Redundancy of the genetic code enables translational pausing

In summary, the conversation discusses the concept of codon redundancy in protein-coding regions of mRNA and its relation to Translational Pausing (TP). It is suggested that this additional layer of Ontological Prescriptive Information (PIo) can affect the translation-decoding process and help with functional folding of the nascent protein. However, there is not enough data to fully support this idea and further research is needed to understand the role of codon choice in protein synthesis and folding.
  • #1
BasicComplex
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Thoughts on this?
http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/full

The codon redundancy (“degeneracy”) found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PIo) purposely slows or speeds up the translation-decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate.(continues)
 
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  • #2
I don't have the molecular background to offer a critique. If valid, It's not surprising to me, given the emphasis on systems biology and emergence in the last couple decades. Context is important in biogy!
 
  • #3
Although translational pausing induced by rare codons is an intriguing idea that makes a lot of sense, there is not a whole lot of data actually showing that this is an important mechanism controlling protein synthesis and folding. For example, when Li et al. used a technique called ribosome profiling to detect ribosome pausing in bacteria, they did not see the ribosome pausing at rare codons (Li et al. 2012. The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484: 538. http://dx.doi.org/10.1038/nature10965 [Broken]). Furthermore, while it was believed that rare codons at the N-terminus of genes affects expression of the protein, it was later shown that the apparent codon bias is a result of a bias against RNA secondary structure (Goodman et al. 2013. Causes and effects of N-terminal codon bias in bacterial genes. Science 342: 475 doi:10.1126/science.1241934).

There are a few published examples where codon choice appears to affect protein folding (for example, Kimchi-Sarfaty et al. 2007. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315:525 doi:10.1126/science.1135308), but its not clear whether changing the codon might also change the secondary structure of the RNA or affect the RNA-binding proteins that might also play a role in controlling translational pausing and protein folding. There definitely is still a lot that needs to be worked out in this area.
 
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1. What is the redundancy of the genetic code?

The redundancy of the genetic code refers to the fact that multiple codons (sequences of three nucleotides) can code for the same amino acid. This allows for some flexibility in the genetic code and protects against potential errors during transcription and translation.

2. How does the redundancy of the genetic code enable translational pausing?

The redundancy of the genetic code allows for certain codons to code for rare or slow-translating tRNAs, which can cause the ribosome to pause during translation. This pausing can have important regulatory functions, such as allowing for proper protein folding or controlling the rate of translation.

3. What are the benefits of translational pausing?

Translational pausing allows for the cell to efficiently regulate gene expression and protein production. It can also prevent potential errors during translation and ensure proper protein folding, which is crucial for protein function.

4. Can translational pausing be harmful?

In some cases, translational pausing can be harmful if it occurs at the wrong time or in the wrong place. This can lead to misfolded proteins or disrupt normal cellular processes. However, when properly regulated, translational pausing is an important mechanism for maintaining cellular homeostasis.

5. How is the redundancy of the genetic code studied in scientific research?

Scientists use a variety of techniques, including bioinformatics and molecular biology methods, to study the redundancy of the genetic code and its impact on translational pausing. This research helps us understand the complex mechanisms of gene expression and protein production, and contributes to advancements in fields such as medicine and biotechnology.

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