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At least 703 records · Page 39Linked to original sources
PubMed2006

Mycobacterium smegmatis whmD and its homologue Mycobacterium tuberculosis whiB2 are functionally equivalent.

Mycobacterium smegmatis whmD is is an essential gene involved in cell division. This paper shows that whmD and its homologue whiB2 in Mycobacterium tuberculosis are functionally equivalent. The genes are syntenous, and share significant homology in both their coding and non-coding DNA sequences. Transcription site mapping showed that the two genes possess near-identical promoter elements, and they displayed comparable promoter strengths in a reporter gene assay. The two proteins show near identity in their C-terminus, and polyclonal antiserum to WhmD specifically cross-reacts with a approximately 15 kDa band in M. tuberculosis lysates. Following overexpression of sense and anti-sense constructs in their cognate mycobacterial hosts, whiB2 and whmD transformants displayed a small-colony phenotype, exhibited filamentation, and showed a reduction in viability. These observations reveal that the two proteins are functionally homologous and that their intracellular concentration is critical for septation in mycobacteria. Colonies of M. tuberculosis overexpressing whiB2 were spherical and glossy, suggesting a change in composition of the cell envelope. Filaments of the conditionally complemented M. smegmatis whmD mutant were non-acid-fast, also indicating changes in characteristics of surface lipids. M. smegmatis transformants carrying a whmD-gfp fusion showed a diffuse pattern of fluorescence, consistent with the putative role of WhmD as a regulator. These observations strongly suggest that M. tuberculosis whiB2 is an essential gene and its protein product in all likelihood regulates the expression of genes involved in the cell division cascade.

Bacterial Proteins↗
PubMed2001

A-6G variant of the angiotensinogen gene and essential hypertension in Han, Tibetan, and Yi populations.

To investigate the relationship between the A-6G variant in the promoter of the angiotensinogen gene and essential hypertension in Han, Tibetan, and Yi populations. All patients with essential hypertension were selected by WHO criteria. And the polymorphism of the A-6G variant was determined by PCR/RFLP. The data were analyzed by t test and chi2 test. There was no significant difference in the genotype or allele frequencies between normotensives and hypertensives in the Han, Tibetan, and Yi populations, respectively. However, when the subjects were divided into male and female subgroups, the genotype distributions among hypertensives and normotensives of the Tibetan female group were as follows: AA, 37% vs. 48%; AG, 52% vs. 48%; GG, 11% vs. 4%, respectively and the frequency of the G allele was significantly higher in hypertensives than in normotensives in the Tibetan female group (0.37 vs. 0.28, chi2=4.25, p<0.05). In addition, we observed that there was a significant difference between the Han and Tibetan normotensive groups in the distributions of the allele and genotype frequencies of the A-6G variant. The frequency of the G allele was 0.29 and 0.17 in the Tibetan normotensive and Han groups, respectively (p<0.001). The G allele of the A-6G variant was associated with hypertension in the Tibetan females, but not in the Yi or Han females. And we confirmed that there was a significant difference in the prevalence of the allele frequencies of the A-6G variant between the Han and Tibetan normotensive groups.

Adult↗
PubMed2003

The Hansenula polymorpha PDD7 gene is essential for macropexophagy and microautophagy.

Hansenula polymorpha PDD genes are involved in the selective degradation of peroxisomes via macropexophagy. We have isolated various novel pdd mutants by a gene-tagging method. Here we describe the isolation and characterisation of PDD7, which encodes a protein with high sequence similarity (40% identity) to Saccharomyces cerevisiae Apg1p/Aut3p, previously described to be involved in random autophagy and the cytoplasm-to-vacuole targeting pathway. Our data indicate that HpPdd7p is essential for two processes that degrade peroxisomes, namely the highly selective process of macropexophagy and microautophagy, which occurs in H. polymorpha upon nitrogen starvation.

Amino Acid Sequence↗
PubMed1991

A genetic mosaic screen of essential zygotic genes in Caenorhabditis elegans.

We have devised a simple genetic mosaic screen, which circumvents the difficulties posed by phenotypic analysis of early lethal mutants, to analyze essential zygotic genes in Caenorhabditis elegans. The screen attempts to distinguish genes involved in cell type and/or lineage specific processes such as determination, differentiation or morphogenesis from genes involved in general processes such as intermediary metabolism by using the pattern of gene function to classify genes: genes required in one or a subset of early blastomeres may have specific functions, whereas genes required in all early blastomeres may have general functions. We found that 12 of 17 genes examined function in specific early blastomeres, suggesting that many zygotic genes contribute to specific early processes. We discuss the advantages and limitations of this screen, which is applicable to other regions of the C. elegans genome.

Alleles↗
PubMed2004

The essential nature of the ubiquitous 26-kilobase circular replicon of Borrelia burgdorferi.

The genome of the type strain (B31) of Borrelia burgdorferi, the causative agent of Lyme disease, is composed of 12 linear and 9 circular plasmids and a linear chromosome. Plasmid content can vary among strains, but one 26-kb circular plasmid (cp26) is always present. The ubiquitous nature of cp26 suggests that it provides functions required for bacterial viability. We tested this hypothesis by attempting to selectively displace cp26 with an incompatible but replication-proficient vector, pBSV26. While pBSV26 transformants contained this incompatible vector, the vector coexisted with cp26, which is consistent with the hypothesis that cp26 carries essential genes. Several cp26 genes with ascribed or predicted functions may be essential. These include the BBB29 gene, which has sequence homology to a gene encoding a glucose-specific phosphotransferase system component, and the resT gene, which encodes a telomere resolvase involved in resolution of the replicated telomeres of the linear chromosome and plasmids. The BBB29 gene was successfully inactivated by allelic exchange, but attempted inactivation of resT resulted in merodiploid transformants, suggesting that resT is required for B. burgdorferi growth. To determine if resT is the only cp26 gene essential for growth, we introduced resT into B. burgdorferi on pBSV26. This did not result in displacement of cp26, suggesting that additional cp26 genes encode vital functions. We concluded that B. burgdorferi plasmid cp26 encodes functions critical for survival and thus shares some features with the chromosome.

Borrelia burgdorferi↗
PubMed1994

Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior.

In a search for genes that regulate circadian rhythms in mammals, the progeny of mice treated with N-ethyl-N-nitrosourea (ENU) were screened for circadian clock mutations. A semidominant mutation, Clock, that lengthens circadian period and abolishes persistence of rhythmicity was identified. Clock segregated as a single gene that mapped to the midportion of mouse chromosome 5, a region syntenic to human chromosome 4. The power of ENU mutagenesis combined with the ability to clone murine genes by map position provides a generally applicable approach to study complex behavior in mammals.

Animals↗
PubMed2000

The rel gene is essential for in vitro growth of Staphylococcus aureus.

The stringent response in Staphylococcus aureus is mediated by the nucleotide guanosine pentaphosphate, whose synthesis is catalyzed by the product of the rel gene. We report here that the rel gene is essential for the in vitro growth of S. aureus, distinguishing it from all other bacteria tested for this requirement.

Genes, Bacterial↗
PubMed1997

[Genetic analysis of responsible genes for essential hypertension].

Recent progress in positional cloning strategy has facilitated analysis of genes responsible for multifactorial diseases such as essential hypertension. To overcome heterogeneous characteristics in essential hypertension, several methods have been developed. Among these, linkage analysis using genetic rat models of hypertension is one of the most promising strategies. We performed linkage analysis using the most commonly used hypertensive model rat, the spontaneously hypertensive rat, finding 3 genomic regions on chromosomes 1, 3 and 10 containing the genes with putative responsibility for hypertension. Since a candidate SA gene was known to be located on chromosome 1, we evaluated this genetic locus in human essential hypertension. Unfortunately, the result did not support the major effects of the SA locus in human essential hypertension. However, with this strategy, we can expect that major genes responsible for hypertension will be identified in the near future.

Animals↗
PubMed2000

Gene disruption and basic phenotypic analysis of nine novel yeast genes from chromosome XIV.

In this work, we describe the disruption of nine ORFs of S. cerevisiae (YNL123w, YNL119w, YNL115c, YNL108c, YNL110c, YNL124w, YNL233w, YNL232w and YNL231c) in two genetic backgrounds: FY1679 and CEN.PK2. For the construction of the deletant strains, we used the strategy of short flanking homology (SFH) PCR. The SFH-deletion cassette was made by PCR amplification of the KanMX4 module with primers containing a 5' region of 40 bases homologous to the target yeast gene and with a 3' region of 20 bases homologous to pFA6a-KanMX4 MCS. Sporulation and tetrad analysis of heterozygous deletants revealed that YNL110c, YNL124w and YNL232w are essential genes. The subcellular localization of the protein encoded by the essential gene YNL110c was investigated using the green fluorescent protein (GFP) approach, revealing a nuclear pattern. Basic phenotypic analysis of the non-essential genes revealed that the growth of ynl119w delta haploid cells was severely affected at 37 degrees C in N3 medium, indicating that this gene is required at high temperatures with glycerol as a non-fermentable substrate. The ynl233w delta haploid cells also showed a particular phenotype under light microscopy and were studied in detail in a separate work.

Chromosomes, Fungal↗
PubMed1996

[Restriction fragment length polymorphism of human renin gene in essential hypertension].

Essential hypertension is a heterogenous multifactorial disease resulting from an interaction between genetic and environmental factors. Nature of genes responsible for the blood pressure regulation is not completely understood. Data from molecular biology studies with animals indicate that renin gene is involved in the pathogenesis of hypertension. Renin gene is one of the major candidate genes contributing to the pathogenesis of essential hypertension in humans. The aim of this study was the assessment of the association of RFLPs of human renin gene with essential hypertension in Polish population and search for the genetic marker of susceptibility to the disease. MspI, HindIII and EcoT141 RFLP in human renin gene locus were studied and polymorphic allele and genotype frequencies in the population of 74 hypertensive and 60 normotensive subjects were compared. MspI and HindIII RFLP analysis has not shown any statistically significant differences in allele and genotype frequencies between hypertensives and normotensives. These RFLPs do not seem to be in association with essential hypertension in studied population. EcoT141 RFLP analysis has not shown statistically significant differences in polymorphic alleles frequencies between examined groups. However, the observed difference between genotype E2O frequencies in hypertensives (0.31) and normotensives (0.12) was statistically significant (p < 0.045). A clinical importance of this finding is not known but genotype E2O seems to be a potential marker of susceptibility to essential hypertension. Further investigations in larger group of patients are required.

Gene Frequency↗
PubMed1988

A family of versatile centromeric vectors designed for use in the sectoring-shuffle mutagenesis assay in Saccharomyces cerevisiae.

A simple assay called the sectoring shuffle was developed to monitor the mutational state of essential genes cloned into yeast centromeric plasmids. The essence of this assay is the creation of a conditional phenotype, colony color sectoring, for an essential gene in the absence of conditional thermosensitive or cold-sensitive alleles of that gene. This allows the quick determination of the mutational state of a cloned essential gene by observing its effect on the sectoring phenotype of the tester strain. During the course of this work we developed a family of 20 Escherichia coli-yeast shuttle vectors, pUN plasmids, containing ARS1 CEN4 and a variety of selectable markers as well as the SUP11 gene which can act as a color marker in the proper background. These vectors are compact and have been very useful for the sectoring-shuffle assay and for gene analysis in general. This paper describes these vectors, the sectoring shuffle and several applications of sectoring phenotypes.

Centromere↗
PubMed2006

In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori.

Availability of genome sequences of pathogens has provided a tremendous amount of information that can be useful in drug target and vaccine target identification. One of the recently adopted strategies is based on a subtractive genomics approach, in which the subtraction dataset between the host and pathogen genome provides information for a set of genes that are likely to be essential to the pathogen but absent in the host. This approach has been used successfully in recent times to identify essential genes in Pseudomonas aeruginosa. We have used the same methodology to analyse the whole genome sequence of the human gastric pathogen Helicobacter pylori. Our analysis revealed that out of the 1590 coding sequences of the pathogen, 40 represent essential genes that have no human homolog. We have further analysed these 40 genes by the protein sequence databases to list some 10 genes whose products are possibly exposed on the pathogen surface. This preliminary work reported here identifies a small subset of the Helicobacter proteome that might be investigated further for identifying potential drug and vaccine targets in this pathogen.

Anti-Bacterial Agents↗
PubMed2026

CREAT: A CRISPR-Based Genome Trimming Strategy for Systematic Identification of Dispensable Regions and Rapid Genome Reduction.

The construction of minimal-genome microbes offers an ideal platform for understanding fundamental biological processes and synthetic biology, yet the research is hindered by incomplete lists of essential genes in microbes and by multiple rounds of genome trimming with a trial-and-error nature. To address this, we introduce CREAT (CRISPR-based genome trimming with a multi-homology-arm template)-a streamlined approach that integrates CRISPR-targeted genome cleavage and homology arm walking to classify essential from non-essential genomic subregions, thus providing the basis for predicting essential genes in a given organism. These essential genes were then assembled into synthetic gene cassettes for one-step replacement of the targeted non-deletable genomic regions for further genome trimming. Eight consecutive rounds of CREAT genome trimming achieved a 20.8% reduction in genome size in Saccharolobus islandicus. Furthermore, Cas9-based CREAT genome trimming was developed for Bacillus subtilis and Escherichia coli, with efficiency greatly enhanced by the &#x3bb;-Red recombinase in the latter. Together, this iterative application of CREAT provides a scalable and generally applicable strategy for rapidly constructing minimal genomes across diverse microorganisms.

CRISPR-Cas Systems↗
PubMed2003

A simple Cre-loxP method for chromosomal N-terminal tagging of essential and non-essential Schizosaccharomyces pombe genes.

To facilitate the N-terminal tagging of essential genes at their genomic locus and under control of their own promoters we have developed a series of novel polymerase chain reaction templates. Initially, a 1.8 kb DNA fragment is integrated upstream of the ATG of the gene of interest. This fragment encodes the tag, a loxP site, a selectable marker, an exogenous nmt1 promoter and a second loxP site. In a single homologous integration event, the gene of interest is placed under control of the thiamine regulated nmt1 promoter, allowing identification of potential integrants on the basis of phenotype. Subsequently, this integrant strain is transformed with a plasmid expressing the Cre recombinase. This results in excision of the marker and nmt1 promoter and leaves sequences encoding an in-frame tag at the N-terminus of the gene of interest under the control of its native promoter. We have created TAP-cdc22, TAP-suc22 and TAP-rad50 strains using this N-tagging system, and developed a range of vectors for introducing TAP-, (His)10HA-, (His)6Myc- and EGFP.

Amino Acid Sequence↗
PubMed1993

The yeast SSS1 gene is essential for secretory protein translocation and encodes a conserved protein of the endoplasmic reticulum.

The SEC61, SEC62 and SEC63 yeast gene products are membrane components of the apparatus that catalyses protein translocation into the endoplasmic reticulum (ER). In the hope of uncovering additional components of the translocation apparatus, we sought yeast genes whose overexpression would restore partial thermoresistance in a sec61 translocation-deficient mutant. The first extragenic Sec sixty-one suppressor, SSS1, is an essential single copy gene whose overexpression restores translocation in the sec61 mutant. Another extragenic suppressor was identified as TDH3, which encodes the major isozyme of the most abundant yeast protein, glyceraldehyde-3-phosphate dehydrogenase. TDH3 overexpression could exert an indirect effect by competitively inhibiting protein synthesis, thereby allowing the impaired translocation apparatus to cope with a reduced flow of newly synthesized secretory proteins. Depletion of the Sss1 protein rapidly results in accumulation of multiple secretory or membrane proteins devoid of post-translational modifications; the normally secreted alpha-factor accumulates on the cytosolic side of ER membranes. Thus, the SSS1 gene is required for continued translocation of secretory preproteins beyond their early association to ER membranes. Consistent with its essential role in protein translocation, the Sss1 protein localizes to the ER and homologues were detected in higher eukaryotes.

Amino Acid Sequence↗
PubMed2002

[The relationship between haplotypes of angiotensinogen gene and essential hypertension].

OBJECTIVE: To investigate the relationship between the polymorphism of angiotensinogen gene (AGT) and the risk for hypertension in a Chinese population. METHODS: Three polymorphisms of AGT gene were analyzed in 335 patients with documented essential hypertension and 196 control subjects by using PCR-restriction fragment length polymorphism. Expectation maximization(EM) algorithm was then used for pairwise linkage disequilibrium test and haplotype analysis of AGT polymorphisms. RESULTS: Linkage disequilibrium between M235T and A-20C, between M235T and A-6G, between A-20C and A-6G was observed (P<10(-4)). The case-control analysis revealed that the frequency of T235 is significantly higher in essential hypertension patients than in control subjects. But all haplotype frequencies showed no significant difference between the patient and control groups. CONCLUSION: No association was noted between the haplotypes of AGT gene and hypertension in tested people, but T235 allele might play an important role in increased risk for essential hypertension.

Alleles↗
PubMed1993

Intronic and 5' flanking sequences of the Drosophila beta 3 tubulin gene are essential to confer ecdysone responsiveness.

The expression of the beta 3 tubulin gene is regulated, at the transcriptional level, by the steroid hormone ecdysone, in Drosophila Kc cells. Using a transient expression assay, we show that 360 bp from the first intron of the beta 3 tubulin gene, associated with the 5' flanking sequences, are essential to confer ecdysone inducibility on a minimum promoter driving the chloramphenicol acetyl transferase (CAT) gene. The 5' flanking region contains ecdysone-independent cis-positive elements located in proximity to the promoter. Deletion analysis of the 360 bp intronic region reveals that a fragment of 57 bp is crucial for the ecdysone response of the beta 3 tubulin gene. This fragment contains 5'-TGA(A/C)C-3' motifs homologous to ecdysone responsive elements (EcRE) half sites. Band shift assays show that this 57-bp fragment is bound by three specific complexes. One of them appears to be involved in the level of the ecdysone response.

Animals↗
PubMed1999

Med8, a subunit of the mediator CTD complex of RNA polymerase II, directly binds to regulatory elements of SUC2 and HXK2 genes.

In a search to identify new factors required for expression of SUC2 gene in Saccharomyces cerevisiae, we have partially purified a 27 kDa protein (p27) that bound both the DRSs of the HXK2 gene and the UASs of SUC2 gene. The amino terminal sequence of p27 identified the MED8 gene (open reading frame YBR193C), located in chromosome II of S. cerevisiae, as the gene coding for the protein. Disruption of this gene has demonstrated that is an essential gene for yeast growth. To determine whether the p27 protein represents the Med8 product, we expressed MED8 gene in E. coli and demonstrated that the heterologous synthesized protein specifically binds to both UASSUC2 and DRS2HXK2. This observation suggests that Med8 may be important for the coupling of the glucose repression pathway of SUC2 gene to the HXK2 gene expression. Med8 has been described as a mediator protein interacting with the CTD of the RNA polymerase II. Thus, the role of Med8 could be to act as coupling factor by linking activating and repressing transcription complexes to the RNA polymerase II holoenzyme transcriptional machinery.

Chromosome Mapping↗