scholarly journals Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa

mSystems ◽  
2021 ◽  
Author(s):  
Kevin S. Myers ◽  
Daniel R. Noguera ◽  
Timothy J. Donohue

Transcription of DNA to RNA by RNA polymerase is essential for cells to grow, develop, and respond to stress. Understanding the process and control of transcription is important for health, disease, the environment, and biotechnology.

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1166
Author(s):  
Krishnaprasad Baby ◽  
Swastika Maity ◽  
Chetan H. Mehta ◽  
Akhil Suresh ◽  
Usha Y. Nayak ◽  
...  

Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), took more lives than combined epidemics of SARS, MERS, H1N1, and Ebola. Currently, the prevention and control of spread are the goals in COVID-19 management as there are no specific drugs to cure or vaccines available for prevention. Hence, the drug repurposing was explored by many research groups, and many target proteins have been examined. The major protease (Mpro), and RNA-dependent RNA polymerase (RdRp) are two target proteins in SARS-CoV-2 that have been validated and extensively studied for drug development in COVID-19. The RdRp shares a high degree of homology between those of two previously known coronaviruses, SARS-CoV and MERS-CoV. Methods: In this study, the FDA approved library of drugs were docked against the active site of RdRp using Schrodinger's computer-aided drug discovery tools for in silico drug-repurposing. Results: We have shortlisted 14 drugs from the Standard Precision docking and interaction-wise study of drug-binding with the active site on the enzyme. These drugs are antibiotics, NSAIDs, hypolipidemic, coagulant, thrombolytic, and anti-allergics. In molecular dynamics simulations, pitavastatin, ridogrel and rosoxacin displayed superior binding with the active site through ARG555 and divalent magnesium. Conclusion: Pitavastatin, ridogrel and rosoxacin can be further optimized in preclinical and clinical studies to determine their possible role in COVID-19 treatment.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 386-386 ◽  
Author(s):  
Ken-ichiro Watanabe ◽  
Yigal Dror

Abstract Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterized by bone marrow failure, pancreatic insufficiency, and a marked propensity for myelodysplastic syndrome and leukemia. Approximately 90% of the patients have mutations in the SBDS gene. Recent studies suggested a role of the yeast SBDS homologue, YLR022C, in RNA processing and ribosomal biogenesis. However, the function of the human SBDS has not been clarified yet. We previously showed that marrow cells from SDS patients are characterized by accelerated apoptosis, overexpression of Fas and hypersensitivity to Fas stimulation. To study the function of SBDS and determine whether the above abnormalities are caused by deficiency of SBDS, we established stably transfected Hela cell lines expressing two different siRNAs against SBDS and lines expressing scrambled siRNA control. SBDS-knockdown was confirmed by Western blotting using polyclonal chicken anti-human SBDS antibody. The SBDS expression in the scrambled siRNA control cells was comparable to that of wild-type Hela cells. DNA content analysis by propidium iodide staining showed a prominent increase in sub-G1 population in asynchronous, non-treated SBDS-knockdown cells, suggesting that these cells are prone to cell death, however, no cell cycle arrest was noted. To further characterize the SBDS-knockdown cells, we examined their sensitivity to four groups of cell death inducers: DNA damaging agents (etoposide, cisplatin, and doxorubicin), transcriptional inhibitors (actinomycin D and α-amanitin), translation blocker (cycloheximide), and Fas pathway activator (agonistic anti-Fas antibody CH-11). Dose-response curves were obtained by MTT assay performed 48 hrs after treatment of the cells with the reagents. Interestingly, SBDS-deleted cells showed marked hypersensitivity to CH-11; while 3 μ g/ml of CH-11 reduced the survival fraction to 50% in wild-type and control cells, a similar effect was obtained at 0.02 μ g/ml in the SBDS-deleted cells. The hypersensitivity to Fas stimulation was also demonstrated by DNA content analysis. Based on the possible role of the yeast SBDS orthologue in RNA metabolism, we anticipated that the SBDS-deficient cells would be hypersensitive to the transcription inhibitors. However, even at concentrations which completely abolished RNA polymerase I or RNA polymerase II activity as determined by BrUTP labeling, the sensitivity of the SBDS-knockdown cells to the transciptional inhibitors was not remarkably different from that of the control or wild type cells. Similarly, the sensitivity to the genotoxic agents and protein synthesis blocker was not obviously different between the SBDS-deficient and proficient cells. To study the mechanism for Fas hypersensitivity, we analyzed Fas expression by flow cytometry using Cy5-conjugated anti-CD95 antibody and found overexpression of Fas in the SBDS-deleted cells in comparison with the Fas expression in the wild-type and control cells. Although further investigation is needed, these results suggest that the SBDS protein might be involved in cell death pathway, especially in the regulation of Fas-mediated apoptosis. The siRNA-mediated SBDS knock-down Hela cells duplicate important features of SDS cells, and may serve as a useful model to investigate the function of the human SBDS protein.


1999 ◽  
Vol 181 (5) ◽  
pp. 1524-1529 ◽  
Author(s):  
Paolo Landini ◽  
Stephen J. W. Busby

ABSTRACT The methylated form of the Ada protein (meAda) activates transcription from the Escherichia coli ada,aidB, and alkA promoters with different mechanisms. In this study we identify amino acid substitutions in region 4 of the RNA polymerase subunit ς70 that affect Ada-activated transcription at alkA. Substitution to alanine of residues K593, K597, and R603 in ς70 region 4 results in decreased Ada-dependent binding of RNA polymerase to thealkA promoter in vitro and impairs alkAtranscription both in vivo and in vitro, suggesting that these residues define a determinant for meAda-ς70interaction. In a previous study (P. Landini, J. A. Bown, M. R. Volkert, and S. J. W. Busby, J. Biol. Chem. 273:13307–13312, 1998), we showed that a set of negatively charged amino acids in ς70 region 4 is involved inmeAda-ς70 interaction at the adaand aidB promoters. However, the alanine substitutions of positively charged residues K593, K597, and R603 do not affectmeAda-dependent transcription at ada andaidB. Unlike the ς70 amino acids involved in the interaction with meAda at the ada andaidB promoters, K593, K597, and R603 are not conserved in ςS, an alternative ς subunit of RNA polymerase mainly expressed during the stationary phase of growth. WhilemeAda is able to promote transcription by the ςS form of RNA polymerase (EςS) atada and aidB, it fails to do so atalkA. We propose that meAda can activate transcription at different promoters by contacting distinct determinants in ς70 region 4 in a manner dependent on the location of the Ada binding site.


2010 ◽  
Vol 285 (20) ◽  
pp. 15380-15392 ◽  
Author(s):  
Boris Shor ◽  
Jiang Wu ◽  
Quazi Shakey ◽  
Lourdes Toral-Barza ◽  
Celine Shi ◽  
...  

1976 ◽  
Vol 73 (9) ◽  
pp. 3201-3205 ◽  
Author(s):  
R. P. Bailey ◽  
M. J. Vrooman ◽  
Y. Sawai ◽  
K. Tsukada ◽  
J. Short ◽  
...  

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12581
Author(s):  
Chunxia Wang ◽  
Hulei Zhang ◽  
Shenhai Wang ◽  
Shengfeng Mao

Leaf spot of Hosta ventricosa is a new disease in China. This disease seriously affects the ornamental value and greening function of H. ventricosa. Identification of the causal agent can prevent and control leaf spot in H. ventricosa and promote the healthy development of the H. ventricosa industry. Known incidents of leaf spot of H. ventricosa occurred in three places, and samples were collected. After the fungus were isolated, its pathogenicity was tested according to Koch’s postulates. Isolates ZE-1b and ZE-2b were identified as Fusarium oxysporum based on morphological features and multigene phylogenetic analyses of calmodulin (CMDA), RNA polymerase II subunit A (RPB1), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1). These results provide a theoretical basis for the control of this disease of H. ventricosa.


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