Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!

Abstract

Previously, leaderless mRNAs (lmRNAs) were perceived to make up only a minor fraction of the transcriptome in bacteria. However, advancements in RNA sequencing technology are uncovering vast numbers of lmRNAs, particularly in archaea, , and extremophiles and thus underline their significance in cellular physiology and regulation. Due to the absence of conventional ribosome binding signals, lmRNA translation initiation is distinct from canonical mRNAs and can therefore be differentially regulated. The ribosome's inherent ability to bind a 5'-terminal AUG can stabilize and protect the lmRNA from degradation or allow ribosomal loading for downstream initiation events. As a result, lmRNAs remain translationally competent during a variety of physiological conditions, allowing them to contribute to multiple regulatory mechanisms. Furthermore, the abundance of lmRNAs can increase during adverse conditions through the upregulation of lmRNA transcription from alternative promoters or by the generation of lmRNAs from canonical mRNAs cleaved by an endonucleolytic toxin. In these ways, lmRNA translation can continue during stress and contribute to regulation, illustrating their importance in the cell. Due to their presence in all domains of life and their ability to be translated by heterologous hosts, lmRNAs appear further to represent ancestral transcripts that might allow us to study the evolution of the ribosome and the translational process.

Pervasive Translation in Mycobacterium tuberculosis

“…Advances in DNA sequencing technology have led to an explosion in the number of sequenced bacterial genomes ( 1 ), with the vast majority of genes identified using automated prediction algorithms ( 2–4 ). While these algorithms typically have a low false-positive rate, they often fail to identify non-canonical open reading frames (ORFs), including short ORFs (sORFs; ≤50 codons; most algorithms have a lower size limit of 30-50 codons), overlapping ORFs ( 5 ), and leaderless ORFs that are translated from mRNAs that lack a 5’ UTR ( 6, 7 ). Ribosome profiling is a powerful experimental approach to identify the translated regions of mRNAs by mapping ribosome-protected RNA fragments ( 8 ).…”

Rewiring the specificity of extra-cytoplasmic function sigma factors

“…Since pyrimidine-purine pairs were present in the approximate TSS for 67.3% of promoters, we assumed that the purine base was the initiating nucleotide (+1) for these promoters. Although both adenine and guanine are commonly used as initiating nucleotides in all phyla, predicted leaderless mRNA promoters were highly enriched for adenine initiating nucleotides (Table 1), as would be expected considering the importance of the AUG codon for recruiting the ribosome to leaderless mRNAs (Beck and Moll 2018).…”

Recent Advances in Archaeal Translation Initiation

“…Because leaderless mRNAs are found in the three domains of life (Janssen, 1993), some data concerning bacteria, and to a lesser extent mitochondria may be relevant to the archaeal case. Leaderless mRNAs can indeed be translated in E. coli (Balakin et al, 1992;Wu and Janssen, 1996;Grill et al, 2000;Moll et al, 2002b;Udagawa et al, 2004;Vesper et al, 2011;Yamamoto et al, 2016;Beck and Moll, 2018) and are even widespread in some bacterial species such as Deinococcus species (de Groot et al, 2014;Bouthier de la Tour et al, 2015) and mycobacterial species (Cortes et al, 2013;Shell et al, 2015;Li et al, 2017).…”

“…Interestingly, several studies have shown that in some non-canonical cases, eukaryotic translation initiation used eIF5B instead of eIF2 for the recruitment of the initiator tRNA ( Terenin et al, 2008 ; Thakor and Holcik, 2012 ; Ho et al, 2018 ; Ross et al, 2018 ). This argues in favor of an ancestral translation initiation mechanism involving e/aIF5B/IF2 and e/aIF1A/IF1 that could have been used in the last common universal ancestor (LUCA) and that should also be discussed in the light of what is known for translation initiation of leaderless mRNAs ( Londei, 2005 ; Beck and Moll, 2018 ).…”