Regulatory Factors in Pochonia chlamydosporia-Induced Gene Expression

2017 ◽  
pp. 99-109
Author(s):  
Aurelio Ciancio ◽  
Isabella Pentimone ◽  
Mariantonietta Colagiero ◽  
Laura Rosso
Keyword(s):  
Gene Expression ◽  
Pochonia Chlamydosporia ◽  
Regulatory Factors

scholarly journals Ethanolamine Utilization and Bacterial Microcompartment Formation Are Subject to Carbon Catabolite Repression

2019 ◽  
Vol 201 (10) ◽  
Author(s):  
Karan Gautam Kaval ◽  
Margo Gebbie ◽  
Jonathan R. Goodson ◽  
Melissa R. Cruz ◽  
Wade C. Winkler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Enterococcus Faecalis ◽  
Small Rna ◽  
Catabolite Repression ◽  
Carbon Catabolite Repression ◽  
Bioinformatics Analysis ◽  
Maximum Efficiency ◽  
Gi Tract ◽  
Content Type ◽  
Regulatory Factors

ABSTRACT Ethanolamine (EA) is a compound prevalent in the gastrointestinal (GI) tract that can be used as a carbon, nitrogen, and/or energy source. Enterococcus faecalis, a GI commensal and opportunistic pathogen, contains approximately 20 ethanolamine utilization (eut) genes encoding the necessary regulatory, enzymatic, and structural proteins for this process. Here, using a chemically defined medium, two regulatory factors that affect EA utilization were examined. First, the functional consequences of loss of the small RNA (sRNA) EutX on the efficacy of EA utilization were investigated. One effect observed, as loss of this negative regulator causes an increase in eut gene expression, was a concomitant increase in the number of catabolic bacterial microcompartments (BMCs) formed. However, despite this increase, the growth of the strain was repressed, suggesting that the overall efficacy of EA utilization was negatively affected. Second, utilizing a deletion mutant and a complement, carbon catabolite control protein A (CcpA) was shown to be responsible for the repression of EA utilization in the presence of glucose. A predicted cre site in one of the three EA-inducible promoters, PeutS, was identified as the target of CcpA. However, CcpA was shown to affect the activation of all the promoters indirectly through the two-component system EutV and EutW, whose genes are under the control of the PeutS promoter. Moreover, a bioinformatics analysis of bacteria predicted to contain CcpA and cre sites revealed that a preponderance of BMC-containing operons are likely regulated by carbon catabolite repression (CCR). IMPORTANCE Ethanolamine (EA) is a compound commonly found in the gastrointestinal (GI) tract that can affect the behavior of human pathogens that can sense and utilize it, such as Enterococcus faecalis and Salmonella. Therefore, it is important to understand how the genes that govern EA utilization are regulated. In this work, we investigated two regulatory factors that control this process. One factor, a small RNA (sRNA), is shown to be important for generating the right levels of gene expression for maximum efficiency. The second factor, a transcriptional repressor, is important for preventing expression when other preferred sources of energy are available. Furthermore, a global bioinformatics analysis revealed that this second mechanism of transcriptional regulation likely operates on similar genes in related bacteria.

scholarly journals Regulatory factors specific for adult and embryonic globin genes may govern their expression in erythroleukemia cells

Blood ◽  
1985 ◽  
Vol 65 (3) ◽  
pp. 705-712 ◽  
Author(s):  
NP Anagnou ◽  
TY Yuan ◽  
E Lim ◽  
J Helder ◽  
S Wieder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Chromosome ◽  
Globin Gene ◽  
Globin Genes ◽  
Chromosome 16 ◽  
Regulatory Factors ◽  
Erythroleukemia Cells ◽  
Erythroleukemia Cell ◽  
Globin Gene Expression ◽  
Mouse Erythroleukemia

Abstract In order to test if trans-acting regulatory factors specific for globin genes of the adult and embryonic stages of development exist in erythroid cells, transcriptionally active embryonic and adult globin genes on the same chromosome were transferred by cell fusion from the human leukemia cell K562 into phenotypically adult mouse erythroleukemia cells. Restriction-fragment-length polymorphisms of the K562 zeta (embryonic) globin genes were used to establish that all three copies of human chromosome 16 present in the K562 cell showed the same pattern of human globin gene expression after transfer to the mouse erythroleukemia cell. Adult (alpha) but not embryonic (zeta) human globin mRNA was detected in all nine of the independently derived mouse erythroleukemia hybrid cells, each of which contained human chromosome 16. Restriction endonuclease studies of the K562 alpha- and zeta-globin genes after transfer into the mouse erythroleukemia cell showed no evidence of rearrangements or deletions that could explain this loss of zeta-globin gene expression. These data suggest that regulation of globin gene expression in these erythroleukemia cells involves trans-acting regulatory factors specific for the adult and embryonic stages of development.

Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice

2015 ◽  
Vol 308 (10) ◽  
pp. E912-E920 ◽  
Author(s):  
Timo Kanzleiter ◽  
Markus Jähnert ◽  
Gunnar Schulze ◽  
Joachim Selbig ◽  
Nicole Hallahan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Dna Methylation ◽  
Exercise Training ◽  
Metabolic Regulation ◽  
Muscle Growth ◽  
Epigenetic Mechanism ◽  
Myogenic Regulatory Factors ◽  
Regulatory Factors ◽  
A Genome

The adaptive response of skeletal muscle to exercise training is tightly controlled and therefore requires transcriptional regulation. DNA methylation is an epigenetic mechanism known to modulate gene expression, but its contribution to exercise-induced adaptations in skeletal muscle is not well studied. Here, we describe a genome-wide analysis of DNA methylation in muscle of trained mice ( n = 3). Compared with sedentary controls, 2,762 genes exhibited differentially methylated CpGs ( P < 0.05, meth diff >5%, coverage >10) in their putative promoter regions. Alignment with gene expression data ( n = 6) revealed 200 genes with a negative correlation between methylation and expression changes in response to exercise training. The majority of these genes were related to muscle growth and differentiation, and a minor fraction involved in metabolic regulation. Among the candidates were genes that regulate the expression of myogenic regulatory factors ( Plexin A2) as well as genes that participate in muscle hypertrophy ( Igfbp4) and motor neuron innervation ( Dok7). Interestingly, a transcription factor binding site enrichment study discovered significantly enriched occurrence of CpG methylation in the binding sites of the myogenic regulatory factors MyoD and myogenin. These findings suggest that DNA methylation is involved in the regulation of muscle adaptation to regular exercise training.

scholarly journals Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia

2011 ◽  
Vol 90 (6) ◽  
pp. 1981-1994 ◽  
Author(s):  
Laura C. Rosso ◽  
Mariella M. Finetti-Sialer ◽  
Penny R. Hirsch ◽  
Aurelio Ciancio ◽  
Brian R. Kerry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptome Analysis ◽  
Pochonia Chlamydosporia ◽  
Differential Gene

Gene expression of myogenic regulatory factors following intramuscular injection of botulinum A toxin in juvenile rats

2005 ◽  
Vol 381 (3) ◽  
pp. 207-210 ◽  
Author(s):  
Jian Shen ◽  
Jianjun Ma ◽  
Gamal A. Elsaidi ◽  
Cassandra A. Lee ◽  
Thomas L. Smith ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intramuscular Injection ◽  
Myogenic Regulatory Factors ◽  
Juvenile Rats ◽  
Regulatory Factors ◽  
Botulinum A Toxin

Altered gene expression of transcriptional regulatory factors in tumor marker-positive cells during chemically induced hepatocarcinogenesis

2006 ◽  
Vol 167 (2) ◽  
pp. 106-113 ◽  
Author(s):  
Shigehiro Osada ◽  
Ayako Naganawa ◽  
Masashi Misonou ◽  
Soken Tsuchiya ◽  
Shigero Tamba ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tumor Marker ◽  
Regulatory Factors ◽  
Altered Gene Expression ◽  
Chemically Induced ◽  
Transcriptional Regulatory ◽  
Altered Gene

scholarly journals OR-009 The expression and roles of lncRNAs in the regeneration of skeletal muscle contusion

2018 ◽  
Vol 1 (2) ◽  
Author(s):  
Lifang Zheng ◽  
Peijie Chen ◽  
Weihua Xiao
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Muscle Regeneration ◽  
Myoblast Differentiation ◽  
Control Group ◽  
Myogenic Regulatory Factors ◽  
Post Injury ◽  
Regulatory Factors ◽  
Expression Levels ◽  
Skeletal Muscle Contusion

Objective In recent years, Accumulating evidence from myoblast differentiation in vitro, cardiotoxin (CTX)-mediated injury or mdx mice suggested that some lncRNAs such as Malat1, H19, linc-MD1, linc-YY1, Sirt1 AS and lnc-mg may modulate myogenesis and muscle regeneration. However, the change of lncRNAs in skeletal muscle contusion and their possible roles are still unclear. We hypothesize that the lncRNAs may be involved in the repair of skeletal muscle contusion. Methods Forty C57BL/6 male mice were randomly divided into two groups, uninjured control group (group C) and muscle contusion group (group S). The mice of group S suffered from contusion injury. All the mice were killed to harvest gastrocnemius at 3, 6, 12 and 24 days post-injury. The gene expression were detected by PCR technique. Gastrocnemius were stained with H & E to evaluate the general morphology. Data were analyzed by One-way analysis of variance, with statistical significance being set at p ≤ 0.05. Results The expression levels of linc-MD1 and Sirt1 AS were significantly higher than that of the uninjured control group at 3, 6 and 12 days post-injury (p<0.01). And Malat1 was highly expressed in the skeletal muscle of the muscle contusion group at 3 days post-injury and continuously up-regulated at 6 days (p<0.01). Moreover, linc-YY1 and H19 were all elevated significantly at 6 days (all p<0.01), but their gene expression levels did not change significantly at 3, 12 and 24 days post-injury, as compared to the uninjured control group. Furthermore, lnc-mg mRNA level did not change significantly in the whole process of regeneration after muscle contusion except the time point of 12 days post-injury which decreased significantly (p<0.01). The expression of myogenic regulatory factors (MyoD, myogenin, myf5, myf6) were studied, they were all elevated significantly at 3 and 6 days (all p<0.01; except myogenin ), and returned to normal at 24 days post-injury, as compared to the uninjured control group. Meanwhile, Pearson correlations showed that there was an correlation between lincRNAs and myogenic regulatory factors mentioned above. Conclusions The expression of myogenic regulatory factors increased significantly after muscle contusion. Meanwhile, varieties of lncRNAs (Malat1, H19, lnc-mg, linc-MD1, linc-YY1, Sirt1 AS) were also up-regulated. Moreover, there was correlation between lncRNAs and myogenic regulatory factors for skeletal muscle regeneration. These results suggest that lncRNAs may play important roles in the regeneration of skeletal muscle contusion.

scholarly journals Intranuclear trafficking of transcription factors: implications for biological control

2000 ◽  
Vol 113 (14) ◽  
pp. 2527-2533 ◽  
Author(s):  
G.S. Stein ◽  
A.J. van Wijnen ◽  
J.L. Stein ◽  
J.B. Lian ◽  
M. Montecino ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Myelogenous Leukemia ◽  
Regulatory Factors ◽  
Acute Myelogenous ◽  
Gene Transcripts ◽  
Targeting Signals ◽  
Discrete Domains

The subnuclear organization of nucleic acids and cognate regulatory factors suggests that there are functional interrelationships between nuclear structure and gene expression. Nuclear proteins that are localized in discrete domains within the nucleus include the leukemia-associated acute myelogenous leukemia (AML) and promyelocytic leukemia (PML) factors, the SC-35 RNA-processing factors, nucleolar proteins and components of both transcriptional and DNA replication complexes. Mechanisms that control the spatial distribution of transcription factors within the three-dimensional context of the nucleus may involve the sorting of regulatory information, as well as contribute to the assembly and activity of sites that support gene expression. Molecular, cellular, genetic and biochemical approaches have identified distinct protein segments, termed intranuclear-targeting signals, that are responsible for directing regulatory factors to specific subnuclear sites. Gene rearrangements that remove or alter intranuclear-targeting signals are prevalent in leukemias and have been linked to altered localization of regulatory factors within the nucleus. These modifications in the intranuclear targeting of transcription factors might abrogate fidelity of gene expression in tumor cells by influencing the spatial organization and/or assembly of machineries involved in the synthesis and processing of gene transcripts.

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