Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); This paper reports on the chromosomal location of 18S rRNA, 5S rRNA and H3 histone multigene families in 4 species of a relatively ancient and diversified group of grasshoppers belonging to the family Proscopiidae. The 5S rRNA and H3 histone genes were highly conserved in the number of sites and chromosomal position in the 4th chromosome pair in all species analyzed, whereas the 18S rRNA genes showed slightly more variation because they were present on one or 2 chromosome pairs, depending on the species. The 5S and 18S rRNA gene families occurred in different chromosomes; in contrast, H3 histone and 5S rRNA genes co-localized in the same chromosomal position, with an apparently interspersed organization. Considering that the Proscopiidae family is a relatively ancient group compared with the Acrididae family, the association of the H3 histone and 5S rRNA multigene families can represent a basal condition for grasshoppers, although more research is needed on other representatives of this insect group to confirm this statement. The presence of such an association of 5S rDNA and H3 histone in mussels and arthropods (beetles...
Cabral-de-Mello, Diogo Cavalcanti; Oliveira, Sarah G.; de Moura, Rita C.; Martins, Cesar
Fonte: Biomed Central Ltd.Publicador: Biomed Central Ltd.
Tipo: Artigo de Revista CientíficaFormato: 12
Relevância na Pesquisa
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Background: Scarabaeinae beetles show a high level of macro-chromosomal variability, although the karyotypic organization of heterochromatin and multigene families (rDNAs and histone genes) is poorly understood in this group. To better understand the chromosomal organization and evolution in this group, we analyzed the karyotypes, heterochromatin distribution and chromosomal locations of the rRNAs and histone H3 genes in beetles belonging to eight tribes from the Scarabaeinae subfamily (Coleoptera, Scarabaeidae).Results: The number of 18S rRNA gene (a member of the 45S rDNA unit) sites varied from one to 16 and were located on the autosomes, sex chromosomes or both, although two clusters were most common. Comparison of the 45S rDNA cluster number and the diploid numbers revealed a low correlation value. However, a comparison between the number of 45S rDNA sites per genome and the quantity of heterochromatin revealed (i) species presenting heterochromatin restricted to the centromeric/pericentromeric region that contained few rDNA sites and (ii) species with a high quantity of heterochromatin and a higher number of rDNA sites. In contrast to the high variability for heterochromatin and 45S rDNA cluster...
Concerted evolution is often invoked to explain the diversity
and evolution of the multigene families of major histocompatibility
complex (MHC) genes and immunoglobulin (Ig) genes. However, this
hypothesis has been controversial because the member genes of these
families from the same species are not necessarily more closely related
to one another than to the genes from different species. To resolve
this controversy, we conducted phylogenetic analyses of several
multigene families of the MHC and Ig systems. The results show that the
evolutionary pattern of these families is quite different from that of
concerted evolution but is in agreement with the birth-and-death model
of evolution in which new genes are created by repeated gene
duplication and some duplicate genes are maintained in the genome for a
long time but others are deleted or become nonfunctional by deleterious
mutations. We found little evidence that interlocus gene conversion
plays an important role in the evolution of MHC and Ig multigene
In this paper, a reverse-transcriptase PCR-based protocol suitable for efficient expression analysis of multigene families is presented. The method combines restriction fragment length polymorphism (RFLP) technology with a gene family-specific version of mRNA differential display and hence is called "RFLP-coupled domain-directed differential display. "With this method, expression of all members of a multigene family at many different developmental stages, in diverse tissues and even in different organisms, can be displayed on one gel. Moreover, bands of interest, representing gene family members, are directly accessible to sequence analysis, without the need for subcloning. The method thus enables a detailed, high-resolution expression analysis of known gene family members as well as the identification and characterization of new ones. Here the technique was used to analyze differential expression of MADS-box genes in male and female inflorescences of maize (Zea mays ssp. mays). Six different MADS-box genes could be identified, being either specifically expressed in the female sex or preferentially expressed in male or female inflorescences, respectively. Other possible applications of the method are discussed.
The tick-borne relapsing fever spirochete Borrelia hermsii evades the mammalian immune system by periodically switching expression among members of two multigene families that encode immunogenic, antigenically distinct outer surface proteins. The type strain, B. hermsii HS1, has at least 40 complete genes and pseudogenes that participate in this multiphasic antigenic variation. Originally termed vmp (for variable major protein) genes, they have been reclassified as vsp (for variable small protein) and vlp (for variable large protein) genes, based on size and amino acid sequence similarities. To date, antigenic variation in B. hermsii has been studied only in the type strain, HS1. Nucleotide sequence comparisons of 23 B. hermsii HS1 genes revealed five distinct groups, the vsp gene family and four subfamilies of vlp genes. We used PCR with family- and subfamily-specific primers, followed by restriction fragment length polymorphism analysis, to compare the vsp and vlp repertoires of HS1 and seven other B. hermsii isolates from Washington, Idaho, and California. This analysis, together with pulsed-field gel electrophoresis genome profiles, revealed that the eight isolates formed three distinct groups, which likely represent clonal lineages. Members of the three groups coexisted in the same geographic area...
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...
We report a technique for the rapid determination of genomic structure of individual members of human interspersed multigene families which circumvents the requirement for genomic clone isolation. In this approach, vectorette libraries were constructed from human/rodent somatic cell hybrid DNA harbouring single members of the gene family. Using these libraries as PCR templates with nested gene-specific primers in combination with a common vectorette primer resulted in the amplification of gene-specific products suitable for the subsequent determination of intron/exon structure. We have applied this technique to characterise members of two gene families.
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.
Random duplication and deletion events generate complex genomes carrying a large amount of dispensable sequences. We have simulated such events in a computer model. We followed the evolution of a genome carrying at least one copy of each type of gene. Partial duplications and deletions of genes generated nonfunctional vestigial sequences that were dispensable. The size of the genome stabilized only when the amount of dispensable sequences had increased to the point that most deletions did not affect vital genes. Within such genomes, the number of copies of specific genes fluctuated, thereby generating small multigene families. The parameters of the model were tested over 100,000 events in both simple and complex genomes. The results indicate that when the size of the genome is not critical to survival, as appears to be the case within limits in most eukaryotic organisms, the genome carries vestigial sequences that are no longer functional and that many genes are present in multigene families by chance.
In a comprehensive study, the temporal replication of tissue-specific genes and flanking sequences was compared in nine cell lines exhibiting different tissue-specific functions. Some of the rules we have determined for the replication of these tissue specific genes include the following. (i) Actively transcribed genes usually replicate during the first quarter of the S phase. (ii) Some immunoglobulin genes replicate during the first half of S phase even when no transcriptional activity is detected but appear to replicate even earlier in cell lines where they are transcribed. (iii) Nontranscribed genes can replicate during any interval of S phase. (iv) Multigene families arranged in clusters of 250 kilobases or less define a temporal compartment comprising approximately one-quarter of S phase. While these rules, and others that are discussed, apply to the tissue-specific genes studied here, all tissue-specific genes may not follow this pattern. In addition, housekeeping genes did not follow some of these rules. These results provide the first molecular evidence that the coordinate timing of replication of contiguous sequences within a multigene family is a general property of the mammalian genome. The relationship between replication very early during S phase and the transcriptional activity within a chromosomal domain is discussed.
DNA restriction endonuclease fragment patterns corresponding to both the rbcS and cab multigene families of pea are each shown to segregate as single Mendelian units in the F2 progeny of two separate crosses. All of the observed variation in each of the multigene families is thus organized on the chromosome in a tightly linked complex. Linkage relationships between both multigene families and an array of morphological and isozyme markers establish the location of the rbcS and cab gene clusters on pea chromosomes 5 and 2, respectively. Our results, which indicate a high level of DNA restriction fragment length polymorphism in pea, suggest sufficient variation to permit the construction of a highly detailed linkage map.
We have characterized a new family of silkmoth chorion genes, called C, which is distinct from previously characterized A and B families. The amino acid compositions of 18 purified C proteins have been determined. Three subgroups are recognized on the basis of compositional similarities and may correspond to distinct gene families or subfamilies. The sequences of two overlapping cDNA clones have been determined in their entirety and shown to correspond to a C-specific sequence. Obvious homology is observed between the middle portions of the C sequence and previously characterized B sequences. By contrast, the arms of the C sequence share no significant similarities either with each other or with the corresponding arms of B sequences. Thus, the same tripartite structure originally observed in A and B family sequences is also present in the C family and may have functional significance. Secondary structure prediction of the C sequence is presented and supports this conclusion. The observed homology between C and B family sequences clearly establishes that silkmoth chorion multigene families constitute a superfamily.
The evolution of multigene families whose members are dispersed into two or more nonhomologous chromosomes is studied from the standpoint of population genetics. By using a simple model of gene conversion, equilibrium and transient properties of the probability of identity of genes belonging to the family are investigated. Also, the time until fixation of a mutant belonging to a subdivided multigene family is studied by an approximation method. It is shown that dispersion of the family into two or more chromosomes has a relatively minor effect on the extent of identity between genes, unless the conversion rate between genes on nonhomologous chromosomes is extremely low, or unless the number of nonhomologous chromosomes on which gene members are dispersed is large.
Evolution of multigene families by gene duplication and subsequent diversification is analyzed assuming a haploid model without interchromosomal crossing over. Chromosomes with more different genes are assumed to have higher fitness. Advantageous and deleterious mutations and duplication/deletion also affect the evolution, as in previous studies. In addition, negative selection on the total number of genes (copy number selection) is incorporated in the model. First, a Markov chain approximation is used to obtain formulas for the average numbers of different alleles, genes without pseudogene mutations, and pseudogenes assuming that mutation rates and duplication/deletion rates are all very small. Computer simulation shows that the approximation works well if the products of population size with mutation and duplication/deletion rates are all small compared to 1. However, as they become large, the approximation underestimates gene numbers, especially the number of pseudogenes. Based on the approximation, the following was found: (1) Gene redundancy measured by the average number of redundant genes decreases as advantageous selection becomes stronger. (2) The number of different genes can be approximately described by a linear pure-birth process and thus has a coefficient of variation around 1. (3) The birth rate is an increasing function of population size without copy number selection...
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.
The PE and PPE (PE/PPE) multigene families of Mycobacterium tuberculosis are particularly GC-rich and share extensive homologous repetitive sequences. We hypothesized that they may undergo homologous recombination events, a mechanism rarely described in the natural evolution of mycobacteria. To test our hypothesis, we developed a specific oligonucleotide-based microarray targeting nearly all of the PE/PPE genes, aimed at detecting signals for homologous recombination. Such a microarray has never before been reported due to the multiplicity and highly repetitive and homologous nature of these sequences. Application of the microarray to a collection of M. tuberculosis clinical isolates (n = 33) representing prevalent spoligotype strain families in Tunisia allowed successful detection of six deleted genomic regions involving a total of two PE and seven PPE genes. Some of these deleted genes are known to be immunodominant or involved in virulence. The four precisely determined deletions were flanked by 400- to 500-bp stretches of nearly identical sequences lying mainly at the conserved N-terminal region of the PE/PPE genes. These highly homologous sequences thus serve as substrates to mediate both intergenic and intragenic homologous recombination events...
The genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, a large and long-lived invertebrate, provides a new perspective on animal immunity. Analysis of this genome uncovered a highly complex immune system in which the gene families that encode homologs of the pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR) sequences, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a 10-fold expansion relative to vertebrates. Given their stereotypic protein structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. A role for these receptors in immune defense is suggested by their similarity to TLRs in other organisms, sequence diversity, and expression in immunologically active tissues, including phagocytes. The complexity of the sea urchin TLR multigene families is largely derived from expansions independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll can be traced to an ancient eumetazoan ancestor. Several other echinoderm sequences are now available...
The Trypanosoma cruzi genome contains the most widely expanded content (∼12,000 genes) of the trypanosomatids sequenced to date. This expansion is reflected in the high number of repetitive sequences and particularly in the large quantity of genes that make up its multigene families. Recently it was discovered that the contents of these families vary between phylogenetically unrelated strains. We review the basic characteristics of trans-sialidases and mucins as part of the mechanisms of immune evasion of T. cruzi and as ligands and factors involved in the cross talk between the host cell and the parasite. We also show recently published data describing two new multigene families, DGF-1 and MASP, that form an important part of the scenario representing the complex biology of T. cruzi.
While it is not possible to directly the observe evolution of multigene
families, the best alternative is to compare orthologous family members among
several closely-related species with varying degrees of reproductive isolation.
Using RT-PCR we show that in pea (Pisum sativum) each member of the
pathogenesis-related PR10 family has a distinct pattern of expression in
response to the fungus Fusarium solani, and in treatment with salicylic acid,
chitosan and abcisic acid. Sequencing reveals that PR10.1, PR10.2 and PR10.3
exist in P. humile, P. elatius and P. fulvum, except that no PR10.2 orthologue
was identified in P. elatius. PR10.1, PR10.2 and PR10.3 appear to have diverged
from a single gene in the common Pisum ancestor. For the recently diverged
PR10.1 and PR10.2, the timing of fungal-induced expression differs greatly
among species. For example, PR10.1 was strongly induced in P. sativum by F.
solani within 8 hours postinoculation (h.p.i.), whereas little PR10.1
expression was seen in pea's closest relative, P. humile, and in the more
distantly-related P. elatius. In P. fulvum, expression did not peak until 48
h.p.i. Expression of the more ancient PR10.4 and PR10.5 genes is more tightly
conserved among Pisum species. These data indicate that expression...
The amount of sequence data available today highly facilitates the access to
genes from many gene families. Universal primers amplifying the desired genes
over a range of species are readily obtained by aligning conserved gene
regions, and laborious gene isolation procedures can often be replaced by
quicker PCR-based approaches. However, in case of multigene families, PCR-based
approaches bear the risk of incomplete isolation of family members. This
problem is most prominent in gene families with highly variable and thus
unpredictable number of gene copies among species, such as in the major
histocompatibility complex (MHC). In the present study we (i) report new
primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds,
and (ii) share our experience with isolating MHCIIB genes from an unprecedented
number of avian species from all over the avian phylogeny. We report important
and usually underappreciated problems encountered during PCR-based multigene
family isolation, and provide a collection of measures that may help to
significantly improve the chance of successfully isolating complete multigene
families using PCR-based approaches.; Comment: 24 pages, 2 Tables, 2 Figures