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Article ; Online: PRL-1/2 phosphatases control TRPM7 magnesium-dependent function to regulate cellular bioenergetics.

Hardy, Serge / Zolotarov, Yevgen / Coleman, Jacob / Roitman, Simon / Khursheed, Hira / Aubry, Isabelle / Uetani, Noriko / Tremblay, Michel L

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 14, Page(s) e2221083120

Abstract: Phosphatases of regenerating liver (PRL-1, PRL-2, PRL-3; also known as PTP4A1, PTP4A2, PTP4A3, respectively) control intracellular magnesium levels by interacting with the CNNM magnesium transport regulators. Still, the exact mechanism governing ... ...

Abstract	Phosphatases of regenerating liver (PRL-1, PRL-2, PRL-3; also known as PTP4A1, PTP4A2, PTP4A3, respectively) control intracellular magnesium levels by interacting with the CNNM magnesium transport regulators. Still, the exact mechanism governing magnesium transport by this protein complex is not well understood. Herein, we have developed a genetically encoded intracellular magnesium-specific reporter and demonstrate that the CNNM family inhibits the function of the TRPM7 magnesium channel. We show that the small GTPase ARL15 increases CNNM3/TRPM7 protein complex formation to reduce TRPM7 activity. Conversely, PRL-2 overexpression counteracts ARL15 binding to CNNM3 and enhances the function of TRPM7 by preventing the interaction between CNNM3 and TRPM7. Moreover, while TRPM7-induced cell signaling is promoted by PRL-1/2, it is reduced when CNNM3 is overexpressed. Lowering cellular magnesium levels reduces the interaction of CNNM3 with TRPM7 in a PRL-dependent manner, whereby knockdown of PRL-1/2 restores the protein complex formation. Cotargeting of TRPM7 and PRL-1/2 alters mitochondrial function and sensitizes cells to metabolic stress induced by magnesium depletion. These findings reveal the dynamic regulation of TRPM7 function in response to PRL-1/2 levels, to coordinate magnesium transport and reprogram cellular metabolism.
MeSH term(s)	Magnesium/metabolism ; TRPM Cation Channels/genetics ; TRPM Cation Channels/metabolism ; Signal Transduction ; Energy Metabolism
Chemical Substances	Magnesium (I38ZP9992A) ; TRPM Cation Channels
Language	English
Publishing date	2023-03-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2221083120
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Article ; Online: De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.

Zolotarov, Yevgen / Strömvik, Martina

PloS one

2015 Volume 10, Issue 6, Page(s) e0129016

Abstract: Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin ... ...

Abstract	Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.
MeSH term(s)	Abscisic Acid/pharmacology ; Base Sequence ; Binding Sites ; GATA Transcription Factors/metabolism ; Gene Expression Regulation, Plant/drug effects ; Genome, Plant ; Light ; Nucleotide Motifs ; Plant Proteins/chemistry ; Plant Proteins/genetics ; Promoter Regions, Genetic ; Protein Binding ; Response Elements ; Temperature
Chemical Substances	GATA Transcription Factors ; Plant Proteins ; dehydrin proteins, plant (134711-03-8) ; Abscisic Acid (72S9A8J5GW)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0129016
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Article ; Online: De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.

Yevgen Zolotarov / Martina Strömvik

PLoS ONE, Vol 10, Iss 6, p e

2015 Volume 0129016

Abstract	Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Physiological and oncogenic roles of the PRL phosphatases.

Hardy, Serge / Kostantin, Elie / Hatzihristidis, Teri / Zolotarov, Yevgen / Uetani, Noriko / Tremblay, Michel L

The FEBS journal

2018 Volume 285, Issue 21, Page(s) 3886–3908

Abstract: The human Phosphatase of Regenerative Liver (PRL) family comprises three members (PRL-1, -2, -3; gene name PTP4A1, PTP4A2, PTP4A3) that are highly expressed in a majority of cancers. This review summarizes our current understanding of PRL biology, ... ...

Abstract	The human Phosphatase of Regenerative Liver (PRL) family comprises three members (PRL-1, -2, -3; gene name PTP4A1, PTP4A2, PTP4A3) that are highly expressed in a majority of cancers. This review summarizes our current understanding of PRL biology, including an overview of their evolutionary relationships and the regulatory mechanisms controlling their expression. We provide an updated view on our current knowledge on the PRL functions in solid tumors, hematological cancer, and normal physiology, particularly emphasizing on the use of in vivo mouse models. We also highlight a novel relationship positioning PRL as a central node controlling magnesium homeostasis through an association with the CNNM proteins, which are involved in magnesium transport.
MeSH term(s)	Cell Cycle Proteins/metabolism ; Homeostasis ; Humans ; Liver Regeneration ; Membrane Proteins/metabolism ; Neoplasm Proteins/metabolism ; Neoplasms/enzymology ; Neoplasms/pathology ; Oncogenes ; Protein Tyrosine Phosphatases/metabolism
Chemical Substances	Cell Cycle Proteins ; Membrane Proteins ; Neoplasm Proteins ; PTP4A1 protein, human (EC 3.1.3.48) ; PTP4A2 protein, human (EC 3.1.3.48) ; PTP4A3 protein, human (EC 3.1.3.48) ; Protein Tyrosine Phosphatases (EC 3.1.3.48)
Language	English
Publishing date	2018-05-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.14503
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Article ; Online: De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome.

Munusamy, Prabhakaran / Zolotarov, Yevgen / Meteignier, Louis-Valentin / Moffett, Peter / Strömvik, Martina V

Scientific reports

2017 Volume 7, Page(s) 43861

Abstract: Gene regulation at the transcriptional and translational level leads to diversity in phenotypes and function in organisms. Regulatory DNA or RNA sequence motifs adjacent to the gene coding sequence act as binding sites for proteins that in turn enable or ...

Abstract	Gene regulation at the transcriptional and translational level leads to diversity in phenotypes and function in organisms. Regulatory DNA or RNA sequence motifs adjacent to the gene coding sequence act as binding sites for proteins that in turn enable or disable expression of the gene. Whereas the known DNA and RNA binding proteins range in the thousands, only a few motifs have been examined. In this study, we have predicted putative regulatory motifs in groups of untranslated regions from genes regulated at the translational level in Arabidopsis thaliana under normal and stressed conditions. The test group of sequences was divided into random subgroups and subjected to three de novo motif finding algorithms (Seeder, Weeder and MEME). In addition to identifying sequence motifs, using an in silico tool we have predicted microRNA target sites in the 3' UTRs of the translationally regulated genes, as well as identified upstream open reading frames located in the 5' UTRs. Our bioinformatics strategy and the knowledge generated contribute to understanding gene regulation during stress, and can be applied to disease and stress resistant plant development.
MeSH term(s)	3' Untranslated Regions/genetics ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Base Sequence ; Binding Sites/genetics ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; MicroRNAs/genetics ; Nucleotide Motifs/genetics ; Open Reading Frames/genetics ; Sequence Homology, Nucleic Acid ; Stress, Physiological
Chemical Substances	3' Untranslated Regions ; Arabidopsis Proteins ; MicroRNAs
Language	English
Publishing date	2017-03-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep43861
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Article ; Online: Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria.

Raymond-Bouchard, Isabelle / Goordial, Jacqueline / Zolotarov, Yevgen / Ronholm, Jennifer / Stromvik, Martina / Bakermans, Corien / Whyte, Lyle G

FEMS microbiology ecology

2018 Volume 94, Issue 4

Abstract: Permafrost accounts for 27% of all soil ecosystems and harbors diverse microbial communities. Our understanding of microorganisms in permafrost, their activities and adaptations, remains limited. Using five subzero-growing (cryophilic) permafrost ... ...

Abstract	Permafrost accounts for 27% of all soil ecosystems and harbors diverse microbial communities. Our understanding of microorganisms in permafrost, their activities and adaptations, remains limited. Using five subzero-growing (cryophilic) permafrost bacteria, we examined features of cold adaptation through comparative genomic analyses with mesophilic relatives. The cryophiles possess genes associated with cold adaptation, including cold shock proteins, RNA helicases, and oxidative stress and carotenoid synthesis enzymes. Higher abundances of genes associated with compatible solutes were observed, important for osmoregulation in permafrost brine veins. Most cryophiles in our study have higher transposase copy numbers than mesophiles. We investigated amino acid (AA) modifications in the cryophiles favoring increased protein flexibility at cold temperatures. Although overall there were few differences with the mesophiles, we found evidence of cold adaptation, with significant differences in proline, serine, glycine and aromaticity, in several cryophiles. The use of cold/hot AA ratios of >1, used in previous studies to indicate cold adaptation, was found to be inadequate on its own. Comparing the average of all cryophiles to all mesophiles, we found that overall cryophiles had a higher ratio of cold adapted proteins for serine (more serine), and to a lesser extent, proline and acidic residues (fewer prolines/acidic residues).
MeSH term(s)	Acclimatization/genetics ; Acclimatization/physiology ; Amino Acids/analysis ; Amino Acids/genetics ; Arctic Regions ; Bacteria/enzymology ; Bacteria/genetics ; Bacteria/metabolism ; Base Sequence ; Carotenoids/biosynthesis ; Carotenoids/genetics ; Cold Shock Proteins and Peptides/genetics ; Cold Temperature ; Genome, Bacterial/genetics ; Genomics ; Microbiota/genetics ; Microbiota/physiology ; Oxidative Stress/genetics ; Permafrost/microbiology ; RNA Helicases/genetics ; Sequence Analysis, DNA ; Soil ; Soil Microbiology
Chemical Substances	Amino Acids ; Cold Shock Proteins and Peptides ; Soil ; Carotenoids (36-88-4) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2018-03-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiy023
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Article ; Online: Transcripts of soybean isoflavone 7-O-glucosyltransferase and hydroxyisoflavanone dehydratase gene homologues are at least as abundant as transcripts of their well known counterparts.

Livingstone, Julie M / Zolotarov, Yevgen / Strömvik, Martina V

Plant physiology and biochemistry : PPB

2011 Volume 49, Issue 9, Page(s) 1071–1075

Abstract: The enzymes of the isoflavonoid pathway produce isoflavones, which have multiple functions in defence and symbiosis. Recently, we identified known and novel homologues of several of these enzymes in the soybean genome sequence. In the present study, we ... ...

Abstract	The enzymes of the isoflavonoid pathway produce isoflavones, which have multiple functions in defence and symbiosis. Recently, we identified known and novel homologues of several of these enzymes in the soybean genome sequence. In the present study, we have investigated the transcript levels of the isoflavone 7-O-glucosyltransferase (GmIF7GT) and 2-hydroxyisoflavanone dehydratase (HIDH) gene homologues in soybean seedling organs (shoot tips, unifoliate leaves, unifoliate nodes, epicotyls, cotyledons, cotyledonary nodes, hypocotyls and roots) as well as flowers, seeds and whole pods using real-time reverse-transcription polymerase chain reaction (real-time RT-PCR). In addition, the transcript levels were also measured in three cell layers of the soybean pod (exocarp, mesocarp and endocarp) dissected using laser capture microdissection (LCM) at two different developmental stages. Statistical analysis has shown that the transcript level of a less known gene homologue of isoflavone 7-O-glucosyltransferase (GmIF7GT4) is significantly higher (about 11-fold) in the roots than the well known gene homologue (GmIF7GT1) and the other less known homologues. It was also shown that the transcript levels of the less known gene homologue of 2-hydroxyisoflavanone dehydratase (HIDH2) do not differ from those of the well known homologue (HIDH1).
MeSH term(s)	Gene Expression Regulation, Enzymologic/physiology ; Gene Expression Regulation, Plant/physiology ; Glucosyltransferases/biosynthesis ; Hydro-Lyases/biosynthesis ; Plant Proteins/biosynthesis ; RNA/biosynthesis ; RNA, Plant/biosynthesis ; Seedlings/enzymology ; Seedlings/genetics ; Glycine max/enzymology ; Glycine max/genetics
Chemical Substances	Plant Proteins ; RNA, Plant ; RNA (63231-63-0) ; Glucosyltransferases (EC 2.4.1.-) ; UDP-glucose-isoflavone 7-O-glucosyltransferase (EC 2.4.1.-) ; Hydro-Lyases (EC 4.2.1.-)
Language	English
Publishing date	2011-06-25
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2011.06.007
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Article: Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria

Raymond-Bouchard, Isabelle / Goordial, Jacqueline / Zolotarov, Yevgen / Ronholm, Jennifer / Stromvik, Martina / Bakermans, Corien / Whyte, Lyle G

FEMS microbiology ecology. 2018 Mar. 08, v. 94, no. 4

2018

Abstract	Permafrost accounts for 27% of all soil ecosystems and harbors diverse microbial communities. Our understanding of microorganisms in permafrost, their activities and adaptations, remains limited. Using five subzero-growing (cryophilic) permafrost bacteria, we examined features of cold adaptation through comparative genomic analyses with mesophilic relatives. The cryophiles possess genes associated with cold adaptation, including cold shock proteins, RNA helicases, and oxidative stress and carotenoid synthesis enzymes. Higher abundances of genes associated with compatible solutes were observed, important for osmoregulation in permafrost brine veins. Most cryophiles in our study have higher transposase copy numbers than mesophiles. We investigated amino acid (AA) modifications in the cryophiles favoring increased protein flexibility at cold temperatures. Although overall there were few differences with the mesophiles, we found evidence of cold adaptation, with significant differences in proline, serine, glycine and aromaticity, in several cryophiles. The use of cold/hot AA ratios of >1, used in previous studies to indicate cold adaptation, was found to be inadequate on its own. Comparing the average of all cryophiles to all mesophiles, we found that overall cryophiles had a higher ratio of cold adapted proteins for serine (more serine), and to a lesser extent, proline and acidic residues (fewer prolines/acidic residues).
Keywords	RNA helicases ; bacteria ; carotenoids ; cold ; cold shock proteins ; cold tolerance ; genes ; genomics ; glycine (amino acid) ; mesophilic microorganisms ; microbial communities ; osmoregulation ; oxidative stress ; permafrost ; proline ; proteins ; serine ; soil ecosystems ; solutes ; temperature ; transposases ; Arctic region
Language	English
Dates of publication	2018-0308
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiy023
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: ARL15 modulates magnesium homeostasis through N-glycosylation of CNNMs.

Zolotarov, Yevgen / Ma, Chao / González-Recio, Irene / Hardy, Serge / Franken, Gijs A C / Uetani, Noriko / Latta, Femke / Kostantin, Elie / Boulais, Jonathan / Thibault, Marie-Pier / Côté, Jean-François / Díaz-Moreno, Irene / Quintana, Antonio Díaz / Hoenderop, Joost G J / Martínez-Cruz, Luis Alfonso / Tremblay, Michel L / de Baaij, Jeroen H F

Cellular and molecular life sciences : CMLS

2021 Volume 78, Issue 13, Page(s) 5427–5445

Abstract: Cyclin M (CNNM1-4) proteins maintain cellular and body magnesium ( ... ...

Abstract	Cyclin M (CNNM1-4) proteins maintain cellular and body magnesium (Mg
MeSH term(s)	ADP-Ribosylation Factors/genetics ; ADP-Ribosylation Factors/metabolism ; Biological Transport ; Cyclins/genetics ; Cyclins/metabolism ; Glycosylation ; HEK293 Cells ; Homeostasis ; Humans ; Magnesium/metabolism ; Models, Molecular ; Protein Binding
Chemical Substances	CNNM3 protein, human ; Cyclins ; ADP-Ribosylation Factors (EC 3.6.5.2) ; ARL15 protein, human (EC 3.6.5.2) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2021-06-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-021-03832-8
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Article: ARL15 modulates magnesium homeostasis through N-glycosylation of CNNMs

Zolotarov, Yevgen / Ma, Chao / González-Recio, Irene / Hardy, Serge / Franken, Gijs A. C. / Uetani, Noriko / Latta, Femke / Kostantin, Elie / Boulais, Jonathan / Thibault, Marie-Pier / Côté, Jean-François / Díaz-Moreno, Irene / Quintana, Antonio Díaz / Hoenderop, Joost G. J. / Martínez-Cruz, Luis Alfonso / Tremblay, Michel L. / de Baaij, Jeroen H. F.

Cellular and molecular life sciences. 2021 July, v. 78, no. 13

2021

Abstract: Cyclin M (CNNM1-4) proteins maintain cellular and body magnesium (Mg²⁺) homeostasis. Using various biochemical approaches, we have identified members of the CNNM family as direct interacting partners of ADP-ribosylation factor-like GTPase 15 (ARL15), a ... ...

Abstract	Cyclin M (CNNM1-4) proteins maintain cellular and body magnesium (Mg²⁺) homeostasis. Using various biochemical approaches, we have identified members of the CNNM family as direct interacting partners of ADP-ribosylation factor-like GTPase 15 (ARL15), a small GTP-binding protein. ARL15 interacts with CNNMs at their carboxyl-terminal conserved cystathionine-β-synthase (CBS) domains. In silico modeling of the interaction between CNNM2 and ARL15 supports that the small GTPase specifically binds the CBS1 and CNBH domains. Immunocytochemical experiments demonstrate that CNNM2 and ARL15 co-localize in the kidney, with both proteins showing subcellular localization in the endoplasmic reticulum, Golgi apparatus and the plasma membrane. Most importantly, we found that ARL15 is required for forming complex N-glycosylation of CNNMs. Overexpression of ARL15 promotes complex N-glycosylation of CNNM3. Mg²⁺ uptake experiments with a stable isotope demonstrate that there is a significant increase of ²⁵Mg²⁺ uptake upon knockdown of ARL15 in multiple kidney cancer cell lines. Altogether, our results establish ARL15 as a novel negative regulator of Mg²⁺ transport by promoting the complex N-glycosylation of CNNMs.
Keywords	Golgi apparatus ; computer simulation ; cyclins ; endoplasmic reticulum ; glycosylation ; guanosinetriphosphatase ; homeostasis ; kidney neoplasms ; kidneys ; magnesium ; neoplasm cells ; plasma membrane ; stable isotopes
Language	English
Dates of publication	2021-07
Size	p. 5427-5445.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-021-03832-8
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