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Nawaz T, Gu L, Gibbons J, Hu Z, Zhou R. Bridging Nature and Engineering: Protein-Derived Materials for Bio-Inspired Applications. Biomimetics (Basel) 2024; 9:373. [PMID: 38921253 PMCID: PMC11201842 DOI: 10.3390/biomimetics9060373] [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: 04/28/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
The sophisticated, elegant protein-polymers designed by nature can serve as inspiration to redesign and biomanufacture protein-based materials using synthetic biology. Historically, petro-based polymeric materials have dominated industrial activities, consequently transforming our way of living. While this benefits humans, the fabrication and disposal of these materials causes environmental sustainability challenges. Fortunately, protein-based biopolymers can compete with and potentially surpass the performance of petro-based polymers because they can be biologically produced and degraded in an environmentally friendly fashion. This paper reviews four groups of protein-based polymers, including fibrous proteins (collagen, silk fibroin, fibrillin, and keratin), elastomeric proteins (elastin, resilin, and wheat glutenin), adhesive/matrix proteins (spongin and conchiolin), and cyanophycin. We discuss the connection between protein sequence, structure, function, and biomimetic applications. Protein engineering techniques, such as directed evolution and rational design, can be used to improve the functionality of natural protein-based materials. For example, the inclusion of specific protein domains, particularly those observed in structural proteins, such as silk and collagen, enables the creation of novel biomimetic materials with exceptional mechanical properties and adaptability. This review also discusses recent advancements in the production and application of new protein-based materials through the approach of synthetic biology combined biomimetics, providing insight for future research and development of cutting-edge bio-inspired products. Protein-based polymers that utilize nature's designs as a base, then modified by advancements at the intersection of biology and engineering, may provide mankind with more sustainable products.
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Affiliation(s)
- Taufiq Nawaz
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA;
| | - Liping Gu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA;
| | | | - Zhong Hu
- Department of Mechanical Engineering, South Dakota State University, Brookings, SD 57007, USA;
| | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA;
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2
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Zedler JAZ, Schirmacher AM, Russo DA, Hodgson L, Gundersen E, Matthes A, Frank S, Verkade P, Jensen PE. Self-Assembly of Nanofilaments in Cyanobacteria for Protein Co-localization. ACS NANO 2023; 17:25279-25290. [PMID: 38065569 PMCID: PMC10754207 DOI: 10.1021/acsnano.3c08600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/27/2023]
Abstract
Cyanobacteria offer great potential as alternative biotechnological hosts due to their photoautotrophic capacities. However, in comparison to established heterotrophic hosts, several key aspects, such as product titers, are still lagging behind. Nanobiotechnology is an emerging field with great potential to improve existing hosts, but so far, it has barely been explored in microbial photosynthetic systems. Here, we report the establishment of large proteinaceous nanofilaments in the unicellular model cyanobacterium Synechocystis sp. PCC 6803 and the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. Transmission electron microscopy and electron tomography demonstrated that expression of pduA*, encoding a modified bacterial microcompartment shell protein, led to the generation of bundles of longitudinally aligned nanofilaments in S. elongatus UTEX 2973 and shorter filamentous structures in Synechocystis sp. PCC 6803. Comparative proteomics showed that PduA* was at least 50 times more abundant than the second most abundant protein in the cell and that nanofilament assembly had only a minor impact on cellular metabolism. Finally, as a proof-of-concept for co-localization with the filaments, we targeted a fluorescent reporter protein, mCitrine, to PduA* by fusion with an encapsulation peptide that natively interacts with PduA. The establishment of nanofilaments in cyanobacterial cells is an important step toward cellular organization of heterologous pathways and the establishment of cyanobacteria as next-generation hosts.
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Affiliation(s)
- Julie A. Z. Zedler
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alexandra M. Schirmacher
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - David A. Russo
- Bioorganic
Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Lorna Hodgson
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Emil Gundersen
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Annemarie Matthes
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Stefanie Frank
- Department
of Biochemical Engineering, University College
London, London, WC1E 6BT, United
Kingdom
| | - Paul Verkade
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Poul Erik Jensen
- Department
of Food Science, University of Copenhagen, 1958 Frederiksberg, Denmark
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3
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Velázquez-Suárez C, Springstein BL, Nieves-Morión M, Helbig AO, Kieninger AK, Maldener I, Nürnberg DJ, Stucken K, Luque I, Dagan T, Herrero A. SepT, a novel protein specific to multicellular cyanobacteria, influences peptidoglycan growth and septal nanopore formation in Anabaena sp. PCC 7120. mBio 2023; 14:e0098323. [PMID: 37650636 PMCID: PMC10653889 DOI: 10.1128/mbio.00983-23] [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: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Multicellular organization is a requirement for the development of complex organisms, and filamentous cyanobacteria such as Anabaena represent a paradigmatic case of bacterial multicellularity. The Anabaena filament can include hundreds of communicated cells that exchange nutrients and regulators and, depending on environmental conditions, can include different cell types specialized in distinct biological functions. Hence, the specific features of the Anabaena filament and how they are propagated during cell division represent outstanding biological issues. Here, we studied SepT, a novel coiled-coil-rich protein of Anabaena that is located in the intercellular septa and influences the formation of the septal specialized structures that allow communication between neighboring cells along the filament, a fundamental trait for the performance of Anabaena as a multicellular organism.
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Affiliation(s)
| | | | - Mercedes Nieves-Morión
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Andreas O. Helbig
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Ann-Katrin Kieninger
- Department of Microbiology/Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Iris Maldener
- Department of Microbiology/Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics and Dahlem Centre of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Karina Stucken
- Department of Food Engineering, Universidad de La Serena, La Serena, Chile
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
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4
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Zhang M, Wang Y, Liu J, Wu X, Shen Y, Zhang D, Pan X. Micron-confined microcapturer-triggered Fenton as efficient and environmentally-friendly method for simultaneously capturing bloom-forming cyanobacteria, inhibiting cell-regrowth and degrading microcystins. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122195. [PMID: 37451589 DOI: 10.1016/j.envpol.2023.122195] [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: 02/28/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The frequent outbreak and continuous expansion of harmful cyanobacteria blooms (HCBs) have become important environmental concerns and public health issues globally. In this study, the "micron-confined Fe(II)-modified-microcapturer (FMC)-triggered Fenton" technology was established as advanced process adaptable to the HCB treatment. Results show that 95.7-99.4% of cyanobacteria cells were captured and separated from the HCB water at the optimum doses of Fe(II) and H2O2 within only 30 s. The chain-like cyanobacteria of A. flos-aquae were easier to be collected by FMCs compared with the unicellular M. aeruginosa. It was confirmed by scanning electron microscopic observation and fluorescence staining flow cytometry measurement that the FMC-carrying Fe(II) played the roles of both cell-gripper and Fenton catalyst. During the one-step process, the FMC-triggered Fenton effectively inhibited the cyanobacteria regrowth via inactivating the cells, and meanwhile, the microcystins of LR and RR were removed. The analyses by continuous flow chemiluminescence and X-ray photoelectron spectroscopy denote that FMCs performed efficiently in capture and Fe(II)-catalytic oxidation through increasing mass transfer, exposing sufficient active reactive oxygen species active-sites on the FMC surface and accelerating electron transfer. The micron-field-confined cascade processes retained the robust performance of Fenton against the high pH of bulk HCB water. This novel interface-dependent Fenton method is a promising tool for HCB treatment owing to its great efficiency, versatility, rapidness and eco-environmental friendliness.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yafeng Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jiayuan Liu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xinyou Wu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yucheng Shen
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China.
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Toida K, Kushida W, Yamamoto H, Yamamoto K, Ishii K, Uesaka K, Kanaly RA, Kutsuna S, Ihara K, Fujita Y, Iwasaki H. The GGDEF protein Dgc2 suppresses both motility and biofilm formation in the filamentous cyanobacterium Leptolyngbya boryana. Microbiol Spectr 2023; 11:e0483722. [PMID: 37655901 PMCID: PMC10581220 DOI: 10.1128/spectrum.04837-22] [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: 12/31/2022] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Colony pattern formations of bacteria with motility manifest complicated morphological self-organization phenomena. Leptolyngbya boryana is a filamentous cyanobacterium, which has been used as a genetic model organism for studying metabolism including photosynthesis and nitrogen fixation. A widely used type strain [wild type (WT) in this article] of this species has not been reported to show any motile activity. However, we isolated a spontaneous mutant strain that shows active motility (gliding activity) to give rise to complicated colony patterns, including comet-like wandering clusters and disk-like rotating vortices on solid media. Whole-genome resequencing identified multiple mutations in the genome of the mutant strain. We confirmed that inactivation of the candidate gene dgc2 (LBDG_02920) in the WT background was sufficient to give rise to motility and morphologically complex colony patterns. This gene encodes a protein containing the GGDEF motif which is conserved at the catalytic domain of diguanylate cyclase (DGC). Although DGC has been reported to be involved in biofilm formation, the dgc2 mutant significantly facilitated biofilm formation, suggesting a role for the dgc2 gene in suppressing both gliding motility and biofilm formation. Thus, Leptolyngbya is expected to be an excellent genetic model for studying dynamic colony pattern formation and to provide novel insights into the role of DGC family genes in biofilm formation. IMPORTANCE Self-propelled bacteria often exhibit complex collective behaviors, such as formation of dense-moving clusters, which are exemplified by wandering comet-like and rotating disk-like colonies; however, the molecular details of how these structures are formed are scant. We found that a strain of the filamentous cyanobacterium Leptolyngbya deficient in the GGDEF protein gene dgc2 elicits motility and complex and dynamic colony pattern formation, including comet-like and disk-like clusters. Although c-di-GMP has been reported to activate biofilm formation in some bacterial species, disruption of dgc2 unexpectedly enhanced it, suggesting a novel role for this GGDEF protein for inhibiting both colony pattern formation and biofilm formation.
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Affiliation(s)
- Kazuma Toida
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Wakana Kushida
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Hiroki Yamamoto
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Kyoka Yamamoto
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Kaichi Ishii
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Robert A. Kanaly
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Shinsuke Kutsuna
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hideo Iwasaki
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
- metaPhorest, Bioaesthetics Platform, Waseda University, Tokyo, Japan
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6
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Joosten ED, Hamelin J, Milferstedt K. Initial type and abundance of cyanobacteria determine morphotype development of phototrophic ecosystems. FEMS Microbiol Ecol 2023; 99:fiad099. [PMID: 37653452 DOI: 10.1093/femsec/fiad099] [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: 04/20/2023] [Revised: 07/24/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023] Open
Abstract
Phototrophic aggregates containing filamentous cyanobacteria occur naturally, for example, as cryoconite on glaciers and microbialites in fresh or marine waters, but their formation is not fully understood. Laboratory models are now available to reproduce aggregation, that is, the formation of different morphotypes like hemispheroids, microbial mats or sphere-like aggregates we call photogranules. In the model, activated sludge as starting matrix is transformed into aggregates enclosed by a phototrophic layer of growing cyanobacteria. These cyanobacteria were either enriched from the matrix or we added them intentionally. We hypothesize that the resulting morphotype depends on the type and concentration of the added cyanobacteria. When cyanobacteria from mature photogranules were added to activated sludge, photogranulation was not observed, but microbial mats were formed. Photogranulation of sludge could be promoted when adding sufficient quantities of cyanobacterial strains that form clumps when grown as isolates. The cyanobacteria putatively responsible for photogranulation were undetectable or only present in low abundance in the final communities of photogranules, which were always dominated by mat-forming cyanobacteria. We suggest that, in a temporal succession, the ecosystem engineer initiating photogranulation eventually disappears, leaving behind its structural legacy. We conclude that understanding phototrophic aggregate formation requires considering the initial succession stages of the ecosystem development.
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Affiliation(s)
| | - Jérôme Hamelin
- INRAE, Univ Montpellier, LBE, 102 Avenue des Etangs, 11100, Narbonne, France
| | - Kim Milferstedt
- INRAE, Univ Montpellier, LBE, 102 Avenue des Etangs, 11100, Narbonne, France
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7
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Hao F, Li X, Wang J, Li R, Zou L, Wang K, Chen F, Shi F, Yang H, Wang W, Tian M. Separation of Bioproducts through the Integration of Cyanobacterial Metabolism and Membrane Filtration: Facilitating Cyanobacteria's Industrial Application. MEMBRANES 2022; 12:963. [PMID: 36295722 PMCID: PMC9611232 DOI: 10.3390/membranes12100963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/10/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
In this work, we propose the development of an efficient, economical, automated, and sustainable method for separating bioproducts from culture medium via the integration of a sucrose-secreting cyanobacteria production process and pressure-driven membrane filtration technology. Firstly, we constructed sucrose-secreting cyanobacteria with a sucrose yield of 600-700 mg/L sucrose after 7 days of salt stress, and the produced sucrose could be fully separated from the cyanobacteria cultures through an efficient and automated membrane filtration process. To determine whether this new method is also economical and sustainable, the relationship between membrane species, operating pressure, and the growth status of four cyanobacterial species was systematically investigated. The results revealed that all four cyanobacterial species could continue to grow after UF filtration. The field emission scanning electron microscopy and confocal laser scanning microscopy results indicate that the cyanobacteria did not cause severe destruction to the membrane surface structure. The good cell viability and intact membrane surface observed after filtration indicated that this innovative cyanobacteria-membrane system is economical and sustainable. This work pioneered the use of membrane separation to achieve the in situ separation of cyanobacterial culture and target products, laying the foundation for the industrialization of cyanobacterial bioproducts.
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Affiliation(s)
- Fei Hao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Xinyi Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Jiameng Wang
- School of Astronautics, Northwestern Polytechnical University, Xi’an 710072, China
| | - Ruoyue Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Liyan Zou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Kai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Fuqing Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Feixiong Shi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Hui Yang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Miao Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
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8
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Zhang M, Liu J, Wang Y, Yu B, Wu X, Qiang Z, Zhang D, Pan X. Morphologically-different cells and colonies cause distinctive performance of coagulative colloidal ozone microbubbles in simultaneously removing bloom-forming cyanobacteria and microcystin-LR. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128986. [PMID: 35487002 DOI: 10.1016/j.jhazmat.2022.128986] [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: 11/30/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Morphology, the important feature of bloom-forming cyanobacteria, was studied for its impacts on the harmful cyanobacterial bloom (HCB) treatment by coagulative colloidal ozone microbubbles (CCOMBs). The globally-appeared HCB species - Microcystis aeruginosa (spherical cells, block mass colonies), Microcystis panniformis (spherical cells, flat penniform-like colonies) and Anabaena flos-aquae (filamentous morphology) were chosen as representative species. CCOMBs were generated by modifying the bubble surface and the gas core with coagulant and ozone, respectively. The removal of spherical cells and filaments was > 99.5% and ≤ 34.6%, individually, and the latter was ascribed to chain breakage. CCOMBs collected Microcystis panniformis via complexing with the fluorescent and non-fluorescent functional groups of cell colonies but captured Anabaena flos-aquae through the fluorescent ones. More Microcystis aeruginosa got membrane-damaged than Microcystis panniformis; nevertheless, the microcystin-LR (MC-LR) removal was guaranteed through efficiently oxidizing the released MC-LR. Although the outer peptidoglycan sheet of Anabaena flos-aquae was destroyed, the inner cyte membrane remained intact, preventing intracellular MC-LR from releasing. The HCBs dominated by single species with spherical cells were more readily treated than those with co-occurred species. The toxicological tests imply that, as a robust tool for HCB treatment, the CCOMB technology could be eco-environmentally friendly to the aquatic environment.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiayuan Liu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yafeng Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Beilei Yu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xinyou Wu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
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9
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Ramos-León F, Ramamurthi K. Cytoskeletal proteins: Lessons learned from bacteria. Phys Biol 2022; 19. [PMID: 35081523 DOI: 10.1088/1478-3975/ac4ef0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/26/2022] [Indexed: 11/11/2022]
Abstract
Cytoskeletal proteins are classified as a group that is defined functionally, whose members are capable of polymerizing into higher order structures, either dynamically or statically, to perform structural roles during a variety of cellular processes. In eukaryotes, the most well-studied cytoskeletal proteins are actin, tubulin, and intermediate filaments, and are essential for cell shape and movement, chromosome segregation, and intracellular cargo transport. Prokaryotes often harbor homologs of these proteins, but in bacterial cells, these homologs are usually not employed in roles that can be strictly defined as "cytoskeletal". However, several bacteria encode other proteins capable of polymerizing which, although they do not appear to have a eukaryotic counterpart, nonetheless appear to perform a more traditional "cytoskeletal" function. In this review, we discuss recent reports that cover the structure and functions of prokaryotic proteins that are broadly termed as cytoskeletal, either by sequence homology or by function, to highlight how the enzymatic properties of traditionally studied cytoskeletal proteins may be used for other types of cellular functions; and to demonstrate how truly "cytoskeletal" functions may be performed by uniquely bacterial proteins that do not display homology to eukaryotic proteins.
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Affiliation(s)
- Félix Ramos-León
- National Institutes of Health, 37 Convent Dr., Bldg 37, Room 5132, Bethesda, Maryland, 20892, UNITED STATES
| | - Kumaran Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, 37 Convent Dr, Bldg 37, Room 5132, Bethesda, Maryland, 20892, UNITED STATES
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10
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Han Y, Jakob A, Engel S, Wilde A, Nils S. PATAN-domain regulators interact with the Type IV pilus motor to control phototactic orientation in the cyanobacterium Synechocystis. Mol Microbiol 2021; 117:790-801. [PMID: 34936151 DOI: 10.1111/mmi.14872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
Many prokaryotes show complex behaviors that require the intricate spatial and temporal organization of cellular protein machineries, leading to asymmetrical protein distribution and cell polarity. One such behavior is cyanobacterial phototaxis which relies on the dynamic localization of the Type IV pilus motor proteins in response to light. In the cyanobacterium Synechocystis, various signaling systems encompassing chemotaxis-related CheY- and PatA-like response regulators are critical players in switching between positive and negative phototaxis depending on the light intensity and wavelength. In this study, we show that PatA-type regulators evolved from chemosensory systems. Using fluorescence microscopy and yeast-two-hybrid analysis, we demonstrate that they localize to the inner membrane, where they interact with the N-terminal cytoplasmic domain of PilC and the pilus assembly ATPase PilB1. By separately expressing the subdomains of the response regulator PixE, we confirm that only the N-terminal PATAN domain interacts with PilB1, localizes to the membrane, and is sufficient to reverse phototactic orientation. These experiments established that the PATAN domain is the principal output domain of PatA-type regulators which we presume to modulate pilus extension by binding to the pilus motor components.
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Affiliation(s)
- Yu Han
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Annik Jakob
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Sophia Engel
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Schuergers Nils
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
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11
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Yadav A, Maertens L, Meese T, Van Nieuwerburgh F, Mysara M, Leys N, Cuypers A, Janssen PJ. Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle. Microorganisms 2021; 9:microorganisms9081626. [PMID: 34442705 PMCID: PMC8400943 DOI: 10.3390/microorganisms9081626] [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: 06/24/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
Two morphotypes of the cyanobacterial Limnospira indica (formerly Arthrospira sp.) strain PCC 8005, denoted as P2 (straight trichomes) and P6 (helical trichomes), were subjected to chronic gamma radiation from spent nuclear fuel (SNF) rods at a dose rate of ca. 80 Gy·h-1 for one mass doubling period (approximately 3 days) under continuous light with photoautotrophic metabolism fully active. Samples were taken for post-irradiation growth recovery and RNA-Seq transcriptional analysis at time intervals of 15, 40, and 71.5 h corresponding to cumulative doses of ca. 1450, 3200, and 5700 Gy, respectively. Both morphotypes, which were previously reported by us to display different antioxidant capacities and differ at the genomic level in 168 SNPs, 48 indels and 4 large insertions, recovered equally well from 1450 and 3200 Gy. However, while the P2 straight type recovered from 5700 Gy by regaining normal growth within 6 days, the P6 helical type took about 13 days to recover from this dose, indicating differences in their radiation tolerance and response. To investigate these differences, P2 and P6 cells exposed to the intermediate dose of gamma radiation (3200 Gy) were analyzed for differential gene expression by RNA-Seq analysis. Prior to batch normalization, a total of 1553 genes (887 and 666 of P2 and P6, respectively, with 352 genes in common) were selected based on a two-fold change in expression and a false discovery rate FDR smaller or equal to 0.05. About 85% of these 1553 genes encoded products of yet unknown function. Of the 229 remaining genes, 171 had a defined function while 58 genes were transcribed into non-coding RNA including 21 tRNAs (all downregulated). Batch normalization resulted in 660 differentially expressed genes with 98 having a function and 32 encoding RNA. From PCC 8005-P2 and PCC 8005-P6 expression patterns, it emerges that although the cellular routes used by the two substrains to cope with ionizing radiation do overlap to a large extent, both strains displayed a distinct preference of priorities.
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Affiliation(s)
- Anu Yadav
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium;
| | - Laurens Maertens
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Research Unit in Biology of Microorganisms (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium
| | - Tim Meese
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (T.M.); (F.V.N.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (T.M.); (F.V.N.)
| | - Mohamed Mysara
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
| | - Natalie Leys
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium;
| | - Paul Jaak Janssen
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Correspondence: ; Tel.: +32-14-332-129
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12
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The cyanobacterial taxis protein HmpF regulates type IV pilus activity in response to light. Proc Natl Acad Sci U S A 2021; 118:2023988118. [PMID: 33723073 DOI: 10.1073/pnas.2023988118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Motility is ubiquitous in prokaryotic organisms including the photosynthetic cyanobacteria where surface motility powered by type 4 pili (T4P) is common and facilitates phototaxis to seek out favorable light environments. In cyanobacteria, chemotaxis-like systems are known to regulate motility and phototaxis. The characterized phototaxis systems rely on methyl-accepting chemotaxis proteins containing bilin-binding GAF domains capable of directly sensing light, and the mechanism by which they regulate the T4P is largely undefined. In this study we demonstrate that cyanobacteria possess a second, GAF-independent, means of sensing light to regulate motility and provide insight into how a chemotaxis-like system regulates the T4P motors. A combination of genetic, cytological, and protein-protein interaction analyses, along with experiments using the proton ionophore carbonyl cyanide m-chlorophenyl hydrazine, indicate that the Hmp chemotaxis-like system of the model filamentous cyanobacterium Nostoc punctiforme is capable of sensing light indirectly, possibly via alterations in proton motive force, and modulates direct interaction between the cyanobacterial taxis protein HmpF, and Hfq, PilT1, and PilT2 to regulate the T4P motors. Given that the Hmp system is widely conserved in cyanobacteria, and the finding from this study that orthologs of HmpF and T4P proteins from the distantly related model unicellular cyanobacterium Synechocystis sp. strain PCC6803 interact in a similar manner to their N. punctiforme counterparts, it is likely that this represents a ubiquitous means of regulating motility in response to light in cyanobacteria.
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13
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Springstein BL, Nürnberg DJ, Weiss GL, Pilhofer M, Stucken K. Structural Determinants and Their Role in Cyanobacterial Morphogenesis. Life (Basel) 2020; 10:E355. [PMID: 33348886 PMCID: PMC7766704 DOI: 10.3390/life10120355] [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: 11/02/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Cells have to erect and sustain an organized and dynamically adaptable structure for an efficient mode of operation that allows drastic morphological changes during cell growth and cell division. These manifold tasks are complied by the so-called cytoskeleton and its associated proteins. In bacteria, FtsZ and MreB, the bacterial homologs to tubulin and actin, respectively, as well as coiled-coil-rich proteins of intermediate filament (IF)-like function to fulfil these tasks. Despite generally being characterized as Gram-negative, cyanobacteria have a remarkably thick peptidoglycan layer and possess Gram-positive-specific cell division proteins such as SepF and DivIVA-like proteins, besides Gram-negative and cyanobacterial-specific cell division proteins like MinE, SepI, ZipN (Ftn2) and ZipS (Ftn6). The diversity of cellular morphologies and cell growth strategies in cyanobacteria could therefore be the result of additional unidentified structural determinants such as cytoskeletal proteins. In this article, we review the current advances in the understanding of the cyanobacterial cell shape, cell division and cell growth.
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Affiliation(s)
- Benjamin L. Springstein
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis J. Nürnberg
- Department of Physics, Biophysics and Biochemistry of Photosynthetic Organisms, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Gregor L. Weiss
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Karina Stucken
- Department of Food Engineering, Universidad de La Serena, La Serena 1720010, Chile;
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Springstein BL, Nürnberg DJ, Woehle C, Weissenbach J, Theune ML, Helbig AO, Maldener I, Dagan T, Stucken K. Two novel heteropolymer-forming proteins maintain the multicellular shape of the cyanobacterium Anabaena sp. PCC 7120. FEBS J 2020; 288:3197-3216. [PMID: 33205554 DOI: 10.1111/febs.15630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/29/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022]
Abstract
Polymerizing and filament-forming proteins are instrumental for numerous cellular processes such as cell division and growth. Their function in stabilization and localization of protein complexes and replicons is achieved by a filamentous structure. Known filamentous proteins assemble into homopolymers consisting of single subunits - for example, MreB and FtsZ in bacteria - or heteropolymers that are composed of two subunits, for example, keratin and α/β tubulin in eukaryotes. Here, we describe two novel coiled-coil-rich proteins (CCRPs) in the filament-forming cyanobacterium Anabaena sp. PCC 7120 (hereafter Anabaena) that assemble into a heteropolymer and function in the maintenance of the Anabaena multicellular shape (termed trichome). The two CCRPs - Alr4504 and Alr4505 (named ZicK and ZacK) - are strictly interdependent for the assembly of protein filaments in vivo and polymerize nucleotide independently in vitro, similar to known intermediate filament (IF) proteins. A ΔzicKΔzacK double mutant is characterized by a zigzagged cell arrangement and hence a loss of the typical linear Anabaena trichome shape. ZicK and ZacK interact with themselves, with each other, with the elongasome protein MreB, the septal junction protein SepJ and the divisome associate septal protein SepI. Our results suggest that ZicK and ZacK function in cooperation with SepJ and MreB to stabilize the Anabaena trichome and are likely essential for the manifestation of the multicellular shape in Anabaena. Our study reveals the presence of filament-forming IF-like proteins whose function is achieved through the formation of heteropolymers in cyanobacteria.
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Affiliation(s)
| | | | | | | | - Marius L Theune
- Institute of General Microbiology, University of Kiel, Germany
| | - Andreas O Helbig
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Germany
| | - Iris Maldener
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen/Organismic Interactions, University of Tübingen, Germany
| | - Tal Dagan
- Institute of General Microbiology, University of Kiel, Germany
| | - Karina Stucken
- Department of Food Engineering, University of La Serena, Chile
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15
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A bacterial cytolinker couples positioning of magnetic organelles to cell shape control. Proc Natl Acad Sci U S A 2020; 117:32086-32097. [PMID: 33257551 DOI: 10.1073/pnas.2014659117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Magnetotactic bacteria maneuver within the geomagnetic field by means of intracellular magnetic organelles, magnetosomes, which are aligned into a chain and positioned at midcell by a dedicated magnetosome-specific cytoskeleton, the "magnetoskeleton." However, how magnetosome chain organization and resulting magnetotaxis is linked to cell shape has remained elusive. Here, we describe the cytoskeletal determinant CcfM (curvature-inducing coiled-coil filament interacting with the magnetoskeleton), which links the magnetoskeleton to cell morphology regulation in Magnetospirillum gryphiswaldense Membrane-anchored CcfM localizes in a filamentous pattern along regions of inner positive-cell curvature by its coiled-coil motifs, and independent of the magnetoskeleton. CcfM overexpression causes additional circumferential localization patterns, associated with a dramatic increase in cell curvature, and magnetosome chain mislocalization or complete chain disruption. In contrast, deletion of ccfM results in decreased cell curvature, impaired cell division, and predominant formation of shorter, doubled chains of magnetosomes. Pleiotropic effects of CcfM on magnetosome chain organization and cell morphology are supported by the finding that CcfM interacts with the magnetoskeleton-related MamY and the actin-like MamK via distinct motifs, and with the cell shape-related cytoskeleton via MreB. We further demonstrate that CcfM promotes motility and magnetic alignment in structured environments, and thus likely confers a selective advantage in natural habitats of magnetotactic bacteria, such as aquatic sediments. Overall, we unravel the function of a prokaryotic cytoskeletal constituent that is widespread in magnetic and nonmagnetic spirilla-shaped Alphaproteobacteria.
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16
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Springstein BL, Arévalo S, Helbig AO, Herrero A, Stucken K, Flores E, Dagan T. A novel septal protein of multicellular heterocystous cyanobacteria is associated with the divisome. Mol Microbiol 2020; 113:1140-1154. [DOI: 10.1111/mmi.14483] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022]
Affiliation(s)
| | - Sergio Arévalo
- Instituto de Bioquímica Vegetal y Fotosíntesis CSIC and Universidad de Sevilla Seville Spain
| | - Andreas O. Helbig
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐Universität zu Kiel Kiel Germany
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis CSIC and Universidad de Sevilla Seville Spain
| | - Karina Stucken
- Department of Food Engineering Universidad de La Serena La Serena Chile
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis CSIC and Universidad de Sevilla Seville Spain
| | - Tal Dagan
- Institute of General Microbiology Christian‐Albrechts‐Universität zu Kiel Kiel Germany
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