Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing

Area of Science:

• Molecular Biology
• Genomics
• Microbiome Research

Background:

• Queuosine (Q) is a crucial tRNA modification impacting translation efficiency and fidelity.
• Mammalian Q-modification relies on queuine from gut bacteria, highlighting microbiome-tRNA interplay.
• Current methods limit high-throughput study of Q-modification biology.

Purpose of the Study:

• To develop a high-throughput sequencing method for profiling Q-modification in tRNAs.
• To enable detection and quantitation of Q-modification and related sulfur modifications.
• To investigate tRNA modifications in different cellular contexts and stress responses.

Main Methods:

• Developed a periodate-treatment method for tRNA sequencing.
• Utilized Next-generation sequencing to detect periodate-induced deletion signatures.
• Introduced PAQS-seq (periodate-dependent analysis of queuosine and sulfur modification sequencing).

Main Results:

• PAQS-seq enables single-base resolution profiling of Q-modification in tRNAs.
• Periodate treatment also detects several 2-thio-modifications (e.g., τm5s2U, mcm5s2U) in human and E. coli tRNAs.
• The study assessed Q- and 2-thio-modifications at the tRNA isodecoder level and changes during stress.

Conclusions:

• PAQS-seq is a versatile tool for studying Q- and 2-thio-modifications in diverse tRNA samples.
• This method facilitates research into translational regulation, microbiome influence, and stress responses.
• PAQS-seq is expected to be widely adopted in mammalian and microbial tRNA studies.