Nonstandard genetic codes and translation termination

Genetic code is not universal. Various nonstandard versions of the code are known for some mitochondrial, prokaryotic, and eukaryotic genomes. The most common deviation is stop codon reassignment; i.e., a stop codon is decoded as a sense codon rather than as a signal for translation termination. Class 1 release factors (RFs: prokaryotic RF1 and RF2 and eukaryotic eRF1) recognize the stop codons and induce hydrolysis of peptidyl-tRNA in the ribosome. The specificity of class 1 RFs changes in organisms with a nonstandard code. The rare amino acids selenocysteine and pyrrolysine utilize essentially different decoding strategies. The review considers several hypotheses of the origin of nonstandard genetic codes. A new hypothesis is advanced, assuming a change in the specificity of class 1 RFs as a starting point for stop codon reassignment.     

吡咯赖氨酸：第 22 种参与蛋白质生物合成的氨基酸

吡咯赖氨酸在产甲烷菌的甲胺甲基转移酶中发现,是目前已知的第 22 种参与蛋白质生物合成的氨基酸,与标准氨基酸不同的是,它由终止密码子 UAG 的有义编码形成 . 与之对应的在产甲烷菌中也含有特异的吡咯赖氨酰 -tRNA 合成酶 (PylRS) 和吡咯赖氨酸 tRNA (tRNA^Pyl). tRNA^Pyl具有不同于经典 tRNA 的特殊结构 . 产甲烷菌通过直接途径和间接途径这两种途径生成吡咯赖氨酰 -tRNA^Pyl(Pyl-tRNA^Pyl) ,它还可能通过 mRNA 上的特殊结构以及其他还未发现的机制,控制 UAG 编码成为终止密码子或者吡咯赖氨酸 . 比较了吡咯赖氨酸与另一种非标准氨基酸,第 21 种氨基酸———硒代半胱氨酸的相似点与不同点 .     

Dual functions of codons in the genetic code

The discovery of the genetic code provided one of the basic foundations of modern molecular biology. Most organisms use the same genetic language, but there are also well-documented variations representing codon reassignments within specific groups of organisms (such as ciliates and yeast) or organelles (such as plastids and mitochondria). In addition, duality in codon function is known in the use of AUG in translation initiation and methionine insertion into internal protein positions as well as in the case of selenocysteine and pyrrolysine insertion (encoded by UGA and UAG, respectively) in competition with translation termination. Ambiguous meaning of CUG in coding for serine and leucine is also known. However, a recent study revealed that codons in any position within the open reading frame can serve a dual function and that a change in codon meaning can be achieved by availability of a specific type of RNA stem-loop structure in the 3′-untranslated region. Thus, duality of codon function is a more widely used feature of the genetic code than previously known, and this observation raises the possibility that additional recoding events and additional novel features have evolved in the genetic code.     

Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors

In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X-ray structures of SelB from the archaeon Methanococcus maripaludis in the apo-, GDP- and GppNHp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. All three SelB structures reveal an EF-Tu:GTP-like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 5' phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNA(Sec) and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a beta barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a 'chalice' observed so far only for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 3' mRNA entrance cleft ready to interact with the downstream secondary structure element.     

Multiple incorporation of non-natural amino acids into a single protein using tRNAs with non-standard structures

The ability to introduce non-natural amino acids into proteins opens up new vistas for the study of protein structure and function. This approach requires suppressor tRNAs that deliver the non-natural amino acid to a ribosome associated with an mRNA containing an expanded codon. The suppressor tRNAs must be absolutely protected from aminoacylation by any of the aminoacyl-tRNA synthetases in the protein synthesizing system, or a natural amino acid will be incorporated instead of the non-natural amino acid. Here, we found that some tRNAs with non-standard structures could work as efficient four-base suppressors fulfilling the above orthogonal conditions. Using these tRNAs, we successfully demonstrated incorporation of three different non-natural amino acids into a single protein.     

第22种氨基酸和无义密码子的重新诠释

遗传密码字典的破译,通用性作为遗传密码的基本特点之一被人们认可.近年来的研究发现了一些例外.除线粒体使用一组密码子其含义有别于核基因之外,原先被认为仅用作终止信号的无义密码子在某些情况下可重新诠释,编码特定的氨基酸.在揭示了硒代半胱氨酸由UGA编码后,最近的研究表明,在某些古细菌和真细菌中,无义密码子UAG可重新诠释,编码组成蛋白质的第22种天然氨基酸——吡咯赖氨酸.     

Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life''s history.     

The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity

Pyrrolysine (Pyl) is co-translationally inserted into a subset of proteins in the Methanosarcinaceae and in Desulfitobacterium hafniense programmed by an in-frame UAG stop codon. Suppression of this UAG codon is mediated by the Pyl amber suppressor tRNA, tRNA(Pyl), which is aminoacylated with Pyl by pyrrolysyl-tRNA synthetase (PylRS). We compared the behavior of several archaeal and bacterial PylRS enzymes towards tRNA(Pyl). Equilibrium binding analysis revealed that archaeal PylRS proteins bind tRNA(Pyl) with higher affinity (K(D)=0.1-1.0 microM) than D. hafniense PylRS (K(D)=5.3-6.9 microM). In aminoacylation the archaeal PylRS enzymes did not distinguish between archaeal and bacterial tRNA(Pyl) species, while the bacterial PylRS displays a clear preference for the homologous cognate tRNA. We also show that the amino-terminal extension present in archaeal PylRSs is dispensable for in vitro activity, but required for PylRS function in vivo.     

Isolation and Identification of Hydrangenol and Umbelliferone from Cultured Cells of Amacha (Hydrangea macrophylla Seringe var. Thunbergii Makino)

2-[1-(1-Alkylamino)alkylidene]- 1,3-dicarbonyl compounds were synthesized as photosynthetic electron transport (PET) inhibitors because of their structural resemblance to the potent new PET inhibitors “cyanoacrylates”. Their functionalities were different from those of other classic photosystem II (PS II) inhibitors, and these compounds inhibited PET at the reducing side of PS II. In this paper, the synthetic approaches to these compounds are discussed.     

Experimental challenges of sense codon reassignment: An innovative approach to genetic code expansion

The addition of new and versatile chemical and biological properties to proteins pursued through incorporation of non-canonical amino acids is at present primarily achieved by stop codon suppression. However, it is critical to find new “blank” codons to increase the variety and efficiency of such insertions, thereby taking ‘sense codon recoding’ to center stage in the field of genetic code expansion. Current thought optimistically suggests the use of the pyrrolysine system coupled with re-synthesis of genomic information towards achieving sense codon reassignment. Upon review of the serious experimental challenges reported in recent studies, we propose that success in this area will depend on the re-synthesis of genomes, but also on ‘rewiring’ the mechanism of protein synthesis and of its quality control.