Plant-Derived, Nodule-Specific Cysteine-Rich Peptides as a Novel Source of Biopesticides for Controlling Citrus Greening Disease

Nodule-specific cysteine-rich (NCR) peptides, encoded in the genome of the Mediterranean legume Medicago truncatula (barrelclover), are known to regulate plant-microbe interactions. A subset of computationally derived 20-mer peptide fragments from 182 NCR peptides was synthesized to identify those with activity against the unculturable vascular pathogen associated with citrus greening disease, 'Candidatus Liberibacter asiaticus' (CLas). Grounded in a design of experiments framework, we evaluated the peptides in a screening pipeline involving three distinct assays: a bacterial culture assay with Liberibacter crescens, a CLas-infected excised citrus leaf assay, and an assay to evaluate effects on bacterial acquisition by the nymphal stage of hemipteran vector Diaphorina citri. A subset of the 20-mer NCR peptide fragments inhibits both CLas growth in citrus leaves and CLas acquisition by D. citri. Two peptides induced higher levels of D. citri mortality. These findings reveal 20-mer NCR peptides as a new class of plant-derived biopesticide molecules to control citrus greening disease.

Plant production of high affinity nanobodies that block SARS-CoV-2 spike protein binding with its receptor, human angiotensin converting enzyme

Nanobodies^® (V_HH antibodies), are small peptides that represent the antigen binding domain, V_HH of unique single domain antibodies (heavy chain only antibodies, HcAb) derived from camelids. Here, we demonstrate production of V_HH nanobodies against the SARS-CoV-2 spike proteins in the solanaceous plant Nicotiana benthamiana through transient expression and their subsequent detection verified through western blot. We demonstrate that these nanobodies competitively inhibit binding between the SARS-CoV-2 spike protein receptor binding domain and its human receptor protein, angiotensin converting enzyme 2. There has been significant interest and a number of publications on the use of plants as biofactories and even some reports of producing nanobodies in plants. Our data demonstrate that functional nanobodies blocking a process necessary to initiate SARS-CoV-2 infection into mammalian cells can be produced in plants. This opens the alternative of using plants in a scheme to rapidly respond to therapeutic needs for emerging pathogens in human medicine and agriculture.

Tad pilus-mediated twitching motility is essential for DNA uptake and survival of Liberibacters

Axenically cultured Liberibacter crescens (Lcr) is a closely related surrogate for uncultured plant pathogenic species of the genus Liberibacter, including ‘Candidatus L. asiaticus’ (CLas) and ‘Ca. L. solanacearum’ (CLso). All Liberibacters encode a completely conserved gene repertoire for both flagella and Tad (Tight Adherence) pili and all are missing genes critical for nucleotide biosynthesis. Both flagellar swimming and Tad pilus-mediated twitching motility in Lcr were demonstrated for the first time. A role for Tad pili in the uptake of extracellular dsDNA for food in Liberibacters was suspected because both twitching and DNA uptake are impossible without repetitive pilus extension and retraction, and no genes encoding other pilus assemblages or mechanisms for DNA uptake were predicted to be even partially present in any of the 35 fully sequenced Liberibacter genomes. Insertional mutations of the Lcr Tad pilus genes cpaA, cpaB, cpaE, cpaF and tadC all displayed such severely reduced growth and viability that none could be complemented. A mutation affecting cpaF (motor ATPase) was further characterized and the strain displayed concomitant loss of twitching, viability and reduced periplasmic uptake of extracellular dsDNA. Mutations of comEC, encoding the inner membrane competence channel, had no effect on either motility or growth but completely abolished natural transformation in Lcr. The comEC mutation was restored by complementation using comEC from Lcr but not from CLas strain psy62 or CLso strain RS100, indicating that unlike Lcr, these pathogens were not naturally competent for transformation. This report provides the first evidence that the Liberibacter Tad pili are dynamic and essential for both motility and DNA uptake, thus extending their role beyond surface adherence.

Peptidomics Approaches for the Identification of Bioactive Molecules from Diaphorina citri

Huanglongbing (HLB), a deadly citrus disease, is primarily associated with Candidatus Liberibacter asiaticus (CLas) and spread by the hemipteran insect Diaphorina citri. Control strategies to combat HLB are urgently needed. In this work, we developed and compared workflows for the extraction of the D. citri peptidome, a dynamic set of polypeptides produced by proteolysis and other cellular processes. High-resolution mass spectrometry revealed bias among methods reflecting the physiochemical properties of the peptides: while TCA/acetone-based methods resulted in enrichment of C-terminally amidated peptides, a modification characteristic of bioactive peptides, larger peptides were overrepresented in the aqueous phase of chloroform/methanol extracts, possibly indicative of reduced co-analytical degradation during sample preparation. Parallel reaction monitoring (PRM) was used to validate the structure and upregulation of peptides derived from hemocyanin, a D. citri immune system protein, in insects reared on healthy and CLas-infected trees. Mining of the data sets also revealed 122 candidate neuropeptides, including PK/PBAN family neuropeptides and kinins, biostable analogs of which have known insecticidal properties. Taken together, this information yields new, in-depth insights into peptidomics methodology. Additionally, the putative neuropeptides identified may lead to psyllid mortality if applied to or expressed in citrus, consequently blocking the spread of HLB disease in citrus groves.

Liberibacter crescens Is a Cultured Surrogate for Functional Genomics of Uncultured Pathogenic 'Candidatus Liberibacter' spp. and Is Naturally Competent for Transformation

'Candidatus Liberibacter' spp. are uncultured insect endosymbionts and phloem-limited bacterial plant pathogens associated with diseases ranging from severe to nearly asymptomatic. 'Ca. L. asiaticus', causal agent of Huanglongbing or citrus "greening," and 'Ca. L. solanacearum', causal agent of potato zebra chip disease, respectively threaten citrus and potato production worldwide. Research on both pathogens has been stymied by the inability to culture these agents and to reinoculate into any host. Only a single isolate of a single species of Liberibacter, Liberibacter crescens, has been axenically cultured. L. crescens strain BT-1 is genetically tractable to standard molecular manipulation techniques and has been developed as a surrogate model for functional studies of genes, regulatory elements, promoters, and secreted effectors derived from the uncultured pathogenic Liberibacters. Detailed, step-by-step, and highly reproducible protocols for axenic culture, transformation, and targeted gene knockouts of L. crescens are described. In the course of developing these protocols, we found that L. crescens is also naturally competent for direct uptake and homology-guided chromosomal integration of both linear and circular plasmid DNA. The efficiency of natural transformation was about an order of magnitude higher using circular plasmid DNA compared with linearized fragments. Natural transformation using a replicative plasmid was obtained at a rate of approximately 900 transformants per microgram of plasmid, whereas electroporation using the same plasmid resulted in 6 × 10⁴ transformants. Homology-guided marker interruptions using either natural uptake or electroporation of nonreplicative plasmids yielded 10 to 12 transformation events per microgram of DNA, whereas similar interruptions using linear fragments via natural uptake yielded up to 34 transformation events per microgram of DNA.

Identification and Characterization of Menadione and Benzethonium Chloride as Potential Treatments of Pierce's Disease of Grapevines

Xylella fastidiosa infects a wide range of plant hosts and causes Pierce's disease (PD) of grapevines. The type 1 multidrug resistance (MDR) efflux system is essential for pathogenicity and survival of bacterial pathogens in planta. X. fastidiosa, with a single MDR system, is significantly more vulnerable to inhibition by small-molecule treatments than most bacterial pathogens that typically carry redundant MDR systems. A high-throughput cell viability assay using a green fluorescent protein-marked strain of X. fastidiosa Temecula 1 was developed to screen two Prestwick combinatorial small-molecule libraries of drugs and phytochemicals (1,600 chemicals in total) approved by the Food and Drug Administration and European Medicines Agency for cell growth inhibition. The screens revealed 215 chemicals that inhibited bacterial growth by >50% at 50 µM concentrations. Seven chemicals proved to lyse X. fastidiosa cells at 25 µM, including four phytochemicals. Menadione (2-methyl-1,4-naphthoquinone, vitamin K) from the phytochemical library and benzethonium chloride (a topical disinfectant) from the chemical library both showed significant bactericidal activity against X. fastidiosa. Both menadione and benzethonium chloride foliar spray (15 and 5 mM, respectively) and soil drench (5 and 25 mM, respectively) treatments were equally effective in reducing PD symptoms by 54 to 59% and revealed that the effects of both chemical treatments became systemic. However, menadione was phytotoxic when applied as a foliar spray at effective concentrations, causing significant loss of photosynthetic capacity.

A Small Wolbachia Protein Directly Represses Phage Lytic Cycle Genes in "Candidatus Liberibacter asiaticus" within Psyllids

Huanglongbing (HLB) is a severe disease of citrus caused by an uncultured alphaproteobacterium "Candidatus Liberibacter asiaticus" and transmitted by Asian citrus psyllids (Diaphorina citri). Two prophage genomes, SC1 and SC2, integrated in "Ca. Liberibacter asiaticus" strain UF506 were described previously, and very similar prophages are found resident in the majority of "Ca. Liberibacter asiaticus" strains described worldwide. The SC1 lytic cycle is marked by upregulation of prophage late genes, including a functional holin (SC1_gp110); these late genes are activated when "Ca. Liberibacter asiaticus" is in planta, but not when infecting the psyllid host. We previously reported that the holin promoter is strongly and constitutively active in Liberibacter crescens (a cultured proxy for uncultured "Ca. Liberibacter asiaticus") but is suppressed in a dose-dependent manner by crude aqueous extracts from D. citri applied exogenously. Here we report that the suppressor activity of the crude psyllid extract was heat labile and abolished by proteinase K treatment, indicating a proteinaceous repressor and of a size smaller than 30 kDa. The repressor was affinity captured from D. citri aqueous extracts using biotinylated holin promoter DNA immobilized on magnetic beads and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein database interrogation was used to identify a small DNA-binding protein encoded by a gene carried by Wolbachia strain wDi, a resident endosymbiont of D. citri as the repressor. The in vitro-translated Wolbachia repressor protein was able to penetrate L. crescens cells, bind to "Ca. Liberibacter asiaticus" promoter DNA, and partially suppress holin promoter-driven β-glucuronidase (GUS) activity, indicating potential involvement of an additional interacting partner(s) or posttranslational modification(s) for complete suppression. Expression of the Wolbachia repressor protein appeared to be constitutive irrespective of "Ca. Liberibacter asiaticus" infection status of the insect host. IMPORTANCE Host acquisition of a new microbial species can readily perturb the dynamics of preexisting microbial associations. Molecular cross talk between microbial associates may be necessary for efficient resource allocation and enhanced survival. Classic examples involve quorum sensing (QS), which detects population densities and is both used and coopted to control expression of bacterial genes, including host adaptation factors. We report that a 56-amino-acid repressor protein made by the resident psyllid endosymbiont Wolbachia can enter cells of Liberibacter crescens, a cultured proxy for the uncultured psyllid endosymbiont "Ca. Liberibacter asiaticus" and repress "Ca. Liberibacter asiaticus" phage lytic cycle genes. Such repression in "Ca. Liberibacter asiaticus" may be critical to survival of both endosymbionts, since phage-mediated lysis would likely breach the immunogenic threshold of the psyllid, invoking a systemic and nonspecific innate immune reaction.

Surface polysaccharides and quorum sensing are involved in the attachment and survival of Xanthomonas albilineans on sugarcane leaves

Xanthomonas albilineans, the causal agent of sugarcane leaf scald, is a bacterial plant pathogen that is mainly spread by infected cuttings and contaminated harvesting tools. However, some strains of this pathogen are known to be spread by aerial means and are able to colonize the phyllosphere of sugarcane before entering the host plant and causing disease. The objective of this study was to identify the molecular factors involved in the survival or growth of X. albilineans on sugarcane leaves. We developed a bioassay to test for the attachment of X. albilineans on sugarcane leaves using tissue-cultured plantlets grown in vitro. Six mutants of strain XaFL07-1 affected in surface polysaccharide production completely lost their capacity to survive on the sugarcane leaf surface. These mutants produced more biofilm in vitro and accumulated more cellular poly-β-hydroxybutyrate than the wild-type strain. A mutant affected in the production of small molecules (including potential biosurfactants) synthesized by non-ribosomal peptide synthetases (NRPSs) attached to the sugarcane leaves as well as the wild-type strain. Surprisingly, the attachment of bacteria on sugarcane leaves varied among mutants of the rpf gene cluster involved in bacterial quorum sensing. Therefore, quorum sensing may affect polysaccharide production, or both polysaccharides and quorum sensing may be involved in the survival or growth of X. albilineans on sugarcane leaves.

Prophage-Encoded Peroxidase in 'Candidatus Liberibacter asiaticus' Is a Secreted Effector That Suppresses Plant Defenses

'Candidatus Liberibacter asiaticus' is transmitted by psyllids and causes huanglongbing (HLB), a lethal disease of citrus. Most pathogenic 'Ca. L. asiaticus' strains carry two nearly identical prophages similar to SC1 and SC2 in strain UF506. SC2 was observed to replicate as a moderately high-copy excision plasmid encoding a reactive oxygen species-scavenging peroxidase (SC2_gp095), a predicted lysogenic conversion factor. SC2_gp095 was expressed at significantly higher levels in periwinkle than in citrus and was suppressed in psyllids. SC2_gp095 was cloned in a shuttle vector and transformed into Escherichia coli and Liberibacter crescens, a culturable proxy for 'Ca. L. asiaticus'. Transformed L. crescens cells showed 20 to 25% enhanced resistance to H₂O₂on agar plates, 47% greater enzymatic activity, and enhanced growth in liquid cultures. A nonclassical secretion potential was predicted for SC2_gp095 and secretion from L. crescens was confirmed by enzymatic and Western blot analyses. Transient expression of SC2_gp095 in planta resulted in strong transcriptional downregulation of RbohB, the key gatekeeper of the H₂O₂-mediated defense signaling in plants, helping explain the surprisingly long incubation period (years) before HLB symptoms appear in 'Ca. L. asiaticus'-infected citrus. 'Ca. L. asiaticus' peroxidase is likely a secreted, horizontally acquired effector that suppresses host symptom development, a tactic used by most biotrophic plant pathogens.

Three New Pierce's Disease Pathogenicity Effectors Identified Using Xylella fastidiosa Biocontrol Strain EB92-1

Xylella fastidiosa (X. fastidiosa) infects a wide range of plant hosts and causes economically serious diseases, including Pierce's Disease (PD) of grapevines. X. fastidiosa biocontrol strain EB92-1 was isolated from elderberry and is infectious and persistent in grapevines but causes only very slight symptoms under ideal conditions. The draft genome of EB92-1 revealed that it appeared to be missing genes encoding 10 potential PD pathogenicity effectors found in Temecula1. Subsequent PCR and sequencing analyses confirmed that EB92-1 was missing the following predicted effectors found in Temecula1: two type II secreted enzymes, including a lipase (LipA; PD1703) and a serine protease (PD0956); two identical genes encoding proteins similar to Zonula occludens toxins (Zot; PD0915 and PD0928), and at least one relatively short, hemagglutinin-like protein (PD0986). Leaves of tobacco and citrus inoculated with cell-free, crude protein extracts of E. coli BL21(DE3) overexpressing PD1703 exhibited a hypersensitive response (HR) in less than 24 hours. When cloned into shuttle vector pBBR1MCS-5, PD1703 conferred strong secreted lipase activity to Xanthomonas citri, E. coli and X. fastidiosa EB92-1 in plate assays. EB92-1/PD1703 transformants also showed significantly increased disease symptoms on grapevines, characteristic of PD. Genes predicted to encode PD0928 (Zot) and a PD0986 (hemagglutinin) were also cloned into pBBR1MCS-5 and moved into EB92-1; both transformants also showed significantly increased symptoms on V. vinifera vines, characteristic of PD. Together, these results reveal that PD effectors include at least a lipase, two Zot-like toxins and a possibly redundant hemagglutinin, none of which are necessary for parasitic survival of X. fastidiosa populations in grapevines or elderberry.

"Candidatus Liberibacter asiaticus" prophage late genes may limit host range and culturability

"Candidatus Liberibacter asiaticus" is an uncultured alphaproteobacterium that systemically colonizes its insect host both inter- and intracellularly and also causes a severe, crop-destroying disease of citrus called huanglongbing, or citrus "greening." In planta, "Ca. Liberibacter asiaticus" is also systemic but phloem limited. "Ca. Liberibacter asiaticus" strain UF506 carries two predicted prophages, SC1 and SC2. Bacteriophage particles have been observed in experimentally "Ca. Liberibacter asiaticus"-infected periwinkle but not in any other host. Comparative gene expression analysis of predicted SC1 late genes showed a much higher level of late gene expression, including holin transcripts (SC1_gp110), in "Ca. Liberibacter asiaticus"-infected periwinkle relative to "Ca. Liberibacter asiaticus"-infected citrus. To functionally characterize predicted holin and endolysin activity, SC1_gp110 and two predicted endolysins, one within SC1 (SC1_gp035) and another well outside the predicted prophage region (CLIBASIA_04790), were cloned and expressed in Escherichia coli. Both SC1 genes inhibited bacterial growth consistent with holin and endolysin function. The holin (SC1_gp110) promoter region was fused with a uidA reporter on pUFR071, a wide bacterial host range (repW) replicon, and used to transform Liberibacter crescens strain BT-1 by electroporation. BT-1 is the only liberibacter strain cultured to date and was used as a proxy for "Ca. Liberibacter asiaticus." pUFR071 was >95% stable without selection in BT-1 for over 20 generations. The reporter construct exhibited strong constitutive glucuronidase (GUS) activity in culture-grown BT-1 cells. However, GUS reporter activity in BT-1 was suppressed in a dose-dependent manner by crude aqueous extracts from psyllids. Taken together with plant expression data, these observations indicate that "Ca. Liberibacter asiaticus" prophage activation may limit "Ca. Liberibacter asiaticus" host range and culturability.

Xanthomonas albilineans OmpA1 appears to be functionally modular and both the OMC and C-like domains are necessary for leaf scald disease of sugarcane

Several EZ-Tn5 insertions in gene locus XALc_0557 (OmpA1) of the sugarcane leaf scald pathogen Xanthomonas albilineans XaFL07-1 were previously found to strongly affect pathogenicity and endophytic stalk colonization. XALc_0557 has a predicted OmpA N-terminal outer membrane channel (OMC) domain and an OmpA C-like domain. Further analysis of mutant M468, with an EZ-Tn5 insertion in the upstream OMC domain coding region, revealed impaired epiphytic and endophytic leaf survival, impaired resistance to sodium dodecyl sulfate (SDS), structural defects in the outer membrane (OM), and hyperproduction of OM vesicles. Cloned full-length XALc_0557 complemented M468 for all phenotypes tested, including pathogenicity, resistance to SDS, and ability to survive both endophytically and epiphytically. Another construct, pCT47.3, which expressed only the C-like domain of XALc_0557, restored resistance to SDS in M468 but failed to complement any other mutant phenotype, indicating that the C-like domain functioned independently of the OMC domain to help maintain OM integrity. pCT47.3 also complemented pathogenicity, resistance to SDS, and stalk colonization in mutant M1152, which carries an EZ-Tn5 insert in the C-like coding region, indicating that both predicted domains are modular and necessary but neither is sufficient for X. albilineans pathogenicity, endophytic survival in, and epiphytic survival on sugarcane.

The RpfCG two-component system negatively regulates the colonization of sugar cane stalks by Xanthomonas albilineans

The genome of Xanthomonas albilineans, the causal agent of sugar cane leaf scald, carries a gene cluster encoding a predicted quorum sensing system that is highly related to the diffusible signalling factor (DSF) systems of the plant pathogens Xylella fastidiosa and Xanthomonas campestris. In these latter pathogens, a cluster of regulation of pathogenicity factors (rpf) genes encodes the DSF system and is involved in control of various cellular processes. Mutation of Xanthomonas albilineans rpfF, encoding a predicted DSF synthase, in Florida strain XaFL07-1 resulted in a small reduction of disease severity (DS). Single-knockout mutations of rpfC and rpfG (encoding a predicted DSF sensor and regulator, respectively) had no effect on DS or swimming motility of the pathogen. However, capacity of the pathogen to cause disease was slightly reduced and swimming motility was severely affected when rpfG and rpfC were both deleted. Similar results were obtained when the entire rpfGCF region was deleted. Surprisingly, when the pathogen was mutated in rpfG or rpfC (single or double mutations) it was able to colonize sugar cane spatially more efficiently than the wild-type. Mutation in rpfF alone did not affect the degree of spatial invasion. We conclude that the DSF signal contributes to symptom expression but not to invasion of sugar cane stalks by Xanthomonas albilineans strain XaFL07-1, which is mainly controlled by the RpfCG two-component system.

'Ca. Liberibacter asiaticus' carries an excision plasmid prophage and a chromosomally integrated prophage that becomes lytic in plant infections

Huanglongbing (HLB), also known as citrus greening, is a lethal disease of citrus caused by several species of 'Candidatus Liberibacter', a psyllid-transmitted, phloem-limited, alpha proteobacteria. 'Ca. Liberibacter asiaticus' is widespread in Florida citrus. The recently published 'Ca. L. asiaticus' psy62 genome, derived from a psyllid, revealed a prophage-like region of DNA in the genome, but phage have not been associated with 'Ca. L. asiaticus' to date. In the present study, shotgun sequencing and a fosmid DNA library of curated 'Ca. L. asiaticus' UF506, originally derived from citrus symptomatic for HLB, revealed two largely homologous, circular phage genomes, SC1 and SC2. SC2 encoded putative adhesin and peroxidase genes that had not previously been identified in 'Ca. L. asiaticus' and which may be involved in lysogenic conversion. SC2 also appeared to lack lytic cycle genes and replicated as a prophage excision plasmid, in addition to being found integrated in tandem with SC1 in the UF506 chromosome. By contrast, SC1 carried suspected lytic cycle genes and was found in nonintegrated, lytic cycle forms only in planta. Phage particles associated with 'Ca. L. asiaticus' were found in the phloem of infected periwinkles by transmission electron microscopy. In psyllids, both SC1 and SC2 were found only as prophage.