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Qiu D, Jian Y, Zhang Y, Xie G. Plant Gravitropism and Signal Conversion under a Stress Environment of Altered Gravity. Int J Mol Sci 2021; 22:ijms222111723. [PMID: 34769154 PMCID: PMC8583895 DOI: 10.3390/ijms222111723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
Humans have been committed to space exploration and to find the next planet suitable for human survival. The construction of an ecosystem that adapts to the long-term survival of human beings in space stations or other planets would be the first step. The space plant cultivation system is the key component of an ecosystem, which will produce food, fiber, edible oil and oxygen for future space inhabitants. Many plant experiments have been carried out under a stimulated or real environment of altered gravity, including at microgravity (0 g), Moon gravity (0.17 g) and Mars gravity (0.38 g). How plants sense gravity and change under stress environment of altered gravity were summarized in this review. However, many challenges remain regarding human missions to the Moon or Mars. Our group conducted the first plant experiment under real Moon gravity (0.17 g) in 2019. One of the cotton seeds successfully germinated and produced a green seedling, which represents the first green leaf produced by mankind on the Moon.
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Affiliation(s)
- Dan Qiu
- Center of Space Exploration, Ministry of Education, Chongqing University, Chongqing 400044, China; (Y.J.); (Y.Z.)
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, School of Life Sciences, Chongqing University, Chongqing 401331, China
- Correspondence: (D.Q.); (G.X.)
| | - Yongfei Jian
- Center of Space Exploration, Ministry of Education, Chongqing University, Chongqing 400044, China; (Y.J.); (Y.Z.)
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yuanxun Zhang
- Center of Space Exploration, Ministry of Education, Chongqing University, Chongqing 400044, China; (Y.J.); (Y.Z.)
| | - Gengxin Xie
- Center of Space Exploration, Ministry of Education, Chongqing University, Chongqing 400044, China; (Y.J.); (Y.Z.)
- Correspondence: (D.Q.); (G.X.)
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A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1436-43. [PMID: 27456266 DOI: 10.1016/j.bbapap.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/11/2016] [Accepted: 07/15/2016] [Indexed: 11/20/2022]
Abstract
Structural comparisons of the cold adapted subtilase VPR and its thermophilic homologue, aqualysin I (AQUI) indicated the presence of additional salt bridges in the latter. Few of those appear to contribute significantly to thermal stability of AQUI. This includes a putative salt bridge between residues Lys142 and Glu172 as its deletion did not have any significant effect on its stability or activity (Jónsdóttir et al. (2014)). Insertion of this putative salt bridge into the structure of VPR, in a double mutant (VPRΔC_Q142K/S172E), however was detrimental to the stability of the enzyme. Incorporation of either the Q142K or S172E mutations into VPR, were found to significantly affect the catalytic properties of the enzyme. The single mutation Q142K was highly effective, as it increased the kcat and kcat/Km more than twofold. When the Q142K mutation was inserted into a thermostabilized, but a low activity mutant of VPR (VPRΔC_N3P/I5P), the activity increased about tenfold in terms of kcat and kcat/Km, while retaining the stability of the mutant. Molecular dynamics simulations of the single mutants were carried out to provide structural rationale for these experimental observations. Based on root mean square fluctuation (RMSF) profiles, the two mutants were more flexible in certain regions of the structure and the Q142K mutant had the highest overall flexibility of the three enzymes. The results suggest that weakening of specific H-bonds resulting from the mutations may be propagated over some distance giving rise to higher flexibility in the active site regions of the enzyme, causing higher catalytic activity in the mutants.
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Scholl ZN, Josephs EA, Marszalek PE. Modular, Nondegenerate Polyprotein Scaffolds for Atomic Force Spectroscopy. Biomacromolecules 2016; 17:2502-5. [PMID: 27276010 PMCID: PMC4940236 DOI: 10.1021/acs.biomac.6b00548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zackary N. Scholl
- Computational Biology and Bioinformatics Program, Edmund
T. Pratt, Jr. School of Engineering, Duke University, Durham, North Carolina, United
States
| | - Eric A. Josephs
- Department of Mechanical Engineering and Materials
Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, North
Carolina, United States
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials
Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, North
Carolina, United States
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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Lenton S, Walsh DL, Rhys NH, Soper AK, Dougan L. Structural evidence for solvent-stabilisation by aspartic acid as a mechanism for halophilic protein stability in high salt concentrations. Phys Chem Chem Phys 2016; 18:18054-62. [PMID: 27327567 DOI: 10.1039/c6cp02684b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Halophilic organisms have adapted to survive in high salt environments, where mesophilic organisms would perish. One of the biggest challenges faced by halophilic proteins is the ability to maintain both the structure and function at molar concentrations of salt. A distinct adaptation of halophilic proteins, compared to mesophilic homologues, is the abundance of aspartic acid on the protein surface. Mutagenesis and crystallographic studies of halophilic proteins suggest an important role for solvent interactions with the surface aspartic acid residues. This interaction, between the regions of the acidic protein surface and the solvent, is thought to maintain a hydration layer around the protein at molar salt concentrations thereby allowing halophilic proteins to retain their functional state. Here we present neutron diffraction data of the monomeric zwitterionic form of aspartic acid solutions at physiological pH in 0.25 M and 2.5 M concentration of potassium chloride, to mimic mesophilic and halophilic-like environmental conditions. We have used isotopic substitution in combination with empirical potential structure refinement to extract atomic-scale information from the data. Our study provides structural insights that support the hypothesis that carboxyl groups on acidic residues bind water more tightly under high salt conditions, in support of the residue-ion interaction model of halophilic protein stabilisation. Furthermore our data show that in the presence of high salt the self-association between the zwitterionic form of aspartic acid molecules is reduced, suggesting a possible mechanism through which protein aggregation is prevented.
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Affiliation(s)
- Samuel Lenton
- School of Physics and Astronomy, University of Leeds, Leeds, UK.
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Hoffmann T, Tych KM, Crosskey T, Schiffrin B, Brockwell DJ, Dougan L. Rapid and Robust Polyprotein Production Facilitates Single-Molecule Mechanical Characterization of β-Barrel Assembly Machinery Polypeptide Transport Associated Domains. ACS NANO 2015; 9:8811-21. [PMID: 26284289 DOI: 10.1021/acsnano.5b01962] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-molecule force spectroscopy by atomic force microscopy exploits the use of multimeric protein constructs, namely, polyproteins, to decrease the impact of nonspecific interactions, to improve data accumulation, and to allow the accommodation of benchmarking reference domains within the construct. However, methods to generate such constructs are either time- and labor-intensive or lack control over the length or the domain sequence of the obtained construct. Here, we describe an approach that addresses both of these shortcomings that uses Gibson assembly (GA) to generate a defined recombinant polyprotein rapidly using linker sequences. To demonstrate the feasibility of this approach, we used GA to make a polyprotein composed of alternating domains of I27 and TmCsp, (I27-TmCsp)3-I27)(GA), and showed the mechanical fingerprint, mechanical strength, and pulling speed dependence are the same as an analogous polyprotein constructed using the classical approach. After this benchmarking, we exploited this approach to facilitiate the mechanical characterization of POTRA domain 2 of BamA from E. coli (EcPOTRA2) by assembling the polyprotein (I27-EcPOTRA2)3-I27(GA). We show that, as predicted from the α + β topology, EcPOTRA2 domains are mechanically robust over a wide range of pulling speeds. Furthermore, we identify a clear correlation between mechanical robustness and brittleness for a range of other α + β proteins that contain the structural feature of proximal terminal β-strands in parallel geometry. We thus demonstrate that the GA approach is a powerful tool, as it circumvents the usual time- and labor-intensive polyprotein production process and allows for rapid production of new constructs for single-molecule studies. As shown for EcPOTRA2, this approach allows the exploration of the mechanical properties of a greater number of proteins and their variants. This improves our understanding of the relationship between structure and mechanical strength, increasing our ability to design proteins with tailored mechanical properties.
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Affiliation(s)
- Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Thomas Crosskey
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Bob Schiffrin
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
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