Biology subjects

Peng, J.-H.

Publications and source records attributed to Peng, J.-H..

3 recordsLinked to original sources

bioRxiv2026

Nonequilibrium States Promote One-Pot Nonenzymatic Carbon Fixation in the Reverse Tricarboxylic Acid Cycle and Amino Acid Synthesis

Several metabolites within the reductive tricarboxylic acid (rTCA) cycle have been found to form prebiotically. However, how these metabolites connect to each other and form rTCA cycle remains unresolved. The rTCA cycle is an ancient route and is considered significant for the emergence of life, since it connects to the routes of amino acids and nucleobases synthesis. A major challenge to complete the rTCA cycle under prebiotic conditions is the thermodynamically unfavorable reductive carboxylation of succinate to -ketoglutarate. Here, we address this challenge by using the nature of energy: nonequilibrium conditions. By calculating the changes in free energy, {Delta}G, of succinate to -ketoglutarate, and its downstream reactions: -ketoglutarate to glutamate and -ketoglutarate to isocitrate under different nonequilibrium conditions, we find that these two-step reactions are exergonic under nonequilibrium conditions at a 10000:1 reactant-to-product ratio at 1.013 bar, pH 10 and 70{degrees}C. To prove the concept, we catalyze succinate to glutamate at a 10000:1 reactant-to-product ratio, with NH2OH and sodium dithionite. The process is catalyzed by Fe(0), Fe3O4, and artificial proto-[4Fe4S] clusters in 1M NaCl at pH 10 and 70{degrees}C under 1 atm of 13CO2 for 48 hours. This nonequilibrium condition and one-pot system successfully promote the formation of -ketoglutarate through carbon fixation with succinate and its subsequent conversion to glutamate. These findings demonstrate nonequilibrium states enable -ketoglutarate formation through succinate and CO2, and suggest that a tendency toward natural thermodynamics may serve as a driving force for autocatalysis in the origin of life. ImportanceHow life began remains open, metabolism provides a key framework for origins. We use a simple and robust energetic principle to show that non-equilibrium conditions can drive the highly endergonic carboxylation step of the reverse tricarboxylic acid (rTCA) cycle, enabling one-pot synthesis of glutamate. This is work bridges the gap between protometabolites and protometabolsim, suggesting that metabolites may have accumulated first, creating concentration gradients that drove reactions and ultimately enabled the emergence of protometabolism. These findings provide a plausible pathway from prebiotic chemistry to the emergence of metabolism.

biochemistry↗

bioRxiv2026

Development of autotrophy in Escherichia coli through adaptive laboratory evolution

Enabling heterotrophic Escherichia coli to use CO2 as its only carbon source remains a great challenge, and previous studies approached autotrophy conversion by metabolic engineering. Although its native carbon fixation routes were identified, the potential to reach autotrophy by itself has long been overlooked. In this study, autotrophy in E. coli was developed through adaptive laboratory evolution. After 1,000 days of consecutive inorganic subculturing, missense mutations were found in isocitrate dehydrogenase icd and isocitrate dehydrogenase kinase/phosphatase aceK genes, determining the metabolic switch between the citrate cycle and the glyoxylate shunt. By transcriptomic comparison of the adapted E. coli between inorganic and organic cultivations, two CO2 fixing enzymes activated in autotrophic mode were found, including the upregulated pyruvate:ferredoxin oxidoreductase YdbK and phosphoenolpyruvate carboxykinase Pck. Connected by the upregulated phosphoenolpyruvate synthase PpsA, a carbon fixation module was constituted, which was the shared foundation of the aspartate-threonine cycle and the citrate-glyoxylate-methylcitrate cycle, and thus integrating into an autotrophic network. By comparing the 13C enrichment patterns in inorganic cultivations between the adapted and initial E. coli, the favorable direction of the autotrophic network was confirmed. IMPORTANCEThis is the first study to accomplish autotrophy in E. coli through long-term evolution alone. Besides missense mutations in icd and aceK genes, adapted E. coli also actively regulated its gene expression to respond to inorganic environment, such as directing the metabolic switch towards the glyoxylate shunt. For biomass formation, a carbon fixation module consisted of the upregulated YdbK, PpsA, and Pck produced pyruvate and oxaloacetate as precursors for two cycles. The aspartate-threonine cycle with a replenishment side loop further accumulated these precursors, and the citrate-glyoxylate-methylcitrate cycle was driven by four overexpressed enzymes to catalyze six reactions. These metabolic pathways were integrated into a novel autotrophic network, and by understanding the nature of E. coli, rational designs for its carbon fixation optimization become attainable by using compatible mechanisms.

microbiology↗

bioRxiv2024

Endophytic pyrroloquinoline quinone enhances banana growth and immunity against Fusarium wilt for plant-microbe mutualisms

Fusarium wilt has a substantial impact on global banana production, posing a threat to food security worldwide. However, breeding new Fusarium-resistant cultivars is difficult and time-consuming. Alternatively, endophytic biostimulants that could combat such pervasive plant diseases provide possible novel solutions. Our prior research demonstrated that a pyrroloquinoline quinone (PQQ)-producing endophytic bacterium, Burkholderia seminalis 869T2, can enhance the growth of various plant species and protect bananas from Fusarium wilt in the field. PQQ is a peptide-derived redox cofactor known to stimulate mitochondrial biogenesis and metabolism in animals, but its molecular roles, especially in plants, remain to be elucidated. In this study, multi-omics approaches were employed to explore the potential mechanisms through which PQQ influences banana plants. The result of in situ imaging mass spectrometry revealed that the endophytic metabolite PQQ does not function through direct antagonism against Fusarium. The follow-up transcriptomic profiling shows it could regulate plant respiration, TCA cycle, oxidative phosphorylation, NAD/NADP-dependent dehydrogenases, MAPK signalling, and various phytohormone signalling pathways. Furthermore, PQQ appeared to trigger plant systemic immunity, thereby enhancing plant health and resistance to biotic stress. Beyond that, the complete genome of 869T2 was determined for follow-up comparative genomics analyses, revealing its genetic contexts, potential evolutionary events of PQQ operons among the Burkholderia species, and the absence of human virulence-facilitating genes within those PQQ-producing agricultural isolates. In summary, this study facilitates our understanding of PQQ in plant-microbe mutualisms and provides scientific evidence for its future application in agriculture. Significance StatementFusarium wilt is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a notorious soil-borne pathogen that attacks bananas vascular system, which critically threatens global banana production and food security. A potential PQQ-producing endophytic strain has been confirmed to protect bananas through in planta biocontrol, reducing the morbidity of Banana Fusarium Wilt (BFW) disease in the field and promoting the growth of banana plants simultaneously. Our results revealed that the endophytic metabolite PQQ does not function through direct antagonism but triggers plant systemic immunity and coordinates energetic metabolisms, thereby improving the overall health of host plants and enhancing their resistance against Fusarium wilt.

plant biology↗