Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria

Control of phosphodiesterase activity in the regulator of biofilm dispersal RbdA from Pseudomonas aeruginosa

The switch between planktonic and biofilm lifestyle correlates with intracellular concentration of the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). While bacteria possess cyclase and phosphodiesterase enzymes to catalyse formation or hydrolysis of c-di-GMP, both enzymatic domains often occur in a single protein. It is tacitly assumed that one of the two enzymatic activities is dominant, and that additional domains and protein interactions enable responses to environmental conditions and control activity. Here we report the structure of the phosphodiesterase domain of the membrane protein RbdA (regulator of biofilm dispersal) in a dimeric, activated state and show that phosphodiesterase activity is controlled by the linked cyclase. The phosphodiesterase region around helices α5/α6 forms the dimer interface, providing a rationale for activation, as this region was seen in contact with the cyclase domain in an auto-inhibited structure previously described. Kinetic analysis supports this model, as the activity of the phosphodiesterase alone is lower when linked to the cyclase. Analysis of a computed model of the RbdA periplasmatic domain reveals an all-helical architecture with a large binding pocket that could accommodate putative ligands. Unravelling the regulatory circuits in multi-domain phosphodiesterases like RbdA is important to develop strategies to manipulate or disperse bacterial biofilms.

Exploring solute binding proteins in Pseudomonas aeruginosa that bind to γ-aminobutyrate and 5-aminovalerate and their role in activating sensor kinases

The standard method of receptor activation involves the binding of signals or signal-loaded solute binding proteins (SBPs) to sensor domains. Many sensor histidine kinases (SHKs), which are activated by SBP binding, are encoded adjacent to their corresponding sbp gene. We examined three SBPs of Pseudomonas aeruginosa PAO1, encoded near the genes for the AgtS (PA0600) and AruS (PA4982) SHKs, to determine how common this arrangement is. Ligand screening and microcalorimetric studies revealed that the SBPs PA0602 and PA4985 preferentially bind to GABA (KD = 2.3 and 0.58 μM, respectively), followed by 5-aminovalerate (KD = 30 and 1.6 μM, respectively) and ethanoldiamine (KD = 2.3 and 0.58 μM, respectively). In contrast, AgtB (PA0604) exclusively recognizes 5-aminovaleric acid (KD = 2.9 μM). However, microcalorimetric titrations did not show any binding between the AgtS sensor domain and AgtB or PA0602, regardless of the presence of ligands. Similarly, bacterial two-hybrid assays did not demonstrate an interaction between PA4985 and the AruS sensor domain. Therefore, sbp and shk genes located nearby are not always functionally linked. We previously identified PA0222 as a GABA-specific SBP. The presence of three SBPs for GABA may be linked to GABA's role as a trigger for P. aeruginosa virulence.

Characterization of the extracellular domain of sensor histidine kinase NagS from Paenibacillus sp. str. FPU-7: nagS interacts with oligosaccharide binding protein NagB1 in complexes with N, N'-diacetylchitobiose

We have previously isolated the Gram-positive chitin-degrading bacterium Paenibacillus sp. str. FPU-7. This bacterium traps chitin disaccharide (GlcNAc)2 on its cell surface using two homologous solute-binding proteins, NagB1 and NagB2. Bacteria use histidine kinase (HK) of the two-component regulatory system as an extracellular environment sensor. In this study, we found that nagS, which encodes a HK, is located next to the nagB1 gene. Biochemical experiments revealed that the NagS sensor domain (NagS30-294) interacts with the NagB1-(GlcNAc)2 complex. However, proof of NagS30-294 interacting with NagB1 without (GlcNAc)2 is currently unavailable. In contrast to NagB1, no complex formation was observed between NagS30-294 and NagB2, even in the presence of (GlcNAc)2. The NagS30-294 crystal structure at 1.8 Å resolution suggested that the canonical tandem-Per-Arnt-Sim fold recognizes the NagB1-(GlcNAc)2 complex. This study provides insight into the recognition of chitin oligosaccharides by bacteria.

The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin

The phytohormone cytokinin has various roles in plant development, including meristem maintenance, vascular differentiation, leaf senescence, and regeneration. Prior investigations have revealed that cytokinin acts via a phosphorelay similar to the two-component system by which bacteria sense and respond to external stimuli. The eventual targets of this phosphorelay are type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs), containing the conserved N-terminal receiver domain (RD), middle DNA binding domain (DBD), and C-terminal transactivation domain. While it has been established for two decades that the phosphoryl transfer from a specific histidyl residue in ARABIDOPSIS HIS PHOSPHOTRANSFER PROTEINS (AHPs) to an aspartyl residue in the RD of B-ARRs results in a rapid transcriptional response to cytokinin, the underlying molecular basis remains unclear. In this work, we determine the crystal structures of the RD-DBD of ARR1 (ARR1RD-DBD) as well as the ARR1DBD-DNA complex from Arabidopsis. Analyses of the ARR1DBD-DNA complex have revealed the structural basis for sequence-specific recognition of the GAT trinucleotide by ARR1. In particular, comparing the ARR1RD-DBD and ARR1DBD-DNA structures reveals that unphosphorylated ARR1RD-DBD exists in a closed conformation with extensive contacts between the RD and DBD. In vitro and vivo functional assays have further suggested that phosphorylation of the RD weakens its interaction with DBD, subsequently permits the DNA binding capacity of DBD, and promotes the transcriptional activity of ARR1. Our findings thus provide mechanistic insights into phosphorelay activation of gene transcription in response to cytokinin.

Role of the Solute-Binding Protein CuaD in the Signaling and Regulating Pathway of Cellobiose and Cellulose Utilization in Ruminiclostridium cellulolyticum

In Ruminiclostridium cellulolyticum, cellobiose is imported by the CuaABC ATP-binding cassette transporter containing the solute-binding protein (SBP) CuaA and is further degraded in the cytosol by the cellobiose phosphorylase CbpA. The genes encoding these proteins have been shown to be essential for cellobiose and cellulose utilization. Here, we show that a second SBP (CuaD), whose gene is adjacent to two genes encoding a putative two-component regulation system (CuaSR), forms a three-component system with CuaS and CuaR. Studies of mutant and recombinant strains of R. cellulolyticum have indicated that cuaD is important for the growth of strains on cellobiose and cellulose. Furthermore, the results of our RT-qPCR experiments suggest that both the three (CuaDSR)- and the two (CuaSR)-component systems are able to perceive the cellobiose signal. However, the strain producing the three-component system is more efficient in its cellobiose and cellulose utilization. As CuaD binds to CuaS, we propose an in-silico model of the complex made up of two extracellular domains of CuaS and two of CuaD. CuaD allows microorganisms to detect very low concentrations of cellobiose due to its high affinity and specificity for this disaccharide, and together with CuaSR, it triggers the expression of the cuaABC-cbpA genes involved in cellodextrins uptake.

β-D-XYLOSIDASE 4 modulates systemic immune signaling in Arabidopsis thaliana

Pectin- and hemicellulose-associated structures of plant cell walls participate in defense responses against pathogens of different parasitic lifestyles. The resulting immune responses incorporate phytohormone signaling components associated with salicylic acid (SA) and jasmonic acid (JA). SA plays a pivotal role in systemic acquired resistance (SAR), a form of induced resistance that - after a local immune stimulus - confers long-lasting, systemic protection against a broad range of biotrophic invaders. β-D-XYLOSIDASE 4 (BXL4) protein accumulation is enhanced in the apoplast of plants undergoing SAR. Here, two independent Arabidopsis thaliana mutants of BXL4 displayed compromised systemic defenses, while local resistance responses to Pseudomonas syringae remained largely intact. Because both phloem-mediated and airborne systemic signaling were abrogated in the mutants, the data suggest that BXL4 is a central component in SAR signaling mechanisms. Exogenous xylose, a possible product of BXL4 enzymatic activity in plant cell walls, enhanced systemic defenses. However, GC-MS analysis of SAR-activated plants revealed BXL4-associated changes in the accumulation of certain amino acids and soluble sugars, but not xylose. In contrast, the data suggest a possible role of pectin-associated fucose as well as of the polyamine putrescine as regulatory components of SAR. This is the first evidence of a central role of cell wall metabolic changes in systemic immunity. Additionally, the data reveal a so far unrecognized complexity in the regulation of SAR, which might allow the design of (crop) plant protection measures including SAR-associated cell wall components.

Structural basis of phosphorylation-induced activation of the response regulator VbrR

<p indent="0mm">Two-component systems typically consist of a paired histidine kinase and response regulator and couple environmental changes to adaptive responses. The response regulator VbrR from <italic>Vibrio parahaemolyticus</italic>, a member of the OmpR/PhoB family, regulates virulence and antibiotic resistance genes. The activation mechanism of VbrR remains unclear. Here, we report the crystal structures of full-length VbrR in complex with DNA in the active conformation and the N-terminal receiver domain (RD) and the C-terminal DNA-binding domain (DBD) in both active and inactive conformations. Structural and biochemical analyses suggest that unphosphorylated VbrR adopts mainly as inactive dimers through the DBD at the autoinhibitory state. The RD undergoes a monomer-to-dimer transition upon phosphorylation, which further induces the transition of DBD from an autoinhibitory dimer to an active dimer and enables its binding with target DNA. Our study suggests a new model for phosphorylation-induced activation of response regulators and sheds light on the pathogenesis of <italic>V</italic>. <italic>parahaemolyticus</italic>. </p>.

Characteristics of the GlnH and GlnX Signal Transduction Proteins Controlling PknG-Mediated Phosphorylation of OdhI and 2-Oxoglutarate Dehydrogenase Activity in Corynebacterium glutamicum

In Corynebacterium glutamicum the protein kinase PknG phosphorylates OdhI and thereby abolishes the inhibition of 2-oxoglutarate dehydrogenase activity by unphosphorylated OdhI. Our previous studies suggested that PknG activity is controlled by the periplasmic binding protein GlnH and the transmembrane protein GlnX, because ΔglnH and ΔglnX mutants showed a growth defect on glutamine similar to that of a ΔpknG mutant. We have now confirmed the involvement of GlnH and GlnX in the control of OdhI phosphorylation by analyzing the OdhI phosphorylation status and glutamate secretion in ΔglnH and ΔglnX mutants and by characterizing ΔglnX suppressor mutants. We provide evidence for GlnH being a lipoprotein and show by isothermal titration calorimetry that it binds l-aspartate and l-glutamate with moderate to low affinity, but not l-glutamine, l-asparagine, or 2-oxoglutarate. Based on a structural comparison with GlnH of Mycobacterium tuberculosis, two residues critical for the binding affinity were identified and verified. The predicted GlnX topology with four transmembrane segments and two periplasmic domains was confirmed by PhoA and LacZ fusions. A structural model of GlnX suggested that, with the exception of a poorly ordered N-terminal region, the entire protein is composed of α-helices and small loops or linkers, and it revealed similarities to other bacterial transmembrane receptors. Our results suggest that the GlnH-GlnX-PknG-OdhI-OdhA signal transduction cascade serves to adapt the flux of 2-oxoglutarate between ammonium assimilation via glutamate dehydrogenase and energy generation via the tricarboxylic acid (TCA) cycle to the availability of the amino group donors l-glutamate and l-aspartate in the environment. IMPORTANCE Actinobacteria comprise a large number of species playing important roles in biotechnology and medicine, such as Corynebacterium glutamicum, the major industrial amino acid producer, and Mycobacterium tuberculosis, the pathogen causing tuberculosis. Many actinobacteria use a signal transduction process in which the phosphorylation status of OdhI (corynebacteria) or GarA (mycobacteria) regulates the carbon flux at the 2-oxoglutarate node. Inhibition of 2-oxoglutarate dehydrogenase by unphosphorylated OdhI shifts the flux of 2-oxoglutarate from the TCA cycle toward glutamate formation and, thus, ammonium assimilation. Phosphorylation of OdhI/GarA is catalyzed by the protein kinase PknG, whose activity was proposed to be controlled by the periplasmic binding protein GlnH and the transmembrane protein GlnX. In this study, we combined genetic, biochemical, and structural modeling approaches to characterize GlnH and GlnX of C. glutamicum and confirm their roles in the GlnH-GlnX-PknG-OdhI-OdhA signal transduction cascade. These findings are relevant also to other Actinobacteria employing a similar control process.

The Repertoire of Solute-Binding Proteins of Model Bacteria Reveals Large Differences in Number, Type, and Ligand Range

Solute-binding proteins (SBPs) are of central physiological relevance for bacteria. They are located in the extracytosolic space, where they present substrates to transporters but also stimulate different types of transmembrane receptors coordinating compound uptake with signal transduction. SBPs are a superfamily composed of proteins recognized by 45 Pfam profiles. The definition of SBP profiles for bacteria is hampered by the fact that these Pfam profiles recognize sensor domains for different types of signaling proteins or cytosolic proteins with alternative functions. We report here the retrieval of the SBPs from 49 bacterial model strains with different lifestyles and phylogenetic distributions. Proteins were manually curated, and the ligands recognized were predicted bioinformatically. There were very large differences in the number and type of SBPs between strains, ranging from 7 SBPs in Helicobacter pylori 26695 to 189 SBPs in Sinorhizobium meliloti 1021. SBPs were found to represent 0.22 to 5.13% of the total protein-encoding genes. The abundance of SBPs was largely determined by strain phylogeny, and no obvious link with the bacterial lifestyle was noted. Most abundant (36%) were SBPs predicted to recognize amino acids or peptides, followed by those expected to bind different sugars (18%). To the best of our knowledge, this is the first comparative study of bacterial SBP repertoires. Given the importance of SBPs in nutrient uptake and signaling, this study enhances the knowledge of model bacteria and will permit the definition of SBP profiles of other strains. IMPORTANCE SBPs are essential components for many transporters, but multiple pieces of more recent evidence indicate that the SBP-mediated stimulation of different transmembrane receptors is a general and widespread signal transduction mechanism in bacteria. The double function of SBPs in coordinating transport with signal transduction remains to a large degree unexplored and represents a major research need. The definition of the SBP repertoire of the 49 bacterial model strains examined here, along with information on their cognate ligand profiles forms the basis to close this gap in knowledge. Furthermore, this study provides information on the forces that have driven the evolution of transporters with different ligand specificities in bacteria that differ in phylogenetics and lifestyle. This article is also a first step in setting up automatic algorithms that permit the large-scale identification of the SBP repertoire in proteomes.

Multivariate insights into enhanced biogas production in thermophilic dry anaerobic co-digestion of food waste with kitchen waste or garden waste: Process properties, microbial communities and metagenomic analyses

Multisubstrate synergetic anaerobic co-digestion can effectively overcome low efficiency of food waste (FW) mono-digestion. This study investigated the effect of supplementing FW with kitchen waste (KW) or garden waste (GW) on thermophilic dry anaerobic co-digestion. FW-KW and FW-GW co-digestion enhanced biogas production by 24.69 % and 44.96 % at organic loading rate (OLR) of 3 g VS L^-1 d^-1, and increased OLR tolerance from 3 to 4 g VS L^-1 d^-1 through mitigating ammonia nitrogen inhibition and volatile fatty acids accumulation. Co-digestion enriched the dominant hydrolytic bacteria Defluviitoga, resulting in an acceleration of substrate hydrolysis. FW-KW co-digestion improved biogas production by increasing gene abundance related to key enzymes in methanogenesis pathways and promoting the conversion of intermediate products into methane. FW-GW co-digestion enhanced biogas production by enriching ABC transporters-associated genes, leading to efficient substrate utilization. This study provides a promising approach for FW treatment with multivariate insights into thermophilic dry anaerobic co-digestion.

Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum

Sugar uptake is of great significance in industrially relevant microorganisms. Clostridium thermocellum has extensive potential in lignocellulose biorefineries as an environmentally prominent, thermophilic, cellulolytic bacterium. The bacterium employs five putative ATP-binding cassette transporters which purportedly take up cellulose hydrolysates. Here, we first applied combined genetic manipulations and biophysical titration experiments to decipher the key glucose and cellodextrin transporters. In vivo gene inactivation of each transporter and in vitro calorimetric and nuclear magnetic resonance (NMR) titration of each putative sugar-binding protein with various saccharides supported the conclusion that only transporters A and B play the roles of glucose and cellodextrin transport, respectively. To gain insight into the structural mechanism of the transporter specificities, 11 crystal structures, both alone and in complex with appropriate saccharides, were solved for all 5 putative sugar-binding proteins, thus providing detailed specific interactions between the proteins and the corresponding saccharides. Considering the importance of transporter B as the major cellodextrin transporter, we further identified its cryptic, hitherto unknown ATPase-encoding gene as clo1313_2554, which is located outside the transporter B gene cluster. The crystal structure of the ATPase was solved, showing that it represents a typical nucleotide-binding domain of the ATP-binding cassette (ABC) transporter. Moreover, we determined that the inducing effect of cellobiose (G2) and cellulose on cellulosome production could be eliminated by deletion of transporter B genes, suggesting the coupling of sugar transport and regulation of cellulosome components. This study provides key basic information on the sugar uptake mechanism of C. thermocellum and will promote rational engineering of the bacterium for industrial application.

Xylose Metabolism in Bacteria—Opportunities and Challenges towards Efficient Lignocellulosic Biomass-Based Biorefineries

In a sustainable society based on circular economy, the use of waste lignocellulosic biomass (LB) as feedstock for biorefineries is a promising solution, since LB is the world’s most abundant renewable and non-edible raw material. LB is available as a by-product from agricultural and forestry processes, and its main components are cellulose, hemicellulose, and lignin. Following suitable physical, enzymatic, and chemical steps, the different fractions can be processed and/or converted to value-added products such as fuels and biochemicals used in several branches of industry through the implementation of the biorefinery concept. Upon hydrolysis, the carbohydrate-rich fraction may comprise several simple sugars (e.g., glucose, xylose, arabinose, and mannose) that can then be fed to fermentation units. Unlike pentoses, glucose and other hexoses are readily processed by microorganisms. Some wild-type and genetically modified bacteria can metabolize xylose through three different main pathways of metabolism: xylose isomerase pathway, oxidoreductase pathway, and non-phosphorylative pathway (including Weimberg and Dahms pathways). Two of the commercially interesting intermediates of these pathways are xylitol and xylonic acid, which can accumulate in the medium either through manipulation of the culture conditions or through genetic modification of the bacteria. This paper provides a state-of-the art perspective regarding the current knowledge on xylose transport and metabolism in bacteria as well as envisaged strategies to further increase xylose conversion into valuable products.

The role of solute binding proteins in signal transduction

The solute binding proteins (SBPs) of prokaryotes are present in the extracytosolic space. Although their primary function is providing substrates to transporters, SBPs also stimulate different signaling proteins, including chemoreceptors, sensor kinases, diguanylate cyclases/phosphodiesterases and Ser/Thr kinases, thereby causing a wide range of responses. While relatively few such systems have been identified, several pieces of evidence suggest that SBP-mediated receptor activation is a widespread mechanism. (1) These systems have been identified in Gram-positive and Gram-negative bacteria and archaea. (2) There is a structural diversity in the receptor domains that bind SBPs. (3) SBPs belonging to thirteen different families interact with receptor ligand binding domains (LBDs). (4) For the two most abundant receptor LBD families, dCache and four-helix-bundle, there are different modes of interaction with SBPs. (5) SBP-stimulated receptors carry out many different functions. The advantage of SBP-mediated receptor stimulation is attributed to a strict control of SBP levels, which allows a precise adjustment of the systeḿs sensitivity. We have compiled information on the effect of ligands on the transcript/protein levels of their cognate SBPs. In 87 % of the cases analysed, ligands altered SBP expression levels. The nature of the regulatory effect depended on the ligand family. Whereas inorganic ligands typically downregulate SBP expression, an upregulation was observed in response to most sugars and organic acids. A major unknown is the role that SBPs play in signaling and in receptor stimulation. This review attempts to summarize what is known and to present new information to narrow this gap in knowledge.

Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria

Gut microbial transformations of flavonoids, an enormous class of polyphenolic compounds abundant in plant-based diets, are closely associated with human health. However, the enzymes that initiate the gut microbial metabolism of flavones and flavonols, the two most abundant groups of flavonoids, as well as their underlying molecular mechanisms of action remain unclear. Here, we discovered a flavone reductase (FLR) from the gut bacterium, Flavonifractor plautii ATCC 49531 (originally assigned as Clostridium orbiscindens DSM 6740), which specifically catalyses the hydrogenation of the C2–C3 double bond of flavones/flavonols and initiates their metabolism as a key step. Crystal structure analysis revealed the molecular basis for the distinct catalytic property of FLR. Notably, FLR and its widespread homologues represent a class of ene-reductases that has not been previously identified. Genetic and biochemical analyses further indicated the importance of FLR in gut microbial consumption of dietary and medicinal flavonoids, providing broader insight into gut microbial xenobiotic transformations and possible guidance for personalized nutrition and medicine.

Flavonoids are abundant polyphenols in plants but it is not well understood how their metabolism is initiated by microbes in the human gut. Here, the authors identify and characterise an ene-reductase from the gut bacterium, Flavonifractor plautii ATCC 49531 that catalyses the hydrogenation of the C2–C3 double bond of flavones and flavonols and present its crystal structure.

Interface switch mediates signal transmission in a two-component system

Two-component systems (TCS), which typically consist of a membrane-embedded histidine kinase and a cytoplasmic response regulator, are the dominant signaling proteins for transduction of environmental stimuli into cellular response pathways in prokaryotic cells. HptRSA is a recently identified TCS consisting of the G6P-associated sensor protein (HptA), transmembrane histidine kinase (HptS), and cytoplasmic effector (HptR). HptRSA mediates glucose-6-phosphate (G6P) uptake to support Staphylococcus aureus growth and multiplication within various host cells. How the mechanism by which HptRSA perceives G6P and triggers a downstream response has remained elusive. Here, we solved the HptA structures in apo and G6P-bound states. G6P binding in the cleft between two HptA domains caused a conformational closing movement. The solved structures of HptA in complex with the periplasmic domain of HptS showed that HptA interacts with HptS through both constitutive and switchable interfaces. The G6P-free form of HptA binds to the membrane-distal side of the HptS periplasmic domain (HptSp), resulting in a parallel conformation of the HptSp protomer pair. However, once HptA associates with G6P, its intramolecular domain closure switches the HptA-HptSp contact region into the membrane-proximal domain, which causes rotation and closure of the C termini of each HptSp protomer. Through biochemical and growth assays of HptA and HptS mutant variants, we proposed a distinct mechanism of interface switch-mediated signaling transduction. Our results provide mechanistic insights into bacterial nutrient sensing and expand our understanding of the activation modes by which TCS communicates external signals.

Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization

Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.

Investigating Nutrient Limitation Role on Improvement of Growth and Poly(3-Hydroxybutyrate) Accumulation by Burkholderia sacchari LMG 19450 From Xylose as the Sole Carbon Source

Burkholderia sacchari LMG19450, a non-model organism and a promising microbial platform, was studied to determine nutrient limitation impact on poly(3-hydroxybutyrate) [P(3HB)] production and bacterial growth from xylose, a major hemicellulosic residue. Nitrogen and phosphorus limitations have been studied in a number of cases to enhance PHA accumulation, but not combining xylose and B. sacchari. Within this strategy, it was sought to understand how to control PHA production and even modulate monomer composition. Nitrogen-limited and phosphorus-limited fed-batch experiments in bioreactors were performed to evaluate each one's influence on cell growth and poly(3-hydroxybutyrate) production. The mineral medium composition was defined based on yields calculated from typical results so that nitrogen was available during phosphorus limitation and residual phosphorus was available when limiting nitrogen. Sets of experiments were performed so as to promote cell growth in the first stage (supplied with initial xylose 15 g/L), followed by an accumulation phase, where N or P was the limiting nutrient when xylose was fed in pulses to avoid concentrations lower than 5 g/L. N-limited fed-batch specific cell growth (around 0.19 1/h) and substrate consumption (around 0.24 1/h) rates were higher when compared to phosphorus-limited ones. Xylose to PHA yield was similar in both conditions [0.37 g_P(3HB)/g_xyl]. We also described pst gene cluster in B. sacchari, responsible for high-affinity phosphate uptake. Obtained phosphorus to biomass yields might evidence polyphosphate accumulation. Results were compared with studies with B. sacchari and other PHA-producing microorganisms. Since it is the first report of the mentioned kinetic parameters for LMG 19450 growing on xylose solely, our results open exciting perspectives to develop an efficient bioprocess strategy with increased P(3HB) production from xylose or xylose-rich substrates.

Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins

Solute binding proteins (SBPs) form a heterogeneous protein family that is found in all kingdoms of life. In bacteria, the ligand-loaded forms bind to transmembrane transporters providing the substrate. We present here the SBP repertoire of Pseudomonas aeruginosa PAO1 that is composed of 98 proteins. Bioinformatic predictions indicate that many of these proteins have a redundant ligand profile such as 27 SBPs for proteinogenic amino acids, 13 proteins for spermidine/putrescine, or 9 proteins for quaternary amines. To assess the precision of these bioinformatic predictions, we have purified 17 SBPs that were subsequently submitted to high-throughput ligand screening approaches followed by isothermal titration calorimetry studies, resulting in the identification of ligands for 15 of them. Experimentation revealed that PA0222 was specific for γ-aminobutyrate (GABA), DppA2 for tripeptides, DppA3 for dipeptides, CysP for thiosulphate, OpuCC for betaine, and AotJ for arginine. Furthermore, RbsB bound D-ribose and D-allose, ModA bound molybdate, tungstate, and chromate, whereas AatJ recognized aspartate and glutamate. The majority of experimentally identified ligands were found to be chemoattractants. Data show that the ligand class recognized by SPBs can be predicted with confidence using bioinformatic methods, but experimental work is necessary to identify the precise ligand profile.

The Molecular Mechanism of Nitrate Chemotaxis via Direct Ligand Binding to the PilJ Domain of McpN

Chemotaxis and energy taxis permit directed bacterial movements in gradients of environmental cues. Nitrate is a final electron acceptor for anaerobic respiration and can also serve as a nitrogen source for aerobic growth. Previous studies indicated that bacterial nitrate taxis is mediated by energy taxis mechanisms, which are based on the cytosolic detection of consequences of nitrate metabolism. Here we show that Pseudomonas aeruginosa PAO1 mediates nitrate chemotaxis on the basis of specific nitrate sensing by the periplasmic PilJ domain of the PA2788/McpN chemoreceptor. The presence of nitrate reduced mcpN transcript levels, and McpN-mediated taxis occurred only under nitrate starvation conditions. In contrast to the NarX and NarQ sensor kinases, McpN bound nitrate specifically and showed no affinity for other ligands such as nitrite. We report the three-dimensional structure of the McpN ligand binding domain (LBD) at 1.3-Å resolution in complex with nitrate. Although structurally similar to 4-helix bundle domains, the ligand binding mode differs since a single nitrate molecule is bound to a site on the dimer symmetry axis. As for 4-helix bundle domains, ligand binding stabilized the McpN-LBD dimer. McpN homologues showed a wide phylogenetic distribution, indicating that nitrate chemotaxis is a widespread phenotype. These homologues were particularly abundant in bacteria that couple sulfide/sulfur oxidation with nitrate reduction. This work expands the range of known chemotaxis effectors and forms the basis for the exploration of nitrate chemotaxis in other bacteria and for the study of its physiological role.IMPORTANCE Nitrate is of central importance in bacterial physiology. Previous studies indicated that movements toward nitrate are due to energy taxis, which is based on the cytosolic sensing of consequences of nitrate metabolism. Here we present the first report on nitrate chemotaxis. This process is initiated by specific nitrate binding to the periplasmic ligand binding domain (LBD) of McpN. Nitrate chemotaxis is highly regulated and occurred only under nitrate starvation conditions, which is helpful information to explore nitrate chemotaxis in other bacteria. We present the three-dimensional structure of the McpN-LBD in complex with nitrate, which is the first structure of a chemoreceptor PilJ-type domain. This structure reveals striking similarities to that of the abundant 4-helix bundle domain but employs a different sensing mechanism. Since McpN homologues show a wide phylogenetic distribution, nitrate chemotaxis is likely a widespread phenomenon with importance for the life cycle of ecologically diverse bacteria.

Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges

Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.