Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5

Abstract

Background: Gluconacetobacter diazotrophicus Pal5 is an endophytic diazotrophic bacterium that lives in association with sugarcane plants. It has important biotechnological features such as nitrogen fixation, plant growth promotion, sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the occurrence of bacteriocins.

Results: Gluconacetobacter diazotrophicus Pal5 is the third diazotrophic endophytic bacterium to be completely sequenced. Its genome is composed of a 3.9 Mb chromosome and 2 plasmids of 16.6 and 38.8 kb, respectively. We annotated 3,938 coding sequences which reveal several characteristics related to the endophytic lifestyle such as nitrogen fixation, plant growth promotion, sugar metabolism, transport systems, synthesis of auxin and the occurrence of bacteriocins. Genomic analysis identified a core component of 894 genes shared with phylogenetically related bacteria. Gene clusters for gum-like polysaccharide biosynthesis, tad pilus, quorum sensing, for modulation of plant growth by indole acetic acid and mechanisms involved in tolerance to acidic conditions were identified and may be related to the sugarcane endophytic and plant-growth promoting traits of G. diazotrophicus. An accessory component of at least 851 genes distributed in genome islands was identified, and was most likely acquired by horizontal gene transfer. This portion of the genome has likely contributed to adaptation to the plant habitat.

Conclusion: The genome data offer an important resource of information that can be used to manipulate plant/bacterium interactions with the aim of improving sugarcane crop production and other biotechnological applications.

Figure 1

Distribution of gene class by groups. Percentage of gene class in three groups: Whole genome (blue), core regions (green) and accessories regions (red). The group energy metabolism includes glycolysis, electron transport. Information transfer includes transcription, translation and DNA/RNA modification. Surface class includes inner and outer membrane, secreted proteins, and lipopolysaccharides.

Figure 2

GC3 analysis of all genes in the chromosome. Each spot represents a gene in the chromosome. In red are the genes that were classified as accessories by the IVOM method. In green are the genes classified as core by quartops analysis. In blue are the genes that were not classified as core or accessories.

Figure 3

Circular representation of G. diazotrophicus PAL5 chromosome. From inside to outside. 1-) GC Content. 2-) GC Skew. 3-) Annotation, colors defined by class, see Methods. 4-) Predicted Highly Expressed genes; in blue genes classified as "Alien" and in red genes classified as putative highly expressed. 5-) Accessory regions determined by GC3 and IVOM. 6-) Reciprocal best hits results, in green from G. oxydans 621H, in blue genes from A. cryptum JF-5 and in red genes from G. bethesdensis CGDNIH. 7-) Reciprocal Best Hits (RBH) with all complete genomes from the order rhizobiales. 8-) RBH with all other complete genomes from Alphaproteobacteria class; 9-) RBH with all complete genomes from Betaproteobacteria class. 10-) RBH with all complete genomes from Gammaproteobacteria class. 11-) RBH with all other complete genomes.

Figure 4

Osmotolerance mechanisms in G. diazotrophicus. Osmotolerance mechanisms in G. diazotrophicus. (1) Sensor protein kdpD (GDI1564). (2) Transcriptional regulatory protein kdpE (GDI1565). (3) Potassium ABC transporter (kdpABC transporter; GDI1566-1568). (4) Glutathione-regulated system protein kefB (GDI0899) and (5) kefC (GDI2585). (6) Proline/betaine transporter (GDI2530). (7) Dpp ABC transporters for di- and tripeptides (GDI0246-GDI0250, GDI0454-GDI0458 and GDI3540-GDI3544). (8) Transporter dtpT, (GDI3819 and GDI0829). (9) Oligopeptide transporter (Opt; GDI3108). (10) Sensor kinase EnVZ (GDI3087). (11) OmpR (GDI3088). (12) Large Conductance MS channel mscL (GDI1732). (13) Small conductance MS channel, mscS, (GDI0793, GDI1149, GDI1789, and GDI3802). (14) glpRDFK (GDI1751-1754). (15) glpDKF (GDI0262, GDI0266, and GDI0267). (16) otsA GDI0917. (17) otsB GDI0916). (18) Periplasmic trehalase (treA GDI1341). The function of the proteins was verified by BLAST and motif searches of the corresponding CDS against public databases.