The evolutionarily conserved checkpoint protein kinase, TOR (target of rapamycin), has emerged as a major effector of cell growth and proliferation via the regulation of protein synthesis. Work in the last decade clearly demonstrates that TOR controls protein synthesis through a stunning number of downstream targets. Some of the targets are phosphorylated directly by TOR, but many are phosphorylated indirectly. In this review, we summarize some recent developments in this fast-evolving field. We describe both the upstream components of the signaling pathway(s) that activates mammalian TOR (mTOR) and the downstream targets that affect protein synthesis. We also summarize the roles of mTOR in the control of cell growth and proliferation, as well as its relevance to cancer and synaptic plasticity.

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Upstream and downstream of mTOR

The genomes of eukaryotic cells are under continuous assault by environmental agents (e.g., UV light and reactive chemicals) as well as the byproducts of normal intracellular metabolism (e.g., reactive oxygen intermediates and inaccurately replicated DNA). Whatever the origin, genetic damage threatens cell survival, and, in metazoans, leads to organ failure, immunodeficiency, cancer, and other pathologic sequelae. To ensure that cells pass accurate copies of their genomes on to the next generation, evolution has overlaid the core cell-cycle machinery with a series of surveillance pathways termed cell-cycle checkpoints. The overall function of these checkpoints is to detect damaged or abnormally structured DNA, and to coordinate cell-cycle progression with DNA repair. Typically, cell-cycle checkpoint activation slows or arrests cell-cycle progression, thereby allowing time for appropriate repair mechanisms to correct genetic lesions before they are passed on to the next generation of daughter cells. In certain cell types, such as thymocytes, checkpoint proteins link DNA strand breaks to apoptotic cell death via induction of p53. Hence, loss of either of two biochemically connected checkpoint kinases, ATM or Chk2, paradoxically increases the resistance of immature (CD4CD8) T cells to ionizing radiation (IR)-induced apoptosis (Xu and Baltimore 1996; Hirao et al. 2000). In a broader context, cell-cycle checkpoints can be envisioned as signal transduction pathways that link the pace of key cell-cycle phase transitions to the timely and accurate completion of prior, contingent events. It is important to recognize that checkpoint surveillance functions are not confined solely to the happenings within the nucleus–extranuclear parameters, such as growth factor availability and cell mass accumulation, also govern the pace of the cell cycle (Stocker and Hafen 2000). However, for the purposes of this review we will focus exclusively on the subset of checkpoints that monitor the status and structure of chromosomal DNA during cell-cycle progression (Fig. 1). These checkpoints contain, as their most proximal signaling elements, sensor proteins that scan chromatin for partially replicated DNA, DNA strand breaks, or other abnormalities, and translate these DNA-derived stimuli into biochemical signals that modulate the functions of specific downstream target proteins. Despite the recent explosion of information regarding the molecular components of cell-cycle checkpoints in eukaryotic cells, we still have only a skeletal understanding of both the identities of the DNA damage sensors and the mechanisms through which they initiate and terminate the activation of checkpoints. However, members of the Rad group of checkpoint proteins, which include Rad17, Rad1, Rad9, Rad26, and Hus1 (nomenclature based on the Schizosaccharomyces pombe gene products) are widely expressed in all eukaryotic cells, and are prime suspects in the lineup of candidate DNA damage sensors (Green et al. 2000; O’Connell et al. 2000). Three of these Rad proteins, Rad1, Rad9, and Hus1, exhibit structural similarity to the proliferating cell nuclear antigen (PCNA), and accumulating evidence supports the idea that this similarity may extend to function as well (Thelen et al. 1999; Burtelow et al. 2000). During DNA replication, PCNA forms a homotrimeric complex that encircles DNA, creating a “sliding clamp” that tethers DNA polymerase to the DNA strand. Rad1, Rad9, and Hus1 are also found as a heterotrimeric complex in intact cells, and it has been postulated that the Rad1–Rad9–Hus1 complex encircles DNA at or near sites of damage to form a checkpoint sliding clamp (CSC) (O’Connell et al. 2000), which could serve as a nucleus for the recruitment of the checkpoint signaling machinery to broken or abnormally structured DNA. The analogy between PCNA and the Rad1–Rad9–Hus1 complex extends even further. The loading of the PCNA clamp onto DNA is controlled by the clamp loading complex, replication factor C (RFC). Interestingly, yet another member of the Rad family, Rad17, bears homology to the RFC subunits and, in fact, associates with RFC subunits to form a putative checkpoint clamp loading complex (CLC) that governs the interaction of the Rad1– Rad9–Hus1 CSC with damaged DNA (Green et al. 2000; O’Connell et al. 2000). Although this model is fascinating, rigorous biochemical evaluations of the interplay between the CLC and CSC complexes, and the interactions of both complexes with damaged chromatin, are needed before the model can be accepted without reservation. Present address: The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA E-MAIL abraham@burnham.org; FAX (858) 713-6268. Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/ gad.914401.

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Cell cycle checkpoint signaling through the ATM and ATR kinases

/pdf/regulation-of-translation-initiation-by-frap-mtor-495vylnz0t.pdf

Regulation of translation initiation by FRAP/mTOR

Rapamycin, a macrocyclic lactone, is a highly specific inhibitor of the serine/threonine protein kinase target of rapamycin (TOR). Although it is clear that TOR controls initiation of protein translation, recent results indicate that TOR is a central controller, integrating a plethora of signalling pathways that respond to growth factors and nutritional status. In addition to the role of rapamycin as an immune suppressant, emerging data indicate that genetic and metabolic changes accompanying malignant transformation might cause hypersensitivity to TOR inhibition.

The tor pathway: a target for cancer therapy

The mammalian target of rapamycin (mTOR) regulates cell growth and survival by integrating nutrient and hormonal signals These signaling functions are distributed between at least two distinct mTOR protein complexes: mTORC1 and mTORC2 mTORC1 is sensitive to the selective inhibitor rapamycin and activated by growth factor stimulation via the canonical phosphoinositide 3-kinase (PI3K)-->Akt-->mTOR pathway Activated mTORC1 kinase up-regulates protein synthesis by phosphorylating key regulators of mRNA translation By contrast, mTORC2 is resistant to rapamycin Genetic studies have suggested that mTORC2 may phosphorylate Akt at S473, one of two phosphorylation sites required for Akt activation; this has been controversial, in part because RNA interference and gene knockouts produce distinct Akt phospho-isoforms The central role of mTOR in controlling key cellular growth and survival pathways has sparked interest in discovering mTOR inhibitors that bind to the ATP site and therefore target both mTORC2 and mTORC1 We investigated mTOR signaling in cells and animals with two novel and specific mTOR kinase domain inhibitors (TORKinibs) Unlike rapamycin, these TORKinibs (PP242 and PP30) inhibit mTORC2, and we use them to show that pharmacological inhibition of mTOR blocks the phosphorylation of Akt at S473 and prevents its full activation Furthermore, we show that TORKinibs inhibit proliferation of primary cells more completely than rapamycin Surprisingly, we find that mTORC2 is not the basis for this enhanced activity, and we show that the TORKinib PP242 is a more effective mTORC1 inhibitor than rapamycin Importantly, at the molecular level, PP242 inhibits cap-dependent translation under conditions in which rapamycin has no effect Our findings identify new functional features of mTORC1 that are resistant to rapamycin but are effectively targeted by TORKinibs These potent new pharmacological agents complement rapamycin in the study of mTOR and its role in normal physiology and human disease

https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1000038&type=printable

Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2.

Control of the translational repressor, PHAS-I, was investigated by expressing proteins with Ser/Thr → Ala mutations in the five (S/T)P phosphorylation sites. Results of experiments with HEK293 cells reveal at least three levels of control. At one extreme is nonregulated phosphorylation, exemplified by constitutive phosphorylation of Ser82. At an intermediate level, amino acids and insulin stimulate the phosphorylation of Thr36, Thr45, and Thr69 via mTOR-dependent processes that function independently of other sites in PHAS-I. At the third level, the extent of phosphorylation of one site modulates the phosphorylation of another. This control is represented by Ser64 phosphorylation, which depends on the phosphorylation of all three TP sites. The five sites have different influences on the electrophoretic properties of PHAS-I and on the affinity of PHAS-I for eukaryotic initiation factor 4E (eIF4E). Phosphorylation of Thr45 or Ser64 results in the most dramatic decreases in eIF4E binding in vitro. However, each of the sites influences mRNA translation, either directly by modulating the binding affinity of PHAS-I and eIF4E or indirectly by affecting the phosphorylation of other sites.

Multiple mechanisms control phosphorylation of PHAS-I in five (S/T)P sites that govern translational repression.

Performance optimization of support vector machine with oppositional grasshopper optimization for acute appendicitis diagnosis

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793%2899%2900762-0

Daqing Yang

Papers

Multiple mechanisms control phosphorylation of PHAS-I in five (S/T)P sites that govern translational repression.

Performance optimization of support vector machine with oppositional grasshopper optimization for acute appendicitis diagnosis

Mutational analysis of sites in the translational regulator, PHAS-I, that are selectively phosphorylated by mTOR