{ "checked": "2026-10-05", "questions": [ { "id": "g1-s-transition-trigger", "theme": "cell-cycle", "title": "What triggers and times the swarmer-to-stalked (G1→S) transition", "question": "What upstream cue sets the length of G1 and triggers the swarmer-to-stalked cell transition in *Caulobacter*?", "known": "Leaving G1 requires clearing active CtrA~P. PleC switches from phosphatase to kinase and, with DivJ, phosphorylates DivK and PleD; c-di-GMP then rises, drives the ShkA–TacA program and flips CckA to phosphatase mode, and CtrA is degraded. PodJ binding restrains PleC kinase; (p)ppGpp and high dNTP pools lengthen G1, while pilus-sensed surface contact shortens it.", "open": "What starts the cascade on time in an unperturbed swarmer cell (what releases the brief PleC kinase pulse and the c-di-GMP rise), and whether G1 length is read from cell size, metabolic state or an internal timer, is unresolved.", "whyItMatters": "G1 length sets the swarmer/stalked make-up of a population and is the main point where *Caulobacter* couples its cell cycle to nutrients and surfaces.", "status": "partly answered", "statusNote": "2024 work shows PodJ restrains PleC kinase to time differentiation, and a 2025 study adds dNTP hydrolysis (FssC) as a G1-exit input, but no single upstream trigger has been identified.", "refs": [ "10.1038/nature14473", "10.1038/s41467-020-14585-6", "10.1073/pnas.1920291117", "10.1128/mbio.02125-23", "10.1073/pnas.2406397121", "10.1128/jb.00145-25" ], "related": { "network": [ "PleC", "DivJ", "DivK", "PleD", "c-di-GMP", "CckA", "CtrA", "PodJ", "ClpXP" ], "pathways": [ "c-di-GMP-signaling" ] }, "tier": "primary" }, { "id": "dnaa-licensing-and-growth-coupling", "theme": "cell-cycle", "title": "How DnaA is licensed once per cycle and coupled to growth", "question": "How is DnaA activity licensed exactly once per cycle at the G1→S transition and scaled to cell growth and nutrient supply?", "known": "Replication starts at *Cori* only after CtrA~P is cleared and DnaA has accumulated. DnaA levels are set by translation, including a nascent-peptide element in *dnaA* that slows elongation on carbon starvation, and by Lon proteolysis. After initiation the replisome-associated HdaA inactivates DnaA (RIDA) and targets it for degradation; HdaB counteracts RIDA in stationary phase.", "open": "Which input limits initiation timing in steady growth (total DnaA, its ATP-bound fraction, or CtrA removal from *Cori*) is unresolved, as is how initiation is coupled to cell mass or growth rate in *Caulobacter*.", "whyItMatters": "Initiating once and only once per cycle is essential for viability, and the coupling explains how nutrient supply sets the rate of proliferation.", "status": "open", "statusNote": "A 2024 review states that the exact molecular mechanisms linking cell growth with replication initiation under different nutrient conditions remain elusive; starvation controls are better understood.", "refs": [ "10.1016/j.bbagrm.2018.01.004", "10.1042/BST20180460", "10.7554/eLife.71611", "10.1093/nar/gkz1193", "10.1371/journal.pgen.1010882", "10.1016/j.mib.2023.102403" ], "related": { "network": [ "DnaA", "CtrA", "Cori", "Lon" ], "pathways": [ "stress-responses" ] }, "tier": "primary" }, { "id": "ccka-kinase-phosphatase-switch", "theme": "cell-cycle", "title": "How CckA is switched between kinase and phosphatase at each pole", "question": "How do DivL, DivK~P, c-di-GMP and the polar microdomain combine to set CckA's kinase or phosphatase mode at each cell pole?", "known": "CckA, via ChpT, is the phosphate source for CtrA. The pseudokinase DivL recruits and activates CckA at the new pole; DivK~P inhibits CckA by binding DivL, and c-di-GMP binding pushes CckA into phosphatase mode. On liposomes DivL toggles CckA directly through its second PAS domain, and the PopZ microdomain concentrates CckA, ChpT and CtrA.", "open": "How DivK~P binding to DivL is transmitted to CckA structurally, and how DivL, c-di-GMP and CckA clustering are weighed against each other in living cells to fix each pole's mode, are not established.", "whyItMatters": "This switch decides which daughter keeps active CtrA, so it encodes the different fates of the swarmer and stalked cells.", "status": "partly answered", "statusNote": "2018 reconstitution and 2020 single-molecule work on polar sequestration explain much of the logic, but a structural mechanism for DivL control of full-length CckA in vivo is still lacking.", "refs": [ "10.1073/pnas.1001767107", "10.1016/j.devcel.2011.01.007", "10.1038/nature14473", "10.1126/sciadv.1600823", "10.1073/pnas.1808543115", "10.1038/s41564-019-0647-7" ], "related": { "network": [ "CckA", "DivL", "DivK", "ChpT", "CtrA", "c-di-GMP", "PopZ" ], "pathways": [ "c-di-GMP-signaling" ] }, "tier": "secondary" }, { "id": "popz-condensate-state-and-clients", "theme": "spatial-organization", "title": "PopZ condensate: material state in cells and client selection", "question": "What is the material state of the PopZ polar condensate in living cells, and how does it select and time its many client proteins?", "known": "PopZ forms ribosome-excluding condensates at the poles. Entry is selective and needs a PopZ-binding route; a helical oligomerization domain and a disordered region tune material properties, and only a narrow range supports division. PopZ assembles into filaments that condense and expose client sites; access can be gated, e.g. by CpdR phosphorylation or by ParA arrival recruiting ChpT.", "open": "Whether PopZ behaves in cells as a liquid, gel or filament network, and the general rules by which many clients with different timing compete for, or are kept out of, the microdomain are unclear.", "whyItMatters": "PopZ is a model bacterial membraneless organelle; its rules govern polar signaling, chromosome anchoring and asymmetric division.", "status": "partly answered", "statusNote": "A 2026 study links PopZ's filamentous ultrastructure to its function and 2024 work shows phospho-gating of CpdR binding, but material state in vivo and general client rules remain open.", "refs": [ "10.1038/s41564-019-0647-7", "10.1038/s41467-022-33221-z", "10.1016/j.jmb.2021.167423", "10.1038/s41594-025-01742-y", "10.1038/s41467-024-53395-y", "10.1016/j.devcel.2021.06.014" ], "related": { "network": [ "PopZ", "CpdR", "ChpT", "CckA", "CtrA", "ClpXP" ], "pathways": [ "chromosome-segregation" ] }, "tier": "primary" }, { "id": "new-pole-identity", "theme": "spatial-organization", "title": "How new-pole identity is set at division and inherited", "question": "What first marks the nascent pole at division, and how is that identity carried into the next cell cycle?", "known": "TipN and TipF go to the septum and newborn pole after cytokinesis; without TipN, progeny size asymmetry is often reversed and flagella form at ectopic sites. PodJ binds PopZ to trigger its new-pole accumulation, SpmX bridges PopZ to DivJ at the stalked pole, and PodJ forms condensates that SpmX restrains.", "open": "Which factor supplies the primary symmetry-breaking cue at the septum, how the partly redundant markers (TipN, PodJ, PopZ and others) are ordered in a hierarchy, and what provides polarity cues when they are missing remain unresolved.", "whyItMatters": "Pole identity decides which daughter builds the flagellum and which the stalk, so it underlies every asymmetric fate decision.", "status": "partly answered", "statusNote": "2023 work identifies PodJ–PopZ binding as a primary trigger for new-pole PopZ, and a 2023 Turing-pattern model reproduces scaffold asymmetry, but the initial septal cue is still undefined.", "refs": [ "10.1016/j.cell.2005.12.040", "10.1016/j.cell.2006.01.019", "10.1128/mBio.02238-16", "10.1038/s41467-022-35000-2", "10.1128/mbio.03218-22", "10.1016/j.isci.2023.106513" ], "related": { "network": [ "PopZ", "PodJ", "SpmX", "DivJ", "PleC" ] }, "tier": "primary" }, { "id": "chromosome-segregation-forces", "theme": "chromosome", "title": "What moves the chromosome beyond the ParABS centromere", "question": "What moves the bulk of the replicated chromosome, and how does ParA generate directed force on the centromere?", "known": "After replication one *parS* centromere is released from PopZ at the stalked pole and moved by ParA–ParB to the new pole, with TipN helping keep direction. Loci then move in replication order to set cell positions. Proposed ParA mechanisms include a DNA relay using chromosome elasticity and a polymer ratchet; replication itself appears to supply extra force.", "open": "Whether DNA far from *parS* follows passively (entropic demixing, extrusion by replication) or needs active machinery, and which ParA mechanism operates in vivo, remain debated.", "whyItMatters": "Faithful segregation of the single chromosome is essential, and *Caulobacter* is a key test case for ParA-based transport used by many bacteria.", "status": "partly answered", "statusNote": "2024 work shows that without replication TipN becomes essential for ParA to move *parS*, pointing to replication as one ParABS-independent force; bulk-DNA mechanics remain unresolved.", "refs": [ "10.1073/pnas.0402606101", "10.1038/ncb2083", "10.1111/j.1365-2958.2011.07899.x", "10.7554/eLife.02758", "10.1093/nar/gkad982", "10.1091/mbc.E23-12-0503" ], "related": { "network": [ "PopZ" ], "pathways": [ "chromosome-segregation" ] }, "tier": "primary" }, { "id": "smc-arm-alignment", "theme": "chromosome", "title": "How SMC aligns the two chromosome arms", "question": "By what mechanism does SMC align the left and right chromosome arms, and how does that alignment aid segregation?", "known": "Hi-C shows the chromosome folds into largely independent domains, with the two arms running side by side along the cell; SMC is needed for this arm co-linearity. SMC is recruited at *parS* in a ParB-dependent way, and highly expressed genes oriented against its path disrupt alignment, consistent with SMC moving away from *parS*.", "open": "Whether *Caulobacter* SMC aligns arms by loop extrusion from *parS*, by tethering the parS-proximal arms, or both has not been shown directly, and how alignment contributes to segregation is unclear.", "whyItMatters": "Arm alignment is a widespread bacterial folding pattern; it shapes replisome behaviour and segregation, linking genome architecture to the cell cycle.", "status": "open", "statusNote": "2021 data-driven models link chromosome extensions to loop-extrusion activity and 2024 work shows alignment shapes replisome pairing, but a direct mechanistic test in *Caulobacter* is lacking.", "refs": [ "10.1126/science.1242059", "10.1016/j.celrep.2017.08.026", "10.1038/s41467-021-22189-x", "10.1038/s41467-024-47849-6" ], "related": { "pathways": [ "chromosome-segregation" ] }, "tier": "secondary" }, { "id": "sister-replisome-organization", "theme": "chromosome", "title": "What organizes and positions the sister replisomes", "question": "Are *Caulobacter*'s sister replisomes held together by a physical linker, and what positions them as replication proceeds?", "known": "The replisome assembles at the origin at the stalked pole and moves toward midcell as replication proceeds, apparently untethered and pushed by new DNA. Live tracking of the β-clamp shows sister replisomes can stay together or split; arm alignment and arm-specific replication–transcription conflicts shape this, and fast segregation can create replisome-like foci.", "open": "Whether any protein linker couples sister replisomes, and what physically sets their position along the cell axis, remain unresolved.", "whyItMatters": "Replisome layout governs how replication, segregation and transcription share one compact chromosome; a single round per cycle makes *Caulobacter* a clean model.", "status": "partly answered", "statusNote": "A 2024 tracking study explains colocalization and splitting by chromosome organization rather than a fixed tether, and 2025 work adds nutrient control of fork speed; a linker has not been directly tested.", "refs": [ "10.1093/emboj/20.17.4952", "10.1038/s41467-024-47849-6", "10.1016/j.cub.2025.03.009" ], "related": { "network": [ "DnaA" ], "pathways": [ "chromosome-segregation" ] }, "tier": "secondary" }, { "id": "cell-size-homeostasis-mechanism", "theme": "division-growth", "title": "Cell-size homeostasis: which rule, and which molecules", "question": "What molecular mechanism implements size homeostasis in *Caulobacter*, and is it best described as an adder, a size-proportional timer, or a mixed rule?", "known": "Single-cell studies agree size is tightly controlled but describe it differently: a constant size added per cycle (adder), division at a fixed multiple (~1.8) of birth size, and a 'mixer' with a timer-like phase before constriction and an adder phase during it. Constriction rate also compensates for size variation.", "open": "Which molecules implement the rule is unknown, and the phenomenological descriptions (adder, multiplicative timer, mixer) have not been reconciled across growth conditions and devices.", "whyItMatters": "Size control is a basic property of all cells; asymmetrically dividing *Caulobacter* tests whether rules found in symmetric dividers like *E. coli* generalize.", "status": "open", "statusNote": "A 2025 preprint reports that ATP-bound DnaA restrains size via the cell-wall enzyme MurD, and 2025 stochastic theory fits size data, but no mechanism has been shown to set the rule.", "refs": [ "10.1073/pnas.1403232111", "10.1016/j.cell.2014.11.022", "10.1038/nmicrobiol.2017.116", "10.1016/j.isci.2018.05.020", "10.1101/2025.02.22.639668", "10.1103/vfhg-gksh" ], "related": { "network": [ "DnaA", "ftsZ" ], "pathways": [ "division-site" ] }, "tier": "primary" }, { "id": "asymmetric-size-partitioning", "theme": "division-growth", "title": "What sets the division plane and the daughter-size ratio", "question": "How does *Caulobacter* place its division site and keep the swarmer-to-stalked daughter size ratio constant?", "known": "MipZ, bound to ParB at the polar origins, forms bipolar gradients that block FtsZ assembly near the poles, so the Z-ring forms in the cell interior; MipZ caps FtsZ polymer ends, and ZapT links the Z-ring to the replication terminus. Swarmer daughters are smaller, and errors in division-site position are corrected early by differential growth of the two compartments.", "open": "How the MipZ gradient is shaped to give the correct asymmetric plane, and what molecular 'growth regulators' make the larger compartment grow more slowly, are unknown.", "whyItMatters": "Size asymmetry gives the two daughters different G1 lengths and fates, tying division geometry to development.", "status": "partly answered", "statusNote": "A 2024 study shows negative feedback between compartment size and growth rate and proposes partitioned growth regulators, but their identity is untested.", "refs": [ "10.1016/j.cell.2006.05.038", "10.1016/j.jtbi.2017.08.011", "10.1128/mBio.00487-20", "10.1073/pnas.2208227119", "10.26508/lsa.202402591" ], "related": { "network": [ "MipZ", "ftsZ" ], "pathways": [ "division-site" ] }, "tier": "secondary" }, { "id": "crescentin-curvature", "theme": "division-growth", "title": "How crescentin curves the cell, and why curvature persists", "question": "How does the crescentin filament bias cell-wall growth to curve the cell, and what advantage maintains curvature in the wild?", "known": "Crescentin, an intermediate-filament-like protein encoded by *creS*, forms a non-polar filament band along the inner (concave) membrane; without it cells are straight. It creates an elongation-rate gradient across the sidewall, apparently via mechanical strain, and can curve *E. coli*. Curvature aids surface colonization under flow and plant-growth promotion.", "open": "How strain in the filament is translated into slower cell-wall growth on the concave side is unknown, and whether flow or other pressures explain why curvature is kept in nature is unsettled.", "whyItMatters": "Crescentin is the founding bacterial intermediate-filament-like protein and a model for how cytoskeletal mechanics shape a cell.", "status": "partly answered", "statusNote": "A 2024 cryo-EM study solved the filament structure and its in-cell band, and a 2025 phylogenomic study traced crescentin's evolution, but the growth-biasing mechanism remains unknown.", "refs": [ "10.1016/s0092-8674(03)00935-8", "10.1038/emboj.2009.61", "10.1038/ncomms4824", "10.1073/pnas.2309984121", "10.1038/s41467-025-65642-x", "10.1371/journal.pone.0249227" ], "tier": "secondary" }, { "id": "stalk-function", "theme": "development", "title": "What the Caulobacter stalk is for", "question": "Is the stalk mainly a nutrient-scavenging antenna, and if not, what advantage explains why cells build it?", "known": "The stalk is a thin extension of the cell envelope that stays short in rich medium but grows up to ~30 µm under phosphate starvation. Stalks carry nutrient-binding and -hydrolysing proteins such as PstS, but not the transporter subunit PstA. Protein diffusion barriers block membrane and periplasmic proteins from moving between stalk and cell body. The holdfast at the stalk tip anchors cells to surfaces.", "open": "Nobody has measured in living cells whether phosphate or other nutrients captured in the stalk reach the cell body at a useful rate across the barriers. The other roles proposed since the barriers were found have not been tested side by side.", "whyItMatters": "The stalk is the textbook case of a bacterial shape with a proposed job. Testing that job is a direct test of how well cell shape can be linked to fitness.", "status": "open", "statusNote": "Klein et al. (2013) wrote that the antenna model \"must be revisited\" once the diffusion barrier was found; no direct in vivo test of uptake through the stalk has been published since (literature checked October 2026).", "refs": [ "10.1073/pnas.0602047103", "10.1046/j.1365-2958.2002.03071.x", "10.1016/j.cell.2012.10.046", "10.4161/cib.24561", "10.1016/j.mib.2025.102661" ], "related": { "pathways": [ "stalk-biogenesis" ] }, "tier": "primary" }, { "id": "holdfast-chemistry", "theme": "development", "title": "Holdfast chemistry, export and the source of its adhesive strength", "question": "What is the full chemical structure of the holdfast, how is it exported, and what gives it its exceptional strength as a wet adhesive?", "known": "The holdfast is a polar adhesin made by the *hfs* genes, secreted with HfsDAB help, and anchored at the stalk tip by an HfaA/B/D complex (plus HfaE) that spans the outer membrane. Extracts contain glucose, 3-O-methylglucose, mannose, N-acetylglucosamine and xylose. Force microscopy shows a stiff core inside a flexible brush, and peptides and DNA are also present.", "open": "The repeating unit and its linkages are not fully solved. Where the peptide signal comes from is unknown, because genetic screens have found no pathway for it. HfsDAB export has no structural model, and which chemical groups make the bond so strong is still hypothesis.", "whyItMatters": "Holdfast is among the strongest biological adhesives ever measured. Knowing its chemistry would explain bacterial wet adhesion and could guide the design of underwater glues.", "status": "partly answered", "statusNote": "The sugars and a 1,4-linked backbone model were reported in 2019. A 2020 spectroscopy study proposed peptide cross-links from an unknown pathway; HfaE joined the anchor in 2022. No full structure exists.", "refs": [ "10.1128/mBio.02359-17", "10.1128/JB.00276-19", "10.1128/mBio.02273-18", "10.1128/JB.00112-19", "10.1021/acs.biochem.0c00625", "10.1128/jb.00273-22" ], "related": { "pathways": [ "pili-holdfast-adhesion" ] }, "tier": "secondary" }, { "id": "surface-sensing-integration", "theme": "development", "title": "How pilus and flagellum signals combine during surface sensing", "question": "How are mechanical signals from Tad pili and the flagellar motor turned into holdfast synthesis and faster cell-cycle progression, and what is the actual sensor?", "known": "When a pilus touches a surface it stops retracting, and that resistance triggers holdfast synthesis within seconds. The flagellar motor senses contact too: its stator-linked cyclase DgcB makes c-di-GMP, which activates the glycosyltransferase HfsJ. Blocking pili raises c-di-GMP through cell-fate kinases and starts replication early. Flagellar defects signal through routes that depend on PleD and on the stator.", "open": "The mechanosensor has not been identified, and the minor pilin CpaL is only a candidate. Two models of pilus signalling disagree: one says obstructed retraction is the signal, the other that PilA in the inner membrane is sensed. How pilus, stator and chemotaxis inputs are weighed against each other is unknown.", "whyItMatters": "Surface sensing is the first step of biofilm formation. Caulobacter is one of few systems where pilus and flagellar mechanosensing can be studied in the same cell.", "status": "partly answered", "statusNote": "2025: deleting the minor-pilin-like gene *cpaL* switched on surface sensing without contact, making CpaL a candidate sensor. 2021: flagellar signals act through two pathways. The mechanism is still open.", "refs": [ "10.1126/science.aan5706", "10.1126/science.aan5353", "10.1073/pnas.1920291117", "10.1073/pnas.1920143117", "10.1128/mBio.03266-20", "10.1128/mbio.02302-25" ], "related": { "network": [ "c-di-GMP", "DgcB", "PleD", "PleC", "pilA" ], "pathways": [ "pili-holdfast-adhesion", "c-di-GMP-signaling", "flagellum-chemotaxis" ] }, "tier": "secondary" }, { "id": "nutrient-replication-coupling", "theme": "stress-physiology", "title": "How nutrient status is wired into the start of replication", "question": "Which molecular sensors turn carbon, nitrogen and phosphate supply into the shut-off of DnaA synthesis and arrest of the cell cycle?", "known": "When carbon, nitrogen or phosphate runs out, *dnaA* translation is inhibited while Lon keeps degrading DnaA. DnaA disappears and replication does not start. On carbon exhaustion, a stretch of the growing DnaA chain slows translation. (p)ppGpp keeps C- and N-starved cells as swarmers, and in stationary phase it induces IncA, which removes the DnaN clamp to halt replication.", "open": "It is unknown what makes the ribosome slow on the DnaA chain and which upstream sensors detect each nutrient. How growth rate sets the timing of initiation during steady growth, as opposed to starvation, is also unresolved.", "whyItMatters": "Every cell must match DNA replication to its food supply. Caulobacter's control of DnaA translation is one of the best-defined bacterial examples, but its sensor is still missing.", "status": "partly answered", "statusNote": "A 2024 review says the mechanisms linking growth to replication under different nutrient conditions 'remain elusive'. A 2025 study added IncA, induced by (p)ppGpp, as a brake on replisomes already copying DNA.", "refs": [ "10.1371/journal.pgen.1005342", "10.7554/eLife.71611", "10.1371/journal.pgen.1010882", "10.1016/j.mib.2023.102403", "10.1016/j.cub.2025.09.042" ], "related": { "network": [ "DnaA", "Lon", "Cori" ], "pathways": [ "stress-responses" ] }, "tier": "primary" }, { "id": "general-stress-inputs", "theme": "stress-physiology", "title": "Which signals feed the general stress response hub", "question": "What do the many kinases upstream of MrrA sense, and how is their input split between stress survival and development?", "known": "The general stress response runs through σT, its anti-σ NepR and the anti-anti-σ PhyR. Phosphate groups reach PhyR through the single-domain regulator MrrA and the phosphotransferase PhyK. At least six histidine kinases phosphorylate MrrA. LovK–LovR soak up phosphate from this flow and tie the pathway to holdfast control. Lon degrades σT, and σT activates the small RNA GsrN.", "open": "For most of the kinases that phosphorylate MrrA, the signal they sense is unknown. It is also unclear how this bow-tie network ranks competing inputs, and how Lon's breakdown of σT is tuned during stress.", "whyItMatters": "This hub ties stress survival to attachment and development across Alphaproteobacteria, including symbionts and pathogens. Without its inputs, the network cannot be predicted.", "status": "partly answered", "statusNote": "The 2018 MrrA paper said these kinases \"likely serve as stress sensors\" but did not define their signals, and Lon turnover of σT was added in 2023; no study has yet mapped the inputs (literature checked October 2026).", "refs": [ "10.1128/JB.00182-12", "10.1128/mBio.00809-18", "10.7554/eLife.33684", "10.1128/jb.00228-23" ], "related": { "network": [ "Lon" ], "pathways": [ "stress-responses", "pili-holdfast-adhesion" ] }, "tier": "secondary" }, { "id": "gene-transfer-agents", "theme": "stress-physiology", "title": "When and why Caulobacter releases gene transfer agents", "question": "Under what natural conditions do wild-type Caulobacter populations make gene transfer agents, and how much does GTA-borne DNA matter for fitness outside the lab?", "known": "Caulobacter carries a prophage-like gene transfer agent (GTA) cluster. RogA represses it, and GafY and GafZ switch it on, with help from IHF and anti-termination by GafZ. The particles carry ~8.3 kb pieces of host DNA. Release needs cell lysis by the defence-like LypABC system. GTA DNA helps recipient cells survive stationary phase and DNA damage by serving as a repair template.", "open": "GTA production was studied mostly in strains lacking *rogA* or overexpressing *gafYZ*. It is not known which cues lift RogA and CdxB repression in wild-type cells, what fraction of cells lyse, or whether GTAs move DNA between strains in nature.", "whyItMatters": "GTAs are domesticated phages found across Alphaproteobacteria. Caulobacter is a tractable system for asking why cells keep a DNA-transfer program that kills the producer.", "status": "partly answered", "statusNote": "Caulobacter GTAs were found in 2022. Papers in 2024 and 2026 worked out how they are switched on (GafYZ, anti-termination) and released (LypABC, CdxB), but no natural trigger has been reported.", "refs": [ "10.1371/journal.pbio.3001790", "10.1371/journal.pbio.3001874", "10.1038/s41467-024-49114-2", "10.1038/s41564-026-02316-4" ], "related": { "pathways": [ "stress-responses" ] }, "tier": "secondary" }, { "id": "natural-habitat-lifestyle", "theme": "ecology-evolution", "title": "Where Caulobacter actually lives and what it does there", "question": "What are the natural niches, lifestyle and ecological roles of C. crescentus and its relatives, beyond the lab strain?", "known": "Caulobacter was long called an aquatic oligotroph, but metagenomes show it on average ~4-fold more abundant in soil than in water. It is common on decaying plant matter and in plant microbiomes. Gene fitness in lake water differs from fitness in lab media. Lake-bloom conditions trigger filamentation. NA1000's lab-derived traits map to five loci.", "open": "Which habitat C. crescentus itself is adapted to is still unclear. Its population sizes and growth rates in the field, its dealings with plants, predators and phages, and how well lab-strain physiology matches wild isolates are largely unmeasured.", "whyItMatters": "To interpret cell-cycle and development genes we need to know the conditions they evolved for. Lab media do not reproduce soil, freshwater or root habitats.", "status": "partly answered", "statusNote": "A 2025 genomic survey of hundreds of Caulobacterales mapped where they occur and which traits they carry, noting that the ecology of model bacteria is often poorly known. Direct field measurements remain scarce.", "refs": [ "10.1128/JB.00255-10", "10.1038/s41396-018-0257-z", "10.1038/s41396-018-0295-6", "10.1128/mBio.01557-19", "10.1007/s11274-022-03237-0", "10.1038/s41467-025-65642-x" ], "tier": "primary" }, { "id": "dimorphism-circuit-evolution", "theme": "ecology-evolution", "title": "Evolution of the dimorphic life cycle and the circuit that runs it", "question": "How did the CtrA-centred cell-cycle circuit and obligate dimorphism evolve across Alphaproteobacteria, and what selective pressures keep them or remove them?", "known": "Orthologs of the CtrA phosphorelay and of the DivJ–PleC–DivK and proteolysis modules occur across Alphaproteobacteria, but they are wired differently. In *Hyphomonas*, DivK is dispensable and CtrA levels are not regulated. In *Brevundimonas*, GcrA and CcrM control mostly different genes than in Caulobacter. Close relatives of C. crescentus have independently lost dimorphic traits.", "open": "No experiment has tested why obligate swarmer–stalked dimorphism is favoured where it persists, or what drives its repeated loss. It is also untested which network features are required and which are historical accident.", "whyItMatters": "Caulobacter's circuit is the reference for alphaproteobacterial cell cycles, including those of pathogens and symbionts. Knowing what is conserved, and why, shows which findings carry over.", "status": "partly answered", "statusNote": "A 2025 Nat Commun survey of Caulobacterales found repeated, independent simplification of the life cycle. A 2025 review discusses only possible selective pressures. Direct tests are missing.", "refs": [ "10.1186/1752-0509-4-52", "10.1371/journal.pgen.1008724", "10.1371/journal.pgen.1009433", "10.1016/j.mib.2025.102661", "10.1038/s41467-025-65642-x" ], "related": { "network": [ "CtrA", "DivK", "DivJ", "PleC", "CckA", "GcrA", "CcrM" ] }, "tier": "primary" }, { "id": "phage-predation-defence", "theme": "ecology-evolution", "title": "Phage predation and antiphage defence in Caulobacter", "question": "Which phages shape Caulobacter populations in nature, and what defence systems does Caulobacter use against them?", "known": "φCbK-like phages first grip the flagellum with a head filament, then infect through pilus portals at the cell pole. Other Caulobacter phages use the S-layer or smooth LPS as receptors. CbK-like phages fall into a temperate clade and an obligately lytic clade. Most strains tested carry restriction–modification systems that had not been annotated, and NA1000 has a 26-kb mobile element that gives phage resistance.", "open": "Caulobacter's antiphage defences have not been systematically catalogued; some restriction genes were not even annotated. Which phages infect wild populations, and how strongly predation shapes them, has not been measured.", "whyItMatters": "Phages use receptors that are made at set points in the cell cycle, such as the flagellum and pili. Predation may therefore have shaped Caulobacter's development.", "status": "partly answered", "statusNote": "2025: unannotated restriction enzymes were found in most strains tested. 2026: a new N4-like phage was shown to need smooth LPS; its authors say understanding of Caulobacter phages 'remains limited'.", "refs": [ "10.1073/pnas.1012388108", "10.1111/1462-2920.16354", "10.3390/v17030311", "10.1128/jb.00488-25" ], "related": { "network": [ "pilA" ], "pathways": [ "flagellum-chemotaxis", "pili-holdfast-adhesion" ] }, "tier": "secondary" }, { "id": "small-rna-functions", "theme": "regulation-systems", "title": "What Caulobacter's small regulatory RNAs do", "question": "What do the dozens of annotated small RNAs do, and how much does post-transcriptional control add to cell-cycle and stress regulation?", "known": "The proteins Hfq and RNase E support small-RNA (sRNA) activity. Known sRNAs include CrfA, ChvR and GsrN. CcnA promotes CtrA accumulation and may block *gcrA* translation. AbnZ represses the essential TamAB module. During carbon starvation, CrfA acts as a sponge that disables the SisA–D sRNAs.", "open": "Only a small fraction of the sRNAs have a known function or target. How much RNA-based control contributes to cell-cycle timing has not been measured, and the CcnA effect on *gcrA* is proposed, not established.", "whyItMatters": "Post-transcriptional control may explain timing and stress effects that transcription factors alone cannot. It is the least-mapped layer of regulation.", "status": "partly answered", "statusNote": "A 2025 Nat Commun paper says 'only a small fraction of its diverse sRNA repertoire has been characterized'. A 2025 overexpression library, CauloSOEP, now allows systematic screens.", "refs": [ "10.1016/j.mib.2021.01.002", "10.7554/eLife.33684", "10.1371/journal.pbio.3001528", "10.1093/nar/gkae1139", "10.1038/s41467-025-65274-1" ], "related": { "network": [ "CtrA", "GcrA" ] }, "tier": "secondary" }, { "id": "unknown-function-genes", "theme": "regulation-systems", "title": "Essential and fitness genes of unknown function", "question": "What do Caulobacter's essential genome elements and fitness-relevant genes of unknown function actually do?", "known": "Saturating transposon sequencing found 1012 essential genome features, including 480 ORFs and 90 intergenic segments of unknown function. When the essential genome was rewritten, 98 genes lost function, exposing misannotations and control signals hidden inside coding sequences. Lake-water screens point to many hypothetical genes. Some unknowns have been solved: the DUF1013 protein TrcR is a cell-cycle regulator.", "open": "Many essential or condition-specific genes and noncoding elements still have no known mechanism. It is unknown which of them carry new cell-cycle or envelope functions, and many hits from pooled screens still need follow-up.", "whyItMatters": "Even in a leading model organism, genes with no known function limit any complete model of the cell cycle.", "status": "partly answered", "statusNote": "2026: the CauloKO ordered mutant library, covering 86% of non-essential genes, was released to speed follow-up. In 2021 an unknown DUF1013 protein turned out to be the regulator TrcR.", "refs": [ "10.1038/msb.2011.58", "10.1073/pnas.1818259116", "10.1038/s41396-018-0295-6", "10.1073/pnas.2010357118", "10.1128/jb.00417-22" ], "related": { "network": [ "CtrA" ] }, "tier": "primary" }, { "id": "two-component-signal-repertoire", "theme": "regulation-systems", "title": "What Caulobacter's two-component systems sense, and how far they cross-talk", "question": "For most of *Caulobacter*'s roughly 100 two-component proteins, what signal does each sensor kinase detect, and how much do the pathways cross-talk inside the cell?", "known": "A 2005 survey counted 106 two-component genes, at least 39 needed for growth, cell-cycle progression or morphogenesis; in vitro, kinases strongly prefer their own regulators. Inputs are known for few: FixL senses oxygen, UzcS responds to uranium, zinc and copper, ChvGI to osmotic and cell-wall stress. Some mix on purpose: ChvGI and NtrYX share target genes, and SkaH forms complexes with LovK and SpdS.", "open": "Most sensor kinases have no identified ligand or physical input (even ChvG's direct signal is unknown), and insulation was inferred mainly from in vitro phosphotransfer, so how much cross-talk occurs across the whole network in vivo is unmeasured.", "whyItMatters": "Two-component systems are the main way *Caulobacter* reads its surroundings; without their inputs, the links between environment, envelope and cell cycle remain unlabeled.", "status": "partly answered", "statusNote": "Inputs are known for a handful of systems (UzcRS 2017, FixL–FixT 2020, ChvGI 2022), and a 2026 study treats ChvGI and NtrYX as almost one four-component system; no network-wide input map exists.", "refs": [ "10.1371/journal.pbio.0030334", "10.1111/mmi.13615", "10.1128/mBio.03383-19", "10.1371/journal.pgen.1008022", "10.1371/journal.pgen.1010465", "10.1111/mmi.70055" ], "related": { "network": [ "CckA", "PleC", "DivJ" ], "pathways": [ "stress-responses", "pili-holdfast-adhesion" ] }, "tier": "secondary" }, { "id": "gantc-hypomethylation-other-methylases", "theme": "regulation-systems", "title": "What unmethylated GANTC sites and the other DNA methylases do", "question": "Do the GANTC sites that escape CcrM methylation, and the marks made by *Caulobacter*'s other DNA methyltransferases, carry regulatory information?", "known": "CcrM methylates GANTC sites once per cycle; this is needed for normal transcription of dozens of cell-cycle genes but not for replication initiation or mismatch repair. A base-resolution methylome found 27 GANTC sites that stay unmethylated, plus other m6A and m5C motifs with constant methylation. MucR binding shields GANTC sites from CcrM, and phosphate limitation reshapes local hypomethylation.", "open": "Whether hypomethylation at particular sites changes nearby gene expression in normal growth is untested, the enzymes for some of the other motifs are unidentified, and whether those marks serve restriction–modification or gene control is unknown.", "whyItMatters": "Methylation is a heritable layer of gene control tied to the cell cycle; knowing which marks matter separates real epigenetic signals from by-products.", "status": "partly answered", "statusNote": "A 2016 study explained much local hypomethylation by MucR occlusion; 2024 nanopore methylomes confirmed CcrM and Lon effects and found no global role for AlkB, but no site-level function has been shown.", "refs": [ "10.1073/pnas.1319315110", "10.1093/nar/gkt1352", "10.1371/journal.pgen.1006499", "10.1128/jb.00083-24" ], "related": { "network": [ "CcrM", "GcrA", "MucR1/2" ] }, "tier": "secondary" }, { "id": "cell-cycle-translation-and-decay", "theme": "cell-cycle", "title": "How translation and mRNA decay are timed across the cell cycle", "question": "What mechanisms give *Caulobacter* genes their cell-cycle-specific translation efficiencies, and does regulated mRNA decay also shape cell-cycle expression?", "known": "Ribosome profiling at six cell-cycle times showed that translation efficiency follows distinct temporal patterns for stalk, flagellum and chemotaxis genes, even within operons. Few mechanisms are known: FlbT, with the flagellin FljJ, blocks flagellin translation until FlaF is made, and nutrients tune DnaA translation via its 5′ leader and a nascent-peptide sequence.", "open": "The regulators behind most translation-efficiency patterns are unidentified. Genome-wide mRNA lifetimes have been measured only in asynchronous cultures, so whether decay rates change across the cycle, and whether BR-bodies take part, is unknown.", "whyItMatters": "Post-transcriptional timing could explain how the flagellum and stalk are assembled on schedule, a layer that transcription-based models of the cycle leave out.", "status": "partly answered", "statusNote": "A 2025 Rif-seq study showed decay is coupled to translation (ribosomes protect mRNA) and BR-bodies are seen at all cell-cycle stages (2018), but no cell-cycle-resolved decay or regulator map exists.", "refs": [ "10.1073/pnas.1614795113", "10.1016/j.devcel.2020.10.005", "10.1371/journal.pgen.1005342", "10.7554/eLife.71611", "10.1016/j.molcel.2018.08.003", "10.1016/j.celrep.2025.116691" ], "related": { "network": [ "DnaA", "CtrA" ], "pathways": [ "flagellum-chemotaxis" ] }, "tier": "secondary" }, { "id": "midcell-elongation-zone", "theme": "division-growth", "title": "What builds the FtsZ-dependent midcell growth zone before constriction", "question": "Which cell-wall synthases insert new peptidoglycan at midcell before constriction in *Caulobacter*, and what switches that zone from elongation to constriction?", "known": "Before constricting, *Caulobacter* elongates from a midcell zone. FtsZ recruits MurG and redirects cell-wall precursor synthesis there, and this growth needs FtsZ but not MreB or PBP2. Constriction later needs FzlA, which links FtsZ to activation of the FtsW–FtsI synthase and interacts with FtsK. Related Caulobacteraceae use other elongation modes, tied to where PBP2 sits.", "open": "The synthase or synthases that build the midcell elongation zone are unidentified, as is the signal that ends this phase and turns the same site into inward septal growth.", "whyItMatters": "This little-studied growth phase ties the division machinery to cell elongation, so it bears on how size, shape and division timing are coupled.", "status": "open", "statusNote": "A 2021 study called the mechanism elusive after ruling out MreB and PBP2; 2024–2025 work explains constriction activation (FzlA–FtsW) and elongation in relatives, not this zone (literature checked October 2026).", "refs": [ "10.1111/j.1365-2958.2007.05720.x", "10.3389/fmicb.2021.732031", "10.1016/j.cub.2019.03.066", "10.1083/jcb.202211026", "10.1038/s41467-025-60005-y" ], "related": { "network": [ "ftsZ" ], "pathways": [ "division-site" ] }, "tier": "secondary" }, { "id": "s-layer-function", "theme": "spatial-organization", "title": "What the RsaA S-layer is for", "question": "What advantage does the RsaA S-layer give *Caulobacter*, given that some predators and phages get through it or even use it?", "known": "RsaA, about 31% of cell protein, is secreted by a type I system and crystallizes, regulated by calcium, into a hexagonal lattice anchored to the LPS O-antigen. New S-layer is inserted at the poles and midcell, following new peptidoglycan, leaving gaps in the lattice. Phage φCr30 uses the S-layer as its receptor.", "open": "Its function is unresolved. An early report that it blocked a predatory vibrio contrasts with *Bdellovibrio exovorus* feeding whether or not the S-layer is present, and the conditions in which RsaA pays for its large cost are undefined.", "whyItMatters": "The S-layer is the cell's outermost surface and consumes a huge share of protein synthesis, so its role bears on how *Caulobacter* survives predators, phages and its habitat.", "status": "open", "statusNote": "Assembly is now well described (2020 LPS-bound structure, 2024 cell-cycle-linked insertion), but a 2024 study found it does not block an epibiotic predator; its function remains unclear.", "refs": [ "10.1128/jb.173.7.2244-2249.1991", "10.1128/jb.173.17.5568-5572.1991", "10.1139/w10-036", "10.1016/j.cell.2019.12.006", "10.1038/s41467-024-47529-5", "10.1038/s41467-024-48042-5" ], "tier": "secondary" }, { "id": "sphingolipid-functions", "theme": "division-growth", "title": "What Caulobacter's sphingolipids and glycolipids do in its outer membrane", "question": "Why does *Caulobacter* make sphingolipids and phosphate-free glycolipids, and how do they stand in for or work alongside LPS and phospholipids in its envelope?", "known": "Unusually for a bacterium, *Caulobacter* makes dihydroceramides and phospho- and glycosphingolipids. Under phosphate starvation it makes glycoglycerolipids and a glycosphingolipid, GSL-2. Ceramide synthesis is needed for stationary-phase survival at high temperature and affects phage and polymyxin sensitivity. In *fur* mutants, the anionic sphingolipid CPG lets cells live without lipid A.", "open": "How these lipids are arranged in the outer membrane, how they pack with or replace LPS, why ceramides change phage and antibiotic sensitivity, and what they contribute in phosphate-poor natural habitats are unknown.", "whyItMatters": "Lipid A is essential in nearly all Gram-negative bacteria; *Caulobacter*'s ability to bypass it makes its sphingolipids a window on other ways to build an outer membrane.", "status": "partly answered", "statusNote": "Biosynthetic genes were defined 2019–2025 (ceramide kinase CpgB 2023, CpgD 2025), and a 2024 study tied phosphosphingolipids to virulence in insect larvae, but their structural role remains unclear.", "refs": [ "10.1128/mBio.00107-19", "10.1111/1462-2920.15280", "10.1016/j.celrep.2022.110888", "10.1016/j.jbc.2023.104894", "10.1371/journal.ppat.1012401", "10.1016/j.jbc.2025.110386" ], "tier": "secondary" }, { "id": "terminus-resolution-at-division", "theme": "chromosome", "title": "How the chromosome terminus is resolved and cleared at division", "question": "How are decatenation, chromosome-dimer resolution and FtsK-driven clearing of the terminus timed relative to constriction in *Caulobacter*?", "known": "ZapT binds the terminus and, through ZauP and ZapA, tethers and compacts it at the Z-ring. FtsK sits at the division plane; its essential C-terminus helps place topoisomerase IV (ParC) at the replisome, and NstA blocks topo IV decatenation early in the cycle under redox control. XerCD act at a *dif* site, and FzlA interacts with FtsK in a pathway with FtsW–FtsI.", "open": "Whether FtsK pumping, XerCD recombination and topo IV decatenation are triggered by constriction, by arrival of the terminus at the Z-ring or by the cell-cycle circuit is unknown, as is how faulty FzlA–FtsK signalling causes DNA damage.", "whyItMatters": "The terminus is the last DNA to leave the closing septum; mistiming here can cut chromosomes, so this is a core genome-integrity step.", "status": "partly answered", "statusNote": "ZapT (2020–2021) and the FzlA–FtsK link (2024) supply parts of the coupling and the main dif site was mapped in 2019, but the timing of the resolution steps relative to constriction is unresolved.", "refs": [ "10.1128/JB.188.4.1497-1508.2006", "10.1101/gad.257030.114", "10.1128/JB.00391-19", "10.1128/mBio.00487-20", "10.1128/mBio.02196-20", "10.1083/jcb.202211026" ], "related": { "network": [ "ftsZ" ], "pathways": [ "division-site", "chromosome-segregation" ] }, "tier": "secondary" }, { "id": "chemoreceptor-ligands-navigation", "theme": "ecology-evolution", "title": "What Caulobacter's chemoreceptors sense, and how it navigates", "question": "What do the roughly 18 putative chemoreceptors of *C. crescentus* detect, and how does its run–reverse–flick swimming turn those signals into navigation?", "known": "Swarmer cells swim with one polar flagellum in a run–reverse–flick pattern. Only the major chemotaxis cluster drives taxis; the second tunes holdfast via *hfiA*. Aerotaxis is strong. Tracked in 3D up a xylose gradient, cells kept motor bias nearly constant and changed forward and backward run lengths, unlike *E. coli*. The receptor *mcpA* is degraded by a ClpX-dependent route as swarmers differentiate.", "open": "Ligands for almost none of the putative chemoreceptors are known; earlier sugar-attractant claims rest mainly on ambiguous soft-agar assays. The proposal that CheY~P alters switching rates without changing bias has not been tested directly, and whether taxis is weak in general or tuned to untested cues is unknown.", "whyItMatters": "Without ligands the chemotaxis system cannot be tied to where Caulobacter finds food or surfaces, and its non-*E. coli* strategy is shared by other singly flagellated bacteria.", "status": "open", "statusNote": "A 2021 3D-tracking study stated that the ligand repertoires of the 18 putative chemoreceptors have not been characterized; no ligand screen was found through 2026 (literature checked October 2026).", "refs": [ "10.1038/s42003-021-02190-2", "10.1128/JB.00071-19", "10.1016/j.bpj.2016.03.028", "10.1103/PhysRevLett.115.198103", "10.1128/JB.183.17.5001-5007.2001", "10.1128/jb.00404-24" ], "related": { "network": [ "chemotaxis", "ClpXP" ], "pathways": [ "flagellum-chemotaxis" ] }, "tier": "secondary" }, { "id": "single-flagellum-number", "theme": "spatial-organization", "title": "What limits each Caulobacter cell to a single flagellum", "question": "*Caulobacter* lacks the FlhF/FlhG switch that sets flagellum number in many polar flagellates, so what restricts assembly to exactly one flagellum per cell?", "known": "Placement is well mapped. The birth-scar protein TipN marks the new pole. TipF, a c-di-GMP receptor with a degenerate EAL domain, is activated by the G1→S rise in c-di-GMP and recruits the positioning factor PflI and switch proteins. Without *tipN* or *pflI*, flagella form at wrong sites, and excess PflI can seed one at the stalked pole. TipF is removed at division as c-di-GMP falls.", "open": "These factors explain where the flagellum goes, not how many are built. Whether one copy follows from a single TipF/PflI nucleation site, from the single CtrA-driven pulse of early flagellar gene expression, or from an active block on extra basal bodies has not been tested, and no number-limiting factor is known.", "whyItMatters": "Each species keeps a fixed flagellation pattern; Caulobacter is a clear case of a polar monotrich that sets its pattern without the widespread FlhF/FlhG system.", "status": "partly answered", "statusNote": "Position factors were defined in 2006–2013, and a 2026 review notes that Caulobacter lacks *flhF*/*flhG* and uses other systems. No study identifying a number-limiting factor was found (literature checked October 2026).", "refs": [ "10.1016/j.cell.2006.01.019", "10.1128/JB.01706-07", "10.1101/gad.222679.113", "10.1093/femsre/fuv034", "10.1128/jb.00329-25" ], "related": { "network": [ "c-di-GMP", "flagellar-class-II", "CtrA" ], "pathways": [ "flagellum-chemotaxis", "c-di-GMP-signaling" ] }, "tier": "primary" }, { "id": "flagellar-ejection-mechanism", "theme": "development", "title": "How the flagellum is ejected at the swarmer-to-stalked transition", "question": "What physically releases the flagellum when a swarmer cell differentiates, and what seals and becomes of the motor relic left at the pole?", "known": "Ejection coincides with ClpAP-dependent degradation of the MS-ring protein FliF, which carries a hydrophobic C-terminal turnover signal; FliF turnover needs PleD and FliL but not the rest of the flagellum. Purified hook-basal bodies are unusually sensitive to protease and acid. Cryo-ET shows that ejection leaves plugged P- and L-ring relics in the outer membrane of the pole that then grows the stalk.", "open": "Whether FliF degradation triggers release or follows it, where the structure breaks, and how the PleD/c-di-GMP signal times the event are unknown. The protein that plugs the PL-ring relic has not been identified, and whether relics affect stalk synthesis at the same pole is untested.", "whyItMatters": "Programmed ejection is a clear bacterial case of an organelle discarded on cue, and it resembles the starvation-induced flagellar loss seen in many species.", "status": "open", "statusNote": "A 2021 cryo-ET study found plugged PL-subcomplex relics after programmed ejection and called the plug protein yet-unidentified; no later study of the ejection mechanism was found (literature checked October 2026).", "refs": [ "10.1046/j.1365-2958.1999.01358.x", "10.1128/JB.186.15.4960-4971.2004", "10.1099/mic.0.27386-0", "10.1371/journal.pbio.3000165", "10.1016/j.jmb.2021.167004" ], "related": { "network": [ "PleD", "c-di-GMP", "flagellar-class-II" ], "pathways": [ "flagellum-chemotaxis", "c-di-GMP-signaling" ] }, "tier": "secondary" }, { "id": "stalk-length-control", "theme": "development", "title": "How phosphate limitation is turned into stalk length", "question": "How does a fall in cytoplasmic phosphate switch on stalk-specific cell-wall synthesis, and what sets how long the stalk grows?", "known": "Stalks grow many-fold longer when phosphate is limiting, and *pst* mutants make long stalks even in rich medium. In 2024, refilling the internal phosphate pool with a foreign transporter abolished long stalks in *pstS* and *phoB* mutants, so internal phosphate, not PhoR–PhoB, drives elongation. Stalk wall is made by a dedicated MreB-dependent complex; ManA, SpdR, ppGpp and NtrC also affect length.", "open": "The 2024 study states that the pathways linking the cytoplasmic phosphate pool to stalk synthesis remain to be determined. What senses internal phosphate, how the signal reaches the stalk synthesis complex, and whether length is set by a ruler, by elongation time or by envelope precursor supply are unknown.", "whyItMatters": "The stalk is an organelle whose length answers one nutrient, so tracing the path would link a metabolite pool directly to cell shape.", "status": "partly answered", "statusNote": "2024: the trigger moved from PhoR–PhoB signalling to the cytoplasmic phosphate level, with the downstream pathway still unknown. 2020 and 2023 work added sugar-phosphate (ManA) and NtrC inputs.", "refs": [ "10.1128/JB.182.2.337-347.2000", "10.1371/journal.pgen.1007897", "10.1128/JB.00468-19", "10.1128/jb.00181-23", "10.1038/s42003-024-06469-y" ], "related": { "pathways": [ "stalk-biogenesis", "stress-responses" ] }, "tier": "secondary" }, { "id": "persister-pathways-ta-systems", "theme": "stress-physiology", "title": "Persister formation beyond HipBA, and what toxin–antitoxin systems do", "question": "Which pathways besides HipBA and SpoT produce antibiotic-tolerant persister cells in *C. crescentus*, and what natural signals activate its many toxin–antitoxin systems?", "known": "Three *hipBA* modules exist. HipA1 and HipA2 phosphorylate the tRNA synthetases GltX and TrpS and promote stationary-phase persistence via SpoT. HipA2 raises free tryptophan, which inactivates glutamine synthetase via GlnE; Lon frees HipA2 by degrading HipB2 under many stresses. HigB is LexA-controlled, and ParDE4 kills cells in low-oxygen biofilm zones to aid dispersal. Seven ParE/RelE toxins are functional.", "open": "Persisters still form without all three *hipBA* operons or without *spoT*, so other routes exist and are unidentified. For most ParE/RelE and other TA pairs, the triggering conditions and targets in natural settings are unknown, and the role of HipA3 is unresolved.", "whyItMatters": "Dormant subpopulations decide survival through starvation and stress in nutrient-poor habitats, and Caulobacter's TA set is large enough to test what such systems are for.", "status": "partly answered", "statusNote": "2020 work found persisters without all *hipBA* operons or *spoT*, implying multiple pathways; 2021 and 2023 studies added HipA2's amino-acid route and oxygen-controlled ParDE4. No full map of persister pathways exists.", "refs": [ "10.1111/j.1365-2958.2010.07207.x", "10.1038/nmicrobiol.2016.8", "10.1038/s41598-020-59283-x", "10.1128/mBio.03020-20", "10.7554/eLife.80808", "10.1007/s00284-021-02549-y" ], "related": { "network": [ "Lon" ], "pathways": [ "stress-responses" ] }, "tier": "secondary" }, { "id": "tonb-receptor-substrates", "theme": "ecology-evolution", "title": "What Caulobacter's 62 TonB-dependent receptors import", "question": "Which substrates do the ~62 predicted TonB-dependent outer-membrane transporters of *C. crescentus* carry, and how do they support growth at very low nutrient levels?", "known": "A minority have assigned roles: MalA (maltodextrins), SucA (sucrose), CciT (iron), HutA (heme), HiuA (ferrioxamine and ferrichrome siderophores made by other microbes) and BugA (an entry route for vancomycin and bacitracin). Xylan is cut on the cell surface, and xylo-oligosaccharide uptake appears to need proton motive force. Several receptors sit in plant-carbohydrate utilization loci.", "open": "For most of the 62 receptors no substrate is known, and ferrichrome can also enter by a route independent of the four Fur-regulated receptors. Which receptors matter in soil, freshwater or on plants, how many substrates each carries, and how their expression is prioritized when nutrients are scarce are open.", "whyItMatters": "Outer-membrane scavenging is likely central to an oligotroph's lifestyle; a substrate map would show which plant- and microbe-derived nutrients Caulobacter lives on.", "status": "partly answered", "statusNote": "Substrates were added in 2026 (HiuA for hydroxamate siderophores; BugA as an antibiotic entry route) and surface xylan breakdown was mapped in 2026, but most receptors remain uncharacterized.", "refs": [ "10.1371/journal.pone.0000224", "10.1128/JB.187.24.8300-8311.2005", "10.1007/s12275-018-8225-x", "10.1128/jb.00400-25", "10.1111/1462-2920.70392", "10.1038/s44318-025-00668-x" ], "tier": "secondary" }, { "id": "uranium-sensing", "theme": "stress-physiology", "title": "How Caulobacter senses uranium, and why it has a uranium response", "question": "How do the UzcRS and UrpRS two-component systems detect uranium, and what natural role does this metal-responsive envelope program play?", "known": "Uranium induces a specific response that includes *urcA*. UzcRS activates it in response to U, Zn and Cu, binds widely across the genome at a non-canonical site, and induces envelope genes including efflux pumps and TonB-dependent receptors. An ABC transporter–peptidase forms a sensory complex with UzcRS, UzcY and UzcZ amplify it and UzcX feeds back. PhoY phosphatase precipitates uranium as phosphate minerals.", "open": "How UzcS or its partners perceive uranium, and tell it from zinc and copper, is unknown, as is the basis of UrpRS's distinct selectivity. Why a soil and freshwater bacterium keeps a uranium-responsive regulon, and whether it matters in natural metal-rich soils or sediments, has not been tested.", "whyItMatters": "Caulobacter is a leading whole-cell uranium biosensor; knowing the sensing chemistry would let sensors be designed rather than screened and explain metal tolerance at contaminated sites.", "status": "partly answered", "statusNote": "Circuit parts were mapped in 2017–2019 and combined into a selective uranium sensor in 2019; no study of how the kinases bind uranium was found (literature checked October 2026).", "refs": [ "10.1128/AEM.01566-07", "10.1128/AEM.01050-14", "10.1111/mmi.13615", "10.1111/mmi.14180", "10.1021/acssynbio.8b00484" ], "related": { "pathways": [ "stress-responses" ] }, "tier": "secondary" }, { "id": "plant-growth-promotion", "theme": "ecology-evolution", "title": "How Caulobacter strains promote plant growth", "question": "Which bacterial factors and plant pathways let plant-associated *Caulobacter* strains increase plant growth?", "known": "Maize isolate RHG1 colonizes Arabidopsis roots and shoots, increases lateral roots and leaf growth, and acts through a route touching brassinosteroid signalling; auxin, cytokinin, nitric oxide and ACC deaminase were ruled out. The *cyo* ubiquinol oxidase operon is needed for growth promotion by two strains, and curvature helps CB15. RHG1 is recognized by root receptor-like kinases and early defence proteins drop.", "open": "No bacterial molecule perceived by the plant has been identified, the link between a respiratory oxidase (*cyo*) and plant growth is unexplained, and whether gnotobiotic Arabidopsis results hold in soil communities or crops is untested.", "whyItMatters": "Caulobacter is a hub taxon in many plant microbiomes; a defined mechanism would make it a tractable model of beneficial plant–bacteria interaction.", "status": "partly answered", "statusNote": "2021 genetics implicated *cyo* and cell shape; a 2026 phosphoproteomics study of RHG1 said the growth-promotion mechanisms remain largely unknown. A 2026 preprint adds a holdfast-free soybean-root isolate.", "refs": [ "10.1094/MPMI-12-18-0347-R", "10.1371/journal.pone.0249227", "10.1007/s00203-021-02702-y", "10.1021/acs.jproteome.6c00044", "10.64898/2026.09.14.750808" ], "tier": "secondary" }, { "id": "cir-repeats", "theme": "regulation-systems", "tier": "secondary", "status": "open", "title": "What do the CIR repeats do?", "question": "What are the CIR intergenic repeats of Caulobacter for, and does the CcrM methylation site at the centre of CIR1 and CIR2 matter?", "known": "A search for sequence motifs around CcrM methylation sites found four long (>100 bp) intergenic repeat families, the CIR sequences, present in up to 21 copies in *C. crescentus*. CIR1 and CIR2 are built as conserved inverted repeats, with a GANTC site at the centre of one arm. A 2024 review of miniature inverted-repeat elements lists CIR among strictly intergenic repeat elements.", "open": "No study has tested what CIRs do: whether they are transcribed or stabilize RNA, bind proteins, move in the genome, or couple methylation state to expression. Because the original search was anchored on CcrM sites, intergenic inverted repeats without a GANTC site would not have been detected.", "whyItMatters": "Conserved intergenic repeats usually have a function; a methylation site at their core suggests one tied to the cell cycle, and the search left room for undiscovered repeat families.", "statusNote": "The 2003 identification is still the only study of CIRs; the papers citing it since are surveys of bacterial repeats, the latest a 2024 review (literature checked October 2026).", "refs": [ "10.1128/jb.185.16.4997-5002.2003", "10.3390/genes15030328" ], "related": { "network": [ "CcrM" ] } } ], "references": [ { "doi": "10.1038/nature14473", "pmid": "25945741", "cite": "Lori C et al. 2015 Nature", "title": "Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication" }, { "doi": "10.1038/s41467-020-14585-6", "pmid": "32041947", "cite": "Kaczmarczyk A et al. 2020 Nat Commun", "title": "Precise timing of transcription by 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