Complete genome sequence of Nakamurella multipartita type strain (Y-104)

Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the monospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Nanobiotechnology in combating CoVid-19

Emergence of novel pandemic viral disease CoVid-19 and its mutational behaviour are alarming. The potential use of nano-biotechnology in combating CoVid-19 is promising. We glean available data to explore such possibility in this short note.     

Ubiquitin Signaling Regulates RNA Biogenesis,Processing, and Metabolism

The fate of eukaryotic proteins, from their synthesis to destruction, is supervised by the ubiquitin–proteasome system (UPS). The UPS is the primary pathway responsible for selective proteolysis of intracellular proteins, which is guided by covalent attachment of ubiquitin to target proteins by E1 (activating), E2 (conjugating), and E3 (ligating) enzymes in a process known as ubiquitylation. The UPS can also regulate protein synthesis by influencing multiple steps of RNA (ribonucleic acid) metabolism. Here, recent publications concerning the interplay between the UPS and different types of RNA are reviewed. This interplay mainly involves specific RNA-binding E3 ligases that link RNA-dependent processes with protein ubiquitylation. The emerging understanding of their modes of RNA binding, their RNA targets, and their molecular and cellular functions are primarily focused on. It is discussed how the UPS adapted to interact with different types of RNA and how RNA molecules influence the ubiquitin signaling components.     

MicroRNA-196a promotes renal cancer cell migration and invasion by targeting BRAM1 to regulate SMAD and MAPK signaling pathways

Rationale: MicroRNAs (miRNAs) are endogenous ~22nt RNAs that play critical regulatory roles in various biological and pathological processes, including various cancers. Their function in renal cancer has not been fully elucidated. It has been reported that miR-196a can act as oncogenes or as tumor suppressors depending on their target genes. However, the molecular target for miR-196a and the underlying mechanism in miR-196a promoted cell migration and invasion in renal cancer is still not clear.Methods: The expression, survival and correlation between miR-196a and BRAM1 were investigated using TCGA analysis and validated by RT-PCR and western blot. To visualize the effect of Bram1 on tumor metastasis in vivo, NOD-SCID gamma (NSG) mice were intravenously injected with RCC4 cells (10⁶ cells/mouse) or RCC4 overexpressing Bram1. In addition, cell proliferation assays, migration and invasion assays were performed to examine the role of miR-196a in renal cells in vitro. Furthermore, immunoprecipitation was done to explore the binding targets of Bram1.Results: TCGA gene expression data from renal clear cell carcinoma patients showed a lower level of Bram1 expression in patients'' specimens compared to adjacent normal tissues. Moreover, Kaplan‑Meier survival data clearly show that high expression of Bram1correlates to poor prognosis in renal carcinoma patients. Our mouse metastasis model confirmed that Bram1 overexpression resulted in an inhibition in tumor metastasis. Target-prediction analysis and dual-luciferase reporter assay demonstrated that Bram1 is a direct target of miR-196a in renal cells. Further, our in vitro functional assays revealed that miR-196a promotes renal cell proliferation, migration, and invasion. Rescue of Bram1 expression reversed miR-196a-induced cell migration. MiR-196a promotes renal cancer cell migration by directly targeting Bram1 and inhibits Smad1/5/8 phosphorylation and MAPK pathways through BMPR1A and EGFR.Conclusions: Our findings thus provide a new mechanism on the oncogenic role of miR-196a and the tumor-suppressive role of Bram1 in renal cancer cells. Dysregulated miR-196a and Bram1 represent potential prognostic biomarkers and may have therapeutic applications in renal cancer.     

Physiological and Genetic Analyses Leading to Identification of a Biochemical Role for the moeA (Molybdate Metabolism) Gene Product in Escherichia coli

A unique class of chlorate-resistant mutants of Escherichia coli which produced formate hydrogenlyase and nitrate reductase activities only when grown in medium with limiting amounts of sulfur compounds was isolated. These mutants failed to produce the two molybdoenzyme activities when cultured in rich medium or glucose-minimal medium. The mutations in these mutants were localized in the moeA gene. Mutant strains with polar mutations in moeA which are also moeB did not produce active molybdoenzymes in any of the media tested. moeA mutants with a second mutation in either cysDNCJI or cysH gene lost the ability to produce active molybdoenzyme even when grown in medium limiting in sulfur compounds. The CysDNCJIH proteins along with CysG catalyze the conversion of sulfate to sulfide. Addition of sulfide to the growth medium of moeA cys double mutants suppressed the MoeA⁻ phenotype. These results suggest that in the absence of MoeA protein, the sulfide produced by the sulfate activation/reduction pathway combines with molybdate in the production of activated molybdenum. Since hydrogen sulfide is known to interact with molybdate in the production of thiomolybdate, it is possible that the MoeA-catalyzed activated molybdenum is a form of thiomolybdenum species which is used in the synthesis of molybdenum cofactor from Mo-free molybdopterin.Molybdoenzymes play essential metabolic roles in most organisms from bacteria to plants and animals (34). All molybdoenzymes other than dinitrogenase contain molybdenum cofactor, which consists of a unique molybdopterin (MPT) complexed with molybdenum (1, 12, 23, 31, 34). In Escherichia coli, the biologically active form of the cofactor in molybdoenzymes is MPT guanine dinucleotide (MGD) (5, 22, 23). Synthesis of this cofactor in an active form requires transport of molybdate into the cell, activation of molybdate, synthesis of the MPT moiety, and incorporation of molybdate into MPT. Although molybdate transport and the various steps in the organic part of MGD biosynthesis are well characterized (17, 24, 33; see references 10, 22, and 23 for reviews), very little is known about the activation and incorporation of molybdenum into the cofactor (22).Mutants which are defective in molybdate metabolism can be isolated as chlorate-resistant mutants (8, 9). A large fraction of these mutants are pleiotropic for all molybdoenzyme activities in the cell, and these comprise the three genetic loci involved in MGD synthesis, moa, mob, and moeB (see references 10, 22, 29, and 31 for reviews). The mod gene products comprise the molybdate transport system through which molybdate is transported into the cell and the Mod⁻ phenotype can be suppressed by increasing molybdate concentration in the medium. The mog mutants which produced formate hydrogenlyase (FHL) activity containing the molybdoenzyme formate dehydrogenase-H (FDH-H) but not nitrate reductase activity was proposed to be defective in molybdochelatase (13, 32). This molybdochelatase is apparently required for production of active nitrate reductase and not for FDH-H.The moe operon codes for two proteins, and only the physiological role of the second gene product, MoeB protein, is known. The MoeB protein activates MPT synthase, which catalyzes the conversion of MPT precursor (precursor Z) to MPT by introducing the needed sulfur to which Mo is coordinated in the molybdenum cofactor (20, 22). The MoeB protein, MPT synthase sulfurylase, is the known S donor in the activation of MPT synthase. The physiological role of MoeA protein coded by the first gene in the two member moe operon is not known. Mutants which are defective in moeA (chlE [29]) produced about 6% of the wild-type levels of MPT (12), although no molybdoenzyme activity was found in these moeA mutants. Since the MoeB protein acts as an S donor in MPT synthesis, it is possible that the first gene product, MoeA protein, also has a similar role in linking S metabolism and Mo metabolism in the cell.During our analysis of molybdate transport-defective mutants, we identified a subgroup of chlorate-resistant mutants with a unique phenotype. Mutations in this class of mutants were mapped in the moeA gene at 18.6 min on the E. coli chromosome (3, 18). The MoeA⁻ phenotype was suppressed when the growth medium was supplemented with sulfide. In this report, we present the physiological and genetic characteristics of E. coli moeA mutants and propose a role for the MoeA protein in the activation of molybdenum by sulfurylation.(This work was presented at the International Symposium on Nitrogen Assimilation: Molecular and Genetic Aspects, 3 to 9 May 1997, Tampa, Fla.)     

Insight into the Enzyme-Inhibitor Interactions of the First Experimentally Determined Human Aromatase

Abstract

Aromatase is an important pharmacological target in the anti-cancer therapy as the intratumoral aromatase is the source of local estrogen production in breast cancer tissues. Suppression of estrogen biosynthesis by aromatase inhibition represents an effective approach for the treatment of hormone-sensitive breast cancer. Because of the membrane-bound character and heme-binding instability, no crystal structure of aromatase was reported for a long time, until recently when crystal structure of human placental aromatase cytochrome P450 in complex with androstenedione was deposited in PDB. The present study is towards understanding the structural and functional characteristics of aromatase to address unsolved mysteries about this enzyme and elucidate the exact mode of binding of aromatase inhibitors. We have performed molecular docking simulation with twelve different inhibitors (ligands), which includes four FDA approved drugs; two flavonoids; three herbal compounds and three compounds having biphenyl motif with known IC₅₀ values into the active site of the human aromatase enzyme. All ligands showed favorable interactions and most of them seemed to interact to hydrophobic amino acids Ile133, Phe134, Phe221, Trp224, Ala306, Val370, Val373, Met374 and Leu477 and hydrophilic Arg115 and neutral Thr310 residues. The elucidation of the actual structure-function relationship of aromatase and the exact binding mode described in this study will be of significant interest as its inhibitors have shown great promise in fighting breast cancer.     

Increased furan tolerance in Escherichia coli due to a cryptic ucpA gene

Expression arrays were used to identify 4 putative oxidoreductases that were upregulated (>3-fold) by furfural (15 mM, 15 min). Plasmid expression of one (ucpA) increased furan tolerance in ethanologenic strain LY180 and wild-type strain W. Deleting ucpA decreased furfural tolerance. Although the mechanism remains unknown, the cryptic ucpA gene is now associated with a phenotype: furan resistance.     

Exploring the interaction of the photodynamic therapeutic agent thionine with bovine serum albumin: multispectroscopic and molecular docking studies

This study explores the binding interaction of thionine (TH) with bovine serum albumin (BSA) under physiological conditions (pH 7.40) using absorption, emission, synchronous emission, circular dichroism (CD) and three‐dimensional (3D) emission spectral studies. The results of emission titration experiments revealed that TH strongly quenches the intrinsic emission of BSA via a static quenching mechanism. The apparent binding constant (K) and number of binding sites (n) were calculated as 2.09 × 10⁵ dm³/mol and n~1, respectively. The negative free energy change value for the BSA–TH system suggested that the binding interaction was spontaneous and energetically favourable. The results from absorption, synchronous emission, CD and 3D emission spectral studies demonstrated that TH induces changes in the microenvironment and secondary structure in BSA. Site marker competitive binding experiments revealed that the binding site of TH was located in subdomain IIA (Sudlow site I) of BSA. The molecular docking study further substantiates Sudlow site I as the preferable binding site of TH in BSA. Copyright © 2014 John Wiley & Sons, Ltd.