Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)

Abstract

The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It consists of 7 circular replicons totalling 5,192,291 bp comprising a circular chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp, 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3, 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined and 5 methylation motifs have been identified. The genome also contains a very high number of transposase/inactivated transposase genes from at least 12 of the 17 recognised insertion sequence families. The Ac-8003 genome has been compared with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain O, the only other member of the Azotobacteraceae determined so far which has a single chromosome of 5,365,318 bp and no plasmids. The chromosomes show significant stretches of synteny throughout but also reveal a history of many deletion/insertion events. The Ac-8003 genome encodes 4628 predicted protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ, and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways and macromolecular architectures and machineries of these organisms appear largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic differences reported for these organisms have also been identified. Also many other potential phenotypic differences have been uncovered. Properties endowed by the plasmids are described including the presence of an entire aerobic corrin synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in pAcX50c. All these findings are related to the potentially different environmental niches from which these organisms were isolated and to emerging theories about how microbes contribute to their communities.

Fig 1. Synteny between the chromosomes of A. chroococcum NCIMB 8003 (ordinate) and A.vinelandii DJ (ATCC BAA-1303).

The nucleotide sequences of the chromosomes of A. chroococcum NCIMB 8003 (ordinate) and A.vinelandii DJ (ATCC BAA-1303) (abscissa) were aligned using BLASTn. The red and blue diagonal lines show the slopes that would be obtained were each chromosome aligned against itself: red, A. chroococcum; blue, A.vinelandii.

Fig 2. Comparison of the gene contents in the chromosomes of A. chroococcum NCIMB 8003 and A.vinelandii DJ (ATCC BAA-1303).

Genes present in both strains are shown in red (“core genes”) whilst the genes present in only that strain (“accessory genes”) are shown in blue. The genome dimensions are marked in bp.

Fig 3. Plasmid- and chromosomal genes involved in Corrin and Adenosyl cobalaimin (B12) uptake, salvage and biosynthesis in Azotobacter chroococcum NCIMB 8003.

A. The region of 16,967 bp from bp 64,013 to 80,225 in plasmid pAcX50f containing a contiguous cluster of genes for corrin synthesis. B. The regions of 12,882 from bp 1,777,467 to 1,789,349; 740,868 to 741,638 and 3,736,258 to 3,738,156 in the chromosome potentially containing genes for corrin and B12 uptake and salvage and the late steps in the synthesis of adenosyl cobalamin.

Fig 4. Physical and genetic map of plasmid pAcX50c from A. chroococcum NCIB 8003.

The map shows the arrangement of deduced genes in the sequence of the potential retro-conjugative plasmid pACX50c. The two clusters of contiguous tra and trb conjugation genes are shown in green and dark blue respectively. Genes for other functions are indicated as follows: replication initiation (trfA: red); partitioning and maintenance (pink), Type I RMS system (AchIII) (yellow); transposases (brown); DNA binding and repair (grey); unidentified or conserved unidentified genes (white).