Biology subjects

Taggart, J. C.

Publications and source records attributed to Taggart, J. C..

3 recordsLinked to original sources

bioRxiv2025

Long-range mRNA folding shapes expression and sequence of bacterial genes

Accessibility of the ribosome binding site (RBS) plays an outsized role in bacterial mRNA decay and translation. Antagonistic mRNA sequences that reduce accessibility and regulate expression have been widely documented near the RBS. To determine whether such sequences are also the primary effectors of expression when placed far from the RBS, we measured impacts of all possible 8-nucleotide substitutions (65,536 variants) at different positions in mRNA in Bacillus subtilis. While the vast majority of substitutions negligibly affect RNA levels, pyrimidine-rich substitutions resembling the anti-Shine-Dalgarno (aSD) sequence exhibit strong inhibitory effects. Even several hundred nucleotides downstream of the RBS, these aSD-like sequences base-pair with the RBS, promote RNA decay, and inhibit translation initiation. We find aSD-like sequences to be depleted throughout endogenous genes, likely due to selective pressure for expression. Taken together, our findings reveal widespread long-range RNA intramolecular interactions in vivo and uncover a key constraint on gene sequence evolution. HIGHLIGHTSO_LILong-range mRNA folding tunes accessibility of the ribosome binding site (RBS) C_LIO_LIShort anti-RBS sequences are major mRNA repressors across the transcript body C_LIO_LIAnti-RBSs, even distally located, can promote RNA decay and inhibit translation C_LIO_LIAnti-RBS sequences are depleted throughout endogenous bacterial coding sequences C_LI

molecular biology↗

bioRxiv2025

Widespread purine bias in bacterial genes driven by runaway transcription

Genes in many bacteria are rich in purine nucleotides and poor in pyrimidines. We show that this purine preference is critical for gene expression because it prevents premature transcription termination in species that exhibit runaway transcription. In contrast to coupled transcription-translation1-5, runaway RNA polymerases that outpace trailing ribosomes have exposed nascent RNA and are vulnerable to the termination factor Rho6,7. Using a massively parallel reporter assay in Bacillus subtilis, we found that Rho-dependent termination requires a high C-to-G skew and high T content. Consequently, purine-rich coding (sense) sequences escape premature termination, whereas the correspondingly pyrimidine-rich antisense sequences are targeted by Rho and transcriptionally silenced. This purine requirement drives biased codon usage in most bacterial species with runaway transcription, except in lineages that have lost Rho. Our results suggest that the avoidance of premature transcription termination imposes major constraints on nucleotide content during genome evolution and adaptation of foreign genes.

microbiology↗

bioRxiv2021

Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3' status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.

molecular biology↗