Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

Riboswitches are cis-acting genetic regulatory elements found in the 5'-untranslated regions of messenger RNAs that control gene expression through their ability to bind small molecule metabolites directly. Regulation occurs through the interplay of two domains of the RNA: an aptamer domain that responds to intracellular metabolite concentrations and an expression platform that uses two mutually exclusive secondary structures to direct a decision-making process. In Gram-positive bacteria such as Bacillus species, riboswitches control the expression of more than 2% of all genes through their ability to respond to a diverse set of metabolites including amino acids, nucleobases and protein cofactors. Here we report the 2.9-angstroms resolution crystal structure of an S-adenosylmethionine (SAM)-responsive riboswitch from Thermoanaerobacter tengcongensis complexed with S-adenosylmethionine, an RNA element that controls the expression of several genes involved in sulphur and methionine metabolism. This RNA folds into a complex three-dimensional architecture that recognizes almost every functional group of the ligand through a combination of direct and indirect readout mechanisms. Ligand binding induces the formation of a series of tertiary interactions with one of the helices, serving as a communication link between the aptamer and expression platform domains.     

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

Riboswitches are metabolite-sensing RNAs, typically located in the non-coding portions of messenger RNAs, that control the synthesis of metabolite-related proteins. Here we describe a 2.05 angstroms crystal structure of a riboswitch domain from the Escherichia coli thiM mRNA that responds to the coenzyme thiamine pyrophosphate (TPP). TPP is an active form of vitamin B1, an essential participant in many protein-catalysed reactions. Organisms from all three domains of life, including bacteria, plants and fungi, use TPP-sensing riboswitches to control genes responsible for importing or synthesizing thiamine and its phosphorylated derivatives, making this riboswitch class the most widely distributed member of the metabolite-sensing RNA regulatory system. The structure reveals a complex folded RNA in which one subdomain forms an intercalation pocket for the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety of TPP, whereas another subdomain forms a wider pocket that uses bivalent metal ions and water molecules to make bridging contacts to the pyrophosphate moiety of the ligand. The two pockets are positioned to function as a molecular measuring device that recognizes TPP in an extended conformation. The central thiazole moiety is not recognized by the RNA, which explains why the antimicrobial compound pyrithiamine pyrophosphate targets this riboswitch and downregulates the expression of thiamine metabolic genes. Both the natural ligand and its drug-like analogue stabilize secondary and tertiary structure elements that are harnessed by the riboswitch to modulate the synthesis of the proteins coded by the mRNA. In addition, this structure provides insight into how folded RNAs can form precision binding pockets that rival those formed by protein genetic factors.     

Glutamate stimulates inositol phosphate formation in striatal neurones

The major excitatory amino acids, glutamate (Glu) and aspartate (Asp), are thought to act at three receptor subtypes in the mammalian central nervous system (CNS). These are termed quisqualate (QA), N-methyl-D-aspartate (NMDA) and kainate (KA) receptors according to the specific agonist properties of these compounds revealed by electrophysiological studies. Although Glu has been shown to stimulate cyclic GMP formation in brain slices, direct regulation of second messenger systems (cyclic AMP, Ca2+ or inositol phosphates) subsequent to activation of excitatory amino-acid receptors, has not been extensively studied. Here we demonstrate that in striatal neurones, excitatory amino acids, but not inhibitory or non-neuroactive amino acids, induce a three- to fourfold increase in inositol mono-, di- and triphosphate (IP, IP, IP) formation with the relative potency QA greater than Glu greater than NMDA, KA. The Glu-evoked formation of inositol phosphates appears to result principally from actions at QA as well as NMDA receptors on striatal neurones. Our results suggest that excitatory amino acids stimulate inositol phosphate formation directly, rather than indirectly by the evoked release and subsequent actions of adenosine or acetylcholine.     

Racemic amino acids from the ultraviolet photolysis of interstellar ice analogues

The delivery of extraterrestrial organic molecules to Earth by meteorites may have been important for the origin and early evolution of life. Indigenous amino acids have been found in meteorites-over 70 in the Murchison meteorite alone. Although it has been generally accepted that the meteoritic amino acids formed in liquid water on a parent body, the water in the Murchison meteorite is depleted in deuterium relative to the indigenous organic acids. Moreover, the meteoritical evidence for an excess of laevo-rotatory amino acids is hard to understand in the context of liquid-water reactions on meteorite parent bodies. Here we report a laboratory demonstration that glycine, alanine and serine naturally form from ultraviolet photolysis of the analogues of icy interstellar grains. Such amino acids would naturally have a deuterium excess similar to that seen in interstellar molecular clouds, and the formation process could also result in enantiomeric excesses if the incident radiation is circularly polarized. These results suggest that at least some meteoritic amino acids are the result of interstellar photochemistry, rather than formation in liquid water on an early Solar System body.     

Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins

Distinct modifications of histone amino termini, such as acetylation, phosphorylation and methylation, have been proposed to underlie a chromatin-based regulatory mechanism that modulates the accessibility of genetic information. In addition to histone modifications that facilitate gene activity, it is of similar importance to restrict inappropriate gene expression if cellular and developmental programmes are to proceed unperturbed. Here we show that mammalian methyltransferases that selectively methylate histone H3 on lysine 9 (Suv39h HMTases) generate a binding site for HP1 proteins--a family of heterochromatic adaptor molecules implicated in both gene silencing and supra-nucleosomal chromatin structure. High-affinity in vitro recognition of a methylated histone H3 peptide by HP1 requires a functional chromo domain; thus, the HP1 chromo domain is a specific interaction motif for the methyl epitope on lysine9 of histone H3. In vivo, heterochromatin association of HP1 proteins is lost in Suv39h double-null primary mouse fibroblasts but is restored after the re-introduction of a catalytically active SWUV39H1 HMTase. Our data define a molecular mechanism through which the SUV39H-HP1 methylation system can contribute to the propagation of heterochromatic subdomains in native chromatin.     

Large differences in the helix propensities of alanine and glycine

The standard view of alpha helix formation in water, based on helix propensities determined by the host-guest method, is that differences in helix propensity among the amino acids are small, except for proline, and that the average value of the helix propagation parameter s is near 1. A contradictory view of alpha helix formation in water is emerging from substitution experiments with short, unique-sequence peptides that contain only naturally occurring amino acids. Short peptides that contain only alanine and lysine, or alanine and glutamate, form surprisingly stable monomeric helices in water and substitution of a single alanine residue by another amino acid in these or related peptides produces a wide range of changes in helix content, depending on which amino acid is substituted for alanine. We show here that the ratio of the helix propensities of alanine to glycine is large, about 100, in substitution experiments with a 17-residue reference peptide containing alanine and lysine. The helix propensity is identified with s, the helix propagation parameter of the statistical mechanics model for alpha helix formation, and the results are interpreted by the Lifson-Roig theory. Single alanine----glycine substitutions have been made at a series of positions in individual peptides. The helix-destabilizing effect of an Ala----Gly substitution depends strongly on its position in the helix, as predicted by the Lifson-Roig theory if the ratio of s values for Ala:Gly is large.     

Interconversion of single and double helices formed from synthetic molecular strands

Synthetic single-helical conformations are quite common, but the formation of double helices based on recognition between the two constituent strands is relatively rare. Known examples include duplex formation through base-pair-specific hydrogen bonding and stacking, as found in nucleic acids and their analogues, and polypeptides composed of amino acids with alternating L and D configurations. Some synthetic polymers and self-assembled fibres have double-helical winding induced by van der Waals interactions. A third mode of non-covalent interaction, coordination of organic ligands to metal ions, can give rise to double, triple and quadruple helices, although in this case the assembly is driven by the coordination geometry of the metal and the structure of the ligands, rather than by direct inter-strand complementarity. Here we describe a family of oligomeric molecules with bent conformations, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands. The bent conformations leading to the helical shape of the molecules result from intramolecular hydrogen bonding within 2'-pyridyl-2-pyridinecarboxamide units, with extensive intermolecular aromatic stacking stabilizing the double-stranded helices that form through dimerization.     

Amino acids from ultraviolet irradiation of interstellar ice analogues

Amino acids are the essential molecular components of living organisms on Earth, but the proposed mechanisms for their spontaneous generation have been unable to account for their presence in Earth's early history. The delivery of extraterrestrial organic compounds has been proposed as an alternative to generation on Earth, and some amino acids have been found in several meteorites. Here we report the detection of amino acids in the room-temperature residue of an interstellar ice analogue that was ultraviolet-irradiated in a high vacuum at 12 K. We identified 16 amino acids; the chiral ones showed enantiomeric separation. Some of the identified amino acids are also found in meteorites. Our results demonstrate that the spontaneous generation of amino acids in the interstellar medium is possible, supporting the suggestion that prebiotic molecules could have been delivered to the early Earth by cometary dust, meteorites or interplanetary dust particles.     

A unique chromatin signature uncovers early developmental enhancers in humans

Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.     

Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein?

Calcium-dependent protease (calcium protease) is apparently involved in a variety of cellular processes. Here we have attempted to clarify the role and regulatory mechanism of calcium protease by analysing its structure. The complete primary structure of calcium protease (relative molecular mass (Mr) 80,000 (80K), 705 amino acids) was deduced from the nucleotide sequence of cloned complementary DNA. The protein contains four distinct domains, and we have observed a marked similarity between the second and fourth domains and the papain-like thiol proteases and calmodulin-like calcium-binding proteins, respectively. This finding suggests that calcium protease arose from the fusion of genes for proteins of completely different function and evolutionary origin. Further, it provides functional insight into cellular regulatory mechanisms mediated by Ca2+ through calcium-binding proteins.     

S-adenosylmethionine--a novel regulator of aspartate kinase

Man derives 70% of his dietary requirements of protein directly from the grains of cereals and legumes. These sources are respectively deficient in lysine (and secondarily threonine) and methionine and much effort is being devoted to their improvement. All three amino acids are derived from aspartate via a common metabolic pathway (Fig. 1) in which the first reaction catalysed by aspartate kinase is a key regulatory step limiting their production. In microorganisms, regulation of aspartate kinase occurs by a variety of mechanisms, commonly involving feedback inhibition of one or more isoenzymes by Lys plus Thr, Lys alone or Thr alone. On the other hand, Met control of this step does not seem to conform to a general pattern. Met represses, but does not inhibit aspartate kinase II of Escherichia coli; in other species Met can enhance or modify the effects of Lys or Thr. Similarly, varied controls involving Lys and Thr have been reported for the enzymes from higher plants with only one report of an effect of Met. In contrast to these previous results, we suggest here that the methionine derivative (S)-S-adenosyl-L-methionine (AdoMet) is an important regulator of the Lys-sensitive aspartate kinase of higher plants, and that this regulatory mechanism is highly conserved. There is thus a major synergistic interaction of the two nutritionally deficient amino acids Lys and Met to inhibit their own syntheses at the primary regulatory step in the pathway.     

绿豆种子蛋白质和氨基酸组成特性的研究

研究了 8个绿豆品种的蛋白质和氨基酸组成 ,结果表明 ,绿豆种子蛋白质以球蛋白为主 ,占 4种蛋白质总量的 60 %以上 ,其次是清蛋白 ,占 2 5%左右 ,这两种蛋白质是绿豆种子的主要贮藏蛋白质部分 ;谷蛋白占 1 0 %左右 ,醇溶谷蛋白在 4种蛋白质中所占的比例最小 ,只是微量水平 氨基酸组成分析表明 ,总蛋白、球蛋白氨基酸组成相似 ,富含赖氨酸 ,缺乏含硫氨基酸 ;清蛋白氨基酸组成基本平衡 ,含硫氨基酸丰富 ,谷蛋白和醇溶蛋白中赖氨酸含量很低     

氨基酸代谢与抗阻训练对骨骼肌mTOR的调节作用研究

抗阻训练在一定程度上能刺激肌肉生长,肌肉收缩和恢复过程中刺激蛋白质分解、合成的分子机制.从氨基酸、抗阻训练对骨骼肌mTOR的调节角度出发,综述了mTOR对细胞生长的作用、mTOR下游靶分子的调节、氨基酸对mTOR的活化作用和抗阻训练对mTOR信号转导调节的研究现状,并探讨了氨基酸与运动对mTOR的调节作用及机制.     

斑马鱼3种胰蛋白酶原基因的克隆、序列分析及组织表达

 胰蛋白酶是丝氨酸蛋白酶类超家族成员之一,在动物蛋白消化中起着重要作用。为深入研究胰蛋白酶在鱼类中的蛋白结构和生理功能,利用RT-PCR和RACE方法,成功获得了斑马鱼3种胰蛋白酶原cDNA序列(zftry1a、zftry1b和zftry2)。结果表明,zftry1a和zftry1b均有242个氨基酸残基组成,其中包括15个氨基酸的信号肽和5个氨基酸(LDDDK)的激活肽。zftry2由247个氨基酸残基组成,其中包括15个氨基酸的信号肽和9个氨基酸(APLGDDDDK)的激活肽。氨基酸序列比对结果显示,三者具备胰蛋白酶原的保守结构特征,如含有催化三联体氨基酸(His-57、Asp-102和Ser-195),12个半胱氨酸,位于底物结合口袋底部Asp-189和口袋开口处的Gly-216、Gly-226等。进化树结果显示,斑马鱼zftry1a和zftry1b属于group I,为阴离子胰蛋白酶原;斑马鱼zftry2属于group II,为阳离子型胰蛋白酶原。RT-PCR结果显示,三者组织分布模式类似,且在肠中有最高表达量。这些结果为研究鱼类胰蛋白酶原的基因进化和功能以及进一步探讨鱼类消化生理的分子机制奠定了基础。     

Orientation of the peptide formation of N-phosphoryl amino acids in solution

The peptide formation of N-phosphoryl amino acids with amino acids proceeds in aqueous solution without any coupling reagents. After being separated in sephadex gel column, the phosphoryl dipeptides were analyzed by the electrospray ionization tandem mass spectrometry (ESIMS/ MS). The result demonstrates that phosphoryl dipeptides were detected in all the reaction systems. It is found that the formation of N-phosphoryl dipeptides is oriented: the N-terminal amino acid residues of the N-phosphoryl dipeptides are from N-phosphoryl amino acids, and the peptide elongation happened at the C-terminal. Only a-dipeptide, no b-dipeptide, is formed in the N-phosphoryl dipeptides, showing that a-carboxylic group is activated selectively by N-phosphorylation. Theoretical calculation shows that the peptide formation of N-phosphoryl amino acids might happen through a penta-coordinate carboxylic-phosphoric intermediate in solution. These results might give some clues to the study on the origin of proteins and protein biosynthesis.