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Results for “Multigene Family”

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PubMed1989

The vitamin D-binding protein, alpha-fetoprotein, albumin multigene family: detection of transcripts in multiple tissues.

The serum vitamin D-binding protein (DBP), a member of a multigene family that includes alpha-fetoprotein (alpha FP) and albumin (ALB), is expressed at high levels in the adult liver. Although several studies have demonstrated the presence of DBP on the cell surface of immunocytes and cytotrophoblasts, evidence of extra-hepatic DBP synthesis remains inconclusive. Using Northern blot analysis of RNA from multiple rat tissues, the DBP transcripts were present in the expected high levels in the adult liver. In addition, DBP mRNA was found in the adult kidney, testis, abdominal fat, and 18-day fetal yolk sac. The concentrations of DBP mRNA in these tissues is 100-1000-fold less than in the liver. Polymerase chain reaction amplification (PCR) of DBP, alpha FP, and ALB cDNAs, reverse transcribed from a wide variety of rat tissue RNA samples, was performed to examine their respective tissue-specific patterns of gene transcripts. The tissues in which DBP gene transcripts were noted by Northern analysis were paralleled at 20 cycles of PCR with liver much greater than kidney, yolk sac, testis, and abdominal fat. Similarly at 20 cycles, alpha FP-amplified fragments were detected in the yolk sac much greater than brain, testes, uterus, liver, and placenta; and ALB-amplified fragments in liver much greater than testis, uterus, placenta, and yolk sac. Unexpectedly, at 32 cycles of PCR, DBP, alpha FP, and ALB mRNAs could be detected at very low levels in all tissues examined. To examine the nature of the DBP mRNA from these nonhepatic sources, a Sprague-Dawley kidney cDNA library was screened, and a single cDNA recombinant was identified. This clone contained a full length DBP cDNA with 14 nucleotide and 3 predicted amino acid differences from the Fischer liver DBP cDNA reported previously. We conclude that the kidney and liver DBP mRNAs are transcription products of the same DBP locus and that DBP, alpha FP, and ALB genes display different spectra of tissue distribution. The unexpected finding that all three spliced RNA transcripts could be detected in at least trace quantities in all tissues studied suggests a leaky level of transcription by this multigene family or their transcription at low levels by an unidentified stromal cell common to all organs studied.

Amino Acid Sequence↗

PubMed1996

Structural analysis of the HLA-A/HLA-F subregion: precise localization of two new multigene families closely associated with the HLA class I sequences.

Positional cloning strategies for the hemochromatosis gene have previously concentrated on a target area restricted to a maximum genomic expanse of 400 kb around the HLA-A and HLA-F loci. Recently, the candidate region has been extended to 2-3 Mb on the distal side of the MHC. In this study, 10 coding sequences [hemochromatosis candidate genes (HCG) I to X] were isolated by cDNA selection using YACs covering the HLA-A/HLA-F subregion. Two of these (HCG II and HCG IV) belong to multigene families, as well as other sequences already described in this region, i.e., P5, pMC 6.7, and HLA class 1. Fingerprinting of the four YACs overlapping the region was performed and allowed partial localization of the different multigene family sequences on each YAC without defining their exact positions. Fingerprinting on cosmids isolated from the ICRF chromosome 6-specific cosmid library allowed more precise localization of the redundant sequences in all of the multigene families and revealed their apparent organization in clusters. Further examination of these intertwined sequences demonstrated that this structural organization resulted from a succession of complex phenomena, including duplications and contractions. This study presents a precise description of the structural organization of the HLA-A/HLA-F region and a determination of the sequences involved in the megabase size polymorphism observed among the A3, A24, and A31 haplotypes.

Cell Line↗

PubMedDate not supplied

Origin and evolution of the Amyrel gene in the alpha-amylase multigene family of Diptera.

Alpha-amylase genes often form multigene families in living organisms. In Diptera, a remote paralog, Amyrel, had been discovered in Drosophila, where this gene is currently used as a population and phylogenetic marker. The putative encoded protein has about 40% divergence with the classical amylases. We have searched the presence of the paralog in other families of Diptera to track its origin and understand its evolution. Amyrel was detected in a number of families of Muscomorpha (Brachycera-Cyclorrapha), suggesting an origin much older than previously thought. It has not been found elsewhere to date, and it is absent from the Anopheles gambiae genome. The intron-exon structures of the genes found so far suggest that the ancestral gene (before the duplication which gave rise to Amyrel) had two introns, and that subsequent, repeated and independent loss of one or both introns occurred in some Muscomorpha families. It seems that the Amyrel protein has experienced specific amino acid substitutions in regions generally well conserved in amylases, raising the possibility of peculiar, functional adaptations of this protein.

Amino Acid Motifs↗

PubMed1995

Structure of the MHC A and B locus promoters in hominoids. Insights on the evolution of the class I MHC multigene family.

The expansion and contraction of mammalian class I multigene families raises the issue as to what determines the loss or retention of family members. We propose that accumulating changes in regulatory regions result in the loss of expression of the gene products during times critical to selection, leading to the extinction of misregulated genes. The structures of promoter regions of MHC class I genes in nonhuman primates support this view. The B promoters are more homogeneous and contain regulatory elements also found in the promoters of the homologous class I genes of more distant mammals, whereas the A locus promoters were significantly more heterogeneous, have fewer sequence motifs related to known transcription factor-binding sites and have accumulated nucleotide substitutions within one of the widely conserved class I promoter elements. These findings are consistent with the view that the more polymorphic B locus is the principal MHC locus encoding functional class I Ag-presenting molecules whereas the less polymorphic A locus is assuming a secondary role as a consequence of promoter defects.

Animals↗

PubMed1991

Pax: a murine multigene family of paired box-containing genes.

A murine multigene family has been identified that shares a conserved sequence motif, the paired box, with developmental control and tissue-specific genes of Drosophila. To date five murine paired box-containing genes (Pax genes) have been described and one, Pax-1, has been associated with the developmental mutant phenotype undulated. Here we describe the paired boxes of three novel Pax genes, Pax-4, Pax-5, and Pax-6. Comparison of the eight murine paired domains of the mouse, the five Drosophila paired domains, and the three human paired domains shows that they fall into six distinct classes: class I comprises Pox meso, Pax-1, and HuP48; class II paired, gooseberry-proximal, gooseberry-distal, Pax-3, Pax-7, HuP1, and HuP2; class III Pax-2, Pax-5, and Pax-8; class IV Pax-4; class V Pox neuro; and class VI Pax-6. Pax-1 and the human gene HuP48 have identical paired domains, as do Pax-3 and HuP2 as well as Pax-7 and HuP1, and are likely to represent homologous genes in mouse and man. Identical intron-exon structure and extensive sequence homology of their paired boxes suggest that several Pax genes represent paralogs. The chromosomal location of all novel Pax genes and of Pax-3 and Pax-7 has been determined and reveals that they are not clustered.

Amino Acid Sequence↗

PubMed1996

Transcriptional silencing of a tRNA1Gly copy from within a multigene family is modulated by distal cis elements.

Individual copies of tRNA1Gly from within the multigene family in Bombyx mori could be classified based on in vitro transcription in homologous nuclear extracts into three categories of highly, moderately, or weakly transcribed genes. Segregation of the poorly transcribed gene copies 6 and 7, which are clustered in tandem within 425 base pairs, resulted in enhancement of their individual transcription levels, but the linkage itself had little influence on the transcriptional status. For these gene copies, when fused together generating a single coding region, transcription was barely detectable, which suggested the presence of negatively regulating elements located in the far flanking sequences. They exerted the silencing effect on transcription overriding the activity of positive regulatory elements. Systematic analysis of deletion, chimeric, and mutant constructs revealed the presence of a sequence element TATATAA located beyond 800 nucleotides upstream to the coding region acting as negative modulator, which when mutated resulted in high level transcription. Conversely, a TATATAA motif reintroduced at either far upstream or far downstream flanking regions exerted a negative effect on transcription. The location of cis-regulatory sequences at such farther distances from the coding region and the behavior of TATATAA element as negative regulator reported here are novel. These element(s) could play significant roles in activation or silencing of genes from within a multigene family, by recruitment or sequestration of transcription factors.

Animals↗

PubMed1996

Cloning, expression, and localization of a new member of a Paracentrotus lividus cell surface multigene family.

We have isolated and characterized a cDNA clone corresponding to a new member of bep (butanol, extracted, proteins) Paracentrotus lividus multigene family coding for cell surface proteins. The cDNA, called bep3, encodes a 370 amino acid protein and shares the same structural organization in the coding region with other members of the same gene family already characterized. Expression of this clone studied by Northern blot and by whole mount hybridization shows that the bep3 messenger is transcribed during oogenesis and utilized till the gastrula stage, whereas at the prism stage, unlike other members of the same gene family, new synthesis of messenger occurs. By whole mount hybridization spatial distribution of bep3 messenger in egg and embryos is established. This messenger appears located in the animal half of the unfertilized egg and moves to the cortical zone after fertilization; it is not present in the structures derived by the vegetal part of the embryo, such as the micromeres of the 16-cell stage, the primary mesenchyme cells of the blastula, and the primary intestine of the gastrula. At the prism stage instead, hybridization of bep3 messenger is restricted to the part of the embryo that will give origin to the oral region as successively confirmed by hybridization at the pluteus stage. The result of whole mount hybridization was confirmed by Northern blot hybridization of separated meso-macromere and micromere RNAs. A Southern blot experiment demonstrates that bep3 is codified by a single copy gene. Conservation of the bep multigene family in several Mediterranean and Japanese sea urchin species has also been analyzed.

Amino Acid Sequence↗

PubMed1997

Differential expression of the fibroblast growth factor receptor (FGFR) multigene family in normal human adult tissues.

This report describes a systematic analysis of the expression of the fibroblast growth factor receptor (FGFR) multigene family (FGFR1, FGFR2, FGFR3, and FGFR4) in archival serial sections of normal human adult tissues representing the major organ systems, using immunohistochemical techniques. Polyclonal antisera specific for FGFR1, FGFR2, FGFR3, and FGFR4 and a three-stage immunoperoxidase technique were employed to determine the cellular distribution of these receptors at the protein level. The expression profiles for the tissue-specific cellular localization of the FGFR multigene family demonstrated wide-spread and striking differential patterns of expression of individual receptors in the epithelia and mesenchyme of multiple tissues (stomach, salivary glands, pancreas, thymus, ureter, and cornea) and co-expression of FGFR1-4 in the same cell types of other tissues. The wide-spread expression of FGFR1-4 in multiple organ systems suggests an important functional role in normal tissue homeostasis. Differences in the spatial patterns of FGFR gene expression may generate functional diversity in response to FGF-1 and FGF-2, both of which bind with equally high affinity to more than one receptor subtype. In vivo, this may lead to functional differences that are crucial for the regulation of normal physiological processes and are responsible for the pathological mechanisms that orchestrate various disease processes.

Adult↗

PubMed1997

A modification in restriction pattern of the Plasmodium falciparum Pf60 multigene family associated with a specific antigenic variation switch in the Palo Alto line.

The wide occurrence of molecular rearrangements associated with expression of specific members within multigene families led us to investigate whether this also happens during antigenic variation of malaria parasites. We have investigated here the Pf60 multigene family restriction patterns of four distinct variants of the Plasmodium falciparum Palo Alto line propagated in Saimiri monkeys. The O and its cloned Oc variant both express the O serotype, while the R variant (derived from O parasites) and the Vc variant (derived from Oc parasites) express distinct serotypes. We show that a specific modification of the restriction pattern could be associated with antigenic switching in this line. The DNA of the variants which expressed the O serotype (O and Oc) had a specific 5.5 kb Hind III/Eco RI restriction fragment which was absent from the R or Vc parasite DNA, whereas both R and Vc DNA presented a 3.5 kb Hind III/Eco RI restriction fragment, which was absent from the O and Oc parasites. These results indicate that both expression and silencing of the O serotype were associated with specific restriction patterns, suggesting that some molecular rearrangement or some modification of the DNA might control expression of the variant surface antigen in malaria parasites.

Animals↗

PubMed2002

A method for estimating the mutation, gene conversion and recombination parameters in small multigene families.

A simple two-locus gene conversion model is considered to investigate the amounts of DNA variation and linkage disequilibrium in small multigene families. The exact solutions for the expectations and variances of the amounts of variation within and between two loci are obtained. It is shown that gene conversion increases the amount of variation within each locus and decreases the amount of variation between two loci. The expectation and variance of the amount of linkage disequilibrium are also obtained. Gene conversion generates positive linkage disequilibrium and the degree of linkage disequilibrium decreases as the recombination rate is increased. Using the theoretical results, a method for estimating the mutation, gene conversion, and recombination parameters is developed and applied to the data of the Amy multigene family in Drosophila melanogaster. The gene conversion rate is estimated to be approximately 60-165 times higher than the mutation rate for synonymous sites.

Animals↗

PubMed1990

Multigene families in African swine fever virus: family 360.

A group of cross-hybridizing DNA segments contained within the restriction fragments RK', RL, RJ, and RD' of African swine fever virus DNA were mapped and sequenced. Analysis of these sequences revealed the presence of a family of homologous open reading frames in regions close to the DNA ends. The whole family is composed of six open reading frames with an average length of 360 coding triplets (multigene family 360), four of which are located in the left part of the genome and two of which are in the right terminal EcoRI fragment. In close proximity to the right terminal inverted repeat, we found an additional small open reading frame which was homologous to the 5'-terminal portion of the other open reading frames, suggesting that most of that open reading frame has been deleted. These repeated sequences account for the previously described inverted internal repetitions (J.M. Sogo, J.M. Almendral, A. Talavera, and E. Viñuela, Virology 133:271-275, 1984). Most of the genes of multigene family 360 are transcribed in African swine fever virus-infected cells. A comparison of the predicted protein sequences of family 360 indicated that several residues are conserved, suggesting that an overall structure is maintained for every member of the family. The transcription direction of each open reading frame, as well as the evolutionary relationships among the genes, suggests that the family originated by gene duplication and translocation of sequences between the DNA ends.

Amino Acid Sequence↗

PubMed1997

Cloning, structural analysis, and mapping of the B30 and B7 multigenic families to the major histocompatibility complex (MHC) and other chromosomal regions.

We present the cloning, structural analysis, and mapping of new members belonging to two multigenic families, the B30-RING finger family and the B7.1-B7.2 family, as well as two genes derived by exon shuffling from members of these families. Eight new members were found and three of them map to the human major histocompatibilitiy complex (MHC) region. Phylogenic and physical mapping analysis allowed us to decipher the evolutionary story of these two multigenic families and to shed light on the evolution of the MHC region. We also show that a deductive analysis can be used to predict the existence of a given gene.

Amino Acid Sequence↗

PubMed1991

The ubiquitin-encoding multigene family of flax, Linum usitatissimum.

Ubiquitin (Ubq), a 76-amino acid (aa) protein, is found in all eukaryotic organisms and is one of the most conserved proteins so far studied. It is implicated in many cellular processes. The Ubq-encoding genes (ubq) are generally present as a multigene family. In flax, we have estimated that this multigene family contains at the most ten members. The initial flax ubq sequences were isolated from a flax genomic library in lambda EMBL4 using a heterologous Arabidopsis thaliana ubq probe. An 916-bp fragment from one of the phage clones was subcloned and sequenced. The aa sequence derived from the nucleotide sequence of this fragment is identical to that of other plant Ubqs. This fragment was then used to isolate additional flax ubq clones. In all, eleven phage lambda clones, which represent six members of the gene family, were restriction-mapped and characterized. These six members are represented as three monomers, three poly-Ubqs, one hexamer and two tetramers. They can be present at either a single locus (two of the monomers and one of the poly-Ubqs) or at two loci (the remaining three genes). The other four members of the family are yet to be cloned and characterized.

Amino Acid Sequence↗

PubMed1983

Comparison of class I (H-2) gene sequences. Derivation of unique probes for members of this multigene family.

The genes for the classical transplantation antigens are unique in that they belong to a multigene family of which each member is represented by a large number of alleles. Since all of these genes are highly related in sequence, it has been difficult to study the expression of individual members of this complex gene family. Based upon our initial suggestion that the 3' noncoding regions of these genes may be useful in identifying mRNA molecules transcribed from different loci, we have compared a large number of sequences from different inbred mouse strains and have been able to assign each of these sequences without ambiguity into distinct allelic series. Such accurate assignment has afforded the opportunity to compare the coding regions of these highly homologous genes and has led to the identification of sequences which are apparently unique to specific genes in the family. Synthetic oligonucleotides corresponding to each of the locus-specific unique regions have been used successfully to type a panel of cDNA sequences, as well as to quantitate the relative amounts of mRNA transcribed from distinct loci. The availability of these specific coding probes will allow the analysis of individual genes and their specific expression without interference from other highly homologous sequences in this multigene family.

Amino Acid Sequence↗

PubMed2005

Transcription of individual tRNA1Gly genes from within a multigene family is regulated by transcription factor TFIIIB.

Members of a multigene family from the silkworm Bombyx mori have been classified based on their transcriptions in homologous nuclear extracts, into three groups of highly, moderately and poorly transcribed genes. Because all these gene copies have identical coding sequences and consequently identical promoter elements (the A and B boxes), the flanking sequences modulate their expression levels. Here we demonstrate the interaction of transcription factor TFIIIB with these genes and its role in regulating differential transcriptions. The binding of TFIIIB to the poorly transcribed gene -6,7 was less stable compared with binding of TFIIIB to the highly expressed copy, -1. The presence of a 5' upstream TATA sequence closer to the coding region in -6,7 suggested that the initial binding of TFIIIC to the A and B boxes sterically hindered anchoring of TFIIIB via direct interactions, leading to lower stability of TFIIIC-B-DNA complexes. Also, the multiple TATATAA sequences present in the flanking regions of this poorly transcribed gene successfully competed for TFIIIB reducing transcription. The transcription level could be enhanced to some extent by supplementation of TFIIIB but not by TATA box binding protein. The poor transcription of -6,7 was thus attributed both to the formation of a less stable transcription complex and the sequestration of TFIIIB. Availability of the transcription factor TFIIIB in excess could serve as a general mechanism to initiate transcription from all the individual members of the gene family as per the developmental needs within the tissue.

Animals↗

PubMed2004

Birth-and-death evolution with strong purifying selection in the histone H1 multigene family and the origin of orphon H1 genes.

Histones are small basic nuclear proteins with critical structural and functional roles in eukaryotic genomes. The H1 multigene family constitutes a very interesting histone class gathering the greatest number of isoforms, with many different arrangements in the genome, including clustered and solitary genes, and showing replication-dependent (RD) or replication-independent (RI) expression patterns. The evolution of H1 histones has been classically explained by concerted evolution through a rapid process of interlocus recombination or gene conversion. Given such intriguing features, we have analyzed the long-term evolutionary pattern of the H1 multigene family through the evaluation of the relative importance of gene conversion, point mutation, and selection in generating and maintaining the different H1 subtypes. We have found the presence of an extensive silent nucleotide divergence, both within and between species, which is always significantly greater than the nonsilent variation, indicating that purifying selection is the major factor maintaining H1 protein homogeneity. The results obtained from phylogenetic analysis reveal that different H1 subtypes are no more closely related within than between species, as they cluster by type in the topologies, and that both RD and RI H1 variants follow the same evolutionary pattern. These findings suggest that H1 histones have not been subject to any significant effect of interlocus recombination or concerted evolution. However, the diversification of the H1 isoforms seems to be enhanced primarily by mutation and selection, where genes are subject to birth-and-death evolution with strong purifying selection at the protein level. This model is able to explain not only the generation and diversification of RD H1 isoforms but also the origin and long-term persistence of orphon RI H1 subtypes in the genome, something that is still unclear, assuming concerted evolution.

Amino Acid Sequence↗

PubMed1996

Localisation and differential expression of the fibroblast growth factor receptor (FGFR) multigene family in normal and atherosclerotic human arteries.

OBJECTIVE: Aberrant expression of FGF-1 and FGF-2 may be central to the atherosclerotic disease process, promoting both intimal hyperplasia and plaque neovascularisation. FGF-1 and FGF-2 mediate their biological effects by binding to a family of specific high-affinity cell surface receptors with protein tyrosine kinase activity. Four receptors have been identified in the human (FGFR1/flg gene product, FGFR2/bek gene product, FGFR3 and FGFR4), but little is known of their in vivo tissue distribution. Characterisation of the spatial distribution of the FGFR multigene family in both normal and atherosclerotic arteries is a prerequisite to further define the functional role of FGF-1 and FGF-2 in atherosclerosis. The objective of this study was to examine the cell-type-specific expression of the FGFR multigene family members in both normal and atherosclerotic human arteries. METHODS: FGFR expression was investigated immunocytochemically with polyclonal antisera to FGFR1-4 and by in situ hybridisation using FGFR1-4 riboprobes in archival material. Total cellular mRNA was analysed using poly d(T) and the levels correlated with the expression of FGFR1-4 mRNA. RESULTS: At the protein level, FGFR1-4 were expressed in the medial smooth muscle cells and adventitial vessels of normal arteries. In simple and advanced lesions, the expression profiles of FGFR1-4 showed variability between individual arteries, and cell-type-specific differential FGFR expression was apparent. Widespread co-expression of FGFR1 and FGFR2 was observed in intimal smooth muscle cells, foam cells and the plaque microvasculature of simple and advanced lesions. FGFR3 and FGFR4 exhibited more restricted patterns of distribution within the plaque. In situ hybridisation with poly d(T) confirmed high cellular transcriptional activity in archival atherosclerotic lesions. The high levels of total cellular mRNA and FGFR protein were not always reciprocated at the FGFR1-4 mRNA level, and only FGFR1 and FGFR2 mRNA transcripts were abundant in intimal lesions. CONCLUSION: These data provide evidence to suggest involvement of the FGF-FGFR multigene families in human atherogenesis. Differential FGFR expression in plaque subtypes may reflect distinct differences in receptor function which may be relevant to lesion progression during atherosclerosis.

Adult↗

PubMed1998

Multigene families encoding the major hemagglutinins in phylogenetically distinct mycoplasmas.

Mycoplasma synoviae has two major membrane antigens, MSPA and MSPB, both of which are phase variable and which may be coordinately involved in adhesion of the organism to erythrocytes. A single gene (vlhA) from M. synoviae was characterized, and polypeptides were expressed from nonoverlapping 5' and 3' regions in Escherichia coli. The expression product of the vlhA 5' region reacted with specific reagents against MSPB, while that of the 3' region reacted with specific reagents against MSPA. Analysis of the predicted amino acid sequence showed a characteristic signal peptidase II cleavage site, and the presence of the acylation site was confirmed by identification of a lipid-associated membrane protein, similar in molecular mass to MSPB, in [3H]palmitate-labelled membrane proteins. Further sequence analysis of the vlhA gene revealed a high identity with the Mycoplasma gallisepticum pMGA1.7 gene, a member of a large translated family. The vlhA gene was shown to hybridize to multiple restriction fragments of the M. synoviae genome, suggesting that it was also a member of a multigene family. These findings indicate that coordinate phase variation of the two major surface antigens of M. synoviae WVU may be due to their expression from the same gene and that homologous gene families encode the major hemagglutinins of two phylogenetically distinct mycoplasmas. The presence of homologous multigene families in such phylogenetically distinct species, but not in the genomes of more closely related species, suggests that the families may have been transferred horizontally.

Amino Acid Sequence↗