Analysis of the Complete Genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and Their Comparison to the Obligate Parasites from ‘Candidatus Phytoplasma'

Abstract

Analysis of the completely determined genomes of the plant-derived Acholeplasma brassicae strain O502 and A. palmae strain J233 revealed that the circular chromosomes are 1,877,792 and 1,554,229 bp in size, have a G + C content of 36 and 29%, and encode 1,690 and 1,439 proteins, respectively. Comparative analysis of these sequences and previously published genomes of A. laidlawii strain PG-8, ‘Candidatus Phytoplasma asteris' strains, ‘Ca. P. australiense' and ‘Ca. P. mali' show a limited shared basic genetic repertoire. The acholeplasma genomes are characterized by a low number of rearrangements, duplication and integration events. Exceptions are the unusual duplication of rRNA operons in A. brassicae and an independently introduced second gene for a single-stranded binding protein in both genera. In contrast to phytoplasmas, the acholeplasma genomes differ by encoding the cell division protein FtsZ, a wide variety of ABC transporters, the F₀F₁ ATP synthase, the Rnf-complex, SecG of the Sec-dependent secretion system, a richly equipped repertoire for carbohydrate metabolism, fatty acid, isoprenoid and partial amino acid metabolism. Conserved metabolic proteins encoded in phytoplasma genomes such as the malate dehydrogenase SfcA, several transporters and proteins involved in host-interaction, and virulence-associated effectors were not predicted for the acholeplasmas.

Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae

“…The 293 to 310 predicted shared proteins (27% to 59%) are consistent with previously calculated numbers for other acholeplasmas [7, 8] (Figure 3). The second highest number of unique proteins (440) is predicted for A. palmae (Figure 4), which is the closest known relative of the phytoplasmas [7] (Figure 2) and is also supported by the highest number of predicted shared proteins with the five completely sequenced phytoplasmas (Additional file 1). In second position among the acholeplasmas, A. oculi shares many of its proteins with the phytoplasmas, supported by its phylogenetic assignment and the received PanOCT results.…”

“…Further studies are needed in this respect, but the results may indicate a mechanism shared by both genera. In contrast, experimentally proven effector proteins or membrane proteins involved in phytoplasma-host interaction were not identified in the acholeplasmas [7]. These genetic elements of phytoplasmas might have originated from horizontal gene transfers.…”

“…Massive gene loss, in combination with duplication events and genome instability, separates the phytoplasmas from the acholeplasmas. The complete genome sequences of eight strains of this family have been published, comprising the acholeplasmas A. laidlawii strain PG-8A [8], A. brassicae strain O502 and A. palmae strain J233 [7] and the phytoplasmas ‘ Ca . P. australiense’ strain rp-A [9] and NZSb11 [10], ‘ Ca .…”

“…In the past, all five phytoplasma strains and A. laidlawii were sequenced by applying the whole genome shotgun approach and using plasmid or fosmid libraries as templates for dye-terminator sequencing (Sanger sequencing). In determining the chromosome sequences of A. brassicae and A. palmae , a combination of Sanger sequencing and next generation sequencing methods (pyrosequencing, 454 Life Sciences/Roche) was applied for the first time to this bacterial family [7]. …”

“…In comparison to acholeplasmas, phytoplasmas lack the F 1 F O ATPase synthetase complex, the cell division protein FtsZ, a wider variety of ABC transporters, the Rnf complex and the membrane protein SecG of the Sec -dependent secretion system. Moreover, acholeplasmas possess a rich repertoire of enzymes involved in carbohydrate metabolism, fatty acids, isoprenoids and partial amino acid metabolism [7]. Because these findings were inferred from the analyses of three acholeplasma and five phytoplasma genome sequences, it remains unclear as to what extent these differences between the two genera can be truly generalised or if the other acholeplasmas might share some of these features of their genetic repertoire with the phytoplasmas.…”