In vivo metal selectivity of metal-dependent biosynthesis of cobalt-type nitrile hydratase in Rhodococcus bacteria: a new look at the nitrile hydratase maturation mechanism?

Metallomics ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1162-1171 ◽  
Author(s):  
Konstantin V. Lavrov ◽  
Anna O. Shemyakina ◽  
Elena G. Grechishnikova ◽  
Andrey D. Novikov ◽  
Tatyana I. Kalinina ◽  
...  
Keyword(s):  
Transcription Regulation ◽  
Nitrile Hydratase ◽  
Metal Selectivity ◽  
Enzyme Maturation ◽  
New Look

Metal-dependent cblA-mediated mechanism of transcription regulation of NHase could not discriminate Ni and Co, but mechanism of NHase enzyme maturation could do this.

scholarly journals Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guillaume Bordet ◽  
Niraj Lodhi ◽  
Danping Guo ◽  
Andrew Kossenkov ◽  
Alexei V. Tulin
Keyword(s):  
Cytochrome P450 ◽  
Transcription Factors ◽  
Transcription Regulation ◽  
Large Scale ◽  
Mobile Elements ◽  
Expression Control ◽  
Genome Wide ◽  
Cytochrome P450 Family ◽  
Parp 1

AbstractPoly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme involved in DNA repair and transcription regulation, among other processes. Malignant transformations, tumor progression, the onset of some neuropathies and other disorders have been linked to misregulation of PARP-1 activity. Despite intensive studies during the last few decades, the role of PARP-1 in transcription regulation is still not well understood. In this study, a transcriptomic analysis in Drosophila melanogaster third instar larvae was carried out. A total of 602 genes were identified, showing large-scale changes in their expression levels in the absence of PARP-1 in vivo. Among these genes, several functional gene groups were present, including transcription factors and cytochrome family members. The transcription levels of genes from the same functional group were affected by the absence of PARP-1 in a similar manner. In the absence of PARP-1, all misregulated genes coding for transcription factors were downregulated, whereas all genes coding for members of the cytochrome P450 family were upregulated. The cytochrome P450 proteins contain heme as a cofactor and are involved in oxidoreduction. Significant changes were also observed in the expression of several mobile elements in the absence of PARP-1, suggesting that PARP-1 may be involved in regulating the expression of mobile elements.

scholarly journals Transcription Regulation by Tandem-Bound FNR at Escherichia coli Promoters

2003 ◽  
Vol 185 (20) ◽  
pp. 5993-6004 ◽  
Author(s):  
Anne M. L. Barnard ◽  
Jeffrey Green ◽  
Stephen J. W. Busby
Keyword(s):  
Escherichia Coli ◽  
Transcription Factor ◽  
Binding Site ◽  
Transcription Regulation ◽  
Transcription Start Site ◽  
Promoter Activity ◽  
Start Site ◽  
Transcription Start ◽  
Substitution Mutant

ABSTRACT FNR is an Escherichia coli transcription factor that regulates the transcription of many genes in response to anaerobiosis. We have constructed a series of artificial FNR-dependent promoters, based on the melR promoter, in which a consensus FNR binding site was centered at position −41.5 relative to the transcription start site. A second consensus FNR binding site was introduced at different upstream locations, and promoter activity was assayed in vivo. FNR can activate transcription from these promoters when the upstream FNR binding site is located at many different positions. However, sharp repression is observed when the upstream-bound FNR is located near positions −85 or −95. This repression is relieved by the FNR G74C substitution mutant, previously identified as being defective in transcription repression at the yfiD promoter. A parallel series of artificial FNR-dependent promoters, carrying a consensus FNR binding site at position −61.5 and a second upstream DNA site for FNR, was also constructed. Again, promoter activity was repressed by FNR when the upstream-bound FNR was located at particular positions.

scholarly journals Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs

2020 ◽  
Vol 118 (1) ◽  
pp. e2008498118
Author(s):  
Mark N. Ragheb ◽  
Christopher Merrikh ◽  
Kaitlyn Browning ◽  
Houra Merrikh
Keyword(s):  
Rna Polymerase ◽  
Transcription Regulation ◽  
Dna Lesions ◽  
Toxin Gene ◽  
Rna Regulation ◽  
Genome Wide ◽  
Highly Sensitive ◽  
Regulatory Rnas ◽  
Dna Translocase

RNA polymerase (RNAP) encounters various roadblocks during transcription. These obstacles can impede RNAP movement and influence transcription, ultimately necessitating the activity of RNAP-associated factors. One such factor is the bacterial protein Mfd, a highly conserved DNA translocase and evolvability factor that interacts with RNAP. Although Mfd is thought to function primarily in the repair of DNA lesions that stall RNAP, increasing evidence suggests that it may also be important for transcription regulation. However, this is yet to be fully characterized. To shed light on Mfd’s in vivo functions, we identified the chromosomal regions where it associates. We analyzed Mfd’s impact on RNAP association and transcription regulation genome-wide. We found that Mfd represses RNAP association at many chromosomal regions. We found that these regions show increased RNAP pausing, suggesting that they are hard to transcribe. Interestingly, we noticed that the majority of the regions where Mfd regulates transcription contain highly structured regulatory RNAs. The RNAs identified regulate a myriad of biological processes, ranging from metabolism to transfer RNA regulation to toxin–antitoxin (TA) functions. We found that cells lacking Mfd are highly sensitive to toxin overexpression. Finally, we found that Mfd promotes mutagenesis in at least one toxin gene, suggesting that its function in regulating transcription may promote evolution of certain TA systems and other regions containing strong RNA secondary structures. We conclude that Mfd is an RNAP cofactor that is important, and at times critical, for transcription regulation at hard-to-transcribe regions, especially those that express structured regulatory RNAs.

scholarly journals Role of an ING1 Growth Regulator in Transcriptional Activation and Targeted Histone Acetylation by the NuA4 Complex

2001 ◽  
Vol 21 (22) ◽  
pp. 7629-7640 ◽  
Author(s):  
Amine Nourani ◽  
Yannick Doyon ◽  
Rhea T. Utley ◽  
Stéphane Allard ◽  
William S. Lane ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Transcription Regulation ◽  
Transcriptional Activation ◽  
Histone Acetyltransferase ◽  
Yeast Cells ◽  
Growth Defect ◽  
Histone H4 ◽  
Phd Finger

ABSTRACT The yeast NuA4 complex is a histone H4 and H2A acetyltransferase involved in transcription regulation and essential for cell cycle progression. We identify here a novel subunit of the complex, Yng2p, a plant homeodomain (PHD)-finger protein homologous to human p33/ING1, which has tumor suppressor activity and is essential for p53 function. Mass spectrometry, immunoblotting, and immunoprecipitation experiments confirm the stable stoichiometric association of this protein with purified NuA4. Yeast cells harboring a deletion of theYNG2 gene show severe growth phenotype and have gene-specific transcription defects. NuA4 complex purified from the mutant strain is low in abundance and shows weak histone acetyltransferase activity. We demonstrate conservation of function by the requirement of Yng2p for p53 to function as a transcriptional activator in yeast. Accordingly, p53 interacts with NuA4 in vitro and in vivo, an interaction reminiscent of the p53-ING1 physical link in human cells. The growth defect of Δyng2 cells can be rescued by the N-terminal part of the protein, lacking the PHD-finger. While Yng2 PHD-finger is not required for p53 interaction, it is necessary for full expression of the p53-responsive gene and other NuA4 target genes. Transcriptional activation by p53 in vivo is associated with targeted NuA4-dependent histone H4 hyperacetylation, while histone H3 acetylation levels remain unchanged. These results emphasize the essential role of the NuA4 complex in the control of cell proliferation through gene-specific transcription regulation. They also suggest that regulation of mammalian cell proliferation by p53-dependent transcriptional activation functions through recruitment of an ING1-containing histone acetyltransferase complex.

scholarly journals Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs

2020 ◽  
Author(s):  
Mark N. Ragheb ◽  
Christopher Merrikh ◽  
Kaitlyn Browning ◽  
Houra Merrikh
Keyword(s):  
Rna Polymerase ◽  
Transcription Regulation ◽  
Living Cells ◽  
Dna Lesions ◽  
Toxin Gene ◽  
Exogenous Dna ◽  
Genome Wide ◽  
Regulatory Rnas ◽  
Dna Translocase

AbstractRNA polymerase (RNAP) encounters various roadblocks during transcription. These obstacles can impede RNAP movement, influence transcription, ultimately necessitating the activity of RNAP associated factors. One such factor is the bacterial protein Mfd; a highly conserved DNA translocase and evolvability factor that interacts with RNAP. Although Mfd is thought to function primarily in the repair of DNA lesions that stall RNAP, increasing evidence suggests that it may also be important for transcription regulation. However, this is yet to be fully characterized.To shed light on Mfd’s in vivo functions, we identified the chromosomal regions where it associates. We analyzed Mfd’s impact on RNAP association and transcription regulation genome-wide. We found that Mfd represses RNAP association at many chromosomal regions. We found that these regions show increased RNAP pausing, suggesting that they are hard-to-transcribe. Interestingly, we noticed that the majority of the regions where Mfd regulates transcription contain highly structured regulatory RNAs. The RNAs identified regulate a myriad of biological processes, ranging from metabolism, to tRNA regulation, to toxin-antitoxin (TA) functions. We found that transcription regulation by Mfd, at least at some TA loci, is critical for cell survival. Lastly, we found that Mfd promotes mutagenesis in at least one toxin gene, suggesting that its function in regulating transcription may promote evolution of certain TA systems, and other regions containing strong RNA secondary structures. We conclude that Mfd is an RNAP co-factor that is important, and at times critical, for transcription regulation at hard-to-transcribe regions, especially those that express structured regulatory RNAs.SignificanceThe bacterial DNA translocase Mfd binds to stalled RNAPs and is generally thought to facilitate transcription-coupled DNA repair. Most of our knowledge about Mfd is based on data from biochemical studies. However, little is known about Mfd’s function in living cells, especially in the absence of exogenous DNA damage. Here, we show that Mfd modulates RNAP association and alters transcription at a variety of chromosomal loci, especially those containing highly structured, regulatory RNAs. As such, this work improves our understanding of Mfd’s function in living cells, and assigns it a new function as a transcription regulator.

scholarly journals Cohesin in space and time: architecture and oligomerization in vivo

2020 ◽  
Author(s):  
Siheng Xiang ◽  
Douglas Koshland
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Transcription Regulation ◽  
Sister Chromatid ◽  
Critical Role ◽  
Coiled Coils ◽  
Biological Functions ◽  
Chromatid Cohesion ◽  
And Function

AbstractCohesin helps mediate sister chromatid cohesion, chromosome condensation, DNA repair and transcription regulation. Cohesin can tether two regions of DNA and can also extrude DNA loops. We interrogated cohesin architecture, oligomerization state and function of cohesin oligomers in vivo through proximity-dependent labeling of cohesin domains. Our results suggest that the hinge and head domains of cohesin both bind DNA, and that cohesin coiled coils bend, bringing the head and hinge together to form a butterfly conformation. Our data also suggest that cohesin efficiently oligomerizes on and off DNA. The levels of oligomers and their distribution on chromosomes are cell cycle regulated. Cohesin oligomerization is blocked by mutations in distinct domains of Smc3p and Mcd1p, or depletion of Pds5p. This unusual subset of mutations specifically blocks the maintenance of cohesion and condensation, suggesting that cohesin oligomerization plays a critical role in these biological functions.

scholarly journals Motif CXCC in nitrile hydratase activator is critical for NHase biogenesis in vivo

FEBS Letters ◽  
2003 ◽  
Vol 553 (3) ◽  
pp. 391-396 ◽  
Author(s):  
Jun Lu ◽  
Yujuan Zheng ◽  
Hiromi Yamagishi ◽  
Masafumi Odaka ◽  
Masanari Tsujimura ◽  
...  
Keyword(s):  
Nitrile Hydratase
Sign in / Sign up

Export Citation Format

Share Document