RESUMO
The Ptr1 (Pseudomonas tomato race 1) locus in Solanum lycopersicoides confers resistance to strains of Pseudomonas syringae pv. tomato expressing AvrRpt2 and Ralstonia pseudosolanacearum expressing RipBN. Here we describe the identification and phylogenetic analysis of the Ptr1 gene. A single recombinant among 585 F2 plants segregating for the Ptr1 locus was discovered that narrowed the Ptr1 candidates to eight nucleotide-binding leucine-rich repeat protein (NLR)-encoding genes. From analysis of the gene models in the S. lycopersicoides genome sequence and RNA-Seq data, two of the eight genes emerged as the strongest candidates for Ptr1. One of these two candidates was found to encode Ptr1 based on its ability to mediate recognition of AvrRpt2 and RipBN when it was transiently expressed with these effectors in leaves of Nicotiana glutinosa. The ortholog of Ptr1 in tomato and in Solanum pennellii is a pseudogene. However, a functional Ptr1 ortholog exists in Nicotiana benthamiana and potato, and both mediate recognition of AvrRpt2 and RipBN. In apple and Arabidopsis, recognition of AvrRpt2 is mediated by the Mr5 and RPS2 proteins, respectively. Phylogenetic analysis places Ptr1 in a distinct clade compared with Mr5 and RPS2, and it therefore appears to have arisen by convergent evolution for recognition of AvrRpt2.
Assuntos
Proteínas de Bactérias/metabolismo , Resistência à Doença/genética , Proteínas de Membrana Transportadoras/genética , Proteínas de Plantas/genética , Solanaceae/genética , Solanum/genética , Evolução Molecular , Solanum lycopersicum/genética , Proteínas de Membrana Transportadoras/fisiologia , Filogenia , Folhas de Planta/metabolismo , Proteínas de Plantas/fisiologia , Pseudogenes/genética , Pseudogenes/fisiologia , Ralstonia/genética , Solanaceae/fisiologia , Solanum tuberosum/genética , Nicotiana/genéticaRESUMO
In this work the complete chloroplast DNAs of Allium paradoxum and Allium ursinum, two edible species of Allium subg. Amerallium (the first lineage), were sequenced, assembled, annotated, and compared with complete Allium plastomes of the second and third evolutionary lines from GenBank database. The A. ursinum plastome contains 90 predicted genes (81 unique) including 5 pseudogenes, while A. paradoxum has 88 predicted genes (79 unique) including 19 pseudogenes. The comparative analysis has revealed that the A. paradoxum plastome differs markedly from those of other species. Due to many deletions, the A. paradoxum plastome is the shortest of known for Allium species, being only 145,819â¯bp long. The most prominent distinctions are (1) a 4825â¯bp long local inversion that spans from the ndhE to the rpl32 gene in the small single copy region and (2) pseudogenization, or the loss of all NADH-genes. In contrast, the plastome of A. ursinum - a species from the first evolutionary line (as well as A. paradoxum) - resembles the Allium species of the second and third evolutionary lines, showing no large rearrangements or discrepancies in gene content. It is unclear yet whether only A. paradoxum was affected by some evolutionary events or its close relatives from both sect. Briseis and other sections of Amerallium were altered as well. We speculate the sunlight-intolerant, shade-loving nature of A. paradoxum and the impairment of the ndh genes in its plastome could be interrelated phenomena.
Assuntos
Allium/genética , Rearranjo Gênico/genética , Genes de Plantas/genética , Cebolas/genética , DNA de Cloroplastos/genética , DNA de Plantas/genética , Evolução Molecular , Genoma de Cloroplastos/genética , Genoma de Planta/genética , Filogenia , Folhas de Planta/genética , Pseudogenes/genética , Análise de Sequência de DNA/métodosRESUMO
Brucella spp. are intracellular pathogens that cause a disease known as brucellosis. Though the genus is highly monomorphic at the genetic level, species have animal host preferences and some defining physiologic characteristics. Of note is the requirement for CO2 supplementation to cultivate particular species, which confounded early efforts to isolate B. abortus from diseased cattle. Differences in the capacity of Brucella species to assimilate CO2 are determined by mutations in the carbonic anhydrase gene, bcaA Ancestral single-nucleotide insertions in bcaA have resulted in frameshifted pseudogenes in B. abortus and B. ovis lineages, which underlie their inability to grow under the low CO2 tension of a standard atmosphere. Incubation of wild-type B. ovis in air selects for mutations that "rescue" a functional bcaA reading frame, which enables growth under low CO2 and enhances the growth rate under high CO2 Accordingly, we show that heterologous expression of functional Escherichia coli carbonic anhydrases enables B. ovis growth in air. Growth of B. ovis is acutely sensitive to a reduction in CO2 tension, while frame-rescued B. ovis mutants are insensitive to CO2 shifts. B. ovis initiates a gene expression program upon CO2 downshift that resembles the stringent response and results in transcriptional activation of its type IV secretion system. Our study provides evidence that loss-of-function insertion mutations in bcaA sensitize the response of B. ovis and B. abortus to reduced CO2 tension relative to that of other Brucella lineages. CO2-dependent starvation and virulence gene expression programs in these species may influence persistence or transmission in natural hosts.IMPORTANCEBrucella spp. are highly related, but they exhibit differences in animal host preference that must be determined by genome sequence differences. B. ovis and the majority of B. abortus strains require high CO2 tension to be cultivated in vitro and harbor conserved insertional mutations in the carbonic anhydrase gene, bcaA, which underlie this trait. Mutants that grow in a standard atmosphere, first reported nearly a century ago, are easily selected in the laboratory. These mutants harbor varied indel polymorphisms in bcaA that restore its consensus reading frame and rescue its function. Loss of bcaA function has evolved independently in the B. ovis and B. abortus lineages and results in a dramatically increased sensitivity to CO2 limitation.
Assuntos
Brucella/genética , Dióxido de Carbono/metabolismo , Anidrases Carbônicas/genética , Pseudogenes/genética , Alelos , Brucella/enzimologia , Brucella/metabolismo , Brucella abortus/enzimologia , Brucella abortus/genética , Brucella abortus/metabolismo , Brucella ovis/enzimologia , Brucella ovis/genética , Brucella ovis/metabolismo , Anidrases Carbônicas/metabolismo , DNA Bacteriano/genética , Mutação da Fase de Leitura/genética , Mutação com Perda de Função/genética , Pseudogenes/fisiologiaRESUMO
Most humans harbor both CD177neg and CD177pos neutrophils but 1-10% of people are CD177null, placing them at risk for formation of anti-neutrophil antibodies that can cause transfusion-related acute lung injury and neonatal alloimmune neutropenia. By deep sequencing the CD177 locus, we catalogued CD177 single nucleotide variants and identified a novel stop codon in CD177null individuals arising from a single base substitution in exon 7. This is not a mutation in CD177 itself, rather the CD177null phenotype arises when exon 7 of CD177 is supplied entirely by the CD177 pseudogene (CD177P1), which appears to have resulted from allelic gene conversion. In CD177 expressing individuals the CD177 locus contains both CD177P1 and CD177 sequences. The proportion of CD177hi neutrophils in the blood is a heritable trait. Abundance of CD177hi neutrophils correlates with homozygosity for CD177 reference allele, while heterozygosity for ectopic CD177P1 gene conversion correlates with increased CD177neg neutrophils, in which both CD177P1 partially incorporated allele and paired intact CD177 allele are transcribed. Human neutrophil heterogeneity for CD177 expression arises by ectopic allelic conversion. Resolution of the genetic basis of CD177null phenotype identifies a method for screening for individuals at risk of CD177 isoimmunisation.
Assuntos
Isoantígenos/biossíntese , Neutropenia/imunologia , Neutrófilos/imunologia , Pseudogenes/genética , Receptores de Superfície Celular/biossíntese , Anticorpos Anticitoplasma de Neutrófilos/biossíntese , Anticorpos Anticitoplasma de Neutrófilos/imunologia , Transfusão de Sangue Autóloga/efeitos adversos , Proteínas Ligadas por GPI/biossíntese , Proteínas Ligadas por GPI/genética , Regulação da Expressão Gênica , Heterogeneidade Genética , Humanos , Isoantígenos/sangue , Isoantígenos/genética , Isoantígenos/imunologia , Neutropenia/patologia , Neutrófilos/metabolismo , Polimorfismo de Nucleotídeo Único , Pseudogenes/imunologia , Receptores de Superfície Celular/genética , Receptores de Superfície Celular/imunologia , Trombocitopenia Neonatal AloimuneRESUMO
Ribosomal DNA (rDNA) repeats often exhibit a high level of within-species homogeneity, but intra-individual polymorphism of rDNA has been found in Camellia species. In order to reveal the evolutionary pattern of rDNA repeats in tea [Camellia sinensis (L.) O. Kuntze], we identified the 45S rDNA loci, estimated their copy number, and cloned partial regions of them from different PCR products and from digested genomic DNA. The results show that there are 3 loci (6 sites) containing 45S rDNA in the tea genome; they are located at the ends of the short arms of 6 chromosomes and consist of a maximum of â¼6500 repeat units. On one hand, 164 sequences of the 26S rDNA cloned from PCR products contained 147 haplotypes, consisting of 62% pseudogenes, 24% putative functional genes, and 14% PCR-mediated recombinants, suggesting that the 45S rDNA of tea maintains an extremely high level of polymorphism and divergence; on the other hand, rDNA fragments cloned directly from genomic DNA exhibited a very high level of homogeneity: only one of 33 rDNA fragments was from a pseudogene. These results demonstrate that although over 60% of the 26S rDNA sequences identified in PCR products belong to pseudogenes, most 45S rDNA repeats are functional genes and have undergone concerted evolution. In this study, strong PCR bias and PCR-mediated recombination greatly increased the apparent proportion of pseudogenes in PCR products. Phylogenetic analysis and genetic divergence values for 26S rDNA sequences obtained in this study show that many pseudogenes have originated independently from functional genes at different times, and despite thus escaping from concerted evolution, they have failed to be eliminated from the tea genome over a long period, some of them having even produced addition copies by rapid expansion. Importantly, our study suggests that in order to determine the true pattern of evolution of rDNA it is necessary to combine data from more than one method rather than relying only on sequences from PCR products.
Assuntos
Camellia sinensis/genética , DNA Ribossômico/genética , Evolução Molecular , Polimorfismo Genético/genética , Pontos de Quebra do Cromossomo , Genoma de Planta/genética , Haplótipos/genética , Filogenia , Reação em Cadeia da Polimerase , Pseudogenes/genética , Recombinação Genética/genética , Chá/genéticaRESUMO
BACKGROUND: Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24. METHODOLOGY/PRINCIPAL FINDINGS: We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian (25 proteins) selenoproteomes, and describe how they evolved along lineages through gene duplication (20 events), gene loss (10 events) and replacement of Sec with cysteine (12 events). We show that an intronless selenophosphate synthetase 2 gene evolved in early mammals and replaced functionally the original multiexon gene in placental mammals, whereas both genes remain in marsupials. Mammalian thioredoxin reductase 1 and thioredoxin-glutathione reductase evolved from an ancestral glutaredoxin-domain containing enzyme, still present in fish. Selenoprotein V and GPx6 evolved specifically in placental mammals from duplications of SelW and GPx3, respectively, and GPx6 lost Sec several times independently. Bony fishes were characterized by duplications of several selenoprotein families (GPx1, GPx3, GPx4, Dio3, MsrB1, SelJ, SelO, SelT, SelU1, and SelW2). Finally, we report identification of new isoforms for several selenoproteins and describe unusually conserved selenoprotein pseudogenes. CONCLUSIONS/SIGNIFICANCE: This analysis represents the first comprehensive survey of the vertebrate and mammal selenoproteomes, and depicts their evolution along lineages. It also provides a wealth of information on these selenoproteins and their forms.
Assuntos
Mamíferos/metabolismo , Proteoma/metabolismo , Selenoproteínas/metabolismo , Vertebrados/metabolismo , Processamento Alternativo , Sequência de Aminoácidos , Animais , Sequência de Bases , Evolução Molecular , Duplicação Gênica , Humanos , Mamíferos/genética , Dados de Sequência Molecular , Mutação , Filogenia , Isoformas de Proteínas/classificação , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteoma/classificação , Proteoma/genética , Proteômica , Pseudogenes/genética , Selenoproteínas/classificação , Selenoproteínas/genética , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido Nucleico , Vertebrados/genéticaRESUMO
The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising â¼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes.
Assuntos
Resistência à Doença/genética , Genoma de Planta , Doenças das Plantas/genética , Proteínas de Plantas/genética , Proteínas/genética , Solanum tuberosum/genética , Sequência de Aminoácidos , Sequência de Bases , Sítios de Ligação , Mapeamento Cromossômico , Cromossomos de Plantas , Sequência Conservada , Resistência à Doença/imunologia , Estudo de Associação Genômica Ampla , Proteínas de Repetições Ricas em Leucina , Dados de Sequência Molecular , Família Multigênica , Nucleotídeos/metabolismo , Filogenia , Doenças das Plantas/imunologia , Proteínas de Plantas/química , Ligação Proteica , Estrutura Terciária de Proteína , Proteínas/química , Pseudogenes/genética , Homologia de Sequência de AminoácidosRESUMO
RNA editing is a process that modifies the information in transcripts of almost all angiosperm mitochondrial protein-coding genes. In order to determine the frequency and distribution of mitochondrial RNA editing in Beta vulgaris, cDNAs were sequenced and compared to the published genome sequence. 357 C to U conversions were identified across the 31 known protein genes and pseudogenes in Beta, the fewest so far for a plant mitochondrial genome. Editing patterns in the putative gene orf518 indicate that it is most likely a functional ccmC homolog, indicating that patterns of editing can be a useful determinant of gene functionality. orf518 also contains a triplicated repeat region whose members are nearly identical yet differentially edited, most likely due to differences in the sequence context of the editing sites. In addition, we show that partial editing in Beta is common at silent editing sites but rare at nonsilent editing sites, extending previous observations to a complete plant mitochondrial genome. Finally, the degree of partial editing observed for certain genes was dependent on the choice of primers used, demonstrating that care must be taken when designing primers for use in editing studies.
Assuntos
Beta vulgaris/genética , Genes Mitocondriais/genética , Edição de RNA/genética , Sequência de Bases , Primers do DNA/metabolismo , Genes de Plantas/genética , Dados de Sequência Molecular , Pseudogenes/genética , Sequências Repetitivas de Ácido Nucleico/genéticaRESUMO
The present work reported the cloning and characterization of two novel human genes--HN1 (hematopoietic- and neurologic-expressed sequence 1) and HN1L (HN1-like gene) which are proposed to be involved in embryo development. HN1 is mapped on chromosome 17q25.2, with two transcripts (1.0 and 1.6 kb in length, respectively) due to alternative splicing. HN1 is expressed abundantly in testis and skeletal muscle among 16 human tissues, and it is localized in the nucleus indicated by GFP fusion expression. Western blot confirmed that HN1 encodes a 16.5-kDa protein. HN1L is on chromosome 16p13.3, with three splicing in the length of 2.0, 4.0 and 4.2 kb, respectively. HN1L is expressed in a variety of tissues such as liver, kidney, prostate, testis and uterus at varying levels. HN1L gene encodes a 20-kDa protein, which is localized in both the nucleus and cytoplasm. Fourteen of HN1 and sixteen of HN1L homologous genes in different species were determined and analyzed by BLAST searches. Silicon analyses of the 14 orthologous proteins of HN1 and 16 orthologous proteins of HN1L revealed that they share great conservation in vertebrate. Additionally, we identified nine pseudogenes of HN1 (six) and HN1L (three) in the genomes of the human, mouse and rat. Based on sequence alignments and phylogenetic analysis, all these homologous genes and pseudogenes were defined as a HN1 gene family.
Assuntos
Evolução Molecular , Perfilação da Expressão Gênica , Proteínas Nucleares/genética , Motivos de Aminoácidos/genética , Sequência de Aminoácidos , Sequência de Bases , Northern Blotting , Western Blotting , Linhagem Celular , Clonagem Molecular , Sequência Conservada/genética , DNA/química , DNA/genética , DNA Complementar/química , DNA Complementar/genética , Éxons , Feminino , Proteínas de Fluorescência Verde , Células HeLa , Humanos , Íntrons , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Masculino , Microscopia de Fluorescência , Dados de Sequência Molecular , Proteínas Nucleares/metabolismo , Filogenia , Pseudogenes/genética , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , TransfecçãoRESUMO
The human TPTE (Transmembrane Phosphatase with TEnsin homology) gene family encodes a PTEN-related tyrosine phosphatase with four potential transmembrane domains. Chromosomal mapping revealed multiple copies of the TPTE gene on chromosomes 13, 15, 21, 22 and Y. Human chromosomes 13 and 21 copies encode two functional proteins, TPIP (TPTE and PTEN homologous Inositol lipid Phosphatase) and TPTE, respectively, whereas only one copy of the gene exists in the mouse genome. In the present study, we show that TPTE and TPIP proteins are expressed in secondary spermatocytes and/or prespermatids. In addition, we report the existence of several novel alternatively spliced isoforms of these two proteins with variable number of transmembrane domains. The latter has no influence on the subcellular localization of these different peptides as shown by co-immunofluorescence experiments. Finally, we identify another expressed TPTE copy, mapping to human chromosome 22, whose transcription appears to be under the control of the LTR of human endogenous retrovirus RTVL-H3.
Assuntos
Processamento Alternativo , Proteínas de Membrana/genética , Proteínas Tirosina Fosfatases/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Células COS , Linhagem Celular , Chlorocebus aethiops , Cromossomos Humanos Par 22/genética , DNA Complementar/química , DNA Complementar/genética , Feminino , Regulação Enzimológica da Expressão Gênica , Proteínas de Fluorescência Verde , Células HeLa , Humanos , Imuno-Histoquímica , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Masculino , Proteínas de Membrana/metabolismo , Microscopia de Fluorescência , Dados de Sequência Molecular , Mutação , PTEN Fosfo-Hidrolase , Monoéster Fosfórico Hidrolases/genética , Monoéster Fosfórico Hidrolases/metabolismo , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteínas Tirosina Fosfatases/metabolismo , Pseudogenes/genética , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Análise de Sequência de DNA , Espermátides/enzimologia , Espermatócitos/enzimologia , Neoplasias Testiculares/enzimologia , Neoplasias Testiculares/genética , Neoplasias Testiculares/patologia , Testículo/enzimologiaRESUMO
Annexin 2 is a calcium-regulated, phospholipid-binding protein present in endothelial cells, macrophages and some tumor cells. Annexin 2 is a substrate for a variety of protein kinases, and plays roles in the regulation of endocytosis, exocytosis and thrombolysis. We have determined the nucleotide sequence of a rat genomic DNA fragment that hybridized to a rat annexin 2 DNA complementary to RNA (cDNA) probe. Sequence analysis revealed that it was an intronless rat annexin 2, consisting of a start-to-stop-codon-length copy of the processed transcript. This pseudogene contained 33 point mutations and two deletion sites in the coding region as compared with the cDNA, and thus displayed typical features of a retroposon. Transitions were more frequent than transversions, and the most frequent type of mutation was G to A transition. We isolated a phage clone that contained a functional rat annexin 2 genomic fragment including coding exons 3 and 4. Polymerase chain reaction and subsequent sequence analysis revealed an intron of approximately 4 kbp at the same site as in humans and mice. Whereas the annexin 2 gene or its cDNA homologues have been detected in various species from Xenopus to humans, its pseudogene has been reported only in humans. In the present study, we demonstrated the presence of an annexin 2 pseudogene in rats.
Assuntos
Anexina A2/genética , Pseudogenes/genética , Animais , Sequência de Bases , DNA/química , DNA/genética , DNA/isolamento & purificação , Genoma , Masculino , Dados de Sequência Molecular , Ratos , Ratos Wistar , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência do Ácido NucleicoRESUMO
The enzyme 5beta-reductase catalyzes the reduction of the 4-ene of 3-ketosteroids, converting them into 5beta-dihydro-3-ketosteroids and, thus, could be involved in the metabolism of 4-cholestene-3-one, progesterone, 17~-hydroxyprogesterone, aldosterone, corticosterone, cortisol, 4-androstenedione, and testosterone. In this study, we report the genomic structure of a human 5beta-reductase gene, its tissue distribution, the characterization of an intronless pseudogene and the substrate selectivity of the enzyme. The gene coding for the active 5beta-reductase contains nine exons like most members of the aldo-keto reductase family, but the sequence covered by the gene, more than 42 kb, is much longer than the sequence of other members of this family. There are many large introns, especially introns 3, 4 and 7 that span approx. 7 kb, and intron 1 that contains more than 10 kb. Northern blot analysis showed three band sizes of 1.3, 2.2 and 2.7 kb. The 1.3 and 2.7 kb bands are highly expressed in the liver while weaker 2.2 and 1.3 kb bands have been observed in the testis and colon, respectively. We also identified an intronless gene having 86% homology with the 5beta-reductase cDNA sequence. Since its sequence contains many stop codons, this gene is most probably a pseudogene. To determine more precisely the substrate selectivity of the enzyme, we established a stable cell line expressing human 5beta-reductase in transformed embryonic kidney (HEK-293) cells. The transfected cells efficiently catalyze the transformation of progesterone, androstenedione, 17alpha-hydroxyprogesterone and testosterone. However, they catalyze much less efficiently the transformation of compounds containing an 11beta-hydroxy group, such as aldosterone, corticosterone and cortisol. In addition to its role in cholesterol catabolism, it is well recognized that 5beta-reductase inactivates active androgens. Indeed, 5beta-dihydrotestosterone (5beta-DHT), the product of the reduction of testosterone by 5beta-reductase, is not active while its 5~-isomer (DHT) is the most potent natural androgen. Recent findings show that 5beta-pregnanes are active ligands in the induction of CYP3A through the orphan receptor hPAR. Our results thus open an opportunity for studying the new role of 5beta-reductase in the formation of a new type of active steroids.
Assuntos
Oxirredutases/genética , Pseudogenes/genética , Sequência de Bases , Northern Blotting , Linhagem Celular , Clonagem Molecular , DNA Complementar/biossíntese , DNA Complementar/química , Humanos , Rim/metabolismo , Fígado/metabolismo , Dados de Sequência Molecular , Oxirredutases/biossíntese , Oxirredutases/química , Alinhamento de Sequência , Especificidade por SubstratoRESUMO
This paper reports the characterization of the human tubulin tyrosine ligase-like 1 gene (TTLL1), which maps to the chromosome region 22q13.1 and has been partially duplicated on three other acrocentric chromosomes: 13, 15 and 21. We describe the complete cDNA, TTLL1a, coding for the putative 423 amino acid long TTLL1 and alternative transcripts coding for truncated TTLL1. Likely TTLL1a corresponds to the 1.8 kb transcript that was detected in a wide range of tissues and has a stronger expression in heart, brain and testis. A 4.8 kb transcript was found only in brain tissues. We present an interspecies sequence comparison, revealing three conserved domains, named TTLD1, TTLD2 and TTLD3, that are specific to the TTLs and TTL-like proteins.
Assuntos
Cromossomos Humanos Par 22/genética , Genes/genética , Peptídeo Sintases/genética , Processamento Alternativo , Sequência de Aminoácidos , Sequência de Bases , Northern Blotting , Mapeamento Cromossômico , DNA Complementar/química , DNA Complementar/genética , Éxons , Etiquetas de Sequências Expressas , Feminino , Humanos , Íntrons , Masculino , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Pseudogenes/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Mapeamento de Híbridos Radioativos , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Distribuição TecidualAssuntos
Genes MHC Classe I/genética , Gorilla gorilla/genética , Antígenos de Histocompatibilidade Classe I/genética , Pan troglodytes/genética , Alelos , Sequência de Aminoácidos , Substituição de Aminoácidos , Animais , Linfócitos B/metabolismo , Sequência de Bases , Linhagem Celular , Cisteína/genética , DNA Complementar/genética , Dissulfetos , Éxons/genética , Gorilla gorilla/imunologia , Antígenos de Histocompatibilidade Classe I/química , Dados de Sequência Molecular , Pan troglodytes/imunologia , Filogenia , Reação em Cadeia da Polimerase , Pseudogenes/genética , Homologia de Sequência de AminoácidosRESUMO
Two alternatively spliced transcripts, psiHLAO1 and psiHLAO2, of a copper-containing monoamine oxidase pseudogene have been isolated from a human-liver cDNA library. The larger psiHLAO1 cDNA (2073bp) contains a 5'-flanking segment of 134bp, followed by an apparent open reading frame (ORF) of 1725bp. The deduced amino acid sequence of this ORF (574 residues) shares 81.0% similarity with the 763-residue monoamine oxidase from human placenta (HPAO) (the N-terminal 533 residues of psiHLAO1 share 86.7% similarity with HPAO). The psiHLAO1 ORF is interrupted by an in-frame stop codon corresponding to amino acid 225 and terminates within a type S(a) dimeric Alu repeat sequence. psiHLAO2 appears to be an alternatively spliced variant of psiHLAO1 that has 413 bases of psiHLAO1 excised according to the 'GT-AG' rule. The slightly longer 3' end of the psiHLAO2 transcript shows that the Alu repeat is followed by an 11-bp poly(A) tract that, in turn, is followed by an AT-rich (81%) sequence of 105bp. A reverse transcriptase-polymerase chain reaction (RT-PCR) protocol was used to confirm that both psiHLAO1 and psiHLAO2 are transcribed in human liver and placenta. A search of the expressed sequence tag (EST) database indicates that, like HPAO, psiHLAO derives also from the region 17q21 of the human genome.
Assuntos
Elementos Alu/genética , Amina Oxidase (contendo Cobre)/genética , DNA Complementar/isolamento & purificação , Monoaminoxidase/genética , Pseudogenes/genética , Processamento Alternativo , Amina Oxidase (contendo Cobre)/química , Sequência de Aminoácidos , Sequência de Bases , Northern Blotting , Mapeamento Cromossômico , Cromossomos Humanos Par 17/genética , Dimerização , Humanos , Fígado/enzimologia , Dados de Sequência Molecular , Monoaminoxidase/química , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Transcrição Gênica/genéticaRESUMO
A human "epidermal-type" 12-lipoxygenase (e-12LO) pseudogene was cloned using a murine e-12LO cDNA probe. Similar to other lipoxygenase genes, the genomic sequence revealed 14 exons and 13 introns covering 6.7 kb of DNA. cDNA corresponding to this gene was amplified from RNA of human skin and hair follicles by RACE-PCR and displayed 65-80% identity to the three murine 12-lipoxygenase cDNAs. Based on several criteria, humans appear to lack a functional e-12LO gene but instead have acquired an expressed pseudogene. The pseudogene designated ALOX12P2 was localized to chromosome 17p13 by analysis of somatic hybrid DNA panels.
Assuntos
Araquidonato 12-Lipoxigenase/genética , Cromossomos Humanos Par 17/genética , Epiderme/enzimologia , Pseudogenes/genética , Sequência de Aminoácidos , Sequência de Bases , Mapeamento Cromossômico , Clonagem Molecular , DNA Complementar/genética , Epiderme/química , Éxons/genética , Humanos , Íntrons/genética , Dados de Sequência Molecular , Análise de Sequência de DNARESUMO
Genes for vicilin, a component of legume seed storage proteins, have been identified in the cultivated lentil (Lens culinaris ssp. culinaris) and in wild species of the genus Lens. Five different types of vicilin sequences (designated A-E) have been identified in each lentil individual. The different types of sequences, and some possible variants of them (also present in each individual) are part of the vicilin family of genes. Type D sequences have the characteristics of nonprocessed pseudogenes. Comparison of nucleotide sequences indicates that lentil vicilin sequences are similar to vicilin sequences of other legume species, in particular to those of the tribe Vicieae, in which the genes Lens is included. Sequence comparison and distance and parsimony trees indicated that two groups or subfamilies of sequences, including, respectively, types A, B, and E (47 kDa vicilins) and types C and D (50 kDa), can be distinguished in lentil and other Vicieae species, and that in the Vicieae species there is no evidence of concerted evolution among the vicilin sequences of different gene subfamilies or sequences groups, as has been suggested for other legume species.
Assuntos
Evolução Molecular , Fabaceae/genética , Genes de Plantas/genética , Proteínas de Plantas/genética , Plantas Medicinais , Composição de Bases , Sequência de Bases , DNA de Plantas/genética , Éxons/genética , Íntrons/genética , Dados de Sequência Molecular , Filogenia , Pseudogenes/genética , Proteínas de Armazenamento de Sementes , Homologia de Sequência do Ácido NucleicoRESUMO
We have recently identified and characterized a Kruppel-like zinc finger protein (BERF-1), that functions as a repressor of beta enolase gene transcription. By interspecific backcross analysis the gene encoding BERF-1 was localized 4.7 cM proximal to the Mtv6 locus on mouse chromosome 16, and an isolated pseudogene was localized to mouse chromosome 8, about 5.3 cM distal to the D8Mit4 marker. Nucleotide sequence identity and chomosome location indicate that the gene encoding BERF-1 is the mouse homologue (Zfp148) of ZNF148 localized to human chromosome 3q21, a common translocation site in acute myeloid leukemia patients.
Assuntos
Mapeamento Cromossômico , Cromossomos Humanos Par 3 , Fosfopiruvato Hidratase/genética , Pseudogenes/genética , Proteínas Repressoras , Dedos de Zinco/genética , Animais , Sequência de Bases , Sequência Conservada , Primers do DNA , DNA Complementar , Proteínas de Ligação a DNA/genética , Regulação Enzimológica da Expressão Gênica , Marcadores Genéticos , Humanos , Células Híbridas/fisiologia , Fatores de Transcrição Kruppel-Like , Camundongos , Reação em Cadeia da Polimerase , Fatores de Transcrição/genética , Transcrição Gênica/genéticaRESUMO
We have applied cDNA hybridization selection to nine YACs spanning 3 Mb of genomic DNA from a region centromeric to HLA-A to the histone cluster that lies telomeric to the human major histocompatibility complex (MHC). In addition to Class I genes and pseudogenes, we describe over 63 genes and 23 additional expressed sequence tags distributed throughout the region. Many of the full-length genes belong to gene families. Prominent among these are a group of genes encoding proteins showing homology to the carboxyl-terminal sequences of butyrophilin and an additional group of zinc finger genes. We also detected several previously undefined genes that are specifically expressed in cells of the immune system, indicating a more complex role of the MHC in the immune response than has been appreciated.
Assuntos
Mapeamento Cromossômico/métodos , DNA Complementar/genética , Genes MHC Classe I/genética , Transcrição Gênica , Sequência de Aminoácidos , Sequência de Bases , Cromossomos Artificiais de Levedura/genética , Evolução Molecular , Expressão Gênica , Humanos , Dados de Sequência Molecular , Família Multigênica/genética , Pseudogenes/genética , RNA Mensageiro/genética , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Dedos de ZincoRESUMO
The L5 ribosomal protein gene (rpl5) and a S14 ribosomal protein pseudogene were identified by sequence analysis in the potato mitochondrial genome. The two genes are separated by one nucleotide and are found upstream of the apocytochrome b gene (cob), an arrangement conserved also in Arabidopsis and Brassica. The rpl5 gene has an intact open reading frame while the rps14 locus is disrupted by a five nucleotide duplication that introduces a frameshift in the reading frame. Editing of rpl5 and pseudorps14 cotranscripts has been studied by cDNA sequence analysis. Eight C residues are edited into U in the rpl5 coding region, resulting in eight amino acid changes that increase the homology between potato and other RPL5 polypeptides. Interestingly, the rps14 pseudogene sequence is not edited at any nucleotide position.