1
|
Boden JS, Zhong J, Anderson RE, Stüeken EE. Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics. Nat Commun 2024; 15:3703. [PMID: 38697988 PMCID: PMC11066067 DOI: 10.1038/s41467-024-47914-0] [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: 08/20/2023] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life's origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS; <1 µM) appeared around the same time or in the Mesoarchean depending on the reconstruction method. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising pathways and hypophosphite-oxidising pathways. CP-lyases are particularly abundant in dissolved phosphate concentrations below 0.1 µM. Our results thus indicate at least local regions of declining phosphate levels through the Archean, possibly linked to phosphate-scavenging Fe(III), which may have limited productivity. However, reduced phosphorus species did not become widely used until after the Paleoproterozoic Great Oxidation Event (2.3 Ga), possibly linked to expansion of the biosphere at that time.
Collapse
Affiliation(s)
- Joanne S Boden
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom.
| | - Juntao Zhong
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Rika E Anderson
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Eva E Stüeken
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom
| |
Collapse
|
2
|
Mao Z, Fleming JR, Mayans O, Frey J, Schleheck D, Schink B, Müller N. AMP-dependent phosphite dehydrogenase, a phosphorylating enzyme in dissimilatory phosphite oxidation. Proc Natl Acad Sci U S A 2023; 120:e2309743120. [PMID: 37922328 PMCID: PMC10636320 DOI: 10.1073/pnas.2309743120] [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: 06/14/2023] [Accepted: 09/20/2023] [Indexed: 11/05/2023] Open
Abstract
Oxidation of phosphite (HPO32-) to phosphate (HPO42-) releases electrons at a very low redox potential (E0'= -690 mV) which renders phosphite an excellent electron donor for microbial energy metabolism. To date, two pure cultures of strictly anaerobic bacteria have been isolated that run their energy metabolism on the basis of phosphite oxidation, the Gram-negative Desulfotignum phosphitoxidans (DSM 13687) and the Gram-positive Phosphitispora fastidiosa (DSM 112739). Here, we describe the key enzyme for dissimilatory phosphite oxidation in these bacteria. The enzyme catalyzed phosphite oxidation in the presence of adenosine monophosphate (AMP) to form adenosine diphosphate (ADP), with concomitant reduction of oxidized nicotinamide adenine dinucleotide (NAD+) to reduced nicotinamide adenine dinucleotide (NADH). The enzyme of P. fastidiosa was heterologously expressed in Escherichia coli. It has a molecular mass of 35.2 kDa and a high affinity for phosphite and NAD+. Its activity was enhanced more than 100-fold by addition of ADP-consuming adenylate kinase (myokinase) to a maximal activity between 30 and 80 mU x mg protein-1. A similar NAD-dependent enzyme oxidizing phosphite to phosphate with concomitant phosphorylation of AMP to ADP is found in D. phosphitoxidans, but this enzyme could not be heterologously expressed. Based on sequence analysis, these phosphite-oxidizing enzymes are related to nucleotide-diphosphate-sugar epimerases and indeed represent AMP-dependent phosphite dehydrogenases (ApdA). A reaction mechanism is proposed for this unusual type of substrate-level phosphorylation reaction.
Collapse
Affiliation(s)
- Zhuqing Mao
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Jennifer R. Fleming
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Jasmin Frey
- Department of Biology, University of Konstanz, Constance78457, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance78457, Germany
| |
Collapse
|
3
|
Mao Z, Müller N, Borusak S, Schleheck D, Schink B. Anaerobic dissimilatory phosphite oxidation, an extremely efficient concept of microbial electron economy. Environ Microbiol 2023; 25:2068-2074. [PMID: 37525971 DOI: 10.1111/1462-2920.16470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/10/2023] [Indexed: 08/02/2023]
Abstract
Phosphite is a stable phosphorus compound that, together with phosphate, made up a substantial part of the total phosphorus content of the prebiotic Earth's crust. Oxidation of phosphite to phosphate releases electrons at an unusually low redox potential (-690 mV at pH 7.0). Numerous aerobic and anaerobic bacteria use phosphite as a phosphorus source and oxidise it to phosphate for synthesis of nucleotides and other phosphorus-containing cell constituents. Only two pure cultures of strictly anaerobic bacteria have been isolated so far that use phosphite as an electron donor in their energy metabolism, the Gram-positive Phosphitispora fastidiosa and the Gram-negative Desulfotignum phosphitoxidans. The key enzyme of this metabolism is an NAD+ -dependent phosphite dehydrogenase enzyme that phosphorylates AMP to ADP. These phosphorylating phosphite dehydrogenases were found to be related to nucleoside diphosphate sugar epimerases. The produced NADH is channelled into autotrophic CO2 fixation via the Wood-Ljungdahl (CO-DH) pathway, thus allowing for nearly complete assimilation of the substrate electrons into bacterial biomass. This extremely efficient type of electron flow connects energy and carbon metabolism directly through NADH and might have been important in the early evolution of life when phosphite was easily available on Earth.
Collapse
Affiliation(s)
- Zhuqing Mao
- Department of Biology, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance, Germany
| | - Sabrina Borusak
- Department of Biology, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| |
Collapse
|
4
|
Willetts A. Bicyclo[3.2.0]carbocyclic Molecules and Redox Biotransformations: The Evolution of Closed-Loop Artificial Linear Biocatalytic Cascades and Related Redox-Neutral Systems. Molecules 2023; 28:7249. [PMID: 37959669 PMCID: PMC10649493 DOI: 10.3390/molecules28217249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
The role of cofactor recycling in determining the efficiency of artificial biocatalytic cascades has become paramount in recent years. Closed-loop cofactor recycling, which initially emerged in the 1990s, has made a valuable contribution to the development of this aspect of biotechnology. However, the evolution of redox-neutral closed-loop cofactor recycling has a longer history that has been integrally linked to the enzymology of oxy-functionalised bicyclo[3.2.0]carbocyclic molecule metabolism throughout. This review traces that relevant history from the mid-1960s to current times.
Collapse
Affiliation(s)
- Andrew Willetts
- Curnow Consultancies Ltd., Trewithen House, Helston TR13 9PQ, Cornwall, UK
| |
Collapse
|
5
|
Abdel-Hady GN, Tajima T, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. A novel salt- and organic solvent-tolerant phosphite dehydrogenase from Cyanothece sp. ATCC 51142. Front Bioeng Biotechnol 2023; 11:1255582. [PMID: 37662428 PMCID: PMC10473253 DOI: 10.3389/fbioe.2023.1255582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Phosphite dehydrogenase (PtxD) is a promising enzyme for NAD(P)H regeneration. To expand the usability of PtxD, we cloned, expressed, and analyzed PtxD from the marine cyanobacterium Cyanothece sp. ATCC 51142 (Ct-PtxD). Ct-PtxD exhibited maximum activity at pH 9.0°C and 50°C and high stability over a wide pH range of 6.0-10.0. Compared to previously reported PtxDs, Ct-PtxD showed increased resistance to salt ions such as Na+, K+, and NH4 +. It also exhibited high tolerance to organic solvents such as ethanol, dimethylformamide, and methanol when bound to its preferred cofactor, NAD+. Remarkably, these organic solvents enhanced the Ct-PtxD activity while inhibiting the PtxD activity of Ralstonia sp. 4506 (Rs-PtxD) at concentrations ranging from 10% to 30%. Molecular electrostatic potential analysis showed that the NAD+-binding site of Ct-PtxD was rich in positively charged residues, which may attract the negatively charged pyrophosphate group of NAD+ under high-salt conditions. Amino acid composition analysis revealed that Ct-PtxD contained fewer hydrophobic amino acids than other PtxD enzymes, which reduced the hydrophobicity and increased the hydration of protein surface under low water activity. We also demonstrated that the NADH regeneration system using Ct-PtxD is useful for the coupled chiral conversion of trimethylpyruvic acid into L-tert-leucine using leucine dehydrogenase under high ammonium conditions, which is less supported by the Rs-PtxD enzyme. These results imply that Ct-PtxD might be a potential candidate for NAD(P)H regeneration in industrial applications under the reaction conditions containing salt and organic solvent.
Collapse
Affiliation(s)
- Gamal Nasser Abdel-Hady
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Department of Genetics, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Takahisa Tajima
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
6
|
Liu W, Zhang Y, Yu M, Xu J, Du H, Zhang R, Wu D, Xie X. Role of phosphite in the environmental phosphorus cycle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163463. [PMID: 37062315 DOI: 10.1016/j.scitotenv.2023.163463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/29/2023] [Accepted: 04/08/2023] [Indexed: 06/01/2023]
Abstract
In modern geochemistry, phosphorus (P) is considered synonymous with phosphate (Pi) because Pi controls the growth of organisms as a limiting nutrient in many ecosystems. The researchers therefore realised that a complete P cycle is essential. Limited by thermodynamic barriers, P was long believed to be incapable of redox reactions, and the role of the redox cycle of reduced P in the global P cycling system was thus not ascertained. Nevertheless, the phosphite (Phi) form of P is widely present in various environments and participates in the global P redox cycle. Herein, global quantitative evidences of Phi are enumerated and the early origin and modern biotic/abiotic sources of Phi are elaborated. Further, the Phi-based redox pathway for P reduction is analysed and global multienvironmental Phi redox cycle processes are proposed on the basis of this pathway. The possible role of Phi in controlling algae in eutrophic lakes and its ecological benefits to plants are proposed. In this manner, the important role of Phi in the P redox cycle and global P cycle is systematically and comprehensively identified and confirmed. This work will provide scientific guidance for the future production and use of Phi products and arouse attention and interest on clarifying the role of Phi in the environmental phosphorus cycle.
Collapse
Affiliation(s)
- Wei Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Yalan Zhang
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Mengqin Yu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Jinying Xu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Hu Du
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Ru Zhang
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Daishe Wu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China; School of Materials and Chemical Engineering, Pingxiang University, Pingxiang 337000, China
| | - Xianchuan Xie
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China.
| |
Collapse
|
7
|
Partipilo M, Claassens NJ, Slotboom DJ. A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells. ACS Synth Biol 2023; 12:947-962. [PMID: 37052416 PMCID: PMC10127272 DOI: 10.1021/acssynbio.3c00070] [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: 01/31/2023] [Indexed: 04/14/2023]
Abstract
The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.
Collapse
Affiliation(s)
- Michele Partipilo
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nico J. Claassens
- Laboratory
of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Jan Slotboom
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
8
|
Murakami H, Sano K, Motomura K, Kuroda A, Hirota R. Assessment of horizontal gene transfer-mediated destabilization of Synechococcus elongatus PCC 7942 biocontainment system. J Biosci Bioeng 2023; 135:190-195. [PMID: 36653270 DOI: 10.1016/j.jbiosc.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/18/2023]
Abstract
Biological containment is a biosafety strategy that prevents the dispersal of genetically modified organisms in natural ecosystems. We previously established a biocontainment system that makes bacterial growth dependent on the availability of phosphite (Pt), an ecologically rare form of phosphorus (P), by introducing Pt metabolic pathway genes and disrupting endogenous phosphate and organic phosphate transporter genes. Although this system proved highly effective, horizontal gene transfer (HGT) mediated recovery of a P transporter gene is considered as a potential pathway to abolish the Pt-dependent growth, resulting in escape from the containment. Here, we assessed the risk of HGT driven escape using the Pt-dependent cyanobacterium Synechococcus elongatus PCC 7942. Transformation experiments revealed that the Pt-dependent strain could regain phosphate transporter genes from the S. elongatus PCC 7942 wild-type genome and from the genome of the closely related strain, S. elongatus UTEX 2973. Transformed S. elongatus PCC 7942 became viable in a phosphate-containing medium. Meanwhile, transformation of the Synechocystis sp. PCC 6803 genome or environmental DNA did not yield escape strains, suggesting that only genetic material derived from phylogenetically-close species confer high risk to generate escape. Eliminating a single gene necessary for natural competence from the Pt-dependent strain reduced the escape occurrence rate. These results demonstrate that natural competence could be a potential risk to destabilize Pt-dependence, and therefore inhibiting exogenous DNA uptake would be effective for enhancing the robustness of the gene disruption-dependent biocontainment.
Collapse
Affiliation(s)
- Hiroki Murakami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kosuke Sano
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kei Motomura
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| |
Collapse
|
9
|
In silico protein engineering shows that novel mutations affecting NAD + binding sites may improve phosphite dehydrogenase stability and activity. Sci Rep 2023; 13:1878. [PMID: 36725973 PMCID: PMC9892502 DOI: 10.1038/s41598-023-28246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Pseudomonas stutzeri phosphite dehydrogenase (PTDH) catalyzes the oxidation of phosphite to phosphate in the presence of NAD, resulting in the formation of NADH. The regeneration of NADH by PTDH is greater than any other enzyme due to the substantial change in the free energy of reaction (G°' = - 63.3 kJ/mol). Presently, improving the stability of PTDH is for a great importance to ensure an economically viable reaction process to produce phosphite as a byproduct for agronomic applications. The binding site of NAD+ with PTDH includes thirty-four residues; eight of which have been previously mutated and characterized for their roles in catalysis. In the present study, the unexplored twenty-six key residues involved in the binding of NAD+ were subjected to in silico mutagenesis based on the physicochemical properties of the amino acids. The effects of these mutations on the structure, stability, activity, and interaction of PTDH with NAD+ were investigated using molecular docking, molecular dynamics simulations, free energy calculations, and secondary structure analysis. We identified seven novel mutations, A155I, G157I, L217I, P235A, V262I, I293A, and I293L, that reduce the compactness of the protein while improving PTDH stability and binding to NAD+.
Collapse
|
10
|
Ma K, Deng L, Wu H, Fan J. Towards green biomanufacturing of high-value recombinant proteins using promising cell factory: Chlamydomonas reinhardtii chloroplast. BIORESOUR BIOPROCESS 2022; 9:83. [PMID: 38647750 PMCID: PMC10992328 DOI: 10.1186/s40643-022-00568-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
Microalgae are cosmopolitan organisms in nature with short life cycles, playing a tremendous role in reducing the pressure of industrial carbon emissions. Besides, microalgae have the unique advantages of being photoautotrophic and harboring both prokaryotic and eukaryotic expression systems, becoming a popular host for recombinant proteins. Currently, numerous advanced molecular tools related to microalgal transgenesis have been explored and established, especially for the model species Chlamydomonas reinhardtii (C. reinhardtii hereafter). The development of genetic tools and the emergence of new strategies further increase the feasibility of developing C. reinhardtii chloroplasts as green factories, and the strong genetic operability of C. reinhardtii endows it with enormous potential as a synthetic biology platform. At present, C. reinhardtii chloroplasts could successfully produce plenty of recombinant proteins, including antigens, antibodies, antimicrobial peptides, protein hormones and enzymes. However, additional techniques and toolkits for chloroplasts need to be developed to achieve efficient and markerless editing of plastid genomes. Mining novel genetic elements and selectable markers will be more intensively studied in the future, and more factors affecting protein expression are urged to be explored. This review focuses on the latest technological progress of selectable markers for Chlamydomonas chloroplast genetic engineering and the factors that affect the efficiency of chloroplast protein expression. Furthermore, urgent challenges and prospects for future development are pointed out.
Collapse
Affiliation(s)
- Ke Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Lei Deng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Jianhua Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, 832003, People's Republic of China.
| |
Collapse
|
11
|
Kumar K, Yadava P, Gupta M, Choudhary M, Jha AK, Wani SH, Dar ZA, Kumar B, Rakshit S. Narrowing down molecular targets for improving phosphorus-use efficiency in maize (Zea mays L.). Mol Biol Rep 2022; 49:12091-12107. [PMID: 35752697 DOI: 10.1007/s11033-022-07679-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
Conventional agricultural practices rely heavily on chemical fertilizers to boost production. Among the fertilizers, phosphatic fertilizers are copiously used to ameliorate low-phosphate availability in the soil. However, phosphorus-use efficiency (PUE) for major cereals, including maize, is less than 30%; resulting in more than half of the applied phosphate being lost to the environment. Rock phosphate reserves are finite and predicted to exhaust in near future with the current rate of consumption. Thus, the dependence of modern agriculture on phosphatic fertilizers poses major food security and sustainability challenges. Strategies to optimize and improve PUE, like genetic interventions to develop high PUE cultivars, could have a major impact in this area. Here, we present the current understanding and recent advances in the biological phenomenon of phosphate uptake, translocation, and adaptive responses of plants under phosphate deficiency, with special reference to maize. Maize is one of the most important cereal crops that is cultivated globally under diverse agro-climatic conditions. It is an industrial, feed and food crop with multifarious uses and a fast-rising global demand and consumption. The interesting aspects of diversity in the root system architecture traits, the interplay between signaling pathways contributing to PUE, and an in-depth discussion on promising candidate genes for improving PUE in maize are elaborated.
Collapse
Affiliation(s)
- Krishan Kumar
- Delhi Unit Office, ICAR - Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
| | - Pranjal Yadava
- ICAR - Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Mamta Gupta
- ICAR - Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India
| | - Mukesh Choudhary
- ICAR - Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India.,School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Abhishek Kumar Jha
- Delhi Unit Office, ICAR - Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology, Khudwani, Srinagar, Jammu and Kashmir, India
| | - Zahoor Ahmed Dar
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology Srinagar, Khudwani, Srinagar, Jammu and Kashmir, India
| | - Bhupender Kumar
- Delhi Unit Office, ICAR - Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Sujay Rakshit
- ICAR - Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India.
| |
Collapse
|
12
|
Inoue H, Tajima K, Mitsumori C, Inoue-Kashino N, Miura T, Ifuku K, Hirota R, Kashino Y, Fujita K, Kinoshita H. Biodiversity risk assessment of genetically modified Chaetoceros gracilis for outdoor cultivation. J GEN APPL MICROBIOL 2022; 68:151-162. [PMID: 35650023 DOI: 10.2323/jgam.2021.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A genetically modified (GM) strain of the diatom Chaetoceros gracilis expressing the phosphite dehydrogenase gene (ptxD), which is a useful gene both for the biological containment and the avoidance of microbial contamination, was characterized to estimate the risk against the biodiversity by laboratory experiments. GM strain could grow in the medium containing phosphite as a sole source of phosphorus, while its general characteristics such as growth, salt tolerance, heat and dehydration resistance in the normal phosphate-containing medium were equivalent to those of wild type (WT) strain. The increase in potential toxicity of GM strain against plant, crustacean, fish and mammal was also disproved. The dispersal ability of WT strain cultured in an outdoor raceway pond was investigated for 28 days by detecting the psb31 gene in vessels, settled at variable distances (between 5 and 60 m) from the pond. The diatom was detected only in one vessel placed 5 m apart. To estimate the influence on the environment, WT and GM strains were inoculated into freshwater, seawater and soil. The influence on the microbiome in those samples was assessed by 16S rRNA gene amplicon sequencing, in addition to the analysis of the survivability of those strains in the freshwater and the seawater. The results indicated that the effect to the microbiome and the survivability were comparable between WT and GM strains. All results showed that the introduction of the ptxD gene into the diatom had a low risk on biodiversity.
Collapse
Affiliation(s)
- Hidetoshi Inoue
- Biological Resource Center, National Institute of Technology and Evaluation (NITE)
| | - Kumiko Tajima
- Biological Resource Center, National Institute of Technology and Evaluation (NITE)
| | - Cristina Mitsumori
- Biological Resource Center, National Institute of Technology and Evaluation (NITE)
| | | | - Takamasa Miura
- Biological Resource Center, National Institute of Technology and Evaluation (NITE)
| | | | - Ryuichi Hirota
- Graduate School of Integrated Sciences for Life, Hiroshima University
| | | | - Katsutoshi Fujita
- Biological Resource Center, National Institute of Technology and Evaluation (NITE)
| | - Hiroshi Kinoshita
- Biological Resource Center, National Institute of Technology and Evaluation (NITE)
| |
Collapse
|
13
|
Harnessing the Algal Chloroplast for Heterologous Protein Production. Microorganisms 2022; 10:microorganisms10040743. [PMID: 35456794 PMCID: PMC9025058 DOI: 10.3390/microorganisms10040743] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
Photosynthetic microbes are gaining increasing attention as heterologous hosts for the light-driven, low-cost production of high-value recombinant proteins. Recent advances in the manipulation of unicellular algal genomes offer the opportunity to establish engineered strains as safe and viable alternatives to conventional heterotrophic expression systems, including for their use in the feed, food, and biopharmaceutical industries. Due to the relatively small size of their genomes, algal chloroplasts are excellent targets for synthetic biology approaches, and are convenient subcellular sites for the compartmentalized accumulation and storage of products. Different classes of recombinant proteins, including enzymes and peptides with therapeutical applications, have been successfully expressed in the plastid of the model organism Chlamydomonas reinhardtii, and of a few other species, highlighting the emerging potential of transplastomic algal biotechnology. In this review, we provide a unified view on the state-of-the-art tools that are available to introduce protein-encoding transgenes in microalgal plastids, and discuss the main (bio)technological bottlenecks that still need to be addressed to develop robust and sustainable green cell biofactories.
Collapse
|
14
|
Liu T, Yuan L, Deng S, Zhang X, Cai H, Ding G, Xu F, Shi L, Wu G, Wang C. Improved the Activity of Phosphite Dehydrogenase and its Application in Plant Biotechnology. Front Bioeng Biotechnol 2021; 9:764188. [PMID: 34900961 PMCID: PMC8655118 DOI: 10.3389/fbioe.2021.764188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/01/2021] [Indexed: 12/02/2022] Open
Abstract
Phosphorus (P) is a nonrenewable resource, which is one of the major challenges for sustainable agriculture. Although phosphite (Phi) can be absorbed by the plant cells through the Pi transporters, it cannot be metabolized by plant and unable to use as P fertilizers for crops. However, transgenic plants that overexpressed phosphite dehydrogenase (PtxD) from bacteria can utilize phosphite as the sole P source. In this study, we aimed to improve the catalytic efficiency of PtxD from Ralstonia sp.4506 (PtxDR4506), by directed evolution. Five mutations were generated by saturation mutagenesis at the 139th site of PtxD R4506 and showed higher catalytic efficiency than native PtxDR4506. The PtxDQ showed the highest catalytic efficiency (5.83-fold as compared to PtxDR4506) contributed by the 41.1% decrease in the K m and 2.5-fold increase in the k cat values. Overexpression of PtxDQ in Arabidopsis and rice showed increased efficiency of phosphite utilization and excellent development when phosphite was used as the primary source of P. High-efficiency PtxD transgenic plant is an essential prerequisite for future agricultural production using phosphite as P fertilizers.
Collapse
Affiliation(s)
- Tongtong Liu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), MOA, Huazhong Agricultural University, Wuhan, China
| | - Lili Yuan
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Suren Deng
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Xiangxian Zhang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongmei Cai
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Guangda Ding
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), MOA, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), MOA, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), MOA, Huazhong Agricultural University, Wuhan, China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chuang Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), MOA, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
15
|
Yuan H, Wang Y, Liu Y, Zhang M, Zou Z. A novel dominant selection system for plant transgenics based on phosphite metabolism catalyzed by bacterial alkaline phosphatase. PLoS One 2021; 16:e0259600. [PMID: 34735551 PMCID: PMC8568168 DOI: 10.1371/journal.pone.0259600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Selective markers are generally indispensable in plant genetic transformation, of which the frequently used are of antibiotic or herbicide resistance. However, the increasing concerns on transgenic biosafety have encouraged many new and safe selective markers emerging, with an eminent representative as phosphite (Phi) in combination to its dehydrogenase (PTDH, e.g. PtxD). As bacterial alkaline phosphatase (BAP) can resemble PtxD to oxidatively convert toxic Phi into metabolizable phosphate (Pi), herein we harnessed it as the substitute of PtxD to develop an alternative Phi-based selection system. We first validated the Escherichia coli BAP (EcBAP) did own an extra enzymatic activity of oxidizing Phi to Pi. We further revealed EcBAP could be used as a dominant selective marker for Agrobacterium-mediated tobacco transformation. Although the involved Phi selection for transformed tobacco cells surprisingly required the presence of Pi, it showed a considerable transformation efficiency and dramatically accelerated transformation procedure, as compared to the routine kanamycin selection and the well-known PtxD/Phi system. Moreover, the EcBAP transgenic tobaccos could metabolize toxic Phi as a phosphorus (P) fertilizer thus underlying Phi-resistance, and competitively possess a dominant growth over wild-type tobacco and weeds under Phi stress. Therefore, this novel BAP/Phi-coupled system, integrating multiple advantages covering biosafe dominant selective marker, plant P utilization and weed management, can provide a PTDH-bypass technological choice to engineer transgenic plant species, especially those of great importance for sustainable agriculture.
Collapse
Affiliation(s)
- Hang Yuan
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
| | - Yuxian Wang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
| | - Yanjuan Liu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
| | - Mengru Zhang
- NHC Key Laboratory of Drug Addiction Medicine, The First Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China
| | - Zhurong Zou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
| |
Collapse
|
16
|
Cutolo E, Tosoni M, Barera S, Herrera-Estrella L, Dall'Osto L, Bassi R. A chimeric hydrolase-PTXD transgene enables chloroplast-based heterologous protein expression and non-sterile cultivation of Chlamydomonas reinhardtii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
17
|
Fontana M, Guillaume T, Bragazza L, Elfouki S, Santonja M, Buttler A, Gerdol R, Brancaleoni L, Sinaj S. Legacy effect of green manure crops fertilized with calcium phosphite on maize production and soil properties. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 295:113092. [PMID: 34182336 DOI: 10.1016/j.jenvman.2021.113092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Recycling phosphorus (P) is crucial to meet future P demand for crop production. We investigated the possibility to use calcium phosphite (Ca-Phi) waste, an industrial by-product, as P fertilizer following the oxidation of phosphite (Phi) to phosphate (Pi) during green manure (GM) cropping in order to target P nutrition of subsequent maize crop. In a greenhouse experiment, four GM crops were fertilized (38 kg P ha-1) with Ca-Phi, triple super phosphate (TSP) or without P (Control) in sandy and clay soils. The harvested GM biomass (containing Phi after Ca-Phi fertilization) was incorporated into the soil before maize sowing. Incorporation of GM residues containing Phi slowed down organic carbon mineralization in clay soil and mass loss of GM residues in sandy soil. Microbial enzymatic activities were affected by Ca-Phi and TSP fertilization at the end of maize crop whereas microbial biomass was similarly influenced by TSP and Ca-Phi in both soils. Compared to Control, Ca-Phi and TSP increased similarly the available P (up to 5 mg P kg-1) in sandy soil, whereas in clay soil available P increased only with Ca-Phi (up to 6 mg P kg-1), indicating that Phi oxidation occurred during GM crops. Accordingly, no Phi was found in maize biomass. However, P fertilization did not enhance aboveground maize productivity and P export, likely because soil available P was not limiting. Overall, our results indicate that Ca-Phi might be used as P source for a subsequent crop since Phi undergoes oxidation during the preliminary GM growth.
Collapse
Affiliation(s)
- Mario Fontana
- Agroscope, Field-Crop Systems and Plant Nutrition, Research Division Plant Production Systems, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Thomas Guillaume
- Agroscope, Field-Crop Systems and Plant Nutrition, Research Division Plant Production Systems, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Luca Bragazza
- Agroscope, Field-Crop Systems and Plant Nutrition, Research Division Plant Production Systems, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Saïd Elfouki
- Agroscope, Field-Crop Systems and Plant Nutrition, Research Division Plant Production Systems, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Mathieu Santonja
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - Alexandre Buttler
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory of Ecological Systems (ECOS), Station 2, CH-1015, Lausanne, Switzerland; Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Site Lausanne, Station 2, CH-1015, Lausanne, Switzerland
| | - Renato Gerdol
- University of Ferrara, Department of Life Science and Biotechnology, Corso Ercole I d'Este 32, I-44121, Ferrara, Italy
| | - Lisa Brancaleoni
- University of Ferrara, Department of Life Science and Biotechnology, Corso Ercole I d'Este 32, I-44121, Ferrara, Italy
| | - Sokrat Sinaj
- Agroscope, Field-Crop Systems and Plant Nutrition, Research Division Plant Production Systems, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland.
| |
Collapse
|
18
|
Giovannoni M, Larini I, Scafati V, Scortica A, Compri M, Pontiggia D, Zapparoli G, Vitulo N, Benedetti M, Mattei B. A novel Penicillium sumatraense isolate reveals an arsenal of degrading enzymes exploitable in algal bio-refinery processes. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:180. [PMID: 34517884 PMCID: PMC8438893 DOI: 10.1186/s13068-021-02030-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 08/30/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Microalgae are coming to the spotlight due to their potential applications in a wide number of fields ranging from the biofuel to the pharmaceutical sector. However, several factors such as low productivity, expensive harvesting procedures and difficult metabolite extractability limit their full utilization at industrial scale. Similarly to the successful employment of enzymatic arsenals from lignocellulolytic fungi to convert lignocellulose into fermentable sugars for bioethanol production, specific algalytic formulations could be used to improve the extractability of lipids from microalgae to produce biodiesel. Currently, the research areas related to algivorous organisms, algal saprophytes and the enzymes responsible for the hydrolysis of algal cell wall are still little explored. RESULTS Here, an algal trap method for capturing actively growing microorganisms was successfully used to isolate a filamentous fungus, that was identified by whole-genome sequencing, assembly and annotation as a novel Penicillium sumatraense isolate. The fungus, classified as P. sumatraense AQ67100, was able to assimilate heat-killed Chlorella vulgaris cells by an enzymatic arsenal composed of proteases such as dipeptidyl- and amino-peptidases, β-1,3-glucanases and glycosidases including α- and β-glucosidases, β-glucuronidase, α-mannosidases and β-galactosidases. The treatment of C. vulgaris with the filtrate from P. sumatraense AQ67100 increased the release of chlorophylls and lipids from the algal cells by 42.6 and 48.9%, respectively. CONCLUSIONS The improved lipid extractability from C. vulgaris biomass treated with the fungal filtrate highlighted the potential of algal saprophytes in the bioprocessing of microalgae, posing the basis for the sustainable transformation of algal metabolites into biofuel-related compounds.
Collapse
Affiliation(s)
- M Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - I Larini
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - V Scafati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - A Scortica
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - M Compri
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - D Pontiggia
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - G Zapparoli
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - N Vitulo
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - M Benedetti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
| | - B Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| |
Collapse
|
19
|
Abstract
Phosphite (Phi)-containing products are marketed for their antifungal and nutritional value. Substantial evidence of the anti-fungal properties of Phi on a wide variety of plants has been documented. Although Phi is readily absorbed by plant leaves and/or roots, the plant response to Phi used as a phosphorus (P) source is variable. Negative effects of Phi on plant growth are commonly observed under P deficiency compared to near adequate plant P levels. Positive responses to Phi may be attributed to some level of fungal disease control. While only a few studies have provided evidence of Phi oxidation through cellular enzymes genetically controlled in plant cells, increasing evidence exists for the potential to manipulate plant genes to enhance oxidation of Phi to phosphate (Pi) in plants. Advances in genetic engineering to sustain growth and yield with Phi + Pi potentially provides a dual fertilization and weed control system. Further advances in genetic manipulation of plants to utilize Phi are warranted. Since Phi oxidation occurs slowly in soils, additional information is needed to characterize Phi oxidation kinetics under variable soil and environmental conditions.
Collapse
|
20
|
Dormatey R, Sun C, Ali K, Fiaz S, Xu D, Calderón-Urrea A, Bi Z, Zhang J, Bai J. ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review. PeerJ 2021; 9:e11809. [PMID: 34395075 PMCID: PMC8323600 DOI: 10.7717/peerj.11809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/27/2021] [Indexed: 12/14/2022] Open
Abstract
Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker genes.
Collapse
Affiliation(s)
- Richard Dormatey
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Chao Sun
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Kazim Ali
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China.,National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Derong Xu
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Alejandro Calderón-Urrea
- Department of Biology, College of Science and Mathematics, California State University, Fresno, CA, USA
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Junlian Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| |
Collapse
|
21
|
Toda N, Murakami H, Kanbara A, Kuroda A, Hirota R. Phosphite Reduces the Predation Impact of Poterioochromonasmalhamensis on Cyanobacterial Culture. PLANTS 2021; 10:plants10071361. [PMID: 34371564 PMCID: PMC8309446 DOI: 10.3390/plants10071361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
Contamination by the predatory zooplankton Poterioochromonas malhamensis is one of the major threats that causes catastrophic damage to commercial-scale microalgal cultivation. However, knowledge of how to manage predator contamination is limited. Previously, we established a phosphite (Pt)-based culture system by engineering Synechococcus elongatus, which exerted a competitive growth advantage against microbial contaminants that compete with phosphate source. Here, we examined whether Pt is effective in suppressing predator-type contamination. Co-culture experiment of Synechococcus with isolated P. malhamensis revealed that, although an addition of Pt at low concentrations up to 2.0 mM was not effective, increased dosage of Pt (~20 mM) resulted in the reduced grazing impact of P. malhamensis. By using unsterilized raw environmental water collected from rivers or ponds, we found that the suppression effect of Pt was dependent on the type of environmental water used. Eukaryotic microbial community analysis of the cultures using environmental water samples revealed that Paraphysomonas, a colorless Chrysophyceae, emerged and dominated under high-Pt conditions, suggesting that Paraphysomonas is insensitive to Pt compared to P. malhamensis. These findings may provide a clue for developing a strategy to reduce the impact of grazer contamination in commercial-scale microalgal cultivation.
Collapse
|
22
|
Fontana M, Bragazza L, Guillaume T, Santonja M, Buttler A, Elfouki S, Sinaj S. Valorization of calcium phosphite waste as phosphorus fertilizer: Effects on green manure productivity and soil properties. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 285:112061. [PMID: 33582477 DOI: 10.1016/j.jenvman.2021.112061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/18/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
The potential to use calcium phosphite (Ca-Phi) as phosphorus (P) fertilizer may represent an effective recycling of P-containing by-products. A greenhouse experiment was conducted to investigate the effect of Ca-Phi (38 kg P ha-1) on soil properties and the growth parameters of four green manure species in clay and sandy soils using Ca-Phi, TSP (triple superphosphate) and control (no fertilization) as treatments. Eight weeks after sowing, we measured aboveground biomass yield, phosphite (Phi) concentration in plant biomass, different soil P pools as well as microbial biomass nutrients. Compared to control, the addition of Ca-Phi did not negatively affect green manure yield, except for lupine (Lupinus albus L.) in clay soil. The Phi concentration in plant biomass varied across species and soil type with a maximum concentration of about 400 mg Phi kg-1 for mustard (Brassica juncea L.) in clay soil. Compared to control, TSP and Ca-Phi fertilization had a similar effect on different P pools and microbial biomass nutrients (C, N and P) although the response was soil-type dependent. In the sandy soil, after Ca-Phi addition the amount of available P (PNHCO3) increased to the same extent as in the TSP treatment (i.e. around 6 mg P kg-1) suggesting that Ca-Phi was, at least partly, oxidized. In the clay soil with high P fixing capacity, Ca-Phi promoted higher PNaHCO3 than TSP likely due to different solubility of chemical P forms. Additional studies are however required to better understand soil microbial responses and to quantify the P agronomical efficiency for the following crop under Ca-Phi fertilization.
Collapse
Affiliation(s)
- Mario Fontana
- Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Luca Bragazza
- Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Thomas Guillaume
- Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Mathieu Santonja
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - Alexandre Buttler
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory of Ecological Systems (ECOS), Station 2, CH-1015, Lausanne, Switzerland; Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Site Lausanne, Station 2, CH-1015, Lausanne, Switzerland
| | - Saïd Elfouki
- Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland
| | - Sokrat Sinaj
- Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260, Nyon, Switzerland.
| |
Collapse
|
23
|
Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
Collapse
Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| |
Collapse
|
24
|
Abdel-Hady GN, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. Engineering Cofactor Specificity of a Thermostable Phosphite Dehydrogenase for a Highly Efficient and Robust NADPH Regeneration System. Front Bioeng Biotechnol 2021; 9:647176. [PMID: 33869158 PMCID: PMC8047080 DOI: 10.3389/fbioe.2021.647176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Nicotinamide adenine dinucleotide phosphate (NADP)-dependent dehydrogenases catalyze a range of chemical reactions useful for practical applications. However, their dependence on the costly cofactor, NAD(P)H remains a challenge which must be addressed. Here, we engineered a thermotolerant phosphite dehydrogenase from Ralstonia sp. 4506 (RsPtxD) by relaxing the cofactor specificity for a highly efficient and robust NADPH regeneration system. The five amino acid residues, Cys174-Pro178, located at the C-terminus of β7-strand region in the Rossmann-fold domain of RsPtxD, were changed by site-directed mutagenesis, resulting in four mutants with a significantly increased preference for NADP. The catalytic efficiency of mutant RsPtxDHARRA for NADP (K cat/K M)NADP was 44.1 μM-1 min-1, which was the highest among the previously reported phosphite dehydrogenases. Moreover, the RsPtxDHARRA mutant exhibited high thermostability at 45°C for up to 6 h and high tolerance to organic solvents, when bound with NADP. We also demonstrated the applicability of RsPtxDHARRA as an NADPH regeneration system in the coupled reaction of chiral conversion of 3-dehydroshikimate to shikimic acid by the thermophilic shikimate dehydrogenase of Thermus thermophilus HB8 at 45°C, which could not be supported by the parent RsPtxD enzyme. Therefore, the RsPtxDHARRA mutant might be a promising alternative NADPH regeneration system for practical applications.
Collapse
Affiliation(s)
- Gamal Nasser Abdel-Hady
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Department of Genetics, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
25
|
Ewens SD, Gomberg AFS, Barnum TP, Borton MA, Carlson HK, Wrighton KC, Coates JD. The diversity and evolution of microbial dissimilatory phosphite oxidation. Proc Natl Acad Sci U S A 2021; 118:e2020024118. [PMID: 33688048 PMCID: PMC7980464 DOI: 10.1073/pnas.2020024118] [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] [Indexed: 11/18/2022] Open
Abstract
Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (Eo') of -650 mV for the PO43-/PO33- couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.
Collapse
Affiliation(s)
- Sophia D Ewens
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Energy & Biosciences Institute, University of California, Berkeley, CA 94720
| | - Alexa F S Gomberg
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Energy & Biosciences Institute, University of California, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| |
Collapse
|
26
|
Feng S, Zeng Y, Cai Z, Wu J, Chan LL, Zhu J, Zhou J. Polystyrene microplastics alter the intestinal microbiota function and the hepatic metabolism status in marine medaka (Oryzias melastigma). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143558. [PMID: 33190902 DOI: 10.1016/j.scitotenv.2020.143558] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
To assess the potential effects of microplastics (MPs) on gut microbiome, a simple investigation of gut microbial structure is not sufficient, and the function and association of gut microbial structure with host health should also be taken into account. Here, the effects of two particle sizes (2 and 200 μm) of polystyrene MPs (PS-MPs) on the gut microbiota of medaka were evaluated following oral administration at 0.3 and 3.0 μg/mg for 28 days. No change in body length and gut histopathology damage were observed. However, the exposure to PS-MPs significantly decreased fish body weight and disrupted the liver anti-oxidative status. The PS-MPs caused a shift in the gut microbial structure of medaka accompanied by changes in community function, including significant environmental stress, increased carbon degradation/fixation activities, and partially modified nitrogen/phosphorus/sulfur metabolic abilities. Furthermore, the PS-MPs exposure disturbed the glycolipid/tyrosine/energy metabolism and the endocrine balance. A potential correlation between the gut microecology and host response to PS-MPs exposure was also observed. These results indicated that the PS-MPs may contribute to gut-liver axis disruption, which could be the underlying toxicological mechanisms of PS-MPs exposure. This work has improved our knowledge about the relationship between gut microbiota dysbiosis and host metabolic disorders following MPs exposure.
Collapse
Affiliation(s)
- Shibo Feng
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Yanhua Zeng
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Jianming Zhu
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China.
| |
Collapse
|
27
|
Liu K, Wang M, Zhou Y, Wang H, Liu Y, Han L, Han W. Exploration of the cofactor specificity of wild-type phosphite dehydrogenase and its mutant using molecular dynamics simulations. RSC Adv 2021; 11:14527-14533. [PMID: 35424015 PMCID: PMC8697927 DOI: 10.1039/d1ra00221j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/12/2021] [Accepted: 04/13/2021] [Indexed: 01/02/2023] Open
Abstract
Phosphite dehydrogenase (Pdh) catalyzes the NAD-dependent oxidation of phosphite to phosphate with the formation of NADH. It can be used in several bioorthogonal systems for metabolic control and related applications, for example, bioelectricity. At present, NAD has poor stability at high concentrations and costs are expensive. Implementation of a non-natural cofactor alternative to the ubiquitous redox cofactor nicotinamide adenosine dinucleotide (NAD) is of great scientific and biotechnological interest. Several Pdhs have been engineered to favor a smaller-sized NAD analogue with a cheaper price and better thermal stability, namely, nicotinamide cytosine dinucleotide (NCD). However, the conformational changes of two cofactors binding to Pdh remain unknown. In this study, five molecular dynamics (MD) simulations were performed to exploit the different cofactors binding to wild-type (WT) Pdh and mutant-type (MT) Pdh (I151R/P176E/M207A). The results were as follows: First, compared with WT Pdh, the cofactor-binding pocket of mutant Pdh became smaller, which may favor a smaller-sized NCD. Second, secondary structure analysis showed that the alpha helices in residues 151–207 partly disappeared in mutant Pdh binding to NAD or NCD. Our theoretical results may provide a basis for further studies on the Pdh family. Phosphite dehydrogenase (Pdh) catalyzes the NAD-dependent oxidation of phosphite to phosphate with the formation of NADH.![]()
Collapse
Affiliation(s)
- Kunlu Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| | - Min Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| | - Yubo Zhou
- High School Attached to Northeast Normal University
- Changchun 130012
- China
| | - Hongxiang Wang
- High School Attached to Northeast Normal University
- Changchun 130012
- China
| | - Yudong Liu
- High School Attached to Northeast Normal University
- Changchun 130012
- China
| | - Lu Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| |
Collapse
|
28
|
Benedetti M, Barera S, Longoni P, Guardini Z, Herrero Garcia N, Bolzonella D, Lopez‐Arredondo D, Herrera‐Estrella L, Goldschmidt‐Clermont M, Bassi R, Dall’Osto L. A microalgal-based preparation with synergistic cellulolytic and detoxifying action towards chemical-treated lignocellulose. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:124-137. [PMID: 32649019 PMCID: PMC7769238 DOI: 10.1111/pbi.13447] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/19/2020] [Accepted: 06/28/2020] [Indexed: 05/28/2023]
Abstract
High-temperature bioconversion of lignocellulose into fermentable sugars has drawn attention for efficient production of renewable chemicals and biofuels, because competing microbial activities are inhibited at elevated temperatures and thermostable cell wall degrading enzymes are superior to mesophilic enzymes. Here, we report on the development of a platform to produce four different thermostable cell wall degrading enzymes in the chloroplast of Chlamydomonas reinhardtii. The enzyme blend was composed of the cellobiohydrolase CBM3GH5 from C. saccharolyticus, the β-glucosidase celB from P. furiosus, the endoglucanase B and the endoxylanase XynA from T. neapolitana. In addition, transplastomic microalgae were engineered for the expression of phosphite dehydrogenase D from Pseudomonas stutzeri, allowing for growth in non-axenic media by selective phosphite nutrition. The cellulolytic blend composed of the glycoside hydrolase (GH) domain GH12/GH5/GH1 allowed the conversion of alkaline-treated lignocellulose into glucose with efficiencies ranging from 14% to 17% upon 48h of reaction and an enzyme loading of 0.05% (w/w). Hydrolysates from treated cellulosic materials with extracts of transgenic microalgae boosted both the biogas production by methanogenic bacteria and the mixotrophic growth of the oleaginous microalga Chlorella vulgaris. Notably, microalgal treatment suppressed the detrimental effect of inhibitory by-products released from the alkaline treatment of biomass, thus allowing for efficient assimilation of lignocellulose-derived sugars by C. vulgaris under mixotrophic growth.
Collapse
Affiliation(s)
- Manuel Benedetti
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
- Present address:
Dipartimento MESVAUniversità dell'AquilaCoppitoAQItaly
| | - Simone Barera
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| | - Paolo Longoni
- Faculty of ScienceInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Zeno Guardini
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| | | | | | - Damar Lopez‐Arredondo
- StelaGenomics MexicoS de RL de CVIrapuato, GuanajuatoMexico
- Institute of Genomics for Crop Abiotic Stress ToleranceTexas Tech UniversityLubbockTXUSA
| | - Luis Herrera‐Estrella
- Laboratorio Nacional de Genómica para la BiodiversidadCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, GuanajuatoMexico
- Institute of Genomics for Crop Abiotic Stress ToleranceTexas Tech UniversityLubbockTXUSA
| | | | - Roberto Bassi
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| | - Luca Dall’Osto
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| |
Collapse
|
29
|
Tensi L, Macchioni A. Extremely Fast NADH-Regeneration Using Phosphonic Acid as Hydride Source and Iridium-pyridine-2-sulfonamidate Catalysts. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02261] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Leonardo Tensi
- Dipartimento di Chimica, Biologia e Biotecnologie and CIRCC, Università degli Studi di Perugia, Via Elce di Sotto, 8-06123 Perugia, Italy
| | - Alceo Macchioni
- Dipartimento di Chimica, Biologia e Biotecnologie and CIRCC, Università degli Studi di Perugia, Via Elce di Sotto, 8-06123 Perugia, Italy
| |
Collapse
|
30
|
Cutolo E, Tosoni M, Barera S, Herrera-Estrella L, Dall’Osto L, Bassi R. A Phosphite Dehydrogenase Variant with Promiscuous Access to Nicotinamide Cofactor Pools Sustains Fast Phosphite-Dependent Growth of Transplastomic Chlamydomonas reinhardtii. PLANTS 2020; 9:plants9040473. [PMID: 32276527 PMCID: PMC7238262 DOI: 10.3390/plants9040473] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 01/23/2023]
Abstract
Heterologous expression of the NAD+-dependent phosphite dehydrogenase (PTXD) bacterial enzyme from Pseudomonas stutzerii enables selective growth of transgenic organisms by using phosphite as sole phosphorous source. Combining phosphite fertilization with nuclear expression of the ptxD transgene was shown to be an alternative to herbicides in controlling weeds and contamination of algal cultures. Chloroplast expression of ptxD in Chlamydomonas reinhardtii was proposed as an environmentally friendly alternative to antibiotic resistance genes for plastid transformation. However, PTXD activity in the chloroplast is low, possibly due to the low NAD+/NADP+ ratio, limiting the efficiency of phosphite assimilation. We addressed the intrinsic constraints of the PTXD activity in the chloroplast and improved its catalytic efficiency in vivo via rational mutagenesis of key residues involved in cofactor binding. Transplastomic lines carrying a mutagenized PTXD version promiscuously used NADP+ and NAD+ for converting phosphite into phosphate and grew faster compared to those expressing the wild type protein. The modified PTXD enzyme also enabled faster and reproducible selection of transplastomic colonies by directly plating on phosphite-containing medium. These results allow using phosphite as selective agent for chloroplast transformation and for controlling biological contaminants when expressing heterologous proteins in algal chloroplasts, without compromising on culture performance.
Collapse
Affiliation(s)
- Edoardo Cutolo
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Matteo Tosoni
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Simone Barera
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA) Cinvestav, 36821 Irapuato, Guanajuato, Mexico;
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Box 42122, Lubbock, TX 79409, USA
| | - Luca Dall’Osto
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Roberto Bassi
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
- Correspondence: ; Tel.: +39-045-802-7916
| |
Collapse
|
31
|
Abstract
Type I Baeyer–Villiger monooxygenases (BVMOs) are flavin-dependent monooxygenases that catalyze the oxidation of ketones to esters or lactones, a reaction otherwise performed in chemical processes by employing hazardous and toxic peracids. Even though various BVMOs are extensively studied for their promising role in industrial biotechnology, there is still a demand for enzymes that are able to retain activity at high saline concentrations. To this aim, and based on comparative in silico analyses, we cloned HtBVMO from the extremely halophilic archaeon Haloterrigena turkmenica DSM 5511. When expressed in standard mesophilic cell factories, proteins adapted to hypersaline environments often behave similarly to intrinsically disordered polypeptides. Nevertheless, we managed to express HtBVMO in Escherichia coli and could purify it as active enzyme. The enzyme was characterized in terms of its salt-dependent activity and resistance to some water–organic-solvent mixtures. Although HtBVMO does not seem suitable for industrial applications, it provides a peculiar example of an alkalophilic and halophilic BVMO characterized by an extremely negative charge. Insights into the behavior and structural properties of such salt-requiring may contribute to more efficient strategies for engineering the tuned stability and solubility of existing BVMOs.
Collapse
|
32
|
Changko S, Rajakumar PD, Young REB, Purton S. The phosphite oxidoreductase gene, ptxD as a bio-contained chloroplast marker and crop-protection tool for algal biotechnology using Chlamydomonas. Appl Microbiol Biotechnol 2020; 104:675-686. [PMID: 31788712 PMCID: PMC6943410 DOI: 10.1007/s00253-019-10258-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/10/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
Edible microalgae have potential as low-cost cell factories for the production and oral delivery of recombinant proteins such as vaccines, anti-bacterials and gut-active enzymes that are beneficial to farmed animals including livestock, poultry and fish. However, a major economic and technical problem associated with large-scale cultivation of microalgae, even in closed photobioreactors, is invasion by contaminating microorganisms. Avoiding this requires costly media sterilisation, aseptic techniques during set-up and implementation of 'crop-protection' strategies during cultivation. Here, we report a strain improvement approach in which the chloroplast of Chlamydomonas reinhardtii is engineered to allow oxidation of phosphite to its bio-available form: phosphate. We have designed a synthetic version of the bacterial gene (ptxD)-encoding phosphite oxidoreductase such that it is highly expressed in the chloroplast but has a Trp→Opal codon reassignment for bio-containment of the transgene. Under mixotrophic conditions, the growth rate of the engineered alga is unaffected when phosphate is replaced with phosphite in the medium. Furthermore, under non-sterile conditions, growth of contaminating microorganisms is severely impeded in phosphite medium. This, therefore, offers the possibility of producing algal biomass under non-sterile conditions. The ptxD gene can also serve as a dominant marker for genetic engineering of any C. reinhardtii strain, thereby avoiding the use of antibiotic resistance genes as markers and allowing the 'retro-fitting' of existing engineered strains. As a proof of concept, we demonstrate the application of our ptxD technology to a strain expressing a subunit vaccine targeting a major viral pathogen of farmed fish.
Collapse
Affiliation(s)
- Saowalak Changko
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Priscilla D Rajakumar
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Rosanna E B Young
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
33
|
Howe GW, van der Donk WA. Temperature-Independent Kinetic Isotope Effects as Evidence for a Marcus-like Model of Hydride Tunneling in Phosphite Dehydrogenase. Biochemistry 2019; 58:4260-4268. [PMID: 31535852 PMCID: PMC6852621 DOI: 10.1021/acs.biochem.9b00732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase catalyzes the transfer of a hydride from phosphite to NAD+, producing phosphate and NADH. We have evaluated the role of hydride tunneling in a thermostable variant of this enzyme (17X-PTDH) by measuring the temperature dependence of the primary 2H kinetic isotope effects (KIEs) between 5 and 45 °C. Pre-steady-state kinetic measurements were used to demonstrate that the hydride transfer is rate-determining across this temperature range and that the observed KIEs are equal to the intrinsic isotope effect on the chemical step. The KIEs on the pre-exponential factor (AH/AD) and the activation energy (ΔEa) were 1.6 ± 0.1 and 0.21 ± 0.05 kcal/mol, respectively, suggesting that 17X-PTDH facilitates extensive tunneling of both isotopes via a Marcus-like model. Site-directed mutagenesis was used to evaluate the role of an active site threonine (Thr104) found on the back face of the nicotinamide in promoting the close packing of the substrates. In mutants with reduced steric bulk at this position, values of AH/AD and ΔEa fall within the range describing semiclassical "over the barrier" reactivity, suggesting that Thr104 acts as a steric backstop to promote tunneling in 17X-PTDH. Whereas hydrogen tunneling is now a widely appreciated feature of C-H activating enzymes, these observations with a P-H activating system are consistent with the proposal that tunneling is likely to be a common feature on all enzymes that catalyze hydrogen transfers.
Collapse
Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| |
Collapse
|
34
|
Sandoval-Vargas JM, Jiménez-Clemente LA, Macedo-Osorio KS, Oliver-Salvador MC, Fernández-Linares LC, Durán-Figueroa NV, Badillo-Corona JA. Use of the ptxD gene as a portable selectable marker for chloroplast transformation in Chlamydomonas reinhardtii. Mol Biotechnol 2019; 61:461-468. [PMID: 30997667 DOI: 10.1007/s12033-019-00177-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic biology and genetic engineering in algae offer an unprecedented opportunity to develop species with traits that can help solve the problems associated with food and energy supply in the 21st century. In the green alga Chlamydomonas reinhardtii, foreign genes can be expressed from the chloroplast genome for molecular farming and metabolic engineering to obtain commodities and high-value molecules. To introduce these genes, selectable markers, which rely mostly on the use of antibiotics, are needed. This has risen social concern associated with the potential risk of horizontal gene transfer across life kingdoms, which has led to a quest for antibiotic-free selectable markers. Phosphorus (P) is a scarce nutrient element that most organisms can only assimilate in its most oxidized form as phosphate (Pi); however, some organisms are able to oxidize phosphite (Phi) to Pi prior to incorporation into the central metabolism of P. As an alternative to the use of the two positive selectable makers already available for chloroplast transformation in C. reinhardtii, the aadA and the aphA-6 genes, that require the use of antibiotics, we investigated if a phosphite-based selection method could be used for the direct recovery of chloroplast transformed lines in this alga. Here we show that following bombardment with a vector carrying the ptxD gene from Pseudomonas stutzeri WM88, only cells that integrate and express the gene proliferate and form colonies using Phi as the sole P source. Our results demonstrate that a selectable marker based on the assimilation of Phi can be used for chloroplasts transformation in a biotechnologically relevant organism. The portable selectable marker we have developed is, in more than 18 years, the latest addition to the markers available for selection of chloroplast transformed cells in C. reinhardtii. The ptxD gene will contribute to the repertoire of tools available for synthetic biology and genetic engineering in the chloroplast of C. reinhardtii.
Collapse
Affiliation(s)
- José M Sandoval-Vargas
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticomán, 07340, Mexico City, Mexico
| | - Luis A Jiménez-Clemente
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticomán, 07340, Mexico City, Mexico
| | - Karla S Macedo-Osorio
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticomán, 07340, Mexico City, Mexico
| | - María C Oliver-Salvador
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticomán, 07340, Mexico City, Mexico
| | - Luis C Fernández-Linares
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticomán, 07340, Mexico City, Mexico
| | - Noé V Durán-Figueroa
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticomán, 07340, Mexico City, Mexico
| | - Jesús A Badillo-Corona
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticomán, 07340, Mexico City, Mexico.
| |
Collapse
|
35
|
Phosphite binding by the HtxB periplasmic binding protein depends on the protonation state of the ligand. Sci Rep 2019; 9:10231. [PMID: 31308436 PMCID: PMC6629693 DOI: 10.1038/s41598-019-46557-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/01/2019] [Indexed: 02/08/2023] Open
Abstract
Phosphorus acquisition is critical for life. In low phosphate conditions, some species of bacteria have evolved mechanisms to import reduced phosphorus compounds, such as phosphite and hypophosphite, as alternative phosphorus sources. Uptake is facilitated by high-affinity periplasmic binding proteins (PBPs) that bind cargo in the periplasm and shuttle it to an ATP-binding cassette (ABC)-transporter in the bacterial inner membrane. PtxB and HtxB are the PBPs responsible for binding phosphite and hypophosphite, respectively. They recognize the P-H bond of phosphite/hypophosphite via a conserved P-H...π interaction, which confers nanomolar dissociation constants for their respective ligands. PtxB also has a low-level binding affinity for phosphate and hypophosphite, whilst HtxB can facilitate phosphite uptake in vivo. However, HtxB does not bind phosphate, thus the HtxBCDE transporter has recently been successfully exploited for biocontainment of genetically modified organisms by phosphite-dependent growth. Here we use a combination of X-ray crystallography, NMR and Microscale Thermophoresis to show that phosphite binding to HtxB depends on the protonation state of the ligand, suggesting that pH may effect the efficiency of phosphite uptake by HtxB in biotechnology applications.
Collapse
|
36
|
What to sacrifice? Fusions of cofactor regenerating enzymes with Baeyer-Villiger monooxygenases and alcohol dehydrogenases for self-sufficient redox biocatalysis. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
37
|
Ram B, Fartyal D, Sheri V, Varakumar P, Borphukan B, James D, Yadav R, Bhatt A, Agrawal PK, Achary VMM, Reddy MK. Characterization of phoA, a Bacterial Alkaline Phosphatase for Phi Use Efficiency in Rice Plant. FRONTIERS IN PLANT SCIENCE 2019; 10:37. [PMID: 30858852 PMCID: PMC6397861 DOI: 10.3389/fpls.2019.00037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Fertilizers and herbicides are two major components in the agriculture system for achieving crop productivity. Massive use of orthophosphate fertilizers and herbicides poses threats to phosphate reserves and aids the evolution of herbicide tolerant weed biotypes. Phosphite (Phi), a phosphate analog, has been proposed as more beneficial than traditionally used phosphate fertilizers and herbicides in the agriculture. We developed phoA overexpressing transgenic rice that minimizes the phosphate loss and contributes to weed management in the agriculture. The phoA rice lines showed improved root, shoot length and total biomass production under phosphite conditions. Additionally, the complete phenotype and productivity of phoA lines under the phosphite treatment attained was similar to that of plants under phosphate sufficient condition. The Phi metabolizing properties of the phoA overexpressed lines improved under the Phi application and phi treatment enabled controlling of weeds without compromising the yield of transgenic rice plants. Our results indicated that phoA alone or in combination with other Phi metabolizing gene(s) can possibly be used as an effective ameliorating system for improving crop plants for phi-based fertilization and weed management strategy in the agriculture.
Collapse
Affiliation(s)
- Babu Ram
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Biotechnology, Uttarakhand Technical University, Dehradun, India
| | - Dhirendra Fartyal
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Biotechnology, Uttarakhand Technical University, Dehradun, India
| | - Vijay Sheri
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Panditi Varakumar
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Bhabesh Borphukan
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Donald James
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Renu Yadav
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Arun Bhatt
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering and Technology, Pauri Garhwal, India
| | - Pawan K. Agrawal
- National Agricultural Science Fund, Indian Council of Agricultural Research, New Delhi, India
| | - V. Mohan M. Achary
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Malireddy K. Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| |
Collapse
|
38
|
Matelska D, Shabalin IG, Jabłońska J, Domagalski MJ, Kutner J, Ginalski K, Minor W. Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase. BMC Evol Biol 2018; 18:199. [PMID: 30577795 PMCID: PMC6303947 DOI: 10.1186/s12862-018-1309-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/27/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members. RESULTS We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase. CONCLUSIONS The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.
Collapse
Affiliation(s)
- Dorota Matelska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA
| | - Jagoda Jabłońska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Marcin J Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA
| | - Jan Kutner
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA. .,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA. .,Department of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland.
| |
Collapse
|
39
|
Howe GW, van der Donk WA. 18O Kinetic Isotope Effects Reveal an Associative Transition State for Phosphite Dehydrogenase Catalyzed Phosphoryl Transfer. J Am Chem Soc 2018; 140:17820-17824. [PMID: 30525552 DOI: 10.1021/jacs.8b06301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase (PTDH) catalyzes an unusual phosphoryl transfer reaction in which water displaces a hydride leaving group. Despite extensive effort, it remains unclear whether PTDH catalysis proceeds via an associative or dissociative mechanism. Here, primary 2H and secondary 18O kinetic isotope effects (KIEs) were determined and used together with computation to characterize the transition state (TS) catalyzed by a thermostable PTDH (17X-PTDH). The large, normal 18O KIEs suggest an associative mechanism. Various transition state structures were computed within a model of the enzyme active site and 2H and 18O KIEs were predicted to evaluate the accuracy of each TS. This analysis suggests that 17X-PTDH catalyzes an associative process with little leaving group displacement and extensive nucleophilic participation. This tight TS is likely a consequence of the extremely poor leaving group requiring significant P-O bond formation to expel the hydride. This finding contrasts with the dissociative TSs in most phosphoryl transfer reactions from phosphate mono- and diesters.
Collapse
Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| |
Collapse
|
40
|
Venkiteshwaran K, McNamara PJ, Mayer BK. Meta-analysis of non-reactive phosphorus in water, wastewater, and sludge, and strategies to convert it for enhanced phosphorus removal and recovery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:661-674. [PMID: 29990914 DOI: 10.1016/j.scitotenv.2018.06.369] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Current and future trends indicate that mining of natural phosphorus (P) reserves is occurring faster than natural geologic replenishment. This mobilization has not only led to P supply concerns, but has also polluted many of the world's freshwater bodies and oceans. Recovery and reuse of this nuisance P offers a long-term solution simultaneously addressing mineral P accessibility and P-based pollution. Available physical, chemical, and biological P removal/recovery processes can achieve low total P (TP) concentrations (≤100 μg/L) and some processes can also recover P for direct reuse as fertilizers (e.g., struvite). However, as shown by our meta-analysis of over 20,000 data points on P quantity and P form, the P in water matrices is not always present in the reactive P (RP) form that is most amenable to recovery for direct reuse. Thus, strategies for removing and recovering other P fractions in water/wastewater are essential to provide environmental protection via P removal and also advance the circular P economy via P recovery. Specifically, conversion of non-reactive P (NRP) to the more readily removable/recoverable RP form may offer a feasible approach; however, extremely limited data on such applications currently exist. This review investigates the role of NRP in various water matrices; identifies NRP conversion mechanisms; and evaluates biological, physical, thermal, and chemical processes with potential to enhance P removal and recovery by converting the NRP to RP. This information provides critical insights into future research needs and technology advancements to enhance P removal and recovery.
Collapse
Affiliation(s)
- Kaushik Venkiteshwaran
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA
| | - Patrick J McNamara
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA.
| |
Collapse
|
41
|
Benedetti M, Vecchi V, Barera S, Dall’Osto L. Biomass from microalgae: the potential of domestication towards sustainable biofactories. Microb Cell Fact 2018; 17:173. [PMID: 30414618 PMCID: PMC6230293 DOI: 10.1186/s12934-018-1019-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022] Open
Abstract
Interest in bulk biomass from microalgae, for the extraction of high-value nutraceuticals, bio-products, animal feed and as a source of renewable fuels, is high. Advantages of microalgal vs. plant biomass production include higher yield, use of non-arable land, recovery of nutrients from wastewater, efficient carbon capture and faster development of new domesticated strains. Moreover, adaptation to a wide range of environmental conditions evolved a great genetic diversity within this polyphyletic group, making microalgae a rich source of interesting and useful metabolites. Microalgae have the potential to satisfy many global demands; however, realization of this potential requires a decrease of the current production costs. Average productivity of the most common industrial strains is far lower than maximal theoretical estimations, suggesting that identification of factors limiting biomass yield and removing bottlenecks are pivotal in domestication strategies aimed to make algal-derived bio-products profitable on the industrial scale. In particular, the light-to-biomass conversion efficiency represents a major constraint to finally fill the gap between theoretical and industrial productivity. In this respect, recent results suggest that significant yield enhancement is feasible. Full realization of this potential requires further advances in cultivation techniques, together with genetic manipulation of both algal physiology and metabolic networks, to maximize the efficiency with which solar energy is converted into biomass and bio-products. In this review, we draft the molecular events of photosynthesis which regulate the conversion of light into biomass, and discuss how these can be targeted to enhance productivity through mutagenesis, strain selection or genetic engineering. We outline major successes reached, and promising strategies to achieving significant contributions to future microalgae-based biotechnology.
Collapse
Affiliation(s)
- Manuel Benedetti
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Valeria Vecchi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Simone Barera
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Luca Dall’Osto
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| |
Collapse
|
42
|
Smith-Moore CM, Grunden AM. Bacteria and archaea as the sources of traits for enhanced plant phenotypes. Biotechnol Adv 2018; 36:1900-1916. [DOI: 10.1016/j.biotechadv.2018.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/12/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
|
43
|
Motomura K, Sano K, Watanabe S, Kanbara A, Gamal Nasser AH, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. Synthetic Phosphorus Metabolic Pathway for Biosafety and Contamination Management of Cyanobacterial Cultivation. ACS Synth Biol 2018; 7:2189-2198. [PMID: 30203964 DOI: 10.1021/acssynbio.8b00199] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent progress in genetic engineering and synthetic biology have greatly expanded the production capabilities of cyanobacteria, but concerns regarding biosafety issues and the risk of contamination of cultures in outdoor culture conditions remain to be resolved. With this dual goal in mind, we applied the recently established biological containment strategy based on phosphite (H3PO3, Pt) dependency to the model cyanobacterium Synechococcus elongatus PCC 7942 ( Syn 7942). Pt assimilation capability was conferred on Syn 7942 by the introduction of Pt dehydrogenase (PtxD) and hypophosphite transporter (HtxBCDE) genes that allow the uptake of Pt, but not phosphate (H3PO4, Pi). We then identified and disrupted the two indigenous Pi transporters, pst (Synpcc7942_2441 to 2445) and pit (Synpcc7942_0184). The resultant strain failed to grow on any media containing various types of P compounds other than Pt. The strain did not yield any escape mutants for at least 28 days with a detection limit of 3.6 × 10-11 per colony forming unit, and rapidly lost viability in the absence of Pt. Moreover, growth competition of the Pt-dependent strain with wild-type cyanobacteria revealed that the Pt-dependent strain could dominate in cultures containing Pt as the sole P source. Because Pt is rarely available in aquatic environments this strategy can contribute to both biosafety and contamination management of genetically engineered cyanobacteria.
Collapse
Affiliation(s)
- Kei Motomura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kosuke Sano
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Satoru Watanabe
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Akihiro Kanbara
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Abdel-Hady Gamal Nasser
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
| |
Collapse
|
44
|
Furukawa N, Miyanaga A, Nakajima M, Taguchi H. Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria. Biochemistry 2018; 57:5388-5406. [PMID: 30149697 DOI: 10.1021/acs.biochem.8b00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
d-Lactate dehydrogenases (d-LDHs) from Fusobacterium nucleatum (FnLDH) and Escherichia coli (EcLDH) exhibit positive cooperativity in substrate binding, and the Pseudomonas aeruginosa enzyme (PaLDH) shows negatively cooperative substrate binding. The apo and ternary complex structures of FnLDH and PaLDH have been determined together with the apo-EcLDH structure. The three enzymes consistently form homotetrameric structures with three symmetric axes, the P-, Q-, and R-axes, unlike Lactobacillus d-LDHs, P-axis-related dimeric enzymes, although apo-FnLDH and EcLDH form asymmetric and distorted quaternary structures. The tetrameric structure allows apo-FnLDH and EcLDH to form wide intersubunit contact surfaces between the opened catalytic domains of the two Q-axis-related subunits in coordination with their asymmetric and distorted quaternary structures. These contact surfaces comprise intersubunit hydrogen bonds and hydrophobic interactions and likely prevent the domain closure motion during initial substrate binding. In contrast, apo-PaLDH possesses a highly symmetrical quaternary structure and partially closed catalytic domains that are favorable for initial substrate binding and forms virtually no intersubunit contact surface between the catalytic domains, which present their negatively charged surfaces to each other at the subunit interface. Complex FnLDH and PaLDH possess highly symmetrical quaternary structures with closed forms of the catalytic domains, which are separate from each other at the subunit interface. Structure-based mutations successfully converted the three enzymes to their dimeric forms, which exhibited no significant cooperativity in substrate binding. These observations indicate that the three enzymes undergo typical sequential allosteric transitions to exhibit their distinctive allosteric functions through the tetrameric structures.
Collapse
Affiliation(s)
- Nayuta Furukawa
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan.,Department of Applied Life Sciences , Niigata University of Pharmacy and Applied Life Sciences , 265-1 Higashijima , Akiha-ku, Niigata 956-8603 , Japan
| | - Akimasa Miyanaga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| |
Collapse
|
45
|
Sandoval-Vargas JM, Macedo-Osorio KS, Durán-Figueroa NV, Garibay-Orijel C, Badillo-Corona JA. Chloroplast engineering of Chlamydomonas reinhardtii to use phosphite as phosphorus source. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
46
|
Miyahara Y, Oota M, Tsuge T. NADPH supply for poly(3-hydroxybutyrate) synthesis concomitant with enzymatic oxidation of phosphite. J Biosci Bioeng 2018; 126:764-768. [PMID: 29910188 DOI: 10.1016/j.jbiosc.2018.05.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 01/07/2023]
Abstract
Acetoacetyl-CoA reductase (PhaB), involved in poly(3-hydroxybutyrate) [P(3HB)] biosynthesis, requires the coenzyme NADPH as a reducing agent. In this study, the effect of NADPH supply on P(3HB) production was investigated in vitro and in vivo using a phosphite dehydrogenase double mutant (PtxDEAAR), which catalyzes oxidation of phosphite to phosphate with the generation of NADH and NADPH. In an in vitro assay using purified enzymes, P(3HB) polymerization was observed only when phosphite and PtxDEAAR were present, confirming that NADPH was supplied to PhaB. In an in vivo assay using Escherichia coli as a production host for P(3HB), the presence of phosphite and PtxDEAAR did not influence the yield of P(3HB) under normal growth conditions. However, P(3HB) yield increased 3.2-fold in non-growing E. coli cells compared to the control, suggesting that PtxDEAAR-mediated NADPH generation is coupled with P(3HB) biosynthesis. This study confirmed the use of PtxDEAAR for supplying NADPH during P(3HB) synthesis in vitro and in vivo.
Collapse
Affiliation(s)
- Yuki Miyahara
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Mino Oota
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Takeharu Tsuge
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan; Department of Materials Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| |
Collapse
|
47
|
Selective fertilization with phosphite allows unhindered growth of cotton plants expressing the ptxD gene while suppressing weeds. Proc Natl Acad Sci U S A 2018; 115:E6946-E6955. [PMID: 29866830 PMCID: PMC6055188 DOI: 10.1073/pnas.1804862115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An increasing number of herbicide-resistant weeds are being reported in the United States, Argentina, and Brazil. This is becoming a global challenge for the production of several major crops, such as cotton, maize, and soybean. New strategies for weed control are required to sustain agricultural production while reducing our dependence on herbicides. Here, we report that selective fertilization of transgenic cotton, expressing a bacterial phosphite dehydrogenase (PTXD), with phosphite provides an effective way to suppress weed growth. Importantly, we show that the ptxD-transgenic cotton plants successfully outcompete a highly aggressive glyphosate-resistant weed. The ptxD/phosphite system represents one of the most promising technologies of recent times with potential to solve many of the agricultural and environmental problems that we encounter currently. Weeds, which have been the bane of agriculture since the beginning of civilization, are managed manually, mechanically, and, more recently, by chemicals. However, chemical control options are rapidly shrinking due to the recent rise in the number of herbicide-resistant weeds in crop fields, with few alternatives on the horizon. Therefore, there is an urgent need for alternative weed suppression systems to sustain crop productivity while reducing our dependence on herbicides and tillage. Such a development will also allay some of the negative perceptions associated with the use of herbicide-resistance genes and heavy dependence on herbicides. Transgenic plants expressing the bacterial phosphite dehydrogenase (ptxD) gene gain an ability to convert phosphite (Phi) into orthophosphate [Pi, the metabolizable form of phosphorus (P)]. Such plants allow for a selective fertilization scheme, based on Phi as the sole source of P for the crop, while offering an effective alternative for suppressing weed growth. Here, we show that, when P is supplied in the form of Phi, ptxD-expressing cotton (Gossypium hirsutum L.) plants outcompete, in both artificial substrates and natural soils from agricultural fields, three different monocot and dicot weed species intentionally introduced in the experiments, as well as weeds naturally present in the tested soils. Importantly, the ptxD/Phi system proved highly efficacious in inhibiting the growth of glyphosate-resistant Palmer amaranth. With over 250 weed species resistant to currently available herbicides, ptxD-transgenic plants fertilized with Phi could provide an effective alternative to suppressing the growth of these weeds while providing adequate nutrition to the crop.
Collapse
|
48
|
Slabu I, Galman JL, Iglesias C, Weise NJ, Lloyd RC, Turner NJ. n-Butylamine as an alternative amine donor for the stereoselective biocatalytic transamination of ketones. Catal Today 2018. [DOI: 10.1016/j.cattod.2017.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
49
|
Archean phosphorus liberation induced by iron redox geochemistry. Nat Commun 2018; 9:1346. [PMID: 29632373 PMCID: PMC5890264 DOI: 10.1038/s41467-018-03835-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 03/15/2018] [Indexed: 11/23/2022] Open
Abstract
The element phosphorus (P) is central to ecosystem growth and is proposed to be a limiting nutrient for life. The Archean ocean may have been strongly phosphorus-limited due to the selective binding of phosphate to iron oxyhydroxide. Here we report a new route to solubilizing phosphorus in the ancient oceans: reduction of phosphate to phosphite by iron(II) at low (<200 °C) diagenetic temperatures. Reduction of phosphate to phosphite was likely widespread in the Archean, as the reaction occurs rapidly and is demonstrated from thermochemical modeling, experimental analogs, and detection of phosphite in early Archean rocks. We further demonstrate that the higher solubility of phosphite compared to phosphate results in the liberation of phosphorus from ferruginous sediments. This phosphite is relatively stable after its formation, allowing its accumulation in the early oceans. As such, phosphorus, not as phosphate but as phosphite, could have been a major nutrient in early pre-oxygenated oceans. Phosphorus is presumed to have been a limiting nutrient in the Archean ocean due to binding to iron oxides. Here, the authors show the heating of iron with phosphate results in the reduction of phosphate to the ion phosphite, which is solubilized and ameliorates the issue of a low Archean phosphorus supply.
Collapse
|
50
|
Liu J, Li H, Zhao G, Caiyin Q, Qiao J. Redox cofactor engineering in industrial microorganisms: strategies, recent applications and future directions. J Ind Microbiol Biotechnol 2018; 45:313-327. [PMID: 29582241 DOI: 10.1007/s10295-018-2031-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/22/2018] [Indexed: 02/07/2023]
Abstract
NAD and NADP, a pivotal class of cofactors, which function as essential electron donors or acceptors in all biological organisms, drive considerable catabolic and anabolic reactions. Furthermore, they play critical roles in maintaining intracellular redox homeostasis. However, many metabolic engineering efforts in industrial microorganisms towards modification or introduction of metabolic pathways, especially those involving consumption, generation or transformation of NAD/NADP, often induce fluctuations in redox state, which dramatically impede cellular metabolism, resulting in decreased growth performance and biosynthetic capacity. Here, we comprehensively review the cofactor engineering strategies for solving the problematic redox imbalance in metabolism modification, as well as their features, suitabilities and recent applications. Some representative examples of in vitro biocatalysis are also described. In addition, we briefly discuss how tools and methods from the field of synthetic biology can be applied for cofactor engineering. Finally, future directions and challenges for development of cofactor redox engineering are presented.
Collapse
Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Huiling Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Guangrong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
| |
Collapse
|