Biochemical properties and crystal structure of isocitrate lyase from Bacillus cereus ATCC 14579

Lee, Seul Hoo; Ki, Dongwoo; Kim, Sang Woo; Kim, Il Kwon; Kim, Kyungjin

doi:10.1016/j.bbrc.2020.09.136

Cited by 3 publications

(1 citation statement)

References 17 publications

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“…Oilseeds convert fats into carbohydrates through the glyoxylic acid cycle and other processes during germination ( Faraoni et al., 2019 ). ICL is one of the key enzymes of the glyoxylate cycle ( Lee et al., 2020 ). Its activity in safflower seeds is inhibited as aging time increases, although it still has a certain activity at C6.…”

Section: Discussionmentioning

confidence: 99%

Comparative changes in sugars and lipids show evidence of a critical node for regeneration in safflower seeds during aging

Zhou

Chen

et al. 2022

Front. Plant Sci.

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During seed aging, there is a critical node (CN) where the population viability drops sharply. Exploring the specific locations of the CN in different species of plants is crucial for understanding the biological storage properties of seeds and refining seed life span management. Safflower, a bulk oil crop that relies on seeds for propagation, has a short seed life. However, at present, its biological characteristics during storage are not clear, especially the changes in metabolic capability and cell structures. Such knowledge is needed to improve the management of safflower seed life span and effective preservation in gene banks. Here, the seed survival curve of oilseed safflower under the controlled deterioration conditions of 60% relative humidity and 50°C was detected. The seed population showed an inverted S shape for the fall in germination. In the first 12 days of aging, germination remained above 86%. Prior to the CN at approximately day 10 (C10), when viability was in the “plateau” interval, seed vigor reduced at the same imbibition time point. Further analysis of the changes in sugar concentration found that the sucrose content decreased slowly with aging and the content of raffinose and two monosaccharides decreased abruptly at C10. Differentially metabolized lipids, namely lysophospholipids [lyso-phosphatidylcholine (LPC) and lyso-phosphatidylethanolamines (LPE)] and PMeOH, increased at day 3 of aging (C3). Fatty acid content increased by C6, and the content of phospholipids [phosphatidylcholines (PC), phosphatidylethanolamines (PE), and phosphatidylinositols (PI) and glycolipids [digalactosyl diacylglycerol, monogalactosyl diacylglycerol, and sulphoquinovosyl diglycerides (SQDG)] decreased significantly from C10. In addition, the activities of raffinose hydrolase alpha-galactosidase and the glyoxylate key enzyme isocitrate lyase decreased with seed aging. Confocal microscopy and transmission electron microscopy revealed shrinkage of the seed plasma membrane at C10 and the later fragmentation. Seedling phenotypic indicators and 2,3,5-triphenyltetrazolium chloride activity assays also verified that there were significant changes in seeds quality at the CN. In summary, the time point C10 is a CN during seed population aging. Before the CN, sugar and lipid metabolism, especially fatty acid metabolism into sugar, can make up for the energy consumed by aging. After this point, the seeds were irreversibly damaged, and their viability was greatly and rapidly reduced as the cell structure became increasingly destroyed.

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Section: Discussionmentioning

confidence: 99%

Comparative changes in sugars and lipids show evidence of a critical node for regeneration in safflower seeds during aging

Zhou

Chen

et al. 2022

Front. Plant Sci.

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Crystal Structure and Molecular Mechanism of Isocitrate Lyase from Chloroflexus aurantiacus

Lee,

Park,

Kim

2024

J. Agric. Food Chem.

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Chloroflexus aurantiacus is a green, nonsulfur bacterium that employs the 3-hydroxypropionate cycle to grow, using carbon dioxide/bicarbonate as its primary carbon source. Like most bacteria, it possesses the glyoxylate cycle, facilitated by malate synthase and isocitrate lyase (ICL), allowing a "tricarboxylic acid cycle" bypass. C. aurantiacus also harbors ICL, an enzyme that catalyzes reversible isocitrate cleavage into glyoxylate and succinate. This study presents the crystal structures of C. aurantiacusderived ICL (CaICL), in its Mg 2+ -bound and Mn 2+ and isocitrate-bound forms, elucidating its substrate-binding mechanism and catalytic loop dynamics. CaICL forms a homotetramer and interacts with isocitrate via critical active-site residues, revealing its catalytic mechanism. The stabilization of the catalytic loop and adjacent terminal regions upon isocitrate binding underscores its functional significance. These findings advance our understanding regarding ICL enzymes, offering a basis for future investigations into their biological roles and potential applications.

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Characterization of a salt-resistant isocitrate lyase gene from mangrove wetland using shotgun metagenomic sequencing

Zhang

et al. 2023

Letters in Applied Microbiology

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Isocitrate lyase, as the key enzyme in the glyoxylate metabolic pathway, plays an important role in metabolic adaptation to environmental changes. In this study, metagenomic DNA from the soil and water microorganism collected from the Dongzhai Harbor Mangroves (DHM) reserve, in Haikou City, China, was high-throughput sequenced using an Illumina HiSeq 4000 platform. The icl121 gene, encoding an isocitrate lyase with the highly conserved catalytic pattern IENQVSDEKQCGHQD was identified. Then, this gene was subcloned into the pET-30a vector and overexpressed in Escherichia coli BL21 (DE3) cells. The maximum enzymatic activity of the recombinant ICL121 protein is 9.47 × 102 U/mg occurring at pH 7.5 and 37 °C. Furthermore, as a metalo-enzyme, ICL121 can utilize the appropriate concentrations of Mg2+, Mn2+, and Na+ ion as cofactors to exhibit high enzymatic activity. In particular, the novel metagenomic-derived icl121 gene displayed distinct salt tolerance (NaCl) and might be useful for generating salt-tolerant crops in the future.

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Biochemical properties and crystal structure of isocitrate lyase from Bacillus cereus ATCC 14579

Cited by 3 publications

References 17 publications

Comparative changes in sugars and lipids show evidence of a critical node for regeneration in safflower seeds during aging

Comparative changes in sugars and lipids show evidence of a critical node for regeneration in safflower seeds during aging

Crystal Structure and Molecular Mechanism of Isocitrate Lyase from Chloroflexus aurantiacus

Characterization of a salt-resistant isocitrate lyase gene from mangrove wetland using shotgun metagenomic sequencing

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