Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont “Candidatus Liberibacter asiaticus” as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats

Abstract

"Candidatus Liberibacter asiaticus" is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of "Ca. Liberibacter" associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (hyv I and hyv II ) were identified in the prophage regions of the Psy62 "Ca. Liberibacter asiaticus" genome. Sequence analyses of the hyv I and hyv II genes in 35 "Ca. Liberibacter asiaticus" DNA isolates collected globally revealed that the hyv I gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while hyv II contains up to 2 NITRs and 4 partial repeats and shares homology with hyv I . Frequent deletions or insertions of these repeats within the hyv I and hyv II genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of "Ca. Liberibacter asiaticus" bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single "Ca. Liberibacter asiaticus"-infected sample. This is the first evidence of different "Ca. Liberibacter asiaticus" populations coexisting in a single HLB-affected sample. The Florida "Ca. Liberibacter asiaticus" isolates contain both hyv I and hyv II , while all other global "Ca. Liberibacter asiaticus" isolates contain either one or the other. Interclade assignments of the putative Hyv I and Hyv II proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple "Ca. Liberibacter asiaticus" populations in the world and a multisource introduction of the "Ca. Liberibacter asiaticus" bacterium into Florida.

Development of Disease and Growth on Six Scion/Rootstock Combinations of Citrus Seedlings under Huanglongbing Pressure

“…Quantification of bacterial titers used a series of primer LJ900fr, forward primer (5-GCCGTTTTAACACAAAAGATGAATATC-3), and reverse primer (5-ATAAATCAATTTGTTCTAGTTTACGAC-3) (Zhou et al, 2011). Real-time PCR reaction mix used 20 µl contained 10 µl of universal real-time mix with SYBR green (Kappa), 1 µl of each primer, 1 µl of DNA sample (50 ng/µl), and 7 µl H 2 O.…”

Detection and Characterization of Miniature Inverted-Repeat Transposable Elements in "Candidatus Liberibacter asiaticus"

“…No transposon was annotated in the complete sequences of three phages/prophages of "Ca. Liberibacter asiaticus," SC1, SC2, and FP2 (23,24). In sequence analyses, two characteristics are highly indicative of transposons: presence of TIRs and identification of a transposase gene (tps).…”

“…In the past few years, there have been several reports of DNA polymorphisms in "Ca. Liberibacter asiaticus" populations using single primer sets (24,(26)(27)(28)(29). By analyzing two Chinese "Ca.…”

The Intracellular Citrus Huanglongbing Bacterium, ‘Candidatus Liberibacter asiaticus’ Encodes Two Novel Autotransporters

“…The lasA I and lasA II , previously reported as hyv I and hy v II , are located in two prophage regions in the Las Psy62 genome [17]. The 2760 bp lasA I encodes a 919 amino-acid hypothetical protein with a predicted molecular mass of 103.5 kDa.…”

“…Within these prophage regions, two hypothetical hypervariable proteins (Hyv I and Hyv II ) were identified that contained multiple, nearly-identical, leucine-rich repeats (LRRs). The diversity and plasticity of these two genes may have implications for how these intracellular bacteria adapt to their host ecological niches [17]. …”