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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #320868

Title: A single prophage carrying a CRISPR/cas system in ‘Candidatus Liberibacter asiaticus’ strain A4 from Guangdong, China

item ZHENG, Z. - South China Agricultural University
item DENG, X. - South China Agricultural University
item BAO, M. - South China Agricultural University
item Chen, Jianchi

Submitted to: PLoS Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2015
Publication Date: 1/10/2016
Citation: Zheng, Z., Deng, X., Bao, M., Chen, J. 2016. A single prophage carrying a CRISPR/cas system in ‘Candidatus Liberibacter asiaticus’ strain A4 from Guangdong, China. PLoS Pathology. 11(1):e0146422. doi: 10.1371/journal.pone.0146422.

Interpretive Summary: Citrus Huanglongbing (HLB, yellow shoot disease, also known as citrus greening disease) is highly destructive to worldwide citrus production. “Candidatus Liberibacter asiaticus” (CLas) is currently considered as the bacterial pathogen that causes HLB. Yet, little is known about CLas because it cannot be cultured in artificial media, which limits research into effective controls for HLB. This study analyzed the genome of a CLas strain collected in Guangdong of China, a place where HLB has been present for over a hundred years. The bacterium was found to harbor a single mobile element, called a phage, with a phage immunity structure called CRISPR/cas. This is the first finding of an immunity system in CLas. The information will facilitate current understanding on how and why CLas vary under different environmental conditions, which is crucial for development of substainable HLB management strategies.

Technical Abstract: “Candidatus Liberibacter asiaticus” (CLas) is an unculturable a-proteobacterium associated with citrus huanglongbing (HLB, yellow shoot disease), a highly destructive disease that affects citrus production worldwide. HLB was observed in Guangdong Province of China over a hundred years ago and remains endemic there. Little is known about the biology of CLas mainly due to the inability to culture the bacterium in vitro. This study analyzed the genome sequence of CLas strain A4 from the historical HLB area of Guangdong. The A4 genome is composed of chromosomal and prophage regions. The A4 chromosome was highly conserved among different CLas strains. Variations between A4 and other published CLas sequences were mainly from single nucleotide polymorphisms (SNPs) and sequence insertions/deletions. The A4 strain had only a single prophage, designated as CGdP2. This is different from the Florida strains (Psy62 and UF506) and the Guangxi strain (gxpsy) from China reported to have two prophages, and the Ishi-1 strain from Japan reported to have a prophage. CGdP2 (38,974 bp) was 97.8% similar to prophage SC2 from Florida. No circular replication form was detected. In silico analyses on the prophage sequence identified a CRISPR (clustered regularly interspaced short palindromic repeats)/cas (CRISPR-associated protein genes) system, containing four 22 bp repeats, three 23 bp spacers, and 11 predicted cas. Similar CRISPR/cas systems were detected in all known CLas prophages with spacer 2 being highly variable. The potential roles of CRISPR/cas in population dynamics of CLas prophages were investigated. This is the first report of CRISPR/cas in bacteria belonging to the “Ca. Liberibacter” genus.