China
Africa
Explore chapters and articles related to this topic
Translation
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
In conclusion, as Li (2015) noted in his recent review, the lack of understanding of the general strategy used by bacteria to tune translation efficiency remains the urgent problem. This urgency was strengthened by forthcoming differences between translation of natural and synthetic mRNAs when the latter are used to express recombinant proteins in bacteria. The problem is going to be solved by the development of array-based oligonucleotide synthesis and ribosome profiling that can provide new approaches to address this issue. At the present day, these high-throughput studies pointed out a statistically significant but mild contribution from the mRNA secondary structure around the start codon, although the major determinant for translation efficiency remains unknown. Li (2015) came to a paradoxical conclusion that bacteria do not use the SD sequence to tune the translation efficiency. In this context, he pointed to the work of Shine and Dalgarno (1974), who noted at that time that the MS2 maturation gene with the strongest SD site was in fact most weakly translated. Therefore, 40 years after their discovery, the major determinant of the translation efficiency is still largely unknown (Li 2015).
Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade
Published in Expert Review of Proteomics, 2021
Jennie R. Lill, William R. Mathews, Christopher M. Rose, Markus Schirle
In addition to developing fit-for-purpose proteome databases through RNA- or Exome-sequencing, ribosome profiling (Ribo-seq) has been growing in popularity as a method to understand the translatome of a biological system. Unlike RNA-Seq or Exome-Seq, Ribo-Seq reveals the portions of the genome that are actively being translated as evidenced by the presence of ribosomes on an RNA molecule. These data can be used alone as evidence of a protein product existing within a cell and in some cases correlates better with protein abundance as compared to RNA-seq [43]. However, Ribo-seq results are more powerful when combined with proteomic analysis that detect the protein product of the translation event. This is particularly true for non-canonical translation events that cannot be predicted from genome sequence alone.
Small, but mighty? Searching for human microproteins and their potential for understanding health and disease
Published in Expert Review of Proteomics, 2018
Annie Rathore, Thomas F. Martinez, Qian Chu, Alan Saghatelian
These discoveries suggested that genomes contain protein-coding smORFs but determining the size of the smORFeome is a challenge. As mentioned, searching the yeast genome for all smORFs between 2 and 99 codons identified approximately 260,000 smORFs [3], but only a small fraction of these are likely translated. Improvements in computational methods, especially the use of homology between closely related species, provided some relief and have improved the prediction of bona fide smORFs. For instance, an informatics analysis of Drosophila melanogaster genome identified ~600,000 potential smORFs that were culled to ~400–4500 smORFs by looking for conservation in another Drosophila species, Drosophila pseudoobscura [6]. The empirical discovery of smORFs took a huge step forward with the advent of Ribosome Profiling (Ribo-Seq) by Weissman and colleagues [7]. Ribo-Seq is based on the deep sequencing of ribosome-protected mRNA fragments called ribosome footprints, and these footprints are used to identify translated regions of the transcriptome. Ribosome-profiling provided the first transcriptome-wide method to empirically and comprehensively measure translation, which has been invaluable in identifying novel smORFs and non-AUG start codons [8]. Thus, improvements in smORF prediction and measurement have revealed the smORFeome to be a large missing fraction of the ORFeome – including smORFs.
Insights into apoptotic proteins in chemotherapy: quantification techniques and informing therapy choice
Published in Expert Review of Proteomics, 2018
How cancer cells globally struggle upon drug exposure before acceding to apoptosis is largely unknown. Wiita et al. [51] addressed this problem using myeloma cells exposed to the proteasome inhibitor (PI) bortezomib. Despite robust transcriptional changes, unbiased quantitative proteomics detected only a few critical anti-apoptotic proteins against a background of general translation inhibition-related proteins. Simultaneous ribosome profiling further revealed potential translational regulation of stress response proteins. Once the apoptotic machinery is engaged, degradation by caspases is largely independent of the upstream effects of bortezomib. Moreover, previously uncharacterized non-caspase proteolytic events also participated in cellular deconstruction. Although, the proteomic analysis seemed to be extensive, the authors admit that low abundance proteins may not be detected by MS. A limiting factor is the inability to observe apoptosis-regulating proteins, particularly in the Bcl-2 family. This is because they are shorter protein sequences that provide few tryptic peptides. Therefore, it is unlikely to observe these proteins in discovery proteomics with LC-MS/MS and necessitates targeted approaches.