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Fan D, Cao S, Zhou Q, Zhang Y, Yue L, Han C, Yang B, Wang Y, Ma Z, Zhu L, Liu C. Exploring the roles of substrate-binding surface of the chaperone site in the chaperone activity of trigger factor. FASEB J 2018; 32:fj201701576. [PMID: 29906241 DOI: 10.1096/fj.201701576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Trigger factor (TF) is a key component of the prokaryotic chaperone network, which is involved in many basic cellular processes, such as protein folding, protein trafficking, and ribosome assembly. The major chaperone site of TF has a cradle-like structure in which protein substrate may fold without interference from other proteins. Here, we investigated in vivo and in vitro the roles of hydrophobic and charged patches on the edge and interior of cradle during TF-assisted protein folding. Our results showed that most of the surface of the cradle was involved in TF-assisted protein folding, which was larger than found in early studies. Although the inner surface of cradle was mostly hydrophobic, both hydrophobic and electrostatic patches were indispensable for TF to facilitate correct protein folding. However, hydrophobic patches were more important for the antiaggregation activity of TF. Furthermore, it was found that the patches on the surface of cradle were involved in TF-assisted protein folding in a spatial and temporal order. These results suggest that the folding-favorable interface between the cradle and substrate was dynamic during TF-assisted protein folding, which enabled TF to be involved in the folding of substrate in an aggressive manner rather than acting as a classic holdase.-Fan, D., Cao, S., Zhou, Q., Zhang, Y., Yue, L., Han, C., Yang, B., Wang, Y., Ma, Z., Zhu, L., Liu, C. Exploring the roles of substrate-binding surface of chaperone site in the chaperone activity of trigger factor.
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Affiliation(s)
- Dongjie Fan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shunan Cao
- Key Laboratory for Polar Science, State Ocean Administration, Polar Research Institute of China, Shanghai, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- ChosenMed Technology Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, China
| | - You Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lei Yue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Chang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Bo Yang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Yu Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhuo Ma
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lingxiang Zhu
- National Research Institute for Family Planning (NRIFP), Beijing, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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Fan D, Zhou Q, Liu C, Zhang J. Functional characterization of the Helicobacter pylori chaperone protein HP0795. Microbiol Res 2016; 193:11-19. [PMID: 27825478 DOI: 10.1016/j.micres.2016.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/09/2016] [Accepted: 08/20/2016] [Indexed: 12/12/2022]
Abstract
Trigger factor (TF) is one of the multiple bacterial chaperone proteins interacting with nascent peptides and facilitating their folding in bacteria. While TF is well-characterized in E. coli, HP0795, a TF-like homologue gene identified earlier in the pathogenic Helicobacter pylori (H. pylori), has not been studied biochemically to date. To characterize its function as a chaperone, we performed 3D-modeling, cross-linking and in vitro enzyme assays to HP0795 in vitro. Our results show that HP0795 possesses peptidyl prolyl cis-trans isomerase activity and exhibits a dimeric structure in solution. In addition, stable expression of HP0795 in a series of well-characterized E. coli chaperone-deficient strains rescued the growth defects in these mutants. Furthermore, we showed that the presence of HP0795 greatly reduced protein aggregation caused by deficiencies of chaperones in these strains. In contrast to other chaperone genes in H. pylori, gene expression of HP0795 displays little induction under acidic pH conditions. Together, our results suggest that HP0795 is a constitutively expressed TF-like protein of the prokaryotic chaperone family that may not play a major role in acid response. Given the pathogenic properties of H. pylori, our insights might provide new avenues for potential future medical intervention for H. pylori-related conditions.
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Affiliation(s)
- Dongjie Fan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin, 150080, China; Beijing CapitalBio MedLab, 88 D2, Branch Six Street, Economic and Technological Development Zone, Beijing 101111, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin, 150080, China
| | - Jianzhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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Fan D, Liu C, Liu L, Zhu L, Peng F, Zhou Q. Large-scale gene expression profiling reveals physiological response to deletion of chaperone dnaKJ in Escherichia coli. Microbiol Res 2016; 186-187:27-36. [PMID: 27242140 DOI: 10.1016/j.micres.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 11/18/2022]
Abstract
Chaperone DnaK and its co-chaperone DnaJ plays various essential roles such as in assisting in the folding of nascent peptides, preventing protein aggregation and maintaining cellular protein homeostasis. Global transcriptional changes in vivo associated with deletion of dnaKJ were monitored using DNA microarray to elucidate the role of DnaKJ at the transcriptional level. Microarray profiling and bioinformatics analysis revealed that a few chaperone and protease genes, stress-related genes and genes involved in the tricarboxylic acid cycle and oxidative phosphorylation were up-regulated, whereas various transporter genes, pentose phosphate pathway and transcriptional regulation related genes were down-regulated. This study is the first to systematically analyze the alterations at the transcriptional level in vivo in deletion of dnaKJ. Fatty acid methyl esters analysis indicated that the amount of unsaturated fatty acid sharply increased and subcellular location prediction analysis showed a marked decrease in transcription of inner-membrane protein genes, which might have triggered the development of aberrant cell shape and susceptibility for some antibiotics in the ΔdnaKJ strain.
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Affiliation(s)
- Dongjie Fan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin 150080, China.
| | - Lushan Liu
- Department of Emergency, Beijing Bo'ai Hospital, 10 Jiaomen North Road, Fengtai District, Beijing, 100068, China; China Rehabilitation Research Center, Capital Medical University, Beijing 100068, China
| | - Lingxiang Zhu
- National Research Institute for Family Planning (NRIFP), Beijing 100081, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan430072, China; Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan 430072, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin 150080, China.
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Thakker C, Lin K, Martini-Stoica H, Bennett GN. Use of transposase and ends of IS608 enables precise and scarless genome modification for modulating gene expression and metabolic engineering applications in Escherichia coli. Biotechnol J 2015; 11:80-90. [PMID: 26282057 DOI: 10.1002/biot.201500205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 06/24/2015] [Accepted: 08/14/2015] [Indexed: 11/11/2022]
Abstract
Various methods have been developed for gene disruption in bacteria; however, extra in vitro manipulation steps or the residual presence of a scar in the host chromosome limits the use of such methods. By utilizing the unique properties of ISHp608, we have developed a simple and precise method for genome manipulation in Escherichia coli that alters the gene sequence without leaving foreign DNA in the chromosome. This strategy involves PCR amplification of a DNA cassette containing ISHp608-LE (left end)-antibiotic resistance gene-counterselection marker-ISHp608-RE (right end) by using primers containing extensions homologous to the adjacent regions of the target gene on the chromosome. The λ Red mediated recombination of the PCR product and antibiotic resistance screening results in transformants with a modified gene target. The ISHp608-LE-antibiotic resistance gene-counterselection marker-ISHp608-RE cassette can then be excised using a temperature sensitive plasmid expressing the TnpA transposase, which precisely cleaves ISHp608-LE and ISHp608-RE without leaving a scar sequence. We demonstrated lacZ gene point mutation repair, two precise disruptions of the lacZ gene and constructed a library of lacZ variants having variable β-galactosidase activity by changing its ribosome binding site sequences using the ISHp608 system. This technique can be used in E. coli genome modification and could be extended for use in other bacteria.
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Affiliation(s)
- Chandresh Thakker
- Department of BioSciences, Rice University, Houston, TX, USA.,TOTAL New Energies USA, Inc., Emeryville, CA, USA
| | - Kevin Lin
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Heidi Martini-Stoica
- Department of BioSciences, Rice University, Houston, TX, USA.,Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
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The DNA-Binding Protein from Starved Cells (Dps) Utilizes Dual Functions To Defend Cells against Multiple Stresses. J Bacteriol 2015. [PMID: 26216848 DOI: 10.1128/jb.00475-15] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Bacteria deficient in the DNA-binding protein from starved cells (Dps) are viable under controlled conditions but show dramatically increased mortality rates when exposed to any of a wide range of stresses, including starvation, oxidative stress, metal toxicity, or thermal stress. It remains unclear whether the protective action of Dps against specific stresses derives from its DNA-binding activity, which may exclude destructive agents from the chromosomal region, or its ferroxidase activity, which neutralizes and sequesters potentially damaging chemical species. To resolve this question, we have identified the critical residues of Escherichia coli Dps that bind to DNA and modulate iron oxidation. We uncoupled the biochemical activities of Dps, creating Dps variants and mutant E. coli strains that are defective in either DNA-binding or ferroxidase activity. Quantification of the contribution of each activity to the protection of DNA integrity and cellular viability revealed that both activities of Dps are required in order to counteract many differing stresses. These findings demonstrate that Dps plays a multipurpose role in stress protection via its dual activities, explaining how Dps can be of vital importance to bacterial viability over a wide range of stresses. IMPORTANCE The DNA-binding protein from starved cells (Dps) protects bacterial cells against many different types of stressors. We find that DNA binding and iron oxidation by Dps are performed completely independently of each other. Both biochemical activities are required to protect E. coli against stressors, as well as to protect DNA from oxidative damage in vitro. These results suggest that many stressors may cause both oxidative stress and direct DNA damage.
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Markerless Deletion System for Escherichia coli Using Short Homologous Sequences and Positive-Negative Selectable Cassette. Appl Biochem Biotechnol 2015; 176:1472-81. [PMID: 25957274 DOI: 10.1007/s12010-015-1658-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
Abstract
Red homologous recombination has been extensively used in recombineering. Because foreign sequences, such as antibiotic resistance genes, FRT-sites, or loxP-sites, are often unwanted in mutant Escherichia coli, we established a markerless deletion system containing short homologous sequences, a positive-selectable marker (kan), and a negative-selectable marker (sacB) for E. coli. For markerless deletion of a specific region of the E. coli genome, a two-step recombination procedure using two different PCR fragments, which were amplified from pUC57-kan-sacB and pUC57-298, was performed. The generation of a pheA-tyrA deficient mutant demonstrated that this markerless deletion system was a simple and efficient method to generate markerless chromosomal deletions in E. coli.
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Madyagol M, Al-Alami H, Levarski Z, Drahovská H, Turňa J, Stuchlík S. Gene replacement techniques for Escherichia coli genome modification. Folia Microbiol (Praha) 2011; 56:253-63. [PMID: 21614539 DOI: 10.1007/s12223-011-0035-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/04/2011] [Indexed: 11/24/2022]
Abstract
The subject of this review covers modern experimental procedures for chromosomal gene replacement in Escherichia coli and related bacteria, which enable the specific substitution of targeted genome sequences with copies of those carrying defined mutations. Two principal methods for gene replacement were established. The first "in-out" method is based on integration of plasmid into bacterial chromosome and subsequent resolving of the cointegrate. The "linear fragment" method (recombineering) is based on homologous recombination mediated by short homology arms at the ends of linear DNA molecule. Many new protocols and improvements in targeted gene replacement were introduced during the last 10 years. These methods are well suited for high-throughput functional gene studies and for many biotechnological applications.
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Affiliation(s)
- Mahesh Madyagol
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 842 15, Bratislava, Slovak Republic
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Efficient gene disruption in Saccharomyces cerevisiae using marker cassettes with long homologous arms prepared by the restriction-free cloning strategy. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0756-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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