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Yang G, Li J, Hu J, Shi JY. Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation. Brief Bioinform 2024; 25:bbae193. [PMID: 38701419 PMCID: PMC11066903 DOI: 10.1093/bib/bbae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
It is a vital step to recognize cyanobacteria promoters on a genome-wide scale. Computational methods are promising to assist in difficult biological identification. When building recognition models, these methods rely on non-promoter generation to cope with the lack of real non-promoters. Nevertheless, the factitious significant difference between promoters and non-promoters causes over-optimistic prediction. Moreover, designed for E. coli or B. subtilis, existing methods cannot uncover novel, distinct motifs among cyanobacterial promoters. To address these issues, this work first proposes a novel non-promoter generation strategy called phantom sampling, which can eliminate the factitious difference between promoters and generated non-promoters. Furthermore, it elaborates a novel promoter prediction model based on the Siamese network (SiamProm), which can amplify the hidden difference between promoters and non-promoters through a joint characterization of global associations, upstream and downstream contexts, and neighboring associations w.r.t. k-mer tokens. The comparison with state-of-the-art methods demonstrates the superiority of our phantom sampling and SiamProm. Both comprehensive ablation studies and feature space illustrations also validate the effectiveness of the Siamese network and its components. More importantly, SiamProm, upon our phantom sampling, finds a novel cyanobacterial promoter motif ('GCGATCGC'), which is palindrome-patterned, content-conserved, but position-shifted.
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Affiliation(s)
- Guang Yang
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
| | - Jianing Li
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
| | - Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
| | - Jian-Yu Shi
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
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2
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Treece TR, Tessman M, Pomeroy RS, Mayfield SP, Simkovsky R, Atsumi S. Fluctuating pH for efficient photomixotrophic succinate production. Metab Eng 2023; 79:118-129. [PMID: 37499856 DOI: 10.1016/j.ymben.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/15/2023] [Accepted: 07/23/2023] [Indexed: 07/29/2023]
Abstract
Cyanobacteria are attracting increasing attention as a photosynthetic chassis organism for diverse biochemical production, however, photoautotrophic production remains inefficient. Photomixotrophy, a method where sugar is used to supplement baseline autotrophic metabolism in photosynthetic hosts, is becoming increasingly popular for enhancing sustainable bioproduction with multiple input energy streams. In this study, the commercially relevant diacid, succinate, was produced photomixotrophically. Succinate is an important industrial chemical that can be used for the production of a wide array of products, from pharmaceuticals to biopolymers. In this system, the substrate, glucose, is transported by a proton symporter and the product, succinate, is hypothesized to be transported by another proton symporter, but in the opposite direction. Thus, low pH is required for the import of glucose and high pH is required for the export of succinate. Succinate production was initiated in a pH 7 medium containing bicarbonate. Glucose was efficiently imported at around neutral pH. Utilization of bicarbonate by CO2 fixation raised the pH of the medium. As succinate, a diacid, was produced, the pH of the medium dropped. By repeating this cycle with additional pH adjustment, those contradictory requirements for transport were overcome. pH affects a variety of biological factors and by cycling from high pH to neutral pH processes such as CO2 fixation rates and CO2 solubility can vary. In this study the engineered strains produced succinate during fluctuating pH conditions, achieving a titer of 5.0 g L-1 after 10 days under shake flask conditions. These results demonstrate the potential for photomixotrophic production as a viable option for the large-scale production of succinate.
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Affiliation(s)
- Tanner R Treece
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | | | - Robert S Pomeroy
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephen P Mayfield
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA; California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA; California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
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3
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Datta D, Weiss EL, Wangpraseurt D, Hild E, Chen S, Golden JW, Golden SS, Pokorski JK. Phenotypically complex living materials containing engineered cyanobacteria. Nat Commun 2023; 14:4742. [PMID: 37550278 PMCID: PMC10406891 DOI: 10.1038/s41467-023-40265-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
The field of engineered living materials lies at the intersection of materials science and synthetic biology with the aim of developing materials that can sense and respond to the environment. In this study, we use 3D printing to fabricate a cyanobacterial biocomposite material capable of producing multiple functional outputs in response to an external chemical stimulus and demonstrate the advantages of utilizing additive manufacturing techniques in controlling the shape of the fabricated photosynthetic material. As an initial proof-of-concept, a synthetic riboswitch is used to regulate the expression of a yellow fluorescent protein reporter in Synechococcus elongatus PCC 7942 within a hydrogel matrix. Subsequently, a strain of S. elongatus is engineered to produce an oxidative laccase enzyme; when printed within a hydrogel matrix the responsive biomaterial can decolorize a common textile dye pollutant, indigo carmine, potentially serving as a tool in environmental bioremediation. Finally, cells are engineered for inducible cell death to eliminate their presence once their activity is no longer required, which is an important function for biocontainment and minimizing environmental impact. By integrating genetically engineered stimuli-responsive cyanobacteria in volumetric 3D-printed designs, we demonstrate programmable photosynthetic biocomposite materials capable of producing functional outputs including, but not limited to, bioremediation.
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Affiliation(s)
- Debika Datta
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
| | - Elliot L Weiss
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Daniel Wangpraseurt
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Erica Hild
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
| | - Shaochen Chen
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
| | - James W Golden
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Susan S Golden
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
| | - Jonathan K Pokorski
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA.
- Center for Nano-ImmunoEngineering and Institute for Materials Discovery and Design, University of California San Diego, La Jolla, CA, USA.
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4
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Patel VK, Das A, Kumari R, Kajla S. Recent progress and challenges in CRISPR-Cas9 engineered algae and cyanobacteria. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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5
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Vamsi Bharadwaj S, Tiwari DS, Ghosh T, Mishra S. Construction of pSM201v: A broad host range replicative vector based on shortening of RSF1010. Heliyon 2023; 9:e14637. [PMID: 37025788 PMCID: PMC10070531 DOI: 10.1016/j.heliyon.2023.e14637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Despite possessing attractive features such as autotrophic growth on minimal media, industrial applications of cyanobacteria are hindered by a lack of genetic manipulative tools. There are two important features that are important for an effective manipulation: a vector which can carry the gene, and an induction system activated through external stimuli, giving us control over the expression. In this study, we describe the construction of an improved RSF1010-based vector as well as a temperature-inducible RNA thermometer. RSF1010 is a well-studied incompatibility group Q (IncQ) vector, capable of replication in most Gram negative, and some Gram positive bacteria. Our designed vector, named pSM201v, can be used as an expression vector in some Gram positive and a wide range of Gram negative bacteria including cyanobacteria. An induction system activated via physical external stimuli such as temperature, allows precise control of overexpression. pSM201v addresses several drawbacks of the RSF1010 plasmid; it has a reduced backbone size of 5189 bp compared to 8684 bp of the original plasmid, which provides more space for cloning and transfer of cargo DNA into the host organism. The mobilization function, required for plasmid transfer into several cyanobacterial strains, is reduced to a 99 bp region, as a result that mobilization of this plasmid is no longer linked to the plasmid replication. The RNA thermometer, named DTT1, is based on a RNA hairpin strategy that prevents expression of downstream genes at temperatures below 30 °C. Such RNA elements are expected to find applications in biotechnology to economically control gene expression in a scalable manner.
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Delatour E, Pagnout C, Zaffino ML, Duval JFL. Comparative Analysis of Cell Metabolic Activity Sensing by Escherichia coli rrnB P1-lux and Cd Responsive-Lux Biosensors: Time-Resolved Experiments and Mechanistic Modelling. BIOSENSORS 2022; 12:763. [PMID: 36140148 PMCID: PMC9496673 DOI: 10.3390/bios12090763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Whole-cell bacterial sensors are used in medical/environmental applications to detect chemicals, and to assess medium toxicity or stress. Non-specific constitutive biosensors generally serve the latter purpose, whereas chemical detection is performed with biosensors involving a specific chemical-inducible promoter. Herein, we show that functioning principles of specific and non-specific whole-cell biosensors are not exclusive as both can probe modulations of cell metabolic activity under stressing conditions. The demonstration is based on (i) time-resolved measurements of bioluminescence produced by constitutive rrnB P1-luxCDABE Escherichia coli biosensor in media differing with respect to carbon source, (ii) theoretical reconstruction of the measured signals using a here-reported theory for bioluminescence generated by constitutive cells, (iii) comparison between time-dependent cell photoactivity (reflecting metabolic activity) retrieved by theory with that we reported recently for cadmium-inducible PzntA-luxCDABE E. coli in media of similar compositions. Whereas signals of constitutive and non-constitutive biosensors differ in terms of shape, amplitude and peak number depending on nutritional medium conditions, analysis highlights the features shared by their respective cell photoactivity patterns mediated by the interplay between stringent response and catabolite repressions. The work advocates for the benefits of a theoretical interpretation for the time-dependent response of biosensors to unravel metabolic and physicochemical contributions to the bioluminescence signal.
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Affiliation(s)
- Eva Delatour
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Christophe Pagnout
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Marie L. Zaffino
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Jérôme F. L. Duval
- Université de Lorraine, CNRS, LIEC, UMR7360, F-54501 Vandoeuvre-lès-Nancy, France
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He H, Li Y, Zhang L, Ding Z, Shi G. Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective. J Adv Res 2022:S2090-1232(22)00205-3. [PMID: 36103961 DOI: 10.1016/j.jare.2022.09.003] [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: 12/13/2021] [Revised: 08/22/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022] Open
Abstract
BACKGROUND Nitrogen sources play an essential role in maintaining the physiological and biochemical activity of bacteria. Nitrogen metabolism, which is the core of microorganism metabolism, makes bacteria able to autonomously respond to different external nitrogen environments by exercising complex internal regulatory networks to help them stay in an ideal state. Although various studies have been put forth to better understand this regulation in Bacillus, and many valuable viewpoints have been obtained, these views need to be presented systematically and their possible applications need to be specified. AIM OF REVIEW The intention is to provide a deep and comprehensive understanding of nitrogen metabolism in Bacillus, an important industrial microorganism, and thereby apply this regulatory logic to synthetic biology to improve biosynthesis competitiveness. In addition, the potential researches in the future are also discussed. KEY SCIENTIFIC CONCEPT OF REVIEW Understanding the meticulous regulation process of nitrogen metabolism in Bacillus not only could facilitate research on metabolic engineering but also could provide constructive insights and inspiration for studies of other microorganisms.
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Affiliation(s)
- Hehe He
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China.
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China.
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8
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Simple transformation of the filamentous thermophilic cyanobacterium Leptolyngbya sp. KC45. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Opel F, Siebert NA, Klatt S, Tüllinghoff A, Hantke JG, Toepel J, Bühler B, Nürnberg DJ, Klähn S. Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria. ACS Synth Biol 2022; 11:1758-1771. [PMID: 35405070 DOI: 10.1021/acssynbio.1c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria have raised great interest in biotechnology due to their potential for a sustainable, photosynthesis-driven production of fuels and value-added chemicals. This has led to a concomitant development of molecular tools to engineer the metabolism of those organisms. In this regard, however, even cyanobacterial model strains lag behind compared to their heterotrophic counterparts. For instance, replicative shuttle vectors that allow gene transfer independent of recombination into host DNA are still scarce. Here, we introduce the pSOMA shuttle vector series comprising 10 synthetic plasmids for comprehensive genetic engineering of Synechocystis sp. PCC 6803. The series is based on the small endogenous plasmids pCA2.4 and pCB2.4, each combined with a replicon from Escherichia coli, different selection markers as well as features facilitating molecular cloning and the insulated introduction of gene expression cassettes. We made use of genes encoding green fluorescent protein (GFP) and a Baeyer-Villiger monooxygenase (BVMO) to demonstrate functional gene expression from the pSOMA plasmids in vivo. Moreover, we demonstrate the expression of distinct heterologous genes from individual plasmids maintained in the same strain and thereby confirmed compatibility between the two pSOMA subseries as well as with derivatives of the broad-host-range plasmid RSF1010. We also show that gene transfer into the filamentous model strain Anabaena sp. PCC 7120 is generally possible, which is encouraging to further explore the range of cyanobacterial host species that could be engineered via pSOMA plasmids. Altogether, the pSOMA shuttle vector series displays an attractive alternative to existing plasmid series and thus meets the current demand for the introduction of complex genetic setups and to perform extensive metabolic engineering of cyanobacteria.
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Affiliation(s)
- Franz Opel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Nina A. Siebert
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Sabine Klatt
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Adrian Tüllinghoff
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Janis G. Hantke
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Toepel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stephan Klähn
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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10
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Parveen H, Yazdani SS. Insights into cyanobacterial alkane biosynthesis. J Ind Microbiol Biotechnol 2022; 49:kuab075. [PMID: 34718648 PMCID: PMC9118987 DOI: 10.1093/jimb/kuab075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 11/12/2022]
Abstract
Alkanes are high-energy molecules that are compatible with enduring liquid fuel infrastructures, which make them highly suitable for being next-generation biofuels. Though biological production of alkanes has been reported in various microorganisms, the reports citing photosynthetic cyanobacteria as natural producers have been the most consistent for the long-chain alkanes and alkenes (C15-C19). However, the production of alkane in cyanobacteria is low, leading to its extraction being uneconomical for commercial purposes. In order to make alkane production economically feasible from cyanobacteria, the titre and yield need to be increased by several orders of magnitude. In the recent past, efforts have been made to enhance alkane production, although with a little gain in yield, leaving space for much improvement. Genetic manipulation in cyanobacteria is considered challenging, but recent advancements in genetic engineering tools may assist in manipulating the genome in order to enhance alkane production. Further, advancement in a basic understanding of metabolic pathways and gene functioning will guide future research for harvesting the potential of these tiny photosynthetically efficient factories. In this review, our focus would be to highlight the current knowledge available on cyanobacterial alkane production, and the potential aspects of developing cyanobacterium as an economical source of biofuel. Further insights into different metabolic pathways and hosts explored so far, and possible challenges in scaling up the production of alkanes will also be discussed.
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Affiliation(s)
- Humaira Parveen
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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11
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Theodosiou E, Tüllinghoff A, Toepel J, Bühler B. Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis. Front Bioeng Biotechnol 2022; 10:855715. [PMID: 35497353 PMCID: PMC9043136 DOI: 10.3389/fbioe.2022.855715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.
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Affiliation(s)
- Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Adrian Tüllinghoff
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- *Correspondence: Bruno Bühler,
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12
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Dykstra PB, Kaplan M, Smolke CD. Engineering synthetic RNA devices for cell control. Nat Rev Genet 2022; 23:215-228. [PMID: 34983970 PMCID: PMC9554294 DOI: 10.1038/s41576-021-00436-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
The versatility of RNA in sensing and interacting with small molecules, proteins and other nucleic acids while encoding genetic instructions for protein translation makes it a powerful substrate for engineering biological systems. RNA devices integrate cellular information sensing, processing and actuation of specific signals into defined functions and have yielded programmable biological systems and novel therapeutics of increasing sophistication. However, challenges centred on expanding the range of analytes that can be sensed and adding new mechanisms of action have hindered the full realization of the field's promise. Here, we describe recent advances that address these limitations and point to a significant maturation of synthetic RNA-based devices.
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Affiliation(s)
- Peter B. Dykstra
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matias Kaplan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,
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13
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The Molecular Toolset and Techniques Required to Build Cyanobacterial Cell Factories. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022. [DOI: 10.1007/10_2022_210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Pathania R, Srivastava A, Srivastava S, Shukla P. Metabolic systems biology and multi-omics of cyanobacteria: Perspectives and future directions. BIORESOURCE TECHNOLOGY 2022; 343:126007. [PMID: 34634665 DOI: 10.1016/j.biortech.2021.126007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacteria are oxygenic photoautotrophs whose metabolism contains key biochemical pathways to fix atmospheric CO2 and synthesize various metabolites. The development of bioengineering tools has enabled the manipulation of cyanobacterial chassis to produce various valuable bioproducts photosynthetically. However, effective utilization of cyanobacteria as photosynthetic cell factories needs a detailed understanding of their metabolism and its interaction with other cellular processes. Implementing systems and synthetic biology tools has generated a wealth of information on various metabolic pathways. However, to design effective engineering strategies for further improvement in growth, photosynthetic efficiency, and enhanced production of target biochemicals, in-depth knowledge of their carbon/nitrogen metabolism, pathway fluxe distribution, genetic regulation and integrative analyses are necessary. In this review, we discuss the recent advances in the development of genome-scale metabolic models (GSMMs), omics analyses (metabolomics, transcriptomics, proteomics, fluxomics), and integrative modeling approaches to showcase the current understanding of cyanobacterial metabolism.
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Affiliation(s)
- Ruchi Pathania
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi 110067, India; DBT-ICGEB Center for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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Lupacchini S, Appel J, Stauder R, Bolay P, Klähn S, Lettau E, Adrian L, Lauterbach L, Bühler B, Schmid A, Toepel J. Rewiring cyanobacterial photosynthesis by the implementation of an oxygen-tolerant hydrogenase. Metab Eng 2021; 68:199-209. [PMID: 34673236 DOI: 10.1016/j.ymben.2021.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022]
Abstract
Molecular hydrogen (H2) is considered as an ideal energy carrier to replace fossil fuels in future. Biotechnological H2 production driven by oxygenic photosynthesis appears highly promising, as biocatalyst and H2 syntheses rely mainly on light, water, and CO2 and not on rare metals. This biological process requires coupling of the photosynthetic water oxidizing apparatus to a H2-producing hydrogenase. However, this strategy is impeded by the simultaneous release of oxygen (O2) which is a strong inhibitor of most hydrogenases. Here, we addressed this challenge, by the introduction of an O2-tolerant hydrogenase into phototrophic bacteria, namely the cyanobacterial model strain Synechocystis sp. PCC 6803. To this end, the gene cluster encoding the soluble, O2-tolerant, and NAD(H)-dependent hydrogenase from Ralstonia eutropha (ReSH) was functionally transferred to a Synechocystis strain featuring a knockout of the native O2 sensitive hydrogenase. Intriguingly, photosynthetically active cells produced the O2 tolerant ReSH, and activity was confirmed in vitro and in vivo. Further, ReSH enabled the constructed strain Syn_ReSH+ to utilize H2 as sole electron source to fix CO2. Syn_ReSH+ also was able to produce H2 under dark fermentative conditions as well as in presence of light, under conditions fostering intracellular NADH excess. These findings highlight a high level of interconnection between ReSH and cyanobacterial redox metabolism. This study lays a foundation for further engineering, e.g., of electron transfer to ReSH via NADPH or ferredoxin, to finally enable photosynthesis-driven H2 production.
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Affiliation(s)
- Sara Lupacchini
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Jens Appel
- Department of Biology, Botanical Institute, University Kiel, 24118, Kiel, Germany
| | - Ron Stauder
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Paul Bolay
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Elisabeth Lettau
- Institute for Chemistry, Technische Universität Berlin, 10623, Berlin, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, 10923, Berlin, Germany
| | - Lars Lauterbach
- Institute for Chemistry, Technische Universität Berlin, 10623, Berlin, Germany; Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule Aachen, 52074, Aachen, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany.
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16
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Gupta JK, Srivastava S. The Effect of Promoter and RBS Combination on the Growth and Glycogen Productivity of Sodium-Dependent Bicarbonate Transporter (SbtA) Overexpressing Synechococcus sp. PCC 7002 Cells. Front Microbiol 2021; 12:607411. [PMID: 33927699 PMCID: PMC8076525 DOI: 10.3389/fmicb.2021.607411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Sodium dependent bicarbonate transporter, SbtA is a high-affinity, inducible bicarbonate transporter in cyanobacterial cells. Our previous work has shown that overexpression of this transporter can significantly increase growth and glycogen accumulation in Synechococcus sp. PCC 7002 cells. In this work, we have tested the effect of two different RBS sequences (RBS1: GGAGGA and RBS2: AGGAGA) and three different promoters (PcpcB, PcpcB560, and PrbcL2) on the growth and glycogen production in SbtA-overexpressing Synechococcus sp. PCC 7002 cells. Our results show that PcpcB or PcpcB560 were more effective than PrbcL2 in increasing the growth and glycogen content. The choice of RBS sequence had relatively minor effect, though RBS2 was more effective than RBS1. The transformant E, with PcpcB560 and RBS2, showed the highest growth. The biomass after 5 days of growth on air or 1% CO2 was increased by about 90% in the strain E compared to PCC 7002 cells. All transformants overexpressing SbtA had higher glycogen content. However, growing the cells with bubbling of 1% CO2 did not increase cellular glycogen content any further. The strain E had about 80% higher glycogen content compared to WT PCC 7002 cells. Therefore, the glycogen productivity of the strain E grown with air-bubbling was about 2.5-fold that of the WT PCC 7002 cells grown similarly. Additionally, some of the transformants had higher chlorophyll content while all the transformants had higher carotenoid content compared to the PCC 7002 cells, suggesting interaction between carbon transport and pigment levels. Thus, this work shows that the choice of photosynthetic promoters and RBSs sequences can impact growth and glycogen accumulation in SbtA-overexpressing cells.
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Affiliation(s)
- Jai Kumar Gupta
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.,Department of Biotechnology-International Centre for Genetic Engineering and Biotechnology (DBT-ICGEB), Centre for Advanced Bioenergy Research, New Delhi, India
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17
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Martin-Pascual M, Batianis C, Bruinsma L, Asin-Garcia E, Garcia-Morales L, Weusthuis RA, van Kranenburg R, Martins Dos Santos VAP. A navigation guide of synthetic biology tools for Pseudomonas putida. Biotechnol Adv 2021; 49:107732. [PMID: 33785373 DOI: 10.1016/j.biotechadv.2021.107732] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Pseudomonas putida is a microbial chassis of huge potential for industrial and environmental biotechnology, owing to its remarkable metabolic versatility and ability to sustain difficult redox reactions and operational stresses, among other attractive characteristics. A wealth of genetic and in silico tools have been developed to enable the unravelling of its physiology and improvement of its performance. However, the rise of this microbe as a promising platform for biotechnological applications has resulted in diversification of tools and methods rather than standardization and convergence. As a consequence, multiple tools for the same purpose have been generated, whilst most of them have not been embraced by the scientific community, which has led to compartmentalization and inefficient use of resources. Inspired by this and by the substantial increase in popularity of P. putida, we aim herein to bring together and assess all currently available (wet and dry) synthetic biology tools specific for this microbe, focusing on the last 5 years. We provide information on the principles, functionality, advantages and limitations, with special focus on their use in metabolic engineering. Additionally, we compare the tool portfolio for P. putida with those for other bacterial chassis and discuss potential future directions for tool development. Therefore, this review is intended as a reference guide for experts and new 'users' of this promising chassis.
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Affiliation(s)
- Maria Martin-Pascual
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Luis Garcia-Morales
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem 4206 AC, The Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, the Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands; LifeGlimmer GmbH, Berlin 12163, Germany.
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18
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Selim KA, Haffner M. Heavy Metal Stress Alters the Response of the Unicellular Cyanobacterium Synechococcus elongatus PCC 7942 to Nitrogen Starvation. Life (Basel) 2020; 10:life10110275. [PMID: 33171751 PMCID: PMC7694984 DOI: 10.3390/life10110275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023] Open
Abstract
Non-diazotrophic cyanobacteria are unable to fix atmospheric nitrogen and rely on combined nitrogen for growth and development. In the absence of combined nitrogen sources, most non-diazotrophic cyanobacteria, e.g., Synechocystis sp. PCC 6803 or Synechococcus elongatus PCC 7942, enter a dormant stage called chlorosis. The chlorosis process involves switching off photosynthetic activities and downregulating protein biosynthesis. Addition of a combined nitrogen source induces the regeneration of chlorotic cells in a process called resuscitation. As heavy metals are ubiquitous in the cyanobacterial biosphere, their influence on the vegetative growth of cyanobacterial cells has been extensively studied. However, the effect of heavy metal stress on chlorotic cyanobacterial cells remains elusive. To simulate the natural conditions, we investigated the effects of long-term exposure of S. elongatus PCC 7942 cells to both heavy metal stress and nitrogen starvation. We were able to show that elevated heavy metal concentrations, especially for Ni2+, Cd2+, Cu2+ and Zn2+, are highly toxic to nitrogen starved cells. In particular, cells exposed to elevated concentrations of Cd2+ or Ni2+ were not able to properly enter chlorosis as they failed to degrade phycobiliproteins and chlorophyll a and remained greenish. In resuscitation assays, these cells were unable to recover from the simultaneous nitrogen starvation and Cd2+ or Ni2+ stress. The elevated toxicity of Cd2+ or Ni2+ presumably occurs due to their interference with the onset of chlorosis in nitrogen-starved cells, eventually leading to cell death.
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