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Journal articles on the topic 'Ribulose-5-phosphate-3-epimerase'

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Published: 7 June 2025

Last updated: 16 July 2025

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Meloni, Maria, Silvia Fanti, Daniele Tedesco, et al. "Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii." Plant Physiology 194, no. 4 (2023): 2263–77. https://doi.org/10.1093/plphys/kiad680.

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<em>This is a pre-copyedited, author-produced version of an article accepted for publication in Plant Physiology following peer review. The version of record [Maria Meloni, Silvia Fanti, Daniele Tedesco, Libero Gurrieri, Paolo Trost, Simona Fermani, Stéphane D. Lemaire, Mirko Zaffagnini, Julien Henri, Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii, Plant Physiology, Volume 194, Issue 4, April 2024, Pages 2263–2277] is available online at: https://academic.oup.com/plphys/article/194/4/2263/7491446 [DOI: 10.1093/plphys/kiad680].</em> <strong>ABSTRACT</strong>Carbon fixation relies on Rubisco and ten additional enzymes in the Calvin-Benson-Bassham cycle. Epimerization of xylulose-5-phosphate (Xu5P) into ribulose-5-phosphate (Ru5P) contributes to the regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco. Ribulose-5-phosphate-3-epimerase (RPE, EC 5.1.3.1) catalyzes the formation of Ru5P, but it can also operate in the pentose phosphate pathway by catalyzing the reverse reaction. Here, we describe the structural and biochemical properties of the recombinant RPE isoform 1 from Chlamydomonas (Chlamydomonas reinhardtii) (CrRPE1). The enzyme is a homo-hexamer that contains a zinc ion in the active site and exposes a catalytic pocket on the top of an α8β8 triose isomerase-type barrel as observed in structurally solved RPE isoforms from both plant and nonplant sources. By optimizing and developing enzyme assays to monitor the reversible epimerization of Ru5P to Xu5P and vice versa, we determined the catalytic parameters that differ from those of other plant paralogues. Despite being identified as a putative target of multiple thiol-based redox modifications, CrRPE1 activity is not affected by both reductive and oxidative treatments, indicating that enzyme catalysis is insensitive to possible redox alterations of cysteine residues. We mapped phosphorylation sites on the crystal structure, and the specific location at the entrance of the catalytic cleft supports a phosphorylation-based regulatory mechanism. This work provides an accurate description of the structural features of CrRPE1 and an in-depth examination of its catalytic and regulatory properties highlighting the physiological relevance of this enzyme in the context of photosynthetic carbon fixation.

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Yew, Wen Shan, and John A. Gerlt. "Utilization of l-Ascorbate by Escherichia coli K-12: Assignments of Functions to Products of the yjf-sga and yia-sgb Operons." Journal of Bacteriology 184, no. 1 (2002): 302–6. http://dx.doi.org/10.1128/jb.184.1.302-306.2002.

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ABSTRACT Escherichia coli K-12 can ferment l-ascorbate. The operon encoding catabolic enzymes in the utilization of l-ascorbate (ula) has been identified; this operon of previously unknown function had been designated the yif-sga operon. Three enzymes in the pathway that produce d-xylulose 5-phosphate have been functionally characterized: 3-keto-l-gulonate 6-phosphate decarboxylase (UlaD), l-xylulose 5-phosphate 3-epimerase (UlaE), and l-ribulose 5-phosphate 4-epimerase (UlaF). Several products of the yia-sgb operon were also functionally characterized, although the substrate and physiological function of the operon remain unknown: 2,3-diketo-l-gulonate reductase (YiaK), 3-keto-l-gulonate kinase (LyxK), 3-keto-l-gulonate 6-phosphate decarboxylase (SgbH), and l-ribulose 5-phosphate 4-epimerase (SgbE).

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Peleato, Maria Luisa, Teresa Muiño-Blanco, José Alvaro Cebrian Pérez, and Manuel José López-Pérez. "Significance of the Non-Oxidative Pentose Phosphate Pathway in Aspergillus oryzae Grown on Different Carbon Sources." Zeitschrift für Naturforschung C 46, no. 3-4 (1991): 223–27. http://dx.doi.org/10.1515/znc-1991-3-411.

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Specific enzyme activities of the non-oxidative pentose phosphate pathway in Aspergillus oryzae mycelia grown on different carbon sources were determined. Mycelia grown on glucose, mannitol and ribose show the highest specific activities, ribose 5-phosphate isomerase being specially very enhanced. Moreover, transketolase, transaldolase, ribose 5-phosphate isomerase and ribulose 5-phosphate 3-epimerase were determined in different developmental stages of mycelia grown on glucose, mannitol and ribose. The non-oxidative pentose phosphate pathway is more active during conidiogenesis, except for ribulose 5-phosphate 3-epimerase, suggesting a fundamental role of this pathway during that stage to supply pentoses for nucleic acids biosynthesis. A general decrease of the enzyme activities was found in sporulated mycelia. Arabinose 5-phosphate was tested as metabolite of the pentose pathway. This pentose phosphate was not converted into hexose phosphates or triose phosphates and inhibits significantly the ribose 5-phosphate utilization, being therefore unappropriate to support the Aspergillus oryzae growth.

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Ibañez, Ester, Rosa Gimenez, Tomas Pedraza, Laura Baldoma, Juan Aguilar, and Josefa Badia. "Role of the yiaR and yiaSGenes of Escherichia coli in Metabolism of Endogenously Formed l-Xylulose." Journal of Bacteriology 182, no. 16 (2000): 4625–27. http://dx.doi.org/10.1128/jb.182.16.4625-4627.2000.

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ABSTRACT Genes yiaP and yiaR of theyiaKLMNOPQRS cluster of Escherichia coli are required for the metabolism of the endogenously formedl-xylulose, whereas yiaS is required for this metabolism only in araD mutants. Like AraD, YiaS was shown to have l-ribulose-5-phosphate 4-epimerase activity. Similarity of YiaR to several 3-epimerases suggested that this protein could catalyze the conversion of l-xylulose-5-phosphate into l-ribulose-5-phosphate, thus completing the pathway between l-xylulose and the general metabolism.

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Wise, Eric L., Julie Akana, John A. Gerlt, and Ivan Rayment. "Structure ofD-ribulose 5-phosphate 3-epimerase fromSynechocystisto 1.6 Å resolution." Acta Crystallographica Section D Biological Crystallography 60, no. 9 (2004): 1687–90. http://dx.doi.org/10.1107/s0907444904015896.

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Caruthers, J., J. Bosch, F. Buckner, et al. "Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum." Proteins: Structure, Function, and Bioinformatics 62, no. 2 (2005): 338–42. http://dx.doi.org/10.1002/prot.20764.

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Le, Simone Balzer, Tonje Marita Bjerkan Heggeset, Tone Haugen, Ingemar Nærdal, and Trygve Brautaset. "6-Phosphofructokinase and ribulose-5-phosphate 3-epimerase in methylotrophic Bacillus methanolicus ribulose monophosphate cycle." Applied Microbiology and Biotechnology 101, no. 10 (2017): 4185–200. http://dx.doi.org/10.1007/s00253-017-8173-0.

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Dallapiccola, Bruno, Giuseppe Novelli, and Aldo Giannotti. "Deletion 2q31.3?2q33.3: gene dosage effect of ribulose 5-phosphate 3-epimerase." Human Genetics 79, no. 1 (1988): 92. http://dx.doi.org/10.1007/bf00291721.

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Hennig, Guido, Carsten Haupka, Luciana F. Brito, et al. "Methanol-Essential Growth of Corynebacterium glutamicum: Adaptive Laboratory Evolution Overcomes Limitation due to Methanethiol Assimilation Pathway." International Journal of Molecular Sciences 21, no. 10 (2020): 3617. http://dx.doi.org/10.3390/ijms21103617.

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Methanol is a sustainable substrate for biotechnology. In addition to natural methylotrophs, metabolic engineering has gained attention for transfer of methylotrophy. Here, we engineered Corynebacterium glutamicum for methanol-dependent growth with a sugar co-substrate. Heterologous expression of genes for methanol dehydrogenase from Bacillus methanolicus and of ribulose monophosphate pathway genes for hexulose phosphate synthase and isomerase from Bacillus subtilis enabled methanol-dependent growth of mutants carrying one of two independent metabolic cut-offs, i.e., either lacking ribose-5-phosphate isomerase or ribulose-5-phosphate epimerase. Whole genome sequencing of strains selected by adaptive laboratory evolution (ALE) for faster methanol-dependent growth was performed. Subsequently, three mutations were identified that caused improved methanol-dependent growth by (1) increased plasmid copy numbers, (2) enhanced riboflavin supply and (3) reduced formation of the methionine-analogue O-methyl-homoserine in the methanethiol pathway. Our findings serve as a foundation for the engineering of C. glutamicum to unleash the full potential of methanol as a carbon source in biotechnological processes.

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Akana, Julie, Alexander A. Fedorov, Elena Fedorov та ін. "d-Ribulose 5-Phosphate 3-Epimerase: Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (β/α)8-Barrel Superfamily†,‡". Biochemistry 45, № 8 (2006): 2493–503. http://dx.doi.org/10.1021/bi052474m.

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Jelakovic, Stefan, Stanislav Kopriva, Karl-Heinz Süss, and Georg E. Schulz. "Structure and Catalytic Mechanism of the Cytosolic d-Ribulose-5-phosphate 3-Epimerase from Rice." Journal of Molecular Biology 326, no. 1 (2003): 127–35. http://dx.doi.org/10.1016/s0022-2836(02)01374-8.

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Süss, Karl-Heinz, Stanislav Kopriva, and Anna Koprivova. "Identification, Cloning, and Properties of Cytosolic d-Ribulose-5-phosphate 3-Epimerase from Higher Plants." Journal of Biological Chemistry 275, no. 2 (2000): 1294–99. http://dx.doi.org/10.1074/jbc.275.2.1294.

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Hu, Lan, Xin Xu, and Manuel S. Valenzuela. "Initiation sites for human DNA replication at a putative ribulose-5-phosphate 3-epimerase gene." Biochemical and Biophysical Research Communications 320, no. 3 (2004): 648–55. http://dx.doi.org/10.1016/j.bbrc.2004.06.018.

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Shi, Rong, Marco Pineda, Eunice Ajamian, Qizhi Cui, Allan Matte, and Miroslaw Cygler. "Structure of l-Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic l-Ascorbate Utilization Pathway of Escherichia coli: Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold." Journal of Bacteriology 190, no. 24 (2008): 8137–44. http://dx.doi.org/10.1128/jb.01049-08.

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ABSTRACT Three catabolic enzymes, UlaD, UlaE, and UlaF, are involved in a pathway leading to fermentation of l-ascorbate under anaerobic conditions. UlaD catalyzes a β-keto acid decarboxylation reaction to produce l-xylulose-5-phosphate, which undergoes successive epimerization reactions with UlaE (l-xylulose-5-phosphate 3-epimerase) and UlaF (l-ribulose-5-phosphate 4-epimerase), yielding d-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway. We describe here crystallographic studies of UlaE from Escherichia coli O157:H7 that complete the structural characterization of this pathway. UlaE has a triosephosphate isomerase (TIM) barrel fold and forms dimers. The active site is located at the C-terminal ends of the parallel β-strands. The enzyme binds Zn2+, which is coordinated by Glu155, Asp185, His211, and Glu251. We identified a phosphate-binding site formed by residues from the β1/α1 loop and α3′ helix in the N-terminal region. This site differs from the well-characterized phosphate-binding motif found in several TIM barrel superfamilies that is located at strands β7 and β8. The intrinsic flexibility of the active site region is reflected by two different conformations of loops forming part of the substrate-binding site. Based on computational docking of the l-xylulose 5-phosphate substrate to UlaE and structural similarities of the active site of this enzyme to the active sites of other epimerases, a metal-dependent epimerization mechanism for UlaE is proposed, and Glu155 and Glu251 are implicated as catalytic residues. Mutation and activity measurements for structurally equivalent residues in related epimerases supported this mechanistic proposal.

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Chen, Yuh-Ru, Frank W. Larimer, Engin H. Serpersu, and Fred C. Hartman. "Identification of a Catalytic Aspartyl Residue ofd-Ribulose 5-Phosphate 3-Epimerase by Site-directed Mutagenesis." Journal of Biological Chemistry 274, no. 4 (1999): 2132–36. http://dx.doi.org/10.1074/jbc.274.4.2132.

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Kopp, Jürgen, Stanislav Kopriva, Karl-Heinz Süss, and Georg E. Schulz. "Structure and mechanism of the amphibolic enzyme d-ribulose-5-phosphate 3-epimerase from potato chloroplasts." Journal of Molecular Biology 287, no. 4 (1999): 761–71. http://dx.doi.org/10.1006/jmbi.1999.2643.

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Azar, Alda Wydia Prihartini, Hasna Dyah Kusumardani, and Haris Maulani. "REVIEW: PRODUKSI LIMONENE MELALUI REKAYASA JALUR PENTOSA FOSFAT MENGGUNAKAN CYANOBACTERIUM Synechocystis sp. PCC 6803." Jurnal Biogenerasi 10, no. 2 (2025): 866–73. https://doi.org/10.30605/biogenerasi.v10i2.5344.

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Limonene, a terpenoid compound found in various plants such as oranges, lemons, and mint, has numerous applications in different industrial fields, including as a fragrance, flavoring agent, and biofuel. Conventional limonene production relies on agricultural outputs vulnerable to fluctuations caused by diseases or climate change. Therefore, metabolic engineering using microorganisms offers an interesting alternative for more efficient and sustainable limonene production. This review article aims to summarize the procedures for limonene production through the modification of the pentose phosphate (PP) and methylerythritol 4-phosphate (MEP) biosynthetic pathways in the cyanobacterium Synechocystis sp. PCC 6803 to produce limonene. Limonene synthase (lims) obtained from C. limon and M. spicata plants was cloned and transformed into cyanobacteria to enhance limonene production. Experimental results showed that genes associated with the limonene biosynthesis pathway, including ribose 5-phosphate isomerase (rpi), ribulose 5-phosphate 3-epimerase (rpe), and geranyl diphosphate synthase (gpps), were successfully expressed in Synechocystis. This study demonstrates that Synechocystis can be an efficient microbial system for limonene and other isoprene compound production, offering a more stable and environmentally friendly alternative than agricultural-based production.

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Guo, Zhang, Li, et al. "Label-Free Proteomic Analysis of Molecular Effects of 2-Methoxy-1,4-naphthoquinone on Penicillium italicum." International Journal of Molecular Sciences 20, no. 14 (2019): 3459. http://dx.doi.org/10.3390/ijms20143459.

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Penicillium italicum is the principal pathogen causing blue mold of citrus. Searching for novel antifungal agents is an important aspect of the post-harvest citrus industry because of the lack of higher effective and low toxic antifungal agents. Herein, the effects of 2-methoxy-1,4-naphthoquinone (MNQ) on P. italicum and its mechanism were carried out by a series of methods. MNQ had a significant anti-P. italicum effect with an MIC value of 5.0 µg/mL. The label-free protein profiling under different MNQ conditions identified a total of 3037 proteins in the control group and the treatment group. Among them, there were 129 differentially expressed proteins (DEPs，up-regulated > 2.0-fold or down-regulated < 0.5-fold, p < 0.05), 19 up-regulated proteins, 26 down-regulated proteins, and 67 proteins that were specific for the treatment group and another 17 proteins that were specific for the control group. Of these, 83 proteins were sub-categorized into 23 hierarchically-structured GO classifications. Most of the identified DEPs were involved in molecular function (47%), meanwhile 27% DEPs were involved in the cellular component and 26% DEPs were involved in the biological process. Twenty-eight proteins identified for differential metabolic pathways by KEGG were sub-categorized into 60 classifications. Functional characterization by GO and KEGG enrichment results suggests that the DEPs are mainly related to energy generation (mitochondrial carrier protein, glycoside hydrolase, acyl-CoA dehydrogenase, and ribulose-phosphate 3-epimerase), NADPH supply (enolase, pyruvate carboxylase), oxidative stress (catalase, glutathione synthetase), and pentose phosphate pathway (ribulose-phosphate 3-epimerase and xylulose 5-phosphate). Three of the down-regulated proteins selected randomly the nitro-reductase family protein, mono-oxygenase, and cytochrome P450 were verified using parallel reaction monitoring. These findings illustrated that MNQ may inhibit P. italicum by disrupting the metabolic processes, especially in energy metabolism and stimulus response that are both critical for the growth of the fungus. In conclusion, based on the molecular mechanisms, MNQ can be developed as a potential anti-fungi agent against P. italicum.

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Miyazaki, K., T. Yamanaka, and N. Ogasawara. "Interstitial deletion 2q32.1----q34 in a child with half normal activity of ribulose 5-phosphate 3-epimerase (RPE)." Journal of Medical Genetics 25, no. 12 (1988): 850–51. http://dx.doi.org/10.1136/jmg.25.12.850.

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Zhan, Ni, Liejian Huang, Zhen Wang, et al. "Comparative transcriptomics and bioinformatics analysis of genes related to photosynthesis in Eucalyptus camaldulensis." PeerJ 10 (November 11, 2022): e14351. http://dx.doi.org/10.7717/peerj.14351.

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The timber species Eucalyptus camaldulensis is one of the most important in southern China. Therefore, it is essential to understand the photosynthetic pattern in eucalyptus leaves. In the present study, eighteen photosynthesis-related genes were analyzed using bioinformatics methods. The results indicated that there were ten differentially expressed ribose-5-phosphate isomerase genes (RPI), and six of them were up-regulated in the mature leaves compared to the young leaves, while others were down-regulated. The differential expression of four rubisco methyltransferase genes (RBCMT) were observed. Two of them were up-regulated, while two were down-regulated in mature leaves compared to young leaves. Furthermore, two ribulose-phosphate-3-epimerase genes (RPE) were up-regulated in the mature leaves compared to the young leaves. In contrast, two genes involved in triosephosphate isomerase (TIM) were down-regulated in mature leaves compared with young leaves. The current study provides basic information about the transcriptome of E. camaldulensis and lays a foundation for further research in developing and utilizing important photosynthetic genes.

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Shen, Ming-Hua, Hao Song, Bing-Zhi Li, and Ying-Jin Yuan. "Deletion of d-ribulose-5-phosphate 3-epimerase (RPE1) induces simultaneous utilization of xylose and glucose in xylose-utilizing Saccharomyces cerevisiae." Biotechnology Letters 37, no. 5 (2014): 1031–36. http://dx.doi.org/10.1007/s10529-014-1759-z.

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Teige, Markus, Michael Melzer, and Karl-Heinz Suss. "Purification, properties and in situ localization of the amphibolic enzymes D-ribulose 5-phosphate 3-epimerase and transketolase from spinach chloroplasts." European Journal of Biochemistry 252, no. 2 (1998): 237–44. http://dx.doi.org/10.1046/j.1432-1327.1998.2520237.x.

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Sobota, J. M., and J. A. Imlay. "Iron enzyme ribulose-5-phosphate 3-epimerase in Escherichia coli is rapidly damaged by hydrogen peroxide but can be protected by manganese." Proceedings of the National Academy of Sciences 108, no. 13 (2011): 5402–7. http://dx.doi.org/10.1073/pnas.1100410108.

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Chen, Yuh-Ru, Fred C. Hartman, Tse-Yuan S. Lu, and Frank W. Larimer. "d-Ribulose-5-Phosphate 3-Epimerase: Cloning and Heterologous Expression of the Spinach Gene, and Purification and Characterization of the Recombinant Enzyme." Plant Physiology 118, no. 1 (1998): 199–207. http://dx.doi.org/10.1104/pp.118.1.199.

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Elleuch, Fatma, Hajer Ben Hlima, Mohamed Barkallah та ін. "Carotenoids Overproduction in Dunaliella Sp.: Transcriptional Changes and New Insights through Lycopene β Cyclase Regulation". Applied Sciences 9, № 24 (2019): 5389. http://dx.doi.org/10.3390/app9245389.

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Dunaliella is a green microalga known for its ability to produce high levels of carotenoids under well-defined growing conditions. Molecular responses to the simultaneous effect of increasing salinity, light intensity and decrease of nitrogen availability were investigated in terms of their effect on different metabolic pathways (isoprenoids synthesis, glycolysis, carbohydrate use, etc.) by following the transcriptional regulation of enolase (ENO), 1-deoxy-D-xylulose 5-phosphate synthase (DXS), lycopene β-cyclase (LCYB), carotene globule protein (CGP), chloroplast-localized heat shock protein (HSP70), and chloroplast ribulose phosphate-3-epimerase (RPE) genes. The intracellular production of carotenoid was increased five times in stressed Dunaliella cells compared to those grown in an unstressed condition. At transcriptional levels, ENO implicated in glycolysis, and revealing about polysaccharides degradation, showed a two-stage response during the first 72 h. Genes directly involved in β-carotene accumulation, namely, CGP and LCYB, revealed the most important increase by about 54 and 10 folds, respectively. In silico sequence analysis, along with 3D modeling studies, were performed to identify possible posttranslational modifications of CGP and LCYB proteins. Our results described, for the first time, their probable regulation by sumoylation covalent attachment as well as the presence of expressed SUMO (small ubiquitin-related modifier) protein in Dunaliella sp.

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Abu Rmaileh, Areej, Balakrishnan Solaimuthu, Mayur Tanna, et al. "Large-Scale Differential Gene Expression Transcriptomic Analysis Identifies a Metabolic Signature Shared by All Cancer Cells." Biomolecules 10, no. 5 (2020): 701. http://dx.doi.org/10.3390/biom10050701.

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Cancer-dependent metabolic rewiring is often manifested by selective expression of enzymes essential for the transformed cells’ viability. However, the metabolic variations between normal and transformed cells are not fully characterized, and therefore, a systematic analysis will result in the identification of unknown cellular mechanisms crucial for tumorigenesis. Here, we applied differential gene expression transcriptome analysis to examine the changes in metabolic gene profiles between a wide range of normal tissues and cancer samples. We found that, in contrast to normal tissues which exhibit a tissue-specific expression profile, cancer samples are more homogenous despite their diverse origins. This similarity is due to a “proliferation metabolic signature” (PMS), composed of 158 genes (87 upregulated and 71 downregulated gene sets), where 143 are common to all proliferative cells but 15 are cancer specific. Intriguingly, the PMS gene set is enriched for genes encoding rate-limiting enzymes, and its upregulated set with genes associated with poor patient outcome and essential genes. Among these essential genes is ribulose-5-phosphate-3-epimerase (RPE), which encodes a pentose phosphate pathway enzyme and whose role in cancer is still unclear. Collectively, we identified a set of metabolic genes that can serve as novel cancer biomarkers and potential targets for drug development.

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Asplund-Samuelsson, Johannes, and Elton P. Hudson. "Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes." PLOS Computational Biology 17, no. 2 (2021): e1008742. http://dx.doi.org/10.1371/journal.pcbi.1008742.

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Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.

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Nowitzki, Ulrich, Ralf Wyrich, Peter Westhoff, Katrin Henze, Claus Schnarrenberger, and William Martin. "Cloning of the amphibolic Calvin cycle/OPPP enzyme d-ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) from spinach chloroplasts: functional and evolutionary aspects." Plant Molecular Biology 29, no. 6 (1995): 1279–91. http://dx.doi.org/10.1007/bf00020468.

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Brautaset, Trygve, Øyvind M. Jakobsen, Michael C. Flickinger, Svein Valla, and Trond E. Ellingsen. "Plasmid-Dependent Methylotrophy in Thermotolerant Bacillus methanolicus." Journal of Bacteriology 186, no. 5 (2004): 1229–38. http://dx.doi.org/10.1128/jb.186.5.1229-1238.2004.

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ABSTRACT Bacillus methanolicus can efficiently utilize methanol as a sole carbon source and has an optimum growth temperature of 50°C. With the exception of mannitol, no sugars have been reported to support rapid growth of this organism, which is classified as a restrictive methylotroph. Here we describe the DNA sequence and characterization of a 19,167-bp circular plasmid, designated pBM19, isolated from B. methanolicus MGA3. Sequence analysis of pBM19 demonstrated the presence of the methanol dehydrogenase gene, mdh, which is crucial for methanol consumption in this bacterium. In addition, five genes (pfk, encoding phosphofructokinase; rpe, encoding ribulose-5-phosphate 3-epimerase; tkt, encoding transketolase; glpX, encoding fructose-1,6-bisphosphatase; and fba, encoding fructose-1,6-bisphosphate aldolase) with deduced roles in methanol assimilation via the ribulose monophosphate pathway are encoded by pBM19. A shuttle vector, pTB1.9, harboring the pBM19 minimal replicon (repB and ori) was constructed and used to transform MGA3. Analysis of the resulting recombinant strain demonstrated that it was cured of pBM19 and was not able to grow on methanol. A pTB1.9 derivative harboring the complete mdh gene could not restore growth on methanol when it was introduced into the pBM19-cured strain, suggesting that additional pBM19 genes are required for consumption of this carbon source. Screening of 13 thermotolerant B. methanolicus wild-type strains showed that they all harbor plasmids similar to pBM19, and this is the first report describing plasmid-linked methylotrophy in any microorganism. Our findings should have an effect on future genetic manipulations of this organism, and they contribute to a new understanding of the biology of methylotrophs.

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Milla, MA Rodriguez, and J. P. Gustafson. "Genetic and physical characterization of chromosome 4DL in wheat." Genome 44, no. 5 (2001): 883–92. http://dx.doi.org/10.1139/g01-089.

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The long arm of chromosome 4D in wheat (Triticum aestivum L.) has been shown in previous studies to harbor genes of agronomic importance. A major dominant gene conferring Aluminum (Al) tolerance (Alt2 in 'Chinese Spring' and AltBH in 'BH 1146'), and the Kna1 locus controlling the K+/Na+ discrimination in saline environments have been mapped to this chromosome arm. However, accurate information on the genetic and physical location of markers related to any of these genes is not available and would be useful for map-based cloning and marker-assisted plant breeding. In the present study, using a population of 91 recombinant inbred lines segregating for Al tolerance, we provide a more extensive genetic linkage map of the chromosome arm 4DL based on RFLP, SSR, and AFLP markers, delimiting the AltBH gene to a 5.9-cM interval between markers Xgdm125 and Xpsr914. In addition, utilizing a set of wheat deletion lines for chromosome arm 4DL, the AltBH gene was physically mapped to the distal region of the chromosome, between deletion breakpoints 0.70 and 0.86, where the kilobase/centimorgan ratio is assumed to be low, making the map-based cloning of the gene a more realistic goal. The polymorphism rates in chromosome arm 4DL for the different types of markers used were extremely low, as confirmed by the physical mapping of AFLPs. Finally, analysis of 1 Mb of contiguous sequence of Arabidopsis chromosome 5 flanking the gene homologous to the BCD1230 clone (a cosegregating marker in our population coding for a ribulose-5-phosphate-3-epimerase gene), revealed a previously identified region of stress-related and disease-resistance genes. This could explain the collinearity observed in comparative mapping studies among different species and the low level of polymorphism detected in the chromosome arm 4DL in hexaploid wheat.Key words: wheat, aluminum, mapping, AFLP, SSR.

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Rodríguez-Milla, Miguel Ángel, and Perry J. Gustafson. "Genetic and physical characterization of chromosome 4DL in wheat." Genome 44, no. 5 (2001): 883–92. https://doi.org/10.1139/g01-089.

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The long arm of chromosome 4D in wheat (Triticum aestivum L.) has been shown in previous studies to harborgenes of agronomic importance. A major dominant gene conferring Aluminum (Al) tolerance (Alt2 in ‘Chinese Spring’and AltBH in ‘BH 1146’), and the Kna1 locus controlling the K+/Na+ discrimination in saline environments have beenmapped to this chromosome arm. However, accurate information on the genetic and physical location of markers relatedto any of these genes is not available and would be useful for map-based cloning and marker-assisted plant breeding. Inthe present study, using a population of 91 recombinant inbred lines segregating for Al tolerance, we provide a more extensivegenetic linkage map of the chromosome arm 4DL based on RFLP, SSR, and AFLP markers, delimiting the AltBHgene to a 5.9-cM interval between markers Xgdm125 and Xpsr914. In addition, utilizing a set of wheat deletion lines forchromosome arm 4DL, the AltBH gene was physically mapped to the distal region of the chromosome, between deletionbreakpoints 0.70 and 0.86, where the kilobase/centimorgan ratio is assumed to be low, making the map-based cloning ofthe gene a more realistic goal. The polymorphism rates in chromosome arm 4DL for the different types of markers usedwere extremely low, as confirmed by the physical mapping of AFLPs. Finally, analysis of 1 Mb of contiguous sequenceof Arabidopsis chromosome 5 flanking the gene homologous to the BCD1230 clone (a cosegregating marker in our populationcoding for a ribulose-5-phosphate-3-epimerase gene), revealed a previously identified region of stress-related anddisease-resistance genes. This could explain the collinearity observed in comparative mapping studies among differentspecies and the low level of polymorphism detected in the chromosome arm 4DL in hexaploid wheat

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Graupner, Stefan, and Wilfried Wackernagel. "A broad-host-range expression vector series including a Ptac test plasmid and its application in the expression of the dod gene of Serratia marcescens (coding for ribulose-5-phosphate 3-epimerase) in Pseudomonas stutzeri." Biomolecular Engineering 17, no. 1 (2000): 11–16. http://dx.doi.org/10.1016/s1389-0344(00)00061-7.

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Makarona, Kalliopi, Valentina Caputo, David Roper, et al. "Gene-Selective Histone Hyperacetylation and Enhanced Sp1 Occupancy Underpin Transcriptional Modulation of Genes of the Glycolytic-Pentose Phosphate Pathway in Response to Histone Deacetylase Inhibitors - Therapeutic Implications." Blood 120, no. 21 (2012): 977. http://dx.doi.org/10.1182/blood.v120.21.977.977.

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Abstract Abstract 977 Transcriptionally active genes, including housekeeping genes, are characterised by co-occupancy and antagonistic actions of histone deacetylases (HDAC) and acetyltransferases (HAT). Transcription is facilitated through the prevailing action of HAT, which maintain histone acetylation. HDAC inhibitors (HDACi) induce widespread histone hyperacetylation and as a consequence are expected to increase expression of transcriptionally active genes. We have previously demonstrated this effect in inherited glycosylphosphatidylinositol (GPI-anchor) deficiency, an autosomal recessive disorder characterised by histone hypoacetylation and transcriptional repression of PIGM due to an in cis mutation which disrupts binding of the transcription factor Sp1 to its core promoter cognate motif. We surmised HDACi-mediated hyperacetylation might lead to increased transcription of other housekeeping genes, such as those of the anaerobic glycolytic and pentose phosphate pathways (GPPP) disruption of which is ameliorated by relatively modest increases in enzymatic activity. HDACi could therefore be of therapeutic value in these disorders. To address these hypotheses, EBV B cell lines were treated with the HDACi sodium butyrate (NaBu; 3mM) and mRNA levels for GPPP genes assessed by RQ-PCR. Of 9 genes tested (glucose-6-phosphate dehydrogenase, G6PD; glucose-6-phosphate isomerase, GPI; triosephosphate isomerase, TPI; pyruvate kinase, PK; 6-phosphogluconolactonase, PGLS; phosphogluconate dehydrogenase, PGD; ribulose-5-phosphate-3-epimerase, RPE; ribose-5-phosphate isomerase A, RPIA; transketolase, TKT), only G6PD mRNA levels increased, in a time-dependent fashion, in response to NaBu (n=3; p<0.01), an effect that was also observed in B cells from a patient with G6PD Brighton a severe, Class I G6PD deficiency (n=3; p<0.01). The increase in G6PD mRNA was observed within 4hrs post NaBu exposure and was not abrogated by the protein synthesis inhibitor cycloheximide suggesting a direct effect of NaBu on G6PD transcription. G6PD protein and enzymatic activity increased commensurately with G6PD mRNA level in both normal (n=4; p<0.01) and G6PD Brighton (n=4; p<0.01) B cells. In G6PD deficient B cells, enzymatic activity was restored to normal levels within 24hrs of treatment with HDACi (n=3; p<0.01). The selective effect of HDACi on transcription of G6PD but not other GPPP genes was also observed in other cell types, including 293T cells, and primary CD36+CD71+ erythroblasts generated from normal cord blood CD34+ cells. Notably, in NaBu-treated (1mM) primary erythroblasts a 2.3-fold increase in G6PD mRNA (n=3; p<0.01) accompanied by a 2.5-fold increase of G6PD protein levels (n=3; p<0.05) and 2.6-fold increase in enzymatic activity (n=3; p<0.05) were observed. The epigenetic correlates of G6PD mRNA induction were assessed by ChIP-Q-PCR. This revealed a dynamic, time-dependent, 3 to 4-fold increase in levels of histone 3 and 4 acetylation and a 4-fold increase in Sp1 and Polymerase II occupancy in the promoter of G6PD but not TPI or GPI. Preliminary pharmacological and shRNA experiments suggest that HDACi-mediated transcriptional upregulation of G6PD is Sp1-dependent. No differences were observed in baseline levels of histone acetylation or Sp1 occupancy of G6PD, TPI and GPI implying a yet to be defined cis acting determinant is required for the selective increase in Sp1 binding and histone hyperacetylation. Finally, in erythroblasts generated from peripheral blood mononuclear cells of two patients with Class I G6PD deficiency (G6PD Brighton and G6PD Harilaou), we confirmed the ability of NaBu to increase mutant G6PD mRNA and protein levels leading to increased G6PD enzymatic activity and its restoration to normal within 24hrs. In conclusion, we show that even within the same metabolic pathway, transcriptional upregulation of active genes in response to HDACi is selective rather than universal and is underpinned by enhanced Sp1 binding and histone hyperacetylation. Our findings raise the prospect of using HDACi to treat severe Class I G6PD deficiency. Disclosures: No relevant conflicts of interest to declare.

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Li, Yonghong, Lianwei Peng, Xiaoqin Wang, and Lin Zhang. "Reduction in chloroplastic ribulose-5-phosphate-3-epimerase decreases photosynthetic capacity in Arabidopsis." Frontiers in Plant Science 13 (October 14, 2022). http://dx.doi.org/10.3389/fpls.2022.813241.

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Chloroplast ribulose-5-phosphate-3-epimerase (RPE) is a critical enzyme involved in the Calvin-Benson cycle and oxidative pentose phosphate pathways in higher plants. Three Arabidopsis rpe mutants with reduced level of RPE were identified through their high NPQ (nonphotochemical quenching) phenotype upon illumination, and no significant difference of plant size was found between these rpe mutants and WT (wild type) plants under growth chamber conditions. A decrease in RPE expression to a certain extent leads to a decrease in CO2 fixation, Vcmax and Jmax. Photosynthetic linear electron transport was partially inhibited and activity of ATP synthase was also decreased in the rpe mutants, but the levels of thylakoid protein complexes and other Calvin-Benson cycle enzymes in rpe mutants were not affected. These results demonstrate that some degree of reduction in RPE expression decreases carbon fixation in chloroplasts, which in turn feedback inhibits photosynthetic electron transport and ATP synthase activity due to the photosynthetic control. Taken together, this work provides evidence that RPE plays an important role in the Calvin-Benson cycle and influences the photosynthetic capacity of chloroplasts.

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Yang, Bin, Yiwen Sun, Shouying Fu, et al. "Improving the Production of Riboflavin by Introducing a Mutant Ribulose 5-Phosphate 3-Epimerase Gene in Bacillus subtilis." Frontiers in Bioengineering and Biotechnology 9 (July 29, 2021). http://dx.doi.org/10.3389/fbioe.2021.704650.

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Ribulose 5-phosphate (Ru5P) and guanosine 5′-triphosphate (GTP) are two key precursors of riboflavin, whereby Ru5P is also a precursor of GTP. Ribulose 5-phosphate 3-epimerase (Rpe) catalyzes the conversion of ribulose 5-phosphate into xylulose 5-phosphate. Inactivation of Rpe can reduce the consumption of Ru5P, enhancing the carbon flux toward riboflavin biosynthesis. Here we investigated the effect of mutation of rpe and other related genes on riboflavin production, physiological and metabolic phenotypes in Bacillus subtilis LY (BSLY). Introducing single nucleotide deletion (generated BSR) or nonsense mutation (generated BSRN) on the genomic copy of rpe, resulting in more than fivefold increase of riboflavin production over the parental strain. BSR process 62% Rpe activity, while BSRN lost the entire Rpe activity and had a growth defect compared with the parent strain. BSR and BSRN exhibited increases of the inosine and guanine titers, in addition, BSRN exhibited an increase of inosine 5′-monophosphate titer in fermentation. The transcription levels of most oxidative pentose phosphate pathway and purine synthesis genes were unchanged in BSR, except for the levels of zwf and ndk, which were higher than in BSLY. The production of riboflavin was increased to 479.90 ± 33.21 mg/L when ribA was overexpressed in BSR. The overexpression of zwf, gntZ, prs, and purF also enhanced the riboflavin production. Finally, overexpression of the rib operon by the pMX45 plasmid and mutant gnd by pHP03 plasmid in BSR led to a 3.05-fold increase of the riboflavin production (977.29 ± 63.44 mg/L), showing the potential for further engineering of this strain.

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Meloni, Maria, Silvia Fanti, Daniele Tedesco, et al. "Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii." Plant Physiology, December 22, 2023. http://dx.doi.org/10.1093/plphys/kiad680.

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Abstract Carbon fixation relies on Rubisco and ten additional enzymes in the Calvin-Benson-Bassham cycle. Epimerization of xylulose-5-phosphate (Xu5P) into ribulose-5-phosphate (Ru5P) contributes to the regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco. Ribulose-5-phosphate-3-epimerase (RPE, EC 5.1.3.1) catalyzes the formation of Ru5P, but it can also operate in the pentose phosphate pathway by catalyzing the reverse reaction. Here, we describe the structural and biochemical properties of the recombinant RPE isoform 1 from Chlamydomonas (Chlamydomonas reinhardtii) (CrRPE1). The enzyme is a homo-hexamer that contains a zinc ion in the active site and exposes a catalytic pocket on the top of an α8β8 triose isomerase-type barrel as observed in structurally solved RPE isoforms from both plant and non-plant sources. By optimizing and developing enzyme assays to monitor the reversible epimerization of Ru5P to Xu5P and vice versa, we determined the catalytic parameters that differ from those of other plant paralogues. Despite being identified as a putative target of multiple thiol-based redox modifications, CrRPE1 activity is not affected by both reductive and oxidative treatments, indicating that enzyme catalysis is insensitive to possible redox alterations of cysteine residues. We mapped phosphorylation sites on the crystal structure, and the specific location at the entrance of the catalytic cleft supports a phosphorylation-based regulatory mechanism. This work provides an accurate description of the structural features of CrRPE1 and an in-depth examination of its catalytic and regulatory properties highlighting the physiological relevance of this enzyme in the context of photosynthetic carbon fixation.

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Meloni, Maria, Libero Gurrieri, Simona Fermani, et al. "Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate." Frontiers in Plant Science 14 (February 16, 2023). http://dx.doi.org/10.3389/fpls.2023.1130430.

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The Calvin-Benson-Bassham (CBB) cycle comprises the metabolic phase of photosynthesis and is responsible for carbon fixation and the production of sugar phosphates. The first step of the cycle involves the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) which catalyzes the incorporation of inorganic carbon into 3-phosphoglyceric acid (3PGA). The following steps include ten enzymes that catalyze the regeneration of ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco. While it is well established that Rubisco activity acts as a limiting step of the cycle, recent modeling studies and experimental evidence have shown that the efficiency of the pathway is also impacted by the regeneration of the Rubisco substrate itself. In this work, we review the current understanding of the structural and catalytic features of the photosynthetic enzymes that catalyze the last three steps of the regeneration phase, namely ribose-5-phosphate isomerase (RPI), ribulose-5-phosphate epimerase (RPE), and phosphoribulokinase (PRK). In addition, the redox- and metabolic-based regulatory mechanisms targeting the three enzymes are also discussed. Overall, this review highlights the importance of understudied steps in the CBB cycle and provides direction for future research aimed at improving plant productivity.

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Wagner, Nils, Frederik Bade, Elly Straube, Kenny Rabe, Cláudio J. R. Frazão, and Thomas Walther. "In vivo implementation of a synthetic metabolic pathway for the carbon-conserving conversion of glycolaldehyde to acetyl-CoA." Frontiers in Bioengineering and Biotechnology 11 (February 9, 2023). http://dx.doi.org/10.3389/fbioe.2023.1125544.

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Ethylene glycol (EG) derived from plastic waste or CO2 can serve as a substrate for microbial production of value-added chemicals. Assimilation of EG proceeds though the characteristic intermediate glycolaldehyde (GA). However, natural metabolic pathways for GA assimilation have low carbon efficiency when producing the metabolic precursor acetyl-CoA. In alternative, the reaction sequence catalyzed by EG dehydrogenase, d-arabinose 5-phosphate aldolase, d-arabinose 5-phosphate isomerase, d-ribulose 5-phosphate 3-epimerase (Rpe), d-xylulose 5-phosphate phosphoketolase, and phosphate acetyltransferase may enable the conversion of EG into acetyl-CoA without carbon loss. We investigated the metabolic requirements for in vivo function of this pathway in Escherichia coli by (over)expressing constituting enzymes in different combinations. Using 13C-tracer experiments, we first examined the conversion of EG to acetate via the synthetic reaction sequence and showed that, in addition to heterologous phosphoketolase, overexpression of all native enzymes except Rpe was required for the pathway to function. Since acetyl-CoA could not be reliably quantified by our LC/MS-method, the distribution of isotopologues in mevalonate, a stable metabolite that is exclusively derived from this intermediate, was used to probe the contribution of the synthetic pathway to biosynthesis of acetyl-CoA. We detected strong incorporation of 13C carbon derived from labeled GA in all intermediates of the synthetic pathway. In presence of unlabeled co-substrate glycerol, 12.4% of the mevalonate (and therefore acetyl-CoA) was derived from GA. The contribution of the synthetic pathway to acetyl-CoA production was further increased to 16.1% by the additional expression of the native phosphate acyltransferase enzyme. Finally, we demonstrated that conversion of EG to mevalonate was feasible albeit at currently extremely small yields.

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Liu, Chuan, Miaomiao Xia, Huan Fang, Fan Xu, Sijia Wang, and Dawei Zhang. "De novo engineering riboflavin production Bacillus subtilis by overexpressing the downstream genes in the purine biosynthesis pathway." Microbial Cell Factories 23, no. 1 (2024). http://dx.doi.org/10.1186/s12934-024-02426-w.

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Abstract Background Bacillus subtilis is widely used in industrial-scale riboflavin production. Previous studies have shown that targeted mutagenesis of the ribulose 5-phosphate 3-epimerase in B. subtilis can significantly enhance riboflavin production. This modification also leads to an increase in purine intermediate concentrations in the medium. Interestingly, B. subtilis exhibits remarkable efficiency in purine nucleoside synthesis, often exceeding riboflavin yields. These observations highlight the importance of the conversion steps from inosine-5’-monophosphate (IMP) to 2,5-diamino-6-ribosylamino-4(3 H)-pyrimidinone-5’-phosphate (DARPP) in riboflavin production by B. subtilis. However, research elucidating the specific impact of these reactions on riboflavin production remains limited. Result We expressed the genes encoding enzymes involved in these reactions (guaB, guaA, gmk, ndk, ribA) using a synthetic operon. Introduction of the plasmid carrying this synthetic operon led to a 3.09-fold increase in riboflavin production compared to the control strain. Exclusion of gmk from the synthetic operon resulted in a 36% decrease in riboflavin production, which was further reduced when guaB and guaA were not co-expressed. By integrating the synthetic operon into the genome and employing additional engineering strategies, we achieved riboflavin production levels of 2702 mg/L. Medium optimization further increased production to 3477 mg/L, with a yield of 0.0869 g riboflavin per g of sucrose. Conclusion The conversion steps from IMP to DARPP play a critical role in riboflavin production by B. subtilis. Our overexpression strategies have demonstrated their effectiveness in overcoming these limiting factors and enhancing riboflavin production.

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Zhang, Runji, Qiuyue Yang, Xin Yao, et al. "Transcriptome analysis reveals the effect of cold storage time on the expression of genes related to oxidative metabolism in Chinese black truffle." Frontiers in Nutrition 11 (June 4, 2024). http://dx.doi.org/10.3389/fnut.2024.1375386.

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Chinese black truffle (Tuber indicum) is a hypogenous fungus of great value due to its distinctive aroma. In this study, both transcriptome and physicochemical analyses were performed to investigate the changes of nutrients and gene expression in truffle fruiting bodies during cold storage. The results of physicochemical analysis revealed the active metabolism of fruiting bodies in cold storage, showing the decreased contents of protein and soluble sugar, the variations in both polyphenol oxidase activity and total phenol content, and the detrimental effect of reactive oxygen species production caused by heavy metals (cadmium and lead) in truffles. Transcriptome analysis identified a total of 139,489 unigenes. Down-regulated expression of genes encoding the catalase-like domain-containing protein (katE), glutaredoxin protein (GRX), a copper/zinc superoxide dismutase (Sod_Cu), and aspartate aminotransferase (AAT) affected the degradation metabolism of intracellular oxides. Ribulose-5-phosphate-3-epimerase (RPE) was a key enzyme in response to oxidative stress in truffle cells through the pentose phosphate pathway (PPP). A total of 51,612 simple sequence repeats were identified, providing valuable resources for further genetic diversity analysis, molecular breeding, and genetic map-ping in T. indicum. Transcription factors GAL4 and SUF4-like protein were involved in glucose metabolism and histone methylation processes, respectively. Our study provided a fundamental characterization of the physicochemical and molecular variations in T. indicum during the cold storage at 4°C, providing strong experimental evidence to support the improvement of storage quality of T. indicum.

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Zhang, Boyan, Xianzhe Jiang, Yue Yu, et al. "Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation." ISME Journal, June 5, 2024. http://dx.doi.org/10.1093/ismejo/wrae098.

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Abstract Gut microbes play a crucial role in transforming primary bile acids (BAs) into secondary forms, which influence systemic metabolic processes. The rumen, a distinctive and critical microbial habitat in ruminants, boasts a diverse array of microbial species with multifaceted metabolic capabilities. There remains a gap in our understanding of BA metabolism within this ecosystem. Herein, through the analysis of 9371 metagenome-assembled genomes and 329 cultured organisms from the rumen, we identified two enzymes integral to BA metabolism: 3-dehydro-bile acid delta4,6-reductase (baiN) and the bile acid:Na + symporter family (BASS). Both in vitro and in vivo experiments were employed by introducing exogenous BAs. We revealed a transformation of BAs in rumen and found an enzyme cluster, including L-ribulose-5-phosphate 3-epimerase and dihydroorotate dehydrogenase. This cluster, distinct from the previously known BA-inducible operon responsible for 7α-dehydroxylation, suggests a previously unrecognized pathway potentially converting primary BAs into secondary BAs. Moreover, our in vivo experiments indicated that microbial BA administration in the rumen can modulate amino acid and lipid metabolism, with systemic impacts underscored by core secondary BAs and their metabolites. Our study provides insights into the rumen microbiome’s role in BA metabolism, revealing a complex microbial pathway for BA biotransformation and its subsequent effect on host metabolic pathways, including those for glucose, amino acids, and lipids. This research not only advances our understanding of microbial BA metabolism but also underscores its wider implications for metabolic regulation, offering opportunities for improving animal and potentially human health.

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Wu, Chao, Ryan Spiller, Nancy Dowe, Yannick J. Bomble, and Peter C. St. John. "Thermodynamic and Kinetic Modeling of Co-utilization of Glucose and Xylose for 2,3-BDO Production by Zymomonas mobilis." Frontiers in Bioengineering and Biotechnology 9 (July 26, 2021). http://dx.doi.org/10.3389/fbioe.2021.707749.

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Prior engineering of the ethanologen Zymomonas mobilis has enabled it to metabolize xylose and to produce 2,3-butanediol (2,3-BDO) as a dominant fermentation product. When co-fermenting with xylose, glucose is preferentially utilized, even though xylose metabolism generates ATP more efficiently during 2,3-BDO production on a BDO-mol basis. To gain a deeper understanding of Z. mobilis metabolism, we first estimated the kinetic parameters of the glucose facilitator protein of Z. mobilis by fitting a kinetic uptake model, which shows that the maximum transport capacity of glucose is seven times higher than that of xylose, and glucose is six times more affinitive to the transporter than xylose. With these estimated kinetic parameters, we further compared the thermodynamic driving force and enzyme protein cost of glucose and xylose metabolism. It is found that, although 20% more ATP can be yielded stoichiometrically during xylose utilization, glucose metabolism is thermodynamically more favorable with 6% greater cumulative Gibbs free energy change, more economical with 37% less enzyme cost required at the initial stage and sustains the advantage of the thermodynamic driving force and protein cost through the fermentation process until glucose is exhausted. Glucose-6-phosphate dehydrogenase (g6pdh), glyceraldehyde-3-phosphate dehydrogenase (gapdh) and phosphoglycerate mutase (pgm) are identified as thermodynamic bottlenecks in glucose utilization pathway, as well as two more enzymes of xylose isomerase and ribulose-5-phosphate epimerase in xylose metabolism. Acetolactate synthase is found as potential engineering target for optimized protein cost supporting unit metabolic flux. Pathway analysis was then extended to the core stoichiometric matrix of Z. mobilis metabolism. Growth was simulated by dynamic flux balance analysis and the model was validated showing good agreement with experimental data. Dynamic FBA simulations suggest that a high agitation is preferable to increase 2,3-BDO productivity while a moderate agitation will benefit the 2,3-BDO titer. Taken together, this work provides thermodynamic and kinetic insights of Z. mobilis metabolism on dual substrates, and guidance of bioengineering efforts to increase hydrocarbon fuel production.

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Rohaun, Sanjay Kumar, Ramakrishnan Sethu, and James A. Imlay. "Microbes vary strategically in their metalation of mononuclear enzymes." Proceedings of the National Academy of Sciences 121, no. 21 (2024). http://dx.doi.org/10.1073/pnas.2401738121.

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Studies have determined that nonredox enzymes that are cofactored with Fe(II) are the most oxidant-sensitive targets inside Escherichia coli . These enzymes use Fe(II) cofactors to bind and activate substrates. Because of their solvent exposure, the metal can be accessed and oxidized by reactive oxygen species, thereby inactivating the enzyme. Because these enzymes participate in key physiological processes, the consequences of stress can be severe. Accordingly, when E. coli senses elevated levels of H 2 O 2 , it induces both a miniferritin and a manganese importer, enabling the replacement of the iron atom in these enzymes with manganese. Manganese does not react with H 2 O 2 and thereby preserves enzyme activity. In this study, we examined several diverse microbes to identify the metal that they customarily integrate into ribulose-5-phosphate 3-epimerase, a representative of this enzyme family. The anaerobe Bacteroides thetaiotaomicron , like E. coli , uses iron. In contrast, Bacillus subtilis and Lactococcus lactis use manganese, and Saccharomyces cerevisiae uses zinc. The latter organisms are therefore well suited to the oxidizing environments in which they dwell. Similar results were obtained with peptide deformylase, another essential enzyme of the mononuclear class. Strikingly, heterologous expression experiments show that it is the metal pool within the organism, rather than features of the protein itself, that determine which metal is incorporated. Further, regardless of the source organism, each enzyme exhibits highest turnover with iron and lowest turnover with zinc. We infer that the intrinsic catalytic properties of the metal cannot easily be retuned by evolution of the polypeptide.

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