gene was characterized by overlapping genomic phage clones. The hSR gene consists of 13 exons and 12 introns with all the splice donor and acceptor sites conforming to the canonical GT/AG rule. By transient reporter gene assays, the wild-type promoter, containing 3.0 kb of the hSR gene 5′ flanking region, was able to drive 5.8±0.6 and 6.6±0.2-fold ( P<0.01) increases in luciferase activities in pancreatic ductule-derived PANC-1 and BPD-1 cells, respectively. By subsequent 5′ and 3′ deletion analysis, a promoter element was identified within −408 to −158, relative to the ATG codon. This promoter element was found to be cell-specific since it could drive reporter gene expression in PANC-1 and BPD-1 cells but not in Hs 262.St, Hs 746T and αT3-1 cells. The study of the transcriptional control of human secretin and its receptor should shed light on the pathological developments of pancreatic cancer and autism in the future.

Human retinoic X receptor beta: complete genomic sequence and mutation search for ossification of posterior longitudinal ligament of the spine.

Ossification of the posterior longitudinal ligament of the spine (OPLL) is characterized by ectopic bone formation in the ligament. OPLL is a very common disorder, in fact it constitutes the leading cause of myelopathy among Japanese. In the previous report, we provided the genetic linkage evidence that the genetic susceptibility of OPLL mapped to HLA complex of chromosome 6. As a candidate gene approach, retinoic X receptor beta (RXR beta), assigned to chromosome 6p21.3 adjacent to HLA class II, was analyzed for a possible causality. To start screening for the molecular variants of RXR beta in OPLL subjects, we first obtained P1 phage genomic clones containing the entire human RXR beta and elucidated the genomic organization of the gene. The human RXR beta is composed of 10 exons spanning over 6.2 kb of genomic DNA. Sequence analysis of the promoter region revealed a GC-rich sequence without TATA motif. We have identified three distinct molecular variants, one was in exon 10 and two were in the intergenic region between RXR beta and collagen 11A2 (COL11A2). Two variants in the intergenic region, 3' end + 140 and 3' end + 561, exhibit statistically significant associations with OPLL in case-control study (p = 0.0028 for 3' end + 140 and p = 0.034 for 3' end + 561). These results indicate that the genetic causality of OPLL lies within or close to the RXR beta/COL11A2 locus.

Characterization of the Human elk-1Promoter: POTENTIAL ROLE OF A DOWNSTREAM INTRONIC SEQUENCE FORelk-1 GENE EXPRESSION IN MONOCYTES

To characterize the human elk-1 promoter, we mapped the transcriptional start site and isolated elk-1-specific genomic phage clones that contained extensive upstream and downstream sequences. A TATA-like motif was identified immediately upstream of the transcriptional start site. Functional analyses of DNA fragments containing the TATA element and the identification of a DNase I-hypersensitive chromatin site (HS 1) in close proximity to the TATA box suggest that the identified TATA motif is important for elk-1 transcription in vivo. Sequences upstream and downstream from the TATA box were found to contribute to elk-1 promoter activity. A second hypersensitive site (HS 2) was identified within the first intron in pre-monocytic cells, which express Elk-1 only when differentiating to monocytes. In a variety of other cell types, which display a constitutive Elk-1 expression, HS 2 did not exist, suggesting that inducibility of elk-1 expression is associated with the presence of HS 2. Egr-1 and the serum response factor were found to interact specifically with the intronic sequence at +265 and +448, respectively. Because Egr-1 mRNA and protein levels were observed to increase significantly before induction of elk-1 expression, we propose that Egr-1 is important for the regulation of elk-1 transcription in differentiating monocytes.

Identification and characterization of the murine FK506 binding protein (FKBP) 12.6 gene.

Identification and characterization of the murine FK506 binding protein (FKBP) 12.6 gene.

Cloning, genomic organization and chromosomal assignment of the mouse p190-B gene

The p190 family of GTPases consists of at least two different isoforms both containing an N-terminal GTPase and a C-terminal Rho GAP domain. Here we have isolated and characterized genomic and cDNA clones spanning the entire coding region of the mouse p190-B gene. Genomic data were obtained by sequencing plasmid subclones of two overlapping mouse genomic phage clones. Interestingly, a single 3.9 kb exon was found to contain approx. 80% of the coding region of the mouse p190-B protein (amino acid residues 1–1238) including the 5′-untranslated region, the N-terminal GTPase domain and a middle domain of unknown function. Missing from this exon, however, was the C-terminal Rho GAP domain, which was cloned from mouse brain mRNA using reverse transcriptase polymerase chain reaction. Comparison of the mouse with the human p190-B proteins revealed that approx. 97% of the amino acid residues were identical. Northern analysis of total RNA from a variety of mouse tissues detected ubiquitous expression of two p190-B transcripts of 4.0 and 6.8 kb in size. Analysis of two multilocus genetic crosses localized the mouse gene, Gfi2, to a position on chromosome 12, consistent with the mapping of the human gene to a position of conserved synteny on chromosome 14. The high level of sequence homology between the human and the mouse suggests that there is a strong selective pressure to maintain the p190-B protein structure.

Molecular analysis and polymorphism of the DLA-DQB genes.

Partial-length cDNA clones and full-length genomic clones corresponding to a complete canine DQB class II gene were isolated. Southern analyses suggested the presence of two DQB genes--one of which appeared to be a pseudogene lacking exon 2 called DQB2. The other DQB gene, called DQB1, was isolated from a genomic phage clone and contained six exons. The DQB1 clone was restriction mapped, and exon 2 was sequenced from 70 dogs. Twenty alleles were found. Most of the amino acid substitutions occurred at putative positions in the peptide binding site. Inheritance of these sequences showed Mendelian segregation with one or two alleles per dog. Cluster analysis of the nucleotide and predicted amino acid sequences subdivided the canine DQB1 alleles into four major allelic groups. The number of nonsynonymous changes was higher than the number of synonymous changes in the putative antigen recognition sites suggestive of positive selection.

A family of pupal-specific cuticular protein genes in the mosquito Anopheles gambiae

We have cloned and sequenced members of a cuticular protein multi-gene family from the mosquito Anopheles gambiae. Three genes ( agcp2a–c), each approximately 1 kb in length, were found in a 17.4 kb genomic phage clone. Analysis of ten cDNAs revealed that at least four related genes are present. The open reading frame of the genes and cDNAs showed 95% sequence identity. Divergence was observed in the sequence of the 3′ ends and the number of copies of two repeated coding sequences. In situ hybridizations with a probe prepared from one of these cuticular protein genes ( agcp2b) showed that the genes physically mapped to two loci, 26B on chromosome 2L and 37A on 3R. Transcription of these An. gambiae cuticular protein genes appears to be limited to pharate pupae and the expressed protein(s) is found in early pupae. The deduced amino acid sequence of these proteins contains a hydrophilic region with significant similarity to other cuticular proteins including the pupal-specific cuticular protein, EDG84, of Drosophila melanogaster ( Apple and Fristrom, 1991).

Genetic polymorphism of the IGHG3 gene in cattle

We cloned and analyzed the gene (IGHG3) encoding cattle IgG3 using a spleen cDNA library and a genomic phage clone. IGHG3 differs most remarkably from IGHG1 and IGHG2 in the structure of its hinge. The IGHG3 hinge is encoded by two exons, one of which encodes a 22 amino acid 3' extension of the CH1 exon. The IGHG3 gene is highly homologous to the C-gamma pseudogene previously reported. Seventy-one DNA samples from different cattle were tested by pulsed-field gel electrophoresis and Southern blot to detect genetic polymorphisms. This analysis revealed two different alleles which we designated IGHG3(a) and IGHG3(b). The two putative alleles differ from each other by a 6 amino acid substitution in the coding region and an 84 base pair insertion in the intron between the CH2 and CH3 exons. Our data also indicate that the cattle heavy chain locus spans approximately 400 kilobases from IGHM to IGHA and encodes only three IgG subclasses, all of which are transcriptionally active.

Anchoring of bovine chromosomes 4, 6, 7, 10, and 14 linkage group telomeric ends via FISH analysis of lambda clones.

We report the placement of 34 new microsatellite (ms) markers, isolated from a lambda phage genomic clone library, on the bovine genetic map by linkage to published markers. Five of these markers lie at or near the ends of linkage groups and are used to establish chromosomal coverage and orientation. Fluorescence in situ hybridization (FISH) analysis demonstrates that the linkage groups on the U.S. Meat Animal Research Center (MARC) map extend to the telomeric region of Chromosomes (Chrs) 7 and 10. Linkage groups on Chrs 4, 6, and 14 appear to be less inclusive.

Restriction mapping of genes by capillary electrophoresis with laser-induced fluorescence detection.

Restriction mapping is one of the essential steps in gene analysis and molecular biology studies. Slab gel electrophoresis is the traditional way to separate DNA fragments for restriction mapping. However, slab gel electrophoresis does not provide sufficient resolution as required in many mapping applications, and the use of radioisotopes in traditional mapping methods creates health hazards. In the present study, capillary electrophoresis coupled with laser-induced fluorescence detection and a modified partial digestion mapping procedure was developed to map DNA fragments. By using capillary electrophoresis, a restriction map of genomic lambda phage clone of human interleukin 5 receptor alpha chain (IL5R alpha) gene was constructed. The IL5R alpha gene was analyzed to have five XbaI enzyme cutting sites at locations 1370, 2290, 2950, 5430, and 9330. The system was further characterized by using pBluescript SK(+) phagemid DNA as a model. Using a sequence-derived map as a reference, the pBluescript SK(+) restriction map constructed by capillary electrophoresis had an accuracy greater than 90%.

Promoter region and alternatively spliced exons of the rat mu-opioid receptor gene.

The actions of exogenous and endogenous opioids are mediated by at least three different opioid receptors, called mu, kappa, and delta. Recently, we have detected a new variant of the rat mu-opioid receptor, which we termed rMOR1B and which differs from rMOR1 (now also called rMOR1A) in the amino acid sequence at the C-terminus. Both isoforms were proposed to be splicing variants of the same gene. To elucidate the molecular mechanism leading to the formation of the new variant, the exon/intron structure of the rat mu-opioid receptor gene in the respective area has been determined by analyzing a genomic P1 phage clone. In addition, we have investigated the putative promoter region of this gene. The present study revealed that rMOR1B is generated by an alternative splicing event whereby a previously unknown exon will be placed behind exon 3 to form rMOR1B mRNA, which is separated from the latter by an intron. Therefore, this new exon has to be called exon 4, whereas the former exon 4, which encodes the C-terminus of MOR1A, now becomes exon 5. Examination of the putative rat promoter region revealed a high degree of nucleotide sequence homology to the mouse gene. Using an RNase protection approach, one single transcription initiation site could be located at 230 bp upstream of the translation start. This is similar to the situation in the mouse, where four major transcription start sites were reported to lie close together around 270 bp upstream of the protein coding region.

Characterization of the regulatory regions of murine α2C2 adrenoceptor subtype gene

In order to delineate the regulatory mechanisms underlying the control of α2 adrenoceptor expression, the sequence of 5′ (1145 bp) and 3′ (2682 bp) flanking regions of murine α2C2 subtype gene were determined and characterized from a genomic phage clone MA2C2. The 5′ flanking region has no TATA box yet with high GC content. The 3′ flanking region is marked by the presence of a polyadenylation signal 2.3 kb down stream from the stop codon. The transcription start site was mapped by 5′ rapid amplification of cDNA ends (RACE) and primer extension assays at nucleotide A, 415 by upstream from the first initiation codon and resides in a motif resembling the consensus sequence of initiator found in many TATA-less promoters. An Ncol fragment (4.7 kb) immediately upstream from the translation initiation site was linked to a reporter gene lacZ Using an in vitro transfection assay, cell lines of renal or neural origin were identified as permissive hosts for α2C2 subtype expression. With its core promoter clearly defined and sequence of the regulatory regions at hand, this in vitro gene transfer system will facilitate the identification of putative cis-elements and transcription factors key to α2C2 adrenoceptor expression.