16S rRNA

FIGURE 12.39 The proposed secondary structure for E. coli 16S rRNA, based on comparative sequence analysis in which the folding pattern is assumed to be conserved across different species. The molecule can be subdivided into four domains—I, II, III, and IV—on the basis of contiguous stretches of the chain that are closed by long-range base-pairing interactions. I, the 5 -domain, includes nucleotides 27 through 556. II, the central domain, runs from nucleotide 564 to 912. Two domains comprise the 3 -end of the molecule. Ill, the major one, comprises nucleotides 923 to 1391. IV, the 3 -terminal domain, covers residues 1392 to 1541. 

Tetracycline has a secondary binding site in the H27 switch region that may also be fimctionally significant. The dtug binds at the interface of the three domains of 16S rRNA, close to helix 44 and between helices 11 and 27. As with the primary binding site, contacts are made from the hydrophilic face of the dtug to the backbone of 16S rRNA. In this binding site, tetracycline may function to stabilize the ram state. 

The universal antibiotic pactamycin targets a highly conserved region of 16S rRNA, contacting the tips of helices 23b and 24a in the central domain. Pactamycin folds up to mimic a RNA dinucleotide in that its... 

Ribosomal Protein Synthesis Inhibitors. Figure 3 The chemical structure of tetracycline and possible interactions with 16S rRNA in the primary binding site. Arrows with numbers indicate distances (in A) between functional groups. There are no interactions obseived between the upper portion of the molecule and 16S rRNA consistent with data that these positions can be modified without affecting inhibitory action (from Brodersen et al. [4] with copynght permission). 

Figure 2. Universal phylogenetic tree determined from rRNA sequence comparisons. A matrix of evolutionary distances (99) was calculated from an alignment (260) of representative 16S RRNA sequences from each of the three urkingdoms. The length of the lines is proportional to the phylogenetic difference. (Reproduced with permission from ret 16. Copyright 19. American Society for Microbiology.)...

Fig. 1. (a) Schematic representation of the three types of anoxygenic ([1] and [2]) and oxygenic ([3]) photosynthesis found in plants and bacteria, (b) Phylogenetic tree based on 16S-rRNA sequence comparisons featuring only photo synthetic phyla. 

Zhao H, D Yang, CR Woese, MP Bryant (1990) Assignment of Clostridium bryantii to Syntrophospora bry-antii gen. nov., comb. nov. on the basis of a 16S rRNA sequence analysis of its crotonate-grown pure culture. Int J Syst Bacteriol 40 40-44. 

Inagaki F et al. (2004) Characterization of Cl-metabolizing prokaryotic communities in methane seep habitat at the Kurishima Knoll, Southern Tyuku Arc, by analysing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70 7445-7455. 

A site at the Agricultural Experimental Station (Ithaca, NY) was treated in microcosms with C-labeled glucose, phenol, caffeine, and naphthalene. Levels of C02 were measured to assess utilization of the substrates, and the populations analyzed by separating the C-labeled DNA by density centrifugation, followed by PCR amplification and sequencing of 16S rRNA (Padmanabhan et al. 2003). Populations contained relatives to a range of bacteria that varied with the substrate. Only relatives of Acinetobacter were found in all samples, and for caffeine only Pantoea. 

It has been established that methane is produced on rice roots by reduction of CO2. This was examined in rice roots using a combination of 16S rRNA sequencing and density gradient fractionation of C-labeled DNA after incubation with C02. The major groups of archaea detected were Methanosarcinaceae that decreased with time to be replaced by the hitherto uncultured Rice Cluster I, although the former subsequently dominated (Lu et al. 2005). 

El Fantroussi S, L Verschuere, W Verstraete, EM Top (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl Environ Microbiol 65 982-988. 

Holoman TRP, MA Elberson, LA Cutter, HD May, KR Sowers (1998) Characterization of a defined 2,3,5,6-tetrachlorobiphenyl-orf/io-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl Environ Microbiol 64 3359-3367. 

Padmanabhan P, S Padmanabhan, C DeRito, A Gray, D Gannon, JR Snape, DC Tsai, W Park, C Jeon, EL Madsen (2003) Respiration of C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of C-labeled soil DNA. Appl Environ Microbiol 69 1614-1622. 

Briglia M, RIL Eggen, WM de Vos et al. (1996) Rapid and sensitive method for the detection of Mycobacterium chlorophenolicum PCP-1 in soil based on 16S rRNA gene-targeted PCR. Appl Environ Microbiol 62 1478-1480. 

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