Occurrence, distribution, and possible functional roles of simple sequence repeats in phytoplasma genomes

Authors: Wei, Wei; Davis, Robert; SUO, XIAOBING - US Department Of The Interior; Zhao, Yan

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2015
Publication Date: 8/1/2015
Publication URL: http://doi:10.1099/ijs.0.000273
Citation: Wei, W., Davis, R.E., Suo, X., Zhao, Y. 2015. Occurrence, distribution, and possible functional roles of simple sequence repeats in phytoplasma genomes. International Journal of Systematic and Evolutionary Microbiology. 65:2748-2760. doi: 10.1099/ijs.0.000273.

Interpretive Summary: Phytoplasmas are small bacteria that parasitize nutrition-transporting vessels of infected plants. These unique pathogens are responsible for numerous diseases in agriculturally important crops worldwide and are spread by insects that feed on diseased plants. The life cycle of phytoplasmas requires rapid responses to significantly different environments, including transitions from infected plant cells to various specialized insect tissues, and adaptations to different plant and insect hosts. Molecular mechanisms enabling such flexibility remain to be uncovered. In the present study, through computational analyses of available genome sequence data, we found that the genomes of phytoplasmas possessed many short, tandemly-repeated DNA tracts termed simple sequence repeats (SSRs), and the occurrence of such repeats was much more frequent than that in the genomes of other bacteria. We also found that the distribution of the SSRs in the phytoplasma genomes was not random: while certain repeat patterns were more abundant within protein coding regions, others were present mainly in non-coding regions. Numerous SSRs were located within sequence variable mosaics (SVM) regions that harbor prophage (integrated virus)-derived multiple gene families and within genomic segments that bear phytoplasma unique genes outside of the SVMs. The SSRs compounded the sequence variability and complexity of multiple gene families, and increased the genetic diversity among phytoplasma strains. Expansions and contractions of SSRs (reversible changes in SSR length by increasing or decreasing the number of repeated units) occur often in living cells, leading to alterations in the transcription and translation of associated genes, and changing in the composition and function of the respective protein products. We therefore envision that SSRs in the phytoplasma genomes play a role in enhancing a phytoplasma’s ability to rapidly adapt their changing environment. Scientists interested in molecular mechanisms of bacterial pathogenesis and scientists interested in genome features determining the physiology of bacterium-host interactions will be interested in the analyses and insights.

Technical Abstract: Phytoplasmas are unculturable, cell wall-less bacteria that parasitize plants and insects. This transkingdom life cycle requires rapid responses to vastly different environments including transitions from plant phloem sieve elements to various insect tissues and alterations of diverse plant hosts. Features enabling such flexibility in other microbes include simple sequence repeats (SSRs) -- mutation-prone, phase variable short DNA tracts that function as “evolutionary rheostats” and enhance rapid adaptations. To gain insights into the occurrence, distribution, and potentially functional roles of SSRs in phytoplasmas, we performed computational analysis on genomes of five completely sequenced phytoplasma strains, including ‘Candidatus Phytoplasma asteris-related strains OYM and AYWB, ‘Candidatus Phytoplasma australiense’-related strains CBWB and SLY, and ‘Candidatus Phytoplasma mali-related strain AP-AT. The overall density of SSRs in phytoplasma genomes was higher than in representative strains of other prokaryotes. While mono- and tri-nucleotide SSRs were significantly overrepresented in the phytoplasma genomes, di-nucleotide SSRs, and other higher order SSRs were underrepresented. The occurrence and distribution of long SSRs in the prophage islands and phytoplasma-unique genetic loci indicated that SSRs played a role in compounding the complexity of sequence mosaics in individual genomes and in increasing allelic diversity among genomes. Findings from computational analyses were further complemented by an examination of SSRs in varied additional phytoplasma strains, which were maintained in greenhouse, with a focus on potential contingency genes. Some SSRs were located in regions that could profoundly alter the regulation of transcription and translation of affected genes, and/or composition of protein products.