SKN-1 domain folding and basic region monomer stabilization upon DNA binding

Carroll, Adam S.; Gilbert, Dara E.; Li, Xiaoying; Cheung, Jim W.; Michnowicz, Jennifer E.; Wagner, Gerhard; Ellenberger, Tom; Blackwell, T. Keith

doi:10.1101/gad.11.17.2227

Cited by 40 publications

(48 citation statements)

References 70 publications

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“…To examine the effect of altered O-GlcNAc synthesis on nuclear pore function, we examined nuclear transport of several well characterized C. elegans transcription factors, including SKN-1, HLH-1, HLH-2, ELT-2, and LIN-26. In C. elegans, SKN-1 is involved in both early blastomere development and the stress response (28)(29)(30)(31). The stress response in larvae and adults causes cytoplasmic SKN-1 in intestinal cells to rapidly translocate to the nucleus (28).…”

Section: Resultsmentioning

confidence: 99%

A Caenorhabditis elegans model of insulin resistance: Altered macronutrient storage and dauer formation in an OGT-1 knockout

Hanover

Forsythe

Hennessey

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

205

269

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O-linked N-acetylglucosamine (O-GlcNAc) is an evolutionarily conserved modification of nuclear pore proteins, signaling kinases, and transcription factors. The O-GlcNAc transferase (OGT) catalyzing O-GlcNAc addition is essential in mammals and mediates the last step in a nutrient-sensing ''hexosamine-signaling pathway.'' This pathway may be deregulated in diabetes and neurodegenerative disease. To examine the function of O-GlcNAc in a genetically amenable organism, we describe a putative null allele of OGT in Caenorhabditis elegans that is viable and fertile. We demonstrate that, whereas nuclear pore proteins of the homozygous deletion strain are devoid of O-GlcNAc, nuclear transport of transcription factors appears normal. However, the OGT mutant exhibits striking metabolic changes manifested in a Ϸ3-fold elevation in trehalose levels and glycogen stores with a concomitant Ϸ3-fold decrease in triglycerides levels. In nematodes, a highly conserved insulin-like signaling cascade regulates macronutrient storage, longevity, and dauer formation. The OGT knockout suppresses dauer larvae formation induced by a temperature-sensitive allele of the insulin-like receptor gene daf-2. Our findings demonstrate that OGT modulates macronutrient storage and dauer formation in C. elegans, providing a unique genetic model for examining the role of O-GlcNAc in cellular signaling and insulin resistance.is a nucleocytoplasmic modification present throughout eukaryotic evolution with the possible exception of yeast (1, 2). Although many intracellular proteins such as nuclear pore components and transcription factors bear O-GlcNAc, the precise function of the modification is unknown. Evidence in mammals suggests a role for O-GlcNAc in the development of insulin resistance associated with noninsulindependent diabetes mellitus (3, 4). A number of lines of evidence also link O-GlcNAc to transcriptional regulation and neurodegeneration (1, 2). O-GlcNAc addition is partly driven by the levels of UDP-GlcNAc derived from the hexosamine biosynthetic pathway. This pathway is a nutrient-sensing pathway implicated in cellular signaling (1, 2). The uncertainty regarding the precise function of O-GlcNAc is perhaps to be expected given the many substrates modified by this glycan addition. Furthermore, O-GlcNAc is a dynamic modification; the levels of O-GlcNAc are maintained by the action of a glycosytransferase [O-linked GlcNAc transferase (OGT)] and a hexosaminidase (O-GlcNAcase) (1, 2). Mammalian O-GlcNAcase exists as two splice variants and is relatively specific for nucleocytoplasmic O-GlcNAc (1, 5, 6). The transferase, OGT, catalyzes the transfer of O-GlcNAc to Ser͞Thr residues. This enzyme has been identified from a number of sources, including plants, human, rat, mouse, and the nematode Caenorhabditis elegans (7,8). In plants, the OGT homolog Spindly is involved in plant-signaling pathways (9, 10). These evolutionarily conserved proteins share a similar overall structure; OGT is composed of multiple protein domains, including tetratricopepti...

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Section: Resultsmentioning

confidence: 99%

A Caenorhabditis elegans model of insulin resistance: Altered macronutrient storage and dauer formation in an OGT-1 knockout

Hanover

Forsythe

Hennessey

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

205

269

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“…Full-length SKN-1 and the SKN domain were expressed by in vitro translation (Promega) as described previously (Carroll et al 1997). Oligonucleotide probes were end-labeled using Klenow and ␣-32 P-labeled dATP and CTP, then purified using QIAquick Kit (QIAGEN).…”

Section: Dna-binding Assaysmentioning

confidence: 99%

“…SKN-1 lacks a ZIP segment, which is essential for bZIP protein DNA binding because it acts as a dimerization element, and stabilizes folding of the BR on the DNA (Talanian et al 1990). In contrast, monomeric SKN-1 DNA binding is comparably stabilized by a flexible "arm" that binds in the minor groove, and by a novel variant of the CNC region, through which SKN-1 is distantly related to a bZIP protein subgroup (Blackwell et al 1994;Carroll et al 1997;Kophengnavong et al 1999). SKN-1 is also similar to two vertebrate CNC-group proteins (NF-E2-related factors Nrf1 and Nrf2) within a 14-amino-acid transactivator element (DIDLID; Fig.…”

mentioning

confidence: 99%

SKN-1 linksC. elegansmesendodermal specification to a conserved oxidative stress response

An¹,

Blackwell²

2003

Genes Dev.

Self Cite

673

877

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During the earliest stages of Caenorhabditis elegans embryogenesis, the transcription factor SKN-1 initiates development of the digestive system and other mesendodermal tissues. Postembryonic SKN-1 functions have not been elucidated. SKN-1 binds to DNA through a unique mechanism, but is distantly related to basic leucine-zipper proteins that orchestrate the major oxidative stress response in vertebrates and yeast. Here we show that despite its distinct mode of target gene recognition, SKN-1 functions similarly to resist oxidative stress in C. elegans. During postembryonic stages, SKN-1 regulates a key Phase II detoxification gene through constitutive and stress-inducible mechanisms in the ASI chemosensory neurons and intestine, respectively. SKN-1 is present in ASI nuclei under normal conditions, and accumulates in intestinal nuclei in response to oxidative stress. skn-1 mutants are sensitive to oxidative stress and have shortened lifespans. SKN-1 represents a connection between developmental specification of the digestive system and one of its most basic functions, resistance to oxidative and xenobiotic stress. This oxidative stress response thus appears to be both widely conserved and ancient, suggesting that the mesendodermal specification role of SKN-1 was predated by its function in these detoxification mechanisms.

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“…65 Additional proteins that form molten globules rather than ordered structure under physiological conditions continue to be discovered. 66,67,68,69,70,71 The information presented above suggests that it is appropriate to reassess the current protein structure / function paradigm. The remainder of this review attempts such a reassessment.…”

Section: Introductionmentioning

confidence: 99%

Intrinsically disordered protein

Dunker

Lawson

Brown

et al. 2001

Journal of Molecular Graphics and Modelling

2,133

2,085

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Proteins can exist in a trinity of structures: the ordered state, the molten globule and the random coil. Five examples follow which suggest that native protein structure can correspond to any of the three states (not just the ordered state) and that protein function can arise from any of the three states and their transitions. 1. In a process that likely mimics infection, fd phage converts from the ordered into the disordered molten globular state. 2. Nucleosome hyperacetylation is crucial to DNA replication and transcription; this chemical modification greatly increases the net negative charge of the nucleosome core particle. We propose that the increased charge imbalance promotes its conversion to a much less rigid form. 3. Clusterin contains an ordered domain and also a native molten globular region. The molten globular domain likely functions as a proteinaceous detergent for cell remodeling and removal of apoptotic debris. 4. In a critical signaling event, a helix in calcineurin becomes bound and surrounded by calmodulin, thereby turning on calcineurin's serine/threonine phosphatase activity.Locating the calcineurin helix within a region of disorder is essential for enabling calmodulin to surround its target upon binding. 5. Calsequestrin regulates calcium levels in the sarcoplasmic reticulum by binding about 50 ions/molecule. Disordered polyanion tails at the carboxy terminus bind many of these calcium ions, perhaps without adopting a unique structure. In addition to these examples, 16 more proteins with native disorder will be discussed. These disordered regions include molecular recognition domains, protein folding inhibitors, flexible linkers, entropic springs, entropic clocks and entropic bristles.Motivated by such examples of intrinsic disorder, we are studying the relationships between amino acid sequence and order/disorder, and from this information we are predicting intrinsic order/disorder from amino acid sequence.The sequence/structure relationships indicate that disorder is an encoded property, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those in the Protein Data Bank. Recent predictions on 29 genomes indicate that proteins from eucaryotes apparently have more intrinsic disorder than those from either bacteria or archaea, with typically > 30 % of eucaryotic proteins having disordered regions of length = 50 consecutive residues.

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SKN-1 domain folding and basic region monomer stabilization upon DNA binding

Cited by 40 publications

References 70 publications

A Caenorhabditis elegans model of insulin resistance: Altered macronutrient storage and dauer formation in an OGT-1 knockout

A Caenorhabditis elegans model of insulin resistance: Altered macronutrient storage and dauer formation in an OGT-1 knockout

SKN-1 linksC. elegansmesendodermal specification to a conserved oxidative stress response

Intrinsically disordered protein

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