Abstract
Although phytoplasma studies are still hampered by the lack of axenic cultivation methods, the availability of genome sequences allowed dramatic advances in the characterization of the virulence mechanisms deployed by phytoplasmas, and highlighted the detection of signal peptides as a crucial step to identify effectors secreted by phytoplasmas. However, various signal peptide prediction methods have been used to mine phytoplasma genomes, and no general evaluation of these methods is available so far for phytoplasma sequences. In this work, we compared the prediction performance of SignalP versions 3.0, 4.0, 4.1, 5.0 and Phobius on several sequence datasets originating from all deposited phytoplasma sequences. SignalP 4.1 with specific parameters showed the most exhaustive and consistent prediction ability. However, the configuration of SignalP 4.1 for increased sensitivity induced a much higher rate of false positives on transmembrane domains located at N-terminus. Moreover, sensitive signal peptide predictions could similarly be achieved by the transmembrane domain prediction ability of TMHMM and Phobius, due to the relatedness between signal peptides and transmembrane regions. Beyond the results presented herein, the datasets assembled in this study form a valuable benchmark to compare and evaluate signal peptide predictors in a field where experimental evidence of secretion is scarce. Additionally, this study illustrates the utility of comparative genomics to strengthen confidence in bioinformatic predictions.
Highlights
Phytoplasmas are bacterial phloem-limited pathogens transmitted by insect vectors that generate diseases in infected plants
In silico analyses of phytoplasma genomes allowed to identify putative virulence factors, and three phytoplasma effectors and their homologs have been the focus of several recent studies
Immunolocalization experiments showed that Tengu and SAP11 were found in plant tissues other than the phloem sieve tubes where phytoplasmas are confined, confirming that these effectors are secreted by phytoplasmas and taken up by host sink tissues (Bai et al, 2009; Hoshi et al, 2009)
Summary
Phytoplasmas are bacterial phloem-limited pathogens transmitted by insect vectors that generate diseases in infected plants. The effector SAP11 impacts the development of the host plant and enhances its capacity to support reproduction of the insect vector through modulation of the jasmonate pathway (Sugio et al, 2011). Detailed molecular structures for SAP54 and its homologs are available (Iwabuchi et al, 2019; Liao et al, 2019) It seems that a major role for SAP54 is to promote the attraction of insect vectors by the host plant (Orlovskis and Hogenhout, 2016). The SWP11 gene product from wheat blue dwarf phytoplasma induced cell death in Nicotiana benthamiana, and strikingly, the SWP12 and SWP21 (Tengu) proteins were able to counteract this process (Wang et al, 2018b). As effectors appear to be major players in the interaction with the host plant, their identification through genome mining stands as a prerequisite for a better understanding of phytoplasma diseases
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