The complete amino acid sequences of ribosomal proteins L9, L20, L21/22, L24 and L32 from the archaebacterium Halobacterium marismorlui were determined. The comparison of the sequences of these proteins with those from other organisms revealed that proteins L21/22 and L24 are homologous to ribosomal protein Yrp29 from yeast and L19 from rat, respectively, and that H . marismortui L20 is homologous to L30 from eubacteria. H. marismortui ribosomal protein L9 showed sequence homology to both L29 from yeast and L15 from eubacteria. No homologous protein was found for H. marismortui L32. These results are discussed with respect to the phylogenetic relationship between eubacteria, archaebacteria and eukaryotes.Archaebacteria were postulated as a third kingdom besides eubacteria and eukaryotes [l]. Since ribosomes occur in all organisms and consist of many components they are ideal objects for studies on phylogenetic relationships between these kingdoms. We have determined the amino acid sequences of a number of ribosomal proteins isolated from the archaebacterium Halobacterium marismortui [2 -91. Comparison of these amino acid sequcnces with those from other organisms has revealed that halobacterial proteins are heterogeneous with respect to the primary structures. Some of the halobacterial ribosomal proteins are homologous only to eubacterial or to eukaryotic proteins, some are homologous to both eubacterial and eukaryotic proteins, whereas others show no homology to any ribosomal proteins so far scquenced.The determination of the amino acid sequences of ribosomal proteins from halobacteria is not only valuable with respect to phylogenetic relationships among organisms but is also important for crystallographic investigations on these ribosomes. Large and well-ordered three-dimensional crystals of intact 50s ribosomal subunits which diffracted to 0.6 nm resolution in a synchrotron beam were obtained from H . marismortui [lo]. Knowledge of the primary structures of the ribosomal components is helpful for the current studies on heavy-atom derivatives and for the crystallographic data evaluation.In this paper, we describe the primary structures of the five ribosomal proteins L9, L20, L21/22, L24 and L32 of H . marismortui, which have recently been isolated in sufficient amounts for sequence determination, and their structural relationships to the counterparts in cubacterial and eukaryotic ribosomes. MATERIALS AND METHODS Purvkation of'rihosomnl proteinsThe ribosomes and their subunits from H . marismortui were prepared as reported previously [l 11. The ribosomal proteins were extracted from 50s ribosomal subunits according to [I 21 and separated by ion-exchange chromatography using DEAE-cellulose in 75 mM Tris/citrate buffer, pH 7.9, containing 30% dimethylformamide 161. Elution was performed by a linear gradient of 0-0.3 M KCI, followed by elution with 0.5 M KC1 in the same buffer. The fractions were pooled after detection of proteins by SDSjPAGE [I31 and dialyzed against water. Proteins were separated either on a TSK ...