Institute for Systems Biology

About: Institute for Systems Biology is a nonprofit organization based out in Seattle, Washington, United States. It is known for research contribution in the topics: Population & Proteomics. The organization has 1277 authors who have published 2777 publications receiving 353165 citations.

Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae

Abstract: Cells have evolved molecular mechanisms for the efficient transmission of organelles during cell division. Little is known about how peroxisomes are inherited. Inp1p is a peripheral membrane protein of peroxisomes of Saccharomyces cerevisiae that affects both the morphology of peroxisomes and their partitioning during cell division. In vivo 4-dimensional video microscopy showed an inability of mother cells to retain a subset of peroxisomes in dividing cells lacking the INP1 gene, whereas cells overexpressing INP1 exhibited immobilized peroxisomes that failed to be partitioned to the bud. Overproduced Inp1p localized to both peroxisomes and the cell cortex, supporting an interaction of Inp1p with specific structures lining the cell periphery. The levels of Inp1p vary with the cell cycle. Inp1p binds Pex25p, Pex30p, and Vps1p, which have been implicated in controlling peroxisome division. Our findings are consistent with Inp1p acting as a factor that retains peroxisomes in cells and controls peroxisome division. Inp1p is the first peroxisomal protein directly implicated in peroxisome inheritance.

A systems view of haloarchaeal strategies to withstand stress from transition metals

Abstract: 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 redox-inactive 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, pH, temperature, and growth-medium components can all influence the metal stress response because they can alter effective free metal ion concentration in the cell (Babich and Stotzky 1980) or influence metal state (Nieto et al. 1989). However, recent studies have cast doubt on whether there is indeed sufficient intracellular free metal ions for metal sensors to directly bind and modulate metal uptake or efflux (Outten and O’Halloran 2001). If so, then protein–protein interactions between metalloproteins and metallochaperones have been proposed to play a more prominent role in metal trafficking (metal sensing and allocation) than previously appreciated (Tottey et al. 2002). In fact, defects in metal trafficking can cause serious medical conditions including Wilson’s and Menkes’ disease (Andrews 2002). Therefore, understanding mechanisms for in vivo trafficking of transition metals and their specific allocation to metalloproteins remains a key goal. It has been proposed that transcriptional responses could serve as a proxy for deciphering in vivo metal specificity of metalloregulators (Tottey et al. 2005). The reasoning being metal ion binding modulates transcription factor activity, thereby resulting in change in gene expression (Tottey et al. 2005). However, to decipher metal-protein speciation from transcriptional responses, one would require knowledge of both genes that respond to a specific metal and the metalloregulatory protein that directly mediates this control. This is further complicated by the fact that transcriptional responses induced by transition metals are a complex mix of direct consequences associated with reversing damage and indirect cellular adjustments necessary for maintaining homeostasis (Moore et al. 2005). Unlike a reductionist approach, a systems approach enables full appreciation of a global stress response of this type, thereby providing insights that help distinguish putative direct changes from indirect responses (Baliga et al. 2002, 2004). In a systems approach, changes at all informational levels (mRNA and protein levels, protein–protein and protein–DNA interactions, protein modifications, etc.) during a cellular response are measured and analyzed simultaneously in context of the relevant environmental perturbations. The goal is to formulate predictive models—mathematical and/or descriptive that can both describe previous observations and also predict how a cell would react to an environmental perturbation (input), appropriately process information (e.g., via gene regulatory network[s]), and elicit a response (output). The model is refined by testing these predictions through additional rounds of systems analyses of targeted genetic and environmental perturbations (Facciotti et al. 2004). An ideal candidate for such global analysis is Halobacterium NRC-1, an archaeon that thrives in a >4.0 M salinity environment. This halophile is easily cultured and manipulated in the laboratory and has a range of systems-analysis tools available for its inquiry (Weston et al. 2003). In this report, we describe systems level responses of Halobacterium NRC-1 to six transition metals (Mn[II], Fe[II], Co[II], Ni[II], Cu[II], and Zn[II]) and an Fe-specific chelator (2, 2′ dipyridyl: DIP). Numerous biological insights were discovered through an integrated analysis of mRNA level changes for all genes in 66 steady-state and time-series experiments, simultaneously with 2187 protein functional associations, ∼6000 protein–DNA interactions and phenotypic analyses on wild-type, and 17 gene knockout strains representing three function categories (ABC transporters [five genes], P1 ATPases [two], and transcription regulators [five]) and a few miscellaneous categories (transposase [one], redoxin [one], putative siderophore biosynthesis [one], and unknown functions [two]). Among the key resistance and regulation mechanisms that were discovered in this study, we provide experimental evidence for roles of (1) two P1 ATPases, ZntA and YvgX, in Co(II), Ni(II), Cu(II), and Zn(II) resistance; (2) Cu-dependent up-regulation of Cu(II)-specific P1 ATPase YvgX by VNG1179C, a Lrp family regulator with a putative metal-binding TRASH domain (Ettema et al. 2003) in Cu(II) resistance; and (3) Mn(II)-dependent repression of active Mn(II) uptake by the MntR family regulator SirR in Mn(II) resistance. We also demonstrate that analysis of global transcriptional responses may indeed provide insights into in vivo metal selectivity for metalloregulatory proteins. Finally, we provide a synthesis of all our findings into a systems scale model of transition metal response. Thus, we demonstrate that a systems approach enables, in a relatively short period of time, detailed reconstruction of whole-cell physiological responses to complex environmental perturbations.

Augmentation of Response to Chemotherapy by microRNA-506 Through Regulation of RAD51 in Serous Ovarian Cancers

Abstract: Epithelial ovarian cancer remains the most lethal gynecological malignancy (1). The current standard of care consists of radical surgery and platinum-based chemotherapy. The five-year survival rate for patients with advanced ovarian cancer is only 30% to 40%, and acquired resistance to platinum is considered a major factor in disease relapse. Platinum-based drugs form intra- and interstrand adducts with DNA, which causes DNA double-strand breaks and triggers DNA damage and repair pathways. Homologous recombination is a critical pathway for DNA double-strand break repair (2) and is responsible for the resistance of high-grade serous ovarian cancer to frontline platinum-based chemotherapy (3). Cells with compromised homologous recombination machinery are highly sensitive to apoptosis triggered by platinum-induced DNA damage through a mechanism termed synthetic lethality (4). Thus, the ability to block homologous recombination-mediated repair is a focus of intense investigation as an approach to improve treatment outcomes in high-grade serous ovarian cancers. Recent studies demonstrated that BRCA2 mutations, and to a lesser extent BRCA1 mutations/methylation, are associated with improved survival and response to therapy in serous ovarian cancer (5,6). Whereas BRCA1 plays diverse roles in DNA damage pathways, the primary role of BRCA2 is to mediate homologous recombination by directly loading the RAD51 protein onto damage sites or stalled replication forks (7,8). RAD51 is a critical component of the homologous recombination-mediated double-strand DNA break repair machinery and assembles onto single-stranded DNA as a nucleoprotein filament and catalyzes the exchange of homologous DNA sequences (9). RAD51 suppression can sensitize cancer cells to DNA-damaging drugs (10–14), and RAD51 overexpression contributes to chemotherapy resistance in human soft tissue sarcoma cells (15). MicroRNAs (miRNAs) are a class of small noncoding RNAs (~22 nt) that regulate gene expression. MiRNAs bind to the 3′-untranslated region (3′-UTR) of target genes, which either leads to mRNA degradation or inhibits protein translation (16). Nearly 2578 miRNAs have been identified in the human genome and are thought to regulate 30% of the transcriptome (17). Increasing evidence has demonstrated that miRNA are highly deregulated in cancer, suggesting they may function as therapeutic tools (17–20). In a recent high-throughput miRNA signature screen, decreased expression of the chrXq27.3-miRNA cluster that included miR-506 was associated with early relapse in patients with advanced-stage epithelial ovarian cancer (21). Our studies established that miR-506 is a potent inhibitor of the epithelial-to-mesenchymal transition (EMT) (22,23), which is also associated with chemoresistance. In addition, we found that miR-506 could suppress proliferation and induce senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer (24). However, it is unknown whether miR-506 is involved in the chemotherapy response.