Owing to their diverse coordination patterns and catalytic mechanisms,non-heme iron-dependent dioxygenases catalyze a variety of biochemical reactions involved in the synthesis of numerous natural products and valuabl...Owing to their diverse coordination patterns and catalytic mechanisms,non-heme iron-dependent dioxygenases catalyze a variety of biochemical reactions involved in the synthesis of numerous natural products and valuable compounds.Recently,we discovered a novel and atypical non-heme iron-dependent dioxygenase,BTG13,that features a unique coordination center consisting of four histidines and a carboxylated lysine(Kcx).This enzyme catalyzes the C–C bond cleavage of anthraquinone through two unconventional steps,with modified Kcx playing a key role in facilitating these processes,as revealed by molecular dynamics simulations and quantum chemical calculations.Phylogenetic analyses and other studies suggest that BTG13-related metalloenzymes are widespread in various organisms.Here,we highlight the significance of this new class of non-heme iron-dependent oxygenases and their potential as novel tools for practical applications in synthetic biology.展开更多
The increasing antimicrobial resistance has seriously threatened human health worldwide over the last three decades.This severe medical crisis and the dwindling antibiotic discovery pipeline require the development of...The increasing antimicrobial resistance has seriously threatened human health worldwide over the last three decades.This severe medical crisis and the dwindling antibiotic discovery pipeline require the development of novel antimicrobial treatments to combat life-threatening infections caused by multidrug-resistant micro-bial pathogens.However,the detailed mechanisms of action,resistance,and toxicity of many antimicrobials remain uncertain,significantly hampering the development of novel antimicrobials.Genome-scale metabolic model(GSMM)has been increasingly employed to investigate microbial metabolism.In this review,we discuss the latest progress of GSMM in antimicrobial pharmacology,particularly in elucidating the complex interplays of multiple metabolic pathways involved in antimicrobial activity,resistance,and toxicity.We also highlight the emerging areas of GSMM applications in modeling non-metabolic cellular activities(e.g.,gene expression),identi-fication of potential drug targets,and integration with machine learning and pharmacokinetic/pharmacodynamic modeling.Overall,GSMM has significant potential in elucidating the critical role of metabolic changes in antimi-crobial pharmacology,providing mechanistic insights that will guide the optimization of dosing regimens for the treatment of antimicrobial-resistant infections.展开更多
Natural occurring aromatic polyketides from actinomycetes indicate a structurally and functionally diverse fam-ily of polycyclic polyphenols.Some of them are consequently suggested as lead structures for drug developm...Natural occurring aromatic polyketides from actinomycetes indicate a structurally and functionally diverse fam-ily of polycyclic polyphenols.Some of them are consequently suggested as lead structures for drug development.Among them,rubromycins are derived from a single C26 polyketide chain and exhibit an unusual bisbenzannu-lated[5,6]-spiroketal system that connects a highly oxygenated naphthazarin motif to an isocoumarin unit.This type of biosynthetically elusive polycyclic polyketides has shown promising pharmacological activities,includ-ing antimicrobial,anticancer,and enzyme inhibition activity.The unique structures,intriguing biosynthesis,and marked bioactivities of rubromycins have drawn considerable attention from several chemists and biologists.This review covers the isolation,characterization,biosynthesis,and biological studies of these structurally diverse and complex rubromycins.展开更多
Formic acid is one of the main weak acids in lignocellulosic hydrolysates that is known to be inhibitory to yeast growth even at low concentrations.In this study,we employed a CRISPR interference(CRISPRi)strain librar...Formic acid is one of the main weak acids in lignocellulosic hydrolysates that is known to be inhibitory to yeast growth even at low concentrations.In this study,we employed a CRISPR interference(CRISPRi)strain library comprising>9000 strains encompassing>98%of all essential and respiratory growth-essential genes,to study formic acid tolerance in Saccharomyces cerevisiae.To provide quantitative growth estimates on formic acid toler-ance,the strains were screened individually on solid medium supplemented with 140 mM formic acid using the Scan-o-Matic platform.Selected resistant and sensitive strains were characterized in liquid medium supplemented with formic acid and in synthetic hydrolysate medium containing a combination of inhibitors.Strains with gR-NAs targeting genes associated with chromatin remodeling were significantly enriched for strains showing formic acid tolerance.In line with earlier findings on acetic acid tolerance,we found genes encoding proteins involved in intracellular vesicle transport enriched among formic acid sensitive strains.The growth of the strains in syn-thetic hydrolysate medium followed the same trend as when screened in medium supplemented with formic acid.Strains sensitive to formic acid had decreased growth in the synthetic hydrolysate and all strains that had im-proved growth in the presence of formic acid also grew better in the hydrolysate medium.Systematic analysis of CRISPRi strains allowed identification of genes involved in tolerance mechanisms and provided novel engineering targets for bioengineering strains with increased resistance to inhibitors in lignocellulosic hydrolysates.展开更多
Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues,such as community stability,keystone species identification,and the manipulation ...Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues,such as community stability,keystone species identification,and the manipulation of community structures.However,exploring these interactions proves challenging within complex natural ecosys-tems.With advances in synthetic biology,the design of synthetic microbial ecosystems has received increasing attention due to their reduced complexity and enhanced controllability.Various ecological relationships,includ-ing commensalism,amensalism,mutualism,competition,and predation have been established within synthetic ecosystems.These relationships are often context-dependent and shaped by physical and chemical environmental factors,as well as by interacting populations and surrounding species.This review consolidates current knowl-edge of synthetic microbial ecosystems and factors influencing their ecological dynamics.A deeper understanding of how these ecosystems function and respond to different variables will advance our understanding of microbial-community interactions.展开更多
Escherichia coli is the most well-studied model prokaryote and has become an indispensable host for the biotech-nological production of proteins and biochemicals.In particular,the probiotic status of one E.coli strain...Escherichia coli is the most well-studied model prokaryote and has become an indispensable host for the biotech-nological production of proteins and biochemicals.In particular,the probiotic status of one E.coli strain,E.coli Nissle 1917(EcN)has helped it become a new favorite amongst synthetic biologists.To broaden its potential applications,here we assemble a comparative study on the genomes,transcriptomes,and metabolic properties of E.coli strains EcN,BL21(DE3),and MG1655.Comparative genomics data suggests that EcN possesses 1404 unique CDSs.In particular,EcN has additional iron transport systems which endow EcN with a higher tolerance to iron scarcity when compared to two other E.coli strains.EcN transcriptome data demonstrates that E.coli strains EcN,BL21(DE3),and MG1655 all have comparable activities of the central metabolic pathway,however only EcN inherits the arginine deiminase pathway.Additionally,we found that EcN displayed a lower expres-sion of ribosomal proteins compared to BL21(DE3)and MG1655.This comparative study on E.coli strains EcN,BL21(DE3),and MG1655 aims to provide a reference for further engineering EcN as a biotechnological tool.展开更多
The present review explores the influence of the gut microbiota on antibiotic resistance dynamics,particularly those associated with dysbiosis.The improper use of antibiotics can induce resistance in pathogens through...The present review explores the influence of the gut microbiota on antibiotic resistance dynamics,particularly those associated with dysbiosis.The improper use of antibiotics can induce resistance in pathogens through various pathways,which is a topic of increasing interest within the scientific community.This review highlights the importance of microbial diversity,gut metabolism,and inflammatory responses against the dysbiosis due to the action of antibiotics.Additionally,it examines how secondary metabolites secreted by pathogens can serve as biomarkers for the early detection of antibiotic resistance.Although significant progress has been made in this field,key research gaps persist,including the need for a deeper understanding of the long-term effects of antibiotic-induced dysbiosis and the specific mechanisms driving the evolution of resistance in gut bacteria.Based on these considerations,this review systematically analyzed studies from PubMed,Web of Science,Embase,Cochrane Library,and Scopus up to July 2024.This study aimed to explore the dynamics of the interactions between gut microbiota and antibiotic resistance,specifically examining how microbial composition influences the development of resistance mechanisms.By elucidating these relationships,this review provides insights into management strategies for drug resistance and improves our understanding of microbial contributions to host health.展开更多
Deciphering gene function is fundamental to engineering of microbiology.The clustered regularly interspaced short palindromic repeats(CRISPR)system has been adapted for gene repression across a range of hosts,creating...Deciphering gene function is fundamental to engineering of microbiology.The clustered regularly interspaced short palindromic repeats(CRISPR)system has been adapted for gene repression across a range of hosts,creating a versatile tool called CRISPR interference(CRISPRi)that enables genome-scale analysis of gene function.This approach has yielded significant advances in the design of genome-scale CRISPRi libraries,as well as in applica-tions of CRISPRi screening in medical and industrial microbiology.This review provides an overview of the recent progress made in pooled and arrayed CRISPRi screening in microorganisms and highlights representative studies that have employed this method.Additionally,the challenges associated with CRISPRi screening are discussed,and potential solutions for optimizing this strategy are proposed.展开更多
The current issues on resources,energy,and the environment of hu-man society drive us to seek sustainable manufacturing methods and de-velopment approaches.Microbes,with a series of advantages of broad substrate range...The current issues on resources,energy,and the environment of hu-man society drive us to seek sustainable manufacturing methods and de-velopment approaches.Microbes,with a series of advantages of broad substrate ranges and diverse metabolic capacities,have great potential to produce fuels and chemicals from renewable resources[1].In recent years,a series of progress has been made in this field in the context of fast-developing synthetic biology technologies and interdisciplinary re-search.The highly abundant renewable resources,including one carbon(C1)compounds and lignocellulose,can be converted to platform chem-icals and then to various products by natural or engineered microbial cell factories[2].展开更多
Toxin-antitoxin(TA)systems are ubiquitous in bacteria and archaea.Most are composed of two neighboring genetic elements,a stable toxin capable of inhibiting crucial cellular processes,including replication,transcrip-t...Toxin-antitoxin(TA)systems are ubiquitous in bacteria and archaea.Most are composed of two neighboring genetic elements,a stable toxin capable of inhibiting crucial cellular processes,including replication,transcrip-tion,translation,cell division and membrane integrity,and an unstable antitoxin to counteract the toxicity of the toxin.Many new discoveries regarding the biochemical properties of the toxin and antitoxin components have been made since the first TA system was reported nearly four decades ago.The physiological functions of TA systems have been hotly debated in recent decades,and it is now increasingly clear that TA systems are important immune systems in prokaryotes.In addition to being involved in biofilm formation and persister cell formation,these modules are antiphage defense systems and provide host defenses against various phage infec-tions via abortive infection.In this review,we explore the potential applications of TA systems based on the recent progress made in elucidating TA functions.We first describe the most recent classification of TA systems and then introduce the biochemical functions of toxins and antitoxins,respectively.Finally,we primarily focus on and devote considerable space to the application of TA complexes in synthetic biology.展开更多
While the typical targets of(chemo-)enzymatic cascades are fine chemicals(e.g.,pharmaceuticals),a chemoen-zymatic cascade,artificial starch anabolic pathway(ASAP),was recently developed to synthesize starch from CO_(2...While the typical targets of(chemo-)enzymatic cascades are fine chemicals(e.g.,pharmaceuticals),a chemoen-zymatic cascade,artificial starch anabolic pathway(ASAP),was recently developed to synthesize starch from CO_(2).The key results and outstanding features of ASAP are discussed here.We envision that ASAP and its mi-crobial counterpart may enable efficient synthesis of food and sequestration of CO_(2)in a circular manner,thus contributing to a sustainable and hunger-free world and future habitation in space.展开更多
The widespread presence of iron and sulfur compounds such as pyrite in marine waterlogged archeological wood(WAW)can cause irreversible damage to the safety of its preservation.This issue has been a longstanding conce...The widespread presence of iron and sulfur compounds such as pyrite in marine waterlogged archeological wood(WAW)can cause irreversible damage to the safety of its preservation.This issue has been a longstanding concern for cultural heritage conservation communities.In this study,we examined the distribution and phase composition of Fe and sulfur compounds in wood samples obtained from the Nanhai I shipwreck using ESEM-EDS,micro-Raman spectroscopy,and an X-ray diffractometer.The removal of iron from WAW samples of the Nanhai I shipwreck using Acidithiobacillus ferrooxidans(A.ferrooxidans)was evaluated using conductivity and ICP-AES analysis.The results showed that A.ferrooxidans effectively improved the removal of iron from WAW.The degradation of fresh healthy wood during treatment was also analyzed using infrared spectroscopy,and the results showed that the treatment had little effect on the samples over a short period.This study demonstrates,for the first time,the feasibility of iron extraction from marine WAW by A.ferrooxidans.This was also the first attempt in China to apply biological oxidation to the removal of iron from marine archeological materials.展开更多
The increasing shortage of fossil resources and environmental pollution has renewed interest in the synthesis of value-added biochemicals from methanol.However,most of native or synthetic methylotrophs are unable to a...The increasing shortage of fossil resources and environmental pollution has renewed interest in the synthesis of value-added biochemicals from methanol.However,most of native or synthetic methylotrophs are unable to assimilate methanol at a sufficient rate to produce biochemicals.Thus,the performance of methylotrophs still needs to be optimized to meet the demands of industrial applications.In this review,we provide an in-depth discussion on the properties of natural and synthetic methylotrophs,and summarize the natural and synthetic methanol assimilation pathways.Further,we discuss metabolic engineering strategies for enabling microbial utilization of methanol for the bioproduction of value-added chemicals.Finally,we highlight the potential of microbial engineering for methanol assimilation and offer guidance for achieving a low-carbon footprint for the biosynthesis of chemicals.展开更多
Small regulatory RNAs(sRNAs)are non-coding RNA molecules that fine-tune various cellular processes and respond to various environmental stimuli.In Bacillus subtilis,the regulatory mechanisms and specific targets of se...Small regulatory RNAs(sRNAs)are non-coding RNA molecules that fine-tune various cellular processes and respond to various environmental stimuli.In Bacillus subtilis,the regulatory mechanisms and specific targets of several sRNAs remain largely unknown.In this study,we identified and characterized S612 as a self-terminating sRNA in B.subtilis.The expression of S612 is regulated by external signals,including nutrient availability and salt concentration.Overexpression of S612 induced filamentous cells with extensive cellular elongation and complete inhibition of sporulation,indicating its potential to control cell morphology and spore formation.S612 directly targets and downregulates genes through post-transcriptional base pairing with mRNAs,including ylmD,trpE,ycxC,yycS,rapH,and amyE,some of which are involved in cell membrane integrity,cell wall synthesis,and sporulation initiation.Therefore,we propose that S612 is an important post-transcriptional regulator of cell morphology and sporulation.展开更多
Essential oil(EO)has significant antifungal activity.However,there is limited information on the mechanism of the synergistic antifungal effect of the effective components of EO against fungi.In the present study,mole...Essential oil(EO)has significant antifungal activity.However,there is limited information on the mechanism of the synergistic antifungal effect of the effective components of EO against fungi.In the present study,molecular electrostatic potential and molecular docking were used for the first time to investigate the synergistic antifungal mechanism of eugenol and citral small molecule(C_(EC))against Penicillium roqueforti.The results showed that the C_(EC)treatment made the activity ofβ-(1,3)-glucan synthase(GS)and chitin synthase(CS)decreas by 20.2%and 11.1%,respectively,and the contents of which decreased by 85.0%and 27.9%,respectively compared with the control group.Molecular docking revealed that C EC small molecules could bind to GS and CS through different amino acid residues,inhibiting their activity and synthesis.The C EC can combine with tryptophan,tyrosine,and phenylalanine in the cell membrane,causing damage to the cell membrane.The binding sites between small molecules and amino acids were mainly around the OH group.In addition,C EC affected the energy metabolism system and inhibited the glycolysis pathway.Simultaneously,C EC treatment reduced the ergosterol content in the cell membrane by 58.2%compared with the control group.Finally,changes in𝛽-galactosidase,metal ion leakage,and relative conductivity confirmed the destruction of the cell membrane,which resulted in the leakage of cell contents.The above results showed that C EC can kill P.roqueforti by inhibiting energy metabolism and destroying the integrity of the cell membrane.展开更多
An imbalance in oral microbial homeostasis is significantly associated with the onset and progression of several systemic diseases.Fusobacterium nucleatum,a ubiquitous periodontitis-causing bacterium in the oral cavit...An imbalance in oral microbial homeostasis is significantly associated with the onset and progression of several systemic diseases.Fusobacterium nucleatum,a ubiquitous periodontitis-causing bacterium in the oral cavity,is frequently detected in focal sites and contributes to the pathogenesis of many extraoral diseases,including cancers,cardiovascular diseases,and adverse pregnancy outcomes(APOs).F.nucleatum is one of the few oral anaerobes that can be cultured purely in vitro and is a‘model species’for studying the impact of oral health on systemic health.The establishment and development of genetic manipulation tools for F.nucleatum and the construction of pathogenic gene-disrupted strains are important strategies for studying the pathogenicity of F.nucleatum.Here,we review the establishment and development of the genetic manipulation systems for F.nucleatum and summarize the characteristics of various genetic manipulation tools,such as suicide plasmid-based systems for gene inactivation,replicable plasmid-based systems controlling gene expression,and transposon-based random mutagenesis systems.Notably,we summarize and analyze their applications in the study of the pathogenic mechanisms of F.nucleatum.We hope to provide reference information and ideas for future research on genetic manipulation tools and the pathogenic mechanisms of F.nucleatum and other Fusobacterium species.展开更多
Diverse microbial community structures(MCS)in wastewater treatment plants(WWTPs)are vital for effectively removing nutrients and chemicals from wastewater.However,the regular monitoring of MCS in WWTP bioreac-tors rem...Diverse microbial community structures(MCS)in wastewater treatment plants(WWTPs)are vital for effectively removing nutrients and chemicals from wastewater.However,the regular monitoring of MCS in WWTP bioreac-tors remains unattractive owing to the skill and cost required for deploying modern microbial molecular tech-niques in the routine assessment of engineered systems.In contrast,low-resolution methods for assessing broad changes in the MCS,such as phospholipid fatty acid(PLFA)analysis,have been used effectively in soil studies for decades.Despite using PLFA analysis in soil remediation studies to capture the long-term effects of envi-ronmental changes on MCS,its application in WWTPs,where the microbial mass is dynamic and operational conditions are more fluid,remains limited.In this study,microbial communities in a controlled pilot plant and 12 full-scale activated sludge plants(ASPs)were surveyed over a two-year period using PLFA analysis.This study revealed that changes in the MCS in wastewater bioreactors could be detected using PLFA analysis.The MCS comprised 59%Gram-negative and 9%Gram-positive bacteria,31%fungi,and 1%actinomycetes.The abun-dances of Gram-negative bacteria and fungi were strongly inversely correlated,with an R^(2)=0.93,while the fatty acids cy17:0 and 16:1𝜔7c positively correlated(R^(2)=0.869).Variations in temperature,solid retention time,and WWTP configuration significantly influenced the MCS in activated sludge reactors.This study showed that WWTP bioreactors can be routinely monitored using PLFA analysis,and changes in the bioreactor profile that may indicate imminent bioreactor failure can be identified.展开更多
The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes.Over the past decades,the accumulated observational evidence reveals a close correlation between the micro...The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes.Over the past decades,the accumulated observational evidence reveals a close correlation between the micro-biome and human health and disease.Many groups are now manipulating individual microbial strains,species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome.Here,we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria,including transformation,transduction,and conjugation.We provide an overview of these approaches and describe the advantages and limitations of each method.In addition,we highlight examples of human mi-crobiome engineering using these approaches.Finally,we provide perspectives for the future of microbiome engineering.展开更多
The recent convergence of microbiology,engineering,genomics,and synthetic biology have fostered a burgeoning discipline:Engineering Microbiology.We can now design and build microbes with desired functions according to...The recent convergence of microbiology,engineering,genomics,and synthetic biology have fostered a burgeoning discipline:Engineering Microbiology.We can now design and build microbes with desired functions according to engineering principles,and this is enabling development of new approaches and unprecedented tools that are supporting major breakthroughs to overcome grand challenges in the environment,health,food,material,and energy.展开更多
This research identified four amino acid residues(Leu174,Asn297,Tyr301,and Gln291)that contribute to sub-strate recognition by the high-affinity glucose transporter Xltr1p from Trichoderma reesei.Potential hotspots af...This research identified four amino acid residues(Leu174,Asn297,Tyr301,and Gln291)that contribute to sub-strate recognition by the high-affinity glucose transporter Xltr1p from Trichoderma reesei.Potential hotspots af-fecting substrate specificity were selected through homology modeling,evolutionary conservation analyses,and substrate-docking modeling of Xltr1p.Variants carrying mutations at these hotspots were subsequently obtained via in silico screening.Replacement of Leu174 or Asn297 in Xltr1p with alanine resulted in loss of hexose trans-port activity,indicating that Leu174 and Asn297 play essential roles in hexose transport.The Y301W variant exhibited accelerated mannose transport,but lost galactose transport capacity,and mutation of Gln291 to ala-nine greatly accelerated mannose transport.These results suggest that amino acids located in transmembrane𝛼-helix 7(Asn297,Tyr301,and Gln291)play critical roles in substrate recognition by the hexose transporter Xltr1p.Our results will help expand the potential applications of this transporter and provide insights into the mechanisms underlying its function and specificity.展开更多
基金funded by the National Natural Science Foundation of China(32270082 and 22207044)the Natural Science Foundation of Jiangsu Province(BK20202002)the Basic Research Program of Jiangsu and the Jiangsu Basic Research Center for Synthetic Biology(BK20233003).
文摘Owing to their diverse coordination patterns and catalytic mechanisms,non-heme iron-dependent dioxygenases catalyze a variety of biochemical reactions involved in the synthesis of numerous natural products and valuable compounds.Recently,we discovered a novel and atypical non-heme iron-dependent dioxygenase,BTG13,that features a unique coordination center consisting of four histidines and a carboxylated lysine(Kcx).This enzyme catalyzes the C–C bond cleavage of anthraquinone through two unconventional steps,with modified Kcx playing a key role in facilitating these processes,as revealed by molecular dynamics simulations and quantum chemical calculations.Phylogenetic analyses and other studies suggest that BTG13-related metalloenzymes are widespread in various organisms.Here,we highlight the significance of this new class of non-heme iron-dependent oxygenases and their potential as novel tools for practical applications in synthetic biology.
文摘The increasing antimicrobial resistance has seriously threatened human health worldwide over the last three decades.This severe medical crisis and the dwindling antibiotic discovery pipeline require the development of novel antimicrobial treatments to combat life-threatening infections caused by multidrug-resistant micro-bial pathogens.However,the detailed mechanisms of action,resistance,and toxicity of many antimicrobials remain uncertain,significantly hampering the development of novel antimicrobials.Genome-scale metabolic model(GSMM)has been increasingly employed to investigate microbial metabolism.In this review,we discuss the latest progress of GSMM in antimicrobial pharmacology,particularly in elucidating the complex interplays of multiple metabolic pathways involved in antimicrobial activity,resistance,and toxicity.We also highlight the emerging areas of GSMM applications in modeling non-metabolic cellular activities(e.g.,gene expression),identi-fication of potential drug targets,and integration with machine learning and pharmacokinetic/pharmacodynamic modeling.Overall,GSMM has significant potential in elucidating the critical role of metabolic changes in antimi-crobial pharmacology,providing mechanistic insights that will guide the optimization of dosing regimens for the treatment of antimicrobial-resistant infections.
基金This work was financially supported by the National Natural Science Foundation of China(No.81903494)the Scientific Research Foun-dation of Qingdao University.
文摘Natural occurring aromatic polyketides from actinomycetes indicate a structurally and functionally diverse fam-ily of polycyclic polyphenols.Some of them are consequently suggested as lead structures for drug development.Among them,rubromycins are derived from a single C26 polyketide chain and exhibit an unusual bisbenzannu-lated[5,6]-spiroketal system that connects a highly oxygenated naphthazarin motif to an isocoumarin unit.This type of biosynthetically elusive polycyclic polyketides has shown promising pharmacological activities,includ-ing antimicrobial,anticancer,and enzyme inhibition activity.The unique structures,intriguing biosynthesis,and marked bioactivities of rubromycins have drawn considerable attention from several chemists and biologists.This review covers the isolation,characterization,biosynthesis,and biological studies of these structurally diverse and complex rubromycins.
基金The authors would like to thank Cecilia Trivellin for providing the original R code for the analysis of the growth curves(available at https://github.com/cectri/Quantification-of-microbial-robustness.git)as well as Luca Torello Pianale for support in strain analysis.We acknowledge the Novo Nordisk Foundation(NF19OC0057685)The Swedish Research Council(Dnr 2018-04713)and the Hasselblad Foundation for financial support.
文摘Formic acid is one of the main weak acids in lignocellulosic hydrolysates that is known to be inhibitory to yeast growth even at low concentrations.In this study,we employed a CRISPR interference(CRISPRi)strain library comprising>9000 strains encompassing>98%of all essential and respiratory growth-essential genes,to study formic acid tolerance in Saccharomyces cerevisiae.To provide quantitative growth estimates on formic acid toler-ance,the strains were screened individually on solid medium supplemented with 140 mM formic acid using the Scan-o-Matic platform.Selected resistant and sensitive strains were characterized in liquid medium supplemented with formic acid and in synthetic hydrolysate medium containing a combination of inhibitors.Strains with gR-NAs targeting genes associated with chromatin remodeling were significantly enriched for strains showing formic acid tolerance.In line with earlier findings on acetic acid tolerance,we found genes encoding proteins involved in intracellular vesicle transport enriched among formic acid sensitive strains.The growth of the strains in syn-thetic hydrolysate medium followed the same trend as when screened in medium supplemented with formic acid.Strains sensitive to formic acid had decreased growth in the synthetic hydrolysate and all strains that had im-proved growth in the presence of formic acid also grew better in the hydrolysate medium.Systematic analysis of CRISPRi strains allowed identification of genes involved in tolerance mechanisms and provided novel engineering targets for bioengineering strains with increased resistance to inhibitors in lignocellulosic hydrolysates.
基金supported by the Hainan Province Science and Tech-nology Special Fund(ZDYF2024XDNY164)National Natural Science Foundation of China(32470065,31971336)+4 种基金Shandong Provincial Nat-ural Science Foundation(ZR2022QC222)Shandong Province Medical and Health Science and Technology Project(202404070807)Science and Technology Development Program of Jinan Municipal Health Com-mission(2024102001)Youth Science Foundation of Shandong First Medical University(202201-132)Talent Introduction of Jinan Cen-tral Hospital(YJRC2022002).
文摘Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues,such as community stability,keystone species identification,and the manipulation of community structures.However,exploring these interactions proves challenging within complex natural ecosys-tems.With advances in synthetic biology,the design of synthetic microbial ecosystems has received increasing attention due to their reduced complexity and enhanced controllability.Various ecological relationships,includ-ing commensalism,amensalism,mutualism,competition,and predation have been established within synthetic ecosystems.These relationships are often context-dependent and shaped by physical and chemical environmental factors,as well as by interacting populations and surrounding species.This review consolidates current knowl-edge of synthetic microbial ecosystems and factors influencing their ecological dynamics.A deeper understanding of how these ecosystems function and respond to different variables will advance our understanding of microbial-community interactions.
基金supported by the National Key Re-search and Development Program of China(2021YFC2100800)the Jiangsu Province Natural Science Fund for Distinguished Young Schol-ars(BK20200025)+1 种基金a grant from the Key Technologies R&D Program of Jiangsu Province(BE2019630)the National First-class Discipline Program of Light Industry Technology and Engineering(LITE2018-16).
文摘Escherichia coli is the most well-studied model prokaryote and has become an indispensable host for the biotech-nological production of proteins and biochemicals.In particular,the probiotic status of one E.coli strain,E.coli Nissle 1917(EcN)has helped it become a new favorite amongst synthetic biologists.To broaden its potential applications,here we assemble a comparative study on the genomes,transcriptomes,and metabolic properties of E.coli strains EcN,BL21(DE3),and MG1655.Comparative genomics data suggests that EcN possesses 1404 unique CDSs.In particular,EcN has additional iron transport systems which endow EcN with a higher tolerance to iron scarcity when compared to two other E.coli strains.EcN transcriptome data demonstrates that E.coli strains EcN,BL21(DE3),and MG1655 all have comparable activities of the central metabolic pathway,however only EcN inherits the arginine deiminase pathway.Additionally,we found that EcN displayed a lower expres-sion of ribosomal proteins compared to BL21(DE3)and MG1655.This comparative study on E.coli strains EcN,BL21(DE3),and MG1655 aims to provide a reference for further engineering EcN as a biotechnological tool.
文摘The present review explores the influence of the gut microbiota on antibiotic resistance dynamics,particularly those associated with dysbiosis.The improper use of antibiotics can induce resistance in pathogens through various pathways,which is a topic of increasing interest within the scientific community.This review highlights the importance of microbial diversity,gut metabolism,and inflammatory responses against the dysbiosis due to the action of antibiotics.Additionally,it examines how secondary metabolites secreted by pathogens can serve as biomarkers for the early detection of antibiotic resistance.Although significant progress has been made in this field,key research gaps persist,including the need for a deeper understanding of the long-term effects of antibiotic-induced dysbiosis and the specific mechanisms driving the evolution of resistance in gut bacteria.Based on these considerations,this review systematically analyzed studies from PubMed,Web of Science,Embase,Cochrane Library,and Scopus up to July 2024.This study aimed to explore the dynamics of the interactions between gut microbiota and antibiotic resistance,specifically examining how microbial composition influences the development of resistance mechanisms.By elucidating these relationships,this review provides insights into management strategies for drug resistance and improves our understanding of microbial contributions to host health.
基金supported by the National Key R&D Program of China(2018YFA0901500)the National Natural Science Foundation of China(32222004 and 32270101)the Youth Innovation Promotion Association of Chinese Academy of Sciences(2021177).
文摘Deciphering gene function is fundamental to engineering of microbiology.The clustered regularly interspaced short palindromic repeats(CRISPR)system has been adapted for gene repression across a range of hosts,creating a versatile tool called CRISPR interference(CRISPRi)that enables genome-scale analysis of gene function.This approach has yielded significant advances in the design of genome-scale CRISPRi libraries,as well as in applica-tions of CRISPRi screening in medical and industrial microbiology.This review provides an overview of the recent progress made in pooled and arrayed CRISPRi screening in microorganisms and highlights representative studies that have employed this method.Additionally,the challenges associated with CRISPRi screening are discussed,and potential solutions for optimizing this strategy are proposed.
文摘The current issues on resources,energy,and the environment of hu-man society drive us to seek sustainable manufacturing methods and de-velopment approaches.Microbes,with a series of advantages of broad substrate ranges and diverse metabolic capacities,have great potential to produce fuels and chemicals from renewable resources[1].In recent years,a series of progress has been made in this field in the context of fast-developing synthetic biology technologies and interdisciplinary re-search.The highly abundant renewable resources,including one carbon(C1)compounds and lignocellulose,can be converted to platform chem-icals and then to various products by natural or engineered microbial cell factories[2].
基金This work was supported by the National Science Foundation of China(31970037,42188102,91951203,31625001,32100030)Science&Technology Fundamental Resources Investigation Program(2022FY100600)+3 种基金Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program(2019BT02Y262)Guangdong Major Project of Basic and Applied Basic Research(2019B030302004)Guangdong Basic and Applied Basic Research Foundation(2022A1515010702)the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)(GML2019ZD0407).
文摘Toxin-antitoxin(TA)systems are ubiquitous in bacteria and archaea.Most are composed of two neighboring genetic elements,a stable toxin capable of inhibiting crucial cellular processes,including replication,transcrip-tion,translation,cell division and membrane integrity,and an unstable antitoxin to counteract the toxicity of the toxin.Many new discoveries regarding the biochemical properties of the toxin and antitoxin components have been made since the first TA system was reported nearly four decades ago.The physiological functions of TA systems have been hotly debated in recent decades,and it is now increasingly clear that TA systems are important immune systems in prokaryotes.In addition to being involved in biofilm formation and persister cell formation,these modules are antiphage defense systems and provide host defenses against various phage infec-tions via abortive infection.In this review,we explore the potential applications of TA systems based on the recent progress made in elucidating TA functions.We first describe the most recent classification of TA systems and then introduce the biochemical functions of toxins and antitoxins,respectively.Finally,we primarily focus on and devote considerable space to the application of TA complexes in synthetic biology.
基金Huazhong Agricultural University for a startup grant and a grant from the Fundamental Research Funds for the Central Uni-versities(Project No.2662021JC006).
文摘While the typical targets of(chemo-)enzymatic cascades are fine chemicals(e.g.,pharmaceuticals),a chemoen-zymatic cascade,artificial starch anabolic pathway(ASAP),was recently developed to synthesize starch from CO_(2).The key results and outstanding features of ASAP are discussed here.We envision that ASAP and its mi-crobial counterpart may enable efficient synthesis of food and sequestration of CO_(2)in a circular manner,thus contributing to a sustainable and hunger-free world and future habitation in space.
基金National Key R&D Program of China(2020YFC1521802).
文摘The widespread presence of iron and sulfur compounds such as pyrite in marine waterlogged archeological wood(WAW)can cause irreversible damage to the safety of its preservation.This issue has been a longstanding concern for cultural heritage conservation communities.In this study,we examined the distribution and phase composition of Fe and sulfur compounds in wood samples obtained from the Nanhai I shipwreck using ESEM-EDS,micro-Raman spectroscopy,and an X-ray diffractometer.The removal of iron from WAW samples of the Nanhai I shipwreck using Acidithiobacillus ferrooxidans(A.ferrooxidans)was evaluated using conductivity and ICP-AES analysis.The results showed that A.ferrooxidans effectively improved the removal of iron from WAW.The degradation of fresh healthy wood during treatment was also analyzed using infrared spectroscopy,and the results showed that the treatment had little effect on the samples over a short period.This study demonstrates,for the first time,the feasibility of iron extraction from marine WAW by A.ferrooxidans.This was also the first attempt in China to apply biological oxidation to the removal of iron from marine archeological materials.
基金supported by the National Natural Science Founda-tion of China(22122806 and 22038005)the Major Project of Natu-ral Science Foundation of Jiangsu Province(BK20212013)+1 种基金the Provin-cial Outstanding Youth Foundation of Jiangsu Province(BK20211529)the Fundamental Research Funds for the Central Universities(JUSRP22031).
文摘The increasing shortage of fossil resources and environmental pollution has renewed interest in the synthesis of value-added biochemicals from methanol.However,most of native or synthetic methylotrophs are unable to assimilate methanol at a sufficient rate to produce biochemicals.Thus,the performance of methylotrophs still needs to be optimized to meet the demands of industrial applications.In this review,we provide an in-depth discussion on the properties of natural and synthetic methylotrophs,and summarize the natural and synthetic methanol assimilation pathways.Further,we discuss metabolic engineering strategies for enabling microbial utilization of methanol for the bioproduction of value-added chemicals.Finally,we highlight the potential of microbial engineering for methanol assimilation and offer guidance for achieving a low-carbon footprint for the biosynthesis of chemicals.
基金supported by the National Natural Science Foundation of China(32370066)。
文摘Small regulatory RNAs(sRNAs)are non-coding RNA molecules that fine-tune various cellular processes and respond to various environmental stimuli.In Bacillus subtilis,the regulatory mechanisms and specific targets of several sRNAs remain largely unknown.In this study,we identified and characterized S612 as a self-terminating sRNA in B.subtilis.The expression of S612 is regulated by external signals,including nutrient availability and salt concentration.Overexpression of S612 induced filamentous cells with extensive cellular elongation and complete inhibition of sporulation,indicating its potential to control cell morphology and spore formation.S612 directly targets and downregulates genes through post-transcriptional base pairing with mRNAs,including ylmD,trpE,ycxC,yycS,rapH,and amyE,some of which are involved in cell membrane integrity,cell wall synthesis,and sporulation initiation.Therefore,we propose that S612 is an important post-transcriptional regulator of cell morphology and sporulation.
基金supported by the National Natural Science Foundation of China(32202192)Special fund for Taishan Scholars Project,and Shandong Provincial Natural Science Foundation(ZR2020MC213).
文摘Essential oil(EO)has significant antifungal activity.However,there is limited information on the mechanism of the synergistic antifungal effect of the effective components of EO against fungi.In the present study,molecular electrostatic potential and molecular docking were used for the first time to investigate the synergistic antifungal mechanism of eugenol and citral small molecule(C_(EC))against Penicillium roqueforti.The results showed that the C_(EC)treatment made the activity ofβ-(1,3)-glucan synthase(GS)and chitin synthase(CS)decreas by 20.2%and 11.1%,respectively,and the contents of which decreased by 85.0%and 27.9%,respectively compared with the control group.Molecular docking revealed that C EC small molecules could bind to GS and CS through different amino acid residues,inhibiting their activity and synthesis.The C EC can combine with tryptophan,tyrosine,and phenylalanine in the cell membrane,causing damage to the cell membrane.The binding sites between small molecules and amino acids were mainly around the OH group.In addition,C EC affected the energy metabolism system and inhibited the glycolysis pathway.Simultaneously,C EC treatment reduced the ergosterol content in the cell membrane by 58.2%compared with the control group.Finally,changes in𝛽-galactosidase,metal ion leakage,and relative conductivity confirmed the destruction of the cell membrane,which resulted in the leakage of cell contents.The above results showed that C EC can kill P.roqueforti by inhibiting energy metabolism and destroying the integrity of the cell membrane.
基金foundation support of the National Natural Science Foundation of China(82270980,82071122)the National Young Scientist Support Foundation(2019),the Major Innovation Projects in Shandong Province(2021SFGC0502)+2 种基金the Oral Microbiome Innovation Team of Shandong Province(2020KJK001)Shandong Province Key Research and Development Program(2021ZDSYS18)Intramural Joint Program Fund of State Key Laboratory of Microbial Technology(SKLMTIJP-2024-08)。
文摘An imbalance in oral microbial homeostasis is significantly associated with the onset and progression of several systemic diseases.Fusobacterium nucleatum,a ubiquitous periodontitis-causing bacterium in the oral cavity,is frequently detected in focal sites and contributes to the pathogenesis of many extraoral diseases,including cancers,cardiovascular diseases,and adverse pregnancy outcomes(APOs).F.nucleatum is one of the few oral anaerobes that can be cultured purely in vitro and is a‘model species’for studying the impact of oral health on systemic health.The establishment and development of genetic manipulation tools for F.nucleatum and the construction of pathogenic gene-disrupted strains are important strategies for studying the pathogenicity of F.nucleatum.Here,we review the establishment and development of the genetic manipulation systems for F.nucleatum and summarize the characteristics of various genetic manipulation tools,such as suicide plasmid-based systems for gene inactivation,replicable plasmid-based systems controlling gene expression,and transposon-based random mutagenesis systems.Notably,we summarize and analyze their applications in the study of the pathogenic mechanisms of F.nucleatum.We hope to provide reference information and ideas for future research on genetic manipulation tools and the pathogenic mechanisms of F.nucleatum and other Fusobacterium species.
文摘Diverse microbial community structures(MCS)in wastewater treatment plants(WWTPs)are vital for effectively removing nutrients and chemicals from wastewater.However,the regular monitoring of MCS in WWTP bioreac-tors remains unattractive owing to the skill and cost required for deploying modern microbial molecular tech-niques in the routine assessment of engineered systems.In contrast,low-resolution methods for assessing broad changes in the MCS,such as phospholipid fatty acid(PLFA)analysis,have been used effectively in soil studies for decades.Despite using PLFA analysis in soil remediation studies to capture the long-term effects of envi-ronmental changes on MCS,its application in WWTPs,where the microbial mass is dynamic and operational conditions are more fluid,remains limited.In this study,microbial communities in a controlled pilot plant and 12 full-scale activated sludge plants(ASPs)were surveyed over a two-year period using PLFA analysis.This study revealed that changes in the MCS in wastewater bioreactors could be detected using PLFA analysis.The MCS comprised 59%Gram-negative and 9%Gram-positive bacteria,31%fungi,and 1%actinomycetes.The abun-dances of Gram-negative bacteria and fungi were strongly inversely correlated,with an R^(2)=0.93,while the fatty acids cy17:0 and 16:1𝜔7c positively correlated(R^(2)=0.869).Variations in temperature,solid retention time,and WWTP configuration significantly influenced the MCS in activated sludge reactors.This study showed that WWTP bioreactors can be routinely monitored using PLFA analysis,and changes in the bioreactor profile that may indicate imminent bioreactor failure can be identified.
基金supported by the National Institutes of Health U01 CA265719(to Y.D.and A.Z.)A.Z.is further supported by R01 EB030134 and received institutional support from NIH P30 DK120515,P30 DK063491,P30 CA014195,P50 AA011999 and UL1 TR001442N.S.is a Biolegend Fellow and is supported by the National Science Foundation Graduate Research Fellowship Program under Grant No.1000340660。
文摘The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes.Over the past decades,the accumulated observational evidence reveals a close correlation between the micro-biome and human health and disease.Many groups are now manipulating individual microbial strains,species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome.Here,we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria,including transformation,transduction,and conjugation.We provide an overview of these approaches and describe the advantages and limitations of each method.In addition,we highlight examples of human mi-crobiome engineering using these approaches.Finally,we provide perspectives for the future of microbiome engineering.
文摘The recent convergence of microbiology,engineering,genomics,and synthetic biology have fostered a burgeoning discipline:Engineering Microbiology.We can now design and build microbes with desired functions according to engineering principles,and this is enabling development of new approaches and unprecedented tools that are supporting major breakthroughs to overcome grand challenges in the environment,health,food,material,and energy.
基金This work was supported by National Key R&D Program of China(No.2018YFA0901700)National Natural Science Foundation of China(No.32271526).
文摘This research identified four amino acid residues(Leu174,Asn297,Tyr301,and Gln291)that contribute to sub-strate recognition by the high-affinity glucose transporter Xltr1p from Trichoderma reesei.Potential hotspots af-fecting substrate specificity were selected through homology modeling,evolutionary conservation analyses,and substrate-docking modeling of Xltr1p.Variants carrying mutations at these hotspots were subsequently obtained via in silico screening.Replacement of Leu174 or Asn297 in Xltr1p with alanine resulted in loss of hexose trans-port activity,indicating that Leu174 and Asn297 play essential roles in hexose transport.The Y301W variant exhibited accelerated mannose transport,but lost galactose transport capacity,and mutation of Gln291 to ala-nine greatly accelerated mannose transport.These results suggest that amino acids located in transmembrane𝛼-helix 7(Asn297,Tyr301,and Gln291)play critical roles in substrate recognition by the hexose transporter Xltr1p.Our results will help expand the potential applications of this transporter and provide insights into the mechanisms underlying its function and specificity.
