Erna Davydova

• Falnes, Pål & Davydova, Erna (2026). The Protein Histidine Methyltransferase METTL9—From Mechanism to Biological Function. Life. 16(3). doi: 10.3390/life16030445. Fulltekst i vitenarkiv
• Schroer, Lisa; Weirich, Sara; Hammerstad, Marta; Hersleth, Hans-Petter; Grønsberg, Ida Andrietta & Hagen, Lars [Vis alle 11 forfattere av denne artikkelen] (2025). Orthologues of the human protein histidine methyltransferase METTL9 display distinct substrate specificities. Journal of Biological Chemistry. ISSN 0021-9258. 301(7). doi: 10.1016/j.jbc.2025.110318. Fulltekst i vitenarkiv Vis sammendrag

  The human (Homo sapiens; Hs) methyltransferase (MTase) METTL9 is the first enzyme shown to generate 1-methylhistidine (π-methylhistidine) in proteins. METTL9 preferentially methylates an alternating histidine (HxH) motif, where “x” is a small, uncharged amino acid, and multiple substrates have been identified. Putative METTL9 orthologues are found in most eukaryotes, and we have here investigated the activity of such enzymes from several species, representing all five eukaryotic supergroups. The majority of the tested enzymes demonstrated in vitro MTase activity on the prototype HsMETTL9 substrates ARMC6 and DNAJB12. We also detected protein methylation activity of the Caenorhabditis elegans METTL9 which had previously been suggested to be a DNA MTase. However, METTL9 from the fruit fly (Drosophila melanogaster; Dm) and the picoplankton Ostreococcus tauri (Ot) displayed distinct substrate specificities, differing from each other and from that of HsMETTL9. These differences were observed when recombinant proteins and short peptides were used as METTL9 substrates. To further analyze substrate specificity, we used peptide arrays to systematically replace the “x” residue and the residues flanking the HxH motif in a substrate peptide. This revealed varying degrees of tolerance among the METTL9 orthologues (Hs > Dm > Ot) for substitutions at these positions. Our results show that the METTL9 orthologues, although requiring an HxH target site, have evolved different substrate specificities, likely due to differing biologically relevant substrates in the respective organisms. Furthermore, we solved the X-ray structure of OtMETTL9, revealing several differences from the previously published HsMETTL9 structures that may explain its distinct substrate specificity.

• Malecki, Jedrzej Mieczyslaw; Weirich, Sara; Ramirez, Manuel; Hagen, Lars; Al-Egly, Jakin Saad & Anonsen, Jan Haug [Vis alle 12 forfattere av denne artikkelen] (2025). Identification of substrates and sequence requirements for CARNMT1-mediated histidine methylation of C3H zinc fingers. Journal of Biological Chemistry. ISSN 0021-9258. 301(7). doi: 10.1016/j.jbc.2025.110335. Fulltekst i vitenarkiv Vis sammendrag

  It has recently become clear that protein histidine methylation is widespread and functionally important in many cellular processes, and human CARNMT1 was recently reported as a novel protein histidine methyltransferase (HMT). We describe our independent uncovering of CARNMT1's protein HMT activity and a comprehensive assessment of its methylation targets and substrate specificity. Using a combination of in vitro methylation of cellular extracts and protein mass spectrometry, we identified several CARNMT1 substrates that were fully methylated in cells, all of which were C3H zinc finger (ZnF) proteins. These include the previously identified U2AF1, ZC3H15, and ZC3H18 but also the unreported RBM22, PPP1R10, PRR3, and RNF113A. Using peptide arrays, we investigated CARNMT1-mediated methylation of 145 candidate sequences, encompassing all C3H ZnFs and selected non-ZnFs. We found that only ∼30% of the tested sequences were methylated, with C3H ZnFs constituting the vast majority of the strongly methylated ones, most of which are also methylated in cells. This establishes peptide methylation as a good predictor of in vivo methylation. To investigate the specificity of CARNMT1, we systematically substituted His-proximal residues in four different substrate peptides. This generated four rather different sequence preference profiles, which were still quite restrictive for each peptide, indicating that substrate sequence recognition by CARNMT1 is context-dependent and that sequence-based prediction of additional CARNMT1 substrates may be challenging. We also identified several homologous methylation events in Caenorhabditis elegans and showed that they could be introduced by nematode CARNMT in vitro. Thus, CARNMT1 is an evolutionarily conserved protein HMT with a complex mode of substrate recognition.

• Prydz, Kristian; Simm, Roger; Davydova, Erna & Åsheim, Hans-Christian (2025). Ephrin-B1 regulates cell surface residency of heparan sulfate proteoglycans (HSPGs) and complexes with the HSPG CD44V3-10 and fibroblast growth factor receptors. Glycobiology. ISSN 0959-6658. 35(6). doi: 10.1093/glycob/cwaf020. Fulltekst i vitenarkiv Vis sammendrag

  The ephrin family of membrane proteins mediate intracellular signalling as ligands of transmembrane Eph tyrosine kinase receptors during cell–cell interactions. Ephrin/Eph signalling regulates processes like cell migration and angiogenesis and is of particular importance during embryonic development. Ephrins-A3 and -B3 can also bind to cell surface-associated and soluble heparan sulfate proteoglycans (HSPGs) that also play important roles during early development. Here we show that ephrins-B1, -B2, and -B3 all can bind in cis to cell surface HSPGs, while only ephrin-B1 interacts with cell surface HSPGs in a way that retards HSPG endocytosis. Expressing ephrin-B1 in HEK293T cells, using polyethyleneimine (PEI) as transfection agent, increased cell surface levels of HSPGs which were detected by an anti-heparan sulfate (HS) antibody or by ephrin-B3-Fc binding. Ephrin-B1 in the plasma membrane seemed to retard PEI-induced HSPG internalisation and degradation. Binding of HSPGs by ephrin-B1 was observed for the human, mouse, xenopus, and zebrafish homologs, and did not require the cytoplasmic tail of ephrin-B1 that contains tyrosines shown to be involved in intracellular signalling. Furthermore, ephrin-B1 could bind the HSPG variant of CD44 (CD44V3–10), a complex that could further associate with fibroblast growth factor receptors (1 and 4) after co-expression with one of these receptors. In summary, our data indicate that ephrin-B1 can regulate cellular HSPG turnover and is able to form complexes of potential biological importance with CD44V3–10 and fibroblast growth factor receptors.

• Falnes, Pål; Malecki, Jedrzej Mieczyslaw; Gonzalez-Molina, Maria del Carmen Herrera; Bengtsen, Mads & Davydova, Erna (2023). Human seven-β-strand (METTL) methyltransferases - conquering the universe of protein lysine methylation. Journal of Biological Chemistry. ISSN 0021-9258. 299(6), s. 1–15. doi: 10.1016/j.jbc.2023.104661. Fulltekst i vitenarkiv Vis sammendrag

  Lysine methylation is an abundant posttranslational modification, which has been most intensively studied in the context of histone proteins, where it represents an important epigenetic mark. Lysine methylation of histone proteins is primarily catalyzed by SET-domain methyltransferases (MTases). However, it has recently become evident that also another MTase family, the so-called seven-β-strand (7BS) MTases, often denoted METTLs (methyltransferase-like), contains several lysine (K)-specific MTases (KMTs). These enzymes catalyze the attachment of up to three methyl groups to lysine residues in specific substrate proteins, using S-adenosylmethionine (AdoMet) as methyl donor. About a decade ago, only a single human 7BS KMT was known, namely the histone-specific DOT1L, but 15 additional 7BS KMTs have now been discovered and characterized. These KMTs typically target a single nonhistone substrate that, in most cases, belongs to one of the following three protein groups: components of the cellular protein synthesis machinery, mitochondrial proteins, and molecular chaperones. This article provides an extensive overview and discussion of the human 7BS KMTs and their biochemical and biological roles.

• Malecki, Jedrzej Mieczyslaw; Davydova, Erna & Falnes, Pål (2022). Protein methylation in mitochondria. Journal of Biological Chemistry. ISSN 0021-9258. 298(4). doi: 10.1016/j.jbc.2022.101791. Fulltekst i vitenarkiv Vis sammendrag

  Many proteins are modified by posttranslational methylation, introduced by a number of methyltransferases (MTases). Protein methylation plays important roles in modulating protein function and thus in optimizing and regulating cellular and physiological processes. Research has mainly focused on nuclear and cytosolic protein methylation, but it has been known for many years that also mitochondrial proteins are methylated. During the last decade, significant progress has been made on identifying the MTases responsible for mitochondrial protein methylation and addressing its functional significance. In particular, several novel human MTases have been uncovered that methylate lysine, arginine, histidine, and glutamine residues in various mitochondrial substrates. Several of these substrates are key components of the bioenergetics machinery, e.g., respiratory Complex I, citrate synthase, and the ATP synthase. In the present review, we report the status of the field of mitochondrial protein methylation, with a particular emphasis on recently discovered human MTases. We also discuss evolutionary aspects and functional significance of mitochondrial protein methylation and present an outlook for this emergent research field.

• Dalum, Alf Seljenes; Kraus, Aurora; Khan, Shanawaz; Davydova, Erna; Rigaudeau, Dimitri & Bjørgen, Håvard [Vis alle 13 forfattere av denne artikkelen] (2021). High-Resolution, 3D Imaging of the Zebrafish Gill-Associated Lymphoid Tissue (GIALT) Reveals a Novel Lymphoid Structure, the Amphibranchial Lymphoid Tissue. Frontiers in Immunology. 12. doi: 10.3389/fimmu.2021.769901. Fulltekst i vitenarkiv Vis sammendrag

  The zebrafish is extensively used as an animal model for human and fish diseases. However, our understanding of the structural organization of its immune system remains incomplete, especially the mucosa-associated lymphoid tissues (MALTs). Teleost MALTs are commonly perceived as diffuse and scattered populations of immune cells throughout the mucosa. Yet, structured MALTs have been recently discovered in Atlantic salmon (Salmo salar L.), including the interbranchial lymphoid tissue (ILT) in the gills. The existence of the ILT was only recently identified in zebrafish and other fish species, highlighting the need for in-depth characterizations of the gill-associated lymphoid tissue (GIALT) in teleosts. Here, using 3-D high-resolution microscopy, we analyze the GIALT of adult zebrafish with an immuno-histology approach that reveals the organization of lymphoid tissues via the labeling of T/NK cells with an antibody directed to a highly conserved epitope on the kinase ZAP70. We show that the GIALT in zebrafish is distributed over at least five distinct sub-regions, an organization found in all pairs of gill arches. The GIALT is diffuse in the pharyngeal part of the gill arch, the interbranchial septum and the filaments/ lamellae, and structured in two sub-regions: the ILT, and a newly discovered lymphoid structure located along each side of the gill arch, which we named the Amphibranchial Lymphoid Tissue (ALT). Based on RAG2 expression, neither the ILT nor the ALT constitute additional thymi. The ALT shares several features with the ILT such as presence of abundant lymphoid cells and myeloid cells embedded in a network of reticulated epithelial cells. Further, the ILT and the ALT are also a site for T/NK cell proliferation. Both ILT and ALT show structural changes after infection with Spring Viraemia of Carp Virus (SVCV). Together, these data suggest that ALT and ILT play an active role in immune responses. Comparative studies show that whereas the ILT seems absent in most neoteleosts (“Percomorphs”), the ALT is widely present in cyprinids, salmonids and neoteleosts, suggesting that it constitutes a conserved tissue involved in the protection of teleosts via the gills.

• Malecki, Jedrzej Mieczyslaw; O'Donohue, Marie-Francoise; Kim, Yeji; Jakobsson, Magnus; Gessa, Luca & Pinto, Rita [Vis alle 14 forfattere av denne artikkelen] (2021). Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function. Nucleic Acids Research (NAR). ISSN 0305-1048. 49(6), s. 3185–3203. doi: 10.1093/nar/gkab088. Fulltekst i vitenarkiv Vis sammendrag

  Abstract Protein methylation occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional nuclear localization signal and accumulates in nucleoli. Recombinant METTL18 methylated a single protein in nuclear extracts and in isolated ribosomes from METTL18 knockout (KO) cells, identified as 60S ribosomal protein L3 (RPL3). We also performed an RPL3 interactomics screen and identified METTL18 as the most significantly enriched MTase. We found that His-245 in RPL3 carries a 3-methylhistidine (3MH; τ-methylhistidine) modification, which was absent in METTL18 KO cells. In addition, both recombinant and endogenous METTL18 were found to be automethylated at His-154, thus further corroborating METTL18 as a histidine-specific MTase. Finally, METTL18 KO cells displayed altered pre-rRNA processing, decreased polysome formation and codon-specific changes in mRNA translation, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. In conclusion, we have here established METTL18 as the second human histidine-specific protein MTase, and demonstrated its functional relevance.

• Davydova, Erna; Shimazu, Tadahiro; Schuhmacher, Maren Kirstin; Jakobsson, Magnus E.; Willemen, Hanneke L.D.M. & Liu, Tongri [Vis alle 28 forfattere av denne artikkelen] (2021). The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes. Nature Communications. 12, s. 1–14. doi: 10.1038/s41467-020-20670-7. Fulltekst i vitenarkiv Vis sammendrag

  Abstract Post-translational methylation plays a crucial role in regulating and optimizing protein function. Protein histidine methylation, occurring as the two isomers 1- and 3-methylhistidine (1MH and 3MH), was first reported five decades ago, but remains largely unexplored. Here we report that METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mouse and human proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where “x” is preferably a small amino acid, allowing METTL9 to methylate a number of HxH-containing proteins, including the immunomodulatory protein S100A9 and the NDUFB3 subunit of mitochondrial respiratory Complex I. Notably, METTL9-mediated methylation enhances respiration via Complex I, and the presence of 1MH in an HxH-containing peptide reduced its zinc binding affinity. Our results establish METTL9-mediated 1MH as a pervasive protein modification, thus setting the stage for further functional studies on protein histidine methylation.

• Kabashi, Saranda; Vindenes, Vigdis; Bryun, Eugeniy Alekseevich; Koshkina, Evgenia A.; Nadezhdin, Alexey V. & Tetenova, Elena J. [Vis alle 16 forfattere av denne artikkelen] (2019). Harmful alcohol use among acutely ill hospitalized medical patients in Oslo and Moscow: A cross-sectional study. Drug and Alcohol Dependence. ISSN 0376-8716. 204:107588, s. 1–9. doi: 10.1016/j.drugalcdep.2019.107588. Fulltekst i vitenarkiv Vis sammendrag

  Background The aim was to estimate the prevalence of harmful alcohol use in relation to socio-demographic characteristics among acutely ill medical patients, and examine identification measures of alcohol use, including the alcohol biomarker phosphatidylethanol 16:0/18:1 (PEth). Methods A cross-sectional study, lasting one year at one hospital in Oslo, Norway and one in Moscow, Russia recruiting acute medically ill patients (≥ 18 years), able to give informed consent. Self-reported data on socio-demographics, mental distress (Symptom Check List-5), alcohol use (Alcohol Use Disorder Identification Test-4 (AUDIT-4) and alcohol consumption past 24 h were collected. PEth and alcohol concentration were measured in whole blood. Results Of 5883 participating patients, 19.2% in Moscow and 21.1% in Oslo were harmful alcohol users, measured by AUDIT-4, while the prevalence of PEth-positive patients was lower: 11.4% in Oslo, 14.3% in Moscow. Men in Moscow were more likely to be harmful users by AUDIT-4 and PEth compared to men in Oslo, except of those being ≥ 71 years. Women in Oslo were more likely to be harmful users compared to those in Moscow by AUDIT-4, but not by PEth for those aged < 61 years. Conclusions The prevalence of harmful alcohol use was high at both study sites. The prevalence of harmful alcohol use was lower when assessed by PEth compared to AUDIT-4. Thus, self-reporting was the most sensitive measure in revealing harmful alcohol use among all groups except for women in Moscow. Hence, screening and identification with objective biomarkers and self-reporting might be a method for early intervention.

• Jakobsson, Magnus; Malecki, Jedrzej Mieczyslaw; Halabelian, Levon; Nilges, Benedikt S.; Pinto, Rita & Kudithipudi, Srikanth [Vis alle 14 forfattere av denne artikkelen] (2018). The dual methyltransferase METTL13 targets N terminus and Lys55 of eEF1A and modulates codon-specific translation rates. Nature Communications. 9:3411, s. 1–15. doi: 10.1038/s41467-018-05646-y. Fulltekst i vitenarkiv Vis sammendrag

  Eukaryotic elongation factor 1 alpha (eEF1A) delivers aminoacyl-tRNA to the ribosome and thereby plays a key role in protein synthesis. Human eEF1A is subject to extensive post-translational methylation, but several of the responsible enzymes remain unknown. Using a wide range of experimental approaches, we here show that human methyltransferase (MTase)-like protein 13 (METTL13) contains two distinct MTase domains targeting the N terminus and Lys55 of eEF1A, respectively. Our biochemical and structural analyses provide detailed mechanistic insights into recognition of the eEF1A N terminus by METTL13. Moreover, through ribosome profiling, we demonstrate that loss of METTL13 function alters translation dynamics and results in changed translation rates of specific codons. In summary, we here unravel the function of a human MTase, showing that it methylates eEF1A and modulates mRNA translation in a codon-specific manner.

• Aileni, Vinay Kumar; Davydova, Erna; Moen, Anders & Falnes, Pål (2017). A System for Enzymatic Lysine Methylation in a Desired Sequence Context. ACS Omega. 2(2), s. 462–469. doi: 10.1021/acsomega.6b00486. Fulltekst i vitenarkiv Vis sammendrag

  A number of lysine-specific methyltransferases (KMTs) are responsible for the post-translational modification of cellular proteins on lysine residues. Most KMTs typically recognize specific motifs in unstructured, short peptide sequences. However, we have recently discovered a novel KMT that appeared to have a more relaxed sequence specificity, namely, valosin-containing protein (VCP)-KMT, which trimethylates Lys-315 in the molecular chaperone VCP. On the basis of this, here, we explored the possibility of using the VCP-KMT/VCP system to obtain specific lysine methylation of desired sequences grafted onto a VCP-derived scaffold. We generated VCP-derived proteins in which three amino acid residues on each side of Lys-315 had been replaced by various sequences representing lysine methylation sites in histone H3. We found that all of these chimeric proteins were subject to efficient VCP-KMT-mediated methylation in vitro, and methylation was also observed in mammalian cells. Thus, we here describe a versatile system for introducing lysine methylation into a desired peptide sequence, and the approach should be readily expandable for generating combinatorial libraries of methylated sequences.

• Falnes, Pål; Jakobsson, Magnus; Davydova, Erna; Ho, Angela Yeuan Yen & Malecki, Jedrzej Mieczyslaw (2016). Protein lysine methylation by seven-β-strand methyltransferases. Biochemical Journal. ISSN 0264-6021. 473(14), s. 1995–2009. doi: 10.1042/BCJ20160117. Fulltekst i vitenarkiv
• Malecki, Jedrzej Mieczyslaw; Dahl, Helge-Andre; Moen, Anders; Davydova, Erna & Falnes, Pål (2016). The METTL20 homologue from agrobacterium tumefaciens is a dual specificity protein-lysine methyltransferase that targets ribosomal protein L7/L12 and the β subunit of electron transfer flavoprotein (ETFβ). Journal of Biological Chemistry. ISSN 0021-9258. 291(18), s. 9581–9595. doi: 10.1074/jbc.M115.709261. Fulltekst i vitenarkiv
• Jakobsson, Magnus; Davydova, Erna; Malecki, Jedrzej Mieczyslaw; Moen, Anders & Falnes, Pål (2015). Saccharomyces cerevisiae eukaryotic elongation factor 1A (eEF1A) is methylated at Lys-390 by a METTL21-like methyltransferase. PLOS ONE. 10(6). doi: 10.1371/journal.pone.0131426. Fulltekst i vitenarkiv Vis sammendrag

  The human methyltransferases (MTases) METTL21A and VCP-KMT (METTL21D) were recently shown to methylate single lysine residues in Hsp70 proteins and in VCP, respectively. The yet uncharacterized MTase encoded by the YNL024C gene in Saccharomyces cerevisiae shows high sequence similarity to METTL21A and VCP-KMT, as well as to their uncharacterized paralogues METTL21B and METTL21C. Despite being most similar to METTL21A, the Ynl024c protein does not methylate yeast Hsp70 proteins, which were found to be unmethylated on the relevant lysine residue. Eukaryotic translation elongation factor eEF1A in yeast has been reported to contain four methylated lysine residues (Lys30, Lys79, Lys318 and Lys390), and we here show that the YNL024C gene is required for methylation of eEF1A at Lys390, the only of these methylations for which the responsible MTase has not yet been identified. Lys390 was found in a partially monomethylated state in wild-type yeast cells but was exclusively unmethylated in a ynl024cΔ strain, and over-expression of Ynl024c caused a dramatic increase in Lys390 methylation, with trimethylation becoming the predominant state. Our results demonstrate that Ynl024c is the enzyme responsible for methylation of eEF1A at Lys390, and in accordance with prior naming of similar enzymes, we suggest that Ynl024c is renamed to Efm6 (Elongation factor MTase 6).

• Zdzalik, Daria; Vågbø, Cathrine Broberg; Kirpekar, F; Davydova, Erna; Puścian, Alicja & Maciejewska, Agnieszka M. [Vis alle 11 forfattere av denne artikkelen] (2014). Protozoan ALKBH8 Oxygenases Display both DNA Repair and tRNA Modification Activities. PLOS ONE. 9(6). doi: 10.1371/journal.pone.0098729. Fulltekst i vitenarkiv Vis sammendrag

  The ALKBH family of Fe(II) and 2-oxoglutarate dependent oxygenases comprises enzymes that display sequence homology to AlkB from E. coli, a DNA repair enzyme that uses an oxidative mechanism to dealkylate methyl and etheno adducts on the nucleobases. Humans have nine different ALKBH proteins, ALKBH1–8 and FTO. Mammalian and plant ALKBH8 are tRNA hydroxylases targeting 5-methoxycarbonylmethyl-modified uridine (mcm5U) at the wobble position of tRNAGly(UCC). In contrast, the genomes of some bacteria encode a protein with strong sequence homology to ALKBH8, and robust DNA repair activity was previously demonstrated for one such protein. To further explore this apparent functional duality of the ALKBH8 proteins, we have here enzymatically characterized a panel of such proteins, originating from bacteria, protozoa and mimivirus. All the enzymes showed DNA repair activity in vitro, but, interestingly, two protozoan ALKBH8s also catalyzed wobble uridine modification of tRNA, thus displaying a dual in vitro activity. Also, we found the modification status of tRNAGly(UCC) to be unaltered in an ALKBH8 deficient mutant of Agrobacterium tumefaciens, indicating that bacterial ALKBH8s have a function different from that of their eukaryotic counterparts. The present study provides new insights on the function and evolution of the ALKBH8 family of proteins.

• Davydova, Erna; Ho, Angela Yeuan Yen; Malecki, Jedrzej Mieczyslaw; Moen, Anders; Enserink, Jorrit & Jakobsson, Magnus [Vis alle 8 forfattere av denne artikkelen] (2014). Identification and characterization of a novel evolutionarily conserved lysine-specific methyltransferase targeting eukaryotic translation elongation factor 2 (eEF2). Journal of Biological Chemistry. ISSN 0021-9258. 289(44), s. 30499–30510. doi: 10.1074/jbc.M114.601658. Fulltekst i vitenarkiv
• Kernstock, Jens Stefan; Davydova, Erna; Jakobsson, Magnus; Moen, Anders; Pettersen, Solveig & Mælandsmo, Gunhild [Vis alle 8 forfattere av denne artikkelen] (2012). Lysine methylation of VCP by a member of a novel human protein methyltransferase family. Nature Communications. 3. doi: 10.1038/ncomms2041. Fulltekst i vitenarkiv

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• Aileni, Vinay Kumar; Davydova, Erna; Kernstock, Jens Stefan; Moen, Anders & Falnes, Pål (2016). VCP-KMT (METTL21D)-mediated lysine methylation of histone H3 peptide sequences grafted onto a VCP-derived scaffold. Fulltekst i vitenarkiv

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