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Wu M.-M.,Key Laboratory of Molecular Microbiology and Technology | Huang H.-D.,Tianjin Agricultural University | Li G.-Q.,Key Laboratory of Molecular Microbiology and Technology | Zhou J.-F.,Key Laboratory of Molecular Microbiology and Technology | Ma T.,Key Laboratory of Molecular Microbiology and Technology
Applied Biochemistry and Microbiology | Year: 2015

Biopolymer Ss of Sphingomonas sanxanigenens strain NX02 is an sphingan that can be extracted using a small quantity of acid, which is a low cost extraction process. A UDP-glucose dehydrogenase gene (ugdG), related to Ss biosynthesis, was cloned from S. sanxanigenens NX02 and expressed in Escherichia coli. It encoded a 454-residue protein of 48.2 kDa. The deduced amino acid sequence had 77% identity with UDP-glucose dehydrogenase (UgdG) from Sphingomonas sp. KC8, and 73% identity with UgdG from Sphingomonas elodea ATCC31461. Purified recombinant UgdG had maximum activity at 35°C and pH 8.0, with Km values of 0.47 and 0.38 mM for UDP-glucose and NAD+, respectively. Overexpression of the ugdG gene in S. sanxanigenens resulted in increased (14.9 ± 0.5)% Ss production and higher fermentation broth viscosity. Furthermore, the weight-average molecular weight of polymer Ss from the recombinant strain was (5.3 ± 0.16)% higher and the viscosity was (74 ± 0.15)% higher than those from the WT strain at a shear rate of 1 rev/min. © 2015, Pleiades Publishing, Inc. Source

Ren Y.,Nankai University | Ren Y.,Engineering and Research Center for Microbial Functional Genomics and Detection Technology | Ren Y.,Key Laboratory of Molecular Microbiology and Technology | Ren Y.,Tianjin Biochip Corporation | And 15 more authors.
Journal of Bacteriology | Year: 2010

Enterobacter cloacae is an important nosocomial pathogen. Here, we report the completion of the genome sequence of E. cloacae ATCC 13047, the type strain of E. cloacae subsp. cloacae. Multiple sets of virulence determinant and heavy-metal resistance genes have been found in the genome. To the best of our knowledge, this is the first complete genome sequence of the E. cloacae species. Copyright © 2010, American Society for Microbiology. All Rights Reserved. Source

Deng X.,Nankai University | Deng X.,Key Laboratory of Molecular Microbiology and Technology | Chen K.,University of Chicago | Chen K.,Howard Hughes Medical Institute | And 10 more authors.
Nucleic Acids Research | Year: 2015

N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent discoveries of demethylases and specific binding proteins of m6A as well as m6A methylomes obtained in mammals, yeast and plants have revealed regulatory functions of this RNA modification. Although m6A is present in the ribosomal RNA of bacteria, its occurrence in mRNA still remains elusive. Here, we have employed ultra-high pressure liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QQQ-MS/MS) to calculate the m6A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m6A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m6A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved m6A pattern that is distinct from those in eukaryotes. Most m6A peaks are located inside open reading frames and carry a unique consensus motif of GCCAU. Functional enrichment analysis of bacterial m6A peaks indicates that the majority of m6A-modified genes are associated with respiration, amino acids metabolism, stress response and small RNAs, suggesting potential functional roles of m6A in these pathways. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. Source

Zhu H.,Nankai University | Zhu H.,Key Laboratory of Molecular Microbiology and Technology | Wang Q.,Nankai University | Wang Q.,Key Laboratory of Molecular Microbiology and Technology | And 12 more authors.
Journal of Clinical Microbiology | Year: 2012

Neisseria meningitidis is a leading pathogen of epidemic bacterial meningitis and fulminant sepsis worldwide. Twelve different N. meningitidis serogroups have been identified to date based on antigenic differences in the capsular polysaccharide. However, more than 90% of human cases of N. meningitidis meningitis are the result of infection with just five serogroups, A, B, C, W135, and Y. Efficient methods of detection and genogrouping of N. meningitidis isolates are needed, therefore, in order to monitor prevalent serogroups as a means of disease control and prevention. The capsular gene complex regions have been sequenced from only seven out of the 12 serogroups. In this study, the capsular gene complexes of the remaining five serogroups were sequenced and analyzed. Primers were designed that were specific for N. meningitidis species and for the 12 individual serogroups, and a multiplex PCR assay using these specific primers was developed for N. meningitidis detection and genogrouping. The assay was tested using 15 reference strains covering all 12 serogroups, 143 clinical isolates, and 21 strains from closely related species or from species that cause meningitis. The assay could detect N. meningitidis serogroups and was shown to be specific, with a detection sensitivity of 1 ng of genomic DNA (equivalent to ∼4 × 10 5 genomes) or 3 × 10 5 CFU/ml in noncultured mock cerebrospinal fluid (CSF) specimens. This study, therefore, describes for the first time the development of a molecular protocol for the detection of all N. meningitidis serogroups. This multiplex PCR-based assay may have use for the clinical diagnosis and epidemiological surveillance of N. meningitidis. Copyright © 2012, American Society for Microbiology. All Rights Reserved. Source

Liu L.,Jiangnan University | Li Y.,Nankai University | Li Y.,Key Laboratory of Molecular Microbiology and Technology | Zhang J.,Jiangnan University | And 8 more authors.
Journal of Bacteriology | Year: 2011

Bacillus megaterium, an industrial strain, has been widely used in protein production and the vitamin C industry. Here we reported a finished, annotated, and compared 4.14-Mbp high-quality genome sequence of B. megaterium WSH-002, which is the companion strain for Ketogulonicigenium vulgare in the vitamin C industry and is stocked in our laboratory. © 2011, American Society for Microbiology. Source

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