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At least 1,153 records · Page 64Linked to original sources
PubMed2002

Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions.

UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signaling via protein kinases. The human homologue of yeast Rad23A (HHR23A) is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of HHR23A UBA(2) showed that the domain forms a compact three-helix bundle. We report the structure of the internal UBA(1) domain of HHR23A. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch. The structural similarity between UBA(1) and UBA(2), in spite of their low level of sequence conservation, leads us to conclude that the structural variability of UBA domains in general is likely to be rather small. On the basis of the structural similarities as well as analysis of sequence conservation, we predict that this hydrophobic surface patch is a common protein-interacting surface present in diverse UBA domains. Furthermore, accumulating evidence that ubiquitin binds to UBA domains leads us to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin. Detailed comparison of the structures of the two UBA domains, combined with previous mutagenesis studies, indicates that the binding site of HIV-1 Vpr on UBA(2) does not completely overlap the ubiquitin binding site.

Amino Acid Sequence↗
PubMed2003

Characterization of the OFD1/Ofd1 genes on the human and mouse sex chromosomes and exclusion of Ofd1 for the Xpl mouse mutant.

Oral-facial-digital type 1 (OFD1) syndrome is an X-linked dominant condition characterized by malformations of the face, oral cavity, and digits. The responsible gene, OFD1, maps to human Xp22 and has an unknown function. We isolated and characterized the mouse Ofd1 gene and showed that it is subject to X-inactivation, in contrast to the human gene. Furthermore, we excluded a role for Ofd1 in the pathogenesis of the spontaneous mouse mutant Xpl, which had been proposed as a mouse model for this condition. Comparative sequence analysis demonstrated that OFD1 is conserved among vertebrates and absent in invertebrates. This analysis allowed the identification of evolutionarily conserved domains in the protein. Finally, we report the identification of 18 apparently nonfunctional OFD1 copies, organized in repeat units on the human Y chromosome. These degenerate OFD1-Y genes probably derived from the ancestral Y homologue of the X-linked gene. The high level of sequence identity among the different units suggests that duplication events have recently occurred during evolution.

Amino Acid Sequence↗
PubMed2003

Tumor metastasis-associated human MTA1 gene and its MTA1 protein product: role in epithelial cancer cell invasion, proliferation and nuclear regulation.

Using differential cDNA library screening techniques based on metastatic and nonmetastatic rat mammary adenocarcinoma cell lines, we previously cloned and sequenced the metastasis-associated gene mta1. Using homology to the rat mta1 gene, we cloned the human MTA1 gene and found it to be over-expressed in a variety of human cell lines (breast, ovarian, lung, gastric and colorectal cancer but not melanoma or sarcoma) and cancerous tissues (breast, esophageal, colorectal, gastric and pancreatic cancer). We found a close similarity between the human MTA1 and rat mta1 genes (88% and 96% identities of the nucleotide and predicted amino acid sequences, respectively). Both genes encode novel proteins that contain a proline rich region (SH3-binding motif), a putative zinc finger motif, a leucine zipper motif and 5 copies of the SPXX motif found in gene regulatory proteins. Using Southern blot analysis the MTA1 gene was highly conserved, and using Northern blot analysis MTA1 transcripts were found in virtually all human cell lines (melanoma, breast, cervix and ovarian carcinoma cells and normal breast epithelial cells). However, the expression level of the MTA1 gene in normal breast epithelial cells was approximately 50% of that found in rapidly growing adenocarcinoma and atypical epithelial cell lines. Experimental inhibition of MTA1 protein expression using antisense phosphorothioate oligonucleotides resulted in inhibition of growth and invasion of human MDA-MB-231 breast cancer cells with relatively high MTA1 expression. Furthermore, the MTA1 protein was localized in the nuclei of cells transfected with a mammalian expression vector containing a full-length MTA1 gene. Although some MTA1 protein was found in the cytoplasm, the vast majority of MTA1 protein was localized in the nucleus. Examination of recombinate MTA1 and related MTA2 proteins suggests that MTA1 protein is a histone deacetylase. It also appears to behave like a GATA-element transcription factor, since transfection of a GATA-element reporter into MTA1-expressing cells resulted in 10-20-fold increase in reporter expression over poorly MTA1-expressing cells. Since it was reported that nucleosome remodeling histone deacetylase complex (NuRD complex) involved in chromatin remodeling contains MTA1 protein and a MTA1-related protein (MTA2), we examined NuRD complexes for the presence of MTA1 protein and found an association of this protein with histone deacetylase. The results suggest that the MTA1 protein may serve multiple functions in cellular signaling, chromosome remodeling and transcription processes that are important in the progression, invasion and growth of metastatic epithelial cells.

Amino Acid Sequence↗
PubMed2006

Differential repression of alternative transcripts: a screen for miRNA targets.

Alternative polyadenylation sites produce transcript isoforms with 3' untranslated regions (UTRs) of different lengths. If a microRNA (miRNA) target is present in the UTR, then only those target-containing isoforms should be sensitive to control by a cognate miRNA. We carried out a systematic examination of 3' UTRs containing multiple poly(A) sites and putative miRNA targets. Based on expressed sequence tag (EST) counts and EST library information, we observed that levels of isoforms containing targets for miR-1 or miR-124, two miRNAs causing downregulation of transcript levels, were reduced in tissues expressing the corresponding miRNA. This analysis was repeated for all conserved 7-mers in 3' UTRs, resulting in a selection of 312 motifs. We show that this set is significantly enriched in known miRNA targets and mRNA-destabilizing elements, which validates our initial hypothesis. We scanned the human genome for possible cognate miRNAs and identified phylogenetically conserved precursors matching our motifs. This analysis can help identify target-miRNA couples that went undetected in previous screens, but it may also reveal targets for other types of regulatory factors.

Animals↗
PubMed1997

Decision support system for the evolutionary classification of protein structures.

The structures of nearly a thousand sequence-unique proteins represent only 300 different 3D shapes. Is structural resemblance between proteins with little sequence similarity the result of physical convergence to favourable folding patterns, or does it reflect a memory of common evolutionary history? Separating these two processes is important for organizing genome data in terms of protein families and for theoretical approaches to protein structure prediction by fold recognition techniques. Achieving separation requires a combination of structure, sequence and functional analysis of proteins. For this purpose, we are developing a decision support system that scans heterogeneous protein sequence and structure related databases, and collects or calculates characters indicative of common functional constraints. The criteria include sequence homology, analysis of 3D clusters of conserved residues, conservation of active sites, and keyword analysis of biological function. Even without extensive refinement, application of a combination of these criteria to a test set representing all currently known protein structures yields 87% coverage with 7% false positives, compared to 53% coverage by only 1D sequence criteria. Thus, the semiautomatic prototype system significantly enhances the efficiency of unifying families of functionally related proteins in spite of long evolutionary distances.

Binding Sites↗
PubMed2001

Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana.

The Arabidopsis genome contains at least 18 genes encoding members of the 70-kilodalton heat shock protein (Hsp70) family, 14 in the DnaK subfamily and 4 in the Hsp110/SSE subfamily. While the Hsp70s are highly conserved, a phylogenetic analysis including all members of this family in Arabidopsis and in yeast indicates the homology of Hsp70s in the subgroups, such as those predicted to localize in the same subcellular compartment and those similar to the mammalian Hsp110 and Grp170. Gene structure and genome organization suggest duplication in the origin of some genes. The Arabidopsis hsp70s exhibit distinct expression profiles; representative genes of the subgroups are expressed at relatively high levels during specific developmental stages and under thermal stress.

Arabidopsis↗
PubMed1993

Identification of a novel zinc finger protein binding a conserved element critical for Pit-1-dependent growth hormone gene expression.

The growth hormone (GH) and prolactin genes require the pituitary-specific POU domain transcription factor Pit-1 for their activation. However, additional factors are necessary for the effective expression of these genes. Analysis of evolutionarily conserved sequences in the proximal GH promoter suggests the critical importance of one highly conserved element located between the two Pit-1 response elements. Mutation of this site decreases expression of a transgene in mice > 100-fold. We have identified a major activity binding to this site as a novel member of the Cys/His zinc finger superfamily, referred to as Zn-15. The Zn-15 DNA-binding domain comprises three zinc fingers separated by unusually long linker sequences that would be expected to interrupt specific DNA site recognition. Zn-15 synergizes with Pit-1 to activate the GH promoter in heterologous cell lines in which this promoter is only minimally responsive to Pit-1 alone. Our data suggest that functional interactions between the tissue-specific POU domain factor Pit-1 and this novel zinc finger factor binding to an evolutionarily conserved region in the GH promoter may constitute an important component of the combinatorial code that underlies the effective expression of the GH gene.

Amino Acid Sequence↗
PubMed2006

Results of a SNP genome screen in a large Costa Rican pedigree segregating for severe bipolar disorder.

We have ascertained in the Central Valley of Costa Rica a new kindred (CR201) segregating for severe bipolar disorder (BP-I). The family was identified by tracing genealogical connections among eight persons initially independently ascertained for a genome wide association study of BP-I. For the genome screen in CR201, we trimmed the family down to 168 persons (82 of whom are genotyped), containing 25 individuals with a best-estimate diagnosis of BP-I. A total of 4,690 SNP markers were genotyped. Analysis of the data was hampered by the size and complexity of the pedigree, which prohibited using exact multipoint methods on the entire kindred. Two-point parametric linkage analysis, using a conservative model of transmission, produced a maximum LOD score of 2.78 on chromosome 6, and a total of 39 loci with LOD scores >1.0. Multipoint parametric and non-parametric linkage analysis was performed separately on four sections of CR201, and interesting (nominal P-value from either analysis <0.01), although not statistically significant, regions were highlighted on chromosomes 1, 2, 3, 12, 16, 19, and 22, in at least one section of the pedigree, or when considering all sections together. The difficulties of analyzing genome wide SNP data for complex disorders in large, potentially informative, kindreds are discussed.

Bipolar Disorder↗
PubMed2000

Computer recognition of skin structures using discriminant and cluster analysis.

BACKGROUND/AIMS: Automated image analysis of complex tissues is usually limited by the difficulty of recognizing special structures by computer. The aim of this study was to test the applicability of discriminant and cluster analysis to the interpretation of skin images. METHODS: Digital images from microscopic, dermatoscopic and clinical views of skin specimens were electronically dissected into elements of equal size and shape, and a set of grey level, colour and texture features was assessed for each element. Elements were classified interactively and submitted to discriminant analysis. Furthermore, hierarchical cluster analysis was used to enable the system to classify the tissue elements automatically, based on the available digital information. The classification results were relocated to the original image in order to evaluate the performance of the procedure. RESULTS: The system performs well in reproducibly detecting different skin structures in digital images. Discriminant analysis of interactively classified elements yielded a correct reclassification in 98 to 100% of tissue elements. Among the cluster analysis procedures, the conservative Ward method after removal of all highly correlated features produced the best results. The method turned out to be applicable irrespective of the image source used. CONCLUSIONS: Discriminant and cluster analysis may be helpful techniques for a user-independent, subjectively unbiased measurement system of skin structures.

Journal Article↗
PubMedDate not supplied

The use of microsatellite analysis in Solanum tuberosum l. in vitro plantlets derived from cryopreserved germplasm.

This study reports the application of the encapsulation/dehydration cryopreservation and microsatellite analysis to the conservation of Solanum tuberosum cultivars Brodick and Golden Wonder. Cryopreserved shoot-tips were capable of up to 40% shoot and plantlet regeneration in Brodick and >60 % for Golden Wonder. Microsatellite analysis was used with genomic DNA of Golden Wonder and Desiree to establish DNA sequence length polymorphisms. As the basis of stability assessments this technique was applied to: (i) individual, field-grown, plants of Golden Wonder; (ii) individual Golden Wonder plants derived from a single parental tuber progeny; (iii) plantlets derived from in vitro cultures of Golden Wonder and Brodick and (iv) Golden Wonder and Brodick plantlets derived from cryopreserved germplasm

Cryopreservation↗
PubMed2005

Phylogeography of the threatened crayfish (genus Austropotamobius) in Italy: implications for its taxonomy and conservation.

A nucleotide sequence analysis of a portion of the mitochondrial large ribosomal subunit was performed to define the phylogeography of the threatened crayfish Austropotamobius (Decapoda; Astacidae) in Italy. We collected 61 specimens from 31 localities across the Italian peninsula. For the phylogenetic inference, we combined the 61 Austropotamobius spp sequences obtained from this study with 18 sequences deposited in GenBank and corresponding to Italian, French, Irish, Swiss, and Slovenian locations. Among the analysed sequences, 34 distinct haplotypes were detected. Our results confirmed the presence of both A. pallipes and A. italicus in the Italian peninsula and the existence within the latter species of a strong intraspecific genetic variation, due to the occurrence of four subspecies with a well-defined geographic distribution. From a conservation viewpoint, Italy, with its high haplotype variability, may be considered a 'hot spot' for the genetic diversity of the European native crayfish Austropotamobius. We suggest that re-introduction programs should be conducted with extreme caution in Italy, since not only the two Austropotamobius species but also the four A. italicus subspecies are genetically and taxonomically separate units and require independent conservation plans.

Animals↗
PubMed2006

A novel lysine-rich domain and GTP binding motifs regulate the nucleolar retention of human guanine nucleotide binding protein, GNL3L.

A variety of G-proteins and GTPases are known to be involved in nucleolar function. We describe here a new evolutionarily conserved putative human GTPase, guanine nucleotide binding protein-like 3-like (GNL3L). Genes encoding proteins related to GNL3L are present in bacteria and yeast to metazoa and suggests its critical role in development. Conserved domain search analysis revealed that the GNL3L contains a circularly permuted G-motif described by a G5-G4-G1-G2-G3 pattern similar to the HSR1/MMR1 GTP-binding protein subfamily. Highly conserved and critical residues were identified from a three-dimensional structural model obtained for GNL3L using the crystal structure of an Ylqf GTPase from Bacillus subtilis. We demonstrate here that GNL3L is transported into the nucleolus by a novel lysine-rich nucleolar localization signal (NoLS) residing within 1-50 amino acid residues. NoLS identified here is necessary and sufficient to target the heterologous proteins to the nucleolus. We show for the first time that the lysine-rich targeting signal interacts with the nuclear transport receptor, importin-beta and transports GNL3L into the nucleolus. Interestingly, depletion of intracellular GTP blocks GNL3L accumulation into the nucleolar compartment. Furthermore, mutations within the G-domains alter the GTP binding ability of GNL3L and abrogate wild-type nucleolar retention even in the presence of functional NoLS, suggesting that the efficient nucleolar retention of GNL3L involves activities of both basic NoLS and GTP-binding domains. Collectively, these data suggest that GNL3L is composed of distinct modules, each of which plays a specific role in molecular interactions for its nucleolar retention and subsequent function(s) within the nucleolus.

Active Transport, Cell Nucleus↗
PubMed2005

Dcode.org anthology of comparative genomic tools.

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website.

Base Sequence↗
PubMed2006

Role of asparagine 1134 in glucosidic bond and transglycosylation specificity of reuteransucrase from Lactobacillus reuteri 121.

Glucansucrases from lactic acid bacteria convert sucrose into various alpha-glucans that differ greatly with respect to the glucosidic bonds present (e.g. dextran, mutan, alternan and reuteran). This study aimed to identify the structural features of the reuteransucrase from Lactobacillus reuteri 121 (GTFA) that determine its reaction specificity. We here report a detailed mutational analysis of a conserved region immediately next to the catalytic Asp1133 (putative transition-state stabilizing) residue in GTFA. The data show that Asn1134 is the main determinant of glucosidic bond product specificity in this reuteransucrase. Furthermore, mutations at this position greatly influenced the hydrolysis/transglycosylation ratio. Changes in this amino acid expands the range of glucan and gluco-oligosaccharide products synthesized from sucrose by mutant GTFA enzymes.

Asparagine↗
PubMed1999

[Molecular cloning of one splicing form of human M6b cDNA].

X-linked, early onset Pelizaeus-Merzbacher disease (PMD) and part of X-linked spastic paraplegia are caused by mutation of proteolipid protein. M6b (U45955) partially cloned by Olinsky was considered as a member of PLP gene family. One novel fragment about 300 bp partially overlapped but differed in 5'part with U45955 was obtained by nested PCR. Assembly of the novel sequence with U45955 make a 1.642kb cDNA sequence with an open reading frame encoding 265 amino acids, which was verified by sequence of PCR products from brain cDNA library. The cDNA (termed M6ba) and its deduced peptide sequence showed significant similarity to murine M6b gene and protein (91.2% and 93.4% respectively). Northern blot, PCR amplification in cDNA library and EST analysis indicated that human M6b gene has at least three splicing forms. M6ba also showed significant similarity to PLP gene, they encode strongly hydrophobic protein and all their hydrophobic region are highly conserved. Gene structure analysis showed that the coding region of M6ba was composed of seven exons.

Amino Acid Sequence↗
PubMed1991

Conserved structural motifs in cyclins identified by sequence analysis.

Cyclins, as regulatory subunits of the ubiquitous p34cdc2 protein kinase, act as key controlling elements of the eukaryotic cell cycle. We have examined published sequences of A- and B-type cyclins for both amino acid and secondary structure homologies. In particular, we sought regions of homology outside the recognised area of sequence conservation known as the "cyclin box', as well as conserved features predicted to lie at the protein surface. Our analysis demonstrates the existence of a number of islands of homology outside the cyclin box, and indicates candidate residues for phosphorylation. One of these, a motif containing the amino acids SPXXXE/D is also present in fission yeast p13suc1, another protein known to interact with p34cdc2. This motif may define a possible p34cdc2 binding or phosphorylation site. A database search revealed that the CDC25 and SCD25 genes of the budding yeast Saccharomyces cerevisiae also contain some of the newly identified motifs, perhaps indicating a common regulatory or degradation pathway.

Amino Acid Sequence↗
PubMed1998

Comparison of genetic variability in wild insular and mainland populations of Eulemur macaco: implications for conservation strategy.

DNA fingerprinting analysis was used to investigate genetic variability within and between three wild populations of Eulemur macaco living on two islands and on the mainland. The analyses revealed that the genetic variability of the population from the smaller island was, as expected, lower than that from the larger island. Surprisingly, on the larger island the genetic variability was greater than on the mainland. These results, in agreement with those previously obtained from blood markers, are discussed in relation to the history of these populations. In addition, the study suggests that settlement of the smallest island was not only by animals originating from the mainland, as previously proposed on the basis of blood marker data, but also by lemurs from the nearby, larger, island. Evidence is presented that reliable information about population structure can be derived only from studies using different genetic markers. This information is important to enable appropriate conservation programmes to be designed.

Animals↗
PubMed1990

Four tightly linked rab genes are differentially expressed in rice.

We have cloned and sequenced the four members of a rice rab (responsive to abscisic acid) gene family that are tandemly arrayed in a locus approximately 30 kbp in length. Each of the genes contains a single, small intron. They are all transcriptionally active and encode proteins of Mr 15,500-16,800 with two highly conserved domains. Northern analysis with gene-specific probes showed slightly different patterns of expression for the four genes in rice plant tissues and in response to osmotic stress. Comparison of the promoter regions revealed a conserved GC-rich sequence (CGG/CCGCGCT) with some homology to the SP1 binding site (Briggs et al., 1986). Another conserved sequence (PuTACGTGGCPu), whose core is found in the promoter regions of ABA-responsive cotton genes, is reminiscent of the cAMP responsive element (Deutsch et al., 1988).

Abscisic Acid↗