Ribosomal analysis

Felske A, Rheims H, Wolterink A, Stackebrandt E, Akkermans AD (1997) Ribosome analysis reveals prominent activity of an uncultured membtu of the class Actinobacteria in grassland soils. Microbiology 143 2983-2989... 

A North American origin for the silverswords clearly emerged from the application of DNA-sequence techniques to members of the alliance and representative Californian species (Baldwin et al., 1990, 1991). The conclusions from these studies, based on chloroplast restriction site analysis were subsequently corroborated by ITS nuclear ribosomal DNA studies. A comprehensive review of these studies can be found in Carlquist et al. (2003). 

D. A. Stahl, D. J. Lane, G. J. Olsen, and N. R. Pace, Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224 409 (1984). 

G. A. Kowalchuk, J. R. Stephen, W. DeBoer, J. 1. Prosser, T. M. Embley, and J. W. Woldendorp, Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified I6S ribosomal DNA fragments. Appl. Environ. Microbiol. 6.1 1489 (1997). 

Infrared spectroscopy, including FTIR Polyacrylamide gel electrophoresis (PAGE) Amplified ribosomal DNA restriction analysis (ARDRA)... 

Sato, T. Hu, J. P Ohki, K. Yamaura, M. Washio, J. Matsuyama, J. Takahashi, N. Identification of mutans streptococci by restriction fragment length polymorphism analysis of polymerase chain reaction-amplified 16S ribosomal RNA genes. Oral Microbiol. Immunol. 2003,18, 323-326. 

Approximately 90% to 95% of whole-cell MALDI MS profiles are representative of the ribosomal proteins abundant in rapid growth whole cells. Although the identification of proteins, from whole bacterial cells, by MALDI-TOF MS analysis is ambiguous, at best, due to the low-mass accuracy and resolving power, several researchers realized that many of the observed... 

Although ribosomal proteins are readily observed as in Figures 13.7 and 13.8 altered matrix conditions can alter the relative ionization of bacterial whole-cell compounds. A systematic analysis involving laser power/fluence and sample preparation conditions reveals that if the concentrated trifluo-roacetic acid is added and the laser power increased above optimal conditions, ionization of bacterial surface compounds can be enhanced. Figure 13.9 is the resulting 9.4 T MALDI-FTMS, seen are both the Braun s lipoprotein56,57 and the Murein lipoprotein. Both of these compounds are complex combinations of hydrocarbon lipids attached to a protein base. This is the first MALDI-FTMS observation of surface proteins desorbed directly from whole cells by influencing ionization conditions. 

FIGURE 13.4 Total ion chromatograms from the ID LC/MS analysis of a yeast ribosomal protein fraction separated using 0.1% TFA (Panel a) and 0.1% formic acid (Panel b) as mobile phase modifiers. TFA produced narrower, more concentrated, peaks for mass analysis that did not overcome the significant electrospray ionization suppression associated with using this modifier for LC/MS studies, resulting in an overall reduction in component intensities. 

FIGURE 13.5 The total ion chromatogram and deconvoluted protein mass map for a ID LC/MS analysis of yeast ribosomal proteins. The bubble size is proportional to component intensity. 

Lee, S.W., Berger, S.J., Martinovic, S., Pasa-Tolic, L., Anderson, G.A., Shen, Y., Zhao, R., Smith, R.D. (2002). Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proc. Natl. Acad. Sci. USA 99, 5942-5947. 

Fig. 1.1. The phylogenetic structure of the Nematoda revealed by small subunit ribosomal RNA analysis. (A) Neighbour-joining (NJ) analysis of aligned ssu rRNA genes from nematodes. The alignment is based on that of Blaxter etal. (1998), with the addition of sequences from Aleshin etal. (1998), Nadler (1998)...

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