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Updated: Sep 11, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
The -10 region adjacent to open reading frames is a common expression pattern in Deinococcus-Thermus
Shitong Zhong1, Linjia Wang1, Shuang Song1
1MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.
Abstract:
Gene transcription and translation are fundamental processes that underpin the vitality of living organisms. In bacteria, the classic promoter elements for transcription include the -35 region and the -10 region, whereas the ribosome binding site (RBS) is essential for translation. Our investigation of the upstream sequences of ORFs in Deinococcus radiodurans has confirmed a -10 region-like motif, which appears as 5'-TANNNT-3' (-10-motif). Through rigorous experimental validation, we have established that this -10-motif functions as the classical -10 region of the promoter during transcription, responsible for initiating transcription of leaderless genes (mRNA products that do not have or only have a very short 5'-UTR), and exhibits specific spacing requirements relative to the ORF. Moreover, our findings suggest that sequences containing -10-motif can serve as promoters for D. radiodurans and introduction of the -35 region at appropriate positions can significantly enhance transcription levels. Genomic analysis revealed that the -10-motif located a few base pairs (bp) upstream of ORFs is common within the Deinococcus-Thermus (D-T) phylum (also known as Deinococcota) and responsible for the transcriptional initiation of leaderless genes. Given these insights, we propose that the -10 region adjacent to the ORF for gene expression via leaderless mRNA constitutes an important mode of expression in the D-T phylum, which may contribute to the extraordinary environmental adaptability observed in this group of microorganisms.
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