1
|
Su X, Zhang L, Meng H, Wang H, Zhao J, Sun X, Song X, Zhang X, Mao L. Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO 2 fixation pathways in coastal saline soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120743. [PMID: 38626484 DOI: 10.1016/j.jenvman.2024.120743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/18/2024]
Abstract
Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.
Collapse
Affiliation(s)
- Xunya Su
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Le Zhang
- China Agricultural University, Agronomy College, Beijing, 100193, China.
| | - Hao Meng
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Han Wang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Jiaxue Zhao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xuezhen Sun
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xianliang Song
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xiaopei Zhang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Lili Mao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| |
Collapse
|
2
|
Zhang X, Xu Y, Li S, Qin Y, Zhu G, Zhang Q, Zhang Y, Guan F, Fan T, Liu H. SIRT2-mediated deacetylation of ACLY promotes the progression of oesophageal squamous cell carcinoma. J Cell Mol Med 2024; 28:e18129. [PMID: 38426936 PMCID: PMC10906381 DOI: 10.1111/jcmm.18129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 03/02/2024] Open
Abstract
ATP citrate lyase (ACLY), as a key enzyme in lipid metabolism, plays an important role in energy metabolism and lipid biosynthesis of a variety of tumours. Many studies have shown that ACLY is highly expressed in various tumours, and its pharmacological or gene inhibition significantly inhibits tumour growth and progression. However, the roles of ACLY in oesophageal squamous cell carcinoma (ESCC) remain unclear. Here, our data showed that ACLY inhibitor significantly attenuated cell proliferation, migration, invasion and lipid synthesis in different ESCC cell lines, whereas the proliferation, migration, invasion and lipid synthesis of ESCC cells were enhanced after ACLY overexpression. Furthermore, ACLY inhibitor dramatically suppressed tumour growth and lipid metabolism in ESCC cells xenografted tumour model, whereas ACLY overexpression displayed the opposite effect. Mechanistically, ACLY protein harboured acetylated modification and interacted with SIRT2 protein in ESCC cells. The SIRT2 inhibitor AGK2 significantly increased the acetylation level of ACLY protein and inhibited the proliferation and migration of ESCC cells, while overexpression of ACLY partially reversed the inhibitory effect of AGK2 on ESCC cells. Overall, these results suggest that targeting the SIRT2/ACLY signalling axis may be a potential therapeutic strategy for ESCC patients.
Collapse
Affiliation(s)
- Xueying Zhang
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yue Xu
- Department of PathologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Shenglei Li
- Department of PathologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Yue Qin
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Guangzhao Zhu
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Qing Zhang
- Translational Medicine Research CenterZhengzhou People's HospitalZhengzhouHenanChina
| | - Yanting Zhang
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Fangxia Guan
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Tianli Fan
- Department of Pharmacology, School of Basic MedicineZhengzhou UniversityZhengzhouHenanChina
| | - Hongtao Liu
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| |
Collapse
|
3
|
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R. Allosteric role of the citrate synthase homology domain of ATP citrate lyase. Nat Commun 2023; 14:2247. [PMID: 37076498 PMCID: PMC10115795 DOI: 10.1038/s41467-023-37986-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
ATP citrate lyase (ACLY) is the predominant nucleocytosolic source of acetyl-CoA and is aberrantly regulated in many diseases making it an attractive therapeutic target. Structural studies of ACLY reveal a central homotetrameric core citrate synthase homology (CSH) module flanked by acyl-CoA synthetase homology (ASH) domains, with ATP and citrate binding the ASH domain and CoA binding the ASH-CSH interface to produce acetyl-CoA and oxaloacetate products. The specific catalytic role of the CSH module and an essential D1026A residue contained within it has been a matter of debate. Here, we report biochemical and structural analysis of an ACLY-D1026A mutant demonstrating that this mutant traps a (3S)-citryl-CoA intermediate in the ASH domain in a configuration that is incompatible with the formation of acetyl-CoA, is able to convert acetyl-CoA and OAA to (3S)-citryl-CoA in the ASH domain, and can load CoA and unload acetyl-CoA in the CSH module. Together, this data support an allosteric role for the CSH module in ACLY catalysis.
Collapse
Affiliation(s)
- Xuepeng Wei
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Kollin Schultz
- Graduate Group in Biochemistry & Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hannah L Pepper
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Emily Megill
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Austin Vogt
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathaniel W Snyder
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Ronen Marmorstein
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Graduate Group in Biochemistry & Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
4
|
Jaziri E, Louis H, Gharbi C, Unimuke TO, Agwamba EC, Mathias GE, Fugita W, Nasr CB, Khedhiri L. Synthesis, X-ray crystallography, molecular electronic property investigation, and leukopoiesis activity of novel 4,6-dimethyl-1,6-dihydropyridin-2-amino nitrate hybrid material. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
5
|
Huang J, Fraser ME. The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase. Acta Crystallogr F Struct Biol Commun 2022; 78:363-370. [PMID: 36189720 PMCID: PMC9527654 DOI: 10.1107/s2053230x22008810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/04/2022] [Indexed: 11/10/2022] Open
Abstract
Succinyl-CoA synthetase (SCS) catalyzes a three-step reaction in the citric acid cycle with succinyl-phosphate proposed as a catalytic intermediate. However, there are no structural data to show the binding of succinyl-phosphate to SCS. Recently, the catalytic mechanism underlying acetyl-CoA production by ATP-citrate lyase (ACLY) has been debated. The enzyme belongs to the family of acyl-CoA synthetases (nucleoside diphosphate-forming) for which SCS is the prototype. It was postulated that the amino-terminal portion catalyzes the full reaction and the carboxy-terminal portion plays only an allosteric role. This interpretation was based on the partial loss of the catalytic activity of ACLY when Glu599 was mutated to Gln or Ala, and on the interpretation that the phospho-citryl-CoA intermediate was trapped in the 2.85 Å resolution structure from cryogenic electron microscopy (cryo-EM). To better resolve the structure of the intermediate bound to the E599Q mutant, the equivalent mutation, E105αQ, was made in human GTP-specific SCS. The structure of the E105αQ mutant shows succinyl-phosphate bound to the enzyme at 1.58 Å resolution when the mutant, after phosphorylation in solution by Mg2+-ATP, was crystallized in the presence of magnesium ions, succinate and desulfo-CoA. The E105αQ mutant is still active but has a specific activity that is 120-fold less than that of the wild-type enzyme, with apparent Michaelis constants for succinate and CoA that are 50-fold and 11-fold higher, respectively. Based on this high-resolution structure, the cryo-EM maps of the E599Q ACLY complex reported previously should have revealed the binding of citryl-phosphate and CoA and not phospho-citryl-CoA.
Collapse
Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
6
|
Verstraete K, Verschueren KHG, Dansercoer A, Savvides SN. Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase. Nat Struct Mol Biol 2021; 28:636-638. [PMID: 34294920 DOI: 10.1038/s41594-021-00624-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 06/16/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Kenneth Verstraete
- VIB-UGent Center for Inflammation Research, Ghent, Belgium. .,Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Koen H G Verschueren
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Ann Dansercoer
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Savvas N Savvides
- VIB-UGent Center for Inflammation Research, Ghent, Belgium. .,Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| |
Collapse
|
7
|
Nguyen VH, Singh N, Medina A, Usón I, Fraser ME. Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion. Protein Sci 2019; 28:1840-1849. [PMID: 31411782 DOI: 10.1002/pro.3708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 01/25/2023]
Abstract
ATP-citrate lyase (ACLY) catalyzes production of acetyl-CoA and oxaloacetate from CoA and citrate using ATP. In humans, this cytoplasmic enzyme connects energy metabolism from carbohydrates to the production of lipids. In certain bacteria, ACLY is used to fix carbon in the reductive tricarboxylic acid cycle. The carboxy(C)-terminal portion of ACLY shows sequence similarity to citrate synthase of the tricarboxylic acid cycle. To investigate the roles of residues of ACLY equivalent to active site residues of citrate synthase, these residues in ACLY from Chlorobium limicola were mutated, and the proteins were investigated using kinetics assays and biophysical techniques. To obtain the crystal structure of the C-terminal portion of ACLY, full-length C. limicola ACLY was cleaved, first non-specifically with chymotrypsin and subsequently with Tobacco Etch Virus protease. Crystals of the C-terminal portion diffracted to high resolution, providing structures that show the positions of active site residues and how ACLY tetramerizes.
Collapse
Affiliation(s)
- Vinh H Nguyen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Noreen Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Ana Medina
- Structural Biology Unit, CSIC, Barcelona, Spain
| | - Isabel Usón
- Structural Biology Unit, CSIC, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Marie E Fraser
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|