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Dietz BR, Olszewski NE, Barney BM. Enhanced extracellular ammonium release in the plant endophyte Gluconacetobacter diazotrophicus through genome editing. Microbiol Spectr 2024; 12:e0247823. [PMID: 38038458 PMCID: PMC10783055 DOI: 10.1128/spectrum.02478-23] [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: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Our results demonstrate increased extracellular ammonium release in the endophyte plant growth-promoting bacterium Gluconacetobacter diazotrophicus. Strains were constructed in a manner that leaves no antibiotic markers behind, such that these strains contain no transgenes. Levels of ammonium achieved by cultures of modified G. diazotrophicus strains reached concentrations of approximately 18 mM ammonium, while wild-type G. diazotrophicus remained much lower (below 50 µM). These findings demonstrate a strong potential for further improving the biofertilizer potential of this important microbe.
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Affiliation(s)
- Benjamin R. Dietz
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Neil E. Olszewski
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Brett M. Barney
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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2
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Gluconacetobacter diazotrophicus Gene Fitness during Diazotrophic Growth. Appl Environ Microbiol 2022; 88:e0124122. [PMID: 36374093 PMCID: PMC9746312 DOI: 10.1128/aem.01241-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant growth-promoting (PGP) bacteria are important to the development of sustainable agricultural systems. PGP microbes that fix atmospheric nitrogen (diazotrophs) could minimize the application of industrially derived fertilizers and function as a biofertilizer. The bacterium Gluconacetobacter diazotrophicus is a nitrogen-fixing PGP microbe originally discovered in association with sugarcane plants, where it functions as an endophyte. It also forms endophyte associations with a range of other agriculturally relevant crop plants. G. diazotrophicus requires microaerobic conditions for diazotrophic growth. We generated a transposon library for G. diazotrophicus and cultured the library under various growth conditions and culture medium compositions to measure fitness defects associated with individual transposon inserts (transposon insertion sequencing [Tn-seq]). Using this library, we probed more than 3,200 genes and ascertained the importance of various genes for diazotrophic growth of this microaerobic endophyte. We also identified a set of essential genes. IMPORTANCE Our results demonstrate a succinct set of genes involved in diazotrophic growth for G. diazotrophicus, with a lower degree of redundancy than what is found in other model diazotrophs. The results will serve as a valuable resource for those interested in biological nitrogen fixation and will establish a baseline data set for plant free growth, which could complement future studies related to the endophyte relationship.
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Tyrosine Kinase Self-Phosphorylation Controls Exopolysaccharide Biosynthesis in Gluconacetobacter diazotrophicus Strain Pal5. Life (Basel) 2021; 11:life11111231. [PMID: 34833106 PMCID: PMC8620434 DOI: 10.3390/life11111231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/28/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
The biosynthesis of exopolysaccharides (EPSs) is essential for endophytic bacterial colonisation in plants bacause this exopolymer both protects bacterial cells against the defence and oxidative systems of plants and acts on the plant colonisation mechanism in Gluconacetobacter diazotrophicus. The pathway involved in the biosynthesis of bacterial EPS has not been fully elucidated, and several areas related to its molecular regulation mechanisms are still lacking. G. diazotrophicus relies heavily on EPS for survival indirectly by protecting plants from pathogen attack as well as for endophytic maintenance and adhesion in plant tissues. Here, we report that EPS from G. diazotrophicus strain Pal5 is a signal polymer that controls its own biosynthesis. EPS production depends on a bacterial tyrosine (BY) kinase (Wzc) that consists of a component that is able to phosphorylate a glycosyltranferase or to self-phosphorylate. EPS interacts with the extracellular domain of Wzc, which regulates kinase activity. In G. diazotrophicus strains that are deficient in EPS production, the Wzc is rendered inoperative by self-phosphorylation. The presence of EPS promotes the phosphorylation of a glycosyltransferase in the pathway, thus producing EPS. Wzc-mediated self-regulation is an attribute for the control of exopolysaccharide biosynthesis in G. diazotrophicus.
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Schwab S, Pessoa CA, de Lima Bergami AA, de Azevedo Figueiredo NL, Dos Santos Teixeira KR, Baldani JI. Isolation and characterization of active promoters from Gluconacetobacter diazotrophicus strain PAL5 using a promoter-trapping plasmid. Arch Microbiol 2016; 198:445-58. [PMID: 26914247 DOI: 10.1007/s00203-016-1203-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/18/2016] [Accepted: 02/07/2016] [Indexed: 12/27/2022]
Abstract
Gluconacetobacter diazotrophicus is a nitrogen-fixing, endophytic bacterium that has the potential to promote plant growth and increase yield. Genetically modified strains might get more benefits to host plants, including through expression of useful proteins, such as Cry toxins from B. thuringiensis, or enzymes involved in phytohormone production, proteins with antagonistic activity for phytopathogens, or that improve nutrient utilization by the plant. For that, expression systems for G. diazotrophicus are needed, which requires active promoters fused to foreign (or innate) genes. This article describes the construction of a G. diazotrophicus PAL5 promoter library using a promoter-less lacZ-bearing vector, and the identification of six active promoters through β-galactosidase activity assays, sequencing and localization in the bacterial genome. The characterized promoters, which are located on distinct regions of the bacterial genome and encoding either sense or antisense transcripts, present variable expression strengths and might be used in the future for expressing useful proteins.
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Affiliation(s)
- Stefan Schwab
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, RJ, Brazil.
| | - Cristiane Alves Pessoa
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, RJ, Brazil
- Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Amanda Aparecida de Lima Bergami
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, RJ, Brazil
- Instituto de Tecnologia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 7, Seropédica, RJ, Brazil
| | - Nathália Lima de Azevedo Figueiredo
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, RJ, Brazil
- Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 7, Seropédica, RJ, Brazil
| | | | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, RJ, Brazil
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5
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Reis VM, Teixeira KRDS. Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture. J Basic Microbiol 2015; 55:931-49. [PMID: 25736602 PMCID: PMC7166518 DOI: 10.1002/jobm.201400898] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/27/2015] [Indexed: 11/17/2022]
Abstract
For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N2 is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth-promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth-promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented.
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de Paula Soares C, Rodrigues EP, de Paula Ferreira J, Simões Araújo JL, Rouws LFM, Baldani JI, Vidal MS. Tn5 insertion in the tonB gene promoter affects iron-related phenotypes and increases extracellular siderophore levels in Gluconacetobacter diazotrophicus. Arch Microbiol 2014; 197:223-33. [DOI: 10.1007/s00203-014-1045-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 08/22/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
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Idogawa N, Amamoto R, Murata K, Kawai S. Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5. Bioengineered 2014; 5:173-9. [PMID: 24717418 DOI: 10.4161/bioe.28792] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production.
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Affiliation(s)
- Nao Idogawa
- Laboratory of Basic and Applied Molecular Biotechnology; Graduate School of Agriculture; Kyoto University; Kyoto, Japan
| | - Ryuta Amamoto
- Laboratory of Basic and Applied Molecular Biotechnology; Graduate School of Agriculture; Kyoto University; Kyoto, Japan
| | - Kousaku Murata
- Laboratory of Basic and Applied Molecular Biotechnology; Graduate School of Agriculture; Kyoto University; Kyoto, Japan
| | - Shigeyuki Kawai
- Laboratory of Basic and Applied Molecular Biotechnology; Graduate School of Agriculture; Kyoto University; Kyoto, Japan
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Urzúa LS, Vázquez-Candanedo AP, Sánchez-Espíndola A, Ramírez CÁ, Baca BE. Identification and characterization of an iron ABC transporter operon in Gluconacetobacter diazotrophicus Pal 5. Arch Microbiol 2013; 195:431-8. [PMID: 23624722 DOI: 10.1007/s00203-013-0890-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 02/02/2013] [Accepted: 02/25/2013] [Indexed: 12/01/2022]
Abstract
Gluconacetobacter diazotrophicus is a nitrogen-fixing bacterium and endophyte of sugarcane. We have cloned and sequenced the genes coding for the components of the iron ABC-type acquisition system of G. diazotrophicus. Sequence analysis revealed three ORFs, (feuA, feuB, and feuC) organized as an operon and encoding polypeptides of 346 (38 kDa), 342 (34.2 kDa), and 240 (26 kDa) amino acids, respectively. The deduced translation products of the feu operon showed similarity with a periplasmic solute-binding protein (FeuA), permease (FeuB), and ATPase (FeuC) involved in Fe transport. The role of FeuB in the survival of G. diazotrophicus under iron depletion was evaluated by comparing the ability of wild-type and FeuB-Km(R) -mutant strains in a medium without iron supplementation and in a medium containing 2, 2'-dipyridyl (DP). Growth of the mutant was affected in the medium containing DP. The operon was expressed at higher levels in cells depleted for iron than in those that contained the metal. A decrease in nitrogenase activity was observed with the FeuB-Km(R) -mutant strain that with the wild-type under iron deficiency conditions, suggesting that the Feu operon play role in Fe nutrition of G. diazotrophicus.
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Affiliation(s)
- Lucia Soto Urzúa
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Apdo. Postal 1622, Puebla, Puebla, Mexico
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Saravanan VS, Madhaiyan M, Osborne J, Thangaraju M, Sa TM. Ecological occurrence of Gluconacetobacter diazotrophicus and nitrogen-fixing Acetobacteraceae members: their possible role in plant growth promotion. MICROBIAL ECOLOGY 2008; 55:130-40. [PMID: 17574542 DOI: 10.1007/s00248-007-9258-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Accepted: 04/14/2007] [Indexed: 05/13/2023]
Abstract
Gluconacetobacter diazotrophicus has a long-standing history of bacterial-plant interrelationship as a symbiotic endophyte capable of fixing atmospheric nitrogen. In low nitrogen fertilized sugarcane fields it plays a significant role and its occurrence was realised in most of the sugarcane growing countries. In this mini review, the association of G. diazotrophicus with sugarcane, other crop plants and with various hosts is discussed. The factors affecting survival in the rhizosphere and the putative soil mode of transmission are emphasized. In addition, other N(2)-fixing Acetobacteraceae members, including Gluconacetobacter azotocaptans, Gluconacetobacter johannae and Swaminathania salitolerans, occurring in coffee, corn and rice plants are also covered. Lastly, the plant-growth-promoting traits identified in this group of bacteria, including N(2) fixation, phytohormone synthesis, P and Zn solubilization and biocontrol, are analysed.
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Affiliation(s)
- V S Saravanan
- School of Bio-Technology, Chemical and Bio-Medical Engineering, Vellore Institute of Technology (VIT) University, Vellore 632 014, Tamil Nadu, India.
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Validation of a Tn5 transposon mutagenesis system for Gluconacetobacter diazotrophicus through characterization of a flagellar mutant. Arch Microbiol 2007; 189:397-405. [DOI: 10.1007/s00203-007-0330-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 10/19/2007] [Accepted: 11/17/2007] [Indexed: 10/22/2022]
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Fisher K, Newton WE. Nitrogenase proteins from Gluconacetobacter diazotrophicus, a sugarcane-colonizing bacterium. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1750:154-65. [PMID: 15925553 DOI: 10.1016/j.bbapap.2005.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Revised: 04/27/2005] [Accepted: 04/28/2005] [Indexed: 10/25/2022]
Abstract
Gluconacetobacter diazotrophicus Pal-5 grew well and expressed nitrogenase activity in the absence of NH4+ and at initial O2 concentrations greater than 5% in the culture atmosphere. G. diazotrophicus nitrogenase consisted of two components, Gd1 and Gd2, which were difficult to separate but were purified individually to homogeneity. Their compositions were very similar to those of Azotobacter vinelandii nitrogenase, however, all subunits were slightly smaller in size. The purified Gd1 protein contained a 12:1 Fe/Mo ratio as compared to 14:1 found for Av1 purified in parallel. Both Gd2 and Av2 contained 3.9 Fe atoms per molecule. Dithionite-reduced Gd1 exhibited EPR features at g=3.69, 3.96, and 4.16 compared with 3.64 and 4.27 for Av1. Gd2 gave an S=1/2 EPR signal identical to that of Av2. A Gd1 maximum specific activity of 1600 nmol H2 (min mg of protein)(-1) was obtained when complemented with either Gd2 or Av2, however, more Av2 was required. Gd2 had specific activities of 600 and 1100 nmol H2 (min mg protein)(-1) when complemented with Av1 and Gd1, respectively. The purified G. diazotrophicus nitrogenase exhibited a narrowed pH range for effective catalysis compared to the A. vinelandii nitrogenase, however, both exhibited maximum specific activity at about pH 7. The Gd-nitrogenase was more sensitive to ionic strength than the Av-nitrogenase.
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Affiliation(s)
- Karl Fisher
- Department of Biochemistry, The Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Perlova O, Ureta A, Nordlund S, Meletzus D. Identification of three genes encoding P(II)-like proteins in Gluconacetobacter diazotrophicus: studies of their role(s) in the control of nitrogen fixation. J Bacteriol 2003; 185:5854-61. [PMID: 13129958 PMCID: PMC193954 DOI: 10.1128/jb.185.19.5854-5861.2003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In our studies on the regulation of nitrogen metabolism in Gluconacetobacter diazotrophicus, an endophytic diazotroph of sugarcane, three glnB-like genes were identified and their role(s) in the control of nitrogen fixation was studied. Sequence analysis revealed that one P(II) protein-encoding gene, glnB, was adjacent to a glnA gene (encoding glutamine synthetase) and that two other P(II) protein-encoding genes, identified as glnK1 and glnK2, were located upstream of amtB1 and amtB2, respectively, genes which in other organisms encode ammonium (or methylammonium) transporters. Single and double mutants and a triple mutant with respect to the three P(II) protein-encoding genes were constructed, and the effects of the mutations on nitrogenase expression and activity in the presence of either ammonium starvation or ammonium sufficiency were studied. Based on the results presented here, it is suggested that none of the three P(II) homologs is required for nif gene expression, that the GlnK2 protein acts primarily as an inhibitor of nif gene expression, and that GlnB and GlnK1 control the expression of nif genes in response to ammonium availability, both directly and by relieving the inhibition by GlnK2. This model includes novel regulatory features of P(II) proteins.
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Affiliation(s)
- Olena Perlova
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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Perlova O, Nawroth R, Zellermann EM, Meletzus D. Isolation and characterization of the glnD gene of Gluconacetobacter diazotrophicus, encoding a putative uridylyltransferase/uridylyl-removing enzyme. Gene 2002; 297:159-68. [PMID: 12384297 DOI: 10.1016/s0378-1119(02)00881-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The glnD gene of Gluconacetobacter diazotrophicus was isolated by complementation of the Azotobacter vinelandii glnD (nfrX) mutant strain MV17 using a pLAFR3 cosmid library. The 5 kb chromosomal DNA region encoding the glnD gene on cosmid pAD401 was identified by introduction of deletions as well as subcloning of restriction fragments followed by subsequent DNA sequencing. Three open reading frames were identified with the deduced amino acid sequence of ORF1 showing significant homologies to known GlnD proteins of other proteobacteria such as Sinorhizobium meliloti, Rhizobium tropici, Escherichia coli and Azotobacter vinelandii.A mutagenesis of the chromosomal glnD gene was carried out by insertion of an interposon carrying the kanamycin resistance gene of Tn5. Mutants carrying the cassette inserted into a central region of glnD could not be isolated, while an interposon mutation at the 3' end of glnD was successful. The resulting strain showed a prolonged generation time in complex growth medium and was unable to utilize ammonium as sole nitrogen source. This phenotype appears to be pleiotropic, since the addition of single amino acids to the minimal medium was not sufficient to allow growth. Furthermore, the glnD mutant was able to express nitrogenase under diazotrophic as well as repressing growth conditions.
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Affiliation(s)
- Olena Perlova
- Universität Bielefeld, Fakultät für Biologie, Lehrstuhl Gentechnologie/Mikrobiologie, D-33615, Bielefeld, Germany
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