To bring this further into perspective, the projected upstream shift caused by the project is less than a mile -- well below normal tidal and seasonal fluctuations.
However, our experimental data (Figure 6A,B) suggest that there is not such a strong preference for an R. The one residue upstream shift by the cTP cleavage site predictor, is most likely a consequence of the build-in preference (based a small set of in vitro cleavage experiments) for cleavage after an R, as explained in [58].
To accommodate the wrong incoming nucleotide in the closed polymerase conformation, the templating base vacates the coding position with an upstream shift in the template strand.
When Pol II GOF alleles are combined with the strong upstream shifting allele tfg2 ∆146-180, the double mutants are inviable on this medium.
The weaker upstream shifting allele tfg2 ∆261-273 also exacerbates MPA sensitivity of Pol II GOF alleles, with the resulting double mutants exhibiting no growth on this medium.
The strongest upstream shifting allele tfg2 ∆146-180 suppressed GalR phenotypes of all Pol II alleles that had the GalR phenotype, whether GOFs or LOFs; tfg2 ∆233-248, an allele with no apparent ADH1 TSS defect, enhanced GalR phenotypes of weak Pol II GOF alleles.
When creating a sequence logo of the predicted cTP from a much larger dataset of 898 annotated Arabidopsis chloroplast proteins (outer envelope proteins were removed) (see further below), we observe a similar consensus sequence as for the original training set and a similar upstream shift of one residue as compared to the experimental consensus sequence presented.
This upstream shift of sedimentation during the Little Ice Age was caused by gradually decreasing runoff resulting from aridification of the upper part of the Hoanib river catchment lying east of the Namib desert margin ≥1.200 m a.s.l.l
We also utilized SUA7 alleles containing substitutions in the "B-reader region": sua7 -1 (encodes E62K in TFIIB), sua7 -3 (encodes R78C in TFIIB) alleles that have been shown to confer downstream TSS shifts by the Hampsey group (Pinto et al. 1994; Wu et al. 1999), and sua7 -58andand sua7 -70A5 mutants previously described as having upstream shift effects (Zhang et al. 2002).
For example, a mutation juxtaposed to a phosphorylation site on position 721 of damage-specific DNA binding protein 1 (DDB1 P721Q) is predicted to cause an upstream shift from CDK1 to ATM and a similar mutation on CCP110 (CCP110 P171leadsads to a predicted upstream rewiring from CDK1 to PLK1 (Table S3).
