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Xu X, Wang T, Niu Y, Liang K, Yang Y. The ubiquitin-like modification by ThiS and ThiF in Escherichia coli. Int J Biol Macromol 2019; 141:351-357. [PMID: 31442507 DOI: 10.1016/j.ijbiomac.2019.08.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/22/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
Abstract
Escherichia coli, one of the most well-studied gram-negative bacterial species, encodes two ubiquitin-like proteins (UBLs), ThiS and MoaD. The studies on prokaryotic UBLs such as Pup, and small archaeal modifier protein have revealed the function of UBLs. However, in gram-negative bacteria, the functions of UBLs in protein modification are still poorly understood to date. Here, we report that ThiS, which has a β-grasp fold and carboxy-terminal diglycine motif similar to ubiquitin, is able to form protein conjugates in vivo and in vitro. We also constructed in vitro ThiS conjugation (thisylation) system and identified the modified lysine sites by MS/MS, this provides an essential platform for studying the UBLs thisylation system in E. coli. The modification system is dependent on lysine 83 (ATPase activity site) and cysteine 169 (zinc binding site) in ThiF and three important substrates, GroEL, PriC, FtsA, were found to be covalently modified by this system in vitro. Taken together, this study provided evidence that the protein conjugation function of β-grasp fold UBLs is conserved in the three major evolutionary lineages of life.
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Affiliation(s)
- Xibing Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; Medical College, Henan University of Science and Technology, Luoyang 471000, China
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yulong Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Ke Liang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
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2
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Abstract
The small protein ubiquitin and its multiple polymers are encountered free in cells and as post-translational modifications on all proteins. Different polyubiquitin three dimensional structures are shown to correlate uniquely with different cellular functions as part of the diverse ubiquitin signaling. At the same time, this multiplicity of structures provides serious challenges to the analytical biochemist. Globally applicable strategies are presented here for the analyses of polyubiquitins and of ubiquitinated proteins, which take advantage of the speed, specificity and sensitivity of top-down tandem mass spectrometry. Particular attention is given to the supervised interpretation of fragmentation as revealed in the MS/MS spectra of these branched proteins. The strategy is compatible with any MS activation technology, is applicable to all polyubiquitin linkage and chain types, can be extended to ubiquitin-like proteins, and will be compatible with and enhanced by continuing advances in LC-MS/MS instrumentation and interpretation software.
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Affiliation(s)
- Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States
| | - Amanda E Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States.
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Characterization of the Sinorhizobium meliloti HslUV and ClpXP Protease Systems in Free-Living and Symbiotic States. J Bacteriol 2019; 201:JB.00498-18. [PMID: 30670545 DOI: 10.1128/jb.00498-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
Symbiotic nitrogen fixation (SNF) in the interaction between the soil bacteria Sinorhizobium meliloti and legume plant Medicago sativa is carried out in specialized root organs called nodules. During nodule development, each symbiont must drastically alter their proteins, transcripts, and metabolites in order to support nitrogen fixation. Moreover, bacteria within the nodules are under stress, including challenges by plant antimicrobial peptides, low pH, limited oxygen availability, and strongly reducing conditions, all of which challenge proteome integrity. S. meliloti stress adaptation, proteome remodeling, and quality control are controlled in part by the large oligomeric protease complexes HslUV and ClpXP1. To improve understanding of the roles of S. meliloti HslUV and ClpXP1 under free-living conditions and in symbiosis with M. sativa, we generated ΔhslU, ΔhslV, ΔhslUV, and ΔclpP1 knockout mutants. The shoot dry weight of M. sativa plants inoculated with each deletion mutant was significantly reduced, suggesting a role in symbiosis. Further, slower free-living growth of the ΔhslUV and ΔclpP1 mutants suggests that HslUV and ClpP1 were involved in adapting to heat stress, the while ΔhslU and ΔclpP1 mutants were sensitive to kanamycin. All deletion mutants produced less exopolysaccharide and succinoglycan, as shown by replicate spot plating and calcofluor binding. We also generated endogenous C-terminal enhanced green fluorescent protein (eGFP) fusions to HslU, HslV, ClpX, and ClpP1 in S. meliloti Using anti-eGFP antibodies, native coimmunoprecipitation experiments with proteins from free-living and nodule tissues were performed and analyzed by mass spectrometry. The results suggest that HslUV and ClpXP were closely associated with ribosomal and proteome quality control proteins, and they identified several novel putative protein-protein interactions.IMPORTANCE Symbiotic nitrogen fixation (SNF) is the primary means by which biologically available nitrogen enters the biosphere, and it is therefore a critical component of the global nitrogen cycle and modern agriculture. SNF is the result of highly coordinated interactions between legume plants and soil bacteria collectively referred to as rhizobia, e.g., Medicago sativa and S. meliloti, respectively. Accomplishing SNF requires significant proteome changes in both organisms to create a microaerobic environment suitable for high-level bacterial nitrogenase activity. The bacterial protease systems HslUV and ClpXP are important in proteome quality control, in metabolic remodeling, and in adapting to stress. This work shows that S. meliloti HslUV and ClpXP are involved in SNF, in exopolysaccharide production, and in free-living stress adaptation.
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Potential Applications of the Escherichia coli Heat Shock Response in Synthetic Biology. Trends Biotechnol 2018; 36:186-198. [DOI: 10.1016/j.tibtech.2017.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/20/2017] [Accepted: 10/20/2017] [Indexed: 01/06/2023]
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BAH1 an E3 Ligase from Arabidopsis thaliana Stabilizes Heat Shock Factor σ 32 of Escherichia coli by Interacting with DnaK/DnaJ Chaperone Team. Curr Microbiol 2017; 75:450-455. [PMID: 29260303 DOI: 10.1007/s00284-017-1401-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
In Escherichia coli, the DnaK/DnaJ chaperone can control the stability and activity of σ32, which is the key factor in heat shock response. Heterologous expression of eukaryotic molecular chaperones protects E. coli from heat stress. Here, we show that BAH1, an E3 ligase from plant that has a similar zinc finger domain to DnaJ, can perform block the effect of DnaK on σ32 in Escherichia coli. By constructing a chimeric DnaJ protein, with the J-domain of DnaJ fused to BAH1, we found BAH1 could partially compensate for the DnaJ' zinc finger domain in vivo, and that it was dependent on the zinc finger domain of BAH1. Furthermore, BAH1 could interact with both σ32 and DnaK to increase the level of HSPs, such as GroEL, DnaK, and σ32. These results suggested that the zinc finger domain was conserved during evolution.
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Plant E3 ligases ubiquitinate Escherichia coli σ 32in vitro. Biochem Biophys Res Commun 2017; 490:1232-1236. [PMID: 28676399 DOI: 10.1016/j.bbrc.2017.06.198] [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: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 11/23/2022]
Abstract
Ubiquitin-like proteins (UBLs) are extremely well-conserved among eukaryotes and prokaryotes allowing interactions between proteins from different organisms. For example, the prokaryotic ubiquitin-like proteins (Pups) and the Proteasome accessory factor A (PafA) of Mycobacterium tuberculosis are sufficient to pupylate at least 51 Escherichia coli proteins. This work shows that the plant E3 ligases BnTR1 and AT1G02860 can ubiquitinate E. coli σ32, but not Hsp70 DnaK in vitro. Molecular biology and biochemical studies confirm that the RING finger domain of BnTR1 and AT1G02860 is essential for their function. These results suggest that the substrates of plant E3 ligases can be prokaryotic protein and therefore the plant ubiquitylation system may have evolved from prokaryote.
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Bittner LM, Arends J, Narberhaus F. When, how and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli. Biol Chem 2017; 398:625-635. [PMID: 28085670 DOI: 10.1515/hsz-2016-0302] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/09/2017] [Indexed: 11/15/2022]
Abstract
Cellular proteomes are dynamic and adjusted to permanently changing conditions by ATP-fueled proteolytic machineries. Among the five AAA+ proteases in Escherichia coli FtsH is the only essential and membrane-anchored metalloprotease. FtsH is a homohexamer that uses its ATPase domain to unfold and translocate substrates that are subsequently degraded without the need of ATP in the proteolytic chamber of the protease domain. FtsH eliminates misfolded proteins in the context of general quality control and properly folded proteins for regulatory reasons. Recent trapping approaches have revealed a number of novel FtsH substrates. This review summarizes the substrate diversity of FtsH and presents details on the surprisingly diverse recognition principles of three well-characterized substrates: LpxC, the key enzyme of lipopolysaccharide biosynthesis; RpoH, the alternative heat-shock sigma factor and YfgM, a bifunctional membrane protein implicated in periplasmic chaperone functions and cytoplasmic stress adaptation.
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Affiliation(s)
- Lisa-Marie Bittner
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
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Schumann W. Regulation of bacterial heat shock stimulons. Cell Stress Chaperones 2016; 21:959-968. [PMID: 27518094 PMCID: PMC5083672 DOI: 10.1007/s12192-016-0727-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 11/28/2022] Open
Abstract
All organisms developed genetic programs to allow their survival under stressful conditions. In most cases, they increase the amount of a specific class of proteins which deal with the stress factor and allow cells to adapt to life-threatening conditions. One class of stress proteins are the heat shock proteins (HSPs) the amount of which is significantly increased after a sudden temperature rise. How is the heat shock response (HSR) regulated in bacteria? This has been studied in detail in Escherichia coli, Bacillus subtilis and Streptomyces spp. Two major mechanisms have been described so far to regulate expression of the HSGs, namely alternative sigma factors and transcriptional repressors. This review focuses on the regulatory details of the different heat shock regulons in the three well-studied bacterial species.
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Affiliation(s)
- Wolfgang Schumann
- Institute of Genetics, University of Bayreuth, 95440, Bayreuth, Germany.
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Xu X, Niu Y, Liang K, Shen G, Cao Q, Yang Y. Analysis of pupylation of Streptomyces hygroscopicus 5008 in vitro. Biochem Biophys Res Commun 2016; 474:126-130. [PMID: 27105915 DOI: 10.1016/j.bbrc.2016.04.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 11/30/2022]
Abstract
Prokaryotic ubiquitin-like protein (Pup) is a post-translational modifier that can be attached to substrate proteins in Actinobacteria. The modification process is defined as pupylation and is associated with proteasome-mediated protein degradation in mycobacteria and streptomycetes. Here, we report the pupylation of Streptomyces hygroscopicus 5008 in vitro. Each component of the Pup system was expressed in Escherichia coli and poly-Pup chains were observed by western blot analysis. Though only one potential Pup substrate (SHJG_3659) was identified using MS/MS, we verified this candidate and other predicted substrates by a reconstituted Pup system in E. coli. In addition, we discuss the depupylation activity of Dop (a Pup activation enzyme). The results presented here show that pupylation exists in S. hygroscopicus and that a reconstituted Pup system can function in vitro in a heterologous host.
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Affiliation(s)
- Xibing Xu
- College of Medicine, Henan University of Science and Technology, Luoyang 471000, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yulong Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Ke Liang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Guomin Shen
- College of Medicine, Henan University of Science and Technology, Luoyang 471000, China
| | - Qing Cao
- College of Medicine, Henan University of Science and Technology, Luoyang 471000, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
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Abstract
The metabolic syndrome (MetS) is comprised of a cluster of closely related risk factors, including visceral adiposity, insulin resistance, hypertension, high triglyceride, and low high-density lipoprotein cholesterol; all of which increase the risk for the development of type 2 diabetes and cardiovascular disease. A chronic state of inflammation appears to be a central mechanism underlying the pathophysiology of insulin resistance and MetS. In this review, we summarize recent research which has provided insight into the mechanisms by which inflammation underlies the pathophysiology of the individual components of MetS including visceral adiposity, hyperglycemia and insulin resistance, dyslipidemia, and hypertension. On the basis of these mechanisms, we summarize therapeutic modalities to target inflammation in the MetS and its individual components. Current therapeutic modalities can modulate the individual components of MetS and have a direct anti-inflammatory effect. Lifestyle modifications including exercise, weight loss, and diets high in fruits, vegetables, fiber, whole grains, and low-fat dairy and low in saturated fat and glucose are recommended as a first line therapy. The Mediterranean and dietary approaches to stop hypertension diets are especially beneficial and have been shown to prevent development of MetS. Moreover, the Mediterranean diet has been associated with reductions in total and cardiovascular mortality. Omega-3 fatty acids and peroxisome proliferator-activated receptor α agonists lower high levels of triglyceride; their role in targeting inflammation is reviewed. Angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and aldosterone blockers comprise pharmacologic therapies for hypertension but also target other aspects of MetS including inflammation. Statin drugs target many of the underlying inflammatory pathways involved in MetS.
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Affiliation(s)
- Francine K Welty
- Division of Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Mass.
| | - Abdulhamied Alfaddagh
- Division of Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Mass
| | - Tarec K Elajami
- Division of Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Mass
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