scholarly journals CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a

2019 ◽  
Author(s):  
Leonardo Martins-Santana ◽  
Renato Graciano de Paula ◽  
Adriano Gomes Silva ◽  
Douglas Christian Borges Lopes ◽  
Roberto do Nascimento Silva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Trichoderma Reesei ◽  
Regulatory Network ◽  
Plant Biomass ◽  
Transcriptional Regulators ◽  
Regulatory Role ◽  
Cellulolytic Enzymes ◽  
Strong Increase ◽  
New Evidence

AbstractBackgroundTrichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Over the last decades, there have been a strong increase in the understanding of the regulatory network controlling cellulase-coding gene expression in response to a number of inducers and environmental signals. In this sense, the role of calcium and the Calcineurin-responsive protein (CRZ1) has been investigated in industrially relevant strains of T. reesei RUT-C30, but this system has not been investigated in wild-type reference strain of this fungus.ResultsHere, we investigated the role of CRZ1 and Ca2+ signaling in the fungus T. reesei QM6a. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reesei Δcrzl strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei, suggesting the existence of additional Ca2+ sensing mechanisms in this fungus.ConclusionsThis work presents new evidence on the regulatory role of CRZ1 and Ca2+ sensing in the regulation of cellulolytic enzymes in T. reesei, evidencing significant and previously unknown function of this Ca2+ sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca2+ transport. Taken together, the data obtained here provide new evidence on the regulatory network of T. reesei related to plant biomass deconstruction.

scholarly journals Regulatory role of indeterminate domain 10 (IDD10) in ammonium-dependent gene expression in rice roots

2013 ◽  
Vol 8 (5) ◽  
pp. e24139 ◽  
Author(s):  
Yuan Hu Xuan ◽  
Ryza A. Priatama ◽  
Vikranth Kumar ◽  
Chang-deok Han
Keyword(s):  
Gene Expression ◽  
Regulatory Role ◽  
Rice Roots

scholarly journals Prefoldins contribute to maintaining the levels of the spliceosome LSM2–8 complex through Hsp90 in Arabidopsis

2020 ◽  
Vol 48 (11) ◽  
pp. 6280-6293 ◽  
Author(s):  
David Esteve-Bruna ◽  
Cristian Carrasco-López ◽  
Noel Blanco-Touriñán ◽  
Javier Iserte ◽  
Julián Calleja-Cabrera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Model Organism ◽  
Transcriptional Regulators ◽  
Hsp90 Inhibitor ◽  
Mrna Splicing ◽  
Core Complex ◽  
Functional Specificity ◽  
U6 Snrna ◽  
Splicing Patterns

Abstract Although originally identified as the components of the complex aiding the cytosolic chaperonin CCT in the folding of actins and tubulins in the cytosol, prefoldins (PFDs) are emerging as novel regulators influencing gene expression in the nucleus. Work conducted mainly in yeast and animals showed that PFDs act as transcriptional regulators and participate in the nuclear proteostasis. To investigate new functions of PFDs, we performed a co-expression analysis in Arabidopsis thaliana. Results revealed co-expression between PFD and the Sm-like (LSM) genes, which encode the LSM2–8 spliceosome core complex, in this model organism. Here, we show that PFDs interact with and are required to maintain adequate levels of the LSM2–8 complex. Our data indicate that levels of the LSM8 protein, which defines and confers the functional specificity of the complex, are reduced in pfd mutants and in response to the Hsp90 inhibitor geldanamycin. We provide biochemical evidence showing that LSM8 is a client of Hsp90 and that PFD4 mediates the interaction between both proteins. Consistent with our results and with the role of the LSM2–8 complex in splicing through the stabilization of the U6 snRNA, pfd mutants showed reduced levels of this snRNA and altered pre-mRNA splicing patterns.

scholarly journals The autophagy protein Ambra1 regulates gene expression by supporting novel transcriptional complexes

2020 ◽  
Vol 295 (34) ◽  
pp. 12045-12057
Author(s):  
Christina Schoenherr ◽  
Adam Byron ◽  
Billie Griffith ◽  
Alexander Loftus ◽  
Jimi C. Wills ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cancer Cell ◽  
Cell Invasion ◽  
Cell Biology ◽  
Protein Complexes ◽  
Transcriptional Regulators ◽  
Adaptor Proteins ◽  
Nuclear Pore ◽  
Biochemical Fractionation

Ambra1 is considered an autophagy and trafficking protein with roles in neurogenesis and cancer cell invasion. Here, we report that Ambra1 also localizes to the nucleus of cancer cells, where it has a novel nuclear scaffolding function that controls gene expression. Using biochemical fractionation and proteomics, we found that Ambra1 binds to multiple classes of proteins in the nucleus, including nuclear pore proteins, adaptor proteins such as FAK and Akap8, chromatin-modifying proteins, and transcriptional regulators like Brg1 and Atf2. We identified biologically important genes, such as Angpt1, Tgfb2, Tgfb3, Itga8, and Itgb7, whose transcription is regulated by Ambra1-scaffolded complexes, likely by altering histone modifications and Atf2 activity. Therefore, in addition to its recognized roles in autophagy and trafficking, Ambra1 scaffolds protein complexes at chromatin, regulating transcriptional signaling in the nucleus. This novel function for Ambra1, and the specific genes impacted, may help to explain the wider role of Ambra1 in cancer cell biology.

Gene expression profiles predict the possible regulatory role of OPN-mediated signaling pathways in rat liver regeneration

Gene ◽  
2016 ◽  
Vol 576 (2) ◽  
pp. 782-790 ◽  
Author(s):  
Gaiping Wang ◽  
Shasha Chen ◽  
Congcong Zhao ◽  
Xiaofang Li ◽  
Ling Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Regeneration ◽  
Signaling Pathways ◽  
Rat Liver ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Regulatory Role ◽  
Rat Liver Regeneration

MINING TIME-DEPENDENT GENE FEATURES

2005 ◽  
Vol 03 (05) ◽  
pp. 1191-1205 ◽  
Author(s):  
ENRICO CAPOBIANCO
Keyword(s):  
Gene Expression ◽  
Dna Damage ◽  
Steady State ◽  
Mutual Information ◽  
Regulatory Network ◽  
Genomic Data ◽  
Genetic Regulatory Network ◽  
Time Dependent ◽  
Cascade Effects

This paper presents an application of the Independent Component Analysis (ICA) method to genomic data. In particular, experimentally produced perturbation effects over the E.coli bacterium are monitored through the changes of gene expression values observed at regular times, and until steady state has been reached. The aim is to control the response of the SOS system to DNA damage. We might assume that only part of the genetic regulatory network is affected directly by the perturbation conditions, as indirect cascade effects might also be present, and some genes may change just because of randomness. ICA decomposes the gene matrix and identifies groups of genes belonging to a certain estimated component by virtue of co-expression; it is of course of interest to establish co-regulation dynamics, which might underlie the captured correlation. Stronger forms of dependence, like Mutual Information, are thus computed and compared with linear correlation in order to validate the results and establish the role of the identified components in determining the network dynamics.

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