Linking RNA polymerase backtracking to genome instability in E. coli.

Frequent codirectional collisions between the replisome and RNA polymerase (RNAP) are inevitable because the rate of replication is much faster than that of transcription. Here we show that, in E. coli, the outcome of such collisions depends on the productive state of transcription elongation complexes (ECs). Codirectional collisions with backtracked (arrested) ECs lead to DNA double-strand breaks (DSBs), whereas head-on collisions do not. A mechanistic model is proposed to explain backtracking-mediated DSBs. We further show that bacteria employ various strategies to avoid replisome collisions with backtracked RNAP, the most general of which is translation that prevents RNAP backtracking. If translation is abrogated, DSBs are suppressed by elongation factors that either prevent backtracking or reactivate backtracked ECs. Finally, termination factors also contribute to genomic stability by removing arrested ECs. Our results establish RNAP backtracking as the intrinsic hazard to chromosomal integrity and implicate active ribosomes and other anti-backtracking mechanisms in genome maintenance.

Rho-dependent termination enables cellular pH homeostasis.

The termination factor Rho, an ATP-dependent RNA translocase, preempts pervasive transcription processes, thereby rendering genome integrity in bacteria. Here, we show that the loss of Rho function raised the intracellular pH to >8.0 in Escherichia coli. The loss of Rho function upregulates tryptophanase-A (TnaA), an enzyme that catabolizes tryptophan to produce indole, pyruvate, and ammonia. We demonstrate that the enhanced TnaA function had produced the conjugate base ammonia, raising the cellular pH in the Rho-dependent termination defective strains. On the other hand, the constitutively overexpressed Rho lowered the cellular pH to about 6.2, independent of cellular ammonia levels. Since Rho overexpression may increase termination activities, the decrease in cellular pH could result from an excess H+ ion production during ATP hydrolysis by overproduced Rho. Furthermore, we performed in vivo termination assays to show that the efficiency of Rho-dependent termination was increased at both acidic and basic pH ranges. Given that the Rho level remained unchanged, the alkaline pH increases the termination efficiency by stimulating Rho's catalytic activity. We conducted the Rho-mediated RNA release assay from a stalled elongation complex to show an efficient RNA release at alkaline pH, compared to the neutral or acidic pH, that supports our in vivo observation. Whereas acidic pH appeared to increase the termination function by elevating the cellular level of Rho. This study is the first to link Rho function to the cellular pH homeostasis in bacteria. IMPORTANCE The current study shows that the loss or gain of Rho-dependent termination alkalizes or acidifies the cytoplasm, respectively. In the case of loss of Rho function, the tryptophanase-A enzyme is upregulated, and degrades tryptophan, producing ammonia to alkalize cytoplasm. We hypothesize that Rho overproduction by deleting its autoregulatory DNA portion increases termination function, causing excessive ATP hydrolysis to produce H+ ions and cytoplasmic acidification. Therefore, this study is the first to unravel a relationship between Rho function and intrinsic cellular pH homeostasis. Furthermore, the Rho level increases in the absence of autoregulation, causing cytoplasmic acidification. As intracellular pH plays a critical role in enzyme function, such a connection between Rho function and alkalization will have far-reaching implications for bacterial physiology.

Proton Conductivity in a Metal-Organic Cube-Based Framework and Derived Hydrogel with Tubular Morphology.

The hydrogels, formed by self-assembly of predesigned, discrete metal-organic cubes (MOCs), have emerged as a new type of functional soft material whose diverse properties are yet to be explored. Here, we explore the proton conductivity of a MOC-based supramolecular porous framework {(Me2NH2)12[Ga8(ImDC)12]·DMF·29H2O} (1) (ImDC = 4,5-imidazole dicarboxylate) and derived hydrogel (MOC-G1). The intrinsic charge-assisted H-bonded (between anionic MOC {[Ga8(ImDC)12]12-} and dimethylammonium cations) framework 1 exhibits an ambient condition proton conductivity value of 2.3 × 10-5 S cm-1 (@40% RH) which increases with increasing temperature (8.2 × 10-4 S cm-1 at 120 °C and 40% RH) and follows the Grotthuss type of mechanism of proton conduction. Self-assembly of the MOCs in the presence of ammonium cations, as molecular binders, resulted in a hydrogel (MOC-G1) that shows directional H-bonded 1D nanotubular morphology. While guest water molecules are immensely important in deciding the proton conductivity of both 1 and MOC-G1, the presence of additional proton carriers, such as DMA and ammonium cations, resulted in at least 1 order increment in the proton conductivity of the latter (1.8 × 10-2 S cm-1) than the former (1.4 × 10-3 S cm-1) under 25 °C and 98% RH condition. The values of proton conductivity of 1 and MOC-G1 are comparable with those of the best proton conduction reports in the literature. This work may pave the way for the development of proton conductors with unique architecture and conductivity requisite for the state-of-the-art technologies by selecting appropriate MOC and molecular binders.

Controlled multimodal hierarchically porous electrode self-assembly of electrochemically exfoliated graphene for fully solid-state flexible supercapacitor.

Supercapacitors constructed from three-dimensional (3D) graphene electrodes with high ion-accessible surface area and durable mechanical flexibility have great potential for wearable devices. For the development of a highly efficient graphene electrode for electrical double layer capacitors (EDLCs), proper control over not only the specific surface area but also the type of pore (macro-, meso- and micro-porous networks) adapted for an appropriate type of electrolyte is crucial to ensure an ideal performance in terms of both energy density and power delivery rate. However, there is still a lack of technology to create graphene structures that combine macro-, meso- and micro-pores by a one-step and facile method. In addition, the ion/electron transport of a solid state electrolyte among such multimodal pore structures is not fully investigated. Here, we report a novel cost-effective technique of concentration dependent self-assembly of electrochemically exfoliated graphene (EC-graphene) to obtain a 3D architecture with controllable macropores (0.39-4.99 µm) and multimodal hierarchical meso- and micro-pores. The better performance of the 3D architecture is obtained due to its optimum micron-sized macropore diameter (∼5 µm) that serves as an ion buffering reservoir, followed by facile ion diffusion kinetics through the well-modulated combination of macro-, meso- and micro-pores. The binder and conductive carbon additive free supercapacitor constructed from the 3D graphene electrode exhibited a specific capacitance of 45.40 F g-1 (6 M KOH) and 23.89 F g-1 (1 M H2SO4 gel electrolyte). A capacitance retention of above 90% (up to 180° folding angle) after 50 bending-relaxing cycles is obtained, implying the superior durability of the device and the worthiness of the synthesis procedure. The method reported here may pave the way for the development of an environment friendly, large scale producible and controlled porous graphene-based architecture for the high performance next generation flexible, all-solid-state and binder-free energy storage devices.

Spectroscopic and computational investigations on the origin of charge transfer between included neutral guest molecules and a functionalized anionic layered host.

Layered double hydroxides (LDHs) or anionic clays are an important class of ion-exchange materials, well known for drug and gene delivery and several other applications including catalysis, bioactive nanocomposite, electroactive and photoactive materials. Their structure is based on positively charged brucite-like inorganic sheets with the interlamellar space being occupied by charge-compensating exchangeable anions. In spite of having a vast scope many of the applications of LDHs are restricted as their host-guest chemistry is limited to ion-exchange reactions. Recently we have shown for the first time that charge-transfer interactions can be used as a driving force for the insertion of neutral guest molecules (ortho- and para-chloranil) within the galleries of an Mg-Al LDH by forming a charge-transfer complex with aniline pre-intercalated as p-aminobenzoate anion. Here, we have performed quantum chemical calculations in combination with molecular dynamics simulations to elucidate the nature of interactions, arrangement and the evaluation of electronic and Raman spectral signatures of the chloranil charge-transfer complex included within the galleries of the Mg-Al LDH. The natural bond orbital (NBO) analysis has been used to understand the nature and origin of the unidirectional charge-transfer that lead to the unusual insertion of chloranil in the galleries of the Mg-Al LDH. The NBO analysis reveals that a considerable amount of electronic charge redistribution occurs from the p-aminobenzoate to the chloranil during latter's insertion within the LDH galleries with a very negligible amount of back donation. This work is expected to pave the way for understanding the host-guest chemistry and targeted and controlled delivery of poorly soluble drugs.

Probing the pseudo-1-D ion diffusion in lithium titanium niobate anode for Li-ion battery.

Comprehensive understanding of the charge transport mechanism in the intrinsic structure of an electrode material is essential in accounting for its electrochemical performance. We present here systematic experimental and theoretical investigations of Li(+)-ion diffusion in a novel layered material, viz. lithium titanium niobate. Lithium titanium niobate (exact composition Li0.55K0.45TiNbO5·1.06H2O) is obtained from sol-gel synthesized potassium titanium niobate (KTiNbO5) by an ion-exchange method. The Li(+)-ions are inserted and de-inserted preferentially into the galleries between the octahedral layers formed by edge and corner sharing TiO6 and NbO6 octahedral units and the effective chemical diffusion coefficient, is estimated to be 3.8 × 10(-11) cm(2) s(-1) using the galvanostatic intermittent titration technique (GITT). Calculations based on density functional theory (DFT) strongly confirm the anisotropic Li(+)-ion diffusion in the interlayer galleries and that Li(+)-ions predominantly diffuse along the crystallographic b-direction. The preferential Li(+)-ion diffusion along the b-direction is assisted by line-defects, which are observed to be higher in concentration along the b-direction compared to the a- and c-directions, as revealed by high resolution electron microscopy. The Li-Ti niobate can be cycled to low voltages (≈0.2 V) and show stable and satisfactory battery performance over 100 cycles. Due to the possibility of cycling to low voltages, cyclic voltammetry and X-ray photoelectron spectroscopy convincingly reveal the reversibility of Ti(3+) ↔ Ti(2+) along with Ti(4+) ↔ Ti(3+) and Nb(5+) ↔ Nb(4+).

An allosteric mechanism of Rho-dependent transcription termination.

Rho is the essential RNA helicase that sets the borders between transcription units and adjusts transcriptional yield to translational needs in bacteria. Although Rho was the first termination factor to be discovered, the actual mechanism by which it reaches and disrupts the elongation complex (EC) is unknown. Here we show that the termination-committed Rho molecule associates with RNA polymerase (RNAP) throughout the transcription cycle; that is, it does not require the nascent transcript for initial binding. Moreover, the formation of the RNAP-Rho complex is crucial for termination. We show further that Rho-dependent termination is a two-step process that involves rapid EC inactivation (trap) and a relatively slow dissociation. Inactivation is the critical rate-limiting step that establishes the position of the termination site. The trap mechanism depends on the allosterically induced rearrangement of the RNAP catalytic centre by means of the evolutionarily conserved mobile trigger-loop domain, which is also required for EC dissociation. The key structural and functional similarities, which we found between Rho-dependent and intrinsic (Rho-independent) termination pathways, argue that the allosteric mechanism of termination is general and likely to be preserved for all cellular RNAPs throughout evolution.

Novel MntR-independent mechanism of manganese homeostasis in Escherichia coli by the ribosome-associated protein HflX.

Manganese is a micronutrient required for activities of several important enzymes under conditions of oxidative stress and iron starvation. In Escherichia coli, the manganese homeostasis network primarily constitutes a manganese importer (MntH) and an exporter (MntP), which are regulated by the MntR dual regulator. In this study, we find that deletion of E. coli hflX, which encodes a ribosome-associated GTPase with unknown function, renders extreme manganese sensitivity characterized by arrested cell growth, filamentation, lower rate of replication, and DNA damage. We demonstrate that perturbation by manganese induces unprecedented influx of manganese in ΔhflX cells compared to that in the wild-type E. coli strain. Interestingly, our study indicates that the imbalance in manganese homeostasis in the ΔhflX strain is independent of the MntR regulon. Moreover, the influx of manganese leads to a simultaneous influx of zinc and inhibition of iron import in ΔhflX cells. In order to review a possible link of HflX with the λ phage life cycle, we performed a lysis-lysogeny assay to show that the Mn-perturbed ΔhflX strain reduces the frequency of lysogenization of the phage. This observation raises the possibility that the induced zinc influx in the manganese-perturbed ΔhflX strain stimulates the activity of the zinc-metalloprotease HflB, the key determinant of the lysis-lysogeny switch. Finally, we propose that manganese-mediated autophosphorylation of HflX plays a central role in manganese, zinc, and iron homeostasis in E. coli cells.

Crystal structure of Mycobacterium tuberculosis CarD, an essential RNA polymerase binding protein, reveals a quasidomain-swapped dimeric structural architecture.

Mycobacterium tuberculosis (Mtb) CarD is an essential transcriptional regulator that binds RNA polymerase and plays an important role in reprogramming transcription machinery under diverse stress conditions. Here, we report the crystal structure of CarD at 2.3 Å resolution, that represents the first structural description of CarD/CdnL-Like family of proteins. CarD adopts an overall bi-lobed structural architecture where N-terminal domain resembles 'tudor-like' domain and C-terminal domain adopts a novel five helical fold that lacks the predicted leucine zipper structural motif. The structure reveals dimeric state of CarD resulting from ß-strand swapping between the N-terminal domains of each individual subunits. The structure provides crucial insights into the possible mode(s) of CarD/RNAP interactions.

Bicyclomycin generates ROS and blocks cell division in Escherichia coli.

The role of reactive oxygen species (ROS) in the killing exerted by antibiotics on bacteria is debated. Evidence attributes part of toxicity of many antibiotics to their ability to generate ROS by interfering with cellular metabolism, but some studies dismiss the role of ROS. Bicyclomycin (BCM) is a broad-spectrum antibiotic that is the only known compound to inhibit E. coli transcription terminator factor Rho with no known other cellular targets. In the present study, we addressed this question by checking whether the induction of oxidative stress could explain the increased sensitivity to Bicyclomycin in the hns deleted strain even in Δkil background in E. coli. BCM evoked the generation of ROS in E. coli cells. BCM is known to cause the cell filamentation phenotype in E. coli. Performing fluorescence microscopic analysis, we show that bicyclomycin-dependent cell filamentation is associated with SOS response. RecA-GFP filaments were found to colocalize with the damaged DNA sites in the cell. Further analysis revealed that the genomic DNA was partitioned but the cell septum formation was severely affected under BCM treatment. Furthermore, we observed biofilm formation by E. coli after BCM treatment. We hypothesize that ROS production after BCM treatment could lead to cell filamentation in bacteria. A better understanding of the mode of toxicity of BCM will help us design better antibiotic treatment regimes for clinical practices, including combinatorial drug therapies. The cell filamentation phenotype observed after BCM treatment makes this antibiotic a promising drug for phage-antibiotic synergy (PAS) therapy.

Multifunctional phosphine stabilized gold nanoparticles: an active catalytic system for three-component coupling reaction.

Multifunctional phosphine based ligands, 1,1,1-tris(diphenylphosphinomethyl)ethane [CH3C(CH2 PPh2)3][P3] and 1,1,1-tris(diphenylphosphinomethyl)ethane trisulphide [CH3C(CH2P(S)Ph2)3][P3S3] have been introduced to stabilize Au(o)-nanoparticles having small core diameter and narrow size distribution. The Au(o)-nanoparticles were synthesized by the reduction of HAuCl4 precursor with NaBH4 in the presence of ligand P3 or P3S3 using two phases, one pot reaction at room temperature. The Au(o)-nanoparticles exhibit face centered cubic (fcc) lattice having different crystalline shape i.e., single crystallite stabilized by P3 while P3S3 forms decahedral shapes. Surface plasmon bands at -520 nm and TEM study indicate particle size below 2 and 4 nm for Au(o)-nanoparticles stabilized by P3 and P3S3 respectively, which are attributable to the stronger interaction of Au(o) (Soft) with P (Soft) than Au(o) (Soft) with S (less Softer than P). Au(o)-nanoparticles stabilized by P3S3 shows higher thermal stability than that of P3. The synthesized Au(o)-nanoparticles serve as an efficient catalyst for one-pot, three-component (A3) coupling of an aldehyde, an amine and an alkyne via C-H alkyne-activation to synthesize propargylamines (85-96%) without any additives and precaution to exclude air.

Unraveling the mechanistic insights of sophorolipid-capped gold nanoparticle-induced cell death in Vibrio cholerae.

IMPORTANCE: Vibrio cholerae, a Gram-negative bacterium, is the causative agent of a fatal disease, "cholera." Prevention of cholera outbreak is possible by eliminating the bacteria from the environment. However, antimicrobial resistance developed in microorganisms has posed a threat and challenges to its treatment. Application of nanoparticles is a useful and effective option for the elimination of such microorganisms. Metal-based nanopaticles exhibit microbial toxicity through non-specific mechanisms. To prevent resistance development and increase antibacterial efficiency, rational designing of nanoparticles is required. Thus, knowledge on the exact mechanism of action of nanoparticles is highly essential. In this study, we explore the possible mechanisms of antibacterial activity of AuNPs-SL against V. cholerae. We show that the interaction of AuNPs-SL with V. cholerae enhances ROS production and membrane depolarization, change in permeability, and leakage of intracellular content. This action leads to the depletion of cellular ATP level, DNA damage, and subsequent cell death.

Accommodating unwelcome guests in inorganic layered hosts: inclusion of chloranil in a layered double hydroxide.

The host-guest chemistry of most inorganic layered solids is limited to ion-exchange reactions. The guest species are either cations or anions to compensate for the charge deficit, either positive or negative, of the inorganic layers. Here, we outline a strategy to include neutral molecules like ortho- and para-chloranil, that are known to be good acceptors in donor-acceptor or charge-transfer complexes, within the galleries of a layered solid. We have succeeded in including neutral ortho- and para-chloranil molecules within the galleries of an Mg-Al layered double hydroxide (LDH) by using charge-transfer interactions with preintercalated p-aminobenzoate ions as the driving force. The p-aminobenzoate ions are introduced in the Mg-Al LDH via ion exchange. The intercalated LDH can adsorb ortho- and para-chloranil from chloroform solutions by forming charge-transfer complexes with the p-aminobenzoate anions present in the galleries. We use X-ray diffraction, spectroscopy, and molecular dynamics simulations to establish the nature of interactions and arrangement of the charge-transfer complex within the galleries of the layered double hydroxide.

An Intrinsic Alkalization Circuit Turns on mntP Riboswitch under Manganese Stress in Escherichia coli.

The trace metal manganese in excess affects iron-sulfur cluster and heme-protein biogenesis, eliciting cellular toxicity. The manganese efflux protein MntP is crucial to evading manganese toxicity in bacteria. Recently, two Mn-sensing riboswitches upstream of mntP and alx in Escherichia coli have been reported to mediate the upregulation of their expression under manganese shock. As the alx riboswitch is also responsive to alkaline shock administered externally, it is intriguing whether the mntP riboswitch is also responsive to alkaline stress. Furthermore, how both manganese and alkaline pH simultaneously regulate these two riboswitches under physiological conditions is a puzzle. Using multiple approaches, we show that manganese shock activated glutamine synthetase (GlnA) and glutaminases (GlsA and GlsB) to spike ammonia production in E. coli. The elevated ammonia intrinsically alkalizes the cytoplasm. We establish that this alkalization under manganese stress is crucial for attaining the highest degree of riboswitch activation. Additional studies showed that alkaline pH promotes a 17- to 22-fold tighter interaction between manganese and the mntP riboswitch element. Our study uncovers a physiological linkage between manganese efflux and pH homeostasis that mediates enhanced manganese tolerance. IMPORTANCE Riboswitch RNAs are cis-acting elements that can adopt alternative conformations in the presence or absence of a specific ligand(s) to modulate transcription termination or translation initiation processes. In the present work, we show that manganese and alkaline pH are both necessary for maximal mntP riboswitch activation to mitigate the manganese toxicity. This study bridges the gap between earlier studies that separately emphasize the importance of alkaline pH and manganese in activating the riboswitches belonging to the yybP-ykoY family. This study also ascribes a physiological relevance as to how manganese can rewire cellular physiology to render cytoplasmic pH alkaline for its homeostasis.

Free spermidine evokes superoxide radicals that manifest toxicity.

Spermidine and other polyamines alleviate oxidative stress, yet excess spermidine seems toxic to Escherichia coli unless it is neutralized by SpeG, an enzyme for the spermidine N-acetyl transferase function. Thus, wild-type E. coli can tolerate applied exogenous spermidine stress, but ΔspeG strain of E. coli fails to do that. Here, using different reactive oxygen species (ROS) probes and performing electron paramagnetic resonance spectroscopy, we provide evidence that although spermidine mitigates oxidative stress by lowering overall ROS levels, excess of it simultaneously triggers the production of superoxide radicals, thereby causing toxicity in the ΔspeG strain. Furthermore, performing microarray experiment and other biochemical assays, we show that the spermidine-induced superoxide anions affected redox balance and iron homeostasis. Finally, we demonstrate that while RNA-bound spermidine inhibits iron oxidation, free spermidine interacts and oxidizes the iron to evoke superoxide radicals directly. Therefore, we propose that the spermidine-induced superoxide generation is one of the major causes of spermidine toxicity in E. coli.

A novel plant lectin, NTL-125, interferes with SARS-CoV-2 interaction with hACE2.

COVID-19 caused by SARS-CoV-2 virus has had profound impact on the world in the past two years. Intense research is going on to find effective drugs to combat the disease. Over the past year several vaccines were approved for immunization. But SARS-CoV-2 being an RNA virus is continuously mutating to generate new variants, some of which develop features of immune escape. This raised serious doubts over the long-term efficacy of the vaccines. We have identified a unique mannose binding plant lectin from Narcissus tazetta bulb, NTL-125, which effectively inhibits SARS-CoV-2 replication in Vero-E6 cell line. In silico docking studies revealed that NTL-125 has strong affinity to viral Spike RBD protein, preventing it from attaching to hACE2 receptor, the gateway to cellular entry. Binding analyses revealed that all the mutant variants of Spike protein also have stronger affinity for NTL-125 than hACE2. The unique α-helical tail of NTL-125 plays most important role in binding to RBD of Spike. NTL-125 also interacts effectively with some glycan moieties of S-protein in addition to amino acid residues adding to the binding strength. Thus, NTL-125 is a highly potential antiviral compound of natural origin against SARS-CoV-2 and may serve as an important therapeutic for management of COVID-19.

Structure-Guided Designing and Evaluation of Peptides Targeting Bacterial Transcription.

The mycobacterial RNA polymerase (RNAP) is an essential and validated drug target for developing antibacterial drugs. The ß-subunit of Mycobacterium tuberculosis (Mtb) RNAP (RpoB) interacts with an essential and global transcription factor, CarD, and confers antibiotic and oxidative stress resistance to Mtb. Compromising the RpoB/CarD interactions results in the killing of mycobacteria, hence disrupting the RpoB/CarD interaction has been proposed as a novel strategy for the development of anti-tubercular drugs. Here, we describe the first approach to rationally design and test the efficacy of the peptide-based inhibitors which specifically target the conserved PPI interface between the bacterial RNAP ß/transcription factor complex. We performed in silico protein-peptide docking studies along with biochemical assays to characterize the novel peptide-based inhibitors. Our results suggest that the top ranked peptides are highly stable, soluble in aqueous buffer, and capable of inhibiting transcription with IC50 > 50 µM concentration. Using peptide-based molecules, our study provides the first piece of evidence to target the conserved RNAP ß/transcription factor interface for designing new inhibitors. Our results may hence form the basis to further improve the potential of these novel peptides in modulating bacterial gene expression, thus inhibiting bacterial growth and combating bacterial infections.

MoSx on Nitrogen-Doped Graphene for High-Efficiency Hydrogen Evolution Reaction: Unraveling the Mechanisms of Unique Interfacial Bonding for Efficient Charge Transport and Stability.

Functional nanostructures with abundant exposed active sites and facile charge transport through conductive scaffolds to active sites are pivotal for developing an advanced and efficient electrocatalyst for water splitting. In the present study, by coating ∼3 nm MoSx on nitrogen-doped graphene (NG) pre-engrafted on a flexible carbon cloth (MNG) as a model system, an extremely low Tafel slope of 39.6 mV dec-1 with cyclic stability up to 5000 cycles is obtained. The specific fraction of N on the NG framework is also analyzed by X-ray photoelectron spectroscopy and X-ray absorption near edge spectroscopy with synchrotron radiation light sources, and it is found that the MoSx particles are selectively positioned on the specific graphitic N sites, forming the unique Mo-N-C bonding state. This Mo-N-C bonding is founded to facilitate highly effective charge transfer directly to the active sulfur sites on the edges of MoSx, leading to a highly improved hydrogen evolution reaction (HER) with excellent stability (95% retention @ 5000 cycles). The functional anchoring of MoSx by such bonding prevents particle aggregation, which plays a significant role in maintaining the stability and activity of the catalyst. Furthermore, it has been revealed that MNG samples with adequately high amounts of both pyridinic and graphitic N result in the best HER performance. This work helps in understanding the mechanisms and bonding interactions within various catalysts and the scaffold electrode.

Properties of HflX, an enigmatic protein from Escherichia coli.

The Escherichia coli gene hflX was first identified as part of the hflA operon, mutations in which led to an increased frequency of lysogenization upon infection of the bacterium by the temperate coliphage lambda. Independent mutational studies have also indicated that the HflX protein has a role in transposition. Based on the sequence of its gene, HflX is predicted to be a GTP-binding protein, very likely a GTPase. We report here purification and characterization of the HflX protein. We also specifically examined its suggested functional roles mentioned above. Our results show that HflX is a monomeric protein with a high (30% to 40%) content of helices. It exhibits GTPase as well as ATPase activities, but it has no role in lambda lysogeny or in transposition.

E. coli HflX interacts with 50S ribosomal subunits in presence of nucleotides.

HflX is a GTP binding protein of unknown function. Based on the presence of the hflX gene in hflA operon, HflX was believed to be involved in the lytic-lysogenic decision during phage infection in Escherichia coli. We find that E. coli HflX binds 16S and 23S rRNA - the RNA components of 30S and 50S ribosomal subunits. Here, using purified ribosomal subunits, we show that HflX specifically interacts with the 50S. This finding is in line with the homology of HflX to GTPases involved in ribosome biogenesis. However, HflX-50S interaction is not limited to a specific nucleotide-bound state of the protein, and the presence of any of the nucleotides GTP/GDP/ATP/ADP is sufficient. In this respect, HflX is different from other GTPases. While E. coli HflX binds and hydrolyses both ATP and GTP, only the GTP hydrolysis activity is stimulated by 50S binding. This work uncovers interesting attributes of HflX in ribosome binding.