The conserved RNA binding protein La recognizes UUU-3OH on its small nuclear RNA ligands and stabilizes them against 3-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome-and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ϳ150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.The RNA binding domain of the conserved La protein consists of a La motif (LaM) and an RNA recognition motif (RRM) that work together to recognize UUU-3ЈOH on small nascent transcripts and to protect them from 3Ј exonucleases (7,45). In addition to this, La proteins can modulate mRNA translation (30,(63)(64)(65). The LaM-RRM arrangement has been found in La-related proteins 1 (LARP1), 1b, 4, 4b, 6, and 7, which have been separately conserved during evolution (8, 10) (LARP4b is also referred to as LARP5 in multiple databases and here will be designated LARP5/4b). LARP7 is specific for 7SK snRNA, which it recognizes in part via UUU-3ЈOH (29, 46). LARP6 binds to a stem-loop in the 5Ј untranslated regions (UTRs) of collagen mRNAs in a uracil-dependent manner (15), and LARP1 was shown to bind poly(U) and to a lesser extent poly(G), but not poly(A) or poly(C) (51). Consistent with these specificities, LARP1, -6, and -7 have conserved all of the amino acids involved in UUU-3ЈOH recognition in La-RNA crystals (37, 66), while LARP4 and -5/4b have diverged, suggesting alternative RNA binding (8). Moreover, an invariant divergence in all of the LARP4 and -5/4b sequences available occurs in a most critical residue involved in base-specific recognition seen in La-RNA crystals, corresponding to human La Q20, suggesting a conserved difference in RNA recognition (8). Although the LaM-RRM in ...

d tRNA isopentenyltransferases (Tit1) modify tRNA position 37, adjacent to the anticodon, to N 6 -isopentenyladenosine (i6A37) in all cells, yet the tRNA subsets selected for modification vary among species, and their relevance to phenotypes is unknown. We examined the function of i6A37 in Schizosaccharomyces pombe tit1؉ and tit1-⌬ cells by using a ␤-galactosidase codon-swap reporter whose catalytic activity is sensitive to accurate decoding of codon 503. i6A37 increased the activity of tRNA Cys at a cognate codon and that of tRNA Tyr at a near-cognate codon, suggesting that i6A37 promotes decoding activity generally and increases fidelity at cognate codons while decreasing fidelity at noncognate codons. S. pombe cells lacking tit1 ؉ exhibit slow growth in glycerol or rapamycin. While existing data link wobble base U34 modifications to translation of functionally related mRNAs, whether this might extend to the anticodon-adjacent position 37 was unknown. Indeed, we found a biased presence of i6A37-cognate codons in high-abundance mRNAs for ribosome subunits and energy metabolism, congruent with the observed phenotypes and the idea that i6A37 promotes translational efficiency. Polysome profiles confirmed the decreased translational efficiency of mRNAs in tit1-⌬ cells. Because subsets of i6A37-tRNAs differ among species, as do their cognate codon-sensitive mRNAs, these genomic variables may underlie associated phenotypic differences.

No abstract

Human quinolinate phosphoribosyltransferase (EC 2.4.2.19) (hQPRTase) is a member of the type II phosphoribosyltransferase family involved in the catabolism of quinolinic acid (QA). It catalyses the formation of nicotinic acid mononucleotide from quinolinic acid, which involves a phosphoribosyl transfer reaction followed by decarboxylation. hQPRTase has been implicated in a number of neurological conditions and in order to study it further, we have carried out structural and kinetic studies on recombinant hQPRTase. The structure of the fully active enzyme overexpressed in Escherichia coli was solved using multiwavelength methods to a resolution of 2.0 A. hQPRTase has a alpha/beta barrel fold sharing a similar overall structure with the bacterial QPRTases. The active site of hQPRTase is located at an alpha/beta open sandwich structure that serves as a cup for the alpha/beta barrel of the adjacent subunit with a QA binding site consisting of three arginine residues (R102, R138 and R161) and two lysine residues (K139 and K171). Mutation of these residues affected substrate binding or abolished the enzymatic activity. The kinetics of the human enzyme are different to the bacterial enzymes studied, hQPRTase is inhibited competitively and non-competitively by one of its substrates, 5-phosphoribosylpyrophosphate (PRPP). The human enzyme adopts a hexameric arrangement, which places the active sites in close proximity to each other.