检索结果-内蒙古大学图书馆

A thermodynamic bottleneck in the TCA cycle contributes to acetate overflow in Staphylococcus aureus

MSPHERE 2025年第1期10卷 e0088324页

作者： Shahreen, Nabia Ahn, Jongsam Alsiyabi, Adil Chowdhury, Niaz Bahar Shinde, Dhananjay Chaudhari, Sujata S. Bayles, Kenneth W. Thomas, Vinai C. Saha, Rajib Univ Nebraska Dept Chem & Biomol Engn Lincoln NE 68588 USA Univ Nebraska Med Ctr Dept Pathol Microbiol & Immunol Omaha NE 68198 USA Univ Nizwa Nat & Med Sci Res Ctr Nizwa Oman

During aerobic growth, S. aureus relies on acetate overflow metabolism, a process where glucose is incompletely oxidized to acetate, for its bioenergetic needs. acetate is not immediately captured as a carbon source and is excreted as waste by cells. The underlying factors governing acetate overflow in S. aureus have not been identified. Here, we show that acetate overflow is favored due to a thermodynamic bottleneck in the TCA cycle specifically involving the oxidation of succinate to fumarate by succinate dehydrogenase. This bottleneck reduces flux through the TCA cycle, making it more efficient for S. aureus to generate ATP via acetate overflow metabolism. Additionally, the protein allocation cost of maintaining ATP flux through the restricted TCA cycle is greater than that of acetate overflow metabolism. Finally, we show that the TCA cycle bottleneck provides S. aureus the flexibility to redirect carbon toward maintaining redox balance through lactate overflow when oxygen becomes limiting, albeit at the expense of ATP production through acetate overflow. Overall, our findings suggest that overflow metabolism offers S. aureus distinct bioenergetic advantages over a thermodynamically constrained TCA cycle, potentially supporting its commensal-pathogenic lifestyle.

关键词： overflow metabolism redox imbalance thermodynamic bottleneck membrane crowding acetate overflow

来源：评论

学校读者我要写书评

暂无评论

Optimal protein allocation controls the inhibition of GltA and AcnB in Neisseria gonorrhoeae

引用

PATHOGENS AND DISEASE 2024年第82期82卷 ftae023页

作者： Shahreen, Nabia Chowdhury, Niaz Bahar Saha, Rajib Univ Nebraska Dept Chem & Biomol Engn Lincoln NE 68588 USA

Neisseria gonorrhea (Ngo) is a major concern for global public health due to its severe implications for reproductive health. Understanding its metabolic phenotype is crucial for comprehending its pathogenicity. Despite Ngo's ability to encode tricarboxylic acid (TCA) cycle proteins, GltA and AcnB, their activities are notably restricted. To investigate this phenomenon, we used the iNgo_557 metabolic model and incorporated a constraint on total cellular protein content. Our results indicate that low cellular protein content severely limits GltA and AcnB activity, leading to a shift toward acetate overflow for Adenosine triphosphate (ATP) production, which is more efficient in terms of protein usage. Surprisingly, increasing cellular protein content alleviates this restriction on GltA and AcnB and delays the onset of acetate overflow, highlighting protein allocation as a critical determinant in understanding Ngo's metabolic phenotype. These findings underscore the significance of Ngo's metabolic adaptation in light of optimal protein allocation, providing a blueprint to understand Ngo's metabolic landscape. The article reveals that optimal protein allocation is key to understanding Neisseria gonorrhoeae's metabolism, impacting critical enzymes and energy production pathways.

关键词： optimal protein allocation constraint-based modeling energy production acetate overflow Neisseria gonorrhoeae

来源：评论

学校读者我要写书评

暂无评论

Silk fibroin production in Escherichia coli is limited by a positive feedback loop between metabolic burden and toxicity stress

引用

METABOLIC ENGINEERING 2023年第1期77卷 231-241页

作者： Xiao, Zhengyang Connor, Alexander J. Worland, Alyssa M. Tang, Yinjie J. Zha, R. Helen Koffas, Mattheos Rensselaer Polytech Inst Dept Chem & Biol Engn Troy NY 12180 USA Washington Univ St Louis Dept Energy Environm & Chem Engn St Louis MO 63130 USA

To investigate the metabolic elasticity and production bottlenecks for recombinant silk proteins in Escherichia coli, we performed a comprehensive characterization of one elastin-like peptide strain (ELP) and two silk protein strains (A5 4mer, A5 16mer). Our approach included 13C metabolic flux analysis, genome-scale modeling, transcription analysis, and 13C-assisted media optimization experiments. Three engineered strains maintained their central flux network during growth, while measurable metabolic flux redistributions (such as the Ent-ner-Doudoroff pathway) were detected. Under metabolic burdens, the reduced TCA fluxes forced the engineered strain to rely more on substrate-level phosphorylation for ATP production, which increased acetate overflow. acetate (as low as 10 mM) in the media was highly toxic to silk-producing strains, which reduced 4mer pro-duction by 43% and 16mer by 84%, respectively. Due to the high toxicity of large-size silk proteins, 16mer ' s productivity was limited, particularly in the minimal medium. Therefore, metabolic burden, overflow acetate, and toxicity of silk proteins may form a vicious positive feedback loop that fractures the metabolic network. Three solutions could be applied: 1) addition of building block supplements (i.e., eight key amino acids: His, Ile, Phe, Pro, Tyr, Lys, Met, Glu) to reduce metabolic burden;2) disengagement of growth and production;and 3) use of non-glucose based substrate to reduce acetate overflow. Other reported strategies were also discussed in light of decoupling this positive feedback loop.

关键词： 13C-MFA acetate overflow Entner-doudoroff pathway Metabolic burden Silk fibroin Toxicity

来源：评论

学校读者我要写书评

暂无评论

Metabolic engineering of Escherichia coli for efficient production of linalool from biodiesel-derived glycerol by targeting cofactors regeneration and reducing acetate accumulation

引用

INDUSTRIAL CROPS AND PRODUCTS 2023年第1期203卷

作者： Wang, Xun Zhang, Xinyi Zhang, Jia Xiao, Longjie Zhou, Yujunjie Wang, Fei Li, Xun Nanjing Forestry Univ Coll Chem Engn Int Innovat Ctr Forest Chem & MatJiangsu Coinnova Jiangsu Prov Key Lab Chem & Utilizat Agroforest Bi Nanjing 210037 Peoples R China Nanjing Forestry Univ Coll Chem Engn 159 Longpan Rd Nanjing 210037 Peoples R China

Linalool is a valuable monoterpenoid compound commercially used in cosmetics and personal care industry as well as a 'drop-in' biofuel. Direct plant extraction or chemical synthesis of linalool suffers from insufficient abundance in plant and inefficient purification procedures. Herein, a powerful green cell factory has been developed to meet the increasing demands for more sustainable and efficient production of this terpene alcohol. The de novo production of linalool from biodiesel-derived glycerol was achieved by engineered Escherichia coli harboring the exogenous mevalonate pathway followed by coupling with geranyl diphosphate synthase and linalool synthase (LIS). Then, the Mentha aquatica LIS showing the most efficient linalool biosynthesis was identified, and subsequently tuned by ribosomal binding site (RBS) engineering and site-directed mutagenesis to facilitate linalool production. A further engineered strain equipped with an engineered NADP+-dependent pyruvate dehydrogenase complex (PDH) and phosphoketolase bypass, remarkably decreasing the by-products formation together with boosting substrate utilization efficiency. A final titer of 1.07 g/L linalool with a yield of 0.10 g/g glycerol was gained in flask culture and further increase to 4.16 g/L in 2-L fed-batch fermentation, which is the highest reported linalool titer and yield in E. coli to the best of our knowledge. In addition, the engineering strategies established here not only lay a potential production platform for linalool and its derivatives, but also provide references to minimize by-products secretion and improve carbon use efficiency.

关键词： Linalool acetate overflow NADPH Phosphoketolase Escherichia coli

来源：评论

学校读者我要写书评

暂无评论

Reprogramming the metabolism of Klebsiella pneumoniae for efficient 1,3-propanediol production

引用

CHEMICAL ENGINEERING SCIENCE 2021年 236卷 116539-116539页

作者： Wang, Weijian Yu, Xiao Wei, Yongjun Ledesma-Amaro, Rodrigo Ji, Xiao-Jun Nanjing Tech Univ Coll Biotechnol & Pharmaceut Engn 30 South Puzhu Rd Nanjing 211816 Peoples R China Zhengzhou Univ Sch Pharmaceut Sci Key Lab Adv Drug Preparat Technol Minist Educ 100 Kexue Ave Zhengzhou 450001 Peoples R China Imperial Coll London Dept Bioengn London SW7 2AZ England Imperial Coll London Imperial Coll Ctr Synthet Biol London SW7 2AZ England

The production of 1,3-propanediol (1,3-PD) from glycerol by Klebsiella pneumoniae is limited by synthesis of numerous byproducts. Among them, the accumulation of acetate has the largest negative impact on the fermentation performance. To address the acetate overflow caused by knocking out lactate dehydrogenase, alcohol dehydrogenase and succinate dehydrogenase, several metabolic engineering manipulations were conducted. First, acetate was reduced through enhancing the acetate assimilation pathway by overexpressing heterologous acetyl-CoA synthetase. Then, the polyhydroxybutyrate (PHB) synthesis pathway was introduced to further reprogram the intracellular carbon metabolism. As a result, the best performed strain Kpr-6 produced up to 91.2 g/L extracellular 1,3-PD and 2.56 g/L intracellular PHB which can be easily separated from each other, while the acetate was dramatically reduced. The metabolic engineering strategies developed in this study would be helpful for constructing the microbial cell factory for other similar bio-based chemical production. (c) 2021 Elsevier Ltd. All rights reserved.

关键词： Metabolic engineering Klebsiella pneumoniae acetate overflow Polyhydroxybutyrate 1 3-Propanediol

来源：评论

学校读者我要写书评

暂无评论

Engineering protein production by rationally choosing a carbon and nitrogen source using E. coli BL21 acetate metabolism knockout strains

引用

MICROBIAL CELL FACTORIES 2019年第1期18卷 151-151页

作者： Terol, Gema Lozano Gallego-Jara, Julia Sola Martinez, Rosa Alba Diaz, Manuel Canovas Puente, Teresa de Diego Univ Murcia Dept Biochem & Mol Biol B & Immunol Fac Chem Campus Espinardo E-30100 Murcia Spain

Background Escherichia coli (E. coli) is a bacteria that is widely employed in many industries for the production of high interest bio-products such as recombinant proteins. Nevertheless, the use of E. coli for recombinant protein production may entail some disadvantages such as acetate overflow. acetate is accumulated under some culture conditions, involves a decrease in biomass and recombinant protein production, and its metabolism is related to protein lysine acetylation. Thereby, the carbon and nitrogen sources employed are relevant factors in cell host metabolism, and the study of the central metabolism of E. coli and its regulation is essential for optimizing the production of biomass and recombinant proteins. In this study, our aim was to find the most favourable conditions for carrying out recombinant protein production in E. coli BL21 using two different approaches, namely, manipulation of the culture media composition and the deletion of genes involved in acetate metabolism and N epsilon-lysine acetylation. Results We evaluated protein overexpression in E. coli BL21 wt and five mutant strains involved in acetate metabolism (Delta acs, Delta ackA and Delta pta) and lysine acetylation (Delta patZ and Delta cobB) grown in minimal medium M9 (inorganic ammonium nitrogen source) and in complex TB7 medium (peptide-based nitrogen source) supplemented with glucose (PTS carbon source) or glycerol (non-PTS carbon source). We observed a dependence of recombinant protein production on acetate metabolism and the carbon and nitrogen source employed. The use of complex medium supplemented with glycerol as a carbon source entails an increase in protein production and an efficient use of resources, since is a sub-product of biodiesel synthesis. Furthermore, the deletion of the ackA gene results in a fivefold increase in protein production with respect to the wt strain and a reduction in acetate accumulation. Conclusion The results showed that the use of diverse carbon and n

关键词： Recombinant proteins acetate overflow Escherichia coli Lysine acetylation GFP Medium composition

来源：评论

学校读者我要写书评

暂无评论

acetate metabolism regulation in Escherichia coli: carbon overflow, pathogenicity, and beyond

引用

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 2016年第21期100卷 8985-9001页

作者： Bernal, Vicente Castano-Cerezo, Sara Canovas, Manuel Ctr Tecnol Repsol Grp Biol Direcc Quim & Nuevas Energias Repsol SA Ctra Extremadura A-5Km 18 Mostoles 28395 Spain Univ Murcia Dept Bioquim & Biol Mol & Inmunol B Fac Quim Campus Reg Excelencia Mare Nostrum E-30100 Murcia Spain

acetate is ubiquitously found in natural environments. Its availability in the gut is high as a result of the fermentation of nutrients, and although it is rapidly absorbed by intestinal mucosa, it can also be used as carbon source by some members of gut microbiota. The metabolism of acetate in Escherichia coli has attracted the attention of the scientific community due to its role in central metabolism and its link to multiple physiological features. In this microorganism, acetate is involved directly or indirectly on the regulation of functional processes, such as motility, formation of biofilms, and responses to stress. Furthermore, it is a relevant nutrient in gut, where it serves additional roles, which regulate or, at least, modulate pathophysiological responses of E. coli and other bacteria. acetate is one of the major by-products of anaerobic (fermenting) metabolism, and it is also produced under fully aerobic conditions. This acetate overflow is recognized as one of the major drawbacks limiting E. coli's productivity in biotechnological processes. This review sums up current knowledge on acetate metabolism in E. coli, explaining the major milestones that have led to deciphering its complex regulation in the K-12 strain. Major differences in the metabolism of acetate in other strains will be underlined, with a focus on strains of biotechnological and biomedical interest.

关键词： acetate overflow Central metabolism Catabolite repression Pathogenic E. coli Protein acetylation Proteome reallocation

来源：评论

学校读者我要写书评

暂无评论

Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli

引用

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 2014年第11期98卷 5131-5143页

作者： Peebo, Karl Valgepea, Kaspar Nahku, Ranno Riis, Gethe Oun, Mikk Adamberg, Kaarel Vilu, Raivo Tallinn Univ Technol Dept Chem EE-19086 Tallinn Estonia Competence Ctr Food & Fermentat Technol EE-12618 Tallinn Estonia Tallinn Univ Technol Food Proc Dept EE-19086 Tallinn Estonia

Elimination of acetate overflow in aerobic cultivation of Escherichia coli would improve many bioprocesses as acetate accumulation in the growth environment leads to numerous negative effects, e.g. loss of carbon, inhibition of growth, target product synthesis, etc. Despite many years of studies, the mechanism and regulation of acetate overflow are still not completely understood. Therefore, we studied the growth of E. coli K-12 BW25113 and several of its mutant strains affecting acetate-related pathways using the continuous culture method accelerostat (A-stat) at various specific glucose consumption rates with the aim of diminishing acetate overflow. Absolute quantitative exo-metabolome and proteome analyses coupled to metabolic flux analysis enabled us to demonstrate that onset of acetate overflow can be postponed and acetate excretion strongly reduced in E. coli by coordinated activation of phosphotransacetylase-acetyl-CoA synthetase (PTA-ACS) and tricarboxylic acid (TCA) cycles. Fourfold reduction of acetate excretion (2 vs. 8 % from total carbon) at fastest growth compared to wild type was achieved by deleting the genes responsible for inactivation of acetyl-CoA synthetase protein (pka) and TCA cycle regulator arcA. The Delta pka Delta arcA strain did not accumulate any other detrimental by-product besides acetate and showed identical mu (max) and only similar to 5 % lower biomass yield compared to wild type. We conclude that a fine-tuned coordination between increasing the recycling capabilities of acetate in the PTA-ACS node through a higher concentration of active acetate scavenging Acs protein and downstream metabolism throughput in the TCA cycle is necessary for diminishing overflow metabolism of acetate in E. coli and achieving higher target product production in bioprocesses.

关键词： acetate overflow Acs Continuous culture Absolute proteomics Acetylation

来源：评论

学校读者我要写书评

暂无评论

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways

引用

BMC SYSTEMS BIOLOGY 2013年第1期7卷 134页

作者： Pey, Jon Valgepea, Kaspar Rubio, Angel Beasley, John E. Planes, Francisco J. Univ Navarra CEIT San Sebastian 20018 Spain Univ Navarra TECNUN San Sebastian 20018 Spain Tallinn Univ Technol Dept Chem EE-12618 Tallinn Estonia Competence Ctr Food & Fermentat Technol EE-12618 Tallinn Estonia Brunel Univ Uxbridge UB8 3PH Middx England

Background: The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essential to efficiently integrate experimental data into metabolic modeling. Results: We present here an in-silico framework to infer relevant metabolic pathways for a particular phenotype under study based on its gene/protein expression data. This framework is based on the Carbon Flux Path (CFP) approach, a mixed-integer linear program that expands classical path finding techniques by considering additional biophysical constraints. In particular, the objective function of the CFP approach is amended to account for gene/protein expression data and influence obtained paths. This approach is termed integrative Carbon Flux Path (iCFP). We show that gene/protein expression data also influences the stoichiometric balancing of CFPs, which provides a more accurate picture of active metabolic pathways. This is illustrated in both a theoretical and real scenario. Finally, we apply this approach to find novel pathways relevant in the regulation of acetate overflow metabolism in Escherichia coli. As a result, several targets which could be relevant for better understanding of the phenomenon leading to impaired acetate overflow are proposed. Conclusions: A novel mathematical framework that determines functional pathways based on gene/protein expression data is presented and validated. We show that our approach is able to provide new insights into complex biological scenarios such as acetate overflow in Escherichia coli.

关键词： acetate overflow Gene expression Proteomics Systems biology Metabolic pathways analysis Mixed-integer linear programming

来源：评论

学校读者我要写书评

暂无评论

acetate scavenging activity in Escherichia coli: interplay of acetyl-CoA synthetase and the PEP-glyoxylate cycle in chemostat cultures

引用

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 2012年第5期93卷 2109-2124页

作者： Renilla, Sergio Bernal, Vicente Fuhrer, Tobias Castano-Cerezo, Sara Pastor, Jose M. Iborra, Jose L. Sauer, Uwe Canovas, Manuel Univ Murcia Fac Chem Dept Biochem & Mol Biol & Immunol B Murcia Spain ETH Inst Mol Syst Biol CH-8093 Zurich Switzerland

Impairment of acetate production in Escherichia coli is crucial for the performance of many biotechnological processes. Aerobic production of acetate (or acetate overflow) results from changes in the expression of central metabolism genes. Acetyl-CoA synthetase scavenges extracellular acetate in glucose-limited cultures. Once converted to acetyl-CoA, it can be catabolized by the tricarboxylic acid cycle or the glyoxylate pathway. In this work, we assessed the significance of these pathways on acetate overflow during glucose excess and limitation. Gene expression, enzyme activities, and metabolic fluxes were studied in E. coli knock-out mutants related to the glyoxylate pathway operon and its regulators. The relevance of post-translational regulation by AceK-mediated phosphorylation of isocitrate dehydrogenase for pathway functionality was underlined. In chemostat cultures performed at increasing dilution rates, acetate overflow occurs when growing over a threshold glucose uptake rate. This threshold was not affected in a glyoxylate-pathway-deficient strain (lacking isocitrate lyase, the first enzyme of the pathway), indicating that it is not relevant for acetate overflow. In carbon-limited chemostat cultures, gluconeogenesis (maeB, sfcA, and pck), the glyoxylate operon and, especially, acetyl-CoA synthetase are upregulated. A mutant in acs (encoding acetyl-CoA synthetase) produced acetate at all dilution rates. This work demonstrates that, in E. coli, acetate production occurs at all dilution rates and that overflow is the result of unbalanced synthesis and scavenging activities. The over-expression of acetyl-CoA synthetase by cAMP-CRP-dependent induction limits this phenomenon in cultures consuming glucose at low rate, ensuring the recycling of the acetyl-CoA and acetyl-phosphate pools, although establishing an energy-dissipating substrate cycle.

关键词： acetate overflow PEP glyoxylate cycle Acetyl-coenzyme A synthetase Chemostat C-13 fluxes Catabolite repression

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：