Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

Abstract

Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major 'islands of catabolic diversity', now an apparent 'archipelago of catabolic diversity', within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism.

Figure 1

Circular representation of the Acinetobacter ADP1 genome. Circles display (from the outside): (i) predicted coding regions transcribed in the clockwise direction. (ii) Predicted coding regions transcribed in the counterclockwise direction. Genes displayed in (i) and (ii) are color coded according to different functional categories: salmon, amino acid biosynthesis; light blue, biosynthesis of cofactors, prosthetic groups and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; green, energy metabolism; purple, fatty acid and phospholipid metabolism; pink, protein fate/synthesis; orange, purines, pyrimidines, nucleosides, nucleotides; blue, regulatory functions; grey, transcription; teal, transport and binding proteins; black, hypothetical and CHPs. (iii) Transposable elements (yellow triangles), phage regions (brown), genes involved in catabolic pathways (red); the five catabolic islands (>20 kb) are numbered from I to V. (iv) tRNAs (light blue) and rRNA (light green). (v) GC bias (G+C/G-C).

Figure 2

Gene content comparisons between Acinetobacter ADP1, P.aeruginosa and P.putida genomes. Putative orthologs are defined as genes showing a minimum of 30% identity and a ratio of 0.8 of the length of the smallest protein, or as two genes included in a synteny group. The intersections between the three circles give the number (and percentage) of genes found in the 2 or 3 compared species. Genes outside these areas are specific to the corresponding organism. The total number of annotated genes is also given under each specie name.

Figure 3

Part of the Acinetobacter ADP1 genome containing a likely horizontally transferred region. The chromosomal segment, extending between positions 553 000 and 583 000 bp, is represented on this graphical map of the MaGe interface developed on our database. Annotated CDSs are represented in the six reading frames of the sequence by red rectangles, and coding prediction curves are superimposed on the predicted CDSs (blue curves). The synteny maps, calculated on a set of selected genomes in the NCBI databank, are displayed below. In contrast to the graphic interface of the Acinetobacter ADP1 genome, there is no notion of scale on the synteny map: a rectangle has the same size of the CDS which is exactly opposite in the ADP1 genome, and it represents a putative ortholog between one CDS of the compared genome and one CDS of the Acinetobacter ADP1 genome. If, for several CDSs co-localized on the ADP1 genome, there are several co-localized orthologs in the compared genome, the rectangles will all be of the same color; otherwise, the rectangle is white. A group of rectangles of the same color thus indicates synteny between Acinetobacter ADP1 and the compared genome. The compared ADP1 chromosomal region is not found in E.coli K12, P.aeruginosa and P.putida genomes. In contrast, very well conserved syntenies are found with P.syringae, V.parahaemolyticus, V.vulnificus and the R.solanacearum megaplasmid.