Sequence specificity of mRNA N6-adenosine methyltransferase

The sequence specificity of chicken mRNA N6-adenosine methyltransferase has been investigated in vivo. Localization of six new N6-methyladenosine sites on Rous sarcoma virus (RSV) virion RNA has confirmed our extended consensus sequence for methylation: RGACU, where R is usually a G (7/12). We have also observed A (2/12) and U (3/12) at the -2 position (relative to m6A at +1) but never a C. At the +3 position, the U was observed 10/12 times; an A and a C were observed once each in weakly methylated sequences. The extent of methylation varied between the different sites up to a maximum of about 90%. To test the significance of this consensus sequence, it was altered by site-specific mutagenesis, and methylation was assayed after transfection of mutated RSV DNA into chicken embryo fibroblasts. We found that changing the G at -1 or the U at +3 to any other residue inhibited methylation. However, inhibition of methylation at all four of the major sites in the RSV src gene did not detectably alter the steady-state levels of the three viral RNA species or viral infectivity. Additional mutants that inactivated the src protein kinase activity produced less virus and exhibited relatively less src mRNA in infected cells.     

Sequence specificity of the human mRNA N6-adenosine methylase in vitro.

N6-adenosine methylation is a frequent modification of mRNAs and their precursors, but little is known about the mechanism of the reaction or the function of the modification. To explore these questions, we developed conditions to examine N6-adenosine methylase activity in HeLa cell nuclear extracts. Transfer of the methyl group from S-[3H methyl]-adenosylmethionine to unlabeled random copolymer RNA substrates of varying ribonucleotide composition revealed a substrate specificity consistent with a previously deduced consensus sequence, Pu[G greater than A]AC[A/C/U]. 32-P labeled RNA substrates of defined sequence were used to examine the minimum sequence requirements for methylation. Each RNA was 20 nucleotides long, and contained either the core consensus sequence GGACU, or some variation of this sequence. RNAs containing GGACU, either in single or multiple copies, were good substrates for methylation, whereas RNAs containing single base substitutions within the GGACU sequence gave dramatically reduced methylation. These results demonstrate that the N6-adenosine methylase has a strict sequence specificity, and that there is no requirement for extended sequences or secondary structures for methylation. Recognition of this sequence does not require an RNA component, as micrococcal nuclease pretreatment of nuclear extracts actually increased methylation efficiency.     

Effect of ribosylzeatin isomers on the enzymatic degradation of N6-(delta2-isopentenyl) adenosine.

Cytokinin oxidase has been partially purified from cultured tobacco tissue. This enzyme converts N6-(delta2-isopentenyl)-adenosine to adenosine. The reaction is inhibited by the two isomers of ribosylzeatin [n6-4-hydroxy-3-methylbut-2-enyl)adenosine]. Trans-ribosylzeatin inhibits the reaction more than the cis-isomer.     

m6A RNA甲基化修饰在心血管疾病中的作用

N6-甲基腺嘌呤（N6-methyladenosine, m6A）是发生在腺嘌呤N6位的甲基化修饰,它是真核生物信使RNA(messenger RNA, mRNA)中最丰富的转录后修饰。m6A修饰是由甲基化酶、去甲基化酶以及结合蛋白质共同调控的动态可逆的过程,并且影响mRNA的生命周期各个阶段,包括稳定性、剪接、核输出、翻译和降解。近年来,有研究报道m6A连续动态调节在心血管疾病中发挥着重要的作用,包括动脉粥样硬化、心肌缺血再灌注损伤、心肌肥厚、心力衰竭、高血压以及腹主动脉瘤等。本文主要对m6A RNA甲基化修饰的作用机制及其在心血管疾病中的最新研究进展进行概述,此外,同时介绍了m6A 单核苷酸多态性（m6A-associated single-nucleotide polymorphisms, m6A-SNPs）在心血管疾病中的应用,以期为心血管疾病的预防及治疗提供新的思路和途径。     

The exploration of N6-deoxyadenosine methylation in mammalian genomes

N6-methyladenine (N6-mA,m6dA,or 6mA),a prevalent DNA modification in prokaryotes,has recently been identified in higher eukaryotes,including mammals.Although 6mA has been well-studied in prokaryotes,the function and regulatory mechanism of 6mA in eukary-otes are still poorly understood.Recent studies indicate that 6mA can serve as an epigenetic mark and play critical roles in various biological processes,from transposable-element suppression to environmental stress response.Here,we review the significant advances in methodology for 6mA detection and major progress in understanding the regulation and function of this non-canonical DNA methylation in eukaryotes,predominantly mammals.     

Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases

DNA methylation is important in cellular, developmental and disease processes, as well as in bacterial restriction-modification systems. Methylation of DNA at the amino groups of cytosine and adenine is a common mode of protection against restriction endonucleases afforded by the bacterial methyltransferases. The first structure of an N:6-adenine methyltransferase belonging to the beta class of bacterial methyltransferases is described here. The structure of M. RSR:I from Rhodobacter sphaeroides, which methylates the second adenine of the GAATTC sequence, was determined to 1.75 A resolution using X-ray crystallography. Like other methyltransferases, the enzyme contains the methylase fold and has well-defined substrate binding pockets. The catalytic core most closely resembles the PVU:II methyltransferase, a cytosine amino methyltransferase of the same beta group. The larger nucleotide binding pocket observed in M. RSR:I is expected because it methylates adenine. However, the most striking difference between the RSR:I methyltransferase and the other bacterial enzymes is the structure of the putative DNA target recognition domain, which is formed in part by two helices on an extended arm of the protein on the face of the enzyme opposite the active site. This observation suggests that a dramatic conformational change or oligomerization may take place during DNA binding and methylation.     

RNA中6-甲基腺嘌呤的研究进展

RNA酶促共价修饰研究, 尤其是m⁶A(6-甲基腺嘌呤), 是RNA生物学研究的一个新兴领域。m⁶A是真核生物mRNA内部序列中最常见的一种转录后修饰形式, 由包含3个独立组分的复合物mRNA: m⁶A甲基转移酶催化生成。最新研究发现肥胖相关蛋白FTO可以脱掉m⁶A上的甲基, 表明该甲基化过程是可逆的。抑制或敲除m⁶A甲基转移酶会引起重要的表型变化, 但是由于过去的检测方法受限, m⁶A确切的作用机制目前为止还不甚清楚。二代测序技术结合免疫沉淀方法为大规模检测m⁶A修饰并研究其作用机制提供了可能。文章主要综述了m⁶A的发现史、生成机制、组织和基因组分布、检测方法、生物学功能等及其最新研究进展, 并通过比较3种IP-seq技术和数据分析的异同及优缺点, 对m⁶A这种RNA表观修饰研究中尚未解决的问题进行了讨论。     

Cross-linking of ribosomal proteins by 4-(6-formyl-3-3-azidophenoxy)butyrimidate, a heterobifunctional, cleavable cross-linker.

For the identification of neighbor relationships between proteins in biological systems 4-(6-formyl-3-azidophenoxy)butyrimidate (FAPB-imidate), a heterobifunctional, cleavable cross-linker was synthesized. The reagent has an imido ester at one end, which is used for the attachment to amino groups of a specific protein whose environment has to be characterized. At the other end, the reagent has both an azido and an aldehyde group. The azido group can be used to cross-link the protein photochemically to a variety of chemical groups of neighboring proteins. The aldehyde group is able to cross-link the protein by reductive alkylatin to amino groups of neighboring proteins. In both cases, the cross-linker can be made radioactive with NaB3H4. the cross-linked complexes can be split at the band originating from the imidate group by treatment with ammonia. Hereby, the radioactive cross-linker remains covalently attached to the unknown neighboring protein, which can be therefore easily identified. In order to explore the usefulness of FAPB-imidate as a cross-linking agent, the compound was attached to ribosomal protein L7. With this modified L7, the existence of the well-known complex between L7 and ribosomal protein L10 could be demonstrated by the photochemical procedure. By the chemical procedure, the presence of dimers of L7 in solution could be shown.     

Choline biosynthesis in sheep. Evidence for extrahepatic synthesis.

Three isomers of methylphytylbenzoquinone have been isolated from lipids of the unicellular alga Scenedesmus obliquus, the most abundant being 2-methyl-6-phytylbenzoquinone (65% of the total). The 2-methyl-3-phytyl and 2-methyl-5-phytyl isomers amounted to 8 and 27% respectively. Previously problems have been encountered in the separation of the 3-phytyl and the 6-phytyl isomers, but in the present study it was found that they separated readily as quinols. Phytyl plastoquinone was also found and the relevance of these compounds to the biosynthesis of alpha-tocopherol is discussed. As well as phylloquinone, a hydroxyphylloquinone was detected, and studies indicated that it is the 5' carbon atom to which the hydroxy group is attached. Such a compound has been found by workers using other unicellular algae.     

Stereo- and biochemical profiles of the 5-6- and 6-6-junction isomers of alpha-D-mannopyranosyl [60]fullerenes

The 5-6- and 6-6-junction isomers of alpha-D-mannopyranosyl [60]fullerene were studied by means of circular dichroism (CD), deuterium labeling, 1H-NMR, molecular-dynamics (MD) calculations, and a lectin-binding assay. The CD spectra of the O-acetylated derivatives allowed clear discrimination of the isomers, while the 1H-NMR spectra, with assistance from deuterium labeling and MD calculations, served to disclose the unique conformation and molecular geometry of each acetylated isomer in chloroform solution. The deprotected 5-6- and 6-6-isomers, which gave colloidal suspensions in aqueous mixtures, displayed marked activity in blocking lectin-induced hemagglutination by concanavalin A.     

杨树溃疡病生防菌株N6-34抗菌活性物质的分离纯化与结构鉴定

【背景】杨树溃疡病是一种主要由葡萄座腔菌引起的杨树枝干病害,危害严重。前期从杨树中分离到一株内生拮抗细菌N6-34,研究表明该菌株拮抗效果好,对多种植物病原菌均有较强的拮抗作用。【目的】对拮抗细菌N6-34产生的抗菌活性物质进行分离纯化,并鉴定了活性物质组分的结构。【方法】通过硫酸铵盐析、甲醇抽提、分子筛、高效液相色谱等方法分离纯化N6-34菌株的抗菌活性物质,并对其进行结构鉴定。【结果】N6-34菌株发酵液经多步分离纯化,共获得14个组分,其中有13个组分具有抗菌活性,经一级质谱分析,获得了13种抗菌活性组分的分子量;经二级质谱分析,将13种抗菌活性物质鉴定为Fengycin A或Fengycin B的同系物或同分异构体。【结论】从N6-34菌株发酵液中分离获得了13种抗菌成分,为杨树溃疡病的生物防治提供了理论依据。     

Critical functions of N6-adenosine methylation of mRNAs in T cells

The existence of N⁶-adenosine methylation (m⁶A) of mRNA has been known for a long time, but only recently its regulatory potential was uncovered. Current research deciphers the molecular determinants leading to the deposition of this modification and consequences for modified mRNAs. It also evaluates the importance of such modifications for specific cell types and programs. In this review, we summarize the current knowledge on m⁶A modification of mRNAs in conventional and regulatory T cells and T-cell-driven immune responses and pathology. We discuss the impact of m⁶A modification on T cell activation including cytokine and antigen receptor signaling or sensing of double-stranded RNAs (dsRNA).     

Interterminal distance and flexibility of a triantennary glycopeptide as measured by resonance energy transfer

Three geometric isomers of a single triantennary glycopeptide, each containing two fluorophores attached to terminal positions in the molecule, were used to probe distance and flexibility of the oligosaccharide in solution. A dansyl group (energy acceptor) was attached to the C6 of Gal at either position 6', 6, or 8, and a naphthyl-2-acetyl group (energy donor) was coupled to the N terminus of the Ala-Asn peptide. (formula; see text) Resonance energy-transfer measurements revealed an average distance of approximately 22, 18, and 17 A between the donor and the acceptor attached to either the 6, 8, or 6' Gal residue, respectively. The lifetime of the donor's emission was nearly a single-exponential decay of 27 ns (96%), whereas the decay of the donor with proximally attached acceptor was fit by nonlinear least-squares analysis to a multiexponential for each glycopeptide probe. Fitting with a Lorentzian function revealed spatially distinct donor/acceptor distances presumably arising from glycopeptide branch flexibility. The results suggest that the acceptor located at Gal 8 is the most rigid relative to the donor with a single population of distances centered at 18.4 A. In contrast, the acceptor attached to either Gal 6' or 6 displayed two populations of different distances from the donor. The Gal 6 isomer contained a major population with average donor/acceptor separation distance of 21.7 A and a minor population with average separation distance of 9.7 A. Similarly, the Gal 6' isomer showed a major population with donor/acceptor separation distance of 18.3 A and a minor population with separation distance of 11.7 A. These data support the earlier conclusions that the Man alpha(1----6)Man linkage found in the core pentasaccharide of all branched N-linked oligosaccharides is flexible. In addition, the data suggest that the branch containing Gal 6 is also flexible in the triantennary glycopeptide.     

Alkylpurine-DNA-N-glycosylase excision of 7-(hydroxymethyl)-1,N6-ethenoadenine, a glycidaldehyde-derived DNA adduct

Glycidaldehyde (GDA) is a bifunctional alkylating agent that has been shown to be mutagenic in vitro and carcinogenic in rodents. However, the molecular mechanism by which it exerts these effects is not established. GDA is capable of forming exocyclic hydroxymethyl-substituted etheno adducts on base residues in vitro. One of them, 7-(hydroxymethyl)-1,N6-ethenoadenine (7-hm-epsilonA), was identified as the principal adduct in mouse skin treated with GDA or a glycidyl ether. In this work, using defined oligonucleotides containing a site-specific 7-hm-epsilonA, the human and mouse alkylpurine-DNA-N-glycosylases (APNGs), responsible for the removal of the analogous 1,N6-ethenoadenine (epsilonA) adduct, are shown to recognize and excise 7-hm-epsilonA. Such an activity can be significantly modulated by both 5' neighboring and opposite sequence contexts. The efficiency of human or mouse APNG for excision of 7-hm-epsilonA is about half that, or similar to the excision of epsilonA, respectively. When human or mouse cell-free extracts were tested, however, the extent of 7-hm-epsilonA excision is dramatically lower than that for epsilonA, suggesting that, in the crude extracts, the APNG activities toward these two adducts are differentially affected. Using cell-free extracts from APNG deficient mice, this enzyme is shown to be the primary glycosylase excising 7-hm-epsilonA. A structural approach, using molecular modeling, was employed to examine how the structure of the 7-hm-epsilonA adduct affects DNA conformation, as compared to the epsilonA adduct. These novel substrate specificities could have both biological and structural implications.     

6-(Methoxymethylene)penicillanic acid: inactivator of RTEM beta-lactamase from Escherichia coli

The Z and E isomers of 6-(methoxymethylene)-penicillanic acid have been synthesized, and their interaction with the RTEM beta-lactamase has been studied. The Z isomer is an inhibitor and an inactivator of the enzyme, and there is some similarity between its behavior and that of other mechanism-based inactivators such as clavulanic acid and the penam sulfones. Kinetic analysis of the interaction of the enzyme with the Z isomer has allowed a detailed evaluation of the factors that are important in the design of anti-beta-lactamase agents. In contrast to the Z compound, the E isomer of 6-(methoxymethylene)penicillanic acid is not a substrate, an inhibitor, or an inactivator of the enzyme.     

A synthesis of N6,N6,N6-trimethyl-L-lysine dioxalate in gram amounts

A procedure is described for the synthesis of crystalline N6,N6,N6-trimethyl-L-lysine dioxalate in gram amounts starting from the commercially available N2-tert-butoxycarbonyl-N6-benzyloxycarbonyl-L-lysine, which is reacted with methyl iodide in methanol in the presence of potassium hydrogen carbonate after deprotection of the side-chain amino group by catalytic hydrogenation. The work-up involves only filtrations and evaporations.