Nature13March2008Volume452Number7184pp127252_PKM2 Nature 13 March 2008 Volume 452 Number 7184, pp127-252 PKM2 Nature 13 March 2008 Volume 452 Number 7184, pp127-252 New Human Famsbase for Nature 13 March 2008 Volume 452 Number 7184, pp127-252 PKM2 wwwpdfamscomindexjahtml http://famshelp.gsc.riken.jp/famsbase/index.html http://www.pd-fams.com/index_ja.html Hideaki Umeyama, Ph.D., Professor School of Pharmacy, Kitasato University 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan phone : +81-3-5791-6330 fax : +81-3-3446-9553 e-mail:umeyamah@pharm.kitasato-u.ac.jp 港区白金5-9-1 北里大学薬学部教授(理化学研究所客員主管研究員) 梅山秀明 http://famshelp.gsc.riken.jp/famsbase/index.html http://www.pd-fams.com/index_ja.html ENSEMBL Homo sapiens (human) hsap0 43797 - Metazoa Chordata ENSEMBL Homo sapiens (human) 137746 - Metazoa Chordata H-Invitational Homo sapiens (human) - Metazoa Chordata NCBI Homo sapiens (cDNA) - Metazoa Chordata Kazusa hsap1 hsap2 28983 huge0 2038 http://apr2007.archive.ensembl.org/Homo_sapiens/index.html http://www.h-invitational.jp/ http://hinv.ddbj.nig.ac.jp/index-j.html http://www.ncbi.nlm.nih.gov/genome/guide/human/ http://www.kazusa.or.jp/huge/ Pyruvate kinase M2 is a phosphotyrosine-binding protein p181 A mechanism whereby the M2 isoform of the glycolytic enzyme pyruvate kinase (PKM2) can be regulated by tyrosine kinase signalling pathways through an ability to bind tyrosine-phosphorylated proteins is revealed. Heather R. Christofk et al. doi:10.1038/nature06667 Abstract | Full Text | PDF > Abstract Article Nature 452, 181-186 (13 March 2008) | doi:10.1038/nature06667; Received 8 November 2007; Accepted 3 January 2008 ピルビン酸キナーゼ M2 はホスホチロシン結合タンパク質である . (Title in English; ).Heather R. Christofk1, Matthew G. Vander Heiden1,3, Ning Wu1, John M. Asara2,4 & Lewis C. Cantley1,4 Department of Systems Biology, Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA Correspondence to: Lewis C. Cantley1,4 Correspondence and requests for materials should be addressed to L.C.C. (Email: lcantley@hms.harvard.edu). Top of pageAbstract 増殖因子は、細胞を刺激して余分な栄養を取り込ませ、それが同 化過程に使われるようにする。これがどのような生化学機構によって遂行されるのかは 完全に解明されていないが、反応はシグナル伝達タンパク質のチロシン残基のリン酸化 によって開始される。ホスホチロシン結合タンパク質探索のために新しくプロテオーム スクリーニングを行い、解糖にかかわる酵素ピルビン酸キナーゼのヒト M2(胎児)型ア イソフォーム(PKM2)が、チロシンのリン酸化されたペプチドに直接、選択的に結合す ることを明らかにした。ホスホチロシンをもつペプチドが PKM2 に結合すると、アロステ リック活性化因子であるフルクトース-1,6-ビスリン酸が解離し、PKM2 の酵素活性が阻 害される。また、細胞が特定の増殖因子によって刺激されると、このホスホチロシンシ グナル伝達を介した PKM2 の調節によって、グルコース代謝物がエネルギー生産から同化 過程へと方向転換されることもわかった。これらを総合すると、このホスホチロシン結 合型のピルビン酸キナーゼの発現が、がん細胞の急激な増殖に不可欠であることが示唆 される。 Top of page M2 isoform of the glycolytic enzyme pyruvate kinase (PKM2) Pyruvate kinase M2 このホスホチロシン結合型のピルビン酸キナーゼの発現が、がん細胞の急激な増殖に不 可欠であることが示唆される。 7: P14618 Reports BLink, Conserved Domains, Links Pyruvate kinase isozymes M1/M2 (Pyruvate kinase muscle isozyme) (Pyruvate kinase 2/3) (Cytosolic thyroid hormone-binding protein) (CTHBP) (THBP1) gi|20178296|sp|P14618.4|KPYM_HUMAN[20178296] LOCUS P14618 531 aa linear PRI 05- FEB-2008 DEFINITION Pyruvate kinase isozymes M1/M2 (Pyruvate kinase muscle isozyme) (Pyruvate kinase 2/3) (Cytosolic thyroid hormone-binding protein) (CTHBP) (THBP1). ACCESSION VERSION DBSOURCE P14618 P14618.4 GI:20178296 swissprot: locus KPYM_HUMAN, accession P14618; class: standard. extra accessions:P14786,Q53GK4,Q96E76,Q9BWB5,Q9UPF2 created: Apr 1, 1990. sequence updated: Jan 23, 2007. annotation updated: Feb 5, 2008. COMMENT On or before Jul 17, 2007 this sequence version replaced gi:74740492, gi:2117873, gi:478822, gi:48429214, gi:266427. [FUNCTION] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. [CATALYTIC ACTIVITY] ATP + pyruvate = ADP + phosphoenolpyruvate. [COFACTOR] Magnesium. [COFACTOR] Potassium. [ENZYME REGULATION] Isoform M2 is allosterically activated by D-fructose 1,6-biphosphate (FBP). Inhibited by oxalate. [BIOPHYSICOCHEMICAL PROPERTIES] Kinetic parameters: KM=2.7 mM for phosphoenolpyruvate; KM=0.17 mM for phosphoenolpyruvate (in the presence of 2mM FBP); KM=0.34 mM for ADP; KM=0.24 mM for ADP (in the presence of 2mM FBP); Note=At pH=8 and 32 degrees Celsius. [PATHWAY] Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 5/5. [SUBUNIT] Homotetramer. [INTERACTION] Q9NQT4:EXOSC5; NbExp=1; IntAct=EBI-353408, EBI-371876; Q92597:NDRG1; NbExp=1; IntAct=EBI-353408, EBI716486; P04049:RAF1; NbExp=3; IntAct=EBI-353408, EBI-365996. [ALTERNATIVE PRODUCTS] Event=Alternative splicing; Named isoforms=2; Name=M2; IsoId=P14618-1; Sequence=Displayed; Name=M1; IsoId=P14618-2, P14786-1; Sequence=VSP_011101. [PTM] Phosphorylated upon DNA damage, probably by ATM or ATR. [MISCELLANEOUS] There are 4 isozymes of pyruvate kinase in mammals: L, R, M1 and M2. L type is major isozyme in the liver, R is found in red cells, M1 is the main form in muscle, heart and brain, and M2 is found in early fetal tissues as well as in most cancer cells. [SIMILARITY] Belongs to the pyruvate kinase family. [WEB RESOURCE] Name=Wikipedia; Note=Pyruvate kinase entry; URL='http://en.wikipedia.org/wiki/Pyruvate_kinase'. FEATURES source Location/Qualifiers 1..531 /organism="Homo sapiens" /db_xref="taxon:9606" gene 1..531 /gene="PKM2" /note="synonyms: PK2, PK3, PKM" Protein 1..531 /gene="PKM2" /product="Pyruvate kinase isozymes M1/M2" /EC_number="2.7.1.40" >gi|20178296|sp|P14618.4|KPYM_HUMAN Pyruvate kinase isozymes M1/M2 (Pyruvate kinase muscle isozyme) (Pyruvate kinase 2/3) (Cytosolic thyroid hormone-binding protein) (CTHBP) (THBP1) MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSV ETLKEMIKSGMN VARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGT AEVELKKGATL KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEV ENGGSLGSKKGVN LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKI ISKIENHEGVRRF DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKK PRPTRAEGSDVAN AVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSD PTEATAVGAVEAS FKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQ EAWAEDVDLRV NFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP Score E Sequences producing significant alignments: (bits) Value SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis p187 SATB1 has been identified as a major regulator of gene expression in breast cancer. SATB1 is often overexpressed in breast tumours, correlating with poor prognosis, and altering the expression of many genes, which leads to enhanced tumourigenesis and metastasis. Hye-Jung Han, Jose Russo, Yoshinori Kohwi and Terumi Kohwi-Shigematsu doi:10.1038/nature06781 Abstract | Full Text | PDF See also: Editor's summary Article Nature 452, 187-193 (13 March 2008) | doi:10.1038/nature06781; Received 11 September 2007; Accepted 22 January 2008 SATB1 は遺伝子発現のリプログラミングを行い、乳がんの増殖と転移を促進する . (Title in English; ).Hye-Jung Han1, Jose Russo2, Yoshinori Kohwi1,3 & Terumi Kohwi-Shigematsu1,3 Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA Breast Cancer Research Laboratory, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA These authors contributed equally to this work. Correspondence to: Yoshinori Kohwi1,3Terumi Kohwi-Shigematsu1,3 Correspondence and requests for materials should be addressed to T.K.-S. (Email: Terumiks@lbl.gov) or Y.K. (Email: YKohwi@lbl.gov). Top of pageAbstract 腫瘍の悪性化に伴い遺伝子発現が大きく変化するが、そのメカニ ズムに関してはほとんどわかっていない。SATB1 は多数の遺伝子を SATB1 のもとに集合 さ せ、さらにクロマチンリモデリングに関与する酵素を呼び込み、クロマチン構造と遺伝 子発現を制御するゲノムオーガナイザーである。本論文では、SATB1 が悪性乳がん細胞 で発現されていることを示し、SATB1 の発現レベルはリンパ節浸潤の有無にかかわらず 、患者の予後と密接な関連性( P <0.0001)がある事実が判明した。悪性度の高い培養 がん細胞(MDA-MB-231)において、RNA 干渉を用いて SATB1 をノックダウンさせると 1,000 を超える遺伝子の発現が変化し、乳腺本来の極性をもった組織形態が回復して腫 瘍形成性が失われ、さらに in vivo で腫瘍増殖や転移能が消失した。逆に、悪性度の 低い培養がん細胞(SKBR3)に SATB1 を強制発現させることで悪性度の高い腫瘍の表現 型 と一致した遺伝子発現パターンを示すようになり、 in vivo で、このがん細胞は新た に転移能を獲得した。SATB1 は標的遺伝子座において特異的なエピジェネティック修飾 を確立し、そして腫瘍抑制遺伝子の発現を抑制する一方で、転移を促進する遺伝子の発 現を増強するという直接的な制御を行っている。SATB1 は乳がん細胞のクロマチン構成 および転写特性をリプログラムすることで、がん細胞の増殖や転移を促進するというこ とから、これは腫瘍悪性化の新しいメカニズムを提供している。 SATB1 SATB1 は乳がん細胞のクロマチン構成および転写特性をリプログラムすることで、がん 細胞の増殖や転移を促進するということから、これは腫瘍悪性化の新しいメカニズムを 提供している。 The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth p230 Many tumour cells express the M2 form of pyruvate kinase rather than the usual M1 form. PKM2 is now shown to promote tumorigenesis and switch the cellular metabolism to increased lactate production and reduced oxygen consumption, recapitulating key aspects of the Warburg effect. Heather R. Christofk et al. doi:10.1038/nature06734 First paragraph | Full Text | PDF See also: Editor's summary Letter Nature 452, 230-233 (13 March 2008) | doi:10.1038/nature06734; Received 18 October 2007; Accepted 19 January 2008 The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth Heather R. Christofk1, Matthew G. Vander Heiden1,2, Marian H. Harris3, Arvind Ramanathan4, Robert E. Gerszten4,5,6, Ru Wei4, Mark D. Fleming3, Stuart L. Schreiber4,7 & Lewis C. Cantley1,8 Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA Department of Pathology, Children's Hospital, Boston, Massachusetts 02115, USA Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA Cardiology Division and Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, Massachusetts 02129, USA Donald W. Reynolds Cardiovascular Clinical Research Center on Atherosclerosis, Harvard Medical School, Boston, Massachusetts 02115, USA Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA Correspondence to: Lewis C. Cantley1,8 Correspondence and requests for materials should be addressed to L.C.C. (Email: lcantley@hms.harvard.edu). Top of pageMany tumour cells have elevated rates of glucose uptake but reduced rates of oxidative phosphorylation. This persistence of high lactate production by tumours in the presence of oxygen, known as aerobic glycolysis, was first noted by Otto Warburg more than 75 yr ago1. How tumour cells establish this altered metabolic phenotype and whether it is essential for tumorigenesis is as yet unknown. Here we show that a single switch in a splice isoform of the glycolytic enzyme pyruvate kinase is necessary for the shift in cellular metabolism to aerobic glycolysis and that this promotes tumorigenesis. Tumour cells have been shown to express exclusively the embryonic M2 isoform of pyruvate kinase2. Here we use short hairpin RNA to knockdown pyruvate kinase M2 expression in human cancer cell lines and replace it with pyruvate kinase M1. Switching pyruvate kinase expression to the M1 (adult) isoform leads to reversal of the Warburg effect, as judged by reduced lactate production and increased oxygen consumption, and this correlates with a reduced ability to form tumours in nude mouse xenografts. These results demonstrate that M2 expression is necessary for aerobic glycolysis and that this metabolic phenotype provides a selective growth advantage for tumour cells in vivo. UNC93B1 delivers nucleotide-sensing toll-like receptors to endolysosomes p234 The membrane protein UNC93B interacts with intracellular Toll-like receptors TLR7 and TLR9. This paper shows that UNC93B specifically controls TLR trafficking from the endoplasmic reticulum to the endolysosome but is not required for ligand recognition or signal initiation. You-Me Kim, Melanie M. Brinkmann, Marie-Eve Paquet & Hidde L. Ploegh doi:10.1038/nature06726 First paragraph | Full Text | PDF Letter Nature 452, 234-238 (13 March 2008) | doi:10.1038/nature06726; Received 5 September 2007; Accepted 3 January 2008; Published online 27 February 2008 UNC93B1 delivers nucleotide-sensing toll-like receptors to endolysosomes You-Me Kim1, Melanie M. Brinkmann1, Marie-Eve Paquet1 & Hidde L. Ploegh1 Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA Correspondence to: You-Me Kim1Hidde L. Ploegh1 Correspondence and requests for materials should be addressed to Y.-M.K. (Email: ykim@wi.mit.edu) or H.L.P. (Email: ploegh@wi.mit.edu). Top of pageSignalling by means of toll-like receptors (TLRs) is essential for the development of innate and adaptive immune responses1, 2, 3. UNC93B1, essential for signalling of TLR3, TLR7 and TLR9 in both humans and mice, physically interacts with these TLRs in the endoplasmic reticulum (ER)4, 5, 6. Here we show that the function of the polytopic membrane protein UNC93B1 is to deliver the nucleotide-sensing receptors TLR7 and TLR9 from the ER to endolysosomes. In dendritic cells of 3d mice, which express an UNC93B1 missense mutant (H412R) incapable of TLR binding, neither TLR7 nor TLR9 exits the ER. Furthermore, the trafficking and signalling defects of the nucleotide-sensing TLRs in 3d dendritic cells are corrected by expression of wild-type UNC93B1. However, UNC93B1 is dispensable for ligand recognition and signal initiation by TLRs. To our knowledge, UNC93B1 is the first protein to be identified as a molecule specifically involved in trafficking of nucleotide-sensing TLRs. By inhibiting the interaction between UNC93B1 and TLRs it should be possible to achieve specific regulation of the nucleotide-sensing TLRs without compromising signalling via the cell-surface-disposed TLRs. Top of page An allylic ketyl radical intermediate in clostridial amino-acid fermentation p239 The pathogenic bacterium Clostridium difficile thrives by fermentation of L-leucine to ammonia, CO2, isovalerate, and isocaproate under anaerobic conditions. Ketyl radicals have been proposed to mediate a key reaction catalysed by an iron?sulphur cluster-containing dehydratase, which requires activation by ATP-dependent electron transfer from a second iron?sulphur protein. A kinetically competent product-related allylic ketyl radical bound to the dehydratase using electron paramagnetic resonance spectroscopy is identified. These results suggest that other 2hydroxyacyl-CoA dehydratases (and the related benzoyl-CoA reductases) may employ ketyl radical intermediates. The absence of radical generators makes these enzymes unprecedented in biochemistry. Jihoe Kim, Daniel J. Darley, Wolfgang Buckel and Antonio J. Pierik doi:10.1038/nature06637 First paragraph | Full Text | PDF See also: Editor's summary | News and Views by Jarrett Abstract Letter Nature 452, 239-242 (13 March 2008) | doi:10.1038/nature06637; Received 6 August 2007; Accepted 10 January 2008 An allylic ketyl radical intermediate in clostridial amino-acid fermentation Jihoe Kim1, Daniel J. Darley1,2, Wolfgang Buckel1 & Antonio J. Pierik1 Laboratorium fur Mikrobiologie, Fachbereich Biologie, PhilippsUniversitat, D35032 Marburg, Germany Present address: Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. Correspondence to: Antonio J. Pierik1 Correspondence and requests for materials should be addressed to A.J.P. (Email: pierik@staff.unimarburg.de). Top of pageThe human pathogenic bacterium Clostridium difficile thrives by the fermentation of l-leucine to ammonia, CO2, 3-methylbutanoate and 4methylpentanoate under anaerobic conditions1. The reductive branch to 4methylpentanoate proceeds by means of the dehydration of (R)-2-hydroxy-4methylpentanoyl-CoA to 4-methylpent-2-enoyl-CoA, which is chemically the most demanding step. Ketyl radicals have been proposed2 to mediate this reaction catalysed by an iron?sulphur-cluster-containing dehydratase, which requires activation by ATP-dependent electron transfer from a second iron?sulphur protein functionally similar to the iron protein of nitrogenase. Here we identify a kinetically competent product-related allylic ketyl radical bound to the enzyme by electron paramagnetic resonance spectroscopy employing isotope-labelled (R)-2-hydroxy-4methylpentanoyl-CoA species. We also found that the enzyme generated the stabilized pentadienoyl ketyl radical from the substrate analogue 2hydroxypent-4-enoyl-CoA, supporting the proposed mechanism. Our results imply that also other 2-hydroxyacyl-CoA dehydratases3 and the related benzoyl-CoA reductases4?present in anaerobically living bacteria?employ ketyl radical intermediates. The absence of radical generators such as coenzyme B12, S-adenosylmethionine or oxygen makes these enzymes unprecedented in biochemistry. Top of page Erratum Top The X-ray crystal structure of RNA polymerase from Archaea p248 Akira Hirata, Brianna J. Klein and Katsuhiko S. Murakami doi:10.1038/nature06844 Full Text | PDF Erratum Nature 452, 248 (13 March 2008) | doi:10.1038/nature06844 The X-ray crystal structure of RNA polymerase from Archaea Akira Hirata, Brianna J. Klein & Katsuhiko S. Murakami Nature 451, 851?854 (2008) In the PDF and print versions of this Letter, the Protein Data Bank (PDB ID) code of the Sulfolobus solfataricus RNA polymerase (RNAP) was wrongly listed as 2PM2. The correct code is 2PMZ. This is correct in the full-text HTML version and on the contents page. Top of page nature online SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin Eriko Michishita et al. doi:10.1038/nature06736 First paragraph | Full Text | PDF Letter Nature advance online publication 12 March 2008 | doi:10.1038/nature06736; Received 3 December 2007; Accepted 23 January 2008; Published online 12 March 2008 SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin Eriko Michishita1,5, Ronald A. McCord1,5, Elisabeth Berber1,5, Mitomu Kioi2, Hesed Padilla-Nash6, Mara Damian1,5, Peggie Cheung3, Rika Kusumoto8, Tiara L. A. Kawahara4, J. Carl Barrett7,9, Howard Y. Chang4, Vilhelm A. Bohr8, Thomas Ried6, Or Gozani3 & Katrin F. Chua1,5 Department of Medicine, Division of Endocrinology, Gerontology and Metabolism, School of Medicine, Department of Radiation Oncology, School of Medicine, Department of Biological Sciences, and, Program in Epithelial Biology, School of Medicine, Stanford University, Stanford, California 94305, USA Geriatric Research, Education and Clinical Center, VA Palo Alto Health Care System, Palo Alto, California 94304, USA Genetics Branch, and, Laboratory of Biosystems and Cancer, Center for Cancer Research, National Cancer Institute/NIH, Bethesda, Maryland 20892, USA Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, Maryland 21224, USA Present address: Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA. Correspondence to: Katrin F. Chua1,5 Correspondence and requests for materials should be addressed to K.F.C. (Email: kfchua@stanford.edu). Top of pageThe Sir2 deacetylase regulates chromatin silencing and lifespan in Saccharomyces cerevisiae 1, 2. In mice, deficiency for the Sir2 family member SIRT6 leads to a shortened lifespan and a premature ageing-like phenotype3. However, the molecular mechanisms of SIRT6 function are unclear. SIRT6 is a chromatin-associated protein3, but no enzymatic activity of SIRT6 at chromatin has yet been detected, and the identity of physiological SIRT6 substrates is unknown. Here we show that the human SIRT6 protein is an NAD+-dependent, histone H3 lysine 9 (H3K9) deacetylase that modulates telomeric chromatin. SIRT6 associates specifically with telomeres, and SIRT6 depletion leads to telomere dysfunction with end-toend chromosomal fusions and premature cellular senescence. Moreover, SIRT6-depleted cells exhibit abnormal telomere structures that resemble defects observed in Werner syndrome, a premature ageing disorder4, 5. At telomeric chromatin, SIRT6 deacetylates H3K9 and is required for the stable association of WRN, the factor that is mutated in Werner syndrome4, 5. We propose that SIRT6 contributes to the propagation of a specialized chromatin state at mammalian telomeres, which in turn is required for proper telomere metabolism and function. Our findings constitute the first identification of a physiological enzymatic activity of SIRT6, and link chromatin regulation by SIRT6 to telomere maintenance and a human premature ageing syndrome. Top of page