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Jiao F, Chen Y, Zhang D, Wu J. Genome-Wide Characterization of Soybean Hexokinase Genes Reveals a Positive Role of GmHXK15 in Alkali Stress Response. PLANTS (BASEL, SWITZERLAND) 2023; 12:3121. [PMID: 37687370 PMCID: PMC10490225 DOI: 10.3390/plants12173121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Hexokinase (HXK) proteins catalyze hexose phosphorylation and are important for the sensing and signaling of sugar. In order to determine the roles played by HXKs in soybean growth and stress responsiveness, seventeen HXK genes (GmHXK1-17) were isolated and analyzed. The phylogenic analysis and subcellular location prediction showed that GmHXKs were clearly classified into type A (GmHXK1-4) and type B (GmHXK5-17). There were similar protein structures and conserved regions in GmHXKs to the HXKs of other plants. An expression analysis of the GmHXK genes in soybean organs or tissues demonstrated that GmHXK3 and GmHXK12, 15, and 16 were the dominant HXKs in all the examined tissues. In addition, salt, osmotic, and alkaline stress treatments dramatically increased the activity and transcripts of GmHXKs. There is the possibility that a type-B isoform (GmHXK15) plays a crucial role in soybean adaptation to alkali, as the expression levels of this isoform correlate well with the HXK enzyme activity. Based on an enzyme assay performed on recombinant plant HXK15 proteins expressed in Escherichia coli, we found that GmHXK15 had functional HXK activities. A further analysis indicated that GmHXK15 specifically targeted the mitochondria, and the overexpression of the GmHXK15 gene could significantly enhance the resistance of transgenic soybean to alkali stress. The present findings will serve as a basis for a further analysis of the function of the GmHXK gene family.
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Affiliation(s)
| | | | | | - Jinhua Wu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (F.J.); (Y.C.); (D.Z.)
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van Tatenhove-Pel RJ, Zwering E, Boreel DF, Falk M, van Heerden JH, Kes MBMJ, Kranenburg CI, Botman D, Teusink B, Bachmann H. Serial propagation in water-in-oil emulsions selects for Saccharomyces cerevisiae strains with a reduced cell size or an increased biomass yield on glucose. Metab Eng 2021; 64:1-14. [PMID: 33418011 DOI: 10.1016/j.ymben.2020.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/26/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022]
Abstract
In S. cerevisiae and many other micro-organisms an increase in metabolic efficiency (i.e. ATP yield on carbon) is accompanied by a decrease in growth rate. From a fundamental point of view, studying these yield-rate trade-offs provides insight in for example microbial evolution and cellular regulation. From a biotechnological point of view, increasing the ATP yield on carbon might increase the yield of anabolic products. We here aimed to select S. cerevisiae mutants with an increased biomass yield. Serial propagation of individual cells in water-in-oil emulsions previously enabled the selection of lactococci with increased biomass yields, and adapting this protocol for yeast allowed us to enrich an engineered Crabtree-negative S. cerevisiae strain with a high biomass yield on glucose. When we started the selection with an S. cerevisiae deletion collection, serial propagation in emulsion enriched hxk2Δ and reg1Δ strains with an increased biomass yield on glucose. Surprisingly, a tps1Δ strain was highly abundant in both emulsion- and suspension-propagated populations. In a separate experiment we propagated a chemically mutagenized S. cerevisiae population in emulsion, which resulted in mutants with a higher cell number yield on glucose, but no significantly changed biomass yield. Genome analyses indicate that genes involved in glucose repression and cell cycle processes play a role in the selected phenotypes. The repeated identification of mutations in genes involved in glucose-repression indicates that serial propagation in emulsion is a valuable tool to study metabolic efficiency in S. cerevisiae.
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Affiliation(s)
- Rinke Johanna van Tatenhove-Pel
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Emile Zwering
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Daan Floris Boreel
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Martijn Falk
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Johan Hendrik van Heerden
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Mariah B M J Kes
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Cindy Iris Kranenburg
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Dennis Botman
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Herwig Bachmann
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands; NIZO Food Research, Kernhemseweg 2, 6718ZB, Ede, the Netherlands.
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Abstract
Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, lead to a novel view of enzymes as active matter. Enzyme chemotaxis and EED may be important in biology and could have practical applications in biotechnology and nanotechnology. They are also of considerable biophysical interest; indeed, their physical mechanisms are still quite uncertain. This review provides an analytic summary of experimental studies of these phenomena and of the mechanisms that have been proposed to explain them and offers a perspective on future directions for the field.
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Affiliation(s)
- Mudong Feng
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA;
| | - Michael K Gilson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA; .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA
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Feng M, Gilson MK. A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion. Biophys J 2019; 116:1898-1906. [PMID: 31053258 PMCID: PMC6531786 DOI: 10.1016/j.bpj.2019.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/02/2019] [Indexed: 01/01/2023] Open
Abstract
A number of enzymes reportedly exhibit enhanced diffusion in the presence of their substrates, with a Michaelis-Menten-like concentration dependence. Although no definite explanation of this phenomenon has emerged, a physical picture of enzyme self-propulsion using energy from the catalyzed reaction has been widely considered. Here, we present a kinematic and thermodynamic analysis of enzyme self-propulsion that is independent of any specific propulsion mechanism. Using this theory, along with biophysical data compiled for all enzymes so far shown to undergo enhanced diffusion, we show that the propulsion speed required to generate experimental levels of enhanced diffusion exceeds the speeds of well-known active biomolecules, such as myosin, by several orders of magnitude. Furthermore, the minimal power dissipation required to account for enzyme enhanced diffusion by self-propulsion markedly exceeds the chemical power available from enzyme-catalyzed reactions. Alternative explanations for the observation of enhanced enzyme diffusion therefore merit stronger consideration.
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Affiliation(s)
- Mudong Feng
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Michael K Gilson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California.
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Haupt C, Weininger U, Kovermann M, Balbach J. Local and Coupled Thermodynamic Stability of the Two-Domain and Bifunctional Enzyme SlyD from Escherichia coli. Biochemistry 2011; 50:7321-9. [DOI: 10.1021/bi2000627] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Caroline Haupt
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Ulrich Weininger
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Michael Kovermann
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Jochen Balbach
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
- Mitteldeutsches Zentrum für
Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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