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1.
Nat Genet ; 31(3): 295-300, 2002 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-12089527

RESUMEN

Only a small proportion of cancers result from familial cancer syndromes with Mendelian inheritance. Nonfamilial, 'sporadic' cancers, which represent most cancer cases, also have a significant hereditary component, but the genes involved have low penetrance and are extremely difficult to detect. Therefore, mapping and cloning of quantitative trait loci (QTLs) for cancer susceptibility in animals could help identify homologous genes in humans. Several cancer-susceptibility QTLs have been mapped in mice and rats, but none have been cloned so far. Here we report the positional cloning of the mouse gene Scc1 (Susceptibility to colon cancer 1) and the identification of Ptprj, encoding a receptor-type protein tyrosine phosphatase, as the underlying gene. In human colon, lung and breast cancers, we show frequent deletion of PTPRJ, allelic imbalance in loss of heterozygosity (LOH) and missense mutations. Our data suggest that PTPRJ is relevant to the development of several different human cancers.


Asunto(s)
Adenocarcinoma/genética , Proteínas de Ciclo Celular/genética , Neoplasias del Colon/genética , Proteínas Tirosina Fosfatasas/genética , Adenocarcinoma/patología , Animales , Neoplasias de la Mama/genética , Proteínas de Ciclo Celular/química , Proteínas Cromosómicas no Histona , Mapeo Cromosómico , Neoplasias del Colon/inducido químicamente , Dimetilhidrazinas , Eliminación de Gen , Silenciador del Gen , Marcadores Genéticos , Humanos , Pérdida de Heterocigocidad , Neoplasias Pulmonares/genética , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos , Proteínas Nucleares , Fosfoproteínas , Polimorfismo Genético , Carácter Cuantitativo Heredable , Proteínas Tirosina Fosfatasas Clase 3 Similares a Receptores , Proteínas de Saccharomyces cerevisiae , Homología de Secuencia de Aminoácido , Homología de Secuencia de Ácido Nucleico
2.
J Bacteriol ; 193(3): 791-2, 2011 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-21097610

RESUMEN

Achromobacter xylosoxidans strain A8 was isolated from soil contaminated with polychlorinated biphenyls. It can use 2-chlorobenzoate and 2,5-dichlorobenzoate as sole sources of carbon and energy. This property makes it a good starting microorganism for further development toward a bioremediation tool. The genome of A. xylosoxidans consists of a 7-Mb chromosome and two large plasmids (98 kb and 248 kb). Besides genes for the utilization of xenobiotic organic substrates, it contains genes associated with pathogenesis, toxin production, and resistance. Here, we report the complete genome sequence.


Asunto(s)
Achromobacter denitrificans/genética , ADN Bacteriano/química , ADN Bacteriano/genética , Genoma Bacteriano , Achromobacter denitrificans/aislamiento & purificación , Achromobacter denitrificans/metabolismo , Carbono/metabolismo , Clorobenzoatos/metabolismo , Cromosomas Bacterianos , Metabolismo Energético , Datos de Secuencia Molecular , Plásmidos , Análisis de Secuencia de ADN , Microbiología del Suelo
3.
Proc Natl Acad Sci U S A ; 105(26): 8989-93, 2008 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-18577593

RESUMEN

Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of dark shielding pigment. Cnidaria as the likely sister group to the Bilateria are the earliest branching phylum with a well developed visual system. Here, we show that camera-type eyes of the cubozoan jellyfish, Tripedalia cystophora, use genetic building blocks typical of vertebrate eyes, namely, a ciliary phototransduction cascade and melanogenic pathway. Our findings indicative of parallelism provide an insight into eye evolution. Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution.


Asunto(s)
Cubomedusas/crecimiento & desarrollo , Ojo/crecimiento & desarrollo , Vertebrados/crecimiento & desarrollo , Animales , Células COS , Chlorocebus aethiops , Cilios/metabolismo , Cilios/ultraestructura , Cristalinas/metabolismo , Ojo/citología , Ojo/ultraestructura , Regulación de la Expresión Génica , Cristalino/metabolismo , Melaninas/metabolismo , Factor de Transcripción Asociado a Microftalmía/genética , Factor de Transcripción Asociado a Microftalmía/metabolismo , Modelos Biológicos , Datos de Secuencia Molecular , Células Fotorreceptoras de Invertebrados/citología , Células Fotorreceptoras de Invertebrados/metabolismo , Células Fotorreceptoras de Invertebrados/ultraestructura , Pigmentación , ARN Mensajero , Opsinas de Bastones/metabolismo , Homología de Secuencia de Ácido Nucleico , Visión Ocular/genética
4.
J Bacteriol ; 192(13): 3545-6, 2010 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-20418398

RESUMEN

Rhodobacter capsulatus SB 1003 belongs to the group of purple nonsulfur bacteria. Its genome consists of a 3.7-Mb chromosome and a 133-kb plasmid. The genome encodes genes for photosynthesis, nitrogen fixation, utilization of xenobiotic organic substrates, and synthesis of polyhydroxyalkanoates. These features made it a favorite research tool for studying these processes. Here we report its complete genome sequence.


Asunto(s)
Genoma Bacteriano/genética , Rhodobacter capsulatus/genética , Sistemas de Lectura Abierta/genética
5.
J Bacteriol ; 192(11): 2701-10, 2010 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-20363938

RESUMEN

The purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in Caulobacter crescentus has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in R. capsulatus shares a high degree of sequence similarity with the C. crescentus protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and ctrA mutant cultures to identify the genes dysregulated by the loss of CtrA in R. capsulatus. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of approximately 6% of genes in the R. capsulatus genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral ctrA gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages.


Asunto(s)
Proteínas Bacterianas/metabolismo , Regulación Bacteriana de la Expresión Génica/fisiología , Rhodobacter capsulatus/genética , Proteínas Bacterianas/genética , Sitios de Unión/genética , Quimiotaxis/genética , Cromatografía Liquida , Flagelos/genética , Regulación Bacteriana de la Expresión Génica/genética , Genoma Bacteriano/genética , Espectrometría de Masas , Análisis de Secuencia por Matrices de Oligonucleótidos , Filogenia , Transducción de Señal/genética
7.
Cancers (Basel) ; 12(11)2020 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-33182777

RESUMEN

Heterogeneous spheroids have recently acquired a prominent position in melanoma research because they incorporate microenvironmental cues relevant for melanoma. In this study, we focused on the analysis of microenvironmental factors introduced in melanoma heterogeneous spheroids by different dermal fibroblasts. We aimed to map the fibroblast diversity resulting from previously acquired damage caused by exposure to extrinsic and intrinsic stimuli. To construct heterogeneous melanoma spheroids, we used normal dermal fibroblasts from the sun-protected skin of a juvenile donor. We compared them to the fibroblasts from the sun-exposed photodamaged skin of an adult donor. Further, we analysed the spheroids by single-cell RNA sequencing. To validate transcriptional data, we also compared the immunohistochemical analysis of heterogeneous spheroids to melanoma biopsies. We have distinguished three functional clusters in primary human fibroblasts from melanoma spheroids. These clusters differed in the expression of (a) extracellular matrix-related genes, (b) pro-inflammatory factors, and (c) TGFß signalling superfamily. We observed a broader deregulation of gene transcription in previously photodamaged cells. We have confirmed that pro-inflammatory cytokine IL-6 significantly enhances melanoma invasion to the extracellular matrix in our model. This supports the opinion that the aspects of ageing are essential for reliable melanoma 3D modelling in vitro.

8.
Cancers (Basel) ; 12(4)2020 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-32224897

RESUMEN

Aberrant regulation of the cell cycle is a typical feature of all forms of cancer. In head and neck squamous cell carcinoma (HNSCC), it is often associated with the overexpression of cyclin D1 (CCND1). However, it remains unclear how CCND1 expression changes between tumor and normal tissues and whether human papillomavirus (HPV) affects differential CCND1 expression. Here, we evaluated the expression of D-type cyclins in a cohort of 94 HNSCC patients of which 82 were subjected to whole genome expression profiling of primary tumors and paired normal mucosa. Comparative analysis of paired samples showed that CCND1 was upregulated in 18% of HNSCC tumors. Counterintuitively, CCND1 was downregulated in 23% of carcinomas, more frequently in HPV-positive samples. There was no correlation between the change in D-type cyclin expression and patient survival. Intriguingly, among the tumors with downregulated CCND1, one-third showed an increase in cyclin D2 (CCND2) expression. On the other hand, one-third of tumors with upregulated CCND1 showed a decrease in CCND2. Collectively, we have shown that CCND1 was frequently downregulated in HNSCC tumors. Furthermore, regardless of the HPV status, our data suggested that a change in CCND1 expression was alleviated by a compensatory change in CCND2 expression.

9.
Trends Genet ; 22(2): 69-73, 2006 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-16356584

RESUMEN

Human processed pseudogenes are copies of cellular RNAs reverse transcribed and inserted into the nuclear genome by the enzymatic machinery of L1 (LINE1) non-LTR retrotransposons. Although it is generally accepted that germline expression is crucial for the heritable retroposition of cellular mRNAs, little is known about the influences of RNA stability, mRNA quality control and compartmentalization of translation on the retroposition of processed pseudogenes. We found that frequently retroposed human mRNAs are derived from stable transcripts with translation-competent functional reading frames that are resistant to nonsense-mediated RNA decay. They are preferentially translated on free cytoplasmic ribosomes and encode soluble proteins. Our results indicate that interactions between mRNAs and L1 proteins seem to occur at free cytoplasmic ribosomes.


Asunto(s)
Elementos de Nucleótido Esparcido Largo/genética , Biosíntesis de Proteínas , Seudogenes/genética , Estabilidad del ARN , Retroelementos/genética , Animales , Expresión Génica , Humanos , ARN Mensajero/genética , ARN Mensajero/metabolismo
10.
Appl Environ Microbiol ; 75(20): 6471-7, 2009 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-19700551

RESUMEN

DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [(13)C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase alpha subunits (BphA) from bacteria that incorporated [(13)C]into DNA in 3-day incubations of the soils with [(13)C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl.


Asunto(s)
Armoracia/microbiología , Bacterias/metabolismo , Compuestos de Bifenilo/metabolismo , Bifenilos Policlorados/metabolismo , Microbiología del Suelo , Contaminantes del Suelo/metabolismo , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Secuencia de Bases , Betaproteobacteria/clasificación , Betaproteobacteria/genética , Betaproteobacteria/aislamiento & purificación , Betaproteobacteria/metabolismo , Isótopos de Carbono , Cartilla de ADN/genética , ADN Bacteriano/genética , Genes Bacterianos , Datos de Secuencia Molecular , Filogenia , ARN Bacteriano/genética , ARN Ribosómico 16S/genética
11.
Evol Dev ; 10(1): 52-61, 2008.
Artículo en Inglés | MEDLINE | ID: mdl-18184357

RESUMEN

Cnidaria is the earliest-branching metazoan phylum containing a well-developed, lens-containing visual system located on specialized sensory structures called rhopalia. Each rhopalium in a cubozoan jellyfish Tripedalia cystophora has a large and a small complex, camera-type eye with a cellular lens containing distinct families of crystallins. Here, we have characterized J2-crystallin and its gene in T. cystophora. The J2-crystallin gene is composed of a single exon and encodes a 157-amino acid cytoplasmic protein with no apparent homology to known proteins from other species. The non-lens expression of J2-crystallin suggests nonoptical as well as crystallin functions consistent with the gene-sharing strategy that has been used during evolution of lens crystallins in other invertebrates and vertebrates. Although nonfunctional in transfected mammalian lens cells, the J2-crystallin promoter is activated by the jellyfish paired domain transcription factor PaxB in co-transfection tests via binding to three paired domain sites. PaxB paired domain-binding sites were also identified in the PaxB-regulated promoters of the J1A- and J1B-crystallin genes, which are not homologous to the J2-crystallin gene. Taken together with previous studies on the regulation of the diverse crystallin genes, the present report strongly supports the idea that crystallin recruitment of multifunctional proteins was driven by convergent changes involving Pax (as well as other transcription factors) in the promoters of nonhomologous genes within and between species as well as within gene families.


Asunto(s)
Cristalinas/metabolismo , Cubomedusas/metabolismo , Evolución Molecular , Factores de Transcripción Paired Box/metabolismo , Regiones Promotoras Genéticas , Animales , Secuencia de Bases , Sitios de Unión , Células COS , Línea Celular , Chlorocebus aethiops , Clonación Molecular , Cristalinas/química , Cristalinas/genética , Cubomedusas/genética , Citoplasma/metabolismo , Exones , Regulación de la Expresión Génica , Humanos , Cristalino/metabolismo , Datos de Secuencia Molecular , Factores de Transcripción Paired Box/genética
12.
Res Microbiol ; 159(2): 118-27, 2008 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-18249097

RESUMEN

The complete 98,192bp nucleotide sequence was determined for plasmid pA81, which is harbored by the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8. The majority of the 103 open reading frames identified on pA81 could be categorized as either "backbone" genes, genes encoding (halo)aromatic compound degradation, or heavy metal resistance determinants. The backbone genes controlled conjugative transfer, replication and plasmid stability, and were well conserved with other IncP1-beta plasmids. Genes encoding (halo)aromatic degradation were clustered within a type I transposon, TnAxI, and included two ring-hydroxylating oxygenases (ortho-halobenzoate oxygenase, salicylate 5-hydroxylase) and a modified ortho-cleavage pathway for chlorocatechol degradation. The cluster of heavy metal resistance determinants was contained within a Type II transposon TnAxII, and included a predicted P-type ATPase and cation diffusion facilitator system. Genes identical to those carried by TnAxI and TnAxII were identified on other biodegradative/resistance plasmids and genomic islands, indicating an evolutionary relationship between these elements. Collectively, these insights further our understanding of how mobile elements, and interactions between mobile elements affect the fate of organic and inorganic toxicants in the environment.


Asunto(s)
Achromobacter denitrificans/genética , ADN Bacteriano/genética , Hidrocarburos Aromáticos/metabolismo , Plásmidos/química , Secuencia de Bases , Elementos Transponibles de ADN , ADN Bacteriano/química , Evolución Molecular , Genes Bacterianos , Metales Pesados/metabolismo , Oxigenasas de Función Mixta/genética , Datos de Secuencia Molecular , Familia de Multigenes , Sistemas de Lectura Abierta , Oxigenasas/genética , Plásmidos/genética , Análisis de Secuencia de ADN
13.
Nucleic Acids Res ; 30(1): 205-6, 2002 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-11752294

RESUMEN

The human endogenous retroviruses database (HERVd) is maintained at the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, and is accessible via the World Wide Web at http://herv.img.cas.cz. The HERVd provides complex information on and analysis of retroviral elements found in the human genome. It can be used for searches of individual HERV families, identification of HERV parts, graphical output of HERV structures, comparison of HERVs and identification of retrovirus integration sites.


Asunto(s)
Bases de Datos de Ácidos Nucleicos , Retrovirus Endógenos/genética , Animales , Sistemas de Administración de Bases de Datos , Evolución Molecular , Genoma Humano , Humanos , Almacenamiento y Recuperación de la Información , Internet , Ratones , Integración Viral
14.
Nucleic Acids Res ; 32(Web Server issue): W48-9, 2004 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-15215348

RESUMEN

Web Alignment Visualization Server contains a set of web-tools designed for quick generation of publication-quality color figures of multiple alignments of nucleotide or amino acids sequences. It can be used for identification of conserved regions and gaps within many sequences using only common web browsers. The server is accessible at http://wavis.img.cas.cz.


Asunto(s)
Gráficos por Computador , Alineación de Secuencia , Análisis de Secuencia , Programas Informáticos , Humanos , Internet , Análisis de Secuencia de ADN , Análisis de Secuencia de Proteína , Análisis de Secuencia de ARN
15.
Nucleic Acids Res ; 32(Database issue): D50, 2004 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-14681356

RESUMEN

An elaboration of HERVd (http://herv.img.cas.cz) is being carried out in two directions. One of them is the integration and better classification of families that diverge considerably from typical retroviral genomes. This leads to a more precise identification of members with individual families. The second improvement is better accessibility of the database and connection with human genome annotation.


Asunto(s)
Bases de Datos Genéticas , Retrovirus Endógenos/genética , Genoma Humano , Biología Computacional , Humanos , Almacenamiento y Recuperación de la Información , Internet
16.
BMC Genomics ; 6: 29, 2005 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-15748293

RESUMEN

BACKGROUND: We generated the gene expression profile of the total testis from the adult C57BL/6J male mice using serial analysis of gene expression (SAGE). Two high-quality SAGE libraries containing a total of 76 854 tags were constructed. An extensive bioinformatic analysis and comparison of SAGE transcriptomes of the total testis, testicular somatic cells and other mouse tissues was performed and the theory of male-biased gene accumulation on the X chromosome was tested. RESULTS: We sorted out 829 genes predominantly expressed from the germinal part and 944 genes from the somatic part of the testis. The genes preferentially and specifically expressed in total testis and testicular somatic cells were identified by comparing the testis SAGE transcriptomes to the available transcriptomes of seven non-testis tissues. We uncovered chromosomal clusters of adjacent genes with preferential expression in total testis and testicular somatic cells by a genome-wide search and found that the clusters encompassed a significantly higher number of genes than expected by chance. We observed a significant 3.2-fold enrichment of the proportion of X-linked genes specific for testicular somatic cells, while the proportions of X-linked genes specific for total testis and for other tissues were comparable. In contrast to the tissue-specific genes, an under-representation of X-linked genes in the total testis transcriptome but not in the transcriptomes of testicular somatic cells and other tissues was detected. CONCLUSION: Our results provide new evidence in favor of the theory of male-biased genes accumulation on the X chromosome in testicular somatic cells and indicate the opposite action of the meiotic X-inactivation in testicular germ cells.


Asunto(s)
Biología Computacional/métodos , Regulación de la Expresión Génica , Testículo/metabolismo , Transcripción Genética , Animales , Análisis por Conglomerados , Interpretación Estadística de Datos , Bases de Datos Genéticas , Perfilación de la Expresión Génica , Biblioteca de Genes , Orden Génico , Ligamiento Genético , Genómica/métodos , Masculino , Ratones , Ratones Endogámicos C57BL , Modelos Estadísticos , Familia de Multigenes , ARN/metabolismo , Análisis de Secuencia de ADN , Cromosoma X
17.
Gene ; 358: 67-72, 2005 Sep 26.
Artículo en Inglés | MEDLINE | ID: mdl-16054306

RESUMEN

Experimental cDNA sequence determinations lag behind in silico gene structure predictions in some recently sequenced genomes. This may be due in part to low transcript abundance and/or the severely spatio-temporarily restricted expression pattern of some genes. Here we characterize the predicted repressed gene of Arabidopsis thaliana (At4g21130) that encodes a homologue of the Arabidopsis U3-55K-like protein (At4g05410) and of the U3-55K (RNU3IP2, Rrp9p) proteins from other eukaryotes. In man and yeast, U3-55K is involved in the processing of the pre-ribosomal RNA. Here we show that treatment with inhibitors of histone deacetylases (trichostatin A, sodium butyrate) or DNA methyltransferases (5-aza-2'-deoxycytidine) induces a low but distinct level of mRNA from the repressed Arabidopsis At4g21130 locus, which can be detected by RT-PCR amplification. Direct sequencing of PCR products reveals the open reading frame that differs, in part, from the hypothetical one and encodes a seven-WD-repeat protein highly conserved when compared to U3-55K proteins from various eukaryotic species. This suggests the conservation of its function. The described approach may help to determine the nucleotide sequences of transcripts from predicted genes with a low level of expression.


Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , ADN Complementario/genética , Regulación de la Expresión Génica de las Plantas/fisiología , Ribonucleoproteínas Nucleolares Pequeñas/genética , Secuencia de Aminoácidos , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Clonación Molecular , Inhibidores Enzimáticos/farmacología , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Inhibidores de Histona Desacetilasas , Histona Desacetilasas/metabolismo , Datos de Secuencia Molecular , Sitios de Carácter Cuantitativo/genética , Procesamiento Postranscripcional del ARN/fisiología , ARN Ribosómico/metabolismo , Ribonucleoproteínas Nucleolares Pequeñas/metabolismo , Análisis de Secuencia de ADN/métodos , Análisis de Secuencia de Proteína/métodos , Homología de Secuencia de Aminoácido
18.
Gene ; 333: 135-41, 2004 May 26.
Artículo en Inglés | MEDLINE | ID: mdl-15177688

RESUMEN

Genome sequencing now permits direct visual representation, at any scale, of GC heterogeneity along the chromosomes of several higher eukaryotes. Plots can be easily obtained from the chromosomal sequences, yet sequence releases of mammalian or plant chromosomes still tend to use small scales or window sizes that obscure important large-scale compositional features. To faithfully reveal, at one glance, the compositional variation at a given scale, we have devised a simple scheme that combines line plots with color-coded shading of the regions underneath the plots. The scheme can be applied to different eukaryotic genomes to facilitate their comparison, as illustrated here for a sample of chromosomes chosen from seven selected species. As a complement to a previously published compact view of isochores in the human genome sequence, we include here an analogous map for the recently sequenced mouse genome, and discuss the contribution of repetitive DNA to the GC variation along the plots. Supplementary information, including a database of color-coded GC profiles for all recently sequenced eukaryotes and the program draw_chromosomes_gc.pl used to obtain them, are available at.


Asunto(s)
Composición de Base/genética , Cromosomas/genética , Células Eucariotas/metabolismo , Animales , Anopheles/genética , Arabidopsis/genética , Caenorhabditis elegans/genética , ADN/genética , Drosophila melanogaster/genética , Genoma , Humanos , Isocoras/genética , Ratones , Secuencias Repetitivas de Ácidos Nucleicos/genética , Saccharomyces cerevisiae/genética , Programas Informáticos
19.
Genome Announc ; 2(2)2014 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-24652983

RESUMEN

We announce the completion of the genome sequence of a phenol derivative-degrading bacterium, Rhodococcus erythropolis strain CCM2595. This bacterium is interesting in the context of bioremediation for its capability to degrade phenol, catechol, resorcinol, hydroxybenzoate, hydroquinone, p-chlorophenol, p-nitrophenol, pyrimidines, and sterols.

20.
Res Microbiol ; 164(10): 1009-18, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24125695

RESUMEN

The cluster of pbtTFYRABC genes is carried by plasmid pA81. Its elimination from Achromobacter xylosoxidans A8 resulted in increased sensitivity towards Pb(2+) and Cd(2+). Predicted pbtTRABC products share strong similarities with Pb(2+) uptake transporter PbrT, transcriptional regulator PbrR, metal efflux P1-ATPases PbrA and CadA, undecaprenyl pyrophosphatase PbrB and its signal peptidase PbrC from Cupriavidus metallidurans CH34. Expression of pbtABC or pbtA in a metal-sensitive Escherichia coli GG48 rendered the strain Pb(2+)-, Cd(2+)- and Zn(2+)-tolerant and caused decreased accumulation of the metal ions. Accumulation of Pb(2+), but not of Cd(2+) or Zn(2+), was promoted in E. coli expressing pbtT. Additional genes of the pbt cluster are pbtF and pbtY, which encode the cation diffusion facilitator (CDF)-like transporter and a putative fatty acid hydroxylase of unknown function, respectively. Expression of pbtF did not confer increased metal tolerance upon E. coli GG48, although the protein showed measurable Pb(2+)-efflux activity. Unlike the pbtT promoter, promoters of pbtABC, pbtF and pbtY contain features characteristic of promoters controlled by metal-responsive transcriptional regulators of the MerR family. Upregulation of pbtABC, pbtF and pbtY upon Pb(2+), Cd(2+) and Zn(2+) exposure was confirmed in wild-type Achromobacter xylosoxidans A8. Gel shift assays proved binding of purified PbtR to the respective promoters.


Asunto(s)
Achromobacter denitrificans/efectos de los fármacos , Cadmio/toxicidad , Tolerancia a Medicamentos , Plomo/toxicidad , Achromobacter denitrificans/genética , Clonación Molecular , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Expresión Génica , Perfilación de la Expresión Génica , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Genes Bacterianos , Familia de Multigenes , Plásmidos
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