In Vitro Translation Assays for Selenocysteine Insertion.

The molecular characterization of the protein and RNA factors that are required for Sec incorporation in mammals has been largely carried out using in vitro translation systems specifically modified for this purpose. This chapter outlines the various systems and modifications that have been used to decipher the mechanism of Sec incorporation.

The utilization of selenocysteine-tRNA[Ser]Sec isoforms is regulated in part at the level of translation in vitro.

The tRNA for the 21st proteinogenic amino acid, selenocysteine, exists in mammalian cells as 2 isoforms differing by a single 2'-O-methylribosyl moiety at position 34 (Um34). These isoforms contain either 5-methoxycarbonylmethyluridine (mcm5U) or 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) at position 34. The accumulation of the mcm5Um isoform is tightly correlated with the expression of nonessential "stress response" selenoproteins such as glutathione peroxidase 1 (GPX1). The expression of essential selenoproteins, such as thioredoxin reductase 1 (TXNRD1), is not affected by changes in Sec-tRNA[Ser]Sec isoform accumulation. In this work we used purified mcm5U and mcm5Um Sec-tRNA[Ser]Sec isoforms to analyze possible differences in binding to the selenocysteine-specific elongation factor, EEFSEC, and the translation of GPX1 and TXNRD1in vitro. Our results indicate that no major distinction between mcm5U and mcm5Um isoforms is made by the translation machinery, but a small consistent increase in GPX1 translation is associated with the mcm5Um isoform. These results implicate fundamental differences in translation efficiency in playing a role in regulating selenoprotein expression as a function of isoform accumulation.

Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.

Selenocysteine is the only proteinogenic amino acid encoded by a recoded in-frame UGA codon that does not operate as the canonical opal stop codon. A specialized translation elongation factor, eEFSec in eukaryotes and SelB in prokaryotes, promotes selenocysteine incorporation into selenoproteins by a still poorly understood mechanism. Our structural and biochemical results reveal that four domains of human eEFSec fold into a chalice-like structure that has similar binding affinities for GDP, GTP and other guanine nucleotides. Surprisingly, unlike in eEF1A and EF-Tu, the guanine nucleotide exchange does not cause a major conformational change in domain 1 of eEFSec, but instead induces a swing of domain 4. We propose that eEFSec employs a non-canonical mechanism involving the distinct C-terminal domain 4 for the release of the selenocysteinyl-tRNA during decoding on the ribosome.

Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1.

It has previously been shown that the Shewanella putrefaciens W3-18-1 strain produces remarkably high current in microbial fuel cells (MFCs) and can form magnetite at 0°C. To explore the underlying mechanisms, we developed a genetic manipulation method by deleting the restriction-modification system genes of the SGI1 (Salmonella genome island 1)-like prophage and analyzed the key genes involved in bacterial respiration. W3-18-1 has less respiratory flexibility than the well-characterized S. oneidensis MR-1 strain, as it possesses fewer cytochrome c genes and lacks the ability to oxidize sulfite or reduce dimethyl sulfoxide (DMSO) and timethylamine oxide (TMAO). W3-18-1 lacks the hydrogen-producing Fe-only hydrogenase, and the hydrogen-oxidizing Ni-Fe hydrogenase genes were split into two separate clusters. Two periplasmic nitrate reductases (NapDAGHB and NapDABC) were functionally redundant in anaerobic growth of W3-18-1 with nitrate as the electron acceptor, though napDABC was not regulated by Crp. Moreover, nitrate respiration started earlier in W3-18-1 than in MR-1 (with NapDAGHB only) under microoxic conditions. These results indicate that Shewanella putrefaciens W3-18-1 is well adapted to habitats with higher oxygen levels. Taken together, the results of this study provide valuable insights into bacterial genome evolution.

Differential microRNA epression in asthma and the role of miR-1248 in regulation of IL-5.

Asthma is a chronic inflammatory disease that can be difficult to manage due to a lack of diagnostic biomarkers and an incomplete understanding of the molecular pathogenesis. MicroRNAs (miRNAs) are small, single-stranded, non-coding RNAs with increasing importance in regulation of immune function and as biomarkers. We profiled miRNAs in the serum of asthmatics and non-asthmatic controls to identify miRNAs that could serve as diagnostic markers and potential regulators of allergic inflammation. Differential expression of miR-1248, miR-26a, Let-7a, and Let-7d were observed in asthmatic patients compared to controls. Predictive algorithm analyses of these miRNAs revealed their specificity for different Th2 cytokines, including IL-5, which has not previously been shown to be post-transcriptionally regulated. Using multiple approaches, we showed that miR-1248 physically interacts with the IL-5 transcript in the 3' untranslated region and serves as a positive regulator to increase IL-5 expression. Collectively, our results demonstrate a previously uncharacterized mode of regulation of IL-5 expression and potential use for miRNAs in the diagnosis and clinical management of asthma.