微生物学报 Pub Date : 2017-02-04

Genfu Wu, Haichun Gao

{"title":"[Endogenous production and physiological functions of hydrogen sulfide in facultative anaerobic bacteria].","authors":"Genfu Wu, Haichun Gao","doi":"","DOIUrl":"","url":null,"abstract":"H2S is the third gaseous signaling molecule next to nitric oxide and carbon monoxide, but studies on its physiological functions in bacteria are just emerging. In this paper, we review recent findings regarding endogenous production and physiological functions of H2S in facultative anaerobic bacteria, partly based on our own research on Shewanella oneidensis. There are two principal H2S producing pathways in S. oneidensis:one is through cysteine degradation, and the other is via inorganic sulfur respiration. Endogenous H2S could either benefit mutual growing bacteria by supplying energy and inorganic, or inhibit competing bacteria. Our review attaches particular importance to the role of H2S in bacterial oxidative stress response. On one hand, H2S is able to directly inhibit heme-containing catalase, enhancing killing by H2O2. On the other hand, H2S could activate oxidative response as a signaling molecule, leading to cell protection from the oxidative stress due to elevated expression of H2O2 scavenging and repairing systems. Intriguingly, the dominance of either role is determined by H2S-treating time, that is, inhibition is the immediate response whereas activation of oxidative stress response needs extended treatment. The elucidation of endogenous production and its physiological function of H2S in facultative anaerobic bacteria would improve understanding of biogeochemical sulfur recycling, and facilitate control of infectious bacterial pathogens.","PeriodicalId":7120,"journal":{"name":"微生物学报","volume":"57 2","pages":"170-8"},"PeriodicalIF":0.0,"publicationDate":"2017-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36089076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Research progress on the genus Microlunatus]. [小月牙属植物的研究进展]。

微生物学报 Pub Date : 2017-02-04

Changfeng Zhang, Liyan Yu, Yuqin Zhang

引用次数: 0

[Identification of non-coding RNA in Haloferax mediterranei]. [黄颡鱼非编码RNA的鉴定]。

微生物学报 Pub Date : 2017-02-04

Lei Wang, Feiyue Cheng, Dahe Zhao, Haibo Yang, Hua Xiang

{"title":"[Identification of non-coding RNA in Haloferax mediterranei].","authors":"Lei Wang, Feiyue Cheng, Dahe Zhao, Haibo Yang, Hua Xiang","doi":"","DOIUrl":"","url":null,"abstract":"Objective: To identify non-coding RNAs in Haloferax mediterranei through high-throughput RNA sequencing, bioinformatics analysis and molecular techniques.Methods: After H. mediterranei cells under log phase of growth were treated with different salt concentrations for 30 minutes, total RNA was extracted for the following strand-specific RNA sequencing and differential RNA sequencing. These RNA-seq data were used to identify the genome-wide ncRNAs and to predict the 5' and 3'-ends of the transcripts by bioinformatics analysis. A few selected ncRNAs were further confirmed by Northern blotting and Circularized RNA reverse transcription-PCR analysis.Results: We identified 105 highly credible ncRNAs. Expression of four ncRNAs showed difference in different salt concentrations. We confirmed the expression, length of transcripts, transcription start and termination sites of incRNA1436 and incRNA1903 by Northern blotting and CR-RT-PCR.Conclusion: We identified the ncRNAs of H. mediterranei in a genome-wide scale, including identification of a few ncRNAs involved in the responses of H. mediterranei to different salt concentrations. Our results have provided fundamental data and novel insights for future study of the function of ncRNA in haloarchaea.","PeriodicalId":7120,"journal":{"name":"微生物学报","volume":"57 2","pages":"220-8"},"PeriodicalIF":0.0,"publicationDate":"2017-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36089083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Transcriptional start site analysis based on genetic fragment analysis system: from prediction to data evaluation]. [基于基因片段分析系统的转录起始位点分析:从预测到数据评价]。

微生物学报 Pub Date : 2017-02-04

Zhifeng Li, Wenyan Zhang, Yang Liu, Shaofeng Qu, Yan Wang, Liping Zhu, Yuezhong Li

{"title":"[Transcriptional start site analysis based on genetic fragment analysis system: from prediction to data evaluation].","authors":"Zhifeng Li, Wenyan Zhang, Yang Liu, Shaofeng Qu, Yan Wang, Liping Zhu, Yuezhong Li","doi":"","DOIUrl":"","url":null,"abstract":"Objective: To establish a pipeline for unknown transcriptional start site (TSS) identification without radioactivity, we used genetic fragment analysis system and replenished two steps regarding prediction and evaluation.Methods: We used unknown TSSs of GroEL genes from M. xanthus as a case. Firstly, we predicted the potential TSSs through bioinformatics databases. According to the prediction, we designed and synthesized fluorescence labeled primers to carry out the reverse transcription reactions. Further, we took advantage of the genetic fragment analysis system to identify TSSs with internal standards. Finally, we applied the normal distribution theory to evaluate the data.Results: We determined the numbers, abundances and accurate sites of the TSSs:GroEL1 has one promoter and the site is TSS(286), whereas GroEL2 has two promoters, and the sites are TSS548 and TSS(502). TSS(286) is 14.3 times more abundant than TSS(548) and TSS(548) is 13.8 times more than TSS(502).Conclusion: The bioinformatics analyzing indicates the range for the experimental design. TSS determination through genetic fragment analysis system is safer, more automatic and accurate. Normal distribution theory further refines the reliability of results. Combination of the three techniques establishes a more complete pipeline of primer extension for unknown TSS determination.","PeriodicalId":7120,"journal":{"name":"微生物学报","volume":"57 2","pages":"254-63"},"PeriodicalIF":0.0,"publicationDate":"2017-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36090469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Identification, cloning and functional verification of U6 promoter from Cryptococcus neoformans]. [新型隐球菌 U6 启动子的鉴定、克隆和功能验证]。

微生物学报 Pub Date : 2017-02-04

Yu Wang, Tingting Xiao, Xiangyang Zhu, Xueru Zhao, Dongsheng Wei, Xudong Zhu

{"title":"[Identification, cloning and functional verification of U6 promoter from Cryptococcus neoformans].","authors":"Yu Wang, Tingting Xiao, Xiangyang Zhu, Xueru Zhao, Dongsheng Wei, Xudong Zhu","doi":"","DOIUrl":"","url":null,"abstract":"Objective: To identify and clone the polymerase Ⅲ U6 promoter from Cryptococcus neoformans (CnU6 promoter), and verify if CnU6 promoter can effectively transcribe shRNA and gRNA of CRISPR/Cas9 system.Methods: Combining the C. neoformans genome information published in GenBank database and RNA-seq library data from our laboratory, we obtained the U6 RNA sequence with high transcriptional level by bioinformatics analysis. The putative CnU6 promoter was ligated upstream of shRNA and gRNA by EasyGeno and overlapping PCR respectively. Based on shRNA-mediated target gene silence phenotype by RNAi and gene mutation by gRNA-guided Cas9 nuclease mediated target sites editing by CRISPR/Cas9 system, we could identify if CnU6 promoter could drive the transcription of short RNA.Results: CnU6 promoter could drive the transcribtion of shRNA, which could silence the target gene, and gRNA, which could guide Cas9 nuclease to cut the target site.Conclusion: The CnU6 promoter from C. neoformans was successfully identified and cloned, which could drive the transcription of shRNA and gRNA efficiently.","PeriodicalId":7120,"journal":{"name":"微生物学报","volume":"57 2","pages":"197-208"},"PeriodicalIF":0.0,"publicationDate":"2017-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36089082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Changes of microbial abundance and functional genes in oil and gas under gaseous hydrocarbon condition]. [气态烃条件下油气微生物丰度及功能基因的变化]。

微生物学报 Pub Date : 2017-01-04

Lei Gu, Ze Mei, Kewei Xu, Yuping Tang, Fan Yang, Yongge Sun

引用次数: 0

[Genetic diversity of psbA of cyanophage from paddy floodwater in northeast China]. [东北水稻洪水中噬藻体psbA的遗传多样性]。

微生物学报 Pub Date : 2017-01-04

Ruiyong Jing, Kun Cao, Junjie Liu, Judong Liu, Jian Jin, Xiaobing Liu, Guanghua Wang

引用次数: 0

[Antioxidant function of the iron binding protein DRA0258 in Deinococcus radiodurans] [耐辐射球菌铁结合蛋白DRA0258的抗氧化功能]

微生物学报 Pub Date : 2017-01-04

Su Yang, Mengjia Liu, Liangyan Wang, Yuejin Hua

{"title":"[Antioxidant function of the iron binding protein DRA0258 in Deinococcus radiodurans]","authors":"Su Yang, Mengjia Liu, Liangyan Wang, Yuejin Hua","doi":"","DOIUrl":"","url":null,"abstract":"Objective: The complete genome of the extreme environmental resistant bacterium Deiococcus radiodurans R1 was analyzed by sequence comparative method and putative ferritin-like protein DRA0258 was screened. Molecular techniques were applied to validate and analyze its function.Methods: We applied sequence alignment to analyze amino acid sequence of the hypothetical protein DRA0258 and detected its iron binding activity after purification. We used triple-fraction-ligation method to construct dra0258 null mutant and detected its survival rate under H2O2 treatment, catalase activity and total antioxidant capacity, using QRT-PCR to examine the relative transcriptional level change of the antioxidant relative enzymes and iron transport relative proteins.Resutls: We confirmed DRA0258 obtained a certain iron binding activity. The survival rate assay with H2O2 treatment suggested that deletion of dra0258 reduced the cellular antioxidant activity of D. radiodurans. The attenuation of catalase activity, total antioxidant capacity as well as the reduction of relative transcriptional levels of antioxidant related genes verified that both the oxidative stress response systems and the iron regulation network were damaged.Conclusion: This study verified DRA0258 is an iron-binding protein. Deletion of this gene would affect cellular iron transport system and reduce cellular antioxidant capability.","PeriodicalId":7120,"journal":{"name":"微生物学报","volume":"57 1","pages":"140-53"},"PeriodicalIF":0.0,"publicationDate":"2017-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36085522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Regulation of sporulation by two-component system YvcPQ in Bacillus thuringiensis]. [双组分体系YvcPQ对苏云金芽孢杆菌产孢的调控]。

微生物学报 Pub Date : 2017-01-04

Qingyun Fan, Shumeng Zhang, Yujing Gong, Jin He

引用次数: 0

[Advances in phosphatase CheZ of bacterial chemotaxis signaling pathway]. 细菌趋化性信号通路中磷酸酶CheZ的研究进展

微生物学报 Pub Date : 2017-01-04

Xiaolin Liu, Wei Liu, Zhihong Xie

引用次数: 0

微生物学报最新文献