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.

Growth phase-specific evolutionary benefits of natural transformation in Acinetobacter baylyi

“…Our model organism A. baylyi (Barbe et al, 2004) is convenient for studying the possible benefits of natural transformation for three reasons: (1) competence is expressed upon dilution into new medium, (2) it stays competent during most of the log phase and (3) most of the cells in a population are competent for DNA uptake at the same time (Bacher et al, 2006;Metzgar et al, 2004).…”

What We Can Deduce about Metabolism in the Moderate Halophile Chromohalobacter Salexigens from its Genomic Sequence

“…So, provided that the latter pathway exists in C. salexigens, we could account for the necessary enzymes of protocatechuate metabolism. Again, unlike in Acinetobacter (Barbe et al, 2004), the three unique enzymes of protocatechuate metabolism are not adjacent to each other in our organism. The expect values indicate the tblastn similarity scores of C. salexigens ORFS against queries from genes from the P. putida TOL plasmid (for the reactions from benzoate to catechol and for the meta pathway) and from Acenitobacter (for the ortho pathway).…”

“…C. salexigens has the "standard" suite of glycolytic enzymes as found in E. coli, and it differs from P. aeruginosa, which lacks phosphofructokinase, and from Acinetobacter, which is devoid of both phosphofructokinase and pyruvate kinase (Barbe et al, 2004). We detected all of the enzymes of the oxidative and non-oxidative branches of the hexose monophosphate shunt as well as the Entner-Doudoroff pathways.…”

“…However, it is possible that we could find better quality matches if we searched the C. salexigens genome with benzoate degradative enzymes from a broader spectrum of organisms. In Acinetobacter, the benzoate degradative enzymes are arranged as a tight cluster (Barbe et al, 2004), but this does not seem to be the case in C. salexigens.…”

“…For the meta-pathway, the genome was queried with ORFs present on the Pseudomonas putida TOL plasmid pWWO (Horn et al, 1991), and for the orthopathway, the genome was searched against the enzymes from Acinetobacter sp. (Barbe et al, 2004).…”