The 5 S RNA.protein complex from an extreme halophile, Halobacterium cutirubrum. Studies on the RNA-protein interaction

Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18

5S rRNA is an essential component of ribosomes of all living organisms, the only known exceptions being mitochondrial ribosomes of fungi, animals, and some protists. An intriguing situation distinguishes mammalian cells: Although the mitochondrial genome contains no 5S rRNA genes, abundant import of the nuclear DNA-encoded 5S rRNA into mitochondria was reported. Neither the detailed mechanism of this pathway nor its rationale was clarified to date. In this study, we describe an elegant molecular conveyor composed of a previously identified human 5S rRNA import factor, rhodanese, and mitochondrial ribosomal protein L18, thanks to which 5S rRNA molecules can be specifically withdrawn from the cytosolic pool and redirected to mitochondria, bypassing the classic nucleolar reimport pathway. Inside mitochondria, the cytosolic 5S rRNA is shown to be associated with mitochondrial ribosomes.

Specific features of 5S rRNA structure - its interactions with macromolecules and possible functions

Small non-coding RNAs are today a topic of great interest for molecular biologists because they can be regarded as relicts of a hypothetical "RNA world" which, apparently, preceded the modern stage of organic evolution on Earth. The small molecule of 5S rRNA (approximately 120 nucleotides) is a component of large ribosomal subunits of all living beings (5S rRNAs are not found only in mitoribosomes of fungi and metazoans). This molecule interacts with various protein factors and 23S (28S) rRNA. This review contains the accumulated data to date concerning 5S rRNA structure, interactions with other biological macromolecules, intracellular traffic, and functions in the cell.

The 5S RNA binding protein from yeast (Saccharomyces cerevisiae) ribosomes. An RNA binding sequence in the carboxyl-terminal region

The carboxyl-terminal half (CN2 fragment) of the yeast 5S RNA binding protein (YL3) retains an ability to form homogeneous ribonucleoprotein complexes with RNA although the N-terminal half (CN1) appears to confer specificity for the 5S RNA molecule [Nazar, R.N., Yaguchi, M., Willick, G.E., Rollin, C.F. and Roy, C. (1979) Eur. J. Biochem. 102, 573-582]. The nucleic acid binding site in this fragment was more clearly delineated by cleaving the CN2 fragment with a variety of enzymatic and chemical reagents and further examining the ability of the products to form RNA-peptide complexes. Hot acetic acid treatment produced a 47-residue subfragment (CN2-A1) which originated from the C terminus and continued to form stable ribonucleopeptide complexes. The amino acid sequence of this subfragment was determined to be: -Pro-Ala-Phe-Lys-Pro-Thr-Glu-Lys50-Phe-Thr-Lys-Glu-Gln-Tyr-Ala-Ala -Glu60-Ser-Ly s -Lys-Tyr-Arg-Gln-Thr-Lys-Leu-Ser70-Lys-Gln-Gln-Arg-Ala-Ala-Arg-Val -Ala-Ala80-Ly s -Ile-Ala-Ala-Leu-Ala-Gly-Gln-Gln-COOH, with 12 of the 16 basic residues in the CN2 fragment being present in this binding site. The amino acid sequence of the CN2-A1 fragment bears a limited homology in both amino acid and charge distribution with histone 2B from mammals and with one of the 5S RNA binding proteins (EL25) from Escherichia coli. The results suggest that many protein binding sites for nucleic acids may share common structural features and further support the notion that the single large eukaryotic 5S RNA protein may have evolved through a fusion of genes for the multiple 5S RNA binding proteins in prokaryotes.

Identification of the protein cross-linked to 3'-terminus of 5 S RNA in rat liver ribosomal 60 S subunits

To cross-link the 3'-terminus of 5 S RNA to its neighbouring proteins, ribosomal 60 S subunits of rat liver were oxidized with sodium periodate and reduced with sodium borohydride. 5 S RNP was then isolated by EDTA treatment followed by sucrose density-gradient centrifugation and subjected to SDS-polyacrylamide gel electrophoresis. The protein with a slower mobility than the L5 protein, which was thought to be cross-linked 5 S RNP, was labeled with 125I, treated with RNAase, and analyzed by two-dimensional polyacrylamide gel electrophoresis, followed by radioautography. A radioactive spot located anodically from L5 protein was observed, suggesting that it is the L5 protein-oligonucleotide complex. When analyzed by SDS slab polyacrylamide gel electrophoresis followed by radioautography, the peptide pattern of the alpha-chymotrypsin digest of this 125I-labeled protein-oligonucleotide complex was similar to that of the digest of 125I-labeled L5 protein. The results indicate that L5 protein binds to the 3'-terminal region of 5 S RNA in rat liver 60 S subunits.

The 5-S RNA binding protein from yeast (Saccharomyces cerevisiae) ribosomes. Evolution of the eukaryotic 5-S RNA binding protein

The ribonucleoprotein complex between 5-S RNA and its binding protein (5-S RNA . protein complex) of yeast ribosomes was released from 60-S subunits with 25 mM EDTA and the protein component was purified by chromatography on DEAE-cellulose. This protein, designated YL3 (Mr = 36000 on dodecylsulfate gels), was relatively insoluble in neutral solutions (pH 4--9) and migrated as one of four acidic 60-S subunit proteins when analyzed by the Kaltschmidt and Wittman two-dimensional gel system. Amino acid analyses indicated lower amounts of lysine and arginine than most ribosomal proteins. Sequence homology was observed in the N terminus of YL3, and two prokaryotic 5-S RNA binding proteins, EL18 from Escherichia coli and HL13 from Halobacterium cutirubrum: Ala1-Phe2-Gln3-Lys4-Asp5-Ala6-Lys7-Ser8-Ser9-Ala10-Tyr11-Ser12-Ser13-Arg14-Phe15-Gln16-Tyr17-Pro18-Phe19-Arg20-Arg21-Arg22-Arg23-Glu24-Gly25-Lys26-Thr27-Asp28-Tyr29-Tyr35; of particular interest was homology in the cluster of basic residues (18--23). Since the protein contained one methionine residue it could be split into two fragments, CN1 (Mr = 24700) and CN2 (Mr = 11300) by CNBr treatment; the larger fragment originated from the N terminus. The N-terminal amino acid sequence of CN2 shared a limited sequence homology with an internal portion of a second 5-S RNA binding protein from E. coli, EL5, and, based also on the molecular weights of the proteins and studies on the protein binding sites in 5-S RNAs, a model for the evolution of the eukaryotic 5-S RNA binding protein is suggested in which a fusion of the prokaryotic sequences may have occurred. Unlike the native 5-S RNA . protein complex, a variety of RNAs interacted with the smaller CN2 fragment to form homogeneous ribonucleoprotein complexes; the results suggest that the CN1 fragment may confer specificity on the natural 5-S RNA-protein interaction.