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1 Proteomic analysis of Bifidobacteria longum strain NCC2705 grown on lactose and glucose

Xiang He , Dawei Liu , Zhongke Sun , Fang Wang , Zheng Jiang , Hongqing Zhao , Xuannan Chen , Liuyu Huang , Jing Yuan

2008, 48(11):1451-1458.

[Abstract](19225) [HTML](0) [PDF 717.24 K](3990)

Abstract:
Abstract: [Objective] Based on a proteomic reference map of the important probiotic organism Bifidobacteria longum NCC2705 constructed by our previous research, we compared the proteomic profiles of Bifidobacteria longum strain NCC2705 grown on lactose or glucose to identify the catabolic route allowing lactose fermentation. [Methods] We con-sidered the proteins differentially expressed if their relative volume deviated more than 3-fold with ImageMaster 2D Elite version 5.0 software. Interesting spots were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis, and phosphorylation analysis of proteins with mobility changes by Pro-Q Diamond Stain. [Results] The identified spots represent 31 protein entries, 14 up-regulated proteins, 17 down-regulated proteins. These identified proteins, which were hydrophilic proteins and their genes with CAI value above 0.5 represented the most abundant proteins, included key stress proteins, metabolism-related proteins, and proteins related to translation. Two proteins including Tal (BL0715, transaldolase, L3) and Pyk (BL0988, pyruvate kinase, G9) exhibited clear post-translational modification. [Conclusion] Proteomic comparison of glucose- and lactose-grown cells revealed that lactose and glucose were catabolized via the same degradation pathway, and the rate of glucose assimilation was higher than that of lactose. Spot and protein analysis revealed that post-translational modifications might be common in these proteins. Pro-Q Diamond staining analysis revealed that lactose trigger Tal phosphorylation at 43 T /47 S, and inhibited Pyk phosphorylation at 65 S. These proteins were identified for the first time as bifidobacterial phosphoproteins.

2 Principle and application of DNA-based stable isotope probing—A review

Zhongjun Jia

2011, 51(12):1585-1594.

[Abstract](6097) [HTML](0) [PDF 738.15 K](8840)

Abstract:
Abstract:Microbial communities are the engines that drive the global biogeochemical cycle of carbon and nitrogen essential for life on Earth． However，microorganisms have evolved as a result of complex interactions with other organisms and environments． Deciphering the metabolism of microorganisms at the community level in nature will be crucial for a better understanding of the mechanisms that lead to the enormous divergence of microbial ecophysiology． Due to the immense number of uncultivated microbial species and the complexity of microbial communities，delineating community metabolism proves a virtually insurmountable hurdle．By tracing the heavy isotope flow of key elements such as carbon and nitrogen，DNA-based stable isotope probing (DNA-SIP) can provide unequivocal evidence for substrate assimilation by microorganisms in complex environments． The essential prerequisite for a successful DNA-SIP is the identification，with confidence，of isotopically enriched 13 C-DNA，of which the amount is generally too low to allow the direct measurement of 13 C atom percent of nucleic acid． The methodological considerations for obtaining unambiguous DNA highly enriched in heavy isotope are presented with emphasis on next-generation sequencing technology and metagenomics．

3 Next-generation sequencing technologies and the application in microbiology - A review

Nan Qin , Dongfang Li , Ruifu Yang

2011, 51(4):445-457.

[Abstract](5366) [HTML](0) [PDF 1.14 M](6897)

Abstract:
Abstract: Since its invention in 1970s, nucleic acid sequencing technology has contributed tremendously to the genomics advances. The next-generation sequencing technologies, represented by Solexa from Illumina, SOLiD from Applied Biosystems and 454 from Roche, re-energized the application of genomics. In this review, we first introduced the next-generation sequencing technologies, then, described their potential applications in the field of microbiology.

4 Transcriptional regulation of cellulases and hemicellulases gene in Hypocrea jecorina

Qi Xin , Jintao Xu , Tianhong Wang , Weifeng Liu? , Guanjun Chen

2010, 50(11):1431-1437.

[Abstract](5021) [HTML](0) [PDF 709.24 K](2531)

Abstract:
Abstract: Hypocrea jecorina（anamorph：Trichoderma reesei）is the main industrial fungi that can produce large amounts of extracellular cellulases and hemicellulases. It also represents a model system to study the mechanism of transcriptional regulation in eukaryotes. The expression of these hydrolases genes in Hypocrea jecorina can be triggered rapidly in the presence of inducers, but differences in the inducing mode of various soluble inducers have been reported. At present, three models have been offered to explain the question of “how an insoluble inducer such as cellulose would initiate the transcription of cellulases?” Moreover, interactions between the identified positive (Xyr1, Ace2, Hap2/3/5) and negative transcriptional regulators (Ace1, Cre1), as well as the interactions between these proteins and the promoters of cellelase and hemicellulase genes have also been primarily characterized. This review focuses on the key factors and the current understanding on the regulation of expression of cellulase and hemicellulase genes in Hypocrea jecorina.

5 Retinoic acid-inducible gene-I-like receptors and RNA virusrecognition—— A review

Chengfeng Qin , Ede Qin

2008, 48(10):1418-1423.

[Abstract](4520) [HTML](0) [PDF 454.70 K](3126)

Abstract:
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) have recently been identified as cytoplasmic sensors for RNA viruses. The RLR signaling cascades induce the production of type I interferons and pro-inflammatory cytokines, which are rigorously regulated by the host. On other side, RNA viruses have evolved strategies to evade RLR signaling. In this review, we present our current understanding of RLR signaling in RNA virus recognition and antiviral innate immunity.

6 A novel archaeal phylum: Thaumarchaeota—A review

Limei Zhang , Jizheng He

2012, 52(4):411-421.

[Abstract](3784) [HTML](0) [PDF 204.47 K](8457)

Abstract:
Abstract:Based on the archaeal 16S rRNA gene phylogenetic tree，the archaeal domain is divided into two major phyla，Euryarchaeota and Crenarchaeota． During the past 20 years，diverse groups of archaea have been found to be widely distributed in moderate environments with the rapid development and application of molecular techniques in microbial ecology． Increasing evidence demonstrated that these archaea，especially ammonia-oxidizing archaea，play a major role in biogeochemical cycles of nitrogen and carbon elements． These mesophilic archaea were placed initially as a sister group of the Crenarchaeota and named as“non-thermophilic Crenarchaeota”．More recently，phylogenetic analyses based on more SSU and SLU rDNA sequences suggested that the non-thermophilic Crenarchaeota constituted a separate phylum of the Archaea that branched off before the separation of Crenarchaeota and Euryarchaeota． The Thaumarchaeota (the Greek “Thaumas”，meaning wonder) was therefore proposed for a novel phylum，as the third archaeal phylum． More studies based on r-proteins and comparative genomics confirm that the Thaumarchaeota are distinct from Crenarchaeota． In this paper，we gave a translated Chinese name for Thaumarchaeota and reviewed the recent progress on the phylogeny position，genetics，ecology and physiology of the Thaumarchaeota．

7 Gene modification in the genome of Epstein-Barr virus cloned as a bacterial artificial chromosome

Jianhong Lu , Yunlian Tang , Ming Zhou , Minghua Wu , Jue Ouyang , Jianming Gao , Liming Zhang , Dan Li , Qiong Chen , Wei Xiong , Xiaoling Li , Ke Tang , Guiyuan Li

2008, 48(3):385-390.

[Abstract](3604) [HTML](0) [PDF 0.00 Byte](3750)

Abstract:
Epstein-Barr virus (EBV) is an oncogenic herpesvirus associated with a variety of malignancies, including Burkitt’s lymphoma and nasopharyngeal carcinoma (NPC). Functions of most EBV genes have not been determined. The use of bacterial artificial chromosome (BAC) to clone and modify the genome of EBV has enhanced the gene function study in the context of genome. Infectious clones of EBV were previously established by using EBV-BAC plasmid p2089. In order to further investigate EBV mutant biology, an easy and efficient method for gene modification in EBV-BAC was developed and detailed. The kanamycin gene (kan) flanked by recombinase FLP recognition targets (FRTs) was amplified from plasmid pKD13 and inserted into the vector of pcDNA3.1(+). Through the introduction of restriction endonuclease BsmBⅠin PCR primers, NPC-derived LMP1 gDNA containing the full-length ORF was then precisely ligated with kan on pcDNA3.1(+). The linear DNA segment of kan-LMP1 was transformed into E.coli DH10B cells containing p2089 and plasmid pKD46, homologous recombination was subsequently mediated by redαβγ system from bacteriophage l. By this linear transformation and ET cloning, the full-length LMP1 in EBV-BAC (p2089) was replaced by the kan-LMP1. The introduced kan gene in EBV-BAC genome was eliminated specifically by the recombinase FLP when transformed by plasmid pCP20, leaving an FRT scar of 69 bp. The mutant could be identified by antibiotic screening and PCR amplifica-tion on bacteria medium. This method allows the gene of interest to be easily modified alone and then to be introduced into EBV-BAC genome. Following this example of gene substitution, other mutations such as deletion, insertion and point mutation become convenient work, and this improved method can be a potential use of gene modification in other BAC-based herpesvirus genome.

8 Screening and identification of plant growth-promoting rhizobacteria

Yijun Kang , Jie Cheng , Lijuan Mei , Shixue Yin

2010, 50(7):853-861.

[Abstract](3501) [HTML](0) [PDF 1.15 M](2845)

Abstract:
Abstract: [Objective] The interaction between plant growth promoting rhizobacteria (PGPR) and plants can be unstable, PGPR with PGP activities may be well adapted to particular soil environment. Based on this, we isolated and identified PGPRs from different rhizosphere soils according to their multiple mechanisms. [Methods] Preliminary screening of PGPRs under the premises of PGPR may having the abilities of N2-fixing, phosphate and potassium solubilization, and resistance against six common pathogenic fungi as well as rhizosphere colonization. After that, multiple PGP activities were detected in vitro. Finally, PGPRs were classified and identified by combining physiological and biochemical tests and 16S rRNA gene sequence analysis. [Results] Fourteen strains having various mechanisms of PGP activities such as NH3, IAA, HCN, siderophore, antibiotics production, phosphate and potassium solubilization, and N2-fixing were isolated from different rhizosphere soils in Yangzhou and Yancheng, Jiangsu province. These 14 isolates could be identified as Pseudomonas (7 isolates), Paenibacillus (3 isolates), Bacillus (2 isolates), Burkholderia (1 isolate) and Erwinia (1 isolate). [Conclusion] Isolates with multiple PGP activities can also be rhizospheric competent, able to survive and colonize in the rhizosphere, providing promising isolates for PGPRs combination to resolve the challenges in field application of PGPR.

9 OSMAC (One Strain Many Compounds) approach in the research of microbial metabolites-A review

Hongjuan Wei , Zhenjian Lin , Dehai Li , Qianqun Gu , Tianjiao Zhu

2010, 50(6):701-709.

[Abstract](3464) [HTML](0) [PDF 1.07 M](3949)

Abstract:
Abstract: Microbial secondary metabolites have a wide range of biological activities due to their structural diversity and have been proved a major source for drug lead compounds. However, the traditional method of a single culture restricts the metabolic pathways of microorganisms and as a result many metabolites cannot be formed. Recently, it has attracted much attention to use various techniques to activate those metabolic pathways restricted by the traditional method to get metabolic products with rich variety of structures. “One strain many compounds” (OSMAC) is a simple and effective approach for activating metabolic pathways and has been successfully applied. This review summarizes the common strategies of the OSMAC approach (altering cultivation parameters, co-cultivation, addition of enzyme inhibitors, etc）and the recent advances of OSMAC combined with genomics scanning. This review also introduces the research of our studies using the OSMAC approach on a fungus Spicaria elegans KLA03 which yielded a series of cytochalasins.

10 Comparative analysis of soil microbial communities by pyrosequencing and DGGE

Weiwei Xia , Zhongjun Jia

2014, 54(12):1489-1499. DOI: 10.13343/j.cnki.wsxb.2014.12.012

[Abstract](3394) [HTML](0) [PDF 1.48 M](7996)

Abstract:
Abstract:［Objective］ We aimed to assess the advantage and disadvantage of next-generation pyrosequencing and traditional Denaturing Gradient Gel Electrophoresis (DGGE) in fingerprinting analysis of soil microbial communities．［Methods］We analyzed microbial compositions，abundance and diversity of typical grassland and forest soils by 16S rRNA gene-based pyrosequencing and DGGE to compare the accuracy and reproducibility of the two techniques on soil microbial communities.［Results］ For grassland soils，pyrosequencing technique revealed 22 phyla，54 classes，60 orders，131 families and 350 genera; DGGE only detected 6 phyla，9 classes，8 orders，10 families and 10 genera. The results show that DGGE greatly underestimated soil community compositions．Similar results were obtained for forest soils，and the detection sensitivity of pyrosequencing of forest soils was 3.8，6.7，6.4，19.2 and 39.4 times higher than that of DGGE at the taxonomic levels of phylum， class， order，family and genera respectively． Furthermore， DGGE overwhelmingly overestimated the relative abundance of dominant microorganisms represented by the high-intensity bands，leading up to a 2000-fold difference． Both DGGE and pyrosequencing showed consistent results of microbial diversity changing patterns，although the DGGE-based diversity index was much lower than pyrosequencing.［Conclusion］ Pyrosequencing thus provides more comprehensive and accurate fingerprints of soil microbial community structure than DGGE. DGGE only can represent a few numerically dominant phylotypes with apparent overestimation of their relative abundance in soil microbial communities.

11 Progress on microbial transformation of arsenic and its application in environmental and medical sciences - A Review

Xu Zhang , Xiumin Yu , Qinjian Xie , Hongyu Li

2008, 48(3):408-412.

[Abstract](3053) [HTML](0) [PDF 0.00 Byte](5148)

Abstract:
Arsenic is widely distributed in the environment. As teratogen, carcinogen or mutagen, it has extremely toxic effect on mammalian health. Recently, as the outbreaks of arsenicosis in many countries such as Bangladesh and China, arsenic toxicity or pollution has been a global problem, severely threatening tens of millions of people’s health. Therefore, studies on the transfer of arsenic toxicity or pollution are important. The threat of pollution and toxicity from the dispersal of naturally occurring and anthropogenic arsenic stimulated extensive studies focusing on the geochemical behaviors, such as mobilization and transformation of arsenic. More evidences suggest that microbes play an important role in the geo-chemical circulation of arsenic. Some microorganisms have evolved to tolerate relatively high concentrations of arsenic by methylation and/or redox. These microbial processes, together with inorganic and physical processes, constitute the global cycle of arsenic. In this article, we review the diversity of microorganisms known to interact with arsenic, and the genes and enzymes involved in these processes. We also briefly discuss the application of arsenic bio-transformation is . Finally, according to the studies in our laboratory, we propose the potential application in medical sciences and its future pros-pects.

12 Construction of ompW knock-out mutants of Escherichia coli to increase sensitivity to neomycinsulphate and ampicillin

Xianbin Wu , Haijie Zou , Lihua Tian , Jianyi Pan , Fukun Zhao

2012, 52(8):1021-1026.

[Abstract](3048) [HTML](0) [PDF 1.25 M](3318)

Abstract:
Abstract:［Objective］To investigate the contribution of an outer membrane protein OmpW to tolerance neomycinsulphate and ampicillin of Escherichia coli K12. ［Methods］The ompW knock-out mutant (ΔompW) of E． coli K12 was generated using λ-Red recombination system． Then the minimal inhibitory concentration (MIC) and the survival rates under 1/2 MIC of neomycinsulphate or ampicillin of ΔompW and E． coli K12 were determined respectively．［Results］The ΔompW was successfully obtained through confirmation of PCR analysis at the gene level and Western blot analysis at the protein level． The MIC of neomycinsulphate of ΔompW is 1.7 μg/mL．The value is much lower than that of E． coli K12，which is 8.0μg/mL． Difference of survival rates under 1 /2 MIC of neomycinsulphate of ΔompW and E． coli K12 was also observed，and their survival rates are 39% and 98% ，respectively． The MIC of ampicillin of ΔompW is 3.3 μg/mL．The value is also lower than that of E． coli K12 (16.0μg/mL)．The survival rates under 1/2 MIC ampicillin of ΔompW and E．coli K12 are 30.3% and 70.38%， respectively．［Conclusion］ The ΔompW is much more sensitive to neomycinsulphate and ampicillin than its parent strain． The result indicated that OmpW played crucial role in bacteria resistance of drug．

13 Heterologous expression of H2O-forming NADH oxidase in Torulopsis glabrata significantly enhance the pyruvate productivity of the host

Zhiyao Dong , Xiufen Li , Liming Liu , Guocheng Du , Jian Chen

2008, 48(8):1061-1066.

[Abstract](2941) [HTML](0) [PDF 0.00 Byte](2919)

Abstract:
[Objective] The aim of this manuscript was to illuminate the effect of NADH oxidation pathway on the glycolytic rate and the pyruvate productivity. [Methods] The noxE gene encoding a water-forming NADH oxidase from Lactococcus lactis, was expressed in a pyruvate producing Torulopsis glabrata CCTCC M202019. A mutant strain T. glabrata-PDnoxE, with specific NADH oxidase activity of 34.8 U/mg protein, was obtained. [Results] During batch fermentation with 100 g/L glucose in the medium, the dry cell weight, the glucose consumption rate and pyruvate production rate were 168%, 44.9% and 12% higher than that of the parent strain, respectively. Only 2.5 g/L residual glucose was detected in the fermentation broth after 36 h culture, then 50 g/L glucose was supplemented to the culture broth and the concentration of pyruvate increased to 67.2 g/L. As the result of NADH oxidase overexpression, the intracellular NADH, NAD+ and ATP concentrations of the mutant and the parent strain were determined, the NADH and ATP content decreased 18.1% and 15.8% respectively, while the NAD+ concentration increased 11.1%. [Conclusion] The increasing of intracellular NAD+ concentration can efficiently enhance the rate of glucose consumption and the pyruvate production.

14 Recent advances in Sphingobium sp． SYK-6 for lignin aromatic compounds degradation-A review

Xiaoyan Zhang , Xue Peng , Eiji Masai

2014, 54(8):854-867. DOI: 10.13343/j.cnki.wsxb.2014.08.002

[Abstract](2916) [HTML](0) [PDF 702.16 K](3198)

Abstract:
Abstract:Lignin is complex heteropolymer produced from hydroxycinnamyl alcohols through radical coupling．In nature，white-rot fungi are assumed initially to attack native lignin and release lignin-derived-low-molecular-weight compounds，and soil bacteria play an importent role for completely degradation of these compounds．Study on the soil bacteria degrading lignin-derived-low-molecular-weight compounds will give way to understand how aromatic compounds recycle in nature，and to utilize lignin compounds as the renewable materials for valuable materials production． Sphingobium sp．SYK-6 that grows on lignin biphenyl (5，5’-dehydrodivanillate) had been isolated from pulp effluent in 1987．We have researched this bacterium more than 25 years，a serious aromatic metabolic pathway has been determined，and related genes have been isolated．As the complete genome sequence of SYK-6 has been opened to the public in 2012，the entire aromatic compounds degradation mechanisms become more clear．Main contents in our review cover: (1) genome information; (2) aryl metabolism; (3) biphenyl metabolism; (4) ferulate metabolism; (5) tetrahydrofolate-dependent O-demethylation system for lignin compound degrdation; (6) protocatechuate 4，5-cleavage pathway; (7) multiple pathways for 3-O-methylgallate metabolism．

15 Recent advance on the genus Nocardioides—A review

Huijing Du , Liyan Yu , Yuqin Zhang

2012, 52(6):671-678.

[Abstract](2844) [HTML](0) [PDF 827.83 K](5100)

Abstract:
Abstract:The Nocardioides genus was established by Prauser H．in 1976 according to morphological and physiological characteristics，as well as partial chemotaxonomic analyses of 17 nocardio-form actinobacteria isolated from soil，based on which a novel species Nocardioides albus was proposed as the type species． With the development in the technologies of isolation，purification and taxonomy，more and more members of this genus with varied morphological，physiological and biochemical characteristics were increasingly discovered from different sources，while all of them shared the same diagnostic characteristics of the genus． In the past 50 years，some of the members of the genus Nocardioides were ever transferred in or out and then some species description was ever emended． Till date，there were 56 validly described species in this genus． Some members of this genus were used in agriculture and industry． The objective of this review is to summarize the research advances in the genus Nocardioides，such as the changes of the taxonomic position and emendation description of the species as well as the application prospect in industry and agriculture．

16 Research progress of CRISPR-Cas system in bacteria

Li Hu , Shi Chen

2017, 57(11):1643-1652. DOI: 10.13343/j.cnki.wsxb.20170162

[Abstract](2817) [HTML](1154) [PDF 1.20 M](4691)

Abstract:
The discovery of CRISPR-Cas system breaks certain theory which adaptive immunity had been long time considered as unique characteristics of eukaryotic organism. CRISPR-Cas, a new adaptive immunity system widespread in bacteria and archaea, protects the host from invasion of exogenous nucleic acids by capturing and using the Cas protein and crRNA to resisting it when invading again. In recent years, CRISPR-Cas system has aroused extensive attention and exploration. From microbial perspective, this article introduces a brief overview on classification, mechanism and application which have achieved significant breakthrough to provide valuable reference for further research on CRISPR-Cas system and its application.

17 Modulating marine ecosystem by marine viruses-A review

Hui Wang , Shijie Bai , Wenwei Cai , Tianling Zheng

2009, 49(5):551-559.

[Abstract](2793) [HTML](0) [PDF 368.61 K](3491)

Abstract:
Abstract: Marine viruses play great roles in the marine ecological system such as modulating the biodiversity and species population, regulating the nutrient cycling, intervening gene transfer and influencing climate changes. Recent research achievements on marine viruses were reviewed in this paper. We focused on the modulating role of marine viruses in marine ecosystem and discussed future research perspectives.

18 Advances in marine actinobacterial research - A review

Xinpeng Tian , Si Zhang , Wenjun Li

2011, 51(2):161-169.

[Abstract](2773) [HTML](0) [PDF 922.79 K](2758)

Abstract:
Abstract: The research on marine actinobacteria has worldwide interest because of their potential to produce special and new metabolites. Based on the research history of marine actinobacteria, we reviewed the research progress, conception, bio-resources and diversity, secondary metabolites, ecological function, genomics of marine actinobacteria and finally introduced the status of marine actinobacterial research in China.

19 Advances in the study of the mechanism and application of nonribosomal peptide synthetases

WANG Shi-yuan

2007, 47(4):734-737.

[Abstract](2771) [HTML](0) [PDF 0.00 Byte](6713)

Abstract:
Many microorganisms could use nonribosomal peptide synthetases (NRPSs) to synthesize various bioactive peptides with complicated structures. Because of their special physical-chemical and pharmacological properties, the nonribosomal peptides (NRPs) had been extensively studied, and would have great potential for commercial application. NRPSs are composed of many iterative modules whose different assembling orders determine the specificity of amino acid sequences of their peptide products. The NRPs are assembled by NRPSs via multiple-carrier thiotemplate mechanism, and the substrate specificity of NRPSs is determined by both adenylation domain and condensation domain. Recently, many expected peptides were synthesized using natural whole NRPSs, some specific domains of NRPSs, or novel NRPSs which were constructed by the combination or hybrid combination of specific modules or domains of some known NRPSs.

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