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PubMed1993

Wild-type adenovirus type 5 transforming genes function as transdominant suppressors of oncogenesis in mutant adenovirus type 5 transformed rat embryo fibroblast cells.

Transformation of cloned rat embryo fibroblast (CREF) cells with the host-range adenovirus type 5 (Ad5) mutant, H5hr1, results in transformants with a fibroblastic morphology which displays a cold-sensitive transformation phenotype and oncogenic potential in both nude mice and syngeneic rats. In contrast, wild-type (wt) Ad5 transformed CREF cells are epithelioid in morphology, temperature independent for transformation, and nontumorigenic. The present studies were conducted to analyze the contribution of the mutated E1A and E1B regions of H5hr1 in regulating the biological properties of H5hr1-transformed CREF cells. CREF cells were constructed which contain the mutated E1A and E1B transforming regions of H5hr1 and either a wt Ad5 E1A gene, a wt Ad5 E1B gene, or both a wt Ad5 E1A and a wt E1B gene. A wt Ad5 E1A gene was sufficient in reversing the cold-sensitive transformation phenotype. By using a wt Ad5 E1A gene under the transcriptional control of a dexamethasone-inducible mouse mammary tumor virus promoter, a direct suppressive effect of wt Ad5 E1A on colony formation in monolayer culture and agar growth of H5hr1-transformed cells was demonstrated. Expression of a wt Ad5 E1A, a wt Ad5 E1B, or both wt transforming genes in H5hr1-transformed CREF cells also suppressed oncogenicity. The ability or inability to form tumors in animals was found not to correlate with sensitivity to natural killer cell-mediated lysis. These results indicate that both the wt Ad5 E1A and wt Ad5 E1B genes can function as dominant suppressors of the oncogenic process when coexpressed in H5hr1-transformed CREF cells. This effect does not require large quantities of wt Ad5 E1A or E1B transforming proteins, nor is it directly related to the acquisition of a natural killer cell cytolysis-susceptible phenotype.

Adenovirus E1A Proteins↗

PubMed1993

Display of biologically active proteins on the surface of filamentous phages: a cDNA cloning system for selection of functional gene products linked to the genetic information responsible for their production.

A cloning and expression system allowing display of functional cDNAs or other gene products on the surface of filamentous phage has been developed, exploiting the high-affinity interaction of the Jun and Fos leucine zippers. Gene jun was expressed from a lacZ promoter as a fusion protein with the viral coat protein, pIII, thereby being structurally incorporated into phage particles during infection with a helper phage. Using a second lacZ promoter of the phagemid, gene fos was co-expressed as an N-terminal fusion peptide to cDNA library gene products, so that the resulting Fos-fusion proteins could become associated with the Jun-decorated phage particles. To avoid interphage exchange of fos-cDNA fusion products, cysteines were engineered at the N- and C-termini of each of the leucine zippers, providing a covalent link of the cDNA gene product to the genetic instructions required for its production. Dissociation between phage and cDNA gene products was readily achieved using reducing agents. Phages displaying gene products covalently anchored on their surface via the modified leucine zippers can be selectively enriched 10(4)-10(6)-fold over nonspecific phages using antibodies. Thus, this cloning system allows rapid isolation of rare mRNA products from complex cDNA libraries by enrichment with appropriate ligands. This approach should allow the expression and cloning of dimeric proteins by cDNA shuffling.

Amino Acid Sequence↗

PubMed1999

Human release factor eRF1: structural organisation of the unique functional gene on chromosome 5 and of the three processed pseudogenes.

In lower and higher eukaryotes, a family of tightly related proteins designated eRF1 (for eukaryotic release factor 1) catalyses termination of protein synthesis at all three stop codons. The human genome contains four eRF1 homologous sequences localised on chromosomes 5, 6, 7 and X. We report here the cloning and the structural analysis of the human eRF1 gene family. It appears that the gene located on chromosome 5 alone is potentially functional, whereas the other three sequences resemble processed pseudogenes. This is the first description of the structural organisation of the human eRF1 gene, which has been remarkably conserved during evolution and which is essential in the translation termination process.

Base Sequence↗

PubMed1995

Mutations in GCR1, a transcriptional activator of Saccharomyces cerevisiae glycolytic genes, function as suppressors of gcr2 mutations.

The Saccharomyces cerevisiae GCR1 and GCR2 genes affect expression of most of the glycolytic genes. Evidence for Gcr1p/Gcr2p interaction has been presented earlier and is now supported by the isolation of mutations in Gcr1p suppressing gcr2, as assessed by growth and enzyme assay. Four specific mutation sites were identified. Together with use of the two-hybrid system of Fields and Song, they show that Gcr1p in its N-terminal half has a potential transcriptional activating function as well as elements for interaction with Gcr2p, which perhaps acts normally to expose an otherwise cryptic activation domain on Gcr1p. Complementation of various gcr1 mutant alleles and results with the two-hybrid system also indicate that Gcr1p itself normally functions as an oligomer.

DNA-Binding Proteins↗

PubMed2026

From Gene Function to Precision Intervention: CRISPR/Cas9 and Stem Cell-Based Strategies as Emerging Disease-Modifying Approaches in PMOS.

Polyendocrine metabolic ovarian syndrome (PMOS) is a complex endocrine-metabolic disorder affecting up to 18% of women worldwide and remains the leading cause of anovulatory infertility. Despite extensive research, current treatments primarily target symptoms, including menstrual irregularities, hyperandrogenism, and metabolic dysfunction, without addressing the underlying molecular and tissue-level disturbances. Advances in multi‑omic profiling have identified disruptions across neuroendocrine, metabolic, inflammatory, and extracellular matrix pathways, alongside genetic susceptibility at loci such as DENND1A, CYP17A1, LHCGR, FSHR, IRS1, and PPARG. However, the functional roles of many variants remain unresolved. CRISPR/Cas9 gene editing enables precise interrogation of these pathways, while stem cell-based platforms, including mesenchymal stem cells (MSCs), exosomes, and gene-edited induced pluripotent stem cells (iPSCs), may serve as complementary platforms for regeneration and disease modeling. Preclinical studies demonstrate that MSCs and their derivatives modulate inflammation, restore ovarian structure, and improve metabolic parameters, while iPSC-based models enable patient-specific investigation of steroidogenic and metabolic abnormalities. Translational challenges remain, including targeted delivery, off-target effects, phenotypic heterogeneity, and regulatory considerations. Integrating CRISPR‑based functional genomics with stem cell research may shift PMOS management from symptom‑focused care to targeted, mechanism‑driven interventions that could modify the course of PMOS (Graphical Abstract).

Humans↗

PubMed1988

Structure and organization of mouse U3B RNA functional genes.

We report the isolation and primary structure of three genes encoding mouse U3B RNA which are expressed after injection into Xenopus laevis oocytes. Over the U3B RNA coding region, their sequences are perfectly identical, showing nine point differences with rat U3B, which do not alter the RNA secondary structure. A comparison of the three mouse sequences for the gene flanks reveals the extensive divergence of the downstream regions, except for a few nucleotides adjacent to the U3 RNA coding region, which contain a motif matching the consensus sequence for the U small nuclear RNA 3' end formation signal. By contrast, the upstream flanking regions are strongly homologous up to position -500, but they completely diverge thereafter. Within the homologous portion of 5' flanks, several motifs can be recognized which are unambiguously related to sequence elements involved in the transcriptional control of other U small nuclear RNA genes: two of these motifs precisely map at the locations (relative to the transcription start site) expected for the proximal and distal (enhancer-like) sequence elements of U small nuclear RNA genes, and "Sp1"-GC boxes and a CCAAT box are also present in their vicinity. The comparison with the rat U3B gene confirms that the preferential preservation of the 5'-flanking sequences extends up to position -500, suggesting the functional importance of sequences well upstream from the distal sequence element of the promoter. Two of the mouse genes are closely linked in genomic DNA (5 kilobase pairs apart, same orientation) and seem to have been homogenized through a recent conversion event. More generally, this small multigene family (at most six to seven copies of functional U3B genes per mouse haploid genome) appears to have undergone a concerted evolution in rodents.

Animals↗

PubMed2006

Anatomy, physiology and pharmacology of Caenorhabditis elegans pharynx: a model to define gene function in a simple neural system.

Invertebrate neuroscience has provided a number of very informative model systems that have been extensively utilized in order to define the neurobiological bases of animal behaviours (Sattelle and Buckingham in Invert Neurosci 6:1-3, 2006). Most eminent among these are a number of molluscs, including Aplysia californica, Lymnaea stagnalis and Helix aspersa, crustacean systems such as the crab stomatogastric ganglion and a wide-range of other arthropods. All of these have been elegantly exploited to shed light on the very important phenomenon of the molecular and cellular basis for synaptic regulation that underpins behavioural plasticity. Key to the successful use of these systems has been the ability to study well-defined, relatively simple neuronal circuits that direct and regulate a quantifiable animal behaviour. Here we describe the pharyngeal system of the nematode C. elegans and its utility as a model for defining the genetic basis of behaviour. The circuitry of the nervous system in this animal is uniquely well-defined. Furthermore, the feeding behaviour of the worm is controlled by the activity of the pharynx and this in turn is regulated in a context-dependent manner by a simple nervous system that integrates external signals, e.g. presence or absence of food, and internal signals, e.g. the nutritional status of the animal to direct an appropriate response. The genetics of C. elegans is being effectively exploited to provide novel insight into genes that function to regulate the neuronal network that controls the pharynx. Here we summarise the progress to date and highlight topics for future research. Two main themes emerge. First, although the anatomy of the pharyngeal system is very well-defined, there is a much poorer understanding of its neurochemistry. Second, it is evident that the neurochemistry is remarkably complex for such a simple circuit/behaviour. This suggests that the pharyngeal activity may be subject to exquisitely precise regulation depending on the animal's environment and status. This therefore provides a very tractable genetic model to investigate neural mechanisms for signal integration and synaptic plasticity in a well-defined neuronal network that directs a quantifiable behaviour, feeding.

Animals↗

PubMed2004

The use of gene function to identify the rate-limiting steps controlling cell fate.

The size and complexity of the genomes of mammals in general, and humans in particular, is such that it will take many years to utilise this information to produce a genuine understanding of the control of cell behaviour. Since there are tens of thousands of genes to consider, the task of identifying those which play the most significant roles, biologically and medically, is both crucial and very demanding. Here we emphasise the importance of functional approaches to answering this question, i.e. the application of techniques which use the function of the gene itself in identifying the critical rate-limiting steps in biological processes. In this review, we use the functional analysis of one of the most important of these processes, the control of survival and apoptosis, to illustrate the power of a number of functional genomic strategies.

Apoptosis↗

PubMed1995

Complete androgen insensitivity syndrome due to a new frameshift deletion in exon 4 of the androgen receptor gene: functional analysis of the mutant receptor.

We studied the androgen receptor gene in a large kindred with complete androgen insensitivity syndrome and negative receptor-binding activity, single-strand conformation polymorphism (SSCP) analysis and sequencing identified a 13 base pair deletion within exon 4. This was responsible for a predictive frameshift in the open reading frame and introduction of a premature stop codon at position 783 instead of 919. The deletion was reproduced in androgen receptor wildtype cDNA and transfected into mammalian cells. Western blot showed a smaller androgen receptor of 94 kDa for the transfected mutated cDNA instead of 110 kDa. Androgen-binding assay of the mutated transfected cells assessed the lack of androgen-binding. Gel retardation assay demonstrated the ability of the mutant to bind target DNA; however, the mutant was unable to transactivate a reporter gene. Although the role of the partial deletion in the lack of androgen action was expected, in vitro analyses highlight the role of the abnormal C-terminal portion in the inhibition of the receptor transregulatory activity of the protein causing androgen resistance in this family.

Androgens↗

PubMed2004

The 5'-untranslated region of the tobacco alcohol dehydrogenase gene functions as an effective translational enhancer in plant.

The alcohol dehydrogenase gene (NtADH) was previously isolated from tobacco BY2 suspension cultured cell. Expression of this gene was dramatically increased only during the early stationary phase, and the 5'-untranslated region (5'-UTR) was hypothesized to be involved in the stimulatory effect at the post-transcriptional level. In this paper, we investigated whether the NtADH 5'-UTR possesses the ability to positively enhance gene expression at the translational level. For easily estimating translational efficiency, we used beta-glucuronidase (GUS) gene as a reporter and tobacco BY2 cell, Arabidopsis thaliana T87 cell, and rice Oryza sativa suspension cultured cells as host cells in a transient assay system. Compared with the control plasmid pBI221, insertion of the NtADH 5'-UTR enhanced GUS expression levels about 30- to 100-fold and 30- to 60-fold in transiently transformed BY2 and T87 cells, respectively. However, in transiently transformed O. sativa cells, expression was barely enhanced. In comparison with the 5'-UTR of tobacco mosaic virus (Omega sequence), a known translational enhancer, the NtADH 5'-UTR enhanced translation to a similar level. Meanwhile, the translational efficiency was affected by the sequence context around the AUG initiation codon at the translational initiation step. Moreover, this NtADH 5'-UTR also worked in stable tobacco transformants. Therefore, it is expected that this 5'-UTR will serve as a powerful tool for enhancing foreign gene expression.

Journal Article↗

PubMed2003

Using natural allelic diversity to evaluate gene function.

Genomics has developed a wide range of tools to identify genes that play roles in specific pathways. However, relating individual genes and alleles to agronomic traits is still quite challenging. We describe how association analysis can be used to relate natural variation at candidate genes with agronomic phenotypes. Association approaches in plants can provide very high resolution and can evaluate a wide range of alleles rapidly. We discuss issues related to experimental design, germplasm sample, molecular assay, population structure, and statistical analysis necessary for association analysis in plants.

Alleles↗

PubMed1993

The mosquito dihydrofolate reductase gene functions as a dominant selectable marker in transfected cells.

An Aedes albopictus dihydrofolate reductase gene was used to construct two chimeric DNA vectors that functioned as dominant selectable markers in transfected, wild type mosquito cells. Stably transformed clones were recovered after 10-15 days in the presence of selective medium containing 1 microM methotrexate. The transformed clones contained an estimated 100-500 copies of transfected DNA per nucleus. Combined data from Southern blots and in situ hybridization to metaphase chromosomes indicated that transfected DNA was likely integrated into chromosomes both as repeated structures and as randomly integrated single copy molecules, with minimal rearrangement of coding sequences. Transfected DNA was stably maintained under selective conditions, but in some cases was lost when cells were maintained for prolonged periods in the absence of methotrexate. These observations provide a general framework for further development of stable gene transfer systems for mosquito cells in culture.

Aedes↗

PubMed1978

[Genetic study of bacteriophage phi81. II. Gene localization in the right arm of the phage chromosome and a comparison of phage phi81 with phages lambda and phi80 in regard to gene functions].

Data on genetic investigation on lambdoid bacteriophage phi81 made possible to localize the cos site on the prophage genetic map. Four essential genes and the gene c1 are located in the right arm of the phage genetic map. Regulatory genes of phage phi81 are found to be uncapable of functional substitution of lambda phages regulatory genes N and Q. It is discovered that some late genes of phage phi80 can be substituted with respective phage phi81 genes. No substitution possibility was observed for a number of early genes of phage phi80.

Chromosome Mapping↗

PubMed2002

Ligand-dependent genetic recombination in fibroblasts : a potentially powerful technique for investigating gene function in fibrosis.

Strategies for conditional induction of transgene expression in mice are likely to be valuable for testing the role of candidate genes in disease pathogenesis. We have developed a system for lineage-specific, ligand-dependent, induction of sustained transgene expression in fibroblastic cells in mice using a chimeric gene encoding the Cre-ER(T) fusion protein, under the control of a fibroblast-specific regulatory sequence from the pro alpha 2(I)collagen gene. Cre-ER(T) operates as a tamoxifen-dependent DNA recombinase to excise fragments flanked by specific LoxP consensus sequences. To test efficiency and ligand dependency of this strategy, Cre-ER(T)-expressing mice were backcrossed with heterozygous ROSA26-LacZ reporter mice, in which a floxed-STOP cassette has been introduced upstream of a bacterial beta-galactosidase (LacZ) reporter gene at a ubiquitously expressed locus. Constitutive or tamoxifen-induced LacZ expression was examined in embryonic, neonatal, and adult compound-transgenic mice. When pregnant ROSA26-LacZ females received a single dose of tamoxifen, high-level expression of LacZ in the skin was demonstrable from 24 hours after injection in double-transgenic embryos harboring both the Cre-ER(T) transgene and the target ROSA26-LacZ allele. High-level expression of LacZ was also induced postnatally by tamoxifen specifically in dermal and visceral fibroblasts. By allowing efficient embryonic or postnatal modification of alleles that have been targeted to incorporate LoxP sites, or to switch on transgenes cloned downstream of the floxed-STOP cassette, this system will allow fibroblast-specific genetic perturbations to be induced at predetermined embryonic or postnatal time points. This should greatly assist in in vivo functional studies of candidate genes in fibrotic diseases such as systemic sclerosis.

Animals↗

PubMed2006

Multiple gene duplication and rapid evolution in the groEL gene: functional implications.

The chaperonins, GroEL and GroES, are present ubiquitously and provide a paradigm in the understanding of assisted protein folding. Due to its essentiality of function, GroEL exhibits high sequence conservation across species. Complete genome sequencing has shown the occurrence of duplicate or multiple copies of groEL genes in bacteria such as Mycobacterium tuberculosis and Corynebacterium glutamicum. Monophyly of each bacterial clade in the phylogenetic tree generated for the GroEL protein suggests a lineage-specific duplication. The duplicated groEL gene in Actinobacteria is not accompanied by the operonic groES despite the presence of upstream regulatory elements. Our analysis suggests that in these bacteria the duplicated groEL genes have undergone rapid evolution and divergence to function in a GroES-independent manner. Evaluation of multiple sequence alignment demonstrates that the duplicated genes have acquired mutations at functionally significant positions including those involved in substrate binding, ATP binding, and GroES binding and those involved in inter-ring and intra-ring interactions. We propose that the duplicate groEL genes in different bacterial clades have evolved independently to meet specific requirements of each clade. We also propose that the groEL gene, although essential and conserved, accumulates nonconservative substitutions to exhibit structural and functional variations.

Adenosine Triphosphate↗

PubMed2003

Highly conserved Drosophila ananassae timeless gene functions as a clock component in Drosophila melanogaster.

The behavior and physiology of Drosophila are subject to rhythms that are controlled by the circadian clock genes, period, timeless, clock and cycle, all of which are thought to participate in central pacemaker control. The molecular mechanism of rhythm in Drosophila has been studied in detail. However, rhythm and clock genes have mostly been analyzed in Drosophila melanogaster. To confirm whether the tim gene exists and works as a clock component in other Drosophila species, we cloned a tim homolog from Drosophila ananassae that shared 85.9% similarity with Drosophila melanogaster tim at the amino acid level. In addition, the PER interaction domains and NLS were highly conserved. Introduction of the D. ananassae tim homolog rescued the rhythm of the locomotor activity of about 44% of a population of D. melanogaster tim(01) flies. At the molecular level, hs-tim introduced not only TIM but PER oscillation in transgenic flies. These results indicate that the tim gene in D. ananassae functions as a component of the circadian clock in D. melanogaster.

Amino Acid Sequence↗

PubMedDate not supplied

HSV gene functions: what have we learned that could be generally applicable to its near and distant cousins?

Herpes simplex virus 1 (HSV-1) encodes at least 84 polypeptides to perform two functions: to enable viral replication and to create the environment in which the entry of the virus into host cells, synthesis of virion components, assembly and egress are optimized. Whereas the former are indispensable for viral replication, the latter, numbering 47, can be deleted without a major effect on viral replication in cells in culture. Of particular interest are gene products whose function is either to modify cellular proteins (set 1) or to block entirely their function (set 2). An example of set 1 is the infected cell protein No. 0 (ICP0), a promiscuous transactivator of genes introduced into cells by infection or transfection. In its nuclear phase this protein binds to cyclin D3, extends its life by many hours, and sequesters it in nuclear structures known as ND10. In its cytoplasmic phase, ICP0 binds the translation elongation factor EF-1 delta. Another viral protein, the UL13 protein kinase, hyper-phosphorylates EF-1 delta. ICP0 and the protein kinase stimulate protein synthesis and cause the cell to induce the synthesis of pre-S phase cellular proteins the virus needs for its replication. The gamma 134.5 protein, a prototype of set 2, also has multiple functions. One, mapped at its carboxyl terminus, blocks the effects of double-stranded RNA-dependent protein kinase R (PKR) that is activated by all wild-type and mutant viruses examined to date. PKR phosphorylates eIF-2 alpha and shuts off protein synthesis. gamma 134.5 protein binds protein phosphatase 1 and redirects it to dephosphorylate eIF-2 alpha. Although PKR is activated in wild-type-infected cells, protein synthesis is unaffected. HSV-1 encodes in addition at least two proteins, ORF O and ORF P that are repressed during productive infection. The ORF P protein localizes in spliceosomes and blocks the synthesis of viral proteins derived from spliced mRNA. The ORF O protein binds ICP4, the major regulatory protein, and prevents it from binding to DNA. The role of ORF O and ORF P proteins in the establishment of latency is uncertain. A significant discovery that has emerged from these studies is that viral proteins can perform several functions that may be totally unrelated.

Gene Expression↗

PubMed1997

Characterization of genes encoding dimethyl sulfoxide reductase of Rhodobacter sphaeroides 2.4.1T: an essential metabolic gene function encoded on chromosome II.

Rhodobacter sphaeroides 2.4.1T is a purple nonsulfur facultative phototrophic bacterium which exhibits remarkable metabolic diversity as well as genomic complexity. Under anoxic conditions, in the absence of light and the presence of dimethyl sulfoxide (DMSO) or trimethylamine N-oxide (TMAO), R. sphaeroides 2.4.1T utilizes DMSO or TMAO as the terminal electron acceptor for anaerobic respiration, which is mediated by the molybdoenzyme DMSO reductase. Sequencing of a 13-kb region of chromosome II revealed the presence of 10 putative open reading frames, of which 5 possess homology to genes encoding the TMAO reductase (the tor system) of Escherichia coli. The dorS and dorR genes encode a sensor-regulator pair of the two-component sensory transduction protein family, homologous to the torS and torR gene products. The dorC gene was shown to encode a 44-kDa DMSO-inducible c-type cytochrome. The dorB gene encodes a membrane protein of unknown function homologous to the torD gene product. The dorA gene encodes DMSO reductase, containing the molybdopterin active site. Mutations were constructed in each of these dor genes, and the resulting mutants were shown to be impaired for DMSO-dependent anaerobic growth in the dark. The mutant strains exhibited negligible levels of DMSO reductase activity compared to the wild-type strain under similar growth conditions. Further, no DorA protein was detected in DorS and DorR mutant strains with anti-DorA antisera, suggesting that the products of these genes are required for the positive regulation of dor expression in response to DMSO. This characterization of the dor gene cluster is the first evidence that genes of chromosome CII encode metabolic functions which are essential under particular growth conditions.

Chromosomes, Bacterial↗