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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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Network-Based Redox Communication Between Abiotic Interactive Materials. iScience 2022; 25:104548. [PMID: 35747390 PMCID: PMC9209720 DOI: 10.1016/j.isci.2022.104548] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/28/2022] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Recent observations that abiotic materials can engage in redox-based interactive communication motivates the search for new redox-active materials. Here we fabricated a hydrogel from a four-armed thiolated polyethylene glycol (PEG-SH) and the bacterial metabolite, pyocyanin (PYO). We show that: (i) the PYO-PEG hydrogel is reversibly redox-active; (ii) the molecular-switching and directed electron flow within this PYO-PEG hydrogel requires both a thermodynamic driving force (i.e., potential difference) and diffusible electron carriers that serve as nodes in a redox network; (iii) this redox-switching and electron flow is controlled by the redox network’s topology; and (iv) the ability of the PYO-PEG hydrogel to “transmit” electrons to a second insoluble redox-active material (i.e., a catechol-PEG hydrogel) is context-dependent (i.e., dependent on thermodynamic driving forces and appropriate redox shuttles). These studies provide an experimental demonstration of important features of redox-communication and also suggest technological opportunities for the fabrication of interactive materials. Thiol-pyocyanin reaction was used to create a redox-active and interactive hydrogel The electron flow and molecular switching requires diffusible mediators These mediators and pyocyanin hydrogel serve as “nodes” in a redox reaction network The networked flow of electrons between two separated hydrogels is reported
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Chlebek D, Płociniczak T, Gobetti S, Kumor A, Hupert-Kocurek K, Pacwa-Płociniczak M. Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits. Int J Mol Sci 2021; 23:ijms23010214. [PMID: 35008639 PMCID: PMC8745256 DOI: 10.3390/ijms23010214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca3(PO4)2, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg−1 h−1). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.
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Maćešić S, Tóth Á, Horváth D. Origins of oscillatory dynamics in the model of reactive oxygen species in the rhizosphere. J Chem Phys 2021; 155:175102. [PMID: 34742207 DOI: 10.1063/5.0062139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oscillatory processes are essential for normal functioning and survival of biological systems, and reactive oxygen species have a prominent role in many of them. A mechanism representing the dynamics of these species in the rhizosphere is analyzed using stoichiometric network analysis with the aim to determine its capabilities to simulate various dynamical states, including oscillations. A detailed analysis has shown that unstable steady states result from four destabilizing feedback cycles, among which the cycle involving hydroquinone, an electron acceptor, and its semi-reduced form is the dominant one responsible for the existence of saddle-node and Andronov-Hopf bifurcations. This requires a higher steady-state concentration for the reduced electron acceptor compared to that of the remaining species, where the level of oxygen steady-state concentration determines whether the Andronov-Hopf or saddle-node bifurcation will occur.
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Affiliation(s)
- Stevan Maćešić
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
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Hui P, Branca M, Limoges B, Mavré F. An autocatalytic organic reaction network based on cross-catalysis. Chem Commun (Camb) 2021; 57:11374-11377. [PMID: 34647564 DOI: 10.1039/d1cc05121k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here we report a simple autocatalytic organic reaction network based on the redox chemistry of quinones and reactive oxygen species. Autocatalysis arises from the cross-activation between the H2O2-catalyzed deprotection of a pro-benzoquinone arylboronic ester probe and the benzoquinone-catalyzed H2O2 production through redox cyling with ascorbate in an aerated buffered solution.
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Affiliation(s)
- Pan Hui
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
| | - Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
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Zhao Z, Ozcan EE, VanArsdale E, Li J, Kim E, Sandler AD, Kelly DL, Bentley WE, Payne GF. Mediated Electrochemical Probing: A Systems-Level Tool for Redox Biology. ACS Chem Biol 2021; 16:1099-1110. [PMID: 34156828 DOI: 10.1021/acschembio.1c00267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Biology uses well-known redox mechanisms for energy harvesting (e.g., respiration), biosynthesis, and immune defense (e.g., oxidative burst), and now we know biology uses redox for systems-level communication. Currently, we have limited abilities to "eavesdrop" on this redox modality, which can be contrasted with our abilities to observe and actuate biology through its more familiar ionic electrical modality. In this Perspective, we argue that the coupling of electrochemistry with diffusible mediators (electron shuttles) provides a unique opportunity to access the redox communication modality through its electrical features. We highlight previous studies showing that mediated electrochemical probing (MEP) can "communicate" with biology to acquire information and even to actuate specific biological responses (i.e., targeted gene expression). We suggest that MEP may reveal an extent of redox-based communication that has remained underappreciated in nature and that MEP could provide new technological approaches for redox biology, bioelectronics, clinical care, and environmental sciences.
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Affiliation(s)
- Zhiling Zhao
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
| | - Evrim E. Ozcan
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - Eric VanArsdale
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jinyang Li
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Eunkyoung Kim
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
| | - Anthony D. Sandler
- Department of General and Thoracic Surgery, Children’s National Hospital, Washington, D.C. 20010, United States
| | - Deanna L. Kelly
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland 21228, United States
| | - William E. Bentley
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
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Li J, Wang SP, Zong G, Kim E, Tsao CY, VanArsdale E, Wang LX, Bentley WE, Payne GF. Interactive Materials for Bidirectional Redox-Based Communication. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007758. [PMID: 33788338 DOI: 10.1002/adma.202007758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Emerging research indicates that biology routinely uses diffusible redox-active molecules to mediate communication that can span biological systems (e.g., nervous and immune) and even kingdoms (e.g., a microbiome and its plant/animal host). This redox modality also provides new opportunities to create interactive materials that can communicate with living systems. Here, it is reported that the fabrication of a redox-active hydrogel film can autonomously synthesize a H2 O2 signaling molecule for communication with a bacterial population. Specifically, a catechol-conjugated/crosslinked 4-armed thiolated poly(ethylene glycol) hydrogel film is electrochemically fabricated in which the added catechol moieties confer redox activity: the film can accept electrons from biological reductants (e.g., ascorbate) and donate electrons to O2 to generate H2 O2 . Electron-transfer from an Escherichia coli culture poises this film to generate the H2 O2 signaling molecule that can induce bacterial gene expression from a redox-responsive operon. Overall, this work demonstrates that catecholic materials can participate in redox-based interactions that elicit specific biological responses, and also suggests the possibility that natural phenolics may be a ubiquitous biological example of interactive materials.
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Affiliation(s)
- Jinyang Li
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Sally P Wang
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
| | - Eric VanArsdale
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
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Liu S, Lin YH, Murphy A, Anderson J, Walker N, Lynn DG, Binns AN, Pierce BD. Mapping Reaction-Diffusion Networks at the Plant Wound Site With Pathogens. FRONTIERS IN PLANT SCIENCE 2020; 11:1074. [PMID: 32765558 PMCID: PMC7379035 DOI: 10.3389/fpls.2020.01074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
The rich collection of microbes colonizing the plant root making up the rhizosphere function as a multigenomic organ for nutrient distribution. The extent to which its dynamic mutualistic cellular order depends on morphogenic signaling, while likely, remains unknown. We have shown that reaction-diffusion chemical networks constructed with model plant and bacterial metabolites can mimic processes ranging from oxidative burst kinetics to traveling waves and extracellular stationary state reaction-diffusion networks for spatiotemporal ordering of the rhizosphere. Plant parasites and pathogens can be limited by host attachment require dynamic informational networks and continue to provide insight into what controls the rhizosphere. Here we take advantage of Agrobacterium tumefaciens, a plant pathogen with a gated receptor that requires simultaneous perception of two plant metabolites. Genetic manipulations have created receptors allowing each metabolite concentration to be correlated with pathogen behavior. The development of the florescent strains used here provide initial maps of the reaction-diffusion dynamics existing in the rhizosphere, revealing significant differences in the signaling landscape of host and non-host plants before and after wounding, specifically highlighting networks that may inform rhizosphere organization.
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Affiliation(s)
- Stephanie Liu
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
| | - Yi-Han Lin
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD, United States
| | - Aidan Murphy
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Josh Anderson
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Nicole Walker
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - David G. Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
| | - Andrew N. Binns
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - B. Daniel Pierce
- Department of Biology, University of Richmond, Richmond, VA, United States
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Goyet V, Wada S, Cui S, Wakatake T, Shirasu K, Montiel G, Simier P, Yoshida S. Haustorium Inducing Factors for Parasitic Orobanchaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:1056. [PMID: 31555315 PMCID: PMC6726735 DOI: 10.3389/fpls.2019.01056] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/30/2019] [Indexed: 05/20/2023]
Abstract
Parasitic plants in the Orobanchaceae family include devastating weed species, such as Striga, Orobanche, and Phelipanche, which infest important crops and cause economic losses of over a billion US dollars worldwide, yet the molecular and cellular processes responsible for such parasitic relationships remain largely unknown. Parasitic species of the Orobanchaceae family form specialized invasion organs called haustoria on their roots to enable the invasion of host root tissues. The process of forming haustoria can be divided into two steps, prehaustorium formation and haustorium maturation, the processes occurring before and after host attachment, respectively. Prehaustorium formation is provoked by host-derived signal molecules, collectively called haustorium-inducing factors (HIFs). Cell wall-related quinones and phenolics have been known for a long time to induce haustoria in many Orobanchaceae species. Although such phenolics are widely produced in plants, structural specificities exist among these molecules that modulate their competency to induce haustoria in different parasitic plant species. In addition, the plant hormone cytokinins, structurally distinct from phenolic compounds, also trigger prehaustorium formation in Orobanchaceae. Recent findings demonstrate their involvement as rhizopsheric HIFs for Orobanche and Phelipanche species and thus address new activities for cytokinins in haustorium formation in Orobanchaceae, as well as in rhizospheric signaling. This review highlights haustorium-inducing signals in the Orobanchaceae family in the context of their host origin, action mechanisms, and species specificity.
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Affiliation(s)
- Vincent Goyet
- Laboratoire de Biologie et Pathologie Végétales, Université de Nantes, Nantes, France
| | - Syogo Wada
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Songkui Cui
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | | | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Gregory Montiel
- Laboratoire de Biologie et Pathologie Végétales, Université de Nantes, Nantes, France
| | - Philippe Simier
- Laboratoire de Biologie et Pathologie Végétales, Université de Nantes, Nantes, France
| | - Satoko Yoshida
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- *Correspondence: Satoko Yoshida,
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