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Soil microbial ecology through the lens of metatranscriptomics

Soil Ecology Letters 2024年第3期6卷 1-15页

作者： Jingjing Peng Xi Zhou Christopher Rensing Werner Liesack Yong-Guan Zhu State key laboratory of Nutrient Use and Management College of Resources and Environmental SciencesNational Academy of Agriculture Green DevelopmentKey Laboratory of Plant-Soil InteractionsMinistry of EducationChina Agricultural UniversityBeijing 100193China Institute of Environmental microbiology College of Resource and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China Max Planck Institute for Terrestrial microbiology Marburg 35043Germany State key laboratory of Urban and Regional Ecology Research Centre for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China key laboratory of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China

Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental *** double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional *** contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA *** this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional *** particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and *** review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.

关键词： metatranscriptomics mRNA MAGs rhizobiont resistome virome

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Gut liver brain axis in diseases:the implications for therapeutic interventions

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Signal Transduction and Targeted Therapy 2024年第1期9卷 79-104页

作者： Mengyao Yan Shuli Man Benyue Sun Long Ma Lanping Guo Luqi Huang Wenyuan Gao State key laboratory of Food Nutrition and Safety Key Laboratory of Industrial MicrobiologyMinistry of EducationTianjin Key Laboratory of Industry MicrobiologyNational and Local United Engineering Lab of Metabolic Control Fermentation TechnologyChina International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal ChemistryCollege of BiotechnologyTianjin University of Science&Technology300457 TianjinChina National Resource Center for Chinese Materia Medica China Academy of Chinese Medical Sciences100700 BeijingChina Tianjin key laboratory for Modern Drug Delivery&High-Efficiency School of Pharmaceutical Science and TechnologyTianjin UniversityWeijin Road300072 TianjinChina

Gut-liver-brain axis is a three-way highway of information interaction system among the gastrointestinal tract,liver,and nervous *** the past few decades,breakthrough progress has been made in the gut liver brain axis,mainly through understanding its formation mechanism and increasing treatment *** this review,we discuss various complex networks including barrier permeability,gut hormones,gut microbial metabolites,vagus nerve,neurotransmitters,immunity,brain toxic metabolites,β-amyloid(Aβ)metabolism,and epigenetic regulation in the gut-liver-brain *** therapies containing antibiotics,probiotics,prebiotics,synbiotics,fecal microbiota transplantation(FMT),polyphenols,low FODMAP diet and nanotechnology application regulate the gut liver brain ***,some special treatments targeting gut-liver axis include farnesoid X receptor(FXR)agonists,takeda G protein-coupled receptor 5(TGR5)agonists,glucagon-like peptide-1(GLP-1)receptor antagonists and fibroblast growth factor 19(FGF19)*** gut-brain axis embraces cognitive behavioral therapy(CBT),antidepressants and tryptophan metabolism-related *** liver-brain axis contains epigenetic regulation and Aβmetabolism-related *** the future,a better understanding of gut-liver-brain axis interactions will promote the development of novel preventative strategies and the discovery of precise therapeutic targets in multiple diseases.

关键词： metabolism therapeutic immunity

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Durable and enhanced immunity against SARS-CoV-2 elicited by manganese nanoadjuvant formulated subunit vaccine

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Signal Transduction and Targeted Therapy 2024年第1期9卷 47-50页

作者： Mengyu Guo Mingjing Cao Jiufeng Sun Ziwei Chen Xin Wang Lianpan Dai George F.Gao Yuliang Zhao Yaling Wang Chunying Chen CAS key laboratory for Biomedical Effects of Nanomaterials and Nanosafety&CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of ChinaBeijingChina Guangdong Provincial Institute of Public Health Guangdong Provincial Center for Disease Control and PreventionGuangzhouChina CAS key laboratory of Pathogen microbiology and Immunology Institute of MicrobiologyBeijingChina

Dear editor,Vaccines are the most efficient and effective means to prevent infectious diseases,but improving the long-term protective efficacy is still a major challenge in contemporary vaccine development.1 The waning immunity varies depending on the diversification of the pathogen and the number of booster doses.1 Strategies to overcome this warrant is using adjuvants that amplify the immune response,and drive the production of memory B and T cells or long-lived plasma cells that recognize the pathogen for durable protection.2–4 Although existing adjuvants have achieved promising results,research on generating durable protective immunity is lacking in promoting vaccine development and staying ahead of global pandemics such as coronavirus disease 2019(COVID-19).The precisely designed nanoadjuvants can enhance lymph node targeting and increase antigenpresenting cell(APCs)uptake,achieving the co-delivery of adjuvants and antigens and activating innate and adaptive immune responses.5 Previously,we reported a manganese nanoadjuvant(MnARK)and receptor-binding domain(RBD)monomer antigen formulated nanovaccine.6 MnARK transported antigens to lymph nodes,activated the STING pathway,elicited strong neutralizing abilities and increased immune memory T cell percentage against the infection of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).6 Regarding the long-term protection potential of MnARK for subunit vaccine development,we further explored the durable immune regulation abilities of MnARK to a SARS-CoV-2 RBD dimer antigen,which has been used in an approved COVID-19 subunit vaccine ZF2001 with aluminum adjuvant(alum).7,8 TEM result revealed that RBD dimer could interact with BSA on MnARK surface and epitope can be well preserved(Supplementary Fig.1a).The size and zeta potential of MnARK-RBD dimer nanovaccine was~58 nm and-14 mV,respectively(Supplementary Fig.1b,c).

关键词： manganese immunity protective

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Jiangsen Mao:a pioneer in Chinese hepatitis A vaccine and interferon research,a virologist at the forefront of times

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Protein & Cell 2024年第1期15卷 1-5页

作者： Huan Liu Kunlan Zuo Zongzhen Wu Hao Cheng University of Science and Technology of China Hefei 230026China State key laboratory of Virology Wuhan 430072China Institute of microbiology Chinese Academy of SciencesBeijing 100101China

There is a renowned virologist who dedicated his life to virology and medicine *** has made important contributions to the study of Chinese polio and hepatitis A vaccines,interferons,and the theory of viral reverse *** invented a live attenuated vaccine for hepatitis A(H2 strain)in the late 1970s,which contributed to the prevention of hepatitis A epidemics in China and earned him the title"Hepatitis A Eradicator"He said.

关键词： prevention hepatitis vaccine

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Acatulides A-G,neuroprotective macrolides from Acaulium album H-JQSF

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Chinese Chemical Letters 2024年第3期35卷 379-383页

作者： Zhi-Wu Tong Ting-Ting Wang Pei Yang Jia-Lin Sun Chen-Peng Zhang Salman Khan Xin-Cun Wang Rui-Hua Jiao Hui-Ming Ge Wen-Ying Zhuang Gang Hu Ren Xiang Tan State key laboratory of Pharmaceutical Biotechnology Institute of Functional BiomoleculesNanjing UniversityNanjing 210023China State key laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese MedicineNanjing 210023China Insitute of microbiology Chinese Academy of SciencesBeijing 100101China

Fungal symbionts co-evolve with hosts and microbial co-inhabitants to acquire an unpredictable potential for producing novel bioactive metabolites,but the knowledge about the topic remains patchy and *** we present the chemical characterization of acatulides A-G(1-7)as architecturally unprecedented macrolides from the solid-state culture of Acaulium album H-JQSF,an arthropod-associated *** acatulide structures were elucidated by spectroscopic analysis,modified Mosher's method and single-crystal X-ray *** plausible biosynthetic pathways for compounds 1-4 are ***,acatulides B-D(2-4)and G(7)were demonstrated to be neuroprotective against the 1-methyl-4-phenylpyridinium(MPP+)-induced damage to SH-SY5Y cells and nematode Caenorhabditis elegans(***).

关键词： Acaulium album Macrolides Acatulides A–G Mosher’s method Neuroprotective

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The RNA-binding domain of DCL3 is required for long-distance RNAi signaling

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aBIOTECH 2024年第1期5卷 17-28页

作者： Jie Li Bo-Sen Zhang Hua-Wei Wu Cheng-Lan Liu Hui-Shan Guo Jian-Hua Zhao State key laboratory of Plant Genomics Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic Interactions University of the Chinese Academy of SciencesBeijing 100049China Qilu Zhongke Academy of Modern microbiology Technology Jinan 250022China

Small RNA(sRNA)-mediated RNA silencing(also known as RNA interference,or RNAi)is a conserved mechanism in eukaryotes that includes RNA degradation,DNA methylation,heterochromatin formation and protein translation *** plants,sRNAs can move either cell-to-cell or systemically,thereby acting as mobile silencing signals to trigger noncell autonomous ***,whether and what proteins are also involved in noncell autonomous silencing have not been *** this study,we utilized a previously reported inducible RNAi plant,PDSi,which can induce systemic silencing of the endogenous PDS gene,and we demonstrated that DCL3 is involved in systemic PDS silencing through its RNA binding *** confirmed that the C-terminus of DCL3,including the predicted RNA-binding domain,is capable of binding short *** affecting RNA binding,but not processing activity,reduced systemic PDS silencing,indicating that DCL3 binding to RNAs is required for the induction of systemic *** mosaic virus infection assays showed that the RNA-binding activity of DCL3 is required for antiviral RNAi in systemically noninoculated *** findings demonstrate that DCL3 acts as a signaling agent involved in noncell autonomous silencing and an antiviral effect in addition to its previously known function in the generation of 24-nucleotide sRNAs.

关键词： RNAi signaling DCL3 RBD RNAs Cucumber mosaic virus

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Disulfide bridge-targeted metabolome mining unravels an antiparkinsonian peptide

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Acta Pharmaceutica Sinica B 2024年第2期14卷 881-892页

作者： Zhiwu Tong Xiahong Xie Huiming Ge Ruihua Jiao Tingting Wang Xincun Wang Wenying Zhuang Gang Hu Renxiang Tan State key laboratory of Pharmaceutical Biotechnology Institute of Functional BiomoleculesSchool of Life SciencesNanjing UniversityNanjing 210023China State key laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese MedicineNanjing 210023China Institute of microbiology Chinese Academy of SciencesBeijing 100101China

Peptides are a particular molecule class with inherent attributes of some small-molecule drugs and macromolecular biologics,thereby inspiring continuous searches for peptides with therapeutic and/or agrochemical ***,the success rate is decreasing,presumably because many interesting but less-abundant peptides are so scarce or labile that they are likely‘overlooked’during the characterization ***,we present the biochemical characterization and druggability improvement of an unprecedented minor fungal RiPP(ribosomally synthesized and post-translationally modified peptide),named acalitide,by taking the relevant advantages of metabolomics approach and disulfide-bridged substructure which is more frequently imprinted in the marketed peptide drug *** is biosynthetically unique in the macrotricyclization via two disulfide bridges and a protease(AcaB)-catalyzed lactamization of AcaA,an unprecedented precursor *** a biosynthetic logic was successfully re-edited for its sample supply renewal to facilitate the identification of the in vitro and in vivo antiparkinsonian efficacy of acalitide which was further confirmed safe and rendered brain-targetable by the liposome encapsulation *** together,the work updates the mining strategy and biosynthetic complexity of RiPPs to unravel an antiparkinsonian drug candidate valuable for combating Parkinson’s disease that is globally prevailing in an alarming manner.

关键词： Fungal RiPPs Biosynthesis Macrocyclic peptide Acalitide Antiparkinsonian

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Crop antiviral defense: Past and future perspective

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Science China Life Sciences 2024年

作者： Zhirui Yang Guangyao Li Yongliang Zhang Fangfang Li Tao Zhou Jian Ye Xianbing Wang Xiaoming Zhang Zongtao Sun Xiaorong Tao Ming Wu Jianguo Wu Yi Li The State key laboratory of Protein and Plant Gene Research School of Life Sciences Peking University State key laboratory of Plant Environmental Resilience Frontiers Science Center for Molecular Design Breeding College of Biological Sciences China Agricultural University State key laboratory for Ecological Pest Control of Fujian and Taiwan Crops Vector-borne Virus Research Center College of Plant Protection Fujian Agriculture and Forestry University State key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences State key laboratory for Agro-Biotechnology and Department of Plant Pathology China Agricultural University State key laboratory of Plant Genomics Institute of Microbiology Chinese Academy of Sciences State key laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of SciencesCAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences State key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province Institute of Plant Virology Ningbo University Department of Plant Pathology The Key Laboratory of Plant Immunity Nanjing Agricultural University

Viral pathogens not only threaten the health and life of humans and animals but also cause enormous crop yield losses and contribute to global food insecurity. To defend against viral pathogens, plants have evolved an intricate immune system to perceive and cope with such attacks. Although most of the fundamental studies were carried out in model plants, more recent research in crops has provided new insights into the antiviral strategies employed by crop plants. We summarize recent advances in understanding the biological roles of cellular receptors, RNA silencing, RNA decay, hormone signaling, autophagy, and ubiquitination in manipulating crop host-mediated antiviral responses. The potential functions of circular RNAs, the rhizosphere microbiome, and the foliar microbiome of crops in plant-virus interactions will be fascinating research directions in the future. These findings will be beneficial for the development of modern crop improvement strategies.

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Insights into effects of thermotolerant nitrifying and sulfur-oxidizing inoculants on nitrogen-sulfur co-metabolism in sewage sludge composting

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Journal of Environmental Sciences 2024年第10期144卷 76-86页

作者： Tingting Hou Yujie Zhou Rongchun Du Jiali Liu Weiguang Li Shumei Zhang Muzi Li Junhong Chu Liqiang Meng Institute of microbiology Heilongjiang Academy of SciencesHarbin 150010China Hebei University of Environmental Engineering Hebei Key Laboratory of Agroecological SafetyQinhuangdao 066102China School of Environment Harbin Institute of TechnologyHarbin 150090China

In this study,high temperature thermotolerant nitrifying bacteria(TNB)and high temperature thermotolerant sulfide oxidizing bacteria(TSOB)were obtained from compost samples and inoculated into sewage sludge(SS)*** effects of inoculation on physical and chemical parameters,ammonia and hydrogen sulfide release,nitrogen form and sulfur compound content change and physical-chemical properties during nitrogen and sulfur conversion were *** results showed that inoculation of TNB and TSOB increased the temperature,pH,OM degradation,C/N ratio and germination index(GI)of *** with the control treatment(CK),the addition of inoculants reduced the release of NH3 and H2S,and transformed them into nitrogen and sulfur compounds,the hydrolysis of polymeric ferrous sulfate was promoted,resulting in relatively high content of sulfite and *** the same time,the physical and chemical properties of SS have a strong correlation with nitrogen and sulfur compounds.

关键词： Sewage sludge Composting Inoculation Thermotolerant nitrifying bacteria Thermotolerant sulfurized oxidizing bacteria

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Engineering Rubisco to enhance CO_(2) utilization

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Synthetic and Systems Biotechnology 2024年第1期9卷 55-68页

作者： Lei Zhao Zhen Cai Yin Li Yanping Zhang CAS key laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China University of Chinese Academy of Sciences Beijing100049China Seeds Research Syngenta Biotechnology ChinaZhong Guan Cun Life Science ParkBeijingChina

Ribulose-1,5-bisphosphate carboxylase/oxygenase(Rubisco)is a pivotal enzyme that mediates the fixation of CO_(2).As the most abundant protein on earth,Rubisco has a significant impact on global carbon,water,and nitrogen ***,the significantly low carboxylation activity and competing oxygenase activity of Rubisco greatly impede high carbon fixation *** review first summarizes the current efforts in directly or indirectly modifying plant Rubisco,which has been challenging due to its high conservation and limitations in chloroplast transformation ***,recent advancements in understanding Rubisco biogenesis with the assistance of chaperones have enabled successful heterologous expression of all Rubisco forms,including plant Rubisco,in *** breakthrough facilitates the acquisition and evaluation of modified proteins,streamlining the measurement of their ***,the establishment of a screening system in *** opens up possibilities for obtaining high-performance mutant enzymes through directed ***,this review emphasizes the utilization of Rubisco in microorganisms,not only expanding their carbon-fixing capabilities but also holding significant potential for enhancing biotransformation processes.

关键词： Rubisco Plant CO_(2)fixation Microbial Carbon fixation pathway Synthetic biology Enzyme engineering

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