Reversible thermal unfolding of a yfdX protein with chaperone-like activity

Thr-to-Ala Mutation Leads to a Larger Aromatic Pair and Reduced Packing Density in α1,α3-Helices during Thioredoxin Cold Adaptation

This study investigates the impact of aromatic-aromatic interactions on the cold adaptation of thioredoxin (Trx), a small redox protein with a conserved Trx-fold structure. Two Trx orthologs, one from the psychrophilic Arctic bacterium Sphingomonas sp. (SpTrx) and the other from the mesophilic Escherichia coli (EcTrx), display distinct aromatic interactions in their α1,α3-helices. SpTrx features a larger Trp11-Phe69 pair, while EcTrx employs a smaller Phe12-Tyr70 pair along with an additional Asp9-Thr66 hydrogen bond. Smaller aromatic residues in SpTrx (Phe-Phe or Phe-Tyr pair) lead to decreased thermal and thermodynamic stabilities, increased conformational flexibility, and reduced enzyme activity. In contrast, EcTrx's thermal stability is primarily influenced by the larger Trp residue, especially in the more hydrophobic Trp-Phe pair compared to the Trp-Tyr pair. Both SpTrx and EcTrx exhibit a strengthening of the Asp-Thr hydrogen bond by a Phe-Tyr pair and a weakening by a Trp-Phe pair. Additionally, the Asp8-Thr65 hydrogen bond in SpTrx contributes to the destabilization of the Phe-Phe pair. Molecular dynamics simulations of SpTrx indicate that a smaller aromatic pair or the Asp-Thr hydrogen bond in the α1,α3-helices further destabilizes the α2-helix across the central β-sheet. Our results suggest that the Thr-to-Ala mutation destabilizes the α1,α3-helices, resulting in a larger aromatic pair and reduced packing density in psychrophilic Trxs during cold adaptation. These findings enhance our understanding of Trx's adaptation to colder temperatures.

Elucidating Protein-Ligand Interactions in Cell Lysates Using High-Throughput Hydrogen-Deuterium Exchange Mass Spectrometry with Integrated Protein Thermal Depletion

Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is a powerful technique for the characterization of protein-ligand interactions. Currently, there is a growing need for breakthroughs in the application of HDX-MS analysis to protein-ligand interactions in highly complex biological samples such as cell lysates. However, HDX-MS analysis in such systems suffers from extreme spectral complexity as a result of high sample complexity and limited LC separation power due to the traditional use of short LC gradients. Here, we introduced protein thermal depletion (PTD) to reduce protein complexity in E. coli cell lysate for our subzero-temperature long gradient UPLC-HDX-MS platform (PTD-HDX-MS) to facilitate high-throughput analysis of protein-ligand interactions in cell lysates. We spiked bovine carbonic anhydrase II (CaII) and its inhibitor acetazolamide (AZM) into E. coli cell lysate as a model system in our study. We demonstrated that PTD at 60 °C greatly reduces protein complexity in cell lysates, while the AZM-targeted CaII complex remains in solution due to improved thermal stability upon binding. Using both PTD to reduce sample complexity and subzero-temperature long gradient UPLC to boost LC separation power, we successfully elucidated the interaction sites between AZM and CaII in E. coli cell lysate from the high-throughput HDX-MS analysis of thousands of deuterated peptides from hundreds of proteins. Our results highlight the great promise of the PTD-HDX-MS platform for the identification of ligand targets and characterization of protein-ligand interactions in highly complex biological samples such as cell lysates.

Crystal structure and biochemical analysis suggest that YjoB ATPase is a putative substrate-specific molecular chaperone

AAA+ ATPases are ubiquitous proteins associated with most cellular processes, including DNA unwinding and protein unfolding. Their functional and structural properties are typically determined by domains and motifs added to the conserved ATPases domain. Currently, the molecular function and structure of many ATPases remain elusive. Here, we report the crystal structure and biochemical analyses of YjoB, a Bacillus subtilis AAA+ protein. The crystal structure revealed that the YjoB hexamer forms a bucket hat-shaped structure with a porous chamber. Biochemical analyses showed that YjoB prevents the aggregation of vegetative catalase KatA and gluconeogenesis-specific glyceraldehyde-3 phosphate dehydrogenase GapB but not citrate synthase, a conventional substrate. Structural and biochemical analyses further showed that the internal chamber of YjoB is necessary for inhibition of substrate aggregation. Our results suggest that YjoB, conserved in the class Bacilli, is a potential molecular chaperone acting in the starvation/stationary phases of B. subtilis growth.

Protein Unfolding: Denaturant vs. Force

While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes it challenging to compare results between studies if different refolding methods were applied. Our current work compares the energetic barriers and folding rates derived from chemical, thermal, and mechanical experiments using an immunoglobulin-like domain from the muscle protein titin as a model system. This domain, I83, has high solubility and low stability relative to other Ig domains in titin, though its stability can be modulated by calcium. Our experiments demonstrated that the free energy of refolding was equivalent with all three techniques, but the refolding rates exhibited differences, with mechanical refolding having slightly faster rates. This suggests that results from equilibrium-based measurements can be compared directly but care should be given comparing refolding kinetics derived from refolding experiments that used different unfolding methods.

Ecology and Function of the Transmissible Locus of Stress Tolerance in Escherichia coli and Plant-Associated Enterobacteriaceae

The transmissible locus of stress tolerance (tLST) is a genomic island which confers resistance to heat and chlorine. In this study, we determined that the tLST is frequent in genomes of those Enterobacteriaceae that occur in association with plants as well as the intestines of humans and animals and are relevant as nosocomial pathogens, e.g., Klebsiella and Cronobacter species. The tLST is more frequent in environmental and clinical isolates of Klebsiella pneumoniae than in animal isolates, and heat and chlorine resistance of tLST-positive strains of K. pneumoniae matched the resistance of tLST-positive strains of Escherichia coli. The function of 13 tLST genes was determined by assessing the heat and chlorine resistance of E. coli MG1655 mutants. The deletion of sHsp20, clpK_GI, sHsp_GI, pscA, pscB, and hdeD_GI reduced both heat and chlorine resistance; deletion of kefB reduced only chlorine resistance. Genes coding for heat shock proteins sHsp20, clpK_GI, and sHsp_GI decreased the oxidation of cytoplasmic proteins, while kefB decreased the oxidation of membrane lipids. The fitness cost of the tLST for E. coli MG1655 was assessed by pairwise competition experiments with isogenic tLST-positive or tLST-negative strains. The tLST imposes a fitness cost that is compensated for by frequent and lethal challenges with chlorine. All core genes need to be present to maintain the ecological advantage relative to the fitness cost. Taken together, core tLST genes are necessary to provide protection for E. coli against heat and chlorine stress, and the selective pressure for the tLST maintains core genes.

IMPORTANCE The transmissible locus of stress tolerance (tLST) is a genomic island comprising 10 core genes that occurs in diverse Enterobacteriaceae and confers resistance to heat and chlorine. Experimentation described in the manuscript describes the physiological function of the core genes by characterization of the resistance of 13 single-knockout (KO) mutants and by characterization of protein and membrane oxidation in these strains after chlorine challenge. Results identify tLST resistance as a genomic island that is specific for those Enterobacteriaceae that occur in plant-associated habitats as well in the intestines of vertebrates. In addition, the ecological function of the genomic island was characterized by large-scale genomic analysis and competition experiments of wild-type and mutant strains. Results suggest that tLST-mediated resistance to chlorine may contribute to the persistence of nosocomial pathogens in hospitals.

Contribution of the Locus of Heat Resistance to Growth and Survival of Escherichia coli at Alkaline pH and at Alkaline pH in the Presence of Chlorine

The locus of heat resistance (LHR) confers resistance to extreme heat, chlorine and oxidative stress in Escherichia coli. This study aimed to determine the function of the LHR in maintaining bacterial cell envelope homeostasis, the regulation of the genes comprising the LHR and the contribution of the LHR to alkaline pH response. The presence of the LHR did not affect the activity of the Cpx two-component regulatory system in E. coli, which was measured to quantify cell envelope stress. The LHR did not alter E. coli MG1655 growth rate in the range of pH 6.9 to 9.2. However, RT-qPCR results indicated that the expression of the LHR was elevated at pH 8.0 when CpxR was absent. The LHR did not improve survival of E. coli MG1655 at extreme alkaline pH (pH = 11.0 to 11.2) but improved survival at pH 11.0 in the presence of chlorine. Therefore, we conclude that the LHR confers resistance to extreme alkaline pH in the presence of oxidizing agents. Resistance to alkaline pH is regulated by an endogenous mechanism, including the Cpx envelope stress response, whereas the LHR confers resistance to extreme alkaline pH only in the presence of additional stress such as chlorine.

PV1 Protein from Plasmodium falciparum Exhibits Chaperone-Like Functions and Cooperates with Hsp100s

Plasmodium falciparum parasitophorous vacuolar protein 1 (PfPV1), a protein unique to malaria parasites, is localized in the parasitophorous vacuolar (PV) and is essential for parasite growth. Previous studies suggested that PfPV1 cooperates with the Plasmodium translocon of exported proteins (PTEX) complex to export various proteins from the PV. However, the structure and function of PfPV1 have not been determined in detail. In this study, we undertook the expression, purification, and characterization of PfPV1. The tetramer appears to be the structural unit of PfPV1. The activity of PfPV1 appears to be similar to that of molecular chaperones, and it may interact with various proteins. PfPV1 could substitute CtHsp40 in the CtHsp104, CtHsp70, and CtHsp40 protein disaggregation systems. Based on these results, we propose a model in which PfPV1 captures various PV proteins and delivers them to PTEX through a specific interaction with HSP101.

RcsB regulation of the YfdX-mediated acid stress response in Klebsiella pneumoniae CG43S3

In Klebsiella pneumoniae CG43S3, deletion of the response regulator gene rcsB reduced the capsular polysaccharide amount and survival on exposure to acid stress. A comparison of the pH 4.4-induced proteomes between CG43S3 and CG43S3ΔrcsB revealed numerous differentially expressed proteins and one of them, YfdX, which has recently been reported as a periplasmic protein, was absent in CG43S3ΔrcsB. Acid survival analysis was then conducted to determine its role in the acid stress response. Deletion of yfdX increased the sensitivity of K. pneumoniae CG43S3 to a pH of 2.5, and transforming the mutant with a plasmid carrying yfdX restored the acid resistance (AR) levels. In addition, the effect of yfdX deletion was cross-complemented by the expression of the periplasmic chaperone HdeA. Furthermore, the purified recombinant protein YfdX reduced the acid-induced protein aggregation, suggesting that YfdX as well as HdeA functions as a chaperone. The following promoter activity measurement revealed that rcsB deletion reduced the expression of yfdX after the bacteria were subjected to pH 4.4 adaptation. Western blot analysis also revealed that YfdX production was inhibited by rcsB deletion and only the plasmid expressing RcsB or the nonphosphorylated form of RcsB, RcsB_D56A, could restore the YfdX production, and the RcsB-mediated complementation was no longer observed when the sensor kinase RcsD gene was deleted. In conclusion, this is the first study demonstrating that YfdX may be involved in the acid stress response as a periplasmic chaperone and that RcsB positively regulates the acid stress response partly through activation of yfdX expression. Moreover, the phosphorylation status of RcsB may affect the YfdX expression under acidic conditions.

Structural and Physiological Exploration of Salmonella Typhi YfdX Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence

YfdX is a prokaryotic protein encoded by several pathogenic bacteria including Salmonella enterica serovar Typhi, which causes one of the most fatal infectious diseases, typhoid fever. YfdX is a product of the yfdXWUVE operon and is known to be under the control of EvgA, a regulator protein controlling the expression of several proteins involved in response to environmental stress, in Escherichia coli. Nevertheless, unlike other proteins encoded by the same operon, the structural and physiological aspects of YfdX have been poorly characterized. Here, we identified a previously unknown pH-dependent stoichiometric conversion of S. Typhi YfdX between dimeric and tetrameric states; this conversion was further analyzed via determining its structure by X-ray crystallography at high resolution and by small-angle X-ray scattering in a solution state and via structure-based mutant studies. Biologically, YfdX was proven to be critically involved in Salmonella susceptibility to two β-lactam antibiotics, penicillin G and carbenicillin, as bacterial growth significantly impaired by its deficiency upon treatment with each of the two antibiotics was recovered by chromosomal complementation. Furthermore, by using Galleria mellonella larvae as an in vivo model of Salmonella infection, we demonstrated that Salmonella virulence was remarkably enhanced by YfdX deficiency, which was complemented by a transient expression of the wild-type or dimeric mutant but not by that of the monomeric mutant. The present study work provides direct evidence regarding the participation of YfdX in Salmonella antibiotic susceptibility and in the modulation of bacterial virulence, providing a new insight into this pathogen's strategies for survival and growth.

Thermal unfolding and refolding of a lytic polysaccharide monooxygenase fromThermoascus aurantiacus

TaLPMO9A regains its catalytic power after a thermal unfolding and refolding cycle.

Characterization of stm3030 and stm3031 genes of Salmonella enterica serovar Typhimurium in relation to cephalosporin resistance

BACKGROUND/PURPOSE

The outer membrane protein STM3031 had been shown to confer Salmonella enterica serovar Typhimurium resistance to ceftriaxone. In this study, the STM3030 was increased in strain R200 and decreased in strain R200(Δstm3031). How stm3030 and stm3031 contributing to antibiotic resistance was investigated.

METHODS

The level of STM3030 protein in R200(Δstm3031) were compared between 01-4, R200, and R200(Δstm3031) by 2-DE analysis. The stm3030 gene deleted strain, R200(Δstm3030), was generated by the one-step inactivation chromosome gene method. The various antibiotic susceptibility of strains 01-4, R200, R200(Δstm3031) and R200(Δstm3030) were determined by agar dilutions assays and E-test. The co-transcription of stm3031 and stm3030 were determined by RT-PCR. The promoter activities of these two genes fused with LacZ were determined. The binding of the regulatory protein BaeR on the promoter of both genes was detected by EMSA. The interaction between STM3030 and STM3031 proteins was determined by GST pull-down assay.

RESULTS

Strain R200(Δstm3030) displayed a 32- to 64-fold reduction in resistance to cephalosporin drugs. Transcription analyses revealed that stm3030 and stm3031 are independent genes and that the promoter of stm3030 is stronger than that of stm3031. The regulator BaeR binds to the promoter region of stm3031 but not that of stm3030. The STM3031 decreased in R200(Δstm3030) compared to R200 by western blot analysis. The pull-down assay revealed that STM3030 and STM3031 bind to each other.

CONCLUSION

Our data indicate that STM3030 has a chaperone-like activity and may modulate or stabilize STM3031, leading to resistance of S. enterica serovar Typhimurium to cephalosporin drugs.

Thermomechanical Response of a Representative Porin for Biomimetics

The thermomechanical response of Omp2a, a representative porin used for the fabrication of smart biomimetic nanomembranes, has been characterized using microcantilever technology and compared with standard proteins. For this purpose, thermally induced transitions involving the conversion of stable trimers to bigger aggregates, local reorganizations based on the strengthening or weakening of intermolecular interactions, and protein denaturation have been detected by the microcantilever resonance frequency and deflection as a function of the temperature. Measurements have been carried out on arrays of 8-microcantilevers functionalized with proteins (Omp2a, lysozyme and bovine serum albumin). To interpret the measured nanofeatures, the response of proteins to temperature has been also examined using other characterization techniques, including real time wide angle X-ray diffraction. Results not only demonstrate the complex behavior of porins, which exhibit multiple local thermal transitions before undergoing denaturation at temperatures higher than 105 °C, but also suggest a posttreatment to control the orientation of immobilized Omp2a molecules in functionalized biomimetic nanomembranes and, thus, increase their efficacy in ion transport.

Molecular dynamics simulations on interaction between bacterial proteins: Implication on pathogenic activities

We perform molecular dynamics simulation studies on interaction between bacterial proteins: an outer-membrane protein STY3179 and a yfdX protein STY3178 of Salmonella Typhi. STY3179 has been found to be involved in bacterial adhesion and invasion. STY3178 is recently biophysically characterized. It is a soluble protein having antibiotic binding and chaperon activity capabilities. These two proteins co-occur and are from neighboring gene in Salmonella Typhi-occurrence of homologs of both STY3178 and STY3179 are identified in many Gram-negative bacteria. We show using homology modeling, docking followed by molecular dynamics simulation that they can form a stable complex. STY3178 belongs to aqueous phase, while the beta barrel portion of STY3179 remains buried in DPPC bilayer with extra-cellular loops exposed to water. To understand the molecular basis of interaction between STY3178 and STY3179, we compute the conformational thermodynamics which indicate that these two proteins interact through polar and acidic residues belonging to their interfacial region. Conformational thermodynamics results further reveal instability of certain residues in extra-cellular loops of STY3179 upon complexation with STY3178 which is an indication for binding with host cell protein laminin.

SDS induced dissociation of STY3178 oligomer: experimental and molecular dynamics studies

STY3178 the yfdX Salmonella Typhi protein dissociates reversibly in presence of sodium dodecyl sulphate from trimer to monomer.