1
|
Ravagnan G, Lesemann J, Müller MF, Poehlein A, Daniel R, Noack S, Kabisch J, Schmid J. Genome reduction in Paenibacillus polymyxa DSM 365 for chassis development. Front Bioeng Biotechnol 2024; 12:1378873. [PMID: 38605990 PMCID: PMC11007031 DOI: 10.3389/fbioe.2024.1378873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
The demand for highly robust and metabolically versatile microbes is of utmost importance for replacing fossil-based processes with biotechnological ones. Such an example is the implementation of Paenibacillus polymyxa DSM 365 as a novel platform organism for the production of value-added products such as 2,3-butanediol or exopolysaccharides. For this, a complete genome sequence is the first requirement towards further developing this host towards a microbial chassis. A genome sequencing project has just been reported for P. polymyxa DSM 365 showing a size of 5,788,318 bp with a total of 47 contigs. Herein, we report the first complete genome sequence of P. polymyxa DSM 365, which consists of 5,889,536 bp with 45 RNAs, 106 tRNAs, 5,370 coding sequences and an average GC content of 45.6%, resulting in a closed genome of P. polymyxa 365. The additional nucleotide data revealed a novel NRPS synthetase that may contribute to the production of tridecaptin. Building on these findings, we initiated the top-down construction of a chassis variant of P. polymyxa. In the first stage, single knock-out mutants of non-essential genomic regions were created and evaluated for their biological fitness. As a result, two out of 18 variants showed impaired growth. The remaining deletion mutants were combined in two genome-reduced P. polymyxa variants which either lack the production of endogenous biosynthetic gene clusters (GR1) or non-essential genomic regions including the insertion sequence ISPap1 (GR2), with a decrease of the native genome of 3.0% and 0.6%, respectively. Both variants, GR1 and GR2, showed identical growth characteristics to the wild-type. Endpoint titers of 2,3-butanediol and EPS production were also unaffected, validating these genome-reduced strains as suitable for further genetic engineering.
Collapse
Affiliation(s)
- Giulia Ravagnan
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Janne Lesemann
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Moritz-Fabian Müller
- Institute of Bio-and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Stephan Noack
- Institute of Bio-and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Johannes Kabisch
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| |
Collapse
|
2
|
Huang XY, Ye XP, Hu YY, Tang ZX, Zhang T, Zhou H, Zhou T, Bai XL, Pi EX, Xie BH, Shi LE. Exopolysaccharides of Paenibacillus polymyxa: A review. Int J Biol Macromol 2024; 261:129663. [PMID: 38278396 DOI: 10.1016/j.ijbiomac.2024.129663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of many metabolically active substances, including polypeptides, volatile organic compounds, phytohormone, hydrolytic enzymes, exopolysaccharide (EPS), etc. Due to the wide range of compounds that it produces, P. polymyxa has been extensively studied as a plant growth promoting bacterium which provides a direct benefit to plants through the improvement of N fixation from the atmosphere and enhancement of the solubilization of phosphorus and the uptake of iron in the soil, and phytohormones production. Among the metabolites from P. polymyxa, EPS exhibits many activities, for example, antioxidant, immunomodulating, anti-tumor and many others. EPS has various applications in food, agriculture, environmental protection. Particularly, in the field of sustainable agriculture, P. polymyxa EPS can be served as a biofilm to colonize microbes, and also can act as a nutrient sink on the roots of plants in the rhizosphere. Therefore, this paper would provide a comprehensive review of the advancements of diverse aspects of EPS from P. polymyxa, including the production, extraction, structure, biosynthesis, bioactivity and applications, etc. It would provide a direction for future research on P. polymyxa EPS.
Collapse
Affiliation(s)
- Xuan-Ya Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Xin-Pei Ye
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yan-Yu Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Zhen-Xing Tang
- School of Culinary Art, Tourism College of Zhejiang, Hangzhou, Zhejiang 311231, China
| | - Tian Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Hai Zhou
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Ting Zhou
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Xue-Lian Bai
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Er-Xu Pi
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Bing-Hua Xie
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
| | - Lu-E Shi
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
| |
Collapse
|
3
|
Wendisch VF, Brito LF, Passaglia LM. Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T. Genet Mol Biol 2024; 46:e20230115. [PMID: 38224489 PMCID: PMC10789242 DOI: 10.1590/1678-4685-gmb-2023-0115] [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: 04/21/2023] [Accepted: 11/20/2023] [Indexed: 01/17/2024] Open
Abstract
Paenibacillus sonchi genomovar Riograndensis SBR5T is a plant growth-promoting rhizobacterium (PGPR) isolated in the Brazilian state of Rio Grande do Sul from the rhizosphere of Triticum aestivum. It fixes nitrogen, produces siderophores as well as the phytohormone indole-3-acetic acid, solubilizes phosphate and displays antagonist activity against Listeria monocytogenes and Pectobacterium carotovorum. Comprehensive omics analysis and the development of genetic tools are key to characterizing and engineering such non-model microorganisms. Therefore, the complete genome of SBR5T was sequenced, and shown to encode 6,705 proteins, 87 tRNAs, and 27 rRNAs and it enabled a landscape transcriptome analysis that unveiled conserved transcriptional and translational patterns and characterized operon structures and riboswitches. The pangenome of P. sonchi species is open with a stable core pangenome. At the same time, the analysis of genes coding for nitrogenases revealed that the trait of nitrogen fixation is sparse within the Paenibacillaceae family and the presence of Fe-only nitrogenase in the P. sonchi group was exclusive to SBR5T. The development of genetic tools for SBR5T enabled genetic transformation, plasmid construction for constitutive and inducible gene expression, and gene repression using the CRISPRi system. Altogether, the work with P. sonchi can guide the study of non-model bacteria with economic potential.
Collapse
Affiliation(s)
- Volker F. Wendisch
- Bielefeld University, Faculty of Biology, Genetics of Prokaryotes, Bielefeld, Germany
- Bielefeld University, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Luciana F. Brito
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway
| | - Luciane M.P. Passaglia
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| |
Collapse
|
4
|
Schilling C, Gansbiller M, Rühmann B, Sieber V, Schmid J. Rheological characterization of artificial paenan compositions produced by Paenibacillus polymyxa DSM 365. Carbohydr Polym 2023; 320:121243. [PMID: 37659800 DOI: 10.1016/j.carbpol.2023.121243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/16/2023] [Accepted: 07/28/2023] [Indexed: 09/04/2023]
Abstract
Microbial exopolysaccharides offer a sustainable alternative to petroleum-based rheological modifiers. Recent studies revealed that the heteroexopolysaccharide produced by Paenibacillus polymyxa is composed of three distinct biopolymers, referred to as paenan I, II and III. Using CRISPR-Cas9 mediated knock-out variants of glycosyltransferases, defined polysaccharide compositions were produced and rheologically characterized in detail. The high viscosity and gel-like character of the wildtype polymer is proposed to originate from the non-covalent interaction between a pyruvate residue of paenan I and the glucuronic acid found in the backbone of paenan III. Paenan II conveys thermostable properties to the exopolysaccharide mixture. In contrast to the wildtype polymer mixture, knock-out variants demonstrated significantly altered rheological behavior. Using the rheological characterization performed in this study, tailor-made paenan variants and mixtures can be generated to be utilized in a wide range of applications including thickening agents, coatings, or high-value biomedical materials.
Collapse
Affiliation(s)
- Christoph Schilling
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Moritz Gansbiller
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany; Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany; School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia 4072, Australia; TUM Catalysis Research Center, Ernst-Otto-Fischer-Straße1, 85748, Garching, Germany
| | - Jochen Schmid
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany; Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany.
| |
Collapse
|