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Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

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Marine Life Science & Technology 2024年第2期6卷 331-348页

作者： Hao Ling Yongxin Lv Yu Zhang Ning‑Yi Zhou Ying Xu state key laboratory of microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China state key of laboratory of Ocean Engineering Shanghai Jiao Tong UniversityShanghai 200240China

Phenolic compounds,as well as other aromatic compounds,have been reported to be abundant in hadal trenches.Although high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds,direct microbiological,genetic and biochemical evidence under in situ pressures remain absent.Here,a microbial consortium and a pure culture of Pseudomonas,newly isolated from Mariana Trench sediments,efficiently degraded phenol under pressures up to 70 and 60 MPa,respectively,with concomitant increase in biomass.By analyzing a high-pressure(70 MPa)culture metatranscriptome,not only was the entire range of metabolic processes under high pressure generated,but also genes encod-ing complete phenol degradation via ortho-and meta-cleavage pathways were revealed.The isolate of Pseudomonas also contained genes encoding the complete degradation pathway.Six transcribed genes(dmpKLMNOP_(sed))were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous expression.In addition,key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial metagenomes.At microbiological,genetic,bioinformatics,and biochemical levels,this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic pressures.This information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

关键词： Hadal trench High hydrostatic pressure Phenolic compounds degradation Piezotolerant microorganisms Widespread distribution

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Rational design of unrestricted pRN1 derivatives and their application in the construction of a dual plasmid vector system for Saccharolobus islandicus

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mLife 2024年第1期3卷 119-128页

作者： Pengpeng Zhao Xiaonan Bi Xiaoning Wang Xu Feng Yulong Shen Guanhua Yuan Qunxin She CRISPR and Archaea Biology Research Center State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina

Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools,which include efficient genome editing,gene silencing,and robust protein expression systems.However,plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic plasmid.Although this plasmid coexists with pRN1 in its original host,early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for Sa.islandicus.We hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this archaeon.We identified a putative target sequence in orf904 encoding a putative replicase on pRN1(target N1).Mutated targets(N1a,N1b,and N1c)were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid inter-ference assay.The results revealed that the original target triggered CRISPR immunity in this archaeon,whereas all three mutated targets did not,indicating that all the designed target mutations evaded host immunity.These mutated targets were then incorporated into orf904 individually,yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed(pN1aSD,pN1bSD,and pN1cSD).Sa.islandicus transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors,but pN1cSD lost the capability for replication.These results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the replicase.We further showed that pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination,and this yielded a dual plasmid system for genetic study with this important archaeal model.

关键词： archaeal genetics CRISPR-Cas CRISPR escape mutations dual plasmid vectors Saccharolobus-E.coli shuttle vectors

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The human-derived novel gut commensal Luoshenia tenuis regulates body weight and food intake in mice

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Food Science and Human Wellness 2024年第2期13卷 830-841页

作者： Yu Jiang Mengxuan Du Lisheng Xie Minzhi Jiang Yaokun Zhang Mingxia Bi Chang Liu Hongwei Liu Shuangjiang Liu state key laboratory of microbial Technology Shandong UniversityQingdao 266237China state key laboratory of microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China College of Life Science Hebei UniversityBaoding 071000China state key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Many studies have revealed that gut microbes modulate host metabolism.In this study,we characterized the therapeutic effects of a novel gut commensal Luoshenia tenuis against host metabolic disorders.First,by in silico analysis,we demonstrated that the L.tenuis was prevalent in the gut microbiomes of healthy humans but were depleted specifically in obesity cohorts.Further in vitro cultivation revealed that L.tenuis produced short chain fatty acids that were verified to modulate host metabolism and some other volatile metabolites to benefit hosts by anti-inflammation and anti-tumor.Second,gavage of the L.tenuis significantly decreased the body weight gain and food intake of high-fat diet-feeding C57BL/6J mice,which was in parallel with the changed expression level of genes related to satiety and feeding behavior.We then performed the gavage trial using diet induced obese mice,and it revealed that the administration of L.tenuis alleviated significantly the abnormal glucose and lipid metabolisms and reduced the inflammatory response.In summary,this study revealed a previously-unknown human gut commensal microbe that benefited host metabolism,and set the stage for the development of novel next-generation probiotic applicable for treatment of obesity and related metabolic disorders.

关键词： Luoshenia tenuis Gut microbe Feeding behavior Obesity Next-generation probiotic

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Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

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Plant Diversity 2024年第3期46卷 372-385页

作者： Shanni Cao Xue Zhao Zhuojin Li Ranran Yu Yuqi Li Xinkai Zhou Wenhao Yan Dijun Chen Chao He state key laboratory of Pharmaceutical biotechnology School of Life SciencesNanjing UniversityNanjing 210023China National key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings.This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological variance.This integration spans a broad spectrum of tissues,including both below-and above-ground parts.Utilizing a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell compositions.We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression.Taken together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.

关键词： Arabidopsis Single cell transcriptome Gene regulatory network Data integration Plant cell atlas

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Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39

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Marine Life Science & Technology 2024年第2期6卷 198-211页

作者： Wanyue Jiang Tongtong Lin Jiao Pan Caitlyn ERivera Clayton Tincher Yaohai Wang Yu Zhang Xiang Gao Yan Wang Ho‑Ching T.Tsui Malcolm E.Winkler Michael Lynch Hongan Long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China laboratory for Marine Biology and biotechnology Laoshan LaboratoryQingdao 266237China Department of Biology Indiana UniversityBloomingtonIN 47405USA School of Mathematics Science Ocean University of ChinaQingdao 266000China state key laboratory of microbial Technology Microbial Technology InstituteSchool of Life ScienceShandong UniversityQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA

Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic stability.However,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)lines.This rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T direction.The high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in nature.In line with this,S.pneumoniae D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among bacteria.Treatment with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and S.pneumoniae lacks a stress response pathway.Our findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.

关键词： Neutral evolution Mutation spectrum Antibiotics DNA mismatch repair Oxidative damage repair

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Identification and characterization of camptothecin tailoring enzymes in Nothapodytes tomentosa

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Journal of Integrative Plant Biology 2024年第6期66卷 1158-1169页

作者： Yin Chen Jian-Ping Huang Yong-Jiang Wang Meng-Ling Tu Junheng Li Bingyan Xu Guoqing Peng Jing Yang Sheng-Xiong Huang state key laboratory of Phytochemistry and Plant Resources in West China and Yunnan key laboratory of Natural Medicinal Chemistry Kunming Institute of Botany Chinese Academy of Sciences University of Chinese Academy of Sciences key laboratory for Economic Plants and biotechnology Kunming Institute of Botany Chinese Academy of Sciences

Camptothecin is a complex monoterpenoid indole alkaloid with remarkable antitumor activity. Given that two C-10 modified camptothecin derivatives,topotecan and irinotecan, have been approved as potent anticancer agents, there is a critical need for methods to access other aromatic ringfunctionalized congeners(e.g., C-9, C-10, etc.).However, contemporary methods for chemical oxidation are generally harsh and low-yielding when applied to the camptothecin scaffold, thereby limiting the development of modified derivatives. Reported herein, we have identified four tailoring enzymes responsible for C-9 modifications of camptothecin from Nothapodytes tomentosa, via metabolomic and transcriptomic analysis. These consist of a cytochrome P450(Nt CPT9H) which catalyzes the regioselective oxidation of camptothecin to 9-hydroxycamptothecin, as well as two methyltransferases(Nt OMT1/2, converting 9-hydroxycamptothecin to 9-methoxycamptothecin),and a uridine diphosphate-glycosyltransferase(Nt UGT5, decorating 9-hydroxycamptothecin to9-β-D-glucosyloxycamptothecin). Importantly, the critical residues that contribute to the specific catalytic activity of Nt CPT9H have been elucidated through molecular docking and mutagenesis experiments. This work provides a genetic basis for producing camptothecin derivatives through metabolic engineering. This will hasten the discovery of novel C-9 modified camptothecin derivatives,with profound implications for pharmaceutical manufacture.

关键词： camptothecin biosynthesis enzymatic assay Nothapodytes tomentosa tailoring enzyme transcriptomic analysis

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Genetic association analysis-based networks and classification of human UCP1 polymorphisms

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Genes & Diseases 2024年第3期11卷 63-65页

作者： Donghai Li state key laboratory of Pharmaceutical biotechnology School of Life SciencesNanjing UniversityJiangsu 210023China

Uncoupling protein 1(UCP1,also known as thermogenin or SLC25A7)plays an important role in the uncoupling of oxidative phosphorylation and adaptive non-shivering thermogenesis(NST).The genomic location for UCP1 is chromosome 4 q31.1:140,555,770--140,568,961(GRCh38/hg38)and its size is 13,192 bases split into 6 exons.In dbSNP,3650 short genetic variations of human UCP1 are documented.In this study,UCP1 serves as an example to construct polymorphism-trait networks and enable a func-tional classification.

关键词： classification. UCP1 networks

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Carbonic anhydrase-like enzymes in the formation of Lycopodium alkaloid

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Chinese Journal of Natural Medicines 2024年第3期22卷 193-194页

作者： DONG Huiwen GE Huiming state key laboratory of Pharmaceutical biotechnology Institute of Functional BiomoleculesSchool of Life SciencesNanjing UniversityNanjing 210023China

Plant alkaloids,renowned for their structural diversity and bioactivity,are prominent in both modern and traditional medicine[1].Unraveling the intricacies of plant alkaloid biosynthesis could pave the way for the discovery of new natural products and pathways.It may also shed light on the roles of existing pathways in host biology and provide valuable tools for metabolic engineering in plants and microbes[2].Unlike other major classes of plant natural products,such as terpenoids and polyketides,the formation of alkaloid scaffolds does not conform to a uniform chemical theme or depend on a singular enzyme class[3].A case in point is the Lycopodium alkaloids in the Lycopodiaceae family,where the enzymes responsible for their core scaffold construction remain unidentified[4].

关键词： Lycopodium alkaloid Carbonic anhydrase-like enzymes Biosynthesis

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Mannanase improves the growth performance of broilers by alleviating inflammation of the intestinal epithelium and improving intestinal microbiota

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Animal Nutrition 2024年第1期16卷 376-394页

作者： Xiaodan Zhang Huiping Xu Lu Gong Jiao Wang Jianyang Fu Zengpeng Lv Liangjuan Zhou Xuejun Li Qiong Liu Pingyu Xia Yuming Guo state key laboratory of Animal Nutrition and Feeding College of Animal Science and Technology China Agricultural University Beijing Strowin biotechnology Co. Ltd.

This experiment aimed to discuss and reveal the effect and mechanism of mannanase on intestinal inflammation in broilers triggered by a soybean meal diet. In this experiment, 384 Arbor Acres broilers at1 d old were randomly divided into 3 treatment groups. The broilers were fed a corn-soybean meal basal diet, a low-energy diet(metabolizable energy reduced by 50 kcal/kg), and a low-energy diet supplemented with 100 mg/kg mannanase for 42 d. The low-energy diet increased feed conversion ratio from0 to 42 d, reduced ileal villus height and villus height-to-crypt depth ratio and upregulated the expression of nuclear factor kappa B(NF-κB) in the ileum(P < 0.05). It also reduced cecal short-chain fatty acids(SCFA), such as acetic acid(P < 0.05). Compared with low-energy diets, the addition of mannanase increased body weight at 42 d, promoted the digestibility of nutrients, and maintained the morphology and integrity of the intestinal epithelium of broilers(P < 0.05). In addition, mannanase upregulated the expression of claudin-1(CLDN1) and zonula occludens-1(ZO-1) in the jejunum at 21 d,downregulated the expression of ileal NF-κB, and increased the content of isobutyric acid in the cecum of broilers(P < 0.05). The results for the ileal microbiota showed that a low-energy diet led to a decrease in the relative abundance of Lactobacillus reuteri in the ileum of broilers. The addition of mannanase increased the relative abundance of Lactobacillus-KC45b and Lactobacillus johnsonii in broilers. Furthermore, a low-energy diet reduced the relative abundance of Butyricicoccus in the intestine of broilers and inhibited oxidative phosphorylation and phosphoinositol metabolism. Mannanase increased the relative abundance of Odoribacter, promoted energy metabolism and N-glycan biosynthesis, and increased the activities of GH3 and GH18. It is concluded that mannanase could improve the growth performance of broilers by reducing the expression of NF-κB in the ileum, increasing the production of SCFA in the cecum, suppressing intestina

关键词： Broiler Low-energy diet Mannanase Intestinal inflammatory response Intestinal microbiota Metagenome

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Improved observation of colonized roots reveals the regulation of arbuscule development and senescence by drought stress in the arbuscular mycorrhizae of citrus

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Horticultural Plant Journal 2024年第2期10卷 425-436页

作者： Xilong Yin Wei Zhang Zengwei Feng Guangda Feng Honghui Zhu Qing Yao College of Horticulture South China Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China)Ministry of Agriculture and Rural AffairsGuangdong Province Key Laboratory of Microbial Signals and Disease ControlGuangzhouGuangdong 510642China key laboratory of Agricultural Microbiomics and Precision Application Ministry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationKey Laboratory of Agricultural MicrobiomicsState Key Laboratory of Applied Microbiology Southern ChinaGuangdong Microbial Culture Collection Center(GDMCC)Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

Citrus is the typical mycorrhizal fruit tree species establishing symbiosis with arbuscular mycorrhizal (AM) fungi. However, arbuscule development and senescence in colonized citrus roots, especially in response to drought stress, remain unclear, which is mainly due to the difficulty in clearing and staining lignified roots with the conventional method. Here, we improved the observation of colonized roots of citrus plants with the sectioning method, which enabled the clear observation of AM fungal structures. Furthermore, we investigated the effects of one week of drought stress on arbuscule development and senescence with the sectioning method. Microscopy observations indicated that drought stress significantly decreased mycorrhizal colonization (F%and M%) although it did not affect plant growth performance. Fluorescence probes (WGA 488 and/or Nile red) revealed that drought stress inhibited arbuscule development by increasing the percentage of arbuscules at the early stage and decreasing the percentages of arbuscules at the midterm and mature stages. Meanwhile, drought stress accelerated arbuscule senescence, which was characterized by the increased accumulation of neutral lipids. Overall, the sectioning method developed in this study enables the in-depth investigation of arbuscule status, and drought stress can inhibit arbuscule development but accelerate arbuscule senescence in the colonized roots of citrus plants. This study paves the way to elaborately dissecting the arbuscule dynamics in the roots of fruit tree species in response to diverse abiotic stresses.

关键词： Arbuscular mycorrhizae Citrus Drought stress Arbuscule development Arbuscule senescence Fruit tree species

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