Theoretical population genetics of repeated genes forming a multigene family

The evolution of repeated genes forming a multigene family in a finite population is studied with special reference to the probability of gene identity, i.e., the identity probability of two gene units chosen from the gene family. This quantity is called clonality and is defined as the sum of squares of the frequencies of gene lineages in the family. The multigene family is undergoing continuous unequal somatic crossing over, ordinary interchromosomal crossing over, mutation and random frequency drift. Two measures of clonality are used: clonality within one chromosome and that between two different chromosomes. The equilibrium properties of the means, the variances and the covariance of the two measures of clonality are investigated by using the diffusion equation method under the assumption of constant number of gene units in the multigene family. Some models of natural selection based on clonality are considered. The possible significance of the variance and covariance of clonality among the chromosomes on the adaptive differentiation of gene families such as those producing antibodies is discussed.     

An Extension of a Model for the Evolution of Multigene Families by Unequal Crossing over

Evolution of a multigene family is studied from the standpoint of population genetics. It is assumed that the multigene family is undergoing continuous interchromosomal unequal crossing over, mutation and random frequency drift. The equilibrium properties of the probability of gene identity (clonality) are investigated, using two measures: identity probability within and between chromosomes. The measures represent homogeneity of genes within a family in one chromosome and similarity of gene families between two homologous chromosomes. The means, the variances and the covariance of these two measures of identity probability are obtained by using the diffusion equation method. It is shown that the means and the variances are generally smaller than those predicted in the previous model assuming intrachromosomal (sister chromatid) unequal crossing over (Ohta 1978a,b).     

In Situ Hybridization Analysis of Chromosomal Homologies in Drosophila Melanogaster and Drosophila Virilis

Twenty-four biotin-labeled recombinant-DNA probes which contained putative unique-sequence Drosophila melanogaster DNA were hybridized to larval salivary-gland chromosomes of D. melanogaster and Drosophila virilis. All probes hybridized to D. melanogaster chromosomes at the expected sites. However, one probe hybridized to at least 16 additional sites, and one hybridized to one additional site. Thirteen probes hybridized strongly to D. virilis chromosomes, four hybridized weakly and infrequently, and seven did not hybridize. Probes representing two multigene families (beta-tubulin and yolk-protein) hybridized as would be expected if all sites had been conserved in the two species on the same chromosomal elements. The multiple hybridization sites of a third probe which may represent a multigene family were also conserved. The results were consistent with H.J. Muller's proposal that chromosomal elements have been conserved during evolution of this genus.     

Chromosomal Mapping of Repetitive DNAs in the Grasshopper Abracris flavolineata Reveal Possible Ancestry of the B Chromosome and H3 Histone Spreading

Supernumerary chromosomes (B chromosomes) occur in approximately 15% of eukaryote species. Although these chromosomes have been extensively studied, knowledge concerning their specific molecular composition is lacking in most cases. The accumulation of repetitive DNAs is one remarkable characteristic of B chromosomes, and the occurrence of distinct types of multigene families, satellite DNAs and some transposable elements have been reported. Here, we describe the organization of repetitive DNAs in the A complement and B chromosome system in the grasshopper species Abracris flavolineata using classical cytogenetic techniques and FISH analysis using probes for five multigene families, telomeric repeats and repetitive C₀t-1 DNA fractions. The 18S rRNA and H3 histone multigene families are highly variable and well distributed in A. flavolineata chromosomes, which contrasts with the conservation of U snRNA genes and less variable distribution of 5S rDNA sequences. The H3 histone gene was an extensively distributed with clusters occurring in all chromosomes. Repetitive DNAs were concentrated in C-positive regions, including the pericentromeric region and small chromosomal arms, with some occurrence in C-negative regions, but abundance was low in the B chromosome. Finally, the first demonstration of the U2 snRNA gene in B chromosomes in A. flavolineata may shed light on its possible origin. These results provide new information regarding chromosomal variability for repetitive DNAs in grasshoppers and the specific molecular composition of B chromosomes.     

Birth-and-death evolution of the internalin multigene family in Listeria

The birth-and-death model of multigene family evolution describes patterns of gene origination, diversification and loss within multigene families. Since it was first developed in the 1990s, the model has been found to characterize a large number of eukaryotic multigene families. In this paper, we report for the first time a bacterial multigene family that undergoes birth-and-death evolution. By analyzing the evolutionary relationships among internalins, a relatively large and diverse family of genes associated with key virulence functions in Listeria, we demonstrate the importance of birth-and-death evolution in the diversification of this important bacterial pathogen. We also detected two instances of lateral gene transfer within the internalins, but the estimated frequency would have been much higher had it not been analyzed within the context of birth-and-death evolutionary dynamics and a phenomenon that we term "paralog-sorting", which involves the unequal transmittal of gene duplicates during or subsequent to the speciation process. As such, in addition to providing the first demonstration of birth-and-death evolution within a bacterial multigene family, our results indicate that the extent of lateral transfer in bacterial multigene families should be re-examined in the light of birth-and-death evolution.     

Chromosome assignment of four photosynthesis-related genes and their variability in wheat species

Copy numbers of four photosynthesis-related genes, PhyA, Ppc, RbcS and Lhcb1 ^*1, in wheat genomes were estimated by slot-blot analysis, and these genes were assigned to the chromosome arms of common wheat by Southern hybridization of DNA from an aneuploid series of the cultivar Chinese Spring. The copy number of PhyA was estimated to be one locus per haploid genome, and this gene was assigned to chromosomes 4AL, 4BS and 4DS. The Ppc gene showed a low copy number of small multigenes, and was located on the short arm of homoeologous group 3 chromosomes and the long arm of chromosomes of homoeologous group 7. RbcS consisted of a multigene family, with approximately 100 copies in the common wheat genome, and was located on the short arm of group 2 chromosomes and the long arm of group 5 chromosomes. Lhcb1 ^*1 also consisted of a multigene family with about 50 copies in common wheat. Only a limited number of restriction fragments (approximately 15%) were used to determine the locations of members of this family on the long arm of group 1 chromosomes owing to the multiplicity of DNA bands. The variability of hybridized bands with the four genes was less in polyploids, but was more in the case of multigene families. RFLP analysis of polyploid wheats and their presumed ancestors was carried out with probes of the oat PhyA gene, the maize Ppc gene, the wheat RbcS gene and the wheat Lhcb1 ^*1 gene. The RFLP patterns of common wheat most closely resembled those of T. Dicoccum (Emmer wheat), T. urartu (A genome), Ae. speltoides (S genome) and Ae. squarrosa (D genome). Diversification of genes in the wheat complex appear to have occurred mainly at the diploid level. Based on RFLP patterns, B and S genomes were clustered into two major groups. The fragment numbers per genome were reduced in proportion to the increase of ploidy level for all four genes, suggesting that some mechanism(s) might operate to restrict, and so keep to a minimum, the gene numbers in the polyploid genomes. However, the RbcS genes, located on 2BS, were more conserved (double dosage), indicating that the above mechanism(s) does not operate equally on individual genes.     

The gene for human chromogranin A (CgA) is located on chromosome 14

Chromogranin A (CgA) is a protein that is present in most neuroendocrine tissues and is co-secreted with their resident hormones. We have assigned the CgA gene to human chromosome 14 by hybridization of a CgA cDNA probe cloned from a cDNA library of human medullary thyroid carcinoma cells to spots of individual human chromosomes flow-sorted onto nitrocellulose filters. Southern analysis of human genomic DNA with the same probe revealed only 1-3 restriction bands. These studies indicate that the CgA gene is probably single copy and not a member of a dispersed, multigene family. The CgA gene is not co-localized with the genes of any of the CgA-associated hormones.     

Human long-chain acyl-CoA synthetase: structure and chromosomal location.

A complementary DNA clone encoding the entire human long-chain acyl-CoA synthetase was isolated and the total 698-amino acid sequence was deduced. The amino acid sequence of human long-chain acyl-CoA synthetase shows 84.9% identity to that of rat long-chain acyl-CoA synthetase. The nucleotide sequences of the protein coding regions between human and rat long-chain acyl-CoA synthetase mRNAs are highly conserved (85.6%), whereas those of the 3' untranslated regions are less conserved (72%). The location of the human long-chain acyl-CoA synthetase gene was identified on chromosome 4 by spot hybridization of flow-sorted chromosomes. Computer-assisted homology search revealed a significant similarity of the enzyme with the enzymes of the luciferase family. Based on this similarity, the structure of human long-chain acyl-CoA synthetase can be divided into five domains: the N-terminus, two domains similar to those in enzymes of the luciferase family, a long gap region between the similar domains and the C-terminus.     

Human metallothionein-II processed gene is located in region p11----q21 of chromosome 4

Metallothionein (MT) genes comprise a multigene family encoding low-molecular-weight, heavy-metal-binding proteins. We have mapped a human MT-II processed gene to chromosome 4, using Southern blotting in combination with a human X mouse hybrid clone panel containing defined subsets of human chromosomes. We have further localized this gene to region p11----q21, using in situ hybridization.     

Physical mapping of the 5S rRNA multigene family in 6x triticale and rye: identification of a new rye locus.

In situ hybridization was used to physically map the 5S rRNA multigene family in three selected lines of hexaploid triticale and five lines of diploid rye. Using this technique, evidence for a new locus on the 3RS arm of the three triticale lines was first obtained, as well as confirmation of the presence of 5S rRNA loci on wheat and rye chromosomes of homoeologous groups 1 and 5. The new locus on the 3RS arm was confirmed in two lines of rye, Secale cereale L., although it was not present in the other rye varieties studied. We propose that the new 5S rRNA locus be referred to as 5SDna-R3.     

Changes in gene position are accompanied by a change in time of replication

The globin and immunoglobulin multigene families have been used to study the effect of chromosomal organization on the time of gene replication. Some of the genes are late-replicating, providing the first identification of late-replicating sequences that are not highly repetitive. One is a member of the mouse alpha-globin gene family, which consists of genes mapping to three different chromosomes. The other genes in this family replicate early during S. Our studies demonstrate that immunoglobulin gene rearrangements and rearrangements between these genes and the c-myc oncogene are accompanied by dramatic differences in their temporal order of replication. We conclude that a gene's position in the chromosome, rather than its sequence, determines the time of replication. We suggest that the differences in association with gene rearrangement result from changes in the proximity of the affected gene to sites that control the temporal order of replication during S.     

Genomic organization of tRNA and aminoacyl-tRNA synthetase genes for two amino acids in Saccharomyces cerevisiae

The genomic organization in Saccharomyces cerevisiae of the tRNA and aminoacyl-tRNA synthetase genes for two amino acids was investigated. Aspartic acid and serine were chosen for the study because of the number and diversity of their tRNA gene sequences and the availability of cloned tRNA and aminoacyl-tRNA synthetase genes. Chromosome assignments were determined by hybridization to DNA gel blots of chromosomal DNA resolved by contour-clamped homogeneous electric field gel electrophoresis. Our results show that the tRNA and the cognate synthetase genes in such a family are dispersed and, therefore, cannot be regulated via a mechanism dependent on close proximity of genes. In general, the genome of S. cerevisiae contains randomly dispersed tRNA genes that are transcribed individually. We have supported and expanded this view by applying the facile method of contour-clamped homogeneous electric field gel electrophoresis to the investigation of these small multigene families.     

The isolation and characterization of a cDNA clone encoding Lupinus angustifolius root nodule glutamine synthetase

Glutamine synthetase, purified from Lupinus angustifolius legume nodules, was carboxymethylated and succinylated prior to chemical or enzymatic cleavage. Peptides were purified and sequenced. An oligonucleotide probe was constructed for the sequence MPGQW. This probe was used to identify a glutamine synthetase cDNA clone, pGS5, from a lupin nodule cDNA library constructed in pBR322. pGS5 was sequenced (1043 bp) and computer-assisted homology searching revealed a high degree of conservation between this lupin partial cDNA clone and other plant glutamine synthetases at both the amino acid (>90%) and nucleotide (>80%) level. Northern and Southern analyses using pGS5 supported the conclusion that a multigene glutamine synthetase family exists in lupin which is differentially expressed in both an organ-specific and temporal manner. Western and Northern blot analyses indicated the accumulation of a glutamine synthetase specific mRNA species during nodule development corresponded to the appearance of a novel glutamine synthetase polypeptide between 8 and 10 days after rhizobial inoculation.     

A large multigene family codes for the polypeptides of the crystalline trichocyst matrix in Paramecium.

The secretory granules (trichocysts) of Paramecium are characterized by a highly constrained shape that reflects the crystalline organization of their protein contents. Yet the crystalline trichocyst content is composed not of a single protein but of a family of related polypeptides that derive from a family of precursors by protein processing. In this paper we show that a multigene family, of unusually large size for a unicellular organism, codes for these proteins. The family is organized in subfamilies; each subfamily codes for proteins with different primary structures, but within the subfamilies several genes code for nearly identical proteins. For one subfamily, we have obtained direct evidence that the different members are coexpressed. The three subfamilies we have characterized are located on different macronuclear chromosomes. Typical 23-29 nucleotide Paramecium introns are found in one of the regions studied and the intron sequences are more variable than the surrounding coding sequences, providing gene-specific markers. We suggest that this multigene family may have evolved to assure a microheterogeneity of structural proteins necessary for morphogenesis of a complex secretory granule core with a constrained shape and dynamic properties: genetic analysis has shown that correct assembly of the crystalline core is necessary for trichocyst function.     

Nitrogen use efficiency. 2. Amino acid metabolism

In a previous article, we highlighted the latest developments in the isolation and characterisation of genes involved in the uptake of nitrogen from the soil, which might be used to improve the nitrogen use efficiency (NUE) of crop plants. In this article, we have concentrated on the genes controlling the enzymes of amino acid metabolism that may be involved in transferring nitrogen to the protein in the grain. Evidence is now accumulating from the use of knockout mutants, of the role of individual isoenzymes involved in amino acid metabolism, which are encoded by specific genes that are often members of a multigene family. In addition, a significant number of overexpressing plant lines have been obtained, which have increased activities of cytosol located, glutamine synthetase, asparagine synthetase and alanine aminotransferase that appear to have improved NUE.     

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

Summary 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.     

Identification and characterization of a novel murine multigene family containing a PHD-finger-like motif

The genes Phf5a and Phf5b-ps are the first two members of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger genes. The Phf5 gene family contains an active locus on mouse chromosome 15, region E and several processed pseudogenes on different chromosomes. The active locus, Phf5a, is expressed ubiquitously in pre- and postnatal murine tissues and encodes a protein of 110 amino acids. The protein is localized in the nucleus in a non-homogenous pattern as the nucleolar subcompartment is almost free of Phf5a. The molecular and biological functions of Phf5a are unknown up-to-date, but the systematic deletion of its yeast homolog is lethal, pointing out that the protein is required for cell viability. Interpretation of our data and review of the literature suggest both basic and essential cellular functions of the Phf5a protein, possibly acting as a chromatin-associated protein.     

High Incidence of Interchromosomal Transpositions in the Evolutionary History of a Subset of Or Genes in Drosophila

In insects, the odorant receptor (Or) multigene family is an intermediate-sized family with genes present in all chromosomes, indicating that duplication followed by interchromosomal transposition played an important role in the early stages of the family evolution. Here, we have explored the occurrence of interchromosomal transpositions in more recent stages through the comparative analysis of a subset of Or genes in Drosophila, where the gene content of chromosomal arms is highly conserved. The studied subset consisted of 11 Or genes located on the left arm of chromosome 3 (Muller’s D element) in D. melanogaster. Our study focused on the number and chromosomal arm location of these members of the family across the 12 Drosophila species with complete genome sequences. In contrast to previous results from in situ hybridization comparative mapping that were mainly based on single-copy genes, our study, based on members of a multigene family of moderate size, revealed repeated interchromosomal transposition events and a complex history of some of the studied genes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The genes coding for the cardiac muscle actin, the skeletal muscle actin and the cytoplasmic beta-actin are located on three different mouse chromosomes.

The actins are a group of highly conserved proteins encoded by a multigene family. We have previously reported that the skeletal muscle actin gene is located on mouse chromosome 3, together with several other unidentified actin DNA sequences. We show here that the gene coding for the cardiac muscle actin, which is closely related to the skeletal muscle actin (1.1% amino acid replacements), is located on mouse chromosome 17. The gene coding for the cytoplasmic beta-actin is located on mouse chromosome 5. Thus, these three actin genes are located on three different chromosomes.