Enzymes with noncanonical amino acids

Enzyme design and engineering strategies rely almost exclusively on nature's alphabet of twenty canonical amino acids. Recent years have seen the emergence of powerful genetic code expansion methods that allow hundreds of structurally diverse amino acids to be installed into proteins in a site-selective manner. Here, we will highlight how the availability of an expanded alphabet of amino acids has opened new avenues in enzyme engineering research. Genetically encoded noncanonical amino acids have provided new tools to probe complex enzyme mechanisms, improve biocatalyst activity and stability, and most ambitiously to design enzymes with new catalytic mechanisms that would be difficult to access within the constraints of the genetic code. We anticipate that the studies highlighted in this article, coupled with the continuing advancements in genetic code expansion technology, will promote the widespread use of noncanonical amino acids in biocatalysis research in the coming years.     

Acidic Aroma Constituents of Turkish Tobacco

The acidic constituents of sun-cured Turkish tobacco have been studied. Of the 93 acidic compounds investigated, 10 compounds are new in nature and 18 are new tobacco constituents. The 93 compounds fall mainly into three groups: fatty acids, aromatic acids, and terpenoid acids, which appear to be derived from macrocyclic thunbergane diterpenoids.     

大杯香菇辐射新株系各类氨基酸的遗传主成分分析

对大杯香菇辐射选育新株系的各类氨基酸总量进行了遗传主成分分析。结果表明,变异系数最大的为硫氨基酸总量,达到13．39％;其次为儿童氨基酸总量,变异系数为7．00％;其它变异系数较小分别为甜味氨基酸总量、芳香族氨基酸总量、必需氨基酸总量、支链氨基酸总量和鲜味氨基酸总量为5．69％、5．64％、5．19％、5．24％和5．06％;在相关性上,鲜味氨基酸总量与甜味氨基酸总量、支链氨基酸总量、芳香族氨基酸总量、儿童氨基酸总量和必需氨基酸总量是呈极显著和显著的正相关,甜味氨基酸总量与支链氨基酸总量、儿童氨基酸总量和芳香族氨基酸总量呈极显著和显著的正相关,硫氨基酸总量与儿童氨基酸总量呈极显著负相关,与必需氨基酸总量是呈极显著正相关;支链氨基酸总量与芳香族氨基酸总量、必需氨基酸总量是呈极显著,与儿童氨基酸总量呈显著正相关;芳香族氨基酸总量与儿童氨基酸总量和必需氨基酸总量是呈极显著和显著的正相关;主成分分析结果表明,前4个特征根在7个特征根中累计贡献率达97．14％,也就是前4个主成分对变异的贡献率达96．07％。在各类氨基酸总量指标选择上,首先对变异大的各类氨基酸总量进行选择是及其重要的。在辐射选育新株系选择时,应注意选择大杯香菇中硫氨基酸总量高的新株系。     

Fatty Acid Profiling of Commercially Important Raw and Boiled Seer Fish <Emphasis Type="Italic">Scomberomorus commerson</Emphasis> (Lacepede, 1800) (Scombridae,Teleostei, Pisces)

The present study aims to determine the fatty acid profiling of commercially important fresh and boiled Scomberomorus commerson. Fatty acids in fresh and boiled fish were separated and quantitatively determined by gas chromatography–mass spectrophotometer using standard methods. The findings revealed that the predominant fatty acids in fresh S. commerson were octadecanoic acid methyl ester, octanoic acid, 1,2-benzenedicarboxylic acid and 3-cyclopentylpropionic acid representing respectively 45.91, 5.69, 6.75 and 8.65% of total fatty acids. Boiled S. commerson showed predominant changes in their fatty acid profiles. In the omega-3 and omega-6 families the dominant fatty acids were doconexent, 3-cyclopentylpropionic acid, octadeconoic acid methyl ester and Hexadecane representing respectively 3.87, 12.08, 44.26 and 3.11% of total fatty acids. After boiling, some fatty acids present in fresh fish are damaged and formed new fatty acids which belonged to ω-3 polyunsaturated fatty acids (PUFA). Boiling increased the concentration of PUFAs from 73.25 to 80.37% of total fatty acids and also formed new fatty acids.     

氨基酸的手性与蛋白质生物合成

生命体中行使生物学功能的重要大分子蛋白质,由其基本单位氨基酸组成. 除甘氨酸外,其余19种常见氨基酸均具有手性,且均为L-构型,称为氨基酸的纯手性（homochirality,或称同手性）.这个现象长久以来困扰着科学家们. 本文简要综述了目前对纯手性起源的一些假说,D-氨基酸在生命体中的存在和可能的作用,以及D-氨基酸在蛋白质合成这个重要过程中的特性,包括D-氨基酸的氨酰化和在新生肽链的掺入. D-氨基酸的研究,让人们对生命有了更深入的认识,为疾病、制药等领域提供了新的思路,也为生命科学的基础研究提供了新的理论支撑和研究方向.     

A new protection/activation strategy for the synthesis of naturally occurring and non-naturalα-N-alkylamino acids

Summary A new method for the preparation of N-methylamino acids and some of their derivatives starting from hexafluoroacetone protected amino acids is described. The new concept results in saving of steps compared to conventional protection/activation techniques. Protection and deprotection proceed without racemization.     

Protein synthesis: twenty three amino acids and counting

The genetic code can be interpreted during translation as 21 amino acids and three termination signals. Recent advances at the interface of chemistry and molecular biology are extending the genetic code to allow assignment of new amino acids to existing codons, providing new functional groups for protein synthesis.     

Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water

Several yellowish-pigmented bacteria with an optimum growth temperature of about 30 degrees C, were recovered from the source (borehole) of bottled mineral water in the Serra da Estrela in Eastern Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strains S-94T , S-97, S-99 and S-92 indicated that these organisms represent a new species of the Betaproteobacteria that is not closely related to any other known species. The major fatty acids of the strains are 16:1 omega7c and 16:0. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. The new strains only assimilated organic acids, glycine and alanine. Casamino acids and a mixture of all natural amino acids are not used as sole carbon and nitrogen sources; these are used as nitrogen source in the presence of organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we are of the opinion that strains S-94T, S-97, S-99 and S-92 represent a new species of a novel genus for which we propose the name Herminiimonas fonticola gen. nov., sp. nov.     

Binding and purification of plasmid DNA using multi-layered carbon nanotubes

We propose a new method for the separation of nucleic acids using multi-layered carbon nanotubes (CNTs) as an adsorbent. According to agarose gel electrophoresis, oxidized water-stable CNTs adsorb certain forms of nucleic acids, such as high molecular weight RNA, chromosomal DNA, linear and denatured forms of plasmid DNA. However, CNTs do not adsorb supercoiled form of plasmid DNA. Nucleic acids bound to CNTs can be readily removed by centrifugation whereas supercoiled plasmid DNA remains in solution. Upon the addition of divalent metal ions supercoiled plasmid DNA forms relatively stable complexes with CNTs due to chelation. Thus, new details about association of nucleic acids with CNTs were revealed and stoichiometry of the complexes was estimated. Our results can be used for fine purification of supercoiled plasmid DNA for gene therapy applications as well as manipulation of nucleic acids for biosensor design.     

氨基酸生产的代谢工程研究进展与发展趋势

氨基酸发酵是我国发酵工业的支柱产业,近年来,随着代谢工程的快速发展,氨基酸的代谢工程育种蓬勃发展。传统的正向代谢工程、基于组学分析与计算机模拟的反向代谢工程以及借鉴自然进化的进化代谢工程,都有越来越多的应用。在氨基酸的工业生产中涌现出了一系列具有高效生产、抗逆性强等优良性状的菌株。日益剧烈的市场竞争对菌株的选育提出了新的要求,如开发高附加值氨基酸品种、菌株代谢的动态调控、适应新工艺的要求等。文中介绍了氨基酸生产相关的代谢工程研究进展以及未来的发展趋势。     

Stereoselective synthesis of chaulmoogric acid and related fatty acid from 2-(±)-cyclopentenecarboxylic acid by Bacillus subtilis (ATCC 7059)

2-(±)-Cyclopentenecarboxylic acid added to the culture medium is incorporated into two new fatty acids by the growing cells of Bacillus subtilis (ATCC 7059). The new fatty acids, amounting to 24% of the total cellular fatty acids, are identified as hydrocarpic [11-(2′-cyclopentenyl)-hendecanoic] and chaulmoogric [13-(2′-cyclopentenyl)-tridecanoic] by gas-liquid chromatography and mass spectrometry. These C₁₆ and C₁₈ fatty acids are optically active, levorotatory, with the specific rotation of ?50.4° as mixture, thus the optical purity of approximately 80%. This indicates that the optical rotation of these bacterial fatty acids are opposite with that of the fatty acids from plant oils.     

Reactions of hydroxyamino acids during hydrochloric acid hydrolysis

Chlorosubstitution reactions occur readily during HCl hydrolysis of delta- and epsilon-hydroxynorleucines (Hnle), the products of deamination of poly-L-lysine by nitrite at low pH. During amino acid analysis, chloronorleucines elute as new peaks after delta- and epsilon-Hnle. To determine if other hydroxyamino acids undergo similar changes during hydrolysis, they were subjected individually to HCl hydrolysis conditions with and without added phenol. Amino acid analyses indicated that terminal hydroxy groups on linear side chains undergo reactions during HCl hydrolysis; the products appear as new peaks which may be chloroderivatives. In contrast, no new peaks are observed in HCl hydrolysates of delta-hydroxylysine or amino acids with beta-hydroxy groups (beta-hydroxynorvaline, serine, and threonine). Phenol did not protect linear amino acids from reactions during HCl hydrolysis but did prevent loss of the cyclic amino acids tyrosine, hydroxyproline, and 3,4-dihydroxyphenylalanine. Although the gamma-hydroxy group of homoserine would be expected to undergo reaction, HCl catalyzes its cyclization to form homoserine lactone instead.     

Comparison of the frequency of functional SH3 domains with different limited sets of amino acids using mRNA display

Although modern proteins consist of 20 different amino acids, it has been proposed that primordial proteins consisted of a small set of amino acids, and additional amino acids have gradually been recruited into the genetic code. This hypothesis has recently been supported by comparative genome sequence analysis, but no direct experimental approach has been reported. Here, we utilized a novel experimental approach to test a hypothesis that native-like globular proteins might be easily simplified by a set of putative primitive amino acids with retention of its structure and function than by a set of putative new amino acids. We performed in vitro selection of a functional SH3 domain as a model from partially randomized libraries with different sets of amino acids using mRNA display. Consequently, a library rich in putative primitive amino acids included a larger number of functional SH3 sequences than a library rich in putative new amino acids. Further, the functional SH3 sequences were enriched from the primitive library slightly earlier than from a randomized library with the full set of amino acids, while the function and structure of the selected SH3 proteins with the primitive alphabet were comparable with those from the 20 amino acid alphabet. Application of this approach to various combinations of codons in protein sequences may be useful not only for clarifying the precise order of the amino acid expansion in the early stages of protein evolution but also for efficiently creating novel functional proteins in the laboratory.     

Asymmetry in the symmetric structure of the genetic code]

The genetic code is characterized by hidden symmetry. Amino acids possessing common antiamino acids are located symmetrically in the graphic models of the code. There is only one exception--apolar amino acids V, M, I, L and F are asymmetrically arranged. Asymmetric disposition of these amino acids is apparently due to divergence in the course of structural evolution of amino acid families as a result of inclusion of new members into the coding system.     

Rapid analysis of amino acids using pre-column derivatization

A new approach to the pre-column derivatization and analysis of amino acids is described. The method is based upon formation of a phenylthiocarbamyl derivative of the amino acids. The derivatization method is rapid, efficient, sensitive, and specific for the analysis of primary and secondary amino acids in protein hydorlyzates. The liquid chromatographic system allows for the rapid, bonded-phase separation with ultraviolet detection of the common amino acids with 12-min analysis time and a 1-pmol sensitivity.     

Evolution of the Genetic Code by Incorporation of Amino Acids that Improved or Changed Protein Function

Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids—valine, alanine, aspartic acid, and glycine—were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.     

四个杏鲍菇品种的氨基酸分析与比较

测定了4个杏鲍菇新品种子实体的氨基酸含量,结果表明,4个新品种的子实体中含有丰富的8种人体必需氨基酸、支链氨基酸和带有胍基的精氨酸,而芳香族氨基酸的含量却很低。在测定过程中,由于采用了酸水解,子实体中的色氨酸被破坏,而其余17种氨基酸均被测出,含量极其丰富。尤其是精氨酸、谷氨酸的含量接近于α-酪蛋白、卵蛋白和大豆球蛋白。     

基于古菌酪氨酰tRNA合成酶非天然氨基酸插入的研究进展

构筑蛋白质的编码信息存在于高度保守的密码子表中,而生物体仅利用20种天然氨基酸,就能排列组合出不同的蛋白质来行使多种生物学功能。通过合成生物学的飞速发展,使得在蛋白质合成中可控地引入非天然氨基酸成为可能。这极大地拓展了蛋白质的结构和功能,并为生物学工具的开发和生物生理过程的研究提供了便利。具有活性基团的非天然氨基酸可以广泛地应用于蛋白质结构研究、蛋白质功能调控以及新型生物材料构建和医药研发等诸多领域。基因密码子拓展技术利用正交翻译系统,通过重新分配密码子改造中心法则,可以在蛋白质的指定位点引入非天然氨基酸。系统地介绍了目前提升密码子拓展技术插入非天然氨基酸效率的方法,包括tRNA以及氨酰tRNA合成酶的各种突变方法和翻译辅助因子的改造。汇总了利用古细菌酪氨酰tRNA合成酶插入的非天然氨基酸和突变位点并总结了密码子拓展技术在生物医药领域的前沿进展。最后讨论了该项技术目前所面临的挑战,如可利用的密码子数量不多、正交翻译系统的种类有限和非天然氨基酸多插效率低下。希望能够帮助研究者建立适合的非天然氨基酸插入方法并推动密码子拓展技术进一步发展。     

Carboxylic acids from hairpencils of male Amauris butterflies (Lep.: Danainae)

63 Carboxylic acids were identified from the male hairpencils of four species of the genus Amauris (Lep.: Danainae), namely A. echeria (Stoll), A. hecate (Butler), A. ochlea (Boisduval) and A. albimaculata Butler. Straight chain saturated as well as unsaturated carboxylic acids, some of which containing an additional oxygen function, contribute to the species-specificity of the odour bouquets. Oxygenated fatty acids form a new class of insect volatiles, 5 of the 10 ketoacids found represent new natural products. (E)-7-Oxo-11-tetradecenoic acid is the main volatile component of the hairpencils of A. echeria, the species with the highest amount of oxygenated fatty acids (70% of the extractable volatiles). 9-Hydroxyoctadecanoic acid is a major compound in both A. ochlea and A. albimaculata while in A. hecate oxygenated carboxylic acids are present in minute amounts only.