Identification and distinct regulation of three di/tripeptide transporters in Aspergillus oryzae

2020 ◽  
Vol 85 (2) ◽  
pp. 452-463
Author(s):  
Mizuki Tanaka ◽  
Keisuke Ito ◽  
Tomomi Matsuura ◽  
Yasuaki Kawarasaki ◽  
Katsuya Gomi
Keyword(s):  
Transcription Factor ◽  
Aspergillus Oryzae ◽  
Ubiquitin Ligase ◽  
Nitrogen Starvation ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Nitrogen Sources ◽  
Regulatory Mechanisms ◽  
Deletion Mutants ◽  
Oligopeptide Transporter

ABSTRACT The uptake of di/tripeptides is mediated by the proton-dependent oligopeptide transporter (POT) family. In this study, 3 POT family transporters, designated PotA, PotB, and PotC were identified in Aspergillus oryzae. Growth comparison of deletion mutants of these transporter genes suggested that PotB and PotC are responsible for di/tripeptide uptake. PotA, which had the highest sequence similarity to yeast POT (Ptr2), contributed little to the uptake. Nitrogen starvation induced potB and potC expression, but not potA expression. When 3 dipeptides were provided as nitrogen sources, the expression profiles of these genes were different. PrtR, a transcription factor that regulates proteolytic genes, was involved in regulation of potA and potB but not in potC expression. Only potC expression levels were dramatically reduced by disruption of ubrA, an orthologue of yeast ubiquitin ligase UBR1 responsible for PTR2 expression. Expression of individual POT genes is apparently controlled by different regulatory mechanisms.

scholarly journals Transcription Factors Indirectly Regulate Genes through Nuclear Colocalization

Cells ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 754 ◽  
Author(s):  
Zhiming Dai
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Biological Process ◽  
Expression Profiles ◽  
Dna Interaction ◽  
Cellular Component ◽  
Regulatory Mechanisms ◽  
Nuclear Positioning ◽  
Conventional View

Various types of data, including genomic sequences, transcription factor (TF) knockout data, TF-DNA interaction and expression profiles, have been used to decipher TF regulatory mechanisms. However, most of the genes affected by knockout of a particular TF are not bound by that factor. Here, I showed that this interesting result can be partially explained by considering the nuclear positioning of TF knockout affected genes and TF bound genes. I found that a statistically significant number of TF knockout affected genes show nuclear colocalization with genes bound by the corresponding TF. Although these TF knockout affected genes are not directly bound by the corresponding TF; the TF tend to be in the same cellular component with the TFs that directly bind these genes. TF knockout affected genes show co-expression and tend to be involved in the same biological process with the spatially adjacent genes that are bound by the corresponding TF. These results demonstrate that TFs can regulate genes through nuclear colocalization without direct DNA binding, complementing the conventional view that TFs directly bind DNA to regulate genes. My findings will have implications in understanding TF regulatory mechanisms.

scholarly journals The Transcription Factor Atf1 Binds and Activates the APC/C Ubiquitin Ligase in Fission Yeast

2009 ◽  
Vol 284 (36) ◽  
pp. 23989-23994 ◽  
Author(s):  
Aslihan Ors ◽  
Margaret Grimaldi ◽  
Yuu Kimata ◽  
Caroline R. M. Wilkinson ◽  
Nic Jones ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Fission Yeast ◽  
Ubiquitin Ligase

scholarly journals Screening Driving Transcription Factors in the Processing of Gastric Cancer

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Guangzhong Xu ◽  
Kai Li ◽  
Nengwei Zhang ◽  
Bin Zhu ◽  
Guosheng Feng
Keyword(s):  
Gastric Cancer ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Profiles ◽  
Functional Enrichment ◽  
Regulatory Mechanisms ◽  
Integrated Analysis ◽  
Transcriptional Regulatory

Background. Construction of the transcriptional regulatory network can provide additional clues on the regulatory mechanisms and therapeutic applications in gastric cancer.Methods. Gene expression profiles of gastric cancer were downloaded from GEO database for integrated analysis. All of DEGs were analyzed by GO enrichment and KEGG pathway enrichment. Transcription factors were further identified and then a global transcriptional regulatory network was constructed.Results. By integrated analysis of the six eligible datasets (340 cases and 43 controls), a bunch of 2327 DEGs were identified, including 2100 upregulated and 227 downregulated DEGs. Functional enrichment analysis of DEGs showed that digestion was a significantly enriched GO term for biological process. Moreover, there were two important enriched KEGG pathways: cell cycle and homologous recombination. Furthermore, a total of 70 differentially expressed TFs were identified and the transcriptional regulatory network was constructed, which consisted of 566 TF-target interactions. The top ten TFs regulating most downstream target genes were BRCA1, ARID3A, EHF, SOX10, ZNF263, FOXL1, FEV, GATA3, FOXC1, and FOXD1. Most of them were involved in the carcinogenesis of gastric cancer.Conclusion. The transcriptional regulatory network can help researchers to further clarify the underlying regulatory mechanisms of gastric cancer tumorigenesis.

scholarly journals Identifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hwang-Yeol Lee ◽  
Yeonsu Jeon ◽  
Yeon Kyung Kim ◽  
Jae Young Jang ◽  
Yun Sung Cho ◽  
...  
Keyword(s):  
Network Model ◽  
Expression Profiles ◽  
Flow Analysis ◽  
Gene Expression Profiles ◽  
Molecular Targets ◽  
Regulatory Mechanisms ◽  
Integrated Network ◽  
Signal Flow ◽  
Biomarkers Of Aging ◽  
Candidate Target

AbstractAging is associated with widespread physiological changes, including skeletal muscle weakening, neuron system degeneration, hair loss, and skin wrinkling. Previous studies have identified numerous molecular biomarkers involved in these changes, but their regulatory mechanisms and functional repercussions remain elusive. In this study, we conducted next-generation sequencing of DNA methylation and RNA sequencing of blood samples from 51 healthy adults between 20 and 74 years of age and identified aging-related epigenetic and transcriptomic biomarkers. We also identified candidate molecular targets that can reversely regulate the transcriptomic biomarkers of aging by reconstructing a gene regulatory network model and performing signal flow analysis. For validation, we screened public experimental data including gene expression profiles in response to thousands of chemical perturbagens. Despite insufficient data on the binding targets of perturbagens and their modes of action, curcumin, which reversely regulated the biomarkers in the experimental dataset, was found to bind and inhibit JUN, which was identified as a candidate target via signal flow analysis. Collectively, our results demonstrate the utility of a network model for integrative analysis of omics data, which can help elucidate inter-omics regulatory mechanisms and develop therapeutic strategies against aging.

Chicken vitellogenin gene-binding protein, a leucine zipper transcription factor that binds to an important control element in the chicken vitellogenin II promoter, is related to rat DBP

1991 ◽  
Vol 11 (10) ◽  
pp. 4863-4875
Author(s):  
S V Iyer ◽  
D L Davis ◽  
S N Seal ◽  
J B Burch
Keyword(s):  
Transcription Factor ◽  
Binding Site ◽  
Binding Protein ◽  
Expression Profiles ◽  
Control Element ◽  
Cdna Expression Library ◽  
Leucine Zippers ◽  
Expression Library ◽  
Positive Elements ◽  
Vitellogenin Gene

We screened a chicken liver cDNA expression library with a probe spanning the distal region of the chicken vitellogenin II (VTGII) gene promoter and isolated clones for a transcription factor that we have named VBP (for vitellogenin gene-binding protein). VBP binds to one of the most important positive elements in the VTGII promoter and appears to play a pivotal role in the estrogen-dependent regulation of this gene. The protein sequence of VBP was deduced from a nearly full length cDNA copy and was found to contain a basic/zipper (bZIP) motif. As expected for a bZIP factor, VBP binds to its target DNA site as a dimer. Moreover, VBP is a stable dimer free in solution. A data base search revealed that VBP is related to rat DBP. However, despite the fact that the basic/hinge regions of VBP and DBP differ at only three amino acid positions, the DBP binding site in the rat albumin promoter is a relatively poor binding site for VBP. Thus, the optimal binding sites for VBP and DBP may be distinct. Similarities between the VBP and DBP leucine zippers are largely confined to only four of the seven helical spokes. Nevertheless, these leucine zippers are functionally compatible and appear to define a novel subfamily. In contrast to the bZIP regions, other portions of VBP and DBP are markedly different, as are the expression profiles for these two genes. In particular, expression of the VBP gene commences early in liver ontogeny and is not subject to circadian control.

scholarly journals Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity

2018 ◽  
Vol 19 (4) ◽  
pp. 289-299 ◽  
Author(s):  
Ruta Skinkyte-Juskiene ◽  
Lisette J.A. Kogelman ◽  
Haja N. Kadarmideen
Keyword(s):  
Transcription Factor ◽  
Regulatory Mechanisms ◽  
Rna Seq
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