Transcriptional response of Corynebacterium glutamicum ATCC 13032 to hydrogen peroxide stress and characterization of the OxyR regulon

Milse, Johanna; Petri, Kathrin; Rückert, Christian; Kalinowski, Jörn

doi:10.1016/j.jbiotec.2014.07.452

Cited by 44 publications

(58 citation statements)

References 70 publications

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“…Genomic DNA was isolated, and libraries were prepared, as described previously (44). Libraries were sequenced on a Genome Analyzer IIx platform (Illumina, San Diego, CA, USA) by using a Single-Read Cluster Generation kit (version 4) according to the manufacturer's instructions.…”

Section: Methodsmentioning

confidence: 99%

Metabolic Engineering of an ATP-Neutral Embden-Meyerhof-Parnas Pathway in Corynebacterium glutamicum: Growth Restoration by an Adaptive Point Mutation in NADH Dehydrogenase

Reddy

Lindner

Wendisch

2015

Appl Environ Microbiol

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Corynebacterium glutamicum uses the Embden-Meyerhof-Parnas pathway of glycolysis and gains 2 mol of ATP per mol of glucose by substrate-level phosphorylation (SLP). To engineer glycolysis without net ATP formation by SLP, endogenous phosphorylating NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was replaced by nonphosphorylating NADPdependent glyceraldehyde-3-phosphate dehydrogenase (GapN) from Clostridium acetobutylicum, which irreversibly converts glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3-PG) without generating ATP. As shown recently (S. Takeno, R. Murata, R. Kobayashi, S. Mitsuhashi, and M. Ikeda, Appl Environ Microbiol 76:7154 -7160, 2010, http://dx.doi.org/10.1128/AEM.01464-10), this ATP-neutral, NADPH-generating glycolytic pathway did not allow for the growth of Corynebacterium glutamicum with glucose as the sole carbon source unless hitherto unknown suppressor mutations occurred; however, these mutations were not disclosed. In the present study, a suppressor mutation was identified, and it was shown that heterologous expression of udhA encoding soluble transhydrogenase from Escherichia coli partly restored growth, suggesting that growth was inhibited by NADPH accumulation. Moreover, genome sequence analysis of second-site suppressor mutants that were able to grow faster with glucose revealed a single point mutation in the gene of non-proton-pumping NADH:ubiquinone oxidoreductase (NDH-II) leading to the amino acid change D213G, which was shared by these suppressor mutants. Since related NDH-II enzymes accepting NADPH as the substrate possess asparagine or glutamine residues at this position, D213G, D213N, and D213Q variants of C. glutamicum NDH-II were constructed and were shown to oxidize NADPH in addition to NADH. Taking these findings together, ATP-neutral glycolysis by the replacement of endogenous NAD-dependent GAPDH with NADP-dependent GapN became possible via oxidation of NADPH formed in this pathway by mutant NADPH-accepting NDH-II D213G and thus by coupling to electron transport phosphorylation (ETP).A TP generation occurs naturally by substrate-level phosphorylation (SLP), electron transport phosphorylation (ETP), photophosphorylation, and decarboxylation phosphorylation. The Embden-Meyerhof-Parnas (EMP) pathway of glycolysis supplies ATP by SLP in the absence of terminal electron acceptors or anaerobic conditions, as well as supplying direct precursors for biomass formation (1). Bacteria and archaea possess one or more of multiple biologically feasible routes for glucose catabolism, such as the EMP pathway, the Entner-Doudoroff (ED) pathway, and the phosphoketolase pathway, which yield zero to 3 ATP molecules per glucose molecule and exist in different variants. In natural habitats, a trade-off between the rate and the yield of ATP production is observed for heterotrophic organisms; faster but less efficient ATP production may be advantageous under conditions characterized by a low abundance of growth substrates (2, 3). For example, Zymomonas mobilis ferments suga...

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Section: Methodsmentioning

confidence: 99%

Metabolic Engineering of an ATP-Neutral Embden-Meyerhof-Parnas Pathway in Corynebacterium glutamicum: Growth Restoration by an Adaptive Point Mutation in NADH Dehydrogenase

Reddy

Lindner

Wendisch

2015

Appl Environ Microbiol

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“…S4B). The proC gene encodes pyrroline carboxylate reductase, a key enzyme in the last step in proline biosynthesis, and katA encodes catalase, both of which play important roles in oxidative or osmotic stress responses (33,34). Based on these studies, NfiS likely controls nitrogenase activity at the transcriptional level through the regulation of both the RpoN/NtrC/NifA regulatory cascade and certain stress response-related genes via unknown mechanisms.…”

Section: Nfis Contributes To the Global And Positive Regulation Of Nimentioning

confidence: 99%

The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

Zhan

Yan

Deng

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Unlike most Pseudomonas, the root-associated bacterium Pseudomonas stutzeri A1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. A genome-wide search for small noncoding RNAs (ncRNAs) in P. stutzeri A1501 identified the novel P. stutzeri-specific ncRNA NfiS in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. The expression of NfiS was RNA chaperone Hfqdependent and activated by the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade. The nfiSdeficient mutant displayed reduced nitrogenase activity, as well as increased sensitivity to multiple stresses, such as osmotic and oxidative stresses. Secondary structure prediction and complementation studies confirmed that a stem-loop structure was essential for NfiS to regulate the nitrogenase gene nifK mRNA synthesis and thus nitrogenase activity. Microscale thermophoresis and physiological analysis showed that NfiS directly pairs with nifK mRNA and ultimately enhances nitrogenase activity by increasing the translation efficiency and the half-life of nifK mRNA. Our data also suggest structural and functional divergence of NfiS evolution in diazotrophic and nondiazotrophic backgrounds. It is proposed that NfiS was recruited by nifK mRNA as a novel regulator to integrate the horizontally acquired nif island into host global networks.nitrogen fixation | Pseudomonas stutzeri | regulatory ncRNA | NfiS | nifK mRNA

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“…In several bacterial species such as Neisseria, OxyRs function in a dual-control manner (both a repressor and an activator) for major H 2 O 2 scavenging proteins and an activator only for other members of their regulons; as a consequence, OxyR-deficient strains are more resistant to H 2 O 2 (10-13). More surprisingly, Corynebacteria OxyRs function primarily as a repressor for more than 20 genes, including those for ROS detoxification enzymes and iron-sequestering proteins (14)(15)(16). In general, the majority of OxyRs are homologous in sequence (30-35% in identity) and similar in structure, and thus functionally exchangeable (10-16).…”

mentioning

confidence: 99%

Defining the binding determinants of Shewanella oneidensis OxyR: Implications for the link between the contracted OxyR regulon and adaptation

Wan

Kong

Gao

2018

Journal of Biological Chemistry

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Transcriptional response of Corynebacterium glutamicum ATCC 13032 to hydrogen peroxide stress and characterization of the OxyR regulon

Cited by 44 publications

References 70 publications

Metabolic Engineering of an ATP-Neutral Embden-Meyerhof-Parnas Pathway in Corynebacterium glutamicum: Growth Restoration by an Adaptive Point Mutation in NADH Dehydrogenase

Metabolic Engineering of an ATP-Neutral Embden-Meyerhof-Parnas Pathway in Corynebacterium glutamicum: Growth Restoration by an Adaptive Point Mutation in NADH Dehydrogenase

The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

Defining the binding determinants of Shewanella oneidensis OxyR: Implications for the link between the contracted OxyR regulon and adaptation

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