Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts

Abstract

Phytoplasmas ("Candidatus Phytoplasma," class Mollicutes) cause disease in hundreds of economically important plants and are obligately transmitted by sap-feeding insects of the order Hemiptera, mainly leafhoppers and psyllids. The 706,569-bp chromosome and four plasmids of aster yellows phytoplasma strain witches' broom (AY-WB) were sequenced and compared to the onion yellows phytoplasma strain M (OY-M) genome. The phytoplasmas have small repeat-rich genomes. This comparative analysis revealed that the repeated DNAs are organized into large clusters of potential mobile units (PMUs), which contain tra5 insertion sequences (ISs) and genes for specialized sigma factors and membrane proteins. So far, these PMUs appear to be unique to phytoplasmas. Compared to mycoplasmas, phytoplasmas lack several recombination and DNA modification functions, and therefore, phytoplasmas may use different mechanisms of recombination, likely involving PMUs, for the creation of variability, allowing phytoplasmas to adjust to the diverse environments of plants and insects. The irregular GC skews and the presence of ISs and large repeated sequences in the AY-WB and OY-M genomes are indicative of high genomic plasticity. Nevertheless, segments of approximately 250 kb located between the lplA and glnQ genes are syntenic between the two phytoplasmas and contain the majority of the metabolic genes and no ISs. AY-WB appears to be further along in the reductive evolution process than OY-M. The AY-WB genome is approximately 154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Furthermore, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M.

FIG. 1.

(A) Genome maps of the 706,569-bp circular chromosome of “Candidatus Phytoplasma asteris” strain AY-WB. Rings present from the inside to outside are as follows: ring 1, rrn operons in red and tRNA in green; ring 2, GC skew over a 2-kb window and 200-bp steps with red denoting G > C and blue denoting C > G; ring 3, predicted ORFs in sense orientation in yellow and antisense orientation in blue; ring 4, location of tra5 ISs presented as angular brackets with yellow indicating sense orientation and blue indicating antisense orientation; ring 5, ORFs present in all sequenced mollicutes in blue and unique to phytoplasmas within the class Mollicutes in red; ring 6, ORFs of predicted secreted proteins in green, secreted membrane proteins in red, and membrane proteins in blue; ring 7, base pair indicator with the first nucleotide of dnaA as nucleotide 1. oriC is most likely located immediately upstream of dnaA as predicted by Oriloc software (32) and by the opposite direction of ORFs surrounding the putative oriC. (B) The four plasmids of AY-WB. ORFs are presented as block arrows with names of the ORFs on the outside of the rings. Numbers on the inside of the rings indicate the locations in base pairs, with the first nucleotide of the repA and rep genes as nucleotide 1. ORFs indicated with an asterisk are predicted to encode membrane-targeted proteins. In the GenBank database, the plasmids are referred to as pAYWB-I through pAYWB-IV. (C) Three chromosomal segments containing ORFs with similarity to plasmid ORFs. The chromosome is presented as a black line. The numbers below the black lines indicate the positions of the first and last nucleotides of the sequence on the AY-WB chromosome in base pairs. ORFs are represented as block arrows. Arrows of paralogous genes on plasmids and chromosomes have the same color, with the exception of the gray arrows, which represent unique genes. The names of the ORFs with predicted functions are indicated above the arrows. RepA, plasmid replication-associated protein with significant similarity to RepA of geminiviruses. rep encodes the phytoplasma-specific plasmid replication protein encodes; ssb encodes the single-stranded DNA-binding protein.

FIG. 2.

Comparative analyses of the AY-WB genome with the genomes of OY-M and other mollicutes. (A) The AY-WB and OY-M genomes are repeat rich. (B) Venn diagram showing the number of shared and unique genes between AY-WB and OY-M. (C) Dot plot comparison of AY-WB and OY-M chromosomes. The numbers on the x and y axes indicate the nucleotides in base pairs. AY-WB and OY-M genome segments in the same orientation are represented as red lines, and those in the reverse orientation are represented as green lines. The arrowheads indicate lplA and glnQ, which flank ∼250 kb of sequences mostly conserved among mollicutes. (D) The number of ORFs unique to phytoplasmas or shared with sequenced SEM clade mollicutes based on blastp analysis of AY-WB and OY-M protein sequences against a database composed of deduced protein sequences of all fully sequenced mollicute genomes (E value, <10⁻⁵). GenBank accession numbers are as follows: Mesoplasma florum L1, AE017263; Mycoplasma gallisepticum R, AE015450; M. genitalium G-37, L43967; M. hyopneumoniae 232, AE017332; M. mobile 163K, AE017308; M. mycoides subsp. mycoides SC strain PG1, BX293980; Mycoplasma penetrans HF-2, BA000026; Mycoplasma pneumoniae M129, U00089; M. pulmonis UAB CTIP, AL445566; OY-M phytoplasma, AP006628; Ureaplasma urealyticum serovar 3 strain ATCC 700970, AF222894.

FIG. 3.

PMUs of the AY-WB chromosome. The chromosome is presented as a black line. The numbers between parentheses at the left indicate the positions of the first and last nucleotides of the PMU on the AY-WB chromosome. ORFs are represented as block arrows. Arrows of paralogous genes have the same color, with the exception of the gray arrows, which represent unique genes. The names of the ORFs with predicted functions are indicated above the arrows, with ORFs of predicted membrane-targeted proteins indicated with *. The ORF numbers below the arrows correspond to annotations listed in Table 3, with # indicating genes that contain mutations separating them into two truncated ORFs. However, the tra5 ORFs of PMU4 contains separate A and B ORFs that may produce a full-length transposase upon a single frameshifting event (58).