Research on Phage Resistance

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Questions and Answers

What effect does the deletion of serU, serT, and prfA have on viral mRNA?

It improves mRNA readability.

It causes ribosome stalling at specific codons. (correct)

It increases the number of available tRNAs.

It maintains normal protein synthesis.

Which codons become unreadable due to the deletion of the specified genes?

AUG, UGC, UUA

UCG, UCA, UAG (correct)

CGA, UGG, AUC

GUA, CUG, UAC

In the propagation of T6 phage, what was the multiplicity of infection (MOI) used?

5 × 10−2 (correct)

1 × 10−3

1 × 10−1

1 × 10−2

What is the total number of codons monitored in the genome of T6 phage as per the article?

3 Signup and view all the answers

What specific role do serU and serT serve before deletion?

They encode tRNAs for specific amino acids. Signup and view all the answers

What was monitored over a duration of 4 hours during the infection of cultures with T6 phage?

Total titer of phages Signup and view all the answers

What is the implication of codon unreadability on the ribosome's action?

The ribosome stops and fails to synthesize proteins. Signup and view all the answers

What are the total values of TCG, TCA, and TAG codons in T6 phage genome?

189, 979, 17 Signup and view all the answers

What is the primary reason for the propagation of phage in the absence of RF1?

Phage can synthesize full-length viral proteins despite stop codon issues. Signup and view all the answers

How much more abundant are sense codons compared to amber codons in viral genomes?

They are at least 10 times more abundant. Signup and view all the answers

What does the inability to read an amber codon imply for viral protein synthesis?

Full-length viral proteins can still be synthesized. Signup and view all the answers

What mechanism enables viral resistance as mentioned in the context?

Reassignment of sense codons. Signup and view all the answers

In which aspect of translation does the TAG stop codon play a significant role?

It rarely serves as a termination signal. Signup and view all the answers

Which statement is true regarding amber codons in viral genes?

They are less important than sense codons. Signup and view all the answers

What might be a potential outcome of having a high abundance of sense codons in viral genomes?

Enhanced ability to explore resistance strategies. Signup and view all the answers

Which of the following statements correctly describes the relationship between sense and amber codons?

Sense codons are more abundant than amber codons. Signup and view all the answers

What are the two distinct monomers involved in the polymerization process described?

A and B Signup and view all the answers

Which of the following statements is true about the polymerization steps?

The polymerization steps can lead to various sequences. Signup and view all the answers

In ribosome-mediated polymerization, what do the A-site and P-site represent?

Substrate roles in the polymerization process. Signup and view all the answers

What is a potential outcome of using noncanonical heteropolymers?

They can lead to emergent properties. Signup and view all the answers

How many distinct sequences can be formed from the four elementary polymerization steps?

Multiple sequences can be composed. Signup and view all the answers

What was the observed effect of deletions of serU and prfA in the Syn61 variant?

Decreased growth rate Signup and view all the answers

Which of the following best describes the relationship between Syn61 and the strain it was derived from?

Syn61 has enhanced viral resistance compared to the parent strain. Signup and view all the answers

What strategy was used to increase the growth rate of the Syn61 strain before the deletion of serT, serU, and prfA?

Random parallel mutagenesis Signup and view all the answers

Which codons are indicated to be decoded by serU and prfA in the context of ncAAs?

TCG, TCA, TAG Signup and view all the answers

What is suggested as a potential reason for the slower growth rate of Syn61 compared to Syn61(ev2)?

Unannotated target codons in the genome Signup and view all the answers

Which aspect of the Syn61D3 strain is noted in the context of viral resistance?

It exhibits stronger resistance compared to wild-type strains. Signup and view all the answers

Which method did researchers apply to generate entirely noncanonical heteropolymers and macrocycles?

Automated dynamic parallel selection Signup and view all the answers

What effect did the growth rate of Syn61 have relative to the strain it was derived from?

Syn61 grew 1.6 times slower than its parent strain. Signup and view all the answers

What strategy was implemented for incorporating non-canonical amino acids (ncAAs)?

Compression and codon reassignment Signup and view all the answers

How many distinct non-canonical amino acids were incorporated into ubiquitin?

Three Signup and view all the answers

Which codons were used for the codon reassignment experiments?

TCG, TCA, TAG Signup and view all the answers

What did the authors anticipate for future work?

To further compress and reassign the genetic code Signup and view all the answers

What contributes to the generality of the approach demonstrated?

Incorporation of multiple ncAAs into a single protein Signup and view all the answers

In which repository are the scripts for analyzing codon usage available?

Zenodo Signup and view all the answers

What was the role of D.C. in the study?

Wrote scripts to analyze codon usage Signup and view all the answers

What were the competing interests declared by the authors?

They declared no competing interests Signup and view all the answers

Study Notes

Viral Resistance and Codon Reassignment

Resistance to viruses is achieved by manipulating codon usage, particularly the TAG stop codon, which is infrequently employed in translation termination.
Phages can propagate without RF1 due to the rarity of the TAG stop codon and the absence of its reading does not hinder the production of full-length viral proteins.
Sense codons (UCG, UCA, TCG) are approximately ten times more prevalent than amber codons in viral genomes.

Genetic Modifications in Phage Resistance

Deletion of specific genes (serU, serT, prfA) in the Syn61D3 strain creates an environment where UCG, UCA, and UAG codons are unreadable, leading to ribosomal stalling.
The Syn61D3 strain exhibits complete resistance to a cocktail of viruses, although it grows 1.6 times slower than its predecessor due to non-targeted codons present in its genome.

Noncanonical Amino Acids and Polymer Synthesis

Synthetic methodologies enable the incorporation of noncanonical amino acids (ncAAs) into proteins in response to target codons.
Example with ubiquitin: three distinct ncAAs were successfully integrated, demonstrating the flexibility and programmability of the reassignment strategy.

Implications for Future Research

The research indicates potential pathways for coding systems to evolve utilizing codon capture similar to natural processes.
Plans for future work include expanding the principles of genetic code reassignment to synthesize a broader array of noncanonical polymers, possibly leading to innovative materials with unique properties.

Polymerization Mechanisms

Linear polymers can be synthesized through various combinations of two monomers (A and B) via specific polymerization steps.
Ribosome-mediated polymerization consists of four fundamental steps, allowing the assembly of any desired sequence.

Data and Materials

Data supporting the findings are available through GenBank and additional scripts for analysis are published on Zenodo.
Collaboration among the authors involved experimental design, data analysis, and manuscript preparation, all without declared competing interests.

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Description

This quiz explores the concept of phage resistance and its specificities. It addresses the nuances of resistance mechanisms that occur in the absence of RF1. Test your understanding of these critical biological concepts.