Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “gene function”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed1978

Construction and characterization of an Escherichia coli plasmid bearing a functional gene G of bacteriophage phiX174.

In order to study the mutagenic effects of site-specific, covalent modifications of biologically active DNA, we need host cells that are permissive for any type of mutation that might be produced in vivo from the modified DNA. Specifically, we require a general, in vivo complementation system for the bacteriophage phiX174 gene G, an essential gene that we have chosen for our initial studies of chemical mutagenesis. Toward this end, we have constructed a plasmid (pphiXG) that carries a functional copy of phiX174 gene G. Three different bacterial strains that are nonpermissive for am9, a gene G amber mutant, have been transformed with pphiXG. The transformants are now permissive for this gene G mutant, but not for the gene A or E mutants that have been tested. This paper describes the construction and the biochemical characterization of this plasmid, pphiXG, and describes some of the biological properties exhibited by the pphiXG-bearing strains.

Coliphages↗
PubMed1979

uvrC gene function in excision repair in toluene-treated Escherichia coli.

We have examined the role of the uvrC gene in UV excision repair by studying incision, excision, repair synthesis, and DNA strand reformation in Escherichia coli mutants made permeable to nucleoside triphosphates by toluene treatment. After irradiation, incisions occur normally in uvrC cells in the presence of nicotinamide mononucleotide (NMN), a ligase-blocking agent, but cannot be detected otherwise. We conclude that repair incisions are followed by a ligation event in uvrC mutants, masking incision. However, a uvrC polA12 mutant accumulates incisions only slightly less efficiently than a polA12 strain without NMN. Excision of pyrimidine dimers is defective in uvrC mutants (polA(+) or polA12) irrespective of the presence or absence of NMN. DNA polymerase I-dependent, NMN-stimulated repair synthesis, which is demonstrable in wild-type cells, is absent in uvrC polA(+) cells, but the uvrC polA12 mutant exhibits a UV-specific, ATP-dependent repair synthesis like parental polA12 strains. A DNA polymerase I-mediated reformation of high-molecular-weight DNA takes place efficiently in uvrC polA(+) mutants after incision accumulation, and the uvrC polA12 mutant shows more reformation than the polA12 strain after incision. These results indicate that normal incision occurs in uvrC mutants, but there appears to be a defect in the excision of pyrimidine dimers, allowing resealing via ligation at the site of the incision. The lack of NMN-stimulated repair synthesis in uvrC polA(+) cells indicates that incision is not the only requirement for repair synthesis.

DNA Polymerase I↗
PubMed2025

Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.).

Finger millet (Eleusine coracana (L.) Gaertn.) is a calcium-rich, nutritious and resilient crop that thrives even in harsh environmental conditions. In such ecologies, seed longevity and seedling vigor are crucial for sustainable crop production amid climate change. The current study explores the genetics of accelerated aging on seed longevity traits across 221 diverse accessions of finger millet through genome-wide association approach (GWAS). A significant variation was identified in germination percentage, germination rate indices, mean germination time, seedling vigor indices and dry weight upon aging treatment. GWAS model from 11,832 high-quality SNPs identified through Genotyping-by-Sequencing (GBS) approach produced 491 marker-trait associations (MTAs) for 27 traits, of which 54 were FDR-corrected. A pleiotropic SNP, FM_SNP_9478 identified on chromosome 7B was associated with the traits viz., germination after aging, germination index after aging and their relative measures. Functional annotation revealed DET1 and expansin-A2 influenced seed coat integrity, critical for germination and aging resilience. Probable protein phosphatase 2C3 and piezo-type ion channels contributed to mechanical sensing and stress adaptation in seeds. Beta-amylase and acetyl-CoA carboxylase 2 were identified for seed metabolism and stress response. These insights lay the framework for targeted breeding efforts to improve seed quality and resilience under diverse production conditions.

Eleusine↗
PubMed1976

Some genetic consequences of changes in the level of recA gene function in Escherichia coli K-12.

Genetic recombination was studied in E. coli mutants that carry lesions in the recA gene but retain some capacity for generating recombinant progeny. We observed that recombination was detectable only at a very low level during the incubation of leaky RecA- merozygotes in broth. However, recombination appeared to occur at much higher frequencies when recombinant progeny were assayed by selection on minimal agar. Analysis of the recombinants obtained with Hfr donors revealed a deficiency of multiple exchanges per unit length of DNA in leaky RecA- strains. In many of these crosses recombinants that inherited donor alleles close to the transfer origin were much reduced in frequency, except when the recipient was also RecB-.

Alleles↗
PubMed2026

Characterization of the gut phageome and functional genes carried by phages in laying hens with fatty liver hemorrhagic syndrome.

BACKGROUND: The gut microbiota is closely associated with the development of fatty liver hemorrhagic syndrome (FLHS); however, the function of its viral component, particularly bacteriophages, remains poorly understood. This study compared clinical parameters and the cecal phageome between 30-week-old (W30) and 50-week-old (W50) laying hens to characterize gut phages in the context of this metabolic disorder. RESULTS: Clinical analysis revealed that the W50 group exhibited typical FLHS, accompanied by elevated serum liver function and lipid markers (P&#x2009;<&#x2009;0.05). Functional prediction of the gut microbiota suggested a reduced lipid-metabolic capacity in W50 compared to the W30 group. A total of 20,274 phage genomes were identified from the two groups. These phages were primarily classified into 67 viral families, including Salasmaviridae, Herelleviridae, Suoliviridae, Peduoviridae, Crevaviridae, and Casjensviridae. The families Druskaviridae, Felixviridae, and Stanwilliamsviridae were uniquely detected in the W50 group. The phage community structure differed significantly between groups, with both phage diversity and richness markedly lower in W50 (P&#x2009;<&#x2009;0.05). LEfSe analysis revealed that phage taxa such as Stegnyidae, Herpelidae, and Chasovidae were significantly enriched in the W50 group, whereas Crewdviridae, Salasmaviridae, and Castroviridae were predominantly enriched in the W30 group. Functional annotation showed that these phages encode numerous metabolism-related genes and carry antimicrobial resistance genes (ARGs) as well as virulence factor genes. Notably, the diversity of ARGs carried by W50 phages was significantly higher (P&#x2009;<&#x2009;0.05), and ARG-rank analysis indicated a greater potential risk to human health. CONCLUSIONS: This study provides the first characterization of the gut phageome associated with FLHS in laying hens and confirms that gut phages constitute an important reservoir of ARGs. These findings offer a new perspective for understanding the pathogenesis of this disease and its associated public health risks. Video Abstract.

Animals↗
PubMed1978

Regulation of the galactose pathway in Saccharomyces cerevisiae: induction of uridyl transferase mRNA and dependency on GAL4 gene function.

In Saccharomyces cerevisiae, utilization of galactose requires four inducible enzyme activities. Three of these activities (galactose-1-phosphate uridyl transferase, EC 2.7.7.10; uridine diphosphogalactose 4-epimerase, EC 5.1.3.2; and galactokinase, EC 2.7.1.6) are specified by three tightly linked genes (GAL7, GAL10, and GAL1, respectively) on chromosome II, whereas the fourth, galactose transport, is specified by a gene (GAL2) located on chromosome XII. Although classic genetic analysis has revealed both positive and negative regulatory genes that coordinately affect the appearance of all four enzyme activities, neither the basic events leading to the appearance of enzyme activities nor the roles of the regulatory genes have yet been determined. Regulation of inducible enzyme activity could be mediated by events related to transcription, translation, or enzyme activation. For the purpose of studying galactose pathway induction and its regulation, we have developed an immunoprecipitation assay that enables us to detect the GAL7 specified uridyl transferase polypeptide in yeast extracts and among the polypeptides synthesized in an RNA-dependent in vitro translation system. Use of this immunoprecipitation assay in conjunction with in vivo labeling experiments demonstrates the presence of [(3)H]leucine-labeled transferase in extracts prepared from cells grown in galactose but not from cells grown in glucose. This galactose-specific induction of transferase polypeptide is mediated by the de novo appearance of a functional mRNA species whose synthetic capacity is detectable by the combination of in vitro translation and immunoprecipitation. The appearance of functional transferase mRNA depends on wild-type expression of the positive regulatory gene, GAL4. Cells carrying a nonsense (amber) mutation in the GAL4 gene fail to produce the transferase mRNA, whereas a nonsense suppressor of the GAL4 amber mutant regains the galactose-specific mRNA response. Our results establish that the induction of the GAL7 specified uridyl transferase activity is mediated by de novo appearance of a functional mRNA and that this galactose-specific response is dependent on a wild-type GAL4 gene product.

Cell-Free System↗
PubMed1975

chlD gene function in molybdate activation of nitrate reductase.

chlD mutants of Escherichia coli lack active nitrate reductase but form normal levels of this enzyme when the medium is supplemented with 10-3 M molybdate. When chlD mutants were grown in unsupplemented medium and then incubated with molybdate in the presence of chloramphenicol, they formed about 5% the normal level of nitrate reductase. Some chlD mutants or the wild type grown in medium supplemented with tungstate accumulated an inactive protein which was electrophoretically identical to active nitrate reductase. Addition of molybdate to those cells in the presence of chloramphenicol resulted in the formation of fully induced levels of nitrate reductase. Two chlD mutants, including a deletion mutant, failed to accumulate the inactive protein and to form active enzyme under the same conditions. Insertion of 99-Mo into the enzyme protein paralleled activation; 185-W could not be demonstrated to be associated with the accumulated inactive protein. The rates of activation of nitrate reductase at varying molybdate concentrations indicated that the chlD gene product facilitates the activation of nitrate reductase at concentrations of molybdate found in normal growth media. At high concentrations, molybdate circumvented this function in chlD mutants and appeared to activate nitrate reductase by a mass action process. We conclude that the chlD gene plays two distinguishable roles in the formation of nitrate reductase in E. coli. It is involved in the accumulation of fully induced levels of the nitrate reductase protein in the cell membrane and it facilitates the insertion of molybdenum to form the active enzyme.

Cell-Free System↗
PubMed2025

Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models.

Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation. Genome-scale metabolic network models (GEMs) - comprehensive representations of metabolic genes and reactions - are widely used to evaluate genetic engineering of biological systems. However, GEMs often fail to accurately predict the behaviour of genetically engineered cells, primarily due to incomplete annotations of gene interactions. The task of learning the intricate genetic interactions within GEMs presents computational and empirical challenges. To efficiently predict using GEM, we describe a novel approach called Boolean Matrix Logic Programming (BMLP) by leveraging Boolean matrices to evaluate large logic programs. We developed a new system, [Formula: see text], which guides cost-effective experimentation and uses interpretable logic programs to encode a state-of-the-art GEM of a model bacterial organism. Notably, [Formula: see text] successfully learned the interaction between a gene pair with fewer training examples than random experimentation, overcoming the increase in experimental design space. [Formula: see text] enables rapid optimisation of metabolic models to reliably engineer biological systems for producing useful compounds. It offers a realistic approach to creating a self-driving lab for biological discovery, which would then facilitate microbial engineering for practical applications.

Active learning↗