https://orcid.org/0000-0002-3993-9467
Figures
Abstract
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.
Citation: Cai L, Jain M, Sena-Vélez M, Jones KM, Fleites LA, Heck M, et al. (2021) Tad pilus-mediated twitching motility is essential for DNA uptake and survival of Liberibacters. PLoS ONE 16(10): e0258583. https://doi.org/10.1371/journal.pone.0258583
Editor: Tushar Kanti Dutta, Indian Agricultural Research Institute, INDIA
Received: July 21, 2021; Accepted: October 1, 2021; Published: October 13, 2021
Copyright: © 2021 Cai et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the manuscript and its Supporting information files.
Funding: This work was supported by the USDA National Institute of Food and Agriculture; Specialty Crops Research Initiative (NIFA-SCRI) grant #2016-70016-24844 to DWG and KMJ. https://nifa.usda.gov/funding-opportunity/specialty-crop-research-initiative-scri. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Introduction
‘Candidatus Liberibacter’ spp. are fastidious and uncultured α-Proteobacteria (order Rhizobiales) that have emerged as a versatile group of phloem-limited plant pathogens. ‘Ca. Liberibacter’ spp. are insect-transmitted, and some are associated with severe diseases, but others cause only mild to asymptomatic infections in several plant hosts [1]. ‘Ca. L. asiaticus’ (CLas) causes Huanglongbing (HLB) or citrus "greening" disease, which is arguably the single most devastating disease of citrus worldwide. HLB is also associated with ‘Ca. L. americanus’ (CLam) in Brazil and ‘Ca. L. africanus’ (CLaf) in Africa. Aberrant assimilate partitioning and nutrient transport in HLB-infected citrus trees leads to progressive decline in productivity and eventual death. ‘Ca. L. solanacearum’ (CLso) causes zebra chip (ZC) disease on potato and is vectored by the tomato and potato psyllid Bactericera cockerelli Šulc (Triozidae) in America and New Zealand [2]. ZC symptoms include purple discoloration and chlorosis of leaves, stolon collapse, browning and necrotic flecking of vascular tissue in the tubers leading to rapid death of infected potato plants. CLso has a wide host range and can also infect several other economically important Solanaceae and Apiaceae crops, including tomato, carrot, fennel, celery, parsnip and parsley [3].
CLas is acquired by Asian citrus psyllid (ACP) Diaphorina citri Kuwayama (Psyllidae) nymphs while feeding and invades the midgut cells. The bacteria recruit endoplasmic reticulum-derived vacuolar vesicles as a unique replicative niche causing localized apoptosis in the midgut of ACP adults [4, 5]. The bacteria form an extensive biofilm on the outer midgut surface before planktonic release to the hemolymph en route to salivary gland invasion. Ultrastructural examination of CLso-infected B. cockerelli suggests colonization of insect midgut cells via an endo/exocytosis-like mechanism [6]. Both CLas and CLso spread inter- and intracellularly in psyllids across multiple organs at relatively high titers but without manifesting overt pathogenic symptoms [5, 6]. By contrast in plants, systemic colonization by CLas [7, 8] and CLso [9] is limited to phloem.
Active bacterial motility is essential for recognition and colonization of host tissues, nutrient resourcing and pathogenesis by many symbiotic and pathogenic bacteria [10, 11]. The complex helical or rotary nanomechanical action of flagella enables directed movement of bacterial cells through aqueous environments either by unicellular swimming or multicellular swarming [12]. Twitching motility is mediated by extension, tethering and retraction of certain Type IV pili (T4P) resulting in forward pulling of bacterial cells under conditions of low water content e.g., within biofilms [13]. Coordinated mechanosensing of host surfaces by rotary flagella and retractable T4P is essential for permanent bacterial attachment [14] and transitioning between biofilm-restricted sessile and planktonic phases [15]. T4P are also involved in biofilm architecture [16], adsorption and uptake of extracellular dsDNA for food and for horizontal gene transfer by naturally competent bacteria [13, 17, 18].
T4P are traditionally categorized into three subclasses, T4aP, T4bP and T4cP, based on morphological, serological, functional and biochemical criteria [19]. T4aP are widespread across several Gram-negative pathogenic and environmental bacteria such as Pseudomonas, Neisseria, Myxococcus etc. T4bP are restricted to the enteropathogenic (EPEC) and enterotoxigenic (ETEC) strains of Escherichia coli, Vibrio cholerae and Salmonella enterica serovar Typhi. T4aP contain NMePhe as the first N-terminus amino acid (aa) residue of the pilin subunit, a characteristic short (5–6 aa) leader peptide and 150–160 aa long mature length. By contrast, T4b pilins lack a conserved N-terminus NMePhe, have longer (15–30 aa) leader peptides and result in 180–200 aa mature pilin subunits [19, 20].
The third subclass, T4cP, includes Tad (Tight adherence) and Flp (Fimbrial low-molecular-weight-protein pili). The Tad pilus apparatus (homologous to Caulobacter crescentus pilus assembly or Cpa) has been implicated in surface anchoring, adhesion, colonization, cellular aggregation and biofilm cohesion [17, 19, 21, 22]. Notably, Tad pili are not considered to be dynamic because they all lack a dedicated retraction ATPase for catalyzing pilin depolymerization, a prerequisite for generating the directional retractile force sufficiently large for active bacterial motility and uptake of extracellular dsDNA in naturally competent bacteria [23]. However, the CpaF motor ATPase of C. crescentus was demonstrated to drive repetitive bidirectional cycles of Tad pilus extension and retraction via ATP hydrolysis, resulting in "walking-like" surface translocation of bacteria in microfluidic chambers [14, 24].
Only one Liberibacter species, L. crescens (Lcr), derived from a diseased mountain papaya, has been axenically cultured in vitro [25], and has no known plant or insect host. Lcr strain BT-1 (GenBank Acc. NC_019907.1) is naturally competent for transformation and is well established as a culturable surrogate for the pathogenic ‘Ca. Liberibacter’ spp., none of which have been axenically cultured [26]. Lcr BT-1 and all 35 sequenced genomes representing all ‘Ca. Liberibacter’ spp. have been annotated as encoding a "nearly" complete set of biosynthetic genes for flagella; all are missing only three minor flagellins: FlaB, FlaC and FlaD [27, 28]. Similarly, a complete set of Tad pilus genes is present and conserved in all Liberibacters [29]. Differential regulation of the CLas Tad pilus operon was described and a potential role for the Tad pilus in bacterial attachment to the ACP midgut was suggested [29]. However, no other potential functional role for these pili in any member of the genus has been suggested. Evidence for surface appendages and their role(s) in motility and systemic colonization in ‘Ca. Liberibacter’ spp. remains largely anecdotal.
In this report we provide ultrastructural evidence for the presence of both flagella and Tad pilus surface appendages in Lcr and demonstrate both flagellar swimming and Tad pilus-mediated twitching motility in the genus Liberibacter for the first time. Based on the presence, transcriptional activity and functional characterization of genes encoding flagella and Tad pili in Lcr, we propose that motility is an essential attribute of pathogenic ‘Ca. Liberibacter’ spp. that likely determines circulative propagation in the psyllid as well as systemic colonization of phloem. More importantly, the demonstration of twitching motility in this genus extends the importance of Tad pili in ‘Ca. Liberibacter’ spp. beyond their traditional role in tenacious surface adherence. Based on (a) the conservation of Tad pilus and DNA uptake genes, (b) our earlier observation of DNA uptake and natural competence in Lcr [26] and (c) the fact that all Liberibacters are deficient in nucleotide biosynthesis [30], we propose that Tad pilus-mediated uptake of extracellular dsDNA for food is likely essential for survival and colonization of ‘Ca. Liberibacter’ spp. in both plant and insect hosts.
Materials and methods
Bacterial strains and growth conditions
The relevant characteristics, source and/or reference for the bacterial strains and plasmids used in this study are listed in Table 1. E. coli was grown in Luria-Bertani (LB) medium at 37°C. Lcr BT-1 was maintained on BM7A medium containing 20 g l-1 N-(2-acetamido)-2-aminoethanesulfonic acid (ACES) buffer (Sigma-Aldrich, St. Louis, MO, USA) [26] with gentle shaking at 110 rpm at 28°C. Antibiotics were used as needed at the following concentrations (in μg/ml): 100 ampicillin (Amp) and 50 kanamycin (Kn) for E. coli; 4.5 Kn, 2.0 chloramphenicol (Cm) and 2.0 gentamycin (Gm) for Lcr.
Transmission electron microscopy (TEM)
Copper grids (400 mesh, 62 μm pitch; Sigma-Aldrich) were placed with the Formvar side down, for 10 sec on a 7-day-old culture of Lcr growing on BM7A medium containing 0.25% or 0.75% agar (w/v; Difco™ Agar, BD diagnostics, VWR, Radnor, PA, USA). Grids were carefully lifted off and the adherent bacterial cells were fixed/stained in a drop of 2% (v/v) uranyl acetate for 60 sec. Excess uranyl acetate was then blotted off and the residue allowed to air dry. Grids were viewed at 100 kV accelerating voltage using a transmission electron microscope (Hitachi H-7000, Hitachi High-Technologies Corporation, Tokyo, Japan) equipped with a Veleta (2k×2k) CCD side mount camera.
Quantification of motility in L. crescens BT-1
Motility assays were performed in BM7A medium solidified with either 0.25% or 0.75% agar for quantification of swimming or twitching phenotype, respectively [12]. Five μl of 5-day-old Lcr culture grown in BM7A medium (OD600 = 0.4) were spot-inoculated on the surface of agar plates. Likewise, 5 μl bacterial inoculum was also stabbed either halfway through the agar, or to the bottom of the petri plate for quantification of twitching phenotype. The inoculated plates were cultured for 3 weeks at 28°C and examined for bacterial motility away from the inoculated site [12]. In case of asymmetric growth, the colony diameter was measured at the widest point. Due to the severely reduced growth of the cpaF mutant strains, the primary transformation colonies were resuspended in liquid BM7A medium (OD600 = 0.4) and used for motility assays. All experiments were repeated at least three times with three replications. Student’s t tests (P = 0.05) were performed to separate treatment means.
Site-directed mutagenesis and complementation of insertional mutants in L. crescens BT-1
Lcr flagellar genes (flgF and flgK), Tad pilus genes (cpaA, cpaB, cpaE, cpaF, tadC) and competence protein gene comEC were interrupted with a kanamycin-resistance gene and the resulting mutant strains were verified by PCR analyses following the strategy outlined in Jain et al. [26]. Partial DNA fragments internal to the coding regions of target genes were PCR-amplified using primer pairs described in Table 2 and the amplicons were cloned into non-replicative (in Lcr) plasmid pCR®2.1-TOPO (Invitrogen, Carlsbad, CA, USA). The resulting suicide plasmids (Table 1) were transformed into Lcr by electroporation.
The Ptryp promoter from pUFZ75 (KnR) [31] was amplified using the primers CLL35F/R and inserted downstream of the lacZ promoter in pBBR1MCS-5 [32] within the KpnI/XhoI sites resulting in plasmid pCLL035 (GmR). Full-length flgF and flgK were PCR-amplified from Lcr using primer pairs CLL38F/R and CLL36F/R, respectively. After sequence verification, the flgF and flgK inserts were directionally subcloned using BamHI/XbaI into pCLL035 and the resulting plasmids pCLL038 and pCLL036 were transformed into mutant Lcr strains flgF::pCLL026 and flgK::pCLL027, respectively, for complementation. Full-length comEC was PCR-amplified using the primer pairs CLL52F/R, CLL53F/R and CLL56F/R from Lcr, CLas strain psy62 [33] and CLso strain ISR100 [34], respectively. Sequence-verified inserts were directionally cloned into pCLL035 using XmaI/BamHI sites and the resulting plasmids (pCLL052, pCLL053 and pCLL056) were transformed into Lcr strain comEC::pMJ054.
Natural transformation of L. crescens BT-1
A 40 μl aliquot of electrocompetent Lcr BT-1 cells [26] was mixed gently with 0.5 μg closed circular plasmid DNA (pUFR071) and 50 μl chitin (1 mM, C-3387, Sigma-Aldrich) or xanthan gum (0.5% w/v in water; G-1253, Sigma-Aldrich). The transformation mix was resuspended in 850 μl liquid BM7A medium, incubated with gentle shaking at 28ºC at 150 rpm for 48 hrs and finally plated on selective BM7A medium containing 4.5 mg l-1 Kn and 2.0 mg l-1 Gm. Natural uptake of pUFR71 by comEC::pMJ054 strains carrying the complementing full-length comEC was selected in the presence of 4.5 mg l-1 Kn and 2.0 mg l-1 each of Gm and Cm.
Nucleic acid extraction and quantitative reverse transcription PCR (qRT-PCR) analyses
For Lcr cultures grown on agar plates, the bacteria were gently scraped off the plates and resuspended in 100–200 μl water and briefly centrifuged to collect the cells in the pellet. Genomic DNA and RNA were extracted using the GenElute™ Bacterial Genomic DNA kit (Sigma-Aldrich) and RNeasy® Mini Kit (Qiagen, Valencia, CA, USA) following manufacturer’s recommendations. RNA was diluted with nuclease free water to 200 ng μl-1 and cleaned with TURBO DNA-free (DNase) Kit (Ambion, Austin, TX, USA). First-strand cDNA was synthesized from one μg purified RNA template using iScript Advanced cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Twenty μL of qPCR reaction consisted of 10 μl of 2× QuantiNova SYBR Green PCR Mix (Qiagen), 1 μl of each primer (5 μM), 4 μl of cDNA template and 5 μl of DNase/RNase free water. The thermal cycling protocol entailed an initial activation step at 95°C for 2 min, followed by 40 cycles of 95°C for 5 s and 60°C for 10 s. All cDNA samples were run in triplicates using a CFX96 Touch Real-Time PCR detection system (Bio-Rad). Optical data were acquired during the annealing step and the fidelity of PCR reaction was monitored by melting curve analysis beginning at 55°C through 95°C, ramped at 0.1°C s-1. The gene-specific primers are listed in Table 2. Transcript levels were normalized using chromosomal reference gene DNA gyrase subunit B (gyrB, B488_RS06700) and transcript values in liquid BM7A were used as calibrator controls (2-ΔΔCt). The data were analyzed using SAS for Windows, version 9.2 (SAS Institute Inc, Cary, NC) and Student’s t tests were performed to separate treatment means. A probability of 5% was used to determine statistically significant differences.
Fluorescence labeling and uptake of DNA
The BamHI/SmaI digested linear insert (2.834 kb) from pCLL04 [26] carrying the internal fragment of the Lcr RIP gene (Type I restriction endonuclease subunit R; B488_RS03405) and Gm resistance gene (aminoglycoside-3-O-acetyltransferase-I, aacC1; 834 bp) from pUFR071 was used for fluorescence labeling of DNA and uptake via natural transformation. Dimeric cyanine nucleic acid dye YOYO™-1 iodide (λex/em 491/509; Invitrogen) was used for noncovalent fluorescent labelling of DNA at a base pair to dye ratio of 1:50. One μg ml-1 YOYO-1-labeled DNA was pretreated with 10 units of DNase I (Sigma-Aldrich) for 10 min and added to the Lcr cell suspension in 100 μl BM7A (OD600 ∼0.4) and incubated for 15–45 min at 28°C. The fluorescence data were captured using an Olympus IX81-DSU Spinning Disc Confocal Microscope (Olympus Corporation, Tokyo, Japan) fitted with Hamamatsu ORCA-Flash 4.0LT+ camera (Hamamatsu Photonics, K.K., Hamamatsu, Japan).
Results
Both flagella and much smaller Tad pili were observed by TEM of L. crescens BT-1
Both flagella and pili were readily distinguished upon ultrastructural examination of Lcr cells. Negatively stained Lcr cells grown on BM7A medium containing 0.25% (w/v) agar revealed the presence of peritrichous flagella distributed on the surface of rod-shaped (~0.5×1.75 μm), asymmetrically dividing bacterial cells. Pili were observed on the surfaces of Lcr cells grown on medium solidified with 0.75% (w/v) agar. By comparison with long, threadlike, electron dense flagella (Fig 1A and 1B), the pili were smaller, shorter and appeared relatively electron lucent (Fig 1C and 1D). Since the only pilus genes encoded by the Lcr genome are Tad pilus genes, we concluded these were Tad pili. Notably, among all the Lcr cell cultures examined, only a small subset of the cell population presented flagella or Tad pili on their surface, and these were observed only on cells grown on semisolid BM7A medium. Neither flagella nor Tad pili were observed on the surfaces of Lcr cells growing in a continuously shaking BM7A broth culture.
(A-D) Ultrastructural and (E-H) functional evidence for the presence of flagella and Tad pili in Lcr BT‐1. Five-day-old Lcr cells were cultured for three weeks on BM7A medium containing 0.25% (A-B, E-F) and 0.75% (C-D, G-H) agar for swimming and twitching assays, respectively. Negatively stained cells were analyzed by transmission electron microscopy. Magnification scales are indicated in the images. Note the swimming zone as outward bacterial growth along the surface (E) and clearly downward within the culture medium when the same colony is photographed at an angle (F). By contrast, Tad pilus-mediated twitching appeared as strictly surface restricted growth (G) or along the agar/polystyrene interface when the inoculum was stabbed to the bottom of the plate (H). Relative expression of (I) flagella and (J) Tad pilus biosynthesis genes in Lcr grown in BM7A broth culture and on BM7A plates containing low (0.25%), medium (0.75%) and high (1.5%) agar concentrations. The transcript abundance of each gene was calibrated against expression in liquid BM7A medium and normalized against the expression levels of the chromosomal reference gene gyrB within each sample. Bars represent average ± the standard deviation for three independent experiments with four replications. Asterisks represent significant differences (P < 0.05) in the transcript abundance.
Both swimming and twitching motility were observed with L. crescens BT-1
Low (0.25%) and medium (0.75%) agar (w/v) concentrations were optimized to differentiate between swimming and twitching motility [12]. Lcr grown in a low (0.25%) agar medium demonstrated swimming behavior as uniform outward growth from the inoculation point along both the surface (Fig 1E) and downward (Fig 1F) within the culture medium. By contrast, twitching motility of Lcr was evident at medium (0.75%) agar concentrations as surface restricted growth if the inoculum was surface-dropped or stabbed half-way through the medium (Fig 1G) and restricted along the medium/polystyrene interface if stabbed to the bottom of the plate (Fig 1H).
Expression of flagella and Tad pilus genes in L. crescens BT-1 was associated with swimming and twitching, respectively
Expression of genes encoding flagella and Tad pili was examined in Lcr cultured in BM7A medium at three agar concentrations; low (0.25%, associated with swimming), medium (0.75%, associated with twitching) and high (1.5%, used for routine microbial maintenance and culturing). By comparison with Lcr grown in liquid cultures, qRT‐PCR analyses demonstrated that the transcription of flagellar biosynthesis genes was significantly downregulated in Lcr cells when cultured on medium (0.75%) or high (1.5%) concentrations of agar but not on 0.25% agar (Fig 1I), associated with the swimming phenotype (Fig 1E and 1F). By contrast, the transcript abundance of the Tad pilus apparatus genes was upregulated compared to liquid BM7A medium only at medium (0.75%) agar concentrations (Fig 1J), associated with the twitching phenotype seen under these conditions (Fig 1G and 1H). No significant changes were observed in the expression level of endogenous housekeeping control gene peptide chain release factor-1 (prfA, B488_RS00360) in cells growing under either liquid or semisolid culture conditions.
Site-directed mutagenesis and complementation of flagella genes affected swimming but not twitching motility in L. crescens BT-1
Insertional mutagenesis of flagellar basal-body rod protein gene flgF (B488_RS00930) and hook-associated protein gene flgK (B488_RS04530) caused 20% and 33% reduction in the swim zone diameters of respective mutant cells flgF::pCLL026 (1.03 ± 0.08 cm) and flgK::pCLL027 (1.19 ± 0.07 cm) in comparison to the wild-type BT-1 (1.51 ± 0.19 cm). The full-length Lcr genes flgF and flgK fully complemented their respective mutant strains flgF::pCLL026/pCLL038 (1.33 ± 0.07 cm) and flgK::pCLL027/pCLL036 (1.48 ± 0.12 cm) (Fig 2A, 2B and 2E). However, no difference in the twitching zone diameters were observed for the wild-type BT-1 (1.03 ± 0.02 cm), flgF::pCLL026 (1.01 ± 0.04 cm), flgF::pCLL026/pCLL038 (1.01 ± 0.02 cm), flgK::pCLL027 (1.02 ± 0.02 cm) and flgK::pCLL027/pCLL036 (1.03 ± 0.01 cm) (Fig 2C–2E). Even though both swimming and twitching motility were observed with wild-type BT-1 (Fig 1), only swimming motility was affected by flagellar mutations (Fig 2). These data clearly show that Lcr was indeed capable of twitching motility independently of the flagella apparatus, and such translocation was deduced to be mediated by Tad pili. The functional role of Tad pilus genes in twitching motility and its association with ComEC-mediated natural competence in Lcr was therefore examined.
(A, B) Swimming and (C, D) twitching motility in the wild-type BT-1, insertional flagellar gene mutants (flgF::pCLL026 and flgK::pCLL027) and complemented (flgF::pCLL026/pCLL038 and flgK::pCLL027/pCLL036) strains on semisolid BM7A plates containing 0.25% and 0.75% agar for swimming and twitching assays, respectively. (E) Swimming and twitching motility zone diameters were measured in three independent assays with three replicates each. The data are average ± standard deviation and the significant differences (P < 0.05, Student’s t test) in swimming behavior are represented by asterisks.
Two distinct Tad pilus ATPase-encoding genes, cpaE and cpaF, are structurally and functionally conserved among all Liberibacters
The Tad pilus operon of all Liberibacters encodes two structurally and functionally distinct genes organized in tandem, a pilus biogenesis ATPase cpaE (B488_RS06245) and a motor ATPase cpaF (B488_RS06240) located immediately downstream. Comparative phylogenetic analyses showed that both CpaE (S1 Fig) and CpaF (Fig 3) are conserved across all α-Proteobacterial lineages examined, including all pathogenic ‘Ca. Liberibacter’ spp. and cultured Lcr.
Sequence alignment of CpaF encoded by L. crescens BT‐1 (WP_015273698.1), ‘Ca. L. asiaticus’ (WP_015452438.1), ‘Ca. L. africanus’ (WP_047264073.1), A. rhizogenes (WP_065114603.1), ‘Ca. L. solanacearum’ (WP_076969128.1), ‘Ca. L. americanus’ (AHA27602.1) and C. crescentus (YP_002518410.1). Invariant residues required for coordination of Mg2+ between β- and γ-phosphate moieties of ATP within the canonical ATP-binding Walker A and Walker B motifs are marked by an asterisk (*). Invariant residues in Asp box and His box motifs are denoted by filled (▲) and open (△) triangles, respectively. Amino acids participating in ATP binding and ATPase activity are denoted by hashtags (#) and those involved in hexamer interface for subunit interactions are denoted by dots (·).
ClustalW [35] analysis revealed that Lcr CpaE (427 aa, 47.3 kDa) has only limited (53–60%) identity between CpaE homologs from ‘Ca. Liberibacter’ spp. and only 42% with C. crescentus and Rhizobium spp. CpaE belongs to the SIMIBI [after signal recognition particle (SRP), MinD, and BioD] ATPase subclass of the large P-loop GTPase superfamily [36] and features an ATPase domain (aa position 164–426) with a deviant Walker A motif, KGGVGSS (aa position 173–179) (S1 Fig).
Activity of all Liberibacter CpaF motor ATPases is likely bidirectional
The Tad pilus motor ATPase CpaF (481 aa, 53.4 kDa) is a soluble and cytoplasmic P-loop NTPase domain superfamily protein [37]. By contrast with CpaE, the CpaF homologs of Lcr, CLas, CLam, CLaf, CLso, C. crescentus and Agrobacterium rhizogenes are all highly similar (app. 70% identical; Fig 3).
ClustalW analysis showed the presence of multiple conserved domains, including an ATP-binding structural domain (aa positions 77–435) with conserved ATP-binding residues L228 and D403 and canonical nucleotide phosphate-binding G-rich Walker A (GGTGSGKT) and Walker B (RIILGE) motifs present between positions 256–263 and 327–332, respectively (Fig 3). Invariant residues T263 of Walker A and E332 of Walker B were present in Lcr CpaF and conserved among all Liberibacters; these residues are known to form coordinate Mg2+ bonds between the β- and γ-phosphate moieties of ATP bound to the conserved K262 of Walker A [38]. Three invariant acidic residues E283, D284 and E287 (within the Asp Box motif) and the two invariant residues H349 and H357 (within the His Box motif) are considered essential for P-loop ATPase activity [23]. All Liberibacter CpaF homologs are therefore likely to form a toroidal homohexameric ring-like structure involved in pilin translocation across the inner membrane via “open” and “closed” conformational changes typical of known P-loop secretion NTPases [22]. Strict conservation of all functional domains (87% query coverage, 70.48% identity, E value 0.0; Fig 3) between Lcr and C. crescentus CpaF [14, 24] indicated that the activity of the Lcr CpaF motor ATPase and by extension, of all Liberibacters, is likely bidirectional and capable of generating the strong retractile force required for twitching motility.
Mutations in Tad pilus genes affected twitching motility and abolished growth in L. crescens BT-1
To functionally validate the role of Tad pili in Lcr twitching motility, site-directed mutations were attempted in genes encoding the pilus biogenesis ATPase cpaE, motor ATPase cpaF, prepilin peptidase cpaA (B488_RS06265), periplasmic subunit cpaB (B488_RS06260) and pilus stabilization protein tadC (B488_RS06230). Insertional mutants of cpaA, cpaB, cpaF and tadC were all severely compromised in growth and very few visible colonies were obtained, and then only after 3–4 months of culture on selective medium. Almost no colonies were subculturable, and even these colonies were not amenable to repetitive subcultures on either solid or liquid media. Despite several attempts, site-directed mutagenesis of cpaE failed to yield any viable colonies. It was also extremely difficult to achieve adequate density of viable cells of mutant strains of Tad pilus genes in liquid cultures to permit further experiments. Multiple attempts to prepare competent cells for complementation via electroporation failed. By contrast, mutations of non-essential Lcr genes typically yield viable colonies in 8–10 weeks [26].
Only cpaF insertional mutant strain (cpaF::pCLL043) was evaluated for twitching phenotype on BM7A plates containing 0.75% agar. A significant reduction of 26% in twitching zone diameter of cpaF mutant strain (1.04 ± 0.06 cm) was observed as compared to the wild-type BT-1 (1.43 ± 0.07 cm) (Fig 4B and 4C). On 0.25% agar plates, significantly altered swimming behavior was clearly observed deep into the agar by the cpaF mutant as compared to wild-type BT-1 (Fig 4A). However, when measured across the surface of the agar only, the cpaF mutant swimming zones (1.25 ± 0.03 cm) on 0.25% agar plates were comparable to those of wild-type BT-1 (1.26 ± 0.04 cm) (Fig 4A and 4C). Further, a significant difference in growth density was also observed between the mutant and wild-type BT-1 on 0.25% agar plates. Impairment of the twitching phenotype in the cpaF mutant strain of Lcr (Fig 4B and 4C), taken together with the high levels of protein sequence similarity among CpaF motor ATPases (Fig 3) confirmed that Tad pili in Lcr and likely in all Liberibacters, are dynamic and involved in surface translocation.
(A-C) Mutation in the Tad pilus motor ATPase gene cpaF had no effect on flagellar swimming (A, C) but reduced twitching motility (B, C) in wild-type BT-1 and the mutant cpaF::pCLL043. (D-F) Mutation in the inner membrane competence protein gene comEC had no effect on flagellar swimming (D, F) or twitching motility (E, F) but completely abolished natural competence for transformation (G). Deficiency in natural competence for transformation in the mutant strain comEC::pMJ054 was fully complemented by full-length comEC gene from Lcr (comEC::pMJ054/pCLL052) but not from CLas strain psy62 (comEC::pMJ054/pCLL053) or CLso strain RS100 (comEC::pMJ054/pCLL056) (G). (H) Insertional mutant strains of Tad pilus genes (cpaA::pMJ081, cpaB::pMJ082, cpaF::pCLL043 and tadC::pMJ083) were severely compromised in growth in culture as compared to wild-type BT‐1, and insertional mutants for flagellar genes (flgF::pCLL026 and flgK::pCLL027) and the competence protein gene (comEC::pMJ054). Motility zone diameters and natural competence for transformation were quantified in three independent experiments with three replicates each. Bacterial growth assays were repeated thrice with five replicates each. The data are average ± standard deviation and the significant differences (P < 0.05, Student’s t test) in bacterial motility, natural transformation and growth are represented by asterisks.
ComEC, necessary for natural competence, is not conserved among ‘Ca. Liberibacter’ spp.
Demonstrably dynamic Tad pili in Lcr and the severity of the growth defects observed with mutations of Lcr Tad pilus genes suggested a correlation between Tad pili and both natural transformation in Lcr [26] and DNA uptake for food in all Liberibacters [30], since dsDNA uptake in bacteria strictly requires a transport assembly through the outer membrane to the periplasm [20].
The adsorption and periplasmic uptake of extracellular dsDNA through the outer membrane is mediated through retraction of T4P, followed by translocation of long ssDNA into the cytoplasm via a conserved comEC/rec2-encoded inner membrane channel protein [39, 40] (also refer Fig 6). Bioinformatic analysis of Lcr comEC (B488_RS05330) (S2 Fig) predicted that ComEC (782 aa, 87.5 kDa) has an N-terminal domain of unknown function DUF4131 (Pfam accession PF13567) followed by a universal transmembrane competence domain (Pfam accession PF03772), an architecture commonly seen in α-Proteobacteria [40]. ComEC in Lcr and ‘Ca. Liberibacter’ spp. lacked the metallo-β-lactamase (Lactamase_B) domain (Pfam accession PF00753) responsible for the degradation of a single strand in the dsDNA that is frequently found in a broad family of DNA and RNA nucleases [39]. The DUF4131 domain (aa position 87–241) participates in oligonucleotide-binding (OB fold) and the competence domain (aa position 291–579) includes a set of core transmembrane helices mediating the transport of ssDNA across the inner membrane (S2 Fig). Topology modeling (using TMHMM-2.0) revealed that the mature ComEC was predicted to be an integral inner membrane protein with 11 transmembrane helices (aa position 61–83, 88–107, 111–133, 311–333, 353–375, 396–418, 454–476, 489–511, 526–545) and a conserved divalent metal-binding motif, GLSHIIAISGLN (aa position 311–322, containing an invariant H314) [41], embedded within the fourth transmembrane helix.
Phylogenetic analyses revealed that only truncated or cryptic homologs of comEC are found in most, if not all, ‘Ca. Liberibacter’ spp. Potentially full-length ComEC homologs were found only in the CLso strains RSTM [42] and LsoNZ1 [43], CLaf strain PTSAPSY [44] and CLam strain São Paulo [45], all containing the oligonucleotide-binding DUF4131 and the universally conserved transmembrane competence domains (S2 Fig).
Mutations in comEC affected natural transformation in L. crescens BT-1, but not motility or growth
A site-directed insertion in comEC had no effect on either swimming (1.21 ± 0.01 cm) (Fig 4D and 4F) or twitching (1.02 ± 0.01 cm) (Fig 4E and 4F) phenotypes as compared to wild-type BT-1 (1.20 ± 0.02 cm and 1.03 ± 0.01 cm, respectively). Wild-type BT-1 had an average natural transformation efficiency of about 380 ± 36 (using 1 mM chitin) and 418 ± 28 (using 0.05% xanthan gum) antibiotic resistant colonies per 500 ng of closed circular pUFR071 plasmid DNA (Fig 4G). However, mutation of comEC nearly abolished natural competence for transformation in the mutant strain (comEC::pMJ054), yielding only 2–3 transformation events under identical conditions. The full-length Lcr comEC gene rescued the natural competence phenotype in the mutant strain comEC::pMJ054/pCLL052 yielding 258 ± 20 (using 1 mM chitin) and 328 ± 24 (using 0.05% xanthan gum) antibiotic resistant colonies. Loci annotated as comEC from CLas strain psy62 [33] and CLso strain ISR100 [34] were found to be nonfunctional, yielding only 1–5 naturally transformed colonies from either pCLL053 (comEC from CLas strain psy62) or pCLL056 (comEC from CLso strain ISR100) in several independent experiments.
While mutations of Tad pilus genes cpaA, cpaB, cpaF and tadC resulted in mutant strains that were severely compromised in growth as compared to wild-type BT-1, mutation of flagellar genes (flgF and flgK) and comEC had no effect on growth in culture (Fig 4H). Addition of sheared salmon sperm DNA (10 μg ml-1 BM7A medium) did not alleviate the growth deficiency of the Tad pilus mutant strains.
The L. crescens BT-1 Tad pilus mediates uptake of extracellular dsDNA
To visualize DNA entry into Lcr cells, a 2.8 kb linear dsDNA fragment was fluorescently labelled with the noncovalent dye YOYO-1. YOYO-1 remains virtually non-fluorescent in aqueous solutions while specifically staining dsDNA by bis-intercalation at base pair to dye ratios of 1:8. After 15 min exposure to fluorescently labeled dsDNA in the presence of DNase I, 48.4 ± 4.2% of the wild-type BT-1 (Fig 5A) and 44.6 ± 4.0% of comEC::pMJ054 (Fig 5I) imported dsDNA into the cells. In contrast, cpaF::pCLL043 cells, lacking retractile Tad pili, had only transiently visible fluorescent foci (15.3 ± 5.9% and 5.9 ± 4.9% cells following DNase I treatment for 15 and 30 min, respectively) (Fig 5E and 5G). While the DNA fluorescence remained stable in wild-type BT-1 (Fig 5D) and comEC::pMJ054 (Fig 5L) cells, fluorescent foci were virtually absent in cpaF::pCLL043 cells after 45 min of DNase I treatment (Fig 5H), due to digestion of DNA outside of the cells.
(A, E and I) Overlay of bright-field and YOYO-1 florescence in Lcr wild-type BT-1, cpaF and comEC insertional mutant strains (cpaF::pCLL043 and comEC::pMJ054, respectively) exposed to YOYO-1-stained dsDNA (1 μg ml-1) for 15 min. Uptake of YOYO-1-stained fluorescent dsDNA by wild-type BT-1, cpaF::pCLL043 and comEC::pMJ054 cells after DNase I exposure for 15 min (B, F and J), 30 min (C, G and K) and 45 min (D, H and L), respectively. Fluorescent DNA foci were transiently observed in cpaF::pCLL043 cells whereas the DNA fluorescence was stable (resistant to DNase I) in wild-type BT-1 and comEC::pMJ054 cells. YOYO-1-stained dsDNA was also pretreated with DNase I for 10 min prior to starting the experiment. Magnification scale = 2 μm.
A working model illustrating the Liberibacter Tad pilus structure, function and conserved gene organization is presented in Fig 6. The data presented herein summarize the unique and critical role of the bifunctional motor ATPase CpaF and several other Tad pilus components in twitching motility and the associated periplasmic uptake and ComEC-mediated cytoplasmic translocation of environmental dsDNA in Lcr for food and natural transformation.
(A) A working model for Tad pilus-mediated uptake of extracellular dsDNA into periplasm and ComEC-mediated cytoplasmic translocation of ssDNA in naturally competent Lcr [26]. Bidirectional motor ATPase CpaF drives pilus extension and retraction via pilin polymerization and depolymerization causing both the twitching motility as well as DNA uptake. Schematic illustration of Tad pilus has been modified from Denise et al. [20]. (B) The structural components of the Tad pilus are named following Andrade and Wang [29]. Essential Tad pilus genes in Lcr encode the biogenesis ATPase (tadZ/cpaE, B488_RS06245), motor ATPase (tadA/cpaF, B488_RS06240), prepilin peptidase (tadV/cpaA, B488_RS06265), inner membrane staging complex (tadB/cpaG, B488_RS06235 and tadC/cpaH, B488_RS06230), secretin (rcpA/cpaC, B488_RS06255), periplasmatic subunits (tadG/cpaB, B488_RS06260 and rcpB/cpaD, B488_RS06250), inner membrane anchor (rcpC/tadG, B488_RS05235) and pilotin (tadD/cpaO, B488_RS05560). The genes encoding the DNA translocation machinery include dsDNA receptor (comEA, B488_RS00175), inner membrane channel protein (comEC, B488_RS05330), ATP-dependent translocase (comF, B488_RS05095), ssDNA binding proteins (ssb, B488_RS01885), DNA processing protein A (dprA, B488_RS04595) and the recombinase protein (recA, B488_RS02195). While Lcr is naturally competent for transformation, in this model, all Liberibacters are presumed to likely assimilate extracellular dsDNA as a food source. Except for comEC, rest of the Tad pilus and natural competence components are well conserved between Lcr and ‘Ca. Liberibacter’ spp. Canonical NTT domain containing nucleotide transporter proteins remain to be identified in Lcr and/or ‘Ca. Liberibacter’ spp. Abbreviations: OM, outer membrane; IM, inner membrane; PP, periplasm; CP, cytoplasm.
Discussion
Active motility and dispersal are fundamental processes that allow bacteria to intercept, explore and colonize host tissue, evade host immune responses, reduce competition for nutrient resourcing and avoid adverse niche environments. Despite significantly reduced (~1.2 Mb) genomes, all 35 sequenced strains of CLas [33], CLam [45] and CLso [2] contain a ‘minimal but complete’ and functional [27, 29, 46, 47] set of flagellar and Tad pilus biosynthetic genes. The present report provides the first empirical evidence for active flagellar swimming and Tad pilus-mediated twitching motility in Lcr, a phylogenetically related and an established surrogate host for functional genomic studies of the uncultured pathogenic ‘Ca. Liberibacter’ spp.
Ca. Liberibacter sp. flagellar genes are suppressed in planta
Innumerable ultrastructural studies of HLB pathogens within their plant hosts have failed to provide any evidence for either flagella or pili to date. Highly coordinated and regulated expression of nearly 30–100 flagellar proteins, their assembly and the rotary function imposes a steep energy drain on the bacterial cell [48]. As opposed to planktonic growth in the psyllid hemolymph, where flagella may be required, CLas and CLso colonization is strictly intracellular in planta where energy intensive flagellar swimming is likely not needed. Pathogenic ‘Ca. Liberibacter’ spp. are incapable of uptake and utilization of sucrose and scavenge ATP from host cell cytoplasm [49] and may therefore, selectively downregulate flagellar biosynthesis to avoid the associated energy drain. It is also conceivable that bacterial transmission into plant phloem cells triggers shedding of flagella, and flagellin expression is repressed as a strategy to prevent PAMP (Pathogen-associated Molecular Pattern) -associated host innate immune responses [29, 50–53].
Tad pilus-mediated twitching motility is required in both psyllid and plant hosts
Chemo- and mechanosensing of tissue surfaces, adhesive forces and the rheology of its surroundings by bacteria is facilitated through Tad pilus-mediated twitching and aggregation [15]. CLas and CLso Tad pilus genes are differentially upregulated in psyllids as compared to the plant hosts [29, 47, 54] and indicate the functional importance of Tad pilus-mediated adherence and motility in insect endosymbiosis. Replicative and circulative colonization by CLas and CLso in insect hosts requires Tad pilus mediated spatial recognition and penetration of psyllid midgut tissue, biofilm formation on the hemocoel surface of midgut, planktonic bacterial growth in the hemolymph, and finally recognition and penetration into the salivary glands’ lumen [4, 6]. Colonization of psyllid salivary glands reaching above a threshold bacterial titer is a prerequisite for efficient transmission of CLas [4] and CLso [55]. Tad pilus-mediated twitching may also explain uneven long-distance cell-to-cell movement of CLas through the plasmodesmata pore units (sieve pore/plasmodesmata complex). The observed uneven spatial and temporal distribution of CLas in citrus [56] argues against strictly passive bacterial movement via bulk symplastic solute flow within the plant hosts. Adherence of CLas to the plasma membrane of the phloem cells specifically adjacent to the sieve pores [7] lends support in favor of Tad-pilus mediated translocation across sieve pore units.
Tad pili in Ca. Liberibacter sp. are retractile and required for twitching and DNA uptake
The current dogma limits the function of Tad pili exclusively to surface adherence, and only the T4aP participate in motility and DNA uptake. Dynamic movement of T4aP in the bacterial outer membrane and periplasm is orchestrated by dedicated cytoplasmic extension (PilB) and retraction (PilT) ATPases belonging to the Additional Strand Catalytic ‘E’ (ASCE) subfamily of AAA+ ATPases [17, 23]. While PilT is dispensable for piliation [23], both PilB and PilT are required for twitching motility and natural competence [57]. PilB and PilT have no known structural or functional homologs encoded within the highly conserved Tad pilus operons of Lcr and ‘Ca. Liberibacter’ spp. Ellison et al. [24] provided the seminal evidence for retractile and dynamic C. crescentus Tad pili driven by the bidirectional activity of CpaF motor ATPase and suggested acquisition of cpaF genes across several bacterial species via widespread horizontal gene transfer events. Phylogenetic and structural similarity between Lcr and C. crescentus motor ATPase CpaF proteins (Fig 3) is consistent with Tad pili being involved in active twitching motility (Fig 4B and 4C) as well as in DNA uptake (Fig 5E–5H). These data extend the function of Tad pili beyond surface adherence in Lcr and pathogenic ‘Ca. Liberibacter’ spp.
A universal prerequisite for all natural competence systems is a structural supramolecular assemblage, such as T4a pili or Type 2 (or rarely Type 4) Secretion Systems (T2SS, T4SS) for transport of DNA across the outer membrane into periplasm and an integral DNA translocation complex for cytoplasmic transport [20]. Natural competence for transformation via uptake of both linear and circular plasmid DNA has previously been demonstrated in Lcr [26]. Adsorption, uptake and cytoplasmic translocation of extracellular dsDNA can readily be explained by a functional and retractile Tad pilus, given the absence of any other T4P or competence pili in any Liberibacter genome. To the best of our knowledge, a requirement for tad-like genes for natural transformation has earlier been shown only in the case of Micrococcus luteus [58], even though the molecular mechanism of retraction was not examined.
Tad pilus-mediated DNA uptake is essential for viability of all Liberibacters
Despite multiple attempts, we were unable to mutagenize the pilus biogenesis ATPase gene cpaE. Pilus biogenesis protein CpaE is required for efficient localization of the motor ATPase CpaF and is the first step of pilus assembly following an inside-out path [36]. Insertional mutation in the Tad pilus motor ATPase gene cpaF resulted in loss of twitching phenotype as well as severely reduced growth in culture (Fig 4B, 4C and 4H). Insertional mutants of cpaA, cpaB, cpaF and tadC were all severely compromised in growth (Fig 4H). Taken together, these data indicate that the dynamics of Tad pili and twitching phenotype are invariably associated with bacterial growth and viability. Although the bidirectional ATPase motor activity of C. crescentus CpaF was demonstrated to drive Tad pilus retraction required for surface sensing, orientation and attachment during biofilm formation [14, 24], a role of CpaF activity in uptake of extracellular dsDNA was not investigated. Both piliation and the CpaF-dependent adsorption and acquisition of extracellular dsDNA by Tad pili (Fig 5) may be crucial for Lcr growth since the enzyme systems for the metabolism of purines and pyrimidines are lacking in the highly reduced Liberibacter genomes [30]. The acquired extracellular dsDNA can be repurposed as the sole C and N source supporting microbial growth [59] or the constituent nucleotides can be salvaged for nucleic acid biosynthesis [60].
Tad pilus mediated DNA uptake is primarily for food in Liberibacters
The cpaF mutation in Lcr severely affected twitching motility (Fig 4B and 4C) and bacterial growth but had no effect on surface-restricted swimming (Fig 4A and 4C). Nonetheless, these poorly growing cpaF mutant cells (Fig 4A and 4H) exhibited an unusually enhanced swimming motility deep into 0.25% agar as compared to the wild-type BT-1 (Fig 4A) likely triggered by nutrient seeking behavior. Flagellar swimming activity is well documented to be stimulated by nutritional need [12]. Several obligate intracellular parasites with reduced genomes encode proton-energized nucleotide transporter (NTT) proteins that mediate net import of nucleotides for DNA replication and energy parasitism compensating for the loss of ATP generation and nucleotide biosynthesis [61]. Except for the nttA-encoded ATP/ADP translocase present only in ‘Ca. Liberibacter’ spp. [49], additional NTT domain containing proteins remain to be identified in Liberibacters. Comparative overview of the COG functional groups revealed 12 additional genes allocated to nucleotide transport and metabolism in CLso haplotype D as compared to Lcr [34].
ComEC mediates DNA uptake for natural competence in L. crescens BT-1
The comEC mutation in Lcr had no effect on bacterial motility functions (Fig 4D–4F) or growth (Fig 4H) but completely abolished natural competence for transformation (Fig 4G). Integral ComEC is required for mediating periplasmic DNA binding, single strand degradation to expose the other strand and passage of ssDNA across the membrane resulting in horizontal gene transfer [39] (refer Fig 6). Since only truncated or cryptic homologs of comEC are found in most, if not all, strains of ‘Ca. Liberibacter’ spp. sequenced to date (S2 Fig and Fig 4G), it is likely that natural competence is limited to only a few strains of Liberibacters, including Lcr.
Conclusions
Active bacterial motility is critical for several aspects of ‘Ca. Liberibacter’ pathogenesis, including acquisition and transmission by the insect vector as well as systemic colonization of both the insect and plant hosts. Fig 6 summarizes the dynamic activity of Tad pilus motor ATPase CpaF, a prerequisite both for motility as well as DNA uptake. We propose that the active process of Tad pilus-mediated uptake of extracellular dsDNA likely fulfills the nucleotide requirements for ‘Ca. Liberibacter’ spp. highlighting the need for externally supplied DNA and a source of ATP [49]. Nucleotide enrichment of culture media may therefore be required to overcome one of many metabolic bottlenecks for successful axenic culturing of pathogenic ‘Ca. Liberibacter’ spp. Conversely, chemical inhibition of the biosynthesis of the sole pilus in ‘Ca. Liberibacter’ spp. would adversely impact pathogen motility and nucleotide acquisition, making this pilus and its components prime targets for disease control.
Supporting information
S1 Fig. Essential motifs of Tad pilus biogenesis ATPase CpaE are conserved among all Liberibacters.
Sequence alignment of CpaE encoded by L. crescens BT‐1 (WP_015273699.1), ‘Ca. L. asiaticus’ (WP_015452437.1), ‘Ca. L. africanus’ (WP_047264074.1), ‘Ca. L. solanacearum’ (WP_103846917.1), ‘Ca. L. americanus’ (WP_144079396.1), Rhizobium spp. CRIBSB (WP_166603675.1) and Caulobacter crescentus (YP_002518411.1). Deviant ATP-binding Walker A motif is marked. Amino acids participating in ATP binding and ATPase activity are denoted by hashtag (#) and residues involved in dimer interface are denoted by dots (·). The ‘signature’ K173 residue in Lcr CpaE is expected to mediate homodimerization by binding to the phosphates of ATP engaged by the other subunit. The deviant Walker A motif of all pathogenic ‘Ca. Liberibacter’ spp. diverges further, where the ‘signature’ K residue is replaced by similar, positively charged and small sized R or H residues.
https://doi.org/10.1371/journal.pone.0258583.s001
(TIF)
S2 Fig. Alignment of ComEC sequences from L. crescens (Lcr) and ‘Ca. Liberibacter’ spp.
The following sequences were used for alignment: Lcr strain BT1 (WP_015273513.1), ‘Ca. L. asiaticus’ (Las) strains psy62 (WP_012778576.1), Ishi-1 (WP_045490146.1) and gxpsy (WP_012778576.1-like), ‘Ca. L. solanacearum’ (Lso) strains ZC1 (WP_080550987.1), RI (ONI59307.1), FIN111 (WP_076969511.1), RSTM (WP_055347849.1) and NZ1 (KJZ82350.1), ‘Ca. L. africanus’ (Laf) strain PTSAPSY (WP_052775004.1) and ‘Ca. L. americanus’ (Lam) strain Sao Paulo (AHA27693.1). The N-terminal domain of unknown function DUF4131 followed by the universal transmembrane competence domain are represented by black and red boxes, respectively. The metal-binding motif is underlined. The invariant H314 and the signal peptide cleavage sites (in Lcr) are denoted by open (△) and filled (▲) triangles, respectively.
https://doi.org/10.1371/journal.pone.0258583.s002
(TIF)
Acknowledgments
We thank Patricia Rayside for excellent technical assistance and Dr. Ofir Bahar, Agricultural Research Organization, Volcani Center, Israel for providing gDNA sample of CLso strain ISR100.
References
- 1.
Gabriel DW, Gottwald TR, Lopes SA, Wulff NA. 2019. Bacterial pathogens. In: The Genus Citrus, 1st Ed., Talon M, Caruso M, Gmitter F, eds. Woodhead Publishing, Elsevier, London.
- 2. Lin H, Lou B, Glynn JM, Doddapaneni H, Civerolo EL, Chen C, et al. 2011. The complete genome sequence of ‘Candidatus Liberibacter solanacearum’, the bacterium associated with potato zebra chip disease. PLoS One 6:e19135 pmid:21552483
- 3. Monger WA, Jeffries CJ. 2018. A survey of ‘Candidatus Liberibacter solanacearum’ in historical seed from collections of carrot and related Apiaceae species. Eur J Plant Pathol 150:803–815.
- 4. Ghanim M, Fattah-Hosseini S, Levy A, Cilia M. 2016. Morphological abnormalities and cell death in the Asian citrus psyllid (Diaphorina citri) midgut associated with ‘Candidatus Liberibacter asiaticus’. Sci Rep 6:33418. pmid:27630042
- 5. Ghanim M, Achor D, Ghosh S, Kontsedalov S, Lebedev G, Levy A. 2017. ‘Candidatus Liberibacter asiaticus’ accumulates inside endoplasmic reticulum associated vacuoles in the gut cells of Diaphorina citri. Sci Rep 7:16945. pmid:29208900
- 6. Cicero JM, Fisher T., Qureshi JA, Stansly P, Brown JK. 2017. Colonization and intrusive invasion of potato psyllid by ‘Candidatus Liberibacter solanacearum’. Phytopathol 107:36–49. pmid:27482628
- 7. Achor D, Welker S, Ben-Mahmoud S, Wang C, Folimonova SY, Dutt M, et al. 2020. Dynamics of Candidatus Liberibacter asiaticus movement and sieve-pore plugging in citrus sink cells. Plant Physiol 182:882–891. pmid:31818905
- 8. Hartung JS, Paul C, Achor D, Brlansky RH. 2010. Colonization of dodder, Cuscuta indecora, by ‘Candidatus Liberibacter asiaticus’ and ‘Ca. L. americanus’. Phytopathol 100:756–762. pmid:20626279
- 9. Levy J, Ravindran A, Gross D, Tamborindeguy C, Pierson E. 2011. Translocation of ‘Candidatus Liberibacter solanacearum’, the zebra chip pathogen, in potato and tomato. Phytopathol 101:1285–1291. pmid:21770778
- 10. Belas R. 2014. Biofilms, flagella, and mechanosensing of surfaces by bacteria. Trends Microbiol 22:517–527. pmid:24894628
- 11. Raina JB Fernandez V, Lambert B, Stocker R, Seymour JR. 2019. The role of microbial motility and chemotaxis in symbiosis. Nat Rev Microbiol 17:284–294. pmid:30923350
- 12. Kearns DB. 2010. A field guide to bacterial swarming motility. Nat Rev Microbiol 8:634–644. pmid:20694026
- 13. Craig L, Forest KT, Maier B. 2019. Type IV pili: dynamics, biophysics and functional consequences. Nat Rev Microbiol 17:429–440. pmid:30988511
- 14. Sangermani M, Hug I, Sauter N, Pfohl T, Jenal U. 2019. Tad pili play a dynamic role in Caulobacter crescentus surface colonization. mBio 10:e01237–19. pmid:31213565
- 15. Bonazzi D, Schiavo VL, Machata S, Djafer-Cherif I, Nivoit P, Manriquez V, et al. 2018. Intermittent pili-mediated forces fluidize Neisseria meningitidis aggregates promoting vascular colonization. Cell 174:143–155. pmid:29779947
- 16. Zöllner R, Cronenberg T, Kouzel N, Welker A, Koomey M, Maier B. 2019. Type IV pilin post-translational modifications modulate material properties of bacterial colonies. Biophys J 116:938–947. pmid:30739725
- 17. Piepenbrink KH. 2019. DNA uptake by type IV filaments. Front Mol Biosci 6:1. pmid:30805346
- 18. Seitz P, Blokesch M 2013. DNA-uptake machinery of naturally competent Vibrio cholerae. Proc Natl Acad Sci USA 110:17987–17992. pmid:24127573
- 19. Pelicic V. 2019. Monoderm bacteria: the new frontier for type IV pilus biology. Mol Microbiol 112:1674–1683. pmid:31556183
- 20. Denise R, Abby SS, Rocha EPC 2019. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PloS Biol 17:e3000390. pmid:31323028
- 21. Ellison CK, Kan J, Dillard RS, Kysela DT, Ducret A, Berne C, et al. 2017. Obstruction of pilus retraction stimulates bacterial surface sensing. Science 358:535–538. pmid:29074778
- 22. Tomich M, Planet PJ, Figurski DH. 2007. The tad locus: postcards from the widespread colonization island. Nat Rev Microbiol 5:363–375. pmid:17435791
- 23. Jakovljevic V, Leonardy S, Hoppert M, Søgaard-Andersen L. 2008. PilB and PilT are ATPases acting antagonistically in type IV pilus function in Myxococcus xanthus. J Bacteriol 190:2411–2421. pmid:18223089
- 24. Ellison CK, Kan J, Chlebek JL, Hummels KR, Panis G, Viollier PH, et al. 2019. A bifunctional ATPase drives Tad pilus extension and retraction. Sci Adv 5: eaay2591. pmid:31897429
- 25. Leonard MT, Fagen JR, Davis-Richardson AG, Davis MJ, Triplett EW. 2012. Complete genome sequence of Liberibacter crescens BT-1. Std Genomic Sci 7:271. pmid:23408754
- 26. Jain M, Cai L, Fleites LA, Munoz-Bodnar A, Davis MJ, Gabriel DW. 2019. Liberibacter crescens is a cultured surrogate for functional genomics of uncultured pathogenic ‘Candidatus Liberibacters’ spp. and is naturally competent for transformation. Phytopathol 109:1811–1819.
- 27. Andrade MO, Pang Z, Achor D., Wang H, Yao T, Singer BH, et al. 2020. The flagella of ‘Candidatus Liberibacter asiaticus’ and its movement in planta. Mol Plant Pathol 21:109–123. pmid:31721403
- 28. Thapa SP, De Francesco A, Trinh J, Gurung FB, Pang Z, Vidalakis G, et al. 2020. Genome wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors. Mol Plant Pathol 21:716–731. pmid:32108417
- 29. Andrade M, Wang N. 2019. The Tad pilus apparatus of ‘Candidatus Liberibacter asiaticus’ and its regulation by VisNR. Mol Plant-Microbe Interact 32:1175–1187. pmid:30925227
- 30. Hartung JS, Shao J, Kuykendall LD. 2011. Comparison of the ‘Ca. Liberibacter asiaticus’ genome adapted for an intracellular lifestyle with other members of the Rhizobiales. PloS One 6:e23289. pmid:21876745
- 31. Zhang Y, Callaway EM, Jones JB, Wilson M. 2009. Visualisation of hrp gene expression in Xanthomonas euvesicatoria in the tomato phyllosphere. Eur J Plant Pathol 124:379–390.
- 32. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM. 1995. Four new derivatives of the broad host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175–176. pmid:8529885
- 33. Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, Lin H, et al. 2009. Complete genome sequence of citrus huanglongbing bacterium, ‘Candidatus Liberibacter asiaticus’ obtained through metagenomics. Mol Plant-Microbe Interact 22:1011–1020. pmid:19589076
- 34. Katsir L, Zhepu R, Santos Garcia D, Piasezky A, Jiang J, Sela N, et al. 2018. Genome analysis of haplotype D of Candidatus Liberibacter solanacearum. Front Microbiol 9:2933. pmid:30619106
- 35. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, et al. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500. pmid:12824352
- 36. Lutkenhaus J. 2012. The ParA/MinD family puts things in their place. Trends Microbiol 20:411–418. pmid:22672910
- 37. Planet P, Kachlany SC, DeSalle R, Figurski DH. 2001. Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification. Proc Natl Acad Sci USA 98:2503–2508. pmid:11226268
- 38. Robien MA, Krumm BE, Sandkvist M, Hol WG. 2003. Crystal structure of the extracellular protein secretion NTPase EpsE of Vibrio cholerae. J Mol Biol 333:657–674. pmid:14556751
- 39. Baker JA, Simkovic F, Taylor HMC, Rigden DJ. 2016. Potential DNA binding and nuclease functions of ComEC domains characterized in silico. Proteins Struct Funct Bioinform 84:1431–1442. pmid:27318187
- 40. Pimentel ZT, Zhang Y. 2018. Evolution of the natural transformation protein, ComEC, in bacteria. Front Microbiol 9:2980. pmid:30627116
- 41. LaBrie SD, Dimond ZE, Harrison KS, Baid S, Wickstrum J, Suchland RJ, et al. 2019. Transposon mutagenesis in Chlamydia trachomatis identifies CT339 as a ComEC homolog important for DNA uptake and lateral gene transfer. mBio 10:e01343–19. pmid:31387908
- 42. Wu F, Deng X, Liang G, Wallis C, Trumble JT, Prager S, et al. 2015. De Novo genome sequence of “Candidatus Liberibacter solanacearum” from a single potato psyllid in California. Genome Announc 3:e01500–15. pmid:26679599
- 43. Thompson SM, Johnson CP, Lu AY, Frampton RA, Sullivan KL, Fiers MW, et al. 2015. Genomes of ‘Candidatus Liberibacter solanacearum’ haplotype A from New Zealand and the United States suggest significant genome plasticity in the species. Phytopathol 105:863–871. pmid:25822188
- 44. Lin H, Pietersen G, Han C, Read DA, Lou B, Gupta G, et al. 2015. Complete genome sequence of “Candidatus Liberibacter africanus,” a bacterium associated with citrus huanglongbing. Genome Announc 3:e00733–15. pmid:26184931
- 45. Wulff NA, Zhang S, Setubal JC, Almeida NF, Martins EC, Harakava R, et al. 2014. The complete genome sequence of ‘Candidatus Liberibacter americanus’, associated with citrus huanglongbing. Mol Plant-Microbe Interact 27:163–176. pmid:24200077
- 46. Cicero JM, Fisher TW, Brown JK. 2016. Localization of ‘Candidatus Liberibacter solanacearum’ and evidence for surface appendages in the potato psyllid vector. Phytopathol 106:142–154. pmid:26551449
- 47. Ibanez F, Levy J, Tamborindeguy C. 2014. Transcriptome analysis of “Candidatus Liberibacter solanacearum” in its psyllid vector, Bactericera cockerelli. PLoS One 9:e100955. pmid:24992557
- 48. Mongiardini E., Quelas JI, Dardis C, Althabegoiti MJ, Lodeiro AR. 2017. Transcriptional control of the lateral-flagellar genes of Bradyrhizobium diazoefficiens. J Bacteriol 199:e00253–17. pmid:28533217
- 49. Jain M, Munoz-Bodnar A, Gabriel DW. 2017. Concomitant loss of the glyoxalase system and glycolysis makes the uncultured pathogen “Candidatus Liberibacter asiaticus” an energy scavenger. Appl Environ Microbiol 83:e01670–17. pmid:28939611
- 50. Jain M, Munoz-Bodnar A, Zhang S, Gabriel DW. 2018. A secreted ‘Candidatus Liberibacter asiaticus’ peroxiredoxin simultaneously suppresses both localized and systemic innate immune responses in planta. Mol Plant-Microbe Interact 31:1312–1322. pmid:29953333
- 51. Shi Q, Febres VJ, Zhang S, Yu F, McCollum G, Hall DG, et al. 2018. Identification of gene candidates associated with huanglongbing tolerance, using ‘Candidatus Liberibacter asiaticus’ flagellin 22 as a proxy to challenge citrus. Mol Plant-Microbe Interact 31:200–211. pmid:29148926
- 52. Zou H, Gowda S, Zhou L, Hajeri S, Chen G, Duan Y. 2012. The destructive citrus pathogen, ‘Candidatus Liberibacter asiaticus’ encodes a functional flagellin characteristic of a pathogen-associated molecular pattern. PLoS One 7:e46447. pmid:23029520
- 53. Hao G, Pitino M, Ding F, Lin H, Stover E, Duan Y 2014. Induction of innate immune responses by flagellin from the intracellular bacterium, ‘Candidatus Liberibacter solanacearum’. BMC Plant Biol 14:211. pmid:25091183
- 54. Yan Q, Sreedharan A, Wei S, Wang J, Pelz‐Stelinski K, Folimonova S, et al. 2013. Global gene expression changes in Candidatus Liberibacter asiaticus during the transmission in distinct hosts between plant and insect. Mol Plant Pathol 14:391–404. pmid:23336388
- 55. Sengoda VG, Cooper WR, Swisher KD, Henne DC, Munyaneza JE. 2014. Latent period and transmission of “Candidatus Liberibacter solanacearum” by the potato psyllid Bactericera cockerelli (Hemiptera: Triozidae). PLoS One 9:e93475. pmid:24682175
- 56. Tatineni S, Sagaram US, Gowda S, Robertson CJ, Dawson WO, Iwanami T, et al. 2008. In planta distribution of ‘Candidatus Liberibacter asiaticus’ as revealed by polymerase chain reaction (PCR) and real-time PCR. Phytopathol 98:592–599.
- 57. Leong CG, Bloomfield RA, Boyd CA, Dornbusch AJ, Lieber L, Liu F, et al. 2017. The role of core and accessory type IV pilus genes in natural transformation and twitching motility in the bacterium Acinetobacter baylyi. PloS One 12:e0182139. pmid:28771515
- 58. Angelov A, Bergen P, Nadler F, Hornburg P, Lichev A, Übelacker M, et al. 2015. Novel Flp pilus biogenesis-dependent natural transformation. Front Microbiol 6:84. pmid:25713572
- 59. Finkel SE, Kolter R. 2001. DNA as a nutrient: novel role for bacterial competence gene homologs. J Bacteriol 183:6288–6293. pmid:11591672
- 60. Chen I, Dubnau D. 2004. DNA uptake during bacterial transformation. Nat Rev Microbiol 2:241–249. pmid:15083159
- 61. Dean P, Sendra KM, Williams TA, Watson AK, Major P, Nakjang S, et al. 2018. Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites. Nat Commun 9:1–12.
- 62. De Feyter R, Gabriel DW. 1991. Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum. J Bacteriol 173:6421–6427. pmid:1655710