The transcriptional activator of the bfp operon in EPEC (PerA) interacts with the RNA polymerase alpha subunit

AbstractEnteropathogenic E. coli virulence genes are under the control of various regulators, one of which is PerA, an AraC/XylS-like regulator. PerA directly promotes its own expression and that of the bfp operon encoding the genes involved in the biogenesis of the bundle-forming pilus (BFP); it also activates PerC expression, which in turn stimulates locus of enterocyte effacement (LEE) activation through the LEE-encoded regulator Ler. Monomeric PerA directly binds to the per and bfp regulatory regions; however, it is not known whether interactions between PerA and the RNA polymerase (RNAP) are needed to activate gene transcription as has been observed for other AraC-like regulators. Results showed that PerA interacts with the alpha subunit of the RNAP polymerase and that it is necessary for the genetic and phenotypic expression of bfpA. Furthermore, an in silico analysis shows that PerA might be interacting with specific alpha subunit amino acids residues highlighting the direction of future experiments.

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Molecular characterization and in silico analysis of RNA polymerase alpha subunit gene (rpoA) in Date Palm (Phoenix dactylifera L.) cv. Deglet Nour

Genes & Genomics ◽

10.1007/s13258-012-0027-7 ◽

2012 ◽

Vol 34 (6) ◽

pp. 599-608 ◽

Cited By ~ 1

Author(s):

Amina Dhieb ◽

Amine Elleuch ◽

Walid Kriaa ◽

Faiza Masmoudi ◽

Nourredine Drira

Keyword(s):

Rna Polymerase ◽

Molecular Characterization ◽

In Silico ◽

Date Palm ◽

In Silico Analysis ◽

Phoenix Dactylifera ◽

Alpha Subunit ◽

Subunit Gene ◽

Phoenix Dactylifera L ◽

Silico Analysis

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Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove

Genes & Development ◽

10.1101/gad.870001 ◽

2001 ◽

Vol 15 (5) ◽

pp. 491-506 ◽

Cited By ~ 68

Author(s):

W. Ross

Keyword(s):

Fine Structure ◽

Rna Polymerase ◽

Minor Groove ◽

Alpha Subunit ◽

E Coli ◽

Rna Polymerase Promoter

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Rice heterotrimeric G-protein alpha subunit (RGA1): In silico analysis of the gene and promoter and its upregulation under abiotic stress

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2012.11.031 ◽

2013 ◽

Vol 63 ◽

pp. 262-271 ◽

Cited By ~ 15

Author(s):

Dinesh K. Yadav ◽

Devesh Shukla ◽

Narendra Tuteja

Keyword(s):

Abiotic Stress ◽

G Protein ◽

In Silico ◽

In Silico Analysis ◽

Alpha Subunit ◽

Heterotrimeric G Protein ◽

G Protein Alpha Subunit ◽

Silico Analysis ◽

Protein Alpha Subunit

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Two Distinct Modes of Lysis Regulation in Campylobacter Fletchervirus and Firehammervirus Phages

Viruses ◽

10.3390/v12111247 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1247

Author(s):

Athina Zampara ◽

Stephen J. Ahern ◽

Yves Briers ◽

Lone Brøndsted ◽

Martine Camilla Holst Sørensen

Keyword(s):

Signal Peptide ◽

In Silico ◽

Protein Domains ◽

In Silico Analysis ◽

Cell Lysis ◽

E Coli ◽

Sec Pathway ◽

Gene Functions ◽

Lytic Genes ◽

Silico Analysis

Campylobacter phages are divided into two genera; Fletchervirus and Firehammervirus, showing only limited intergenus homology. Here, we aim to identify the lytic genes of both genera using two representative phages (F352 and F379) from our collection. We performed a detailed in silico analysis searching for conserved protein domains and found that the predicted lytic genes are not organized into lysis cassettes but are conserved within each genus. To verify the function of selected lytic genes, the proteins were expressed in E. coli, followed by lytic assays. Our results show that Fletchervirus phages encode a typical signal peptide (SP) endolysin dependent on the Sec-pathway for translocation and a holin for activation. In contrast, Firehammervirus phages encode a novel endolysin that does not belong to currently described endolysin groups. This endolysin also uses the Sec-pathway for translocation but induces lysis of E. coli after overexpression. Interestingly, co-expression of this endolysin with an overlapping gene delayed and limited cell lysis, suggesting that this gene functions as a lysis inhibitor. These results indicate that Firehammervirus phages regulate lysis timing by a yet undescribed mechanism. In conclusion, we found that the two Campylobacter phage genera control lysis by two distinct mechanisms.

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Molecular characterization, modeling, in silico analysis of equine pituitary gonadotropin alpha subunit and docking interaction studies with ganirelix

In Silico Pharmacology ◽

10.1007/s40203-017-0025-1 ◽

2017 ◽

Vol 5 (1) ◽

Author(s):

Anuradha Bhardwaj ◽

Varij Nayan ◽

Parvati Sharma ◽

Sanjay Kumar ◽

Yash Pal ◽

...

Keyword(s):

Molecular Characterization ◽

In Silico ◽

In Silico Analysis ◽

Alpha Subunit ◽

Interaction Studies ◽

Pituitary Gonadotropin ◽

Docking Interaction ◽

Silico Analysis

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Overexpression of the RNA Polymerase Alpha Subunit Reduces Transcription of Bvg-Activated Virulence Genes inBordetella pertussis

Journal of Bacteriology ◽

10.1128/jb.182.2.529-531.2000 ◽

2000 ◽

Vol 182 (2) ◽

pp. 529-531 ◽

Cited By ~ 7

Author(s):

Nicholas H. Carbonetti ◽

Alla Romashko ◽

Teresa J. Irish

Keyword(s):

Rna Polymerase ◽

Virulence Factor ◽

Pertussis Toxin ◽

Bordetella Pertussis ◽

Virulence Genes ◽

Transcriptional Activator ◽

Alpha Subunit ◽

Terminal Domain

ABSTRACT Overexpression of the RNA polymerase alpha subunit inBordetella pertussis reduces expression of the virulence factor pertussis toxin. Here we show that this reduction is at the level of transcription, is reversed by overexpression of the transcriptional activator BvgA, and is dependent on the C-terminal domain of alpha.

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In Silico Analysis of Some Phytochemicals as Potent Anti-tubercular Agents Targeting Mycobacterium tuberculosis RNA Polymerase and InhA Protein

10.20944/preprints202010.0098.v1 ◽

2020 ◽

Author(s):

Md Emran ◽

Md. Mofijur Rahman ◽

Afroza Khanam Anika ◽

Sultana Hossain Nasrin ◽

Abu Tayab Moin

Keyword(s):

Mycobacterium Tuberculosis ◽

Rna Polymerase ◽

In Silico ◽

Acyl Carrier Protein ◽

Low Cost ◽

In Silico Analysis ◽

The Past ◽

Two Agents ◽

In Silico Biology ◽

Silico Analysis

Tuberculosis (TB) is a contagious disease, caused by Mycobacterium tuberculosis (MTB) that has infected and killed a lot of people in the past. At present treatments against TB are available at a very low cost. Since these chemical drugs have many adverse effects on health, more attention is now given on the plant-derived phytochemicals as potential agents to fight against TB. In this study, 5 phytochemicals, 4-hydroxybenzaldehyde, benzoic acid, bergapten, psoralen, and p-hydroxybenzoic acid, are selected to test their potentiality, safety, and efficacy against two potential targets, the MTB RNA polymerase and enoyl-acyl carrier protein (ACP) reductase, the InhA protein, using various tools of in silico biology. The molecular docking experiment, drug-likeness property test, ADME/T-test, P450 SOM prediction, pharmacophore mapping, and modeling, solubility testing, DFT calculations, and PASS prediction study had confirmed that all the molecules had the good potentiality to inhibit the two targets. However, two agents, 4-hydroxybenzaldehyde and bergapten were considered as the best agents among the five selected agents and they also showed far better results than the two currently used drugs, that function in these pathways, rifampicin (MTB RNA polymerase) and isoniazid (InhA protein). These two agents can be used effectively to treat tuberculosis.

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Haemophilus influenzae HP1 Bacteriophage Encodes a Lytic Cassette with a Pinholin and a Signal-Arrest-Release Endolysin

International Journal of Molecular Sciences ◽

10.3390/ijms21114013 ◽

2020 ◽

Vol 21 (11) ◽

pp. 4013

Author(s):

Monika Adamczyk-Popławska ◽

Zuzanna Tracz-Gaszewska ◽

Przemysław Lasota ◽

Agnieszka Kwiatek ◽

Andrzej Piekarowicz

Keyword(s):

Haemophilus Influenzae ◽

Gene Product ◽

Transmembrane Protein ◽

In Silico Analysis ◽

Viable Cell ◽

Cell Lysis ◽

Gene Products ◽

E Coli ◽

Myoviridae Family ◽

Silico Analysis

HP1 is a temperate bacteriophage, belonging to the Myoviridae family and infecting Haemophilus influenzae Rd. By in silico analysis and molecular cloning, we characterized lys and hol gene products, present in the previously proposed lytic module of HP1 phage. The amino acid sequence of the lys gene product revealed the presence of signal-arrest-release (SAR) and muraminidase domains, characteristic for some endolysins. HP1 endolysin was able to induce lysis on its own when cloned and expressed in Escherichia coli, but the new phage release from infected H. influenzae cells was suppressed by inhibition of the secretion (sec) pathway. Protein encoded by hol gene is a transmembrane protein, with unusual C-out and N-in topology, when overexpressed/activated. Its overexpression in E. coli did not allow the formation of large pores (lack of leakage of β-galactosidase), but caused cell death (decrease in viable cell count) without lysis (turbidity remained constant). These data suggest that lys gene encodes a SAR-endolysin and that the hol gene product is a pinholin. HP1 SAR-endolysin is responsible for cell lysis and HP1 pinholin seems to regulate the cell lysis and the phage progeny release from H. influenzae cells, as new phage release from the natural host was inhibited by deletion of the hol gene.

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