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Kremer M, Schulze S, Eisenbruch N, Nagel F, Vogt R, Berndt L, Dörre B, Palm GJ, Hoppen J, Girbardt B, Albrecht D, Sievers S, Delcea M, Baumann U, Schnetz K, Lammers M. Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism. Nat Commun 2024; 15:1674. [PMID: 38395951 PMCID: PMC10891134 DOI: 10.1038/s41467-024-46039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.
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Affiliation(s)
- Magdalena Kremer
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Nadja Eisenbruch
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Felix Nagel
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Vogt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Leona Berndt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Babett Dörre
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Jens Hoppen
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Britta Girbardt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Michael Lammers
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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Stojowska-Swędrzyńska K, Kuczyńska-Wiśnik D, Laskowska E. Influence of N ε-Lysine Acetylation on the Formation of Protein Aggregates and Antibiotic Persistence in E. coli. Molecules 2024; 29:383. [PMID: 38257296 PMCID: PMC10819833 DOI: 10.3390/molecules29020383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/07/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous studies indicate that reversible Nε-lysine acetylation in bacteria may play a key role in the regulation of metabolic processes, transcription and translation, biofilm formation, virulence, and drug resistance. Using appropriate mutant strains deficient in non-enzymatic acetylation and enzymatic acetylation or deacetylation pathways, we investigated the influence of protein acetylation on cell viability, protein aggregation, and persister formation in Escherichia coli. Lysine acetylation was found to increase protein aggregation and cell viability under the late stationary phase. Moreover, increased lysine acetylation stimulated the formation of persisters. These results suggest that acetylation-dependent aggregation may improve the survival of bacteria under adverse conditions (such as the late stationary phase) and during antibiotic treatment. Further experiments revealed that acetylation-favorable conditions may increase persister formation in Klebsiella pneumoniae clinical isolate. However, the exact mechanisms underlying the relationship between acetylation and persistence in this pathogen remain to be elucidated.
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Affiliation(s)
| | | | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (K.S.-S.); (D.K.-W.)
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3
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Li Z, Gong T, Wu Q, Zhang Y, Zheng X, Li Y, Ren B, Peng X, Zhou X. Lysine lactylation regulates metabolic pathways and biofilm formation in Streptococcus mutans. Sci Signal 2023; 16:eadg1849. [PMID: 37669396 DOI: 10.1126/scisignal.adg1849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 08/11/2023] [Indexed: 09/07/2023]
Abstract
In eukaryotes, lactate produced during glycolysis is involved in regulating multiple metabolic processes through lysine lactylation (Kla). To explore the potential link between metabolism and Kla in prokaryotes, we investigated the distribution of Kla in the cariogenic bacterium Streptococcus mutans during planktonic growth in low-sugar conditions and in biofilm-promoting, high-sugar conditions. We identified 1869 Kla sites in 469 proteins under these two conditions, with the biofilm growth state showing a greater number of lactylated sites and proteins. Although high sugar increased Kla globally, it reduced lactylation of RNA polymerase subunit α (RpoA) at Lys173. Lactylation at this residue inhibited the synthesis of extracellular polysaccharides, a major constituent of the cariogenic biofilm. The Gcn5-related N-acetyltransferase (GNAT) superfamily enzyme GNAT13 exhibited lysine lactyltransferase activity in cells and lactylated Lys173 in RpoA in vitro. Either GNAT13 overexpression or lactylation of Lys173 in RpoA inhibited biofilm formation. These results provide an overview of the distribution and potential functions of Kla and improve our understanding of the role of lactate in the metabolic regulation of prokaryotes.
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Affiliation(s)
- Zhengyi Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qinrui Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yixin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Tan Y, Liu W, Chen Y, Zhou Y, Song K, Cao S, Zhang Y, Song Y, Deng H, Yang R, Du Z. Comparative Lysine Acetylome Analysis of Y. pestis YfiQ/CobB Mutants Reveals that Acetylation of SlyA Lys73 Significantly Promotes Biofilm Formation of Y. pestis. Microbiol Spectr 2023; 11:e0046023. [PMID: 37458592 PMCID: PMC10433856 DOI: 10.1128/spectrum.00460-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/10/2023] [Indexed: 08/19/2023] Open
Abstract
Increasing evidence shows that protein lysine acetylation is involved in almost every aspect of cellular physiology in bacteria. Yersinia pestis is a flea-borne pathogen responsible for millions of human deaths in three global pandemics. However, the functional role of lysine acetylation in this pathogen remains unclear. Here, we found more acetylated proteins and a higher degree of acetylation in Y. pestis grown under mammalian host (Mh) conditions than under flea vector (Fv) conditions, suggesting that protein acetylation could significantly change during fleabite transmission. Comparative acetylome analysis of mutants of YfiQ and CobB, the major acetyltransferase and deacetylase of Y. pestis, respectively, identified 23 YfiQ-dependent and 315 CobB-dependent acetylated proteins. Further results demonstrated that acetylation of Lys73 of the SlyA protein, a MarR-family transcriptional regulator, inhibits its binding to the promoter of target genes, including hmsT that encodes diguanylate cyclase responsible for the synthesis of c-di-GMP, and significantly enhances biofilm formation of Y. pestis. Our study presents the first extensive acetylome data of Y. pestis and a critical resource for the functional study of lysine acetylation in this pathogen. IMPORTANCE Yersinia pestis is the etiological agent of plague, historically responsible for three global pandemics. The 2017 plague epidemic in Madagascar was a reminder that Y. pestis remains a real threat in many parts of the world. Plague is a zoonotic disease that primarily infects rodents via fleabite, and transmission of Y. pestis from infected fleas to mammals requires rapid adaptive responses to adverse host environments to establish infection. Our study provides the first global profiling of lysine acetylation derived from mass spectrometry analysis in Y. pestis. Our data set can serve as a critical resource for the functional study of lysine acetylation in Y. pestis and provides new molecular insight into the physiological role of lysine acetylation in proteins. More importantly, we found that acetylation of Lys73 of SlyA significantly promotes biofilm formation of Y. pestis, indicating that bacteria can use lysine acetylation to fine-tune the expression of genes to improve adaptation.
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Affiliation(s)
- Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wanbing Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yazhou Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shiyang Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Choi JH, Kim JW, Oh MH. Identification of Feronia-interacting proteins in Arabidopsis thaliana. Genes Genomics 2022; 44:1477-1485. [PMID: 36053485 DOI: 10.1007/s13258-022-01292-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Plant growth and development are complex processes modulated by numerous genes, transcription factors, hormones, and peptides. Several reports implicate the membrane-localized Catharanthus roseus receptor-like kinase1 (CrRLK1L) protein, FERONIA (FER), involved in plant development. However, protein targets of FER remain poorly characterized. OBJECTIVE FER recombinant proteins were analyzed, and FER-interacting proteins were identified, to better understand the function of the Arabidopsis thaliana FER (AtFER) gene in plant development. METHODS AtFER-interacting proteins were identified through Yeast-Two Hybrid (Y2H) and validated by bimolecular fluorescence complementation (BiFC). Autophosphorylation activity was evaluated in AtFER site-directed and deletion mutants. RESULTS AtFER cytoplasmic kinase domain (Flag-FER-CD) is autophosphorylated at the Thr residue (s), with T559 and T664 as important sites for AtFER kinase activity. In addition, the carboxy terminal region is essential for AtFER kinase activity. Y2H identified an Armadillo (ARM)-repeat protein (At4g16490) with tandem copies of a degenerate protein sequence motif, a U-BOX 9 (PUB9, At3g07360), IQ-DOMAIN 7 (IQD7, At1g17480), and heteroglycan glucosidase 1 (HGL1, At3g23640) as AtFER-interacting proteins. BiFC confirmed the in vivo interactions between these four proteins and AtFER in tobacco (Nicotiana benthamiana) leaf transient expression assays. The RAPID ALKALINIZATION FACTOR1 (RALF1) peptide, which is a FER ligand, induced the expression of genes encoding the four AtFER-interacting proteins. CONCLUSION The AtFER-interacting proteins identified in this study are likely involved in FER-mediated intracellular signaling pathways that are essential in plant growth and development, and possibly plant immunity.
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Affiliation(s)
- Jae-Han Choi
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea
| | - Ji-Woo Kim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea
| | - Man-Ho Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea.
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Teng AY, Che TL, Zhang AR, Zhang YY, Xu Q, Wang T, Sun YQ, Jiang BG, Lv CL, Chen JJ, Wang LP, Hay SI, Liu W, Fang LQ. Mapping the viruses belonging to the order Bunyavirales in China. Infect Dis Poverty 2022; 11:81. [PMID: 35799306 PMCID: PMC9264531 DOI: 10.1186/s40249-022-00993-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Viral pathogens belonging to the order Bunyavirales pose a continuous background threat to global health, but the fact remains that they are usually neglected and their distribution is still ambiguously known. We aim to map the geographical distribution of Bunyavirales viruses and assess the environmental suitability and transmission risk of major Bunyavirales viruses in China. METHODS We assembled data on all Bunyavirales viruses detected in humans, animals and vectors from multiple sources, to update distribution maps of them across China. In addition, we predicted environmental suitability at the 10 km × 10 km pixel level by applying boosted regression tree models for two important Bunyavirales viruses, including Crimean-Congo hemorrhagic fever virus (CCHFV) and Rift Valley fever virus (RVFV). Based on model-projected risks and air travel volume, the imported risk of RVFV was also estimated from its endemic areas to the cities in China. RESULTS Here we mapped all 89 species of Bunyavirales viruses in China from January 1951 to June 2021. Nineteen viruses were shown to infect humans, including ten species first reported as human infections. A total of 447,848 cases infected with Bunyavirales viruses were reported, and hantaviruses, Dabie bandavirus and Crimean-Congo hemorrhagic fever virus (CCHFV) had the severest disease burden. Model-predicted maps showed that Xinjiang and southwestern Yunnan had the highest environmental suitability for CCHFV occurrence, mainly related to Hyalomma asiaticum presence, while southern China had the highest environmental suitability for Rift Valley fever virus (RVFV) transmission all year round, mainly driven by livestock density, mean precipitation in the previous month. We further identified three cities including Guangzhou, Beijing and Shanghai, with the highest imported risk of RVFV potentially from Egypt, South Africa, Saudi Arabia and Kenya. CONCLUSIONS A variety of Bunyavirales viruses are widely distributed in China, and the two major neglected Bunyavirales viruses including CCHFV and RVFV, both have the potential for outbreaks in local areas of China. Our study can help to promote the understanding of risk distribution and disease burden of Bunyavirales viruses in China, and the risk maps of CCHFV and RVFV occurrence are crucial to the targeted surveillance and control, especially in seasons and locations at high risk.
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Affiliation(s)
- Ai-Ying Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Tian-Le Che
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - An-Ran Zhang
- Department of Research, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China
| | - Yuan-Yuan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Qiang Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Tao Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Yan-Qun Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Chen-Long Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Jin-Jin Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China
| | - Li-Ping Wang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Simon I Hay
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA. .,Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, 98121, USA.
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China.
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai, Beijing, 100071, People's Republic of China.
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Complete genome sequence of a novel arlivirus from a yellow spotted stink bug (Erthesina fullo (Thunberg, 1783)). Arch Virol 2022; 167:1205-1209. [PMID: 35246733 DOI: 10.1007/s00705-022-05399-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/17/2022] [Indexed: 11/02/2022]
Abstract
Arlivirus is currently the only genus in the newly established viral family Lispiviridae. In this study, the complete genome sequence of a novel arlivirus, tentatively named "Nbu stink bug virus 1" (NbuSBV-1), was identified in an individual yellow spotted stink bug, Erthesina fullo (family Pentatomidae, order Hemiptera), which is a widely distributed phytophagous pest in Asia. NbuSBV-1 has a single negative-stranded RNA genome of 13,605 nucleotides in length, and it was predicted to contain six open reading frames (ORFs). Conserved domains of NbuSBV-1 were predicted in ORF1 (a nucleoprotein), ORF4 (a glycoprotein domain), ORF5 (a zinc-finger domain), and ORF6 (an RNA-directed RNA polymerase [RdRP] domain, an mRNA cap domain, and a methyltransferase domain). NbuSBV-1 shares 50.54% amino acid sequence identity in the RdRP region with its closest homolog, Lĭshì spider virus 2. In RdRP-based phylogenetic analysis, NbuSBV-1 was clearly clustered in a clade with other arliviruses. Furthermore, NbuSBV-1-derived small interfering RNAs (siRNAs) showed typical patterns of virus-derived siRNAs produced by the host antiviral RNA interference pathway. As far as we know, NbuSBV-1 is the first arlivirus identified in an insect of the family Pentatomidae.
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Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
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Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
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9
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Liu M, Guo L, Fu Y, Huo M, Qi Q, Zhao G. Bacterial protein acetylation and its role in cellular physiology and metabolic regulation. Biotechnol Adv 2021; 53:107842. [PMID: 34624455 DOI: 10.1016/j.biotechadv.2021.107842] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/22/2021] [Accepted: 10/03/2021] [Indexed: 12/28/2022]
Abstract
Protein acetylation is an evolutionarily conserved posttranslational modification. It affects enzyme activity, metabolic flux distribution, and other critical physiological and biochemical processes by altering protein size and charge. Protein acetylation may thus be a promising tool for metabolic regulation to improve target production and conversion efficiency in fermentation. Here we review the role of protein acetylation in bacterial physiology and metabolism and describe applications of protein acetylation in fermentation engineering and strategies for regulating acetylation status. Although protein acetylation has become a hot topic, the regulatory mechanisms have not been fully characterized. We propose future research directions in protein acetylation.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China; CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Yingxin Fu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Meitong Huo
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China; CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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10
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Wang J, Liu C, Chen Y, Zhao Y, Ma Z. Protein acetylation and deacetylation in plant-pathogen interactions. Environ Microbiol 2021; 23:4841-4855. [PMID: 34398483 DOI: 10.1111/1462-2920.15725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022]
Abstract
Protein acetylation and deacetylation catalysed by lysine acetyltransferases (KATs) and deacetylases (KDACs), respectively, are major mechanisms regulating various cellular processes. During the fight between microbial pathogens and host plants, both apply a set of measures, including acetylation interference, to strengthen themselves while suppressing the other. In this review, we first summarize KATs and KDACs in plants and their pathogens. Next, we introduce diverse acetylation and deacetylation mechanisms affecting protein functions, including the regulation of enzyme activity and specificity, protein-protein or protein-DNA interactions, subcellular localization and protein stability. We then focus on the current understanding of acetylation and deacetylation in plant-pathogen interactions. Additionally, we also discuss potential acetylation-related approaches for controlling plant diseases.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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11
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Herrmann B, Butler BE. Hearing loss and brain plasticity: the hyperactivity phenomenon. Brain Struct Funct 2021; 226:2019-2039. [PMID: 34100151 DOI: 10.1007/s00429-021-02313-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/03/2021] [Indexed: 12/22/2022]
Abstract
Many aging adults experience some form of hearing problems that may arise from auditory peripheral damage. However, it has been increasingly acknowledged that hearing loss is not only a dysfunction of the auditory periphery but also results from changes within the entire auditory system, from periphery to cortex. Damage to the auditory periphery is associated with an increase in neural activity at various stages throughout the auditory pathway. Here, we review neurophysiological evidence of hyperactivity, auditory perceptual difficulties that may result from hyperactivity, and outline open conceptual and methodological questions related to the study of hyperactivity. We suggest that hyperactivity alters all aspects of hearing-including spectral, temporal, spatial hearing-and, in turn, impairs speech comprehension when background sound is present. By focusing on the perceptual consequences of hyperactivity and the potential challenges of investigating hyperactivity in humans, we hope to bring animal and human electrophysiologists closer together to better understand hearing problems in older adulthood.
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Affiliation(s)
- Björn Herrmann
- Rotman Research Institute, Baycrest, Toronto, ON, M6A 2E1, Canada. .,Department of Psychology, University of Toronto, Toronto, ON, Canada.
| | - Blake E Butler
- Department of Psychology & The Brain and Mind Institute, University of Western Ontario, London, ON, Canada.,National Centre for Audiology, University of Western Ontario, London, ON, Canada
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12
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Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. J Mol Evol 2021; 89:329-340. [PMID: 34059925 DOI: 10.1007/s00239-021-10013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022]
Abstract
Preventing and controlling epidemics caused by vector-borne viruses are particularly challenging due to their diverse pool of hosts and highly adaptive nature. Many vector-borne viruses belong to the Flavivirus genus, whose members vary greatly in host range and specificity. Members of the Flavivirus genus can be categorized to four main groups: insect-specific viruses that are maintained solely in arthropod populations, mosquito-borne viruses and tick-borne viruses that are transmitted to vertebrate hosts by mosquitoes or ticks via blood feeding, and those with no-known vector. The mosquito-borne group encompasses the yellow fever, dengue, and West Nile viruses, all of which are globally spread and cause severe morbidity in humans. The Flavivirus genus is genetically diverse, and its members are subject to different host-specific and vector-specific selective constraints, which do not always align. Thus, understanding the underlying genetic differences that led to the diversity in host range within this genus is an important aspect in deciphering the mechanisms that drive host compatibility and can aid in the constant arms-race against viral threats. Here, we review the phylogenetic relationships between members of the genus, their infection bottlenecks, and phenotypic and genomic differences. We further discuss methods that utilize these differences for prediction of host shifts in flaviviruses and can contribute to viral surveillance efforts.
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13
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Sun L, Yao Z, Guo Z, Zhang L, Wang Y, Mao R, Lin Y, Fu Y, Lin X. Comprehensive analysis of the lysine acetylome in Aeromonas hydrophila reveals cross-talk between lysine acetylation and succinylation in LuxS. Emerg Microbes Infect 2020; 8:1229-1239. [PMID: 31448697 PMCID: PMC6735345 DOI: 10.1080/22221751.2019.1656549] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lysine acetylation and succinylation are both prevalent protein post-translational modifications (PTMs) in bacteria species, whereas the effect of the cross-talk between both PTMs on bacterial biological function remains largely unknown. Our previously study found lysine succinylated sites on proteins play important role on metabolic pathways in fish pathogenic Aeromonas hydrophila. A total of 3189 lysine-acetylation sites were further identified on 1013 proteins of this pathogen using LC-MS/MS in this study. Functional examination of these PTMs peptides showed associations with basal biological processes, especially metabolic pathways. Additionally, when comparing the obtained lysine acetylome to a previously obtained lysine succinylome, 1198 sites in a total of 547 proteins were found to be in common and associated with various metabolic pathways. As the autoinducer-2 (AI-2) synthase involved in quorum sensing of bacteria, the site-directed mutagenesis of LuxS at the K165 site was performed and revealed that the cross-talk between lysine acetylation and succinylation exerts an inverse influence on bacterial quorum sensing and on LuxS enzymatic activity. In summary, this study provides an in-depth A. hydrophila lysine acetylome profile and for the first time reveals the role of cross-talk between lysine acetylation and succinylation, and its potential impact on bacterial physiological functions.
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Affiliation(s)
- Lina Sun
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Zujie Yao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences , Shanghai , People's Republic of China
| | - Zhuang Guo
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Ranran Mao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Yuexu Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Yuying Fu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China.,Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China
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14
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Abstract
Over the past decade the number and variety of protein post-translational modifications that have been detected and characterized in bacteria have rapidly increased. Most post-translational protein modifications occur in a relatively low number of bacterial proteins in comparison with eukaryotic proteins, and most of the modified proteins carry low, substoichiometric levels of modification; therefore, their structural and functional analysis is particularly challenging. The number of modifying enzymes differs greatly among bacterial species, and the extent of the modified proteome strongly depends on environmental conditions. Nevertheless, evidence is rapidly accumulating that protein post-translational modifications have vital roles in various cellular processes such as protein synthesis and turnover, nitrogen metabolism, the cell cycle, dormancy, sporulation, spore germination, persistence and virulence. Further research of protein post-translational modifications will fill current gaps in the understanding of bacterial physiology and open new avenues for treatment of infectious diseases.
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15
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Xu Z, Zhang H, Zhang X, Jiang H, Liu C, Wu F, Qian L, Hao B, Czajkowsky DM, Guo S, Xu Z, Bi L, Wang S, Li H, Tan M, Yan W, Feng L, Hou J, Tao SC. Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP. EMBO J 2019; 38:e100948. [PMID: 31418899 DOI: 10.15252/embj.2018100948] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis of acetyl-CoA. Interestingly, we also found that one of the key enzymes directly involved in c-di-GMP production, DgcZ, is a substrate of CobB. Deacetylation of DgcZ by CobB enhances its activity and thus the production of c-di-GMP. Our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.
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Affiliation(s)
- Zhaowei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hainan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xingrun Zhang
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Hewei Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chengxi Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fanlin Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lili Qian
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bingbing Hao
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijing Xu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lijun Bi
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Shihua Wang
- School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Feng
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Jingli Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
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16
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Christensen DG, Baumgartner JT, Xie X, Jew KM, Basisty N, Schilling B, Kuhn ML, Wolfe AJ. Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes. mBio 2019; 10:e02708-18. [PMID: 30967470 PMCID: PMC6456759 DOI: 10.1128/mbio.02708-18] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.
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Affiliation(s)
- D G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| | - J T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - X Xie
- Buck Institute for Research on Aging, Novato, California, USA
| | - K M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - N Basisty
- Buck Institute for Research on Aging, Novato, California, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, California, USA
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
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17
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Suzuki S, Kondo N, Yoshida M, Nishiyama M, Kosono S. Dynamic changes in lysine acetylation and succinylation of the elongation factor Tu in Bacillus subtilis. MICROBIOLOGY-SGM 2018; 165:65-77. [PMID: 30394869 DOI: 10.1099/mic.0.000737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nε-lysine acetylation and succinylation are ubiquitous post-translational modifications in eukaryotes and bacteria. In the present study, we showed a dynamic change in acetylation and succinylation of TufA, the translation elongation factor Tu, from Bacillus subtilis. Increased acetylation of TufA was observed during the exponential growth phase in LB and minimal glucose conditions, and its acetylation level decreased upon entering the stationary phase, while its succinylation increased during the late stationary phase. TufA was also succinylated during vegetative growth under minimal citrate or succinate conditions. Mutational analysis showed that triple succinylation mimic mutations at Lys306, Lys308 and Lys316 in domain-3 of TufA had a negative effect on B. subtilis growth, whereas the non-acylation mimic mutations at these three lysine residues did not. Consistent with the growth phenotypes, the triple succinylation mimic mutant showed 67 % decreased translation activity in vitro, suggesting a possibility that succinylation at the lysine residues in domain-3 decreases the translation activity. TufA, including Lys308, was non-enzymatically succinylated by physiological concentrations of succinyl-CoA. Lys42 in the G-domain was identified as the most frequently modified acetylation site, though its acetylation was likely dispensable for TufA translation activity and growth. Determination of the intracellular levels of acetylating substrates and TufA acetylation revealed that acetyl phosphate was responsible for acetylation at several lysine sites of TufA, but not for Lys42 acetylation. It was speculated that acetyl-CoA was likely responsible for Lys42 acetylation, though AcuA acetyltransferase was not involved. Zn2+-dependent AcuC and NAD+-dependent SrtN deacetylases were responsible for deacetylation of TufA, including Lys42. These findings suggest the potential regulatory roles of acetylation and succinylation in controlling TufA function and translation in response to nutrient environments in B. subtilis.
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Affiliation(s)
- Shota Suzuki
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoko Kondo
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Minoru Yoshida
- 2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,3Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,4RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Makoto Nishiyama
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Saori Kosono
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,4RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.,2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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18
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Avrahami EM, Levi S, Zajfman E, Regev C, Ben-David O, Arbely E. Reconstitution of Mammalian Enzymatic Deacylation Reactions in Live Bacteria Using Native Acylated Substrates. ACS Synth Biol 2018; 7:2348-2354. [PMID: 30207693 PMCID: PMC6198279 DOI: 10.1021/acssynbio.8b00314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Lysine deacetylases
(KDACs) are enzymes that catalyze the hydrolysis
of acyl groups from acyl-lysine residues. The recent identification
of thousands of putative acylation sites, including specific acetylation
sites, created an urgent need for biochemical methodologies aimed
at better characterizing KDAC-substrate specificity and evaluating
KDACs activity. To address this need, we utilized genetic code expansion
technology to coexpress site-specifically acylated substrates with
mammalian KDACs, and study substrate recognition and deacylase activity
in live Escherichia coli. In this system the bacterial
cell serves as a “biological test tube” in which the
incubation of a single mammalian KDAC and a potential peptide or full-length
acylated substrate transpires. We report novel deacetylation activities
of Zn2+-dependent deacetylases and sirtuins in bacteria.
We also measure the deacylation of propionyl-, butyryl-, and crotonyl-lysine,
as well as novel deacetylation of Lys310-acetylated RelA by SIRT3,
SIRT5, SIRT6, and HDAC8. This study highlights the importance of native
interactions to KDAC-substrate recognition and deacylase activity.
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Affiliation(s)
- Emanuel M. Avrahami
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Shahar Levi
- Department of Chemistry and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Eyal Zajfman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Clil Regev
- Department of Chemistry and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Oshrit Ben-David
- Department of Chemistry and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Eyal Arbely
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Department of Chemistry and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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19
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Bontemps-Gallo S, Gaviard C, Richards CL, Kentache T, Raffel SJ, Lawrence KA, Schindler JC, Lovelace J, Dulebohn DP, Cluss RG, Hardouin J, Gherardini FC. Global Profiling of Lysine Acetylation in Borrelia burgdorferi B31 Reveals Its Role in Central Metabolism. Front Microbiol 2018; 9:2036. [PMID: 30233522 PMCID: PMC6127242 DOI: 10.3389/fmicb.2018.02036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
The post-translational modification of proteins has been shown to be extremely important in prokaryotes. Using a highly sensitive mass spectrometry-based proteomics approach, we have characterized the acetylome of B. burgdorferi. As previously reported for other bacteria, a relatively low number (5%) of the potential genome-encoded proteins of B. burgdorferi were acetylated. Of these, the vast majority were involved in central metabolism and cellular information processing (transcription, translation, etc.). Interestingly, these critical cell functions were targeted during both ML (mid-log) and S (stationary) phases of growth. However, acetylation of target proteins in ML phase was limited to single lysine residues while these same proteins were acetylated at multiple sites during S phase. To determine the acetyl donor in B. burgdorferi, we used mutants that targeted the sole acetate metabolic/anabolic pathway in B. burgdorferi (lipid I synthesis). B. burgdorferi strains B31-A3, B31-A3 ΔackA (acetyl-P- and acetyl-CoA-) and B31-A3 Δpta (acetyl-P+ and acetyl-CoA-) were grown to S phase and the acetylation profiles were analyzed. While only two proteins were acetylated in the ΔackA mutant, 140 proteins were acetylated in the Δpta mutant suggesting that acetyl-P was the primary acetyl donor in B. burgdorferi. Using specific enzymatic assays, we were able to demonstrate that hyperacetylation of proteins in S phase appeared to play a role in decreasing the enzymatic activity of at least two glycolytic proteins. Currently, we hypothesize that acetylation is used to modulate enzyme activities during different stages of growth. This strategy would allow the bacteria to post-translationally stimulate the activity of key glycolytic enzymes by deacetylation rather than expending excessive energy synthesizing new proteins. This would be an appealing, low-energy strategy for a bacterium with limited metabolic capabilities. Future work focuses on identifying potential protein deacetylase(s) to complete our understanding of this important biological process.
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Affiliation(s)
- Sébastien Bontemps-Gallo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Charlotte Gaviard
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Crystal L Richards
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Takfarinas Kentache
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Sandra J Raffel
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Kevin A Lawrence
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Joseph C Schindler
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Joseph Lovelace
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Daniel P Dulebohn
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Robert G Cluss
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Julie Hardouin
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Frank C Gherardini
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
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20
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Kremer M, Kuhlmann N, Lechner M, Baldus L, Lammers M. Comment on 'YcgC represents a new protein deacetylase family in prokaryotes'. eLife 2018; 7:37798. [PMID: 29939131 PMCID: PMC6023612 DOI: 10.7554/elife.37798] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
Lysine acetylation is a post-translational modification that is conserved from bacteria to humans. It is catalysed by the activities of lysine acetyltransferases, which use acetyl-CoA as the acetyl-donor molecule, and lysine deacetylases, which remove the acetyl moiety. Recently, it was reported that YcgC represents a new prokaryotic deacetylase family with no apparent homologies to existing deacetylases (Tu et al., 2015). Here we report the results of experiments which demonstrate that YcgC is not a deacetylase.
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Affiliation(s)
- Magdalena Kremer
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Nora Kuhlmann
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marius Lechner
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Linda Baldus
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Michael Lammers
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Institute of Biochemistry, Synthetic and Structural Biochemistry, University of Greifswald, Greifswald, Germany
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21
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Venkat S, Chen H, Stahman A, Hudson D, McGuire P, Gan Q, Fan C. Characterizing Lysine Acetylation of Isocitrate Dehydrogenase in Escherichia coli. J Mol Biol 2018; 430:1901-1911. [PMID: 29733852 PMCID: PMC5988991 DOI: 10.1016/j.jmb.2018.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 12/21/2022]
Abstract
The Escherichia coli isocitrate dehydrogenase (ICDH) is one of the tricarboxylic acid cycle enzymes, playing key roles in energy production and carbon flux regulation. E. coli ICDH was the first bacterial enzyme shown to be regulated by reversible phosphorylation. However, the effect of lysine acetylation on E. coli ICDH, which has no sequence similarity with its counterparts in eukaryotes, is still unclear. Based on previous studies of E. coli acetylome and ICDH crystal structures, eight lysine residues were selected for mutational and kinetic analyses. They were replaced with acetyllysine by the genetic code expansion strategy or substituted with glutamine as a classic approach. Although acetylation decreased the overall ICDH activity, its effects were different site by site. Deacetylation tests demonstrated that the CobB deacetylase could deacetylate ICDH both in vivo and in vitro, but CobB was only specific for lysine residues at the protein surface. On the other hand, ICDH could be acetylated by acetyl-phosphate chemically in vitro. And in vivo acetylation tests indicated that the acetylation level of ICDH was correlated with the amounts of intracellular acetyl-phosphate. This study nicely complements previous proteomic studies to provide direct biochemical evidence for ICDH acetylation.
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Affiliation(s)
- Sumana Venkat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States
| | - Hao Chen
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States
| | - Alleigh Stahman
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Denver Hudson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Paige McGuire
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States.
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22
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Gallego-Jara J, Écija Conesa A, de Diego Puente T, Lozano Terol G, Cánovas Díaz M. Characterization of CobB kinetics and inhibition by nicotinamide. PLoS One 2017; 12:e0189689. [PMID: 29253849 PMCID: PMC5734772 DOI: 10.1371/journal.pone.0189689] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022] Open
Abstract
Lysine acetylation has emerged as a global protein regulation system in all domains of life. Sirtuins, or Sir2-like enzymes, are a family of histone deacetylases characterized by their employing NAD+ as a co-substrate. Sirtuins can deacetylate several acetylated proteins, but a consensus substrate recognition sequence has not yet been established. Product inhibition of many eukaryotic sirtuins by nicotinamide and its analogues has been studied in vitro due to their potential role as anticancer agents. In this work, the kinetics of CobB, the main Escherichia coli deacetylase, have been characterized. To our knowledge, this is the first kinetic characterization of a sirtuin employing a fully acetylated and natively folded protein as a substrate. CobB deacetylated several acetyl-CoA synthetase acetylated lysines with a single kinetic rate. In addition, in vitro nicotinamide inhibition of CobB has been characterized, and the intracellular nicotinamide concentrations have been determined under different growth conditions. The results suggest that nicotinamide can act as a CobB regulator in vivo. A nicotinamidase deletion strain was thus phenotypically characterized, and it behaved similarly to the ΔcobB strain. The results of this work demonstrate the potential regulatory role of the nicotinamide metabolite in vivo.
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Affiliation(s)
- Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
- * E-mail:
| | - Ana Écija Conesa
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Gema Lozano Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
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23
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Venkat S, Gregory C, Gan Q, Fan C. Biochemical Characterization of the Lysine Acetylation of Tyrosyl-tRNA Synthetase in Escherichia coli. Chembiochem 2017; 18:1928-1934. [PMID: 28741290 PMCID: PMC5629106 DOI: 10.1002/cbic.201700343] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein synthesis. As a member of the aaRS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown in proteomic studies to be acetylated at multiple lysine residues. However, these putative acetylation targets have not yet been biochemically characterized. In this study, we applied a genetic-code-expansion strategy to site-specifically incorporate Nϵ -acetyl-l-lysine into selected positions of TyrRS for in vitro characterization. Enzyme assays demonstrated that acetylation at K85, K235, and K238 could impair the enzyme activity. In vitro deacetylation experiments showed that most acetylated lysine residues in TyrRS were sensitive to the E. coli deacetylase CobB but not YcgC. In vitro acetylation assays indicated that 25 members of the Gcn5-related N-acetyltransferase family in E. coli, including YfiQ, could not acetylate TyrRS efficiently, whereas TyrRS could be acetylated chemically by acetyl-CoA or acetyl-phosphate (AcP) only. Our in vitro characterization experiments indicated that lysine acetylation could be a possible mechanism for modulating aaRS enzyme activities, thus affecting translation.
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Affiliation(s)
- Sumana Venkat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Caroline Gregory
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 727011, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
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24
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Xuan W, Yao A, Schultz PG. Genetically Encoded Fluorescent Probe for Detecting Sirtuins in Living Cells. J Am Chem Soc 2017; 139:12350-12353. [PMID: 28857557 DOI: 10.1021/jacs.7b05725] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Sirtuins are NAD+ dependent protein deacetylases, which are involved in many biological processes. We now report a novel genetically encoded fluorescent probe (EGFP-K85AcK) that responds to sirtuins in living cells. The probe design exploits a lysyl residue in EGFP that is essential for chromophore maturation, and is also an efficient deacetylation substrate for sirtuins. Analysis of activity in Escherichia coli ΔcobB revealed that the probe can respond to various human sirtuins, including SIRT1, SIRT2, SIRT3 and SIRT5. We also directly monitored SIRT1 and SIRT2 activity in HEK293T cells with an mCherry fusion of EGFP-K85AcK, and showed that this approach can be extended to other fluorescent proteins. Finally, we demonstrate that this approach can be used to examine the activity of sirtuins toward additional lysyl posttranslational modifications, and show that sirtuins can act as erasers of HibK modified proteins.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry and Skaggs Institute for Chemical Biology, the Scripps Research Institute , 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Anzhi Yao
- Department of Chemistry and Skaggs Institute for Chemical Biology, the Scripps Research Institute , 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, the Scripps Research Institute , 10550 N Torrey Pines Road, La Jolla, California 92037, United States
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25
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Abstract
Nε-Lysine acetylation is now recognized as an abundant posttranslational modification (PTM) that influences many essential biological pathways. Advancements in mass spectrometry-based proteomics have led to the discovery that bacteria contain hundreds of acetylated proteins, contrary to the prior notion of acetylation events being rare in bacteria. Although the mechanisms that regulate protein acetylation are still not fully defined, it is understood that this modification is finely tuned via both enzymatic and nonenzymatic mechanisms. The opposing actions of Gcn5-related N-acetyltransferases (GNATs) and deacetylases, including sirtuins, provide the enzymatic control of lysine acetylation. A nonenzymatic mechanism of acetylation has also been demonstrated and proven to be prominent in bacteria, as well as in mitochondria. The functional consequences of the vast majority of the identified acetylation sites remain unknown. From studies in mammalian systems, acetylation of critical lysine residues was shown to impact protein function by altering its structure, subcellular localization, and interactions. It is becoming apparent that the same diversity of functions can be found in bacteria. Here, we review current knowledge of the mechanisms and the functional consequences of acetylation in bacteria. Additionally, we discuss the methods available for detecting acetylation sites, including quantitative mass spectrometry-based methods, which promise to promote this field of research. We conclude with possible future directions and broader implications of the study of protein acetylation in bacteria.
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26
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Xu Z, Li X, Zhou S, Xie W, Wang J, Cheng L, Wang S, Guo S, Xu Z, Cao X, Zhang M, Yu B, Narimatsu H, Tao SC, Zhang Y. Systematic identification of the protein substrates of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T1/T2/T3 using a human proteome microarray. Proteomics 2017; 17. [PMID: 28394504 DOI: 10.1002/pmic.201600485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/31/2017] [Accepted: 04/07/2017] [Indexed: 12/12/2022]
Abstract
O-GalNAc glycosylation is the initial step of the mucin-type O-glycosylation. In humans, it is catalyzed by a family of 20 homologous UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts). So far, there is very limited information on their protein substrate specificities. In this study, we developed an on-chip ppGalNAc-Ts assay that could rapidly and systematically identify the protein substrates of each ppGalNAc-T. In detail, we utilized a human proteome microarray as the protein substrates and UDP-GalNAz as the nucleotide sugar donor for click chemistry detection. From a total of 16 368 human proteins, we identified 570 potential substrates of ppGalNAc-T1, T2, and T3. Among them, 128 substrates were overlapped, while the rest were isoform specific. Further cluster analysis of these substrates showed that the substrates of ppGalNAc-T1 had a closer phylogenetic relationship with that of ppGalNAc-T3 compared with ppGalNAc-T2, which was consistent with the topology of the phylogenetic tree of these ppGalNAc-Ts. Taken together, our microarray-based enzymatic assay comprehensively reveals the substrate profile of the ppGalNAc-T1, T2, and T3, which not only provides a plausible explanation for their partial functional redundancy as reported, but clearly implies some specialized roles of each enzyme in different biological processes.
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Affiliation(s)
- Zhijue Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xing Li
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Shumin Zhou
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenxian Xie
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Jing Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Microbial metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Li Cheng
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, P. R. China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Sheng Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Zhaowei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xin Cao
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Menghui Zhang
- State Key Laboratory of Microbial metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Biao Yu
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- SCSB (China) - AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, P. R. China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Microbial metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
- SCSB (China) - AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai Jiao Tong University, Shanghai, P. R. China
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27
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Venkat S, Gregory C, Sturges J, Gan Q, Fan C. Studying the Lysine Acetylation of Malate Dehydrogenase. J Mol Biol 2017; 429:1396-1405. [PMID: 28366830 PMCID: PMC5479488 DOI: 10.1016/j.jmb.2017.03.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022]
Abstract
Protein acetylation plays important roles in many biological processes. Malate dehydrogenase (MDH), a key enzyme in the tricarboxylic acid cycle, has been identified to be acetylated in bacteria by proteomic studies, but no further characterization has been reported. One challenge for studying protein acetylation is to get purely acetylated proteins at specific positions. Here, we applied the genetic code expansion strategy to site-specifically incorporate Nε-acetyllysine into MDH. The acetylation of lysine residues in MDH could enhance its enzyme activity. The Escherichia coli deacetylase CobB could deacetylate acetylated MDH, while the E. coli acetyltransferase YfiQ cannot acetylate MDH efficiently. Our results also demonstrated that acetyl-CoA or acetyl-phosphate could acetylate MDH chemically in vitro. Furthermore, the acetylation level of MDH was shown to be affected by carbon sources in the growth medium.
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Affiliation(s)
- Sumana Venkat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
| | - Caroline Gregory
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jourdan Sturges
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
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28
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Ye Q, Ji QQ, Yan W, Yang F, Wang ED. Acetylation of lysine ϵ-amino groups regulates aminoacyl-tRNA synthetase activity in Escherichia coli. J Biol Chem 2017; 292:10709-10722. [PMID: 28455447 DOI: 10.1074/jbc.m116.770826] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/16/2017] [Indexed: 11/06/2022] Open
Abstract
Previous proteomic analyses have shown that aminoacyl-tRNA synthetases in many organisms can be modified by acetylation of Lys. In this present study, leucyl-tRNA synthetase and arginyl-tRNA synthetase from Escherichia coli (EcLeuRS and EcArgRS) were overexpressed and purified and found to be acetylated on Lys residues by MS. Gln scanning mutagenesis revealed that Lys619, Lys624, and Lys809 in EcLeuRS and Lys126 and Lys408 in EcArgRS might play important roles in enzyme activity. Furthermore, we utilized a novel protein expression system to obtain enzymes harboring acetylated Lys at specific sites and investigated their catalytic activity. Acetylation of these Lys residues could affect their aminoacylation activity by influencing amino acid activation and/or the affinity for tRNA. In vitro assays showed that acetyl-phosphate nonenzymatically acetylates EcLeuRS and EcArgRS and suggested that the sirtuin class deacetylase CobB might regulate acetylation of these two enzymes. These findings imply a potential regulatory role for Lys acetylation in controlling the activity of aminoacyl-tRNA synthetases and thus protein synthesis.
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Affiliation(s)
- Qing Ye
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Quan-Quan Ji
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Wei Yan
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Fang Yang
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - En-Duo Wang
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and .,the School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
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29
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Ren J, Sang Y, Lu J, Yao YF. Protein Acetylation and Its Role in Bacterial Virulence. Trends Microbiol 2017; 25:768-779. [PMID: 28462789 DOI: 10.1016/j.tim.2017.04.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 12/13/2022]
Abstract
Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the protein acetyltransferase Pat, and nonenzymatically by metabolic intermediates (e.g., acetyl phosphate) in bacteria. Protein acetylation plays a role in bacterial chemotaxis, metabolism, DNA replication, and other cellular processes. Recently, accumulating evidence has suggested that protein acetylation might be involved in bacterial virulence because a number of bacterial virulence factors are acetylated. In this review, we summarize the progress in understanding bacterial protein acetylation and discuss how it mediates bacterial virulence.
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Affiliation(s)
- Jie Ren
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Sang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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30
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Li S, Zhang Q, Xu Z, Yao YF. Acetylation of Lysine 243 Inhibits the oriC Binding Ability of DnaA in Escherichia coli. Front Microbiol 2017; 8:699. [PMID: 28473824 PMCID: PMC5397419 DOI: 10.3389/fmicb.2017.00699] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/05/2017] [Indexed: 12/23/2022] Open
Abstract
DNA replication initiation is a central event in the cell cycle, and it is strictly controlled by multiple regulatory mechanisms. Our previous work showed that acetylation of residue lysine (K) 178 prevents DnaA from binding to ATP, which leads to the inhibition of DNA replication initiation. Here, we show that another residue, K243, is critical for DnaA full activity in vivo. K243 can be acetylated, and its acetylation level varies with cell growth. A homogeneous, recombinant DnaA that contains N𝜀-acetyllysine at K243 (K243Ac) retained its ATP/ADP binding ability, but showed decreased binding activity to the oriC region. A DNase I footprinting assay showed that DnaA K243Ac failed to recognize DnaA boxes I3, C1, and C3, and, thus, it formed an incomplete initiation complex with oriC. Finally, we found that acetyl phosphate and the deacetylase CobB can regulate the acetylation level of K243 in vivo. These findings suggest that DnaA K243 acetylation disturbs its binding to low-affinity DnaA boxes, and they provide new insights into the regulatory mechanisms of DNA replication initiation.
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Affiliation(s)
- Shuxian Li
- Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Qiufen Zhang
- Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, Shanghai Jiao Tong University School of MedicineShanghai, China.,Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of MedicineShanghai, China
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31
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Wei W, Liu T, Li X, Wang R, Zhao W, Zhao G, Zhao S, Zhou Z. Lysine acetylation regulates the function of the global anaerobic transcription factor FnrL in Rhodobacter sphaeroides. Mol Microbiol 2017; 104:278-293. [PMID: 28118511 DOI: 10.1111/mmi.13627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 01/04/2023]
Abstract
The metabolism of the purple non-sulfur bacterium Rhodobacter sphaeroides is versatile and it can grow under various conditions. Here, we report evidence that the anaerobic photosynthetic metabolism of R. sphaeroides is regulated by protein lysine acetylation. Using a proteomic approach, 59 acetylated peptides were detected. Among them is the global anaerobic transcription factor FnrL, which regulates the biosynthetic pathway of tetrapyrroles and synthesis of the photosynthetic apparatus. Lysine 223 of FnrL was identified as acetylated. We show that all three lysines in the DNA binding domain (K223, K213 and K175) of FnrL can be acetylated by acetyl-phosphate in vitro. A bacterial deacetylase homolog, RsCobB can deacetylate FnrL in vitro. The transcription of genes downstream of FnrL decreased when the DNA binding domain of FnrL was acetylated, as revealed by chromatin immunoprecipitation and acetylation-mimicking mutagenesis. An increasing number of acetylated lysines resulted in a further decrease in DNA binding ability. These results demonstrate that the lysine acetylation can fine tune the function of the oxygen-sensitive FnrL; thus, it might regulate anaerobic photosynthetic metabolism of R. sphaeroides.
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Affiliation(s)
- Wei Wei
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, 650091, China
| | - Xinfeng Li
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ruofan Wang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shimin Zhao
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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32
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Gu J, Chen Y, Guo H, Sun M, Yang M, Wang X, Zhang X, Deng J. Lysine acetylation regulates the activity of Escherichia coli pyridoxine 5'-phosphate oxidase. Acta Biochim Biophys Sin (Shanghai) 2017; 49:186-192. [PMID: 28039149 DOI: 10.1093/abbs/gmw129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 11/14/2022] Open
Abstract
Nɛ-lysine acetylation is one of the most abundant post-translational modifications in eukaryote and prokaryote. Protein acetylome of Escherichia coli has been screened using mass spectrometry (MS) technology, and many acetylated proteins have been identified, including the pyridoxine 5'-phosphate oxidase (EcPNPOx), but the biological roles played by lysine acetylation in EcPNPOx still remain unknown. In this study, EcPNPOx was firstly overexpressed and purified, and two acetylated lysine residues were identified by the subsequent liquid chromatography-tandem mass spectrometry analysis. Site-directed mutagenesis analysis demonstrated that acetylated lysine residues play important roles in the enzymatic activity and enzymatic properties of the protein. EcPNPOx could be non-enzymatically acetylated by acetyl-phosphate and deacetylated by CobB in vitro. Furthermore, enzymatic activities of acetylated and deacetylated EcPNPOx were compared in vitro, and results showed that acetylation led to a decrease of its enzymatic activity, which could be rescued by CobB deacetylation. Taken together, our data suggest that CobB modulates the enzymatic activity of EcPNPOx in vitro.
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Affiliation(s)
- Jing Gu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yuanyuan Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Huazhong Agricultural University, Wuhan 430070, China
| | - Hongsen Guo
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Huazhong Agricultural University, Wuhan 430070, China
| | - Manluan Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mingkun Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xude Wang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xian'en Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaoyu Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Qin R, Sang Y, Ren J, Zhang Q, Li S, Cui Z, Yao YF. The Bacterial Two-Hybrid System Uncovers the Involvement of Acetylation in Regulating of Lrp Activity in Salmonella Typhimurium. Front Microbiol 2016; 7:1864. [PMID: 27909434 PMCID: PMC5112231 DOI: 10.3389/fmicb.2016.01864] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/04/2016] [Indexed: 12/14/2022] Open
Abstract
N𝜀-lysine acetylation is an abundant and important Post-translational modification in bacteria. We used the bacterial two-hybrid system to screen the genome library of the Salmonella Typhimurium to identify potential proteins involved in acetyltransferase Pat - or deacetylase CobB-mediated acetylation. Then, the in vitro (de)acetylation assays were used to validate the potential targets, such as STM14_1074, NrdF, RhaR. Lrp, a leucine-responsive regulatory protein and global regulator, was shown to interact with Pat. We further demonstrate that Lrp could be acetylated by Pat and deacetylated by NAD+-dependent CobB in vitro. Specifically, the conserved lysine residue 36 (K36) in helix-turn-helix (HTH) DNA-binding domain of Lrp was acetylated. Acetylation of K36 impaired the function of Lrp through altering the affinity with the target promoter. The mutation of K36 in chromosome mimicking acetylation enhanced the transcriptional level of itself and attenuated the mRNA levels of Lrp-regulated genes including fimA, which was confirmed by yeast agglutination assay. These findings demonstrate that the acetylation regulates the DNA-binding activity of Lrp, suggesting that acetylation modification of transcription factors is a conserved regulatory manner to modulate gene expression in bacteria and eukaryotes.
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Affiliation(s)
- Ran Qin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Yu Sang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Jie Ren
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Qiufen Zhang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Shuxian Li
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of MedicineShanghai, China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of MedicineShanghai, China
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Kuczyńska-Wiśnik D, Moruno-Algara M, Stojowska-Swędrzyńska K, Laskowska E. The effect of protein acetylation on the formation and processing of inclusion bodies and endogenous protein aggregates in Escherichia coli cells. Microb Cell Fact 2016; 15:189. [PMID: 27832787 PMCID: PMC5105262 DOI: 10.1186/s12934-016-0590-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/03/2016] [Indexed: 12/21/2022] Open
Abstract
Background Acetylation of lysine residues is a reversible post-translational modification conserved from bacteria to humans. Several recent studies have revealed hundreds of lysine-acetylated proteins in various bacteria; however, the physiological role of these modifications remains largely unknown. Since lysine acetylation changes the size and charge of proteins and thereby may affect their conformation, we assumed that lysine acetylation can stimulate aggregation of proteins, especially for overproduced recombinant proteins that form inclusion bodies. Results To verify this assumption, we used Escherichia coli strains that overproduce aggregation-prone VP1GFP protein. We found that in ΔackA-pta cells, which display diminished protein acetylation, inclusion bodies were formed with a delay and processed faster than in the wild-type cells. Moreover, in ΔackA-pta cells, inclusion bodies exhibited significantly increased specific GFP fluorescence. In CobB deacetylase-deficient cells, in which protein acetylation was enhanced, the formation of inclusion bodies was increased and their processing was significantly inhibited. Similar results were obtained with regard to endogenous protein aggregates formed during the late stationary phase in ΔackA-pta and ΔcobB cells. Conclusions Our studies revealed that protein acetylation affected the aggregation of endogenous E. coli proteins and the yield, solubility, and biological activity of a model recombinant protein. In general, decreased lysine acetylation inhibited the formation of protein aggregates, whereas increased lysine acetylation stabilized protein aggregates. These findings should be considered during the designing of efficient strategies for the production of recombinant proteins in E. coli cells. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0590-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dorota Kuczyńska-Wiśnik
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - María Moruno-Algara
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Karolina Stojowska-Swędrzyńska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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Bernal V, Castaño-Cerezo S, Cánovas M. Acetate metabolism regulation in Escherichia coli: carbon overflow, pathogenicity, and beyond. Appl Microbiol Biotechnol 2016; 100:8985-9001. [DOI: 10.1007/s00253-016-7832-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022]
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Sun M, Guo H, Lu G, Gu J, Wang X, Zhang XE, Deng J. Lysine acetylation regulates the activity of Escherichia coli S-adenosylmethionine synthase. Acta Biochim Biophys Sin (Shanghai) 2016; 48:723-31. [PMID: 27421658 DOI: 10.1093/abbs/gmw066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/29/2016] [Indexed: 12/31/2022] Open
Abstract
Lysine acetylation is one of the most abundant post-translational modifications. However, physiological roles of this modification in bacteria are largely unknown. Previous protein acetylome analysis showed that Escherichia coli adenosylmethionine synthase (MAT) undergoes acetylation in vivo, but the biological functions of this modification still need to be uncovered. In this study, MAT of E. coli was over-expressed and purified. Subsequent mass spectrometry analysis showed that 12 lysine residues of the protein were acetylated. Site-directed mutagenesis analysis was performed and the results showed that acetylated lysine residues play important roles in the enzymatic activity of MAT. Next, deacetylation assay was performed by using CobB as the deacetylase, and the results showed that CobB could deacetylate MAT in vitro In addition, the enzymatic activities of acetylated and deacetylated MAT were compared in vitro, and results showed that acetylation led to a decrease in its enzymatic activity, which could be reversed by CobB deacetylation. Altogether, our data suggest that CobB modulates the enzymatic activity of E. coli MAT in vitro.
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Affiliation(s)
- Manluan Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hongsen Guo
- State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Lu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jing Gu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xude Wang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaoyu Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Abstract
Gene organization and control are described by models conceived in the 1960s. These models explain basic gene regulatory mechanisms and underpin current genome annotation. However, such models struggle to explain recent genome-scale observations. For example, accounts of RNA synthesis initiating within genes, widespread antisense transcription and non-canonical DNA binding by gene regulatory proteins are difficult to reconcile with traditional thinking. As a result, unexpected observations have often been dismissed and downstream consequences ignored. In this paper I will argue that, to fully understand the biology of bacterial chromosomes, we must embrace their hidden layers of complexity.
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Affiliation(s)
- David C Grainger
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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38
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Acetylation of Lysine 201 Inhibits the DNA-Binding Ability of PhoP to Regulate Salmonella Virulence. PLoS Pathog 2016; 12:e1005458. [PMID: 26943369 PMCID: PMC4778762 DOI: 10.1371/journal.ppat.1005458] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/25/2016] [Indexed: 12/21/2022] Open
Abstract
The two-component system PhoP-PhoQ is highly conserved in bacteria and regulates virulence in response to various signals for bacteria within the mammalian host. Here, we demonstrate that PhoP could be acetylated by Pat and deacetylated by deacetylase CobB enzymatically in vitro and in vivo in Salmonella Typhimurium. Specifically, the conserved lysine residue 201(K201) in winged helix-turn-helix motif at C-terminal DNA-binding domain of PhoP could be acetylated, and its acetylation level decreases dramatically when bacteria encounter low magnesium, acid stress or phagocytosis of macrophages. PhoP has a decreased acetylation and increased DNA-binding ability in the deletion mutant of pat. However, acetylation of K201 does not counteract PhoP phosphorylation, which is essential for PhoP activity. In addition, acetylation of K201 (mimicked by glutamine substitute) in S. Typhimurium causes significantly attenuated intestinal inflammation as well as systemic infection in mouse model, suggesting that deacetylation of PhoP K201 is essential for Salmonella pathogenesis. Therefore, we propose that the reversible acetylation of PhoP K201 may ensure Salmonella promptly respond to different stresses in host cells. These findings suggest that reversible lysine acetylation in the DNA-binding domain, as a novel regulatory mechanism of gene expression, is involved in bacterial virulence across microorganisms.
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39
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A novel family of bacterial protein deacetylases. Nat Rev Microbiol 2016. [DOI: 10.1038/nrmicro.2016.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Clark LF, Kodadek T. And then there were two. eLife 2015; 4. [PMID: 26716612 PMCID: PMC4744185 DOI: 10.7554/elife.12724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 11/26/2015] [Indexed: 11/22/2022] Open
Abstract
A second enzyme that removes acetyl groups from lysine residues in E. coli been discovered and represents the founding member of a new enzyme family.
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Affiliation(s)
- Lorraine F Clark
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Jupiter, United States
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