Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts

Abstract

Candidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.

Establishment of a Cuscuta campestris‐mediated enrichment system for genomic and transcriptomic analyses of ‘Candidatus Liberibacter asiaticus’

“…Few studies have reported the in planta genome‐wide transcriptome profiling of CLas, until a recent study that employed RNA sequencing for analyses of CLas expression profile by using phloem‐enriched samples from CLas‐infected citrus trees (Zuñiga et al ., 2020). However, less than 0.53% of total reads were identified as CLas reads in RNA‐Seq data derived from CLas‐infected citrus phloem samples (Zuñiga et al ., 2020). The use of CLas‐enriched dodder RNA sample in this study provided a higher resolution of CLas transcripts, and we observed similar gene expression patterns of CLas both in citrus host and dodders.…”

“…However, few studies have been reported CLas transcriptome profiling by using RNA‐Seq, mainly due to low abundance of CLas RNA compared with host RNA. A recent study analysed in citrus and psyllids CLas expression profiles using RNA‐Seq, but the analysis lacked enough depth because CLas reads were minoritary (Zuñiga et al, 2020). Therefore, to gain insight into CLas–host interaction during infection, higher resolution of in planta CLas transcripts is required.…”

The Genome of “Candidatus Liberibacter asiaticus” Is Highly Transcribed When Infecting the Gut of Diaphorina citri

“…This value falls in the range observed by other authors, such as the mapping of 0.50% of transcriptome reads of the whole body of B. cockerelli against the Lso genome ( Ibanez et al, 2014 ). Transcriptome analysis of Las was comparatively carried out in citrus and in dodder, with read mapping ranging from 0.11% to 1.44%, respectively ( Li et al, 2021 ), while in adventitious citrus roots in culture media and in alimentary canals of D. citri , 0.28% to 2.51% of reads mapped to Las genome ( Zuñiga et al, 2020 ). In contrast, only 0.01% of reads obtained from infected grapevine mapped against the flavescence dorée phytoplasma ( Abbà et al, 2014 ).…”

“…In contrast, only 0.01% of reads obtained from infected grapevine mapped against the flavescence dorée phytoplasma ( Abbà et al, 2014 ). Las DNA detection in relation to host DNA is higher in psyllids than in citrus ( Selvaraj et al, 2018 ), and this favors the obtention of Las nucleic acid from psyllids for metagenomic ( Duan et al, 2009 ; Lin et al, 2013 ) and metatranscriptomic ( Zuñiga et al, 2020 ) analysis.…”

“…Transcriptome analysis of Las genome in citrus and dodder has shown a high correlation in gene expression in both hosts, expected since dodder was parasitizing citrus, and in both hosts, Las encounters similar nutrients and micro-environmental conditions ( Li et al, 2021 ). A predicted model of metabolite usage was created for Liberibacter crescens growing in culture media and for Las in plant and psyllid hosts, using RNA-seq data ( Zuñiga et al, 2020 ). A transcriptome analysis of Bactericera cockerelli indicated a high percentage of “ Ca.…”