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Zhou Y, Zheng J, Wu H, Yang Y, Han H. A novel toolbox to record CLE peptide signaling. FRONTIERS IN PLANT SCIENCE 2024; 15:1468763. [PMID: 39206038 PMCID: PMC11349659 DOI: 10.3389/fpls.2024.1468763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Affiliation(s)
- Yong Zhou
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Jie Zheng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
| | - Hao Wu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
| | - Youxin Yang
- Jiangxi Provincial Key Laboratory for Postharvest Storage and Preservation of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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2
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Posadas N, Conaco C. Gene networks governing the response of a calcareous sponge to future ocean conditions reveal lineage-specific XBP1 regulation of the unfolded protein response. Ecol Evol 2024; 14:e11652. [PMID: 38952658 PMCID: PMC11214833 DOI: 10.1002/ece3.11652] [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: 03/12/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
Marine sponges are predicted to be winners in the future ocean due to their exemplary adaptive capacity. However, while many sponge groups exhibit tolerance to a wide range of environmental insults, calcifying sponges may be more susceptible to thermo-acidic stress. To describe the gene regulatory networks that govern the stress response of the calcareous sponge, Leucetta chagosensis (class Calcarea, order Clathrinida), individuals were subjected to warming and acidification conditions based on the climate models for 2100. Transcriptome analysis and gene co-expression network reconstruction revealed that the unfolded protein response (UPR) was activated under thermo-acidic stress. Among the upregulated genes were two lineage-specific homologs of X-box binding protein 1 (XBP1), a transcription factor that activates the UPR. Alternative dimerization between these XBP1 gene products suggests a clathrinid-specific mechanism to reversibly sequester the transcription factor into an inactive form, enabling the rapid regulation of pathways linked to the UPR in clathrinid calcareous sponges. Our findings support the idea that transcription factor duplication events may refine evolutionarily conserved molecular pathways and contribute to ecological success.
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Affiliation(s)
- Niño Posadas
- Marine Science Institute, University of the Philippines DilimanQuezon CityPhilippines
- Present address:
Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayIreland
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines DilimanQuezon CityPhilippines
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3
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Eom K, Jung J, Kim B, Hyun JH. Molecular tools for recording and intervention of neuronal activity. Mol Cells 2024; 47:100048. [PMID: 38521352 PMCID: PMC11021360 DOI: 10.1016/j.mocell.2024.100048] [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: 12/15/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024] Open
Abstract
Observing the activity of neural networks is critical for the identification of learning and memory processes, as well as abnormal activities of neural circuits in disease, particularly for the purpose of tracking disease progression. Methodologies for describing the activity history of neural networks using molecular biology techniques first utilized genes expressed by active neurons, followed by the application of recently developed techniques including optogenetics and incorporation of insights garnered from other disciplines, including chemistry and physics. In this review, we will discuss ways in which molecular biological techniques used to describe the activity of neural networks have evolved along with the potential for future development.
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Affiliation(s)
- Kisang Eom
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jinhwan Jung
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Byungsoo Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jung Ho Hyun
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; Center for Synapse Diversity and Specificity, DGIST, Daegu 42988, Republic of Korea.
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4
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Ren H, Cheng Y, Wen G, Wang J, Zhou M. Emerging optogenetics technologies in biomedical applications. SMART MEDICINE 2023; 2:e20230026. [PMID: 39188295 PMCID: PMC11235740 DOI: 10.1002/smmd.20230026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/17/2023] [Indexed: 08/28/2024]
Abstract
Optogenetics is a cutting-edge technology that merges light control and genetics to achieve targeted control of tissue cells. Compared to traditional methods, optogenetics offers several advantages in terms of time and space precision, accuracy, and reduced damage to the research object. Currently, optogenetics is primarily used in pathway research, drug screening, gene expression regulation, and the stimulation of molecule release to treat various diseases. The selection of light-sensitive proteins is the most crucial aspect of optogenetic technology; structural changes occur or downstream channels are activated to achieve signal transmission or factor release, allowing efficient and controllable disease treatment. In this review, we examine the extensive research conducted in the field of biomedicine concerning optogenetics, including the selection of light-sensitive proteins, the study of carriers and delivery devices, and the application of disease treatment. Additionally, we offer critical insights and future implications of optogenetics in the realm of clinical medicine.
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Affiliation(s)
- Haozhen Ren
- Department of Hepatobiliary SurgeryHepatobiliary InstituteNanjing Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Yi Cheng
- Department of Vascular SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
| | - Gaolin Wen
- Department of Hepatobiliary SurgeryHepatobiliary InstituteNanjing Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Jinglin Wang
- Department of Hepatobiliary SurgeryHepatobiliary InstituteNanjing Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Min Zhou
- Department of Vascular SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
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5
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Larsen B, Hofmann R, Camacho IS, Clarke RW, Lagarias JC, Jones AR, Jones AM. Highlighter: An optogenetic system for high-resolution gene expression control in plants. PLoS Biol 2023; 21:e3002303. [PMID: 37733664 PMCID: PMC10513317 DOI: 10.1371/journal.pbio.3002303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Abstract
Optogenetic actuators have revolutionized the resolution at which biological processes can be controlled. In plants, deployment of optogenetics is challenging due to the need for these light-responsive systems to function in the context of horticultural light environments. Furthermore, many available optogenetic actuators are based on plant photoreceptors that might crosstalk with endogenous signaling processes, while others depend on exogenously supplied cofactors. To overcome such challenges, we have developed Highlighter, a synthetic, light-gated gene expression system tailored for in planta function. Highlighter is based on the photoswitchable CcaS-CcaR system from cyanobacteria and is repurposed for plants as a fully genetically encoded system. Analysis of a re-engineered CcaS in Escherichia coli demonstrated green/red photoswitching with phytochromobilin, a chromophore endogenous to plants, but also revealed a blue light response likely derived from a flavin-binding LOV-like domain. We deployed Highlighter in transiently transformed Nicotiana benthamiana for optogenetic control of fluorescent protein expression. Using light to guide differential fluorescent protein expression in nuclei of neighboring cells, we demonstrate unprecedented spatiotemporal control of target gene expression. We implemented the system to demonstrate optogenetic control over plant immunity and pigment production through modulation of the spectral composition of broadband visible (white) light. Highlighter is a step forward for optogenetics in plants and a technology for high-resolution gene induction that will advance fundamental plant biology and provide new opportunities for crop improvement.
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Affiliation(s)
- Bo Larsen
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Roberto Hofmann
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ines S. Camacho
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, Teddington, United Kingdom
| | - Richard W. Clarke
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, Teddington, United Kingdom
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California, United States of America
| | - Alex R. Jones
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, Teddington, United Kingdom
| | - Alexander M. Jones
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
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6
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Höfte H. A dive into the cell wall with Arabidopsis. C R Biol 2023; 345:41-60. [PMID: 36847119 DOI: 10.5802/crbiol.101] [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: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
One of the many legacies of the work of Michel Caboche is our understanding of plant cell wall synthesis and metabolism thanks to the use of Arabidopsis mutants. Here I describe how he was instrumental in initiating the genetic study of plant cell walls. I also show, with a few examples for cellulose and pectins, how this approach has led to important new insights in cell wall synthesis and how the metabolism of pectins contributes to plant growth and morphogenesis. I also illustrate the limitations of the use of mutants to explain processes at the scale of cells, organs or whole plants in terms of the physico-chemical properties of cell wall polymers. Finally, I sketch how new approaches can cope with these limitations.
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Kumar A, Baldia A, Rajput D, Kateriya S, Babu V, Dubey KK. Multiomics and optobiotechnological approaches for the development of microalgal strain for production of aviation biofuel and biorefinery. BIORESOURCE TECHNOLOGY 2023; 369:128457. [PMID: 36503094 DOI: 10.1016/j.biortech.2022.128457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Demand and consumption of fossil fuels is increasing daily, and oil reserves are depleting. Technological developments are required towards developing sustainable renewable energy sources and microalgae are emerging as a potential candidate for various application-driven research. Molecular understanding attained through omics and system biology approach empowering researchers to modify various metabolic pathways of microalgal system for efficient extraction of biofuel and important biomolecules. This review furnish insight into different "advanced approaches" like optogenetics, systems biology and multi-omics for enhanced production of FAS (Fatty Acid Synthesis) and lipids in microalgae and their associated challenges. These new approaches would be helpful in the path of developing microalgae inspired technological platforms for optobiorefinery, which could be explored as source material to produce biofuels and other valuable bio-compounds on a large scale.
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Affiliation(s)
- Akshay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Anshu Baldia
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepanshi Rajput
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vikash Babu
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Kashyap Kumar Dubey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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8
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Salihoglu R, Srivastava M, Liang C, Schilling K, Szalay A, Bencurova E, Dandekar T. PRO-Simat: Protein network simulation and design tool. Comput Struct Biotechnol J 2023; 21:2767-2779. [PMID: 37181657 PMCID: PMC10172639 DOI: 10.1016/j.csbj.2023.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks. It enables simulation outputs with in-depth analysis of the type, strength, duration and pathway of the protein interactions on the website. Furthermore, the user can efficiently edit and analyse the effect of network modifications and engineering experiments. In case studies, applications of PRO-Simat are demonstrated: (i) understanding mutually exclusive differentiation pathways in Bacillus subtilis, (ii) making Vaccinia virus oncolytic by switching on its viral replication mainly in cancer cells and triggering cancer cell apoptosis and (iii) optogenetic control of nucleotide processing protein networks to operate DNA storage. Multilevel communication between components is critical for efficient network switching, as demonstrated by a general census on prokaryotic and eukaryotic networks and comparing design with synthetic networks using PRO-Simat. The tool is available at https://prosimat.heinzelab.de/ as a web-based query server.
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Affiliation(s)
- Rana Salihoglu
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Chunguang Liang
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Klaus Schilling
- Informatics VII, Robotics and Telematics, Department of Mathematics and Informatics, Am Hubland, University of Würzburg, D-97074 Würzburg, Germany
| | - Aladar Szalay
- Dept. of Biochemistry, Biocenter, Am Hubland, University of Würzburg, D-97074 Würzburg, Germany
- Department of Radiation Medicine and Applied Sciences, Rebecca & John Moores Comprehensive Cancer Center, University of California, San Diego, CA, USA
- Dept. of Pathology, Center of Immune technologies, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Corresponding author.
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- Corresponding author at: Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.
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9
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Couée I. Perspectives in Plant Abiotic Stress Signaling. Methods Mol Biol 2023; 2642:429-444. [PMID: 36944892 DOI: 10.1007/978-1-0716-3044-0_23] [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: 03/23/2023]
Abstract
State-of-the-art collections of strategies, approaches, and methods are immediately useful for ongoing characterizations or for novel discoveries in the scientific field of plant abiotic stress signaling. It must however be kept in mind that, in the future, these strategies, approaches, and methods will be facing a number of increasingly complex issues. The development of the necessary confrontation of laboratory-based knowledge on abiotic stress signaling mechanisms with real-life in natura situations of plant-stress interactions involves at least five levels of complexity: (i) plant biodiversity, (ii) the spatio-temporal heterogeneity of stress-related parameters, (iii) the unknowns of future stress-related constraints, (iv) the influence of biotic interactions, (v) the crosstalk between various signaling pathways and their final integration into physiological responses. These complexities are major bottlenecks for assessing the evolutionary, ecological, and agronomical relevance of abiotic stress signaling studies. All of the presently-described strategies, approaches, and methods will have to be gradually complemented with the development of real-time and in natura tools, with systematic application of mathematical modeling to complex interactions and with further research on the impact of stress memory mechanisms on long-term responses.
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Affiliation(s)
- Ivan Couée
- UMR 6553 ECOBIO (Ecosystems-Biodiversity-Evolution), Centre National de la Recherche Scientifique (CNRS), University of Rennes, Rennes, France.
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Couée I, Gouesbet G. Protein-Protein Interactions in Abiotic Stress Signaling: An Overview of Biochemical and Biophysical Methods of Characterization. Methods Mol Biol 2023; 2642:319-330. [PMID: 36944886 DOI: 10.1007/978-1-0716-3044-0_17] [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: 03/23/2023]
Abstract
The identification and characterization of bona fide abiotic stress signaling proteins can occur at different levels of the complete in vivo signaling cascade or network. Knowledge of a particular abiotic stress signaling protein could theoretically lead to the characterization of complete networks through the analysis of unknown proteins that interact with the previously known protein. Such signaling proteins of interest can indeed be experimentally used as bait proteins to catch interacting prey proteins, provided that the association of bait proteins and prey proteins should yield a biochemical or biophysical signal that can be detected. To this end, several biochemical and biophysical techniques are available to provide experimental evidence for specific protein-protein interactions, such as co-immunoprecipitation, bimolecular fluorescence complementation, tandem affinity purification coupled to mass spectrometry, yeast two hybrid, protein microarrays, Förster resonance energy transfer, or fluorescence correlation spectroscopy. This array of methods can be implemented to establish the biochemical reality of putative protein-protein interactions between two proteins of interest or to identify previously unknown partners related to an initially known protein of interest. The ultimate validity of these methods however depends on the in vitro/in vivo nature of the approach and on the heterologous/homologous context of the analysis. This chapter will review the application and success of some classical methods of protein-protein interaction analysis in the field of plant abiotic stress signaling.
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Affiliation(s)
- Ivan Couée
- UMR 6553 ECOBIO (Ecosystems-Biodiversity-Evolution), CNRS, Université de Rennes, Brittany, France.
| | - Gwenola Gouesbet
- UMR 6553 ECOBIO (Ecosystems-Biodiversity-Evolution), CNRS, Université de Rennes, Brittany, France
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11
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Shikata H, Denninger P. Plant optogenetics: Applications and perspectives. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102256. [PMID: 35780691 DOI: 10.1016/j.pbi.2022.102256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
To understand cell biological processes, like signalling pathways, protein movements, or metabolic processes, precise tools for manipulation are desired. Optogenetics allows to control cellular processes by light and can be applied at a high temporal and spatial resolution. In the last three decades, various optogenetic applications have been developed for animal, fungal, and prokaryotic cells. However, using optogenetics in plants has been difficult due to biological and technical issues, like missing cofactors, the presence of endogenous photoreceptors, or the necessity of light for photosynthesis, which potentially activates optogenetic tools constitutively. Recently developed tools overcome these limitations, making the application of optogenetics feasible also in plants. Here, we highlight the most useful recent applications in plants and give a perspective for future optogenetic approaches in plants science.
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Affiliation(s)
- Hiromasa Shikata
- Division of Plant Environmental Responses, National Institute for Basic Biology, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Japan.
| | - Philipp Denninger
- Technical University of Munich, School of Life Sciences, Plant Systems Biology, Emil-Ramann-Strasse 8, 85354 Freising, Germany.
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Poddar H, Heyes DJ, Zhang S, Hardman SJ, Sakuma M, Scrutton NS. An unusual light-sensing function for coenzyme B 12 in bacterial transcription regulator CarH. Methods Enzymol 2022; 668:349-372. [PMID: 35589201 DOI: 10.1016/bs.mie.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coenzyme B12 is one of the most complex cofactors found in nature and synthesized de novo by certain groups of bacteria. Although its use in various enzymatic reactions is well characterized, only recently an unusual light-sensing function has been ascribed to coenzyme B12. It has been reported that the coenzyme B12 binding protein CarH, found in the carotenoid biosynthesis pathway of several thermostable bacteria, binds to the promoter region of DNA and suppresses transcription. To overcome the harmful effects of light-induced damage in the cells, CarH releases DNA in the presence of light and promotes transcription and synthesis of carotenoids, thereby working as a photoreceptor. CarH is able to achieve this by exploiting the photosensitive nature of the CoC bond between the adenosyl moiety and the cobalt atom in the coenzyme B12 molecule. Extensive structural and spectroscopy studies provided a mechanistic understanding of the molecular basis of this unique light-sensitive reaction. Most studies on CarH have used the ortholog from the thermostable bacterium Thermus thermophilus, due to the ease with which it can be expressed and purified in high quantities. In this chapter we give an overview of this intriguing class of photoreceptors and report a step-by-step protocol for expression, purification and spectroscopy experiments (both static and time-resolved techniques) employed in our laboratory to study CarH from T. thermophilus. We hope the contents of this chapter will be of interest to the wider coenzyme B12 community and apprise them of the potential and possibilities of using coenzyme B12 as a light-sensing probe in a protein scaffold.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Samantha J Hardman
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom.
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13
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Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
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14
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Boral A, Khamaru M, Mitra D. Designing synthetic transcription factors: A structural perspective. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:245-287. [PMID: 35534109 DOI: 10.1016/bs.apcsb.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this chapter, we discuss different design strategies of synthetic proteins, especially synthetic transcription factors. Design and engineering of synthetic transcription factors is particularly relevant for the need-based manipulation of gene expression. With recent advances in structural biology techniques and with the emergence of other precision biochemical/physical tools, accurate knowledge on structure-function relations is increasingly becoming available. Besides discussing the underlying principles of design, we go through individual cases, especially those involving four major groups of transcription factors-basic leucine zippers, zinc fingers, helix-turn-helix and homeodomains. We further discuss how synthetic biology can come together with structural biology to alter the genetic blueprint of life.
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Affiliation(s)
- Aparna Boral
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Madhurima Khamaru
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.
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15
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Dwijayanti A, Zhang C, Poh CL, Lautier T. Toward Multiplexed Optogenetic Circuits. Front Bioeng Biotechnol 2022; 9:804563. [PMID: 35071213 PMCID: PMC8766309 DOI: 10.3389/fbioe.2021.804563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Owing to its ubiquity and easy availability in nature, light has been widely employed to control complex cellular behaviors. Light-sensitive proteins are the foundation to such diverse and multilevel adaptive regulations in a large range of organisms. Due to their remarkable properties and potential applications in engineered systems, exploration and engineering of natural light-sensitive proteins have significantly contributed to expand optogenetic toolboxes with tailor-made performances in synthetic genetic circuits. Progressively, more complex systems have been designed in which multiple photoreceptors, each sensing its dedicated wavelength, are combined to simultaneously coordinate cellular responses in a single cell. In this review, we highlight recent works and challenges on multiplexed optogenetic circuits in natural and engineered systems for a dynamic regulation breakthrough in biotechnological applications.
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Affiliation(s)
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Thomas Lautier
- CNRS@CREATE, Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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16
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Molina-Hidalgo FJ, Vazquez-Vilar M, D'Andrea L, Demurtas OC, Fraser P, Giuliano G, Bock R, Orzáez D, Goossens A. Engineering Metabolism in Nicotiana Species: A Promising Future. Trends Biotechnol 2021; 39:901-913. [PMID: 33341279 DOI: 10.1016/j.tibtech.2020.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/31/2022]
Abstract
Molecular farming intends to use crop plants as biofactories for high value-added compounds following application of a wide range of biotechnological tools. In particular, the conversion of nonfood crops into efficient biofactories is expected to be a strong asset in the development of a sustainable bioeconomy. The 'nonfood' status combined with the high metabolic versatility and the capacity of high-yield cultivation highlight the plant genus Nicotiana as one of the most appropriate 'chassis' for molecular farming. Nicotiana species are a rich source of valuable industrial, active pharmaceutical ingredients and nutritional compounds, synthesized from highly complex biosynthetic networks. Here, we review and discuss approaches currently used to design enriched Nicotiana species for molecular farming using new plant breeding techniques (NPBTs).
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Affiliation(s)
- Francisco Javier Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Lucio D'Andrea
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Olivia C Demurtas
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, London, UK
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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17
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Christie JM, Zurbriggen MD. Optogenetics in plants. THE NEW PHYTOLOGIST 2021; 229:3108-3115. [PMID: 33064858 DOI: 10.1111/nph.17008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
The last two decades have witnessed the emergence of optogenetics; a field that has given researchers the ability to use light to control biological processes at high spatiotemporal and quantitative resolutions, in a reversible manner with minimal side-effects. Optogenetics has revolutionized the neurosciences, increased our understanding of cellular signalling and metabolic networks and resulted in variety of applications in biotechnology and biomedicine. However, implementing optogenetics in plants has been less straightforward, given their dependency on light for their life cycle. Here, we highlight some of the widely used technologies in microorganisms and animal systems derived from plant photoreceptor proteins and discuss strategies recently implemented to overcome the challenges for using optogenetics in plants.
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Affiliation(s)
- John M Christie
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Duesseldorf, Duesseldorf, 40225, Germany
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18
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Sinha S, Samaddar S, Das Gupta SK, Roy S. Network approach to mutagenesis sheds insight on phage resistance in mycobacteria. Bioinformatics 2021; 37:213-220. [PMID: 33416849 DOI: 10.1093/bioinformatics/btaa1103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 12/08/2020] [Accepted: 01/01/2021] [Indexed: 01/03/2023] Open
Abstract
MOTIVATION A rigorous yet general mathematical approach to mutagenesis, especially one capable of delivering systems-level perspectives would be invaluable. Such systems-level understanding of phage resistance is also highly desirable for phage-bacteria interactions and phage therapy research. Independently, the ability to distinguish between two graphs with a set of common or identical nodes and identify the implications thereof, is important in network science. RESULTS Herein we propose a measure called shortest path alteration fraction (SPAF) to compare any two networks by shortest paths, using sets. When SPAF is one, it can identify node pairs connected by at least one shortest path, which are present in either network but not both. Similarly, SPAF equaling zero identifies identical shortest paths, which are simultaneously present between a node pair in both networks. We study the utility of our measure theoretically in five diverse microbial species, to capture reported effects of well-studied mutations and predict new ones. We also scrutinise the effectiveness of our procedure through theoretical and experimental tests on Mycobacterium smegmatis mc2155 and by generating a mutant of mc2155, which is resistant to mycobacteriophage D29. This mutant of mc2155, which is resistant to D29 exhibits significant phenotypic alterations. Whole-genome sequencing identifies mutations, which cannot readily explain the observed phenotypes. Exhaustive analyses of protein-protein interaction network of the mutant and wild-type, using the machinery of topological metrics and differential networks does not yield a clear picture. However, SPAF coherently identifies pairs of proteins at the end of a subset of shortest paths, from amongst hundreds of thousands of viable shortest paths in the networks. The altered functions associated with the protein pairs are strongly correlated with the observed phenotypes.
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Affiliation(s)
- Saptarshi Sinha
- Department of Physics, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, WB, 700009, India
| | - Sourabh Samaddar
- Department of Microbiology, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kolkata, WB, 700 054, India
| | - Sujoy K Das Gupta
- Department of Microbiology, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kolkata, WB, 700 054, India
| | - Soumen Roy
- Department of Physics, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, WB, 700009, India
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19
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Sureda-Vives M, Sarkisyan KS. Bioluminescence-Driven Optogenetics. Life (Basel) 2020; 10:E318. [PMID: 33260589 PMCID: PMC7760859 DOI: 10.3390/life10120318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 02/04/2023] Open
Abstract
Bioluminescence-based technologies are among the most commonly used methods to quantify and visualise physiology at the cellular and organismal levels. However, the potential of bioluminescence beyond reporter technologies remains largely unexplored. Here, we provide an overview of the emerging approaches employing bioluminescence as a biological light source that triggers physiological events and controls cell behaviour and discuss its possible future application in synthetic biology.
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Affiliation(s)
- Macià Sureda-Vives
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK;
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Karen S. Sarkisyan
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK;
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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20
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Deb A, Grewal RK, Roy S, Mitra D. Residue interaction dynamics in
Vaucheria
aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments. Proteins 2020; 88:1660-1674. [DOI: 10.1002/prot.25984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/04/2020] [Accepted: 07/12/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Anwesha Deb
- Department of Life Sciences Presidency University Kolkata India
| | | | - Soumen Roy
- Department of Physics Bose Institute Kolkata India
| | - Devrani Mitra
- Department of Life Sciences Presidency University Kolkata India
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21
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MARTINIÈRE A, MOREAU P. Complex roles of Rabs and SNAREs in the secretory pathway and plant development: a never‐ending story. J Microsc 2020; 280:140-157. [DOI: 10.1111/jmi.12952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/22/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
Affiliation(s)
- A. MARTINIÈRE
- Univ Montpellier, CNRS, INRAE, Montpellier SupAgro BPMP Montpellier France
| | - P. MOREAU
- UMR 5200 Membrane Biogenesis Laboratory CNRS and University of Bordeaux, INRAE Bordeaux Villenave d'Ornon France
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22
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Lee YT, He L, Zhou Y. Expanding the Chemogenetic Toolbox by Circular Permutation. J Mol Biol 2020; 432:3127-3136. [PMID: 32277990 DOI: 10.1016/j.jmb.2020.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 12/18/2022]
Abstract
To expand the repertoire of chemogenetic tools tailored for molecular and cellular engineering, we describe herein the design of cpRAPID as a circularly permuted rapamycin-inducible dimerization system composed of the canonical FK506-binding protein (FKBP) and circular permutants of FKBP12-rapamycin binding domain (cpFRB). By permuting the topology of the four helices within FRB, we have created cpFRB-FKBP pairs that respond to ligand with varying activation kinetics and dynamics. The cpRAPID system enables chemical-controllable subcellular redistribution of proteins, as well as inducible transcriptional activation when coupled with the CRISPR activation (CRISPRa) technology to induce a GFP reporter and endogenous gene expression. We have further demonstrated the use of cpRAPID to generate chemically switchable split nanobody (designated Chessbody) for ligand-gated antigen recognition in living cells. Collectively, the circular permutation approach offers a powerful means for diversifying the chemogenetics toolbox to benefit the burgeoning synthetic biology field.
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Affiliation(s)
- Yi-Tsang Lee
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA; Department of Medical Physiology, College of Medicine, Texas A&M University, Bryan, TX 77807, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA.
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