This study employed integrated multi-omics approaches to elucidate,from the perspective of amino acid metabolism,the adaptive mechanism of Penicillium digitatum under modified atmosphere packaging(MAP)conditions.Compa...This study employed integrated multi-omics approaches to elucidate,from the perspective of amino acid metabolism,the adaptive mechanism of Penicillium digitatum under modified atmosphere packaging(MAP)conditions.Comparative analysis of natural air(Air),controlled atmosphere(CA),and MAP treatments revealed that MAP upregulated the expression of the hercynylcysteine S-oxide synthase(HCSOS),aldehyde dehydrogenase(ALDH),and monoamine oxidase(MAO)genes,thereby enhancing histidine-derived ergothioneine and methionine levels,and subsequently boosting glutathione-mediated redox homeostasis.Meanwhile,MAP induced the expression of the dihydroxyacid dehydratase(DHAD),saccharopine dehydrogenase(SDH),and arginosuccinate lyase(ASL)genes,redirecting valine,lysine,and arginine into the tricarboxylic acid(TCA)cycle to fuel ATP production.MAP also enhanced ASL-mediated arginine degradation and urea cycle activity,reducing arginine accumulation when compared to CA treatment.In contrast,while MAP induced upregulated expression of the pyrroline-5-carboxylate dehydrogenase(P5CDH)and D-amino acid oxidase(DAAO)genes,CA treatment promoted proline accumulation,reflecting stress-specific metabolic flexibility.Collectively,these findings demonstrate that MAP triggers transcriptional reprogramming of amino acid metabolism to coordinate oxidative defense,energy generation,and osmotic balance.By modulating these metabolic pathways and regulatory genes under MAP conditions,fungal adaptability can be disrupted.Hence,this study provides a promising strategy for suppressing green mold development,extending the postharvest shelf life,and improving the quality of fruits and vegetables.展开更多
Manganese-oxidizing microbes are capable of oxidizing Mn(Ⅱ) to manganese oxides through direct enzymatic and indirect mechanisms.However,bacterial Mn(Ⅱ) oxidation in alkaline environment remains unclear.This study i...Manganese-oxidizing microbes are capable of oxidizing Mn(Ⅱ) to manganese oxides through direct enzymatic and indirect mechanisms.However,bacterial Mn(Ⅱ) oxidation in alkaline environment remains unclear.This study isolated an alkali-tolerant bacterium Pseudorhizobium flavum MXJ-1 from marine surface sediments that can oxidize Mn(Ⅱ) to biogenic manganese oxides(BioMnO_(x)).Characterization of BioMnO_(x) reveals that rod-shaped bacterial cells produce amorphous BioMnO_(x) containing mixed valences of Mn.The effects of different pH,carbon and nitrogen sources,metal ions on growth and Mn(Ⅱ) oxidation activity of strain MXJ-1 were investigated.Results elucidate that strain MXJ-1 adapts to a broad range of pH from 5.0 to 10.0,achieves a maximum Mn(Ⅱ) oxidation percentage of 69.41 %,but there is no significant correlation between biomass and Mn(Ⅱ) oxidation.Cu(Ⅱ) inhibited Mn(Ⅱ) oxidation at concentration as low as 20 μmol/L,and Mn(Ⅱ) oxidation decreased with Mn(Ⅱ) levels increasing to 500 μmol/L.Genomic analysis identified two genes encoding animal heme peroxidases(AHPs) and three encoding dihydrolipoyl dehydrogenases(DLDHs),highlighting the potential role of superoxide in Mn(Ⅱ) oxidation.Several alkali-tolerance genes,including those encoding Na+/H+ antiporter,were also identified,which probably associated with alkali-tolerance of MXJ-1.Superoxide detection by nitro blue tetrazolium(NBT) assay indicates it involved in Mn(Ⅱ) oxidation.This study isolated a Mn(Ⅱ)-oxidizing,alkali-tolerant bacterium,expanding insights into microbial Mn(Ⅱ) oxidation in extreme environments.展开更多
Bacterial growth requires strategic allocation of limited intracellular resources,especially under cold stress,where stabilized messenger ribonucleic acid(mRNA)secondary structures slow translation by impairing riboso...Bacterial growth requires strategic allocation of limited intracellular resources,especially under cold stress,where stabilized messenger ribonucleic acid(mRNA)secondary structures slow translation by impairing ribosome binding.Escherichia coli(E.coli)counters this bottleneck by inducing the cold-shock protein A(CspA),an RNA chaperone that remodels inhibitory structures.However,synthesizing CspA diverts biosynthetic capacity from ribosome production and metabolism,creating a fundamental resource-allocation trade-off.In this work,we develop a dynamical model capturing the interplay between metabolic precursors,ribosomes,and CspA,and use it to examine how growth and allocation patterns shift with temperature.Steady-state analysis shows that each temperature produces a distinct,locally stable equilibrium,illustrating how cold environments reshape cellular priorities.We then formulate growth maximization as an optimal control problem,solved using Pontryagin’s Maximum Principle,to identify allocation strategies that balance translation maintenance and biomass production.The resulting optimal strategies exhibit bang-bang and singular structures,highlighting periods of extreme and intermediate allocation that reflect how bacteria might dynamically prioritize competing cellular functions.These control patterns converge to their corresponding steady state allocations and provide quantitative insight into optimal resource management under cold stress.These results provide a quantitative optimal-control framework linking RNA-level cold-shock adaptation to proteome allocation and growth,yielding testable predictions for how bacteria balance translational maintenance and biomass production at suboptimal temperatures.展开更多
文摘This study employed integrated multi-omics approaches to elucidate,from the perspective of amino acid metabolism,the adaptive mechanism of Penicillium digitatum under modified atmosphere packaging(MAP)conditions.Comparative analysis of natural air(Air),controlled atmosphere(CA),and MAP treatments revealed that MAP upregulated the expression of the hercynylcysteine S-oxide synthase(HCSOS),aldehyde dehydrogenase(ALDH),and monoamine oxidase(MAO)genes,thereby enhancing histidine-derived ergothioneine and methionine levels,and subsequently boosting glutathione-mediated redox homeostasis.Meanwhile,MAP induced the expression of the dihydroxyacid dehydratase(DHAD),saccharopine dehydrogenase(SDH),and arginosuccinate lyase(ASL)genes,redirecting valine,lysine,and arginine into the tricarboxylic acid(TCA)cycle to fuel ATP production.MAP also enhanced ASL-mediated arginine degradation and urea cycle activity,reducing arginine accumulation when compared to CA treatment.In contrast,while MAP induced upregulated expression of the pyrroline-5-carboxylate dehydrogenase(P5CDH)and D-amino acid oxidase(DAAO)genes,CA treatment promoted proline accumulation,reflecting stress-specific metabolic flexibility.Collectively,these findings demonstrate that MAP triggers transcriptional reprogramming of amino acid metabolism to coordinate oxidative defense,energy generation,and osmotic balance.By modulating these metabolic pathways and regulatory genes under MAP conditions,fungal adaptability can be disrupted.Hence,this study provides a promising strategy for suppressing green mold development,extending the postharvest shelf life,and improving the quality of fruits and vegetables.
基金supported by the National Natural Science Foundation of China(No.42277107)Liaoning Province Natural Science Foundation Joint Funds(Ph.D.Scientific Research Program)(No.2023-BSBA-024/DUT24BS004)the Open Project of State Key Laboratory of Urban Water Resource and Environment,China,Harbin Institute of Technology(No.HC202330)。
文摘Manganese-oxidizing microbes are capable of oxidizing Mn(Ⅱ) to manganese oxides through direct enzymatic and indirect mechanisms.However,bacterial Mn(Ⅱ) oxidation in alkaline environment remains unclear.This study isolated an alkali-tolerant bacterium Pseudorhizobium flavum MXJ-1 from marine surface sediments that can oxidize Mn(Ⅱ) to biogenic manganese oxides(BioMnO_(x)).Characterization of BioMnO_(x) reveals that rod-shaped bacterial cells produce amorphous BioMnO_(x) containing mixed valences of Mn.The effects of different pH,carbon and nitrogen sources,metal ions on growth and Mn(Ⅱ) oxidation activity of strain MXJ-1 were investigated.Results elucidate that strain MXJ-1 adapts to a broad range of pH from 5.0 to 10.0,achieves a maximum Mn(Ⅱ) oxidation percentage of 69.41 %,but there is no significant correlation between biomass and Mn(Ⅱ) oxidation.Cu(Ⅱ) inhibited Mn(Ⅱ) oxidation at concentration as low as 20 μmol/L,and Mn(Ⅱ) oxidation decreased with Mn(Ⅱ) levels increasing to 500 μmol/L.Genomic analysis identified two genes encoding animal heme peroxidases(AHPs) and three encoding dihydrolipoyl dehydrogenases(DLDHs),highlighting the potential role of superoxide in Mn(Ⅱ) oxidation.Several alkali-tolerance genes,including those encoding Na+/H+ antiporter,were also identified,which probably associated with alkali-tolerance of MXJ-1.Superoxide detection by nitro blue tetrazolium(NBT) assay indicates it involved in Mn(Ⅱ) oxidation.This study isolated a Mn(Ⅱ)-oxidizing,alkali-tolerant bacterium,expanding insights into microbial Mn(Ⅱ) oxidation in extreme environments.
基金supported by NASA Oklahoma Established Program to Stimulate Competitive Research(EPSCoR)Infrastructure Development,“Machine Learning Ocean World Biosignature Detection from Mass Spec,”(PI:Brett McKinney),Grant No.80NSSC24M0109Tandy School of Computer Science,The University of Tulsa.
文摘Bacterial growth requires strategic allocation of limited intracellular resources,especially under cold stress,where stabilized messenger ribonucleic acid(mRNA)secondary structures slow translation by impairing ribosome binding.Escherichia coli(E.coli)counters this bottleneck by inducing the cold-shock protein A(CspA),an RNA chaperone that remodels inhibitory structures.However,synthesizing CspA diverts biosynthetic capacity from ribosome production and metabolism,creating a fundamental resource-allocation trade-off.In this work,we develop a dynamical model capturing the interplay between metabolic precursors,ribosomes,and CspA,and use it to examine how growth and allocation patterns shift with temperature.Steady-state analysis shows that each temperature produces a distinct,locally stable equilibrium,illustrating how cold environments reshape cellular priorities.We then formulate growth maximization as an optimal control problem,solved using Pontryagin’s Maximum Principle,to identify allocation strategies that balance translation maintenance and biomass production.The resulting optimal strategies exhibit bang-bang and singular structures,highlighting periods of extreme and intermediate allocation that reflect how bacteria might dynamically prioritize competing cellular functions.These control patterns converge to their corresponding steady state allocations and provide quantitative insight into optimal resource management under cold stress.These results provide a quantitative optimal-control framework linking RNA-level cold-shock adaptation to proteome allocation and growth,yielding testable predictions for how bacteria balance translational maintenance and biomass production at suboptimal temperatures.
