scholarly journals Transcriptional Profiling of Methyltransferase Genes during Growth of Methanosarcina mazei on Trimethylamine

2009 ◽  
Vol 191 (16) ◽  
pp. 5108-5115 ◽  
Author(s):  
Christian Krätzer ◽  
Paul Carini ◽  
Raymond Hovey ◽  
Uwe Deppenmeier
Keyword(s):  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Exponential Growth Phase ◽  
Methane Formation ◽  
Rt Pcr ◽  
Transcript Levels ◽  
Methanosarcina Mazei ◽  
Depth Analysis ◽  
Genes Encoding

ABSTRACT The genomic expression patterns of Methanosarcina mazei growing with trimethylamine were measured in comparison to those of cells grown with methanol. We identified a total of 72 genes with either an increased level (49 genes) or a decreased level (23 genes) of mRNA during growth on trimethylamine with methanol-grown cells as the control. Major differences in transcript levels were observed for the mta, mtb, mtt, and mtm genes, which encode enzymes involved in methane formation from methanol and trimethylamine, respectively. Other differences in mRNA abundance were found for genes encoding enzymes involved in isopentenyl pyrophosphate synthesis and in the formation of aromatic amino acids, as well as a number of proteins with unknown functions. The results were verified by in-depth analysis of methyltransferase genes using specific primers for real-time quantitative reverse transcription-PCR (RT-PCR). The monitored transcript levels of genes encoding corrinoid proteins involved in methyl group transfer from methylated C1 compounds (mtaC, mtbC, mttC, and mtmC) indicated increased amounts of mRNA from the mtaBC1, mtaBC2, and mtaBC3 operons in methanol-grown cells, whereas mRNA of the mtb1-mtt1 operon was found in high concentrations during trimethylamine consumption. The genes of the mtb1-mtt1 operon encode methyltransferases that are responsible for sequential demethylation of trimethylamine. The analysis of product formation of trimethylamine-grown cells at different optical densities revealed that large amounts of dimethylamine and monomethylamine were excreted into the medium. The intermediate compounds were consumed only in the very late exponential growth phase. RT-PCR analysis of key genes involved in methanogenesis led to the conclusion that M. mazei is able to adapt to changing trimethylamine concentrations and the consumption of intermediate compounds. Hence, we assume that the organism possesses a regulatory network for optimal substrate utilization.

DFR and PAL gene transcription and their correlation with anthocyanin accumulation in Rhodomyrtus tomentosa (Aiton.) Hassk.

2018 ◽  
Vol 44 (3) ◽  
pp. 289-298
Author(s):  
Bao-Jun Zhu ◽  
Qian Wang ◽  
Jing-Hui Wang ◽  
Lin-Lin Gao ◽  
Jing-Wen Zhang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Pcr Analysis ◽  
Anthocyanin Synthesis ◽  
Anthocyanin Content ◽  
Transcript Levels ◽  
Color Development ◽  
Phenylalanine Ammonialyase ◽  
Maturity Period ◽  
Late Maturity ◽  
Rhodomyrtus Tomentosa

Abstract Objectives Rhodomyrtus tomentosa (Aiton.) Hassk. (R. tomentosa) is rich in nutrients and has multiple pharmacological applications. Anthocyanins confer color to the flowers and berries of R. tomentosa and provide protection against photodamage. The dihydroflavonol 4-reductase gene (DFR) and phenylalanine ammonialyase gene (PAL) are crucial for anthocyanin synthesis. Methods DFR and PAL transcript levels and anthocyanin content in the pigmented organs of R. tomentosa were investigated through qRT-PCR analysis and spectrophotometry, respectively. The glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was selected as the reference gene for the normalization of DFR and PAL transcript levels. Results Transcript levels of DFR and PAL were higher in organs with vigorous metabolism than those in senescent organs. DFR and PAL transcript levels were up-regulated during the initial and middle-maturity periods of fruit. These expression patterns are consistent with fruit color development. The highest transcript levels of PAL and DFR were observed during the middle-maturity period or the red-fruit period. Conclusion During the late maturity period of R. tomentosa fruit, the transcript levels of the two genes were down-regulated even though anthocyanins were continuously accumulated, which was different from the accumulation of anthocyanins in some late mature fruits.

scholarly journals microRNA and mRNA profiles in the amygdala are relevant to fear memory induced by physical or psychological stress

2019 ◽  
Vol 122 (3) ◽  
pp. 1002-1022 ◽  
Author(s):  
Yan Sun ◽  
Wei Lu ◽  
Kaixin Du ◽  
Jin-Hui Wang
Keyword(s):  
Psychological Stress ◽  
High Throughput Sequencing ◽  
Fear Memory ◽  
Physical Stress ◽  
Luciferase Reporter ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Genes Encoding ◽  
Reporter Assays ◽  
Molecular Profiles

Anxiety is presumably driven by fear memory. Molecular profiles in the amygdala of mice with fear memory induced by psychological and physical stresses remain to be elucidated. Fear memory in mice was induced by a paradigm of social defeat. Physical and psychological stresses (PPS) to an intruder were given by attacks from an aggressive resident. Psychological stress (PS) to an observer was given by the witnessing of aggressor attacks. Amygdala tissues from these mice showing fear memory and anxiety vs. tissues from control mice were harvested to analyze mRNA and microRNA profiles by high-throughput sequencing. In the amygdala of intruders and observers with fear memory, the genes encoding 5-HTR1b, 5-HTR2a, DAR2, AChRM3, and IP3R1 are upregulated, whereas genes encoding GPγ11, GPγ13, GPγT2, RasC3, and P450 are downregulated, indicating that these molecules are involved in fear memory induced by physical/psychological stresses. In the comparison of intruders with observers, the upregulation of genes encoding 5-HTR6, GPγ8, P2R7, NFκ2, CREB3/1, and Itgα9 as well as the downregulation of genes encoding DAR5, 5-HTR1a, and HSP1a are involved in fear memory induced by physical stress. The upregulation of genes encoding DAR1, 5-HTR5a and SSR2/3 as well as the downregulation of AdRα1, CREB3/1, GPγ13 and GPγ8 are involved in fear memory induced by psychological stress. Results obtained by sequencing mRNA and microRNA profiles are consistent with results of quantitative RT-PCR analysis and dual-luciferase reporter assays performed for validation. In conclusion, fear memories and anxiety induced by PPS vs. PS are caused by the imbalanced regulation of different synapses and signaling pathways in the amygdala. NEW & NOTEWORTHY The current study identifies the molecular mechanism underlying fear memory and anxiety induced by psychological stress vs. physical stress, in which the imbalanced expression of microRNA-regulated mRNAs relevant to dopaminergic, adrenergic, and serotonergic synapses in the amygdala plays an important role. This result reveals different molecular profiles for psychological and physical stresses.

scholarly journals Low Concentrations of Bile Salts Induce Stress Responses and Reduce Motility in Bacillus cereus ATCC 14570

2007 ◽  
Vol 189 (14) ◽  
pp. 5302-5313 ◽  
Author(s):  
Simen M. Kristoffersen ◽  
Solveig Ravnum ◽  
Nicolas J. Tourasse ◽  
Ole Andreas Økstad ◽  
Anne-Brit Kolstø ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Stress Responses ◽  
Bile Salts ◽  
Expression Patterns ◽  
Food Poisoning ◽  
Soft Agar ◽  
Exponential Growth Phase ◽  
Specific Response ◽  
Genes Encoding ◽  
General Response

ABSTRACT Tolerance to bile salts was investigated in forty Bacillus cereus strains, including 17 environmental isolates, 11 dairy isolates, 3 isolates from food poisoning outbreaks, and 9 other clinical isolates. Growth of all strains was observed at low bile salt concentrations, but no growth was observed on LB agar plates containing more than 0.005% bile salts. Preincubation of the B. cereus type strain, ATCC 14579, in low levels of bile salts did not increase tolerance levels. B. cereus ATCC 14579 was grown to mid-exponential growth phase and shifted to medium containing bile salts (0.005%). Global expression patterns were determined by hybridization of total cDNA to a 70-mer oligonucleotide microarray. A general stress response and a specific response to bile salts were observed. The general response was similar to that observed in cultures grown in the absence of bile salts but at a higher (twofold) cell density. Up-regulation of several putative multidrug exporters and transcriptional regulators and down-regulation of most motility genes were observed as part of the specific response. Motility experiments in soft agar showed that motility decreased following bile salts exposure, in accordance with the transcriptional data. Genes encoding putative virulence factors were either unaffected or down-regulated.

scholarly journals Differential Gene Expression in the Laccase Gene Family from Basidiomycete I-62 (CECT 20197)

1998 ◽  
Vol 64 (2) ◽  
pp. 771-774 ◽  
Author(s):  
Mariana Mansur ◽  
Teresa Suárez ◽  
Aldo E. González
Keyword(s):  
Expression Patterns ◽  
Veratryl Alcohol ◽  
Culture Conditions ◽  
Laccase Gene ◽  
Transcript Levels ◽  
The Third ◽  
Stages Of Growth ◽  
Genes Encoding ◽  
Differential Gene ◽  
Laccase Genes

ABSTRACT A family of genes encoding laccases has recently been described for the basidiomycete I-62 (CECT 20197). Transcript levels of geneslcc1, lcc2, and lcc3 were analyzed under four different culture conditions to study their expression patterns. Two of the laccase genes were clearly inducible by veratryl alcohol: the lcc1 gene is inducible in early stages of growth, and the lcc2 gene is also inducible but only when the organism reaches the stationary phase. Transcript levels for the third gene, lcc3, were uninduced by veratryl alcohol and repressed by glucose.

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.

scholarly journals Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Isaac M Chiu ◽  
Lee B Barrett ◽  
Erika K Williams ◽  
David E Strochlic ◽  
Seungkyu Lee ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Molecular Diversity ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Molecular Signatures ◽  
Qrt Pcr ◽  
Somatosensory Neurons ◽  
Overlapping Classes ◽  
Somatosensory Nervous System

The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation.

scholarly journals Identification of the gene for disaggregatase fromMethanosarcina mazei

Archaea ◽  
2008 ◽  
Vol 2 (3) ◽  
pp. 185-191 ◽  
Author(s):  
Naoki Osumi ◽  
Yoshihiro Kakehashi ◽  
Shiho Matsumoto ◽  
Kazunari Nagaoka ◽  
Junichi Sakai ◽  
...  
Keyword(s):  
Amino Acid ◽  
Single Cells ◽  
Pcr Analysis ◽  
Amino Acid Residues ◽  
Wall Function ◽  
Rt Pcr ◽  
Methanosarcina Mazei ◽  
C Terminus ◽  
First Time

The gene sequences encoding disaggregatase (Dag), the enzyme responsible for dispersion of cell aggregates ofMethanosarcina mazeito single cells, were determined for three strains ofM. mazei(S-6T, LYC and TMA). Thedaggenes of the three strains were 3234 bp in length and had almost the same sequences with 97% amino acid sequence identities. Dag was predicted to comprise 1077 amino acid residues and to have a molecular mass of 120 kDa containing three repeats of the DNRLRE domain in the C terminus, which is specific to the genusMethanosarcinaand may be responsible for structural organization and cell wall function. Recombinant Dag was overexpressed inEscherichia coliand preparations of the expressed protein exhibited enzymatic activity. The RT-PCR analysis showed thatdagwas transcribed to mRNA inM. mazeiLYC and indicated that the gene was expressed in vivo. This is the first time the gene involved in the morphological change ofMethanosarcinaspp. from aggregate to single cells has been identified.

Transcriptional Inactivation of p53, Bax, Bcl-2 and Mdm2 Correlates with Malignant Transformation of the Uterine Cervix

2005 ◽  
Vol 20 (1) ◽  
pp. 18-27 ◽  
Author(s):  
G. Soufla ◽  
S. Baritaki ◽  
S. Sifakis ◽  
A. Zafiropoulos ◽  
D.A. Spandidos
Keyword(s):  
Mrna Expression ◽  
Malignant Transformation ◽  
Uterine Cervix ◽  
Expression Patterns ◽  
Cellular Transformation ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Cervical Lesions ◽  
Transcript Levels ◽  
Mdm2 Mrna

Deregulation of the apoptotic machinery plays a major role in cell death, cellular transformation and cancer. p53, Bcl-2, Bcl-XL, Bax and Mdm2 mRNA expression patterns were evaluated in tissue samples with cervical intraepithelial neoplasia (CIN) and cervical cancer compared to those of normal cervical tissues, and correlated with the underlying cervical lesions. Transcript levels of the above genes were assessed by RT-PCR analysis in a total of 44 cervical specimens. p53, Bcl-2, Bax and Mdm2 transcript levels were significantly different in the normal, CIN and cancer specimen groups (p=0.003, p=0.009, p=0.040 and p=0.001, respectively). Specifically, p53, Bax and Bcl-2 exhibited substantially lower transcript levels in CIN lesions compared to controls, whereas Bax mRNA levels showed a significant decrease in cancer compared to normal specimens. Mdm2 mRNA expression was considerably lower in cancer than in CIN lesions or normal cervix. High-grade squamous intraepithelial lesions exhibited lower p53 and Bcl-2 mRNA levels than controls (p=0.002, p=0.016). Coexpression analysis revealed more correlations between the above apoptosis-related molecules in normal tissues compared to CIN or cancer specimens. p53 showed significant coexpression with Bax, Bcl-2 and Mdm2 (p=0.040, p=0.013 and p=0.015, respectively) in normal cervical specimens. Bax and Bcl-XL mRNA expression was negatively correlated. Mdm2 transcriptional levels correlated significantly with those of Bax, Bcl-XL and Bcl-2. Our findings show that p53, Bax, Bcl-2 and Mdm2 mRNA expression levels correlate with the malignant transformation of the uterine cervix. mRNA coexpression patterns of the members of the pro- and anti-apoptotic family examined in cervical carcinogenesis were found to be disrupted in CIN and cancer, as already demonstrated at the protein level.

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.

Quantitative RT-PCR analysis of multiple genes encoding putative metronidazole nitroreductases from Helicobacter pylori

2000 ◽  
Vol 15 (1) ◽  
pp. 31-36 ◽  
Author(s):  
Dong H Kwon ◽  
Michael S Osato ◽  
David Y Graham ◽  
Fouad A.K El-Zaatari
Keyword(s):  
Helicobacter Pylori ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Multiple Genes ◽  
Genes Encoding
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