A Cluster of Early Eggshell Protein Genes in \u3cem\u3eDrosophila melanogaster\u3c/em\u3e: Gene Structure, Expression and Regulation

The formation of the insect eggshell is a popular model system in which to study molecular mechanisms involved in the production of complex structures. The eggshell, secreted by ovarian follicle cells during the later stages of oocyte maturation, is deposited in several layers. The vitelline membrane is deposited during stages 8-10, and the several layers of the chorion are secreted during stages 11-14. We are examining the expression of early eggshell genes. I have characterized a cluster of follicle cell specific genes expressed during the period of vitelline membrane formation in Drosophila. Four genes are clustered in 8 kilobase pairs of genomic DNA from the 26A region of the second chromosome. Three of these genes encode 700 nucleotide long RNAs; the two most abundantly expressed code for major vitelline membrane proteins. Hybrid selected translation and sequencing studies suggest the product of the third gene is a minor eggshell protein. The fourth gene of the cluster specifies a 1400 nucleotide RNA of unknown function. The direction of transcription, intron-less structures and positions of these genes have been determined by northern blot analysis and S1 protection studies. Northern blot analysis demonstrates that these genes are expressed specifically in the female\u27s ovary and are only detected in eggchambers of stages producing vitelline membrane. The follicle cell specific expression of these genes has been demonstrated by in situ hybridization to ovarian tissue sections or by S1 protection studies with RNA isolated from follicle cell or nurse cell fractions of cut stage 10 eggchambers. Gel electrophoresis-DNA binding studies with nuclear proteins isolated from expressing tissue have identified two potential cis-regulatory regions of one of the major vitelline membrane protein genes. One region is 5\sp\prime to the gene, between $-$146 and $-$53; the second region is within the transcribed portion of the gene, upstream of +153. The location of the 5\sp\prime region is similar to that of elements required for proper tissue and temporal specificity of both early and late chorion protein genes

List of base-pair substitutions found in Mutation Accumulation lines of Escherichia coli K-12 PFM2 and its derivative strains (DNA repair)

List of base-pair substitutions found in mutation accumulation of the following E. coli strains: 1. K12 PFM2 (LB) 2. K12 PFM2 (minimal) 3. ED1a 4. IAI1 5. PFM101 6. PFM133 7. PFM35 8. PFM40 9. PFM88 10. PFM180 11. PFM22 12. PFM91 13. PFM61 14. PFM6 15. PFM94Multidisciplinary University Research Initiative Award W911NF-09-1-0444 from the US Army Research OfficePlease refer to Foster et al. PNAS (2015)Microsoft Excel for Mac 2011 Version 14.3.8 (130913

Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair Defective Escherichia coli

Mismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defective Escherichia coli strains yielded ≈30,000 base-pair substitutions (BPSs), revealing mutational patterns across the entire chromosome. The BPS spectrum was dominated by A:T to G:C transitions, which occurred predominantly at the center base of 5'NAC3'+5'GTN3' triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for BPSs, and the rate at which these occurred increased with run length. Comparison with ≈2000 BPSs accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In an mmr ndk double mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone, or less well corrected by proofreading, than was leading strand synthesis