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Title: Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter' asiaticus and other rhizbiales

item Kuykendall, Larry
item Shao, Jonathan
item Hartung, John

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2011
Publication Date: 4/1/2012
Citation: Kuykendall, L.D., Shao, J.Y., Hartung, J.S. 2012. Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter' asiaticus and other rhizbiales. PLoS One. 7(4):e34673.

Interpretive Summary: A bacterium called ‘Liberibacter’ lives inside the cells of sweet orange trees where it is picked up by insects feeding on the tree, who then spread it to other sweet orange trees. ‘Liberibacter’ is considered to be the pathogen responsible for citrus greening, or huanglongbing disease, which is now causing tremendous losses in the citrus industries of Florida and Brazil. Control methods include eradication of infected trees and insecticidal spray programs, which are expected to provide short term control only. The lack of sustainable methods of disease control is because the details of the metabolism and reproduction of ‘Liberibacter’ are not well understood. Interestingly, ‘Liberibacter’ is related to useful nitrogen-fixing bacteria, as well as to another plant pathogen, and an intracellular pathogen of cats. Although the full genome sequences of these bacteria are available, detailed comparisons among them are lacking. We used this set of five bacteria to investigate questions related to the evolution, metabolism and reproduction of ‘Liberibacter’, and the mechanisms that it may use to induce disease in citrus trees and be spread by the insect vector. We did this by comparing the genomic data among the five bacteria to identify genes common to all, and to subsets of the five bacteria. By doing this we have identified eight genes common to ‘Liberibacter’ and the pathogen of cats. Although the hosts could not be more different, these bacteria share an intracellular lifestyle and common evolutionary origin. These genes presumably condition the host cells for colonization by the pathogens. We have also identified a set of 319 genes unique to ‘Liberibacter’ as well as other smaller sets of genes shared by ‘Liberibacter’ and the other bacteria studied. ‘Liberibacter’ also has a remarkably small genome as compared to its relatives. We have studied the structure of the ‘Liberibacter’ genome in detail and show that in the course of evolution it has adopted a modified version of the standard genetic code that allows it to reproduce at a low energy cost. This analysis has also revealed a set of ten genes not found in intracellular pathogens from other hosts. These genes may be involved in specific interactions with the citrus or insect hosts of ‘Liberibacter’. Our research will be of interest to the rapidly expanding community of researchers working on citrus greening disease and may lead to useful insights needed to develop effective long-term control methods for citrus greening disease.

Technical Abstract: The intracellular plant pathogen ‘Ca. Liberibacter asiaticus’ is a member of the Rhizobiales, as are the nitrogen fixing Sinorhizobium meliloti and Bradyrhizobium japonicum, the plant pathogen Agrobacterium tumefaciens and the intracellular mammalian pathogen Bartonella henselae. Whole genome comparisons identified 42 clusters of conserved orthologous genes found in all five metabolically diverse species. Although local regions of microsynteny remain, blocks of orthologous geneshave been extensively reordered in genome by genome comparisons. The intracellular pathogens, ‘Ca. Liberibacter asiaticus’ and Bartonella henselae have drastically reduced genomes with low content of guanine and cytosine. Codon and amino acid preferences that emphasize low guanosine and cytosine usage are employed globally in these genomes including regions of microsynteny and within signature sequences of orthologous proteins. The length of orthologous proteins is conserved, but not their isoelectric points, consistent with extensive amino acid substitutions to accommodate the low GC content of the genome. The ‘Ca. Liberibacter asiaticus’ genome has 319 unique coding sequences not shared with the other members of the Rhizobiales from a total of 1136 coding sequences. ‘Ca. Liberibacter asiaticus’ also has members of all 100 COGs previously found in all bacteria to support basic physiological functions, but also has representatives of ten COGs that have been lost in other intracellular pathogens. These COGS, as well as eight proteins uniquely shared by ‘Ca. Liberibacter asiaticus’ and Bartonella henselae may condition host cells for intracellular colonization or facilitate transmission by insects. Only two protein encoding genes were uniquely shared by ‘Ca. Liberibacter asiaticus’ and Agrobacterium tumefaciens, the other plant pathogen in the study. These genes may also be important to the host-pathogen interaction. Ten and twelve genes were uniquely shared between ‘Ca. Liberibacter asiaticus’ and Sinorhizobium meliloti and Bradyrhizobium japonicum, respectively.