DNA-directed RNA Polymerase Subunit Research Articles

Homology modeling and in silico toxicity assessment of potential inhibitors of cytidylate kinase from Mycobacterium tuberculosis

Cytidylate kinase (CMK) plays a central role in the phosphorylation of ATP to nucleoside diphosphates in the purine and pyrimidine pathway in Mycobacterium tuberculosis (MTB). The enzyme is specific to bacteria, fungi, and plants and it shares the same pathway with a DNA-directed RNA polymerase subunit beta, the known target of rifampicin (RIF). Therefore, it serves as an attractive alternative target to inhibit the purine and pyrimidine pathway in MTB. In this study, the novel inhibitors of CMK were identified using in silico approach. Homology modeling was used to build the three-dimensional (3D) structure of CMK using program implemented in Modeller 9.16 and based on the template (3R20) obtained from Mycobacterium smegmatis. Structural analysis of CMK showed that it has P-loop or core in the ATP binding domain, nucleoside monophosphate binding (NMP) site, and a LID domain. Inhibition of any of the residues that formed the nucleoside binding site or ATP binding site blocks the catalytic activity of the CMK. Eleven thousand four hundred and fifty-four compounds that had an affinity to bind to the CMK with minimum binding energies were obtained through virtual screening from Zinc and PubChem databases using PyRx 8.0. These compounds were further filtered for Lipinski rule of five, molecular docking analysis, and ADMET properties (absorption distribution, metabolism, excretion, and toxicity). Four compounds (ZINC95485891 = − 8.80 kcal/mol, ZINC95485880 = − 8.44 kcal/mol, ZINC95485900 = − 8.24 kcal/mol, and ZINC95486231 = − 8.20 kcal/mol) with good binding energies and desirable pharmacokinetic properties were selected. These compounds were further subjected to molecular dynamic (MD) simulation and molecular mechanics generalized Born and surface area (MM-GBSA) analyses. The results of the analyses showed that all the four ligands formed a stable complex and had good free binding energy after 50 ns MD simulation. Therefore, these compounds were considered as possible inhibitors of MTB after experimental validation.

Interactions of protein translocation machinery components of Streptococcus mutans

BackgroundPivotal virulence properties of the cariogenic bacterium Streptococcus mutans depend on secreted and integral membrane proteins. Bacterial protein trafficking involves the signal recognition particle (SRP) pathway components Ffh, scRNA and FtsY, the SecYEG translocon, the SecA motor protein, and membrane‐localized YidC chaperone/insertases. Unlike Escherichia coli, S. mutans survives loss of the SRP pathway. In addition, S. mutans has two yidC paralogs. The phenotype of a DyidC2 mutant largely parallels that of Dffh, while that of DyidC1 is far less severe. Also in S. mutans, YlxM acts as an accessory factor of the SRP that modulates GTP hydrolysis activities of Ffh and FtsY. The goal of this study is to identify interactions among S. mutans transport machinery components to better understand the respective functions of YidC1 and YidC2 alone and in concert with the SRP, ribosome, and/or Sec translocon that can affect the destiny of translocated proteins.MethodsA chemical cross‐linking approach was employed, whereby whole cell lysates (wcl) were treated with formaldehyde followed by Western blotting using anti‐Ffh, FtsY, YidC1 and YidC2 antibodies and mass spectrometry (MS) analysis of corresponding gel‐shifted bands. Wcl from WT and DyidC2 strains were also reacted with a‐YidC2 antibodies coupled to magnetic Dynabeads™ and co‐captured proteins identified by MS. In addition, biolayer interferometry (BLI) was used to evaluate specific interactions of the C‐terminal tails of YidC1 and YidC2, engineered as glutathione‐S‐transferase fusion proteins (GST‐C1 and GST‐C2), with the SRP components Ffh and YlxM. The same GST‐constructs were also subjected to 2D Difference Gel Electrophoresis (DIGE), in which each was reacted with wcl, captured with glutathione affinity resin, and labelled individually with fluorescent dyes. Spots unique to the GST‐C1 and/or GST‐C2 samples were analysed by MS.Results and ConclusionBand‐shift patterns detected with anti‐Ffh, FtsY and YidC2 antisera were similar to one another and distinct from that of anti‐YidC1. Cross‐linked proteins included elongation factor Tu, DNA‐directed RNA polymerase subunit b, and HSP 70. Immunocaptured proteins from anti‐YidC2 Dynabeads™ included two small, transmembrane proteins, LemA and SMU_1719c, which may represent translocation substrates. Both GST‐C1 and GST‐C2 interacted with Ffh by BLI with binding influenced by YlxM. Over one hundred spots were identified by DIGE. Among differentially identified proteins in the GST‐C1 sample were DnaK, RNA polymerase subunit d, and cell division protein FtsH. Ribosomal proteins S7 and L13 were prevalent in spots of the GST‐C2 sample, whereas ribosomal protein L2, DNA polymerase III g/t subunit, and the Cas5 homolog were all more abundant in spots from GST‐C1 and GST‐C2 samples compared to GST. This information suggests a coupled cellular machinery that integrates transcription and translation with protein transport and folding.Support or Funding InformationNIH R01DE008007This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Selection of Optimized Reference Genes for qRT-PCR Normalization in Xanthomonas campestris pv. campestris Cultured in Different Media.

Black rot is a cruciferous disease caused by Xanthomonas campestris pv. campestris (Xcc) and results in significant economic losses worldwide; therefore, elucidation of the mechanism of Xcc pathogenesis is urgently required. In this study, we aimed to select optimized reference genes to verify the relative quantification of virulent genes in Xcc. Xcc strains were cultured in three different media [basic medium (MMX), hrp-inducing medium (MMXC) and rich medium (NYG)] and the expression stability of five candidate genes [thymidylate synthase (thyA), DNA gyrase subunit B (gyrB), DNA-directed RNA polymerase subunit beta, glyceraldehyde-3-phosphate dehydrogenase and 16S ribosomal RNA (16S rRNA)] was evaluated using BestKeeper, GeNorm, and NormFinder software programs. Quantitative real-time PCR (qRT-PCR) analysis confirmed that two Xcc effector genes were hrpX/hrpG-regulated in MMXC using selected genes as controls. Finally, gyrB and thyA were validated as the optimized reference genes of Xcc cultured in MMXC, and qRT-PCR analysis was demonstrated to be an efficient alternative to Gus-activity detection for the analysis of Xcc expression. This information will be useful in the future studies of Xcc, especially those seeking new functional genes.

Sensitive and visual detection of Cronobacter spp. in powdered infant formula by saltatory rolling circle amplification method

Cronobacter species are opportunistic foodborne pathogens involved in neonatal infections from powdered infant formula (PIF). In this study, a novel saltatory rolling circle amplification (SRCA) method has been developed for detecting Cronobacter spp. in PIF. 16 of Cronobacter spp. strains and 32 of non-Cronobacter strains were examined by using the DNA-directed RNA polymerase subunit beta (rpoB) gene. All Cronobacter strains were identified in pure cultures, whereas no SRCA products were found in non-Cronobacter strains. The detection limits were 3.4 × 102 CFU/mL through observing the white precipitate by naked eye, while 3.4 × 101 CFU/mL by fluorescence visualization. After enrichment, the detection limits of SRCA method in PIF were 8.7 × 100 CFU/g and 8.7 × 10−1 CFU/g by visualization with white precipitate and fluorescence, respectively. Compared with the conventional PCR method, the SRCA has at least 100-fold higher sensitivity and 100-fold lower detection limit. In addition, 85 of PIF samples were investigated for the Cronobacter contamination, and the results were 100% sensitivity, 97.62% specificity and 97.65% accuracy compared with the ISO method. Therefore, the results show that SRCA is a sensitive and visual detection method for the detection of Cronobacter spp. in PIF with great potential.

Identification of a new diagnostic antigen for glanders using immunoproteome analysis.

Glanders is a disease of horses, donkeys and mules. The causative agent Burkholderia mallei, is a biorisk group 3 pathogen and is also a biothreat agent. Simple and rapid diagnostic tool is essential for control of glanders. Using a proteomic approach and immunoblotting with equine sera, we identified 12 protein antigens that may have diagnostic potential. Various immunoreactive proteins e.g. GroEL, translation elongation factor Tu, elongation factor Ts, arginine deiminase, malate dehydrogenase, DNA directed RNA polymerase subunit alpha were identified on 2-dimentional immunoblots. One of these proteins, GroEL, was cloned and expressed in E. coli and purified using Ni-NTA affinity chromatography. The recombinant GroEL protein was evaluated in ELISA format on a panel of glanders positive (n=49) and negative (n=79) equine serum samples to determine its diagnostic potential. The developed ELISA had a sensitivity and specificity of 96 and 98.7% respectively. The results of this study highlight the potential of GroEL in serodiagnosis of glanders.

ITRAQ-based quantitative proteomic analysis of Microcystis aeruginosa exposed to spiramycin at different nutrient levels

Research on the combined effects of antibiotic contaminants and environmental factors in cyanobacteria is still limited. This study focused on the action and its mechanism of spiramycin combined with changes in nitrogen and phosphorus level in Microcystis aeruginosa at environmentally relevant concentrations. Though photosynthetic activity was stimulated by spiramycin at a high nutrient level, no significant correlation (p>0.05) was found between photosynthesis-related proteins and growth-related proteins, and the growth rate was inhibited by 200ngL−1 of spiramycin. At low nitrogen and low phosphorus levels, up-regulated photosynthesis-related proteins were closely correlated with (p<0.05) stress response-related, transcription-related and cell division-related proteins, which consequently led to stimulated growth of M. aeruginosa under spiramycin exposure. Spiramycin exposure also regulated the production of microcystins (MCs) and the expression of two microcystin synthetases (mcyB and mcyC). The spiramycin-induced protein secretion process and the up-regulation of ATP binding cassette transporters might contribute to the increased MC release. Enolase, superoxide dismutase, protein GrpE, DNA-directed RNA polymerase subunit alpha and serine protease were candidate target proteins of spiramycin in M. aeruginosa under different nutrient conditions. Coexisting spiramycin mitigated the threat of cyanobacteria to aquatic environments at a high nutrient level but aggravated cyanobacterial bloom at a low nitrogen level.

Immunoproteomic profiling of Rickettsia parkeri and Rickettsia amblyommii

Rickettsia parkeri is an Amblyomma-associated, spotted fever group Rickettsia species that causes an eschar-associated, febrile illness in multiple countries throughout the Western Hemisphere. Many other rickettsial species of known or uncertain pathogenicity have been detected in Amblyomma spp. ticks in the Americas, including Rickettsia amblyommii, “Candidatus Rickettsia andeanae” and Rickettsia rickettsii. In this study, we utilized an immunoproteomic approach to compare antigenic profiles of low-passage isolates of R. parkeri and R. amblyommii with serum specimens from patients with PCR- and culture-confirmed infections with R. parkeri. Five immunoreactive proteins of R. amblyommii and nine immunoreactive proteins of R. parkeri were identified by matrix-assisted laser desorption ionization tandem time-of-flight mass spectrometry. Four of these, including the outer membrane protein (Omp) A, OmpB, translation initiation factor IF-2, and cell division protein FtsZ, were antigens common to both rickettsiae. Serum specimens from patients with R. parkeri rickettsiosis reacted specifically with cysteinyl–tRNA synthetase, DNA-directed RNA polymerase subunit alpha, putative sigma (54) modulation protein, chaperonin GroEL, and elongation factor Tu of R. parkeri which have been reported as virulence factors in other bacterial species. Unique antigens identified in this study may be useful for further development of the better serological assays for diagnosing infection caused by R. parkeri.

Anther proteomic characterization in temperature sensitive Bainong male sterile wheat

Male sterile line is a useful material for hybridization, but its sterility mechanism, especially proteomic profile, is still not entirely clear. In wheat (Triticum aestivum L.), a male sterile Bainong (BNS) genotype whose sterility could be manipulated by temperature was recently selected. We focused on the proteomic profile change of anthers from the male sterile line (SL) and its conversional line (CL). Two-dimensional gel electrophoresis and MALDI-TOF-MS technologies were utilized for proteomic profiles analysis. Differently abundant protein spots (over 2-fold, P < 0.05) were selected for identification analysis. Compared to CL, 24 up-regulated and 23 down-regulated proteins were identified in SL. Protein metabolism-related proteins, which included a ubiquitin-conjugating enzyme E2 (23 kDa) and an ATP-dependent Clp protease proteolytic subunit, were over-accumulated in SL anthers. Alcohol dehydrogenase ADH1A, fructose-bisphosphate aldolase, chloroplast fructose-bisphosphate aldolase, and NADP-dependent malic enzyme were notably down-regulated in SL anthers. Up-regulated prohibitin protein Wph and a translationallycontrolled tumor protein homolog, and down-regulated histone acetyltransferases HAT1 and HAT2, and DNA directed RNA polymerase subunit α were identified in SL anthers. These dramatically changed proteins may play a crucial role in abnormal anther development and pollen abortion in BNS.

Anti-tubercular agents from Glycyrrhiza glabra.

Bioactivity guided isolation of Glycyrrhiza glabra (Leguminosae / Fabaceae) roots resulted in the characterization of 18β-glycyrrhetinic acid as a major anti-tubercular agent. Further, GA-1 was semi-synthetically converted into its nine derivatives, which were in-vitro evaluated for their antitubercular potential against Mycobacterium tuberculosis H37Rv using BACTEC-460 radiometric susceptibility assay. All the derivatives were active, but the benzylamide (GA-8, MIC 12.5μg/ml) and ethyl oxylate (GA-3, MIC 25.0 μg/ml) derivatives were significantly active against the pathogen. This was further supported by the molecular docking studies, which showed adequate docking (LibDock) scores for GA-3 (120.3) and GA-8 (112.6) with respect to the standard anti-tubercular drug, rifampicin (92.94) on the DNA-directed RNA polymerase subunit beta (rpoB) target site. Finally, the in silico pharmacokinetic and drug-likeness studies showed that GA-3 and GA- 8 possesses drug-like properties. This is the first ever report on the anti-tubercular potential of GA and its derivatives. These results may be of great help in anti-tubercular drug development from a very common, inexpensive, and non toxic natural product.

Expression, crystallization and preliminary X-ray crystallographic analysis of DNA-directed RNA polymerase subunit L from Thermococcus onnurineus NA1.

RNA polymerase (RNAP) plays a crucial role in gene expression in all organisms. It is a multiprotein complex that produces primary transcript RNA. Generally, the basal transcription apparatus in archaea is simpler than the eukaryotic RNA polymerase II counterpart. To understand the structure and function of archaeal RNAP, the TON-0309 gene encoding DNA-directed RNA polymerase subunit L (ToRNAP_L) from Thermococcus onnurineus NA1 was cloned and the protein was overexpressed in Escherichia coli, purified and crystallized. The purified protein was crystallized using the hanging-drop vapour-diffusion method and the crystal diffracted to 2.10 Å resolution. The crystal belonged to the hexagonal space group P6122, with unit-cell parameters a = b = 42.3, c = 211.2 Å. One molecule was present in the asymmetric unit, with a corresponding VM of 2.5 Å(3) Da(-1) and a solvent content of 50.0%.

Understanding Rifampicin Resistance in Tuberculosis through a Computational Approach.

The disease tuberculosis, caused by Mycobacterium tuberculosis (MTB), remains a major cause of morbidity and mortality in developing countries. The evolution of drug-resistant tuberculosis causes a foremost threat to global health. Most drug-resistant MTB clinical strains are showing resistance to isoniazid and rifampicin (RIF), the frontline anti-tuberculosis drugs. Mutation in rpoB, the beta subunit of DNA-directed RNA polymerase of MTB, is reported to be a major cause of RIF resistance. Amongst mutations in the well-defined 81-base-pair central region of the rpoB gene, mutation at codon 450 (S450L) and 445 (H445Y) is mainly associated with RIF resistance. In this study, we modeled two resistant mutants of rpoB (S450L and H445Y) using Modeller9v10 and performed a docking analysis with RIF using AutoDock4.2 and compared the docking results of these mutants with the wild-type rpoB. The docking results revealed that RIF more effectively inhibited the wild-type rpoB with low binding energy than rpoB mutants. The rpoB mutants interacted with RIF with positive binding energy, revealing the incapableness of RIF inhibition and thus showing resistance. Subsequently, this was verified by molecular dynamics simulations. This in silico evidence may help us understand RIF resistance in rpoB mutant strains.

Isolation of differentially expressed genes related to salt tolerance in peanut

Salinity is one of the most serious environmental factors influencing crop growth and development, especially during germination period. In peanut, screening for salinity tolerance has been reported by several investigators, but there are few reports regarding isolation and identification of salt responsive genes from salt tolerant genotypes. In this study, we compared gene expression profile of a large-seeded saline tolerant peanut line 10L19 imbibed in 1.0% sodium chloride solution and seeds of the same genotype treated with distilled water, using the annealing control primer (ACP)-based GeneFishing technology. Total RNAs were extracted from seeds sampled at 1, 6 and 24 h after imbibition initiation. With 40 ACPs, a total of 20 differentially expressed transcripts were isolated. Thirteen of them were found to have high homology to genes with known functions in GenBank nr database. BLAST search revealed that those genes were related to gene expression regulation, signalling transduction, development and stress tolerance, among which S-38 was of direct relevance to hyperosmotic salinity response. S-14, S-15, S-17, S-28, S-31, S-32 and S-38, encoding ethylene-responsive element binding factor 4, DNA-directed RNA polymerase subunit, oleosin 5, polygalacturonase-inhibiting protein, vacuolarprocessing enzyme precursor, ribosomal protein s7 and nac domain protein, respectively, were selected and their relative expression levels determined by qRT-PCR using β-actin as internal control. The results confirmed that all the seven genes were expressed differentially in stressed and control peanut seeds. The highest relative expression for S-17 and S-38 was both at 6 h, while that for the rest genes was at 24 h.

Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples

To identify possible novel biomarkers in gingival crevicular fluid (GCF) samples from chronic periodontitis (CP) and periodontally healthy individuals using high-throughput proteomic analysis. Gingival crevicular fluid samples were collected from 12 CP and 12 periodontally healthy subjects. Samples were trypically digested with trypsin, eluted using high-performance liquid chromatography, and fragmented using tandem mass spectrometry (MS/MS). MS/MS spectra were analysed using PILOT_PROTEIN to identify all unmodified proteins within the samples. Using the database derived from Homo sapiens taxonomy and all bacterial taxonomies, 432 human (120 new) and 30 bacterial proteins were identified. The human proteins, angiotensinogen, clusterin and thymidine phosphorylase were identified as biomarker candidates based on their high-scoring only in samples from periodontal health. Similarly, neutrophil defensin-1, carbonic anhydrase-1 and elongation factor-1 gamma were associated with CP. Candidate bacterial biomarkers include 33 kDa chaperonin, iron uptake protein A2 and phosphoenolpyruvate carboxylase (health-associated) and ribulose biphosphate carboxylase, a probable succinyl-CoA:3-ketoacid-coenzyme A transferase, or DNA-directed RNA polymerase subunit beta (CP-associated). Most of these human and bacterial proteins have not been previously evaluated as biomarkers of periodontal conditions and require further investigation. The proposed methods for large-scale comprehensive proteomic analysis may lead to the identification of novel biomarkers of periodontal health or disease.

Identification of Enterococci from Broiler Products and a Broiler Processing Plant and Description of Enterococcus viikkiensis sp. nov

In two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genus Enterococcus. Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (rpoA) and phenylalanyl-tRNA synthetase α chain (pheS) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in the Enterococcus avium group, with E. devriesei being the closest phylogenetic neighbor. The DNA-DNA hybridization levels with E. devriesei ranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The name Enterococcus viikkiensis sp. nov. is proposed, with strain DSM 24043(T) (LMG 26075(T)) being the type strain. Our study demonstrated that the identification of enterococci within the E. avium phylogenetic group demands polyphasic taxonomic approaches. The rpoA and pheS gene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) between E. viikkiensis and its closest phylogenetic neighbor, E. devriesei, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in the E. avium group were also highly similar, and some traits were found to be misleading for enterococci, such as E. viikkiensis does not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within the E. avium group.

Novel domains and orthologues of eukaryotic transcription elongation factors.

The passage of RNA polymerase II across eukaryotic genes is impeded by the nucleosome, an octamer of histones H2A, H2B, H3 and H4 dimers. More than a dozen factors in the yeast Saccharomyces cerevisiae are known to facilitate transcription elongation through chromatin. In order to better understand the evolution and function of these factors, their sequences have been compared with known protein, EST and DNA sequences. Elongator subcomplex components Elp4p and Elp6p are shown to be homologues of ATPases, yet with substitutions of amino acids critical for ATP hydrolysis, and novel orthologues of Elp5p are detectable in human, and other animal, sequences. The yeast CP complex is shown to contain a likely inactive homologue of M24 family metalloproteases in Spt16p/Cdc68p and a 2-fold repeat in Pob3p, the orthologue of mammalian SSRP1. Archaeal DNA-directed RNA polymerase subunit E" is shown to be the orthologue of eukaryotic Spt4p, and Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. Spt6p is found to contain a domain homologous to the YqgF family of RNases, although this domain may also lack catalytic activity. These findings imply that much of the transcription elongation machinery of eukaryotes has been acquired subsequent to their divergence from prokaryotes.

Rifampicin resistance in Neisseria meningitidis: evidence from a study of sibling strains, description of new mutations and notes on population genetics.

To provide direct evidence for the mechanism leading to resistance to rifampicin, two Neisseria meningitidis strains from one clonal lineage (so-called sibling strains) were studied; one of these strains was resistant, the other sensitive to rifampicin. The polymerase chain reaction (PCR) was used to amplify fragments of the known rifampicin resistance region on the rpoB gene coding for the beta subunit of DNA-directed RNA polymerase and the amplimers were then sequenced. In addition to the DNA from the sibling strains, DNA from further strains was analysed, including two Spanish, rifampicin-resistant strains, eight further N. meningitidis strains, strains of four further Neisseria spp. and one reference strain. The results demonstrated how quickly and easily N. meningitidis can acquire resistance to rifampicin, and also suggest a clonal population structure within the collection of strains studied. This finding is discussed with respect to recent studies that indicate a more panmictic population structure within particular serogroups of N. meningitidis.