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Yugi K, Kubota H, Toyoshima Y, Noguchi R, Kawata K, Komori Y, Uda S, Kunida K, Tomizawa Y, Funato Y, Miki H, Matsumoto M, Nakayama KI, Kashikura K, Endo K, Ikeda K, Soga T, Kuroda S. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep 2014; 8:1171-83. [PMID: 25131207 DOI: 10.1016/j.celrep.2014.07.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/13/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis is regulated by signals through multiple molecular networks that include protein phosphorylation and metabolites. However, where and when the signal flows through a network and regulates homeostasis has not been explored. We have developed a reconstruction method for the signal flow based on time-course phosphoproteome and metabolome data, using multiple databases, and have applied it to acute action of insulin, an important hormone for metabolic homeostasis. An insulin signal flows through a network, through signaling pathways that involve 13 protein kinases, 26 phosphorylated metabolic enzymes, and 35 allosteric effectors, resulting in quantitative changes in 44 metabolites. Analysis of the network reveals that insulin induces phosphorylation and activation of liver-type phosphofructokinase 1, thereby controlling a key reaction in glycolysis. We thus provide a versatile method of reconstruction of signal flow through the network using phosphoproteome and metabolome data.
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Affiliation(s)
- Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kubota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; PRESTO, Japan Science and Technology Corporation, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yu Toyoshima
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rei Noguchi
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kentaro Kawata
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasunori Komori
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinsuke Uda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Katsuyuki Kunida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoko Tomizawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Kasumi Kashikura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Keiko Endo
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Kazutaka Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Corporation, Bunkyo-ku, Tokyo 113-0033, Japan.
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Seki Y, Sato K, Kono T, Akiba Y. Two types of phosphofructokinase-1 differentially regulate the glycolytic pathway in insulin-stimulated chicken skeletal muscle. Comp Biochem Physiol B Biochem Mol Biol 2006; 143:344-50. [PMID: 16413217 DOI: 10.1016/j.cbpb.2005.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 12/04/2005] [Accepted: 12/05/2005] [Indexed: 11/21/2022]
Abstract
To elucidate the precise regulation of glucose homeostasis in chicken skeletal muscle, expression of muscle- and liver-type phosphofructokinase-1 (EC:2.7.1.11, PFK-M, PFK-L) was characterized in the insulin-stimulated state by Real-Time PCR. Firstly, chicken PFK-M and PFK-L full-length cDNA sequences were identified. The deduced amino acid sequences were 81.6% and 86.5% identical with human PFK-M and PFK-L, respectively. In pectoralis superficialis (PS) muscle and extensor digitorum longus (EDL), PFK-M mRNA levels were unchanged following insulin stimulation. Surprisingly, although mammalian PFK-L has been reported to be expressed in liver, kidney and brain, chicken PFK-L was not detected in liver and kidney, however, strong expression was detected in skeletal muscle and brain by Northern blot analysis. However, using PCR, PFK-L mRNA was detected in liver. Taken together, chicken PFK-L mRNA expression was at a very low level, below the detection limit of Northern blot analysis. Chicken PFK-L mRNA levels were increased 200% in PS muscle but decreased by 40% in EDL following insulin stimulation. These results suggest that two types of PFK regulate the glycolytic pathway in the insulin-stimulated state and, therefore, that glucose metabolism in chicken skeletal muscle may be regulated in a very different manner compared to mammals.
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MESH Headings
- Amino Acid Sequence
- Animals
- Chickens/metabolism
- Cloning, Molecular
- Gene Expression
- Glucose/metabolism
- Glycolysis/genetics
- Insulin/pharmacology
- Liver/chemistry
- Molecular Sequence Data
- Muscle, Skeletal/chemistry
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/enzymology
- Phosphofructokinase-1, Liver Type/genetics
- Phosphofructokinase-1, Liver Type/metabolism
- Phosphofructokinase-1, Muscle Type/genetics
- Phosphofructokinase-1, Muscle Type/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/metabolism
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Affiliation(s)
- Yoshinori Seki
- Animal Nutrition, Division of Life Sciences, Graduate School of Agricultural Science, Tohoku University, Sendai, 981-8555, Japan
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Mannick EE, Bonomolo JC, Horswell R, Lentz JJ, Serrano MS, Zapata-Velandia A, Gastanaduy M, Himel JL, Rose SL, Udall JN, Hornick CA, Liu Z. Gene expression in mononuclear cells from patients with inflammatory bowel disease. Clin Immunol 2004; 112:247-57. [PMID: 15308118 DOI: 10.1016/j.clim.2004.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 03/17/2004] [Indexed: 01/16/2023]
Abstract
OBJECTIVES Discovery of Nod2 as the inflammatory bowel disease 1 (IBD1) susceptibility gene has brought to light the significance of mononuclear cells in inflammatory bowel disease pathogenesis. The purpose of this study was to examine changes in gene expression in peripheral blood mononuclear cells in patients with untreated Crohn's disease (CD) and ulcerative colitis (UC) as compared to patients with other inflammatory gastrointestinal disorders and to healthy controls. METHODS We used a 2400 gene cDNA glass slide array (MICROMAX) to examine gene expression in peripheral blood mononuclear cells from seven patients with Crohn's disease, five patients with ulcerative colitis, 10 patients with other inflammatory gastrointestinal disorders, and 22 age- and sex-matched controls. Results. Novel categories of genes differentially expressed in Crohn's disease and ulcerative colitis patients included genes regulating hematopoietic cell differentiation and leukemogenesis, lipid raft-associated signaling, the actin cytoskeleton, and vesicular trafficking. CONCLUSIONS Altered gene expression in mononuclear cells may contribute to inflammatory bowel disease pathogenesis.
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Winger QA, Hill JR, Shin T, Watson AJ, Kraemer DC, Westhusin ME. Genetic reprogramming of lactate dehydrogenase, citrate synthase, and phosphofructokinase mRNA in bovine nuclear transfer embryos produced using bovine fibroblast cell nuclei. Mol Reprod Dev 2000; 56:458-64. [PMID: 10911395 DOI: 10.1002/1098-2795(200008)56:4<458::aid-mrd3>3.0.co;2-l] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Adult animal cloning has progressed to allow the production of offspring cloned from adult cells, however many cloned calves die prenatally or shortly after birth. This study examined the expression of three important metabolic enzymes, lactate dehydrogenase (LDH), citrate synthase, and phosphofructokinase (PFK), to determine if their detection in nuclear transfer (NT) embryos mimics that determined for in vitro produced embryos. A day 40 nuclear transfer produced fetus derived from an adult cell line was collected and fetal fibroblast cultures were established and maintained. Reconstructed NT embryos were then produced from this cell line, and RT-PCR was used to evaluate mRNA reprogramming. All three mRNAs encoding these enzymes were detected in the regenerated fetal fibroblast cell line. Detection patterns were first determined for IVF produced embryos (1-cell, 2-cell, 6-8 cell, morula, and blastocyst stages) to compare with their detection in NT embryos. PFK has three subunits: PFK-L, PFK-M, and PFK-P. PFK-L and PFK-P were not detected in bovine oocytes. PFK subunits were not detected in 6-8 cell embryos but were detected in blastocysts. Results from NT embryo RT-PCR demonstrated that PFK was not detected in 8-cell NT embryos but was detected in NT blastocysts indicating that proper nuclear reprogramming had occurred. Citrate synthase was detected in oocytes and throughout development to the blastocyst stage in both bovine IVF and NT embryos. LDH-A and LDH-B were detected in bovine oocytes and in all stages of IVF and NT embryos examined up to the blastocyst stage. A third subunit, LDH-C was not detected at the blastocyst stage in IVF or NT embryos but was detected in all earlier stages and in mature oocytes. In addition, LDH-C mRNA was detected in gonad isolated from the NT and an in vivo produced control fetus. These results indicate that the three metabolic enzymes maintain normal expression patterns and therefore must be properly reprogrammed following nuclear transfer.
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Affiliation(s)
- Q A Winger
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine, Texas A&M University, College Station 77843-4466, USA
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Nakajima H, Noguchi T, Hamaguchi T, Tomita K, Hanafusa T, Kono N, Tanaka T, Kuwajima M, Matsuzawa Y. Expression of mouse phosphofructokinase-M gene alternative transcripts: evidence for the conserved two-promoter system. Biochem J 1994; 303 ( Pt 2):449-53. [PMID: 7980403 PMCID: PMC1137348 DOI: 10.1042/bj3030449] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular cloning of the 5' part of mouse phosphofructokinase-M cDNA was performed. In the 46 cDNA clones isolated, there were two classes of 5' untranslated sequences. One had an EcoRI site within its 5' untranslated sequence. This showed 83.0% similarity with human type B mRNA for phosphofructokinase-M. The other lacked an EcoRI site, showing 92.9% similarity with human type C mRNA. Using the reverse-transcription PCR technique, we found that the transcript with an EcoRI site was exclusively expressed in cardiac and skeletal muscles, while that without an EcoRI site was expressed in all the mouse tissues examined. The results suggested that the mouse phosphofructokinase-M gene was transcribed through alternative splicing by the multiple promoters. This transcription mechanism was considered to be evolutionarily conserved. The level of phosphofructokinase-M gene expression in mouse cardiac and skeletal muscles decreased in the ketotic diabetic state. Although the regulatory mechanism and the physiological significance are not fully known, this would indicate that phosphofructokinase-M gene transcripts are affected during the diabetic state.
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MESH Headings
- Animals
- Base Sequence
- Blotting, Northern
- Cloning, Molecular
- Conserved Sequence
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Diabetes Mellitus, Experimental/enzymology
- Diabetes Mellitus, Experimental/genetics
- Gene Expression Regulation, Enzymologic/genetics
- Humans
- Male
- Mice
- Mice, Inbred ICR
- Molecular Sequence Data
- Muscles/enzymology
- Myocardium/enzymology
- Nucleic Acid Hybridization
- Phosphofructokinase-1/genetics
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rabbits
- Rats
- Sequence Alignment
- Sequence Homology, Amino Acid
- Specific Pathogen-Free Organisms
- Transcription, Genetic/genetics
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Affiliation(s)
- H Nakajima
- Second Department of Internal Medicine, Osaka University Medical School, Suita, Japan
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Vaisanen PA, Reddy GR, Sharma PM, Kohani R, Johnson JL, Raney AK, Babior BM, McLachlan A. Cloning and characterization of the human muscle phosphofructokinase gene. DNA Cell Biol 1992; 11:461-70. [PMID: 1388024 DOI: 10.1089/dna.1992.11.461] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A 35-kbp region of genomic DNA encoding the human muscle phosphofructokinase (HPFK-M) gene including all of the coding exons (1-22) plus 2.2-kbp of 5'-flanking sequence has been cloned. The exon boundaries are the same as has been observed for the rabbit muscle phosphofructokinase (RPFK-M), the human liver phosphofructokinase (HPFK-L), and the mouse liver phosphofructokinase (MPFK-L) genes. Characterization of the structure of the HPFK-M gene and its transcript in Epstein-Barr virus transformed B-cell lines derived from patients with glycogen storage disease type VII (GSDVII or Tarui's disease) demonstrated that this single-copy gene encodes a normal sized 3.0-kb transcript in the four cases examined. This suggests the lesion in these cases represents either a point mutation or possibly a small insertion or deletion resulting in the synthesis of a defective HPFK-M protein. Analysis of the 5'-flanking region demonstrated the presence of a functional promoter located within 114 nucleotides of a proposed transcription initiation site. This promoter was active in the human cervical carcinoma cell line, HeLa S3, the dedifferentiated human hepatoma cell line, HepG2.1, and the mouse myoblast cell line, C2C12, suggesting this promoter has a broad cell-type specificity. In addition, from the known HPFK-M cDNA sequences, this observation indicates that the HPFK-M gene has a second promoter located upstream from the genomic region isolated in this study.
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Affiliation(s)
- P A Vaisanen
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037
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