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PubMed1984

A multigene family of intron lacking and containing genes, encoding for mouse ribosomal protein L7.

Mouse ribosomal protein L7 is encoded by a multigene family. Screening of two mouse genomic libraries with cloned L7 cDNA, has resulted in the isolation of nine independent lambda Charon 4A recombinant phages which include seven different L7 genes. Restriction enzyme mapping of six of these genes (L7-1, L7-16, L7-18, L7-28, L7-35 and L7- 16b ) reveals dissimilarity in sites within the L7 sequences as well as in the flanking regions. Electron microscopic analysis of heteroduplex and S1 nuclease mapping demonstrate that the first five genes contain the entire L7 mRNA sequence but lack introns. Based on these features we propose that these are processed genes. Of the L7 genes described here only one (L7- 16b ) exhibits a high degree of homology with L7 mRNA and contains introns. We discuss the possibility that this low representation of intron containing L7 genes may reflect the proportion of functional L7 genes in this multigene family.

Animals↗

PubMed1986

The silkmoth late chorion locus. II. Gradients of gene conversion in two paired multigene families.

The late chorion locus of Bombyx mori is composed of two multigene families arranged as divergently oriented pairs irregularly spaced over 140 X 10(3) bases of DNA. The average sequence homology is 91% for the 15 members of each family. DNA sequence analysis reveals: that most of the sequence variants found in individual members of a family are shared by two or more members of that family; that family members sharing a particular variant are scattered throughout the locus; and adjacent variants in individual genes are often shared by different subsets of family members. The large number of shared variants scored and their distribution is most simply explained by numerous sequence transfers similar to gene conversions. These sequence transfers are not uniformly distributed along each gene pair. Sequence transfer is highest near the 3' end of each gene and lowest in the common 5' region between the divergent genes. A model is presented that explains these gradients by assuming that the events leading to gene conversion preferentially initiate in a simple-sequence DNA repeat. The resulting heteroduplexes extend to distances influenced by features of the sequence affecting their stability. The simple-sequence DNA is part of the major exon in both gene families and encodes tandem copies of the sequence Cys-Gly-Gly and Cys-Gly. Striking identity in the precise pattern of codon biases of these repeated sequences in the two families suggests that repeated sequence transfers occur also between families in this simple-sequence region.

Animals↗

PubMed2001

Differential expression of potato U1A spliceosomal protein genes: a rapid method for expression profiling of multigene families.

The spliceosomal protein, UIA, is a component of the U1snRNP essential to pre-mRNA splicing. From the ubiquitous nature of the splicing machinery, expression of U1A genes is expected to be constitutive. However, many plant genes are organised in multigene families that exhibit variation in expression profiles. Without detailed knowledge of the size of the U1A gene family or their degree of sequence variation, we examined the expression of the U1A genes using a novel approach. The approach was based on 5' RACE with [32P]-labelled primers and separation of products on high-resolution DNA sequencing gels to give a 'snapshot' of the expression of U1A genes. This was followed by sequencing of cloned 5' RACE products and of products re-amplified from excised bands. In combination with RT-PCR/SSCP, these analyses allowed the rapid identification of different gene transcripts and assessment of their relative expression profiles. Transcripts from four U1A genes (U1A-1 to U1A-4) were identified, of which U1A-1 and U1A-2 were expressed much more highly than U1A-3 and U1A-4. Differential expression of the two most highly expressed genes, U1A-1 and UIA-2, was observed in that only U1A-2 was expressed in flowers. Upstream sequences of U1A-1 and U1A-2 were cloned and the gene-specific promoters identified on the basis of the sequence variation defined from the 5' RACE products. The differential expression of these genes may be due to a 1.3 kb insertion less than 200 bp upstream of the U1A-1 coding sequence. This approach can be used more generally to examine expression profiles of multigene families, and in particular to refine information from EST or microarray analyses, and to isolate rapidly gene-specific promoters.

Base Sequence↗

PubMed2004

The class III peroxidase multigenic family in rice and its evolution in land plants.

Plant peroxidases (class III peroxidases, E.C. 1.11.1.7) are secreted glycoproteins known to be involved in the mechanism of cell elongation, in cell wall construction and differentiation, and in the defense against pathogens. They usually form large multigenic families in angiosperms. The recent completion of rice (Oryza sativa japonica c.v. Nipponbare) genome sequencing allowed drawing up the full inventory of the genes encoding class III peroxidases in this plant. We found 138 peroxidase genes distributed among the 12 rice chromosomes. In contrast to several other gene families studied so far, peroxidase genes are twice as numerous in rice as in Arabidopsis. This large number of genes results from various duplication events that were tentatively traced back using a phylogenetic tree based on the alignment of conserved amino acid sequences. We also searched for peroxidase encoding genes in the major phyla of plant kingdom. In addition to gymnosperms and angiosperms, sequences were found in liverworts, mosses and ferns, but not in unicellular green algae. Two rice and one Arabidopsis peroxidase genes appeared to be rather close to the only known sequence from the liverwort Marchantia polymorpha. The possible relationship of these peroxidases with the putative ancestor of peroxidase genes is discussed, as well as the connection between the development of the class III peroxidase multigenic family and the emergence of the first land plants.

Amino Acid Sequence↗

PubMed1994

Chimerism in PCR products from a multigene family.

This paper describes a potential hazard in obtaining sequences of a multigene family by amplifying the mixed population by the polymerase chain reaction with primers from conserved sequences. We describe a product which appears to be a chimera formed during the PCR reaction from two different but related sequences.

Base Sequence↗

PubMed1989

Expression and hormonal control of a new larval cuticular multigene family at the onset of metamorphosis of the tobacco hornworm.

The pattern of cuticular protein synthesis by the epidermis of the tobacco hornworm larva changes during the final day of feeding, leading to an alteration in cuticular structure and a stiffening of the cuticle. We have isolated a small multigene family which codes for at least three of the new cuticular proteins made at this time. The five genes which were isolated from this family map to two different genomic regions. Sequencing shows that one of the genes is 1.9 kb and consists of three exons coding for a 12.2-kDa acidic (pI = 5.26) protein that is predominantly hydrophilic. The deduced amino acid sequence shows regions of similarity to proteins from flexible lepidopteran cuticles and from Drosophila larval and pupal cuticles, but not to proteins found in highly sclerotized cuticles. This gene family is first expressed late on the penultimate day (Day 2) of feeding in the final larval instar and ceases expression 2 days later when metamorphosis begins. In situ hybridization shows that this gene family is expressed in all the epidermal cells of Day 3 larvae except the bristle cells and those at the muscle attachment site. Expression can be induced in Day 1 epidermis by exposure to 50 ng/ml 20-hydroxyecdysone in vitro, but only if juvenile hormone is absent. Its developmental expression, tissue specificity, and hormonal regulation strongly suggest that this multigene family is involved in the structural changes that occur in the larval cuticle just prior to the onset of metamorphosis.

Amino Acid Sequence↗

PubMed1977

Mathematical models for the evolution of multigene families by unequal crossing over.

Mathematical models of homologous but unequal crossing over between sister chromatids are presented. For mispairing by one repeat, the evolution of a multigene family by unequal crossing over can be represented by a linear birth-death process. The fixation rate of one repeat in a multigene family is estimated. For mispairing by more than one repeat, some approximate results are obtained.

Alleles↗

PubMed1998

Evolution of the trappin multigene family in the Suidae.

Trappins are a group of secretory proteins containing a WAP motif with an anchoring domain. Previous studies showed that their genes, especially those of pig, have undergone rapid evolution, which produced trappins with a broad spectrum of actions. To understand the evolution of such a rapidly evolving multigene family, we isolated trappin genes of the Artiodactyla, including pig, wart hog, collared peccary, hippopotamus, and cow, by means of polymerase chain reaction (PCR). Two genes newly isolated from wart hog are orthologs of trappin-1 (SPAI) and trappin-2 (elafin), the others are novel members of the trappin family and named trappins-6 to 11. The divergence of the sequences is greatest in the region that encodes the reactive site, and intron sequences appear to be more highly conserved than the protein-coding sequences, especially among the pig paralogs. Phylogenetic analysis showed that the trappin multigene family members of pig were generated through gene duplication after the divergence of the Suidae (pig and wart hog) and Tayassuidae (collared peccary). Similarities in the gene structure with seminal vesicle clotting proteins (REST) and WAP motif-containing proteins suggest that trappins are naturally occurring fusion proteins created through exon shuffling between ancestral REST and WAP motif-coding genes.

Amino Acid Sequence↗

PubMed2000

Molecular evolution of the histone 3 multigene family in the Drosophila melanogaster species subgroup.

Molecular evolution of the histone multigene family was studied by cloning and sequencing regions of the histone 3 gene in the Drosophila melanogaster species subgroup. Analysis of the nucleotide substitution pattern showed that in the coding region synonymous changes occurred more frequently to A or T in contrast to the GC-rich base composition, while in the 3' region the nucleotide substitutions were most likely in equilibrium. These results suggested that the base composition at the third codon position of the H3 gene, i.e., codon usage, has been changing to A or T in the Drosophila melanogaster species subgroup.

Animals↗

PubMed1996

Differential display-mediated rapid identification of different members of a multigene family, HSP 16.9 in wheat.

Isolation of cDNAs encoding individual members of a gene family is essential for assessing their role in a biological phenomenon. However, this process is often laborious and slow due to highly conserved protein-coding region that interferes with the isolation of the individual members. Identification of gene-specific probes from 3' non-coding regions of different members can assist in the fast retrieval and characterization of individual members of a multigene family. We used the recent technique of differential display for the same purpose. As an example of a multigene family in plants, we selected a heat shock protein gene family, HSP16.9 from wheat, with estimated 12 members. We modified the original differential display technique for selective amplification of the 3' non-coding regions of different wheat HSP16.9 genes by replacing the random 10-mer in the original method with a conserved HSP16.9 gene family-specific primer. Sixteen cDNA fragments from these experiments were sequenced and they represent 8 different members of a 12 member gene family. Our success can be attributed to shorter 3' non-coding regions that are typical of higher-plant genes and use of highly conserved gene family-specific primer in these experiments. This modified differential display technique can be of general application to other plant systems where cloning of the different members of a gene family is desired.

Amino Acid Sequence↗

PubMed1986

Chromosomal proteins HMG-14 and HMG-17. Distinct multigene families coding for similar types of transcripts.

Human nonhistone chromosomal proteins HMG-14 and HMG-17 are encoded by genes which are part of multigene families. Southern analysis of human, mouse, and rat genomic restriction digests reveals that the two families are distinct. Although the cDNAs of HMG-14 and HMG-17 do not cross-hybridize, they have several similar structural features: the open reading frame comprises only 23% of the transcripts, the 5'-untranslated region is extremely GC rich whereas the 3'-untranslated region is unusually long and AT rich. The overall sequence homology between the two transcripts is highest (71%) in the 90 nucleotides coding for the DNA-binding domains of the proteins. The sequence of the human HMG-14 and HMG-17 proteins, deduced from the open reading frame, differs by more than 50%; the DNA-binding domains of the proteins show 74% sequence homology. However, even in this 30-residue long peptide there are significant differences between the proteins as the proline content of HMG-17 (8 residues) is twice that of HMG-14. The two proteins have different hydropathy index profiles and are serologically distinct. The multigene families may have evolved independently from similar genetic elements or from a shared ancestral gene in which the nucleotide sequence coding for the DNA-binding domain of the protein is the most conserved region. The structural differences between the molecules and the differences in their DNA-binding domains suggest that the proteins may be involved in distinguishable cellular functions.

Amino Acid Sequence↗

PubMed1997

Evidence for distinct prototype sequences within the Plasmodium falciparum Pf60 multigene family.

Using oligonucleotides derived from Pf60.1, a member of the Plasmodium falciparum Pf60 multigene family, numerous fragments were amplified from genomic and cDNA from the 3D7 P. falciparum clone. DNA sequencing showed that the various fragments presented considerable diversity, indicating that the 3D7 repertoire contains at least 20 distinct versions of the region analysed. The various sequences aligned with either of two prototype sequences. Characteristic of the A-type was the presence of a 21 bp motif, present in variable copy number, as well as a sequence homologous to the Babesia sp. RAP-1 consensus. The B prototype sequence did not present such features and substantially differed from the A-type, due to accumulation of point mutations and numerous triplet deletions. Consistent with the marked differences between both sub-families, individual members from each sub-family did not cross-hybridise, produced distinct multiple band patterns on Southern blots and distinct chromosome profiles. Numerous hybrid sequences were observed. Interestingly, most var genes and var-related unspliced cDNAs described so far are of A/B hybrid type. These data suggest that the family has evolved by successive amplifications from two ancestral copies, with accumulation of mutations, as well as recombination and/or gene conversion events.

Amino Acid Sequence↗

PubMed1999

The map1 gene of Cowdria ruminantium is a member of a multigene family containing both conserved and variable genes.

Heartwater is an economically important disease of ruminants caused by the tick-transmitted rickettsia Cowdria ruminantium. The disease is present in Africa and the Caribbean and there is a risk of spread to the Americas, particularly because of a clinically asymptomatic carrier state in infected livestock and imported wild animals. The causative agent is closely related taxonomically to the human and animal pathogens Ehrlichia chaffeensis and Ehrlichia canis. A dominant immune response of infected animals or people is directed against variable outer membrane proteins of these agents known, in E. chaffeensis and E. canis, to be encoded by polymorphic multigene families. We demonstrate, by sequence analysis, that map1 encoding the major outer membrane protein of C. ruminantium is also encoded by a polymorphic multigene family. Two members of the gene family are located in tandem in the genome. The upstream member, orf2, is conserved, encoding only 2 amino acid substitutions among six different rickettsial strains from diverse locations in Africa and the Caribbean. In contrast, the downstream member, map1, contains variable and conserved regions between strains. Interestingly, orf2 is more closely related in sequence to omp1b of E. chaffeensis than to map1 of C. ruminantium. The regions that differ among orf2, map1, and omp1b correspond to previously identified variable sequences in outer membrane protein genes of E. chaffeensis and E. canis. These data suggest that diversity in these outer membrane proteins may arise by recombination among gene family members and offer a potential mechanism for persistence of infection in carrier animals.

Africa↗

PubMed1996

Rubisco in marine symbiotic dinoflagellates: form II enzymes in eukaryotic oxygenic phototrophs encoded by a nuclear multigene family.

Genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) were cloned from dinoflagellate symbionts (Symbiodinium spp) of the giant clam Tridacna gigas and characterized. Strikingly, Symbiodinium Rubisco is completely different from other eukaryotic (form I) Rubiscos: it is a form II enzyme that is approximately 65% identical to Rubisco from Rhodospirillum rubrum (Rubisco forms I and II are approximately 25 to 30% identical); it is nuclear encoded by a multigene family; and the predominantly expressed Rubisco is encoded as a precursor polyprotein. One clone appears to contain a predominantly expressed Rubisco locus (rbcA), as determined by RNA gel blot analysis of Symbiodinium RNA and sequencing of purified Rubisco protein. Another contains an enigmatic locus (rbcG) that exhibits an unprecedented pattern of amino acid replacement but does not appear to be a pseudogene. The expression of rbcG has not been analyzed; it was detected only in the minor of two taxa of Symbiodinium that occur together in T. gigas. This study confirms and describes a previously unrecognized branch of Rubisco's evolution: a eukaryotic form II enzyme that participates in oxygenic photosynthesis and is encoded by a diverse, nuclear multigene family.

Amino Acid Sequence↗

PubMed1997

The Cmv1 host resistance locus is closely linked to the Ly49 multigene family within the natural killer cell gene complex on mouse chromosome 6.

Natural killer (NK) cells play important roles in controlling tumor cells and against a range of infectious organisms. Recent studies of mouse NK cell surface receptors, which may be involved in the specificity of NK cells, have shown that many of these molecules are encoded by the Ly49 and Ly55 (Nkrp1) multigene families that map to distal mouse chromosome 6. Also mapping to this NK cell gene complex (NKC) is the resistance locus, Cmv1, which is involved in genetically determined resistance to murine cytomegalovirus (MCMV). The aim of this study was to localize Cmv1 more precisely in relation to other NKC loci by generating a high-resolution genetic map of the region. We have analyzed 1250 backcross mice comprising panels of 700 (BALB/c x C57BL/6J)F1 x BALB/c and 550 (A/J x C57BL/6J)F1 x A/J progeny. A total of 25 polymorphic genes or microsatellite markers were analyzed over a region of 10 map units from D6Mit134 to D6Mit59. The Cmv1 phenotypes of mice recombinant in this interval were tested by infection with MCMV. The results obtained indicate that the functionally important NKC region is a tightly linked cluster of loci spanning at least 0.4 map units. Furthermore, Cmv1 maps distal to, but very closely linked to, the Ly49 multigene family (< 0.2 map units), suggesting that MCMV resistance may be conferred by MHC class I-specific NK cell receptors.

Animals↗

PubMed2004

Characterization of a major outer membrane protein multigene family in Ehrlichia ruminantium.

Ehrlichia ruminantium is a tick-transmitted rickettsial pathogen, which causes heartwater or cowdriosis in wild and domestic ruminants. A dominant antibody response of animals infected with E. ruminantium is directed against the outer membrane protein MAP1 (major antigenic protein 1). Part of the locus containing map1 has been characterized and consists of four map1 paralogs, designated map1-2, map1-1, map1 and map1+1, indicating that map1 is encoded by a multigene family. The purpose of this study was to determine the total number of map1 paralogs and their transcriptional activities. Using genome walking and data from an ongoing E. ruminantium genome sequencing project at the Onderstepoort Veterinary Institute, we found 16 paralogs of the map1 gene tandemly arranged in a 25 kb region of the E. ruminantium genome. The map1 multigene family is downstream of a hypothetical transcriptional regulator gene and upstream of the secA gene. Thirteen paralogs at the 5' end of the 25-kb locus were connected by short intergenic spaces (ranging from 0 to 42 bp) and the remaining three paralogs at the 3' end were connected by longer intergenic spaces (ranging from 375 to 1612 bp). All 16 map1 paralogs were transcriptionally active in E. ruminantium grown in endothelial cells and paralogs with short intergenic spaces were co-transcribed with their adjacent genes.

Antigens, Bacterial↗

PubMed2003

Natural killer cell receptors in cattle: a bovine killer cell immunoglobulin-like receptor multigene family contains members with divergent signaling motifs.

Natural killer (NK) cells recognize and kill certain tumor cells, virally infected cells and MHC class I-disparate normal hematopoietic cells. NK cell cytotoxicity is regulated by a multitude of receptors with either activating or inhibitory signaling function. We here report the molecular cloning of bovine CD94 [killer cell lectin-like receptor (KLR)-D1] and NKp46 orthologues, four members of a bovine CD158 [killer cell immunoglobulin-like receptor (KIR)] family, and a novel KLR. This novel receptor was termed KLRJ1 and is most similar to Ly-49 (KLRA). The KLRD1 and KLRJ1 loci were mapped to a bovine NK gene complex on chromosome 5 by radiation hybrid mapping, whereas KIR2DL1 and NKP46 were localized to chromosome 18. Two of the bovine KIR(KIR2DL1 and KIR3DL1) contain immunoreceptor tyrosine-based inhibition motifs (ITIM), suggesting an inhibitory function. Bovine KIR2DS1 and KIR3DS1 lack ITIM but have an arginine-containing motif in their transmembrane domain, similar to primate KIR2DL4. Thus, KIR multigene families with divergent signaling motifs do not only exist in primates. Based on sequence comparison, it appears that the primate and bovine KIR multigene families may have evolved independently.

Amino Acid Motifs↗

PubMed1997

Characterization of multigene families in the micronuclear genome of Paramecium tetraurelia reveals a germline specific sequence in an intron of a centrin gene.

In Paramecium, as in other ciliates, the transcriptionally active macronucleus is derived from the germline micronucleus by programmed DNA rearrangements, which include the precise excision of thousands of germline-specific sequences (internal eliminated sequences, IESs). We report the characterization of micronuclear versions of genes encoding Paramecium secretory granule proteins (trichocyst matrix proteins, TMPs) and Paramecium centrins. TMP and centrin multigene families, previously studied in the macronuclear genome, consist of genes that are co-expressed to provide mixtures of related polypeptides that co-assemble to form respectively the crystalline trichocyst matrix and the infraciliary lattice, a contractile cytoskeletal network. We present evidence that TMP and centrin genes identified in the macronucleus are also present in the micronucleus, ruling out the possibility that these novel multigene families are generated by somatic rearrangements during macronuclear development. No IESs were found in TMP genes, however, four IESs in or near germline centrin genes were characterized. The only intragenic IES is 75 bp in size, interrupts a 29 bp intron and is absent from at least one other closely related centrin gene. This is the first report of an IES in an intron in Paramecium.

Amino Acid Sequence↗