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1.
Mol Immunol ; 111: 209-219, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31096062

RESUMO

We have previously reported Israa, immune-system-released activating agent, as a novel gene nested in intron 8 of the mouse Zmiz1 gene. We have also shown that Israa encodes for a novel FYN-binding protein and might be involved in the regulation of T-cell activation. In this report, we demonstrate that Israa gene product regulates the expression of a pool of genes involved in T-cell activation and signaling. Real time PCR and GFP knock-in expression analysis showed that Israa is transcribed and expressed in the spleen mainly by CD3+CD8+ cells as well as in the thymus by CD3+ (DP and DN), CD4+SP and CD8+SP cells at different developmental stages. We also showed that Israa is downregulated in T-cells following activation of T-cell receptor. Using yeast two-hybrid analysis, we identified ELF1, a transcription factor involved in T-cell regulation, as an ISRAA-binding partner. Transcriptomic analysis of an EL4 cell line overexpressing ISRAA revealed differential expression of several genes involved in T-cell signaling, activation and development. Among these genes, Prkcb, Mib2, Fos, Ndfip2, Cxxc5, B2m, Gata3 and Cd247 were upregulated whereas Itk, Socs3, Tigit, Ifng, Il2ra and FoxJ1 were downregulated. Our findings support the existence in mouse of a novel FYN-related T-cell regulation pathway involving the product of an intron-nested gene.


Assuntos
Íntrons/imunologia , Ativação Linfocitária/imunologia , Linfócitos/imunologia , Linfocinas/imunologia , Genes Inseridos/imunologia , Transdução de Sinais/imunologia , Linfócitos T/imunologia , Animais , Complexo CD3/imunologia , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD8-Positivos/imunologia , Linhagem Celular , Regulação para Baixo/imunologia , Feminino , Expressão Gênica/imunologia , Camundongos , Camundongos Endogâmicos C57BL , Receptores de Antígenos de Linfócitos T/imunologia , Fatores de Transcrição/imunologia , Regulação para Cima/imunologia
2.
Virology ; 478: 112-22, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25666524

RESUMO

Barley yellow striate mosaic virus (BYSMV), a member of the genus Cytorhabdovirus, causes serious crop losses in agriculture. Here, we have cloned the BYSMV-derived small interfering RNAs (siRNAs), assembled the siRNAs and used RT-PCR to reconstruct the BYSMV genome. The genome consists of 12,706 nucleotides and encodes ten predicted genes from the antigenomic strand. The major BYSMV structural proteins share identities ranging from 35% to 62% with northern cereal mosaic virus (NCMV) counterparts. A notable difference is that BYSMV contains three transcriptional units residing between the P and M genes compared with four units in the corresponding region of NCMV. Unexpectedly, the middle mRNA in this region encodes gene5 nested in an alternative frame within gene4 via a leaky scanning mechanism. The gene5 encodes a small hydrophobic protein targeting to the endoplasmic reticulum (ER). To our knowledge, this is the first report of nested gene in plant rhabdoviruses.


Assuntos
Genoma Viral , Interações Hidrofóbicas e Hidrofílicas , Genes Inseridos , RNA Viral/genética , Rhabdoviridae/genética , Proteínas Virais/química , Proteínas Virais/genética , Sequência de Aminoácidos , Sequência de Bases , Genes Virais , Hordeum/virologia , Dados de Sequência Molecular , Rhabdoviridae/isolamento & purificação , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos
3.
Genetics ; 199(3): 729-37, 2015 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-25571900

RESUMO

The essential neurotransmitter acetylcholine functions throughout the animal kingdom. In Caenorhabditis elegans, the acetylcholine biosynthetic enzyme [choline acetyltransferase (ChAT)] and vesicular transporter [vesicular acetylcholine transporter (VAChT)] are encoded by the cha-1 and unc-17 genes, respectively. These two genes compose a single complex locus in which the unc-17 gene is nested within the first intron of cha-1, and the two gene products arise from a common pre-messenger RNA (pre-mRNA) by alternative splicing. This genomic organization, known as the cholinergic gene locus (CGL), is conserved throughout the animal kingdom, suggesting that the structure is important for the regulation and function of these genes. However, very little is known about CGL regulation in any species. We now report the identification of an unusual type of splicing regulation in the CGL of C. elegans, mediated by two pairs of complementary sequence elements within the locus. We show that both pairs of elements are required for efficient splicing to the distal acceptor, and we also demonstrate that proper distal splicing depends more on sequence complementarity within each pair of elements than on the sequences themselves. We propose that these sequence elements are able to form stem-loop structures in the pre-mRNA; such structures would favor specific splicing alternatives and thus regulate CGL splicing. We have identified complementary elements at comparable locations in the genomes of representative species of other animal phyla; we suggest that this unusual regulatory mechanism may be a general feature of CGLs.


Assuntos
Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , Colina O-Acetiltransferase/genética , Genes Inseridos , Processamento de RNA , Proteínas Vesiculares de Transporte de Acetilcolina/genética , Animais , Evolução Molecular
4.
Genome Biol Evol ; 5(10): 1978-85, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24084778

RESUMO

Nearly 10% of the genes in the genome of Drosophila melanogaster are in nested structures, in which one gene is completely nested within the intron of another gene (nested and including gene, respectively). Even though the coding sequences and untranslated regions of these nested/including gene pairs do not overlap, their intimate structures and the possibility of shared regulatory sequences raise questions about the evolutionary forces governing the origination and subsequent functional and evolutionary impacts of these structures. In this study, we show that nested genes experience weaker evolutionary constraint, have faster rates of protein evolution, and are expressed in fewer tissues than other genes, while including genes show the opposite patterns. Surprisingly, despite completely overlapping with each other, nested and including genes are less likely to display correlated gene expression and biological function than the nearby yet nonoverlapping genes. Interestingly, significantly fewer nested genes are transcribed from the same strand as the including gene. We found that same-strand nested genes are more likely to be single-exon genes. In addition, same-strand including genes are less likely to have known lethal or sterile phenotypes than opposite-strand including genes only when the corresponding nested genes have introns. These results support our hypothesis that selection against potential erroneous mRNA splicing when nested and including genes are on the same strand plays an important role in the evolution of nested gene structures.


Assuntos
Evolução Molecular , Íntrons/genética , Genes Inseridos , Regiões não Traduzidas/genética , Sequência de Aminoácidos , Animais , Drosophila melanogaster/genética , Éxons/genética , Fenótipo , Processamento de RNA/genética , Transcrição Genética
5.
PLoS One ; 6(10): e26099, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-22022525

RESUMO

BACKGROUND: Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs) and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals. CONCLUSIONS/SIGNIFICANCE: Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.


Assuntos
Éxons/genética , Íntrons/genética , Genes Inseridos/genética , Poliadenilação/genética , Retroelementos/genética , Transcrição Genética , Transportadores de Cassetes de Ligação de ATP/genética , Sequência de Bases , Etiquetas de Sequências Expressas , Células HeLa , Humanos , Internet , Modelos Biológicos , Fases de Leitura Aberta/genética , Especificidade de Órgãos/genética , Sítios de Splice de RNA/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Vírus 40 dos Símios/genética , Transfecção
6.
Cell Mol Life Sci ; 68(15): 2493-8, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21598020

RESUMO

Alpha-T-Catenin (CTNNA3) is a key protein of the adherens junctional complex in epithelial cells playing a crucial role in cellular adherence. What makes this gene particularly interesting is that it is located within a common fragile site, is epigenetically regulated, is transcribed through multiple promoters, and generates a variety of alternate transcripts. Finally, CTNNA3 has a nested gene (LRTMM3) embedded within its genomic context transcribed in the opposite direction. Apart from the complexity of its regulation, alterations in both CTNNA3 and LRTMM3 are implicated in human disease.


Assuntos
Genes Inseridos/genética , alfa Catenina/genética , alfa Catenina/fisiologia , Doença de Alzheimer/genética , Animais , Adesão Celular/genética , Epigênese Genética/fisiologia , Regulação da Expressão Gênica , Humanos , Proteínas de Membrana/genética , Proteínas do Tecido Nervoso/genética , Genes Inseridos/fisiologia
7.
Yi Chuan ; 32(9): 914-20, 2010 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-20870612

RESUMO

In the genome one gene, whose entire or the most part of the sequence localizes in an intronic or UTR region of another larger gene, is called nested gene. A nested gene pair consists of a host and a nested gene. Here, we conducted a systematic scanning and analysis to identify all cis-nested gene pairs and their structural features in the human genome. Meanwhile, we also explored possible mechanism for evolution of nested gene and the relationship between the host and the cis-nested gene (denoted as nested gene in short). Our analysis indicated that evolution of nested gene pair probably arose from the transposition, de novo mutation, and the mutations occurred in transcription start or termination sites. The change in transcription starting or ending site could be a unique mechanism driving evolution of nested gene pair. Gene Ontology analysis indicated the gene products of the nested gene and its host counterpart have no functional correlation.


Assuntos
Genoma Humano/genética , Íntrons/genética , Genes Inseridos/fisiologia , Transcrição Genética/fisiologia , Sequência de Bases , Evolução Molecular , Genoma Humano/fisiologia , Humanos , Íntrons/fisiologia , Genes Inseridos/genética
8.
Cytogenet Genome Res ; 129(1-3): 35-46, 2010 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-20516662

RESUMO

The 35S ribosomal DNA (rDNA) intergenic spacer (IGS) of Allium cernuum is examined. Initial sequencing of IGS clones revealed that some rDNA units contain a truncated retrotransposon sequence most similar to members of the Copia superfamily. Fluorescence in situ hybridisation (FISH) to metaphase chromosomes indicates that this element is dispersed along both pairs of major rDNA arrays. Southern hybridisation confirmed the presence of this 'relic' Copia-like element in more than 10% of 35S rDNA units, in the same position within the IGS. To measure the intragenomic divergence of the relic retroelement and its flanking sequences amongst different rDNA units, a 1.1-kb region was amplified and cloned. These data collectively point to a single origin for units containing the putative retrotransposon fragment. It is likely that units containing the putative retroelement increased in copy number and dispersed via rDNA homogenisation mechanisms, rather than by multiple retrotransposition events.


Assuntos
Allium/genética , DNA de Plantas/genética , DNA Espaçador Ribossômico/genética , Retroelementos/genética , Allium/classificação , Sequência de Bases , Southern Blotting , Cromossomos de Plantas/genética , Primers do DNA/genética , Evolução Molecular , Variação Genética , Genoma de Planta , Hibridização in Situ Fluorescente , Genes Inseridos , Filogenia , Especificidade da Espécie
10.
Eukaryot Cell ; 8(6): 899-912, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19286988

RESUMO

We describe a novel pair of nested genes, CDA12 and CDA13, from Tetrahymena thermophila. Both are implicated in membrane trafficking associated with cell division and conjugation. Green fluorescent protein localization reveals Cda12p decoration of diverse membrane-bound compartments, including mobile, subcortical tubulovesicular compartments; perinuclear vesicles; and candidates for recycling endosomes. Cda13p decorates intracellular foci located adjacent to cortically aligned mitochondria and their neighboring Golgi networks. The expression of antisense CDA12 RNA in transformants produces defects in cytokinesis, macronuclear segregation, and the processing of pinosomes to downstream compartments. Antisense CDA13 RNA expression produces a conjugation phenotype, resulting in the failure of mating pairs to separate, as well as failures in postconjugation cytokinesis and macronuclear fission. This study offers insight into the membrane trafficking events linking endosome and Golgi network activities, cytokinesis, and karyokinesis and the unique membrane-remodeling events that accompany conjugation in the ciliate T. thermophila. We also highlight an unusual aspect of genome organization in Tetrahymena, namely, the existence of nested, antisense genes.


Assuntos
Membrana Celular/metabolismo , Genes Inseridos , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , Tetrahymena thermophila/genética , Tetrahymena thermophila/metabolismo , Animais , Membrana Celular/genética , Citocinese , Dados de Sequência Molecular , Transporte Proteico , Tetrahymena thermophila/citologia
11.
PLoS One ; 3(12): e3839, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-19052635

RESUMO

Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequencing of the transcriptomes of reciprocal F1 mouse neonatal brains and identified 26 genes with parent-of-origin dependent differential allelic expression. Allele-specific Pyrosequencing verified 17 of them, including three novel imprinted genes. The known and novel imprinted genes all are found in proximity to previously reported differentially methylated regions (DMRs). Ten genes known to be imprinted in placenta had sufficient expression levels to attain a read depth that provided statistical power to detect imprinting, and yet all were consistent with non-imprinting in our transcript count data for neonatal brain. Three closely linked and reciprocally imprinted gene pairs were also discovered, and their pattern of expression suggests transcriptional interference. Despite the coverage of more than 5000 genes, this scan only identified three novel imprinted refseq genes in neonatal brain, suggesting that this tissue is nearly exhaustively characterized. This approach has the potential to yield an complete catalog of imprinted genes after application to multiple tissues and developmental stages, shedding light on the mechanism, bioinformatic prediction, and evolution of imprinted genes and diseases associated with genomic imprinting.


Assuntos
Encéfalo/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Impressão Genômica/genética , Alelos , Animais , Animais Recém-Nascidos , Encéfalo/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Camundongos , Camundongos Endogâmicos AKR , Camundongos Endogâmicos C3H , Camundongos Endogâmicos C57BL , Genes Inseridos , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA
12.
Zoolog Sci ; 25(8): 811-20, 2008 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-18795815

RESUMO

The rice frog, Fejervarya multistriata, is an amphibian widely distributed in China. In this study, we sampled the species across its distributional area in China and sequenced the mtDNA D-loop to investigate the genetic diversity and geographical pattern of the frog population. The results revealed 38 haplotypes in the population, with K2P values varying from 0.19% to 4.22%. Both a phylogenetic analysis and a nested clade analysis (NCA) detected two geographically isolated lineages respectively distributed around the Yangtze drainage (Yangtze lineage) and the south of China (southern lineage). NCA inferred a contiguous range expansion within the Yangtze lineage and allopatric fragmentation within the southern lineage, which might be partly due to the limited samples from this lineage. Accordingly, Fu's Fs test also indicated a population expansion after glacial movement. Therefore, we assumed that the species history responding to glacial events shaped the present population pattern of F. multistriata on the Chinese mainland.


Assuntos
DNA Mitocondrial/genética , Haplótipos/genética , Filogenia , Ranidae/genética , Animais , Sequência de Bases , China , Evolução Molecular , Variação Genética , Genética Populacional , Geografia , Dados de Sequência Molecular , Genes Inseridos , Reação em Cadeia da Polimerase , Ranidae/classificação
13.
Trends Genet ; 24(10): 475-8, 2008 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-18774620

RESUMO

The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.


Assuntos
Genoma , Genes Inseridos/fisiologia , Animais , Evolução Molecular , Genoma/fisiologia , Humanos , Filogenia
14.
Genome Res ; 18(9): 1484-99, 2008 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-18599681

RESUMO

Mobile DNA elements play a major role in genome plasticity and other evolutionary processes, an insight gained primarily through the study of transposons and retrotransposons (generally approximately 1000 nt or longer). These elements spawn smaller parasitic versions (generally >100 nt) that propagate through proteins encoded by the full elements. Highly repeated sequences smaller than 100 nt have been described, but they are either nonmobile or their origins are not known. We have surveyed the genome of the multicellular cyanobacterium, Nostoc punctiforme, and its relatives for small dispersed repeat (SDR) sequences and have identified eight families in the range of from 21 to 27 nucleotides. Three of the families (SDR4, SDR5, and SDR6), despite little sequence similarity, share a common predicted secondary structure, a conclusion supported by patterns of compensatory mutations. The SDR elements are found in a diverse set of contexts, often embedded within tandemly repeated heptameric sequences or within minitransposons. One element (SDR5) is found exclusively within instances of an octamer, HIP1, that is highly over-represented in the genomes of many cyanobacteria. Two elements (SDR1 and SDR4) often are found within copies of themselves, producing complex nested insertions. An analysis of SDR elements within cyanobacterial genomes indicate that they are essentially confined to a coherent subgroup. The evidence indicates that some of the SDR elements, probably working through RNA intermediates, have been mobile in recent evolutionary time, making them perhaps the smallest known mobile elements.


Assuntos
Cianobactérias/genética , Genoma Bacteriano , Sequências Repetitivas Dispersas/genética , Proteínas de Bactérias/genética , Sequência de Bases , Modelos Biológicos , Dados de Sequência Molecular , Mutação , Genes Inseridos , Conformação de Ácido Nucleico , Filogenia
15.
Zhonghua Gan Zang Bing Za Zhi ; 16(4): 265-9, 2008 Apr.
Artigo em Chinês | MEDLINE | ID: mdl-18423147

RESUMO

OBJECTIVE: To investigate the influence of combined hepatitis B immune globulin (HBIG) and lamivudine (LMV) treatment on hepatitis B virus (HBV) surface antigen and polymerase overlapping gene mutations in HBV reinfected liver transplant recipients. METHODS: From June 2002 to December 2003, 320 patients who underwent liver transplantations due to HBV-related end-stage liver diseases were followed-up for 1.5 to 3 years postoperatively. Fourteen patients developed HBV reinfection. They had LMV before their liver transplantations and had LMV and HBIG after the transplantations to prevent HBV infections. Their serum levels of HBV DNA were measured by polymerase chain reaction. Gene sequencing method was used to analyze HBV genotype and mutations of the S gene. Micro-particle enzyme immunoassay was used to measure the serum concentration of HBIG. RESULTS: (1) There was no obvious difference in the number of amino acid mutation sites in S and P regions before and after the transplantations. (2) The HBV genotypes were B-type (n=2) and C-type (n=12) in the reinfected group before the transplantations, and genotypes after the transplantations remained the same. (3) HBIG concentrations were 0 U/L in 7 patients, less than 100 U/L in 5 patients, and more than 100 U/L in 2 patients. Mutations were detected as I126S, T131N, S143T and G145R in 'a' determinant and L110F, I113S, T160K in up- or down-stream of 'a' determinant. (4) Mutations in S gene caused missense mutation in the surface antigen region. These mutations also caused corresponding missense mutations in the polymerase region. The missense mutation in the polymerase region involved lamivudine mutation sites and other mutation sites. CONCLUSION: Immunosuppressant therapy has no obvious influence on the numbers of mutations, but it can influence the sites of the mutations. Besides 'a' determinant mutations, there exist mutations in up- or down-streams of 'a' determinant and they may cause HBV reinfection.


Assuntos
Vírus da Hepatite B/genética , Hepatite B/virologia , Transplante de Fígado , Mutação , Adulto , Feminino , Frequência do Gene , Genoma Viral , Genótipo , Hepatite B/tratamento farmacológico , Antígenos de Superfície da Hepatite B/genética , Humanos , Imunoglobulinas/uso terapêutico , Lamivudina/uso terapêutico , Masculino , Pessoa de Meia-Idade , Genes Inseridos , Recidiva
16.
Eukaryot Cell ; 7(8): 1289-98, 2008 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-18310357

RESUMO

The genomic architecture of the budding yeast Saccharomyces cerevisiae is typical of other eukaryotes in that genes are spatially organized into discrete and nonoverlapping units. Inherent in this organizational model is the assumption that protein-coding sequences do not overlap completely. Here, we present evidence to the contrary, defining a previously overlooked yeast gene, NAG1 (for nested antisense gene) nested entirely within the coding sequence of the YGR031W open reading frame in an antisense orientation on the opposite strand. NAG1 encodes a 19-kDa protein, detected by Western blotting of hemagglutinin (HA)-tagged Nag1p with anti-HA antibodies and by beta-galactosidase analysis of a NAG1-lacZ fusion. NAG1 is evolutionarily conserved as a unit with YGR031W in bacteria and fungi. Unlike the YGR031WP protein product, however, which localizes to the mitochondria, Nag1p localizes to the cell periphery, exhibiting properties consistent with those of a plasma membrane protein. Phenotypic analysis of a site-directed mutant (nag1-1) disruptive for NAG1 but silent with respect to YGR031W, defines a role for NAG1 in yeast cell wall biogenesis; microarray profiling of nag1-1 indicates decreased expression of genes contributing to cell wall organization, and the nag1-1 mutant is hypersensitive to the cell wall-perturbing agent calcofluor white. Furthermore, production of Nag1p is dependent upon the presence of the cell wall integrity pathway mitogen-activated protein kinase Slt2p and its downstream transcription factor Rlm1p. Thus, NAG1 is important for two reasons. First, it contributes to yeast cell wall biogenesis. Second, its genomic context is novel, raising the possibility that other nested protein-coding genes may exist in eukaryotic genomes.


Assuntos
Elementos Antissenso (Genética)/genética , Regulação Fúngica da Expressão Gênica/genética , Proteínas de Membrana/genética , Genes Inseridos/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Parede Celular/genética , Parede Celular/metabolismo , Genoma Fúngico/genética , Proteínas de Domínio MADS , Proteínas de Membrana/isolamento & purificação , Proteínas de Membrana/metabolismo , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/isolamento & purificação , Proteínas de Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/metabolismo
17.
BMC Evol Biol ; 8: 21, 2008 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-18215328

RESUMO

BACKGROUND: Pleistocene glaciations had considerable impact on phylogeographic patterns within and among closely related species of many vertebrates. Compared to Europe and North America, research on the phylogeography of vertebrates in East Asia, particularly in China, remains limited. The black-spotted frog (Pelophylax nigromaculata) is a widespread species in East Asia. The wide distribution of this species in China makes it an ideal model for the study of palaeoclimatic effects on vertebrates in East Asia. Our previous studies of P. nigromaculata revealed significant subdivisions between the northeast China populations and populations in other regions of the mainland. In the present study, we aim to see whether the deepest splits among lineages and perhaps subsequent genealogical divisions are temporally consistent with a Pleistocene origin and whether clade geographic distributions, with insight into expansion patterns, are similarly spatially consistent with this model. RESULTS: Using 1143 nucleotides of the mitochondrial cytochrome b gene from 262 individuals sampled from 28 localities, two main clades (clade A and clade B) differing by c. 7.72% sequence divergence were defined from parsimony analyses. The corresponding timing of lineage divergence, 0.92 Mya, indicates a most likely Pleistocene split. The A clade is further subdivided into two sub-clades, A1 and A2 with 1.22% sequence divergence. Nested clade phylogeographical and population demographic analyses suggested that the current distribution of this frog species was the result of range expansion from two independent refugia during the last interglacial period. We discovered a population within which haplotype lineages A and B of P. nigromaculata coexist in the Dongliao area of China by nucleotide sequences, PCR-RFLP and ISSR (inter simple sequence repeat) patterns. The ISSR result in particular supported divergence between the mitochondrial clades A and B and implied introgressive gene flow between the two divergent lineages. CONCLUSION: Nested clade phylogeographical and population demographic analyses indicate that the current distribution of P. nigromaculata is the result of range expansion from two independent refugia during the last interglacial period in late Pleistocene. One refugium was in east China and the lower elevations of south-western plateau. The distribution of the other mitochondrial clade is consistent with the presence of a refugium in the Korean Peninsula. The gene flow as detected by ISSR markers suggests a range expansion of the two refugia and a secondary contact between the two highly divergent lineages in the Dongliao (DL) area of northeast China.


Assuntos
Filogenia , Ranidae/genética , Animais , China , Citocromos b/genética , DNA Mitocondrial/genética , Demografia , Evolução Molecular , Variação Genética , Geografia , Haplótipos , Genes Inseridos , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição
18.
J Mol Biol ; 375(5): 1212-21, 2008 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-18076902

RESUMO

The gene pgaM is involved in the biosynthesis of an angucycline-type polyketide antibiotic in Streptomyces sp. PGA64. It encodes a two-domain polypeptide consisting of an N-terminal flavoprotein oxygenase and a C-terminal short-chain alcohol dehydrogenase/reductase, which are fused together at the translational level as a result of end codon deletion. Here we show that translation also initiates at an internal start codon that enables independent expression of a separate reductase subunit, PgaMred. This confirms that the gene exhibits a rare viral-like arrangement of two overlapping reading frames that allows simultaneous expression of two alternative forms of the protein. Together, these two proteins associate to form a stable non-covalent complex, the native form of PgaM. The reductase subunit PgaMred is shown to provide enzyme stability and to affect the redox state of the oxygenase domain FAD. Finally, a model for the quaternary structure of the complex that explains the necessity for a nested gene system and the unusual behaviour of the protein subunits in vitro is presented.


Assuntos
Genes Bacterianos , Genes Inseridos , Estrutura Quaternária de Proteína/genética , Proteínas/genética , Streptomyces/genética , Álcool Desidrogenase/química , Sequência de Aminoácidos , Sequência de Bases , Catálise , Códon de Iniciação , Dimerização , Escherichia coli/genética , Isoenzimas , Oxigenases de Função Mista/química , Modelos Moleculares , Dados de Sequência Molecular , Família Multigênica , Fases de Leitura Aberta , Oxirredução , Plasmídeos , Policetídeo Sintases/biossíntese , Estrutura Terciária de Proteína , Subunidades Proteicas/química , Análise de Sequência de Proteína
19.
Physiol Genomics ; 28(2): 168-78, 2007 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-16985004

RESUMO

Nested genes are fairly common within the mammalian nervous system, yet few studies have examined whether the guest and host genes might be coordinately regulated. Tissue inhibitors of metalloproteinase (TIMPs) inhibit extracellular matrix proteolysis mediated by metzincin proteases. TIMP-2 is the only TIMP not nested within a synapsin gene. It does, however, serve as a host for differential display clone 8 (DDC8), a testis-specific gene whose expression is upregulated during spermatogenesis. Here, we demonstrate that DDC8 is not testis specific. Furthermore, DDC8 expression in nonneural and neural tissues mimics that of TIMP-2, including its upregulation in response to traumatic brain injury, suggesting a potential regulatory relationship. The most striking observation is that the TIMP-2 knockout mouse brain contains TIMP-2 mRNA encoding exons 2-5, which are downstream of DDC8, but not exon 1, which contains the signal sequence and cysteine residue required for MMP inhibition, indicating a functional knockout. That TIMP-2 transcripts in wild-type brain contain DDC8 sequence suggests alternative splicing between the two genes.


Assuntos
Regulação da Expressão Gênica , Genes Inseridos/genética , Proteínas/genética , Inibidor Tecidual de Metaloproteinase-2/genética , Sequência de Aminoácidos , Animais , Northern Blotting , Western Blotting , Encéfalo/metabolismo , Éxons/genética , Feminino , Perfilação da Expressão Gênica , Hibridização In Situ , Masculino , Camundongos , Camundongos Knockout , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Alinhamento de Sequência , Testículo/metabolismo , Inibidor Tecidual de Metaloproteinase-2/metabolismo , Transcrição Genética/genética
20.
Eur J Oral Sci ; 114 Suppl 1: 133-8; discussion 164-5, 380-1, 2006 May.
Artigo em Inglês | MEDLINE | ID: mdl-16674675

RESUMO

The AMELX gene encoding the enamel matrix protein, amelogenin, is located within (and in the opposite orientation to) the first intron of the ARHGAP6 gene, which encodes a GTPase-activating protein. The orientation of these two genes with respect to each other raises the possibility that they may undergo simultaneous convergent transcription during amelogenesis. The aim of this study was to use atomic force microscopy (AFM) to study a transcriptionally active amelogenin DNA template and to investigate the binding of RNA polymerase to convergently aligned promoters. Images of RNA polymerases stalled on DNA templates were obtained following incubation of the template with RNA polymerases and ribonucleotide triphosphates. A linear DNA template incorporating an intact rat amelogenin cDNA flanked by convergently aligned coliphage T7 and T3 promoters was constructed and shown to be transcriptionally active in vitro. Atomic force microscopy images of transcription complexes revealed globular structures, corresponding to single RNA polymerase molecules bound at specific locations on the DNA templates. These results indicate that AFM allows the visualization of individual RNA polymerases on DNA templates, offering a realistic approach to investigating the concept of convergent transcription of nested genes, which may lead to an understanding of whether the simultaneous expression of AMELX and ARHGAP6 is possible during the formation of tooth enamel.


Assuntos
Amelogênese/genética , RNA Polimerases Dirigidas por DNA/genética , Proteínas do Esmalte Dentário/genética , Microscopia de Força Atômica , Transcrição Genética/genética , Amelogenina , Animais , DNA Complementar/genética , RNA Polimerases Dirigidas por DNA/ultraestrutura , Esmalte Dentário/ultraestrutura , Proteínas do Esmalte Dentário/ultraestrutura , Proteínas Ativadoras de GTPase/genética , Íntrons/genética , Genes Inseridos/genética , Regiões Promotoras Genéticas/genética , Ratos , Ribonucleotídeos/genética , Moldes Genéticos , Proteínas rho de Ligação ao GTP/genética
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