scholarly journals Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription

2013 ◽  
Vol 41 (2) ◽  
pp. 542-547 ◽  
Author(s):  
Charles J. Dorman
Keyword(s):  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Complex Nature ◽  
Regulation Of Transcription ◽  
Transcription Control ◽  
Dna Relaxation ◽  
Bacterial Transcription ◽  
Associated Proteins ◽  
Topological State ◽  
Bacterial Genes

DNA supercoiling and NAPs (nucleoid-associated proteins) contribute to the regulation of transcription of many bacterial genes. The horizontally acquired SPI (Salmonella pathogenicity island) genes respond positively to DNA relaxation, they are activated and repressed by the Fis (factor for inversion stimulation) and H-NS (histone-like nucleoid-structuring) NAPs respectively, and are positively controlled by the OmpR global regulatory protein. The ompR gene is autoregulated and responds positively to DNA relaxation. Binding of the Fis and OmpR proteins to their targets in DNA is differentially sensitive to its topological state, whereas H-NS binds regardless of the topological state of the DNA. These data illustrate the overlapping and complex nature of NAP and DNA topological contributions to transcription control in bacteria.

scholarly journals Glycosylation and biogenesis of a family of serine-rich bacterial adhesins

Microbiology ◽  
2009 ◽  
Vol 155 (2) ◽  
pp. 317-327 ◽  
Author(s):  
Meixian Zhou ◽  
Hui Wu
Keyword(s):  
Biosynthetic Pathway ◽  
Protein Glycosylation ◽  
Second Step ◽  
Complex Nature ◽  
Bacterial Physiology ◽  
Bacterial Proteins ◽  
New Family ◽  
Bacterial Adhesins ◽  
Platelet Binding ◽  
Associated Proteins

Glycosylation of bacterial proteins is an important process for bacterial physiology and pathophysiology. Both O- and N-linked glycan moieties have been identified in bacterial glycoproteins. The N-linked glycosylation pathways are well established in Gram-negative bacteria. However, the O-linked glycosylation pathways are not well defined due to the complex nature of known O-linked glycoproteins in bacteria. In this review, we examine a new family of serine-rich O-linked glycoproteins which are represented by fimbriae-associated adhesin Fap1 of Streptococcus parasanguinis and human platelet-binding protein GspB of Streptococcus gordonii. This family of glycoproteins is conserved in streptococcal and staphylococcal species. A gene cluster coding for glycosyltransferases and accessory Sec proteins has been implicated in the protein glycosylation. A two-step glycosylation model is proposed. Two glycosyltransferases interact with each other and catalyse the first step of the protein glycosylation in the cytoplasm; the cross-talk between glycosylation-associated proteins and accessory Sec components mediates the second step of the protein glycosylation, an emerging mechanism for bacterial O-linked protein glycosylation. Dissecting the molecular mechanism of this conserved biosynthetic pathway offers opportunities to develop new therapeutic strategies targeting this previously unrecognized pathway, as serine-rich glycoproteins have been shown to play a role in bacterial pathogenesis.

Activation by TyrR in Escherichia coli K-12 by Interaction between TyrR and the α-subunit of RNA polymerase

2021 ◽  
Author(s):  
Helen Camakaris ◽  
Ji Yang ◽  
Tadashi Fujii ◽  
James Pittard
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Regulatory Protein ◽  
Aromatic Amino Acids ◽  
Regulation Of Transcription ◽  
Plant Interactions ◽  
Α Subunit ◽  
Partial Suppression ◽  
K 12

A novel selection was developed for RpoA α-CTD mutants altered in activation by the TyrR regulatory protein of E. coli K-12. This allowed the identification of an aspartate to asparagine substitution in residue 250 (DN250) as an Act - mutation. Amino acid residues known to be close to D250 were altered by in vitro mutagenesis, and substitutions DR250, RE310 and RD310 were all shown to be defective in activation. None of these mutations caused defects in UP regulation. The rpoA mutation DN250 was transferred onto the chromosome to facilitate the isolation of suppressor mutations. TyrR Mutations EK139 and RG119 caused partial suppression of rpoA DN250, and TyrR RC119, RL119, RP119, RA77 and SG100 caused partial suppression of rpoA RE310. Additional activation-defective rpoA mutants (DT250, RS310, EG288) were also isolated, using the chromosomal rpoA DN250 strain. Several new Act - tyrR mutants were isolated in an rpoA + strain, adding positions R77, D97, K101, D118, R119, R121 and E141 to known residues, S95 and D103, and defining the ‘activation patch’ on the NTD of TyrR. These results support a model for activation of TyrR-regulated genes where the ‘activation patch’ on the TyrR NTD interacts with the ‘TyrR-specific patch’ on the αCTD of RNA polymerase. Given known structures, both these sites appear to be surface exposed, and suggest a model for activation by TyrR. They also help resolve confusing results in the literature that implicated residues within the 261 and 265 determinants, as Activator contact sites. IMPORTANCE Regulation of transcription by RNA polymerases is fundamental for adaptation to a changing environment and for cellular differentiation, across all kingdoms of life. The gene TyrR in Escherichia coli is a particularly useful model because it is involved in both activation and repression of a large number of operons by a range of mechanisms, and it interacts with all three aromatic amino acids and probably other effectors. Furthermore TyrR has homologues in many other genera, regulating many different genes, utilizing different effector molecules, and in some cases affecting virulence, and important plant interactions.

scholarly journals Differential behaviors of Staphylococcus aureus and Escherichia coli type II DNA topoisomerases.

1996 ◽  
Vol 40 (12) ◽  
pp. 2714-2720 ◽  
Author(s):  
F Blanche ◽  
B Cameron ◽  
F X Bernard ◽  
L Maton ◽  
B Manse ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Strong Support ◽  
Dna Gyrase ◽  
Dna Supercoiling ◽  
Type Ii ◽  
Topoisomerase Iv ◽  
E Coli ◽  
Dna Relaxation

Staphylococcus aureus gyrA and gyrB genes encoding DNA gyrase subunits were cloned and coexpressed in Escherichia coli under the control of the T7 promoter-T7 RNA polymerase system, leading to soluble gyrase which was purified to homogeneity. Purified gyrase was catalytically indistinguishable from the gyrase purified from S. aureus and did not contain detectable amounts of topoisomerases from the E. coli host. Topoisomerase IV subunits GrlA and GrlB from S. aureus were also expressed in E. coli and were separately purified to apparent homogeneity. Topoisomerase IV, which was reconstituted by mixing equimolar amounts of GrlA and GrlB, had both ATP-dependent decatenation and DNA relaxation activities in vitro. This enzyme was more sensitive than gyrase to inhibition by typical fluoroquinolone antimicrobial agents such as ciprofloxacin or sparfloxacin, adding strong support to genetic studies which indicate that topoisomerase IV is the primary target of fluoroquinolones in S. aureus. The results obtained with ofloxacin suggest that this fluoroquinolone could also primarily target gyrase. No cleavable complex could be detected with S. aureus gyrase upon incubation with ciprofloxacin or sparfloxacin at concentrations which fully inhibit DNA supercoiling. This suggests that these drugs do not stabilize the open DNA-gyrase complex, at least under standard in vitro incubation conditions, but are more likely to interfere primarily with the DNA breakage step, contrary to what has been reported with E. coli gyrase. Both S. aureus gyrase-catalyzed DNA supercoiling and S. aureus topoisomerase IV-catalyzed decatenation were dramatically stimulated by potassium glutamate or aspartate (500- and 50-fold by 700 and 350 mM glutamate, respectively), whereas topoisomerase IV-dependent DNA relaxation was inhibited 3-fold by 350 mM glutamate. The relevance of the effect of dicarboxylic amino acids on the activities of type II topoisomerases is discussed with regard to the intracellular osmolite composition of S. aureus.

scholarly journals The Global Regulatory Cyclic AMP Receptor Protein (CRP) Controls Multifactorial Fluoroquinolone Susceptibility in Salmonella enterica Serovar Typhimurium

2017 ◽  
Vol 61 (11) ◽  
Author(s):  
Stefani C. Kary ◽  
Joshua R. K. Yoneda ◽  
Stephen C. Olshefsky ◽  
Laura A. Stewart ◽  
Steven B. West ◽  
...  
Keyword(s):  
Cyclic Amp ◽  
Salmonella Enterica ◽  
Topoisomerase I ◽  
Multiple Drug Resistance ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Receptor Protein ◽  
Multiple Drug ◽  
Topoisomerase Iv ◽  
Fluoroquinolone Antibiotics

ABSTRACT Fluoroquinolone antibiotics are prescribed for the treatment of Salmonella enterica infections, but resistance to this family of antibiotics is growing. Here we report that loss of the global regulatory protein cyclic AMP (cAMP) receptor protein (CRP) or its allosteric effector, cAMP, reduces susceptibility to fluoroquinolones. A Δcrp mutation was synergistic with the primary fluoroquinolone resistance allele gyrA83, thus able to contribute to clinically relevant resistance. Decreased susceptibility to fluoroquinolones could be partly explained by decreased expression of the outer membrane porin genes ompA and ompF with a concomitant increase in the expression of the ciprofloxacin resistance efflux pump gene acrB in Δcrp cells. Expression of gyrAB, which encode the DNA supercoiling enzyme GyrAB, which is blocked by fluoroquinolones, and expression of topA, which encodes the dominant supercoiling-relaxing enzyme topoisomerase I, were unchanged in Δcrp cells. Yet Δcrp cells maintained a more relaxed state of DNA supercoiling, correlating with an observed increase in topoisomerase IV (parCE) expression. Surprisingly, the Δcrp mutation had the unanticipated effect of enhancing fitness in the presence of fluoroquinolone antibiotics, which can be explained by the observation that exposure of Δcrp cells to ciprofloxacin had the counterintuitive effect of restoring wild-type levels of DNA supercoiling. Consistent with this, Δcrp cells did not become elongated or induce the SOS response when challenged with ciprofloxacin. These findings implicate the combined action of multiple drug resistance mechanisms in Δcrp cells: reduced permeability and elevated efflux of fluoroquinolones coupled with a relaxed DNA supercoiling state that buffers cells against GyrAB inhibition by fluoroquinolones.

DNA relaxation mediated by Ustilago maydis type I topoisomerase; modulation by chromatin associated proteins

1993 ◽  
Vol 1173 (2) ◽  
pp. 155-164 ◽  
Author(s):  
Manimekalai M. Thiyagarajan ◽  
Hidehito Kotani ◽  
William K. Holloman ◽  
Eric B. Kmiec
Keyword(s):  
Ustilago Maydis ◽  
Type I ◽  
Dna Relaxation ◽  
Associated Proteins

Toxicoproteomic Analysis of Poly(ADP-Ribose)-Associated Proteins Induced by Oxidative Stress in Human Proximal Tubule Cells

2019 ◽  
Vol 171 (1) ◽  
pp. 117-131
Author(s):  
Argel Islas-Robles ◽  
Deepthi Yedlapudi ◽  
Serrine S Lau ◽  
Terrence J Monks
Keyword(s):  
Oxidative Stress ◽  
Cell Death ◽  
Proximal Tubule ◽  
Calcium Influx ◽  
Regulation Of Transcription ◽  
Loss Of Function ◽  
Proximal Tubule Cells ◽  
Associated Proteins ◽  
Tubule Cells ◽  
Parp 1

Abstract 2,3,5-Tris-(glutathion-S-yl)hydroquinone (TGHQ) is a nephrotoxic and nephrocarcinogenic metabolite of hydroquinone. TGHQ generates reactive oxygen species (ROS), causing DNA-strand breaks, hyperactivation of PARP-1, increases in intracellular calcium ([Ca2+]i), and cell death. PARP-1 catalyzes the attachment of ADP-ribose polymers (PAR) to target proteins. In human kidney proximal tubule cells, ROS-mediated PARP-1 hyperactivation and elevations in [Ca2+]i are reciprocally coupled. The molecular mechanism of this interaction is unclear. The aim of the present study was to identify ROS-induced PAR-associated proteins to further understand their potential role in cell death. PAR-associated proteins were enriched by immunoprecipitation, identified by LC-MS/MS, and relative abundance was obtained by spectral counting. A total of 356 proteins were PAR-modified following TGHQ treatment. A total of 13 proteins exhibited gene ontology annotations related to calcium. Among these proteins, the general transcription factor II-I (TFII-I) is directly involved in the modulation of [Ca2+]i. TFII-I binding to phospholipase C (PLC) leads to calcium influx via the TRPC3 channel. However, inhibition of TRPC3 or PLC had no effect on TGHQ-mediated cell death, suggesting that their loss of function may be necessary but insufficient to cause cell death. Nevertheless, TGHQ promoted a time-dependent translocation of TFII-I from the nucleus to the cytosol concomitant with a decrease in tyrosine phosphorylation in α/β-TFII-I. Therefore it is likely that ROS have an important impact on the function of TFII-I, such as regulation of transcription, and DNA translesion synthesis. Our data also shed light on PAR-mediated signaling during oxidative stress, and contributes to the development of strategies to prevent PAR-dependent cell death.

Regulatory protein genes and microRNAs in response to selenium stimuli in Pueraria lobata (Willd.) Ohwi

Metallomics ◽  
2020 ◽  
Author(s):  
Yanni Li ◽  
Meijun He ◽  
Jishuang Li ◽  
Yiwei Yao ◽  
Li Zhu ◽  
...  
Keyword(s):  
Structural Gene ◽  
Target Genes ◽  
Regulatory Protein ◽  
Enrichment Analysis ◽  
Regulation Of Transcription ◽  
Pueraria Lobata ◽  
Ros Scavenging ◽  
Edible Plant ◽  
Go Enrichment ◽  
Highly Correlated

Abstract Regulatory protein genes and microRNAs (miRNAs) play important roles in response to abiotic and biotic stress, and the biosynthesis of secondary metabolites in plants. However, their responses to selenium (Se) stimuli have not been comprehensively studied in Pueraria lobata (Willd.) Ohwi, a Selenocompound-rich medicinal and edible plant. In this study, we identified a total of 436/556/1161/624 transcription factors (TFs), 134/157/308/172 transcriptional regulators (TRs) and 341/456/250/518 protein kinases (PKs), which were coexpressed with at least one Selenocompound-related structural gene/sulfate transporter or phosphate transporter/ROS scavenging structural gene/isoflavone-related structural gene, respectively. Then, we identified a total of 87 expressed miRNAs by Se disposure, in which 11 miRNAs, including miR171f-3p, miR390b-3P, miR-N111b, miR-N118, miR-N30, miR-N38-3P, miR-N61a, miR-N61b, miR-N80-3p, miR-N84-3P and miR-N90.2-3P were significantly up-regulated. We also identified a total of 1172 target genes for the 87 expressed miRNAs. Go enrichment analysis of these target genes showed that terms of regulation of transcription, DNA-templated, integral component of membrane, nucleus, ATP binding and plasma membrane are the top five subclassifications. Finally, we revealed that 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one Selenocompound-related structural gene or transporter gene; 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one ROS scavenging structural gene; 5 miRNAs targeted 9 regulatory protein genes, which are potentially involved in the isoflavone biosynthesis. Overall, the study provides us the comprehensive insight of the roles of regulatory proteins and miRNAs in response to Se stimuli in P. lobata.

scholarly journals G-Quadruplex loops regulate PARP-1 enzymatic activation

2020 ◽  
Author(s):  
Andrea D Edwards ◽  
John C Marecki ◽  
Alicia K Byrd ◽  
Jun Gao ◽  
Kevin D Raney
Keyword(s):  
Dna Repair ◽  
Enzymatic Activity ◽  
Regulation Of Transcription ◽  
Dna Structures ◽  
Repair Enzymes ◽  
G Quadruplex ◽  
Associated Proteins ◽  
Enzymatic Activation ◽  
Forming Characteristics ◽  
Parp 1

Abstract G-Quadruplexes are non-B form DNA structures present at regulatory regions in the genome, such as promoters of proto-oncogenes and telomeres. The prominence in such sites suggests G-quadruplexes serve an important regulatory role in the cell. Indeed, oxidized G-quadruplexes found at regulatory sites are regarded as epigenetic elements and are associated with an interlinking of DNA repair and transcription. PARP-1 binds damaged DNA and non-B form DNA, where it covalently modifies repair enzymes or chromatin-associated proteins respectively with poly(ADP-ribose) (PAR). PAR serves as a signal in regulation of transcription, chromatin remodeling, and DNA repair. PARP-1 is known to bind G-quadruplexes with stimulation of enzymatic activity. We show that PARP-1 binds several G-quadruplex structures with nanomolar affinities, but only a subset promote PARP-1 activity. The G-quadruplex forming sequence found in the proto-oncogene c-KIT promoter stimulates enzymatic activity of PARP-1. The loop-forming characteristics of the c-KIT G-quadruplex sequence regulate PARP-1 catalytic activity, whereas eliminating these loop features reduces PARP-1 activity. Oxidized G-quadruplexes that have been suggested to form unique, looped structures stimulate PARP-1 activity. Our results support a functional interaction between PARP-1 and G-quadruplexes. PARP-1 enzymatic activation by G-quadruplexes is dependent on the loop features and the presence of oxidative damage.

scholarly journals The nucleoid-associated proteins H-NS and FIS modulate the DNA supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium Dickeya dadantii

2012 ◽  
Vol 40 (10) ◽  
pp. 4306-4319 ◽  
Author(s):  
Zghidi-Abouzid Ouafa ◽  
Sylvie Reverchon ◽  
Thomas Lautier ◽  
Georgi Muskhelishvili ◽  
William Nasser
Keyword(s):  
Virulence Factors ◽  
Plant Pathogen ◽  
Dna Supercoiling ◽  
Dickeya Dadantii ◽  
Associated Proteins
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