Abstract
The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 is under evolutionary constraints to maintain the specific secondary structures that provide functionality. A link between function, structure and evolution could contribute an understanding to each other and recently has created a growing point of sequence-structure phylogeny of ITS2. Here we briefly review the current knowledge of ITS2 processing in ribosome biogenesis, focusing on the conservative characteristics of ITS2 secondary structure, including structure form, structural motifs, cleavage sites, and base-pair interactions. We then review the phylogenetic implications and applications of this structure information, including structure-guiding sequence alignment, base-pair mutation model, and species distinguishing. We give the rationale for why incorporating structure information into tree construction could improve reliability and accuracy, and some perspectives of bioinformatics coding that allow for a meaningful evolutionary character to be extracted. In sum, this review of the integration of function, structure and evolution of ITS2 will expand the traditional sequence-based ITS2 phylogeny and thus contributes to the tree of life. The generality of ITS2 characteristics may also inspire phylogenetic use of other similar structural regions.
Highlights
The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures
Site-specific mutagenesis that the cryo-electron microscopy (cryo-EM) and the recent high-throughput RNA structure probing method indicate that the 5.8S25S base-paired proximal stem occurs as early as the co-transcription of pre-rRNAs [7]
To avoid misused Compensatory base change (CBC), we suggest evolutionary changes occurring in ITS2 secondary structure should be mapped onto the phylogeny using sufficient inter- and intraspecific sampling
Summary
The ribonucleoprotein nano-machinery that translates genetic codes into amino acids, is indispensable to all life forms. Ribosome biogenesis is a highly complex process involving folding, modifying, processing, assembling and transporting of the precursor rRNAs (pre-rRNAs), orchestrated by more than 200 assembly factors (AFs). Such a complicated process begins in the nucleolus with the massive transcription of ribosomal DNA (rDNA) by RNA polymerase I, accounting for approximately 60% of total cellular RNA. ITS2 location and processing in pre-rRNA from genome to transcriptome. The endonucleolytic cleavage sites are labelled A–E on the pre-rRNA. (b) ITS2A–E location the secondary region is highlighted in dark red in each state. Structure, which was recently shown by cryo-electron microscopy (cryo-EM) [8,9,10,11]
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