The phosphoinositide phosphatase Sac1 regulates cell shape and microtubule stability in the developing Drosophila eye.

Epithelial patterning in the developing Drosophila melanogaster eye requires the Neph1 homolog Roughest (Rst), an immunoglobulin family cell surface adhesion molecule expressed in interommatidial cells (IOCs). Here, using a novel temperature-sensitive (ts) allele, we show that the phosphoinositide phosphatase Sac1 is also required for IOC patterning. Sac1ts mutants have rough eyes and retinal patterning defects that resemble rst mutants. Sac1ts retinas exhibit elevated levels of phosphatidylinositol 4-phosphate (PI4P), consistent with the role of Sac1 as a PI4P phosphatase. Indeed, genetic rescue and interaction experiments reveal that restriction of PI4P levels by Sac1 is crucial for normal eye development. Rst is delivered to the cell surface in Sac1ts mutants. However, Sac1ts mutant IOCs exhibit severe defects in microtubule organization, associated with accumulation of Rst and the exocyst subunit Sec8 in enlarged intracellular vesicles upon cold fixation ex vivo Together, our data reveal a novel requirement for Sac1 in promoting microtubule stability and suggest that Rst trafficking occurs in a microtubule- and exocyst-dependent manner.

Genome-scale analysis of anti-metabolite directed strain engineering.

Classic strain engineering methods have previously been limited by the low-throughput of conventional sequencing technology. Here, we applied a new genomics technology, scalar analysis of library enrichments (SCALEs), to measure >3 million Escherichia coli genomic library clone enrichment patterns resulting from growth selections employing three aspartic-acid anti-metabolites. Our objective was to assess the extent to which access to genome-scale enrichment patterns would provide strain-engineering insights not reasonably accessible through the use of conventional sequencing. We determined that the SCALEs method identified a surprisingly large range of anti-metabolite tolerance regions (423, 865, or 909 regions for each of the three anti-metabolites) when compared to the number of regions (1-3 regions) indicated by conventional sequencing. Genome-scale methods uniquely enable the calculation of clone fitness values by providing concentration data for all clones within a genomic library before and after a period of selection. We observed that clone fitness values differ substantially from clone concentration values and that this is due to differences in overall clone fitness distributions for each selection. Finally, we show that many of the clones of highest fitness overlapped across all selections, suggesting that inhibition of aspartate metabolism, as opposed to specific inhibited enzymes, dominated each selection. Our follow up studies confirmed our observed growth phenotypes and showed that intracellular amino-acid levels were also altered in several of the identified clones. These results demonstrate that genome-scale methods, such as SCALEs, can be used to dramatically improve understanding of classic strain engineering approaches.

Functional genomic analysis of the 61D-61F region of the third chromosome of Drosophila melanogaster.

Assigning functional significance to completed genome sequences is one of the next challenges in biological science. Conventional genetic tools such as deficiency chromosomes help assign essential complementation groups to their corresponding genes. We describe an F2 genetic screen to identify lethal mutations within cytogenetic region 61D-61F of the third chromosome of Drosophila melanogaster. One hundred sixteen mutations were identified by their failure to complement both Df(3L)bab-PG and Df(3L)3C7. These alleles were assigned to 14 complementation groups and 9 deficiency intervals. Complementation groups were ordered using existing deficiencies, as well as new deficiencies generated in this study. With the aid of the genomic sequence, genetic and physical maps in the region were correlated by use of PCR to localize the breakpoints of deficiencies within a 268-kb genomic contig (GenBank accession No. AC005847). Six essential complementation groups were assigned to specific genes, including genes encoding a porphobilinogen deaminase and a Sac1-like protein.

The Sac1 lipid phosphatase regulates cell shape change and the JNK cascade during dorsal closure in Drosophila.

The Sac1 lipid phosphatase dephosphorylates several phosphatidylinositol (PtdIns) phosphates and, in yeast, regulates a diverse range of cellular processes including organization of the actin cytoskeleton and secretion. We have identified mutations in the gene encoding Drosophila Sac1. sac1 mutants die as embryos with defects in dorsal closure (DC). DC involves the migration of the epidermis to close a hole in the dorsal surface of the embryo occupied by the amnioserosa. It requires cell shape change in both the epidermis and amnioserosa and activation of a Jun N-terminal kinase (JNK) MAPK cascade in the leading edge cells of the epidermis [2]. Loss of Sac1 leads to the improper activation of two key events in DC: cell shape change in the amnioserosa and JNK signaling. sac1 interacts genetically with other participants in these two events, and our data suggest that loss of Sac1 leads to upregulation of one or more signals controlling DC. This study is the first report of a role for Sac1 in the development of a multicellular organism.

Comparative modeling of the phosphatase and kinase domains of protein tyrosine phosphatase and insulin receptor kinase from Drosophila melanogaster (DPTP61fm), and a computational study of their mutual interactions.

The components and functions of the insulin receptor kinase signaling pathway have been conserved in a broad range of Metazoa ranging from mammals to insects and nematodes. There is a high degree of sequence homology and functional similarity between the human insulin receptor kinase (IRK) and the drosophila (Drosophila melanogaster) form (DIRK) of this enzyme. Similarly, a high degree of homology exists between human protein tyrosine phosphatase 1B (PTP1B) (which directly regulates IRK) and its drosophila counterpart DPTP61F (DPTP). However, genetic and biochemical studies have yet to demonstrate that DPTP61F acts in the DIRK pathway. Comparative structural modeling techniques using the known structures of human IRK and PTP1B as templates have yielded structures for the drosophila enzymes. The derived structures confirm that there is a high level of structural conservation at the tertiary level. Association of the DIRK and DPTP enzymes with each other was then investigated with a view to ascertaining whether DIRK might be a substrate of the DPTP. Evaluation of the interaction surfaces, including hydrophobic patch, shape, hydrogen bonding, and electrostatic compatibility, strongly suggested that the drosophila insulin receptor is a substrate of the DPTP. The interaction surfaces of the human and drosophila enzymes are structurally similar, although changes in critical residues modify possible electrostatic and hydrogen-bonding interactions. This suggests that in the mixed systems, DPTP-IRK or PTP1B-DIRK, the kinase domain will be a comparatively poor substrate for phosphatase activity when compared with the native systems.