ABSTRACT
A bacterial RNA functioning as both tRNA and mRNA, transfer-messenger RNA (tmRNA) rescues stalled ribosomes and clears the cell of incomplete polypeptides. For function, Escherichia coli tmRNA requires an elaborate interplay between a tRNA-like structure and an internal mRNA domain that are connected by a 295 nt long compact secondary structure. The tRNA-like structure is surrounded by 16 unpaired nt, including 10 residues that are >95% conserved among the known 140 tmRNA sequences. All these residues were mutated to define their putative role(s) in trans-translation. Both the extent of aminoacylation and the alanine incorporation into the tag sequence, reflecting the two functions of tmRNA, were measured in vitro for all variants. As anticipated from the low sequence conservation, mutating positions 8-12 and position 15 affects neither aminoacylation nor protein tagging. Mutating a set of two conserved positions 13 and 14 abolishes both functions. Probing the solution conformation indicates that this defective mutant adopts an alternate conformation of its acceptor stem that is no more aminoacylatable, and thus inactive in protein tagging. Selected point mutations at the conserved nucleotide stretches 16-20 and 333-335 seriously impair protein tagging with only minor changes in their solution conformations and aminoacylation. Point mutations at conserved positions 19 and 334 abolish trans-translation and 70S ribosome binding, although retaining nearly normal aminoacylation capacities. Two proteins that are known to interact with tmRNA were purified, and their interactions with the defective RNA variants were examined in vitro. Based on phylogenetic and functional data, an additional structural motif consisting of a quartet composed of non-Watson-Crick base pairs 5'-YGAC-3':5'-GGAC-3' involving some of the conserved nucleotides next to the tRNA-like portion is proposed. Overall, the highly conserved nucleotides around the tRNA-like portion are maintained for both structural and functional requirements during evolution.
Subject(s)
Bacterial Proteins/metabolism , Conserved Sequence/genetics , Escherichia coli/genetics , RNA, Bacterial/metabolism , Acylation , Alanine/metabolism , Arginine/metabolism , Base Sequence , Binding Sites/genetics , Blotting, Northern , Escherichia coli/metabolism , Molecular Sequence Data , Mutation , Nucleic Acid Conformation , Open Reading Frames/genetics , Peptide Elongation Factor Tu/metabolism , RNA, Bacterial/chemistry , RNA, Bacterial/genetics , RNA, Messenger/chemistry , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Transfer/chemistry , RNA, Transfer/genetics , RNA, Transfer/metabolism , Ribosomal Proteins/metabolism , Ribosomes/metabolism , Serine/metabolism , Threonine/metabolismABSTRACT
This paper provides further characterization of a receptor that, in cells lacking the LDL receptor (FH fibroblasts), mediates lipoprotein binding, uptake, and degradation when incubated with oleate at concentrations not exceeding albumin binding capacity. This oleate-activated receptor is genetically distinct from the LDL receptor and is hereafter referred to as the lipolysis-stimulated receptor (LSR). Its apparent affinity was higher for triglyceride-rich lipoproteins (chylomicrons, VLDL) and for lipid emulsions supplemented with recombinant apoE, than for LDL which contains solely apoB. In contrast, VLDL isolated from a Type III hyperlipidemic patient (apoE2/2 phenotype) failed to bind to the LSR. Five lines of evidence indicated that the LSR is distinct from the LDL receptor-related protein (LRP): (1) the LRP ligand, alpha 2-macroglobulin-methylamine (alpha 2-MG*), did not bind to the oleate-induced LDL binding site; (2) oleate had no effect on the binding of alpha 2-MG* to LRP; (3) the LRP-associated protein, RAP, which inhibits LRP, had no effect on the LSR; (4) binding of lipoproteins to LSR was independent of Ca2+; and (5) LSR activity resolved as two proteins smaller than LRP (apparent molecular masses as determined by ligand blots: 115 and 85 kDa). That LSR provides a new candidate receptor contributing to the clearance of chylomicron remnants (CMR) is supported by the observation that LSR was inhibited by lactoferrin, a milk protein that delays CMR clearance when injected in vivo. Furthermore, in primary cultures of rat hepatocytes, oleate stimulated binding, uptake, and degradation of LDL with kinetic characteristics similar to that of LSR expressed in FH fibroblasts.(ABSTRACT TRUNCATED AT 250 WORDS)