1
|
Ning J, Sala M, Reina J, Kalagiri R, Hunter T, McCullough BS. Histidine Phosphorylation: Protein Kinases and Phosphatases. Int J Mol Sci 2024; 25:7975. [PMID: 39063217 PMCID: PMC11277029 DOI: 10.3390/ijms25147975] [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: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Phosphohistidine (pHis) is a reversible protein post-translational modification (PTM) that is currently poorly understood. The P-N bond in pHis is heat and acid-sensitive, making it more challenging to study than the canonical phosphoamino acids pSer, pThr, and pTyr. As advancements in the development of tools to study pHis have been made, the roles of pHis in cells are slowly being revealed. To date, a handful of enzymes responsible for controlling this modification have been identified, including the histidine kinases NME1 and NME2, as well as the phosphohistidine phosphatases PHPT1, LHPP, and PGAM5. These tools have also identified the substrates of these enzymes, granting new insights into previously unknown regulatory mechanisms. Here, we discuss the cellular function of pHis and how it is regulated on known pHis-containing proteins, as well as cellular mechanisms that regulate the activity of the pHis kinases and phosphatases themselves. We further discuss the role of the pHis kinases and phosphatases as potential tumor promoters or suppressors. Finally, we give an overview of various tools and methods currently used to study pHis biology. Given their breadth of functions, unraveling the role of pHis in mammalian systems promises radical new insights into existing and unexplored areas of cell biology.
Collapse
Affiliation(s)
- Jia Ning
- Correspondence: (J.N.); (B.S.M.)
| | | | | | | | | | - Brandon S. McCullough
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (M.S.); (J.R.); (R.K.); (T.H.)
| |
Collapse
|
2
|
Brenner M, Zink C, Witzinger L, Keller A, Hadamek K, Bothe S, Neuenschwander M, Villmann C, von Kries JP, Schindelin H, Jeanclos E, Gohla A. 7,8-Dihydroxyflavone is a direct inhibitor of human and murine pyridoxal phosphatase. eLife 2024; 13:RP93094. [PMID: 38856179 PMCID: PMC11164532 DOI: 10.7554/elife.93094] [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] [Indexed: 06/11/2024] Open
Abstract
Vitamin B6 deficiency has been linked to cognitive impairment in human brain disorders for decades. Still, the molecular mechanisms linking vitamin B6 to these pathologies remain poorly understood, and whether vitamin B6 supplementation improves cognition is unclear as well. Pyridoxal 5'-phosphate phosphatase (PDXP), an enzyme that controls levels of pyridoxal 5'-phosphate (PLP), the co-enzymatically active form of vitamin B6, may represent an alternative therapeutic entry point into vitamin B6-associated pathologies. However, pharmacological PDXP inhibitors to test this concept are lacking. We now identify a PDXP and age-dependent decline of PLP levels in the murine hippocampus that provides a rationale for the development of PDXP inhibitors. Using a combination of small-molecule screening, protein crystallography, and biolayer interferometry, we discover, visualize, and analyze 7,8-dihydroxyflavone (7,8-DHF) as a direct and potent PDXP inhibitor. 7,8-DHF binds and reversibly inhibits PDXP with low micromolar affinity and sub-micromolar potency. In mouse hippocampal neurons, 7,8-DHF increases PLP in a PDXP-dependent manner. These findings validate PDXP as a druggable target. Of note, 7,8-DHF is a well-studied molecule in brain disorder models, although its mechanism of action is actively debated. Our discovery of 7,8-DHF as a PDXP inhibitor offers novel mechanistic insights into the controversy surrounding 7,8-DHF-mediated effects in the brain.
Collapse
Affiliation(s)
- Marian Brenner
- Institute of Pharmacology and Toxicology, University of WürzburgWürzburgGermany
| | - Christoph Zink
- Institute of Pharmacology and Toxicology, University of WürzburgWürzburgGermany
| | - Linda Witzinger
- Institute of Pharmacology and Toxicology, University of WürzburgWürzburgGermany
| | - Angelika Keller
- Institute of Pharmacology and Toxicology, University of WürzburgWürzburgGermany
| | - Kerstin Hadamek
- Institute of Pharmacology and Toxicology, University of WürzburgWürzburgGermany
| | - Sebastian Bothe
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | | | - Carmen Villmann
- Institute of Clinical Neurobiology, University Hospital, University of WürzburgWürzburgGermany
| | | | - Hermann Schindelin
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | - Elisabeth Jeanclos
- Institute of Pharmacology and Toxicology, University of WürzburgWürzburgGermany
| | - Antje Gohla
- Institute of Pharmacology and Toxicology, University of WürzburgWürzburgGermany
| |
Collapse
|
3
|
Jindal M, Chhetri A, Ludhiadch A, Singh P, Peer S, Singh J, Brar RS, Munshi A. Neuroimaging Genomics a Predictor of Major Depressive Disorder (MDD). Mol Neurobiol 2024; 61:3427-3440. [PMID: 37989980 DOI: 10.1007/s12035-023-03775-0] [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: 06/01/2023] [Accepted: 11/05/2023] [Indexed: 11/23/2023]
Abstract
Depression is a complex psychiatric disorder influenced by various genetic and environmental factors. Strong evidence has established the contribution of genetic factors in depression through twin studies and the heritability rate for depression has been reported to be 37%. Genetic studies have identified genetic variations associated with an increased risk of developing depression. Imaging genetics is an integrated approach where imaging measures are combined with genetic information to explore how specific genetic variants contribute to brain abnormalities. Neuroimaging studies allow us to examine both structural and functional abnormalities in individuals with depression. This review has been designed to study the correlation of the significant genetic variants with different regions of neural activity, connectivity, and structural alteration in the brain as detected by imaging techniques to understand the scope of biomarkers in depression. This might help in developing novel therapeutic interventions targeting specific genetic pathways or brain circuits and the underlying pathophysiology of depression based on this integrated approach can be established at length.
Collapse
Affiliation(s)
- Manav Jindal
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Bathinda, India
| | - Aakash Chhetri
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, India
| | - Abhilash Ludhiadch
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, India
| | - Paramdeep Singh
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Bathinda, India
| | - Sameer Peer
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Bathinda, India
| | - Jawahar Singh
- Department of Psychiatry, All India Institute of Medical Sciences, Bathinda, India
| | - Rahatdeep Singh Brar
- Department of Diagnostic and Interventional Radiology, Homi Bhabha Cancer Hospital & Research Center, Mohali, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, India.
| |
Collapse
|
4
|
Reina J, Vallmajo-Martin Q, Ning J, Michi AN, Yeung K, Wahl GM, Hunter T. LHPP expression in triple-negative breast cancer promotes tumor growth and metastasis by modulating the tumor microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590151. [PMID: 38712081 PMCID: PMC11071390 DOI: 10.1101/2024.04.19.590151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive and metastatic form of breast cancer that lacks an effective targeted therapy. To identify new therapeutic targets, we investigated the phosphohistidine phosphatase, LHPP, which has been implicated in the development of several types of cancer. However, the full significance of LHPP in cancer progression remains unclear due to our limited understanding of its molecular mechanism. We found that levels of the LHPP phosphohistidine phosphatase were significantly increased in human breast cancer patients compared to normal adjacent tissues, with the highest levels in the TNBC subtype. When LHPP was knocked out in the MDA-MB-231 human TNBC cell line, cell proliferation, wound healing capacity, and invasion were significantly reduced. However, LHPP knockout in TNBC cells did not affect the phosphohistidine protein levels. Interestingly, LHPP knockout in MDA-MB-231 cells delayed tumor growth and reduced metastasis when orthotopically transplanted into mouse mammary glands. To investigate LHPP's role in breast cancer progression, we used next-generation sequencing and proximity-labeling proteomics, and found that LHPP regulates gene expression in chemokine-mediated signaling and actin cytoskeleton organization. Depletion of LHPP reduced the presence of tumor-infiltrating macrophages in mouse xenografts. Our results uncover a new tumor promoter role for LHPP phosphohistidine phosphatase in TNBC and suggest that targeting LHPP phosphatase could be a potential therapeutic strategy for TNBC.
Collapse
Affiliation(s)
- Jeffrey Reina
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Jia Ning
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Aubrey N Michi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kay Yeung
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| |
Collapse
|
5
|
Slane EG, Tambrini SJ, Cummings BS. Therapeutic potential of lipin inhibitors for the treatment of cancer. Biochem Pharmacol 2024; 222:116106. [PMID: 38442792 DOI: 10.1016/j.bcp.2024.116106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/28/2024] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
Lipins are phosphatidic acid phosphatases (PAP) that catalyze the conversion of phosphatidic acid (PA) to diacylglycerol (DAG). Three lipin isoforms have been identified: lipin-1, -2 and -3. In addition to their PAP activity, lipin-1 and -2 act as transcriptional coactivators and corepressors. Lipins have been intensely studied for their role in regulation of lipid metabolism and adipogenesis; however, lipins are hypothesized to mediate several pathologies, such as those involving metabolic diseases, neuropathy and even cognitive impairment. Recently, an emerging role for lipins have been proposed in cancer. The study of lipins in cancer has been hampered by lack of inhibitors that have selectivity for lipins, that differentiate between lipin family members, or that are suitable for in vivo studies. Such inhibitors have the potential to be extremely useful as both molecular tools and therapeutics. This review describes the expression and function of lipins in various tissues and their roles in several diseases, but with an emphasis on their possible role in cancer. The mechanisms by which lipins mediate cancer cell growth are discussed and the potential usefulness of selective lipin inhibitors is hypothesized. Finally, recent studies reporting the crystallization of lipin-1 are discussed to facilitate rational design of novel lipin inhibitors.
Collapse
Affiliation(s)
- Elizabeth G Slane
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Samantha J Tambrini
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Brian S Cummings
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| |
Collapse
|
6
|
Zhuang L, Gao W, Chen Y, Fang W, Lo H, Dai X, Zhang J, Chen W, Ye Q, Chen X, Zhang J. LHPP in Glutamatergic Neurons of the Ventral Hippocampus Mediates Depression-like Behavior by Dephosphorylating CaMKIIα and ERK. Biol Psychiatry 2024; 95:389-402. [PMID: 37678540 DOI: 10.1016/j.biopsych.2023.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/09/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND LHPP was recently shown to be a risk gene for major depressive disorder. LHPP has been proven to dephosphorylate the residues of histidine, serine, threonine, and tyrosine. However, much remains unknown about how LHPP contributes to depression. METHODS In the current study, we addressed this issue by integrating approaches of genetics, molecular biology, behavioral testing, and electrophysiology. RESULTS We found that levels of LHPP were upregulated in glutamatergic neurons of the ventral hippocampus in mice that displayed stress-induced depression-like behaviors. Knockout of LHPP in glutamatergic neurons of the brain improved the spontaneous activity of LHPPflox/flox·CaMKIIαCre+ (conditional knockout) mice. Adeno-associated virus-mediated LHPP knockdown in the ventral hippocampus enhanced resistance against chronic social defeat stress in mice. Manipulations of LHPP levels impacted the density of dendritic spines and excitability of CA1 pyramidal neurons by mediating the expressions of BDNF (brain-derived neurotrophic factor) and PSD95 via the modulation of the dephosphorylation of CaMKIIα and ERK. Notably, compared with wild-type LHPP, human mutant LHPP (E56K, S57L) significantly increased the activity of the CaMKIIα/ERK-BDNF/PSD95 signaling pathway. Finally, esketamine, not fluoxetine, markedly alleviated the LHPP upregulation-induced depression-like behaviors. CONCLUSIONS These findings provide evidence that LHPP contributes to the pathogenesis of depression via threonine and serine hydrolases, thereby identifying LHPP as a potential therapeutic target in treating patients with major depressive disorder.
Collapse
Affiliation(s)
- Lvping Zhuang
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Weijie Gao
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yanbing Chen
- Institute of Neurosciences, Xiamen University Medical College, Xiamen, China
| | - Wenting Fang
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Hsuan Lo
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Xiaoman Dai
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Jie Zhang
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China; Institute of Neurosciences, Xiamen University Medical College, Xiamen, China
| | - Wanjing Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qinyong Ye
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Xiaochun Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China.
| | - Jing Zhang
- Department of Neurology, Fujian Medical University Union Hospital, Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China.
| |
Collapse
|
7
|
Yang L, Wu X, Liu S, Zhang L, Li T, Cao Y, Duan Q. Comprehensive Analysis of BrHMPs Reveals Potential Roles in Abiotic Stress Tolerance and Pollen–Stigma Interaction in Brassica rapa. Cells 2023; 12:cells12071096. [PMID: 37048168 PMCID: PMC10093364 DOI: 10.3390/cells12071096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/28/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Although HMPs have been identified in several plants, no studies to date have identified the HMPs in Brassica rapa (B. rapa). Here, we identified 85 potential HMPs in B. rapa by bioinformatic methods. The promoters of the identified genes contain many elements associated with stress responses, including response to abscisic acid, low-temperature, and methyl jasmonate. The expression levels of BrHMP14, BrHMP16, BrHMP32, BrHMP41, and BrHMP42 were upregulated under Cu2+, Cd2+, Zn2+, and Pb2+ stresses. BrHMP06, BrHMP30, and BrHMP41 were also significantly upregulated after drought treatment. The transcripts of BrHMP06 and BrHMP11 increased mostly under cold stress. After applying salt stress, the expression of BrHMP02, BrHMP16, and BrHMP78 was induced. We observed increased BrHMP36 expression during the self-incompatibility (SI) response and decreased expression in the compatible pollination (CP) response during pollen–stigma interactions. These changes in expression suggest functions for these genes in HMPs include participating in heavy metal transport, detoxification, and response to abiotic stresses, with the potential for functions in sexual reproduction. We found potential co-functional partners of these key players by protein–protein interaction (PPI) analysis and found that some of the predicted protein partners are known to be involved in corresponding stress responses. Finally, phosphorylation investigation revealed many phosphorylation sites in BrHMPs, suggesting post-translational modification may occur during the BrHMP-mediated stress response. This comprehensive analysis provides important clues for the study of the molecular mechanisms of BrHMP genes in B. rapa, especially for abiotic stress and pollen–stigma interactions.
Collapse
Affiliation(s)
- Lin Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Xiaoyu Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Shangjia Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Lina Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Ting Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Yunyun Cao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Qiaohong Duan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| |
Collapse
|
8
|
Lin D, Li L, Chen WB, Chen J, Ren D, Zheng ZH, Zhao C, Zhong Y, Luo B, Jing H, Chen P, Zou S, Lai X, Zhou T, Ding N, Li L, Pan BX, Fei E. LHPP, a risk factor for major depressive disorder, regulates stress-induced depression-like behaviors through its histidine phosphatase activity. Mol Psychiatry 2023; 28:908-918. [PMID: 36460727 DOI: 10.1038/s41380-022-01893-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Histidine phosphorylation (pHis), occurring on the histidine of substrate proteins, is a hidden phosphoproteome that is poorly characterized in mammals. LHPP (phospholysine phosphohistidine inorganic pyrophosphate phosphatase) is one of the histidine phosphatases and its encoding gene was recently identified as a susceptibility gene for major depressive disorder (MDD). However, little is known about how LHPP or pHis contributes to depression. Here, by using integrative approaches of genetics, behavior and electrophysiology, we observed that LHPP in the medial prefrontal cortex (mPFC) was essential in preventing stress-induced depression-like behaviors. While genetic deletion of LHPP per se failed to affect the mice's depression-like behaviors, it markedly augmented the behaviors upon chronic social defeat stress (CSDS). This augmentation could be recapitulated by the local deletion of LHPP in mPFC. By contrast, overexpressing LHPP in mPFC increased the mice's resilience against CSDS, suggesting a critical role of mPFC LHPP in stress-induced depression. We further found that LHPP deficiency increased the levels of histidine kinases (NME1/2) and global pHis in the cortex, and decreased glutamatergic transmission in mPFC upon CSDS. NME1/2 served as substrates of LHPP, with the Aspartic acid 17 (D17), Threonine 54 (T54), or D214 residue within LHPP being critical for its phosphatase activity. Finally, reintroducing LHPP, but not LHPP phosphatase-dead mutants, into the mPFC of LHPP-deficient mice reversed their behavioral and synaptic deficits upon CSDS. Together, these results demonstrate a critical role of LHPP in regulating stress-related depression and provide novel insight into the pathogenesis of MDD.
Collapse
Affiliation(s)
- Dong Lin
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Luhui Li
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Wen-Bing Chen
- Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Jiang Chen
- Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Dongyan Ren
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zhi-Heng Zheng
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Changqin Zhao
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yanzi Zhong
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Bin Luo
- Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Hongyang Jing
- Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Peng Chen
- Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Suqi Zou
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xinsheng Lai
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.,Institute of Life Science, Nanchang University, Nanchang, 330031, China
| | - Tian Zhou
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Ning Ding
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Lei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Bing-Xing Pan
- School of Life Sciences, Nanchang University, Nanchang, 330031, China. .,Institute of Life Science, Nanchang University, Nanchang, 330031, China.
| | - Erkang Fei
- School of Life Sciences, Nanchang University, Nanchang, 330031, China. .,Institute of Life Science, Nanchang University, Nanchang, 330031, China.
| |
Collapse
|
9
|
Johansson M, Steffen A, Lewinski M, Kobi N, Staiger D. HDF1, a novel flowering time regulator identified in a mutant suppressing sensitivity to red light reduced 1 early flowering. Sci Rep 2023; 13:1404. [PMID: 36697433 PMCID: PMC9876914 DOI: 10.1038/s41598-023-28049-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Arabidopsis SENSITIVITY TO RED LIGHT REDUCED 1 (SRR1) delays the transition from vegetative to reproductive development in noninductive conditions. A second-site suppressor screen for novel genes that overcome early flowering of srr1-1 identified a range of suppressor of srr1-1 mutants flowering later than srr1-1 in short photoperiods. Here, we focus on mutants flowering with leaf numbers intermediate between srr1-1 and Col. Ssm67 overcomes srr1-1 early flowering independently of day-length and ambient temperature. Full-genome sequencing and linkage mapping identified a causative SNP in a gene encoding a Haloacid dehalogenase superfamily protein, named HAD-FAMILY REGULATOR OF DEVELOPMENT AND FLOWERING 1 (HDF1). Both, ssm67 and hdf1-1 show increased levels of FLC, indicating that HDF1 is a novel regulator of this floral repressor. HDF1 regulates flowering largely independent of SRR1, as the effect is visible in srr1-1 and in Col, but full activity on FLC may require SRR1. Furthermore, srr1-1 has a delayed leaf initiation rate that is dependent on HDF1, suggesting that SRR1 and HDF1 act together in leaf initiation. Another mutant flowering intermediate between srr1-1 and wt, ssm15, was identified as a new allele of ARABIDOPSIS SUMO PROTEASE 1, previously implicated in the regulation of FLC stability.
Collapse
Affiliation(s)
- Mikael Johansson
- RNA Biology and Molecular Physiology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany.
| | - Alexander Steffen
- RNA Biology and Molecular Physiology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Martin Lewinski
- RNA Biology and Molecular Physiology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Natalie Kobi
- RNA Biology and Molecular Physiology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany.
| |
Collapse
|
10
|
Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [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: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
Collapse
Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
| |
Collapse
|
11
|
Glycolytic flux control by drugging phosphoglycolate phosphatase. Nat Commun 2022; 13:6845. [PMID: 36369173 PMCID: PMC9652372 DOI: 10.1038/s41467-022-34228-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting the intrinsic metabolism of immune or tumor cells is a therapeutic strategy in autoimmunity, chronic inflammation or cancer. Metabolite repair enzymes may represent an alternative target class for selective metabolic inhibition, but pharmacological tools to test this concept are needed. Here, we demonstrate that phosphoglycolate phosphatase (PGP), a prototypical metabolite repair enzyme in glycolysis, is a pharmacologically actionable target. Using a combination of small molecule screening, protein crystallography, molecular dynamics simulations and NMR metabolomics, we discover and analyze a compound (CP1) that inhibits PGP with high selectivity and submicromolar potency. CP1 locks the phosphatase in a catalytically inactive conformation, dampens glycolytic flux, and phenocopies effects of cellular PGP-deficiency. This study provides key insights into effective and precise PGP targeting, at the same time validating an allosteric approach to control glycolysis that could advance discoveries of innovative therapeutic candidates.
Collapse
|
12
|
Hunter T. A journey from phosphotyrosine to phosphohistidine and beyond. Mol Cell 2022; 82:2190-2200. [PMID: 35654043 DOI: 10.1016/j.molcel.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/22/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
Protein phosphorylation is a reversible post-translational modification. Nine of the 20 natural amino acids in proteins can be phosphorylated, but most of what we know about the roles of protein phosphorylation has come from studies of serine, threonine, and tyrosine phosphorylation. Much less is understood about the phosphorylation of histidine, lysine, arginine, cysteine, aspartate, and glutamate, so-called non-canonical phosphorylations. Phosphohistidine (pHis) was discovered 60 years ago as a mitochondrial enzyme intermediate; since then, evidence for the existence of histidine kinases and phosphohistidine phosphatases has emerged, together with examples where protein function is regulated by reversible histidine phosphorylation. pHis is chemically unstable and has thus been challenging to study. However, the recent development of tools for studying pHis has accelerated our understanding of the multifaceted functions of histidine phosphorylation, revealing a large number of proteins that are phosphorylated on histidine and implicating pHis in a wide range of cellular processes.
Collapse
Affiliation(s)
- Tony Hunter
- Molecular Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| |
Collapse
|
13
|
Sledzieski S, Singh R, Cowen L, Berger B. D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Syst 2021; 12:969-982.e6. [PMID: 34536380 PMCID: PMC8586911 DOI: 10.1016/j.cels.2021.08.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/01/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022]
Abstract
We combine advances in neural language modeling and structurally motivated design to develop D-SCRIPT, an interpretable and generalizable deep-learning model, which predicts interaction between two proteins using only their sequence and maintains high accuracy with limited training data and across species. We show that a D-SCRIPT model trained on 38,345 human PPIs enables significantly improved functional characterization of fly proteins compared with the state-of-the-art approach. Evaluating the same D-SCRIPT model on protein complexes with known 3D structure, we find that the inter-protein contact map output by D-SCRIPT has significant overlap with the ground truth. We apply D-SCRIPT to screen for PPIs in cow (Bos taurus) at a genome-wide scale and focusing on rumen physiology, identify functional gene modules related to metabolism and immune response. The predicted interactions can then be leveraged for function prediction at scale, addressing the genome-to-phenome challenge, especially in species where little data are available.
Collapse
Affiliation(s)
- Samuel Sledzieski
- Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rohit Singh
- Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, MA 02155, USA.
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
14
|
The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins. Biochem J 2021; 478:3575-3596. [PMID: 34624072 DOI: 10.1042/bcj20210533] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 01/12/2023]
Abstract
Histidine phosphorylation is an important and ubiquitous post-translational modification. Histidine undergoes phosphorylation on either of the nitrogens in its imidazole side chain, giving rise to 1- and 3- phosphohistidine (pHis) isomers, each having a phosphoramidate linkage that is labile at high temperatures and low pH, in contrast with stable phosphomonoester protein modifications. While all organisms routinely use pHis as an enzyme intermediate, prokaryotes, lower eukaryotes and plants also use it for signal transduction. However, research to uncover additional roles for pHis in higher eukaryotes is still at a nascent stage. Since the discovery of pHis in 1962, progress in this field has been relatively slow, in part due to a lack of the tools and techniques necessary to study this labile modification. However, in the past ten years the development of phosphoproteomic techniques to detect phosphohistidine (pHis), and methods to synthesize stable pHis analogues, which enabled the development of anti-phosphohistidine (pHis) antibodies, have accelerated our understanding. Recent studies that employed anti-pHis antibodies and other advanced techniques have contributed to a rapid expansion in our knowledge of histidine phosphorylation. In this review, we examine the varied roles of pHis-containing proteins from a chemical and structural perspective, and present an overview of recent developments in pHis proteomics and antibody development.
Collapse
|
15
|
Szabó K, Miskei M, Farkas I, Dombrádi V. The phosphatome of opportunistic pathogen Candida species. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
16
|
Relationship of MDR1 gene polymorphism and P-glycoprotein expression in Chinese refractory lupus nephritis. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AbstractTo evaluate the association of multidrug resistance 1 (MDR1) polymorphism and the expression of P-glycoprotein (Pgp) in Chinese refractory lupus nephritis (LN) patients. Polymerase chain reaction-direct sequencing was used to analyze MDR1 polymorphism. The genotype distribution of MDR1 polymorphism in 132 SLE (systemic lupus erythematosus) patients was evaluated. ELISA was used to measure the expression of Pgp. Relationship among Pgp expression, MDR1 polymorphism, SLEDAI (SLE disease activity index), and kidney pathological score was analyzed by using One-way ANOVA and Pearson linear correlation. The frequency distribution of the MDR1 gene was consistent with the Hardy-Weinberg equilibrium. Compared with CT and CC, patients with T/T homozygote in MDR1 C3435T had significantly increased Pgp expression in the refractory group (p < 0.05). Additionally, SLEDAI score was positively correlated with Pgp expression (r = 0.481, p < 0.05). Also, Pgp expression was positively correlated with renal pathological activity index (r = 0.76, p < 0.05). MDR1 C3435T polymorphism is significantly associated with Pgp expression in patients with refractory LN. Pgp expression is closely related to SLEDAI and renal pathological score. Thus, Pgp may be useful in evaluation of the prognosis of patients with refractory LN.
Collapse
|
17
|
Possik E, Al-Mass A, Peyot ML, Ahmad R, Al-Mulla F, Madiraju SRM, Prentki M. New Mammalian Glycerol-3-Phosphate Phosphatase: Role in β-Cell, Liver and Adipocyte Metabolism. Front Endocrinol (Lausanne) 2021; 12:706607. [PMID: 34326816 PMCID: PMC8313997 DOI: 10.3389/fendo.2021.706607] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022] Open
Abstract
Cardiometabolic diseases, including type 2 diabetes, obesity and non-alcoholic fatty liver disease, have enormous impact on modern societies worldwide. Excess nutritional burden and nutri-stress together with sedentary lifestyles lead to these diseases. Deranged glucose, fat, and energy metabolism is at the center of nutri-stress, and glycolysis-derived glycerol-3-phosphate (Gro3P) is at the crossroads of these metabolic pathways. Cellular levels of Gro3P can be controlled by its synthesis, utilization or hydrolysis. The belief that mammalian cells do not possess an enzyme that hydrolyzes Gro3P, as in lower organisms and plants, is challenged by our recent work showing the presence of a Gro3P phosphatase (G3PP) in mammalian cells. A previously described phosphoglycolate phosphatase (PGP) in mammalian cells, with no established physiological function, has been shown to actually function as G3PP, under physiological conditions, particularly at elevated glucose levels. In the present review, we summarize evidence that supports the view that G3PP plays an important role in the regulation of gluconeogenesis and fat storage in hepatocytes, glucose stimulated insulin secretion and nutri-stress in β-cells, and lipogenesis in adipocytes. We provide a balanced perspective on the pathophysiological significance of G3PP in mammals with specific reference to cardiometabolic diseases.
Collapse
Affiliation(s)
- Elite Possik
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
| | - Anfal Al-Mass
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Marie-Line Peyot
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
| | - Rasheed Ahmad
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Fahd Al-Mulla
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - S. R. Murthy Madiraju
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
- *Correspondence: Marc Prentki, ; S. R. Murthy Madiraju,
| | - Marc Prentki
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
- *Correspondence: Marc Prentki, ; S. R. Murthy Madiraju,
| |
Collapse
|
18
|
Ahn S, Jung H, Kee JM. Quest for the Crypto-phosphoproteome. Chembiochem 2020; 22:319-325. [PMID: 33094900 DOI: 10.1002/cbic.202000583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/14/2020] [Indexed: 11/05/2022]
Abstract
Protein phosphorylation is one of the most studied post-translational modifications (PTMs). Despite the remarkable advances in phosphoproteomics, a chemically less-stable subset of the phosphosites, which we call the crypto-phosphoproteome, has remained underexplored due to technological challenges. In this Viewpoint, we briefly summarize the current understanding of these elusive protein phosphorylations and identify the missing pieces for future studies.
Collapse
Affiliation(s)
- Seungmin Ahn
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Hoyoung Jung
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Jung-Min Kee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| |
Collapse
|
19
|
Hauser A, Hwang S, Sun H, Hackenberger CPR. Combining free energy calculations with tailored enzyme activity assays to elucidate substrate binding of a phospho-lysine phosphatase. Chem Sci 2020; 11:12655-12661. [PMID: 34094459 PMCID: PMC8163145 DOI: 10.1039/d0sc03930f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022] Open
Abstract
Studying enzymes that are involved in the regulation of dynamic post-translational modifications (PTMs) is of key importance in proteomics research. Such investigations can be particularly challenging when the modification itself is intrinsically labile. In this article, we elucidate the enzymatic activity of Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase (LHPP) towards different O- and N-phosphorylated peptides by a combined experimental and computational approach. LHPP has been previously described to hydrolyze the phosphoramidate bonds in different small molecule substrates, including phosphorylated lysine (pLys). Taking the instability of the phosphoramidate bond into account, we conducted a carefully adjusted enzymatic assay with various pLys pentapeptides to confirm enzymatic phosphatase activity with LHPP. Molecular docking was employed to explore possible binding poses of the substrates in complex with the enzyme. Molecular dynamics based free energy calculations, which are unique in their accuracy and solid theoretical basis, were further applied to predict relative binding affinity of different substrates. Comparison of simulations with experiments clearly suggested a distinct binding motif of pLys peptides as well as a very narrow promiscuity of LHPP. We believe this integrated approach can be widely adopted to study the structure and interaction of poorly characterized enzyme-substrate complexes, in particular with synthetically challenging or labile substrates.
Collapse
Affiliation(s)
- Anett Hauser
- Department of Chemical Biology II, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin Germany
- Institute for Chemistry, Humboldt-Universität zu Berlin Berlin Germany
| | - Songhwan Hwang
- Group of Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin Germany
| | - Han Sun
- Group of Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin Germany
| | - Christian P R Hackenberger
- Department of Chemical Biology II, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin Germany
- Institute for Chemistry, Humboldt-Universität zu Berlin Berlin Germany
| |
Collapse
|
20
|
Adam K, Ning J, Reina J, Hunter T. NME/NM23/NDPK and Histidine Phosphorylation. Int J Mol Sci 2020; 21:E5848. [PMID: 32823988 PMCID: PMC7461546 DOI: 10.3390/ijms21165848] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022] Open
Abstract
The NME (Non-metastatic) family members, also known as NDPKs (nucleoside diphosphate kinases), were originally identified and studied for their nucleoside diphosphate kinase activities. This family of kinases is extremely well conserved through evolution, being found in prokaryotes and eukaryotes, but also diverges enough to create a range of complexity, with homologous members having distinct functions in cells. In addition to nucleoside diphosphate kinase activity, some family members are reported to possess protein-histidine kinase activity, which, because of the lability of phosphohistidine, has been difficult to study due to the experimental challenges and lack of molecular tools. However, over the past few years, new methods to investigate this unstable modification and histidine kinase activity have been reported and scientific interest in this area is growing rapidly. This review presents a global overview of our current knowledge of the NME family and histidine phosphorylation, highlighting the underappreciated protein-histidine kinase activity of NME family members, specifically in human cells. In parallel, information about the structural and functional aspects of the NME family, and the knowns and unknowns of histidine kinase involvement in cell signaling are summarized.
Collapse
Affiliation(s)
| | | | | | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (K.A.); (J.N.); (J.R.)
| |
Collapse
|
21
|
Jeanclos E, Knobloch G, Hoffmann A, Fedorchenko O, Odersky A, Lamprecht AK, Schindelin H, Gohla A. Ca 2+ functions as a molecular switch that controls the mutually exclusive complex formation of pyridoxal phosphatase with CIB1 or calmodulin. FEBS Lett 2020; 594:2099-2115. [PMID: 32324254 DOI: 10.1002/1873-3468.13795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 11/09/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) is an essential cofactor for neurotransmitter metabolism. Pyridoxal phosphatase (PDXP) deficiency in mice increases PLP and γ-aminobutyric acid levels in the brain, yet how PDXP is regulated is unclear. Here, we identify the Ca2+ - and integrin-binding protein 1 (CIB1) as a PDXP interactor by yeast two-hybrid screening and find a calmodulin (CaM)-binding motif that overlaps with the PDXP-CIB1 interaction site. Pulldown and crosslinking assays with purified proteins demonstrate that PDXP directly binds to CIB1 or CaM. CIB1 or CaM does not alter PDXP phosphatase activity. However, elevated Ca2+ concentrations promote CaM binding and, thereby, diminish CIB1 binding to PDXP, as both interactors bind in a mutually exclusive way. Hence, the PDXP-CIB1 complex may functionally differ from the PDXP-Ca2+ -CaM complex.
Collapse
Affiliation(s)
- Elisabeth Jeanclos
- Institute of Pharmacology and Toxicology, University of Würzburg, Germany
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Germany
- Leibniz Institute for Analytical Sciences ISAS, Dortmund, Germany
| | - Gunnar Knobloch
- Institute of Pharmacology and Toxicology, University of Würzburg, Germany
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Germany
| | - Axel Hoffmann
- Institute of Pharmacology and Toxicology, University of Würzburg, Germany
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Germany
- Institute of Biochemistry and Molecular Biology II, Heinrich Heine University Düsseldorf, Germany
| | - Oleg Fedorchenko
- Institute of Biochemistry and Molecular Biology II, Heinrich Heine University Düsseldorf, Germany
| | - Andrea Odersky
- Institute of Biochemistry and Molecular Biology II, Heinrich Heine University Düsseldorf, Germany
| | - Anna-Karina Lamprecht
- Institute of Pharmacology and Toxicology, University of Würzburg, Germany
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Germany
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Germany
| | - Antje Gohla
- Institute of Pharmacology and Toxicology, University of Würzburg, Germany
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Germany
- Institute of Biochemistry and Molecular Biology II, Heinrich Heine University Düsseldorf, Germany
| |
Collapse
|
22
|
Much More Than a Scaffold: Cytoskeletal Proteins in Neurological Disorders. Cells 2020; 9:cells9020358. [PMID: 32033020 PMCID: PMC7072452 DOI: 10.3390/cells9020358] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/08/2023] Open
Abstract
Recent observations related to the structure of the cytoskeleton in neurons and novel cytoskeletal abnormalities involved in the pathophysiology of some neurological diseases are changing our view on the function of the cytoskeletal proteins in the nervous system. These efforts allow a better understanding of the molecular mechanisms underlying neurological diseases and allow us to see beyond our current knowledge for the development of new treatments. The neuronal cytoskeleton can be described as an organelle formed by the three-dimensional lattice of the three main families of filaments: actin filaments, microtubules, and neurofilaments. This organelle organizes well-defined structures within neurons (cell bodies and axons), which allow their proper development and function through life. Here, we will provide an overview of both the basic and novel concepts related to those cytoskeletal proteins, which are emerging as potential targets in the study of the pathophysiological mechanisms underlying neurological disorders.
Collapse
|
23
|
Biochemical and Molecular Characterization of PvNTD2, a Nucleotidase Highly Expressed in Nodules from Phaseolus vulgaris. PLANTS 2020; 9:plants9020171. [PMID: 32024086 PMCID: PMC7076459 DOI: 10.3390/plants9020171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022]
Abstract
Nucleotides are molecules of great importance in plant physiology. In addition to being elementary units of the genetic material, nucleotides are involved in bio-energetic processes, play a role as cofactors, and are also components of secondary metabolites and the hormone cytokinin. The common bean (Phaseolus vulgaris) is a legume that transports the nitrogen fixed in nodules as ureides, compounds synthetized from purine nucleotides. The first step in this pathway is the removal of the 5’-phosphate group by a phosphatase. In this study, a gene that codes for a putative nucleotidase (PvNTD2) has been identified in P. vulgaris. The predicted peptide contains the conserved domains for haloacid dehalogenase-like hydrolase superfamily. The protein has been overexpressed in Escherichia coli, and the purified protein showed molybdate-resistant phosphatase activity with nucleoside monophosphates as substrates, confirming that the identified gene codes for a nucleotidase. The optimum pH for the activity was 7–7.5. The recombinant enzyme did not show special affinity for any particular nucleotide, although the behaviour with AMP was different from that with the other nucleotides. The activity was inhibited by adenosine, and a regulatory role for this nucleoside was proposed. The expression pattern of PvNTD2 shows that it is ubiquitously expressed in all the tissues analysed, with higher expression in nodules of adult plants. The expression was maintained during leaf ontogeny, and it was induced during seedling development. Unlike PvNTD1, another NTD previously described in common bean, the high expression of PvNTD2 was maintained during nodule development, and its possible role in this organ is discussed.
Collapse
|