A novel human NatA Nα-terminal acetyltransferase complex: hNaa16p-hNaa10p (hNat2-hArd1)

Background  

Protein acetylation is among the most common protein modifications. The two major types are post-translational N^ε-lysine acetylation catalyzed by KATs (Lysine acetyltransferases, previously named HATs (histone acetyltransferases) and co-translational N^α-terminal acetylation catalyzed by NATs (N-terminal acetyltransferases). The major NAT complex in yeast, NatA, is composed of the catalytic subunit Naa10p (N alpha acetyltransferase 10 protein) (Ard1p) and the auxiliary subunit Naa15p (Nat1p). The NatA complex potentially acetylates Ser-, Ala-, Thr-, Gly-, Val- and Cys- N-termini after Met-cleavage. In humans, the homologues hNaa15p (hNat1) and hNaa10p (hArd1) were demonstrated to form a stable ribosome associated NAT complex acetylating NatA type N-termini in vitro and in vivo.     

A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants

The core histones, H2A, H2B, H3 and H4, undergo post‐translational modifications (PTMs) including lysine acetylation, methylation and ubiquitylation, arginine methylation and serine phosphorylation. Lysine residues may be mono‐, di‐ and trimethylated, the latter resulting in an addition of mass to the protein that differs from acetylation by only 0.03639 Da, but that can be distinguished either on high‐performance mass spectrometers with sufficient mass accuracy and mass resolution or via retention times. Here we describe the use of chemical derivatization to quantify methylated and acetylated histone isoforms by forming deuteroacetylated histone derivatives prior to tryptic digestion and bottom‐up liquid chromatography‐mass spectrometric analysis. The deuteroacetylation of unmodified or mono‐methylated lysine residues produces a chemically identical set of tryptic peptides when comparing the unmodified and modified versions of a protein, making it possible to directly quantify lysine acetylation. In this work, the deuteroacetylation technique is used to examine a single histone H3 peptide with methyl and acetyl modifications at different lysine residues and to quantify the relative abundance of each modification in different deacetylase and methylase knockout yeast strains. This application demonstrates the use of the deuteroacetylation technique to characterize modification ‘cross‐talk’ by correlating different PTMs on the same histone tail. Copyright © 2013 John Wiley & Sons, Ltd.     

Reactivity and adduct formation of a polyaromatic hydrocarbon, 7-bromomethylbenz[a]anthracene, with chromatin histone proteins

The alkylation of histones by the direct-acting carcinogen 7-bromomethylbenz[a]anthracene was demonstrated both in vivo and in vitro. The relative molar reactivity for mouse liver histones in vivo was H3 greater than H1 greater than H2b greater than H4 greater than H2a. The in vitro modification of histone H3 was examined in detail. Amino acid adducts stable to acid hydrolysis were separated after acetylation by reversed-phase high-performance liquid chromatography and characterized using ultraviolet absorbance spectra and synthetic amino acid adduct standards. Three major adducts were observed and tentatively identified as cysteinyl, lysyl and histidinyl adducts of histone H3.     

Mapping Post-translational Modifications of Histones H2A, H2B and H4 in Schizosaccharomyces pombe

Core histones are known to carry a variety of post-translational modifications (PTMs), including acetylation, phosphorylation, methylation and ubiquitination, which play important roles in the epigenetic control of gene expression. The nature and biological functions of these PTMs in histones from plants, animals and budding yeast have been extensively investigated. In contrast, the corresponding studies for fission yeast were mainly focused on histone H3. In the present study, we applied LC-nano-ESI-MS/MS, coupled with multiple protease digestion, to identify PTMs in histones H2A, H2B and H4 from Schizosaccharomyces pombe (S. pombe), the typical model organism of fission yeast. Various protease digestions provided high sequence coverage for PTM mapping, and accurate mass measurement of fragment ions allowed for unambiguous differentiation of acetylation from tri-methylation. Many modification sites conserved in other organisms were identified in S. pombe. In addition, some unique modification sites, including N-terminal acetylation in H2A and H2B as well as K123 acetylation in H2A.β, were observed. Our results provide a comprehensive picture of the PTMs of histones H2A, H2B and H4 in S. pombe, which serves as a foundation for future investigations on the regulation and functions of histone modifications in this important model organism.     

Aminopeptidase B,a glucagon-processing enzyme: site directed mutagenesis of the Zn<Superscript>2+</Superscript>-binding motif and molecular modelling

Background  

Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the N-terminus of peptides and processes glucagon into miniglucagon. The enzyme exhibits, in vitro, a residual ability to hydrolyze leukotriene A₄ into the pro-inflammatory lipid mediator leukotriene B₄. The potential bi-functional nature of Ap-B is supported by close structural relationships with LTA₄ hydrolase (LTA₄H ; EC 3.3.2.6). A structure-function analysis is necessary for the detailed understanding of the enzymatic mechanisms of Ap-B and to design inhibitors, which could be used to determine the complete in vivo functions of the enzyme.     

Spectral characterization of novel <Emphasis Type="Italic">bis</Emphasis> heterocycles comprising both piperidine and thiohydantoin nuclei

Abstract  

A series of bis heterocycles comprising both piperidine and thiohydantoin nuclei namely 3-(3-alkyl-2,6-diarylpiperin-4-ylidene)-2-thioxoimidazolidin-4-ones is synthesized and characterized by melting point, elemental analysis, MS, FT–IR, one-dimensional NMR (¹H, D₂O exchanged ¹H and ¹³C), two-dimensional HOMOCOSY, and NOESY spectroscopic data.     

Identification and fractionation of the total histone of the cotton plant

In order to isolate individual fractions of the histones of the cotton plant of variety 108-F and to investigate them further, the total histone has been chromatographed on Acrylex P-60 and Bio-Gel P-30. It has been shown that the most complete fractionation is achieved on a Acrylex P-60. By electrophoresis of the fractions in 15% PAAG in the presence of 6.25 M urea and on the basis of amino acid compositions, the following order of elution of the histones has been established: H1, H2B + H2A, H3, and H4. In a comparison of the amino acid composition of the H3 and H4 histones of the cotton plant with histones enriched with arginine from other species, a somewhat higher lysine : arginine ratio in these fractions has been found. On comparing the electrophoretic mobilities of the histone fractions from the cotton plant with the histones of calf thymus, some difference is observed which is apparently connected with a difference in their molecular weights.     

Examining histone modification crosstalk using immobilized libraries established from ligation-ready nucleosomes

Chromatin signaling relies on a plethora of posttranslational modifications (PTM) of the histone proteins which package the long DNA molecules of our cells in reoccurring units of nucleosomes. Determining the biological function and molecular working mechanisms of different patterns of histone PTMs requires access to various chromatin substrates of defined modification status. Traditionally, these are achieved by individual reconstitution of single nucleosomes or arrays of nucleosomes in conjunction with modified histones produced by means of chemical biology. Here, we report an alternative strategy for establishing a library of differentially modified nucleosomes that bypasses the need for many individual syntheses, purification and assembly reactions by installing modified histone tails on ligation-ready, immobilized nucleosomes reconstituted in a single batch. Using the ligation-ready nucleosome strategy with sortase-mediated ligation for histone H3 and intein splicing for histone H2A, we generated libraries of up to 280 individually modified nucleosomes in 96-well plate format. Screening these libraries for the effects of patterns of PTMs onto the recruitment of a well-known chromatin factor, HP1 revealed a previously unknown long-range cross-talk between two modifications. H3S28 phosphorylation enhances recruitment of the HP1 protein to the H3K9 methylated H3-tail only in nucleosomal context. Detailed structural analysis by NMR measurements implies negative charges at position 28 to increase nucleosomal H3-tail dynamics and flexibility. Our work shows that ligation-ready nucleosomes enable unprecedented access to the ample space and complexity of histone modification patterns for the discovery and dissection of chromatin regulatory principles.

280 different patterns of histone modifications were installed in preassembled nucleosomes using PTS and SML enabling screening of readout crosstalk.     

Identification and fractionation of the total histone of the cotton plant

In order to isolate individual fractions of the histones of the cotton plant of variety 108-F and to investigate them further, the total histone has been chromatographed on Acrylex P-60 and Bio-Gel P-30. It has been shown that the most complete fractionation is achieved on a Acrylex P-60. By electrophoresis of the fractions in 15% PAAG in the presence of 6.25 M urea and on the basis of amino acid compositions, the following order of elution of the histones has been established: H1, H2B + H2A, H3, and H4. In a comparison of the amino acid composition of the H3 and H4 histones of the cotton plant with histones enriched with arginine from other species, a somewhat higher lysine : arginine ratio in these fractions has been found. On comparing the electrophoretic mobilities of the histone fractions from the cotton plant with the histones of calf thymus, some difference is observed which is apparently connected with a difference in their molecular weights.V. I. Nikitin Institute of Chemistry, Academy of Sciences of the TadzhSSR, Dushanbe. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 832–838, November–December, 1979.     

A bacterial acetyltransferase capable of regioselective N-acetylation of antibiotics and histones

The Salmonella enterica chromosomally encoded AAC(6')-Iy has been shown to confer broad aminoglycoside resistance in strains in which the structural gene is expressed. The three-dimensional structures reported place the enzyme in the large Gcn5-related N-acetyltransferase (GNAT) superfamily. The structure of the CoA-ribostamycin ternary complex allows us to propose a chemical mechanism for the reaction, and comparison with the Mycobacterium tuberculosis AAC(2')-CoA-ribostamycin complex allows us to define how regioselectivity of acetylation is achieved. The AAC(6')-Iy dimer is most structurally similar to the Saccharomyces cerevisiae Hpa2-encoded histone acetyltransferase. We demonstrate that AAC(6')-Iy catalyzes both acetyl-CoA-dependent self-alpha-N-acetylation and acetylation of eukaryotic histone proteins and the human histone H3 N-terminal peptide. These structural and catalytic similarities lead us to propose that chromosomally encoded bacterial acetyltransferases, including those functionally identified as aminoglycoside acetyltransferases, are the evolutionary progenitors of the eukaryotic histone acetyltransferases.     

One-pot synthesis of diphenyl pyrazolylmethylanilines via reductive amination using NaBH<Subscript>4</Subscript>/I<Subscript>2</Subscript> and their antimicrobial screening

Abstract  

Direct reductive amination of 1,3-diphenyl-1H-pyrazole-4-carbaldehyde and 3-(4-methylphenyl)-1-phenyl-1H-pyrazole-4-carbaldehyde with various substituted aromatic amines using NaBH₄ in the presence of I₂ as reducing agent is described. The reaction has been carried out in anhydrous methanol under neutral conditions at room temperature. The structure of newly synthesized diphenyl pyrazolylmethylanilines was established on the basis of IR, ¹H, ¹³C NMR, and mass spectral data. All diphenyl pyrazolylmethylaniline derivatives were tested in vitro for their antifungal and antibacterial activity against different strains of fungi and bacteria. Most of the compound exhibited considerable antifungal activity but poor antibacterial activity against the test strains.     

Conformational properties of <Emphasis Type="Italic">ortho</Emphasis>-nitrobenzenesulfonamide in gas and crystalline phases. Intra- and intermolecular hydrogen bond

A combined gas-phase electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pvtz, MP2/cc-pvtz) study of molecular structure of 2-nitrobenzenesulfonamide (2-NBSA) was carried out. Quantum chemical calculations showed that 2-NBSA has four conformers, two of which are stabilized by intramolecular hydrogen bond. The latter (with the S–N bond in a close to orthogonal position around the phenyl ring and differing from each other by staggered or eclipsed positions of the N–H and S=O bonds in the SO₂NH₂ group) presented in a saturated vapor over 2-NBSA at T = 433 (3) K in commensurable amounts. Experimental internuclear distances (Ǻ) for the staggered conformer are (?): r _h1(C–H)_av. = 1.071(9), r _h1(C–C)_av. = 1.390(4), r _h1(C–S) = 1.789(8), r _h1(S=O)_av. = 1.427(6), r _h1(S–N) = 1.644(6), r _h1(N–O)_av. = 1.221(4), r _h1(C′–N) = 1.487(8), r _h1(N–H)_av. = 1.014. Calculations at B3LYP/cc-pvtz level were performed to determine the structure and the energies of the transition states between conformers. It was shown that the conformer structures of free molecule differ from those of a molecule stabilized by intermolecular hydrogen bonds in a crystal. Influence of a substituent X (X = –CH₃, –NO₂) on conformational features of the ortho-substituted benzenesulfonamide was established.