Lysyl tRNA Synthetase binds to mutant SOD1. Endonuclease is decreased in ALS. Ku is associated with all 3 molecules.

---

http://genome.cshlp.org/content/11/8/1365.full.html

Genome Res. 2001 11: 1365-1374

Prokaryotic Homologs of the Eukaryotic DNA-End-Binding Protein Ku, Novel Domains in the Ku Protein and Prediction of a Prokaryotic Double-Strand Break Repair System

L. Aravind1 and Eugene V. Koonin

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health,
Bethesda, Maryland 20894, USA

Homologs of the eukaryotic DNA-end-binding protein Ku were identified in several bacterial and one archeal
genome using iterative database searches with sequence profiles. Identification of prokaryotic Ku homologs
allowed the dissection of the Ku protein sequences into three distinct domains, the Ku core that is conserved in eukaryotes and prokaryotes, a derived von Willebrand A domain that is fused to the amino terminus of the core in eukaryotic Ku proteins, and the newly recognized helix–extension–helix (HEH) domain that is fused to the carboxyl terminus of the core in eukaryotes and in one of the Ku homologs from the Actinomycete Streptomyces coelicolor. The version of the HEH domain present in eukaryotic Ku proteins represents the previously described DNA-binding domain called SAP. The Ku homolog from S. coelicolor contains a distinct version of the HEH domain that belongs to a previously unnoticed family of nucleic-acid-binding domains, which also includes HEH domains from the bacterial transcription termination factor Rho, bacterial and eukaryotic lysyl-tRNA synthetases, bacteriophage T4 endonuclease VII, and several uncharacterized proteins. The distribution of the Ku homologs in bacteria coincides with that of the archeal-eukaryotic-type DNA primase and genes for prokaryotic Ku homologs form predicted operons with genes coding for an ATP-dependent DNA ligase and/or archeal-eukaryotic-type DNA primase. Some of these operons additionally encode an uncharacterized protein that may function as nuclease or an Slx1p-like predicted nuclease containing a URI domain. A hypothesis is proposed that the Ku homolog, together with the associated gene products, comprise a previously unrecognized prokaryotic system for repair of double strand breaks in DNA.

Hi Donna,

I'd sent this in recently. I wonder whether anyone can comment on whether IP6 would be beneficial. Many posts in the archives suggest that enhancing the NHEJ pathway is the way to go. It would seem to be a great candidate to move through to trial.

Mary

"http://www.jhsph.edu/publichealthnews/magazine/archive/Mag_Fall04/microcosmos/enemy_within.html

That’s what Leslyn Hanakahi wants to know. Hanakahi, PhD, assistant professor of Biochemistry and Molecular Biology, thinks part of the answer lies in inositol hexakisphosphate (IP6). Hanakahi discovered the chemical in 2000 while doing her postdoctoral work at Cancer Research UK. “We came across IP6 with a huge dose of luck,” she says. “I was looking for a protein and came up with a chemical.” She discovered that, in a test tube, IP6 stimulated the NHEJ pathway. "

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WG1-45F4M9F-S&_user=10&_coverDate=12%2F01%2F2000&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1199225567&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=36570e457da5f478ae54a57a0497d559

Genetic Mapping of a Mouse Modifier Gene That Can Prevent ALS Onset

Catherine B. Kunsta, 1, Laurel Messera, Jon Gordonb, Jonathan Hainesc and David Pattersona

a Eleanor Roosevelt Institute, 1899 Gaylord Street, Denver, Colorado, 80206
b Mount Sinai School of Medicine, 2050 Annenberg, 1 Gustave L. Levy Place, New York, New York, 10029
c Vanderbilt University Medical Center, 519 Light Hall, Nashville, Tennessee, 37232

Abstract
Mutations in the cytoplasmic Cu/Zn superoxide dismutase (SOD1) gene on human chromosome 21q22.1 cause 10–20% of familial amyotrophic lateral sclerosis (ALS) cases. The expression of the ALS phenotype in mice carrying the murine G86R SOD1 mutation is highly dependent upon the mouse genetic background. This is similar to the phenotypic variation observed in ALS patients containing identical SOD1 mutations. In the FVB/N background, mice expressing mG86R SOD1 develop an ALS phenotype at 100 days. However, when these mice were bred into a mixed background of C57Bl6/129Sv, the onset of the ALS phenotype was delayed (143 days to >2 years). Using 129 polymorphic autosomal markers in a whole genome scan, we have identified a major genetic modifier locus with a maximum lod score of 5.07 on mouse chromosome 13 between D13mit36 and D13mit76. This 5- to 8-cM interval contains the spinal muscular atrophy (SMA)-associated gene Smn (survival motor neuron) and seven copies of Naip (neuronal apoptosis inhibitory protein), suggesting a potential link between SMA and ALS.

Genomics Volume 70, Issue 2, 1 December 2000, Pages 181-189

Hi Donna,

Thanks. Does this mean that SMN is part of the NHEJ pathway. I see that Artemis has an SMN1 domain. Thy write below that "proteins and enzymes of NHEJ include Ku, DNA-PKcs, Artemis, DNA polymerase mu (Pol mu), DNA polymerase lambda (Pol lambda), XLF (also called Cernunnos), XRCC4, and DNA ligase IV."

I'll see if there are others on mouse Chr 13 besides SMN1 and XRCC4. Not sure how close they are.

Mary

http://www.coursehero.com/file/2879958/Lect3-EA-101408/

Based upon the homology to SMN proteins they guess that Artemis might be a nuclease.

http://jem.rupress.org/cgi/content/full/197/5/543

Future experiments using point mutants of Artemis to separate the catalytic versus the architectural role of the protein will be very informative. One such mutant might be the one used by Ma et al. (14). The mutation (D165N, numbering according to reference 14), identified in a SCID patient, resides in the conserved SMN1 domain and the resulting mutant protein is unable to open hairpin substrates.


Curr Biol. 2002 Mar 5;12(5):397-402.

Oxygen metabolism causes chromosome breaks and is associated with the neuronal apoptosis observed in DNA double-strand break repair mutants.
Karanjawala ZE, Murphy N, Hinton DR, Hsieh CL, Lieber MR.

Department of Pathology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles 90089-9176, USA.

Comment in:

Curr Biol. 2002 Apr 2;12(7):R262-4.

Cells deficient in a major DNA double-strand break repair pathway (nonhomologous DNA end joining [NHEJ]) have increased spontaneous chromosome breaks; however, the source of these chromosome breaks has remained undefined. Here, we show that the observed spontaneous chromosome breaks are partially suppressed by reducing the cellular oxygen tension. Conversely, elevating the level of reactive oxygen species by overexpressing the antioxidant enzyme superoxide dismutase 1 (SOD1), in a transgenic mouse, increases chromosome breakage. The effect of SOD1 can also be modulated by cellular oxygen tension. The elevated chromosome breakage correlates histologically with a significant increase in the amount of neuronal cell death in Ku86(-/-) SOD1 transgenic embryos over that seen in Ku86(-/-) embryos. Therefore, oxygen metabolism is a major source of the genomic instability observed in NHEJ-deficient cells and, presumably, in all cells.

PMID: 11882291 [PubMed - indexed for MEDLINE]


Subcell Biochem. 2010;50:279-96.

Nonhomologous DNA End Joining (NHEJ) and Chromosomal Translocations in Humans.
Lieber MR, Gu J, Lu H, Shimazaki N, Tsai AG.

USC Norris Comprehensive Cancer Center, Los Angeles, CA, 90089-9176, USA, lieber@usc.edu.

Double-strand breaks (DSBs) arise in dividing cells about ten times per cell per day. Causes include replication across a nick, free radicals of oxidative metabolism, ionizing radiation, and inadvertent action by enzymes of DNA metabolism (such as failures of type II topoisomerases or cleavage by recombinases at off-target sites). There are two major double-strand break repair pathways. Homologous recombination (HR) can repair double-strand breaks, but only during S phase and typically only if there are hundreds of base pairs of homology. The more commonly used pathway is nonhomologous DNA end joining, abbreviated NHEJ. NHEJ can repair a DSB at any time during the cell cycle and does not require any homology, although a few nucleotides of terminal microhomology are often utilized by the NHEJ enzymes, if present. The proteins and enzymes of NHEJ include Ku, DNA-PKcs, Artemis, DNA polymerase mu (Pol mu), DNA polymerase lambda (Pol lambda), XLF (also called Cernunnos), XRCC4, and DNA ligase IV. These enzymes constitute what some call the classical NHEJ pathway, and in wild type cells, the vast majority of joining events appear to proceed using these components. NHEJ is present in many prokaryotes, as well as all eukaryotes, and very similar mechanistic flexibility evolved both convergently and divergently. When two double-strand breaks occur on different chromosomes, then the rejoining is almost always done by NHEJ. The causes of DSBs in lymphomas most often involve the RAG or AID enzymes that function in the specialized processes of antigen receptor gene rearrangement.

PMID: 20012587 [PubMed - in process]

Should reduced levels of SMN1 result in artemis deficiency, does that help to explain the immunodeficiency reported in spinal muscular atrophy in the first link? Does reduced NHEJ pathway function in the SOD1 mice explain why all these mice carry a staph aureus infection and why they were more likely to succumb to that infection in the apocynin trial? Is there a limit for NHEJ repair before you deplete artemis? Do the mice develop IBD as the disease progresses?

Mary

http://www.springerlink.com/content/m7h1470042449n60/


Chronic Inflammatory Bowel Disease as Key Manifestation of Atypical ARTEMIS Deficiency
Journal Journal of Clinical Immunology
Publisher Springer Netherlands
ISSN 0271-9142 (Print) 1573-2592 (Online)
DOI 10.1007/s10875-009-9349-x
Subject Collection Biomedical and Life Sciences
SpringerLink Date Friday, December 04, 2009


Chronic Inflammatory Bowel Disease as Key Manifestation of Atypical ARTEMIS Deficiency
Jan Rohr1, Ulrich Pannicke2, Michaela Döring3, Annette Schmitt-Graeff4, Elisabeth Wiech4, Andreas Busch5, Carsten Speckmann1, Ingo Müller3, Peter Lang3, Rupert Handgretinger3, Paul Fisch4, Klaus Schwarz2, 6, 7 and Stephan Ehl7

(1) Centre of Pediatrics and Adolescent Medicine, University Medical Center, Freiburg, Germany
(2) Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
(3) Department of General Pediatrics, Hematology and Oncology, University Children’s Hospital, Tübingen, Germany
(4) Institute of Pathology, University Medical Center, Freiburg, Germany
(5) Division of Pediatric Gastroenterology, University Children’s Hospital, Tübingen, Germany
(6) Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service, Ulm, Baden–Württemberg–Hessen, Germany
(7) Centre of Chronic Immunodeficiency, University Medical Center, Mathildenstr. 1, 79106 Freiburg, Germany

Received: 10 September 2009 Accepted: 11 November 2009 Published online: 5 December 2009

Abstract
Introduction We describe a girl presenting at age 6 years with a history of chronic ulcerating intestinal inflammation since 9 months of age. She exhibited a severe, steroid-dependent clinical course of intestinal inflammation over several years in the absence of serious infections.
Results and Discussion Immunodeficiency was first considered at 6 years of age due to chronic lymphopenia. Immunophenotyping revealed low B and T cell counts with few naïve T cells, a skewed TCR repertoire, and TCR γ/δ T cell predominance, suggesting a defect of lymphocyte development. Genetic and functional analyses identified a hypomorphic mutation in the DCLRE1C (ARTEMIS) gene compromising V(D)J recombination efficiency, but allowing residual T and B cell development. Hematopoetic stem cell transplantation reconstituted the lymphocyte compartment and cured the inflammatory bowel disease.
Conclusion This report illustrates that a genetic disorder of lymphocyte development can present with chronic inflammatory bowel disease as the dominant phenotype in the absence of severe infection susceptibility.

Autoantigen Ku is implicated in lupus. Secreted autoantigen Lysyl tRNA synthetase is implicated in increased expression of tumor necrosis factor (TNF) and activation of macrophages. Human Islet cell autoantigen 1-like protein in ALS2 codes for RHO.

An autoantigen is defined an antigen that despite being a normal tissue constituent is the target of a humoral or cell-mediated immune response, as in autoimmune disease (Free Dictionary). The function of chemotaxis may to be a distinguishing characteristic.

How can ALS present as a TH1 disease and be associated with autoantigens implicated in autoimmune
TH2 diseases? Perhaps, in the future, the newly derived HEH2 will provide a clue.

HEH2 (inner nuclear membrane protein with helix-extension-helix) is associated with Ku 70, Ku 80, RHO-N, and endonuclease VII-T4, SAP, and lysyl tRNA synthetase.

HEH interacts with NUP49 (subunit of nuclear pore complex)
which interacts with SEN1 CIK3 (senataxin/ALS4: helicase for RNA processing/polymerase II termination)
which interacts with MSK1 (mitochondrial lysyl tRNA synthetase).

RHO (which contains the HEH2 protein) is encoded by the human Islet cell autoantigen 1-like protein in ALS2. Juvenile ALS2 correlates with mRNA sequence AK023024.1 Homo sapiens cDNA FLJ12962 which is weakly similar to X-Linked Retinitis Pigmentosa GTPase Regulator. Similarly, the function of the HERC gene may also be lost in ALS2. It codes for ubiquitin3 ligases with RCC1-like domains that function as GTPases regulators. Mutations are associated with retinitis pigmentosa, amyotrophic lateral sclerosis, and cancer.

An increased immune response to autoantigen Ku has been observed in human ocular ciliary epithelium and in a human nonpigmented (NPE) ciliary epithelial cell line where Ku is highly expressed along with SOD. The ciliary epithelial cells have been found to be involved in non-visual phototransduction which may be similar to the function of light activated AMPA receptors implicated in ALS.

Donna C. King

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The following research provides a table of therapeutic agents researched for use in retinitis pigmentosa that may also benefit patients with ALS.

http://hmg.oxfordjournals.org/cgi/reprint/ddn202v1.pdf

Pharmacological manipulation of gain-of-function and dominant negative
mechanisms in rhodopsin retinitis pigmentosa

Hugo F. Mendes and Michael E. Cheetham*

UCL Institute of Ophthalmology, London, UK

HMG Advance Access published July 17, 2008

p. 32 Table 1. Summary of drug effects on P23H opsin

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2188621/pdf/je17241049.pdf

The Autoantigen Ku Is Indistinguishable from NF IV, a Protein Forming Multimeric Protein-DNA Complexes

By Maarten H. Stuiver, Frank E. J. Coenjaerts,
and Peter C. van der Vliet

From the Laboratory for Physiological Chemistry, University ofUtrecht, The Netherlands

We have isolated a cDNA encoding the 84-kD subunit of NFIV (nuclear Factor IV). Tryptic peptide sequences were identified within the coding sequences, confirming its proper identity. The primary sequence of the protein is identical to that of the large subunit of the Ku autoantigen . A missing NFIV peptide sequence was identified within the sequence of the small subunit of Ku. In addition, the proteins are identical in immunological aspects. We suggest that the Ku and NFIV proteins are identical. This connection adds new biochemical data to our knowledge of the Ku autoantigen .

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http://mcb.asm.org/cgi/content/abstract/29/11/3163

Molecular and Cellular Biology, June 2009, p. 3163-3172, Vol. 29, No. 11

Structural and Functional Interaction between the Human DNA Repair Proteins DNA Ligase IV and XRCC4 ,

Peï-Yu Wu,1,2 Philippe Frit,1,2* SriLakshmi Meesala,3 Stéphanie Dauvillier,1,2 Mauro Modesti,4 Sara N.

CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale),Toulouse, France,1
Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France,2
Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario , Canada,3
CNRS, Unité Propre de Recherche 3081, Genome Instability and Carcin. Conventionné, Univ. d'Aix-Marseille,4
Departments of Internal Medicine and Human Genetics, University of Michigan Ann Arbor,5
Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario

Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.

---

http://genome.cshlp.org/content/11/8/1365.full.pdf+html

p. 7 Figure 4
p. 9 Figure 6

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http://www.thebiogrid.org/SearchResults/summary/32512

HEH2 Saccharomyces cerevisiae Aliases: YDR458C

---

http://www.thebiogrid.org/SearchResults/summary/33081

NUP49 Saccharomyces cerevisiae

---

http://www.thebiogrid.org/SearchResults/summary/31689

SEN1 Saccharomyces cerevisiae

---

http://www.thebiogrid.org/SearchResults/summary/35750

MSK1 Saccharomyces cerevisiae

---

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4BRT39G-1&_user=10&_origUdi=B6WBK-45GW75F-JG&_fmt=high&_coverDate=03%2F26%2F2004&_rdoc=1&_orig=article&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=4ee3994100f559b11756250c0255fffb

Journal of Molecular Biology Volume 337, Issue 3, 26 March 2004, Pages 503-511

The Membrane-associated Form of the DNA Repair Protein Ku is Involved in Cell Adhesion to Fibronectin

Sylvie Monferrana, Catherine Muller, a, , Lionel Moureya, Philippe Frita and Bernard Sallesa

aInstitut de Pharmacologie et de Biologie Structurale, Toulouse Cedex, France

Abstract
The Ku heterodimer (Ku70/Ku80) plays a central role in DNA double-strand breaks recognition and repair. However, Ku is expressed also on the surface of different types of cells along with its intracellular pool within the nucleus and the cytoplasm. Participation of membrane-associated Ku in cell–cell interaction has been reported recently. Here, we describe a novel function of cell-surface Ku as an adhesion receptor for fibronectin (Fn). The role of Ku in cell adhesion was investigated by comparing the Ku80 deficient Chinese hamster ovary (CHO) cell line, xrs-6, with clones transfected stably with either the hamster or human Ku80 cDNA. Ku expression in transfectant cells resulted in a significant increased adhesion on Fn and type IV collagen as compared to control cells. The observed increase in cell adhesion relied on Ku cell-surface expression, since antibodies directed against Ku70 or Ku80 subunit inhibited adhesion on Fn of Ku80, but not control vector, transfected xrs-6 cells. In addition, both Ku70 and Ku80 present a structural relationship with integrin I (or A) domains and the A1 and A3 domains of von Willebrand factor, domains known to be involved in Fn binding. Both Ku70 and Ku80 exhibit a complete set of residues compatible in their position and chemical nature with the formation of a metal ion-dependent adhesion (MIDAS) site implicated in ligand binding and integrin activation. Taken together, these functional and structural approaches support a new role for Ku as an adhesion receptor for Fn.

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http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WBK-45GW75F-JG&_user=10&_coverDate=08%2F11%2F1999&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b1f18188e360762ba4a5ea60307f491a
Biochemical and Biophysical Research Communications Volume 261, Issue 3, 11 August 1999, Pages 802-807

Defining Functional Domains of Ku80: DNA End Binding and Survival after Radiation

O. Osipovicha, R. J. Duhea, P. Hastyb, S. K. Duruma and K. Mueggea

a Laboratory of Molecular Immunoregulation, SAIC, National Cancer Institute
b Lexicon Genetics Inc. The Woodlands, Texas, 77382

Abstract
The Ku heterodimeric protein (Ku80/Ku70) is an essential component of the double-strand break DNA repair pathway in mammalian cells. We have recently defined a central region within Ku80 that is required for heterodimerization with Ku70. We now identified a core region within Ku80 (amino acids 210 to 531) that is necessary for binding of Ku to DNA ends. Interaction with Ku70 and DNA end binding are important for Ku80 function in vivo, since Ku80 mutants lacking DNA end binding activity were unable to restore radiation resistance in Ku80 deficient fibroblast cell lines. However, Ku80 mutants were identified that retained DNA end binding activity but were unable to restore radiation survival, thus pointing to additional functional properties of Ku80. An N-terminal deletional mutant of Ku80 was able to suppress wild type Ku80 function for radiation survival in several cell lines, thus demonstrating dominant negative function.

Mary Reid posted Huntington ...Sunday, June 14, 2009 8:14:25 PM

Neurobiol Dis. 2006 Nov;24(2):213-25. Epub 2006 Sep 6. Links

Induction of multiple heat shock proteins and neuroprotection in a primary culture model of familial amyotrophic lateral sclerosis.
Batulan Z, Taylor DM, Aarons RJ, Minotti S, Doroudchi MM, Nalbantoglu J, Durham HD.
Montreal Neurological Institute, McGill University, 3801 University St., Montreal, Quebec, Canada H3A 2B4.

High threshold for stress-induced activation of the heat shock transcription factor, Hsf1, may contribute to vulnerability of motor neurons to disease and limit efficacy of agents promoting expression of neuroprotective heat shock proteins (Hsps) through this transcription factor. Plasmid encoding a constitutively active form of Hsf1, Hsf1act, and chemicals shown to activate Hsf1 in other cells were investigated in a primary culture model of familial amyotrophic lateral sclerosis. Hsf1act and the Hsp90 inhibitor, geldanamycin, induced high expression of multiple Hsps in cultured motor neurons and conferred dramatic neuroprotection against SOD1G93A in comparison to Hsp70 or Hsp25 alone. Two other Hsp90 inhibitors, 17-allylamino-17-demethoxygeldanamycin (17-AAG) and radicicol, and pyrrolidine dithiocarbamate induced robust expression of Hsp70 and Hsp40 in motor neurons, but at cytotoxic concentrations. 17-AAG, which penetrates the blood-brain barrier, has exhibited a higher therapeutic index than geldanamycin, but this may not be the case when activation of Hsf1 in neurons is targeted.

Hi Donna,

I see that MSK1 encodes the mitochondrial lysyl-tRNA synthetase in yeast. I'm not sure if there are different genes in humans. Lysyl-tRNA synthetase in humans is known as KARS. It is of interest however that it is the mitochondrial form which binds mutant SOD1. Binding partners of MSK1 in the first link. It's also of interest that a normal function of MSK1 is to induce the expression of prions. Reduced prion protein expression is reported in an SOD1 mutant and reduced prion protein expression has been reported to accelerate the disease process. Does mitochondrial lysyl-tRNA snythetase induce the expression of prion protein and might the binding by mutant SOD1 inhibit this?

Mary

http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=MSK1


http://newsarchive.asm.org/aug00/topic4.asp
This conformation-shifting reaction is "very specific," Wickner says. "It does not induce other proteins, but picks out" only one in the mixture. Moreover, the "same part of the URE2 protein that induces prion formation in vivo induces amyloid formation in vitro." After entering this conformation, the protein becomes highly resistant to proteolytic digestion, a trait that is due in part to its assuming extensive beta-sheet structure. This whole process apparently is under metabolic control in yeast, with the expression of the MSK1 gene increasing [URE3], whereas deletion of MSK1 eliminates it. Moreover, if the RAS2 gene is activated, it becomes capable of blocking [URE3] prion induction, he notes. Precisely how MSK1 promotes prion formation remains a mystery, but these genes in yeast represent the first known genetic circuitry for generating prions and maintaining them under some form of metabolic control within cells, he says.

Mary,

Thanks for the info. Very interesting correlation of KARS with prions.

SUP35 implicated with prion proteins contains elongation factor EF-1 alpha.

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http://www.thebiogrid.org/SearchResults/summary/35750

MSK1 Saccharomyces cerevisiae

Intereacts with ELP3

Subunit of Elongator complex, which is required for modification of wobble nucleosides in tRNA; exhibits histone acetyltransferase activity that is directed to histones H3 and H4; disruption confers resistance to K. lactis zymotoxin

Gene Ontology
Function
• histone acetyltransferase activity (IDA)
• histone acetyltransferase activity (ISS)

Process
• tRNA wobble uridine modification (IMP)
• regulation of transcription from RNA polymera ... (IMP)
• RNA modification (RCA)
• tRNA metabolic process (RCA)

Component
• nucleus (IDA)
• Elongator holoenzyme complex (IDA)
• cytoplasm (IDA)

---

http://www.ncbi.nlm.nih.gov/pubmed/8469113

Mol Microbiol. 1993 Mar;7(5):683-92.

Deletion analysis of the SUP35 gene of the yeast Saccharomyces cerevisiae reveals two non-overlapping functional regions in the encoded protein.

Ter-Avanesyan MD, Kushnirov VV, Dagkesamanskaya AR, Didichenko SA, Chernoff YO, Inge-Vechtomov SG, Smirnov VN.

Institute of Experimental Cardiology, Cardiology Research Centre, Moscow, Russia.

SUP35 is an omnipotent suppressor gene of Saccharomyces cerevisiae coding for a protein consisting of a C-terminal part similar to the elongation factor EF-1 alpha and a unique N-terminal sequence of 253 amino acids. Twelve truncated versions of the SUP35 gene were generated by the deletion of fragments internal to the coding sequence. Functional studies of these deletion mutants showed that: (i) only the EF-1 alpha-like C-terminal part of the Sup35 protein is essential for the cell viability; (ii) overexpression of either the N-terminal part of the Sup35 protein or the full-length Sup35 protein decreases translational fidelity, resulting in omnipotent suppression and reduced growth of [psi+] strains; (iii) expression of the C-terminal part of the Sup35 protein generates an antisuppressor phenotype; and (iv) both the N- or C-terminal segments of the Sup35 protein can bind to 80S ribosomes. Thus, the data obtained define two domains within the Sup35 protein which are responsible for different functions.

PMID: 8469113 [PubMed - indexed for MEDLINE]

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T0G-4XSVRH9-4&_user=10&_coverDate=01%2F18%2F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1203759068&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=61c607596d39ea40d8eb38b007f2abc0

Neuroscience Letters Volume 469, Issue 1, 18 January 2010, Pages 112-116

Degradation of TDP-43 and its pathogenic form by autophagy and the ubiquitin-proteasome system

Xiaoju Wanga, Huadong Fana, Zheng Yinga, Bin Lia, Hongfeng Wanga and Guanghui Wang, a,

a Hefei National Laboratory for Physical Sciences at Microscale and Department of Neurobiology, School of Life Sciences, University of Science & Technology of China

Abstract
TAR DNA-binding protein-43 (TDP-43) is a nuclear protein functioning in the regulation of transcription and mRNA splicing. TDP-43 is accumulated in ubiquitinated inclusions in frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U) and amyotrophic lateral sclerosis (ALS) diseased brains. However, the pathways involved in the clearance of TDP-43 and its pathogenic form (TDP-25), a truncated form of TDP-43, are still not elucidated. In this study, we demonstrated that the protein levels of TDP-43 and TDP-25 were increased in cells treated with a proteasome inhibitor, MG132, or an autophagy inhibitor, 3-MA, whereas, they were decreased in cells treated with an enhancer of autophagy, trehalose. Furthermore, more protein level changes of TDP-25 than TDP-43 were observed in cells treated with above inhibitors or enhancer. Thus, our data suggest that TDP-43 and TDP-25 are degraded by both proteasome and autophagy with TDP-25 being more regulated.