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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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Gibbons J, Gu L, Qiu Y, Zhou R. Single Crossover to Inactivate Target Gene in Cyanobacteria. Methods Mol Biol 2022; 2489:289-298. [PMID: 35524056 DOI: 10.1007/978-1-0716-2273-5_15] [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] [Indexed: 06/14/2023]
Abstract
Anabaena sp. PCC 7120 (hereafter Anabaena 7120) is a model cyanobacterium for studying pathways such as photosynthesis and nitrogen fixation along with many other metabolic pathways common to plants. In addition, since Anabaena 7120 forms specialized N2-fixing cells, called heterocysts, to perform uniquely solar-powered, oxic nitrogen fixation under fixed-nitrogen depleted conditions, this cyanobacterium provides the unique opportunity to study cellular differentiation in bacteria. Since more than 155,810 sequenced prokaryotic genomes are currently available (Zhang et al., Microbiome 8(1):134, 2020), target gene inactivation, combined with analyses of the corresponding mutant's phenotype, has become a powerful tool to assess gene function through detecting a loss-of-function in the knockout mutant. In the method described here, a single crossover approach is used to knockout a target gene in Anabaena 7120. The method requires inserting an internal fragment of the target gene into the cyanobacterial integration vector pZR606 to create a knockout plasmid, and then is introduced to Anabaena 7120 via conjugative transformation. A single crossover, occurring via homologous recombination, disrupts the target gene, creating 3'- and 5'-deleted fragments (Fig. 1). The mutant containing the inactivated gene can then be studied to determine any loss of function, thereby defining the gene's function. This gene inactivation approach is based on an integrative vector pZR606 (Chen et al., Appl Microbiol Biotechnol 99:1779-1793, 2015), which may be broadly applied to gene inactivation in other cyanobacterial species as well as other prokaryotic organisms.
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Affiliation(s)
- Jaimie Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Liping Gu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yeyan Qiu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.
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He P, Cai X, Chen K, Fu X. Identification of small RNAs involved in nitrogen fixation in Anabaena sp. PCC 7120 based on RNA-seq under steady state conditions. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01557-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Abstract
Purpose
Anabaena sp. PCC7120 is a genetically tractable model organism for nitrogen fixation and photosynthesis research. The importance of small regulatory RNAs (sRNAs) as mediators of a number of cellular processes in bacteria has begun to be recognized. Bacterial sRNA binds to target genes through base pairing, and play a regulatory role. Many studies have shown that bacterial sRNA can regulate cell stress response, carbon and nitrogen fixation, and so on. However, little is known about sRNAs in Anabaena sp. PCC 7120 regarded to nitrogen fixation under later steady state.
Methods
To provide a comprehensive study of sRNAs in this model organism, the sRNA (< 200 nt) extracted from Anabaena sp. PCC 7120 under nitrogen step-down treatment of 12 days, together with the sRNA from the control, was analyzed using deep RNA sequencing. Possible target genes regulated by all identified putative sRNAs were predicted by IntaRNA and further analyzed for functional categorizations for biological pathways.
Result
Totally, 14,132 transcripts were produced from the de novo assembly. Among them, transcripts that are located either in the intergenic region or antisense strand were kept, which resulted in 1219 sRNA candidates, for further analysis. RPKM-based differential expression analysis showed that 418 sRNAs were significantly differentially expressed between the samples from control (nitrogen addition, N+) and nitrogen depletion, (N−). Among them, 303 sRNAs were significantly upregulated, whereas 115 sRNAs were significantly downregulated. RT-PCR of 18 randomly chosen sRNAs showed a similar pattern as RNA-seq result, which confirmed the reliability of the RNA-seq data. In addition, the possible target genes regulated by unique sRNAs of Anabaena sp. PCC 7120 under nitrogen addition (N+) condition or that under nitrogen depletion (N−) condition were analyzed for functional categorization and biological pathways, which provided the evidences that sRNAs were indeed involved in many different metabolic pathways.
Conclusion
The information from the present study provides a valuable reference for understanding the sRNA-mediated regulation of the nitrogen fixation in Anabaena PCC 7120 under steady state conditions.
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Ge YD, Jiang LL, Hou SL, Su FZ, Wang P, Zhang G. Heteroexpression and biochemical characterization of thermostable citrate synthase from the cyanobacteria Anabaena sp. PCC7120. Protein Expr Purif 2019; 168:105565. [PMID: 31887428 DOI: 10.1016/j.pep.2019.105565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/26/2019] [Accepted: 12/26/2019] [Indexed: 11/25/2022]
Abstract
The present study recombinantly expressed a citrate synthase from cyanobacteria Anabaena sp. PCC7120 (AnCS) in Escherichia coli and characterized its enzymatic activity. The molecular mass of native AnCS was 88,533.1 Da containing two 44,162.7 Da subunits. Recombinant AnCS revealed the highest activity at pH 9.0 and 25 °C. AnCS displayed high thermal stability with a half-life time (t1/2) of approximately 6.5 h at 60 °C, which was more thermostable than most CS from general organisms, but less than those from hyperthermophilic bacteria. The Km values of oxaloacetate and acetyl-CoA were 138.50 and 18.15 μM respectively, suggesting a higher affinity to acetyl-CoA than oxaloacetate. Our inhibition assays showed that AnCS activity was not severely affected by most metal ions, but was strongly inhibited by Cu2+ and Zn2+. Treatments with ATP, ADP, AMP, NADH, and DTT depressed the AnCS activity. Overall, our results provide information on the enzymatic properties of AnCS, which contributes to the basic knowledge on CS selection for industrial utilizations.
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Affiliation(s)
- Ya-Dong Ge
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Lu-Lu Jiang
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Shao-Lin Hou
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Feng-Zhi Su
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Peng Wang
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Gen Zhang
- Shenzhen GenProMetab Biotechnology Company Limited, Shenzhen, 518000, China.
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Gibbons J, Gu L, Zhu H, Gibbons W, Zhou R. Identification of two genes required for heptadecane production in a N 2-fixing cyanobacterium Anabaena sp. strain PCC 7120. AMB Express 2018; 8:167. [PMID: 30317393 PMCID: PMC6186262 DOI: 10.1186/s13568-018-0700-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/09/2018] [Indexed: 12/27/2022] Open
Abstract
Cyanobacteria photosynthetically produce long-chain hydrocarbons, which are considered as infrastructure-compatible biofuels. However, native cyanobacteria do not produce these hydrocarbons at sufficient rates or yields to warrant commercial deployment. This research sought to identify specific genes required for photosynthetic production of alkanes to enable future metabolic engineering for commercially viable production of alkanes. The two putative genes (alr5283 and alr5284) required for long-chain hydrocarbon production in Anabaena sp. PCC 7120 were knocked out through a double crossover approach. The knockout mutant abolished the production of heptadecane (C17H36). The mutant is able to be complemented by a plasmid bearing the two genes along with their native promoters only. The complemented mutant restored photosynthetic production of heptadecane. This combined genetic and metabolite (alkanes) profiling approach may be broadly applicable to characterization of knockout mutants, using N2-fixing cyanobacteria as a cellular factory driven by solar energy to produce a wide range of commodity chemicals and drop-in-fuels from atmospheric gases (CO2 and N2 gas) and mineralized water.
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Ueno K, Sakai Y, Shono C, Sakamoto I, Tsukakoshi K, Hihara Y, Sode K, Ikebukuro K. Applying a riboregulator as a new chromosomal gene regulation tool for higher glycogen production in Synechocystis sp. PCC 6803. Appl Microbiol Biotechnol 2017; 101:8465-8474. [PMID: 29038975 DOI: 10.1007/s00253-017-8570-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/18/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Abstract
Cyanobacteria are one of the most attractive hosts for biofuel production; however, genetic approaches to regulate specific chromosomal genes in cyanobacteria remain limited. With the aim of developing a novel method to regulate chromosomal gene expression in cyanobacteria, we focused on riboregulatory technology. Riboregulators are composed of two RNA fragments whose interaction leads to target gene regulation with high specificity. In this study, we inserted a riboregulator sequence upstream of the chromosomal gene encoding AbrB-like transcriptional regulator, cyAbrB2, to investigate the utility of this tool. The inserted riboregulator was able to regulate cyabrB2 gene expression, with a high ON-OFF ratio up to approximately 50-fold. The transcription levels of several genes for which cyAbrB2 acts as a transcriptional upregulator were also decreased. Further, the cyAbrB2 expression-repressed mutant showed high glycogen accumulation, equivalent to that in the cyabrB2 deletion mutant (ΔcyabrB2). Phenotypic similarities between the cyabrB2 expression-repressed mutant and the ΔcyabrB2 mutant suggest that the riboregulator can potentially be used as a new chromosomal gene regulation tool in cyanobacteria.
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Affiliation(s)
- Kinuko Ueno
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yuta Sakai
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Chika Shono
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Ippei Sakamoto
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Fu W, Chaiboonchoe A, Khraiwesh B, Nelson DR, Al-Khairy D, Mystikou A, Alzahmi A, Salehi-Ashtiani K. Algal Cell Factories: Approaches, Applications, and Potentials. Mar Drugs 2016; 14:md14120225. [PMID: 27983586 PMCID: PMC5192462 DOI: 10.3390/md14120225] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 12/26/2022] Open
Abstract
With the advent of modern biotechnology, microorganisms from diverse lineages have been used to produce bio-based feedstocks and bioactive compounds. Many of these compounds are currently commodities of interest, in a variety of markets and their utility warrants investigation into improving their production through strain development. In this review, we address the issue of strain improvement in a group of organisms with strong potential to be productive “cell factories”: the photosynthetic microalgae. Microalgae are a diverse group of phytoplankton, involving polyphyletic lineage such as green algae and diatoms that are commonly used in the industry. The photosynthetic microalgae have been under intense investigation recently for their ability to produce commercial compounds using only light, CO2, and basic nutrients. However, their strain improvement is still a relatively recent area of work that is under development. Importantly, it is only through appropriate engineering methods that we may see the full biotechnological potential of microalgae come to fruition. Thus, in this review, we address past and present endeavors towards the aim of creating productive algal cell factories and describe possible advantageous future directions for the field.
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Affiliation(s)
- Weiqi Fu
- Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
| | - Amphun Chaiboonchoe
- Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
| | - Basel Khraiwesh
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
| | - David R Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
| | - Dina Al-Khairy
- Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
| | - Alexandra Mystikou
- Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, P.O. Box 129188 Saadiyat Island, Abu Dhabi, UAE.
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Johnson TJ, Gibbons JL, Gu L, Zhou R, Gibbons WR. Molecular genetic improvements of cyanobacteria to enhance the industrial potential of the microbe: A review. Biotechnol Prog 2016; 32:1357-1371. [DOI: 10.1002/btpr.2358] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/30/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Tylor J. Johnson
- Dept. of Biology and MicrobiologySouth Dakota State UniversityBrookings SD57007
- Dept. of MicrobiologyThe University of TennesseeKnoxville TN37996
| | - Jaimie L. Gibbons
- Dept. of Biology and MicrobiologySouth Dakota State UniversityBrookings SD57007
| | - Liping Gu
- Dept. of Biology and MicrobiologySouth Dakota State UniversityBrookings SD57007
| | - Ruanbao Zhou
- Dept. of Biology and MicrobiologySouth Dakota State UniversityBrookings SD57007
| | - William R. Gibbons
- Dept. of Biology and MicrobiologySouth Dakota State UniversityBrookings SD57007
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Chen K, Zhu H, Gu L, Tian S, Zhou R. Target Gene Inactivation in Cyanobacterium Anabaena sp. PCC 7120. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Xu X, Gu L, He P, Zhou R. Characterization of five putative aspartate aminotransferase genes in the N2-fixing heterocystous cyanobacterium Anabaena sp. strain PCC 7120. MICROBIOLOGY-SGM 2015; 161:1219-30. [PMID: 25808172 DOI: 10.1099/mic.0.000083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Aspartate and glutamate are two key amino acids used in biosynthesis of many amino acids that play vital role in cellular metabolism. Aspartate aminotransferases (AspATs) are required for channelling nitrogen (N(2)) between Glu and Asp in all life forms. Biochemical and genetic characterization of AspATs have been lacking in N(2)-fixing cyanobacteria. In this report, five putative AspAT genes (alr1039, all2340, alr2765, all4327 and alr4853) were identified in the N(2)-fixing heterocystous cyanobacterium Anabaena sp. PCC 7120. Five recombinant C-terminal hexahistidine-tagged AspATs (AspAT-H(6)) were overexpressed in Escherichia coli and purified to homogeneity. Biochemical analysis demonstrated that these five putative AspATs have authentic AspAT activity in vitro using aspartate as an amino donor. However, the enzymic activities of the five AspATs differed in vitro. Alr4853-H(6) showed the highest AspAT activity, while the enzymic activity for the other four AspATs ranged from 6.5 to 53.7 % activity compared to Alr4853 (100 %). Genetic characterization of the five AspAT genes was also performed by inactivating each individual gene. All of the five AspAT knockout mutants exhibited reduced diazotrophic growth, and alr4853 was further identified to be a Fox gene (requiring fixed N(2) for growth in the presence of oxygen). Four out of five P(aspAT)-gfp transcriptional fusions were constitutively expressed in both diazotrophic and nitrate-dependent growth conditions. Quantitative reverse transcriptase PCR showed that alr4853 expression was increased by 2.3-fold after 24 h of N(2) deprivation. Taken together, these findings add to our understanding of the role of AspATs in N(2)-fixing within heterocystous cyanobacteria.
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