1
|
Kim S, Koo J. Recent advances in utilization of ferredoxins for biosynthesis of valuable compounds. World J Microbiol Biotechnol 2022; 38:178. [PMID: 35941298 DOI: 10.1007/s11274-022-03371-9] [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: 07/02/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022]
Abstract
Ferredoxin (Fd) is a small metalloprotein holding one or two Fe-S clusters in its inner shell. Like many other metalloproteins, Fd is redox active and involved in electron transfer during cellular metabolism. The electrons from reduced Fd are mostly used to regenerate NADPH under physiological conditions. Increasing number of attempts have been reported, however, where Fd delivers electrons to enable biosynthesis of valuable compounds. Various compounds ranging from H2 to vitamin D3 have been synthesized successfully using electrons mediated by Fd molecules. In this review, we provide an overview of the engineering studies utilizing Fd for biosynthesis of targeted molecules. The emphasis is on the role and activity of Fd as well as the methods used to improve the rate of electron transfer. Both microbial and electrochemical biosynthesis technologies are described and compared with respect to productivity and the compound being produced. In addition to the ferredoxins from the microbial organisms, artificially designed de novo types are described, highlighting the potential of the emerging computational methods used in metabolic and protein engineering. We believe that the recent advances in utilization of Fd for biosynthesis can result in breakthrough innovation across the biotechnology industry.
Collapse
Affiliation(s)
- Seongwon Kim
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, 04066, Republic of Korea.
| |
Collapse
|
2
|
Mo S, Li J, Li B, Kashif M, Nie S, Liao J, Su G, Jiang Q, Yan B, Jiang C. L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis. WATER 2021; 13:3053. [DOI: 10.3390/w13213053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.
Collapse
|
3
|
Mo S, Li J, Li B, Kashif M, Nie S, Liao J, Su G, Jiang Q, Yan B, Jiang C. L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis. WATER 2021; 13:3053. [DOI: https:/doi.org/10.3390/w13213053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.
Collapse
|
4
|
Luu Trinh MD, Miyazaki D, Ono S, Nomata J, Kono M, Mino H, Niwa T, Okegawa Y, Motohashi K, Taguchi H, Hisabori T, Masuda S. The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I. iScience 2021; 24:102059. [PMID: 33554065 PMCID: PMC7848650 DOI: 10.1016/j.isci.2021.102059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 11/21/2022] Open
Abstract
In natural habitats, plants have developed sophisticated regulatory mechanisms to optimize the photosynthetic electron transfer rate at the maximum efficiency and cope with the changing environments. Maintaining proper P700 oxidation at photosystem I (PSI) is the common denominator for most regulatory processes of photosynthetic electron transfers. However, the molecular complexes and cofactors involved in these processes and their function(s) have not been fully clarified. Here, we identified a redox-active chloroplast protein, the triplet-cysteine repeat protein (TCR). TCR shared similar expression profiles with known photosynthetic regulators and contained two triplet-cysteine motifs (CxxxCxxxC). Biochemical analysis indicated that TCR localizes in chloroplasts and has a [3Fe-4S] cluster. Loss of TCR limited the electron sink downstream of PSI during dark-to-light transition. Arabidopsis pgr5-tcr double mutant reduced growth significantly and showed unusual oxidation and reduction of plastoquinone pool. These results indicated that TCR is involved in electron flow(s) downstream of PSI, contributing to P700 oxidation. P700 oxidation at photosystem I is important for regulation of photosynthesis TCR is a redox active chloroplast protein harboring a 3Fe-4S iron-sulfur cluster TCR controls electron flow around photosystem I, contributing to P700 oxidation
Collapse
Affiliation(s)
- Mai Duy Luu Trinh
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Daichi Miyazaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Sumire Ono
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Jiro Nomata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masaru Kono
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Mino
- Division of Materials Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yuki Okegawa
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Ken Motohashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toru Hisabori
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
- Corresponding author
| |
Collapse
|
5
|
Grayson KJ, Anderson JLR. Designed for life: biocompatible de novo designed proteins and components. J R Soc Interface 2019; 15:rsif.2018.0472. [PMID: 30158186 PMCID: PMC6127164 DOI: 10.1098/rsif.2018.0472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
A principal goal of synthetic biology is the de novo design or redesign of biomolecular components. In addition to revealing fundamentally important information regarding natural biomolecular engineering and biochemistry, functional building blocks will ultimately be provided for applications including the manufacture of valuable products and therapeutics. To fully realize this ambitious goal, the designed components must be biocompatible, working in concert with natural biochemical processes and pathways, while not adversely affecting cellular function. For example, de novo protein design has provided us with a wide repertoire of structures and functions, including those that can be assembled and function in vivo. Here we discuss such biocompatible designs, as well as others that have the potential to become biocompatible, including non-protein molecules, and routes to achieving full biological integration.
Collapse
Affiliation(s)
- Katie J Grayson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK .,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| |
Collapse
|