2026 年 14 巻 2 号 p. 113-130
Dickeya dadantii is a destructive bacterial phytopathogen responsible for soft rot and blackleg diseases in numerous crops worldwide. Its pathogenicity depends largely on the massive secretion of cell wall-degrading enzymes via complex regulatory networks in response to environmental and host-derived signals. Previous studies have mainly examined regulatory systems and virulence factors separately at the individual level, resulting in a fragmented understanding of virulence regulation in D. dadantii. However, pathogen infection is a dynamic and stage-dependent process. Here, we propose a structured framework that organizes D. dadantii regulatory networks into four infection stages: prepenetration, penetration, infection, and colonization. In this review, the stage-based infection framework is applied to explain dynamic shifts in virulence regulation during host colonization. Furthermore, the major regulatory pathways that control virulence in D. dadantii are discussed, including quorum-sensing systems (N-acyl homoserine lactone [AHL] and virulence factor modulating [VFM]), transcriptional regulators (e.g., KdgR, PecS, and PecT), the second messenger c-di-GMP, and two-component regulatory systems. Understanding these pathways provides a foundation for the development of disease management strategies targeting virulence regulation, such as interfering with signal transduction pathways, disrupting virulence activation, suppressing virulence gene expression, and targeting quorum-sensing signaling.
Dickeya is a genus of soft-rot bacterial pathogens that cause tissue decay in plants. The genus was reclassified from Erwinia chrysanthemi based on genetic and taxonomic analyses [1]. Currently, there are 14 recognized species in the genus, including the recently described Dickeya colocasiae and Dickeya ananatis [2, 3, 4]. Dickeya dadantii, especially strain 3937, has been studied extensively as a model soft-rot pathogen owing to its well-characterized virulence mechanism [5, 6]. This bacterium infects a wide range of plants, including crops, trees, and ornamental plants, causing significant yield losses [2, 7, 8, 9].
The pathogenicity of D. dadantii relies on the coordinated production of multiple virulence factors [10]. Infection involves the extensive secretion of cell wall-degrading enzymes (CWDEs), particularly pectinases, which efficiently degrade pectin in the middle lamella and primary cell walls of plants [11, 12]. Other virulence determinants include secretion systems (T2SS, T3SS, and T6SS), quorum-sensing networks, iron acquisition systems, motility mechanisms, and secondary metabolites, collectively contributing to host tissue maceration and effective colonization [6, 14, 15, 16, 17, 18].
Virulence gene expression in D. dadantii is regulated by complex regulatory networks that integrate environmental signals during infection [18]. Consistent with this complexity, approximately 9% of the genome of D. dadantii 3937 is predicted to encode transcriptional regulators, enabling the bacterium to precisely coordinate virulence gene expression and rapidly adapt to changing environmental and host-derived signals during infection [6]. Several key regulators have been identified, including KdgR, PecS, and PecT, which modulate the expression of CWDEs and other virulence determinants [11, 13, 16, 19, 20, 21, 22]. In addition to transcriptional regulators, global regulatory systems, such as quorum sensing and the second messenger c-di-GMP, contribute to the coordination of virulence-related behaviors [23, 24, 25, 26].
Successful infection by D. dadantii involves multiple stages, including host recognition, tissue penetration, disease progression, and colonization [27]. During the initial stage of infection, D. dadantii must recognize diverse host-derived signals to locate the entry site [28]. This process relies on chemotaxis and flagellum-mediated motility, which enable bacterial cells to navigate chemical gradients released from plant tissues [20, 29]. Virulence gene expression is tightly regulated to prevent premature activation before host entry occurs [30]. Once the bacterium reaches the host surface, tissue penetration occurs via the secretion of CWDEs, leading to the degradation of plant cell walls and the release of nutrients that support bacterial growth [13, 31].
Following entry into plant tissues, D. dadantii encounters a complex and often hostile environment within the apoplast, including acidic conditions and oxidative stress generated by plant defense responses [27]. To survive these stresses, the bacterium deploys a range of adaptive strategies, including oxidative stress resistance mechanisms and metabolic pathways that facilitate survival in nutrient-limited environments [32]. As bacterial populations increase within host tissues, quorum-sensing systems coordinate the large-scale production of virulence factors, ultimately resulting in extensive tissue maceration and disease symptom development [33]. Finally, during the colonization stage, the pathogen establishes a persistent population through biofilm formation and the production of extracellular polysaccharides, supporting long-term survival within plant tissues [34].
Numerous studies have identified individual regulators and signaling pathways involved in D. dadantii virulence. However, a comprehensive understanding of how these regulatory networks coordinate virulence gene expression throughout the infection cycle is still lacking. This review aims to summarize current knowledge on the regulatory mechanisms controlling virulence in D. dadantii, with particular emphasis on transcriptional regulators, quorum-sensing systems, and second messenger signaling pathways, and to discuss how these regulatory layers contribute to the different stages of plant infection.
The prepenetration stage in D. dadantii represents the shift from environmental survival to locating potential host entry sites [27]. During this phase, the bacterium senses various environmental and host-derived chemical cues that function as chemoattractants and stimulate bacterial chemotaxis [35]. These signals activate the flagellar motility system through the FlhDC–FliA regulatory hierarchy, enabling the bacterium to move toward susceptible plant tissues [36, 37]. After reaching the host surface, initial attachment allows the cells to maintain close contact with plant tissues prior to invasion. At this stage, the bacterium prepares for host entry without yet causing extensive tissue damage, as virulence genes remain repressed to prevent premature cell wall degradation [30].
Mechanistically, the prepenetration phase begins with host sensing of plant-derived signals. Several compounds released from wounded or metabolically active plant tissues act as chemoattractants that guide bacterial movement. Among the most important cues are jasmonic acid (JA), a plant wound hormone, and xylose, a pentose sugar released during hemicellulose modification. These molecules are detected by specific chemoreceptors; for example, in D. dadantii, the candidate receptors ABF-0020167 for JA and ABF-0046680 for xylose have been identified [35]. In addition to these plant-derived signals, recent studies have revealed the role of interkingdom signaling molecules, such as acetylcholine (ACh), in the stimulation of swimming motility and early host localization [20 , 38]. In D. dadantii and D. solani, ACh is recognized with high affinity (19–92 µM) by the dCache1-type receptors DdaA [36] and MkcA [35, 39]. Notably, a ddaA mutant showed reduced competitive infectivity compared with that of wild-type D. dadantii 3937, emphasizing the critical role of DdaA-mediated chemotaxis toward ACh in plant infection and competitive fitness [38].
Signal perception is translated into directed movement through the bacterial chemotaxis system. Upon detection of attractant molecules, chemoreceptors transmit signals to the canonical CheA–CheY phosphorelay pathway [35, 40]. Activated CheY interacts with components of the flagellar motor, including FliG and FliM, thereby modulating flagellar rotation and guiding bacterial movement along chemical gradients [35, 36]. Mutations in key chemotaxis genes, such as cheW, cheB, cheY, and cheZ, significantly reduce swimming motility, highlighting the importance of this signaling pathway for host localization [36].
Bacterial movement during this stage is driven by peritrichous flagella, whose synthesis and function are controlled by the master regulator FlhDC. This regulatory complex acts as a central switch that activates the expression of genes required for flagellar assembly as well as the alternative sigma factor FliA [36, 41]. In D. dadantii strain 3937, deletion of the flhDC operon significantly reduces fliA promoter activity, confirming that FlhDC directly regulates the flagellar gene cascade [24, 37]. This regulatory hierarchy coordinates motility and chemotaxis in D. dadantii for efficient navigation toward wounded plant tissues.
Complementing this transcriptional hierarchy, the sugar transporter MfsX, a member of the Major Facilitator Superfamily, serves as a vital functional component for the physical biogenesis of the flagellar machinery in D. dadantii 3937. While FlhDC provides the regulatory command, MfsX is essential for structural assembly; mutants lacking mfsX exhibit drastic reductions in flagellin production and the number of flagellar filaments [42].
Once the bacterium reaches the plant surface, it must transition from a motile state to a stable attachment phase. Initial attachment is mediated by bacterial adhesins and the recognition of host surface receptors. During this process, D. dadantii produces cellulose fibrils, which facilitate transient adhesion to plant tissues and promote early colonization [34, 43]. Cellulose biosynthesis is regulated by the second messenger cyclic di-GMP (c-di-GMP), which functions as a key molecular switch controlling the transition between motility and sessile behavior [44].
Elevated intracellular c-di-GMP levels activate the cellulose synthase complex encoded by the bcsABCD operon. Binding of c-di-GMP to the PilZ domain of BcsA stimulates the polymerization of UDP-glucose into β-1,4-glucan chains, which are extruded across the cell envelope and assembled into cellulose microfibrils [36, 43, 45]. At the same time, c-di-GMP interacts with the flagellar brake protein YcgR, which binds to the flagellar motor and reduces rotational activity, thereby halting bacterial movement. These coordinated processes allow D. dadantii to shift from active swimming to stable surface attachment [45].
The timing of this transition is tightly regulated by several global regulatory systems. The nucleoid-associated protein Fis represses the bcs operon during early growth phases, preventing premature biofilm formation [43]. Environmental signals within the plant apoplast are also sensed by the PhoP–PhoQ two-component system, which responds to low-magnesium conditions and modulates both motility and attachment genes [46]. The synthesis of c-di-GMP in response to these host-specific cues is partially mediated by the GGDEF-domain protein AdrA, which triggers the catalytic activity of BcsA to produce cellulose fibrils [47]. In addition, the ArcBA regulatory system integrates metabolic signals, such as oxygen availability, to fine-tune biofilm formation and host colonization in D. dadantii 3937 [27, 45, 48]. However, it is important to note that in strain 3937, arcB is a pseudogene due to a nonsense mutation at codon 383, suggesting that the response regulator ArcA interacts with alternative sensor kinases or functions through non-canonical signaling routes in this strain [48].
The structural stability of the initial attachment is reinforced by the Type III Secretion System (T3SS), which is required for the formation of a stable pellicle-biofilm at the air–liquid interface. During this early interaction phase, virulence genes remain tightly controlled. The MarR-family regulator PecS represses the expression of pectate lyases and other CWDEs, celZ, the Type II Secretion System (T2SS), also known as the Out-secretion system, and the virulence factor modulating (VFM) system, preventing premature tissue maceration, which could trigger host defense responses [13, 31, 41, 49]. This regulatory strategy allows the bacterium to maintain a relatively “silent” presence on the host surface until favorable conditions for invasion are reached. This repression is relieved when PecS detects anionic lipophilic ligands, including plant-derived phenolic acids, which weaken their DNA-binding ability and act as a molecular switch that initiates virulence activation [30] (Figure 1).
In the transition from chemotaxis-driven motility to surface attachment during early host interactions, host-derived signals are detected by chemoreceptors and transduced through the CheA–CheY pathway, enabling flagella-mediated movement via the FlhDC–FliA regulatory cascade. Upon surface contact, increased intracellular cyclic-di-GMP acts as a central molecular switch that suppresses motility through the flagellar brake protein YcgR and promotes cellulose biosynthesis via BcsA, facilitating bacterial attachment and early colonization. Environmental regulators, including PhoP–PhoQ, AdrA, and ArcBA, modulate c-di-GMP signaling in response to host-associated conditions. During this stage, virulence gene expression is repressed by PecS/PecT, preventing premature CWDEs and secretion systems. Created using https://BioRender.com (→ (solid arrow): direct signaling or regulatory flow; ⊣ (inhibition line): direct repression)
During the penetration stage, D. dadantii begins the transition from surface colonization to active invasion of host tissues [5]. This transition is driven by the regulated production of CWDEs, enabling the bacterium to access the apoplast and initiate infection [5, 50, 51, 52]. Among CWDEs, pectinases play a central role in penetration because pectin is a major structural component of plant cell walls. These enzymes act sequentially to degrade the pectin matrix, thereby facilitating bacterial entry into host tissues. Pectate lyases (Pels) encoded by the pel gene family represent the most important virulence factors in D. dadantii. Several pel genes, particularly pelA, pelD, and pelE, contribute significantly to pathogenicity [5, 51, 53]. These genes encode enzymes that cleave homogalacturonan chains and release oligogalacturonides, which promote cell wall degradation and induce virulence gene expression. These enzymes are secreted through T2SS, which delivers CWDEs into the extracellular environment [40, 54, 55, 56]. This system ensures efficient enzyme deployment at the plant–bacterium interface, enabling localized pectin degradation during penetration [54].
The activation of the pectinolytic system depends on the differential expression of pel genes. pelE exhibits relatively high basal expression and likely initiates early enzymatic activity, whereas pelD is strongly inducible by pectin-derived signals and amplifies the virulence response as infection progresses [57, 58, 59]. This regulatory process is primarily controlled by KdgR, a master repressor of pectin catabolism genes. Upon pectin degradation, the intracellular accumulation of 2-keto-3-deoxygluconate (KDG) inactivates KdgR, leading to derepression of pel genes and initiation of CWDE production [10, 57, 59].
In parallel, the VFM quorum-sensing system synchronizes virulence gene expression in response to the increasing bacterial population density. Through the response regulator VfmH, this system integrates population signals with intracellular metabolic cues, including c-di-GMP and the cAMP–CRP complex, ensuring that CWDE production is coordinated with the physiological state of the pathogen [14, 51].
Additional regulators further refine this network. PecT represses multiple pel genes during early infection, preventing premature enzyme production [5]. This early repression is reinforced during the penetration stage, where the acidic environment of the plant apoplast promotes MfbR accumulation in a virulence-inactive state. Together, these regulatory mechanisms prevent the untimely expression of CWDEs, allowing the pathogen to establish a latent infection without triggering an early host immune response [41, 60, 61].
Importantly, these regulators do not function independently but operate as an integrated network that coordinates environmental sensing, metabolic status, and population density. KdgR-mediated derepression initiates the response, which is subsequently amplified and synchronized through quorum sensing and environmental feedback mechanisms. This multilayered regulation ensures that CWDE production is precisely timed, allowing the pathogen to optimize energy use while maximizing infection efficiency.
This regulatory configuration is particularly critical during the penetration stage, where the transition from surface colonization to tissue invasion requires precise temporal control of virulence activation. Together, the coordinated activity of CWDE production, T2SS-mediated enzyme secretion, and transcriptional regulation by KdgR, PecT, and MfbR enables D. dadantii to efficiently breach the plant cell wall barrier during penetration. Rather than a constitutive response, virulence activation is tightly coupled to host-derived signals, bacterial population density, and metabolic status, ensuring that enzymatic activity is deployed only under conditions that maximize infection efficiency. This regulatory precision facilitates successful host invasion and represents a critical checkpoint that governs the transition from surface colonization to aggressive tissue colonization in subsequent stages of disease development (Fig. 2a).
a) During penetration, pectin degradation by pectate lyases generates oligogalacturonides and intracellular KDG, which inactivates KdgR and derepresses pel genes, thereby promoting CWDE production and T2SS-mediated secretion for localized cell wall degradation and tissue entry. This process is further coordinated by differential pel gene expression, the VFM quorum sensing system, cyclic-di-GMP–mediated signal integration, and additional modulators, such as PecT and the pH-responsive regulator MfbR, which ensure proper timing of virulence activation. b) After entry into the apoplast, oxidative stress, iron limitation, and pH shifts activate stress-response regulators, including OxyR, RpoS, and Fur, while indigoidine and LfaR contribute to oxidative protection and fine-tuning of virulence. Together, these interconnected regulatory pathways sustain CWDE secretion, promote stress adaptation, and drive tissue maceration and bacterial spread. Created using https://BioRender.com (→ (solid arrow): direct signaling or regulatory flow; ⊣ (inhibition line): direct repression)
After penetrating host tissues, D. dadantii establishes itself in the apoplast, where it encounters multiple host-derived stresses, such as acidic conditions (pH 4.0–6.5), oxidative bursts, antimicrobial compounds, and nutrient limitation [62, 63, 64]. Under these conditions, rapid transcriptional reprogramming is required to maintain bacterial survival while sustaining virulence activity [32]. To counteract oxidative stress generated by plant immune responses, D. dadantii activates antioxidant defense systems regulated by OxyR and RpoS [39, 48, 58, 65, 66]. These regulators induce the expression of antioxidant enzymes, including catalases (KatE and KatG), superoxide dismutases (SodA and SodC), the alkyl hydroperoxide reductase AhpCF, and the ferritin-like protein Dps, which collectively detoxify ROS and protect bacterial cells from oxidative damage [6, 32, 39, 67].
In addition to enzymatic detoxification, the pathogen produces the blue pigment indigoidine, which functions as an efficient ROS scavenger and enhances bacterial survival within host tissues [5]. Indigoidine production allows D. dadantii to withstand the oxidative burst contributing to plant defense [40].
Nutrient limitation, particularly iron restriction, represents another major constraint during infection [16]. To overcome this restriction, D. dadantii activates siderophore-mediated iron acquisition systems regulated by the ferric uptake regulator Fur [39, 67]. Two major siderophores are involved in this process: achromobactin, which is produced under moderate iron limitation, and chrysobactin, which becomes predominant under severe iron deficiency [39, 68]. Under iron-limited conditions, Fur derepresses genes involved in siderophore production and transport, enabling efficient iron acquisition and supporting bacterial growth within the apoplast [67].
Environmental changes during infection, including shifts in apoplastic pH resulting from ongoing pectin degradation, further influence virulence. These changes activate MfbR, a pH-responsive transcriptional regulator that stimulates the expression of genes encoding CWDEs, such as pelA, pelB, and celA, facilitating further tissue degradation and supporting the progression of infection [60, 69, 70]. This differs from the penetration stage, where the acidic apoplast (pH 5.0–6.5) maintains MfbR in an inactive state [60].
Several two-component systems contribute to bacterial responses to fluctuating host environments [16, 39]. For example, in response to low magnesium and acidic conditions, the PhoP–PhoQ system regulates genes associated with stress tolerance and virulence [2, 46].
Recent studies have identified the role of LfaR, a member of the LacI-family transcriptional regulators, in the regulatory network controlling virulence in D. dadantii [18, 71]. Disruption of lfaR significantly increases the production of extracellular enzymes, including pectate lyases, polygalacturonases, cellulases, and proteases, and enhances traits associated with pathogenicity, such as bacterial motility and indigoidine synthesis. These findings indicate that LfaR acts primarily as a negative regulator of virulence factor expression, contributing to the precise regulation of extracellular enzyme production during infection. By inhibiting excessive virulence activation, LfaR likely helps balance bacterial proliferation with host tissue degradation during the infection process [71].
Environmental stress within the apoplast also affects DNA topology, providing an additional layer of gene regulation. Changes in DNA supercoiling influence the activity of nucleoid-associated proteins, such as FIS and H-NS, which modulate global transcriptional patterns and contribute to the coordinated regulation of virulence and stress-response genes during infection [72].
Notably, the infection process integrates diverse regulatory pathways that link stress adaptation with metabolic control and virulence maintenance. Oxidative stress responses, iron acquisition, and environmental sensing pathways are tightly interconnected, ensuring a balance between bacterial survival and sustained virulence under hostile host conditions. Together, these adaptive responses enable D. dadantii to withstand host immune defenses while preserving the metabolic flexibility needed to sustain infection. Consequently, the infection stage is a critical phase in which precise regulatory control determines the transition toward extensive tissue colonization and progressive disease development (Fig. 2b).
During the colonization stage, D. dadantii populations expand within plant tissues, requiring the coordinated regulation of community-level behaviors to support persistent infection. This stage is characterized by a high cell density, which activates regulatory systems that synchronize gene expression across the bacterial population [14, 73].
Population expansion activates the N-acyl homoserine lactone (AHL) quorum-sensing system, which regulates gene expression in a cell density-dependent manner [74]. Signaling molecules produced by the AHL synthase ExpI, primarily 3-oxo-C6-HSL (OHHL), accumulate as bacterial density increases. Once a threshold concentration is reached, these signals are detected by the transcriptional regulator ExpR, triggering coordinated expression of genes associated with colonization and community formation [33, 75, 76].
Transcript levels of expI and expR typically increase during the second half of the exponential growth phase and peak during the late exponential phase, when bacterial population densities are high [75]. At this stage, the AHL system functions primarily to coordinate the transition from individual planktonic cells to multicellular communities [33]. Although the AHL system in D. dadantii plays a relatively limited role in regulating pectinase production compared with those of other virulence regulatory pathways, it is crucial for synchronizing population-level behaviors required for long-term persistence within host tissues [74].
The AHL system induces biofilm formation, which enhances bacterial persistence within host tissues [43]. Biofilms consist of bacterial aggregates embedded within an extracellular matrix composed of polysaccharides and structural polymers [44]. In D. dadantii, biofilm formation is closely associated with c-di-GMP, which promotes cellulose production through activation of the cellulose synthase BcsA [43, 44, 51]. Cellulose fibrils, synthesized by the bcsABCD operon, provide structural stability and facilitate bacterial attachment, while additional extracellular polysaccharides contribute to matrix formation and protection against environmental stress [43, 44, 77].
The establishment of biofilms and extracellular matrix structures supports long-term bacterial survival and spread within plant tissues [78]. For example, cellulose-deficient mutants of D. dadantii display a 3.7- to 6-fold reduction in colonization ability on chicory leaves compared with that of wild-type strains [43]. These findings highlight the critical role of cellulose-based extracellular matrices in stabilizing bacterial communities and promoting persistent infection within plant tissues. These multicellular structures enhance resistance to host defense responses and allow the bacterial population to persist within the nutrient-rich environment created by earlier plant cell wall degradation [79].
As colonization progresses, coordinated enzyme activity enhances tissue maceration, releasing nutrients that support continued bacterial growth and expansion. Notably, quorum sensing, second messenger signaling, and extracellular matrix production are functionally interconnected during colonization. AHL-mediated communication coordinates population-level gene expression, while c-di-GMP signaling drives the structural organization of biofilms. This regulatory interplay ensures that community formation, nutrient acquisition, and persistence are tightly aligned during the late stages of infection. Collectively, these processes position the colonization stage as a critical phase in which population-level regulatory mechanisms drive the establishment of stable bacterial communities and facilitate widespread tissue invasion and long-term persistence (Fig. 3).
During colonization, the increasing bacterial density within plant tissues activates the AHL quorum sensing system through ExpI-produced 3-oxo-C6-HSL and its detection by ExpR, thereby coordinating population-level gene expression and promoting the transition from planktonic cells to multicellular communities. In parallel, cyclic-di-GMP stimulates cellulose biosynthesis through BcsA (bcsABCD), leading to extracellular matrix formation, biofilm development, and enhanced attachment, protection, and persistence. Nutrients released from previously macerated tissues support bacterial growth and expansion. Together, quorum sensing and c-di-GMP signaling function as interconnected regulatory systems that coordinate community formation, biofilm stability, and long-term colonization within host tissues. Created using https://BioRender.com (→ (solid arrow): direct signaling or regulatory flow; ⊣ (inhibition line): direct repression; (⇄) indicate functional interconnection or regulatory cross-talk between signaling pathways)
D. dadantii infection is regulated by a continuous and highly coordinated system, rather than discrete and independent processes [5]. Virulence expression in the pathogen is dynamically controlled by combining environmental sensing, motility control, metabolic activation, stress adaptation, and population density-based communication into an integrated regulatory network [5, 39, 57, 63, 73, 80]. This regulatory continuum begins before tissue penetration, specifically in the prepenetration phase, where bacteria detect signals originating from the host and prepare for invasion [2]. At this stage, regulatory control is dominated by a coordinated module integrating chemotaxis, motility, adhesion, and virulence repression [35]. The CheA–CheY phosphorelay system drives bacteria toward host-derived chemical gradients, while the FlhDC–FliA hierarchy controls flagella production and motility [35, 36, 81]. Structural components, such as MfsX, contribute to flagellar assembly and functionality, supporting this motility system [42]. Intracellular cyclic-di-GMP suppresses flagellar rotation and activates cellulose production to switch bacteria from motility to adhesion when they approach the host surface [12, 40, 48, 51]. Transcriptional regulators, such as PecS, suppress CWDEs, retaining the metabolic activity of bacteria without exerting destructive effects. Collectively, these regulators form an integrated pre-infection module that prepares the bacterium for host contact [13, 30, 31, 82, 83]
This “ready” state is directly linked to the next layer of regulation at the penetration stage, where metabolic sensing becomes the primary driver of virulence activation. Initial degradation of plant cell wall components produces intracellular metabolites, including KDG, which inactivates the KdgR repressor and activates pectinase enzymes [19, 58, 40]. Pectinase enzyme activation results from the integration of several regulators, including KdgR, working simultaneously. PecT continues to suppress the expression of virulence genes at the early stage to prevent premature enzyme production. MfbR regulates gene expression in response to changes in environmental conditions, including the apoplastic pH during pectin degradation; in particular, pelA is uniquely induced by the initial acidic stress of the apoplast, promoting pectin degradation during the early stages of infection [22, 84, 85,]. Additionally, the quorum-sensing system, particularly through the VFM system and VfmH regulator, begins to synchronize gene expression with the bacterial population density and integrate metabolic signals with the physiological status of the cell through intracellular signaling molecules, such as c-di-GMP and the cAMP–CRP complex [21, 51]. Thus, the penetration stage represents a convergence point involving the initial integration of metabolic signals, transcriptional regulation, environmental conditions, and intercellular communication, resulting in spatially and temporally controlled virulence activation to support efficient tissue invasion.
As the infection progresses within the plant tissue, the regulatory network expands by incorporating stress response pathways, which are functionally integrated with metabolic and virulence systems. Within the apoplast, oxidative stress, nutrient limitations, and fluctuating physicochemical conditions [32, 63] are detected and coordinated by global regulators, such as OxyR, RpoS, Fur, and MfbR, which control antioxidant defenses, iron homeostasis, and metabolic activity. These stress response pathways do not operate independently but rather reinforce and refine the virulence program that was initiated at the penetration stage, allowing the bacteria to maintain infection under unfavorable host conditions [5, 28, 48].
As bacterial population density increases, quorum sensing is introduced as an additional regulatory layer that synchronizes gene expression across the population [80]. The ExpI–ExpR system mediated by AHL enhances the production of virulence factors and coordinates collective behavior, thereby increasing the efficiency of processes initially triggered by metabolic signals [33, 76, 78]. Simultaneously, cyclic-di-GMP continues to function as a cross-stage integrator by promoting biofilm formation and extracellular matrix production, thereby linking early adhesion mechanisms with later-stage persistence and structural organization [2, 40].
Importantly, these regulatory systems are interconnected through multiple feedback mechanisms and shared signaling pathways [23]. Metabolic activity influences intracellular signaling molecules, stress conditions modulate transcriptional regulators, and quorum sensing reinforces previously activated pathways [10, 55]. Therefore, infection by D. dadantii should be viewed as a continuum of regulation, rather than a series of linear events. Each stage is not defined by isolated mechanisms but by the dynamic integration of multiple regulatory inputs that continuously adjust to the host's conditions. This layered coordination allows bacteria to balance growth, survival, and virulence, which ultimately determines the success of infection.
Thus, the pathogenicity of D. dadantii depends on the integration of various key regulatory nodes, including the chemotaxis and motility system (Che–FlhDC–MfsX), intracellular signaling molecules (c-di-GMP), transcriptional repressors and activators (PecS/PecT and KdgR), global stress regulators (OxyR, RpoS, and Fur), and the quorum-sensing system (ExpI/ExpR), into a coherent and adaptive network [5, 10, 13, 16, 19, 30, 31, 33, 35, 36, 39, 42, 57, 60, 61, 80, 81, 84, 85]. This cross-stage regulatory architecture highlights critical control points that could potentially be targeted to inhibit disease progression (Table 1).
| Regulatory node | Input | Target | Outcome | Reference |
|---|---|---|---|---|
| CheA-CheY system |
Host-derived chemoattractants (JA, xylose, Ach, Nitrate) | Flagellar motor (FliG, FliM); Flagellar rotation machinery (via CheY-P) |
Directed chemotaxis toward host tissues | [11, 36, 87] |
| FlhDC–FliA | Plant-derived chemical gradients (via CheA–CheY system) | fliA, fliC, motility genes, Flagellar gene cascade; flhDC → fliA (σ28) → fliC, motA/B | Flagellar biosynthesis, motility activation and host localization | [11, 43, 44] |
| MfsX | Cellular metabolic state; Surface/contact signals; | Flagellar assembly machinery | Proper flagellar biogenesis and motility efficiency, Functional flagella formation | [88] |
| c-di-GMP | Environmental signals, surface contact, nutrient status | bcsABCD operon (synthesis cellulose), YcgR (rem flagella) | Transition from motility to adhesion; cellulose production; Motility inhibition and cellulose-mediated attachment Switch from motility → attachment/biofilm |
[89] |
| AdrA (GGDEF protein) | Host environmental signals | c-di-GMP synthesis | Activation of cellulose production | [47] |
| Fis | Growth phase signals | bcs operon | Repression of premature biofilm formation | [43] |
| PecS | Absence of plant-derived inducers | CWDE genes (pel, cel, T2SS, VFM) | Repression of virulence during prepenetration | [11, 64] |
| KdgR | KDG (pectin degradation product) | pel genes CWDEs (pectate lyases), kdu, kdg genes | Derepression of CWDEs and initiation of tissue maceration; Activation of pectin degradation and invasion | [11, 55] |
| PecT | Early infection signals | pel genes | Prevention of premature CWDE production | [5] |
| VFM system (VfmH) | Population density + metabolic signals | Virulence gene network, including pectate lyases (Pels), CWDEs | Coordinates virulence factor expression in response to population density and environmental cues | [14, 21, 51] |
| cAMP–CRP | Carbon availability / metabolic status | CWDE genes, and metabolic genes | Links carbon availability and metabolic status to virulence gene regulation; Activation of virulence under nutrient limitation | [14, 51] |
| MfbR (cross-stage regulator) | Apoplastic pH changes, environmental cues | pel genes and virulence regulators | Fine-tuning of virulence expression across stages | [22, 84] |
| OxyR | Oxidative stress (ROS) | Antioxidant genes (kat, sod, ahp) katG, ahpC | Protection against oxidative damage | [32, 39] |
| RpoS (σS) | General stress signals ( nutrient limitation, host environment) | Stress-response genes | Survival under host stress conditions | [39] |
| Fur | Iron limitation | Siderophore biosynthesis genes | Iron acquisition and growth in host tissues | [67, 90] |
| PhoP–PhoQ | Low Mg²⁺, acidic pH | Stress response and virulence genes Motility and virulence genes |
Adaptation to apoplastic conditions | [2, 46] |
| LfaR | Intracellular metabolic signals | CWDE and motility genes | Negative regulation of virulence (fine control) | [71] |
| ExpI–ExpR (AHL system) | High cell density (AHL accumulation) | Population-level gene expression; pel, prt, cel, hrp genes; biofilm genes | Coordination of collective behavior and persistence | [74, 75] |
| c-di-GMP | High c-di-GMP (Colonization stage) QS + environmental signals; surface attachment |
Biofilm matrix genes (cellulose, EPS) | Promotes biofilm formation and long-term colonization | [43, 44, 51, 89] |
| ArcA / ArcBA | Oxygen availability | Biofilm and metabolic genes | Regulation of colonization and energy adaptation | [45, 48] |
| DNA supercoiling (FIS / H-NS) | Environmental stress | Global transcription | Fine-tuning of virulence and stress genes | [72] |
Several regulators such as c-di-GMP, MfbR, and quorum sensing systems function as cross-stage integrators, linking early host sensing with later-stage persistence and population-level coordination.
The regulatory complexity underlying D. dadantii pathogenesis provides a strong foundation for the development of virulence-targeting disease management strategies. Rather than targeting bacterial viability, these approaches aim to disrupt key regulatory nodes that control virulence activation, thereby reducing pathogenicity while minimizing selective pressure for resistance. Central regulatory systems, including KdgR-mediated metabolic sensing, OxyR-dependent oxidative stress responses, and quorum-sensing pathways, represent critical intervention points [2, 5, 10, 19]. Disrupting these systems can impair the precise coordination required for successful infection. For example, interference with quorum sensing can disrupt the coordination of population-level responses, reducing the efficiency of virulence factor production and biofilm formation. Targeting intracellular signaling pathways, such as cyclic-di-GMP, can destabilize the transition between motility, attachment, and persistence, ultimately compromising bacterial fitness within host tissues. Targeting early-stage regulatory mechanisms governing CWDE production may prevent the timely activation of tissue invasion, effectively blocking disease progression [23, 44, 51, 86].
These strategies reflect a broader shift toward sustainable plant disease management, where modulation of pathogen behavior is prioritized over eradication. Approaches such as quorum quenching, the use of plant-derived signaling inhibitors, and the application of beneficial microorganisms offer promising avenues to interfere with pathogen regulatory networks in an environmentally sustainable manner.
Despite these advances, a major challenge remains in translating mechanistic insights into effective field applications. In particular, the dynamic behavior of regulatory networks in planta and responsiveness to complex environmental conditions are not yet fully understood. Future research should focus on identifying robust regulatory nodes that remain effective under field conditions and on elucidating how regulatory pathways interact across infection stages. Overall, targeting the regulatory architecture of virulence represents a promising and sustainable strategy for controlling soft-rot diseases caused by D. dadantii, shifting the focus from pathogen elimination to functional disarmament.
Plant pathogenic bacteria, such as D. dadantii, rely on extensive transcriptional flexibility to coordinate virulence across different stages of infection. Rather than being governed by isolated regulatory events, metabolic sensing, stress adaptation, and population-level communication are progressively integrated to determine pathogenesis. This stage-dependent reprogramming allows the bacterium to precisely control the timing and intensity of virulence factor expression in response to changing host conditions.
Central to this process is the coordinated activity of multiple regulatory systems, including metabolic regulators such as KdgR, global repressors such as PecS and PecT, quorum-sensing systems (AHL and VFM), and stress-responsive regulators. These elements do not operate independently but form a multilayered regulatory architecture in which host-derived signals, intracellular metabolic status, and bacterial population density converge to modulate virulence expression. This integration ensures that energetically costly processes, such as CWDE production, secretion, and biofilm formation, are activated only under conditions that maximize infection efficiency and bacterial survival.
The interplay between virulence regulation and metabolic adaptation represents a key feature of D. dadantii pathogenesis. The coupling of pectin degradation with nutrient acquisition highlights how regulatory networks coordinate both host tissue breakdown and resource utilization. This tight linkage enables the bacterium to continuously adjust its infection strategy in response to environmental fluctuations within host tissues.
These insights provide a conceptual framework for developing novel disease management strategies based on the disruption of virulence regulation rather than direct bacterial elimination. Targeting key regulatory nodes, including quorum-sensing systems, metabolic regulators, and signaling pathways, may offer promising avenues for reducing pathogenicity while limiting the development of resistance. Future research should therefore focus on elucidating cross-stage regulatory interactions, validating these mechanisms in planta, and identifying effective strategies to interfere with regulatory network coordination.
Overall, understanding the dynamic and integrated nature of virulence regulation in D. dadantii advances our knowledge of soft-rot pathogenesis and provides a foundation for the development of more sustainable and targeted approaches to disease control.
TW: Conceptualization, Investigation, Writing – original draft. HH: Resources, Writing – review & editing. TJ: Resources. NO: Conceptualization, Supervision.
We thank Edanz ( https://jp.edanz.com/ac) for editing a draft of this manuscript.
