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Hanasaki M, Yaku K, Yamauchi M, Nakagawa T, Masumoto H. Deletion of the GAPDH gene contributes to genome stability in Saccharomyces cerevisiae. Sci Rep 2020; 10:21146. [PMID: 33273685 PMCID: PMC7713361 DOI: 10.1038/s41598-020-78302-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 11/17/2020] [Indexed: 12/30/2022] Open
Abstract
Cellular metabolism is directly or indirectly associated with various cellular processes by producing a variety of metabolites. Metabolic alterations may cause adverse effects on cell viability. However, some alterations potentiate the rescue of the malfunction of the cell system. Here, we found that the alteration of glucose metabolism suppressed genome instability caused by the impairment of chromatin structure. Deletion of the TDH2 gene, which encodes glyceraldehyde 3-phospho dehydrogenase and is essential for glycolysis/gluconeogenesis, partially suppressed DNA damage sensitivity due to chromatin structure, which was persistently acetylated histone H3 on lysine 56 in cells with deletions of both HST3 and HST4, encoding NAD+-dependent deacetylases. tdh2 deletion also restored the short replicative lifespan of cells with deletion of sir2, another NAD+-dependent deacetylase, by suppressing intrachromosomal recombination in rDNA repeats increased by the unacetylated histone H4 on lysine 16. tdh2 deletion also suppressed recombination between direct repeats in hst3∆ hst4∆ cells by suppressing the replication fork instability that leads to both DNA deletions among repeats. We focused on quinolinic acid (QUIN), a metabolic intermediate in the de novo nicotinamide adenine dinucleotide (NAD+) synthesis pathway, which accumulated in the tdh2 deletion cells and was a candidate metabolite to suppress DNA replication fork instability. Deletion of QPT1, quinolinate phosphoribosyl transferase, elevated intracellular QUIN levels and partially suppressed the DNA damage sensitivity of hst3∆ hst4∆ cells as well as tdh2∆ cells. qpt1 deletion restored the short replicative lifespan of sir2∆ cells by suppressing intrachromosomal recombination among rDNA repeats. In addition, qpt1 deletion could suppress replication fork slippage between direct repeats. These findings suggest a connection between glucose metabolism and genomic stability.
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Affiliation(s)
- Miki Hanasaki
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Keisuke Yaku
- Department of Metabolism and Nutrition, Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Motohiro Yamauchi
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Takashi Nakagawa
- Department of Metabolism and Nutrition, Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Hiroshi Masumoto
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
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Tang X, Ding X, Hou YL. Comparative analysis of transcriptomes revealed the molecular mechanism of development of Tricholoma matsutake at different stages of fruiting bodies. Food Sci Biotechnol 2020; 29:939-951. [PMID: 32582456 DOI: 10.1007/s10068-020-00732-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/17/2019] [Accepted: 01/02/2020] [Indexed: 11/27/2022] Open
Abstract
The purpose of the study is to investigate the molecular mechanisms of development of Tricholoma matsutake fruiting body at the primordial stage (TM-1), the intermediate stage (TM-2) and the mature stage (TM-3) using RNA-Seq sequencing technology. The analysis of gene expression level revealed that the Spn2 and Eef1a1 gene were the key genes in the primordial stage of T. matsutake by regulating cytokinesis, protein synthesis, and cell growth. And the Ubc, Atp6, Cytb, and Pth2 gene were the key genes in the mature stage of T. matsutake by regulating energy metabolism and protein synthesis. Differential expression genes (DEGs) analysis results showed that Cdc28, Rad53, Dun1, Pho85 and Pho81 were the key DEGs regulating cell cycle genes of T. matsutake from primordial stage to intermediate stage. And APC, Cyr1, Cdc45, Spo11 and Rec8 genes were the key DEGs for the meiosis and sporogenesis of T. matsutake from the intermediate stage to the mature stage.
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Affiliation(s)
- Xian Tang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, 1# Shida Road, Nanchong, 637009 Sichuan Province China
| | - Xiang Ding
- College of Environmental Science and Engineering, China West Normal University, 1# Shida Road, Nanchong, 637009 Sichuan Province China
| | - Yi-Ling Hou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, 1# Shida Road, Nanchong, 637009 Sichuan Province China
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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Huang WC, Liao JH, Hsiao TC, Wei TYW, Maestre-Reyna M, Bessho Y, Tsai MD. Binding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA. Chembiochem 2018; 20:140-146. [PMID: 30378729 DOI: 10.1002/cbic.201800436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/30/2018] [Indexed: 01/01/2023]
Abstract
Human tumor necrosis factor receptor associated factor (TRAF)-interacting protein, with a forkhead-associated domain (TIFA), is a key regulator of NF-κB activation. It also plays a key role in the activation of innate immunity in response to bacterial infection, through heptose 1,7-bisphosphate (HBP); a metabolite of lipopolysaccharide (LPS). However, the mechanism of TIFA function is largely unexplored, except for the suggestion of interaction with TRAF6. Herein, we provide evidence for direct binding, albeit weak, between TIFA and the TRAF domain of TRAF6, and it is shown that the binding is enhanced for a rationally designed double mutant, TIFA S174Q/M179D. Enhanced binding was also demonstrated for endogenous full-length TRAF6. Furthermore, the structures of the TRAF domain complexes with the consensus TRAF-binding peptides from the C terminus of wild-type and S174Q/M179D mutant TIFA, showing salt-bridge formation between residues 177-181 of TIFA and the binding pocket residues of the TRAF domain, were solved. Taken together, the results provide direct evidence and a structural basis for the TIFA-TRAF6 interaction, and show how this important biological function can be modulated.
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Affiliation(s)
- Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Tzu-Chun Hsiao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Tong-You Wade Wei
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan.,Institute of Biochemical Sciences, National (Taiwan) University, 1, Roosevelt Road Sec. 4, Taipei, 106, Taiwan
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Xie C, He C, Jiang Y, Yu H, Cheng L, Nshogoza G, Ala MS, Tian C, Wu J, Shi Y, Li F. Structural insights into the recognition of phosphorylated Hop1 by Mek1. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1027-1038. [PMID: 30289413 DOI: 10.1107/s2059798318011993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022]
Abstract
The FHA domain-containing protein Mek1 is a meiosis-specific kinase that is involved in the regulation of interhomolog recombination in meiosis in Saccharomyces cerevisiae. The recruitment and activation of Mek1 require the phosphorylation of the chromosome axis protein Hop1 at Thr318 (pT318), which is necessary for recognition by the Mek1 FHA domain. Here, crystal structures of the Mek1 FHA domain in the apo state and in complex with the Hop1 pT318 peptide are presented, demonstrating that the hydrophobic residues Phe320 and Val321 at the pT+2 and pT+3 positions in the ligand contribute to the preferential recognition. It was further found that in Schizosaccharomyces pombe Mek1 FHA binds both pT15 in its N-terminal SQ/TQ cluster domain (SCD) and pT270 in the Hop1 SCD. The results revealed the structural basis for the preferential recognition of phosphorylated Hop1 by Mek1 in S. cerevisiae and facilitate the understanding of the interaction between the S. pombe Mek1 FHA domain and its binding targets.
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Affiliation(s)
- Changlin Xie
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Hailong Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Lin Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Moududee Sayed Ala
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Yunyu Shi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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