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Xu M, Zhang X, Yu J, Guo Z, Li Y, Song X, He K, Li G, Chi Y. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus niger in Peanuts. Front Microbiol 2021; 12:719337. [PMID: 34489910 PMCID: PMC8418202 DOI: 10.3389/fmicb.2021.719337] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/30/2021] [Indexed: 01/10/2023] Open
Abstract
Aspergillus niger is a very destructive pathogen causing severe peanut root rot, especially in the seeding stage of peanuts (Arachis hypogaea), and often leading to the death of the plant. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected post-translational modification identified in several species. In this study, we identified 5041 Khib sites on 1,453 modified proteins in A. niger. Compared with five other species, A. niger has conserved and novel proteins. Bioinformatics analysis showed that Khib proteins are widely distributed in A. niger and are involved in many biological processes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that Khib proteins were significantly enriched in many cellular compartments and pathways, such as ribosomes and proteasome subunits. A total of 223 Khib proteins were part of the PPI network, thus, suggesting that Khib proteins are associated with a large range of protein interactions and diverse pathways in the life processes of A. niger. Several identified proteins are involved in pathogenesis regulation. Our research provides the first comprehensive report of Khib and an extensive database for potential functional studies on Khib proteins in this economically important fungus.
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Affiliation(s)
- Manlin Xu
- Shandong Peanut Research Institute, Qingdao, China
| | - Xia Zhang
- Shandong Peanut Research Institute, Qingdao, China
| | - Jing Yu
- Shandong Peanut Research Institute, Qingdao, China
| | - Zhiqing Guo
- Shandong Peanut Research Institute, Qingdao, China
| | - Ying Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Xinying Song
- Shandong Peanut Research Institute, Qingdao, China
| | - Kang He
- Shandong Peanut Research Institute, Qingdao, China
| | - Guowei Li
- Institute of Crop Germplasm Resources, SAAS, Jinan, China
| | - Yucheng Chi
- Shandong Peanut Research Institute, Qingdao, China
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52
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Metabolic enzymes function as epigenetic modulators: A Trojan Horse for chromatin regulation and gene expression. Pharmacol Res 2021; 173:105834. [PMID: 34450321 DOI: 10.1016/j.phrs.2021.105834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 02/08/2023]
Abstract
Epigenetic modification is a fundamental biological process in living organisms, which has significant impact on health and behavior. Metabolism refers to a set of life-sustaining chemical reactions, including the uptake of nutrients, the subsequent conversion of nutrients into energy or building blocks for organism growth, and finally the clearance of redundant or toxic substances. It is well established that epigenetic modifications govern the metabolic profile of a cell by modulating the expression of metabolic enzymes. Strikingly, almost all the epigenetic modifications require substrates produced by cellular metabolism, and a large proportion of metabolic enzymes can transfer into nucleus to locally produce substrates for epigenetic modification, thereby providing an alternative link between metabolism, epigenetic modification and gene expression. Here, we summarize the recent literature pertinent to metabolic enzymes functioning as epigenetic modulators in the regulation of chromatin architecture and gene expression.
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53
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Zheng L, Li C, Ma X, Zhou H, Liu Y, Wang P, Yang H, Tamada Y, Huang J, Wang C, Hu Z, Wang X, Wang G, Li H, Hu J, Liu X, Zhou C, Zhang Y. Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation. Nucleic Acids Res 2021; 49:7347-7360. [PMID: 34165567 PMCID: PMC8287917 DOI: 10.1093/nar/gkab536] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 02/03/2023] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation whose prevalence and function in plants remain unclear. Here, we identified 41 Khib sites on histones in Arabidopsis thaliana, which did not overlap with frequently modified N-tail lysines (e.g. H3K4, H3K9 and H4K8). Chromatin immunoprecipitation-sequencing (ChIP-seq) assays revealed histone Khib in 35% of protein-coding genes. Most Khib peaks were located in genic regions, and they were highly enriched at the transcription start sites. Histone Khib is highly correlated with acetylation (ac), particularly H3K23ac, which it largely resembles in its genomic and genic distribution. Notably, co-enrichment of histone Khib and H3K23ac correlates with high gene expression levels. Metabolic profiling, transcriptome analyses, and ChIP-qPCR revealed that histone Khib and H3K23ac are co-enriched on genes involved in starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis, and help fine-tune plant response to dark-induced starvation. These findings suggest that Khib and H3K23ac may act in concert to promote high levels of gene transcription and regulate cellular metabolism to facilitate plant adaption to stress. Finally, HDA6 and HDA9 are involved in removing histone Khib. Our findings reveal Khib as a conserved yet unique plant histone mark acting with lysine acetylation in transcription-associated epigenomic processes.
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Affiliation(s)
- Lanlan Zheng
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Chen Li
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xueping Ma
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU) /Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Yuan Liu
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU) /Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Ping Wang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Huilan Yang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Yosuke Tamada
- School of Engineering, Utsunomiya University, Utsunomiya 321-8585, Japan
| | - Ji Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003, USA
| | - Chunfei Wang
- Center for Multi-Omics Research, Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Science, Henan University, Kaifeng 475001, China
| | - Zhubing Hu
- Center for Multi-Omics Research, Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Science, Henan University, Kaifeng 475001, China
| | - Xuening Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an Shaanxi 710119, China
| | - Guodong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an Shaanxi 710119, China
| | - Haihong Li
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Juntao Hu
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU) /Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
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54
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Qi T, Li J, Wang H, Han X, Li J, Du J. Global analysis of protein lysine 2-hydroxyisobutyrylation (K hib) profiles in Chinese herb rhubarb (Dahuang). BMC Genomics 2021; 22:542. [PMID: 34266380 PMCID: PMC8283887 DOI: 10.1186/s12864-021-07847-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered protein posttranslational modification (PTM) and is involved in the broad-spectrum regulation of cellular processes that are found in both prokaryotic and eukaryotic cells, including in plants. The Chinese herb rhubarb (Dahuang) is one of the most widely used traditional Chinese medicines in clinical applications. To better understand the physiological activities and mechanism of treating diseases with the herb, it is necessary to conduct intensive research on rhubarb. However, Khib modification has not been reported thus far in rhubarb. RESULTS In this study, we performed the first global analysis of Khib-modified proteins in rhubarb by using sensitive affinity enrichment combined with high-accuracy HPLC-MS/MS tandem spectrometry. A total of 4333 overlapping Khib modification peptides matched on 1525 Khib-containing proteins were identified in three independent tests. Bioinformatics analysis showed that these Khib-containing proteins are involved in a wide range of cellular processes, particularly in protein biosynthesis and central carbon metabolism and are distributed mainly in chloroplasts, cytoplasm, nucleus and mitochondria. In addition, the amino acid sequence motif analysis showed that a negatively charged side chain residue (E), a positively charged residue (K), and an uncharged residue with the smallest side chain (G) were strongly preferred around the Khib site, and a total of 13 Khib modification motifs were identified. These identified motifs can be classified into three motif patterns, and some motif patterns are unique to rhubarb and have not been identified in other plants to date. CONCLUSIONS A total of 4333 Khib-modified peptides on 1525 proteins were identified. The Khib-modified proteins are mainly distributed in the chloroplast, cytoplasm, nucleus and mitochondria, and involved in a wide range of cellular processes. Moreover, three types of amino acid sequence motif patterns, including EKhib/KhibE, GKhib and k.kkk….Khib….kkkkk, were extracted from a total of 13 Khib-modified peptides. This study provides comprehensive Khib-proteome resource of rhubarb. The findings from the study contribute to a better understanding of the physiological roles of Khib modification, and the Khib proteome data will facilitate further investigations of the roles and mechanisms of Khib modification in rhubarb.
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Affiliation(s)
- Tong Qi
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China
| | - Jinping Li
- International Cooperation Department of Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China
| | - Xiaofan Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China
| | - Junrong Li
- Bathurst Future Agri-Tech Institute of Qingdao Agricultural University, Qingdao, China
| | - Jinzhe Du
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China.
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55
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Nitsch S, Zorro Shahidian L, Schneider R. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Rep 2021. [PMID: 34159701 DOI: 10.5252/embr.202152774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Santander, Spain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
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56
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Nitsch S, Zorro Shahidian L, Schneider R. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Rep 2021; 22:e52774. [PMID: 34159701 PMCID: PMC8406397 DOI: 10.15252/embr.202152774] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/08/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC)University of CantabriaSantanderSpain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Faculty of BiologyLudwig‐Maximilians Universität MünchenPlanegg‐MartinsriedGermany
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57
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Dong J, Li Y, Zheng F, Chen W, Huang S, Zhou X, Wang K, Cai W, Liu H, Yin L, Li Q, Tang D, Dai Y. Co-occurrence of Protein Crotonylation and 2-Hydroxyisobutyrylation in the Proteome of End-Stage Renal Disease. ACS OMEGA 2021; 6:15782-15793. [PMID: 34179622 PMCID: PMC8223210 DOI: 10.1021/acsomega.1c01161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/25/2021] [Indexed: 05/16/2023]
Abstract
End-stage renal disease (ESRD) is gradually becoming a major public healthcare burden worldwide. Post-translational modifications carrying epigenetic information play a crucial role in the pathogenesis of many chronic diseases. We performed lysine crotonylation (KCr) and lysine 2-hydroxyisobutyrylation (Khib) analyses with liquid chromatography-tandem mass spectrometry to obtain a comprehensive profile and reveal the specific pathogenesis of peripheral blood mononuclear cells in ESRD patients. 218 overlap proteins among differentially modified proteins (DMPs) of both 2-hydroxyisobutyrylation and crotonylation were identified. KEGG analysis enriched pathways of protein processing in endoplasmic reticulum (ER) and glycolysis/gluconeogenesis which is closely related with cell apoptosis. In Bip, a master regulator in the ER, eight sites were identified as having both KCr and Khib modifications. Five differentially KCr modification sites and three differentially Khib-modified sites were detected between ESRD patients and normal controls. Besides Bip, other proteins (GRP94, CNX, CRT, PDIs, GlcII, ERP57, Bap31, Hsp70, and Hsp90) happened both KCr and Khib modifications. Nine DMPs having both KCr and Khib modifications were related to the glycolysis/gluconeogenesis pathway containing two key regulatory enzymes of hexokinase-1 and pyruvate kinase. The two most abundant dual modification proteins were ENO1 and PGK1 with 15 sites and 8 sites, respectively. Lysine residue K228 with both KCr and Khib modifications in ENO1 was on its surface and made it accessible for p300 mediating dynamic modifications. Overall, we hypothesize that KCr and Khib comodifications may influence the number of immunocytes and further induce immune senescence in ESRD patients through the glycolysis/gluconeogenesis pathway and protein processing in the ER process, which may be a potential therapeutic direction in the future.
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Affiliation(s)
- Jingjing Dong
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Yixi Li
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Fengping Zheng
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wenbiao Chen
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Shaoying Huang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Xianqing Zhou
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
| | - Kang Wang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wanxia Cai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - HaiPing Liu
- The
Second People’s Hospital of Lianping County, Heyuan517139, Guangdong , China
| | - Lianghong Yin
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
| | - Qiang Li
- Dongguan
Hospital of Guangzhou University of Traditional Chinese Medicine, Dongguan 523000, Guangdong, China
- . Phone: +86 0769 26385192
| | - Donge Tang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- . Phone: +86 0755 22942106
| | - Yong Dai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
- . Phone: +86 0755 22942780
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Feng B, Li S, Wang Z, Cao F, Wang Z, Li G, Liu K. Systematic analysis of lysine 2-hydroxyisobutyrylation posttranslational modification in wheat leaves. PLoS One 2021; 16:e0253325. [PMID: 34138952 PMCID: PMC8211214 DOI: 10.1371/journal.pone.0253325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/02/2021] [Indexed: 01/15/2023] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered post-translational modification (PTM) showing diverse biological functions and effects in living organisms. However, the study of Khib in plant species is still relatively limited. Wheat (Triticum aestivum L.) is a global important cereal plant. In this study, the systematic Khib analysis was performed in wheat leave tissues. A total of 3004 Khib sites in 1104 proteins were repeatedly identified. Structure characterization of these Khib peptides revealed 12 conserved sequence motifs. Function classification and enrichment analysis indicated these Khib proteins showed a wide function and pathway distribution, of which ribosome activity, protein biosynthesis and photosynthesis were the preferred biological processes. Subcellular location predication indicated chloroplast was the dominant subcellular compartment where Khib was distributed. There may be some crosstalks among Khib, lysine acetylation and lysine succinylation modification because some proteins and sites were modified by all these three acylations. The present study demonstrated the critical role of Khib in wheat biological and physiology, which has expanded the scope of Khib in plant species. Our study is an available resource and reference of Khib function demonstration and structure characterization in cereal plant, as well as in plant kingdom.
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Affiliation(s)
- Bo Feng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Shengdong Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Zongshuai Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Fang Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Zheng Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Geng Li
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, P. R. China
| | - Kaichang Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
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59
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Wang M, Lin H. Understanding the Function of Mammalian Sirtuins and Protein Lysine Acylation. Annu Rev Biochem 2021; 90:245-285. [PMID: 33848425 DOI: 10.1146/annurev-biochem-082520-125411] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein lysine acetylation is an important posttranslational modification that regulates numerous biological processes. Targeting lysine acetylation regulatory factors, such as acetyltransferases, deacetylases, and acetyl-lysine recognition domains, has been shown to have potential for treating human diseases, including cancer and neurological diseases. Over the past decade, many other acyl-lysine modifications, such as succinylation, crotonylation, and long-chain fatty acylation, have also been investigated and shown to have interesting biological functions. Here, we provide an overview of the functions of different acyl-lysine modifications in mammals. We focus on lysine acetylation as it is well characterized, and principles learned from acetylation are useful for understanding the functions of other lysine acylations. We pay special attention to the sirtuins, given that the study of sirtuins has provided a great deal of information about the functions of lysine acylation. We emphasize the regulation of sirtuins to illustrate that their regulation enables cells to respond to various signals and stresses.
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Affiliation(s)
- Miao Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA; .,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
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60
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Dou L, Yang F, Xu L, Zou Q. A comprehensive review of the imbalance classification of protein post-translational modifications. Brief Bioinform 2021; 22:6217722. [PMID: 33834199 DOI: 10.1093/bib/bbab089] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/17/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Post-translational modifications (PTMs) play significant roles in regulating protein structure, activity and function, and they are closely involved in various pathologies. Therefore, the identification of associated PTMs is the foundation of in-depth research on related biological mechanisms, disease treatments and drug design. Due to the high cost and time consumption of high-throughput sequencing techniques, developing machine learning-based predictors has been considered an effective approach to rapidly recognize potential modified sites. However, the imbalanced distribution of true and false PTM sites, namely, the data imbalance problem, largely effects the reliability and application of prediction tools. In this article, we conduct a systematic survey of the research progress in the imbalanced PTMs classification. First, we describe the modeling process in detail and outline useful data imbalance solutions. Then, we summarize the recently proposed bioinformatics tools based on imbalanced PTM data and simultaneously build a convenient website, ImClassi_PTMs (available at lab.malab.cn/∼dlj/ImbClassi_PTMs/), to facilitate the researchers to view. Moreover, we analyze the challenges of current computational predictors and propose some suggestions to improve the efficiency of imbalance learning. We hope that this work will provide comprehensive knowledge of imbalanced PTM recognition and contribute to advanced predictors in the future.
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Affiliation(s)
- Lijun Dou
- University of Electronic Science and Technology of China and the Shenzhen Polytechnic, China
| | - Fenglong Yang
- University of Electronic Science and Technology of China and the Shenzhen Polytechnic, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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61
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Vizán P, Di Croce L, Aranda S. Functional and Pathological Roles of AHCY. Front Cell Dev Biol 2021; 9:654344. [PMID: 33869213 PMCID: PMC8044520 DOI: 10.3389/fcell.2021.654344] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/24/2021] [Indexed: 11/25/2022] Open
Abstract
Adenosylhomocysteinase (AHCY) is a unique enzyme and one of the most conserved proteins in living organisms. AHCY catalyzes the reversible break of S-adenosylhomocysteine (SAH), the by-product and a potent inhibitor of methyltransferases activity. In mammals, AHCY is the only enzyme capable of performing this reaction. Controlled subcellular localization of AHCY is believed to facilitate local transmethylation reactions, by removing excess of SAH. Accordingly, AHCY is recruited to chromatin during replication and active transcription, correlating with increasing demands for DNA, RNA, and histone methylation. AHCY deletion is embryonic lethal in many organisms (from plants to mammals). In humans, AHCY deficiency is associated with an incurable rare recessive disorder in methionine metabolism. In this review, we focus on the AHCY protein from an evolutionary, biochemical, and functional point of view, and we discuss the most recent, relevant, and controversial contributions to the study of this enzyme.
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Affiliation(s)
- Pedro Vizán
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
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62
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Bo F, Shengdong L, Zongshuai W, Fang C, Zheng W, Chunhua G, Geng L, Ling'an K. Global analysis of lysine 2-hydroxyisobutyrylation in wheat root. Sci Rep 2021; 11:6327. [PMID: 33737719 PMCID: PMC7973580 DOI: 10.1038/s41598-021-85879-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring post-translational modification. The system Khib identification at proteomics level has been performed in various species and tissues to characterize the role of Khib in biological activities. However, the study of Khib in plant species is relatively less. In the present study, the first plant root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat with antibody immunoprecipitation affinity, high resolution mass spectrometry-based proteomics and bioinformatics analysis. In total, 6328 Khib sites in 2186 proteins were repeatedly identified in three replicates. These Khib proteins showed a wide subcellular location distribution. Function and pathways characterization of these Khib proteins indicated that many cellular functions and metabolism pathways were potentially affected by this modification. Protein and amino acid metabolism related process may be regulated by Khib, especially ribosome activities and proteins biosynthesis process. Carbohydrate metabolism and energy production related processes including glycolysis/gluconeogenesis, TCA cycle and oxidative phosphorylation pathways were also affected by Khib modification. Besides, root sulfur assimilation and transformation related enzymes exhibited Khib modification. Our work illustrated the potential regulation role of Khib in wheat root physiology and biology, which could be used as a useful reference for Khib study in plant root.
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Affiliation(s)
- Feng Bo
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Li Shengdong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Wang Zongshuai
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Cao Fang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Wang Zheng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Gao Chunhua
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Li Geng
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
| | - Kong Ling'an
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China.
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63
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Qian H, Wang L, Ma X, Yi X, Wang B, Liang W. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylated Proteins in Fusarium oxysporum. Front Microbiol 2021; 12:623735. [PMID: 33643252 PMCID: PMC7902869 DOI: 10.3389/fmicb.2021.623735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022] Open
Abstract
Protein lysine 2-hydroxyisobutyrylation (K hib ), a new type of post-translational modification, occurs in histones and non-histone proteins and plays an important role in almost all aspects of both eukaryotic and prokaryotic living cells. Fusarium oxysporum, a soil-borne fungal pathogen, can cause disease in more than 150 plants. However, little is currently known about the functions of K hib in this plant pathogenic fungus. Here, we report a systematic analysis of 2-hydroxyisobutyrylated proteins in F. oxysporum. In this study, 3782 K hib sites in 1299 proteins were identified in F. oxysporum. The bioinformatics analysis showed that 2-hydroxyisobutyrylated proteins are involved in different biological processes and functions and are located in diverse subcellular localizations. The enrichment analysis revealed that K hib participates in a variety of pathways, including the ribosome, oxidative phosphorylation, and proteasome pathways. The protein interaction network analysis showed that 2-hydroxyisobutyrylated protein complexes are involved in diverse interactions. Notably, several 2-hydroxyisobutyrylated proteins, including three kinds of protein kinases, were involved in the virulence or conidiation of F. oxysporum, suggesting that K hib plays regulatory roles in pathogenesis. Moreover, our study shows that there are different K hib levels of F. oxysporum in conidial and mycelial stages. These findings provide evidence of K hib in F. oxysporum, an important filamentous plant pathogenic fungus, and serve as a resource for further exploration of the potential functions of K hib in Fusarium species and other filamentous pathogenic fungi.
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Affiliation(s)
- Hengwei Qian
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Lulu Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | | | - Xingling Yi
- Micron Biotechnology Co., Ltd., Hangzhou, China
| | - Baoshan Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Wenxing Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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64
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Huang S, Zheng F, Lin H, Zhou X, Xu H, Zhang C, Dai W, Hocher B, Zhang X, Tang D, Dai Y. Quantitative proteomics analysis of lysine 2-hydroxyisobutyrylation in IgA nephropathy. Clin Proteomics 2021; 18:7. [PMID: 33557746 PMCID: PMC7869230 DOI: 10.1186/s12014-021-09314-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/15/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Protein posttranslational modification is an indispensable regulatory element that can fine-tune protein functions and regulate diverse cellular processes. Lysine 2-hydroxyisobutyrylation (Khib) is a protein posttranslational modification that was recently identified and is thought to play a role in a wide variety of active cellular functions. METHODS In this report, for the first time, we comparatively studied the 2-hydroxyisobutyrylation proteome in peripheral blood mononuclear cells from a biopsy-proven immunoglobulin A nephropathy (IgAN) group and a normal control group based on liquid chromatography-tandem mass spectrometry. RESULTS Altogether, 7405 proteins were identified and added to a Khib library. Of these proteins, we identified 111 with upregulated expression and 83 with downregulated expression. Furthermore, we identified 428 Khib modification sites on 290 Khib-modified proteins, including 171 sites with increased modification on 122 Khib-modified proteins and 257 specific sites with reduced modification on 168 Khib-modified proteins. CONCLUSIONS Importantly, the abundance of lipocalin 2 was increased in the differentially expressed proteins, and a KEGG-based functional enrichment analysis showed that Khib proteins clustered in the IL-17 signaling pathway and phagosome category, which may have important associations with IgAN. Our data enlighten our understanding of Khib in IgAN and indicate that Khib may have important regulatory roles in IgAN.
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Affiliation(s)
- Shaoying Huang
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 Guangdong People’s Republic of China
| | - Fengping Zheng
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 Guangdong People’s Republic of China
| | - Hua Lin
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department of Guilin NO. 924 Hospital, Guilin, 541002 People’s Republic of China
| | - Xianqing Zhou
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department of Guilin NO. 924 Hospital, Guilin, 541002 People’s Republic of China
| | - Huixuan Xu
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 Guangdong People’s Republic of China
| | - Cantong Zhang
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 Guangdong People’s Republic of China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, Texas 78712 USA
| | - Berthold Hocher
- Department of Medicine Nephrology, Medical Faculty Mannheim Heidelberg University, Mannheim, Germany
| | - Xinzhou Zhang
- Department of Nephrology, the Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 People’s Republic of China
| | - Donge Tang
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 Guangdong People’s Republic of China
| | - Yong Dai
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 Guangdong People’s Republic of China
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department of Guilin NO. 924 Hospital, Guilin, 541002 People’s Republic of China
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65
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Abstract
C. albicans is one of the most commonly reported fungal pathogens in mucosal and systemic infections. A better understanding of its growth habits and metabolic processes in the host should help improve defense strategies. Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we surveyed the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans. Using an antibody enrichment approach along with the traditional liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, we analyzed the pattern of Khib-modified proteins and sites in one wild-type strain of C. albicans. We identified 1,438 Khib-modified proteins with 6,659 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism, of which the ribosome pathway is the most affected pathway. Even compared with the reported numbers of lysine acetylation (Kac) and succinylation (Ksuc) sites, the numbers of Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Findings in this study may provide new insights for studying posttranslational modification (PTM)-associated mechanisms in fungal development and pathogenicity. IMPORTANCEC. albicans is one of the most commonly reported fungal pathogens in mucosal and systemic infections. A better understanding of its growth habits and metabolic processes in the host should help improve defense strategies. The newly discovered protein posttranslational modification (PTM) on histones is one epigenetic mechanism which has been linked to many pathogenic events, including cancers. The types of PTM and their pathogenic roles in C. albicans are still somewhat poorly understood, even though studies of C. albicans based on acetylation inhibitors have shed some light on their function, and it seems that PTMs regulate pathogenic adhesion factors. Here, we quantified and analyzed the occurrence of lysine 2-hydroxyisobutyrylation (Khib) in C. albicans. The Khib-modified proteins are enriched with respect to carbon metabolism, ribosomal biogenesis, and protein translation in C. albicans.
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66
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Chen X, Li X, Li P, Chen X, Liu H, Huang J, Luo C, Hsiang T, Zheng L. Comprehensive identification of lysine 2-hydroxyisobutyrylated proteins in Ustilaginoidea virens reveals the involvement of lysine 2-hydroxyisobutyrylation in fungal virulence. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:409-425. [PMID: 33427395 DOI: 10.1111/jipb.13066] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib ) is a newly identified post-translational modification (PTM) that plays important roles in transcription and cell proliferation in eukaryotes. However, its function remains unknown in phytopathogenic fungi. Here, we performed a comprehensive assessment of Khib in the rice false smut fungus Ustilaginoidea virens, using Tandem Mass Tag (TMT)-based quantitative proteomics approach. A total of 3 426 Khib sites were identified in 977 proteins, suggesting that Khib is a common and complex PTM in U. virens. Our data demonstrated that the 2-hydroxyisobutyrylated proteins are involved in diverse biological processes. Network analysis of the modified proteins revealed a highly interconnected protein network that included many well-studied virulence factors. We confirmed that the Zn-binding reduced potassium dependency3-type histone deacetylase (UvRpd3) is a major enzyme that removes 2-hydroxyisobutyrylation and acetylation in U. virens. Notably, mutations of Khib sites in the mitogen-activated protein kinase (MAPK) UvSlt2 significantly reduced fungal virulence and decreased the enzymatic activity of UvSlt2. Molecular dynamics simulations demonstrated that 2-hydroxyisobutyrylation in UvSlt2 increased the hydrophobic solvent-accessible surface area and thereby affected binding between the UvSlt2 enzyme and its substrates. Our findings thus establish Khib as a major post-translational modification in U. virens and point to an important role for Khib in the virulence of this phytopathogenic fungus.
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Affiliation(s)
- Xiaoyang Chen
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiabing Li
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pingping Li
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaolin Chen
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Liu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junbin Huang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaoxi Luo
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Lu Zheng
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
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67
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Huang H, Zhang D, Weng Y, Delaney K, Tang Z, Yan C, Qi S, Peng C, Cole PA, Roeder RG, Zhao Y. The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway. SCIENCE ADVANCES 2021; 7:7/9/eabe2771. [PMID: 33627428 PMCID: PMC7904266 DOI: 10.1126/sciadv.abe2771] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/12/2021] [Indexed: 05/07/2023]
Abstract
Metabolism-mediated epigenetic changes represent an adapted mechanism for cellular signaling, in which lysine acetylation and methylation have been the historical focus of interest. We recently discovered a β-hydroxybutyrate-mediated epigenetic pathway that couples metabolism to gene expression. However, its regulatory enzymes and substrate proteins remain unknown, hindering its functional study. Here, we report that the acyltransferase p300 can catalyze the enzymatic addition of β-hydroxybutyrate to lysine (Kbhb), while histone deacetylase 1 (HDAC1) and HDAC2 enzymatically remove Kbhb. We demonstrate that p300-dependent histone Kbhb can directly mediate in vitro transcription. Moreover, a comprehensive analysis of Kbhb substrates in mammalian cells has identified 3248 Kbhb sites on 1397 substrate proteins. The dependence of histone Kbhb on p300 argues that enzyme-catalyzed acylation is the major mechanism for nuclear Kbhb. Our study thus reveals key regulatory elements for the Kbhb pathway, laying a foundation for studying its roles in diverse cellular processes.
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Affiliation(s)
- He Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yejing Weng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kyle Delaney
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Cong Yan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shankang Qi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Peng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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68
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Zheng Y, Dong H, Bai X, Cui H, Li MJ, Wu HY, Zhang K. Effects of lysine 2-hydroxyisobutyrylation on bacterial FabI activity and resistance to triclosan. Biochimie 2021; 182:197-205. [PMID: 33485933 DOI: 10.1016/j.biochi.2021.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 10/22/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel protein posttranslational modification conserved in eukaryotes and prokaryotes. However, the biological significance of Khib remains largely unknown. Here, through screening the proteome-wide Khib modification sites in bacteria using a bioinformatic method, we identified a potential Khib site (K201hib) targeted by de-2-hyroxyisobutyrylase CobB at the substrate-binding site of FabI, an enoyl-acyl carry protein reductase (EnvM or FabI) in fatty acid biosynthesis pathway. First, we confirmed that the previously identified de-2-hyroxyisobutyrylase CobB can remove Khib of FabI in an in vitro experiment. To investigate the biological effects of the Khib on FabI's activity, amino acid substitutes were introduced to the modification sites of the protein of E. coli origin to mimic modified/unmodified status. We found that the mutant mimicking K201hib reduced FabI activity with decreased Michaelis constant (Km) and catalytic turnover number (kcat), while the mutant mimicking the unmodified form and the recombinant wild-type protein treated with CobB exhibited increased activity. However, the dissociation constant (KD) between FabI and NADH was not affected by the mutation mimicking the modification, suggesting that K201hib didn't alter the binding between NADH and FabI. We also found that K201hib tended to increase the resistance of E. coli to triclosan (TCL), a widely-used antibiotics targeting FabI. Taken together, this study identified the regulatory role of Khib on FabI activity and pointed to a novel mechanism related to antibiotic resistance.
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Affiliation(s)
- Yiqiang Zheng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Hanyang Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Hui Cui
- Department of Pharmacology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Pharmacology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hui-Yuan Wu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China.
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69
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Xu Y, Li X, Liang W, Liu M. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea. Front Microbiol 2020; 11:585614. [PMID: 33329453 PMCID: PMC7728723 DOI: 10.3389/fmicb.2020.585614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Posttranslational modifications (PTMs) of the whole proteome have become a hot topic in the research field of epigenetics, and an increasing number of PTM types have been identified and shown to play significant roles in different cellular processes. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected PTM, and the 2-hydroxyisobutyrylome has been identified in several species. Botrytis cinerea is recognized as one of the most destructive pathogens due to its broad host distribution and very large economic losses; thus the many aspects of its pathogenesis have been continuously studied. However, distribution and function of Khib in this phytopathogenic fungus are not clear. In this study, a proteome-wide analysis of Khib in B. cinerea was performed, and 5,398 Khib sites on 1,181 proteins were identified. Bioinformatics analysis showed that the 2-hydroxyisobutyrylome in B. cinerea contains both conserved proteins and novel proteins when compared with Khib proteins in other species. Functional classification, functional enrichment and protein interaction network analyses showed that Khib proteins are widely distributed in cellular compartments and involved in diverse cellular processes. Significantly, 37 proteins involved in different aspects of regulating the pathogenicity of B. cinerea were detected as Khib proteins. Our results provide a comprehensive view of the 2-hydroxyisobutyrylome and lay a foundation for further studying the regulatory mechanism of Khib in both B. cinerea and other plant pathogens.
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Affiliation(s)
- Yang Xu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiaoxia Li
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mengjie Liu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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70
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Nie LB, Liang QL, Elsheikha HM, Du R, Zhu XQ, Li FC. Global profiling of lysine 2-hydroxyisobutyrylome in Toxoplasma gondii using affinity purification mass spectrometry. Parasitol Res 2020; 119:4061-4071. [PMID: 33057814 DOI: 10.1007/s00436-020-06923-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/06/2020] [Indexed: 11/28/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered and evolutionarily conserved form of protein post-translational modification (PTM) found in mammalian and yeast cells. Previous studies have shown that Khib plays roles in the activity of gene transcription and Khib-containing proteins are closely related to the cellular metabolism. In this study, a global Khib-containing analysis using the latest databases (ToxoDB 46, 8322 sequences, downloaded on April 16, 2020) and sensitive immune-affinity enrichment coupled with liquid chromatography-tandem mass spectrometry was performed. A total of 1078 Khib modification sites across 400 Khib-containing proteins were identified in tachyzoites of Toxoplasma gondii RH strain. Bioinformatics and functional enrichment analysis showed that Khib-modified proteins were associated with various biological processes, such as ribosome, glycolysis/gluconeogenesis, and central carbon metabolism. Interestingly, many proteins of the secretory organelles (e.g., microneme, rhoptry, and dense granule) that play roles in the infection cycle of T. gondii were found to be Khib-modified, suggesting the involvement of Khib in key biological process during T. gondii infection. We also found that histone proteins, key enzymes related to cellular metabolism, and several glideosome components had Khib sites. These results expanded our understanding of the roles of Khib in T. gondii and should promote further investigations of how Khib regulates gene expression and key biological functions in T. gondii.
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Affiliation(s)
- Lan-Bi Nie
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China
| | - Qin-Li Liang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China. .,College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, People's Republic of China.
| | - Fa-Cai Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China.,College of Veterinary Medicine, Southwest University, Chongqing, 400715, People's Republic of China
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71
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Zhang L, Zou Y, He N, Chen Y, Chen Z, Li L. DeepKhib: A Deep-Learning Framework for Lysine 2-Hydroxyisobutyrylation Sites Prediction. Front Cell Dev Biol 2020; 8:580217. [PMID: 33015075 PMCID: PMC7509169 DOI: 10.3389/fcell.2020.580217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/17/2020] [Indexed: 11/28/2022] Open
Abstract
As a novel type of post-translational modification, lysine 2-Hydroxyisobutyrylation (K hib ) plays an important role in gene transcription and signal transduction. In order to understand its regulatory mechanism, the essential step is the recognition of K hib sites. Thousands of K hib sites have been experimentally verified across five different species. However, there are only a couple traditional machine-learning algorithms developed to predict K hib sites for limited species, lacking a general prediction algorithm. We constructed a deep-learning algorithm based on convolutional neural network with the one-hot encoding approach, dubbed CNN OH . It performs favorably to the traditional machine-learning models and other deep-learning models across different species, in terms of cross-validation and independent test. The area under the ROC curve (AUC) values for CNN OH ranged from 0.82 to 0.87 for different organisms, which is superior to the currently available K hib predictors. Moreover, we developed the general model based on the integrated data from multiple species and it showed great universality and effectiveness with the AUC values in the range of 0.79-0.87. Accordingly, we constructed the on-line prediction tool dubbed DeepKhib for easily identifying K hib sites, which includes both species-specific and general models. DeepKhib is available at http://www.bioinfogo.org/DeepKhib.
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Affiliation(s)
- Luna Zhang
- School of Data Science and Software Engineering, Qingdao University, Qingdao, China
| | - Yang Zou
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ningning He
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yu Chen
- School of Data Science and Software Engineering, Qingdao University, Qingdao, China
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Lei Li
- School of Data Science and Software Engineering, Qingdao University, Qingdao, China
- School of Basic Medicine, Qingdao University, Qingdao, China
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Qi W, Li XX, Guo YH, Bao YZ, Wang N, Luo XG, Yu CD, Zhang TC. Integrated metabonomic-proteomic analysis reveals the effect of glucose stress on metabolic adaptation of Lactococcus lactis ssp. lactis CICC23200. J Dairy Sci 2020; 103:7834-7850. [PMID: 32684472 DOI: 10.3168/jds.2019-17810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/14/2020] [Indexed: 12/30/2022]
Abstract
A combined proteomic and metabonomic approach was used to investigate the metabolism of Lactococcus lactis ssp. lactis subjected to glucose stress treatment. A proteomic method was used to determine 1,427 altered proteins, including 278 proteins with increased expression and 255 proteins with decreased expression. A metabonomic approach was adopted to identify 98 altered metabolites, including 62 metabolites with increased expression and 26 metabolites with decreased expression. The integrated analysis indicated that the RNA and DNA mismatch repair process and energy metabolism were enhanced in response to high-glucose stress in L. lactis. Lactococcus lactis responded to glucose stress by up-regulating oxidoreductase activity, which acted on glycosyl bonds, hydrolase activity, and organic acid transmembrane transporter activity. This led to an improvement in the metabolic flux from glucose to pyruvate, lactate, acetate, and maltose. Down-regulation of amino acid transmembrane transporter, aminoacyl-transfer RNA ligase, hydroxymethyl-, formyl-, and related transferase activities resulted in a decrease in the nitrogen metabolism-associated metabolic pathway, which might be related to inhibition of the production of biogenic amines. Overall, we highlight the response of metabolism to glucose stress and provide potential possibilities for the reduced formation of biogenic amines in improved level of sugar in the dairy fermentation industry. Moreover, according to the demand for industrial production, sugar concentration in fermented foods should be higher, or lower, than a set value that is dependent on bacterial strain and biogenic amine yield.
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Affiliation(s)
- Wei Qi
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin 300457, P.R. China; National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China.
| | - Xiao-Xue Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin 300457, P.R. China; National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China
| | - Yao-Hua Guo
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin 300457, P.R. China; National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China
| | - Yan-Zhou Bao
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin 300457, P.R. China; National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin 300457, P.R. China; National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China
| | - Xue-Gang Luo
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin 300457, P.R. China; National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China
| | - Chun-Di Yu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, P.R. China
| | - Tong-Cun Zhang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education, Tianjin 300457, P.R. China; National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P.R. China.
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Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly identified post-translational modifications (PTMs) primitively identified by mass spectrometry (MS). Research in animals suggests that histone Khib is related to regulation of chromatin and cellular functions. However, there is no review to summarize and elaborate on the current understanding of Khib. In this review, we start with the basic description of Khib, such as sequence preference and subcellular localization. We then analyze the lysine 2-hydroxyisobutyrylated sites with the purpose of learning its functions and activities. We finally discuss the regulation toward Khib and the way it regulates, thus opening an avenue for us to illustrate the diverse cellular metabolites associated with (Khib).
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Affiliation(s)
- Shaoying Huang
- Department of Clinical Medical Research Center, Shenzhen People's Hospital, Shenzhen, CHN
| | - Donge Tang
- Department of Clinical Medical Research Center, Shenzhen People's Hospital, Shenzhen, CHN
| | - Yong Dai
- Department of Clinical Medical Research Center, Shenzhen People's Hospital, Shenzhen, CHN
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74
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Wang YG, Huang SY, Wang LN, Zhou ZY, Qiu JD. Accurate prediction of species-specific 2-hydroxyisobutyrylation sites based on machine learning frameworks. Anal Biochem 2020; 602:113793. [DOI: 10.1016/j.ab.2020.113793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/25/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
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75
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Short-chain fatty acid, acylation and cardiovascular diseases. Clin Sci (Lond) 2020; 134:657-676. [PMID: 32219347 DOI: 10.1042/cs20200128] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/16/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide. Metabolic dysfunction is a fundamental core mechanism underlying CVDs. Previous studies generally focused on the roles of long-chain fatty acids (LCFAs) in CVDs. However, a growing body of study has implied that short-chain fatty acids (SCFAs: namely propionate, malonate, butyrate, 2-hydroxyisobutyrate (2-HIBA), β-hydroxybutyrate, crotonate, succinate, and glutarate) and their cognate acylations (propionylation, malonylation, butyrylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, crotonylation, succinylation, and glutarylation) participate in CVDs. Here, we attempt to provide an overview landscape of the metabolic pattern of SCFAs in CVDs. Especially, we would focus on the SCFAs and newly identified acylations and their roles in CVDs, including atherosclerosis, hypertension, and heart failure.
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76
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Xue C, Qiao Z, Chen X, Cao P, Liu K, Liu S, Ye L, Gong Z. Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa. RICE (NEW YORK, N.Y.) 2020; 13:34. [PMID: 32572646 PMCID: PMC7310055 DOI: 10.1186/s12284-020-00389-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/11/2020] [Indexed: 06/09/2023]
Abstract
BACKGROUND Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed. RESULTS In this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalk of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms. CONCLUSIONS In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.
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Affiliation(s)
- Chao Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhongying Qiao
- Suzhou Academy of Agricultural Sciences, North of Wangting Town, Suzhou, 215128, China
| | - Xu Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Penghui Cao
- Suzhou Academy of Agricultural Sciences, North of Wangting Town, Suzhou, 215128, China
| | - Kai Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Shuai Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Lu Ye
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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77
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Ju Z, Wang SY. Prediction of 2-hydroxyisobutyrylation sites by integrating multiple sequence features with ensemble support vector machine. Comput Biol Chem 2020; 87:107280. [PMID: 32505881 DOI: 10.1016/j.compbiolchem.2020.107280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a new type of histone mark, which has been found to affect the association between histone and DNA. To better understand the molecular mechanism of Khib, it is important to identify 2-hydroxyisobutyrylated substrates and their corresponding Khib sites accurately. In this study, a novel bioinformatics tool named KhibPred is proposed to predict Khib sites in human HeLa cells. Three kinds of effective features, the composition of k-spaced amino acid pairs, binary encoding and amino acid factors, are incorporated to encode Khib sites. Moreover, an ensemble support vector machine is employed to overcome the imbalanced problem in the prediction. As illustrated by 10-fold cross-validation, the performance of KhibPred achieves a satisfactory performance with an area under receiver operating characteristic curve of 0.7937. Therefore, KhibPred can be a useful tool for predicting protein Khib sites. Feature analysis shows that the polarity factor features play significant roles in the prediction of Khib sites. The conclusions derived from this study might provide useful insights for in-depth investigation into the molecular mechanisms of Khib.
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Affiliation(s)
- Zhe Ju
- College of Science, Shenyang Aerospace University, 110136, People's Republic of China.
| | - Shi-Yun Wang
- College of Science, Shenyang Aerospace University, 110136, People's Republic of China.
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78
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Diehl KL, Muir TW. Chromatin as a key consumer in the metabolite economy. Nat Chem Biol 2020; 16:620-629. [PMID: 32444835 DOI: 10.1038/s41589-020-0517-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/05/2020] [Indexed: 12/31/2022]
Abstract
In eukaryotes, chromatin remodeling and post-translational modifications (PTMs) shape the local chromatin landscape to establish permissive and repressive regions within the genome, orchestrating transcription, replication, and DNA repair in concert with other epigenetic mechanisms. Though cellular nutrient signaling encompasses a huge number of pathways, recent attention has turned to the hypothesis that the metabolic state of the cell is communicated to the genome through the type and concentration of metabolites in the nucleus that are cofactors for chromatin-modifying enzymes. Importantly, both epigenetic and metabolic dysregulation are hallmarks of a range of diseases, and this metabolism-chromatin axis may yield a well of new therapeutic targets. In this Perspective, we highlight emerging themes in the inter-regulation of the genome and metabolism via chromatin, including nonenzymatic histone modifications arising from chemically reactive metabolites, the expansion of PTM diversity from cofactor-promiscuous chromatin-modifying enzymes, and evidence for the existence and importance of subnucleocytoplasmic metabolite pools.
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Affiliation(s)
- Katharine L Diehl
- Department of Chemistry, Princeton University, Princeton, NJ, USA. .,Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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79
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Cheng YM, Peng Z, Chen HY, Pan TT, Hu XN, Wang F, Luo T. Posttranslational lysine 2-hydroxyisobutyrylation of human sperm tail proteins affects motility. Hum Reprod 2020; 35:494-503. [PMID: 32142584 DOI: 10.1093/humrep/dez296] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/26/2019] [Indexed: 12/15/2022] Open
Abstract
STUDY QUESTION Does lysine 2-hydroxyisobutyrylation, a newly identified protein posttranslational modification (PTM), occur in human sperm and affect human sperm function? SUMMARY ANSWER Lysine 2-hydroxyisobutyrylation mainly occurs in human sperm tail proteins, and excessive lysine 2-hydroxyisobutyrylation affects human sperm motility. WHAT IS KNOWN ALREADY PTM is regarded as an important pathway in regulating sperm function since mature sperm are almost transcriptionally silent. However, only phosphorylation was extensively studied in mature sperm to date. Lysine 2-hydroxyisobutyrylation, a newly characterised PTM, is broadly conserved in both eukaryotic and prokaryotic cells. Although histone lysine 2-hydroxyisobutyrylation has been shown to be associated with active gene expression in spermatogenic cells, the presence, regulatory elements and function of lysine 2-hydroxyisobutyrylation have not been characterised in mature sperm. STUDY DESIGN, SIZE, DURATION Sperm samples were obtained from normozoospermic men and asthenozoospermic men who visited the reproductive medical centre at Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, China, between May 2017 and November 2018. In total, 58 normozoospermic men and 65 asthenozoospermic men were recruited to participate in this study. PARTICIPANTS/MATERIALS, SETTING, METHODS Lysine 2-hydroxyisobutyrylation was examined using immunoblotting and immunofluorescence assays using a previously qualified pan anti-lysine 2-hydroxyisobutyrylation antibody. The immunofluorescence assay was imaged using super-resolution structured illumination microscopy. Sperm viability was examined by using the eosin staining method, and sperm motility parameters were assessed by computer-assisted sperm analysis. Sperm penetration ability was determined by evaluating the ability of the sperm to penetrate a 1% (w/v) methylcellulose solution. The level of intracellular adenosine triphosphate (ATP) was detected using a rapid bioluminescent ATP assay kit. MAIN RESULTS AND THE ROLE OF CHANCE Lysine 2-hydroxyisobutyrylation was present in several proteins (20-100 kDa) mainly located in the tail of human sperm. Sperm lysine 2-hydroxyisobutyrylation was derived from 2-hydroxyisobutyrate (2-Hib) and was regulated by acyltransferase P300 and nicotinamide adenine dinucleotide-dependent lysine deacylase sirtuins. Elevation of sperm lysine 2-hydroxyisobutyrylation by 2-Hib decreased total motility, progressive motility, penetration ability and ATP level of human sperm. Interestingly, the level of sperm lysine 2-hydroxyisobutyrylation was higher in asthenozoospermic men than that in normozoospermic men and was negatively correlated with the progressive motility of human sperm. Furthermore, high levels of lysine 2-hydroxyisobutyrylation in asthenozoospermic men accompanied decreased ATP levels. LIMITATIONS, REASONS FOR CAUTION Although the present study indicated the involvement of sperm lysine 2-hydroxyisobutyrylation in regulating human sperm motility, the underlying mechanism needs to be further illustrated. WIDER IMPLICATIONS OF THE FINDINGS The findings of this study provide insight into the novel role of lysine 2-hydroxyisobutyrylation in human sperm and suggest that abnormality of sperm lysine 2-hydroxyisobutyrylation may be one of the causes for asthenozoospermia. STUDY FUNDING/COMPETING INTEREST(S) National Natural Science Foundation of China (81771644 to T.L. and 81871207 to H.C.); Natural Science Foundation of Jiangxi province (20171ACB21006). The authors have no conflicts of interest to declare.
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Affiliation(s)
- Yi-Min Cheng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi 330031, PR China
| | - Zhen Peng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi 330031, PR China.,Department of Pharmacy, the First People's Hospital of Yichun City in Jiangxi Province, Yichun 336000, China
| | - Hou-Yang Chen
- Reproductive Medical Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, PR China
| | - Ting-Ting Pan
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi 330031, PR China
| | - Xiao-Nian Hu
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi 330031, PR China
| | - Fang Wang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi 330031, PR China
| | - Tao Luo
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi 330031, PR China
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80
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Dong H, Zhai G, Chen C, Bai X, Tian S, Hu D, Fan E, Zhang K. Protein lysine de-2-hydroxyisobutyrylation by CobB in prokaryotes. SCIENCE ADVANCES 2019; 5:eaaw6703. [PMID: 31328167 PMCID: PMC6636992 DOI: 10.1126/sciadv.aaw6703] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/13/2019] [Indexed: 05/06/2023]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) has recently been shown to be an evolutionarily conserved histone mark. Here, we report that CobB serves as a lysine de-2-hydroxyisobutyrylation enzyme that regulates glycolysis and cell growth in prokaryotes. We identified the specific binding of CobB to Khib using a novel self-assembled multivalent photocrosslinking peptide probe and demonstrated that CobB can catalyze lysine de-2-hydroxyisobutyrylation both in vivo and in vitro. R58 of CobB is a critical site for its de-2-hydroxyisobutyrylase activity. Using a quantitative proteomics approach, we identified 99 endogenous substrates that are targeted by CobB for de-2-hydroxyisobutyrylation. We further demonstrated that CobB can regulate the catalytic activities of enolase (ENO) by removing K343hib and K326ac of ENO simultaneously, which account for changes of bacterial growth. In brief, our study dissects a Khib-mediated molecular mechanism that is catalyzed by CobB for the regulation of the activity of metabolic enzymes as well as the cell growth of bacteria.
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Affiliation(s)
- Hanyang Dong
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Guijin Zhai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Cong Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xue Bai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Deqing Hu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Freiburg, Germany
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Corresponding author.
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81
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Wang Y, Wang F, Bao X, Fu L. Systematic analysis of lysine acetylome reveals potential functions of lysine acetylation in Shewanella baltica, the specific spoilage organism of aquatic products. J Proteomics 2019; 205:103419. [PMID: 31212084 DOI: 10.1016/j.jprot.2019.103419] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/19/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023]
Abstract
Protein lysine acetylation is a major post-translational modification and plays a critical regulatory role in almost every aspect in both eukaryotes and prokaryotes, yet there have been no data on Shewanella baltica, which is one of the specific spoilage organism (SSO) of aquatic products. Here, we performed the first global acetylproteome analysis of S. baltica. 2929 lysine acetylation sites were identified in 1103 proteins, accounting for 26.1% of the total proteins which participate in a wide variety of biological processes, especially in the constituent of ribosome, the biosynthesis of aminoacyl-tRNA, the amino acids and fatty acid metabolism. Besides, 14 conserved acetylation motifs were detected in S. baltica. Notably, various directly or indirectly spoilage-related proteins were prevalently acetylated, including enzymes involved in the unsaturated fatty acids biosynthesis closely related to the cold adaptability, cold shock proteins, pivotal enzymes involved in the putrescine biosynthesis, and a LuxR-type protein in quorum sensing system. The acetylome analysis in Shewanella can supplement the database and provide new insight into uncovering the spoilage mechanisms of S. baltica. The provided dataset illuminates the potential role of reversible acetylation in S. baltica, and serves as an important resource for exploring the physiological role of lysine acetylation in prokaryotes. SIGNIFICANCE: The psychrotrophic nature and the ability of S. baltica to make good use of "habitat" nutrients explain its importance in spoilage of seafood stored at low temperatures. However, the underlying mechanism of spoilage potential from the perspective of protein post-translational modification was rarely studied. This work identifies the first comprehensive survey of a lysine acetylome in S. baltica and uncovers the involvement of lysine acetylation in the diverse biological processes, especially in the closely spoilage-related pathways. This study provides a resource for functional analysis of acetylated proteins and creates opportunities for in-depth elucidation of the physiological role of protein acetylation in Shewanella spp.
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Affiliation(s)
- Yangbo Wang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; Zhejiang Engineering Institute of Food Quality and Safety, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Feifei Wang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xingyue Bao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Linglin Fu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; Zhejiang Engineering Institute of Food Quality and Safety, Zhejiang Gongshang University, Hangzhou 310018, China.
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82
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Ringel AE, Tucker SA, Haigis MC. Chemical and Physiological Features of Mitochondrial Acylation. Mol Cell 2019; 72:610-624. [PMID: 30444998 DOI: 10.1016/j.molcel.2018.10.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/15/2018] [Accepted: 10/15/2018] [Indexed: 01/09/2023]
Abstract
Growing appreciation of the diversity of post-translational modifications (PTMs) in the mitochondria necessitates reevaluation of the roles these modifications play in both health and disease. Compared to the cytosol and nucleus, the mitochondrial proteome is highly acylated, and remodeling of the mitochondrial "acylome" is a key adaptive mechanism that regulates fundamental aspects of mitochondrial biology. It is clear that we need to understand the underlying chemistry that regulates mitochondrial acylation, as well as how chemical properties of the acyl chain impact biological functions. Here, we dissect the sources of PTMs in the mitochondria, review major mitochondrial pathways that control levels of PTMs, and highlight how sirtuin enzymes respond to the bioenergetic state of the cell via NAD+ availability to regulate mitochondrial biology. By providing a framework connecting the chemistry of these modifications, their biochemical consequences, and the pathways that regulate the levels of acyl PTMs, we will gain a deeper understanding of the physiological significance of mitochondrial acylation and its role in mitochondrial adaptation.
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Affiliation(s)
- Alison E Ringel
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Sarah A Tucker
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA.
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83
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Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 2019; 63:97-107. [PMID: 30940741 PMCID: PMC6484784 DOI: 10.1042/ebc20180061] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.
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84
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Huang H, Tang S, Ji M, Tang Z, Shimada M, Liu X, Qi S, Locasale JW, Roeder RG, Zhao Y, Li X. p300-Mediated Lysine 2-Hydroxyisobutyrylation Regulates Glycolysis. Mol Cell 2019; 70:663-678.e6. [PMID: 29775581 DOI: 10.1016/j.molcel.2018.04.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/24/2018] [Accepted: 04/12/2018] [Indexed: 12/25/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is an evolutionarily conserved and widespread histone mark like lysine acetylation (Kac). Here we report that p300 functions as a lysine 2-hyroxyisobutyryltransferase to regulate glycolysis in response to nutritional cues. We discovered that p300 differentially regulates Khib and Kac on distinct lysine sites, with only 6 of the 149 p300-targeted Khib sites overlapping with the 693 p300-targeted Kac sites. We demonstrate that diverse cellular proteins, particularly glycolytic enzymes, are targeted by p300 for Khib, but not for Kac. Specifically, deletion of p300 significantly reduces Khib levels on several p300-dependent, Khib-specific sites on key glycolytic enzymes including ENO1, decreasing their catalytic activities. Consequently, p300-deficient cells have impaired glycolysis and are hypersensitive to glucose-depletion-induced cell death. Our study reveals an p300-catalyzed, Khib-specific molecular mechanism that regulates cellular glucose metabolism and further indicate that p300 has an intrinsic ability to select short-chain acyl-CoA-dependent protein substrates.
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Affiliation(s)
- He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Shuang Tang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ming Ji
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shankang Qi
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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85
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Prominent action of butyrate over β-hydroxybutyrate as histone deacetylase inhibitor, transcriptional modulator and anti-inflammatory molecule. Sci Rep 2019; 9:742. [PMID: 30679586 PMCID: PMC6346118 DOI: 10.1038/s41598-018-36941-9] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/26/2018] [Indexed: 12/16/2022] Open
Abstract
Butyrate and R-β-hydroxybutyrate are two related short chain fatty acids naturally found in mammals. Butyrate, produced by enteric butyric bacteria, is present at millimolar concentrations in the gastrointestinal tract and at lower levels in blood; R-β-hydroxybutyrate, the main ketone body, produced by the liver during fasting can reach millimolar concentrations in the circulation. Both molecules have been shown to be histone deacetylase (HDAC) inhibitors, and their administration has been associated to an improved metabolic profile and better cellular oxidative status, with butyrate inducing PGC1α and fatty acid oxidation and R-β-hydroxybutyrate upregulating oxidative stress resistance factors FOXO3A and MT2 in mouse kidney. Because of the chemical and functional similarity between the two molecules, we compared here their impact on multiple cell types, evaluating i) histone acetylation and hydroxybutyrylation levels by immunoblotting, ii) transcriptional regulation of metabolic and inflammatory genes by quantitative PCR and iii) cytokine secretion profiles using proteome profiling array analysis. We confirm that butyrate is a strong HDAC inhibitor, a characteristic we could not identify in R-β-hydroxybutyrate in vivo nor in vitro. Butyrate had an extensive impact on gene transcription in rat myotubes, upregulating PGC1α, CPT1b, mitochondrial sirtuins (SIRT3-5), and the mitochondrial anti-oxidative genes SOD2 and catalase. In endothelial cells, butyrate suppressed gene expression and LPS-induced secretion of several pro-inflammatory genes, while R-β-hydroxybutyrate acted as a slightly pro-inflammatory molecule. Our observations indicate that butyrate induces transcriptional changes to a higher extent than R-β-hydroxybutyrate in rat myotubes and endothelial cells, in keep with its HDAC inhibitory activity. Also, in contrast with previous reports, R-β-hydroxybutyrate, while inducing histone β-hydroxybutyrylation, did not display a readily detectable HDAC inhibitor activity and exerted a slight pro-inflammatory action on endothelial cells.
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86
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Wu Q, Ke L, Wang C, Fan P, Wu Z, Xu X. Global Analysis of Lysine 2-Hydroxyisobutyrylome upon SAHA Treatment and Its Relationship with Acetylation and Crotonylation. J Proteome Res 2018; 17:3176-3183. [PMID: 30109935 DOI: 10.1021/acs.jproteome.8b00289] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysine 2-hydroxyisobutyrylation is a newly discovered protein acylation and was reported to share acyltransferases and deacylases with the widely studied lysine acetylation. The well-known acetyltransferase Tip60 and histone deacetylases HDAC 2 and HDAC 3 were discovered to be "writer" and "eraser" of this new PTM on histones. However, the acyltransferases and deacylases for nonhistone proteins are still unclear. In this work, lysine 2-hydroxyisobutyrylome on both histones and nonhistone proteins upon SAHA treatment were intensively studied and 8765 lysine 2-hydroxyisobutyrylation sites on 2484 proteins were identified in A549 cells. This is the largest data set of lysine 2-hydroxyisobutyrylome in mammalian cells to date. It was found that lysine 2-hydroxyisobutyrylation participates in varieties of biological functions and processes including ribosome, glycolysis/gluconeogenesis, and transcription. More importantly, it was found that most quantified sites on core histones were up-regulated upon SAHA treatment for all 2-hydroxyisobutyrylation, crotonylation, and acetylation and the fold changes upon SAHA of 2-hydroxyisobutyrylation and crotonylation on nonhistone proteins were highly correlated, while their fold changes have little correlations with acetylation on nonhistone proteins.
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Affiliation(s)
- Quan Wu
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China.,Department of Microbiology and Immunobiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Li Ke
- Department of Thoracic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Chi Wang
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Pingsheng Fan
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Zhiwei Wu
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Xiaoling Xu
- Department of Respiration, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
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87
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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc 2018; 140:9478-9485. [PMID: 29991262 PMCID: PMC6070418 DOI: 10.1021/jacs.8b03572] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module's molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.
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Affiliation(s)
- Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Matthew D. Gibson
- Department of Physics, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael T. Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Division of Genetics, Brigham and Women’s Hospital; Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Ave Louis Pasteur, HMS New Research Building, Boston, Massachusetts 02115, USA
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88
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Meng X, Xing S, Perez LM, Peng X, Zhao Q, Redoña ED, Wang C, Peng Z. Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds. Sci Rep 2017; 7:17486. [PMID: 29235492 PMCID: PMC5727541 DOI: 10.1038/s41598-017-17756-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022] Open
Abstract
Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants. Functional annotation analyses indicated that a wide variety of vital biological processes were preferably targeted by lysine 2-hydroxyisobutyrylation, including glycolysis/gluconeogenesis, TCA cycle, starch biosynthesis, lipid metabolism, protein biosynthesis and processing. Our finding showed that 2-hydroxyisobutyrylated histone sites were conserved across plants, human, and mouse. A number of 2-hydroxyisobutyryl sites were shared with other lysine acylations in both histone and non-histone proteins. Comprehensive analysis of the lysine 2-hydroxyisobutyrylation sites illustrated that the modification sites were highly sequence specific with distinct motifs, and they had less surface accessibility than other lysine residues in the protein. Overall, our study provides the first systematic analysis of lysine 2-hydroxyisobutyrylation proteome in plants, and it serves as an important resource for future investigations of the regulatory mechanisms and functions of lysine 2-hydroxyisobutyrylation.
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Affiliation(s)
- Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
| | - Shihai Xing
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, Anhui, 230000, China
| | - Loida M Perez
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou, 310018, China
| | - Qingyong Zhao
- Institute of Crop Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Edilberto D Redoña
- Delta Research and Extension Center, Stoneville, P.O. Box 197, Mississippi, 38776, USA
| | - Cailin Wang
- Institute of Crop Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA.
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