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PubMedDate not supplied

The complement inhibitor CD59 and the lymphocyte function-associated antigen-3 (LFA-3, CD58) genes possess functional binding sites for the p53 tumor suppressor protein.

p53 is an oncosuppressor protein, which acts via transcriptional and non-transcriptional mechanisms. The transcriptional function of p53 is mediated by specific responsive elements. In the present study we found active responsive elements, specific for the p53 within the 5'flanking region and within the first intron of the gene encoding for the CD59 membrane inhibitor of reactive lysis, and within the first intron of the gene encoding for the CD58 membrane protein (LFA-3). The results suggest that p53 may enhance the transcription of both CD59 and CD58 and imply a novel role for p53 as a direct regulator of the immune response.

Base Sequence↗
PubMed2005

Strategies to investigate gene expression and function in granule cells.

Studying gene expression in granule cells is a major route to understanding the factors required for many key cellular processes such as specification, proliferation, migration, differentiation, apoptosis, tumour formation and neurodegeneration. A greater understanding of these processes will not only provide insight into cerebellum development, but also diseases of the cerebellum. Granule cells can be readily grown in culture and both viral and non-viral strategies have been optimised to allow gene transfer and expression in cultured cells. However, granule cell migration and maturation are inherent parts of cerebellum development and these rely on interactions with other cells. Hence, a true picture of gene function in these cells can only be obtained when tissue context is maintained. Studies of gene function in this context can be achieved by creation of mouse models. Conditional mouse models, where loss of gene expression is restricted as far as possible to granule cells, are by far the most informative resource in this respect. Despite their obvious benefits, the production of mouse models is both costly and time-consuming and this may be further compounded by a potential lack of phenotype due to redundancy of gene function. Organotypic slice cultures, on the other hand, are a comparatively cheap and accessible model for studies of gene function where tissue context is maintained. Recent technologies have provided the means to manipulate gene expression in such systems and are beginning to yield valuable insights into the molecular regulation of cerebellum development.

Animals↗
PubMed2006

Annotating the human proteome: beyond establishing a parts list.

The completion of the human genome has shifted the attention from deciphering the sequence to the identification and characterisation of the functional components, including genes. Improved gene prediction algorithms, together with the existing transcript and protein information, have enabled the identification of most exons in a genome. Availability of the 'parts list' has fostered the development of experimental approaches to systematically interrogate gene function on the genome, transcriptome and proteome level. Studying gene function at the protein level is vital to the understanding of how cells perform their functions as variations in protein isoforms and protein quantity which may underlie a change in phenotype can often not be deduced from sequence or transcript level genomics experiments alone. Recent advancements in proteomics have afforded technologies capable of measuring protein expression, post-translational modifications of these proteins, their subcellular localisation and assembly into complexes and pathways. Although an enormous amount of data already exists on the function of many human proteins, much of it is scattered over multiple resources. Public domain databases are therefore required to manage and collate this information and present it to the user community in both a human and machine readable manner. Of special importance here is the integration of heterogeneous data to facilitate the creation of resources that go beyond a mere parts list.

Humans↗
PubMed1993

Structurally engineered cytochromes with unusual ligand-binding properties: expression of Saccharomyces cerevisiae Met-80-->Ala iso-1-cytochrome c.

A strategy has been developed to express and purify a recombinant, nonfunctional axial-ligand mutant of iso-1-cytochrome c (Met-80-->Ala) in Saccharomyces cerevisiae in quantities necessary for extensive biophysical characterization. It involves coexpressing in the same plasmid (YEp213) the nonfunctional gene with a functional gene copy for complementation in a selective medium. The functional gene encodes a product with an engineered metal-chelating dihistidine site (His-39 and Leu-58-->His) that enables efficient separation of the two isoforms by immobilized metal-affinity chromatography. The purified Met-80-->Ala protein possesses a binding site for dioxygen and other exogenous ligands. Absorption spectra of several derivatives of this mutant show striking similarities to those of corresponding derivatives of horseradish peroxidase, myoglobin, and cytochrome P450. The use of a dual-gene vector for cytochrome c expression together with metal-affinity separation opens the way for the engineering of variants with dramatically altered structural and catalytic properties.

Alanine↗
PubMed2003

Trait-to-gene: a computational method for predicting the function of uncharacterized genes.

The function of unknown genes is often inferred from comparisons to well-characterized homologs. In this paper, we show that, even if all of the homologs of a gene are unannotated, its function may be deduced through phylogenetic profiling. We have designed a series of algorithms that make functional predictions of genes based on orthology and set theory, but our approach to predicting gene function requires no previous knowledge of homolog function. With this technique, we successfully identified 94% of the clusters of orthologous groups that are known to be involved in flagella development or function. As a test, we removed the function of three putative flagellar genes that had been previously uncharacterized in Bacillus subtilis. We observed a motility phenotype for two of these three genes. Thus, these algorithms allow for high-throughput functional prediction of genes beyond that provided by simple orthology-based annotation endeavors.

Algorithms↗
PubMed1999

Two E2F sites control growth-regulated and cell cycle-regulated transcription of the Htf9-a/RanBP1 gene through functionally distinct mechanisms.

The gene encoding Ran-binding protein 1 (RanBP1) is transcribed in a cell cycle-dependent manner. The RanBP1 promoter contains two binding sites for E2F factors, named E2F-c, located proximal to the transcription start, and E2F-b, falling in a more distal promoter region. We have now induced site-directed mutagenesis in both sites. We have found that the distal E2F-b site, together with a neighboring Sp1 element, actively controls up-regulation of transcription in S phase. The proximal E2F-c site plays no apparent role in cycling cells yet is required for transcriptional repression upon growth arrest. Protein binding studies suggest that each E2F site mediates specific interactions with individual E2F family members. In addition, transient expression assays with mutagenized promoter constructs indicate that the functional role of each site is also dependent on its position relative to other regulatory elements in the promoter context. Thus, the two E2F sites play opposite genetic functions and control RanBP1 transcription through distinct molecular mechanisms.

3T3 Cells↗
PubMed1993

Wilms' tumour gene and function.

The Wilms' tumour gene, WT1, encodes a protein with four zinc fingers that is probably a transcription factor. In humans, WT1 mutations can lead to childhood kidney tumours and to developmental defects of the kidney and gonad. The WT1 gene may have a role in the mesenchyme to epithelial switch in a range of mesodermally derived tissues. Furthermore, growth-factor genes may be targets for repression by the WT1 protein during development. WT1 is the first example of a tumour-suppressor gene with a specific developmental role.

Animals↗
PubMedDate not supplied

The tumor suppressor gene RIZ in cancer gene therapy (review).

In recent years, significant progress has been made in understanding the nature of the human genome and the role that genes and their related proteins play in both normal and diseased cells. It has been proven that many cancers are caused by the mutation of certain genes or lack of gene function. The introduction of those genes into cancer cells where gene function is compromised, can work to restore gene function and stop tumor progression. There have been numerous clinical trials, which have shown that gene therapy products are efficacious in humans. The RIZ1 gene is a member of a superfamily of histone/protein methyltransferases. The gene is commonly inactivated in human cancers. Gene knock-out study has established RIZ1 as a tumor susceptibility gene in mice. The gene has potent tumor suppressive activities in causing apoptosis, G2/M arrest, or both. Preclinical animal studies have shown that a recombinant adenovirus expressing the gene, AdRIZ1, can suppress the growth of colon cancer xenografts. Therefore, AdRIZ1 shows promise as a new generation of gene therapy products to enter the clinic.

DNA-Binding Proteins↗
PubMed2002

Regulation of the cell expansion gene RHD3 during Arabidopsis development.

The RHD3 (ROOT HAIR DEFECTIVE3) gene encodes a putative GTP-binding protein required for appropriate cell enlargement in Arabidopsis. To obtain insight into the mechanisms of RHD3 regulation, we conducted a molecular genetic dissection of RHD3 gene expression and function. Gene fusion and complementation studies show that the RHD3 gene is highly expressed throughout Arabidopsis development and is controlled by two major regulatory regions. One regulatory region is located between -1,500 and -600 bp upstream of the RHD3 gene and is required for vascular tissue expression. The other region is intragenically located and includes the 558-bp first intron, which is responsible for high-level expression of RHD3 throughout the plant. The presence and location of this intron is essential for gene function because constructs lacking this intron or constructs with the intron in an abnormal position are unable to functionally complement the rhd3 mutations. We also analyzed the role of other RHD genes and the plant hormones auxin and ethylene in RHD3 regulation, and we determined that these act downstream or independently from the RHD3 pathway. This study shows that multiple levels of regulation are employed to ensure the appropriate expression of RHD3 throughout Arabidopsis development.

Arabidopsis↗
PubMed2003

A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference.

RNA interference (RNAi) has recently emerged as a specific and efficient method to silence gene expression in mammalian cells either by transfection of short interfering RNAs (siRNAs; ref. 1) or, more recently, by transcription of short hairpin RNAs (shRNAs) from expression vectors and retroviruses. But the resistance of important cell types to transduction by these approaches, both in vitro and in vivo, has limited the use of RNAi. Here we describe a lentiviral system for delivery of shRNAs into cycling and non-cycling mammalian cells, stem cells, zygotes and their differentiated progeny. We show that lentivirus-delivered shRNAs are capable of specific, highly stable and functional silencing of gene expression in a variety of cell types and also in transgenic mice. Our lentiviral vectors should permit rapid and efficient analysis of gene function in primary human and animal cells and tissues and generation of animals that show reduced expression of specific genes. They may also provide new approaches for gene therapy.

Animals↗
PubMed2006

EMS mutagenesis of Arabidopsis.

A powerful approach for determining the biological functions of genes in an organism is to produce mutants with altered phenotypes and physiological responses. Various approaches for mutagenesis involving chemical, irradiation, and insertional methods have been developed; each has advantages and disadvantages for the study of gene function. In this post-genomic era, the use of reverse genetic approaches to understanding the role of genes in growth and development has become widespread. With development of new techniques such as targeting induced local lesions in genomes (TILLING), ethyl methanesulfonate (EMS) mutagenesis can be used for both forward and reverse genetic studies. Generation of diverse mutant alleles in the same gene provides critical tools to understand the role of these genes in the function of the organism. Here we describe the general method of EMS mutagenesis for the molecular genetic model plant Arabidopsis thaliana.

Arabidopsis↗
PubMed1992

Functional homologs of the Arabidopsis RPM1 disease resistance gene in bean and pea.

We showed that a bacterial avirulence (avr) gene function, avrPpiA1, from the pea pathogen Pseudomonas syringae pv pisi, is recognized by some, but not all, genotypes of Arabidopsis. Thus, an avr gene functionally defined on a crop species is also an avr gene on Arabidopsis. The activity of avrPpiA1 on a series of Arabidopsis genotypes is identical to that of the avrRpm1 gene from P.s. pv maculicola previously defined using Arabidopsis. The two avr genes are homologous and encode nearly identical predicted products. Moreover, this conserved avr function is also recognized by some bean and pea cultivars in what has been shown to be a gene-for-gene manner. We further demonstrated that the Arabidopsis disease resistance locus, RPM1, conditioning resistance to avrRpm1, also conditions resistance to bacterial strains carrying avrPpiA1. Therefore, bean, pea, and conceivably other crop species contain functional and potentially molecular homologs of RPM1.

Amino Acid Sequence↗
PubMed2001

Cytochrome P450 2D6 genotype and methadone steady-state concentrations.

A genetic polymorphism of cytochrome P450 2D6 has been described with the existence of poor (zero functional genes), extensive (one or two functional genes), and ultrarapid metabolizers (three or more functional genes). The authors measured the steady-state trough (R)- (i.e., the active enantiomer), (S)-, and (R,S)-methadone plasma levels in opiate-dependent patients receiving methadone maintenance treatment (MMT) and genotyped them for cytochrome P4502D6. The patients' medical records were reviewed to assess the outcome of the MMT with regard to the absence of illicit opiate consumption and to the absence of withdrawal complaints in ultrarapid and poor metabolizers. Of 256 patients included, 18 were found to be poor metabolizers, 228 to be extensive metabolizers, and 10 to be ultrarapid metabolizers. Significant differences were found between genotypes for (R)- (p = 0.024), (S)- (p = 0.033), and (R,S)-methadone (p = 0.026) concentrations to dose-to-weight ratios. For (R)-methadone, a significant difference was found between ultrarapid metabolizers and poor metabolizers (p = 0.009), with the median value in the former group being only 54% of the median value in the latter group. These results confirm the involvement of cytochrome P450 2D6 in methadone metabolism. Although the difference was nonsignificant (p = 0.103), 13 (72%) of the 18 poor metabolizers and only 4 (40%) of the 10 ultrarapid metabolizers were considered successful in their treatment. More studies are needed to examine the influence of the ultrarapid metabolizer status on the outcome of the MMT.

Adolescent↗
PubMed2002

A comparative analysis of the avirulence and translational transactivator functions of gene VI of Cauliflower mosaic virus.

The primary function associated at present with the gene VI product of Cauliflower mosaic virus (CaMV) is that of a translational transactivator (TAV). In this capacity, it alters the host translational machinery to allow reinitiation of translation of other CaMV genes on the polycistronic 35S RNA of CaMV. In addition, the gene VI protein can elicit a specific type of plant defense response called the hypersensitive response (HR) in Nicotiana edwardsonii. In this study, we have adapted the agroinfiltration technique to compare the sequences of CaMV gene VI required for TAV function and elicitation of HR. To measure the activity of the TAV, we coagroinfiltrated gene VI of CaMV strain W260 with a bicistronic GUS reporter plasmid. TAV function could be assayed 4 days postinfiltration, before the onset of HR in N. edwardsonii. Through the use of the TAV and HR assays, we could show that the TAV functions of gene VI of CaMV strains W260 and D4 were equivalent, but only W260 gene VI elicited HR. A mutational analysis of W260 gene VI showed that the structural requirements for elicitation of HR were much more stringent than those for TAV function. Small deletions from either the 5' or 3' end of W260 gene VI abolished its ability to elicit HR, although the TAV function was retained in the mutant. The TAV function could also tolerate a small insertion within gene VI; this insertion abolished the elicitor function. This study provides direct evidence that the TAV function of gene VI is separate from its role as an elicitor of HR.

Caulimovirus↗
PubMed1990

The rat cytochrome c oxidase subunit IV gene family: tissue-specific and hormonal differences in subunit IV and cytochrome c mRNA expression.

We have isolated three members of the rat cytochrome c oxidase subunit IV gene family: one functional gene and two processed pseudogenes. The pseudogenes appear to represent the only other closely related sequences in this family. The functional gene encodes an isoform which is expressed in all tissues examined and has features characteristic of 'housekeeping' genes. These include multiple transcription start sites mapped to within an approximately 50 bp region and a GC-rich promoter lacking typical CCAAT or TATAA sequences. Although the subunit IV gene is expressed at its highest levels in cardiac and skeletal muscle, consistent with the high energy demand in those tissues, its expression differs from that of cytochrome c in several respects. 1) Subunit IV mRNA abundance in various tissues is relatively uniform when compared to the highly variable levels of cytochrome c mRNAs. 2) Unlike cytochrome c, subunit IV mRNA is expressed at a surprisingly high level in testis. 3) While cytochrome c mRNA levels in liver are increased markedly in response to thyroid hormone treatment, subunit IV mRNA is not significantly affected. Differences in the expression of these two nuclear-encoded respiratory genes are consistent with differences in regulatory elements within their promoters. Therefore, the regulation of nuclear-encoded respiratory genes in response to tissue demands for cellular energy may not be satisfactorily explained by a set of universal regulators common to all such genes.

Animals↗
PubMed2004

Understanding endothelin-1 function during craniofacial development in the mouse and zebrafish.

Morphogenesis of the face and neck is driven by an intricate relay of signaling molecules and transcription factors organized into hierarchical pathways. The coordinated action of these pathways regulates the development of neural crest cells within the pharyngeal arches, resulting in proper spatiotemporal formation of bone, cartilage, and connective tissue. While the functions of many genes involved in these processes were initially elucidated through the use of knockout technology in the mouse, increasing numbers of zebrafish craniofacial mutants have led to a rapid expansion in the identification of genes involved in craniofacial development. A comparative analysis of signaling pathways involved in these processes between mouse and zebrafish holds the potential not only to pinpoint conserved and therefore crucial gene functions in craniofacial development, but also to rapidly identify and study downstream effectors. These complementary approaches will also allow rapid identification of candidate genes and gene functions disrupted in human craniofacial dysmorphologies. In this brief review, we present a comparative analysis of one molecule involved in craniofacial development, endothelin-1, a small, secreted protein that is crucial for patterning the neural crest cells that give rise to lower jaw and throat structures.

Animals↗
PubMed1998

Inducible gene expression in the nervous system of transgenic mice.

Gene function during mammalian development is often studied by making irreversible changes to the genome. This approach has a major drawback in that the function of the gene in question must be deduced from the phenotype of animals that have been deficient for the product of the disrupted gene throughout ontogeny. Compensation for the loss of the gene product could yield an apparently unaltered phenotype. Alternatively, the changes in the regulation of other genes could yield a misleading phenotype. If the genetic manipulation results in embryonic or neonatal lethality, gene function at later stages of development cannot be analyzed. It would thus be highly advantageous if the expression of a particular gene could be restricted both temporally and spatially through the use of an inducible genetic system. This paper describes the various inducible genetic expression systems developed for use in mammalian cells, with particular emphasis on their application in the nervous system of transgenic mice.

Animals↗
PubMed2006

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

Escherichia coli↗