PMC

OCT findings baseline to follow-up after 6 months are presented as boxplots. The horizontal lines in the middle of the boxplots demonstrate the medians. The interquartile range (IQR) is presented by the box, and the minimum and maximum values by whiskers (excluding outliers). Outliers defined as values 1.5 to 3.0 times outside the IQR are presented as circles and extreme outliers defined as values of more than 3.0 times outside the IQR are presented as asterisks. (A) On the left the macular retinal nerve fiber layer (mRNFL) thickness of the symptomatic nasal retinal sector with a significant (p < 0.05) reduction at follow-up after 6 months compared to baseline, N = 8, on the right the macular optical coherence tomography (OCT) sector grid with the affected nasal sector marked in red. (B) On the left the macular inner retinal layer (mIRL) thickness of the symptomatic nasal retinal sector at baseline with a significant (p < 0.05) reduction at follow-up after 6 months compared to baseline, N = 8, on the right the macular OCT sector grid with the affected nasal sector marked in red. (C) On the left the peripapillary retinal nerve fiber layer (pRNFL) thickness of the symptomatic temporal inferior retinal sector with a significant (p < 0.05) reduction at follow-up after 6 months compared to baseline, N = 12, on the right the peripapillary OCT sector grid with the affected temporal inferior sector marked in red. (D) On the left the pRNFL thickness of the symptomatic temporal superior retinal sector with a significant (p < 0.05) reduction at follow-up after 6 months compared to baseline, N = 12, on the right the peripapillary OCT sector grid with the affected temporal superior sector marked in red.

Evidence for a function of the Hsp70 sector in allosteric coupling. Examination of sector positions in the nucleotide-binding domain (blue) and in the substrate-binding domain (green) reveals many experimentally characterized sites implicated in allostery (colored in red; see text for details) (A) In the ATP-binding site, sector residues include determinants of nucleotide hydrolysis and nucleotide-mediated conformational change. (B) At nucleotide-binding domain surface contacting the substrate-binding domain, a patch of sector residues includes many known to perturb allostery upon mutation. (C) In the substrate-binding domains, the sector contains residues both proximal and distal from the substrate-binding site, and includes the functionally critical interdomain linker (390–392). (D) At the substrate-binding domain surface that comprises the interface with the nucleotide-binding domain, sector residues include many that display defects in allostery upon mutation. (E) Across the interdomain interface, mutation at residues Q152 and F216 (not shown) partially suppress the loss-of-function mutations at position 462 on the substrate-binding domain. Also shown are positions 415 and 326, sector residues that contact across the interdomain interface and are previously untested with regard to allosteric function.

Analysis of the growth phenotypes conferred by the L20Δ1, L20Δ2, and L20ΔN truncations. (A,B) L20Δ1 and L20Δ2 display complementation defects. The E. coli ΔrplT strain IBPC6801 was transformed with either plasmid pBL20ec, expressing wild-type L20 (L20 sector) or its derivatives pBL20ecΔ6–20 (L20Δ1 sector) or pBL20ecΔ6–29 (L20Δ2 sector) expressing the L20Δ1 and L20Δ2 truncations, respectively. The pBL20ecΔ6–20 and pBL20ecΔ6–29 transformants were cotransformed with the compatible plasmids pSGL6 expressing wild-type L20 (L20Δ1 + L20 and L20Δ2 + L20 sectors) or pSUrplTW61Stop expressing the N-terminal domain of L20 (L20Δ1 + L20N and L20Δ2 + L20N sectors). Growth was followed at 37°C upon induction of the expression of the different rplT alleles with 1 mM IPTG (A) and in noninducing conditions (B). (C) Overproduction of L20ΔN results in a dominant-lethal phenotype. The E. coli IBPC5311[λMQ21ΔNB] lysogen was transformed with either pBR322 (empty vector sector) or with plasmids pBL20ec (L20 sector) or its derivative pBL20ecΔN expressing the L20ΔN truncation (L20ΔN sector). The pBL20ecΔN transformant was cotransformed with the compatible plasmids pSGL6 expressing wild-type L20 (L20ΔN + L20 sector) or pSUrplTW61Stop expressing the N-terminal domain of L20 (L20ΔN + L20N sector). Induction was carried out with 1 mM IPTG.

A fraction of Gcn4p target genes is induced by 3AT in gcn4Δ cells. (A) Venn diagram depicting the overlap among 613 genes for which statistically significant data were obtained (P ≤ 0.05) and that showed an induction ratio of ≥2 in the WT ± 3AT (set C), GCN4/gcn4Δ, or gcn4Δ ± 3AT experiments. There are 229 Gcn4p target genes (sectors A and B) found at the intersection between 462 genes induced by 3AT in the WT (sectors A, B, C, and D) and 311 genes showing Gcn4p dependence for induction in the GCN4/gcn4Δ experiment (sectors F, B, and A). There were 280 genes induced by 3AT in the gcn4Δ ± 3AT experiment (sectors A, C, and E). The 151 genes in sector B are Gcn4p targets that were not induced by 3AT in the gcn4Δ strain and thus are completely dependent on Gcn4p for induction. Sector A contains the subset of Gcn4p target genes that were also induced by 3AT in the gcn4Δ mutant. These 78 genes are subject to dual regulation and require Gcn4p only for maximal induction by 3AT. Sector C is comprised of the 133 genes induced by 3AT in both gcn4Δ and WT cells which showed little or no dependence on Gcn4p in the GCN4/gcn4Δ experiment (induction ratio of <2-fold). These genes are induced by 3AT independently of Gcn4p. Thus, ∼50% of the genes induced by 3AT in the WT are designated Gcn4p targets because of their dependence on Gcn4p for maximal induction ([A + B]/[A + B + C + D]), and 34% of these target genes (A/[A + B]) can be induced by 3AT even in the absence of Gcn4p. The genes in sector F showed greater expression in WT cells than in gcn4Δ cells in the presence of 3AT but were not induced by 3AT in the WT. This class includes additional Gcn4p targets that depend on Gcn4p primarily to prevent repression in histidine-starved cells (see text). The genes in sector E were induced only in gcn4Δ cells and thus belong to the class of genes induced by 3AT independently of Gcn4p. The results obtained for the 100 genes in sector D marked with an asterisk are paradoxical in that any genes induced by 3AT in the WT should be either dependent on (sector A or B) or independent of (sector C) Gcn4p for their induction. Close examination of this group revealed that 28 genes were induced only in the single WT ± 3AT experiment used to construct this diagram (data set C) but not in other experiments of the same type (data set A, B, or D); hence, these 28 genes probably are not 3AT inducible. Fifty of the remaining genes in sector D showed induction ratios between 1.5 and 2.0 in the GCN4/gcn4Δ experiment and most likely belong to sector A or B, comprising the Gcn4p targets. Fifteen of the remaining genes had induction ratios between 1.5 and 2.0 in the gcn4Δ ± 3AT experiment and probably belong to sector C or E, comprising the Gcn4p-independent 3AT-inducible genes. Among the 133 genes assigned to sector C, 53 had induction ratios between 1.5- and 2-fold in the GCN4/gcn4Δ experiment, suggesting that they belong to sector A: Gcn4p targets that are also inducible by a Gcn4p-independent mechanism. (B) Color display plot of the expression ratios of selected Gcn4p target genes that were induced ≥1.9-fold by 3AT in the gcn4Δ strain. The log₁₀ ratios of expression are depicted using the color code described for Fig. , with the brightest red depicting log₁₀ ratios of ≥1.0 and black signifying no significant change in expression (P > 0.05). Data were taken from the different experiments listed across the top (as defined in Fig. and Table ) for the genes listed on the right.