Structural basis for chitin acquisition by marine Vibrio species

A Dynamic Sugar-Selective Bacterial Nanopore for Targeted Antibiotic Transport

Bacterial porins are essential for molecule transport, yet their functionality in pathogens remains underexplored. Here, a monomeric porin CymAKp is identified and characterized from a pathogen Klebsiella pneumoniae, featuring a specialized constricted segment (1-25 residues) in the pore. Single-channel recordings reveal the formation of fluctuating CymAKp nanopores that exhibit gating in symmetrical and asymmetrical lipid bilayers. The movement of the constricted segment drives these gating events, and the deletion of this segment results in stable nanopores establishing dynamic functionality of the pores. Furthermore, it is shown that CymAKp functions as a sugar-selective nanopore, facilitating the permeation of cyclic hexasaccharide while excluding larger cyclic sugars. Aminoglycoside antibiotics, structurally similar to cyclic sugars, exploit this sugar-selective pathway for translocation, and their translocation kinetics is quantified. Remarkably, molecular dynamics simulations reveal two distinct translocation pathways: one for cyclic hexasaccharides, where the constricted segment is displaced, and another for antibiotics, where the constricted segment remains within the pore. Studies establish the charged affinity site and constricted segment role in the porin as key regulators of dynamic molecular transport in pathogenic porins and provide new insights for developing nanopore-based drug delivery systems.

A suite of ddPCR assays targeting microbial pathogens for improved management of shellfish aquaculture

The shellfish aquaculture industry is one of the fastest-growing sectors of global food production, but it is currently facing major challenges stemming from microbial pathogens. This study presents an optimized and validated suite of droplet digital PCR (ddPCR) assays using water samples proximal to oyster farms in North Carolina to quantify pathogens relevant to the aquaculture industry. Two of the molecular assays enable the quantification of the pathogens, Vibrio parahaemolyticus and Perkinsus marinus, that threaten human health and oyster performance, respectively. This work also introduces two ddPCR assays that enable the simultaneous quantification of at least nine ecologically relevant Vibrio spp. using only two sets of primers and probes targeting the glycosyl hydrolase family 18 (GH18) domain of the chiA gene in Vibrio bacteria. The entire suite of assays was applied to single assessments at 12 sites, revealing heterogeneity in microbial pathogen concentrations across the coastal landscape and variability of abundances within individual estuarine river systems. Additionally, a longitudinal study conducted at a demonstration lease elucidated unique temporal trends for all microbial targets. Notably, when concentrations of Vibrio spp. quantified using the two assays targeting the chiA gene reached their maximum, the daily probability of mortality increased, suggesting a role for other ecologically pertinent Vibrio spp. in the progression of mortality that would otherwise be missed. This study highlights the utility of ddPCR for the advancement of shellfish management by offering insights into the spaciotemporal dynamics of microbial pathogens.

IMPORTANCE

Climate change is drastically altering the environment and changing the abundance and geographical distribution of marine pathogens. These microbial species put additional pressure on the aquaculture industry by acting as sources of disease for animals important to the food industry as well as for humans upon consumption of contaminated food. To address growing concerns, high-resolution monitoring of pathogens can offer insights for effective management in a critical industry. Validated in the field, the suite of molecular droplet digital PCR assays presented here improves upon current methods, enabling the simultaneous quantification of several targets. This technology makes it possible to track pathogens as they move through the environment and reveals changes in abundance that may inform adjustments to farming practices aimed at mitigating negative outcomes. Additionally, this work presents a unique approach to molecular assay design that unveils potential drivers of ecological shifts and emerging etiologies of disease more efficiently.

Secretome analysis of the chitinolytic machinery of Chitiniphilus shinanonensis and its implication in chitooligosaccharide production

Chitin's robust structure poses significant challenges for degradation, necessitating the study of microbial processes in chitin-rich environments. We assessed the chitinolytic bacterium Chitiniphilus shinanonensis DSM 23277T (SAY3T) for converting chitin biomass into valuable saccharides using various substrates (chitin flakes, α-chitin, and β-chitin) in shake flask cultures. The bacterium successfully grew on all substrates, achieving complete degradation, although chitin flakes required more time. Maximum growth was observed on β-chitin, followed by α-chitin and chitin flakes. Scanning electron microscopy confirmed bacterial colonization and potential hydrolytic activity on chitin flakes. Proteomic analysis via nanoLC-MS/MS identified 32 chitin-degrading enzymes distributed across secretome, periplasmic, and intracellular fractions, with a notable expression of glycoside hydrolases (families 18, 19, and 20), carbohydrate esterases (family 4), and auxiliary activity proteins (family 10). Among the family 18 chitinases, ChiM, ChiI, and ChiL were significantly upregulated on all chitinous substrates compared to glucose. The chitin-active-secretome exhibited optimal activity at pH 8.0 and 45 °C in 50 mM Tris-HCl. Moreover, the chitin-active-secretome effectively degraded chitin flakes, α-chitin, and β-chitin into chitobiose and GlcNAc, with β-chitin yielding the highest chitobiose levels. The diverse chitin-degrading enzymes of C. shinanonensis efficiently utilize recalcitrant chitin as a carbon and energy source, underscoring its industrial potential for chitin degradation.

Functional genomics of chitin degradation by Vibrio parahaemolyticus reveals finely integrated metabolic contributions to support environmental fitness

Vibrio species are marine prokaryotes that inhabit diverse ecological niches, colonizing abiotic and biotic surfaces. These bacteria are vital players in the global carbon cycle, assimilating billions of tonnes of chitin for carbon (and nitrogen) metabolites. Many bacterial proteins involved in the process-including chitinases, sugar transporters, and modifying enzymes-have been well studied. However, the genetic functional interplay and key drivers of Vibrio competitive survival in the presence of chitin as the dominant carbon source is not understood. To address this question, we carried out transposon sequencing (Tn-seq) to determine the genetic fitness of Vibrio parahaemolyticus mutants grown on chitin as a sole carbon source. Along with validating known Vibrio genes associated with chitin metabolism, our data newly identified vital roles for an unclassified OprD-like import chitoporin and a HexR family transcriptional regulator. Furthermore, we functionally implicated HexR in regulating multiple physiological processes involved in V. parahaemolyticus environmental survival including carbon assimilation and cell growth, biofilm formation, and cell motility. Under nutrient limiting conditions, our data revealed a requirement for HexR in filamentous cell morphology, a critical trait for V. parahaemolyticus environmental fitness. Therefore, a vital import porin and genomic regulation mediated by HexR support multiple physiological processes for Vibrio chitinolytic growth and environmental fitness.

Specialists regulate microbial network and community assembly in subtropical seagrass sediments under differing land use conditions

Microorganisms in the sediment play a pivotal role in the functioning and stability of seagrass ecosystems and their dynamics are influenced by the nutrient acquisition strategies of host plants. While the distinct impacts of microbial generalists and specialists on community dynamics are recognized, their distribution patterns and ecological roles within seagrass ecosystems remain largely unexplored. To address this issue, we conducted an analysis of community assembly processes and co-occurrence relationships of both microbial generalists and specialists within sediment profiles (0-100 cm) from seagrass habitats subjected to differing land use conditions. The results revealed that seagrasses in Yifeng Estuary experienced the large proportion of cultivated land and exhibited higher organic carbon content in the 0-20 cm surface sediment layer. Nitrogen-cycling bacteria were predominantly associated with seagrasses from Yifeng Estuary, whereas Vibrio spp. was more prevalent in seagrasses from Liusha Bay. Notably, seagrass Halophia beccarii (YHB) in Yifeng Estuary harbored higher niche breadths for both microbial generalist and specialist compared to Halodule uninervis (LHU) and Halophia ovalis (LHO) from Liusha Bay. Stochastic processes were pivotal in shaping seagrass sediment microbial communities, with a higher immigration rate observed in YHB, suggesting greater microbial turnover in this area. Additionally, YHB sediment presented lower drift and higher dispersal limitation among generalists compared to LHU and LHO, whereas the pattern was reversed among specialists. Specialists were found to play a crucial role in shaping microbial interactions within YHB sediment, with genera Halioglobus identified as keystone species in the network. The specialists were further found to significantly influence microbial β-diversity in seagrass sediment directly. Overall, our findings illustrated how microbial generalists and specialists were distributed in seagrass sediments in response to land use changes and provided new insights into the potential roles of microbial regulation in degraded seagrass ecosystems.

Nanodots functionalized with chitooligosaccharides for blocking chitoporins

We report the synthesis of functionalized nanodots as potential powerful blockers of solute transport through a chitoporin. Ultrasmall silica nanocapsules with a diameter of ∼ 6 nm were coated with chitooligosaccharides to be used as a "lid" binding to the opening of the chitoporin VhChiP of Vibrio campbellii. Efficient blocking is attributed to the adequate size of the nanodots and their functionalization with oligochitosan, which has strong affinity towards the Vibrio chitoporin. This strategy paves the way towards the development of nanomaterials for blocking other porins.

Conformational flexibility driving charge-selective substrate translocation across a bacterial transporter

Bacterial membrane porins facilitate the translocation of small molecules while restricting large molecules, and this mechanism remains elusive at the molecular level. Here, we investigate the selective uptake of large cyclic sugars across an unusual passive membrane transporter, CymA, comprising a charged zone and a constricting N terminus segment. Using a combination of electrical recordings, protein mutagenesis and molecular dynamics simulations, we establish substrate translocation across CymA governed by the electrostatic pore properties and conformational dynamics of the constriction segment. Notably, we show that the variation in pH of the environment resulted in reversible modulation of the substrate binding site in the pore, thereby regulating charge-selective transport of cationic, anionic and neutral cyclic sugars. The quantitative kinetics of cyclic sugar translocation across CymA obtained in electrical recordings at different pHs are comparable with molecular dynamics simulations that revealed the transport pathway, energetics and favorable affinity sites in the pore for substrate binding. We further define the molecular basis of cyclic sugar translocation and establish that the constriction segment is flexible and can reside inside or outside the pore, regulating substrate translocation distinct from the ligand-gated transport mechanism. Our study provides novel insights into energy-independent large molecular membrane transport for targeted drug design strategies.

Enzymatically prepared neoagarooligosaccharides improve gut health and function through promoting the production of spermidine by Faecalibacterium in chickens

Maintaining animal gut health through modulating the gut microbiota is a constant need when antibiotics are not used in animal feed during the food animal production process. Prebiotics is regarded as one of the most promising antibiotic alternatives for such purpose. As an attractive prebiotic, the role and mechanisms of neoagarooligosaccharides (NAOS) in promoting animal growth and gut health have not been elucidated. In this study, we first cloned and expressed marine bacterial β-agarase in yeast to optimize the NAOS preparation and then investigated the role and the underlying mechanisms of the prepared NAOS in improving chicken gut health and function. The marine bacterial β-agarase PDE13B was expressed in Pichia pastoris GS115 and generated even-numbered NAOS. Dietary the prepared NAOS promoted chicken growth and improved intestinal morphology, its barrier, and digestion capabilities, and absorption function. Metagenomic analysis indicated that NAOS modulated the chicken gut microbiota structure and function, and microbial interactions, and promoted the growth of spermidine-producing bacteria especially Faecalibacterium. Through integration of gut metagenome, gut content metabolome, and gut tissue transcriptome, we established connections among NAOS, gut microbes, spermidine, and chicken gut gene expression. The spermidine regulation of genes related to autophagy, immunity, and inflammation was further confirmed in chicken embryo intestinal epithelium cells. We also verified that NAOS can be utilized by Faecalibacterium prausnitzii to grow and produce spermidine in in vitro experiments. Collectively, we provide a systematic investigation of the role of NAOS in regulating gut health and demonstrate the microbial spermidine-mediated mechanism involved in prebiotic effects of NAOS, which lays foundation for future use of NAOS as a new antibiotic alternative in animal production.

Structural insights of a SusD-like protein in marine Bacteroidetes bacteria reveal the molecular basis for chitin recognition and acquisition

Efficient recognition and transportation of chitin oligosaccharides are crucial steps for the utilization of chitin by heterotrophic bacteria. In this study, we employed structural biological and biochemical approaches to investigate the substrate recognition and acquisition mechanism of a novel chitin-binding SusD-like protein, AqSusD, which is derived from the chitin utilization gene cluster of a marine Bacteroides strain (Aquimarina sp. SCSIO 21287). We resolved the crystal structures of the AqSusD apo-protein and its complex with chitin oligosaccharides. Our results revealed that some crucial residues (Gln67, Phe87, and Asp276) underwent significant conformational changes to form tighter substrate binding sites for ligand binding. Moreover, we identified the functions of key amino acid residues and discovered that π-π stacking and hydrogen bonding between AqSusD and the ligand played significant roles in recognition of the protein for chitin oligosaccharide binding. Based on our findings and previous investigations, we put forward a model for the mechanism of chitin oligosaccharide recognition, capture, and transport by AqSusD, in collaboration with the membrane protein AqSusC. Our study deepens the understanding of the molecular-level "selfish" use of polysaccharides such as chitin by Bacteroides.

Complete genome sequence of a winter season Vibrio facilitates discovery of a novel subclade of cold-adapted species in the albus clade

In temperate marine climate zones, seasonal changes in water temperature contribute to distinct populations of warm- and cold-water vibrios. We report here the complete genome sequence (BUSCO score=94.8) of the novel strain Vibrio sp. VB16 isolated in late winter from the intertidal zone near Virginia Beach, Virginia, USA with the ability to form colonies at 4 °C. The 5.2 Mbp genome is composed of a large (3.6 Mbp) and small (1.6 Mbp) chromosome. Based on paired average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH), V. sp. VB16 is the same species as V. sp. UBA2437 from a North Sea tidal flat and is closely related to V. sp. DW001 from Antarctic sea ice. Our phylogenomic and bioinformatic analyses placed VB16, UBA2437 and DW001 into a cold-tolerant subclade within the albus clade, along with two non-cold-tolerant subclades. Orthovenn analysis indicated that VB16 and its other albus clade members shared 1544 gene orthologue clusters, including clusters for biosynthesis of polar flagella and tight adhesion pili that predict multiple lifestyles, either free-living or as an opportunistic pathogen within a marine eukaryotic host. The cold-tolerant subclade shared 552 orthologue proteins, including genes known to promote survival in cold or freezing temperatures, such as the eicosapentaenoic acid biosynthetic gene cluster, syp exopolysaccharide gene cluster and novel giant proteins with ice-binding domains. This subclade represents a group of psychrotolerant or 'moderate psychrophile' winter season Vibrio species. The discovery of this subclade opens the door for experimental work on the physiological features, virulence potential and ecological importance of this subclade.

Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation

Periplasmic solute-binding proteins (SBPs) specific for chitooligosaccharides, (GlcNAc)n (n = 2, 3, 4, 5 and 6), are involved in the uptake of chitinous nutrients and the negative control of chitin signal transduction in Vibrios. Most translocation processes by SBPs across the inner membrane have been explained thus far by two-domain open/closed mechanism. Here we propose three-domain mechanism of the (GlcNAc)n translocation based on experiments using a recombinant VcCBP, SBP specific for (GlcNAc)n from Vibrio cholerae. X-ray crystal structures of unliganded or (GlcNAc)3-liganded VcCBP solved at 1.2-1.6 Å revealed three distinct domains, the Upper1, Upper2 and Lower domains for this protein. Molecular dynamics simulation indicated that the motions of the three domains are independent and that in the (GlcNAc)3-liganded state the Upper2/Lower interface fluctuated more intensively, compared to the Upper1/Lower interface. The Upper1/Lower interface bound two GlcNAc residues tightly, while the Upper2/Lower interface appeared to loosen and release the bound sugar molecule. The three-domain mechanism proposed here was fully supported by binding data obtained by thermal unfolding experiments and ITC, and may be applicable to other translocation systems involving SBPs belonging to the same cluster.

Inherited chitinases enable sustained growth and rapid dispersal of bacteria from chitin particles

Many biogeochemical functions involve bacteria utilizing solid substrates. However, little is known about the coordination of bacterial growth with the kinetics of attachment to and detachment from such substrates. In this quantitative study of Vibrio sp. 1A01 growing on chitin particles, we reveal the heterogeneous nature of the exponentially growing culture comprising two co-existing subpopulations: a minority replicating on chitin particles and a non-replicating majority which was planktonic. This partition resulted from a high rate of cell detachment from particles. Despite high detachment, sustained exponential growth of cells on particles was enabled by the enrichment of extracellular chitinases excreted and left behind by detached cells. The 'inheritance' of these chitinases sustains the colonizing subpopulation despite its reduced density. This simple mechanism helps to circumvent a trade-off between growth and dispersal, allowing particle-associated marine heterotrophs to explore new habitats without compromising their fitness on the habitat they have already colonized.

Structural bioinformatics studies of bacterial outer membrane beta-barrel transporters and their AlphaFold2 predicted water-soluble QTY variants

Beta-barrel outer membrane proteins (OMP) are integral components of Gram-negative bacteria, eukaryotic mitochondria, and chloroplasts. They play essential roles in various cellular processes including nutrient transport, membrane stability, host-pathogen interactions, antibiotic resistance and more. The advent of AlphaFold2 for accurate protein structure predictions transformed structural bioinformatic studies. We previously used a QTY code to convert hydrophobic alpha-helices to hydrophilic alpha-helices in over 50 membrane proteins with all alpha-helices. The QTY code systematically replaces hydrophobic leucine (L), isoleucine (I), valine (V), and phenylalanine (F) with hydrophilic glutamine (Q), threonine (T), and tyrosine (Y). We here present a structural bioinformatic analysis of five outer membrane beta-barrel proteins with known molecular structures, including a) BamA, b) Omp85 (also called Sam50), c) FecA, d) Tsx, and e) OmpC. We superposed the structures of five native beta-barrel outer membrane proteins and their AlphaFold2-predicted corresponding QTY variant structures. The superposed structures of OMPs and their QTY variants exhibit remarkable structural similarity, as evidenced by residue mean square distance (RMSD) values between 0.206Å to 0.414Å despite the replacement of at least 22% (Transmembrane variation) of the amino acids in the transmembrane regions. We also show that native outer membrane proteins and QTY variants have different hydrophobicity patches. Our study provides important insights into the differences between hydrophobic and hydrophilic beta-barrels and validates the QTY code for studying beta-barrel membrane proteins and perhaps other hydrophobic aggregated proteins. Our findings demonstrate that the QTY code can be used as a simple tool for designing hydrophobic proteins in various biological contexts.

Structural displacement model of chitooligosaccharide transport through chitoporin

VhChiP is a chitooligosaccharide-specific porin identified in the outer membrane of Vibrio campbellii type strain American Type Culture Collection BAA 1116. VhChiP contains three identical subunits, and in each subunit, the 19-amino acid N-terminal segment serves as a molecular plug (the "N-plug") that controls the closed/open dynamics of the neighboring pores. In this study, the crystal structures of VhChiP lacking the N-plug were determined in the absence and presence of chitohexaose. Binding studies of sugar-ligand interactions by single-channel recordings and isothermal microcalorimetry experiments suggested that the deletion of the N-plug peptide significantly weakened the sugar-binding affinity due to the loss of hydrogen bonds around the central affinity sites. Steered molecular dynamic simulations revealed that the movement of the sugar chain along the sugar passage triggered the ejection of the N-plug, while the H-bonds transiently formed between the reducing end GlcNAc units of the sugar chain with the N-plug peptide may help to facilitate sugar translocation. The findings enable us to propose the structural displacement model, which enables us to understand the molecular basis of chitooligosaccharide uptake by marine Vibrio bacteria.

Bioconversion of chitin into chitin oligosaccharides using a novel chitinase with high chitin-binding capacity

Chitin is the second largest renewable biomass resource in nature, it can be enzymatically degraded into high-value chitin oligosaccharides (CHOSs) by chitinases. In this study, a chitinase (ChiC8-1) was purified and biochemically characterized, its structure was analyzed by molecular modeling. ChiC8-1 had a molecular mass of approximately 96 kDa, exhibited its optimal activity at pH 6.0 and 50 °C. The K_m and V_max values of ChiC8-1 towards colloidal chitin were 10.17 mg mL^-1 and 13.32 U/mg, respectively. Notably, ChiC8-1 showed high chitin-binding capacity, which may be related to the two chitin binding domains in the N-terminal. Based on the unique properties of ChiC8-1, a modified affinity chromatography method, which combines protein purification with chitin hydrolysis process, was developed to purify ChiC8-1 while hydrolyzing chitin. In this way, 9.36 ± 0.18 g CHOSs powder was directly obtained by hydrolyzing 10 g colloidal chitin with crude enzyme solution. The CHOSs were composed of 14.77-2.83 % GlcNAc and 85.23-97.17 % (GlcNAc)₂ at different enzyme-substrate ratio. This process simplifies the tedious purification and separation steps, and may enable its potential application in the field of green production of chitin oligosaccharides.

Shell disease syndromes of decapod crustaceans

The term shell disease subsumes a number of debilitating conditions affecting the outer integument (the carapace) of decapod crustaceans, such as lobsters and crabs. Herein, we seek to find commonality in the aetiology and pathology of such conditions, and those cases that result in the progressive erosion of the cuticle through to the visceral tissues by a cocktail of microbial-derived enzymes including lipases, proteases and chitinases. Aquimarina spp. are involved in shell disease in many different crustaceans across a wide geographical area, but the overall view is that the condition is polymicrobial in nature leading to dysbiosis within the microbial consortium of the damaged cuticle. The role of environment, decapod behaviour and physiology in triggering this disease is also reviewed. Finally, we provide a conceptual model for disease aetiology and suggest several avenues for future research that could improve our understanding of how such factors trigger, or exacerbate, this condition.

Synergic chitin degradation by Streptomyces sp. SCUT-3 chitinases and their applications in chitinous waste recycling and pathogenic fungi biocontrol

The genus Streptomyces comprises the most important chitin decomposers in soil and revealing their chitinolytic machinery is beneficial for the conversion of chitinous wastes. Streptomyces sp. SCUT-3, a chitin-hydrolyzing and a robust feather-degrading bacterium, was isolated previously. The potential chitin-degrading enzymes produced by SCUT-3 were analyzed in the present study. Among these enzymes, three chitinases were successfully expressed in Pichia pastoris at comparatively high yields of 4.8 U/mL (SsExoChi18A), 11.2 U/mL (SsExoChi18B), and 17.8 U/mL (SsEndoChi19). Conserved motifs and constructive 3D structures of these three exo- and endochitinases were also analyzed. These chitinases hydrolyzed colloidal chitin to chitin oligomers. SsExoChi18A showed apparent synergic effects with SsEndoChi19 in colloidal chitin and shrimp shell hydrolysis, with an improvement of 29.3 % and 124.9 %, respectively. Compared with SsExoChi18B and SsEndoChi19, SsExoChi18A exhibited the strongest antifungal effects against four plant pathogens by inhibiting mycelial growth and spore germination. This study provided good candidates for chitinous waste-processing enzymes and antifungal biocontrol agents. These synergic chitin-degrading enzymes of SCUT-3 are good targets for its further genetical modification to construct super chitinous waste-degrading bacteria with strong abilities to hydrolyze both protein and chitin, thereby providing a direction for the future path of the chitinous waste recycling industry.

Single-channel characterization of the chitooligosaccharide transporter chitoporin (SmChiP) from the opportunistic pathogen Serratia marcescens

Serratia marcescens is an opportunistic pathogen that can utilize chitin as a carbon source, through its ability to produce chitin-degrading enzymes to digest chitin and membrane transporters to transport the degradation products (chitooligosaccharides) into the cells. Further characterization of these proteins is important to understand details of chitin metabolism. Here, we investigate the properties and function of the S. marcescens chitoporin, namely SmChiP, a chitooligosaccharide transporter. We show that SmChiP is a monomeric porin that forms a stable channel in artificial phospholipid membranes, with an average single-channel conductance of 0.5 ± 0.02 nS in 1 M KCl electrolyte. Additionally, we demonstrated that SmChiP allowed the passage of small molecules with a size exclusion limit of <300 Da and exhibited substrate specificity toward chitooligosaccharides, both in membrane and detergent-solubilized forms. We found that SmChiP interacted strongly with chitopentaose (K_d = 23 ± 2.0 μM) and chitohexaose (K_d = 17 ± 0.6 μM) but did not recognize nonchitose oligosaccharides (maltohexaose and cellohexaose). Given that S. marcescens can use chitin as a primary energy source, SmChiP may serve as a target for further development of nutrient-based antimicrobial therapies directed against multidrug antibiotic-resistant S. marcescens infections.

Selective Translocation of Cyclic Sugars through Dynamic Bacterial Transporter

The selective translocation of molecules through membrane pores is an integral process in cells. We present a bacterial sugar transporter, CymA of unusual structural conformation due to a dynamic N terminus segment in the pore, reducing its diameter. We quantified the translocation kinetics of various cyclic sugars of different charge, size, and symmetry across native and truncated CymA devoid of the N terminus using single-channel recordings. The chemically divergent cyclic hexasaccharides bind to the native and truncated pore with high affinity and translocate effectively. Specifically, these sugars bind and translocate rapidly through truncated CymA compared to native CymA. In contrast, larger cyclic heptasaccharides and octasaccharides do not translocate but bind to native and truncated CymA with distinct binding kinetics highlighting the importance of molecular charge, size and symmetry in translocation consistent with liposome assays. Based on the sugar-binding kinetics, we suggest that the N terminus most likely resides inside the native CymA barrel, regulating the transport rate of cyclic sugars. Finally, we present native CymA as a large nanopore sensor for the simultaneous single-molecule detection of various sugars at high resolution, establishing its functional versatility. This natural pore is expected to have several applications in nanobiotechnology and will help further our understanding of the fundamental mechanism of molecular transport.

Recognition of discrete export signals in early flagellar subunits during bacterial Type III secretion

Type III Secretion Systems (T3SS) deliver subunits from the bacterial cytosol to nascent cell surface flagella. Early flagellar subunits that form the rod and hook substructures are unchaperoned and contain their own export signals. A gate recognition motif (GRM) docks them at the FlhBc component of the FlhAB-FliPQR export gate, but the gate must then be opened and subunits must be unfolded to pass through the flagellar channel. This induced us to seek further signals on the subunits. Here, we identify a second signal at the extreme N-terminus of flagellar rod and hook subunits and determine that key to the signal is its hydrophobicity. We show that the two export signal elements are recognised separately and sequentially, as the N-terminal signal is recognised by the flagellar export machinery only after subunits have docked at FlhB_C via the GRM. The position of the N-terminal hydrophobic signal in the subunit sequence relative to the GRM appeared to be important, as a FlgD deletion variant (FlgD_short), in which the distance between the N-terminal signal and the GRM was shortened, 'stalled' at the export machinery and was not exported. The attenuation of motility caused by FlgD_short was suppressed by mutations that destabilised the closed conformation of the FlhAB-FliPQR export gate, suggesting that the hydrophobic N-terminal signal might trigger opening of the flagellar export gate.

The C2 entity of chitosugars is crucial in molecular selectivity of the Vibrio campbellii chitoporin

The marine bacterium Vibrio campbellii expresses a chitooligosaccharide-specific outer-membrane channel (chitoporin) for the efficient uptake of nutritional chitosugars that are externally produced through enzymic degradation of environmental host shell chitin. However, the principles behind the distinct substrate selectivity of chitoporins are unclear. Here, we employed black lipid membrane (BLM) electrophysiology, which handles the measurement of the flow of ionic current through porins in phospholipid bilayers for the assessment of porin conductivities, to investigate the pH dependency of chitosugar-chitoporin interactions for the bacterium's natural substrate chitohexaose and its deacetylated form, chitosan hexaose. We show that efficient passage of the N-acetylated chitohexaose through the chitoporin is facilitated by its strong affinity for the pore. In contrast, the deacetylated chitosan hexaose is impermeant; however, protonation of the C2 amino entities of chitosan hexaose allows it to be pulled through the channel in the presence of a transmembrane electric field. We concluded from this the crucial role of C2-substitution as the determining factor for chitoporin entry. A change from N-acetylamino- to amino-substitution effectively abolished the ability of approaching molecules to enter the chitoporin, with deacetylation leading to loss of the distinctive structural features of nanopore opening and pore access of chitosugars. These findings provide further understanding of the multistep pathway of chitin utilization by marine Vibrio bacteria and may guide the development of solid-state or genetically engineered biological nanopores for relevant technological applications.

A structural model for (GlcNAc)2 translocation via a periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria

VhCBP is a periplasmic chitooligosaccharide-binding protein mainly responsible for translocation of the chitooligosaccharide (GlcNAc)₂ across the double membranes of marine bacteria. However, structural and thermodynamic understanding of the sugar-binding/-release processes of VhCBP is relatively less. VhCBP displayed the greatest affinity toward (GlcNAc)₂, with lower affinity for longer-chain chitooligosaccharides [(GlcNAc)_3–4]. (GlcNAc)₄ partially occupied the closed sugar-binding groove, with two reducing-end GlcNAc units extending beyond the sugar-binding groove and barely characterized by weak electron density. Mutation of three conserved residues (Trp³⁶³, Asp³⁶⁵, and Trp⁵¹³) to Ala resulted in drastic decreases in the binding affinity toward the preferred substrate (GlcNAc)₂, indicating their significant contributions to sugar binding. The structure of the W513A–(GlcNAc)₂ complex in a ‘half-open’ conformation unveiled the intermediary step of the (GlcNAc)₂ translocation from the soluble CBP in the periplasm to the inner membrane–transporting components. Isothermal calorimetry data suggested that VhCBP adopts the high-affinity conformation to bind (GlcNAc)₂, while its low-affinity conformation facilitated sugar release. Thus, chitooligosaccharide translocation, conferred by periplasmic VhCBP, is a crucial step in the chitin catabolic pathway, allowing Vibrio bacteria to thrive in oceans where chitin is their major source of nutrients.

Inward-facing glycine residues create sharp turns in β-barrel membrane proteins

The transmembrane region of outer-membrane proteins (OMPs) of Gram-negative bacteria are almost exclusively β-barrels composed of between 8 and 26 β-strands. To explore the relationship between β-barrel size and shape, we modeled and simulated engineered variants of the Escherichia coli protein OmpX with 8, 10, 12, 14, and 16 β-strands. We found that while smaller barrels maintained a roughly circular shape, the 16-stranded variant developed a flattened cross section. This flat cross section impeded its ability to conduct ions, in agreement with previous experimental observations. Flattening was determined to arise from the presence of inward-facing glycines at sharp turns in the β-barrel. An analysis of all simulations revealed that glycines, on average, make significantly smaller angles with residues on neighboring strands than all other amino acids, including alanine, and create sharp turns in β-barrel cross sections. This observation was generalized to 119 unique structurally resolved OMPs. We also found that the fraction of glycines in β-barrels decreases as the strand number increases, suggesting an evolutionary role for the addition or removal of glycine in OMP sequences.

Probing the physiological roles of the extracellular loops of chitoporin from Vibrio campbellii

VhChiP, a sugar-specific porin found on the outer membrane of Vibrio campbellii, is responsible for the transport of chitooligosaccharides, allowing the bacterium to thrive in aquatic environments using chitin as a nutrient. We previously showed that VhChiP is composed of three identical subunits, each containing a 16-stranded β-barrel connected by eight extracellular loops and eight short periplasmic turns. This study is focused on the specific roles of three prominent extracellular loops of VhChiP-L2, L3, and L8. The deletion of L2 completely disrupted the L2-L2 interactions, thus destabilizing the protein trimers as well as the integrity of the secondary structure. The deletion of L3 caused a drastic loss in the binding affinity for sugar substrates because of the absence of a cluster of key amino acid residues that form the affinity sites. The removal of L8 induced pronounced gating, which is highly responsive to elevated potentials. Our data provide further information on the important roles of the three prominent loops of VhChiP: loop L2 maintains the trimeric structure and the integrity of secondary structure, loop L3 controls the binding affinity for sugar substrates, and loop L8 retains the stably open state of the channel.

Genome sequence of Vibrio fluvialis 362.3 isolated from coral Mussismilia braziliensis reveals genes related to marine environment adaptation

Vibrio fluvialis is a halophilic bacterium frequently found in estuarine and coastal waters environments. The strain 362.3 was isolated from Mussismilia braziliensis coral of Abrolhos Bank. In this study, to gain insights into the marine adaptation in V. fluvialis, we sequenced the genome of 362.3 strain, which comprised 4,607,294 bp with a G + C content of 50.2%. In silico analysis showed that V. fluvialis 362.2 encodes genes related to chitin catabolic pathway, iron metabolism, osmotic stress and membrane transport.

How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics

Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.

Links among extracellular enzymes, lignin degradation and cell growth establish the models to identify marine lignin-utilizing bacteria

A major conundrum in the isolation of prokaryotes from open environments is stochasticity. It is especially difficult to study low abundance groups where very little biological information exists, although single-cell genomics and metagenomics have alleviated some of this bottleneck. Here, we report an approach to capture lignin-utilizing bacteria by linking a physical model to actual organisms. Extracellular enzymes, lignin degradation and cell growth are crucial phenotypes of lignin-utilizing bacteria, but their interrelationships remain poorly understood. In this study, the phenotypes of bacteria isolated from in situ lignocellulose enrichment samples in coastal waters were traced and statistically analysed. It suggested cell growth, dye-decolorizing peroxidase (DyP) and reactive oxygen species (ROS) were significantly correlated with lignin degradation, exhibiting a genus-specific property. The established models enabled us to efficiently capture lignin-utilizing bacteria and rapidly evaluate lignin degradation for Bacillus and Vibrio strains. Through the model, we identified several previously unrecognized marine bacterial lignin degraders. Moreover, it demonstrated that the isolated marine lignin-utilizing bacteria employ a DyP-based system and ROS for lignin depolymerization, providing insights into the mechanism of marine bacterial lignin degradation. Our findings should have implications beyond the capture of lignin-utilizing bacteria, in the isolation of other microorganisms with as-yet-unknown molecular biomarkers.

Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization

Serratia marcescens is an opportunistic pathogen that commonly causes hospital-acquired infections and can utilize chitin-enriched nutrients as an alternative energy source. This study reports the identification of a chitoporin (ChiP), termed SmChiP, from the outer membrane of S. marcescens. Sequence alignment with genetically characterized ChiPs suggests that SmChiP is more closely related to the monomeric EcChiP from Escherichia coli than to the trimeric VhChiP from Vibrio campbellii. A single crystal of SmChiP grown under the condition 22%(w/v) PEG 8000, 0.1 M calcium acetate, 0.1 M MES pH 6.0 diffracted X-ray synchrotron radiation to 1.85 Å resolution. SmChiP co-crystallized with chitohexaose under the condition 19%(w/v) PEG 1500, 2 M ammonium phosphate monobasic, 0.1 M HEPES pH 7.0 diffracted X-rays to 2.70 Å resolution. Preliminary crystallographic analysis shows that both SmChiP crystal forms contain one molecule per asymmetric unit and that they belong to the tetragonal space groups P42212 and P41212, respectively. The SmChiP crystal has unit-cell parameters a = 82.97, b = 82.97, c = 189.53 Å, α = β = γ = 90°, while the crystal of SmChiP in complex with chitohexaose has unit-cell parameters a = 73.24, b = 73.24, c = 213.46 Å, α = β = γ = 90°. Initial assessment of the complex structure clearly revealed electron density for the sugar ligand. Structure determination of SmChiP in the absence and presence of chitohexaose should reveal the molecular basis of chitin utilization by S. marcescens.

Vibrio campbellii chitoporin: Thermostability study and implications for the development of therapeutic agents against Vibrio infections

Vibrio campbellii (formerly Vibrio harveyi) is a bacterial pathogen that causes vibriosis, which devastates fisheries and aquaculture worldwide. V. campbellii expresses chitinolytic enzymes and chitin binding/transport proteins, which serve as excellent targets for antimicrobial agent development. We previously characterized VhChiP, a chitooligosaccharide-specific porin from the outer membrane of V. campbellii BAA-1116. This study employed far-UV circular dichroism and tryptophan fluorescence spectroscopy, together with single channel electrophysiology to demonstrate that the strong binding of chitoligosaccharides enhanced thermal stability of VhChiP. The alanine substitution of Trp¹³⁶ at the center of the affinity sites caused a marked decrease in the binding affinity and decreased the thermal stability of VhChiP. Tryptophan fluorescence titrations over a range of temperatures showed greater free-energy changes on ligand binding (ΔG°_binding) with increasing chain length of the chitooligosaccharides. Our findings suggest the possibility of designing stable channel-blockers, using sugar-based analogs that serve as antimicrobial agents, active against Vibrio infection.

Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria

β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.

Single-channel properties, sugar specificity, and role of chitoporin in adaptive survival of Vibrio cholerae type strain O1

Vibrio cholerae is a Gram-negative, facultative anaerobic bacterial species that causes serious disease and can grow on various carbon sources, including chitin polysaccharides. In saltwater, its attachment to chitin surfaces not only serves as the initial step of nutrient recruitment but is also a crucial mechanism underlying cholera epidemics. In this study, we report the first characterization of a chitooligosaccharide-specific chitoporin, VcChiP, from the cell envelope of the V. cholerae type strain O1. We modeled the structure of VcChiP, revealing a trimeric cylinder that forms single channels in phospholipid bilayers. The membrane-reconstituted VcChiP channel was highly dynamic and voltage induced. Substate openings O1', O2', and O3', between the fully open states O1, O2, and O3, were polarity selective, with nonohmic conductance profiles. Results of liposome-swelling assays suggested that VcChiP can transport monosaccharides, as well as chitooligosaccharides, but not other oligosaccharides. Of note, an outer-membrane porin (omp)-deficient strain of Escherichia coli expressing heterologous VcChiP could grow on M9 minimal medium supplemented with small chitooligosaccharides. These results support a crucial role of chitoporin in the adaptive survival of bacteria on chitinous nutrients. Our findings also suggest a promising means of vaccine development based on surface-exposed outer-membrane proteins and the design of novel anticholera agents based on chitooligosaccharide-mimicking analogs.

Nanopore Passport Control for Substrate-Specific Translocation

Membrane protein pores have demonstrated applications in nanobiotechnology and single-molecule chemistry for effective detection of biomolecules. Here, we define the molecular basis of carbohydrate polymers translocation through a substrate-specific bacterial nanopore, CymA, which has a 15-residue N terminus segment inside the pore, restricting its diameter. Using single-channel recordings, we determined the kinetics of cationic cyclic oligosaccharide binding and elucidated the translocation mechanism across the pore in real-time. The cationic cyclic hexasaccharide binds to the densely packed negatively charged residues at the extracellular side of the pore with high affinity, facilitating its entry into the pore driven by the applied voltage. Further, the dissociation rate constant increased with increasing voltages, indicating unidirectional translocation toward the pore exit. Specifically, a larger cationic cyclic octasaccharide rapidly blocked the pore more effectively, resulting in the complete closure of the pore with increasing voltage, implying only strong binding. Further, we show that uncharged oligosaccharides exclusively bind to the extracellular side of the pore and the electroosmotic flow most likely drives their translocation. We propose that CymA favors selective translocation of cyclic hexasaccharide and linear maltooligosaccharides due to an asymmetrical charge pattern and the N terminus that regulates the substrate transport. We suggest that this substrate-specific nanopore with sophisticated geometry will be useful for complex biopolymer characterization.

Membrane directed expression in Escherichia coli of BBA57 and other virulence factors from the Lyme disease agent Borrelia burgdorferi

Membrane-embedded proteins are critical to the establishment, survival and persistence in the host of the Lyme disease bacterium Borrelia burgdorferi (Bb), but to date, there are no solved structures of transmembrane proteins representing these attractive therapeutic targets. All available structures from the genus Borrelia represent proteins expressed without a membrane-targeting signal peptide, thus avoiding conserved pathways that modify, fold and assemble membrane protein complexes. Towards elucidating structure and function of these critical proteins, we directed translocation of eleven expression-optimized Bb virulence factors, including the signal sequence, to the Escherichia coli membrane, of which five, BBA57, HtrA, BB0238, BB0323, and DipA, were expressed with C-terminal His-tags. P66 was also expressed using the PelB signal sequence fused to maltose binding protein. Membrane-associated BBA57 lipoprotein was solubilized by non-ionic and zwitterionic detergents. We show BBA57 translocation to the outer membrane, purification at a level sufficient for structural studies, and evidence for an α-helical multimer. Previous studies showed multiple critical roles of BBA57 in transmission, joint arthritis, carditis, weakening immune responses, and regulating other Bb outer surface proteins. In describing the first purification of membrane-translocated BBA57, this work will support subsequent studies that reveal the precise mechanisms of this important Lyme disease virulence factor.

Understanding microbial community dynamics to improve optimal microbiome selection

BACKGROUND

Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown.

RESULTS

Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms.

CONCLUSIONS

The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.

Effects of H-bonds on sugar binding to chitoporin from Vibrio harveyi

BACKGROUND

VhChiP is a sugar-specific-porin present in the outer membrane of the marine bacterium Vibrio harveyi and responsible for chitin uptake, with a high selectivity for chitohexaose.

METHODS

VhChiP and its mutants were expressed and purified from BL21 (DE3) Omp8 Rosetta strain. After reconstitution into planar lipid bilayers, the ion current fluctuations caused by chitohexaose entering the channel were measured in deuterium oxide and in water.

RESULTS

The role of hydrogen-bonding in sugar binding was investigated by comparing channel occlusion by chitohexaose in buffers containing H₂O and D₂O. The BLM results revealed the significant contribution of hydrogen bonding to the binding of chitohexaose in the constriction zone of VhChiP. Replacing H₂O as solvent by D₂O significantly decreased the on- and off-rates of sugar penetration into the channel. The importance of hydrogen bonding inside the channel was more noticeable when the hydrophobicity of the constriction zone was diminished by replacing Trp¹³⁶ with the charged residues Asp or Arg. The on- and off-rates decreased up to 2.5-fold and 4-fold when Trp¹³⁶ was replaced by Arg, or 5-fold and 3-fold for Trp¹³⁶ replacement by Asp, respectively. Measuring the on-rate at different temperatures and for different channel mutants revealed the activation energy for chitohexaose entrance into VhChiP channel.

CONCLUSIONS

Hydrogen-bonds contribute to sugar permeation.

Structural features underlying recognition and translocation of extracellular polysaccharides

Essentially all living systems produce complex carbohydrates as an energy source, structural component, protective coat or adhesive for cell attachment. Many polysaccharides are displayed on the cell surface or are threaded through proteinaceous tunnels for degradation. Dictated by their chemical composition and mode of polymerization, the physical properties of complex carbohydrates differ substantially, from amphipathic water-insoluble polymers to highly hydrated hydrogel-forming macromolecules. Accordingly, diverse recognition and translocation mechanisms evolved to transport polysaccharides to their final destinations. This review will summarize and compare diverse polysaccharide transport mechanisms implicated in the biosynthesis and degradation of cell surface polymers in pro- and eukaryotes.