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At least 19 recordsLinked to original sources
PubMed2026

Contribution of the Arg-33-His replacement in the histidine kinase CpxA to carbapenem and cefiderocol resistance in Serratia marcescens.

OBJECTIVE: The Serratia marcescens ROT_R clinical isolate, which was resistant to almost all β-lactams, including cefiderocol (4 mg/L), was recovered from a neonate 2 months after the isolation of the S. marcescens ROT_S strain that was susceptible to extended-spectrum cephalosporins (ESCs). In this study, we attempted to decipher the mechanism of resistance displayed by the ROT_R isolate. METHODS: The genomes of ROT_S and ROT_R were sequenced using the Illumina and the Oxford Nanopore Technologies. Long and short reads were assembled together, giving rise to a circularized hybrid genome. RESULTS: Genomic comparison between ROT_S and ROT_R disclosed only one mutation (G98A) in the cpxA gene of ROT_R, which led to the Arg-33-His substitution in the histidine kinase of the two-component system CpxA/CpxR. The cpxA alleles of ROT_S and ROT_R were amplified and cloned, thus giving rise to the pCpxA_WT and pCpxA_R33H recombinant plasmids, respectively, which were subsequently introduced into the S. marcescens HatR recipient strain, which lacks functional CpxA. The S. marcescens HatR (pCpxA_R33H) recombinant clone, which produced the altered CpxA_R33H variant, differed from the S. marcescens HatR (pCpxA_WT) recombinant clone, which produced the wild-type CpxA, by enhanced MICs of carbapenems and ESCs, including cefiderocol (1 mg/L). CONCLUSIONS: This study demonstrates that CpxA alteration, such as Arg-33-His substitution, can contribute to cefiderocol resistance. Although it increases slightly the MIC of cefiderocol without resulting per se in clinical resistance, it can contribute, in combination with other additional mechanisms, to achieve a high level of resistance to this siderophore cephalosporin.

Cefiderocol↗
PubMed2025

Functional and Pangenomic Exploration of Roc Two-Component Regulatory Systems Identifies Novel Players Across Pseudomonas Species.

The opportunistic pathogen Pseudomonas aeruginosa relies on a large collection of two-component regulatory systems (TCSs) to sense and adapt to changing environments. Among them, the Roc (regulation of cup) system is a one-of-a-kind network of branched TCSs, composed of two histidine kinases (HKs-RocS1 and RocS2) interacting with three response regulators (RRs-RocA1, RocR, and RocA2), which regulate virulence, antibiotic resistance, and biofilm formation. Based on extensive work on the Roc system, previous data suggested the existence of other key regulators yet to be discovered. In this work, we identified PA4080, renamed RocA3, as a fourth RR that is activated by RocS1 and RocS2 and that positively controls the expression of the cupB operon. Comparative genomic analysis of the locus identified a gene-rocR3-adjacent to rocA3 in a subpopulation of strains that encodes a protein with structural and functional similarity to the c-di-GMP phosphodiesterase RocR. Furthermore, we identified a fourth branch of the Roc system consisting of the PA2583 HK, renamed RocS4, and the Hpt protein HptA. Using a bacterial two-hybrid system, we showed that RocS4 interacts with HptA, which in turn interacts with RocA1, RocA2, and RocR3. Finally, we mapped the pangenomic RRs repertoire, establishing a comprehensive view of the plasticity of such regulators among clades of the species. Overall, our work provides a comprehensive inter-species definition of the Roc system, nearly doubling the number of proteins known to be involved in this interconnected network of TCSs controlling pathogenicity in Pseudomonas species.

Gene Expression Regulation, Bacterial↗
PubMed1979

Brain pyridoxal kinase. Purification, substrate specificities, and sensitized photodestruction of an essential histidine.

Pyridoxal kinase has been purified 2,000-fold from pig brain. The enzyme preparation migrates as a single protein and activity band on analytical gel electrophoresis. Pyridoxal kinase, 60,000 molecular weight, catalyzes the phosphorylation of pyridoxal (Km = 2.5 x 10(-5) M) and pyridoxine (Km = 1.7 x 10(-5) M). Pyridoxamine is not a substrate of the purified kinase. Irradiation of the kinase in the presence of riboflavin leads to irreversible loss of catalytic activity. Riboflavin binds to the kinase with a KD = 5 microM as shown by fluorometric titrations. Singlet excited oxygen, generated by energy transfer from the lowest triplet of riboflavin to oxygen, acts as the oxidizing agent of approximately one histidine residue per mol of enzyme. The amino acid residues tyrosine, tryptophan, and cysteine are not photooxidized by the sensitizer bound to the enzyme. It is postulated that histidine is involved in the binding of the substrate ATP to the catalytic site of pyridoxal kinase.

Animals↗
PubMed2025

Specificities of chemosensory receptors in the human gut microbiota.

The human gut is rich in metabolites and harbors a complex microbial community, yet surprisingly little is known about the spectrum of chemical signals detected by the large variety of sensory receptors present in the gut microbiome. Here, we systematically mapped the ligand specificities of selected extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. Twenty-five metabolites from different chemical classes-including amino acids, nucleobase derivatives, amines, indole, and carboxylates-were identified as specific ligands for fifteen sensory domains from nine bacterial species, which represent all three major functional classes of transmembrane receptors: chemotaxis receptors, histidine kinases, and enzymatic sensors. We have further characterized the specificity and evolution of ligand binding to Cache superfamily sensors specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs). Structural and biochemical analysis of the dCache sensor of uracil and SCFAs revealed that its two different ligand types bind at distinct sensory modules. Overall, combining experimental identification with computational analyses, we were able to assign ligands to approximately half of the Cache-type chemotaxis receptors found in the eleven gut commensal genomes from our set, with carboxylic acids representing the largest ligand class. Among these, the most commonly found ligand specificities were for lactate and formate, indicating a particular importance of these metabolites in the human gut microbiota and consistent with their observed growth-promoting effects on selected bacterial commensals.

Humans↗
PubMed2025

A widespread Actinobacterial G Protein System regulates production of specialized metabolites in Streptomyces coelicolor.

Actinobacterial G protein systems (AGPSs), also known as conservons, are regulatory systems that are broadly distributed within Actinomycetota. AGPSs are composed of a minimum of four proteins, including a sensor histidine kinase, a small Ras-like GTPase, a roadblock/MglB protein (likely a GTPase activating protein), and protein with a domain of unknown function that likely functions as a guanine-nucleotide exchange factor (GEF). While progress has been made in understanding AGPS function at the mechanistic level, the phylogenetic distribution of individual AGPSs, and the genes and processes they regulate, remain largely unmapped. Previously, the Cvn8 AGPS of Streptomyces coelicolor was found to influence expression of genes in multiple specialized metabolic pathways during interspecies interactions with other actinomycetes. However, the impact of the Cvn8 AGPS on specialized metabolism has not been assessed at the chemical level. Here, we investigated the phylogenetic distribution of the Cvn8 AGPS clade,and assessed the impact of the Cvn8 AGPS on natural product biosynthesis using untargeted metabolomics. In a set of 485 actinobacterial genomes, we found that members of the clade that includes the Cvn8 AGPS from S. coelicolor are widely distributed in the lineages known to produce specialized metabolites. We also found that in S. coelicolor, the pattern of specialized metabolite production varied in mutants lacking specific components of the Cvn8 AGPS. Specifically, normal production of the pigmented antibiotic actinorhodin during interspecies interactions required cvnA8 and cvnF8, while a ΔcvnD8 overproduced undecylprodigiosin. Together, these results connect a widespread AGPS to control of specialized metabolism in a model actinomycete.

Journal Article↗
PubMed2025

Sucrose and malic acid in the tobacco plant induce hrp regulon in a phytopathogen Ralstonia pseudosolanacearum.

Genes encoding a type III secretion system in Ralstonia pseudosolanacearum are regulated by HrpB as an hrp regulon and induced only in plants. This study aimed to identify the plant signals that induce the hrp regulon and confirm the signal recognition mechanism. Signaling molecules that induce hrpB expression were screened using resting cells of the hrpB-lacZ reporter strain. Only the soluble fraction of smashed tobacco seedlings induced hrpB expression. The heated soluble fraction retained its hrpB-inducing activity, indicating that the signaling molecules were not proteins. When the soluble fraction was fractionated into acidic, neutral, and basic components, both the acidic and neutral fractions induced hrpB expression. As neutral compounds, sucrose, glucose, and fructose have been found to induce hrpB expression. Sucrose-induced hrpB expression was greatly reduced in the prhA mutant, indicating that the TonB-dependent receptor PrhA perceives sugars. Among the organic acids found in the acidic fractions, malic acid most efficiently induced hrpB expression, which was reduced by the mutation of a hybrid histidine kinase gene of a two-component system, rsc1598, indicating that Rsc1598 may sense malic acid. We demonstrated direct binding of Rsc1598 to malic acid using isothermal titration calorimetry.IMPORTANCESimilar to other Gram-negative plant pathogens, the type III secretion system (T3SS) is the most important virulence factor in Ralstonia pseudosolanacearum. The genes for the T3SS are regulated as an hrp regulon, activated only when the pathogen encounters the plants, indicating that the pathogen must sense plant signals. For the first time, we identified two signaling compounds, sucrose and malic acid, that are abundantly found in tobacco roots. The hrp operon was induced even in non-host plants, possibly because sucrose and malic acid are common in plants. We also found that R. pseudosolanacearum membrane proteins received sucrose and malic acid independently. As a next step, antagonists of signaling molecules can be screened.

Malates↗
PubMed2026

Time-resolved proteomic adaptation of multidrug-resistant Acinetobacter baumannii to antimicrobial stress induced by partially purified fraction from Caesalpinia pulcherrima flower using DEqMS.

UNLABELLED: The global prevalence of multidrug-resistant (MDR) bacteria represents an urgent public health challenge, emphasizing the critical need for novel antimicrobial agents. MDR Acinetobacter baumannii, a nosocomial pathogen of critical global concern owing to its capacity to acquire and disseminate antimicrobial resistance, was employed as a bacterial model to investigate the antimicrobial potential of natural products derived from Caesalpinia pulcherrima (L.) Sw. (Fabaceae). This medicinal plant represents a promising reservoir of novel bioactive compounds; however, its molecular effects on the A. baumannii proteome had not previously been characterized. The partially purified ethyl acetate fraction of C. pulcherrima flowers (CPF4) exhibited potent bactericidal activity against susceptible A. baumannii (minimum inhibitory concentration and minimum bactericidal concentration = 31.25 µg/mL), and time-resolved label-free quantitative LC-MS/MS proteomics was subsequently performed on MDR A. baumannii cultures treated with CPF4 at 24 h, 48 h, and 72 h post-treatment alongside untreated controls in biological triplicate, with differential protein expression assessed using differential expression of quantified mass spectrometry data. No significantly differentially expressed proteins were detected at 24 h or 48 h relative to the control, indicating that the proteomic effects of CPF4 manifest predominantly at the late treatment stage. In contrast, a robust late-phase response was identified at 72 h, comprising the coordinated induction of proteins associated with DNA damage repair, transcriptional regulation, and cell surface glycosylation remodeling. The sensor histidine kinase PmrB was significantly upregulated at 72 h vs 48 h (adjusted P = 0.029), implicating the PmrA/PmrB two-component system in late-phase colistin tolerance acquisition under sustained CPF4 exposure. IMPORTANCE: These findings provide mechanistic insight into the adaptive survival strategies employed by multidrug-resistant Acinetobacter baumannii in response to plant-derived antimicrobial challenge and support the further development of Caesalpinia pulcherrima-derived natural products as candidate antimicrobial agents.

Acinetobacter baumannii↗
PubMed2025

The NmpRSTU multi-component signaling system of Myxococcus xanthus regulates expression of an oxygen utilization regulon.

UNLABELLED: Myxococcus xanthus has numerous two-component signaling systems (TCSs), many of which regulate the complex social behaviors of this soil bacterium. A subset of TCSs consists of NtrC-like response regulators (RRs) and their cognate histidine sensor kinases (SKs). We have previously demonstrated that a multi-component, phosphorelay TCS named NmpRSTU plays a role in M. xanthus social motility. NmpRSTU was discovered through a screen that identified mutations in nmp genes that restored Type-IV pili-dependent motility to a nonmotile strain. The Nmp pathway begins with the SK NmpU, which is predicted to be active in the presence of oxygen. NmpU phosphorylates another SK, NmpS, a hybrid kinase containing an RR domain and a HisKA-CA domain. These two kinases work in a reciprocal fashion: when NmpU is active, NmpS is inactive, and vice versa. Finally, the phosphorelay culminates in NmpS phosphorylating the NtrC-like RR NmpR. To better understand the role of NmpRSTU in M. xanthus physiology, we determined the NmpR regulon by combining in silico predictions of the NmpR consensus binding sequence with in vitro electromobility shift assays (EMSAs) and in vivo transcriptional reporters. We identified several NmpR-dependent, upregulated genes likely to be important in oxygen utilization. Additionally, we demonstrate NmpRSTU plays a role in fruiting body development, suggesting a role for oxygen sensing in this behavior. We propose that NmpRSTU senses oxygen-limiting conditions, and NmpR upregulates genes associated with optimal utilization of that oxygen. This may be necessary for M. xanthus physiology and behaviors in the highly dynamic soil where oxygen concentrations vary dramatically. IMPORTANCE: Bacteria use two-component signaling systems (TCSs) to respond to a multitude of environmental signals and subsequently regulate complex cellular physiology and behaviors. Myxococcus xanthus is a ubiquitous soil bacterium that encodes numerous two-component systems to respond to the conditions of its soil environment and coordinate multicellular behaviors such as coordinated motility, microbial predation, fruiting body development, and sporulation. To better understand how this bacterium uses a two-component system that has been linked to the sensing of oxygen concentrations, NmpRSTU, we determined the gene regulatory network of this system. We identified several genes regulated by NmpR that are likely important in oxygen utilization and for the M. xanthus response to varied oxygen concentrations in the dynamic soil environment.

Myxococcus xanthus↗
PubMed2002

Microarray-based identification of htrA, a Streptococcus pneumoniae gene that is regulated by the CiaRH two-component system and contributes to nasopharyngeal colonization.

Nasopharyngeal carriage is the reservoir from which most disease with Streptococcus pneumoniae arises. Survival as a commensal in this environment is likely to require a set of adaptations distinct from those needed to cause disease, some of which may be mediated by two-component signal transduction systems (TCSTS). We examined the contributions of nine pneumococcal TCSTS to the process of nasopharyngeal colonization by using an infant rat model. Whereas deletions in all but one of these systems have been associated previously with a high degree of attenuation in a murine model of pneumonia, only the CiaRH system was necessary for efficient carriage. Transcriptional analysis by using microarray hybridization identified a locus consisting of two adjacent genes, htrA and spoJ, that was specifically and strongly downregulated in a DeltaciaRH-null mutant. A S. pneumoniae strain lacking the htrA gene encoding a putative serine protease, but not one lacking spoJ, showed decreased fitness in a competitive model of colonization, a finding consistent with this gene mediating a portion of the carriage deficit observed with the DeltaciaRH strain.

Animals↗
PubMed1977

Characterization of lambda Escherichia coli hybrids carrying chemotaxis genes.

Molecular cloning techniques were used to construct hybrid Escherichia coli lambda phage and isolate Col E1 factors that carried the cheB region of the E. coli genome. The products of these genes were examined by using a series of deletions in the phage to stimulate specific polypeptide synthesis in ultraviolet-irradiated cells and by using Col factor to program protein synthesis in minicells. Seven flagellar related polypeptides were synthesized. Three of these with apparent molecular weights of 38,000, 28,000, and 8,000 were associated with the cheB region; three polypeptides 63,000, 61,000, and 60,000 were associated with the region that maps between cheB and cheA. These bands were referred to as the triplet group. We suggest that these polypeptides are the same as the methyl-accepting chemotaxis protein described by Kort et al. (Proc. Natl. Acad. Sci. U.S.A. 72:3939-3943, 1975). Another polypeptide with a molecular weight of 12,000 is associated with the cheA region which also produces at least three gene products. We conclude that the cheA-cheB region in E. coli is complex. Further genetic and biochemical analyses are required to describe all of these products.

Bacterial Proteins↗
PubMed1975

Comparative study of two ATP : L-arginine phosphotransferases of molecular weight 84 000.

Solen ensisensis muscle arginine kinase (ATP : L-arginine phosphotransferase, EC 2.7.3.3) was isolated in an homogeneous state. Its molecular weight was found to be about 80 000. The properties of this enzyme were compared with those of arginine kinase from Sipunculus nudus, an enzyme which also has a molecular weight of about 80 000. Both enzymes have several reactive thiol groups (8 thiol groups in the Solen kinase and 12 in the Sipunculus enzyme were titrateable with 5,5'-dithio-bis-(2-nitrobenzoic) acid and histidine residues (both enzymes have 6 reactive histidine residues). These kinases were, therefore, highly susceptible to oxidation. Both enzymes show the same pH optimum and absolute specificity towards the guanidine substrate, L-arginine. The reaction kinetics of both enzymes are of the sequential type. In the presence of alpha-aminoacids of Mg2+-ADP, similar spectral effects were obtained. The enzymes differ in their enzymic activities and in their rate of recovery following urea denaturation. The most important difference that appeared to be a special feature of the Sipunculus enzyme is that the spectrum of the Mg2+-ADP-enzyme complex is strongly intensified by L-arginine.

Adenosine Diphosphate↗
PubMed1977

Studies on the mechanism of action of histone kinase dependent on adenosine 3':5'-monophosphate. Evidence for involvement of histidine and lysine residues in the phosphotransferase reaction.

The reaction of the phosphate residue transfer catalysed by histone kinase dependent on adenosine 3':5'-monophosphate (cyclic AMP) was studied. The phosphotransferase reaction was shown to obey the mechanism of ping-pong bi-bi type. After incubation of the catalytic subunit of histone kinase with [gamma-32P]ATP the incorporation of one mole of [32P]phosphage per mole of protein was observed. The tryptic [32P]phosphohistidine-containing peptide was isolated and its N-terminus and amino acid composition were determined. The 2',3'-dialdehyde derivative of ATP (oATP) was used as the affinity label for the catalytic subunit of cyclic-AMP-dependent histone kinase. The inhibitor formed an alidmine bond with epsilon-amino group of the lysine residue of the active site and was irreversibly bound to the enzyme after reduction by sodium borohydride with concurrent irreversible inactivation of the enzyme. After inactivation, about one mole of 14C-labelled inhibitor was incorporated per mole of the enzyme. ATP effectively protected the catalytic subunit of histone kinase against inactivation by oATP. Tryptic digestion of the enzyme-inhibitor complex led to the isolation of the 14C-labelled peptide of the active site of histone kinase. Basing on these results, the role of histidine and lysine residues in the active site of the catalytic subunit of histone kinase was suggested.

Amino Acids↗
PubMed1976

Inhibition of growth and aspartokinase activity of Salmonella typhimurium by thialysine.

Thialysine (S-2-aminoethyl cysteine) is an analog of lysine and has been reported to inhibit the lysyl-tRNA synthetase activity of Escherichia coli. This analog inhibits the growth of Salmonella typhimurium when added to glucose minimal medium at concentrations of 1.25 mM or greater. The addition of lysine with thialysine restores the normal growth rate, whereas, methionine, valine, or leucine each enhances the growth inhibition casued by thialysine. Enzyme assays demonstrate that thialysine inhibits not only the lysyl-tRNA synthetase from S. typhimurium, but also the aspartokinase activity. Lysine and thialysine appear to inhibit the same 40% of the total aspartokinase because simultaneous addition of the two compounds to the reaction mixture does not increase the inhibition caused by either alone. Furthermore, the slow growth of cells in the presence of 2.5 mM thialysine decreases the level of aspartokinase activity, suggesting that thialysine causes repression of enzyme synthesis as well as inhibition of activity.

Amino Acids↗
PubMed1975

Crystalline adenylate kinase from carp muscle.

1. The concentration of adenylate kinase in carp muscle is about 0.3 mg/g. An improved isolation procedure makes use of a dilute solution of the substrates, ATP and AMP, to elute the enzyme from a phosphocellulose column in overall yields of 60% before crystallization. By the hexokinase--pH-stat assay the specific activity is 3550 units/mg. The preparation has been found to be essentially homogeneous by dodecylsulfate gel electrophoresis, isoelectrofocusing and gel filtration. 2. The molecular weight has been determined to be 22000 by several methods. The absorbance of a 1% solution at 280 nm is 6.9 and the isoelectric point by electrofocusing is pH 5.9. 3. The crystals of carp adenylate kinase have the space group P4-1-22 or P4-3-22. 4. The amino acid composition has been determined. There is no tryptophan, no cystine. There is one amino acid residue each of cysteine and histidine which are at or close to the catalytic center. 5. Several peptides derived by tryptic hydrolysis have been isolated and identified with corresponding peptides of porcine adenylate kinase. Consideration is given to histidine and cysteine being a part of the active site.

Adenylate Kinase↗
PubMed1979

The reaction of rabbit muscle creatine kinase with diethyl pyrocarbonate.

The reaction of rabbit muscle creatine kinase with diethyl pyrocarbonate was studied. It was found that up to five of the sixteen histidine groups per enzyme subunit could be modified, and under the conditions employed, there was no evidence for formation of the disubstituted derivative of histidine. Evidence was obtained for small but significant amounts of modification of lysine and cysteine groups; tyrosine groups were not modified. Modification of the enzyme led to inactivation; this could be protected against by inclusion of substrates or, more effectively, by inclusion of the combination MgADP plus creatine plus nitrate, which is thought to produce a 'transition-stage-analogue' complex. Analysis of data on the rates of inactivation and the stoicheiometry of modification suggested that there was one essential histidine group per enzyme subunit, modification of which led to inactivation.

Adenosine Diphosphate↗
PubMed1976

Integration of biochemical functions of different cells of rat gastric mucosa for hydrochloric acid secretion.

The regulation patterns of gastric acid secretion in rats were investigated. Pentagastrin and histamine stimulate gastric acid secretion, but the inhibitors of DNA-dependent synthesis of RNA and of proteins prevent only the pentagastrin action. It has been found that pentagastrin induces histidine decarboxylase in gastric mucosa, ensuring local accumulation of histamine. The latter activates adenylate cyclase and results in 3',5'-AMP accumulation in gastric tissues. The administration of pentagastrin, histamine or 3',5'-AMP enhances the activity of gastric carbonic anhydrase, the enzyme which takes part in HCl formation. The data suggest that these three compounds act sequentially (pentagastrin leads to histamine leads to3',5'-AMP) and the effect of the last one could be mediated through 3',5'-AMP dependent protein kinase. The experiments in vitro demonstrated that gastric carbonic anhydrase can be separated into two isoenzymes and thephosphorylation of one of them by the 3',5'-AMP dependent protein kinase sharply increases its activity. The findings raise the possibility that histamine and 3',5'-AMP, mediating gastrin action, form together with enzymes (histidine decarboxylase, adenylate cyclase, protein kinase, carbonic anhydrase) a caascade of amplifiers. Autoradiographic studies have shown that [3H]-pentagastrin is not bound by oxyntic cells but adheres preferentially to histamine-producing alpha-like endocrine cells and to the chief cells, while 3H-histamine adheres preferentially to oxyntic and to chief cells. Electron microscopy indicates that only pentagastrin (but not histamine) initiates in alpha-like endocrine cells ultrastructural changes characteristic for induction. Pentagastrin, histamine and 3',5'-AMP administration produces in oxyntic cells ultrastructural changes typical for the secretion processes. These results lead to assumption that pentagastrin (gastrin) induces histidine decarboxylase in alpha-like endocrine cells of gastric glands. Histamine which is secreted enhances adenylate cyclase activity in the neighbouring oxyntic cells where 3',5'-AMP dependent protein kinase activates carbonic anhydrase by means of phosphorylation. These different cells form, probably, a multicellular functional unit for gastric acid secretion.

Adenosine Triphosphatases↗