Comparative sequence analysis

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. 

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. 

Comparative sequence analysis based on MALDI-TOF-MS analysis of nucleic acids cleaved at specific bases and reference sequences used to construct in silico cleavage patterns enable cross-correlation of theoretical and experimental mass signal patterns. Observed signal pattern differences are indicators of sequence variations and... 

Given these Lego concepts, some aspects of comparative sequence analysis are reviewed next. First it is clear that there can be at least two levels of background sequence similarity that do not reflect common ancestry. The first is the local similarity between similar types of secondary elements, and second is that between sequences of secondary elements in similar folds. Thus one should anticipate that all four-helix bundles would have greater sequence similarity than that between an all-ce and an all-/3 protein, as well as greater than that between truly random sequences. This will complicate our ability to distinguish true homology from structural similarity (Henikoff and Henikoff, 1991 Claverie, 1995),... 

Figure 12.4A shows the interaction of the first CUE domain of Cue2 interacting with ubiquitin, which might serve as a general model for the interaction mode of other UBA-like domains. The CUE domain binds to the Ile-44 patch of ubiquitin, in accordance with the chemical shift perturbation results of the UBA ubiquitin interaction [52], On the side of the CUE domain, residues of the first and third helix participate in this interaction surface. These residues include the Phe-Pro and Leu-Leu motifs, which had been predicted to be important for ubiquitin binding, based on comparative sequence analysis of CUE-A and CUE-B domains [62]. Positions in close contact with ubiquitin are also indicated in the alignment of Figure 12.3. The two available structures of the CUE ubiquitin complexes offer little expla-...

Most plant peroxidases contain 2 His and an Arg which are essential for activity (22,23). Our recent EPR and resonance Raman evidence (IJ see above) demonstrates the presence of a proximal His ligated to the neme iron of MnP-1. Comparative sequence analysis (Fig. 2) indicates that the sequences flanking the proximal His and the distal His and Arg are conserved in the MnP-1 protein. In addition, very little variation is observed in the locations of the proximal His (residue 176) and the distal His and Arg (residues 46 and 42, respectively), suggesting that all of these peroxidases evolved from a common precursor. 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

Michel, F., and Westhof, E. (1990). Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216, 585-610. Milligan, J. F., and Uhlenbeck, O. C. (1989). Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51—62. 

COMPARATIVE SEQUENCE ANALYSIS USING BASE-SPECIFIC CLEAVAGE AND MALDI-TOF MS... 

Hartmer R, Storm N, Boecker S, Rodi CP, Hillenkamp F, Jurinke C, van den Boom D. RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis. Nucleic Acids Res 2003 31 e47. 

Matsushima, N., Tanaka, T., Enkhbayar, P., Mikami, T., Taga, M., Yamada, K., Kuroki, Y. Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. BMC Genomics 8 (2007) 124. 

F)G. 7. Comparative sequence analysis of PDl. Reproduced with permission from Park-konen el at. (1988). 

Thamatrakoln, K., Alverson, A., and Hildebrand, M. (2006) Comparative sequence analysis of diatom sflicon transporters Toward a mechanistic model of silicon transport. J. Phycol. 42, 822-834. 

Reznikoff WS, Bordenstein SR, Apodaca J. Comparative sequence analysis of IS50/Tn5 transposase. J. Bacteriol. 2004 186 8240-8247. 

Eichel-Streiber Cv, Laufenberg-Feldmann R, Sartingen S, etal. (1992) Comparative sequence analysis of the Clostridium difficile toxins A and B. In Mol Gen Genet, 233 260-268. 

In the absence of reliable predictive methods for assessing potential immunological cross-reactivity, a comparative sequence analysis approach can be used to identify whether or not known epitopes from human proteins exist in a candidate vaccine antigen. The Immune Epitope Database (IEDB) provides a comprehensive reference data set for known epitopes.78 When screening potential vaccine candidates, the presence of known human-derived epitopes can be ruled out by comparison against the IEDB (www.iedb.org). 

Kazianis, S., L. Gan, L. Della Coletta, B. Santi, D.C. Morizot and R.S. Nairn. Cloning and comparative sequence analysis ofTP53 in Xiphophorus fish hybrid melanoma models. Gene 212 31-38, 1998. 

Comparative sequence analysis of even well described inter-protein interactions (i.e., from X-ray structure of multi-domain or subunit proteins) has only recently been possible initial results have however shown some common features of quaternary interactions. There is hope that interactions in naturally selfassociating proteins will be similar to those that lead to irreversible interactions in refolded proteins, and that one can then use this knowledge to prevent precipitation. For example, fibrin clots can be dissolved by adding the tetra-peptide Gly-Pro-Arg-Pro, the amino acids at the N-termini of fibrinogen molecules after thrombin cleavage. A related peptide, Arg-Gly-Asp-Ser, from the carboxy- terminus of fibrinogen, inhibits platelet aggregation. ... 

One of the most important steps in comparative sequence analysis is the selection of suitable training sets of sequences. If a training set of promoters consists only of constitutively expressed sequences (constant level of expression, no or little regulation) little can be learned about any kind of tissue-specific expression regardless of the methods applied. Also inclusion of too many wrong sequences (e.g., that are no promoters at all) may prevent any meaningful analysis. Although this appears a bit trivial at first, it is a real issue when data are scarce and less well-characterized sequences have to used. 

This category of methods introduces the functional context in form of heuristic rules or tries to learn the context from comparative sequence analysis. 

Rinner, O. and Morgenstern, B. (2002) AGenDA gene prediction by comparative sequence analysis. In Silico Biol. 2, 195-205. 

Rivas, E. and Eddy, S. R. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics. 2, 8. 

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