La proteins couple use of sequence-specific and non-specific binding modes to engage RNA substrates

Figures & data

Figure 1. Regions of the La module associated with RNA interaction. Top: schematic comparing domain organization of human La and S. pombe La. NRE: nuclear retention element. SBM: short basic motif. S366: site of phosphorylation. NLS: nuclear localization signal. Bottom: High-resolution structure of the human La motif (light grey) and RNA recognition motif 1 (RRM1; dark grey) with highlighted amino acids, including alignments showing conservation of residues linked to RNA function. Pink: amino acids previously shown to make direct contacts to UUU-3ʹOH in La module-UUU-3ʹOH co-crystal structures [55,56]. Note I140 on RRM1 colored in pink as this contacts UUU-3ʹOH, but side chain and conservation of I140 not included as this contact is to peptide backbone. Tan: amino acids in loop 3 of RRM1 whose mutation results in reduced tRNA binding, defective tRNA mediated suppression and impaired RNA chaperone activity [19]. Blue: β-sheet and canonical RNA binding surface of RRM1; mutation of aromatic amino acids conserved in RNP1 and RNP2 motifs (highlighted) causes defective tRNA mediated suppression and decreased RNA chaperone activity [17,24]. Green: alpha helical extension C-terminal to canonical RRM fold; mutation of highlighted amino acids results in defective tRNA mediated suppression and decreased RNA chaperone activity [24]. Orange: amino acids in first wing of winged-helix fold of La motif; mutation results in defects in binding to A20 and binding to poly(A) in human cells. PDB for figure: 2VON [56]. Schematic generated using [51]

Figure 2. Hypothesized arrangement of structural domains during La binding to pre-tRNAs and poly(A). Top: schematic of domains in human La. Bottom left: arrangement of domains during binding to poly(A). Bottom right: arrangement of domains during binding to pre-tRNA. Protein-RNA contacts validated by co-crystal structures (UUU-3ʹOH) shown in black dashed lines [55,56]. Protein-protein or protein-RNA contacts hypothesized from mutagenesis experiments shown in green and red dashed lines, respectively. During binding to UUU-3ʹOH or pre-tRNA, interdomain contact between RRM1-α1 (green) and RRM2-α3/NRE (blue) that is present during poly(A) binding is disrupted [75]. Binding to pre-tRNA also involves contacts to α3 helix of RRM2 (possibly through the 5ʹ leader [75],) and loop 3 of RRM1 [19]. Binding to poly(A) hypothesized to involve winged-helix face of La motif and relies also on contact to RRM1, although specific amino acids of RRM1 important for this are not yet known (see ‘?’ [42];). Similarly, the region of the tRNA contacted by the β2-β3 loop of RRM1 is not known (see ‘?’ [18];) Poly(A) not drawn to scale

Teplova M, Yuan Y-R, Phan AT, et al. Structural basis for recognition and sequestration of UUU(OH) 3ʹ temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen. Mol Cell. 2006;21:75–85.

 PubMed Web of Science ®Google Scholar

Kotik-Kogan O, Valentine ER, Sanfelice D, et al. Structural analysis reveals conformational plasticity in the recognition of RNA 3ʹ ends by the human La protein. Struct Lond Engl. 2008;1993(16):852–862.

 Google Scholar

Brown KA, Sharifi S, Hussain R, et al. distinct dynamic modes enable the engagement of dissimilar ligands in a promiscuous atypical RNA recognition motif. Biochemistry. 2016;55:7141–7150.

 Web of Science ®Google Scholar

Huang Y, Bayfield MA, Intine RV, et al. Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation. Nat Struct Mol Biol. 2006;13:611–618.

 PubMed Web of Science ®Google Scholar

Naeeni AR, Conte MR, Bayfield MA. RNA chaperone activity of human La protein is mediated by variant RNA recognition motif. J Biol Chem. 2012;287:5472–5482.

 PubMed Web of Science ®Google Scholar

Ren J, Wen L, Gao X, et al. DOG 1.0: illustrator of protein domain structures. Cell Res. 2009;19:271–273.

 PubMed Web of Science ®Google Scholar

Marrella S, Brown K, Mansouri-Noori F, et al. An interdomain bridge influences RNA binding of the human La protein. J Biol Chem. 2019;294:1529–1540.

 PubMedGoogle Scholar

Vinayak J, Marrella SA, Hussain RH, et al. Human La binds mRNAs through contacts to the poly(A) tail. Nucleic Acids Res. 2018;46:4228–4240.

 PubMed Web of Science ®Google Scholar

Bayfield MA, Maraia RJ. Precursor-product discrimination by La protein during tRNA metabolism. Nat Struct Mol Biol. 2009;16:430–437.

 PubMed Web of Science ®Google Scholar