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Detailed profiling of carbon fixation of in silico synthetic autotrophy with reductive tricarboxylic acid cycle and calvin-benson-bassham cycle in Esherichia coli using hydrogen as an energy source

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Synthetic and Systems Biotechnology 2019年第3期4卷 165-172页

作者： Hsieh-Ting-Yang Cheng Shou-Chen Lo Chieh-Chen Huang Tsung-Yi Ho Ya-Tang Yang Department of Computer Science National Tsing Hua UniversityHsinchu30013TaiwanR.O.C Department of Life Sciences National Chung-Hsing UniveristyTaichungTaiwanR.O.C Department of Electrical Engineering National Tsing Hua UniversityHsinchu30013TaiwanR.O.C Program in Microbial Genomics National Chung Hsing UniversityTaichungTaiwanR.O.C Innovation and Development Center of Sustainable Agriculture National Chung Hsing UniversityTaichungTaiwanR.O.C

Carbon fixation is the main route of inorganic carbon in the form of CO2 into the biosphere.In nature,RuBisCO is the most abundant protein that photosynthetic organisms use to fix CO2 from the atmosphere through the calvin-benson-bassham(CBB)cycle.However,the CBB cycle is limited by its low catalytic rate and low energy efficiency.In this work,we attempt to integrate the reductive tricarboxylic acid and CBB cycles in silico to further improve carbon fixation capacity.Key heterologous enzymes,mostly carboxylating enzymes,are inserted into the Esherichia coli core metabolic network to assimilate CO2 into biomass using hydrogen as energy source.Overall,such a strain shows enhanced growth yield with simultaneous running of dual carbon fixation cycles.Our key results include the following.(i)We identified two main growth states:carbon-limited and hydrogenlimited;(ii)we identified a hierarchy of carbon fixation usage when hydrogen supply is limited;and(iii)we identified the alternative sub-optimal growth mode while performing genetic perturbation.The results and modeling approach can guide bioengineering projects toward optimal production using such a strain as a microbial cell factory.

关键词： Reductive tricarboxylic acid cycle calvin-benson-bassham cycle Carbon fixation Metabolism

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Glycolytic Shunts Replenish the calvin-benson-bassham cycle as Anaplerotic Reactions in Cyanobacteria

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Molecular Plant 2020年第3期13卷 471-482页

作者： Alexander Makowka Lars Nichelmann Dennis Schulze Katharina Spengler Christoph Wittmann Karl Forchhammer Kirstin Gutekunst Department of Biology Botanical InstituteUniversity Kiel24118 KielGermany Institute for Systems Biotechnology Saarland University66123 SaarbruckenGermany Organismic Interactions Department Interfaculty Institute for Microbiology and Infection MedicineUniversity

The recent discovery of the Entner-Doudoroff(ED)pathway as a third glycolytic route beside Embden-Meyerhof-Parnas(EMP)and oxidative pentose phosphate(OPP)pathway in oxygenic photoautotrophs requires a revision of their central carbohydrate metabolism.In this study,unexpectedly,we observed that deletion of the ED pathway alone,and even more pronounced in combination with other glycolytic routes,diminished photoautotrophic growth in continuous light in the cyanobacterium Synechocystis sp.PCC 6803.Furthermore,we found that the ED pathway is required for optimal glycogen catabolism in parallel to an operating calvin-benson-bassham(CBB)cycle.It is counter-intuitive that glycolytic routes,which are a reverse to the CBB cycle and do not provide any additional biosynthetic intermediates,are important under photoautotrophic conditions.However,observations on the ability to reactivate an arrested CBB cycle revealed that they form glycolytic shunts that tap the cellular carbohydrate reservoir to replenish the cycle.Taken together,our results suggest that the classical view of the CBB cycle as an autocatalytic,completely autonomous cycle that exclusively relies on its own enzymes and C02 fixation to regenerate ribulose-1,5-bisphosphate for Rubisco is an oversimplification.We propose that in common with other known autocatalytic cycles,the CBB cycle likewise relies on anaplerotic reactions to compensate for the depletion of intermediates,particularly in transition states and under fluctuating light conditions that are common in nature.

关键词： central carbohydrate metabolism calvin-benson-bassham cycle Entner-Doudoroff pathway oxidative pentose phosphate pathway Embden-Meyerhof-Parnas pathway cyanobacteria

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Distribution characteristics and diversities of cbb and coxL genes in paddy soil profiles from southern China

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Pedosphere 2021年第6期31卷 954-963页

作者： Wentao PENG Yan WANG Xiuxiu ZHU Liufeng XU Juan ZHAO Zhongli CUI Hui CAO College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture and Rural AffairsNanjing Agricultural UniversityNanjing 210095(China) Rubber Research Institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101(China)

The calvin-benson-bassham cycle and Wood-Ljungdahl pathway are two well-known ones in the six carbon sequestration pathways,but the current knowledge of their occurrence in different layers of agricultural soil profiles is poor.In this study,the diversities of three genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase(Rubis CO),i.e.,genes encoding the green-like(cbbLG)and red-like(cbbLR)forms of Rubis COⅠ and encoding Rubis COⅡ(cbbM),and the gene encoding carbon monoxide dehydrogenase large subunit(coxL)from five paddy soils in southern China were investigated by real-time quantitative polymerase chain reaction,restriction fragment length polymorphism(RFLP)analysis,and clone library.The abundances of the four genes ranged from 10^(7) to 10^(9) copies g^(-1) soil,and the cbbLR gene outnumbered the other three genes in all soil samples,suggesting important roles they play in carbon dioxide(CO_(2))fixation.In addition,it was found that the copy numbers of cbbLR and cbbLG decreased with increasing soil depth,while the copy numbers of cbbM and coxL decreased in the shallow depths but increased with increasing soil depth.The results of RFLP showed a larger Shannon index(H)in the deeper soil layers among the four gene clone libraries,indicating that the community diversity in these soil layers was greater.The cbbLG gene had relatively low diversity(at genus level),and most of the sequences were classified as Sideroxydans and Thiobacillus.In contrast,the highly diverse groups were found in the other three gene clone libraries(cbbLR,cbbM,and coxL),most of which were distantly related to known sequences,even forming separate clusters.In summary,this study provides a new insight into CO_(2) fixers along agricultural soil profiles by comparing four bacterial genes.

关键词： calvin-benson-bassham cycle carbon dioxide fixation carbon monoxide dehydrogenase ribulose-1 5-bisphosphate carboxylase/oxygenase

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