Expression and biochemical characterization of α-ketoglutarate decarboxylase from cyanobacterium Synechococcus sp. PCC7002

Lei, Guofeng; Wang, Xiaoqin; Lai, Chongde; Zhang, Wei; Xie, Congcong; Wang, Fei; Wu, Xiaoyu; Li, Zhimin

doi:10.1016/j.ijbiomac.2018.03.112

Cited by 7 publications

(13 citation statements)

References 32 publications

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“…Indeed, this is a logical interpretation. It has also been reported that in bacteria, succinate-semialdehyde dehydrogenase can also convert succinate-semialdehyde to succinate during the fission of the pyridine ring, and, moreover, the succinate-semialdehyde dehydrogenase part of the nicotine catabolic pathway is expressed in our data set. Therefore, it is reasonable to postulate that nicotine catabolism replenishes the Krebs cycle via anaplerotic reactions, not only through pyruvate carboxylase but also through alpha-ketoglutarate decarboxylase and succinate-semialdehyde dehydrogenase.…”

Section: Resultssupporting

confidence: 66%

Time-Dependent Analysis of Paenarthrobacter nicotinovorans pAO1 Nicotine-Related Proteome

et al. 2021

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Paenarthrobacter nicotinovorans is a soil Gram-positive nicotine-degrading microorganism (NDM) that harbors a 165 kb pAO1 catabolic megaplasmid. The nicotine catabolic genes on pAO1 have been sequenced, but not all the details on the regulation and interplay of this pathway with the general metabolism of the cell are available. To address this issue at the protein level, a time-based shotgun proteomics study was performed. P. nicotinovorans was grown in the presence or absence of nicotine, and the cells were harvested at three different time intervals: 7, 10, and 24 h after inoculation. The cells were lysed, separated on SDS-PAGE, and digested by in-gel digestion using trypsin, and the resulting peptide mixture was analyzed using nanoliquid chromatography tandem mass spectrometry. We found an extensive number of proteins that are both plasmidal- and chromosomal-encoded and that work together in the energetic metabolism via the Krebs cycle and nicotine pathway. These data provide insight into the adaptation of the bacterial cells to the nicotine metabolic intermediates and could serve as a basis for future attempts to genetically engineer the pAO1-encoded catabolic pathway for increased bioremediation efficiency or for the production of valuable chemicals. The mass-spectrometry-based proteomics data have been deposited to the PRIDE partner repository with the data set identifier PXD012577.

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Section: Resultssupporting

confidence: 66%

Time-Dependent Analysis of Paenarthrobacter nicotinovorans pAO1 Nicotine-Related Proteome

et al. 2021

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“…In this work, αKDH, SSADH, and THIC were highlighted so they might play a critical role. Zhang and Bryant (2011) and Lei et al (2018) investigated that αKDC and SSADH might form succinic acid via succinic semialdehyde by using cofactors of thiamine phosphate in Synechococcus sp. PCC7002.…”

Section: The Essential Role Of the Biosynthesis Of Amino Acids And Nu...mentioning

confidence: 99%

Unraveling the Role of Acetic Acid Bacteria Comparing Two Acetification Profiles From Natural Raw Materials: A Quantitative Approach in Komagataeibacter europaeus

et al. 2022

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The industrial production of vinegar is carried out by the activity of a complex microbiota of acetic acid bacteria (AAB) working, mainly, within bioreactors providing a quite specific and hard environment. The “omics” sciences can facilitate the identification and characterization analyses of these microbial communities, most of which are difficult to cultivate by traditional methods, outside their natural medium. In this work, two acetification profiles coming from the same AAB starter culture but using two natural raw materials of different alcoholic origins (fine wine and craft beer), were characterized and compared and the emphasis of this study is the effect of these raw materials. For this purpose, the composition and natural behavior of the microbiota present throughout these profiles were analyzed by metaproteomics focusing, mainly, on the quantitative protein profile of Komagataeibacter europaeus. This species provided a protein fraction significantly higher (73.5%) than the others. A submerged culture system and semi-continuous operating mode were employed for the acetification profiles and liquid chromatography with tandem mass spectrometry (LC-MS/MS) for the protein analyses. The results showed that neither of two raw materials barely modified the microbiota composition of the profiles, however, they had an effect on the protein expression changes in different biological process. A molecular strategy in which K. europaeus would prevail over other species by taking advantage of the different features offered by each raw material has been suggested. First, by assimilating the excess of inner acetic acid through the TCA cycle and supplying biosynthetic precursors to replenish the cellular material losses; second, by a previous assimilation of the excess of available glucose, mainly in the beer medium, through the glycolysis and the pentose phosphate pathway (PPP); and third, by triggering membrane mechanisms dependent on proton motive force to detoxify the cell at the final moments of acetification. This study could complement the current knowledge of these bacteria as well as to expand the use of diverse raw materials and optimize operating conditions to obtain quality vinegars.Clinical Trial Registration:[www.ClinicalTrials.gov], identifier [PXD031147].

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“…PCC6803 (StKGD encoded by sll1981 gene) and Synechococcus sp. PCC7002 (ScKGD encoded by SYNPCC7002_A2770 gene) were previously reported by our laboratory [16,17]. It was observed that the activity of ScKGD was about 500-fold higher than that of StKGD with α-KG as a substrate, although these two enzymes shared over 80% amino acids sequences identities (Figure S1 and Table S1).…”

Section: Introductionmentioning

confidence: 82%

Biochemical and Structural Insights into a Thiamine Diphosphate-Dependent α-Ketoglutarate Decarboxylase from Cyanobacterium Microcystis aeruginosa NIES-843

Li,

Hu,

Wang

et al. 2023

IJMS

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α-Ketoglutarate decarboxylase is a crucial enzyme in the tricarboxylic acid cycle of cyanobacteria, catalyzing the non-oxidative decarboxylation of α-ketoglutarate to produce succinate semialdehyde and CO2. The decarboxylation process is reliant on the cofactor of thiamine diphosphate. However, this enzyme’s biochemical and structural properties have not been well characterized. In this work, two α-ketoglutarate decarboxylases encoded by MAE_06010 and MiAbw_01735 genes from Microcystis aeruginosa NIES-843 (MaKGD) and NIES-4325 (MiKGD), respectively, were overexpressed and purified by using an Escherichia coli expression system. It was found that MaKGD exhibited 9.2-fold higher catalytic efficiency than MiKGD, which may be attributed to the absence of glutamate decarboxylase in Microcystis aeruginosa NIES-843. Further biochemical investigation of MaKGD demonstrated that it displayed optimum activity at pH 6.5–7.0 and was most activated by Mg2+. Additionally, MaKGD showed substrate specificity towards α-ketoglutarate. Structural modeling and autodocking results revealed that the active site of MaKGD contained a distinct binding pocket where α-ketoglutarate and thiamine diphosphate interacted with specific amino acid residues via hydrophobic interactions, hydrogen bonds and salt bridges. Furthermore, the mutagenesis study provided strong evidence supporting the importance of certain residues in the catalysis of MaKGD. These findings provide new insights into the structure-function relationships of α-ketoglutarate decarboxylases from cyanobacteria.

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Expression and biochemical characterization of α-ketoglutarate decarboxylase from cyanobacterium Synechococcus sp. PCC7002

Cited by 7 publications

References 32 publications

Time-Dependent Analysis of Paenarthrobacter nicotinovorans pAO1 Nicotine-Related Proteome

Time-Dependent Analysis of Paenarthrobacter nicotinovorans pAO1 Nicotine-Related Proteome

Unraveling the Role of Acetic Acid Bacteria Comparing Two Acetification Profiles From Natural Raw Materials: A Quantitative Approach in Komagataeibacter europaeus

Biochemical and Structural Insights into a Thiamine Diphosphate-Dependent α-Ketoglutarate Decarboxylase from Cyanobacterium Microcystis aeruginosa NIES-843

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