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Ji X.,Fudan University | Li Y.,Fudan University | Jia Y.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | Ding W.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | Zhang Q.,Fudan University
Angewandte Chemie - International Edition | Year: 2016

The radical S-adenosyl-l-methionine (SAM) enzyme NosL catalyzes the transformation of l-tryptophan into 3-methyl-2-indolic acid (MIA), which is a key intermediate in the biosynthesis of a clinically interesting antibiotic nosiheptide. NosL catalysis was investigated by using the substrate analogue 2-methyl-3-(indol-3-yl)propanoic acid (MIPA), which can be converted into MIA by NosL. Biochemical assays with different MIPA isotopomers in D2O and H2O unambiguously indicated that the 5′-deoxyadenosyl (dAdo)-radical-mediated hydrogen abstraction is from the amino group of l-tryptophan and not a protein residue. Surprisingly, the dAdo-radical-mediated hydrogen abstraction occurs at two different sites of MIPA, thereby partitioning the substrate into different reaction pathways. Together with identification of an α,β-unsaturated ketone shunt product, our study provides valuable mechanistic insight into NosL catalysis and highlights the remarkable catalytic flexibility of radical SAM enzymes. Two roads diverged: The radical S-adenosyl-L-methionine enzyme NosL, which catalyzes the transformation of L-tryptophan into 3-methyl-2-indolic acid (MIA), was investigated with the substrate analogue 2-methyl-3-(indol-3-yl)propanoic acid (MIPA). Radical-mediated hydrogen abstraction was found to be from the amino group of L-tryptophan and occurs at two different sites of MIPA, thus partitioning the substrate into different reaction pathways. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Liu W.,CAS Lanzhou Cold and Arid Regions Environmental and Engineering Research Institute | Liu W.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | Zhang W.,CAS Lanzhou Cold and Arid Regions Environmental and Engineering Research Institute | Zhang W.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | And 5 more authors.
Journal of Arid Land | Year: 2016

Soil salinization or alkalization is a form of soil desertification. Coastal saline-alkali soil represents a type of desert and a key system in the network of ecosystems at the continent-ocean interface. Tamarix chinensis is a drought-tolerant plant that is widely distributed in the coastal saline-alkali soil of Bohai Bay, China. In this study, we used 454 pyrosequencing techniques to investigate the characteristics and distribution of the microbial diversity in coastal saline-alkali soil of the T. chinensis woodland at Bohai Bay. A total of 20,315 sequences were obtained, representing 19 known bacterial phyla and a large proportion of unclassified bacteria at the phylum level. Proteobacteria, Acidobacteria and Actinobacteria were the predominant phyla. The coverage of T. chinensis affected the microbial composition. At the phylum level, the relative abundance of γ-Proteobacteria and Bacteroidetes decreased whereas Actinobacteria increased with the increasing coverage of T. chinensis. At the genus level, the proportions of Steroidobacter, Lechevalieria, Gp3 and Gp4 decreased with the increase of the vegetation coverage whereas the proportion of Nocardioides increased. A cluster analysis showed that the existing T. chinensis changed the niches for the microorganisms in the coastal saline-alkali soil, which caused changes in the microbial community. The analysis also distinguished the microbial community structure of the marginal area from those of the dense area and sparse area. Furthermore, the results also indicated that the distance to the seashore line could also affect certain groups of soil bacteria in this coastal saline-alkali soil, such as the family Cryomorphaceae and class Flavobacteria, whose population decreased as the distance increased. In addition, the seawater and temperature could be the driving factors that affected the changes. © 2016, Xinjiang Institute of Ecology and Geography, the Chinese Academy of Sciences and Springer - Verlag GmbH. Source


Zhang G.,CAS Lanzhou Cold and Arid Regions Environmental and Engineering Research Institute | Zhang G.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | Chen T.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | Chen T.,Chinese Academy of Sciences | And 16 more authors.
Journal of Biotechnology | Year: 2016

Acinetobacter sp. strain TTH0-4 was isolated from a permafrost region in Qinghai-Tibet Plateau. With its capability to degrade crude oil at low temperature, 10 °C, the strain could be an excellent candidate for the bioremediation of crude oil pollution in cold areas or at cold seasons. We sequenced and annotated the whole genome to serve as a basis for further elucidation of the genetic background of this promising strain, and provide opportunities for investigating the metabolic and regulatory mechanisms and optimizing the biodegradative activity in cold environment. © 2016. Source


Liu G.,CAS Lanzhou Cold and Arid Regions Environmental and Engineering Research Institute | Liu G.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | Zhang M.,CAS Lanzhou Cold and Arid Regions Environmental and Engineering Research Institute | Zhang M.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | And 9 more authors.
Biochemical and Biophysical Research Communications | Year: 2015

This work reports the 13C-assisted metabolic flux analysis of Haladaptatus paucihalophilus, a halophilic archaeon possessing an intriguing osmoadaption mechanism. We showed that the carbon flow is through the oxidative tricarboxylic acid (TCA) cycle whereas the reductive TCA cycle is not operative in H. paucihalophilus. In addition, both threonine and the citramalate pathways contribute to isoleucine biosynthesis, whereas lysine is synthesized through the diaminopimelate pathway and not through the α-aminoadipate pathway. Unexpected, the labeling patterns of glycine from the cells grown on [1-13C]pyruvate and [2-13C]pyruvate suggest that, unlike all the organisms investigated so far, in which glycine is produced exclusively from the serine hydroxymethyltransferase (SHMT) pathway, glycine biosynthesis in H. paucihalophilus involves different pathways including SHMT, threonine aldolase (TA) and the reverse reaction of glycine cleavage system (GCS), demonstrating for the first time that other pathways instead of SHMT can also make a significant contribution to the cellular glycine pool. Transcriptional analysis confirmed that both TA and GCS genes were transcribed in H. paucihalophilus, and the transcriptional level is independent of salt concentrations in the culture media. This study expands our understanding of amino acid biosynthesis and provides valuable insights into the metabolism of halophilic archaea. © 2015 Elsevier Inc. Source


Baogui Z.,CAS Lanzhou Cold and Arid Regions Environmental and Engineering Research Institute | Baogui Z.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering | Baogui Z.,University of Chinese Academy of Sciences | Wei Z.,CAS Lanzhou Cold and Arid Regions Environmental and Engineering Research Institute | And 13 more authors.
Nature Environment and Pollution Technology | Year: 2015

Variations in the culturable terrestrial bacterial communities and soil biochemical parameters along an altitude gradient (from 1260m to 4111m) upstream of the Shule River, Qinghai-Tibetan Plateau, were investigated. The results showed that the number of cultivable bacteria varied between 0.4×107 and 3.3×107 CFU/g, with an average of 1.6×107 CFU/g. 168 isolates from these soils were clustered into 34 groups by amplified ribosomal DNA restriction analysis (ARDRA). These groups are affiliated to 15 genera that belong to six taxa, β-Proteobacteria, γ-Proteobacteria, α-Proteobacteria, Actinobacteria, Firmicutes and Bacteroides, of which Bacillus and Arthrobacter were the dominant species at the level of the genus. The relative abundance of Arthrobacter increased significantly at high altitude. Correlation analysis showed that the total number of culturable bacteria in the soils decreased first and then increased below 3000m, and these trends significantly positively correlated to the soil organic C, total N and the activities of soil sucrase, and positively correlated to the activities of soil urease and catalase. However, when the altitude exceeded 3000m, cultivable bacterial number dramatically declined, although soil organic carbon, total nitrogen and enzyme activities were relatively high. While the diversity index of bacteria increased along with the increased altitude as a whole and there existed a significantly positive correlation between altitude and bacteria diversity. Together, these results illustrated that culturable bacterial numbers were mainly influenced by soil biochemical properties while bacterial diversity was mainly influenced by altitude in this region. Source

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