Extracurricular Functions of tRNA Modifications in Microorganisms

Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. These molecules undergo a variety of post-transcriptional modifications, which expand their chemical reactivity while influencing their structure, stability, and functionality. Chemical modifications to tRNA ensure translational competency and promote cellular viability. Hence, the placement and prevalence of tRNA modifications affects the efficiency of aminoacyl tRNA synthetase (aaRS) reactions, interactions with the ribosome, and transient pairing with messenger RNA (mRNA). The synthesis and abundance of tRNA modifications respond directly and indirectly to a range of environmental and nutritional factors involved in the maintenance of metabolic homeostasis. The dynamic landscape of the tRNA epitranscriptome suggests a role for tRNA modifications as markers of cellular status and regulators of translational capacity. This review discusses the non-canonical roles that tRNA modifications play in central metabolic processes and how their levels are modulated in response to a range of cellular demands.

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Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation

10.21203/rs.3.pex-1031/v1 ◽

2021 ◽

Author(s):

Otis Pinkard ◽

Sean Mcfarland ◽

Thomas Sweet ◽

Jeff Coller

Keyword(s):

Messenger Rna ◽

Protein Production ◽

Rna Stability ◽

Amino Acid Identity ◽

Rna Modifications ◽

Transfer Rnas ◽

Trna Modifications ◽

Mammalian Tissues ◽

Trna Sequencing ◽

Regulatory Landscape

Abstract Transfer RNAs (tRNA) are quintessential in deciphering the genetic code; disseminating nucleic acid triplets into correct amino acid identity. While this decoding function is clear, an emerging theme is that tRNA abundance and functionality can powerfully impact protein production rate, folding, activity, and messenger RNA stability. Importantly, however, the expression pattern of tRNAs is obliquely known. Here we present Quantitative Mature tRNA sequencing (QuantM-tRNA seq), a technique to monitor tRNA abundance and sequence variants secondary to RNA modifications. With QuantM-tRNA seq we assess the tRNA transcriptome in mammalian tissues. We observe dramatic distinctions in isodecoder expression and known tRNA modifications between tissues. Remarkably, despite dramatic changes in tRNA isodecoder gene expression, the overall anticodon pool of each tRNA family is similar across tissues. These findings suggest that while anticodon pools appear to be buffered via an unknown mechanism, underlying transcriptomic and epitranscriptomic differences suggest a more complex tRNA regulatory landscape.

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Recombinant thiopeptides containing noncanonical amino acids

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1602733113 ◽

2016 ◽

Vol 113 (13) ◽

pp. 3615-3620 ◽

Cited By ~ 40

Author(s):

Xiaozhou Luo ◽

Claudio Zambaldo ◽

Tao Liu ◽

Yuhan Zhang ◽

Weimin Xuan ◽

...

Keyword(s):

Amino Acids ◽

Chemical Reactivity ◽

Biological Activities ◽

Structural Diversity ◽

Trna Synthetase ◽

Aminoacyl Trna Synthetase ◽

Noncanonical Amino Acids ◽

Amber Suppressor ◽

Modified Peptides ◽

Biophysical Probes

Thiopeptides are a subclass of ribosomally synthesized and posttranslationally modified peptides (RiPPs) with complex molecular architectures and an array of biological activities, including potent antimicrobial activity. Here we report the generation of thiopeptides containing noncanonical amino acids (ncAAs) by introducing orthogonal amber suppressor aminoacyl-tRNA synthetase/tRNA pairs into a thiocillin producer strain ofBacillus cereus. We demonstrate that thiopeptide variants containing ncAAs with bioorthogonal chemical reactivity can be further postbiosynthetically modified with biophysical probes, including fluorophores and photo-cross-linkers. This work allows the site-specific incorporation of ncAAs into thiopeptides to increase their structural diversity and probe their biological activity; similar approaches can likely be applied to other classes of RiPPs.

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