The RNA chaperone La promotes pre-tRNA maturation via indiscriminate binding of both native and misfolded targets

Abstract

Non-coding RNAs have critical roles in biological processes, and RNA chaperones can promote their folding into the native shape required for their function. La proteins are a class of highly abundant RNA chaperones that contact pre-tRNAs and other RNA polymerase III transcripts via their common UUU-3′OH ends, as well as through less specific contacts associated with RNA chaperone activity. However, whether La proteins preferentially bind misfolded pre-tRNAs or instead engage all pre-tRNA substrates irrespective of their folding status is not known. La deletion in yeast is synthetically lethal when combined with the loss of tRNA modifications predicted to contribute to the native pre-tRNA fold, such as the N2, N2-dimethylation of G26 by the methyltransferase Trm1p. In this work, we identify G26 containing pre-tRNAs that misfold in the absence of Trm1p and/or La (Sla1p) in Schizosaccharomyces pombe cells, then test whether La preferentially associates with such tRNAs in vitro and in vivo. Our data suggest that La does not discriminate a native from misfolded RNA target, and highlights the potential challenges faced by RNA chaperones in preferentially binding defective substrates.

A missense variant impairing TRMT1 function in tRNA modification is linked to intellectual disability

“…The m2,2G modification has been predicted to prevent the folding of certain nuclearencoded tRNAs into alternative conformers found in mitochondrial tRNAs (Steinberg and Cedergren 1995). Moreover, previous studies in S. cerevisiae have found that certain tRNA isoacceptors exhibit decreased accumulation in the absence of Trm1, suggesting that the m2,2G modification plays a role in the proper folding of certain tRNAs (Dewe et al 2012;Vakiloroayaei et al 2017). Interestingly, we have found that TRMT1-deficient human cells exhibit similar steadystate levels of all tested nuclear-and mitochondrial-encoded tRNAs (Dewe et al 2017).…”

“…While S. cerevisiae strains lacking Trm1 are viable, Trm1-null strains display temperature sensitivity and defects in tRNA stability that are further exacerbated by combined deletion of either the Trm4p tRNA methyltransferase or the La RNA binding protein (Copela et al 2006;Dewe et al 2012). Furthermore, studies in Schizosaccahromyces pombe have identified particular tRNAs that are dependent upon Trm1p and/or La for proper folding, aminoacylation and accumulation (Vakiloroayaei et al 2017). These observations highlight a key role for Trm1p-catalyzed m2,2G modifications in the stabilization of tRNA structure and function.…”

An intellectual disability‐associated missense variant in TRMT1 impairs tRNA modification and reconstitution of enzymatic activity

“…Moreover, previous studies in S. cerevisiae have found that certain tRNA isoacceptors exhibit decreased accumulation in the absence of Trm1, suggesting that the m2,2G modification plays a role in the proper folding of certain tRNAs (Dewe, Whipple, Chernyakov, Jaramillo, & Phizicky, 2012;Vakiloroayaei, Shah, Oeffinger, & Bayfield, 2017). Interestingly, we have found that TRMT1-deficient ZHANG ET AL.…”

“…The m2,2G modification has been predicted to prevent the folding of certain nuclear‐encoded tRNAs into alternative conformers found in mitochondrial tRNAs (Steinberg & Cedergren, 1995). Moreover, previous studies in S. cerevisiae have found that certain tRNA isoacceptors exhibit decreased accumulation in the absence of Trm1, suggesting that the m2,2G modification plays a role in the proper folding of certain tRNAs (Dewe, Whipple, Chernyakov, Jaramillo, & Phizicky, 2012; Vakiloroayaei, Shah, Oeffinger, & Bayfield, 2017). Interestingly, we have found that TRMT1‐deficient human cells exhibit similar steady‐state levels of all tested nuclear‐ and mitochondrial‐encoded tRNAs (Dewe et al, 2017).…”

Human La binds mRNAs through contacts to the poly(A) tail

“…Often, these UUU-3’OH independent binding modes have been implicated in La function as an RNA chaperone. RNA chaperone activity in human La has been mapped to the RRM1 as well as the disordered CTD ( 17 , 20 ), and it has been proposed that one of the functions of the UUU-3’OH depending binding mode is to recruit non-specific La-associated RNA chaperone activity to UUU-3’OH containing substrates ( 21 ). It is thus hypothesized that binding of La to RNA targets in vivo occurs through the co-operation of a number of RNA binding modes in combination ( 15 , 22 ), and that the specificity determinants for some of these binding modes are still nebulous.…”