Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia

Abstract

Giardia lamblia is an early diverging and evolutionarily successful protozoan as it can enter into a dormant cyst stage from a vegetative trophozoite. During dormant stage, its metabolic rate decreases dramatically. However, to date, the regulatory molecules participating in the initiation and maintenance of this process have not been fully investigated. In this study, we have identified a class of abundant small RNAs named sitRNAs, which are ∼46 nucleotides in length and accumulate in G. lamblia encysting cultures. Remarkably, they are derived from the 3′ portion of fully matured tRNAs by cleavage of the anticodon left arm, with the 3′ terminal CCA triplex still connected. During differentiation, only a limited portion of mature tRNAs is cleaved, but this cleavage occurs almost in the entire tRNA family. sitRNAs begin to accumulate as early as 3 h after initiation of encystation and are maintained at a relatively stable level during the whole process, exhibiting an expression peak at around 24 hr. Our studies further show that sitRNAs can be induced by several other stress factors, and in the case of serum deprivation, both tRNAs and sitRNAs degrade rapidly, with the accumulation of tRNA being halved. Our results may provide new insight into a novel mechanism for stressed G. lamblia to regulate gene expression globally.

A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)

“…Below the mature tRNA bands, there are additional bands of intermediate size (35-60 nt long) that could correspond to the tRNA cleavage products that were reported recently (Lee and Collins 2005;Haiser et al 2008;Jochl et al 2008;Kawaji et al 2008;Li et al 2008;Thompson et al 2008;Zhang et al 2009). tRF-1001 was also measured by splinted ligation assays (Supplemental Fig.…”

“…tRNA fragments of 30-35 nt have been identified in bacteria, fungi, plants, and animals (Lee and Collins 2005;Haiser et al 2008;Jochl et al 2008;Kawaji et al 2008;Li et al 2008;Thompson et al 2008;Zhang et al 2009). These tRNA fragments are different from the ones reported here in that they are derived from a cleavage at or around the anti-codon loop by Rny1p in yeast (Thompson and Parker 2009) or angiogenin in humans (Yamasaki et al 2009).…”

Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryote Giardia lamblia

“…Intriguingly, four probes targeting to the 5′ end of tRNAs could also detect a novel kind of sRNAs with a slightly longer length (∼50 nt) than sitRNAs (stress-induced tRNA-derived RNAs) (∼46 nt), which were identified by our previous work and could not be detected by probe target to the tRNA 5′ end (17). Notably, the length of this novel sRNA (∼50 nt) is approximately equal to the sum of the lengths of 5tasRNAs (∼29 nt) and actasRNAs (∼21 nt), suggesting that this novel sRNA shares the same 3′ end with actasRNAs.…”

“…The cleavage site and frequency did not change during the differentiation of Giardia. Interestingly, the CSI is the cleavage site used to generate the 3sitRNAs by Giardia, which we reported years ago (17), and the 3′ end of 5sitRNA is located at CSII, implying a connection between the biogenesis of tasRNAs and sitRNAs. It is possible that the endonuclease cleavage of CSI and CSII in the mature tRNAs was activated in the differentiation of Giardia and produced five sRNA products simultaneously (Fig.…”

“…4 and 5), which indicates that tRNA-derived sRNAs may also play a pivotal role in the differentiation of Giardia. Although tRNA-derived sRNAs were proven to be biologically functional in eukaryotes (9,17), little is known about their biogenesis, characteristics, and classification. Results from this study clearly showed comprehensive tRNAderived sRNAs in the early evolution of eukaryotes (Fig.…”