1
|
Mallén-Ponce MJ, Florencio FJ, Huertas MJ. Thioredoxin A regulates protein synthesis to maintain carbon and nitrogen partitioning in cyanobacteria. Plant Physiol 2024:kiae101. [PMID: 38386687 DOI: 10.1093/plphys/kiae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024]
Abstract
Thioredoxins play an essential role in regulating enzyme activity in response to environmental changes, especially in photosynthetic organisms. They are crucial for metabolic regulation in cyanobacteria, but the key redox-regulated central processes remain to be determined. Physiological, metabolic, and transcriptomic characterization of a conditional mutant of the essential Synechocystis sp. PCC 6803 thioredoxin trxA gene (STXA2) revealed that decreased TrxA levels alter cell morphology and induce a dormant-like state. Furthermore, TrxA depletion in the STXA2 strain inhibited protein synthesis and led to changes in amino acid pools and nitrogen/carbon reserve polymers, accompanied by oxidation of the EF-Tu elongation factor. Transcriptomic analysis of TrxA depletion in STXA2 revealed a robust transcriptional response. Down-regulated genes formed a large cluster directly related to photosynthesis, ATP synthesis, and CO2 fixation. In contrast, up-regulated genes were grouped into different clusters related to respiratory electron transport, carotenoid biosynthesis, amino acid metabolism, and protein degradation, among others. These findings highlight the complex regulatory mechanisms that govern cyanobacterial metabolism, where TrxA acts as a critical regulator that orchestrates the transition from anabolic to maintenance metabolism and regulates carbon and nitrogen balance.
Collapse
Affiliation(s)
- Manuel J Mallén-Ponce
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, Profesor García González, 1, 41012, Sevilla, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092, Sevilla, Spain
| | - Francisco Javier Florencio
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, Profesor García González, 1, 41012, Sevilla, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092, Sevilla, Spain
| | - María José Huertas
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, Profesor García González, 1, 41012, Sevilla, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092, Sevilla, Spain
| |
Collapse
|
2
|
Sharon I, Grogg M, Hilvert D, Schmeing TM. The structure of cyanophycinase in complex with a cyanophycin degradation intermediate. Biochim Biophys Acta Gen Subj 2022; 1866:130217. [PMID: 35905922 DOI: 10.1016/j.bbagen.2022.130217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Cyanophycinases are serine protease family enzymes which are required for the metabolism of cyanophycin, the natural polymer multi-L-arginyl-poly(L-aspartic acid). Cyanophycinases degrade cyanophycin to β-Asp-Arg dipeptides, which enables use of this important store of fixed nitrogen. METHODS We used genetic code expansion to incorporate diaminopropionic acid into cyanophycinase in place of the active site serine, and determined a high-resolution structure of the covalent acyl-enzyme intermediate resulting from attack of cyanophycinase on a short cyanophycin segment. RESULTS The structure indicates that cyanophycin dipeptide residues P1 and P1' bind shallow pockets adjacent to the catalytic residues. We observe many cyanophycinase - P1 dipeptide interactions in the co-complex structure. Calorimetry measurements show that at least two cyanophycin dipeptides are needed for high affinity binding to cyanophycinase. We also characterized a putative cyanophycinase which we found to be structurally very similar but that shows no activity and could not be activated by mutation of its active site. GENERAL SIGNIFICANCE Despite its peptidic structure, cyanophycin is resistant to degradation by peptidases and other proteases. Our results help show how cyanophycinase can specifically bind and degrade this important polymer.
Collapse
Affiliation(s)
- Itai Sharon
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
| |
Collapse
|
3
|
Lu Z, Ye J, Chen Z, Xiao L, Lei L, Han BP, Paerl HW. Cyanophycin accumulated under nitrogen-fluctuating and high-nitrogen conditions facilitates the persistent dominance and blooms of Raphidiopsis raciborskii in tropical waters. Water Res 2022; 214:118215. [PMID: 35228039 DOI: 10.1016/j.watres.2022.118215] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Nutrient storage is considered a critical strategy for algal species to adapt to a fluctuating nutrient supply. Luxury phosphorus (P) uptake into storage of polyphosphate extends the duration of cyanobacterial dominance and their blooms under P deficiency. However, it is unclear whether nitrogen (N) storage in the form of cyanophycin supports persistent cyanobacterial dominance or blooms in the tropics where N deficiency commonly occurs in summer. In this study, we examined genes for cyanophycin synthesis and degradation in Raphidiopsis raciborskii, a widespread and dominant cyanobacterium in tropical waters; and detected the cyanophycin accumulation under fluctuating N concentrations and its ecological role in the population dynamics of the species. The genes for cyanophycin synthesis (cphA) and degradation (cphB) were highly conserved in 21 out of 23 Raphidiopsis strains. This suggested that the synthesis and degradation of cyanophycin are evolutionarily conserved to support the proliferation of R. raciborskii in N-fluctuating and/or deficient conditions. Isotope 15N-NaNO3 labeling experiments showed that R. raciborskii QDH7 always commenced to synthesize and accumulate cyanophycin under fluctuating N conditions, regardless of whether exogenous N was deficient. When the NO3--N concentration exceeded 1.2 mg L-1, R. raciborskii synthesized cyanophycin primarily through uptake of 15N-NaNO3. However, when the NO3--N concentration was below 1.0 mg L-1, cyanophycin-based N was derived from unlabeled N2, as evidenced by increased dinitrogenase activity. Cells grown under NO3--N < 1.0 mg L-1 had lower cyanophycin accumulation rates than cells grown under NO3--N > 1.2 mg L-1. Our field investigation in a large tropical reservoir underscored the association between cyanophycin content and the population dynamics of R. raciborskii. The cyanophycin content was high in N-sufficient (NO3--N > 0.45 mg L-1) periods, and decreased in N-deficient summer. In summer, R. raciborskii sustained a relatively high biomass and produced few heterocysts (< 1%). These findings indicated that cyanophycin-released N, rather than fixed N, supported persistent R. raciborskii blooms in N-deficient seasons. Our study suggests that the highly adaptive strategy in a N2-fixing cyanobacterial species makes mitigating its bloom more difficult than previously assumed.
Collapse
Affiliation(s)
- Zhe Lu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Jinmei Ye
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Zhijiang Chen
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Lijuan Xiao
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Lamei Lei
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Hans W Paerl
- Institute of Marine Sciences, The University of North Carolina at Chapel Hill, Morehead City, United States of America
| |
Collapse
|
4
|
Wördemann R, Wiefel L, Wendisch VF, Steinbüchel A. Incorporation of alternative amino acids into cyanophycin by different cyanophycin synthetases heterologously expressed in Corynebacterium glutamicum. AMB Express 2021; 11:55. [PMID: 33856569 PMCID: PMC8050183 DOI: 10.1186/s13568-021-01217-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/07/2021] [Indexed: 11/10/2022] Open
Abstract
Cyanophycin (multi-L-arginyl-poly-L-aspartic acid; also known as cyanophycin grana peptide [CGP]) is a biopolymer that could be used in various fields, for example, as a potential precursor for the synthesis of polyaspartic acid or for the production of CGP-derived dipeptides. To extend the applications of this polymer, it is therefore of interest to synthesize CGP with different compositions. A recent re-evaluation of the CGP synthesis in C. glutamicum has shown that C. glutamicum is a potentially interesting microorganism for CGP synthesis with a high content of alternative amino acids. This study shows that the amount of alternative amino acids can be increased by using mutants of C. glutamicum with altered amino acid biosynthesis. With the DM1729 mutant, the lysine content in the polymer could be increased up to 33.5 mol%. Furthermore, an ornithine content of up to 12.6 mol% was achieved with ORN2(Pgdh4). How much water-soluble or insoluble CGP is synthesized is strongly related to the used cyanophycin synthetase. CphADh synthesizes soluble CGP exclusively. However, soluble CGP could also be isolated from cells expressing CphA6308Δ1 or CphA6308Δ1_C595S in addition to insoluble CGP in all examined strains. The point mutation in CphA6308Δ1_C595S partially resulted in a higher lysine content. In addition, the CGP content could be increased to 36% of the cell dry weight under optimizing growth conditions in C. glutamicum ATCC13032. All known alternative major amino acids for CGP synthesis (lysine, ornithine, citrulline, and glutamic acid) could be incorporated into CGP in C. glutamicum.
Collapse
|
5
|
Elbahloul Y, Steinbüchel A. Characterization of an efficient extracellular cyanophycinase and its encoding cphE Strept. gene from Streptomyces pratensis strain YSM. J Biotechnol 2020; 319:15-24. [PMID: 32473189 DOI: 10.1016/j.jbiotec.2020.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022]
Abstract
Until now, no enzymes were described that hydrolyze cyanophycin granular protein (CGP) from a species of the genus Streptomyces. An isolate able to hydrolyze CGP was identified as Streptomyces pratensis strain YSM. The CGPase from S. pratensis strain YSM had an optimum activity at 42 °C and pH 8.5, and was able to degrade CGP at a rate of 12 ± 0.3 μg/mL min. Additionally, this CGPase hydrolyzes water-soluble CGP significantly faster than water-insoluble CGP. The molecular mass of CGPase subunits from S. pratensis strain YSM as determined by SDS-PAGE was about 43 kDa, and the enzyme was entirely inhibited by serine-protease inhibitors. The CGPase coding gene (cphEStrept.) was amplified from genomic DNA using primers designed form consensus sequence of putative CGPase sequences. The cphEStrept. was 1427 bp encoding a CGPase of 420 amino acids that showed about 44% and 22% similarities to CGPase from Pseudomonas anguilliseptica BI and Synechocystis sp. PCC 6803, respectively. The catalytic triad and serine-protease residues (GXSXG) were identified in the CphEStrept. sequence. Dipeptides and tetrapeptides were identified as hydrolysis products. Biotechnological exploitation of S. pratensis strain YSM for CGPase production might have an advantage due to the reduction of separation costs and its ability to degrade CGP in phosphate buffer saline using actively growing or resting cells.
Collapse
Affiliation(s)
- Yasser Elbahloul
- Biology Department, College of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia; Botany and Microbiology Department, Faculty of Science, Alexandria University, 21511, Alexandria, Egypt; Institut Für Molekulare Mikrobiologie Und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Corrensstraße 3, 48149, Münster, Germany.
| | - Alexander Steinbüchel
- Institut Für Molekulare Mikrobiologie Und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Corrensstraße 3, 48149, Münster, Germany; Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
6
|
Du J, Li L, Zhou S. Microbial production of cyanophycin: From enzymes to biopolymers. Biotechnol Adv 2019; 37:107400. [PMID: 31095967 DOI: 10.1016/j.biotechadv.2019.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 05/11/2019] [Indexed: 11/20/2022]
Abstract
Cyanophycin is an attractive biopolymer with chemical and material properties that are suitable for industrial applications in the fields of food, medicine, cosmetics, nutrition, and agriculture. For efficient production of cyanophycin, considerable efforts have been exerted to characterize cyanophycin synthetases (CphAs) and optimize fermentations and downstream processes. In this paper, we review the characteristics of diverse CphAs from cyanobacteria and non-cyanobacteria. Furthermore, strategies for cyanophycin production in microbial strains, including Escherichia coli, Pseudomonas putida, Ralstonia eutropha, Rhizopus oryzae, and Saccharomyces cerevisiae, heterologously expressing different cphA genes are reviewed. Additionally, chemical and material properties of cyanophycin and its derivatives produced through biological or chemical modifications are reviewed in the context of their industrial applications. Finally, future perspectives on microbial production of cyanophycin are provided to improve its cost-effectiveness.
Collapse
|
7
|
Wiefel L, Wohlers K, Steinbüchel A. Re-evaluation of cyanophycin synthesis in Corynebacterium glutamicum and incorporation of glutamic acid and lysine into the polymer. Appl Microbiol Biotechnol 2019; 103:4033-4043. [PMID: 30937497 DOI: 10.1007/s00253-019-09780-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/05/2019] [Accepted: 03/18/2019] [Indexed: 11/29/2022]
Abstract
Corynebacterium glutamicum was only examined in the early 2000s as a possible microorganism for the production of the polyamide cyanophycin (multi-L-arginyl-poly-[L-aspartic acid], CGP). CGP is a potential precursor for the synthesis of polyaspartic acid and CGP-derived dipeptides which may be of use in peptide-based clinical diets, as dietary supplements, or in livestock feeds. In the past, C. glutamicum was disregarded for CGP production due to low CGP contents and difficulties in isolating the polymer. However, considering recent advances in CGP research, the capabilities of this organism were revisited. In this study, several cyanophycin synthetases (CphA) as well as expression vectors and cultivation conditions were evaluated. The ability of C. glutamicum to incorporate additional amino acids such as lysine and glutamic acid was also examined. The strains C. glutamicum pVWEx1::cphAΔ1 and C. glutamicum pVWEx1::cphABP1 accumulated up to 14% of their dry weight CGP, including soluble CGP containing more than 40 mol% of the alternative side-chain amino acid lysine. The soluble, lysine-rich form of the polymer was not detected in C. glutamicum in previous studies. Additionally, an incorporation of up to 6 mol% of glutamic acid into the backbone of CGP synthesized by C. glutamicum pVWEx1::cphADh was detected. The strain accumulated up to 17% of its dry weight in soluble CGP. Although glutamic acid had previously been found to replace arginine in the side chain, this is the first time that glutamic acid was found to substitute aspartic acid in the backbone.
Collapse
Affiliation(s)
- Lars Wiefel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Corrensstraße 3, 48149, Münster, Germany
| | - Karen Wohlers
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Corrensstraße 3, 48149, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Corrensstraße 3, 48149, Münster, Germany. .,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia.
| |
Collapse
|
8
|
Ponndorf D, Broer I, Nausch H. Expression of CphB- and CphE-type cyanophycinases in cyanophycin-producing tobacco and comparison of their ability to degrade cyanophycin in plant and plant extracts. Transgenic Res 2017; 26:491-499. [PMID: 28432544 DOI: 10.1007/s11248-017-0019-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/17/2017] [Indexed: 11/28/2022]
Abstract
Increasing the arginine (Arg) content in plants used as feed or food is of interest, since the supplementation of food with conditionally essential Arg has been shown to have nutritional benefits. An increase was achieved by the expression of the Arg-rich bacterial storage component, cyanophycin (CGP), in the chloroplast of transgenic plants. CGP is stable in plants and its degradation into β-aspartic acid (Asp)-Arg dipeptides, is solely catalyzed by bacterial cyanophycinases (CGPase). Dipeptides can be absorbed by animals even more efficiently than free amino acids (Matthews and Adibi 1976; Wenzel et al. 2001). The simultaneous production of CGP and CGPase in plants could be a source of β-Asp-Arg dipeptides if CGP degradation can be prevented in planta or if dipeptides are stable in the plants. We have shown for the first time that it is possible to co-express CGP and CGPase in the same plant without substrate degradation in planta by transient expression of the cyanobacterial CGPase CPHB (either in the plastid or cytosol), and the non-cyanobacterial CGPase CPHE (cytosol) in CGP-producing Nicotiana tabacum plants. We compared their ability to degrade CGP in planta and in crude plant extracts. No CGP degradation appeared prior to cell homogenization independent of the CGPase produced. In crude plant extracts, only cytosolic CPHE led to a fast degradation of CGP. CPHE also showed higher stability and in vitro activity compared to both CPHB variants. This work is the next step to increase Arg in forage plants using a stable, Arg-rich storage protein.
Collapse
Affiliation(s)
- Daniel Ponndorf
- Department of Agrobiotechnology and Risk Assessment for Bio- and Gene Technology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig Weg 8, 18059, Rostock, Germany
| | - Inge Broer
- Department of Agrobiotechnology and Risk Assessment for Bio- and Gene Technology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig Weg 8, 18059, Rostock, Germany.
| | - Henrik Nausch
- Department of Agrobiotechnology and Risk Assessment for Bio- and Gene Technology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig Weg 8, 18059, Rostock, Germany
| |
Collapse
|
9
|
Nausch H, Hausmann T, Ponndorf D, Hühns M, Hoedtke S, Wolf P, Zeyner A, Broer I. Tobacco as platform for a commercial production of cyanophycin. N Biotechnol 2016; 33:842-851. [PMID: 27501906 DOI: 10.1016/j.nbt.2016.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 01/22/2023]
Abstract
Cyanophycin (CP) is a proteinogenic polymer that can be substituted for petroleum in the production of plastic compounds and can also serve as a source of valuable dietary supplements. However, because there is no economically feasible system for large-scale industrial production, its application is limited. In order to develop a low-input system, CP-synthesis was established in the two commercial Nicotiana tabacum (N. tabacum) cultivars 'Badischer Geudertheimer' (BG) and 'Virginia Golta' (VG), by introducing the cyanophycin-synthetase gene from Thermosynecchococcus elongatus BP-1 (CphATe) either via crossbreeding with transgenic N. tabacum cv. Petit Havana SR1 (PH) T2 individual 51-3-2 or by agrobacterium-mediated transformation. Both in F1 hybrids (max. 9.4% CP/DW) and T0 transformants (max. 8.8% CP/DW), a substantial increase in CP content was achieved in leaf tissue, compared to a maximum of 1.7% CP/DW in PH T0 transformants of Hühns et al. (2008). In BG CP, yields were homogenous and there was no substantial difference in the variation of the CP content between primary transformants (T0), clones of T0 individuals, T1 siblings and F1 siblings of hybrids. Therefore, BG meets the requirements for establishing a master seed bank for continuous and reliable CP-production. In addition, it was shown that the polymer is not only stable in planta but also during silage, which simplifies storage of the harvest prior to isolation of CP.
Collapse
Affiliation(s)
- Henrik Nausch
- University of Rostock, Faculty of Agricultural and Environmental Sciences, Department of Agrobiotechnology and Risk Assessment for Bio- und Gene Technology, Justus-von-Liebig Weg 8, Mecklenburg-Western Pomerania, 18059, Rostock, Germany.
| | - Tina Hausmann
- University of Rostock, Faculty of Agricultural and Environmental Sciences, Department of Agrobiotechnology and Risk Assessment for Bio- und Gene Technology, Justus-von-Liebig Weg 8, Mecklenburg-Western Pomerania, 18059, Rostock, Germany
| | - Daniel Ponndorf
- University of Rostock, Faculty of Agricultural and Environmental Sciences, Department of Agrobiotechnology and Risk Assessment for Bio- und Gene Technology, Justus-von-Liebig Weg 8, Mecklenburg-Western Pomerania, 18059, Rostock, Germany
| | - Maja Hühns
- University of Rostock, Faculty of Agricultural and Environmental Sciences, Department of Agrobiotechnology and Risk Assessment for Bio- und Gene Technology, Justus-von-Liebig Weg 8, Mecklenburg-Western Pomerania, 18059, Rostock, Germany
| | - Sandra Hoedtke
- University of Rostock, Faculty of Agricultural and Environmental Sciences, Department of Nutrition Physiology and Animal Nutrition, Justus-von-Liebig-Weg 6b, Mecklenburg-Western Pomerania, 18059, Rostock, Germany
| | - Petra Wolf
- University of Rostock, Faculty of Agricultural and Environmental Sciences, Department of Nutrition Physiology and Animal Nutrition, Justus-von-Liebig-Weg 6b, Mecklenburg-Western Pomerania, 18059, Rostock, Germany
| | - Annette Zeyner
- Martin-Luther-University Halle-Wittenberg, Institute for Agricultural and Nutritional Sciences, Chair of Animal Nutrition, Theodor-Lieser-Str. 11, 06120, Halle (Saale), Germany
| | - Inge Broer
- University of Rostock, Faculty of Agricultural and Environmental Sciences, Department of Agrobiotechnology and Risk Assessment for Bio- und Gene Technology, Justus-von-Liebig Weg 8, Mecklenburg-Western Pomerania, 18059, Rostock, Germany
| |
Collapse
|
10
|
Gonzalez-Esquer CR, Smarda J, Rippka R, Axen SD, Guglielmi G, Gugger M, Kerfeld CA. Cyanobacterial ultrastructure in light of genomic sequence data. Photosynth Res 2016; 129:147-157. [PMID: 27344651 DOI: 10.1007/s11120-016-0286-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/14/2016] [Indexed: 06/06/2023]
Abstract
Cyanobacteria are physiologically and morphologically diverse photosynthetic microbes that play major roles in the carbon and nitrogen cycles of the biosphere. Recently, they have gained attention as potential platforms for the production of biofuels and other renewable chemicals. Many cyanobacteria were characterized morphologically prior to the advent of genome sequencing. Here, we catalog cyanobacterial ultrastructure within the context of genomic sequence information, including high-magnification transmission electron micrographs that represent the diversity in cyanobacterial morphology. We place the image data in the context of tabulated protein domains-which are the structural, functional, and evolutionary units of proteins-from the 126 cyanobacterial genomes comprising the CyanoGEBA dataset. In particular, we identify the correspondence between ultrastructure and the occurrence of genes encoding protein domains related to the formation of cyanobacterial inclusions. This compilation of images and genome-level domain occurrence will prove useful for a variety of analyses of cyanobacterial sequence data and provides a guidebook to morphological features.
Collapse
Affiliation(s)
- C R Gonzalez-Esquer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - J Smarda
- Department of Biology, Faculty of Medicine, Masaryk University, University Campus, Building A6, Kamenice 5, 625 00, Brno, Czech Republic
| | - R Rippka
- Unité des Cyanobactéries, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée (URA) 2172, 75724, Paris Cedex 15, France
| | - S D Axen
- Bioinformatics Graduate Group, University of California, San Francisco, CA, 94158, USA
| | - G Guglielmi
- Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Ecole Normale Supérieure, 75005, Paris, France
| | - M Gugger
- Unité des Cyanobactéries, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée (URA) 2172, 75724, Paris Cedex 15, France
| | - C A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.
- Berkeley Synthetic Biology Institute, UC Berkeley, Berkeley, CA, USA.
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|