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At least 307 records · Page 17Linked to original sources
PubMed1997

Molecular aspects of the E. coli nucleoid protein, H-NS: a central controller of gene regulatory networks.

The nucleoid-associated protein H-NS has a central role in the structuring and control of the enteric bacterial chromosome. This protein has been demonstrated to contribute to the regulation of expression for approximately thirty genes. In this article, the molecular aspects of H-NS structure and function are briefly reviewed. H-NS contains at least two independent structural domains: a C-terminal domain, involved in the DNA-protein interactions, and a N-terminal domain, likely involved in protein-protein interactions. Recent reports have revealed that H-NS is a key factor in a multi-component gene regulatory system. Factors have now been discovered which can backup or antagonise H-NS action at certain promoters. These recent findings are summarised and discussed in relationship to the role of H-NS in DNA packaging and nucleoid structure.

Bacterial Proteins↗
PubMed2005

Circadian rhythms in Neurospora crassa: clock gene homologues in fungi.

Computer-based analysis of a total of 17 filamentous fungal and yeasts genomes has shown: (1) homologues of frq, wc-1, wc-2, and vvd, key gene components of the Neurospora crassa clock, are present in Magnaporthe grisea, Gibberella zeae, and Podospora anserina, suggesting an frq-based oscillator in these organisms; (2) some fungal species that are more distantly related to Neurospora, such as Rhizopus oryzae do not appear to have frq homologues; (3) many fungal species that do not appear to contain frq, such as Aspergillus nidulans, do contain wc homologues; (4) of 11 well-described genes classified as clock-controlled genes (ccgs), in Neurospora, all of them were found to have homologues in other fungi; (5) the ccg-8 gene of N. crassa has homologies to opi1p, a transcriptional regulatory gene in Saccharomyces cerevisiae involved in inositol regulation. This suggests the possibilities of rhythmic inositol regulation, and/or a cascade of rhythmic activation of other genes in N. crassa.

Biological Clocks↗
PubMed1995

The Marek's disease virus (MDV) unique short region: alphaherpesvirus-homologous, fowlpox virus-homologous, and MDV-specific genes.

Despite its previous classification as a gammaherpesvirus, primarily due to its lymphotropism, Marek's disease virus (MDV), an oncogenic avian herpesvirus, is phylogenetically more related to the "neurotropic" alphaherpesviruses, characterized by its prototype, herpes simplex virus (HSV) (Buckmaster et al., 1988, J. Gen. Virol. 69, 2033-2042). In this report we present the DNA sequence of an 11,286-bp DNA segment encompassing the entire 11,160-bp-long Us region of the oncogenic avian herpesvirus, Marek's disease virus. Eleven open reading frames (ORFs) likely to code for proteins were identified; of these, 7 represent homologs exclusive to alphaherpesvirus S component genes. These include MDV counterparts of HSV US1 (ICP22), US2, US3 (a serine-threonine protein kinase), US6, US7, and US8 (HSV glycoproteins gD, gI, and gE, respectively), and US10. Three additional ORFs were identified with no apparent relation to any sequences currently present in the SwissProt or GenBank/EMBL databases, while a fourth was found to exhibit significant homology to an uncharacterized fowlpox virus (FPV) ORF. Having precisely identified the IRs-U(s) and U(s)-TRs junctions, we have corrected and clarified their previously reported locations. By characterizing genes encoding three new alphaherpesvirus-related homologs (US1, US8, and US10), completing the sequence for a fourth (US7), and identifying 2 new MDV-specific ORFs (SORF1 and SORF3) and a fowlpox homolog (SORF2), our sequence analysis of the "virulent" GA strain of MDV (vMDV) extends upon that of a 5255-bp segment located in the U(s) region of the "very virulent" RB1B strain of MDV (vvMDV) (Ross et al., 1991, J. Gen. Virol. 72, 939-947; 949-954). These two sequences were found to exhibit 99% identity at both nucleotide and predicted amino acid levels. Combined with the fact that MDV U(s) sequences failed to show statistically significant CpG deficiencies, our analysis is consistent with MDV bearing a closer phylogenetic relation to alphaherpesviruses than to gammaherpesviruses. Because alphaherpesvirus-specific U(s) region genes are primarily nonessential for virus replication, they are thought to be important biological property determinants. Thus, our sequence provides a foundation for further MDV studies aimed at resolving the apparent discrepancy between MDV's genetic and biologic properties.

Amino Acid Sequence↗
PubMed2000

Ethylene: a gaseous signal molecule in plants.

Ethylene regulates a multitude of plant processes, ranging from seed germination to organ senescence. Of particular economic importance is the role of ethylene as an inducer of fruit ripening. Ethylene is synthesized from S-adenosyl-L-methionine via 1-aminocyclopropane-1-carboxylic acid (ACC). The enzymes catalyzing the two reactions in this pathway are ACC synthase and ACC oxidase. Environmental and endogenous signals regulate ethylene biosynthesis primarily through differential expression of ACC synthase genes. Components of the ethylene signal transduction pathway have been identified by characterization of ethylene-response mutants in Arabidopsis thaliana. One class of mutations, exemplified by etr1, led to the identification of the ethylene receptors, which turned out to be related to bacterial two-component signaling systems. Mutations that eliminate ethylene binding to the receptor yield a dominant, ethylene-insensitive phenotype. CTR1 encodes a Raf-like Ser/Thr protein kinase that acts downstream from the ethylene receptor and may be part of a MAP kinase cascade. Mutants in CTR1 exhibit a constitutive ethylene-response phenotype. Both the ethylene receptors and CTR1 are negative regulators of ethylene responses. EIN2 and EIN3 are epistatic to CTR1, and mutations in either gene lead to ethylene insensitivity. Whereas the function of EIN2 in ethylene transduction is not known, EIN3 is a putative transcription factor involved in regulating expression of ethylene-responsive genes. Biotechnological modifications of ethylene synthesis and of sensitivity to ethylene are promising methods to prevent spoilage of agricultural products such as fruits, whose ripening is induced by ethylene.

Ethylenes↗
PubMed2004

Identification of the nonA and nonB loci of Bacillus subtilis Marburg permitting the growth of SP10 phage.

Mutational inactivation of both nonA and nonB genes are required for the permissiveness of Bacillus subtilis Marburg cells to infection by phage SP10. By transformational analysis of the nonA strain with DNAs from gently lysed protoplasts carrying the integrative plasmid pMUTIN (em) insertions in every 20 kb along the whole chromosome, we have identified the nonA to be the cured state of endogenous prophage SPbeta. Direct DNA sequencing, on the other hand, revealed one nonsense mutation of nonB in ydiR, which is a component gene of the intrinsic restriction system BsuMR of B.subtilis Marburg. Introduction of the wild type ydiR into the nonB strain at aprE locus resulted in complementation of nonB. Furthermore, as the SP10 genome was found to possess multiple BsuM target sites, it is considered that SP10 can infect and multiply in B.subtilis cells, which are SPbeta free and possess a defective BsuMR restriction system.

Bacillus subtilis↗
PubMed1992

Familial recurrence-pattern analysis of cleft lip with or without cleft palate.

Cleft lip with or without cleft palate (CL/P) is a common congenital malformation with an incidence in European white populations of about 1/1,000. The familial clustering of CL/P has been extensively characterized, and epidemiological studies have proposed monogenic models (with reduced penetrance), multifactorial/threshold models, and mixed major-gene/multifactorial models to explain its inheritance. The recognition of an association between two RFLPs at the transforming growth factor alpha (TGFA) locus and CL/P supports a major-gene component to the etiology of CL/P. Risch has shown that the recurrence risk ratio lambda R (risk to relatives, vs. population prevalence) is a useful pointer to the mode of inheritance. Here we further develop the use of lambda R to analyze recurrence-risk data for CL/P. Recurrence risks for first-, second-, and third-degree relatives equate well with oligogenic models with as few as four loci. A monogenic/additive model is strongly rejected. The limited available twin data are also consistent with this model. A "major gene" interacting epistatically with an oligogenic background is shown to be a plausible alternative. Power calculations for a linkage study to map the CL/P major-risk locus suggest that a sample of 50 affected sib pairs will be adequate, but linkage to minor-risk loci will require very much larger samples.

Chromosome Mapping↗
PubMed1993

Proteins with molecular masses of 50 and 80 kilodaltons encoded by genes downstream from the fimbrilin gene (fimA) are components associated with fimbriae in the oral anaerobe Porphyromonas gingivalis.

Flanking DNA regions of the fimbrilin gene (designated fimA), which encodes the major subunit protein of Porphyromonas (Bacteroides) gingivalis fimbriae, were cloned in several manners from the P. gingivalis chromosome into Escherichia coli by screening with probes derived from a 2.5-kb SacI DNA fragment previously cloned. A total of 10.4 kb of DNA fragments from the P. gingivalis genome was cloned in the pUC plasmid. Expression of the fimA gene and possible flanking genes in the fragments cloned was examined in a pUC plasmid vector system and in a bacteriophage T7 RNA polymerase-promoter expression vector system. The results show that in the pUC plasmid system, a 45-kDa protein, a product of fimA, was only poorly expressed as a precursor of the fimbrilin protein (FimA) and could be detected from cell extracts in Western blotting (immunoblotting) analysis as a sharp band but not in colony immunoblotting analysis. On the other hand, in the T7 RNA polymerase-promoter system, the product of fimA and products of the possible flanking genes responsible for fimbriation were overproduced as thick bands of the 45-kDa protein and as 63-, 50-, and 80-kDa proteins, respectively, in stained electrophoresis gels. All of the recombinant proteins were insoluble and seemed to be expressed as precursors with leader peptides. The 63-kDa, 45-k*Da (a truncated protein of the 50-kDa protein), and 80-kDa proteins were purified after solubilization with sodium dodecyl sulfate. N-terminal amino acid sequences of the 45-k*Da and 80-kDa proteins were analyzed up to the first 35 residues with a gas-phase sequencer. Monospecific antibodies directed to the recombinant proteins, i.e., the 63-kDa, 45-k*Da, and 80-kDa proteins, were raised in rabbits. By using the antibodies, localization of their matured proteins in P. gingivalis was investigated by Western blotting analysis. Immunoblotting analysis suggests that at least the 50- and 80-kDa proteins, encoded by genes downstream from the fimA gene, are minor components associated with fimbriae.

Amino Acid Sequence↗
PubMed2005

Methylation of tumor suppressor genes p16(INK4a), p27(Kip1) and E-cadherin in carcinogenesis.

Not only genomic mutations but also abnormal epigenetic methylation can significantly contribute to gene silencing and carcinogenesis. Methylation is particularly often observed in the CpG islands of the promoter regions in the regulatory genes. However, there are considerable differences in the incidence of methylation e.g. in the tumor suppressor genes, so that aberrant methylation of p16(INK4a) is relatively frequently observed in tumors, p27(Kip1) methylation is rare, and the incidence of E-cadherin methylation occurs at an intermediate rate. Although true genomic defects are generally much less common than methylation, parallel tendencies for both are often observed, probably reflecting the different levels of evolutionary advantage for tumor cells from inactivation of different genes. This also suggests that loss of p27 expression could be more a consequence of carcinogenesis, while lost p16 expression is a true oncogenic event. Due to the role of p27 in maintaining cellular quiescence, however, loss of its expression can still be a useful partial indicator of the aggressiveness of cancer. Loss of E-cadherin or its catenin partners of cellular adhesion will result in increasing invasiveness and metastatic potential of neoplastic cells but, because of several alternative routes to the same effect, incidence of lost expression for one component gene like E-cadherin does not need to be very high. Similarly, there must be a relatively high number of genes with modest or low incidence of aberrant silencing by methylation, to reflect multiple alternatives for the multistep process of carcinogenesis. Nevertheless, methylation of different genes also shows characteristic differences between different cancer and tumor types, and the epigenetic methylation patterns therefore have considerable diagnostic and prognostic potential. Realising this potential requires efficient methods for profiling the status of methylation. Such profiling methods have only recently become available and are still under relatively rapid development.

Cadherins↗
PubMed2000

Ki-ras point mutation and p53 expression in human pancreatic cancer: a comparative study among Chinese, Japanese, and Western patients.

The aim of this study was to clarify features of Ki-ras point mutation (PM) and p53 expression in Chinese pancreatic cancer and to compare those with that in other countries. Dot blot hybridization and immunohistochemical methods were performed in 59 Chinese patients. The results showed that Ki-ras PMs at codon 12 and p53 expression were frequent in this group. No relationships were found between Ki-ras PM alone and p53 expression alone, and clinicopathological parameters, including age, gender, clinical stage, and histological grade and classification in Chinese patients. However, their cooperation was significantly associated with a poor prognosis in this group. Comparison showed that there were significant differences in the overall frequency and substitution of Ki-ras PM and in the ratio of transition:transversion in pancreatic cancer among various countries. In addition, the effect of Ki-ras PM and p53 expression on a poor prognosis of pancreatic cancer may be different among various countries. These findings suggested that not only Ki-ras PM and p53 expression are frequent in Chinese pancreatic cancer, but also a gene component to pancreatic cancer may be different between Asian and Western pancreatic cancer. In addition, it seems that cooperation of Ki-ras PM and p53 expression may predict a poor prognosis in Chinese patients with pancreatic cancer.

Adult↗
PubMed1999

Segregation analysis of body mass index in a large sample selected for obesity: the Swedish Obese Subjects study.

OBJECTIVE: To investigate a major gene hypothesis for body mass index (BMI) in a large sample of probands (n = 2580, ages 37-57 years) who were selected for obesity (BMI> or =34 kg/m2 for males and > or =38 kg/m2 for females), along with their spouses and first-degree relatives (n = 11,204 family members). The probands were recruited as part of an intervention trial assessing whether mortality and morbidity were improved after surgical intervention for obesity as part of the Swedish Obese Subjects (SOS) study. METHODS AND PROCEDURES: The current analyses were based on BMI measures obtained before intervention. Segregation analysis was carried out using the mixed model implementation in PAP (Pedigree Analysis Package), which allowed for ascertainment correction and for genotype-dependent effects of covariates (sex and age) in both the major gene component and the multifactorial (i.e., polygenic and familial environment) component. RESULTS: Both a major effect and a multifactorial effect were significant. The percentage of the total variance accounted for by the multifactorial effect was 17%-24% (increasing as a function of age), and by the major effect, 8%-34% (decreasing as a function of age). Although tests on the transmission probabilities (taus) were not compatible with Mendelian expectations of 1, 1/2, and 0, the equal taus model was rejected (i.e., the effect is transmitted in families) and the point estimates (0.96, 0.60, and 0.17) compared favorably to Mendelian expectations. The major effect was transmitted in a codominant fashion, consistent with a gene-environment interaction. DISCUSSION: These results suggest both multifactorial and major effect etiologies for BMI in these families of extremely obese probands. Before 20 years of age, the major effect dominates the BMI expression, but after age 20, multifactorial effects account for the most variance. Although the major effect is transmitted in these families, the pattern does not appear to be consistent with a simple Mendelian trait. The possibility of additional major loci (i.e., epistasis) and gene by environment interactions may explain these findings.

Adult↗
PubMed1987

Sequence analysis of a cDNA clone of a gene encoding a component of a putative phosphorylcholine-specific T suppressor factor and functional property of its gene product.

We have isolated a putative phosphorylcholine (PC)-T cell suppressor factor (TsF) cDNA clone, p6-5, from a cDNA library of a T hybridoma which constitutively secretes a PC-TsF in vitro [8]. In the present study, we determined the nucleotide sequence of the p6-5 gene and found that the p6-5 sequence is 86% homologous to rat preproelastase 1 gene, one of the serine protease genes. An oligopeptide (14 mer, TsF14) deduced from the p6-5 sequence was synthesized and antisera against TsF14 were prepared in rabbits. Anti-TsF14-conjugated Sepharose 4B specifically absorbed the PC-TsF activity from the culture supernatant of PC-TsF-secreting T hybridomas. In contrast, the binding molecule eluted from the anti-TsF14-conjugated Sepharose suppressed the antibody response PC specifically. These results indicated that the p6-5 polypeptide is a component of the PC-TsF molecule.

Amino Acid Sequence↗
PubMed2006

GeneTrees: a phylogenomics resource for prokaryotes.

The GeneTrees phylogenomics system pursues comparative genomic analyses from the perspective of gene phylogenies for individual genes. The GeneTrees project has the goal of providing detailed evolutionary models for all protein-coding gene components of the fully sequenced genomes. Currently, a database of alignments and trees for all protein sequences for 325 fully sequenced and annotated prokaryote genomes is available. The prokaryote database contains 890,000 protein sequences organized into over 100,000 alignments, each described by a phylogenetic tree. An original homology group discovery tool assembles sets of related proteins from all versus all pairwise alignments. Multiple alignments for each homology group are stored and subjected to phylogenetic tree inference. A graphical web interface provides visual exploration of the GeneTrees database. Homology groups can be queried by sequence identifiers or annotation terms. Genomes can be browsed visually on a gene map of each chromosome or plasmid. Phylogenetic trees with support values are displayed in conjunction with the associated sequence alignment. A variety of classes of information can be selected to label the tree tips to aid in visual evaluation of annotation and gene function. This web interface is available at http://genetrees.vbi.vt.edu.

Bacterial Proteins↗
PubMed2002

The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator.

Mammalian circadian rhythms are generated by a feedback loop in which BMAL1 and CLOCK, players of the positive limb, activate transcription of the cryptochrome and period genes, components of the negative limb. Bmal1 and Per transcription cycles display nearly opposite phases and are thus governed by different mechanisms. Here, we identify the orphan nuclear receptor REV-ERBalpha as the major regulator of cyclic Bmal1 transcription. Circadian Rev-erbalpha expression is controlled by components of the general feedback loop. Thus, REV-ERBalpha constitutes a molecular link through which components of the negative limb drive antiphasic expression of components of the positive limb. While REV-ERBalpha influences the period length and affects the phase-shifting properties of the clock, it is not required for circadian rhythm generation.

ARNTL Transcription Factors↗
PubMed2005

The atypical resistance gene, RPW8, recruits components of basal defence for powdery mildew resistance in Arabidopsis.

Genetic studies have identified a number of components of signal transduction pathways leading to plant disease resistance and the accompanying hypersensitive response (HR) following detection of pathogens by plant resistance (R) genes. In Arabidopsis, the majority of R proteins so far characterized belong to a plant superfamily that have a central nucleotide-binding site and C-terminal leucine-rich-repeats (NB-LRRs). Another much less prevalent class comprises RPW8.1 and RPW8.2, two related proteins that possess a putative N-terminal transmembrane domain and a coiled-coil motif, and confer broad-spectrum resistance to powdery mildew. Here we investigated whether RPW8.1 and RPW8.2 engage known pathway(s) for defence signalling. We show that RPW8.1 and RPW8.2 recruit, in addition to salicylic acid and EDS1, the other NB-LRR gene-signalling components PAD4, EDS5, NPR1 and SGT1b for activation of powdery mildew resistance and HR. In contrast, NDR1, RAR1 and PBS3 that are required for function of certain NB-LRR R genes, and COI1 and EIN2 that operate, respectively, in the jasmonic acid and ethylene signalling pathways, do not contribute to RPW8.1 and RPW8.2-mediated resistance. We further demonstrate that EDR1, a gene encoding a conserved MAPKK kinase, exerts negative regulation on HR cell death and powdery mildew resistance by limiting the transcriptional amplification of RPW8.1 and RPW8.2. Our results suggest that RPW8.1 and RPW8.2 stimulate a conserved basal defence pathway that is negatively regulated by EDR1.

Arabidopsis↗
PubMed2003

The Bacillus cereus bceT enterotoxin sequence reappraised.

Bacillus cereus is a known opportunistic human pathogen belonging to the B. cereus group. Establishment of the pathogenesis most likely involves several gene products. One of these gene products, a single gene component named bceT, has been cloned and described from B. cereus B-4ac [Agata et al., Microbiology 141 (1995) 983-988]. However, our sequences of the bceT region from 16 B. cereus group strains showed inconsistency with the published bceT sequence. Only part of the bceT sequence had homology to our sequences. This initiated a more thorough investigation of the bceT sequence. Restriction site search and database searches intimated that the cloned bceT was created by an incidental joining of four DNA fragments during ligation. One of these fragments had 93% homology to an open reading frame (ORF 101) located within the pathogenic island of the Bacillus anthracis pXO1 virulence plasmid. We suggest that the reported enterotoxic activity of the original cloned bceT construct could be due to either the fusion gene or the fragment with homology to ORF 101 in pXO1.

Bacillus cereus↗
PubMed2002

An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology.

Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function. With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available for an increasing number of microorganisms. This has resulted in substantial research efforts in assigning function to all identified open reading frames - referred to as functional genomics. In both metabolic engineering and functional genomics there is a trend towards application of a macroscopic view on cell function, and this leads to an expanded role of the classical approach applied in microbial physiology. With the increased understanding of the molecular mechanisms it is envisaged that in the future it will be possible to describe the interaction between all the components in the system (the cell), also at the quantitative level, and this is the goal of systems biology. Clearly this will have a significant impact on microbial physiology as well as on metabolic engineering.

Aspergillus↗
PubMed1991

RNA polymerase activity may regulate transcription initiation and attenuation in the rplKAJLrpoBC operon in Escherichia coli.

The relationship between global RNA transcription capacity and transcript initiation, attenuation, and stability in the rplKAJLrpoBC operon of Escherichia coli has been examined. The rplKAJLrpoBC operon encodes in order the four large ribosome subunit proteins, L11, L1, L10, and L12, and the two large beta and beta' subunits of RNA polymerase. Operon transcripts are initiated at two promoters, PL11 and PL10. The L12-beta intergenic space contains a transcription attenuator which, during balanced growth, terminates about 80% of the transcripts exiting the L12 gene; the remaining transcripts read through into the beta and beta' encoding genes. The capacity for global transcription initiation was modulated using a strain carrying a temperature-sensitive, initiation-defective mutation in rpoC. Following a shift to 39 degrees C, the global transcription initiation capacity was reduced to about one-half the level at 30 degrees C. This partial restriction resulted in a decrease in the stability of distal beta mRNA, whereas the stability of proximal L11-L1 and L10-L12 mRNA was not changed. Measurements of the synthesis rates of L11-L1, L10-L12, and beta mRNAs relative to total RNA synthesis indicated that this operon was selectively transcribed when the initiation capacity of RNA polymerase was limited. The synthesis rates of L11-L1 and L10-L12 mRNA increased about 2-fold, whereas the synthesis rate of beta mRNA increased nearly 5-fold. The relative transcription of other ribosome component genes and the alpha subunit gene exhibited only a modest increase during the partial restriction. Protection from S1 nuclease was used to demonstrate that the preferential transcription within the operon of beta mRNA was the consequence of active regulation of termination-antitermination at the attenuator structure in the L12-beta intergenic space. These results demonstrate that global transcription capacity may be an important parameter in determining both initiation and attenuation of transcription of the rplKAJLrpoBC ribosomal protein-RNA polymerase operon.

Base Sequence↗
PubMed1987

Genome size variation in North American minnows (Cyprinidae). II. Variation among 20 species.

Genome sizes (nuclear DNA contents) from 200 individuals representing 20 species of North American cyprinid fishes (minnows) were examined spectrophotometrically. The distributions of DNA values of individuals within populations of the 20 species were essentially continuous and normal; the distribution of DNA values among species was continuous and overlapping. These observations suggest that changes in DNA quantity in cyprinids are small in amount, involve both gains and losses of DNA, and are cumulative and independent in effect. Significant heterogeneity in mean genome size occurs both between individuals within populations of species and among species. The former averages maximally around 6% of the cyprinid genome and is nearly the same as the amount of DNA theoretically needed for the entire cyprinid structural gene component. The majority of the DNA content variation among the 20 species is distributed above the level of individuals within populations. Comparisons of average genome size difference or distance between individuals drawn from different levels of taxonomic organization indicate that considerably greater divergence in genome size has occurred in the extremely speciose cyprinid genus Notropis as compared with other North American cyprinid genera. This may suggest that genome size change is concentrated in speciation episodes. Finally, no associations were found between interspecific variation in genome size and five life-history characters. This suggests that much of the variation in genome size within and among the 20 species may be phenotypically inconsequential.

Animals↗