Compensatory mutations

The globin fold has been used to study evolutionary constraints for maintaining structure and function. Evolutionary divergence is primarily constrained by conservation of the hydrophobicity of buried residues. In contrast, neither conserved sequence nor size-compensatory mutations in the hydrophobic core are important. Proteins adapt to mutations in buried residues by small changes of overall structure that in the globins involve movements of entire helices relative to each other. 

As for HIV, the selection of HCV drug resistant variants can be accompanied by a decrease in RC. For HCV protease inhibitor resistant variants, the level of resistance seems to be inversely related to viral fitness (Sarrazin et al. 2007 Tong et al. 2006 Yi et al. 2006). There is some evidence that viral RC can be restored by the selection of compensatory mutations within the protease gene (Sarrazin et al. 2007 Tong et al. 2006 Yi et al. 2006). However, further research is warranted to investigate to what extent viral fitness can be restored and by which mutations. Also for the nucleoside and non-nucleoside inhibitors, the selection of resistance results in a fitness defect. It remains to be investigated whether or not compensatory mutations can be selected. 

The evolution of antiviral resistance for viruses discussed in this chapter (HIV, HBV, HCV, and Influenza virus) shares some common features. Replication in vivo results in the generation of viral variation and selection of preexisting viruses from the population occurs under particular conditions. This will only happen when the escaping viruses have a sufficient level of both resistance and RC. In most cases, the resistance level subsequently increases further by the gradual acquisition of further mutations. Additional compensatory mutations then accumulate that help to restore full RC in the third stage. 

While the effect of primary mutations on reduced binding affinities of inhibitors can be at least partially explained in view of the accumulated structural data, the function of secondary, or compensatory mutations in the resistant HIV PR is difficult to rationalize as yet. The predominant compensatory mutations observed in the resistant variants involve residues Leu63/63, 1 71/7 , Met46/46, ... 

Fig. 12.2. Consensus structure and dot plot for die alignment of 9 RNAI sequences. Encircled bases in tire consensus structure mark consistent and compensatory mutations.

If certain amino acids (such as disulfide bonds or crucial amino acids in the hydrophobic core) are indispensable for protein stability, these positions can be changed by site-directed mutagenesis (Proba et al., 1998). To avoid back-mutations during the evolution process or the selection of a residual wild-type contamination, the pool is amplified after each round of ribosome display with a primer that reintroduces the destabilizing mutation. If the mutation is not close to one of the termini, the coding sequence has to be amplified in two parts, which are then reassembled by PCR. Thus, to evolve improved stabilities this strategy first removes known crucial stabilizing factors to select for compensatory mutations at different positions. 

Stock, J., Borezuk, A., Chiou, F., Burchenal, J. E. B. (1985). Compensatory mutations in receptor function a re-evaluation of the role of methylation in bacterial chemotaxis. Proc. Natl. Acad. Sci. USA 82, 8364-8368. 

This sorts the output by the Combinations/Pair value, i.e., by compensatory mutations supporting the structure (explained in Note 5). 

Sequence covariations are a direct consequence of RNA basepairing rules. RNA helices normally contain only 6 out of the 16 possible combinations the Watson-Crick pairs GC, CG, AU, UA, and the somewhat weaker wobble pairs GU and UG. Mutations in helical regions therefore have to be correlated. In particular, we often find compensatory mutations where a mutation on one side of the helix is compensated by a second mutation on the other side, e.g., a C G pair changes into a U A pair. Mutations where only one pairing partner changes (such as C G to U G) are termed consistent mutations. ... 

Finally, the in silico two-hybrid system implies that traces of the coevolution of interacting proteins can be detected in the form of patterns of possible compensatory mutations in the interface of the two proteins. The so-called correlated mutations have been useful for predicting the tendency of interacting residue pairs to be located in the proximity of protein interfaces [58]. As in the case of mirror tree, this method has also been applied to large datasets [59]. 

For the mutant, one point mutation enhancing photosynthetic growth occurred at LI 87, which reverted a mutagenic Phe residue back to Leu (as found in WT). Residue L187 is closest to the center of Hg [6]. Another revertant had a compensatory mutation that mapped to residue L237 and substituted a Pro for an Ala residue. According to the x-ray structure [17], residue L237 is actually in the E helix and in the vicinity of Ha (not Hb). 

Parent Strain Reversion Compensatory mutations Occurrence PS assay ... 

These results are difficult to interpret but they do lead to interesting h>yotheses. Since the RC has been symmetrized, one possibility is second site mutations in either subunit could produce similar effects that stabilize the RC structure. A speculative but more interesting possibility is that the symmetrization of the RC causes the two chromophore branches to have the same potential for electron transfer. If the two chromophore branches in the RC are structurally and functionally similar in these helix exchange mutants, either branch could be activated by a secondary mutation. Because of the symmetry, a compensatory mutation activating the A-branch would be homologous to a mutation that activates the B-branch. Future experiments will be aimed at detecting such aberrant electron transfer in these mutants. 

STUDY OF REACTION CENTER FUNCTION BY ANALYSIS OF THE EFFECTS OF SITE-SPECIFIC AND COMPENSATORY MUTATIONS... 

Lethal or ts mutations under nonpermissive conditions often generate revert-ants. Revertants arise from point mutations and insertions, but not from deletions. Reversion in point mutations may involve the reversal of the original mutation true reversion) or a compensatory mutation elsewhere in the gene (second-site or more generally suppressor mutation). The reversion from insertional mutations usually occurs by appropriate deletion of the inserted part. The suppression restores a wild- or pseudo-wild-type phenotype to a mutant organism in which the primary mutation is still maintained. 

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