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PubMed2005

Structural genomics of GPCRs.

G protein-coupled receptors (GPCRs) are targets for 60-70% of drugs in development today. Traditionally, the drug discovery process has relied on screening of chemical compounds to identify novel and more-efficient drug molecules. Structure-based drug design, however, provides a targeted approach but has been severely hampered by limited knowledge of high-resolution structures of GPCRs owing to the difficulties encountered in their expression, purification and crystallization. In addition to individual laboratories studying specific GPCRs, structural genomics initiatives have been established as large networks with a wide range of expertise in protein expression, purification and crystallography. Several of these national and international consortia have included GPCRs in their programs. Milligram quantities of GPCRs can now be expressed in several expression systems and purified to high homogeneity. However, success in crystallization still requires major technological improvement.

Crystallization↗
PubMed2025

Genomic structure of class 1 and 2 integrons in non-typhoidal Salmonella isolated from food animals and related meat products in the USA.

OBJECTIVES: Integrons facilitate the capture and expression of exogenous genes, including antimicrobial resistance (AMR) genes. This study aimed to detect the presence of integrons, examine their genomic structure and location, and analyse integron-associated AMR, virulence and stress response genes in Salmonella using WGS. METHODS: WGS data from 193 Salmonella strains, representing 38 serotypes isolated from food animals and related meat products (2001-2019), were analysed using bioinformatic tools to assess integron presence and characterize their genomic architectures. RESULTS: Of 193 isolates, 116 (60.1%) harboured class 1 and/or class 2 integrons. Class 1 integrons alone were detected in 105 isolates, with some containing multiple copies. One S. Infantis isolate harboured only class 2 integrons, whereas 10 others contained both classes. No class 3-5 integrons were found. Twenty-seven class 1 integrons were chromosomal; the rest were plasmid-associated, linked to various plasmid incompatibility (Inc) types. Sixty-nine distinct AMR genes conferring resistance to 11 antimicrobial classes were found in integron cassettes or integron-associated plasmids. Genes linked to resistance to quaternary ammonium compounds and heavy metals, as well as ISs and transposons, were also identified. Significant virulence and stress response genes and proteins such as groES-groEL, LysR and EAL (glutamate, alanine and leucine) were common in integron cassettes. CONCLUSIONS: Class 1 integrons are prevalent in MDR Salmonella isolates from food animals and related meat products and are linked to diverse plasmid types. Their association with AMR, virulence and stress response genes underscores their role in AMR dissemination, and bacterial adaptation and pathogenicity.

Integrons↗
PubMed2026

"Tissue-specific mitochondrial dysfunction in keratoconus: An integrated structural, genomic, and functional analysis".

PURPOSE: Keratoconus (KC) is a progressive corneal ectasia characterized by stromal thinning, conical protrusion, and irregular astigmatism, leading to visual impairment. Although oxidative stress is implicated in KC, the role of mitochondrial dysfunction remains unclear. We evaluated mitochondrial structural, genomic, and functional abnormalities in corneal tissues and blood from KC patients. METHODS: This prospective study enrolled 110&#x202f;KC patients and 55 controls. Transmission electron microscopy (TEM) and immunohistochemistry (IHC) were performed on epithelial and stromal tissues from 10&#x202f;KC to 5 control corneas assessing mitochondrial morphology, oxidative phosphorylation (OXPHOS) complexes and pro-apoptotic protein NOXA. Whole mitochondrial DNA (mtDNA) sequencing and relative mtDNA copy number analysis were performed on paired blood and corneal tissues from 50&#x202f;KC patients and 35 controls including both epithelial and stromal samples. Gene expression of mitochondrial biogenesis and oxidative stress-related genes was analysed by qRT-PCR in corneal epithelium from independent 50&#x202f;KC patients and 15 controls. RESULTS: TEM revealed cristolysis, membrane disruption, and reduced mitochondrial density in KC corneas. IHC showed reduced expression of OXPHOS complexes and increased NOXA expression (p&#x202f;<&#x202f;0.05). Sequencing identified 1107 mtDNA variants, with more variants in corneal tissues than matched blood (929 vs. 576; p&#x202f;=&#x202f;0.0002). Recurrent likely pathogenic variants were enriched in complex I-encoding genes (ND4, ND5). KC corneas showed reduced mtDNA copy number, downregulated POLRMT, upregulated NOX4, and significant downregulation of multiple antioxidant genes (p&#x202f;<&#x202f;0.0001). CONCLUSION: KC patients exhibit tissue-specific mitochondrial abnormalities and impaired oxidative stress regulation, supporting a role for mitochondrial dysfunction in disease pathogenesis and highlighting potential therapeutic targets.

Corneal pathology↗
PubMed1994

Mouse homologue of C33 antigen (CD82), a member of the transmembrane 4 superfamily: complementary DNA, genomic structure, and expression.

C33 Ag (CD82) is a member of the transmembrane 4 superfamily (TM4SF) and an activation Ag of T-cells. Recent studies have shown that CD82 associates with CD4 or CD8 and delivers costimulatory signals for the TCR/CD3 pathway. We have isolated cDNA and genomic clones of mouse CD82. Mouse CD82 has 266 amino acid residues with 76% identity to human CD82. The mouse CD82 gene consists of nine exons and spans more than 20 kb of genomic DNA. The genomic organization of CD82 is quite similar to that of three other TM4SF members whose genomic structures were described, i.e., Tapa-1 (CD81), CD53, and CD63. By mapping the 5' end of CD82 transcripts, we found a single major transcription initiation site 144 bp upstream of the ATG initiation codon. We also determined the sequence of the 5' flanking region of CD82 gene for about 2 kb. The 5' flanking sequence has a housekeeping promoter with potential binding motifs for various transcriptional factors. Northern blot analysis showed quite variable expression of the CD82 gene among different organs. The highest expression was seen in the spleen and the kidney. The expression was low in skeletal muscle and hardly detectable in the heart. Northern blot analysis was also carried out for CD81, CD53, and CD63. The expression of the CD81 gene was ubiquitous and similar among different organs, while that of CD53 was seen only in the spleen. The expression of the CD63 gene was ubiquitous, with the highest expression in the kidney. These results together with the comparison of the structures of 5' flanking sequences of these genes indicate distinct regulations of gene expression for these four members of TM4SF.

Amino Acid Sequence↗
PubMed2000

A 500-kb region on chromosome 16p13.1 contains the pseudoxanthoma elasticum locus: high-resolution mapping and genomic structure.

We have recently mapped the genetic defect underlying pseudoxanthoma elasticum (PXE), an inherited disorder characterized by progressive calcification of elastic fibers in skin, eye, and cardiovascular system, to chromosome 16p 13.1. Here we report further data on the fine-mapping and genomic structure of this locus. Haplotype analysis of informative PXE families narrowed the locus to an interval of less than 500 kb located between markers D16B9621 and D16S764. Three overlapping YAC clones were found to cover this region through YAC-STS content mapping. An overlapping BAC contig was then constructed to cover this interval and the surrounding region. About 80% of this chromosomal region has been fully sequenced using the BAC shotgun technique. Gene content and sequence analysis predicted four genes (MRP1, MRP6, PM5, and a novel transcript) and two pseudogenes (ARA and PKDI) within this interval. By screening a somatic cell hybrid panel we were able to precision-map the breakpoint of Cy185 and the starting point of a chromosomal duplication within 20 kb of BAC A962B4. The present data further refine the localization of PXE, provide additional physical cloning resources, and will aid in the eventual identification of the genetic defect causing PXE.

Adult↗
PubMed1995

Genomic structure of SAS, a member of the transmembrane 4 superfamily amplified in human sarcomas.

SAS is a recently identified member of the transmembrane 4 superfamily (TM4SF) that is frequently amplified in human sarcomas. To further its characterization and to confirm its classification, the genomic structure of the SAS gene was determined. The SAS gene covers approximately 3.2 kb of DNA. It contains six exons within its translated region, three of which are highly conserved in the TM4SF. 5' to the translation start site are two putative transcription start sites, two CCAAT consensus sequences, and potential binding sites for both Sp1 and ATF transcription factors. Comparison of SAS organization to human ME491, CD9, and CD53 and murine CD53 and TAPA-1 confirms that SAS is a member of this family of genes and is consistent with the theory that these genes arose through duplication and divergent evolution.

Amino Acid Sequence↗
PubMed1997

Genomic structure of human cystatin A.

Cystatin A is a cysteine proteinase inhibitor with a molecular mass of 11 kDa, and is located mainly in the keratohyaline granules of the stratum granulosum and the cornified envelope of the stratum corneum in the epidermis. In this study, we demonstrated the genomic structure of this proteinase inhibitor in which there were three exons of 111 bp, 102 bp and 226 bp in length, while the lengths of the 1st and 2nd intron were approximately 14 Kbp and 4 Kbp, respectively. The conserved sequence of QVVAG was encoded in the 2nd exon and was not inserted by any introns. There were binding sites for SP-1 and AP-2 in the promoter region and an AP-1 binding site in the 1st intron. The successful amplification of each exon of cystatin A may possibly contribute to the detection of the genomic abnormality of some skin disorders e.g. keratinization disorder, chronic bacterial infection or photophobia.

Amino Acid Sequence↗
PubMed2001

Genomic structure and transcriptional regulation of human Galbeta1,3GalNAc alpha2,3-sialyltransferase (hST3Gal I) gene.

Previous studies have shown that hST3Gal I mRNA is overexpressed in colorectal cancer tissues and primary breast carcinoma compared with nonmalignant or benign tissue, suggesting that the transcriptional regulation of hST3Gal I gene is altered during malignant transformation. We report transcriptional regulation of the hST3Gal I gene in colon adenocarcinoma and leukemia cell lines. To determine the genomic structure of the 5'-untranslated region, we cloned and identified the 5'-untranslated region of hST3Gal I from a human genome library. The 5'-untranslated region was found to be divided into three exons, namely, exons Y, X, and C1. The transcription initiation sites map at -1035 bp from the translation initiation site. Our results indicate that the transcriptional regulation of hST3Gal I depends on the pI promoter that exists 5'-upstream of exon Y in these cell lines. The results of luciferase assay suggest that the nt -304 to -145 region is important for transcriptional activity of hST3Gal I gene in both cell lines. The nt -304 to -145 region contains two sequences similar to the Sp1 recognition elements (GC-box) and one USF binding site. The results of site-directed mutagenesis indicated that the Sp1 binding sites and USF binding site of the pI promoter are involved in the transcription of hST3Gal I mRNA. However, the triple mutant of these sites still exhibits about 50% transcriptional activity, suggesting that there are other transcription factors involved in the transcription of hST3Gal I mRNA. These results suggest that these factors may play a critical role in the up-regulation of the hST3Gal I gene during malignant transformation.

Base Sequence↗
PubMed1998

Human DCTN1: genomic structure and evaluation as a candidate for Alström syndrome.

The human dynactin 1 gene (DCTN1) is positioned on chromosome 2p13, the candidate region for various diseases including Alström syndrome, limb-girdle muscle dystrophy, and Miyoshi myopathy. Here, we report the exon-intron structure of DCTN1 along with characterization of the 5' upstream sequence and alternative splice variants previously identified by Tokito et al. (1996), Mol. Biol. Cell 7: 1167-1180). Knowledge of the genomic structure of DCTN1allowed us to design intronic primers necessary for analyzing mutations in families segregating for diseases linked to this gene. These primers were tested on a French Acadian kindred segregating for Alström syndrome. No mutations were observed within the coding region of DCTN1 in this family. However, the intronic primers should allow for the rapid amplification of the coding region for mutational analysis of additional Alström families and other diseases tightly linked to the DCTN1locus on chromosome 2p13.

Alternative Splicing↗
PubMed1999

Characterization of the genomic structure of the murine Spam1 gene and its promoter: evidence for transcriptional regulation by a cAMP-responsive element.

The Sperm Adhesion Molecule 1 (SPAM1), also known as PH-20, is a sperm membrane-bound protein that has been shown to have bifunctional roles in fertilization. It is encoded by a gene that is widely conserved in mammalian species, underscoring its importance in the fertilization process. Here we determined the genomic structure of the murine homologue, Spam1, using PCR analysis, and studied its transcriptional regulation. The gene covers approximately 10.5 kb of genomic DNA, is encoded by four exons, and the splice site consensus sequence is maintained in all intron-exon junctions, similar to that reported for the human homologue. With primer extension analysis, two transcription initiation sites were detected. One was assigned to the residue C and the other (a minor site) to the residue G, at positions 1 and -56, respectively. These are at 313 and 369 nucleotides upstream of the translation initiation codon, ATG. In about 770 bp upstream region of Spam1 that has been cloned and sequenced, multiple transcription factor binding sites including a CRE (cAMP-responsive element) were found. We specifically studied the function of the eight nucleotide CRE sequence (TGATGTCA) at -57 (or -62 depending on the strain of mice) of the promoter region. It can bind to the transcription factor CREM (cAMP-responsive element modulator) in gel mobility shift assays using mouse testis nuclear extract, and the binding can be inhibited by a 28 bp oligonucleotide containing the CRE sequence. Similar binding and inhibition assays using rat nuclear extract suggest the existence of a rat CRE sequence and the involvement of CREM in rat Spam1 expression. In vitro transcription assays suggest that CRE is necessary for the transcriptional activity of the murine promoter, and Northern analysis shows that Spam1 transcripts are absent in CREM-knockout mice. The results strongly suggest that the murine Spam1 expression is under the control of CREM, and that this transcriptional regulator for Spam1 might be conserved in other mammals, at least in the rat.

Animals↗
PubMed2001

Genomic structure, functional comparison, and tissue distribution of mouse Cd59a and Cd59b.

CD59 is a crucial complement regulatory protein that inhibits the terminal step of the complement activation cascade by interfering with the binding of C9 to C5b-8, thus preventing the formation of the membrane attack complex (MAC). We recently reported that the mouse genome contains two Cd59 genes, while the human and rat genomes each contain only one Cd59 gene (Qian et al. 2000). Here, we describe the genomic structure, comparative activity, and tissue distribution of these two mouse genes, designated Cd59a and Cd59b. The mouse Cd59 genes encompass a total of 45.6 kb with each gene having four exons. Cd59a spans 19 kb, and Cd59b spans 15 kb, with approximately 11.6 kb of genomic DNA separating the two genes. The overall sequence similarity between Cd59a and Cd59b is approximately 60%. The sequence similarity between exon 2, exon 3, and exon 4 and the respective flanking regions between the two genes is over 85%, but exon 1 and its flanking regions are totally different. Comparative studies of the activity of both genes as inhibitors of MAC formation revealed that Cd59b has a specific activity that is six times higher than that of Cd59a. Using polyclonal antibodies specific to either Cd59a or Cd59b, we showed that Cd59a and Cd59b are both widely expressed in the kidneys, brain, lungs, spleen, and testis, as well as in the blood vessels of most mouse tissues. Interestingly, testicular Cd59a appeared to be expressed exclusively in spermatids, whereas Cd59b was expressed in more mature sperm cells. These results suggest that even though Cd59a and Cd59b are expressed in multiple tissues, they may play some different roles, particularly in reproduction.

Animals↗
PubMed2000

Genomic structure and chromosomal localization of the gene encoding TRAX, a Translin-associated factor X.

The TRAX gene encodes a Translin-associated 33-kDa protein partner, TRAX. The TRAX protein has extensive amino acid homology with Translin, and contains bipartite nuclear targeting sequences, suggesting a possible role in the selective nuclear transport of Translin lacking any nuclear targeting motifs. In the present study, genomic clones of the human TRAX gene were isolated to determine the complete genomic organization. The genomic structure of the human TRAX gene was similar to that of the human Translin gene, consisting of six exons and five introns, encompassing approximately 27kb in genomic DNA. Northern blot analysis revealed a predominant transcript of approximately 2.7kb, and its distribution in various tissues was like that of Translin. Chromosomal mapping by fluorescence in situ hybridization (FISH) analysis allowed localization of the TRAX gene to human chromosome lq41.

Carrier Proteins↗
PubMed1998

hSmad5 gene, a human hSmad family member: its full length cDNA, genomic structure, promoter region and mutation analysis in human tumors.

hSmad (mothers against decapentaplegic)-related proteins are important messengers within the Transforming Growth Factor-beta1 (TGF-beta1) superfamily signal transduction pathways. To further characterize a member of this family, we obtained a full length cDNA of the human hSmad5 (hSmad5) gene by rapid amplification of cDNA ends (RACE) and then determined the genomic structure of the gene. There are eight exons and two alternative transcripts; the shorter transcript lacks exon 2. We identified the hSmad5 promoter region from a human genomic YAC clone by obtaining the nucleotide sequence extending 1235 base pairs upstream of the 5' end of the cDNA. We found a CpG island consistent with a promoter region, and we demonstrated promoter activity in a 1232 bp fragment located upstream of the transcription initiation site. To investigate the frequency of somatic hSmad5 mutations in human cancers, we designed intron-based primers to examine coding regions by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. Neither homozygous deletions or point mutations were found in 40 primary gastric tumors and 51 cell lines derived from diverse types of human cancer including 20 cell lines resistant to the growth inhibitory effects of TGF-beta1. These results suggest that the hSmad5 gene is not commonly mutated and that other genetic alterations mediate the loss of TGF-beta1 responsiveness in human cancers.

Alternative Splicing↗
PubMed2001

Molecular cloning and genomic structure of a gene encoding interferon regulatory factor in the pufferfish (Fugu rubripes).

Interferon regulatory factors (IRFs) are a large family of transcription factors involved in regulating the transcriptional response of vertebrates to interferons and viral infection. In this report we describe the cloning and genomic organization of an IRF gene from the pufferfish (Fugu rubripes). The fugu IRF gene spans 2.7 kb from the transcription start site to the polyadenylation signal. It consists of 10 exons and 9 introns and encodes a protein of 296 amino acids. The overall amino acid sequence of fugu IRF displays 55% identity to flounder IRF and approximately 44% identity to avian and mammalian IRF-1 and IRF-2. On the basis of the genomic structure and the absence of a transcriptional repression domain, we conclude that the fugu IRF is a member of the IRF-1 family. The fugu IRF gene is expressed in a wide range of tissues. While a single transcript of 1.4 kb was detected in most tissues, several larger transcripts generated using alternative polyadenylation signals were found in the gills.

Journal Article↗
PubMed1996

Tissue distribution, genomic structure, and chromosome mapping of mouse and human eukaryotic initiation factor 4E-binding proteins 1 and 2.

Two related eukaryotic initiation factor-4E binding proteins (4E-BP1 and 4E-BP2) were recently characterized for their capacity to bind specifically to eIF4E and inhibit its function. Here, we determined the cDNA sequence, tissue distribution, genomic structure, and chromosome localization of murine and human 4E-BP1 and 4E-BP2. Mouse 4E-BP1 and 4E-BP2 consist of 117 and 120 amino acids and exhibit 91. 5 and 95.0% identity, respectively, to their human homologues. 4E-BP1 mRNA is expressed in most tissues, but is most abundant in adipose tissue, pancreas, and skeletal muscle, while 4E-BP2 mRNA is ubiquitously expressed. The structures of the mouse 4E-BP1 and 4E-BP2 were determined. The 4E-BP1 gene consists of three exons and spans approximately 16 kb. In addition, two 4E-BP1 pseudogenes exist in the mouse genome. The 4E-BP2 gene spans approximately 20 kb and exhibits an identical genomic organization to that of 4E-BP1, with the protein coding portion of the gene divided into three exons. There are no pseudogenes for 4E-BP2. The chromosomal locations of 4E-BP1 and 4E-BP2 were determined in both mice and humans by fluorescence in situ hybridization analysis. Mouse 4E-BP1 and 4E-BP2 map to chromosomes 8 (A4-B1) and 10 (B4-B5), respectively, and human 4E-BP1 and 4E-BP2 localize to chromosomes 8p12 and 10q21-q22, respectively.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Genomic structure and promoter characterization of the gene encoding the ErbB ligand betacellulin.

Betacellulin (BTC) belongs to the epidermal growth factor (EGF) family of peptide ligands that are characterized by a six-cysteine consensus motif (EGF-motif) that forms three intra-molecular disulfide bonds, crucial for binding the ErbB receptor family. A variety of in vitro studies have identified BTC as an important factor in the growth and/or differentiation of pancreatic islet cells. The molecular mechanisms that regulate the transcription of the BTC gene however have not been delineated. As an initial step, we have characterized the genomic structure of the mouse BTC (mBTC) gene. mBTC cDNA was used as a probe to screen a mouse 129/SVJ genomic bacterial artificial chromosome (BAC) library. Three positive clones containing the entire gene were isolated. DNA sequence analysis identified six exons (1-6) and five introns (A-E); a structure conserved among the EGF family. PCR analysis showed that introns A-E are approximately 7.8, 8.9, 3.8, 1.4 and 1.4 kb in length, respectively. The EGF-motif is encoded by exons 3 and 4 with an intron (intron C) disrupting the coding sequence between the second and third disulfide loops. All exon-intron boundaries are consistent with the "gt-ag" rule. Multiple transcription start sites and one poly(A) site, located 18 bp downstream of a polyadenylation signal sequence, were identified by 5'- and 3'-RACE, respectively. Approximately 2.6 kb of 5'-flanking region was sequenced and was shown to lack consensus TATA and CCAAT boxes, but was found to contain several putative cis-acting regulatory elements. These included consensus binding sites for transcription factors HNF3 beta, USF, Nkx2-5, AP-4, and Sp1. Functional promoter analysis of the 5'-flanking region in COS-7 cells, using 5'-deletion fragments (-168/+335; -635/+335; -732/+335; -1175/+335; -1698/+335) cloned into a promoterless firefly luciferase reporter vector, identified basal promoter activity and both positive and negative cis-acting elements.

5' Untranslated Regions↗
PubMed1998

The mouse Hoxc11 gene: genomic structure and expression pattern.

The mouse and human Hox complex consists of 39 genes in four linkage groups (A-D). Although the structure and expression patterns of most of these genes have been reported, the 5' members of the Hox C linkage group have been only partially characterized. Herein we report the primary and genomic structure of the mouse Hoxc11 gene as well as its expression pattern. The Hoxc11 gene encodes a 304 amino acid protein which is translated from a 2.2 kb transcript, derived from two exons. Hoxc11 mRNA is found in the most posterior region of the developing embryo commencing at 9.5 days of gestation. Expression is detected in the posterior neural tube, dorsal root ganglia, prevertebrae and hindlimbs. Expression is also found in metanephric mesenchyme which, later in development, becomes restricted to the cortical region of the developing kidney. In the developing genitalia, prominent expression is first observed in the posterior urogenital sinus that gives rise to the urethra, vagina and prostate. Later, expression is seen in paramesonephric and mesonephric ducts and in the genital tubercle. In the hindlimbs, Hoxc11 expression is seen in the mesenchyme posterior to the region forming the femur and fibula, but does not extend anteriorly to the region giving rise to the tibia or distally to the tarsal bones.

Amino Acid Sequence↗