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F M Nazmul Hassan, Radhey S Gupta
Deinococcus species display a high degree of resistance to radiation and desiccation due to their ability to protect critical proteome from oxidatively generated damage; however, the underlying mechanisms are not understood. Comparative analysis of DNA repair proteins reported here has identified 22 conserved signature indels (CSIs) in the proteins UvrA1, UvrC, UvrD, UvsE, MutY, MutM, Nth, RecA, RecD, RecG, RecQ, RecR, RuvC, RadA, PolA, DnaE, LigA, GyrA and GyrB, that are uniquely shared by all/most Deinococcus homologs...
March 8, 2018: Genes
S Behera, R Rana, P K Gupta, D Kumar, Sonal, V Rekha, T R Arun, D Jena
Mycoplasma bovis is one of the important bovine mycoplasma involved in economically important clinical conditions like respiratory diseases, otitis media, and mastitis. The present study was undertaken with the objective of developing a SYBR Green dye-based real-time PCR assay targeting uvrC gene for the diagnosis of M. bovis. The analytical sensitivity and specificity of the assay were evaluated. The test showed 103-fold more sensitivity than conventional PCR and detected down to 100 fg level of DNA. It was found to be specific, as no cross reactivity was shown with other related bacteria and Mycoplasma species...
January 15, 2018: Tropical Animal Health and Production
Aqeela Ashraf, Muhammad Imran, Tahir Yaqub, Muhammad Tayyab, Wasim Shehzad, Claro N Mingala, Yung-Fu Chang
Mycoplasma mastitis is often difficult to control due to a lack of rapid and accurate diagnostic tools. The aim of the current study was to develop a loop-mediated isothermal amplification (LAMP) assay for the detection of Mycoplasma bovis (M. bovis) in mastitic milk. The assay was developed using primers designed for three different target genes: uvrC, 16S rRNA, and gyrB, and validated using mastitic milk samples previously found positive for the target pathogen. Specificity of the developed assay was determined by testing cross-reactivity of LAMP primers against closely related bovine mastitis bacterial pathogens...
December 14, 2017: Folia Microbiologica
Luke Springall, Craig D Hughes, Michelle Simons, Stavros Azinas, Bennett Van Houten, Neil M Kad
Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA...
December 12, 2017: Nucleic Acids Research
Samarpita Lahiri, Menico Rizzi, Franca Rossi, Riccardo Miggiano
During its life cycle Mycobacterium tuberculosis (MTB) must face a variety of environmental and endogenous physical and chemical stresses that could produce genotoxic damage. However, MTB possesses efficient systems to counteract the harmful effects of DNA-damaging assaults. The nucleotide excision repair (NER) is a highly conserved multi-enzymatic cascade that is initiated by the concerted action of three core proteins, that is UvrA, UvrB, and UvrC. Although the functional roles of these enzymes are well characterized, the intra-pathway coordination of the NER components and the dynamics of their association is still a matter of debate...
January 2018: Proteins
Xiaochen Yin, Michelle R Salemi, Brett S Phinney, Velitchka Gotcheva, Angel Angelov, Maria L Marco
We identified the proteins synthesized by Lactobacillus delbrueckii subsp. bulgaricus strain LBB.B5 in laboratory culture medium (MRS) at 37°C and milk at 37 and 4°C. Cell-associated proteins were measured by gel-free, shotgun proteomics using high-performance liquid chromatography coupled with tandem mass spectrophotometry. A total of 635 proteins were recovered from all cultures, among which 72 proteins were milk associated (unique or significantly more abundant in milk). LBB.B5 responded to milk by increasing the production of proteins required for purine biosynthesis, carbohydrate metabolism (LacZ and ManM), energy metabolism (TpiA, PgK, Eno, SdhA, and GapN), amino acid synthesis (MetE, CysK, LBU0412, and AspC) and transport (GlnM and GlnP), and stress response (Trx, MsrA, MecA, and SmpB)...
September 2017: MSystems
Patricia Bell-Rogers, Lois Parker, Hugh Y Cai
A total of 217 Mycoplasma bovis isolates cultured from clinical cases in Ontario, Canada, over the past 30 y were selected to be characterized by a multi-locus sequence typing (MLST) method. Eleven housekeeping genes were evaluated for suitability for MLST; 2 loci that had been used in prior MLST schemes, dnaN and metS, along with hsp70 were chosen for further sequence analysis. The remaining loci- adk, efp, gmk, gyrB, polC, rpoB, tpiA, and uvrC genes-were not used because they had little to no sequence variation...
September 1, 2017: Journal of Veterinary Diagnostic Investigation
Irshad M Sulaiman, Emily Jacobs, Steven Simpson, Khalil Kerdahi
The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa...
June 2017: Journal of Food Protection
Shigeru Shimamura, Takashi Kaneko, Genki Ozawa, Mamiko Nishino Matsumoto, Takeru Koshiishi, Yoshihiro Takaki, Chiaki Kato, Ken Takai, Takao Yoshida, Katsunori Fujikura, James P Barry, Tadashi Maruyama
Intracellular thioautotrophic symbionts of deep-sea vesicomyid clams lack some DNA repair genes and are thought to be undergoing reductive genome evolution (RGE). In this study, we addressed two questions, 1) how these symbionts lost their DNA repair genes and 2) how such losses affect RGE. For the first question, we examined genes associated with nucleotide excision repair (NER; uvrA, uvrB, uvrC, uvrD, uvrD paralog [uvrDp] and mfd) in 12 symbionts of vesicomyid clams belonging to two clades (5 clade I and 7 clade II symbionts)...
2017: PloS One
Christopher P Selby
In 1989, transcription-repair coupling (TRC) was first described in Escherichia coli, as the transcription-dependent, preferential nucleotide excision repair (NER) of UV photoproducts located in the template DNA strand. This finding led to pioneering biochemical studies of TRC in the laboratory of Professor Aziz Sancar, where, at the time, major contributions were being made toward understanding the roles of the UvrA, UvrB and UvrC proteins in NER. When the repair studies were extended to TRC, template but not coding strand lesions were found to block RNA polymerase (RNAP) in vitro, and unexpectedly, the blocked RNAP inhibited NER...
January 2017: Photochemistry and Photobiology
Anthonige Vidya Perera, James Brian Mendenhall, Charmain Tan Courcelle, Justin Courcelle
DNA interstrand cross-links are complex lesions that covalently link both strands of the duplex DNA. Lesion removal is proposed to be initiated via the UvrABC nucleotide excision repair complex; however, less is known about the subsequent steps of this complex repair pathway. In this study, we characterized the contribution of nucleotide excision repair mutants to survival in the presence of psoralen-induced damage. Unexpectedly, we observed that the nucleotide excision repair mutants exhibit differential sensitivity to psoralen-induced damage, with uvrC mutants being less sensitive than either uvrA or uvrB We show that Cho, an alternative endonuclease, acts with UvrAB and is responsible for the reduced hypersensitivity of uvrC mutants...
November 15, 2016: Journal of Bacteriology
Jun Fan, Mathieu Leroux-Coyau, Nigel J Savery, Terence R Strick
Escherichia coli Mfd translocase enables transcription-coupled repair by displacing RNA polymerase (RNAP) stalled on a DNA lesion and then coordinating assembly of the UvrAB(C) components at the damage site. Recent studies have shown that after binding to and dislodging stalled RNAP, Mfd remains on the DNA in the form of a stable, slowly translocating complex with evicted RNAP attached. Here we find, using a series of single-molecule assays, that recruitment of UvrA and UvrAB to Mfd-RNAP arrests the translocating complex and causes its dissolution...
August 11, 2016: Nature
Qiuhua Bao, Yuqin Song, Haiyan Xu, Jie Yu, Wenyi Zhang, Bilige Menghe, Heping Zhang, Zhihong Sun
Lactobacillus casei is a lactic acid bacterium used in manufacturing of many fermented food products. To investigate the genetic diversity and population biology of this food-related bacterium, 224 Lb. casei isolates and 5 reference isolates were examined by multilocus sequence typing (MLST). Among them, 224 Lb. casei isolates were isolated from homemade fermented foods, including naturally fermented dairy products, acidic gruel, and Sichuan pickles from 38 different regions in China and Mongolia. The MLST scheme was developed based on the analysis of 10 selected housekeeping genes (carB, clpX, dnaA, groEL, murE, pyrG, pheS, recA, rpoC, and uvrC)...
July 2016: Journal of Dairy Science
Tong Dan, Wenjun Liu, Yuqin Song, Haiyan Xu, Bilige Menghe, Heping Zhang, Zhihong Sun
BACKGROUND: Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). RESULTS: MLST analysis of 203 isolates of L...
2015: BMC Microbiology
Samuel Million-Weaver, Ariana N Samadpour, Daniela A Moreno-Habel, Patrick Nugent, Mitchell J Brittnacher, Eli Weiss, Hillary S Hayden, Samuel I Miller, Ivan Liachko, Houra Merrikh
We previously reported that lagging-strand genes accumulate mutations faster than those encoded on the leading strand in Bacillus subtilis. Although we proposed that orientation-specific encounters between replication and transcription underlie this phenomenon, the mechanism leading to the increased mutagenesis of lagging-strand genes remained unknown. Here, we report that the transcription-dependent and orientation-specific differences in mutation rates of genes require the B. subtilis Y-family polymerase, PolY1 (yqjH)...
March 10, 2015: Proceedings of the National Academy of Sciences of the United States of America
Wenyi Zhang, Wenjun Liu, Yuqing Song, Haiyan Xu, Bilige Menghe, Heping Zhang, Zhihong Sun
Leuconostoc mesenteroides strains play an important role in food fermentation. In this study, 136 strains from different dairy products in China and Mongolia were examined by multilocus sequence typing of 9 housekeeping genes. In total, 82 polymorphic sites were detected among the 9 loci. The number of polymorphic nucleotide sites varied between 4 (dnaA) and 18 (uvrC), whereas the nucleotide diversity per site among the 9 genes varied from 0.00379 in dnaA to 0.01195 in uvrC, suggesting a relatively low level of sequence diversity...
April 2015: Journal of Dairy Science
Tong Dan, Wenjun Liu, Zhihong Sun, Qiang Lv, Haiyan Xu, Yuqin Song, Heping Zhang
BACKGROUND: Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level...
2014: BMC Microbiology
Bennett Van Houten, Neil Kad
Despite three decades of biochemical and structural analysis of the prokaryotic nucleotide excision repair (NER) system, many intriguing questions remain with regard to how the UvrA, UvrB, and UvrC proteins detect, verify and remove a wide range of DNA lesions. Single-molecule techniques have begun to allow more detailed understanding of the kinetics and action mechanism of this complex process. This article reviews how atomic force microscopy and fluorescence microscopy have captured new glimpses of how these proteins work together to mediate NER...
August 2014: DNA Repair
Alexandra Vaisman, John P McDonald, Donald Huston, Wojciech Kuban, Lili Liu, Bennett Van Houten, Roger Woodgate
Stringent steric exclusion mechanisms limit the misincorporation of ribonucleotides by high-fidelity DNA polymerases into genomic DNA. In contrast, low-fidelity Escherichia coli DNA polymerase V (pol V) has relatively poor sugar discrimination and frequently misincorporates ribonucleotides. Substitution of a steric gate tyrosine residue with alanine (umuC_Y11A) reduces sugar selectivity further and allows pol V to readily misincorporate ribonucleotides as easily as deoxynucleotides, whilst leaving its poor base-substitution fidelity essentially unchanged...
November 2013: PLoS Genetics
Rishikesh S Parulekar, Sagar H Barage, Chidambar B Jalkute, Maruti J Dhanavade, Prayagraj M Fandilolu, Kailas D Sonawane
Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacterium, is the leading causative agent of most cases of tuberculosis. The pathogenicity of the bacteria is enhanced by its developed DNA repair mechanism which consists of machineries such as nucleotide excision repair. Nucleotide excision repair consists of excinuclease protein UvrABC endonuclease, multi-enzymatic complex which carries out repair of damaged DNA in sequential manner. UvrC protein is a part of this complex and thus helps to repair the damaged DNA of M...
August 2013: Protein Journal
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