Haloarcula marismortui, ribosomal

The origin of the idea that a ribosome might be a ribozyme is derived from the experiment in which peptidyl transferase activity was observed even after digestion of protein components of the ribosome [15]. This was surprising because the most important biological function involved in the synthesis of proteins is catalyzed by RNA. Recently, a large ribosomal subunit from Haloarcula marismortui was determined at a resolution of 2.4 A [16, 155]. Importantly, because of the absence of proteins at the active site, it was concluded that the key peptidyl transferase reaction is accomplished by the ribosomal RNA (rRNA) itself, not by proteins. How does it work ... 

More recently, however, this mechanism was questioned by several researchers [156-158]. In the case of E. coli 50S subunits, the pH-dependent modification of A2451 by DMS (A2486 in Haloarcula marismortui) occurred only in its inactive conformation [157]. Under the conditions wherein the ribosomes were fully active, in contrast, the modification of A2451 by DMS could not be recognized. These results indicate that A2451 becomes shielded from chemical modification by a conformational change upon activation. Thus, it was concluded that the conditional modification of A2451 by DMS... 

This small RNA is found in the central protuberance of the 50S ribosomal subunit. See Fig 29-4A. Photocrosslinking using thiouridine-containing 5S RNA suggested a close proximity of U89 (marked by arrow) with nucleotide 2477 of the 23S RNA in the loop end of helix 89 (Fig. 29-4).93 (B) Stereoscopic view of the 5S RNA as observed in ribosomes of Haloarcula marismortui. From Ban et al 7 Courtesy of Thomas A. Steitz. 

Figure 29-6 Some protein-RNA interactions within the ribosome. (A) A space-filling model of the 23S and 5S RNA with associated proteins from the ribosome of Haloarcula marismortui. The CCA ends of bound tRNA molecules in the A, P, and E sites are also included. The view is looking into the active site cleft. The proteins with e after the number are related to eukaryotic ribosomal proteins more closely than to those of E. coli.17 Courtesy of T. A. Steitz. (B) Three-dimensional structure of a 70S ribosome from Thermus thermophilus. The 30S subunit is to the right of the 50S subunit. Courtesy of Yusupov et al.33a (C) Stereoscopic view of the helix 21 to helix 23b region of the 16S RNA with associated proteins S6 (upper left), S18 (upper center, front), and S15 (lower back) from T. thermophilus. Courtesy of Agalarov et at.31 (D) Simplified in vitro assembly map of the central domain of the 30S bacterial ribosome. Courtesy of Gloria Culver. (E) Contacts of proteins with the central (platform) domain of the 16S RNA component. The sequence shown is that of Thermus thermophilus. Courtesy of Agalarov et al. (F) Three drawings showing alternative location of the four copies of protein L7/L12. The N-terminal and C-terminal...

Structures for three 16-membered macrolides and one 15-memberered macrolide bound to the archaeal ribosome of Haloarcula marismortui (Hm) are available [8], as are structures for four 14-membered macrolides bound to the bacterial ribosome of Ddnococcus radiodurans Dr) [4]. Interestingly, it appears that the 14-mem-bered macrolides do not bind to the bacterial ribosomes in the same way that the... 

Since all the r-proteins from both the large (L) and the small (S) ribosomal subunits of E. coli are sequenced and well characterized [106], homologous proteins from other organisms are named according to their E. coli counterpart. For example, proteins homologous to L23 of E. coli (Eco L23) will be called Sac L23 in Sulfolobus acidocaldarius, Hma L23 in Haloarcula marismortui and See L23 in Saccharomyces cerevisiae. In Table 2 (below), we have used this nomenclature to identify any r-protein that, from its sequence similarity, was equivalent to a known E. coli r-protein. Proteins which have no counterparts in E. coli (or where the sequence similarity is too weak to identify the relationship) are listed by the numbers described in the original publications and a trivial name. These numbers usually refer to the mobility of the protein in a 2D polyacrylamide gel. For example, HS15 is a protein from the small ribosomal subunit of H. marismortui which has no counterpart in E. co/j [107]. 

In this chapter, the molecular-biological mode of action of macrolide antibiotics and the biochemical and genetic mechanisms of resistance to MLS antibiotics are reviewed. Based on a recent X-ray crystallographic study on a 50S ribosomal subunit from Haloarcula marismortui and the finding of intracellular macrolide accumulation, the mode of action from the viewpoint of a new hypothetical concept, deposition binding, and mechanisms of drug resistance in clinically isolated bacteria are discussed. In addition, recent major developments in macrolide antibiotics are briefly described. 

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the SOS subunit of ribosomes of Haloarcula marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban rf Courtesy of Thomas A. Steitz. (B) The corresponding structure of...

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the SOS subunit of ribosomes of Haloarcula marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban cf Courtesy of Thomas A. Steitz. (B) The corresponding structure of the 23S RNA from Thermus thermophilus. Courtesy of Yusupov et alP (C) Simplified drawing of the secondary structure of . coli 23S RNA showing the six domains. The peptidyltransferase loop (see also Fig. 29-14) is labeled. This diagram is customarily presented in two halves, which are here connected by dashed lines. Stem-loop 1, which contains both residues 1 and 2000, is often shown in both halves but here only once. From Merryman et al7 Similar diagrams for Haloarcula marismortui and for the mouse reveal a largely conserved structure with nearly identical active sites. (D) Cryo-electron microscopic (Cryo-EM) reconstruction of a SOS subunit of a modified E. coli ribosome. The RNA has been modified genetically to have an...

However, the exact number of proteins present in the archaeal ribosome is still unknown. The number quoted by various investigators, based on 2D polyacrylamide gel electrophoresis, depends on the resolving power of the gel system used. Recent studies by Casiano et al. [11] suggest that the Sulfolobus 508 ribosomal subunit could contain as many as 43 r-proteins, and work from our laboratory [12] on the structure of the Sulfolobus r-proteins and from Wittmann s laboratory [13] on Haloarcula (formerly Halobacterium) marismortui r-proteins indicates an increasing number of proteins present in the archaeal ribosome that are not present in the bacterial ribosome. It may well be that the archaeal ribosome contains more proteins than are present in the bacterial E. coll) ribosome, or the bacterial ribosome contains proteins not found in the archaeal ribosome (see section 6). 

Haloferax (formerly Halobacterium) volcanii, a moderately halophilic species. A close relative of Haloferax volcanii is Haloferax phenon K isolate Aa 2.2 [4]. Halobacterium marismortui, the subject of extensive work on ribosomal proteins, is not closely related to Halobacterium salinarium, instead, it belongs in the genus Haloarcula [2]. 

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