scholarly journals Transcription Profiling of Cyclic AMP Signaling inCandida albicans

2004 ◽  
Vol 15 (10) ◽  
pp. 4490-4499 ◽  
Author(s):  
Doreen Harcus ◽  
André Nantel ◽  
Anne Marcil ◽  
Tracey Rigby ◽  
Malcolm Whiteway
Keyword(s):  
Gene Expression ◽  
Adenylyl Cyclase ◽  
Regulation Of Gene Expression ◽  
Ribosomal Subunit ◽  
Primary Role ◽  
Cellular Regulation ◽  
Transcription Profiling ◽  
Downstream Effector ◽  
Genes Encoding ◽  
Modulation Of Gene Expression

We used transcription profiling in Candida albicans to investigate cellular regulation involving cAMP. We found that many genes require the adenylyl cyclase Cdc35p for proper expression. These include genes encoding ribosomal subunit proteins and RNA polymerase subunit proteins, suggesting that growth could be controlled in part by cAMP-mediated modulation of gene expression. Other genes influenced by loss of adenylyl cyclase are involved in metabolism, the cell wall, and stress response and include a group of genes of unknown function that are unique to C. albicans. The profiles generated by loss of the adenylyl cyclase regulator Ras1p and a downstream effector Efg1p were also examined. The loss of Ras1p function disturbs the expression of a subset of the genes regulated by adenylyl cyclase, suggesting both that the primary role of Ras1p in transcriptional regulation involves its influence on the function of Cdc35p and that there are Ras1p independent roles for Cdc35p. The transcription factor Efg1p is also needed for the expression of many genes; however, these genes are distinct from those modulated by Cdc35p with the exception of a class of hyphal-specific genes. Therefore transcription profiling establishes that cAMP plays a key role in the overall regulation of gene expression in C. albicans, and enhances our detailed understanding of the circuitry controlling this regulation.

scholarly journals ARID2 Chromatin Remodeler in Hepatocellular Carcinoma

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2152
Author(s):  
Robin Loesch ◽  
Linda Chenane ◽  
Sabine Colnot
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Associated Factors ◽  
Regulation Of Gene Expression ◽  
Specific Gene ◽  
Chromatin Remodeler ◽  
Chromatin Remodelers ◽  
Genes Encoding ◽  
Gene Alterations

Chromatin remodelers are found highly mutated in cancer including hepatocellular carcinoma. These mutations frequently occur in ARID (AT-rich Interactive Domain) genes, encoding subunits of the ATP-dependent SWI/SNF remodelers. The increasingly prevalent complexity that surrounds the functions and specificities of the highly modular BAF (BG1/BRM-associated factors) and PBAF (polybromo-associated BAF) complexes, including ARID1A/B or ARID2, is baffling. The involvement of the SWI/SNF complexes in diverse tissues and processes, and especially in the regulation of gene expression, multiplies the specific outcomes of specific gene alterations. A better understanding of the molecular consequences of specific mutations impairing chromatin remodelers is needed. In this review, we summarize what we know about the tumor-modulating properties of ARID2 in hepatocellular carcinoma.

Regulation of type II adenylyl cyclase mRNA in rabbit skeletal muscle by chronic motor nerve pacing

1996 ◽  
Vol 271 (2) ◽  
pp. E253-E260 ◽  
Author(s):  
C. E. Torgan ◽  
W. E. Kraus
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Protein Kinase ◽  
Adenylyl Cyclase ◽  
Regulation Of Gene Expression ◽  
Rabbit Skeletal Muscle ◽  
Type Ii ◽  
Wide Range ◽  
Electrical Pacing ◽  
Fast Twitch

Skeletal muscle exhibits a wide range in functional phenotype in response to changes in physiological demands. We have observed that, in response to changes in work patterns, alterations in gene expression of some proteins coincide with changes in adenylyl cyclase (AC) activity [Kraus, W.E., J.P. Longabaugh, and S. B. Liggett. Am. J. Physiol 263 (Endocrinol. Metab. 26): E266-E230, 1992]. We now examine AC isoform transcript prevalence in various rabbit skeletal muscles and in response to changing work demands. Using reverse transcriptase-polymerase chain reaction, we detected type II AC isoform transcripts in rabbit skeletal muscle. Ribonuclease protection analyses revealed that expression of the type II isoform significantly correlated with the percentage of fast-twitch type IIb/IId fibers (r2 = 0.765, P < 0.01). When a fast-twitch muscle was converted to a slow-twitch muscle via chronic electrical pacing, expression of type II AC mRNA significantly decreased. This response occurred 3 days after the onset of stimulation (78% decrease) and was still present after 21 days of stimulation (76% decrease). As type II AC is relatively insensitive to calcium regulation while sensitive to protein kinase C (PKC) signaling, these data provide further impetus for investigations of protein kinase A and PKC cross-talk signaling mechanisms in the regulation of gene expression.

Effect of hypothyroidism on adenylyl cyclase activity and subtype gene expression in brown adipose tissue

1997 ◽  
Vol 273 (2) ◽  
pp. R762-R767 ◽  
Author(s):  
A. Chaudhry ◽  
J. G. Granneman
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Brown Adipose Tissue ◽  
Adenylyl Cyclase ◽  
Regulation Of Gene Expression ◽  
Mrna Levels ◽  
Adrenergic Stimulation ◽  
Functional Responses ◽  
Synergistic Interactions ◽  
Brown Adipose

Brown adipose tissue (BAT) expresses several adenylyl cyclase (AC) subtypes, and adrenergic stimulation selectively upregulates AC-III gene expression. Previous studies have described synergistic interactions between the sympathetic nervous system (SNS) and 3,5,3'-triiodothyronine (T3) on the regulation of gene expression in BAT. Because adrenergic stimulation also increases the activity of BAT type II thyroxine 5'-deiodinase (DII) and local T3 generation is important for many functional responses in BAT, we examined the effects of thyroid hormone status on the expression of various AC subtypes. Hypothyroidism selectively increased AC-III mRNA levels in BAT but not in white adipose tissue. Of the other subtypes examined, hypothyroidism did not alter AC-VI mRNA levels and slightly reduced AC-IX mRNA levels in BAT. The increase in AC-III expression was paralleled by an increase in forskolin-stimulated AC activity in BAT membranes. Sympathetic denervation of BAT abolished the increase in both AC activity and AC-III mRNA expression produced by hypothyroidism, but did not affect the expression of other subtypes. Surgical denervation also prevented the induction of AC-III in the cold-stressed euthyroid rat, but injections of T3 failed to alter AC-III expression in intact or denervated BAT. Our results indicate that T3 does not directly affect expression of AC-III. Rather, hypothyroidism increases BAT AC-III expression indirectly via an increase in sympathetic stimulation. Furthermore, our results strongly indicate that the increase in AC activity in hypothyroid BAT is due to increased expression of AC-III.

scholarly journals Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1545-1563 ◽  
Author(s):  
Ramona Lütkenhaus ◽  
Stefanie Traeger ◽  
Jan Breuer ◽  
Laia Carreté ◽  
Alan Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Comparative Transcriptomics ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development ◽  
Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

Manganese transport and its regulation in bacteria

2002 ◽  
Vol 30 (4) ◽  
pp. 768-771 ◽  
Author(s):  
M. Bhattacharyya-Pakrasi ◽  
H. B. Pakrasi ◽  
T. Ogawa ◽  
R. Aurora
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Structural Analysis ◽  
Calcium Ions ◽  
Regulation Of Gene Expression ◽  
Zinc Transport ◽  
Synechocystis 6803 ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Manganese Transport

Regulation of manganese acquisition by bacteria occurs by both biochemical regulation of the activity of the transporters and transcriptional regulation of gene expression. Structural analysis suggests that calcium ions may regulate the function of an Mn ATP-binding cassette (ABC)-permease in Synechocystis 6803, a cyanobacterium, as well as in a number of other bacteria. The expression of genes encoding the manganese transporter in Synechocystis 6803 is regulated by a twocomponent signal-transduction mechanism that has not been previously observed for manganese and zinc transport in bacteria.

scholarly journals Regulation by the Modulation of Gene Expression Variability

2015 ◽  
Vol 197 (12) ◽  
pp. 1974-1975 ◽  
Author(s):  
David Dubnau
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Content Type ◽  
Expression Variability ◽  
Link Type ◽  
Article Type ◽  
Modulation Of Gene Expression ◽  
The Mean ◽  
Cell Changes ◽  
Expression Variance

Classically, transcription is regulated so that the average expression per cell changes, often with a distribution that extends across the population. Roggiani and Goulian (M. Roggiani and M. Goulian, J. Bacteriol. 197:1976–1987, 2015, doi:http://dx.doi.org/10.1128/JB.00074-15) have shown that this is what happens when thetorCADoperon ofEscherichia coliis induced anaerobically by the addition of trimethylamine-N-oxide (TMAO). However, when the same inducer is added to aerobically growing cells, only a subset of the cells respond, although the mean expression per cell is similar to that obtained anaerobically. Thus, in the presence of oxygen, the variance but not the expression mean is altered. The regulation of gene expression variance appears to be due to noise in the phosphorelay that governstorCADtranscription.

scholarly journals Iron and Fur Regulation in Vibrio cholerae and the Role of Fur in Virulence

2005 ◽  
Vol 73 (12) ◽  
pp. 8167-8178 ◽  
Author(s):  
Alexandra R. Mey ◽  
Elizabeth E. Wyckoff ◽  
Vanamala Kanukurthy ◽  
Carolyn R. Fisher ◽  
Shelley M. Payne
Keyword(s):  
Gene Expression ◽  
Vibrio Cholerae ◽  
Iron Acquisition ◽  
Bacterial Species ◽  
Regulation Of Gene Expression ◽  
Transport Systems ◽  
Infant Mouse ◽  
Genes Encoding ◽  
Regulatory Functions

ABSTRACT Regulation of iron uptake and utilization is critical for bacterial growth and for prevention of iron toxicity. In many bacterial species, this regulation depends on the iron-responsive master regulator Fur. In this study we report the effects of iron and Fur on gene expression in Vibrio cholerae. We show that Fur has both positive and negative regulatory functions, and we demonstrate Fur-independent regulation of gene expression by iron. Nearly all of the known iron acquisition genes were repressed by Fur under iron-replete conditions. In addition, genes for two newly identified iron transport systems, Feo and Fbp, were found to be negatively regulated by iron and Fur. Other genes identified in this study as being induced in low iron and in the fur mutant include those encoding superoxide dismutase (sodA), fumarate dehydratase (fumC), bacterioferritin (bfr), bacterioferritin-associated ferredoxin (bfd), and multiple genes of unknown function. Several genes encoding iron-containing proteins were repressed in low iron and in the fur mutant, possibly reflecting the need to reserve available iron for the most critical functions. Also repressed in the fur mutant, but independently of iron, were genes located in the V. cholerae pathogenicity island, encoding the toxin-coregulated pilus (TCP), and genes within the V. cholerae mega-integron. The fur mutant exhibited very weak autoagglutination, indicating a possible defect in expression or assembly of the TCP, a major virulence factor of V. cholerae. Consistent with this observation, the fur mutant competed poorly with its wild-type parental strain for colonization of the infant mouse gut.

scholarly journals Microarray Transcription Profiling of a Shewanella oneidensis etrA Mutant

2002 ◽  
Vol 184 (16) ◽  
pp. 4612-4616 ◽  
Author(s):  
Alex S. Beliaev ◽  
Dorothea K. Thompson ◽  
Matthew W. Fields ◽  
Liyou Wu ◽  
Douglas P. Lies ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Regulation Of Gene Expression ◽  
Shewanella Oneidensis ◽  
Transcript Abundance ◽  
Mrna Levels ◽  
Transcription Profiling ◽  
Cellular Processes ◽  
Metabolism Regulation ◽  
Microarray Study

ABSTRACT DNA microarrays were used to examine the effect of an insertional mutation in the Shewanella oneidensis etrA (electron transport regulator) locus on gene expression under anaerobic conditions. The mRNA levels of 69 genes with documented functions in energy and carbon metabolism, regulation, transport, and other cellular processes displayed significant alterations in transcript abundance in an etrA-mutant genetic background. This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in S. oneidensis MR-1.

scholarly journals Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance

2021 ◽  
Author(s):  
Agata Tyczewska ◽  
Joanna Gracz-Bernaciak ◽  
Jakub Szymkowiak ◽  
Tomasz Twardowski
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Differential Susceptibility ◽  
Inbred Lines ◽  
Specific Gene ◽  
Genes Encoding ◽  
Shock Proteins

AbstractDNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.

scholarly journals Petri nets and ODE as complementary tools in analysis of signaling pathways

10.29007/542h ◽  
2019 ◽  
Author(s):  
Daria Kogut ◽  
Kaja Gutowska ◽  
Aleksandra Poterała-Hejmo ◽  
Jarosław Śmieja ◽  
Dorota Formanowicz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Ribosomal Subunit ◽  
Antioxidant Systems ◽  
Main Function ◽  
Oxygen Species ◽  
Radical Oxygen Species ◽  
Apoptosis Pathway ◽  
Elongation Process ◽  
Post Transcriptional Regulation

Regulation of gene expression is one of the most important problems analyzed in systems biology. It involves, among other, interactions of mRNA with miRNA - a small (21-25 nt) single–stranded non–coding RNA molecule. Its main function is post-transcriptional regulation of gene expression leading to gene silencing. It is achieved either by inhibition of translation or by degradation of mRNA. The detailed mechanisms employed include inhibition of attaching the 60s ribosomal subunit, premature ribosome drop-off or inhibition of protein elongation process, cleavage of mRNA or destabilization of mRNA. Another mechanism of regulation of gene expression involves reactive oxygen species (ROS - radical and non-radical oxygen species formed by the partial reduction of oxygen) which, being released from mitochondrium cytochrome C and inducing DNA damage, induce the apoptosis pathway. ROS level can be regulated by antioxidant systems existing in a cell. This paper presents analysis of a model of gene regulation based on these molecules, in which Petri net is used to find the key reactions and, subsequently, an ODE-based model is used to verify these conclusions.

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