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PubMed2003

Reg gene family and human diseases.

Regenerating gene (Reg or REG) family, within the superfamily of C-type lectin, is mainly involved in the liver, pancreatic, gastric and intestinal cell proliferation or differentiation. Considerable attention has focused on Reg family and its structurally related molecules. Over the last 15 years, 17 members of the Reg family have been cloned and sequenced. They have been considered as members of a conserved protein family sharing structural and some functional properties being involved in injury, inflammation, diabetes and carcinogenesis. We previously identified Reg IV as a strong candidate for a gene that was highly expressed in colorectal adenoma when compared to normal mucosa based on suppression subtractive hybridization (SSH), reverse Northern blot, semi-quantitative reverse transcriptase PCR (RT-PCR) and Northern blot. In situ hybridization results further support that overexpression of Reg IV may be an early event in colorectal carcinogenesis. We suggest that detection of Reg IV overexpression might be useful in the early diagnosis of carcinomatous transformation of adenoma. This review summarizes the roles of Reg family in diseases in the literature as well as our recent results of Reg IV in colorectal cancer. The biological properties of Reg family and its possible roles in human diseases are discussed. We particularly focus on the roles of Reg family as sensitive reactants of tissue injury, prognostic indicators of tumor survival and early biomarkers of carcinogenesis. In addition to our current understanding of Reg gene functions, we postulate that there might be relationships between Reg family and microsatellite instability, apoptosis and cancer with a poor prognosis. Investigation of the correlation between tumor Reg expression and survival rate, and analysis of the Reg gene status in human malignancies, are required to elucidate the biologic consequences of Reg gene expression, the implications for Reg gene regulation of cell growth, tumorigenesis, and the progression of cancer. It needs to be further attested whether Reg gene family is applicable in early detection of cancer and whether Reg and Reg-related molecules can offer novel molecular targets for anticancer therapeutics. This has implications with regard to prognosis, such as in monitoring cancer initiation, progression and recurrence, as well as the design of chemotherapeutic drugs.

Diabetes Mellitus↗

PubMed1997

Tumor-suppressive pathways in pancreatic carcinoma.

During tumorigenesis, positive selection is exerted upon those tumor cells that alter rate-limiting regulatory pathways. A corollary of this principle is that mutation of one gene abrogates the need for alteration of another gene in the same pathway and also that the coexistence in a single tumor of mutations in different genes implies their involvement in distinct tumor-suppressive pathways. We studied 42 pancreatic adenocarcinomas for genetic alterations in the K-ras oncogene and the p16, p53, and DPC4 tumor suppressor genes. All of them had the K-ras gene mutated. Thirty-eight % of the tumors had four altered genes, another 38% had three altered genes, 15% had two altered genes, and 8% of the tumors had one altered gene. Interestingly, we noted a high concordance of DPC4 and p16 inactivations (P = 0.007), suggesting that the genetic inactivation of p16 increases the selective advantage of subsequent mutation in DPC4. No statistically significant association was identified between the alteration of these cancer genes and pathological or clinical parameters. This type of multigenic analysis in human tumors may serve to substantiate experimental tumor models and thus increase our understanding of the truly physiologically relevant tumor-suppressive pathways that are abrogated during human tumorigenesis.

Adenocarcinoma↗

PubMed2004

Multigene family for Bowman-Birk type proteinase inhibitors of wild soja and soybean: the presence of two BBI-A genes and pseudogenes.

Genes for Bowman-Birk type protease inhibitors (BBIs) of wild soja (Glycine soja) and soybean (Glycine max) comprise a multigene family. The organization of the genes for wild soja BBIs (wBBIs) was elucidated by an analysis of their cDNAs and the corresponding genomic sequences, and compared with the counterparts in the soybean. The cDNAs encoding three types of wild soja BBIs (wBBI-A, -C, and -D) were cloned. Two subtypes of cDNAs for wBBI-A, designated wBBI-A1 and -A2, were further identified. Similar subtypes (sBBI-A1 and -A2) were also found in the soybean genome. cDNA sequences for wBBIs were highly homologous to those for the respective soybean homologs. Phylogenetic analysis of these cDNAs demonstrated the evolutional proximity between these two leguminae strains.

Base Sequence↗

PubMed1992

VACUOLAR-TYPE H+-TRANSLOCATING ATPases IN PLANT ENDOMEMBRANES: SUBUNIT ORGANIZATION AND MULTIGENE FAMILIES.

Acidification of endomembrane compartments by the vacuolar-type H+-translocating ATPase (V-ATPase) is vital to the growth and development of plants. The V-ATPase purified from oat roots is a large complex of 650x10(3 )Mr that contains 10 different subunits of 70, 60, 44, 42, 36, 32, 29, 16, 13 and 12x10(3 )Mr. This set of ten polypeptides is sufficient to couple ATP hydrolysis to proton pumping after reconstitution of the ATPase into liposomes. Unlike some animal V-ATPases, the purified and reconstituted V-ATPase from oat is directly stimulated by Cl-. The peripheral complex of the ATPase includes the nucleotide-binding subunits of 70 and 60x10(3 )Mr and polypeptides of 44, 42, 36 and 29x10(3 )Mr. Six copies of the 16x10(3 )Mr proteolipid together with three other polypeptides are thought to make up the integral sector that forms the H+-conducting pathway. Release of the peripheral complex from the native membrane completely inactivates the pump; however, the peripheral subunits can be reassembled with the membrane sector to form a functional H+ pump. Comparison of V-ATPases from several plants indicates considerable variations in subunit composition. Hence, several forms of the V-ATPase may exist among, and probably within, plant species. At least four distinct cDNAs encode the 16x10(3 )Mr proteolipid subunit in oat. Multiple genes could encode different subtypes of the H+ pump that are regulated by the developmental stage and physiological function specific to the cell or tissue type.

Journal Article↗

PubMed1980

A computer simulation of evolutionary forces controlling the size of a multigene family.

A Monte Carlo-type simulation of the evolution of a multigene family was performed. The model was designed to study the selective forces which may control the size of a multigene family. As expected, we find that direct selection on the size of the multigene family can control its size. More important, we find that selection acting upon the family as a single functional unit, in conjunction with homologous but unequal crossing over, can also control the size of a multigene family.

Animals↗

PubMed2001

S100: a multigenic family of calcium-modulated proteins of the EF-hand type with intracellular and extracellular functional roles.

S100 is a multigenic family of non-ubiquitous Ca(2+)-modulated proteins of the EF-hand type expressed in vertebrates exclusively and implicated in intracellular and extracellular regulatory activities. Within cells, most of S100 members exist in the form of antiparallelly packed homodimers (in some cases heterodimers), capable of functionally crossbridging two homologous or heterologous target proteins in a Ca(2+)-dependent (and, in some instances, Ca(2+)-independent) manner. S100 oligomers can also form, under the non-reducing conditions found in the extracellular space and/or within cells upon changes in the cell redox status. Within cells, S100 proteins have been implicated in the regulation of protein phosphorylation, some enzyme activities, the dynamics of cytoskeleton components, transcription factors, Ca(2+) homeostasis, and cell proliferation and differentiation. Certain S100 members are released into the extracellular space by an unknown mechanism. Extracellular S100 proteins stimulate neuronal survival and/or differentiation and astrocyte proliferation, cause neuronal death via apoptosis, and stimulate (in some cases) or inhibit (in other cases) the activity of inflammatory cells. A cell surface receptor, RAGE, has been identified on inflammatory cells and neurons for S100A12 and S100B, which transduces S100A12 and S100B effects. It is not known whether RAGE is a universal S100 receptor, S100 members interact with other cell surface receptors, or S100 protein interaction with other extracellular factors specifies the biological effects of a given S100 protein on a target cell. The variety of intracellular target proteins of S100 proteins and, in some cases, of a single S100 protein, and the cell specificity of expression of certain S100 members suggest that these proteins might have a role in the fine regulation of effector proteins and/or specific steps of signaling pathways/cellular functions. Future analyses should discriminate between functionally relevant S100 interactions with target proteins and in vitro observations devoid of physiological importance.

Animals↗

PubMed1993

Replication timing and Xenopus 5S RNA gene transcription in vitro.

The influence of DNA replication in a chromosomal environment on the transcription of Xenopus laevis 5S RNA genes has been examined using low-speed extracts of Xenopus eggs and Xenopus sperm nuclei. The major oocyte- and somatic-type 5S RNA multigene families of X. laevis are differentially expressed in these extracts dependent on limiting transcription factors and replicate in different compartments of S-phase. Under these particular experimental conditions the timing of replication of the somatic 5S RNA genes appears to be independent of their transcriptional activity. Moreover, differential transcription of the oocyte- and somatic-type 5S RNA genes is not influenced by the replication process.

Animals↗

PubMed1990

Induction of heat shock (stress) genes in the mammalian brain by hyperthermia and other traumatic events: a current perspective.

Is the heat shock response physiologically relevant? For example, following hyperthermia or ischemia, what neural cell types show induction of heat shock genes and what is the time course of the effect? Initial experiments in this area demonstrated the prominent induction of a 70 kDa heat shock protein (hsp70) when labeled brain proteins isolated from hyperthermic animals were analyzed. Recently, in situ hybridization and immunocytochemistry have been utilized to map out the pattern of expression of both constitutively expressed and stress-inducible members of the hsp70 multigene family. Different types of neural trauma have been found to induce characteristic cellular responses in the mammalian brain with regard to the type of brain cell that responds by inducing hsp70 and the timing of the induction response. Fever-like temperature causes a dramatic induction of hsp70 mRNA within 1 hr in fiber tracts of the forebrain and cerebellum, a pattern consistent with a strong glial response to heat shock. Tissue injury, namely, a small surgical cut in the cerebral cortex, induces a rapid and highly localized induction of hsp70 mRNA in cells proximal to the injury site. Using an immunocytochemical approach, a neuronal pattern of induction of hsp70 has been demonstrated following ischemia or kainic acid-induced seizures. It is apparent that the pattern of induction of hsp70 may be a useful early marker of cellular injury and may identify previously unrecognized areas of vulnerability in the nervous system.

Animals↗

PubMed2005

The complete genomic sequence of the carp fast skeletal myosin heavy chain gene.

We have determined the complete DNA nucleotide sequence of the carp Cyprinus carpio fast skeletal myosin heavy chain (MYH) gene. Introns and exons were predicted by comparison with the corresponding carp MYH cDNAs previously reported. The gene encoded the entire mRNA transcript and contained 5958 nucleotides (nt) including 77 nt 5'-untranslated region, 5796 nt coding region for 1931 amino acids, and 85 nt 3'-untranslated region. The coding region was split by 38 introns and the complete gene contained 11,385 nt. This integration of the carp fast skeletal MYH gene was comparable to those of the rat and chicken embryonic MYH genes, which have 41 and 40 exons, respectively. However, the entire gene size of carp MYH was about half those of rat and chicken due to much smaller size of carp introns. We have also demonstrated that this carp MYH gene belonged to so-called intermediate type in a multigene family of carp fast skeletal muscle MYH in comparison of its nucleotide and deduced amino acid sequences to those of carp MYH cDNAs reported previously.

3' Untranslated Regions↗

PubMed2005

Searching QTL by gene expression: analysis of diabesity.

BACKGROUND: Recent developments in sequence databases provide the opportunity to relate the expression pattern of genes to their genomic position, thus creating a transcriptome map. Quantitative trait loci (QTL) are phenotypically-defined chromosomal regions that contribute to allelically variant biological traits, and by overlaying QTL on the transcriptome, the search for candidate genes becomes extremely focused. RESULTS: We used our novel data mining tool, ExQuest, to select genes within known diabesity QTL showing enriched expression in primary diabesity affected tissues. We then quantified transcripts in adipose, pancreas, and liver tissue from Tally Ho mice, a multigenic model for Type II diabetes (T2D), and from diabesity-resistant C57BL/6J controls. Analysis of the resulting quantitative PCR data using the Global Pattern Recognition analytical algorithm identified a number of genes whose expression is altered, and thus are novel candidates for diabesity QTL and/or pathways associated with diabesity. CONCLUSION: Transcription-based data mining of genes in QTL-limited intervals followed by efficient quantitative PCR methods is an effective strategy for identifying genes that may contribute to complex pathophysiological processes.

Algorithms↗

PubMed1991

Ly-49 multigene family. New members of a superfamily of type II membrane proteins with lectin-like domains.

Ly-49 (YE1/48, A1) is a dimer protein expressed on subpopulations of murine NK cells. It is a member of a superfamily of type II transmembrane proteins containing carbohydrate recognition domains (CRD). In the mouse genome, the detection of multiple restriction fragments that cross-hybridize with Ly-49 cDNA probes suggests the presence of related genes. In this study, we have isolated several genomic clones encoding portions of CRD sequences highly homologous to the CRD of Ly-49. By using primers based on the consensus sequences of the genomic clones, expression of Ly-49-related genes was detected by the polymerase chain reaction in various organs, including lung, kidney, liver, spleen, and thymus. Two full-length cDNA clones that are highly homologous to the Ly-49 gene were subsequently isolated from a lung cDNA library. At the nucleotide level, the two clones are 72% and 80% identical to Ly-49 in their translated regions, but their sequences are different from those of the genomic clones characterized to date. The two cDNA clones potentially encode type II transmembrane proteins containing CRD that are very similar to Ly-49. These amino acid sequences are also homologous to other members of the superfamily of CRD-containing type II transmembrane proteins, including hepatic lectins and the low affinity IgER (CD23). The homology is most evident in the CRD but is also significant in other domains. These results demonstrate the existence of several functional genes that are highly related to Ly-49. These genes comprise a subfamily within the superfamily of type II transmembrane proteins containing CRD.

Amino Acid Sequence↗

PubMed1997

Multigene antiviral vectors inhibit diverse human immunodeficiency virus type 1 clades.

The chronicity of infection by the human immunodeficiency virus (HIV) calls for therapeutic regimens that offer sustained antiviral effects, such as gene therapy. Recent studies have demonstrated that expression of HIV mutant transdominant proteins, RNA decoys, and ribozymes efficiently inhibited HIV replication. We have previously shown that an RNA decoy (stem-loop II of the Rev response element of HIV type 1 [HIV-1], named SL2) and a ribozyme (Rz) targeting the U5 region of the HIV-1 5' long terminal repeat (LTR), combined in a fusion molecule, was more efficient in inhibiting HIV-1 replication than the ribozyme or the decoy alone. In this study, we expressed this fusion molecule in a retrovirus-based double-copy vector to obtain higher expression of this molecule. Furthermore, we inserted a sequence internally to drive expression of another fusion molecule with a ribozyme targeting the env/rev region linked to SL2 to obtain a triple-copy vector. These multigene antiviral vectors were subsequently transduced or transfected into human CD4+ T cells (Molt-4). Results showed that the translocation of the SL2-Rz cassette from the 3' to the 5' LTR occurred in 80% of the transduced cells. The numbers of ribozyme RNA transcripts, estimated by competitive-quantitative reverse transcription (RT)-PCR, were 1.2 x 10(5), 1.2 x 10(4), and 1.5 x 10(3) copies per cell for the triple-copy, double-copy, and single-copy vectors, respectively. Cell challenge with multiple subtypes of HIV-1 (clades A to E) showed commensurate levels of virus inhibition for the three vectors. This study suggests that the combination of multiple anti-HIV genes, such as ribozymes and decoys, targeting multiple sites of HIV RNA and expressed at high levels are promising for the treatment of HIV-1 infection.

Animals↗

PubMed1992

A cell-free recombination system for site-specific integration of multigenic shuttle plasmids into the herpes simplex virus type 1 genome.

This report describes a novel method for complementation studies of defective herpes simplex virus (HSV) genes. Viral test gene and nonviral reporter gene cassettes were rapidly integrated into the HSV genome in a site-specific and reversible manner by using the P1 phage-based Cre-lox recombination system. Shuttle plasmids contained a functional loxP recombination site, an expressible form of the bacterial lacZ gene, and a copy of the wild-type glycoprotein B (gB) gene or double mutant gB allele containing both a temperature-sensitive (ts) mutation and a syncytium (syn)-forming mutation. A recipient viral genome, K delta T::lox1, was constructed from the HSV type 1 (syn) gB-deficient mutant virus, K delta T, by marker transfer of the loxP recombination site into the viral thymidine kinase locus. Shuttle plasmids of up to 12.9 kb in length were recombined with high efficiency (11 to 20%) into the K delta T::lox1 genome in cell-free, Cre-mediated recombination reactions. Expression of a functional wild-type or double mutant gB polypeptide complemented the nonfunctional polypeptide expressed from the deleted, normal gB locus and allowed production of either wild-type or Syn- plaques on Vero cells. The latter recombinant virus was also ts for growth. The ability to express viral genes from plasmids which can be shuttled into and out of the HSV genome in cell-free recombination reactions makes this a powerful method for performing genetic studies of the biologic properties of viral gene products.

Animals↗

PubMed2005

The chicken leukocyte receptor complex: a highly diverse multigene family encoding at least six structurally distinct receptor types.

The chicken Ig-like receptors (CHIR) have been described as two Ig domain molecules with long cytoplasmic tails containing inhibitory motifs. In this study, we demonstrate that CHIR form a large family, with multiple members showing great sequence variability among members as well as a great diversity in domain organization and properties of the transmembrane and cytoplasmic segments. We characterize various novel receptor types with motifs indicative of inhibitory, activating, or both functions. In addition to the inhibitory receptors with two ITIM, receptors with a single immunoreceptor tyrosine-based switch motif or receptors lacking a cytoplasmic domain were isolated. Activating receptors with a short cytoplasmic domain and a transmembrane arginine assembled with the newly identified chicken FcepsilonRIgamma chain. Three bifunctional receptor types were characterized composed of one or two C2-type Ig-like domains, a transmembrane region with a positively charged residue and combinations of cytoplasmic motifs such as ITIM, immunoreceptor tyrosine-based switch motif, and YXXM. RT-PCR revealed distinct expression patterns of individual CHIR. All receptor types shared a conserved genomic architecture, and in single Ig domain receptors a pseudoexon replaced the second Ig exon. Southern blot analyses with probes specific for the Ig1 domain were indicative of a large multigene family. Of 103 sequences from the Ig1 domain of a single animal, 41 unique sequences were obtained that displayed extensive variability within restricted Ig regions. Fluorescence in situ hybridization localized the CHIR gene cluster to microchromosome 31 and identified this region as orthologous to the human leukocyte receptor complex.

Amino Acid Sequence↗

PubMed1986

Structures of two HaeIII-type genes in the human salivary proline-rich protein multigene family.

Two members of the human salivary proline-rich protein (PRP) multigene family have been isolated and completely sequenced. These PRP genes, PRH1 and PRH2, are of the HaeIII-type subfamily and code for acidic PRP proteins. Both genes are approximately 3.5 kilobase pairs (kb) in length and contain four exons. Exon 3 encodes the proline-rich part of the protein and includes five 63-base pair (bp) repeats. CAT and ATA boxes and several possible enhancer sequences occur in a 1-kb region 5' to exon 1. Two sets of repeats occur in the sequenced region in addition to the 63-bp repeats: one pair of about 140 bp flanks 500 bp of DNA in the first intervening sequence, and the other pair of 72 bp is tandemly repeated 1.4 kb 5' to the PRH1 gene. The 4-kb region of sequenced DNA from PRH1 differs by an average of 8.7% from the same region in PRH2, but the nucleotide sequences of the exon 3 of the two genes differ by only 0.2%. This result suggests the occurrence of a recent gene conversion event. The regions containing the 5-fold repeated sequences of 63 bp are identical in the two genes, PRH1 and PRH2. A comparison of the human HaeIII and BstNI subfamily repeats and a comparison of the human, mouse, and rat repeats suggest that the individual repeats have evolved in a concerted fashion within each gene and within the PRP gene family as a whole.

Animals↗

PubMed2025

A paradoxical population structure of var DBLα types in Africa.

The var multigene family encodes Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), central to host-parasite interactions. Genome structure studies have identified three major groups of var genes by specific upstream sequences (upsA, B, or C). Var with these ups groups have different chromosomal locations, transcriptional directions, and associations with disease severity. Here we explore temporal and spatial diversity of a region of var genes encoding the DBLα domain of PfEMP1 in Africa. By applying a novel ups classification algorithm (cUps) to publicly-available DBLα sequence datasets, we categorised DBLα according to association with the three ups groups, thereby avoiding the need to sequence complete genes. Data from deep sequencing of DBLα types in a local population in northern Ghana surveyed seven times from 2012 to 2017 found variants with rare-to-moderate-to-extreme frequencies, and the common variants were temporally stable in this local endemic area. Furthermore, we observed that every isolate repertoire, whether mono- or multiclonal, comprised DBLα types occurring with these frequency ranges implying a common genome structure. When comparing African countries of Ghana, Gabon, Malawi, and Uganda, we report that some DBLα types were consistently found at high frequencies in multiple African countries while others were common only at the country level. The implication of these local and pan-Africa population patterns is discussed in terms of advantage to the parasite with regards to within-host adaptation and resilience to malaria control.

Plasmodium falciparum↗

PubMed1999

Activation of the mouse inositol 1,4,5-trisphosphate receptor type 1 promoter by AP-2.

Inositol 1,4,5-trisphosphate receptor (IP3R) functions as a Ca2+ channel that increases the intracellular Ca2+ upon binding to inositol trisphosphates. IP3R is expressed ubiquitously and consists of a multigene family. Since the type 1 IP3R (IP3R1) is highly expressed in the cerebellar Purkinje cells and moderately in hippocampus in the mammalian central nervous system (CNS), it is regarded as a neural member of this gene family. In this work, we investigated transcriptional regulation of the mouse ip3r1 gene. A DNaseI footprinting assay demonstrated that a sequence from -95 to -75, designated as box-II, was a binding site for a cerebellum-enriched factor. A consensus sequence for AP-2 was located in box-II. An electrophoretic mobility shift assay with anti-AP-2 antibody revealed that AP-2 is capable of binding to box-II. Deletion analysis of box-II showed that flanking sequences beside the box-II motif were required for the stable binding. We demonstrated by transient luciferase assay that exogenously expressed AP-2 activated box-II-dependent transcription. Moreover, we showed that endogenous AP-2 induced by retinoic acid also activated transcription via box-II in P19 cells. In-situ hybridization of the mouse brain revealed that AP-2 was predominantly expressed in the cerebellar Purkinje cells and hippocampal CA1 region, where IP3R1 is also highly expressed. From these observations, AP-2 binding to box-II is thought to be responsible for IP3R1 gene regulation in the CNS.

Animals↗

PubMed1986

Nakahara memorial lecture. Non-receptor type protein-tyrosine kinases closely related to src and yes compose a multigene family.

We have determined the total coding sequence of human c-yes, a non-receptor type protein-tyrosine kinase gene, and found that the c-yes gene closely resembles the c-src gene. Recently, two new genes, syn and lyn, were found to encode proteins closely related to the yes product. In addition, we also determined the partial sequence of fgr. These genes together with lck reported by two American groups have very closely related structures and are thought to compose a closely related group of non-receptor type protein-tyrosine kinases. Partial analysis of the structures of these genes indicated that they have identical splicing junctions at all sites so far examined. On the other hand, the erbB-1/EGF (epidermal growth factor) receptor gene and the erbB-2/neu gene have completely different splicing junctions from those of the above gene group even in the kinase domain, although these genes also have protein kinase activity specific for tyrosine residues and the erbB-1 and -2 genes share splicing sites. These results suggest that the genes of the group of six non-receptor type kinases and those of the erbB-1 and erbB-2 gene group are descendants evolved by duplication of two distinct ancestor genes and are members of two distinct multi-gene families. The genes coding for protein kinases may be members of a super-family including multiple distinct gene families.

Amino Acid Sequence↗