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《Journal of molecular biology》2022,434(8):167424
Various post-translational modifications can naturally occur on proteins, regulating the activity, subcellular localization, interaction, or stability of the proteins. However, it can be challenging to decipher the biological implication or physiological roles of site-specific modifications due to their dynamic and sub-stoichiometric nature. Genetic code expansion method, relying on an orthogonal aminoacyl-tRNA synthetase/tRNA pair, enables site-specific incorporation of non-canonical amino acids. Here we focus on the application of genetic code expansion to study site-specific protein post-translational modification in vitro and in vivo. After a brief introduction, we discuss possibilities of incorporating non-canonical amino acids containing post-translational modifications or their mimics into target proteins. This approach is applicable for Ser/Thr/Tyr phosphorylation, Tyr sulfation/nitration/hydroxylation, Lys acetylation/acylation, Lys/His mono-methylation, as well as Arg citrullination. The next section describes the use of a precursor non-canonical amino acid followed by chemical and/or enzymatic reactions to afford the desired modification, such as Cys/Lys acylation, ubiquitin and ubiquitin-like modifications, as well as Lys/Gln methylation. We also discuss means for functional regulation of enzymes involving in post-translational modifications through genetically incorporated non-canonical amino acids. Lastly, the limitations and perspectives of genetic code expansion in studying protein post-translational modification are described. 相似文献
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Shin-ichi Yokobori Tsutomu Suzuki Kimitsuna Watanabe 《Journal of molecular evolution》2001,53(4-5):314-326
Characteristic features of tRNA such as the anticodon sequence and modified nucleotides in the anticodon loop are thought
to be crucial effectors for promoting or restricting codon reassignment. Our recent findings on basepairing rules between
anticodon and codon in various metazoan mitochondria suggest that the complete loss of a codon is not necessarily essential
for codon reassignment to take place. We postulate that a possible competition between two tRNAs with cognate anticodon sequences
towards the relevant codon to be varied has a potential role in codon reassignment. Our proposition can be viewed as an expanded
version of the codon capture theory proposed by Osawa and Jukes (J Mol Evol 28: 271–278, 1989).
Received: 28 December 2000 / Accepted: 12 March 2001 相似文献
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Coding Rules for Amino Acids in the Genetic Code: The Genetic Code is a Minimal Code of Mutational Deterioration 总被引:3,自引:0,他引:3
Coding rules for amino acids in the genetic code are discussed from the point that the genetic code is a minimal code ofmutational deterioration. The global mutational deterioration(GMD) function is defined through several parameters describingsingle base mutations and amino acid distances. The problem ofsearching for the global minimum of the GMD function is discussedin some detail. From GMD minimization under initial constraintswe have succeeded in deducing the standard genetic code. 相似文献
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An algebraic and geometrical approach is used to describe the primaeval RNA code and a proposed Extended RNA code. The former
consists of all codons of the type RNY, where R means purines, Y pyrimidines, and N any of them. The latter comprises the
16 codons of the type RNY plus codons obtained by considering the RNA code but in the second (NYR type), and the third, (YRN
type) reading frames. In each of these reading frames, there are 16 triplets that altogether complete a set of 48 triplets,
which specify 17 out of the 20 amino acids, including AUG, the start codon, and the three known stop codons. The other 16
codons, do not pertain to the Extended RNA code and, constitute the union of the triplets YYY and RRR that we define as the
RNA-less code. The codons in each of the three subsets of the Extended RNA code are represented by a four-dimensional hypercube
and the set of codons of the RNA-less code is portrayed as a four-dimensional hyperprism. Remarkably, the union of these four
symmetrical pairwise disjoint sets comprises precisely the already known six-dimensional hypercube of the Standard Genetic
Code (SGC) of 64 triplets. These results suggest a plausible evolutionary path from which the primaeval RNA code could have
originated the SGC, via the Extended RNA code plus the RNA-less code. We argue that the life forms that probably obeyed the
Extended RNA code were intermediate between the ribo-organisms of the RNA World and the last common ancestor (LCA) of the
Prokaryotes, Archaea, and Eucarya, that is, the cenancestor. A general encoding function, E, which maps each codon to its corresponding amino acid or the stop signal is also derived. In 45 out of the 64 cases, this
function takes the form of a linear transformation F, which projects the whole six-dimensional hypercube onto a four-dimensional hyperface conformed by all triplets that end
in cytosine. In the remaining 19 cases the function E adopts the form of an affine transformation, i.e., the composition of F with a particular translation. Graphical representations of the four local encoding functions and E, are illustrated and discussed. For every amino acid and for the stop signal, a single triplet, among those that specify
it, is selected as a canonical representative. From this mapping a graphical representation of the 20 amino acids and the
stop signal is also derived. We conclude that the general encoding function E represents the SGC itself. 相似文献
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Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of
codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation:
erroneous codons are either synonymous or code for an amino acid with chemical properties very similar to those of the one
that would have been present had the error not occurred. This work has suggested that the second base of codons is less efficient
in this respect, by about three orders of magnitude, than the first and third bases. These results are based on the assumption
that all forms of error at all bases are equally likely. We extend this work to investigate (1) the effect of weighting transition
errors differently from transversion errors and (2) the effect of weighting each base differently, depending on reported mistranslation
biases. We find that if the bias affects all codon positions equally, as might be expected were the code adapted to a mutational
environment with transition/transversion bias, then any reasonable transition/transversion bias increases the relative efficiency
of the second base by an order of magnitude. In addition, if we employ weightings to allow for biases in translation, then
only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only
that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects
biases in these errors, as might be expected were the code the product of selection.
Received: 25 July 1997 / Accepted: 9 January 1998 相似文献
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作为生命信息的基本遗传单位,基因组遗传密码的破译对于人们加深对生命本质的认识具有重要的理论价值和现实意义.目前,遗传密码子的研究重心已由遗传密码子的破译及反常密码子的发现转入到遗传密码子的起源与进化及扩张等研究.遗传密码子的起源与进化是当今基因组学研究的热点命题之一,相关的学说、假设层出不穷,但尚未取得实质性突破.另一方面,无义密码子的再定义及遗传密码的扩张等研究却极大的丰富和发展了遗传密码子的科学内涵,推动了生命科学研究的发展.文章综述了遗传密码子的多态性、起源与进化、无义密码子的再定义及遗传密码的扩张等方面的研究进展,并就其应用价值作了评述,期待为其在基因组学、医学等相关领域的应用研究提供参考. 相似文献
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遗传密码子研究进展 总被引:2,自引:0,他引:2
作为生命信息的基本遗传单位,基因组遗传密码的破译对于人们加深对生命本质的认识具有重要的理论价值和现实意义。目前,遗传密码子的研究重心已由遗传密码子的破译及反常密码子的发现转入到遗传密码子的起源与进化及扩张等研究。遗传密码子的起源与进化是当今基因组学研究的热点命题之一,相关的学说、假设层出不穷,但尚未取得实质性突破。另一方面,无义密码子的再定义及遗传密码的扩张等研究却极大的丰富和发展了遗传密码子的科学内涵,推动了生命科学研究的发展。文章综述了遗传密码子的多态性、起源与进化、无义密码子的再定义及遗传密码的扩张等方面的研究进展,并就其应用价值作了评述,期待为其在基因组学、医学等相关领域的应用研究提供参考。 相似文献
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The genetic code is the syntactic foundation underlying the structure and function of every protein in the history of the
biological world. Its highly ordered degenerate complexity suggests an incremental evolution, the result of a combination
of selective, mechanistic, and random processes. These evolutionary processes are still poorly understood and remain an open
question in the study of early life on Earth. We perform a compositional analysis of ribosomal proteins and ATPase subunits
in bacterial and archaeal lineages, using conserved positions that came and remained under purifying selection before and
up to the most recent common ancestor. An observable shift in amino acid usage at these conserved positions likely provides
an untapped window into the history of protein sequence space, allowing events of genetic code expansion to be identified.
We identify Cys, Glu, Phe, Ile, Lys, Val, Trp, and Tyr as recent additions to the genetic code, with Asn, Gln, Gly, and Leu
among the more ancient. Our observations are consistent with a scenario in which genetic code expansion primarily favored
amino acids that promoted an increase in polypeptide size and functionality. We propose that this expansion would have been
critical in the takeover of many RNA-mediated processes, as well as the addition of novel biological functions inaccessible
to an RNA-based physiology, such as crossing lipid membranes. Thus, expansion of the genetic code likely set the stage for
the transition from RNA-based to protein-based life.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Amino-acid Sequence Invariance and Genetic Code 总被引:1,自引:0,他引:1
A. C. T. NORTH 《Nature: New biology》1972,239(90):76-77
FROM the complete nucleotide sequence of the gene coding for the coat protein of coliphage MS2, Min Jou et al.1 have suggested a scheme for base-pairing between certain stretches of the polynucleotide chain. Their hypothesis leads to the formation of double helices in their “flower” model and to the consequent implication that nucleic acids have a well-defined tertiary structure. Such a scheme remains to be proved by direct observation of the structure, but the indirect arguments of Min Jou et al. and others appear so convincing and the notion that the genetic material has a definite tertiary structure seems so probable, that there can be little doubt that the “flower” model is on the right lines in principle, even though it may be incorrect in detail. 相似文献
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Capnocytophaga canimorsus, a commensal bacterium from canine oral flora, has been isolated throughout the world from severe human infections caused by dog bites. Due to the low level of evolutionary relationship to Proteobacteria, genetic methods suitable for the genus Capnocytophaga needed to be established. Here, we show that Tn4351, derived from Bacteroides fragilis, could be introduced by conjugation into C. canimorsus and conferred resistance to erythromycin. By mapping and sequencing a naturally occurring plasmid isolated from a clinical isolate of C. canimorsus, we identified a repA gene that allowed us to construct Escherichia coli-Capnocytophaga shuttle vectors. Most commonly used antibiotic markers were not functional in C. canimorsus, but cefoxitin (cfxA), tetracycline (tetQ), and erythromycin (ermF) resistances could be used as markers for plasmid maintenance in C. canimorsus and even in some other Capnocytophaga spp. Shuttle vectors were introduced into C. canimorsus either by conjugation using the origin of transfer (oriT) of RP4 or by electrotransformation. Taking advantage of the promoter of ermF, an expression vector was constructed. Finally, a method that allows site-directed mutagenesis is described. All these genetic tools pave the way, not only for molecular studies of the pathogenesis of C. canimorsus, but also for studies of other oral Capnocytophaga species. 相似文献
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We isolated RNAs by selection–amplification, selecting for affinity to Phe–Sepharose and elution with free l-phenylalanine. Constant sequences did not contain Phe condons or anticodons, to avoid any possible confounding influence
on initially randomized sequences. We examined the eight most frequent Phe-binding RNAs for inclusion of coding triplets.
Binding sites were defined by nucleotide conservation, protection, and interference data. Together these RNAs comprise 70%
of the 105 sequenced RNAs. The K
D for the strongest sites is ≈50 μM free amino acid, with strong stereoselectivity. One site strongly distinguishes free Phe from Trp and Tyr, a specificity
not observed previously. In these eight Phe-binding RNAs, Phe codons are not significantly associated with Phe binding sites.
However, among 21 characterized RNAs binding Phe, Tyr, Arg, and Ile, containing 1342 total nucleotides, codons are 2.7-fold
more frequent within binding sites than in surrounding sequences in the same molecules. If triplets were not specifically related to binding sites, the probability of this distribution would be 4.8 × 10−11. Therefore, triplet concentration within amino acid binding sites taken together is highly likely. In binding sites for Arg,
Tyr, and Ile cognate codons are overrepresented. Thus Arg, Tyr, and Ile may be amino acids whose codons were assigned during
an era of direct RNA–amino acid affinity. In contrast, Phe codons arguably were assigned by another criterion, perhaps during
later code evolution. 相似文献
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It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters. 相似文献
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The asymmetry of digit folidosis and the correlation of exterior characteristics have been studied in 20 passerine species. The level of the characteristic asymmetry depends on the phylopatry level and regularly increases in the species disposed to annual change of the nesting site. We assume that the revealed variability reflects interpopulation flow of genes. Age-, sex-, and biotope-related changes associated with urbanization have been revealed in the correlation of characteristics. Older birds have more pronounced correlation of characteristics; it is also more specific for males than females. Correlation of characteristics is less pronounced in the urban avian populations. These differences are interpreted in terms of stabilizing selection within intraspecific groups. 相似文献