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Wen Y, Tang C, Shen Q, Dong S, Wang Y, Li Y, Shao S. An efficient ratiometric fluorescence and colorimetric dual-mode probe for convenient determination of nitrite in real samples and E. coli. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 38973349 DOI: 10.1039/d4ay00417e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Developing an effective and convenient nitrite detection method is indispensable in food safety, environmental monitoring, clinical diagnosis of diseases, and many other areas. Herein, a dicyanoisophorone derivative, TMN-NH2 with large Stokes shift and near-infrared (NIR) emission, was proposed as a ratiometric fluorescence and colorimetric dual-mode probe for the rapid determination of NO2- in acidic media, showing excellent selectivity and high sensitivity. The sensing mechanism is based on the diazotization of TMN-NH2 with NO2- and subsequent diazonium salt hydrolysis to form a hydroxyl-substituted product (TMN-OH). Under the optimized conditions of reaction and detection, a new quantitative analysis method based on TMN-NH2 was established for NO2- detection, exhibiting good linear relationships to NO2- in the range of 0.5 to 15 μM with practical detection limits of 26.6 nM and 17.6 nM for the colorimetric and fluorescent readout, respectively. The quantitative detection of NO2- in real samples demonstrated satisfactory recoveries and repeatability. Moreover, TMN-NH2 was successfully applied for monitoring NO2- in Escherichia coli by confocal fluorescence imaging.
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Affiliation(s)
- Yujie Wen
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Cong Tang
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qing Shen
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shuqing Dong
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Yaya Wang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Yunchun Li
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Shijun Shao
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
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Thapliyal C, Mishra R. The Chaperone-Active State of HdeB at pH 4 Arises from Its Conformational Rearrangement and Enhanced Stability Instead of Surface Hydrophobicity. Biochemistry 2024; 63:1147-1161. [PMID: 38640496 DOI: 10.1021/acs.biochem.4c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
HdeA and HdeB are dimeric ATP-independent acid-stress chaperones, which protect the periplasmic proteins of enteric bacteria at pH 2.0 and 4.0, respectively, during their passage through the acidic environment of the mammalian stomach. Despite being structurally similar, they exhibit distinct functional pH optima and conformational prerequisite for their chaperone action. HdeA undergoes a dimer-to-monomer transition at pH 2.0, whereas HdeB remains dimeric at pH 4.0. The monomerization of HdeA exposes its hydrophobic motifs, which facilitates its interaction with the partially folded substrates. How HdeB functions despite maintaining its dimeric conformation has been poorly elucidated in the literature. Herein, we characterized the conformational states and stability of HdeB at its physiologically relevant pH and compared the data with those of HdeA. At pH 4.0, HdeB exhibited distinct spectroscopic signatures and higher stability against heat and guanidine-HCl-induced denaturation than at pH 7.5. We affirm that the pH 4.0 conformer of HdeB was distinct from that at pH 7.5 and that these two conformational states were hierarchically unrelated. Salt-bridge mutations that perturbed HdeB's intersubunit interactions resulted in the loss of its stability and function at pH 4.0. In contrast, mutations affecting intrasubunit interactions enhanced its function, albeit with a reduction in stability. These findings suggest that, unlike HdeA, HdeB acts as a noncanonical chaperone, where pH-dependent stability and conformational rearrangement at pH 4.0 play a core role in its chaperone function rather than its surface hydrophobicity. Such rearrangement establishes a stability-function trade-off that allows HdeB to function while maintaining its stable dimeric state.
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Affiliation(s)
- Charu Thapliyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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Dubinkina V, Bhogale S, Hsieh PH, Dibaeinia P, Nambiar A, Maslov S, Yoshikuni Y, Sinha S. A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains. Microbiol Spectr 2024; 12:e0253623. [PMID: 38018981 PMCID: PMC10783018 DOI: 10.1128/spectrum.02536-23] [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: 06/16/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Issatchenkia orientalis is a promising industrial chassis to produce biofuels and bioproducts due to its high tolerance to multiple environmental stresses such as low pH, heat, and other chemicals otherwise toxic for the most widely used microbes. Yet, little is known about specific mechanisms of such tolerance in this organism, hindering our ability to engineer this species to produce valuable biochemicals. Here, we report a comprehensive study of the mechanisms of acidic tolerance in this species via transcriptome profiling across variable pH for 12 different strains with different phenotypes. We found multiple regulatory mechanisms involved in tolerance to low pH in different strains of I. orientalis, marking potential targets for future gene editing and perturbation experiments.
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Affiliation(s)
- Veronika Dubinkina
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA
| | - Shounak Bhogale
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Ping-Hung Hsieh
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Payam Dibaeinia
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Ananthan Nambiar
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Yasuo Yoshikuni
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Saurabh Sinha
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical Engineering at Georgia Tech and Emory University, Atlanta, Georgia, USA
- Department of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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4
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Zhang R, Wang Y. EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance. Appl Environ Microbiol 2023; 89:e0157723. [PMID: 38019025 PMCID: PMC10734491 DOI: 10.1128/aem.01577-23] [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] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE EvgS/EvgA, one of the five unorthodox two-component systems in Escherichia coli, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.
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Affiliation(s)
- Ruizhen Zhang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yan Wang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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5
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Zeng S, Liu X, Kafuti YS, Kim H, Wang J, Peng X, Li H, Yoon J. Fluorescent dyes based on rhodamine derivatives for bioimaging and therapeutics: recent progress, challenges, and prospects. Chem Soc Rev 2023; 52:5607-5651. [PMID: 37485842 DOI: 10.1039/d2cs00799a] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Since their inception, rhodamine dyes have been extensively applied in biotechnology as fluorescent markers or for the detection of biomolecules owing to their good optical physical properties. Accordingly, they have emerged as a powerful tool for the visualization of living systems. In addition to fluorescence bioimaging, the molecular design of rhodamine derivatives with disease therapeutic functions (e.g., cancer and bacterial infection) has recently attracted increased research attention, which is significantly important for the construction of molecular libraries for diagnostic and therapeutic integration. However, reviews focusing on integrated design strategies for rhodamine dye-based diagnosis and treatment and their wide application in disease treatment are extremely rare. In this review, first, a brief history of the development of rhodamine fluorescent dyes, the transformation of rhodamine fluorescent dyes from bioimaging to disease therapy, and the concept of optics-based diagnosis and treatment integration and its significance to human development are presented. Next, a systematic review of several excellent rhodamine-based derivatives for bioimaging, as well as for disease diagnosis and treatment, is presented. Finally, the challenges in practical integration of rhodamine-based diagnostic and treatment dyes and the future outlook of clinical translation are also discussed.
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Affiliation(s)
- Shuang Zeng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Xiaosheng Liu
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Yves S Kafuti
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Heejeong Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea.
| | - Jingyun Wang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
| | - Haidong Li
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
- Provincial Key Laboratory of Interdisciplinary Medical Engineering for Gastrointestinal Carcinoma, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, Liaoning 110042, China
| | - Juyoung Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea.
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Jia YL, Li J, Nong FT, Yan CX, Ma W, Zhu XF, Zhang LH, Sun XM. Application of Adaptive Laboratory Evolution in Lipid and Terpenoid Production in Yeast and Microalgae. ACS Synth Biol 2023; 12:1396-1407. [PMID: 37084707 DOI: 10.1021/acssynbio.3c00179] [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: 04/23/2023]
Abstract
Due to the complexity of metabolic and regulatory networks in microorganisms, it is difficult to obtain robust phenotypes through artificial rational design and genetic perturbation. Adaptive laboratory evolution (ALE) engineering plays an important role in the construction of stable microbial cell factories by simulating the natural evolution process and rapidly obtaining strains with stable traits through screening. This review summarizes the application of ALE technology in microbial breeding, describes the commonly used methods for ALE, and highlights the important applications of ALE technology in the production of lipids and terpenoids in yeast and microalgae. Overall, ALE technology provides a powerful tool for the construction of microbial cell factories, and it has been widely used in improving the level of target product synthesis, expanding the range of substrate utilization, and enhancing the tolerance of chassis cells. In addition, in order to improve the production of target compounds, ALE also employs environmental or nutritional stress strategies corresponding to the characteristics of different terpenoids, lipids, and strains.
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Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Jin Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Fang-Tong Nong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Chun-Xiao Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Wang Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiao-Feng Zhu
- College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Li-Hui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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7
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Xu J, Guo L, Zhao N, Meng X, Zhang J, Wang T, Wei X, Fan M. Response mechanisms to acid stress of acid-resistant bacteria and biotechnological applications in the food industry. Crit Rev Biotechnol 2023; 43:258-274. [PMID: 35114869 DOI: 10.1080/07388551.2021.2025335] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Acid-resistant bacteria are more and more widely used in industrial production due to their unique acid-resistant properties. In order to survive in various acidic environments, acid-resistant bacteria have developed diverse protective mechanisms such as sensing acid stress and signal transduction, maintaining intracellular pH homeostasis by controlling the flow of H+, protecting and repairing biological macromolecules, metabolic modification, and cross-protection. Acid-resistant bacteria have broad biotechnological application prospects in the food field. The production of fermented foods with high acidity and acidophilic enzymes are the main applications of this kind of bacteria in the food industry. Their acid resistance modules can also be used to construct acid-resistant recombinant engineering strains for special purposes. However, they can also cause negative effects on foods, such as spoilage and toxicity. Herein, the aim of this paper is to summarize the research progress of molecular mechanisms against acid stress of acid-resistant bacteria. Moreover, their effects on the food industry were also discussed. It is useful to lay a foundation for broadening our understanding of the physiological metabolism of acid-resistant bacteria and better serving the food industry.
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Affiliation(s)
- Junnan Xu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Li Guo
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Ning Zhao
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Xuemei Meng
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Jie Zhang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Tieru Wang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
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8
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Jroundi F, Povedano-Priego C, Pinel-Cabello M, Descostes M, Grizard P, Purevsan B, Merroun ML. Evidence of microbial activity in a uranium roll-front deposit: Unlocking their potential role as bioenhancers of the ore genesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160636. [PMID: 36464038 DOI: 10.1016/j.scitotenv.2022.160636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) roll-front deposits constitute a valuable source for an economical extraction by in situ recovery (ISR) mining. Such technology may induce changes in the subsurface microbiota, raising questions about the way their activities could build a functional ecosystem in such extreme environments (i.e.: oligotrophy and high SO4 concentration and salinity). Additionally, more information is needed to dissipate the doubts about the microbial role in the genesis of such U orebodies. A U roll-front deposit hosted in an aquifer driven system (in Zoovch Ovoo, Mongolia), intended for mining by acid ISR, was previously explored and showed to be governed by a complex bacterial diversity, linked to the redox zonation and the geochemical conditions. Here for the first time, transcriptional activities of microorganisms living in such U ore deposits are determined and their metabolic capabilities allocated in the three redox-inherited compartments, naturally defined by the roll-front system. Several genes encoding for crucial metabolic pathways demonstrated a strong biological role controlling the subsurface cycling of many elements including nitrate, sulfate, metals and radionuclides (e.g.: uranium), through oxidation-reduction reactions. Interestingly, the discovered transcriptional behaviour gives important insights into the good microbial adaptation to the geochemical conditions and their active contribution to the stabilization of the U ore deposits. Overall, evidences on the importance of these microbial metabolic activities in the aquifer system are discussed that may clarify the doubts on the microbial role in the genesis of low-temperature U roll-front deposits, along the Zoovch Ovoo mine.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - Cristina Povedano-Priego
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - María Pinel-Cabello
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Michael Descostes
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France; Centre de Géosciences, MINES ParisTech, PSL University, 35 rue St Honoré, 77300 Fontainebleau, France
| | - Pierre Grizard
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France
| | - Bayaarma Purevsan
- Badrakh Energy LLC, Jamyan Gun Avenue - 9, Sukhbaatar district, 1st khoroo, UB-14240, Mongolia
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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10
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Vaughn B, Abu Kwaik Y. Idiosyncratic Biogenesis of Intracellular Pathogens-Containing Vacuoles. Front Cell Infect Microbiol 2021; 11:722433. [PMID: 34858868 PMCID: PMC8632064 DOI: 10.3389/fcimb.2021.722433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
While most bacterial species taken up by macrophages are degraded through processing of the bacteria-containing vacuole through the endosomal-lysosomal degradation pathway, intravacuolar pathogens have evolved to evade degradation through the endosomal-lysosomal pathway. All intra-vacuolar pathogens possess specialized secretion systems (T3SS-T7SS) that inject effector proteins into the host cell cytosol to modulate myriad of host cell processes and remodel their vacuoles into proliferative niches. Although intravacuolar pathogens utilize similar secretion systems to interfere with their vacuole biogenesis, each pathogen has evolved a unique toolbox of protein effectors injected into the host cell to interact with, and modulate, distinct host cell targets. Thus, intravacuolar pathogens have evolved clear idiosyncrasies in their interference with their vacuole biogenesis to generate a unique intravacuolar niche suitable for their own proliferation. While there has been a quantum leap in our knowledge of modulation of phagosome biogenesis by intravacuolar pathogens, the detailed biochemical and cellular processes affected remain to be deciphered. Here we discuss how the intravacuolar bacterial pathogens Salmonella, Chlamydia, Mycobacteria, Legionella, Brucella, Coxiella, and Anaplasma utilize their unique set of effectors injected into the host cell to interfere with endocytic, exocytic, and ER-to-Golgi vesicle traffic. However, Coxiella is the main exception for a bacterial pathogen that proliferates within the hydrolytic lysosomal compartment, but its T4SS is essential for adaptation and proliferation within the lysosomal-like vacuole.
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Affiliation(s)
- Bethany Vaughn
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States.,Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, KY, United States
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The challenges and prospects of Escherichia coli as an organic acid production host under acid stress. Appl Microbiol Biotechnol 2021; 105:8091-8107. [PMID: 34617140 DOI: 10.1007/s00253-021-11577-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production. IMPORTANCE However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment. ELABORATION This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application. IMPLICATION At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value. KEY POINTS • E. coli is a potential host for high value-added organic acids production. • Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules. • Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.
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12
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Tran VG, Zhao H. Engineering robust microorganisms for organic acid production. J Ind Microbiol Biotechnol 2021; 49:6373449. [PMID: 34549297 PMCID: PMC9118992 DOI: 10.1093/jimb/kuab067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/11/2021] [Indexed: 11/24/2022]
Abstract
Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.
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Affiliation(s)
- Vinh G Tran
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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13
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Wu D, Qi W, Nie W, Lu Z, Ye Y, Li J, Sun T, Zhu Y, Cheng H, Wang X. BacFlash signals acid-resistance gene expression in bacteria. Cell Res 2021; 31:703-712. [PMID: 33159153 PMCID: PMC8169942 DOI: 10.1038/s41422-020-00431-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/14/2020] [Indexed: 11/08/2022] Open
Abstract
Intracellular pH (pHi) homeostasis is crucial for cellular functions and signal transduction across all kingdoms of life. In particular, bacterial pHi homeostasis is important for physiology, ecology, and pathogenesis. Here we report an exquisite bacterial acid-resistance (AR) mechanism in which proton leak elicits a pre-emptive AR response. A single bacterial cell undergoes quantal electrochemical excitation, termed "BacFlash", which consists of membrane depolarization, transient pHi rise, and bursting production of reactive oxygen species. BacFlash ignition is dictated by acid stress in the form of proton leak across the plasma membrane and the rate of BacFlash occurrence is reversely correlated with the pHi buffering capacity. Through genome-wide screening, we further identify the ATP synthase Fo complex subunit a as the putative proton sensor for BacFlash biogenesis. Importantly, persistent BacFlash hyperactivity activates transcription of a panel of key AR genes and predisposes the cells to survive imminent extreme acid stress. These findings demonstrate a prototypical coupling between electrochemical excitation and nucleoid gene expression in prokaryotes.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Wenfeng Qi
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Wei Nie
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China
| | - Zhengyuan Lu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Yongxin Ye
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Jinghang Li
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Tao Sun
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Yufei Zhu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China.
| | - Xianhua Wang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China.
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14
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Kim H, Wu K, Lee C. Stress-Responsive Periplasmic Chaperones in Bacteria. Front Mol Biosci 2021; 8:678697. [PMID: 34046432 PMCID: PMC8144458 DOI: 10.3389/fmolb.2021.678697] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 01/14/2023] Open
Abstract
Periplasmic proteins are involved in a wide range of bacterial functions, including motility, biofilm formation, sensing environmental cues, and small-molecule transport. In addition, a wide range of outer membrane proteins and proteins that are secreted into the media must travel through the periplasm to reach their final destinations. Since the porous outer membrane allows for the free diffusion of small molecules, periplasmic proteins and those that travel through this compartment are more vulnerable to external environmental changes, including those that result in protein unfolding, than cytoplasmic proteins are. To enable bacterial survival under various stress conditions, a robust protein quality control system is required in the periplasm. In this review, we focus on several periplasmic chaperones that are stress responsive, including Spy, which responds to envelope-stress, DegP, which responds to temperature to modulate chaperone/protease activity, HdeA and HdeB, which respond to acid stress, and UgpB, which functions as a bile-responsive chaperone.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, South Korea
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
| | - Kevin Wu
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
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15
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Bollen C, Dewachter L, Michiels J. Protein Aggregation as a Bacterial Strategy to Survive Antibiotic Treatment. Front Mol Biosci 2021; 8:669664. [PMID: 33937340 PMCID: PMC8085434 DOI: 10.3389/fmolb.2021.669664] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/29/2021] [Indexed: 11/18/2022] Open
Abstract
While protein aggregation is predominantly associated with loss of function and toxicity, it is also known to increase survival of bacteria under stressful conditions. Indeed, protein aggregation not only helps bacteria to cope with proteotoxic stresses like heat shocks or oxidative stress, but a growing number of studies suggest that it also improves survival during antibiotic treatment by inducing dormancy. A well-known example of dormant cells are persisters, which are transiently refractory to the action of antibiotics. These persister cells can switch back to the susceptible state and resume growth in the absence of antibiotics, and are therefore considered an important cause of recurrence of infections. Mounting evidence now suggests that this antibiotic-tolerant persister state is tightly linked to-or perhaps even driven by-protein aggregation. Moreover, another dormant bacterial phenotype, the viable but non-culturable (VBNC) state, was also shown to be associated with aggregation. These results indicate that persisters and VBNC cells may constitute different stages of the same dormancy program induced by progressive protein aggregation. In this mini review, we discuss the relation between aggregation and bacterial dormancy, focusing on both persisters and VBNC cells. Understanding the link between protein aggregation and dormancy will not only provide insight into the fundamentals of bacterial survival, but could prove highly valuable in our future battle to fight them.
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Affiliation(s)
- Celien Bollen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
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16
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Ionescu D, Zoccarato L, Zaduryan A, Schorn S, Bizic M, Pinnow S, Cypionka H, Grossart HP. Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems. Mol Biol Evol 2021; 38:1040-1059. [PMID: 33169788 PMCID: PMC7947748 DOI: 10.1093/molbev/msaa273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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
Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.
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Affiliation(s)
- Danny Ionescu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
| | - Luca Zoccarato
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Artur Zaduryan
- Department of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mina Bizic
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
| | - Solvig Pinnow
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Heribert Cypionka
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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17
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Wang Y, Li J, Zhou Z, Zhou R, Sun Q, Wu P. Halo-fluorescein for photodynamic bacteria inactivation in extremely acidic conditions. Nat Commun 2021; 12:526. [PMID: 33483514 PMCID: PMC7822816 DOI: 10.1038/s41467-020-20869-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/22/2020] [Indexed: 02/05/2023] Open
Abstract
Aciduric bacteria that can survive in extremely acidic conditions (pH < 4.0) are challenging to the current antimicrobial approaches, including antibiotics and photodynamic bacteria inactivation (PDI). Here, we communicate a photosensitizer design concept of halogenation of fluorescein for extremely acidic PDI. Upon halogenation, the well-known spirocyclization that controls the absorption of fluorescein shifts to the acidic pH range. Meanwhile, the heavy atom effect of halogens boosts the generation of singlet oxygen. Accordingly, several photosensitizers that could work at even pH < 2.0 were discovered for a broad band of aciduric bacteria families, with half maximal inhibitory concentrations (IC50) lower than 1.1 μM. Since one of the discovered photosensitizers is an FDA-approved food additive (2',4',5',7'-tetraiodofluorescein, TIF), successful bacteria growth inhibition in acidic beverages was demonstrated, with greatly extended shelf life from 2 days to ~15 days. Besides, the in vivo PDI of Candidiasis with TIF under extremely acidic condition was also demonstrated.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, 610064, Chengdu, China
- Analytical & Testing Center, Sichuan University, 610064, Chengdu, China
| | - Jiazhuo Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, 610064, Chengdu, China
- Analytical & Testing Center, Sichuan University, 610064, Chengdu, China
| | - Zhiwei Zhou
- College of Life Science, Sichuan University, 610064, Chengdu, China
| | - Ronghui Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041, Chengdu, China
| | - Qun Sun
- College of Life Science, Sichuan University, 610064, Chengdu, China
| | - Peng Wu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, 610064, Chengdu, China.
- Analytical & Testing Center, Sichuan University, 610064, Chengdu, China.
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18
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Yu L, Zhang S, Xu Y, Mi X, Xing T, Li J, Zhang L, Gao F, Jiang Y. Acid resistance of E. coli O157:H7 and O26:H11 exposure to lactic acid revealed by transcriptomic analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Detection of key sites of dimer dissociation and unfolding initiation during activation of acid-stress chaperone HdeA at low pH. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140576. [PMID: 33253897 DOI: 10.1016/j.bbapap.2020.140576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022]
Abstract
HdeA is a small acid-stress chaperone protein with a unique activity profile. At physiological pH, it forms a folded, but inactive, dimer. Below pH 3.0, HdeA unfolds and dissociates into disordered monomers, utilizing exposed hydrophobic patches to bind other unfolded proteins and prevent their irreversible aggregation. In this way, HdeA has a key role in helping pathogenic bacteria survive our acidic stomach and colonize our intestines, facilitating the spread of dysentery. Despite numerous publications on the topic, there remain questions about the mechanism by which HdeA unfolding and activation are triggered. Previous studies usually assessed HdeA unfolding over pH increments that are too far apart to gain fine detail of the process of unfolding and dimer dissociation, and often employed techniques that prevented thorough evaluation of specific regions of the protein. We used a variety of heteronuclear NMR experiments to investigate changes to backbone and side chain structure and dynamics of HdeA at four pHs between 3.0 and 2.0. We found that the long loop in the dimer interface is an early site of initiation of dimer dissociation, and that a molecular "clasp" near the disulfide bond is broken open at low pH as part, or as a trigger, of unfolding; this process also results in the separation of C-terminal helices and exposure of key hydrophobic client binding sites. Our results highlight important regions of HdeA that may have previously been overlooked because they lie too close to the disulfide bond or are thought to be too dynamic in the folded state to influence unfolding processes.
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20
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Paquette SJ, Reuter T. Escherichia coli: Physiological Clues Which Turn On the Synthesis of Antimicrobial Molecules. Vet Sci 2020; 7:E184. [PMID: 33233401 PMCID: PMC7712815 DOI: 10.3390/vetsci7040184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 11/17/2022] Open
Abstract
Zoonotic pathogens, like Shiga toxin-producing Escherichia coli (STEC) are a food safety and health risk. To battle the increasing emergence of virulent microbes, novel mitigation strategies are needed. One strategy being considered to combat pathogens is antimicrobial compounds produced by microbes, coined microcins. However, effectors for microcin production are poorly understood, particularly in the context of complex physiological responses along the gastro-intestinal tract (GIT). Previously, we identified an E. coli competitor capable of producing a strong diffusible antimicrobial with microcin-associated characteristics. Our objective was to examine how molecule production of this competitor is affected by physiological properties associated with the GIT, namely the effects of carbon source, bile salt concentration and growth phase. Using previously described liquid- and agar-based assays determined that carbon sources do not affect antimicrobial production of E. coli O103F. However, bile salt concentrations affected production significantly, suggesting that E. coli O103F uses cues along the GIT to modulate the expression of antimicrobial production. Furthermore, E. coli O103F produces the molecule during the exponential phase, contrary to most microcins identified to date. The results underscored the importance of experimental design to identify producers of antimicrobials. To detect antimicrobials, conventional microbiological methods can be a starting point, but not the gold standard.
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Affiliation(s)
- Sarah-Jo Paquette
- University of Lethbridge, Lethbridge, AB T1K 3M4, Canada;
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada
| | - Tim Reuter
- University of Lethbridge, Lethbridge, AB T1K 3M4, Canada;
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada
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21
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Molecular evaluation of quorum quenching potential of vanillic acid against Yersinia enterocolitica through transcriptomic and in silico analysis. J Med Microbiol 2020; 69:1319-1331. [DOI: 10.1099/jmm.0.001261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Introduction.
Yersinia enterocolitica
is one of the leading food-borne entero-pathogens causing various illnesses ranging from gastroenteritis to systemic infections. Quorum sensing (QS) is one of the prime mechanisms that control the virulence in
Y. enterocolitica
.
Hypothesis/Gap Statement. Vanillic acid inhibits the quorum sensing and other virulence factors related to
Y. enterocolitica
. It has been evaluated by transcriptomic and Insilico analysis. Therefore, it can be a prospective agent to develop a therapeutic combination against
Y. enterocolitica
.
Aim. The present study is focused on screening natural anti-quorum-sensing agents against
Y. enterocolitica
. The effect of selected active principle on various virulence factors was evaluated.
Methodology. In total, 12 phytochemicals were screened by swarming assay. MATH assay, EPS and surfactant production assay, SEM analysis, antibiotic and blood sensitivity assay were performed to demonstrate the anti-virulence activity. Further, RNA sequencing and molecular docking studies were carried out to substantiate the anti-QS activity.
Results. Vanillic acid (VA) has exhibited significant motility inhibition, thus indicating the anti-QS activity with MQIC of 400 µg ml−1 without altering the cell viability. It has also inhibited the violacein production in
Chromobacterium violaceum
ATCC 12472, which further confirms the anti-QS activity. VA has inhibited 16 % of cell-surface hydrophobicity (CSH), 52 % of EPS production and 60 % of surfactant production. Moreover, it has increased the sensitivity of
Y. enterocolitica
towards antibiotics. It has also made the cells upto 91 % more vulnerable towards human immune cells. The transcriptomic analysis by RNA sequencing revealed the down regulation of genes related to motility, virulence, chemotaxis, siderophores and drug resistance. VA treatment has also positively regulated the expression of several stress response genes. In furtherance, the anti-QS potential of VA has been validated with QS regulatory protein YenR by in silico molecular simulation and docking study.
Conclusion. The present study is possibly the first attempt to demonstrate the anti-QS and anti-pathogenic potential of VA against
Y. enterocolitica
by transcriptomic and in silico analysis. It also deciphers that VA can be a promising lead to develop biopreservative and therapeutic regimens to treat
Y. enterocolitica
infections.
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22
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Lund PA, De Biase D, Liran O, Scheler O, Mira NP, Cetecioglu Z, Fernández EN, Bover-Cid S, Hall R, Sauer M, O'Byrne C. Understanding How Microorganisms Respond to Acid pH Is Central to Their Control and Successful Exploitation. Front Microbiol 2020; 11:556140. [PMID: 33117305 PMCID: PMC7553086 DOI: 10.3389/fmicb.2020.556140] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022] Open
Abstract
Microbes from the three domains of life, Bacteria, Archaea, and Eukarya, share the need to sense and respond to changes in the external and internal concentrations of protons. When the proton concentration is high, acidic conditions prevail and cells must respond appropriately to ensure that macromolecules and metabolic processes are sufficiently protected to sustain life. While, we have learned much in recent decades about the mechanisms that microbes use to cope with acid, including the unique challenges presented by organic acids, there is still much to be gained from developing a deeper understanding of the effects and responses to acid in microbes. In this perspective article, we survey the key molecular mechanisms known to be important for microbial survival during acid stress and discuss how this knowledge might be relevant to microbe-based applications and processes that are consequential for humans. We discuss the research approaches that have been taken to investigate the problem and highlight promising new avenues. We discuss the influence of acid on pathogens during the course of infections and highlight the potential of using organic acids in treatments for some types of infection. We explore the influence of acid stress on photosynthetic microbes, and on biotechnological and industrial processes, including those needed to produce organic acids. We highlight the importance of understanding acid stress in controlling spoilage and pathogenic microbes in the food chain. Finally, we invite colleagues with an interest in microbial responses to low pH to participate in the EU-funded COST Action network called EuroMicropH and contribute to a comprehensive database of literature on this topic that we are making publicly available.
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Affiliation(s)
- Peter A Lund
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory affiliated to the Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
| | - Oded Liran
- Department of Plant Sciences, MIGAL - Galilee Research Institute, Kiryat-Shemona, Israel
| | - Ott Scheler
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Nuno Pereira Mira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Sara Bover-Cid
- IRTA, Food Safety Programme, Finca Camps i Armet, Monells, Spain
| | - Rebecca Hall
- School of Biosciences, Kent Fungal Group, University of Kent, Canterbury, United Kingdom
| | - Michael Sauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Conor O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland
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23
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Pacheco S, Widjaja MA, Gomez JS, Crowhurst KA, Abrol R. The complex role of the N-terminus and acidic residues of HdeA as pH-dependent switches in its chaperone function. Biophys Chem 2020; 264:106406. [PMID: 32593908 PMCID: PMC8276670 DOI: 10.1016/j.bpc.2020.106406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/03/2020] [Accepted: 05/16/2020] [Indexed: 10/24/2022]
Abstract
HdeA is a small acid-stress chaperone protein found in the periplasm of several pathogenic gram-negative bacteria. In neutral pH environments HdeA is an inactive folded homodimer but when exposed to strong acidic environments it partially unfolds and, once activated, binds to other periplasmic proteins, protecting them from irreversible aggregation. Here we use a combination of hydrogen/deuterium exchange NMR experiments and constant pH molecular dynamics simulations to elucidate the role of HdeA's N-terminus in its activation mechanism. Previous work indicates that the N-terminus is flexible and unprotected at high pH while exhibiting interactions with some HdeA client binding site residues. It, however, becomes partially solvent-protected at pH 2.6 - 2.8 and then loses protection again at pH 2.0. This protection is not due to the appearance of new secondary structure, but rather increased contacts between N-terminal residues and the C-terminus of the other protomer in the dimer, as well as concurrent loosening of its hold on the client binding site residues, priming HdeA for interactions with periplasmic client proteins. This work also uncovers unusual protonation profiles of some titratable residues and suggests their complex role in chaperone function.
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Affiliation(s)
- Sayuri Pacheco
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America
| | - Marlyn A Widjaja
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America
| | - Jafaeth S Gomez
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America
| | - Karin A Crowhurst
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America.
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24
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Hu Y, Li C, He L, Jin C, Liu M. Mechanisms of Chaperones as Active Assistant/Protector for Proteins: Insights from NMR Studies. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.201900441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, Peking University Beijing 100871 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
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25
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A Short Peptide Designed from Late Embryogenesis Abundant Protein Enhances Acid Tolerance in Escherichia coli. Appl Biochem Biotechnol 2020; 191:164-176. [PMID: 32096062 DOI: 10.1007/s12010-020-03262-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/13/2020] [Indexed: 01/09/2023]
Abstract
Unsuitable pH is a major limiting factor for all organisms, and a low pH can lead to organism death. Late embryogenesis abundant (LEA) peptides confer tolerance to abiotic stresses including salinity, drought, high and low temperature, and ultraviolet radiation same as the LEA proteins from which they originate. In this study, LEA peptides derived from group 3 LEA proteins of Polypedilum vanderplanki were used to enhance low pH tolerance. Recombinant Escherichia coli BL21 (DE3) cells expressing the five designed LEA peptides were grown at pH 4, 3, and 2. The transformants showed higher growth capacity at low pH as compared to control cells. These results indicate that LEA peptide could prevent E. coli cell death under low pH conditions.
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26
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He YU, Wang S, Yin X, Sun F, He B, Liu X. Comparison of Extracellular Proteins from Virulent and Avirulent Vibrio parahaemolyticus Strains To Identify Potential Virulence Factors. J Food Prot 2020; 83:155-162. [PMID: 31860395 DOI: 10.4315/0362-028x.jfp-19-188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Vibrio parahaemolyticus is a leading seafood-borne pathogen that causes gastroenteritis, septicemia, and serious wound infections due to the actions of virulence-associated proteins. We compared the extracellular proteins of nonvirulent JHY20 and virulent ATCC 33847 V. parahaemolyticus reference strains. Eighteen extracellular proteins were identified from secretory profiles, and 11 (68.75%) of the 16 proteins in ATCC 33847 are associated with virulence and/or protection against adverse conditions: trigger factor, chaperone SurA, aspartate-semialdehyde dehydrogenase, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, glutamate 5-kinase, alanine dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, outer membrane protein OmpV, ribosome-associated inhibitor A, chaperone protein Skp, and universal stress protein. Two nontoxic-related proteins, amino acid ABC transporter substrate-binding protein and an uncharacterized protein, were identified in JHY20. The results provide a theoretical basis for supporting safety risk assessment of aquatic foods, illuminate the pathogenic mechanisms of V. parahaemolyticus, and assist the identification of novel vaccine candidates for foodborne pathogens.
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Affiliation(s)
- Y U He
- College of Food (Biotechnology) Engineering.,Key Construction Laboratory of Food Resources Development and the Quality Safety, Xuzhou University of Technology, Jiangsu, Xuzhou 221018, People's Republic of China
| | - Shuai Wang
- College of Food (Biotechnology) Engineering.,Key Construction Laboratory of Food Resources Development and the Quality Safety, Xuzhou University of Technology, Jiangsu, Xuzhou 221018, People's Republic of China
| | | | - Fengjiao Sun
- Logistics & Security Department, Shanghai Civil Aviation College, Shanghai 201300, People's Republic of China
| | - Bin He
- Environment Monitoring Station, Zaozhuang Municipal Bureau of Ecology and Environment, Shandong 277100, People's Republic of China
| | - Xiao Liu
- Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450001, People's Republic of China
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27
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Guan N, Liu L. Microbial response to acid stress: mechanisms and applications. Appl Microbiol Biotechnol 2020; 104:51-65. [PMID: 31773206 PMCID: PMC6942593 DOI: 10.1007/s00253-019-10226-1] [Citation(s) in RCA: 229] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 02/07/2023]
Abstract
Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.
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Affiliation(s)
- Ningzi Guan
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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28
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Du B, Yang L, Lloyd CJ, Fang X, Palsson BO. Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. PLoS Comput Biol 2019; 15:e1007525. [PMID: 31809503 PMCID: PMC6897400 DOI: 10.1371/journal.pcbi.1007525] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022] Open
Abstract
Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle by passing through the stomach to colonize the digestive tract. To develop a fundamental understanding of this response, we established a molecular mechanistic description of acid stress mitigation responses in E. coli and integrated them with a genome-scale model of its metabolism and macromolecular expression (ME-model). We considered three known mechanisms of acid stress mitigation: 1) change in membrane lipid fatty acid composition, 2) change in periplasmic protein stability over external pH and periplasmic chaperone protection mechanisms, and 3) change in the activities of membrane proteins. After integrating these mechanisms into an established ME-model, we could simulate their responses in the context of other cellular processes. We validated these simulations using RNA sequencing data obtained from five E. coli strains grown under external pH ranging from 5.5 to 7.0. We found: i) that for the differentially expressed genes accounted for in the ME-model, 80% of the upregulated genes were correctly predicted by the ME-model, and ii) that these genes are mainly involved in translation processes (45% of genes), membrane proteins and related processes (18% of genes), amino acid metabolism (12% of genes), and cofactor and prosthetic group biosynthesis (8% of genes). We also demonstrated several intervention strategies on acid tolerance that can be simulated by the ME-model. We thus established a quantitative framework that describes, on a genome-scale, the acid stress mitigation response of E. coli that has both scientific and practical uses.
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Affiliation(s)
- Bin Du
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Laurence Yang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Colton J. Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, Denmark
- * E-mail:
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29
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Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. Adaptive laboratory evolution of Escherichia coli under acid stress. MICROBIOLOGY-SGM 2019; 166:141-148. [PMID: 31625833 DOI: 10.1099/mic.0.000867] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ability of Escherichia coli to tolerate acid stress is important for its survival and colonization in the human digestive tract. Here, we performed adaptive laboratory evolution of the laboratory strain E. coli K-12 MG1655 at pH 5.5 in glucose minimal medium. After 800 generations, six independent populations under evolution had reached 18.0 % higher growth rates than their starting strain at pH 5.5, while maintaining comparable growth rates to the starting strain at pH 7. We characterized the evolved strains and found that: (1) whole genome sequencing of isolated clones from each evolved population revealed mutations in rpoC appearing in five of six sequenced clones; and (2) gene expression profiles revealed different strategies to mitigate acid stress, which are related to amino acid metabolism and energy production and conversion. Thus, a combination of adaptive laboratory evolution, genome resequencing and expression profiling revealed, on a genome scale, the strategies that E. coli uses to mitigate acid stress.
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Affiliation(s)
- Bin Du
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor A Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Patrick V Phaneuf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ke Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Muyao Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Sibei Xu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ye Gao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
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30
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Fu X, Chang Z. Biogenesis, quality control, and structural dynamics of proteins as explored in living cells via site-directed photocrosslinking. Protein Sci 2019; 28:1194-1209. [PMID: 31002747 DOI: 10.1002/pro.3627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
Protein biogenesis and quality control are essential to maintaining a functional pool of proteins and involve numerous protein factors that dynamically and transiently interact with each other and with the substrate proteins in living cells. Conventional methods are hardly effective for studying dynamic, transient, and weak protein-protein interactions that occur in cells. Herein, we review how the site-directed photocrosslinking approach, which relies on the genetic incorporation of a photoreactive unnatural amino acid into a protein of interest at selected individual amino acid residue positions and the covalent trapping of the interacting proteins upon ultraviolent irradiation, has become a highly efficient way to explore the aspects of protein contacts in living cells. For example, in the past decade, this approach has allowed the profiling of the in vivo substrate proteins of chaperones or proteases under both physiologically optimal and stressful (e.g., acidic) conditions, mapping residues located at protein interfaces, identifying new protein factors involved in the biogenesis of membrane proteins, trapping transiently formed protein complexes, and snapshotting different structural states of a protein. We anticipate that the site-directed photocrosslinking approach will play a fundamental role in dissecting the detailed mechanisms of protein biogenesis, quality control, and dynamics in the future.
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Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province, 350117, China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Center for Protein Science, Beijing, 100871, China
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31
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The Plasmid-Encoded pGP3 Promotes Chlamydia Evasion of Acidic Barriers in Both Stomach and Vagina. Infect Immun 2019; 87:IAI.00844-18. [PMID: 30858342 DOI: 10.1128/iai.00844-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Although Chlamydia trachomatis is a human genital tract pathogen, chlamydial organisms have frequently been detected in both vaginal and rectal swab samples of animals and humans. The plasmid-encoded pGP3, a genital tract virulence factor, is essential for Chlamydia muridarum to colonize the mouse gastrointestinal tract. However, intracolon inoculation to bypass the gastric barrier rescued the colonization ability of a pGP3-deficient C. muridarum mutant, suggesting that pGP3 is required for C. muridarum to reach but not to colonize the large intestine. The pGP3-deficient mutant was rapidly cleared in the stomach and was 100-fold more susceptible to gastric killing. In mice genetically deficient in gastrin, a key regulator for gastric acid production, or pharmacologically treated with a proton pump inhibitor, the ability of pGP3-deficient C. muridarum to colonize the gastrointestinal tract was rescued. The pGP3-dependent resistance was further recapitulated in vitro with treatments with HCl, pepsin, or sarkosyl. In the genital tract, deficiency in pGP3 significantly reduced C. muridarum survival in the mouse vagina and increased C. muridarum susceptibility to vaginal killing by ∼8 times. The pGP3-deficient C. muridarum was more susceptible to lactic acid killing, and the pGP3 deficiency also significantly increased C. trachomatis susceptibility to lactic acid. The above-described observations together suggest that Chlamydia may have acquired the plasmid-encoded pGP3 to overcome the gastric barrier during its adaptation to the gastrointestinal tract and the pGP3-dependent resistance may enable chlamydial evasion of the female lower genital tract barrier during sexual transmission.
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Abstract
The biogenesis of periplasmic and outer membrane proteins (OMPs) in Escherichia coli is assisted by a variety of processes that help with their folding and transport to their final destination in the cellular envelope. Chaperones are macromolecules, usually proteins, that facilitate the folding of proteins or prevent their aggregation without becoming part of the protein's final structure. Because chaperones often bind to folding intermediates, they often (but not always) act to slow protein folding. Protein folding catalysts, on the other hand, act to accelerate specific steps in the protein folding pathway, including disulfide bond formation and peptidyl prolyl isomerization. This review is primarily concerned with E. coli and Salmonella periplasmic and cellular envelope chaperones; it also discusses periplasmic proline isomerization.
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33
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Liu CJ, Lin CT, Chiang JD, Lin CY, Tay YX, Fan LC, Peng KN, Lin CH, Peng HL. RcsB regulation of the YfdX-mediated acid stress response in Klebsiella pneumoniae CG43S3. PLoS One 2019; 14:e0212909. [PMID: 30818355 PMCID: PMC6394985 DOI: 10.1371/journal.pone.0212909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
In Klebsiella pneumoniae CG43S3, deletion of the response regulator gene rcsB reduced the capsular polysaccharide amount and survival on exposure to acid stress. A comparison of the pH 4.4-induced proteomes between CG43S3 and CG43S3ΔrcsB revealed numerous differentially expressed proteins and one of them, YfdX, which has recently been reported as a periplasmic protein, was absent in CG43S3ΔrcsB. Acid survival analysis was then conducted to determine its role in the acid stress response. Deletion of yfdX increased the sensitivity of K. pneumoniae CG43S3 to a pH of 2.5, and transforming the mutant with a plasmid carrying yfdX restored the acid resistance (AR) levels. In addition, the effect of yfdX deletion was cross-complemented by the expression of the periplasmic chaperone HdeA. Furthermore, the purified recombinant protein YfdX reduced the acid-induced protein aggregation, suggesting that YfdX as well as HdeA functions as a chaperone. The following promoter activity measurement revealed that rcsB deletion reduced the expression of yfdX after the bacteria were subjected to pH 4.4 adaptation. Western blot analysis also revealed that YfdX production was inhibited by rcsB deletion and only the plasmid expressing RcsB or the nonphosphorylated form of RcsB, RcsBD56A, could restore the YfdX production, and the RcsB-mediated complementation was no longer observed when the sensor kinase RcsD gene was deleted. In conclusion, this is the first study demonstrating that YfdX may be involved in the acid stress response as a periplasmic chaperone and that RcsB positively regulates the acid stress response partly through activation of yfdX expression. Moreover, the phosphorylation status of RcsB may affect the YfdX expression under acidic conditions.
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Affiliation(s)
- Chia-Jui Liu
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Ching-Ting Lin
- School of Chinese Medicine, China Medical University, Taichung, Taiwan, Republic of China
| | - Jo-Di Chiang
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Chen-Yi Lin
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Yen-Xi Tay
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Li-Cheng Fan
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Kuan-Nan Peng
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Chih-Huan Lin
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- * E-mail:
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34
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Challenges and Adaptations of Life in Alkaline Habitats. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 172:85-133. [DOI: 10.1007/10_2019_97] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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35
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Protease-Mediated Protein Quality Control for Bacterial Acid Resistance. Cell Chem Biol 2019; 26:144-150.e3. [DOI: 10.1016/j.chembiol.2018.10.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/10/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022]
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36
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Yu XC, Hu Y, Ding J, Li H, Jin C. Structural basis and mechanism of the unfolding-induced activation of HdeA, a bacterial acid response chaperone. J Biol Chem 2018; 294:3192-3206. [PMID: 30573682 DOI: 10.1074/jbc.ra118.006398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
The role of protein structural disorder in biological functions has gained increasing attention in the past decade. The bacterial acid-resistant chaperone HdeA belongs to a group of "conditionally disordered" proteins, because it is inactive in its well-structured state and becomes activated via an order-to-disorder transition under acid stress. However, the mechanism for unfolding-induced activation remains unclear because of a lack of experimental information on the unfolded state conformation and the chaperone-client interactions. Herein, we used advanced solution NMR methods to characterize the activated-state conformation of HdeA under acidic conditions and identify its client-binding sites. We observed that the structure of activated HdeA becomes largely disordered and exposes two hydrophobic patches essential for client interactions. Furthermore, using the pH-dependent chemical exchange saturation transfer (CEST) NMR method, we identified three acid-sensitive regions that act as structural locks in regulating the exposure of the two client-binding sites during the activation process, revealing a multistep activation mechanism of HdeA's chaperone function at the atomic level. Our results highlight the role of intrinsic protein disorder in chaperone function and the self-inhibitory role of ordered structures under nonstress conditions, offering new insights for improving our understanding of protein structure-function paradigms.
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Affiliation(s)
- Xing-Chi Yu
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Yunfei Hu
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences
| | - Hongwei Li
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Changwen Jin
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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37
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Pennacchietti E, D'Alonzo C, Freddi L, Occhialini A, De Biase D. The Glutaminase-Dependent Acid Resistance System: Qualitative and Quantitative Assays and Analysis of Its Distribution in Enteric Bacteria. Front Microbiol 2018; 9:2869. [PMID: 30498489 PMCID: PMC6250119 DOI: 10.3389/fmicb.2018.02869] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/08/2018] [Indexed: 12/22/2022] Open
Abstract
Neutralophilic bacteria have developed several strategies to overcome the deleterious effects of acid stress. In particular, the amino acid-dependent systems are widespread, with their activities overlapping, covering a rather large pH range, from 6 to <2. Recent reports showed that an acid resistance (AR) system relying on the amino acid glutamine (AR2_Q), the most readily available amino acid in the free form, is operative in Escherichia coli, Lactobacillus reuteri, and some Brucella species. This system requires a glutaminase active at acidic pH and the antiporter GadC to import L-glutamine and export either glutamate (the glutamine deamination product) or GABA. The latter occurs when the deamination of glutamine to glutamate, via acid-glutaminase (YbaS/GlsA), is coupled to the decarboxylation of glutamate to GABA, via glutamate decarboxylase (GadB), a structural component of the glutamate-dependent AR (AR2) system, together with GadC. Taking into account that AR2_Q could be widespread in bacteria and that until now assays based on ammonium ion detection were typically employed, this work was undertaken with the aim to develop assays that allow a straightforward identification of the acid-glutaminase activity in permeabilized bacterial cells (qualitative assay) as well as a sensitive method (quantitative assay) to monitor in the pH range 2.5-4.0 the transport of the relevant amino acids in vivo. The qualitative assay is colorimetric, rapid and reliable and provides several additional information, such as co-occurrence of AR2 and AR2_Q in the same bacterial species and assessment of the growth conditions that support maximal expression of glutaminase at acidic pH. The quantitative assay is HPLC-based and allows to concomitantly measure the uptake of glutamine and the export of glutamate and/or GABA via GadC in vivo and depending on the external pH. Finally, an extensive bioinformatic genome analysis shows that the gene encoding the glutaminase involved in AR2_Q is often nearby or in operon arrangement with the genes coding for GadC and GadB. Overall, our results indicate that AR2_Q is likely to be of prominent importance in the AR of enteric bacteria and that it modulates the enzymatic as well as antiport activities depending on the imposed acidic stress.
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Affiliation(s)
- Eugenia Pennacchietti
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory Affiliated to the Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
| | - Chiara D'Alonzo
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory Affiliated to the Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
| | - Luca Freddi
- Institut de Recherche en Infectiologie de Montpellier, CNRS, University of Montpellier, Montpellier, France
| | - Alessandra Occhialini
- Institut de Recherche en Infectiologie de Montpellier, CNRS, University of Montpellier, Montpellier, France
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory Affiliated to the Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
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38
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Fu X, Wang Y, Shao H, Ma J, Song X, Zhang M, Chang Z. DegP functions as a critical protease for bacterial acid resistance. FEBS J 2018; 285:3525-3538. [DOI: 10.1111/febs.14627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 06/03/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Yan Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Heqi Shao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Jing Ma
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Xinwen Song
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Meng Zhang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
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39
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Zhang Q, Li R, Li J, Shi H. Optimal Allocation of Bacterial Protein Resources under Nonlethal Protein Maturation Stress. Biophys J 2018; 115:896-910. [PMID: 30122293 DOI: 10.1016/j.bpj.2018.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 11/25/2022] Open
Abstract
Under different environmental stresses, bacteria optimize the allocation of cellular resources through a variety of mechanisms. Recently, researchers have used phenomenological models to quantitatively characterize the allocation of bacterial protein resources under metabolic and translational limitations. Some stresses interfere with protein maturation, thereby enhancing the expression of chaperones and proteases. However, the reallocation of protein resources caused by such environmental stresses has not been modeled quantitatively. Here, we developed a dynamic model of coarse-grained protein resource fluxes based on a self-replicator that includes protein maturation and degradation. Through flux balance analysis, it produces a constrained optimization problem that can be solved analytically. Accordingly, we predicted protein allocation fractions as functions of growth rate under different limitations, which are basically in line with empirical data. We cultured Escherichia coli in media containing different concentrations of chloramphenicol, acetic acid, and paraquat and measured the functional relationship between the expression level of β-galactosidase driven by a constitutive promoter and the bacterial growth rate, respectively. Taking into account the possible mode of stress limitation on the fluxes, our model reproduces this experimentally measured relationship. In addition, our model is in good agreement with the experimental relationship between growth rate and proteome fraction of unnecessary protein in E. coli, considering the unoptimized upregulation of chaperones with useless protein overexpression. The results provide a more systematic view of bacterial stress adaptation that may help in designing for bioengineering or medical interventions.
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Affiliation(s)
- Qing Zhang
- Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China.
| | - Rui Li
- Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Junbai Li
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Hualin Shi
- Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China.
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40
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Yu XC, Yang C, Ding J, Niu X, Hu Y, Jin C. Characterizations of the Interactions between Escherichia coli Periplasmic Chaperone HdeA and Its Native Substrates during Acid Stress. Biochemistry 2017; 56:5748-5757. [PMID: 29016106 DOI: 10.1021/acs.biochem.7b00724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial acid-resistant chaperone HdeA is a "conditionally disordered" protein that functions at low pH when it undergoes a transition from a well-folded dimer to an unfolded monomer. The dimer dissociation and unfolding processes result in exposure of hydrophobic surfaces that allows binding to a broad range of client proteins. To fully elucidate the chaperone mechanism of HdeA, it is crucial to understand how the activated HdeA interacts with its native substrates during acid stress. Herein, we present a nuclear magnetic resonance study of the pH-dependent HdeA-substrate interactions. Our results show that the activation of HdeA is not only induced by acidification but also regulated by the presence of unfolded substrates. The variable extent of unfolding of substrates differentially regulates the HdeA-substrate interaction, and the binding further affects the HdeA conformation. Finally, we show that HdeA binds its substrates heterogeneously, and the "amphiphilic" model for HdeA-substrate interaction is discussed.
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Affiliation(s)
- Xing-Chi Yu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Chengfeng Yang
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Jienv Ding
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Changwen Jin
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
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41
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Hussain HI, Iqbal Z, Seleem MN, Huang D, Sattar A, Hao H, Yuan Z. Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken. Sci Rep 2017; 7:8335. [PMID: 28827616 PMCID: PMC5567091 DOI: 10.1038/s41598-017-07798-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/03/2017] [Indexed: 02/01/2023] Open
Abstract
Numerous studies have examined the prevalence of pathogenic Escherichia coli in poultry and poultry products; however, limited data are available regarding their resistance- and virulence-associated gene expression profiles. This study was designed to examine the resistance and virulence of poultry E. coli strains in vitro and in vivo via antibiotic susceptibility, biofilm formation and adhesion, and invasion and intracellular survivability assays in Caco-2 and Raw 264.7 cell lines as well as the determination of the median lethal dose in two-day old chickens. A clinical pathogenic multidrug-resistant isolate, E. coli 381, isolated from broilers, was found to be highly virulent in cell culture and 1000-fold more virulent in a chicken model than other strains; accordingly, the isolate was subsequently selected for transcriptome analysis. The comparative gene expression profile of MDR E. coli 381 and the reference human strain E. coli ATCC 25922 was completed with Illumina HiSeq. 2500 transcriptome analysis. Differential gene expression analysis indicates that there are multiple pathways involved in the resistance and virulence of this highly virulent strain. The results garnered from this study provide critical information about the highly virulent MDR E. coli strain of poultry origin and warrant further investigation due to its significant threat to public health.
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Affiliation(s)
- Hafiz I Hussain
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zahid Iqbal
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
- University College of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Deyu Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Adeel Sattar
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.
| | - Zonghui Yuan
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China.
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42
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Yu K, Wang Z, Zhou F, Jiang J, Liu Y, Hu M, Liu X. Quantitative analysis of Shigella flexneri protein expression under acid stress. Proteomics 2017; 17. [PMID: 28221718 DOI: 10.1002/pmic.201600381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/10/2017] [Accepted: 02/17/2017] [Indexed: 11/10/2022]
Abstract
As an important foodborne pathogen, Shigella flexneri can cause widespread enteric infection with bacteria as few as hundreds. This is, at least in part, attributed to its robust anti-acid strategies because passage through the highly acidic human digestive tract is a prerequisite for successful bacterial infection. Nevertheless, our understanding of these mechanisms and the impact of acid stress on Shigella protein expression still remains largely incomplete. Herein we conducted a proteomic survey of Shigella spp. under acid stress. Out of 1754 protein identifications, we found 131 altered proteins, most of which were down-regulated, including virulence factors and cell envelope proteins. Rather, many metabolic enzymes and pyrimidine/amino acid biosynthesis proteins were up-regulated. In addition to induction of many known anti-acid systems, we also found marked increase of 2-oxoglutarate dehydrogenase (SucAB), a metabolic enzyme in the tricarboxylic acid cycle. Importantly, overproduction of this enzyme significantly enhanced Shigella acid resistance and hence SucAB-mediated metabolic pathways may represent novel anti-acid strategies.
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Affiliation(s)
- Kaiwen Yu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Zhen Wang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Fan Zhou
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Jiezhang Jiang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yanhua Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Mo Hu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
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43
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Zhang S, He D, Lin Z, Yang Y, Song H, Chen PR. Conditional Chaperone-Client Interactions Revealed by Genetically Encoded Photo-cross-linkers. Acc Chem Res 2017; 50:1184-1192. [PMID: 28467057 DOI: 10.1021/acs.accounts.6b00647] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The cell envelope is an integral and essential component of Gram-negative bacteria. As the front line during host-pathogen interactions, it is directly challenged by host immune responses as well as other harsh extracellular stimuli. The high permeability of the outer-membrane and the lack of ATP energy system render it difficult to maintain important biological activities within the periplasmic space under stress conditions. The HdeA/B chaperone machinery is the only known acid resistant system found in bacterial periplasm, enabling enteric pathogens to survive through the highly acidic human stomach and establish infections in the intestine. These two homologous chaperones belong to a fast growing family of conditionally disordered chaperones that conditionally lose their well-defined three-dimensional structures to exert biological activities. Upon losing ordered structures, these proteins commit promiscuous binding of diverse clients in response to environmental stimulation. For example, HdeA and HdeB are well-folded inactive dimers at neutral pH but become partially unfolded to protect a wide array of acid-denatured proteins upon acid stress. Whether these conditionally disordered chaperones possess client specificities remains unclear. This is in part due to the lack of efficient tools to investigate such versatile and heterogeneous protein-protein interactions under living conditions. Genetically encoded protein photo-cross-linkers have offered a powerful strategy to capture protein-protein interactions, showing great potential in profiling protein interaction networks, mapping binding interfaces, and probing dynamic changes in both physiological and pathological settings. Despite great success, photo-cross-linkers that can simultaneously capture the promiscuous binding partners and directly identify the interaction interfaces remain technically challenging. Furthermore, methods for side-by-side profiling and comparing the condition-dependent client pools from two homologous chaperones are lacking. Herein, we introduce our recent efforts in developing a panel of versatile genetically encoded photo-cross-linkers to study the disorder-mediated chaperone-client interactions in living cells. In particular, we have developed a series of proteomic-based strategies relying on these new photo-cross-linkers to systematically compare the client profiles of HdeA and HdeB, as well as to map their interaction interfaces. These studies revealed the mode-of-action, particularly the client specificity, of these two conditionally disordered chaperones. In the end, some recent elegant work from other groups that applied the genetically encoded photo-cross-linking strategy to illuminate important protein-protein interactions within bacterial cell envelope is also discussed.
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Affiliation(s)
- Shuai Zhang
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dan He
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhi Lin
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Yang
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haiping Song
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R. Chen
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
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44
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Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection. Clin Microbiol Rev 2017; 29:819-36. [PMID: 27464994 DOI: 10.1128/cmr.00031-16] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial pathogens have coevolved with humans in order to efficiently infect, replicate within, and be transmitted to new hosts to ensure survival and a continual infection cycle. For enteric pathogens, the ability to adapt to numerous host factors under the harsh conditions of the gastrointestinal tract is critical for establishing infection. One such host factor readily encountered by enteric bacteria is bile, an innately antimicrobial detergent-like compound essential for digestion and nutrient absorption. Not only have enteric pathogens evolved to resist the bactericidal conditions of bile, but these bacteria also utilize bile as a signal to enhance virulence regulation for efficient infection. This review provides a comprehensive and up-to-date analysis of bile-related research with enteric pathogens. From common responses to the unique expression of specific virulence factors, each pathogen has overcome significant challenges to establish infection in the gastrointestinal tract. Utilization of bile as a signal to modulate virulence factor expression has led to important insights for our understanding of virulence mechanisms for many pathogens. Further research on enteric pathogens exposed to this in vivo signal will benefit therapeutic and vaccine development and ultimately enhance our success at combating such elite pathogens.
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45
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Enterohemorrhagic Escherichia coli pathogenesis: role of Long polar fimbriae in Peyer's patches interactions. Sci Rep 2017; 7:44655. [PMID: 28317910 PMCID: PMC5357955 DOI: 10.1038/srep44655] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/13/2017] [Indexed: 11/14/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) are major food-borne pathogens whose survival and virulence in the human digestive tract remain unclear owing to paucity of relevant models. EHEC interact with the follicle-associated epithelium of Peyer’s patches of the distal ileum and translocate across the intestinal epithelium via M-cells, but the underlying molecular mechanisms are still unknown. Here, we investigated the involvement of Long polar fimbriae (Lpf) in EHEC pathogenesis. Of the 236 strains tested, a significant association was observed between the presence of lpf operons and pathogenicity. In sophisticated in vitro models of the human gastro-intestinal tract, lpf expression was induced during transit through the simulated stomach and small intestine, but not in the colonic compartment. To investigate the involvement of Lpf in EHEC pathogenesis, lpf isogenic mutants and their relative trans-complemented strains were generated. Translocation across M-cells, interactions with murine ileal biopsies containing Peyer’s patches and the number of hemorrhagic lesions were significantly reduced with the lpf mutants compared to the wild-type strain. Complementation of lpf mutants fully restored the wild-type phenotypes. Our results indicate that (i) EHEC might colonize the terminal ileum at the early stages of infection, (ii) Lpf are an important player in the interactions with Peyer’s patches and M-cells, and could contribute to intestinal colonization.
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46
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Tong ZX, Liu W, Huang H, Chen HZ, Liu XJ, Kuang YQ, Jiang JH. A ratiometric fluorescent pH probe based on keto–enol tautomerization for imaging of living cells in extreme acidity. Analyst 2017; 142:3906-3912. [DOI: 10.1039/c7an01103b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A ratiometric fluorescent pH probe (DDXC) has been developed for extreme acidity, the sensing mechanism of which is based on the reversible protonation of the carbonyl oxygen followed by keto–enol tautomerization.
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Affiliation(s)
- Zong-Xuan Tong
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Wei Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Hui Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Hong-Zong Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Xian-Jun Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Yong-Qing Kuang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
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47
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Ge Y, Fan X, Chen PR. A genetically encoded multifunctional unnatural amino acid for versatile protein manipulations in living cells. Chem Sci 2016; 7:7055-7060. [PMID: 28451140 PMCID: PMC5355830 DOI: 10.1039/c6sc02615j] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/01/2016] [Indexed: 01/20/2023] Open
Abstract
The genetic code expansion strategy allowed incorporation of unnatural amino acids (UAAs) bearing diverse functional groups into proteins, providing a powerful toolkit for protein manipulation in living cells. We report a multifunctional UAA, Nε-p-azidobenzyloxycarbonyl lysine (PABK), that possesses a panel of unique properties capable of fulfilling various protein manipulation purposes. In addition to being used as a bioorthogonal ligation handle, an infrared probe and a photo-affinity reagent, PABK was shown to be chemically decaged by trans-cyclooctenols via a strain-promoted 1,3-dipolar cycloaddition, which provides a new bioorthogonal cleavage strategy for intracellular protein activation. The biocompatibility and efficiency of this method were demonstrated by decaging of a PABK-caged firefly luciferase under living conditions. We further extended this method to chemically rescue a bacterial toxin OspF inside mammalian host cells.
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Affiliation(s)
- Yun Ge
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
- Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China
| | - Peng R Chen
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
- Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China
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48
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Mendoza JA, Weinberger KK, Swan MJ. The Hsp60 protein of helicobacter pylori displays chaperone activity under acidic conditions. Biochem Biophys Rep 2016; 9:95-99. [PMID: 28955994 PMCID: PMC5614549 DOI: 10.1016/j.bbrep.2016.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 10/26/2022] Open
Abstract
The heat shock protein, Hsp60, is one of the most abundant proteins in Helicobacter pylori. Given its sequence homology to the Escherichia coli Hsp60 or GroEL, Hsp60 from H. pylori would be expected to function as a molecular chaperone in this organism. H. pylori is an organism that grows on the gastric epithelium, where the pH can fluctuate between neutral and 4.5 and the intracellular pH can be as low as 5.0. This study was performed to test the ability of Hsp60 from H. pylori to function as a molecular chaperone under mildly acidic conditions. We report here that Hsp60 could suppress the acid-induced aggregation of alcohol dehydrogenase (ADH) in the 7.0-5.0 pH range. Hsp60 was found to undergo a conformational change within this pH range. It was also found that exposure of hydrophobic surfaces of Hsp60 is significant and that their exposure is increased under acidic conditions. Although, alcohol dehydrogenase does not contain exposed hydrophobic surfaces, we found that their exposure is triggered at low pH. Our results demonstrate that Hsp60 from H. pylori can function as a molecular chaperone under acidic conditions and that the interaction between Hsp60 and other proteins may be mediated by hydrophobic interactions.
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Affiliation(s)
- Jose A Mendoza
- Department of Chemistry and Biochemistry, California State University San Marcos, CA 92096-0001, United States
| | - Kevin K Weinberger
- Department of Chemistry and Biochemistry, California State University San Marcos, CA 92096-0001, United States
| | - Matthew J Swan
- Department of Chemistry and Biochemistry, California State University San Marcos, CA 92096-0001, United States
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49
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Socher E, Sticht H. Probing the Structure of the Escherichia coli Periplasmic Proteins HdeA and YmgD by Molecular Dynamics Simulations. J Phys Chem B 2016; 120:11845-11855. [PMID: 27787971 DOI: 10.1021/acs.jpcb.6b06091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HdeA and YmgD are structurally homologous proteins in the periplasm of Escherichia coli. HdeA has been shown to represent an acid-activated chaperone, whereas the function of YmgD has not yet been characterized. We performed pH-titrating molecular dynamics simulations (pHtMD) to investigate the structural changes of both proteins and to assess whether YmgD may also exhibit an unfolding behavior similar to that of HdeA. The unfolding pathway of HdeA includes partially unfolded dimer structures, which represent a prerequisite for subsequent dissociation. In contrast to the coupled unfolding and dissociation of HdeA, YmgD displays dissociation of the folded subunits, and the subunits do not undergo significant unfolding even at low pH values. The differences in subunit stability between HdeA and YmgD may be explained by the structural features of helix D, which represents the starting point of unfolding in HdeA. In summary, the present study suggests that YmgD either is not an acid-activated chaperone or, at least, does not require unfolding for activation.
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Affiliation(s)
- Eileen Socher
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) , Fahrstraße 17, 91054 Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) , Fahrstraße 17, 91054 Erlangen, Germany
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50
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Dahl JU, Koldewey P, Bardwell JCA, Jakob U. Detection of the pH-dependent Activity of Escherichia coli Chaperone HdeB In Vitro and In Vivo. J Vis Exp 2016. [PMID: 27805614 DOI: 10.3791/54527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Bacteria are frequently exposed to environmental changes, such as alterations in pH, temperature, redox status, light exposure or mechanical force. Many of these conditions cause protein unfolding in the cell and have detrimental impact on the survival of the organism. A group of unrelated, stress-specific molecular chaperones have been shown to play essential roles in the survival of these stress conditions. While fully folded and chaperone-inactive before stress, these proteins rapidly unfold and become chaperone-active under specific stress conditions. Once activated, these conditionally disordered chaperones bind to a large number of different aggregation-prone proteins, prevent their aggregation and either directly or indirectly facilitate protein refolding upon return to non-stress conditions. The primary approach for gaining a more detailed understanding about the mechanism of their activation and client recognition involves the purification and subsequent characterization of these proteins using in vitro chaperone assays. Follow-up in vivo stress assays are absolutely essential to independently confirm the obtained in vitro results. This protocol describes in vitro and in vivo methods to characterize the chaperone activity of E. coli HdeB, an acid-activated chaperone. Light scattering measurements were used as a convenient read-out for HdeB's capacity to prevent acid-induced aggregation of an established model client protein, MDH, in vitro. Analytical ultracentrifugation experiments were applied to reveal complex formation between HdeB and its client protein LDH, to shed light into the fate of client proteins upon their return to non-stress conditions. Enzymatic activity assays of the client proteins were conducted to monitor the effects of HdeB on pH-induced client inactivation and reactivation. Finally, survival studies were used to monitor the influence of HdeB's chaperone function in vivo.
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Affiliation(s)
- Jan-Ulrik Dahl
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan;
| | - Philipp Koldewey
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan; Howard Hughes Medical Institute, University of Michigan
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan; Howard Hughes Medical Institute, University of Michigan;
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
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