Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by ‘Candidatus Liberibacter asiaticus’

Authors: Ramsey, John - John; CHIN, ELIZABETH - University Of California; CHAVEZ, JUAN - University Of Washington; SAHA, SURYA - Boyce Thompson Institute; MISCHUK, DARYA - University Of California; MAHONEY, JACLYN - Boyce Thompson Institute; MOHR, JARED - Cornell University; ROBISON, FAITH - Boyce Thompson Institute; GODFREY, KRIS - University Of California; LEVESQUE, CYNTHIA - Citrus Research Board; FOSTER, LYZZ - University Of Washington; XU, YIMIN - Boyce Thompson Institute; STRICKLER, SUSAN - Boyce Thompson Institute; FERNANDEZ, NOE - Boyce Thompson Institute; Polek, Marylou; Giovannoni, James; MUELLER, LUKAS - Boyce Thompson Institute; SLUPSKY, CAROLYN - University Of California; BRUCE, JAMES - University Of Washington; Heck, Michelle

Submitted to: Journal of Proteome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2020
Publication Date: 4/27/2020
Citation: Ramsey, J.S., Chin, E., Chavez, J., Saha, S., Mischuk, D., Mahoney, J., Mohr, J., Robison, F., Godfrey, K., Levesque, C., Foster, L., Xu, Y., Strickler, S., Fernandez, N., Polek, M., Giovannoni, J.J., Mueller, L., Slupsky, C., Bruce, J., Heck, M.L. 2020. Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by ‘Candidatus Liberibacter asiaticus’. Journal of Proteome Research. 19:2247-2263. https://doi.org/10.1021/acs.jproteome.9b00802.
DOI: https://doi.org/10.1021/acs.jproteome.9b00802

Interpretive Summary: Diagnosis of citrus trees infected with citrus greening relies on detection of DNA from the bacteria associated with the disease, but bacterial DNA detection in infected trees can be unreliable for several months or years after infection. We developed a set of early infection biomarkers in Lisbon lemon. The biomarkers were effective as early as 10 weeks post infection, at a time when the detection of bacterial DNA was unreliable. These biomarkers will serve as the basis to develop diagnostic technologies to classify trees as healthy or infected. In addition, increased understanding of the plant response to infection over time revealed citrus genes that may be targeted to develop resistant varieties.

Technical Abstract: Early detection of citrus trees infected with ‘Candidatus Liberibacter asiaticus’, the bacterial pathogen associated with Huanglongbing (citrus greening disease), is critical to controlling the spread of the disease. Lemon (Citrus limon) trees were graft inoculated with either Ca. L. asiaticus infected or control budwood, and leaf samples collected over the course of a longitudinal study were analyzed for discovery of plant changes associated with Ca. L. asiaticus infection. RNA, protein, and metabolite samples extracted from leaves were analyzed using RNAseq, mass spectrometry, and 1H NMR spectroscopy, respectively. All three methods recorded the most dramatic differences between CLas infected and control plants at 10 weeks post graft. At this time point, Ca. L. asiaticus-upregulated lemon transcripts identified by RNAseq have predicted functions in the biosynthesis and perception of the hormones jasmonic acid and ethylene, aromatic amino acid and terpenoid biosynthesis, and the phenylpropanoid pathway. Plant proteins found to be more abundant in infected plants at 10 weeks post graft include protease inhibitors, photosynthesis proteins, and proteins involved in carbon, iron, lipid and abscisic acid metabolism. In 1H NMR analysis of 25 metabolites, galactose, glucose, aspartate, lysine, and leucine were all detected at significantly higher levels in infected compared to control trees at the 10 week time point. Significant differences between Ca. L. asiaticus and control grafted trees were detected at two weeks post graft - twice as many transcripts were found to be downregulated as were upregulated in the infected trees, with several heat shock protein transcripts among those showing the greatest downregulation in response to Ca. L. asiaticus. A heat shock protein was among the three proteins, all involved in stress or defense, found to be less abundant in Ca. L. asiaticus infected trees two weeks post graft. At the earliest stages of infection, suppression of plant defense and manipulation of host cell endocytosis may be a component of the bacterial strategy to promote its invasion and spread within the phloem. This study has used an integrated approach to quantify plant molecular changes in leaves of asymptomatic, infected trees, enabling the development of a diagnostic technology for early disease detection as part of efforts to control the spread of Huanglongbing.