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1.
Sci Adv ; 10(18): eadl4450, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38701202

ABSTRACT

Caulobacter crescentus Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular ß sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its ß region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in Escherichia coli, maintaining infectivity against C. crescentus, which presents promising applications, including RNA delivery and phage display.


Subject(s)
Caulobacter crescentus , Fimbriae, Bacterial , Caulobacter crescentus/virology , Caulobacter crescentus/metabolism , Fimbriae, Bacterial/metabolism , Fimbriae, Bacterial/chemistry , Fimbriae, Bacterial/ultrastructure , Protein Binding , Cryoelectron Microscopy , Fimbriae Proteins/metabolism , Fimbriae Proteins/chemistry , Fimbriae Proteins/genetics , RNA Phages/metabolism , RNA Phages/chemistry , Models, Molecular
2.
Nat Commun ; 15(1): 3355, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38637514

ABSTRACT

Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.


Subject(s)
Bacterial Proteins , Caulobacter crescentus , Bacterial Proteins/metabolism , Caulobacter crescentus/metabolism , Membrane Glycoproteins/metabolism , Cell Division , Cell Membrane/metabolism
3.
Nat Commun ; 15(1): 3460, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38658616

ABSTRACT

DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial species, driving the hypothesis that a physical linker may tether them together. However, replisome splitting has also been reported in many of the same species, leaving the principles behind replisome organization a long-standing puzzle. Here, by tracking the replisome ß-clamp subunit in live Caulobacter crescentus, we find that rapid DNA segregation can give rise to a second focus which resembles a replisome, but does not replicate DNA. Sister replisomes can remain colocalized, or split apart to travel along DNA separately upon disruption of chromosome inter-arm alignment. Furthermore, chromosome arm-specific replication-transcription conflicts differentially modify replication speed on the two arms, facilitate the decoupling of the two replisomes. With these observations, we conclude that the dynamic chromosome organization flexibly shapes the organization of sister replisomes, and we outline principles which can help to reconcile previously conflicting models of replisome architecture.


Subject(s)
Bacterial Proteins , Caulobacter crescentus , Chromosomes, Bacterial , DNA Replication , Caulobacter crescentus/metabolism , Caulobacter crescentus/genetics , Chromosomes, Bacterial/metabolism , Chromosomes, Bacterial/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , DNA, Bacterial/metabolism , DNA, Bacterial/genetics , Chromosome Segregation
4.
Mol Biol Cell ; 35(6): ar78, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38598301

ABSTRACT

Microfluidic platforms enable long-term quantification of stochastic behaviors of individual bacterial cells under precisely controlled growth conditions. Yet, quantitative comparisons of physiological parameters and cell behaviors of different microorganisms in different experimental and device modalities is not available due to experiment-specific details affecting cell physiology. To rigorously assess the effects of mechanical confinement, we designed, engineered, and performed side-by-side experiments under otherwise identical conditions in the Mother Machine (with confinement) and the SChemostat (without confinement), using the latter as the ideal comparator. We established a protocol to cultivate a suitably engineered rod-shaped mutant of Caulobacter crescentus in the Mother Machine and benchmarked the differences in stochastic growth and division dynamics with respect to the SChemostat. While the single-cell growth rate distributions are remarkably similar, the mechanically confined cells in the Mother Machine experience a substantial increase in interdivision times. However, we find that the division ratio distribution precisely compensates for this increase, which in turn reflects identical emergent simplicities governing stochastic intergenerational homeostasis of cell sizes across device and experimental configurations, provided the cell sizes are appropriately mean-rescaled in each condition. Our results provide insights into the nature of the robustness of the bacterial growth and division machinery.


Subject(s)
Caulobacter crescentus , Cell Division , Stochastic Processes , Caulobacter crescentus/physiology , Caulobacter crescentus/metabolism , Caulobacter crescentus/cytology , Microfluidics/methods
5.
mBio ; 15(4): e0315323, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38511926

ABSTRACT

The alphaproteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate the translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the Hfq-bound sRNA RusT is transcriptionally controlled by the NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis, we determine 16 candidate target transcripts that are deregulated, many of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limited.IMPORTANCEThe conserved RNA-binding protein Hfq contributes significantly to the adaptation of bacteria to different environmental conditions. Hfq not only stabilizes associated sRNAs but also promotes inter-molecular base-pairing interactions with target transcripts. Hfq plays a pivotal role for growth and survival, controlling central metabolism and cell wall synthesis in the oligotroph Caulobacter crescentus. However, direct evidence for Hfq-dependent post-transcriptional regulation and potential oligotrophy in C. crescentus has been lacking. Here, we identified sRNAs and mRNAs associated with Hfq in vivo, and demonstrated the requirement of Hfq for sRNA-mediated regulation, particularly of outer membrane transporters in C. crescentus.


Subject(s)
Caulobacter crescentus , RNA, Small Untranslated , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , RNA, Small Untranslated/metabolism , RNA, Bacterial/metabolism , RNA, Messenger/genetics , Membrane Transport Proteins/metabolism , Host Factor 1 Protein/genetics , Host Factor 1 Protein/metabolism , Gene Expression Regulation, Bacterial
6.
Proc Natl Acad Sci U S A ; 121(7): e2309984121, 2024 Feb 13.
Article in English | MEDLINE | ID: mdl-38324567

ABSTRACT

The protein crescentin is required for the crescent shape of the freshwater bacterium Caulobacter crescentus (vibrioides). Crescentin forms a filamentous structure on the inner, concave side of the curved cells. It shares features with eukaryotic intermediate filament (IF) proteins, including the formation of static filaments based on long and parallel coiled coils, the protein's length, structural roles in cell and organelle shape determination and the presence of a coiled coil discontinuity called the "stutter." Here, we have used electron cryomicroscopy (cryo-EM) to determine the structure of the full-length protein and its filament, exploiting a crescentin-specific nanobody. The filament is formed by two strands, related by twofold symmetry, that each consist of two dimers, resulting in an octameric assembly. Crescentin subunits form longitudinal contacts head-to-head and tail-to-tail, making the entire filament non-polar. Using in vivo site-directed cysteine cross-linking, we demonstrated that contacts observed in the in vitro filament structure exist in cells. Electron cryotomography (cryo-ET) of cells expressing crescentin showed filaments on the concave side of the curved cells, close to the inner membrane, where they form a band. When comparing with current models of IF proteins and their filaments, which are also built from parallel coiled coil dimers and lack overall polarity, it emerges that IF proteins form head-to-tail longitudinal contacts in contrast to crescentin and hence several inter-dimer contacts in IFs have no equivalents in crescentin filaments. Our work supports the idea that intermediate filament-like proteins achieve their shared polymerization and mechanical properties through a variety of filament architectures.


Subject(s)
Caulobacter crescentus , Intermediate Filaments , Intermediate Filaments/metabolism , Bacterial Proteins/metabolism , Cytoskeleton/metabolism , Intermediate Filament Proteins/metabolism , Caulobacter crescentus/metabolism
7.
PLoS Genet ; 19(11): e1011048, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37972151

ABSTRACT

The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and bacteriophage, regulate diverse features of bacterial cell physiology and impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of a paralogous XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. crescentus. We further discovered related XRE TFs throughout the class Alphaproteobacteria and its phages, including the φCbK Caulophage, suggesting that members of this cluster impact host-phage interactions. Here we show that a closely related group of XRE transcription factors encoded by both C. crescentus and φCbK can physically interact and function to control the transcription of a common gene set, influencing processes including holdfast development and the production of φCbK virions. The φCbK-encoded XRE paralog, tgrL, is highly expressed at the earliest stages of infection and can directly inhibit transcription of host genes including hfiA, a potent holdfast inhibitor, and gafYZ, an activator of prophage-like gene transfer agents (GTAs). XRE proteins encoded from the C. crescentus chromosome also directly repress gafYZ transcription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting the C. crescentus XRE transcription factors reduced φCbK burst size, while overexpressing these host genes or φCbK tgrL rescued this burst defect. We conclude that this XRE TF gene cluster, shared by C. crescentus and φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection.


Subject(s)
Bacteriophages , Caulobacter crescentus , Caulobacter , Transcription Factors/genetics , Transcription Factors/metabolism , Bacteriophages/genetics , Caulobacter/genetics , Caulobacter/metabolism , Ecosystem , Xenobiotics/metabolism , Caulobacter crescentus/metabolism , Adhesins, Bacterial/genetics , Response Elements
8.
PLoS Genet ; 19(11): e1010882, 2023 Nov.
Article in English | MEDLINE | ID: mdl-38011258

ABSTRACT

Upon nutrient depletion, bacteria stop proliferating and undergo physiological and morphological changes to ensure their survival. Yet, how these processes are coordinated in response to distinct starvation conditions is poorly understood. Here we compare the cellular responses of Caulobacter crescentus to carbon (C), nitrogen (N) and phosphorus (P) starvation conditions. We find that DNA replication initiation and abundance of the replication initiator DnaA are, under all three starvation conditions, regulated by a common mechanism involving the inhibition of DnaA translation. By contrast, cell differentiation from a motile swarmer cell to a sessile stalked cell is regulated differently under the three starvation conditions. During C and N starvation, production of the signaling molecules (p)ppGpp is required to arrest cell development in the motile swarmer stage. By contrast, our data suggest that low (p)ppGpp levels under P starvation allow P-starved swarmer cells to differentiate into sessile stalked cells. Further, we show that limited DnaA availability, and consequently absence of DNA replication initiation, is the main reason that prevents P-starved stalked cells from completing the cell cycle. Together, our findings demonstrate that C. crescentus decouples cell differentiation from DNA replication initiation under certain starvation conditions, two otherwise intimately coupled processes. We hypothesize that arresting the developmental program either as motile swarmer cells or as sessile stalked cells improves the chances of survival of C. crescentus during the different starvation conditions.


Subject(s)
Caulobacter crescentus , DNA-Binding Proteins , DNA-Binding Proteins/genetics , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , Phosphates/metabolism , Guanosine Pentaphosphate/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , DNA Replication/genetics , Cell Cycle/genetics , Cell Differentiation
9.
Nucleic Acids Res ; 51(22): 12275-12287, 2023 Dec 11.
Article in English | MEDLINE | ID: mdl-37933842

ABSTRACT

Chromosomal maintenance is vital for the survival of bacteria. In Caulobacter crescentus, chromosome replication initiates at ori and segregation is delayed until the nearby centromere-like region parS is replicated. Our understanding of how this sequence of events is regulated remains limited. The segregation of parS has been shown to involve multiple steps including polar release from anchoring protein PopZ, slow movement and fast ParA-dependent movement to the opposite cell pole. In this study, we demonstrate that ParA's competing attractions from PopZ and from DNA are critical for segregation of parS. Interfering with this balance of attractions-by expressing a variant ParA-R195E unable to bind DNA and thus favoring interactions exclusively between ParA-PopZ-results in cell death. Our data revealed that ParA-R195E's sole interactions with PopZ obstruct PopZ's ability to release the polar anchoring of parS, resulting in cells with multiple parS loci fixed at one cell pole. We show that the inability to separate and segregate multiple parS loci from the pole is specifically dependent on the interaction between ParA and PopZ. Collectively, our results reveal that the initial steps in chromosome segregation are highly regulated.


Subject(s)
Caulobacter crescentus , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Caulobacter crescentus/metabolism , Centromere/genetics , Centromere/metabolism , Chromosome Segregation , Chromosomes, Bacterial/genetics , Chromosomes, Bacterial/metabolism , DNA/metabolism
10.
J Bacteriol ; 205(11): e0022823, 2023 11 21.
Article in English | MEDLINE | ID: mdl-37930077

ABSTRACT

IMPORTANCE: Regulated protein degradation is a critical process in all cell types, which contributes to the precise regulation of protein amounts in response to internal and external cues. In bacteria, protein degradation is carried out by ATP-dependent proteases. Although past work revealed detailed insights into the operation principles of these proteases, there is limited knowledge about the substrate proteins that are degraded by distinct proteases and the regulatory role of proteolysis in cellular processes. This study reveals a direct role of the conserved protease Lon in regulating σT, a transcriptional regulator of the general stress response in α-proteobacteria. Our work is significant as it underscores the importance of regulated proteolysis in modulating the levels of key regulatory proteins under changing conditions.


Subject(s)
Caulobacter crescentus , Protease La , Proteolysis , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Caulobacter crescentus/metabolism , Gene Expression Regulation, Bacterial , Protease La/genetics , Protease La/metabolism , Sigma Factor/genetics , Sigma Factor/metabolism
11.
Mol Cell Proteomics ; 22(12): 100679, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37979947

ABSTRACT

The ability of an organism to respond to environmental changes is paramount to survival across a range of conditions. The bacterial heme nitric oxide/oxygen binding proteins (H-NOX) are a family of biofilm-regulating gas sensors that enable bacteria to respond accordingly to the cytotoxic molecule nitric oxide. By interacting with downstream signaling partners, H-NOX regulates the production of the bacterial secondary messenger cyclic diguanylate monophosphate (c-di-GMP) to influence biofilm formation. The aquatic organism Caulobacter crescentus has the propensity to attach to surfaces as part of its transition into the stalked S-phase of its life cycle. This behavior is heavily influenced by intracellular c-di-GMP and thus poses H-NOX as a potential influencer of C. crescentus surface attachment and cell cycle. By generating a strain of C. crescentus lacking hnox, our laboratory has demonstrated that this strain exhibits a considerable growth deficit, an increase in biofilm formation, and an elevation in c-di-GMP. Furthermore, in our comprehensive proteome study of 2779 proteins, 236 proteins were identified that exhibited differential expression in Δhnox C. crescentus, with 132 being downregulated and 104 being upregulated, as determined by a fold change of ≥1.5 or ≤0.66 and a p value ≤0.05. Our systematic analysis unveiled several regulated candidates including GcrA, PopA, RsaA, FtsL, DipM, FlgC, and CpaE that are associated with the regulation of the cellular division process, surface proteins, flagellum, and pili assembly. Further examination of Gene Ontology and pathways indicated that the key differences could be attributed to several metabolic processes. Taken together, our data indicate a role for the HNOX protein in C. crescentus cell cycle progression.


Subject(s)
Caulobacter crescentus , Hemeproteins , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , Nitric Oxide/metabolism , Cyclic GMP/metabolism , Hemeproteins/genetics , Hemeproteins/metabolism , Oxygen/metabolism , Bacterial Proteins/metabolism , Cell Cycle , Heme/metabolism , Gene Expression Regulation, Bacterial
12.
J Bacteriol ; 205(10): e0020623, 2023 10 26.
Article in English | MEDLINE | ID: mdl-37730540

ABSTRACT

The bacterial DNA damage response is a critical, coordinated response to endogenous and exogenous sources of DNA damage. Response dynamics are dependent on coordinated synthesis and loss of relevant proteins. While much is known about its global transcriptional control, changes in protein abundance that occur upon DNA damage are less well characterized at the system level. Here, we perform a proteome-wide survey of the DNA damage response in Caulobacter crescentus. We find that while most protein abundance changes upon DNA damage are readily explained by changes in transcription, there are exceptions. The survey also allowed us to identify the novel DNA damage response factor, YaaA, which has been overlooked by previously published, transcription-focused studies. A similar survey in a ∆lon strain was performed to explore lon's role in DNA damage survival. The ∆lon strain had a smaller dynamic range of protein abundance changes in general upon DNA damage compared to the wild-type strain. This system-wide change to the dynamics of the response may explain this strain's sensitivity to DNA damage. Our proteome survey of the DNA damage response provides additional insight into the complex regulation of stress response and nominates a novel response factor that was overlooked in prior studies. IMPORTANCE The DNA damage response helps bacteria to react to and potentially survive DNA damage. The mutagenesis induced during this stress response contributes to the development of antibiotic resistance. Understanding how bacteria coordinate their response to DNA damage could help us to combat this growing threat to human health. While the transcriptional regulation of the bacterial DNA damage response has been characterized, this study is the first to our knowledge to assess the proteomic response to DNA damage in Caulobacter.


Subject(s)
Caulobacter crescentus , Humans , Caulobacter crescentus/metabolism , DNA, Bacterial/metabolism , Proteomics , Proteome , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , DNA Damage , Gene Expression Regulation, Bacterial
13.
Mol Microbiol ; 120(3): 307-323, 2023 09.
Article in English | MEDLINE | ID: mdl-37487601

ABSTRACT

Bacteria frequently store excess carbon in hydrophobic granules of polyhydroxybutyrate (PHB) that in some growth conditions can occupy most of the cytoplasmic space. Different types of proteins associate to the surface of the granules, mainly enzymes involved in the synthesis and utilization of the reserve polymer and a diverse group of proteins known as phasins. Phasins have different functions, among which are regulating the size and number of the granules, modulating the activity of the granule-associated enzymes and helping in the distribution of the granules inside the cell. Caulobacter crescentus is an oligotrophic bacterium that shows several morphological and regulatory traits that allow it to grow in very nutrient-diluted environments. Under these conditions, storage compounds should be particularly relevant for survival. In this work, we show an initial proteomic characterization of the PHB granules and describe a new type of phasin (PhaH) characterized by the presence of an N-terminal hydrophobic helix followed by a helix-hairpin-helix (HhH) domain. The hydrophobic helix is required for maximal PHB accumulation and maintenance during the stationary phase while the HhH domain is involved in determining the size of the PHB granules and their distribution in the cell.


Subject(s)
Caulobacter crescentus , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , Proteomics , Bacterial Proteins/metabolism , Hydroxybutyrates/metabolism , Polyesters/metabolism
14.
J Bacteriol ; 205(2): e0038422, 2023 02 22.
Article in English | MEDLINE | ID: mdl-36715542

ABSTRACT

First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.


Subject(s)
Caulobacter crescentus , Caulobacter crescentus/metabolism , Cell Cycle , Cell Division , Bacterial Proteins/genetics
15.
Nucleic Acids Res ; 51(4): 1960-1970, 2023 02 28.
Article in English | MEDLINE | ID: mdl-36715319

ABSTRACT

Canonical bacterial transcription activators bind to their cognate cis elements at the upstream of transcription start site (TSS) in a form of dimer. Caulobacter crescentus GcrA, a non-canonical transcription activator, can activate transcription from promoters harboring its cis element at the upstream or downstream of TSS in a form of monomer. We determined two cryo-EM structures of C. crescentus GcrA-bound transcription activation complexes, GcrA TACU and GcrA TACD, which comprise GcrA, RNAP, σ70 and promoter DNA with GcrA cis elements at either the upstream or downstream of TSS at 3.6 and 3.8 Å, respectively. In the GcrA-TACU structure, GcrA makes bipartite interactions with both σ70 domain 2 (σ702) and its cis element, while in the GcrA-TACD structure, GcrA retains interaction with σ702 but loses the interaction with its cis element. Our results suggest that GcrA likely forms a functionally specialized GcrA-RNAP-σA holoenzyme, in which GcrA first locates its cis element and then facilitates RNAP to load on core promoter at its proximal region. The sequence-specific interaction of GcrA and DNA is disrupted either at the stage of RPo formation or promoter escape depending on the location of GcrA cis elements relative to TSS.


Subject(s)
Bacterial Proteins , Caulobacter crescentus , Transcription Factors , Transcriptional Activation , Bacterial Proteins/metabolism , Caulobacter crescentus/metabolism , DNA/metabolism , DNA-Directed RNA Polymerases/metabolism , Gene Expression Regulation, Bacterial , Transcription Factors/metabolism , Transcription, Genetic
16.
Curr Biol ; 33(2): 228-240.e7, 2023 01 23.
Article in English | MEDLINE | ID: mdl-36516849

ABSTRACT

Proper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the ⍺-proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell-wall-targeting antibiotics, EstG does not demonstrate biochemical activity toward cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. This molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which are important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.


Subject(s)
Caulobacter crescentus , Caulobacter , Caulobacter/metabolism , Esterases , Cell Membrane/metabolism , Cell Wall/metabolism , Caulobacter crescentus/metabolism , Anti-Bacterial Agents , Bacterial Proteins/genetics , Bacterial Proteins/metabolism
17.
Biotechnol Appl Biochem ; 70(2): 688-696, 2023 Apr.
Article in English | MEDLINE | ID: mdl-35932185

ABSTRACT

The bacterium Caulobacter crescentus secretes an adhesive polysaccharide called holdfast, which is the known strongest underwater adhesive in nature. The deacetylase encoded by hfs (holdfast synthesis) H gene is a key factor affecting the adhesion of holdfast. Its structure and function are not yet clear, and whether other polysaccharide deacetylases exist in C. crescentus is still unknown. The screening of both HfsH and its structural analogue as well as their purification from the artificial expression products of Escherichia coli is the first step to clarify these questions. Here, we determined the conserved domains of HfsH via sequence alignment among carbohydrate esterase family 4 enzymes and screened out its structural analogue (CC_2574) in C. crescentus. The recombinant HfsH and CC_2574 were effectively expressed in E. coli. Both of them were purified by chromatography from their corresponding productions in E. coli and were then functionally analyzed. The results indicated that a high deacetylase activity (61.8 U/mg) was observed in recombinant HfsH but not in CC_2574, which suggesting that HfsH might be the irreplaceable gene mediating adhesion of holdfast in C. crescentus. Moreover, the divalent metal ions Zn2+ , Mg2+ , and Mn2+ could promote the activity of recombinant HfsH at the concentration from 0.05 to 1 mM, but inhibit its activity when the concentration exceeds 1 mM. In sum, our study first realized the artificial production of polysaccharide deacetylase HfsH and its structural analogue, and further explored their functions, both of which laid the foundation for the development of new adhesive materials.


Subject(s)
Bacterial Adhesion , Caulobacter crescentus , Bacterial Adhesion/genetics , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Follicle Stimulating Hormone, Human/metabolism , Polysaccharides/metabolism , Bacterial Proteins/genetics
18.
Nucleic Acids Res ; 50(22): 12896-12912, 2022 12 09.
Article in English | MEDLINE | ID: mdl-36484102

ABSTRACT

The replicative DNA helicase translocates on single-stranded DNA to drive replication forks during chromosome replication. In most bacteria the ubiquitous replicative helicase, DnaB, co-evolved with the accessory subunit DciA, but how they function remains incompletely understood. Here, using the model bacterium Caulobacter crescentus, we demonstrate that DciA plays a prominent role in DNA replication fork maintenance. Cell cycle analyses using a synchronized Caulobacter cell population showed that cells devoid of DciA exhibit a severe delay in fork progression. Biochemical characterization revealed that the DnaB helicase in its default state forms a hexamer that inhibits self-loading onto single-stranded DNA. We found that upon binding to DciA, the DnaB hexamer undergoes conformational changes required for encircling single-stranded DNA, thereby establishing the replication fork. Further investigation of the functional structure of DciA revealed that the C-terminus of DciA includes conserved leucine residues responsible for DnaB binding and is essential for DciA in vivo functions. We propose that DciA stimulates loading of DnaB onto single strands through topological isomerization of the DnaB structure, thereby ensuring fork progression. Given that the DnaB-DciA modules are widespread among eubacterial species, our findings suggest that a common mechanism underlies chromosome replication.


Subject(s)
Bacterial Proteins , Caulobacter crescentus , Chromosomes, Bacterial , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , DNA Replication/genetics , DNA, Single-Stranded/metabolism , DnaB Helicases/metabolism , Chromosomes, Bacterial/genetics , Chromosomes, Bacterial/metabolism
19.
PLoS Biol ; 20(11): e3001790, 2022 11.
Article in English | MEDLINE | ID: mdl-36327213

ABSTRACT

Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package approximately 5 to 15 kbp fragments of the host genome that can then be transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer (HGT) in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the α-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a newly identified transcription factor, RogA, that represses gafYZ, the direct activators of GTA synthesis. Cells lacking rogA or expressing gafYZ produce GTAs harboring approximately 8.3 kbp fragment of the genome that can, after cell lysis, be transferred into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual HGT mechanism.


Subject(s)
Caulobacter crescentus , Prophages , Prophages/genetics , Prophages/metabolism , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , Gene Transfer, Horizontal/genetics , Genome, Bacterial , DNA Repair/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Gene Expression Regulation, Bacterial
20.
J Bacteriol ; 204(11): e0038622, 2022 Nov 15.
Article in English | MEDLINE | ID: mdl-36286485

ABSTRACT

In the Caulobacterales, a highly adhesive polysaccharide called the holdfast mediates attachment to exogenous surfaces. The mechanism by which this polysaccharide is anchored to the cell envelope is not well defined. N. K. Chepkwony, G. G. Hardy, and Y. V. Brun (J Bacteriol 204:e00273-22, 2022, https://doi.org/10.1128/jb.00273-22) report the characterization of HfaE, a localized surface protein with amyloid-like properties that is required for robust holdfast anchoring. This study expands our understanding of the protein factors that attach a bacterial "superglue" to the surface of the cell.


Subject(s)
Caulobacter crescentus , Caulobacter crescentus/metabolism , Adhesins, Bacterial/metabolism , Bacterial Adhesion , Polysaccharides/metabolism , Cell Membrane/metabolism
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