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Choi Y, Kim YH. Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13. J Microbiol 2022; 60:411-418. [DOI: 10.1007/s12275-022-2018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
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Zhang Y, Zhao M, Chen W, Yu H, Jia W, Pan H, Zhang X. Multi-Omics Techniques for Analysis Antifungal Mechanisms of Lipopeptides Produced by Bacillus velezensis GS-1 against Magnaporthe oryzae In Vitro. Int J Mol Sci 2022; 23:ijms23073762. [PMID: 35409115 PMCID: PMC8998706 DOI: 10.3390/ijms23073762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Magnaporthe oryzae is a fungal pathogen that causes rice blast, a highly destructive disease. In the present study, the bacteria strain GS-1 was isolated from the rhizosphere soil of ginseng and identified as Bacillus velezensis through 16S rRNA gene sequencing, whole genome assembly, and average nucleotide identity analysis. B. velezensis strain GS-1 exhibited significant antagonistic activity to several plant fungal pathogens. Through whole genome sequencing, 92 Carbohydrate-Active Enzymes and 13 gene clusters that encoded for secondary metabolites were identified. In addition, strain GS-1 was able to produce the lipopeptide compounds, surfactin, fengycin, and plantazolicin. The inhibitory effects of lipopeptide compounds on M. oryzae were confirmed, and the antagonistic mechanism was explored using transcriptomics and metabolomics analysis. Differential expressed genes (DEGs) and differential accumulated metabolites (DAMs) revealed that the inhibition of M. oryzae by lipopeptide produced by GS-1 downregulated the expression of genes involved in amino acid metabolism, sugar metabolism, oxidative phosphorylation, and autophagy. These results may explain why GS-1 has antagonistic activity to fungal pathogens and revealed the mechanisms underlying the inhibitory effects of lipopeptides produced by GS-1 on fungal growth, which may provide a theoretical basis for the potential application of B. velezensis GS-1 in future plant protection.
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Kim J, Pham H, Baek Y, Jo I, Kim YH, Ha NC. Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering. Acta Crystallogr D Struct Biol 2022; 78:104-112. [PMID: 34981766 DOI: 10.1107/s2059798321011724] [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: 07/22/2021] [Accepted: 11/04/2021] [Indexed: 11/11/2022] Open
Abstract
The YxaL protein was isolated from the soil bacterium Bacillus velezensis and has been shown to promote the root growth of symbiotic plants. YxaL has further been suggested to act as an exogenous signaling protein to induce the growth and branching of plant roots. Amino acid sequence analysis predicted YxaL to exhibit an eight-bladed β-propeller fold stabilized by six tryptophan-docking motifs and two modified motifs. Protein engineering to improve its structural stability is needed to increase the utility of YxaL as a plant growth-promoting factor. Here, the crystal structure of YxaL from B. velezensis was determined at 1.8 Å resolution to explore its structural features for structure-based protein engineering. The structure showed the typical eight-bladed β-propeller fold with structural variations in the third and fourth blades, which may decrease the stability of the β-propeller fold. Engineered proteins targeting the modified motifs were subsequently created. Crystal structures of the engineered YxaL proteins showed that the typical tryptophan-docking interaction was restored in the third and fourth blades, with increased structural stability, resulting in improved root growth-promoting activity in Arabidopsis seeds. The work is an example of structure-based protein engineering to improve the structural stability of β-propellor fold proteins.
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Affiliation(s)
- Jiheon Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Ha Pham
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu 42472, Republic of Korea
| | - Yeongjin Baek
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong Hak Kim
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu 42472, Republic of Korea
| | - Nam Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
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Nadeem SM, Ahmad M, Tufail MA, Asghar HN, Nazli F, Zahir ZA. Appraising the potential of EPS-producing rhizobacteria with ACC-deaminase activity to improve growth and physiology of maize under drought stress. PHYSIOLOGIA PLANTARUM 2021; 172:463-476. [PMID: 32949405 DOI: 10.1111/ppl.13212] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/15/2020] [Indexed: 05/25/2023]
Abstract
Rhizobacteria containing 1-aminocyclopropane-1-carboxylic acid-deaminase (ACC-deaminase) and exopolysaccharides (EPS) activity are important to induce stress tolerance in plants. The present study was conducted to screen and characterize plant growth-promoting rhizobacteria (PGPR) with ACC-deaminase and EPS-producing activity for improving maize growth under drought stress. Eighty-five rhizobacterial strains were isolated from the rain-fed areas, among those 69 isolates were able to utilize ACC and 31 strains were found positive for EPS production. These strains containing ACC-deaminase and/or EPS-producing activity were subjected to drought tolerance assay by inducing water stress in media using polyethylene glycol 6000. Based on results of the drought tolerance bioassay, 12 most prominent strains were selected to evaluate their growth-promoting abilities in maize under water-stressed conditions by conducting jar trial. The impact of strains on maize growth parameters was variable. Strains with co-existence of ACC-deaminase and EPS-producing activity showed comparatively better results than those with either ACC-deaminase or EPS-producing activity only. These strains were also significantly better in improving the plant physiological parameters including photosynthesis rate, stomatal conductance, vapor pressure, water-use efficiency and transpiration rate. The strain D3 with co-existence of ACC-deaminase and EPS-producing activity was significantly better in colonizing maize roots, improving plant growth and physiological parameters. The strain was named as Bacillus velezensis strain D3 (accession number MT367633) as confirmed through results of 16S rRNA partial gene sequencing. It is concluded that the strains with co-existence of ACC-deaminase and EPS-producing activity could be better suited for improving crop growth and physiology under drought stress.
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Affiliation(s)
- Sajid M Nadeem
- Sub-campus Burewala, University of Agriculture Faisalabad, Vehari, Pakistan
| | - Maqshoof Ahmad
- Department of Soil Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad A Tufail
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Hafiz N Asghar
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Farheen Nazli
- Pesticide Quality Control Laboratory, Punjab Agriculture Department, Bahawalpur, Government of Punjab, Pakistan
| | - Zahir A Zahir
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
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A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. Commun Biol 2021; 4:582. [PMID: 33990691 PMCID: PMC8121941 DOI: 10.1038/s42003-021-02107-z] [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: 02/13/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
The conjugative plasmid (pBV71) possibly confers a selective advantage to Bacillus velezensis strain GH1-13, although a selective marker gene is yet to be identified. Here we show that few non-mucoid wild-type GH1-13 cells are spontaneously converted to mucoid variants with or without the loss of pBV71. Mucoid phenotypes, which contain or lack the plasmid, become sensitive to bacitracin, gramicidin, selenite, and tellurite. Using the differences in antibiotic resistance and phenotype, we isolated a reverse complement (COM) and a transconjugant of strain FZB42 with the native pBV71. Transformed COM and FZB42p cells were similar to the wild-type strain GH1-13 with high antibiotic resistance and slow growth rates on lactose compared to those of mucoid phenotypes. RT-PCR analysis revealed that the expression of plasmid-encoded orphan aspartate phosphatase (pRapD) was coordinated with a new quorum-sensing (QS) cassette of RapF2-PhrF2 present in the chromosome of strain GH1-13, but not in strain FZB42. Multi-omics analysis on wild-type and plasmid-cured cells of strain GH1-13 suggested that the conjugative plasmid expression has a crucial role in induction of early envelope stress response that promotes cell morphogenesis, biofilm formation, catabolite repression, and biosynthesis of extracellular-matrix components and antibiotics for protection of host cell during exponential phase.
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Ichikawa S, Tsuge Y, Karita S. Metabolome Analysis of Constituents in Membrane Vesicles for Clostridium thermocellum Growth Stimulation. Microorganisms 2021; 9:microorganisms9030593. [PMID: 33805707 PMCID: PMC8002186 DOI: 10.3390/microorganisms9030593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 11/24/2022] Open
Abstract
The cultivation of the cellulolytic bacterium, Clostridium thermocellum, can have cost-effective cellulosic biomass utilizations, such as consolidated bioprocessing, simultaneous biological enzyme production and saccharification. However, these processes require a longer cultivation term of approximately 1 week. We demonstrate that constituents of the C. thermocellum membrane vesicle fraction significantly promoted the growth rate of C. thermocellum. Similarly, cell-free Bacillus subtilis broth was able to increase C. thermocellum growth rate, while several B. subtilis single-gene deletion mutants, e.g., yxeJ, yxeH, ahpC, yxdK, iolF, decreased the growth stimulation ability. Metabolome analysis revealed signal compounds for cell–cell communication in the C. thermocellum membrane vesicle fraction (ethyl 2-decenoate, ethyl 4-decenoate, and 2-dodecenoic acid) and B. subtilis broth (nicotinamide, indole-3-carboxaldehyde, urocanic acid, nopaline, and 6-paradol). These findings suggest that the constituents in membrane vesicles from C. thermocellum and B. subtilis could promote C. thermocellum growth, leading to improved efficiency of cellulosic biomass utilization.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
- Correspondence: ; Tel.: +89-59-231-9254; Fax: +89-59-231-9352
| | - Yoichiro Tsuge
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
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Draft Genome Sequence of Bacillus velezensis BZR 336g, a Plant Growth-Promoting Antifungal Biocontrol Agent Isolated from Winter Wheat. Microbiol Resour Announc 2020; 9:9/30/e00450-20. [PMID: 32703828 PMCID: PMC7378027 DOI: 10.1128/mra.00450-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bacillus velezensis strain BZR 336g is a plant growth-promoting rhizobacterium isolated from a winter wheat rhizoplane from the Krasnodar region in Russia. In this study, we report the genome, including genes with known phenotypic function, i.e., the biosynthesis of secondary metabolites with fungicidal and plant growth-promoting activities. We sequenced and analyzed the complete BZR 336g genome using two different DNA preparation methods to help us better understand the origin of the antimicrobial and antifungal abilities and to weigh the biocontrol properties of this strain.
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Reva ON, Larisa SA, Mwakilili AD, Tibuhwa D, Lyantagaye S, Chan WY, Lutz S, Ahrens CH, Vater J, Borriss R. Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains. Appl Microbiol Biotechnol 2020; 104:7643-7656. [PMID: 32651600 DOI: 10.1007/s00253-020-10767-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/11/2020] [Accepted: 07/02/2020] [Indexed: 01/29/2023]
Abstract
The application of biocontrol biopesticides based on plant growth-promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Biosciences' Single Molecule Real-Time (PacBio SMRT) platform, have allowed researchers to gain deeper insights into the molecular and genetic mechanisms of PGPR activities, and to compare whole genome sequences and global patterns of epigenetic modifications. In the current work, this approach was used to sequence and compare four Bacillus strains that exhibited various PGPR activities including the strain UCMB5140, which is used in the commercial biopesticide Phytosubtil. Whole genome comparison and phylogenomic inference assigned the strain UCMB5140 to the species Bacillus velezensis. Strong biocontrol activities of this strain were confirmed in several bioassays. Several factors that affect the evolution of active PGPR B. velezensis strains were identified: (1) horizontal acquisition of novel non-ribosomal peptide synthetases (NRPS) and adhesion genes; (2) rearrangements of functional modules of NRPS genes leading to strain specific combinations of their encoded products; (3) gain and loss of methyltransferases that can cause global alterations in DNA methylation patterns, which eventually may affect gene expression and regulate transcription. Notably, we identified a horizontally transferred NRPS operon encoding an uncharacterized polypeptide antibiotic in B. velezensis UCMB5140. Other horizontally acquired genes comprised a possible adhesin and a methyltransferase, which may explain the strain-specific methylation pattern of the chromosomal DNA of UCMB5140. KEY POINTS: • Whole genome sequence of the active PGPR Bacillus velezensis UCMB5140. • Identification of genetic determinants responsible for PGPR activities. • Role of methyltransferases and epigenetic mechanisms in evolution of bacteria.
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Affiliation(s)
- Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hillcrest, Lynnwood Rd., Pretoria, South Africa.
| | - Safronova A Larisa
- Innovation and Technology Transfer Laboratory, DK Zabolotny Institute of Microbiology and Virology, 154 Zabolotnogo Str, Kyiv, 03143, Ukraine
| | - Aneth D Mwakilili
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania.,Plant Protection Department, Swedish University of Agricultural Sciences (SLU), Alnarp, Sweden
| | - Donatha Tibuhwa
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Sylvester Lyantagaye
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Wai Yin Chan
- Biotechnology Platform (BTP), Agricultural Research Council, Onderstepoort Veterinary Research Campus, Old Soutpan Rd, Onderstepoort, South Africa.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Forestry and Agricultural Biotechnology Institute (FABI), DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB), University of Pretoria, Pretoria, South Africa
| | - Stefanie Lutz
- Agroscope, Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Müller-Thurgau-Str. 29, 8820, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Müller-Thurgau-Str. 29, 8820, Wädenswil, Switzerland
| | | | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany
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Reva ON, Swanevelder DZH, Mwita LA, Mwakilili AD, Muzondiwa D, Joubert M, Chan WY, Lutz S, Ahrens CH, Avdeeva LV, Kharkhota MA, Tibuhwa D, Lyantagaye S, Vater J, Borriss R, Meijer J. Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics. Front Microbiol 2019; 10:2610. [PMID: 31803155 PMCID: PMC6873887 DOI: 10.3389/fmicb.2019.02610] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well understood, nor is it clear why several strains outperform other same species isolates by their bioactivities. The main objective of this work was to demonstrate versatility of bioactivities and lifestyle strategies of the selected B. velezensis strains suitable to serve as model organisms in future studies. Here, we performed a comparative study of newly sequenced genomes of four B. velezensis isolates with distinct phenotypes and isolation origin, which were assessed by RNA sequencing under the effect of root exudate stimuli and profiled by epigenetic modifications of chromosomal DNA. Among the selected strains, UCMB5044 is an oligotrophic PGPR strain adapted to nutrient poor desert soils. UCMB5113 and At1 are endophytes that colonize plants and require nutrient rich media. In contrast, the probiotic strain, UCMB5007, is a copiotroph, which shows no propensity to colonize plants. PacBio and Illumina sequencing approaches were used to generate complete genome assemblies, tracing epigenetic modifications, and determine gene expression profiles. All sequence data was deposited at NCBI. The strains, UCMB5113 and At1, show 99% sequence identity and similar phenotypes despite being isolated from geographically distant regions. UCMB5007 and UCMB5044 represent another group of organisms with almost identical genomes but dissimilar phenotypes and plant colonization propensity. The two plant associated strains, UCMB5044 and UCMB5113, share 398 genes putatively associated with root colonization, which are activated by exposure to maize root exudates. In contrast, UCMB5007 did not respond to root exudate stimuli. It was hypothesized that alterations in the global methylation pattern and some other epigenetic modifications enable adaptation of strains to different habitats and therefore may be of importance in terms of the biotechnological applicability of these bacteria. Contrary, the ability to grow on root exudates as a sole source of nutrients or a strong antagonism against phytopathogens showed by the strains in vitro cannot be considered as good predictors of PGPR activities.
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Affiliation(s)
- Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Liberata A Mwita
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Aneth David Mwakilili
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania.,Department of Plant Protection, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Dillon Muzondiwa
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Monique Joubert
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Wai Yin Chan
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Forestry and Agricultural Biotechnology Institute, DST-NRF Centre of Excellence in Tree Health Biotechnology, University of Pretoria, Pretoria, South Africa
| | - Stefanie Lutz
- Agroscope, Molecular Diagnostics, Genomics and Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics and Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Lylia V Avdeeva
- Department of Antibiotics, D.K. Zabolotny Institute of Microbiology and Virology, Kyiv, Ukraine
| | - Maksim A Kharkhota
- Department of Antibiotics, D.K. Zabolotny Institute of Microbiology and Virology, Kyiv, Ukraine
| | - Donatha Tibuhwa
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Sylvester Lyantagaye
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | | | - Rainer Borriss
- Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Johan Meijer
- Department of Plant Biology, Linnéan Center for Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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