基于结构生物学的微生物环境适应机制研究

   

071010-生物化学与分子生物学
071005-微生物学

微生物降解污染物及适应环境的机制
结构生物学

2001-09--2006-06   中国科学院生物物理研究所   理学博士
1997-09--2001-07   武汉大学   理学学士

研究生

博士

   

2018-02~现在, 中国科学院微生物研究所, 项目研究员
2006-07~2018-01,中国科学院生物物理研究所, 助理研究员/副研究员/项目研究员

2022-01-01-2025-12-31,Applied and Environmental Microbiology编委, 编委
2021-09-30-2026-09-30,中国微生物学会环境微生物学专业委员会委员, 委员
2021-09-30-2026-09-30,《微生物学通报》编委, 编委

   

（1） 中国科学院青年创新促进会会员, 院级, 2014

[1] 一株产碱杆菌HC-1及其应用. 2023-09-08.

[2] 一种耐盐的石油烃降解菌及其应用. 2023-09-28.

[3] 刘志培, 刘双江, 李德峰, 苗莉莉, 吴梦茹, 刘缨, 侯婷婷. 一种氧化酶及其应用. CN: CN114763541A, 2022-07-19.

[4] 刘志培, 刘双江, 李德峰, 苗莉莉, 吴梦茹, 刘缨, 侯婷婷. 一种氧化酶及其应用. CN: CN114763541B, 2023-08-29.

   

（1） Paraflavitalea pollutisoli sp. nov., Pollutibacter soli gen. nov. sp. nov., Polluticoccus soli gen. nov. sp. nov., and Terrimonas pollutisoli sp. nov., four new members of the family Chitinophagaceae from polluted soil., Syst Appl Microbiol., 2024, 通讯作者
（2） The ligand binding domain of a type IV pilus chemoreceptor PilJ has a different fold from that of another PilJ-type receptor McpN., Biochem Biophys Res Commun., 2024, 通讯作者
（3） A hydrogel-modified electrochemical biosensor for the rapid detection of ammonia‑nitrogen-resistant bacteria, Sci Total Environ, 2024, 通讯作者
（4） Attractant and repellent induce opposing changes in the four-helix bundle ligand-binding domain of a bacterial chemoreceptor., PLoS Biol., 2023, 通讯作者
（5） Flagellar brake protein YcgR interacts with motor proteins MotA and FliG to regulate the flagellar rotation speed and direction., Front Microbiol., 2023, 通讯作者
（6） Agromyces chromiiresistens sp. nov., Novosphingobium album sp. nov., Sphingobium arseniciresistens sp. nov., Sphingomonas pollutisoli sp. nov., and Salinibacterium metalliresistens sp. nov.: five new members of Microbacteriaceae and Sphingomonadaceae from polluted soil., Front Microbiol., 2023, 通讯作者
（7） Identification and characterization of a novel hydroxylamine oxidase, DnfA, that catalyzes the oxidation of hydroxylamine to N 2, THE JOURNAL OF BIOLOGICAL CHEMISTRY, 2022, 通讯作者
（8） Crystal structure of the chromosome partition protein MukE homodimer, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2022, 第 4 作者
（9） Desymmetric hydrolysis of prochiral imide for S-pregabalin synthesis by rationally designed d-hydantoinase, GREEN CHEMISTRY, 2022, 第 5 作者
（10） Structural insights into the substrate specificity of 5-chloro-2-hydroxymuconate tautomerase CnbG, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2022, 通讯作者
（11） Mutations in surface-sensing receptor WspA lock the Wsp signal transduction system into a constitutively active state, ENVIRONMENTAL MICROBIOLOGY, 2022, 第 10 作者
（12） The Response Regulator FlmD Regulates Biofilm Formation in Comamonas testosteroni through the Transcriptional Activator SoxR, MICROORGANISMS, 2022, 第 6 作者
（13） Genetic Foundations of Direct Ammonia Oxidation (Dirammox) to N-2 and MocR-Like Transcriptional Regulator DnfR in Alcaligenes faecalis Strain JQ135, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2022, 第11作者
（14） Crystal Structure of the Core Module of the Yeast Paf1 Complex, JOURNAL OF MOLECULAR BIOLOGY, 2022, 通讯作者
（15） Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites, Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites, ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY, 2022, 其他（合作组作者）
（16） PapA, a peptidoglycan-associated protein, interacts with OmpC and maintains cell envelope integrity, ENVIRONMENTAL MICROBIOLOGY, 2021, 第 8 作者
（17） Structural and Biochemical Analysis Reveals a Distinct Catalytic Site of Salicylate 5-Monooxygenase NagGH from Rieske Dioxygenases, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2021, 通讯作者
（18） Single-Component and Two-Component para-Nitrophenol Monooxygenases: Structural Basis for Their Catalytic Difference, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2021, 第 2 作者
（19） Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N-2 with a previously unknown pathway, ENVIRONMENTAL MICROBIOLOGY, 2021, 其他（合作组作者）
（20） Hexachlorobenzene Monooxygenase Substrate Selectivity and Catalysis: Structural and Biochemical Insights, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2021, 第 2 作者
（21） Biochemical insights into Paf1 complex-induced stimulation of Rad6/Bre1-mediated H2B monoubiquitination, Proc. Natl. Acad. Sci. USA, 2021, 通讯作者
（22） Characterization of the Methanomicrobial Archaeal RNase Zs for Processing the CCA-Containing tRNA Precursors, FRONTIERS IN MICROBIOLOGY, 2020, 第 5 作者
（23） A New State I-plus Observed for the L, D- transpeptidase LdtMt2-ertapenem Adduct, PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 2020, 通讯作者
（24） Structural insights into the mechanism of c-di-GMP?bound YcgR regulating flagellar motility in Escherichia coli, JOURNAL OF BIOLOGICAL CHEMISTRY, 2020, 通讯作者
（25） A newly identified duplex RNA unwinding activity of archaeal RNase J depends on processive exoribonucleolysis coupled steric occlusion by its structural archaeal loops, RNA BIOLOGY, 2020, 通讯作者
（26） Crystal structure of the glycoside hydrolase PssZ from Listeria monocytogenes, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2019, 第 3 作者
（27） The 1-beta-methyl group confers a lower affinity of L,D-transpeptidase Ldt(Mt2) for ertapenem than for imipenem, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2019, 通讯作者
（28） The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure, MOLECULAR MICROBIOLOGY, 2019, 通讯作者
（29） Huang Z, Wang YH, Zhu HZ, Andrianova EP, Jiang CY, Li D, Ma L, Feng J, Liu ZP, Xiang H, Zhulin IB, Liu SJ.Cross Talk between Chemosensory Pathways That Modulate Chemotaxis and Biofilm Formation., MBio. ;10(1). pii: e02876-18., 2019, 
（30） Cross Talk between Chemosensory Pathways That Modulate Chemotaxis and Biofilm Formation, MBIO, 2019, 第 6 作者
（31） Biochemical and structural characterization of a highly active branched-chain amino acid aminotransferase from Pseudomonas sp. for efficient biosynthesis of chiral amino acids, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2019, 第 6 作者
（32） 山药中的致痒物质及致痒机制研究, Study on Itching Substance and Mechanism in Chinese Yam (Dioscoreae Rhizoma), PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 2019, 通讯作者
（33） The C2′- and C3′-endo equilibrium for AMP molecules bound in the cystathionine-beta-synthase domain, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2018, 通讯作者
（34） A potential substrate binding pocket of BdcA plays a critical role in NADPH recognition and biofilm dispersal, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2018, 通讯作者
（35） Structural and Functional Characterization of the FadR Regulatory Protein from Vibrio alginolyticus, FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2017, 第 2 作者
（36） Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis, SCIENTIFIC REPORTS, 2017, 第 2 作者
（37） Mycobacterium tuberculosis proteasomal ATPase Mpa has a β-grasp domain that hinders docking with the proteasome core protease, MOLECULAR MICROBIOLOGY, 2017, 第 3 作者
（38） New molecular insights into an archaeal rnase j reveal a conserved processive exoribonucleolysis mechanism of the rnase j family, MOLECULAR MICROBIOLOGY, 2017, 通讯作者
（39） Deciphering MCR-2 Colistin Resistance, MBIO, 2017, 第 7 作者
（40） Dissemination and Mechanism for the MCR-1 Colistin Resistance, PLOS PATHOGENS, 2016, 第 10 作者
（41） Origin, dissemination and entry of the pandemic Zika viruses, SCIENCE BULLETIN, 2016, 第 3 作者
（42） Molecular Structural Basis for the Cold Adaptedness of the Psychrophilic β-Glucosidase BglU in Micrococcus antarcticus, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2016, 第 7 作者
（43） Crystal Structure of the ERp44-Peroxiredoxin 4 Complex Reveals the Molecular Mechanisms of Thiol-Mediated Protein Retention, STRUCTURE, 2016, 第 2 作者
（44） Molecular Structural Basis for the Cold Adaptedness of the Psychrophilic beta-Glucosidase BglU in Micrococcus antarcticus, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2016, 第 7 作者
（45） Crystal structure of Rv3899c 184–410 , a hypothetical protein from Mycobacterium tuberculosis, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2016, 第 3 作者
（46） Crystallographic observation of the movement of the membrane-distal domain of the T7SS core component EccB1 from Mycobacterium tuberculosis, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2016, 第 4 作者
（47） Structure of the MarR family protein Rv0880 from Mycobacterium tuberculosis, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2015, 第 4 作者
（48） Structure and function of Mycobacterium smegmatis 7-keto-8-aminopelargonic acid (KAPA) synthase, INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 2015, 
（49） Structural Basis of Specific Recognition of Non-Reducing Terminal N-Acetylglucosamine by an Agrocybe aegerita Lectin, PLOS ONE, 2015, 第 2 作者
（50） Biochemical and structural characterization of a novel ubiquitin-conjugating enzyme E2 from Agrocybe aegeria reveals Ube2w family-specific properties, SCIENTIFIC REPORTS, 2015, 第 2 作者
（51） Core component EccB1 of the Mycobacterium tuberculosis type VII secretion system is a periplasmic ATPase, FASEB JOURNAL, 2015, 第 2 作者
（52） Structure and function of Mycobacterium smegmatis 7-keto-8-aminopelargonic acid (KAPA) synthase, INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND CELL BIOLOGY, 2015, 第 2 作者
（53） Purification, crystallization and preliminary X-ray crystallographic studies of Rv3899c from Mycobacterium tuberculosis, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2015, 
（54） Structural basis of a mutant Y195I alpha-cyclodextrin glycosyltransferase with switched product specificity from alpha-cyclodextrin to beta-/gamma-cyclodextrin, JOURNAL OF BIOTECHNOLOGY, 2014, 第 3 作者
（55） Purification and X-ray crystallographic analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase from Mycobacterium smegmatis, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2014, 
（56） Crystallization and preliminary crystallographic studies of AAL-2, a novel lectin from Agrocybe aegerita that binds nonreducing terminal N-acetylglucosamine, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2013, 第 3 作者
（57） Interaction between DAHP synthase and chorismate mutase endows new regulation on DAHP synthase activity in Corynebacterium glutamicum, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2013, 第 2 作者
（58） His-234是毛白杨对香豆酸 ∶ CoA连接酶的重要酶催化活性残基, His-234 is an Essential Residue for Populus tomentosa 4-coumarate ∶ CoA Ligase Enzymatic Mechanisms, PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 2013, 第 2 作者
（59） Crystal structure of L,D-transpeptidase Ldt(Mt2) in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis, CELL RESEARCH, 2013, 第 2 作者
（60） Structural, enzymatic and biochemical studies on Helicobacter pylori arginase, INTERNATIONALJOURNALOFBIOCHEMISTRYCELLBIOLOGY, 2013, 第 9 作者
（61） Expression, crystallization and preliminary crystallographic study of GluB from Corynebacterium glutamicum, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2013, 第 2 作者
（62） Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor, ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2013, 
（63） The expression, purification and crystallization of a ubiquitin-conjugating enzyme E2 from Agrocybe aegerita underscore the impact of His-tag location on recombinant protein properties, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2013, 第 1 作者
（64） Crystallization and preliminary X-ray analysis of the flagellar motor 'brake' molecule YcgR with c-di-GMP from Escherichia coli, ACTACRYSTALLOGRAPHICASECTIONFSTRUCTURALBIOLOGYCOMMUNICATIONS, 2013, 通讯作者
（65） Structural Basis of the Novel S. pneumoniae Virulence Factor, GHIP, a Glycosyl Hydrolase 25 Participating in Host-Cell Invasion, PLOS ONE, 2013, 第 10 作者
（66） Crystallization and preliminary crystallographic analysis of 2-aminophenol 1,6-dioxygenase complexed with substrate and with an inhibitor, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2012, 第 1 作者
（67） Modeling studies with Helicobacter pylori octaprenyl pyrophosphate synthase reveal the enzymatic mechanism of trans-prenyltransferases, INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 2012, 
（68） The TetR-Type Transcriptional Repressor RolR from Corynebacterium glutamicum Regulates Resorcinol Catabolism by Binding to a Unique Operator, rolO, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2012, 第 4 作者
（69） Crystal Structure of TNF-alpha-Inducing Protein from Helicobacter Pylori in Active Form Reveals the Intrinsic Molecular Flexibility for Unique DNA-Binding, PLOS ONE, 2012, 第 2 作者
（70） Crystallization and preliminary crystallographic analysis of 2-aminophenol 1,6-dioxygenase complexed with substrate and with an inhibitor, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 2012, 第 1 作者
（71） Expression, Purification and Characterization of Arginase from Helicobacter pylori in Its Apo Form, PLOS ONE, 2011, 第 9 作者
（72） A Novel Binding Pattern Unique in Two Ligands for One Carbohydrate Recognition Domain in Galectins, PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 2011, 
（73） Crystal Structures of the Transcriptional Repressor RoIR Reveals a Novel Recognition Mechanism between Inducer and Regulator, PLOS ONE, 2011, 通讯作者
（74） Identification and clarification of the role of key active site residues in bacterial glutathione S-transferase zeta/maleylpyruvate isomerase, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2011, 第 2 作者
（75） Expression, crystallization and preliminary crystallographic study of octaprenyl pyrophosphate synthase from Helicobacter pylori, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2011, 第 5 作者
（76） Crystallization and preliminary crystallographic studies of Helicobacter pylori arginase, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2011, 第 5 作者
（77） 半乳糖凝集素糖结合的新模式：一个糖结合域的双重配体结合, A Novel Binding Pattern Unique in Two Ligands for One Carbohydrate Recognition Domain in Galectins, 生物化学与生物物理进展, 2011, 第 3 作者
（78） Structural Basis for Distinct Binding Properties of the Human Galectins to Thomsen-Friedenreich Antigen, PLOS ONE, 2011, 第 4 作者
（79） Crystal Structures of a Populus tomentosa 4-Coumarate:CoA Ligase Shed Light on Its Enzymatic Mechanisms, PLANT CELL, 2010, 
（80） Crystallization and preliminary crystallographic studies of CorC, a magnesium-ion transporter, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2010, 通讯作者
（81） Crystal structure of human programmed cell death 10 complexed with inositol-(1,3,4,5)-tetrakisphosphate: A novel adaptor protein involved in human cerebral cavernous malformation, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2010, 
（82） A nuclear ligand MRG15 involved in the proapoptotic activity of medicinal fungal galectin AAL (Agrocybe aegerita lectin), BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 2010, 
（83） Structural insights into the recognition mechanism between an antitumor galectin AAL and the Thomsen-Friedenreich antigen, FASEB JOURNAL, 2010, 
（84） Structural Basis for the Tumor Cell Apoptosis-Inducing Activity of an Antitumor Lectin from the Edible Mushroom Agrocybe aegerita, JOURNAL OF MOLECULAR BIOLOGY, 2009, 
（85） Importance of nuclear localization for the apoptosis-induced activity of a fungal galectin AAL (Agrocybe aegerita lectin), BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2009, 
（86） Crystal structure of Mabinlin II: A novel structural type of sweet proteins and the main structural basis for its sweetness, JOURNAL OF STRUCTURAL BIOLOGY, 2008, 

   

（ 1 ） 镁离子转运蛋白CorC受腺苷类配体以及镁离子调控的分子机理的生物化学和结构生物学研究, 负责人, 国家任务, 2013-01--2016-12
（ 2 ） 芳香烃降解相关的调控蛋白NCgl1110以及其与芳香烃配体、核酸复合物的晶体结构和功能研究, 负责人, 国家任务, 2009-01--2011-12
（ 3 ） 重要病原微生物感染与耐药性相关的膜蛋白结构功能研究, 负责人, 国家任务, 2013-01--2017-12
（ 4 ） 结核病耐药相关的基础和应用研究, 负责人, 中国科学院计划, 2013-01--2015-12
（ 5 ） 重要生命活动中关键膜蛋白及蛋白质复合物的结构与功能研究, 参与, 国家任务, 2011-01--2015-12
（ 6 ） 微生物结构生物学, 负责人, 研究所自主部署, 2018-02--2020-02
（ 7 ） 微生物趋化运动和运动调控的分子机制, 负责人, 研究所自主部署, 2018-01--2020-12
（ 8 ） 趋化受体MCP2201介导的趋化激活和抑制的机理研究, 负责人, 国家任务, 2019-01--2022-12
（ 9 ） 活性污泥人工多细胞体系构建与应用-课题1-3, 负责人, 国家任务, 2020-01--2024-12
（ 10 ） 土壤复合污染过程和生物修复-课题3-3, 负责人, 国家任务, 2020-01--2024-12
（ 11 ） 岩溶地下水系统寡营养条件下的微生物碳代谢研究, 负责人, 国家任务, 2021-01--2023-12
（ 12 ） 典型工业污染场地微生物群落分析及菌剂研发, 负责人, 国家任务, 2021-01--2024-12
（ 13 ） 新型直接氨氧化途径中羟胺氧化酶的分子机制及其分布和影响因素研究, 负责人, 国家任务, 2024-01--2027-12
（ 14 ） 水圈微生物驱动碳氮硫循环的代谢新机制-微生物所子课题, 负责人, 国家任务, 2024-01--2024-12

（1）直接氨氧化 (到氮气)微生物的机制、分布和应用潜力   第二十四次全国环境微生物学学术会议   2023-08-02
（2）从异养硝化-好氧反硝化到直接氨氧化   中国微生物学会成立七十周年庆祝大会暨 2022 年学术年会   2022-12-18
（3）趋化受体介导细菌负趋化运动的机制研究   第二十三次全国环境微生物学学术研讨会   2022-08-23
（4）邻氨基苯酚-1,6-双加氧酶APD和水杨酸-5-加羟酶NagGH的比较研究   第二十一次全国环境微生物学学术研讨会   李德峰   2018-12-07
（5）Structural studies of bacterial transmembrane chemoreceptor MCP2201   中德微生物趋化、环境污染物的生物降解与污染环境修复双边研讨会   2016-10-16

现指导学生

韩群  硕士研究生  085238-生物工程  

秦亚玲  博士研究生  071010-生物化学与分子生物学