Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases

Tomkuvienė, Miglė; Clouet‐d’Orval, Béatrice; Černiauskas, Ignas; Weinhold, Elmar G.; Klimašauskas, Saulius

doi:10.1093/nar/gks381

Cited by 95 publications

(104 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, SeAdoYn follows a different mechanism and directly forms the selenoether 20h, 28. SeAdoYn is used as a substrate for transalkylation by a large variety of wild‐type MTases, which is in contrast with many of the AdoMet analogues with larger transferable groups, which are only active with mutated MTases 9b, 19a, 20h, 28, 29…”

Section: Labeling Strategies Using Adomet‐dependent Mtasesmentioning

confidence: 99%

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

et al. 2017

View full text Add to dashboard Cite

Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S‐adenosyl‐l‐Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly‐activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet‐dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.

show abstract

Section: Labeling Strategies Using Adomet‐dependent Mtasesmentioning

confidence: 99%

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Small-molecule methyltransferases such as NovO, CouO and catechol O-methyltransferease were shown to be active toward other sulfonium-substituted SAM analogues [•26,•27]. Certain SAM analogues such as ProSeAM and EnYn-SAM (see the discussion below) were also shown to be active toward native RNA methyltransferases (Figure 2) [28–29]. Most of the active SAM analogue cofactors contain a sulfonium-β-sp 1 /sp 2 -substituent, an anticipated feature to stabilize the S N 2 transition states of the transalkylation reactions catalyzed by native methyltransferases [••24, ••30, ••31].…”

Section: Sam Analogues With Clickable Moieties For Transalkylation Rementioning

confidence: 99%

A journey toward Bioorthogonal Profiling of Protein Methylation inside living cells

Wang

2013

Current Opinion in Chemical Biology

View full text Add to dashboard Cite

Human protein methyltransferases (PMTs) play essential roles through methylating histone and nonhistone targets. It is very challenging to profile global methylation (or methylome) in the context of relevant cellular settings. Unlike other posttranslational modifications such as lysine acetylation or Ser/Thr/Tyr/His phosphorylation, methylation of lysine or arginine does not significantly alter its physical properties (e.g. charge and size) and therefore may not be probed readily by conventional biological tools such antibodies. It is also not trivial to assign unambiguously dynamic methylation events to specific PMTs given their potential redundancy. This review focuses on the decade-long progress in developing complementary chemical tools to elucidate targets of designated PMTs. One of such efforts was to develop the Bioorthogonal Profiling of Protein Methylation (BPPM) technology in vitro and inside living cells.

show abstract

“…Typically, they are used to transfer side chains with unique chemical groups (chemical reporters), like amino, alkyne and azide groups, for chemo-selective labeling in a second step 8,21 . Figure 3) is accepted by wild-type DNA, RNA and protein MTases [30][31][32] which abrogate the need for protein engineering in many cases. This is exemplified by fluorescence protein labeling with the histone H3 lysine 4 (H3K4) MTase Set7/9 33 ( Figure 3, see protocol section 3: Two-step protein labeling via double activated cofactors).…”

Section: Introductionmentioning

confidence: 99%

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

Hanz

Jung

Giesbertz

et al. 2014

JoVE

Self Cite

View full text Add to dashboard Cite

S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific positions in DNA, RNA, proteins and small biomolecules. This natural methylation reaction can be expanded to a wide variety of alkylation reactions using synthetic cofactor analogues. Replacement of the reactive sulfonium center of AdoMet with an aziridine ring leads to cofactors which can be coupled with DNA by various DNA MTases. These aziridine cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific Methyltransferase-Induced Labeling of DNA (SMILing DNA). As a typical example we give a protocol for biotinylation of pBR322 plasmid DNA at the 5'-ATCGAT-3' sequence with the DNA MTase M.BseCI and the aziridine cofactor 6BAz in one step. Extension of the activated methyl group with unsaturated alkyl groups results in another class of AdoMet analogues which are used for methyltransferase-directed Transfer of Activated Groups (mTAG). Since the extended side chains are activated by the sulfonium center and the unsaturated bond, these cofactors are called double-activated AdoMet analogues. These analogues not only function as cofactors for DNA MTases, like the aziridine cofactors, but also for RNA, protein and small molecule MTases. They are typically used for enzymatic modification of MTase substrates with unique functional groups which are labeled with reporter groups in a second chemical step. This is exemplified in a protocol for fluorescence labeling of histone H3 protein. A small propargyl group is transferred from the cofactor analogue SeAdoYn to the protein by the histone H3 lysine 4 (H3K4) MTase Set7/9 followed by click labeling of the alkynylated histone H3 with TAMRA azide. MTase-mediated labeling with cofactor analogues is an enabling technology for many exciting applications including identification and functional study of MTase substrates as well as DNA genotyping and methylation detection. Video LinkThe video component of this article can be found at

show abstract

Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases

Cited by 95 publications

References 41 publications

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

A journey toward Bioorthogonal Profiling of Protein Methylation inside living cells

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

Contact Info

Product

Resources

About