Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects on diverse aspects of cellular physiology. Therefore, in an attempt to characterize unique and shared responses to chemically similar metals, we have reconstructed physiological behaviors of Halobacterium NRC-1, an archaeal halophile, in sublethal levels of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II). Over 20% of all genes responded transiently within minutes of exposure to Fe(II), perhaps reflecting immediate large-scale physiological adjustments to maintain homeostasis. At steady state, each transition metal induced growth arrest, attempts to minimize oxidative stress, toxic ion scavenging, increased protein turnover and DNA repair, and modulation of active ion transport. While several of these constitute generalized stress responses, up-regulation of active efflux of Co(II), Ni(II), Cu(II), and Zn(II), down-regulation of Mn(II) uptake and up-regulation of Fe(II) chelation, confer resistance to the respective metals. We have synthesized all of these discoveries into a unified systems-level model to provide an integrated perspective of responses to six transition metals with emphasis on experimentally verified regulatory mechanisms. Finally, through comparisons across global transcriptional responses to different metals, we provide insights into putative in vivo metal selectivity of metalloregulatory proteins and demonstrate that a systems approach can help rapidly unravel novel metabolic potential and regulatory programs of poorly studied organisms.[Supplemental material is available online at www.genome.org. The microarray data from this study have been submitted to GEO under accession nos. GSM109343-GSM109461 and GSM109514-GSM109522.]Transition metals such as manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni) copper (Cu), and zinc (Zn) are essential cofactors in the physiology of all organisms. In fact, recent estimates suggest that over half of all proteins in every organism are metalloproteins (Degtyarenko 2000). Although essential in trace amounts, at higher levels these metals can be toxic to cells because they directly or indirectly compromise DNA, protein, and membrane integrity and function. For example, cycling in redox states of metals such as Fe and Cu and antioxidant scavenging by redoxinactive metals such as Zn can both cause oxidative damage to cell components through increased production of reactive oxygen species (ROS) (Nelson 1999). Organisms usually avoid metal toxicity through selective uptake, trafficking, and efflux of metal ions, enzymatic conversion of metals into non-or less-toxic redox states, or sequestering toxic metal ions with ferritins and metallothioneins (Silver 1992;Blindauer et al. 2002;Reindel et al. 2002;Zeth et al. 2004). These mechanisms are believed to be often regulated by free metal-ion concentration (Raab and Feldman 2003). In this regard, other factors such as salinity,...

Niemann-Pick type C (NPC) is an autosomal recessive disease that affects children at a young age with hepatosplenomegaly and neurodegeneration that ultimately leads to mortality. The disease is due to a mutation in the NPC1 protein that leads to the intracellular accumulation of cholesterol within the cell due to a disruption in unesterified cholesterol trafficking. The specifics of how mutations in NPC1 cells inhibit the cholesterol movement pathway are still yet to be explained, but previous research suggests that intracellular movement of cholesterol-rich lipid rafts may be involved. To understand better the nature and role of these rafts, proteomic analysis will identify proteins important in the structures and function of these domains. The importance of this research is to not only perfect the protein extraction and 2-D gel electrophoresis but to start the preliminary steps in analyzing the difference in proteins present in NPC normal, NPC carriers, and NPC mutants, which will give possible candidates involved in cholesterol trafficking and an hypothesis of the cholesterol trafficking pathway. The perfected techniques of 2-D gel electrophoresis produced gels for wild-type, carrier, and mutant of NPC1 protein. These three gels showed distinct similarities and differences. The similarities were depicted to show consistency within the gels that demonstrate not only successful gel runs but proteins that are continually not affected by NPC. The differences showed either positive or inverse relationships with the expression of NPC1; these proteins are candidates for possible further research since they show a correlation to the expression of NPC1 and may be involved in the cholesterol trafficking pathway. The next step is to identify the proteins that are changed by NPC1 expression, and through further experimentation with Sypro staining and computer analysis—which has recently begun—will give insight into these proteins and ultimately the pathway of cholesterol trafficking. The current results have given a stepping stone in focusing on a successful protocol that has given evidence of other possible proteins that are affected by NPC1 and create the devastating NPC disease.