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Synthetic and Systems Biotechnology 2024年第3期9卷 540-548页

作者： Xin-jing Yue Jia-rui Wang Jun-ning Zhao Zhuo Pan Yue-zhong Li State Key Laboratory of microbial Technology Institute of Microbial TechnologyShandong UniversityQingdaoPR China

The chromosomal position effect can significantly affect the transgene expression,which may provide an efficient strategy for the inauguration of alien genes in new hosts,but has been less explored *** bacterium Myxococcus xanthus harbors a large circular high-GC genome,and the position effect in this chassis may result in a thousand-fold expression variation of alien natural *** this study,we conducted transposon insertion at TA sites on the *** genome,and used enrichment and dilution indexes to respectively appraise high and low expression potentials of alien genes at insertion *** enrichment sites are characteristically distributed along the genome,and the dilution sites are overlapped well with the horizontal transfer *** experimentally demonstrated the enrichment sites as high expression integration sites(HEISs),and the dilution sites unsuitable for gene integration *** work highlights that HEISs are the plug-and-play sites for efficient expression of integrated genes.

关键词： Position effect High expression integration sites(HEISs) Myxococcus xanthus Tn-seq

Construction of an alternative NADPH regeneration pathway improves ethanol production in Saccharomyces cerevisiae with xylose metabolic pathway

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Synthetic and Systems Biotechnology 2024年第2期9卷 269-276页

作者： Yali Qiu Wei Liu Meiling Wu Haodong Bao Xinhua Sun Qin Dou Hongying Jia Weifeng Liu Yu Shen State Key Laboratory of microbial Technology Institute of Microbial TechnologyShandong UniversityQingdao266237China Advanced Medical Research Institute Shandong UniversityJinan250012China

Full conversion of glucose and xylose from lignocellulosic hydrolysates is required for obtaining a high ethanol ***,glucose and xylose share flux in the pentose phosphate pathway(PPP)and glycolysis pathway(EMP),with glucose having a competitive advantage in the shared metabolic *** this work,we knocked down ZWF1 to preclude glucose from entering the *** reduced the[NADPH]level and disturbed growth on both glucose or xylose,confirming that the oxidative PPP,which begins with Zwf1p and ultimately leads to CO_(2) production,is the primary source of NADPH in both glucose and *** glucose depletion,gluconeogenesis is necessary to generate glucose-6-phosphate,the substrate of *** re-established the NADPH regeneration pathway by replacing the endogenous NAD^(+)-dependent glyceraldehyde-3-phosphate dehydrogenase(GAPDH)gene TDH3 with heterogenous NADP^(+)-GAPDH genes GDH,gapB,and *** the resulting strains,the strain BZP1(zwf1Δ,tdh3::GDP1)exhibited a similar xylose consumption rate before glucose depletion,but a 1.6-fold increased xylose consumption rate following glucose depletion compared to the original strain BSGX001,and the ethanol yield for total consumed sugars of BZP1 was 13.5%higher than *** suggested that using the EMP instead of PPP to generate NADPH reduces the wasteful metabolic cycle and excess CO_(2)^(++) release from oxidative ***,we used a copper-repressing promoter to modulate the expression of ZWF1 and optimize the timing of turning off the ZWF1,therefore,to determine the competitive equilibrium between glucose-xylose *** strategy allowed fast growth in the early stage of fermentation and low waste in the following stages of fermentation.

关键词： Saccharomyces cerevisiae Xylose Ethanol NADPH Glyceraldehyde-3-phosphate dehydrogenase

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

Acarbose glycosylation by AcbE for the production of acarstatins with enhancedα-amylase inhibitory activity

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Synthetic and Systems Biotechnology 2024年第2期9卷 359-368页

作者： Xin Zhang Qungang Huang Ziyue Guo Feifei Cai Qianjin Kang Linquan Bai State Key Laboratory of microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China College of Life science Tarim UniversityAlar843300China

Acarbose is a potent glycosidase inhibitor widely used in the clinical treatment of type 2 diabetes mellitus(T2DM).Various acarbose analogs have been identified while exploring compounds with improved pharmacological *** this study,we found that AcbE from Actinoplanes ***50/110 catalyzes the production of acarbose analogs that exhibit significantly improved inhibitory activity towardsα-amylase than *** AcbE mainly catalyzed the formation of two new compounds,namely acarstatins A and B,using acarbose as *** high-resolution mass spectrometry,nuclear magnetic resonance,and glycosidase hydrolysis,we elucidated their chemical structures as O-α-d-maltosyl-(1→4)-acarbose and O-α-d-maltotriosyl-(1→4)-acarbose,*** A and B exhibited 1584-and 1478-fold greater inhibitory activity towards human salivaryα-amylase than ***,both acarstatins A and B exhibited complete resistance to microbiome-derived acarbose kinase 1-mediated phosphorylation and partial resistance to acarbose-preferred glucosidase-mediated ***,acarstatins A and B have great potential as candidate therapeutic agents for T2DM.

关键词： Acarbose analogs α-amylase inhibitory activity Actinoplanes sp. Transglycosylase

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 *** this study,we characterized the therapeutic effects of a novel gut commensal Luoshenia tenuis against host metabolic ***,by in silico analysis,we demonstrated that the *** was prevalent in the gut microbiomes of healthy humans but were depleted specifically in obesity *** in vitro cultivation revealed that *** produced short chain fatty acids that were verified to modulate host metabolism and some other volatile metabolites to benefit hosts by anti-inflammation and ***,gavage of the *** 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 *** then performed the gavage trial using diet induced obese mice,and it revealed that the administration of *** alleviated significantly the abnormal glucose and lipid metabolisms and reduced the inflammatory *** 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

Exploring the characteristics of microbial community and enzyme activity in the aged refuse landfill environment of Taiyuan, China

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Pedosphere 2024年第5期34卷 879-891页

作者： Fen HOU Junjie DU Yuzhou MENG Xihui WU Department of Land Resource Management School of Public Administration Shanxi University of Finance and Economics College of Life science Shanxi Engineering Research Center of Microbial Application Technologies Shanxi Normal University

Municipal solid waste landfill is the main disposal option for domestic garbage, in which microbial activities play an important role. However, despite the widespread practice of landfilling, the metagenomic microbial profiles of landfill sites remain poorly characterized. In this study, we used a combination of physicochemical analysis, ultraviolet-visible spectrophotometry, and high-throughput Illumina shotgun sequencing to systematically investigate the changes in soil enzyme activities, microbial community structure, and functional attributes in aged refuse collected from the Xingou Municipal Solid Waste Landfill in Taiyuan, China, with ordinary topsoil from an area within 5 km of the landfill as control soil. Except for neutral phosphatase (P=0.065), the activities of urease, laccase, dehydrogenase, sucrase, neutral protease, and β-glucosidase were all significantly reduced (P microbial communities, as reflected by the higher values of community richness estimators (Chao 1 and ACE) and diversity indices (Shannon and Simpson). In total, 186 phyla, 4 354 genera, and 34 459 species were identified, with 132 phyla, 1 914 genera, and7 369 species showing significantly different abundances between the aged refuse and the control soil. Actinobacteria and Acidobacteria were identified as the dominant phyla in the control soil, whereas Proteobacteria, Euryarchaeota (archaea), and Firmicutes were found to predominate in the aged ***, Euryarchaeota and Methanoculleus were the major taxa detected in the aged refuse, but were almost completely absent in the control soil. Xenobiotic biodegradation and bacterial chemotaxis were the main functions of the microflora in the aged refuse, whereas the carbohydrate, amino acid,

关键词： functional attribute metabolism pathway municipal solid waste landfill resource utilization soil microflora

Coupled strategy based on regulator manipulation and medium optimization empowers the biosynthetic overproduction of lincomycin

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Synthetic and Systems Biotechnology 2024年第1期9卷 134-143页

作者： Xinlu Cai Wanlian Xu Yang Zheng Sendi Wu Rundong Zhao Nian Wang Yaqian Tang Meilan Ke Qianjin Kang Linquan Bai Buchang Zhang Hang Wu School of Life sciences Institute of Physical Science and Information TechnologyAnhui UniversityHefei230601China State Key Laboratory of microbial Metabolism Shanghai Jiao Tong UniversityShanghai200240China

The biosynthesis of bioactive secondary metabolites,specifically antibiotics,is of great scientific and economic *** control of antibiotic production typically involves different processes and molecular *** numerous efforts to improve antibiotic yields,joint engineering strategies for combining genetic manipulation with fermentation optimization remain *** A(Lin-A),a lincosamide antibiotic,is industrially fermented by Streptomyces ***,the leucine-responsive regulatory protein(Lrp)-type regulator SLCG_4846 was confirmed to directly inhibit the lincomycin biosynthesis,whereas indirectly controlled the transcription of SLCG_2919,the first reported repressor in *** of SLCG_4846 in the high-yield *** LA219X(LA219XΔ4846)increases the Lin-A production and deletion of SLCG_2919 in LA219XΔ4846 exhibits superimposed yield *** the effect of the double deletion on cellular primary metabolism of ***,Plackett-Burman design,steepest ascent and response surface methodologies were utilized and employed to optimize the seed medium of this double mutant in shake flask,and Lin-A yield using optimal seed medium was significantly increased over the *** strategies were performed in a 15-L *** maximal yield of Lin-A in LA219XΔ4846-2919 reached 6.56 g/L at 216 h,55.1%higher than that in LA219X at the parental cultivation(4.23 g/L).This study not only showcases the potential of this strategy to boost lincomycin production,but also could empower the development of high-performance actinomycetes for other antibiotics.

关键词： Streptomyces Transcription factor Genetic engineering Fermentation optimization Lincomycin

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 ***,plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic *** 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 *** hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this *** 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 *** 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 *** mutated targets were then incorporated into orf904 individually,yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed(pN1aSD,pN1bSD,and pN1cSD).*** transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors,but pN1cSD lost the capability for *** results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the *** 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

Nitrogen-based fertilizers differentially affect protist community composition in paddy field soils

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Soil Ecology Letters 2024年第3期6卷 35-44页

作者： Seda Ozer Bodur Solomon Oloruntoba Samuel Kazuki Suzuki Naoki Harada Rasit Asiloglu Graduate School of science and Technology Niigata UniversityNiigataJapan Department of Plant and microbial Biology North Carolina State UniversityRaleighNCUSA Institute of science and Technology Niigata UniversityNiigataJapan

Protists are one of the most diverse and dominant microbial groups and they play critical roles in the soil *** nitrogen fertilizers have a profound impact on protist communities,still less is known about how different nitrogen fertilizer types affect protist community composition in different soil *** we investigated the effects of six inorganic nitrogen fertilizers(urea,ammonium nitrate,ammonium sulfate,potassium nitrate,ammonium chloride,and diammonium hydrogen phosphate)and an organic fertilizer(a mixture of rice husk and cow manure)on protist community composition in three paddy field soils using a high-throughput sequencing *** effect of the fertilizers on the functional groups of protists,namely consumers(predators and decomposers),photoautotrophs,and parasites(plant pathogens and animal parasites)was also *** results showed that nitrogen fertilizers had distinctive effects on the beta diversity of the protists,while we also observed that the same fertilizer had slightly different effects depending on the soil *** and Rhizaria were the most affected protist taxonomical groups,while predatory protists were the main functional groups that were affected by nitrogen *** forest analysis showed that most of the fertilizer-affected protists were predators,among which Cercozoa was the most affected *** conclusion,our results provide important insights into the impact of nitrogen fertilizers on soil protist communities.

关键词： nitrogen fertilizer bottom-up paddy field predatory protist soil protist community

An upgraded Myxococcus xanthus chassis with enhanced growth characteristics for efficient genetic manipulation

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Engineering Microbiology 2024年第3期4卷 62-66页

作者： Weifeng Hu Yan Wang Xiaoran Yue Weiwei Xue Wei Hu Xinjing Yue Yuezhong Li State Key Laboratory of microbial Technology Institute of Microbial TechnologyShandong UniversityQingdao 266237China

Myxobacteria are well known for multicellular social behaviors and valued for biosynthesis of natural *** social behaviors such as clumping growth severely hamper strain cultivation and genetic *** Myxococcus xanthus DK1622,we engineered Hu04,which is deficient in multicellular behavior and ***04,while maintaining nutritional growth and a similar metabolic background,exhibits improved dispersed growth,streamlining operational *** achieves high cell densities in culture and is promising for synthetic biology applications.

关键词： Myxococcus xanthus Operation deficiency Phenotypic optimization Chassis Genetic performance