scholarly journals The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the β-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria

Microbiology ◽  
2005 ◽  
Vol 151 (11) ◽  
pp. 3713-3722 ◽  
Author(s):  
Hiroshi Habe ◽  
Jin-Sung Chung ◽  
Ayako Ishida ◽  
Kano Kasuga ◽  
Kazuki Ide ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Tricarboxylic Acid Cycle ◽  
Bacterial Species ◽  
Linear Plasmid ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Rt Pcr ◽  
Gene Encoding ◽  
Positive Trait ◽  
Tricarboxylic Acid Cycle Intermediates

Terrabacter sp. strain DBF63 is capable of degrading fluorene (FN) to tricarboxylic acid cycle intermediates via phthalate and protocatechuate. Genes were identified for the protocatechuate branch of the β-ketoadipate pathway (pcaR, pcaHGBDCFIJ) by sequence analysis of a 70 kb DNA region of the FN-catabolic linear plasmid pDBF1. RT-PCR analysis of RNA from DBF63 cells grown with FN, dibenzofuran, and protocatechuate indicated that the pcaHGBDCFIJ operon was expressed during both FN and protocatechuate degradation in strain DBF63. The gene encoding β-ketoadipate enol-lactone hydrolase (pcaD) was not fused to the next gene, which encodes γ-carboxymuconolactone decarboxylase (pcaC), in strain DBF63, even though the presence of the pcaL gene (the fusion of pcaD and pcaC) within a pca gene cluster has been thought to be a Gram-positive trait. Quantitative RT-PCR analysis revealed that pcaD mRNA levels increased sharply in response to protocatechuate, and a biotransformation experiment with cis,cis-muconate using Escherichia coli carrying both catBC and pcaD indicated that PcaD exhibited β-ketoadipate enol-lactone hydrolase activity. The location of the pca gene cluster on the linear plasmid, and the insertion sequences around the pca gene cluster suggest that the ecologically important β-ketoadipate pathway genes, usually located chromosomally, may be spread widely among bacterial species via horizontal transfer or transposition events.

scholarly journals Cloning of Two Gene Clusters Involved in the Catabolism of 2,4-Dinitrophenol by Paraburkholderia sp. Strain KU-46 and Characterization of the Initial DnpAB Enzymes and a Two-Component Monooxygenase DnpC1C2

2019 ◽  
Author(s):  
Taisei Yamamoto ◽  
Yaxuan Liu ◽  
Nozomi Kohaya ◽  
Yoshie Hasegawa ◽  
Peter C.K. Lau ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Tricarboxylic Acid Cycle ◽  
Gene Clusters ◽  
Degradation Pathway ◽  
Pcr Analysis ◽  
Gram Negative Bacteria ◽  
Protein Database ◽  
Gene Encoding ◽  
Gram Negative ◽  
Two Component

AbstractBesides an industrial pollutant, 2,4-dinitrophenol (DNP) has been used illegally as a weight loss drug that had claimed human lives. Little is known about the metabolism of DNP, particularly among Gram-negative bacteria. In this study, two non-contiguous genetic loci of Paraburkholderia (formerly Burkholderia) sp. strain KU-46 genome were identified and four key initial genes (dnpA, dnpB, and dnpC1C2) were characterized to provide molecular and biochemical evidence for the degradation of DNP via the formation of 4-nitrophenol (NP), a pathway that is unique among DNP utilizing bacteria. Reverse transcription PCR analysis indicated that the dnpA gene encoding the initial hydride transferase (28 kDa), and the dnpB gene encoding a nitrite-eliminating enzyme (33 kDa), are inducible by DNP and the two genes are organized in an operon. Purified DnpA and DnpB from overexpression clones in Escherichia coli effected the transformation of DNP to NP via the formation of hydride-Meisenheimer complex of DNP. The function of DnpB appears new since all homologs of DnpB sequences in the protein database are annotated as putative nitrate ABC transporter substrate-binding proteins. The gene cluster responsible for the degradation of DNP after NP formation was designated dnpC1C2DXFER. DnpC1 and DnpC2 were functionally characterized as the respective FAD reductase and oxygenase components of the two-component NP monooxygenase. Both NP and 4-nitrocatechol were shown to be substrates, producing hydroquinone and hydroxyquinol, respectively. Elucidation of the hqdA1A2BCD gene cluster allows the delineation of the final degradation pathway of hydroquinone to ß-ketoadipate prior to its entry to the tricarboxylic acid cycle.ImportanceThis study fills a gap in our knowledge and understanding of the genetic basis and biochemical pathway for the degradation of 2,4-dinitrophenol (DNP) in Gram-negative bacteria, represented by the prototypical Paraburkholderia sp. strain KU-46 that metabolizes DNP through the formation of 4-nitrophenol, a pathway unseen by other DNP utilizers. The newly cloned genes could serve as DNA probes in biomonitoring as well as finding application in new biocatalyst development to access green chemicals. By and large, knowledge of the diverse strategies used by microorganisms to degrade DNP will contribute to the development of bioremediation solutions since DNP is an industrial pollutant used widely in the chemical industry for the synthesis of pesticides, insecticides, sulfur dyes, wood preservatives, and explosives, etc. (119 words)

scholarly journals Phenotypical and Functional Characteristics of Human Regulatory T Cells during Ex Vivo Maturation from CD4+ T Lymphocytes

2021 ◽  
Vol 11 (13) ◽  
pp. 5776
Author(s):  
Varvara G. Blinova ◽  
Natalia S. Novachly ◽  
Sofya N. Gippius ◽  
Abdullah Hilal ◽  
Yulia A. Gladilina ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Ex Vivo ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Rt Pcr ◽  
Inflammatory Reactions ◽  
Effector Cells ◽  
Cycle Regulation ◽  
Further Development

Regulatory T cells (Tregs) participate in the negative regulation of inflammatory reactions by suppressing effector cells. In a number of autoimmune disorders, the suppressive function and/or the number of Tregs is compromised. The lack of active functioning Tregs can be restored with adoptive transfer of expanded ex vivo autologous Tregs. In our study, we traced the differentiation and maturation of Tregs CD4+CD25+FoxP3+CD127low over 7 days of cultivation from initial CD4+ T cells under ex vivo conditions. The resulting ex vivo expanded cell population (eTregs) demonstrated the immune profile of Tregs with an increased capacity to suppress the proliferation of target effector cells. The expression of the FoxP3 gene was upregulated within the time of expansion and was associated with gradual demethylation in the promotor region of the T cell-specific demethylation region. Real-time RT-PCR analysis revealed changes in the expression profile of genes involved in cell cycle regulation. In addition to FOXP3, the cells displayed elevated mRNA levels of Ikaros zinc finger transcription factors and the main telomerase catalytic subunit hTERT. Alternative splicing of FoxP3, hTERT and IKZF family members was demonstrated to be involved in eTreg maturation. Our data indicate that expanded ex vivo eTregs develop a Treg-specific phenotype and functional suppressive activity. We suggest that eTregs are not just expanded but transformed cells with enhanced capacities of immune suppression. Our findings may influence further development of cell immunosuppressive therapy based on regulatory T cells.

Identification of a gene cluster for cell-surface genes of the SRS superfamily inNeospora caninumand characterization of the novelSRS9gene

Parasitology ◽  
2011 ◽  
Vol 138 (14) ◽  
pp. 1832-1842 ◽  
Author(s):  
V. RISCO-CASTILLO ◽  
V. MARUGÁN-HERNÁNDEZ ◽  
A. FERNÁNDEZ-GARCÍA ◽  
A. AGUADO-MARTÍNEZ ◽  
E. JIMÉNEZ-RUIZ ◽  
...  
Keyword(s):  
Western Blot ◽  
Gene Cluster ◽  
Neospora Caninum ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Specific Expression ◽  
Initial Characterization ◽  
Hydrophilic Region

SUMMARYHere we present the detection of a gene cluster forNeospora caninumsurface genes, similar to theToxoplasma gondiiSRS9 locus, and the cloning and characterization of the NcSRS9gene. PCR genome walking, using NcBSR4gene as a framework, allows the identification, upstream NcBSR4, of 2 sequences homologous to theSRS5and the Ubiquinol-cytochrome C reductase genes and, downstream NcBSR4, of an ORF of 1191 bp coding for a 396-amino acid polypeptide with 59% similarity to the TgSRS9 antigen. A putative 39-residue signal peptide was found at the NH2-terminus followed by a hydrophilic region, and a potential site for a glycosylphosphatidylinositol anchor at the COOH-terminus. A recombinant NcSRS9 protein was produced and was recognized on a Western blot by a low proportion of sera from a panel of naturally infected cows and calves. In addition, Western blot analysis using polyclonal anti-rNcSRS9 revealed stage-specific expression of NcSRS9 in bradyzoites but not in tachyzoites, and immunohistochemistry on brain from a congenitally infected calf showed NcSRS9 recognition in bradyzoites contained in tissue cysts. However, bradyzoite-specific expression of NcSRS9 could not be proven by immunofluorescence on bradyzoites obtainedin vitroand RT-PCR analysis showed no significant variations of NcSRS9transcripts duringin vitrotachyzoite-bradyzoite switch, probably due to incomplete maturity ofin vitrobradyzoites. Initial characterization of NcSRS9 in this study may lead to further studies for a better understanding ofN. caninumpersistence.

scholarly journals Expression and homologous regulation of GH secretagogue receptor mRNA in rat adrenal gland

2002 ◽  
pp. 677-688 ◽  
Author(s):  
ML Barreiro ◽  
L Pinilla ◽  
E Aguilar ◽  
M Tena-Sempere
Keyword(s):  
Biological Effects ◽  
Biologically Active ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
R Gene ◽  
Rt Pcr ◽  
Short Term ◽  
Opposite Pattern ◽  
Corticosterone Secretion

OBJECTIVE: GH secretagogues (GHSs) elicit a variety of biological effects in several endocrine and non-endocrine target tIssues, including activation of the hypothalamic-pituitary-adrenal axis. The latter is mainly carried out through a central hypothalamic action; yet the possibility of additional effects directly at the adrenal level cannot be ruled out. The aims of this study were to evaluate the expression and homologous regulation of the GHS-receptor (GHS-R) gene in rat adrenal and to assess the effects of synthetic (GH releasing peptide-6 - GHRP-6) and natural (ghrelin) ligands of GHS-R upon basal and ACTH-stimulated corticosterone secretion in vitro. DESIGN AND METHODS: Analysis of adrenal expression of target mRNAs (GHS-R, GHS-R1a, ghrelin, and several steroidogenic factors) was conducted by means of primer-specific, semi-quantitative RT-PCR. Evaluation of corticosterone secretion by incubated adrenal tIssue was carried out by specific RIA. RESULTS: RT-PCR analysis demonstrated expression of the GHS-R gene, but not of the gene encoding the cognate ligand ghrelin, in rat adrenal. Moreover, expression of the mRNA coding for the type 1a GHS-R (GHS-R1a), i.e. the biologically active receptor form, was demonstrated. The adrenal expression of the GHS-R message appeared under the regulation of homologous signals in vitro, as short-term incubation of adrenal samples in serum-free medium induced a significant increase in GHS-R mRNA levels that was inhibited by exposure to different doses of GHRP-6 (10(-9)-10(-5) mol/l) or ghrelin (10(-7) mol/l). Notably, an opposite pattern of homologous regulation of GHS-R gene expression was observed at the pituitary. Finally, short-term stimulation with increasing concentrations of GHRP-6 (10(-9)-10(-5) mol/l) or ghrelin (10(-7) mol/l) failed to alter basal and ACTH-stimulated corticosterone secretion in vitro, neither did it modify ACTH-stimulated mRNA expression levels of several upstream elements in the steroidogenic route: the steroidogenic acute regulatory (StAR) protein, and the enzymes P450 cholesterol side-chain cleavage (P450scc) and 3beta-hydroxysteroid dehydrogenase (3beta-HSD). CONCLUSIONS: Our study provides novel evidence for the expression and homologous regulation of the GHS-R gene in rat adrenal. However, our results cast doubts on the possibility of direct adrenal actions of ligands of the GHS-R in the regulation of corticosterone secretion in the rat.

scholarly journals Transcript Profiling Provides Insights into the Molecular Mechanisms of Harvesting-activated Latex Regeneration in Virgin Rubber Trees

2021 ◽  
Author(s):  
Yujie Fan ◽  
Xiaohu Xiao ◽  
Jianghua Yang ◽  
Jiyan Qi ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Rubber Tree ◽  
Transcript Profiling ◽  
Raw Material ◽  
Limiting Factors ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Rubber Biosynthesis ◽  
Latex Regeneration

Abstract Background: Natural rubber, an important industrial raw material with wide applications, is harvested in the form of latex (cytoplasm of rubber-producing laticifers) from Hevea brasiliensis (para rubber tree) by the way of tapping, i.e. removing a slice of trunk bark by a special knife. In regularly tapped rubber trees, latex regeneration consists of one of the main yield-limiting factors for rubber productivity. Conspicuous stimulation on latex production for the first few tappings makes virgin (untapped before) rubber trees an ideal model to investigate the regulatory mechanisms of latex regeneration. To understand the underlying mechanisms, genome-wide transcript profiling was conducted with a silver-staining cDNA-AFLP technology against the latex samples for the first five tappings.Results: A total of 505 non-redundant differentially expressed (DE) transcript-derived fragments (TDFs) were identified, of which 217 were up-regulated, 180 down-regulated, and 108 bell type-regulated among the five tappings. About 72.5% of these DE-TDFs were functionally annotated, and classified into 11 functional categories, which were discussed with reference to harvesting-stimulated latex regeneration. The importance of sugar metabolism and rubber biosynthesis was highlighted, due to the fact that most of the DE-TDFs annotated in sucrose transport, sugar catabolism, glycolysis, tricarboxylic acid cycle and pentose-phosphate pathway and nine of the ten rubber biosynthesis pathway DE-TDFs were up-regulated by the tapping treatment. More than one tenth of the total DE-TDFs were randomly selected for expression validation by semi-quantitative RT-PCR, and 83.8% showed patterns consistent with their original cDNA-AFLP gel profiles. Moreover, quantitative RT-PCR analysis revealed an 89.7% consistency for the 29 latex-regeneration related DE-TDFs examined.Conclusions: In brief, our results indicate the tapping treatment incurs extensive physiological and molecular changes in the laticifers of virgin rubber trees. The vast numbers of tapping-responsive DE-TDFs identified here provide a basis for unravelling the gene regulatory network for latex regeneration in regularly harvested rubber trees.

scholarly journals Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from Sphingomonas sp. strain A4

Microbiology ◽  
2006 ◽  
Vol 152 (8) ◽  
pp. 2455-2467 ◽  
Author(s):  
Atsushi Kouzuma ◽  
Onruthai Pinyakong ◽  
Hideaki Nojiri ◽  
Toshio Omori ◽  
Hisakazu Yamane ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Gene Disruption ◽  
Pcr Analysis ◽  
Nucleotide Sequence Analysis ◽  
Rt Pcr ◽  
Transcription Start ◽  
Ferredoxin Reductase ◽  
Genes Encoding ◽  
Dna Fragment ◽  
Putative Binding Site

Sphingomonas sp. strain A4 is capable of utilizing acenaphthene as its sole carbon and energy source. To isolate the genes responsible for acenaphthene degradation, transposon mutagenesis was performed on strain A4 and four mini-Tn5-inserted mutants lacking the ability to utilize acenaphthene were isolated. In three of the four mini-Tn5 inserted mutants, the mini-Tn5s were inserted into the same locus (within about 16 kb) as the arhA1A2 genes, which had previously been identified as the genes encoding the terminal oxygenase components for the initial oxygenation of acenaphthene. The nucleotide sequence analysis of the corresponding 16.4 kb DNA fragment revealed the existence of 16 ORFs and a partial ORF. From these ORFs, the genes encoding the ferredoxin (ArhA3) and ferredoxin reductase (ArhA4) complementary to ArhA1A2 were identified. RT-PCR analysis suggested that a 13.5 kb gene cluster, consisting of 13 ORFs and including all the arhA genes, forms an operon, although it includes several ORFs that are apparently unnecessary for acenaphthene degradation. Furthermore, using gene disruption and quantitative RT-PCR analyses, the LysR-type activator, ArhR, required for expression of the 13.5 kb gene cluster was also identified. Transcription of the gene cluster by ArhR was induced in the presence of acenaphthene (or its metabolite), and a putative binding site (T-N11-A motif) for ArhR was found upstream from the transcription start point of arhA3.

Molecular characterization and expression analysis of a gene encoding mannose-binding lectin from bulb of Zephyranthes grandiflora

Biologia ◽  
2006 ◽  
Vol 61 (6) ◽  
Author(s):  
Guoyin Kai ◽  
Yang Lu ◽  
Zhongying Qian ◽  
Yongting Luo ◽  
Genyu Zhou ◽  
...  
Keyword(s):  
Mannose Binding Lectin ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Gene Encoding ◽  
Acid Protein ◽  
Mannose Binding ◽  
Lectin Family ◽  
Binding Lectin ◽  
Amino Acid Protein ◽  
Chinese Medicinal Plant

AbstractIn this paper we report on the molecular cloning, sequencing and partially characterisation of a lectin from bulb of the Chinese medicinal plant Zephyranthes grandiflora. The full-length cDNA of Z. grandiflora bulb lectin (ZGBL) consisted of 986 bp and contained a 576 bp ORF encoding a 191 amino acid protein. Bioinformatics analysis results clearly indicate that ZGBL belongs to the monocot mannose-binding lectin family, which contains 3 putative mannose-binding sites per subunit. RT-PCR analysis results indicate that ZGBL is constitutively expressed in all the tested tissue types including root, bulb, leaf and flower. Interestingly, ZGBL is more closely related to the Orchidaceae rather than the Amaryllidaceae family on molecular evolution.

Upregulation of corin gene expression in hypertrophic cardiomyocytes and failing myocardium

2004 ◽  
Vol 287 (4) ◽  
pp. H1625-H1631 ◽  
Author(s):  
Katherine L. Tran ◽  
Xiangru Lu ◽  
Ming Lei ◽  
Qingping Feng ◽  
Qingyu Wu
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Mrna Expression ◽  
Rat Model ◽  
Left Ventricular ◽  
Biologically Active ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Rt Pcr ◽  
Neonatal Cardiomyocytes

High levels of plasma atrial natriuretic peptides (ANP) are associated with pathological conditions such as congestive heart failure (CHF). Recently, we have identified a cardiac serine protease, corin, that is the pro-ANP convertase. In this study, we examined the regulation of corin gene expression in cultured hypertrophic cardiomyocytes and in the left ventricular (LV) myocardium of a rat model of heart failure. Quantitative RT-PCR analysis showed that both corin and ANP mRNA levels were significantly increased in phenylephrine (PE)-stimulated rat neonatal cardiomyocytes in culture. The increase in corin mRNA correlated closely with the increase in cell size and ANP mRNA expression in the PE-treated cells ( r = 0.95, P < 0.01; r = 0.92, P < 0.01, respectively). The PE-treated cardiomyocytes had an increased activity in converting recombinant human pro-ANP to biologically active ANP, as determined by a pro-ANP processing assay and a cell-based cGMP assay. In a rat model of heart failure induced by ligation of the left coronary artery, corin mRNA expression in the noninfarcted LV myocardium was significantly higher than that of control heart tissues from sham-operated animals, when examined by Northern blot analysis and RT-PCR at 8 wk. These results indicate that the corin gene is upregulated in hypertrophic cardiomyocytes and failing myocardium. Increased corin expression may contribute to elevation of ANP in the setting of cardiac hypertrophy and heart failure.

scholarly journals β-Tubulin mRNA as a Marker ofCryptosporidium parvum Oocyst Viability

1999 ◽  
Vol 65 (4) ◽  
pp. 1584-1588 ◽  
Author(s):  
Giovanni Widmer ◽  
Elizabeth A. Orbacz ◽  
Saul Tzipori
Keyword(s):  
Pcr Analysis ◽  
Mrna Levels ◽  
Rt Pcr ◽  
Prolonged Incubation ◽  
Mrna Species ◽  
Viability Analysis ◽  
Viability Assay ◽  
Pcr Products ◽  
Tubulin Mrna ◽  
Β Tubulin

ABSTRACT Determining the viability of waterborne Cryptosporidium parvum oocysts remains a technical challenge. rRNA and mRNA were evaluated in a reverse transcription (RT)-PCR assay as potential markers of oocyst viability. The rationale for this approach is the rapid turnover and postmortem decay of cellular RNA. The β-tubulin mRNA and an anonymous mRNA transcript were chosen as potential markers because they are the only mRNA species in C. parvum known to possess introns. This feature facilitated the distinction between genuine RT-PCR products and PCR products originating from copurifying DNA. Prolonged incubation at room temperature of initially viable oocysts resulted in a gradual decrease in mRNA levels, which correlated with the loss of oocyst infectivity to neonatal mice. In contrast, oocysts stored at 4°C for over 39 weeks maintained their infectivity and displayed no decrease in the level of β-tubulin RT-PCR product. The postmortem decay of two mRNA species demonstrates that RT-PCR analysis can provide information on the viability of C. parvum oocysts. The methodological similarity between PCR detection and RT-PCR viability analysis could facilitate the development of a combined detection and viability assay.

scholarly journals Liver receptor homologue-1 is expressed in the adrenal and can regulate transcription of 11 beta-hydroxylase

2001 ◽  
Vol 27 (2) ◽  
pp. 255-258 ◽  
Author(s):  
ZN Wang ◽  
M Bassett ◽  
WE Rainey
Keyword(s):  
Adrenal Glands ◽  
Pcr Analysis ◽  
Orphan Nuclear Receptor ◽  
Rt Pcr ◽  
Hormone Production ◽  
Mobility Shift ◽  
Gene Encoding ◽  
Liver And Pancreas ◽  
Genes Encoding ◽  
Mobility Shift Assay

Liver receptor homologue-1 (LRH-1, designated NR5A2) is a mammalian homologue of Drosophila fushi tarazu factor (dFTZ-F1) and structurally belongs to the orphan nuclear receptor superfamily. LRH-1 can recognize the DNA sequence 5'-AAGGTCA-3', the canonical recognition motif for steroidogenic factor 1 (SF-1). Herein, we hypothesized that LRH-1 might play a role in the regulation of human adrenal expression of steroidogenic enzymes. To test this hypothesis, LRH-1 expression in human adult and fetal adrenal glands was examined by RT-PCR analysis. The fetal and adult adrenal glands, as well as liver and pancreas, were observed to express LRH-1 mRNA using RT-PCR. The ability of LRH-1 to enhance transcription of the gene encoding human 11 beta- hydroxylase (hCYP11B1) was then examined using the H295R adrenal cell line. LRH-1 co-transfection with hCYP11B1 luciferase promoter constructs caused a 25-fold induction of luciferase activity. Furthermore, co-transfection of a hCYP11B1 reporter construct containing a mutation in the SF-1 binding cis-element abolished the stimulatory effect of both SF-1 and LRH-1. Electrophoretic mobility shift assay (EMSA) demonstrated that LRH-1 could bind to the SF-1 response element. Taken together, our data suggested that LRH-1 is expressed in the adrenal, and can substitute for SF-1 to enhance transcription of genes encoding certain of the steroid-metabolizing enzymes. A role for LRH-1 in the regulation of adrenal or gonadal steroid hormone production should be further studied.

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