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Selected Papers from the 13th International NME Conference: NME/NDPK/AWD 2023
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Selected Papers from the 13th International NME Conference: NME/NDPK/AWD 2023

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 4583

Special Issue Editors

Prof. Dr. Chris M. Bunce

E-Mail Website
Guest Editor
School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
Interests: haematological cancers; tumour microenvironment; NME/NDPK protein family; inflammasome
Prof. Dr. Uwe Schlattner

E-Mail Website
Guest Editor
Laboratory of Fundamental and Applied Bioenergetics, University Grenoble Alpes, 38185 Grenoble, France
Interests: energy homeostasis; mitochondrial signaling; AMP-activated protein kinase; NME/NDPK protein family
Special Issues, Collections and Topics in MDPI journals
Dr. Farhat Latif Khanim

E-Mail Website
Guest Editor
Institute of Clinical Sciences, Medical School, University of Birmingham, Birmingham B15 2TT, UK
Interests: NME/NDPK protein family; leukaemias and lymphomas; tumour immune microenvironment; drug repurposing

Special Issue Information

Dear Colleagues,

The nucleoside diphosphate kinase (NME, AWD) gene/protein family encompasses a highly complex family of proteins that are evolutionarily conserved from bacteria to humans. The kinase function of NME proteins regulates the conversion of nucleoside diphosphates to nucleoside triphosphates, impacting many functions including energy regulation and signalling pathways. Many members of the NME gene/protein family have acquired important additional functions that are crucial in bioenergetics, cell signalling, and cancer and its metastasis or development, and act not only on nucleotides but also on interacting proteins, membrane lipids or DNA in different cellular compartments. This Special Issue of IJMS will address the entire diversity of current NME research and allow for first-hand insight into recent progress made in the field.

Prof. Dr. Chris M. Bunce
Prof. Dr. Uwe Schlattner
Dr. Farhat Latif Khanim
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • NDPK
  • NME
  • AWD
  • cancer
  • metastasis
  • development
  • bioenergetics
  • cell signalling

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Related Special Issue

Published Papers (4 papers)

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Research

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19 pages, 4525 KiB  
Article
Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes
by Rezan Amjadi, Sebastiaan Werten, Santosh Kumar Lomada, Clara Baldin, Klaus Scheffzek, Theresia Dunzendorfer-Matt and Thomas Wieland
Int. J. Mol. Sci. 2024, 25(18), 9768; https://doi.org/10.3390/ijms25189768 - 10 Sep 2024
Viewed by 652
Abstract
Nucleoside diphosphate kinases (NDPKs) are encoded by nme genes and exist in various isoforms. Based on interactions with other proteins, they are involved in signal transduction, development and pathological processes such as tumorigenesis, metastasis and heart failure. In this study, we report a [...] Read more.
Nucleoside diphosphate kinases (NDPKs) are encoded by nme genes and exist in various isoforms. Based on interactions with other proteins, they are involved in signal transduction, development and pathological processes such as tumorigenesis, metastasis and heart failure. In this study, we report a 1.25 Å resolution structure of human homohexameric NDPK-C bound to ADP and describe the yet unknown complexes formed with GDP, UDP and cAMP, all obtained at a high resolution via X-ray crystallography. Each nucleotide represents a distinct group of mono- or diphosphate purine or pyrimidine bases. We analyzed different NDPK-C nucleotide complexes in the presence and absence of Mg2+ and explain how this ion plays an essential role in NDPKs’ phosphotransferase activity. By analyzing a nucleotide-depleted NDPK-C structure, we detected conformational changes upon substrate binding and identify flexible regions in the substrate binding site. A comparison of NDPK-C with other human isoforms revealed a strong similarity in the overall composition with regard to the 3D structure, but significant differences in the charge and hydrophobicity of the isoforms’ surfaces. This may play a role in isoform-specific NDPK interactions with ligands and/or important complex partners like other NDPK isoforms, as well as monomeric and heterotrimeric G proteins. Considering the recently discovered role of NDPK-C in different pathologies, these high-resolution structures thus might provide a basis for interaction studies with other proteins or small ligands, like activators or inhibitors. Full article
(This article belongs to the Special Issue Selected Papers from the 13th International NME Conference: NME/NDPK/AWD 2023)
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15 pages, 2792 KiB  
Article
Mitochondrial NME6 Influences Basic Cellular Processes in Tumor Cells In Vitro
by Bastien Proust, Anđela Horvat, Ana Tadijan, Ignacija Vlašić and Maja Herak Bosnar
Int. J. Mol. Sci. 2024, 25(17), 9580; https://doi.org/10.3390/ijms25179580 - 4 Sep 2024
Viewed by 725
Abstract
NME6 belongs to the family of nucleoside diphosphate kinase enzymes, whose major role is to transfer the terminal phosphate from NTPs, mostly ATP, to other (d)NDPs via a high-energy intermediate. Beside this basic enzymatic activity, the family, comprising 10 genes/proteins in humans, executes [...] Read more.
NME6 belongs to the family of nucleoside diphosphate kinase enzymes, whose major role is to transfer the terminal phosphate from NTPs, mostly ATP, to other (d)NDPs via a high-energy intermediate. Beside this basic enzymatic activity, the family, comprising 10 genes/proteins in humans, executes a number of diverse biochemical/biological functions in the cell. A few previous studies have reported that NME6 resides in the mitochondria and influences oxidative phosphorylation while interacting with RCC1L, a GTPase involved in mitochondrial ribosome assembly and translation. Considering the multifunctional role of NME family members, the goal of the present study was to assess the influence of the overexpression or silencing of NME6 on fundamental cellular events of MDA-MB-231T metastatic breast cancer cells. Using flow cytometry, Western blotting, and a wound-healing assay, we demonstrated that the overexpression of NME6 reduces cell migration and alters the expression of EMT (epithelial–mesenchymal transition) markers. In addition, NME6 overexpression influences cell cycle distribution exclusively upon DNA damage and impacts the MAPK/ERK signaling pathway, while it has no effect on apoptosis. To conclude, our results demonstrate that NME6 is involved in different cellular processes, providing a solid basis for future, more precise investigations of its role. Full article
(This article belongs to the Special Issue Selected Papers from the 13th International NME Conference: NME/NDPK/AWD 2023)
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Review

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41 pages, 1964 KiB  
Review
Histidine Phosphorylation: Protein Kinases and Phosphatases
by Jia Ning, Margaux Sala, Jeffrey Reina, Rajasree Kalagiri, Tony Hunter and Brandon S. McCullough
Int. J. Mol. Sci. 2024, 25(14), 7975; https://doi.org/10.3390/ijms25147975 - 21 Jul 2024
Cited by 1 | Viewed by 1850
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Selected Papers from the 13th International NME Conference: NME/NDPK/AWD 2023)
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9 pages, 1165 KiB  
Review
Nucleoside Diphosphate Kinases Are ATP-Regulated Carriers of Short-Chain Acyl-CoAs
by Domenico Iuso, Julie Guilliaumet, Uwe Schlattner and Saadi Khochbin
Int. J. Mol. Sci. 2024, 25(14), 7528; https://doi.org/10.3390/ijms25147528 - 9 Jul 2024
Cited by 1 | Viewed by 825
Abstract
Nucleoside diphosphate (NDP) kinases 1 and 2 (NME1/2) are well-characterized enzymes known for their NDP kinase activity. Recently, these enzymes have been shown by independent studies to bind coenzyme A (CoA) or acyl-CoA. These findings suggest a hitherto unknown role for NME1/2 in [...] Read more.
Nucleoside diphosphate (NDP) kinases 1 and 2 (NME1/2) are well-characterized enzymes known for their NDP kinase activity. Recently, these enzymes have been shown by independent studies to bind coenzyme A (CoA) or acyl-CoA. These findings suggest a hitherto unknown role for NME1/2 in the regulation of CoA/acyl-CoA-dependent metabolic pathways, in tight correlation with the cellular NTP/NDP ratio. Accordingly, the regulation of NME1/2 functions by CoA/acyl-CoA binding has been described, and additionally, NME1/2 have been shown to control the cellular pathways consuming acetyl-CoA, such as histone acetylation and fatty acid synthesis. NME1/2-controlled histone acetylation in turn mediates an important transcriptional response to metabolic changes, such as those induced following a high-fat diet (HFD). This review discusses the CoA/acyl-CoA-dependent NME1/2 activities and proposes that these enzymes be considered as the first identified carriers of CoA/short-chain acyl-CoAs. Full article
(This article belongs to the Special Issue Selected Papers from the 13th International NME Conference: NME/NDPK/AWD 2023)
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