Sharon A. Boylan

Isolation of a secY homologue from Bacillus subtilis: evidence for a common protein export pathway in eubacteria

Genetic and biochemical studies have shown that the product of the Escherichia coli secY gene is an integral membrane protein with a central role in protein secretion. We found the Bacillus subtilis secY homologue within the spc‐alpha ribosomal protein operon at the same position occupied by E. coli secY. B. subtilis secY coded for a hypothetical product 41% identical to E. coli SecY, a protein thought to contain 10 membrane‐spanning segments and 11 hydrophilic regions, six of which are exposed to the cytoplasm and five to the periplasm. We predicted similar segments in B. subtilis SecY, and the primary sequences of the second and third cytoplasmic regions and the first, second, fourth, fifth, seventh, and tenth membrane segments were particularly conserved, sharing greater than 50% identity with E. coli SecY. We propose that the conserved cytoplasmic regions interact with similar cytoplasmic secretion factors in both organisms and that the conserved membrane‐spanning segments actively participate in protein export. Our results suggest that despite the evolutionary differences reflected in cell wall architecture, Gram‐negative and Gram‐positive bacteria possess a similar protein export apparatus.

The expression of native and cultured human retinal pigment epithelial cells grown in different culture conditions

Aim: To determine the transcriptional proximity of retinal pigment epithelium (RPE) cells grown under different culture conditions and native RPE. Methods: ARPE-19 cells were grown under five conditions in 10% CO2: “subconfluent” in DMEM/F12 + 10% FBS, “confluent” in serum and serum withdrawn, and “differentiated” for 2.5 months in serum and serum withdrawn medium. Native RPE was laser microdissected. Total RNA was extracted, reverse transcribed, and radiolabelled probes were hybridised to an array containing 5353 genes. Arrays were evaluated by hierarchical cluster analysis and significance analysis of microarrays. Results: 78% of genes were expressed by native RPE while 45.3–47.7% were expressed by ARPE-19 cells, depending on culture condition. While the most abundant genes were expressed by native and cultured cells, significant differences in low abundance genes were seen. Hierarchical cluster analysis showed that confluent and differentiated, serum withdrawn cultures clustered closest to native RPE, and that serum segregated cultured cells from native RPE. The number of differentially expressed genes and their function, and profile of expressed and unexpressed genes, demonstrate differences between native and cultured cells. Conclusions: While ARPE-19 cells have significant value for studying RPE behaviour, investigators must be aware of how culture conditions can influence the mRNA phenotype of the cell.

Genetic and transcriptional organization of the Bacillus subtilis spc-α region

Abstract We used chromosomal walking methods to isolate a 10.8-kb region from the major ribosomal protein (r-protein) gene cluster of Bacillus subtilis (Bs). The gene order in this region, given by gene product, was r-proteins L16-L29-S17-L14-L24-L5-S14-S8-L6-L18-S5-L30-L15-SecY-adenylate kinase (Adk)-methionine aminopeptidase (Map)-initiation factor 1 (IF1)-L36-S13-S11-α subunit of RNA polymerase-L17. The region cloned, therefore, contains the homologues for the last three genes of the Escherichia coli (Ec) S10 operon, together with entire spc and α operons. This Bs organization differs from the corresponding region in Ec by the inclusion of the genes encoding Adk, Map and IF1 between the genes encoding SecY and L36. Plasmid integration experiments indicated that all 22 genes comprise a single large transcriptional unit controlled from a major promoter which lies upstream from the gene encoding r-protein L16. Promoter probe experiments located lesser activities internal to this large transcriptional unit, the secY and map promoters. The secY promoter region (psecY) contained two activities, each principally functioning in the stationary growth phase when high protein export is required. Thus, the Bs S10-spc-α region differs from its Ec counterpart in both genetic and transcriptional organization. Given this difference in transcriptional organization, the mechanisms coordinating expression of the translational apparatus are also likely to differ between Ec and Bs

Two genes from Bacillus subtilis under the sole control of the general stress transcription factor σB

The general stress response of Bacillus subtilis is triggered by a variety of environmental and metabolic stresses which activate the sigmaB transcription factor. Among the more than 100 genes controlled by sigmaB (the csb genes), the functions identified thus far include resistance to oxidative stress, resistance to protein denaturation and resistance to osmotic stress. To understand the breadth of functions in which csb genes participate, the transcriptional organization and predicted products of two such genes previously identified in a screen for sigmaB-dependent lacZ fusions were analysed. The csb-22::Tn917lacZ and csb-34::Tn917lacZ fusions are unusual among csb genes in that their expression appears to be completely dependent upon sigmaB. By plasmid-integration experiments, fusion analyses and site-directed mutagenesis, stress-inducible, sigmaB-dependent promoters for both these fusions were identified. The csb-34 fusion marked an ORF (yxcC or csbC) which by sequence analysis lay in a monocistronic transcriptional unit. This ORF encoded a predicted 461-residue product which had high identity with Class I sugar transporters of the major facilitator superfamily. It was speculated that the csbC product could serve either a nutritional or an osmotic protection function. In contrast, the csb-22 fusion identified an ORF (ywmG or csbD) which appeared to be the second gene of a two-gene operon. This ORF encoded a predicted 62-residue product which resembled a small Escherichia coli protein of unknown function. The sigmaB. dependent promoter lay immediately upstream from csbD and appeared to be an internal promoter for the operon.

Early-blocked sporulation mutations alter expression of enzymes under carbon control in Bacillus subtilis

SummaryThe physiological roles of the gene subset defined by early-blocked sporulation mutations (spo0) and their second-site suppressor alleles (rvtA11 and crsA47) remain cryptic for both vegetative and sporulating Bacillus subtilis cells. To test the hypothesis that spo0 gene products affect global regulation, we assayed the levels of carbon- and nitrogen-sensitive enzymes in wild-type and spo0 strains grown in a defined minimal medium containing various carbon and nitrogen sources. All the spo0 mutations (except spo0J) affected both histidase and arabinose isomerase levels in an unexpected way: levels of both carbon-sensitive enzymes were two- to six-fold higher in spo0 strains compared to wild type, when cells were grown on the derepressing carbon sources arabinose or maltose. There was no difference in enzyme levels with glucose-grown cells, nor was there a significant difference in levels of the carbonindependent enzymes glutamine synthetase and glucose-6-phosphate dehydrogenase. This effect was not due to a slower growth rate for the spo0 mutants on the poor carbon and nitrogen sources used. The levels of carbon-sensitive enzymes were not simply correlated with sporulation ability in genetically suppressed spo0 mutants, but the rvtA and crsA suppressors each had such marked effects on wild-type growth and enzyme levels that these results were difficult to interpret. We conclude that directly or indirectly the spo0 mutations, although blocking the sporulation process, increase levels of carbon-sensitive enzymes, possibly at the level of gene expression.

An optimized protocol for first strand cDNA synthesis from laser capture microdissected tissue.

An Optimized Protocol for First Strand cDNA Synthesis from Laser Capture Microdissected Tissue

Acute hyperoxia-induced transcriptional response in the mouse RPE/choroid.

Oxidative stress has been studied in the retinal pigmented epithelium (RPE) in vitro but not in vivo. Our purpose, therefore, was to develop an in vivo model of acute oxidative stress in the C57BL/6J mouse. Mice were exposed to > or = 98% oxygen for 0, 2, or 6 h, and amplified total RNA from the RPE/choroid was applied to microarrays examining about 2200 unique genes. Statistical analysis determined that 642 genes, out of a total of 1349 expressed, were significantly downregulated at only 2 h, only 6 h, or both 2 and 6 h, and a single gene, ubiquitin, was upregulated. These genes are involved in all aspects of cellular functions, and there are no major differences among the three groups. The effect of hyperoxia on the RPE/choroid in vivo appears to be very similar to oxidative stress studies performed with an RPE cell line in vitro. All 11 genes identified as being regulated by all three oxidants in our previous study, and were expressed by mouse, were also differentially regulated by hyperoxia. At least for the initial response to an oxidative challenge, the in vitro ARPE-19 cell line is a reasonable model for in vivo studies.