Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator

Optogenetic control of RNA function and metabolism using engineered light-switchable RNA-binding proteins

RNA-binding proteins (RBPs) play an essential role in regulating the function of RNAs in a cellular context, but our ability to control RBP activity in time and space is limited. Here, we describe the engineering of LicV, a photoswitchable RBP that binds to a specific RNA sequence in response to blue light irradiation. When fused to various RNA effectors, LicV allows for optogenetic control of RNA localization, splicing, translation and stability in cell culture. Furthermore, LicV-assisted CRISPR-Cas systems allow for efficient and tunable photoswitchable regulation of transcription and genomic locus labeling. These data demonstrate that the photoswitchable RBP LicV can serve as a programmable scaffold for the spatiotemporal control of synthetic RNA effectors.

OUP accepted manuscript

Regulated transcription termination provides an efficient and responsive means to control gene expression. In bacteria, rho-independent termination occurs through the formation of an intrinsic RNA terminator loop, which disrupts the RNA polymerase elongation complex, resulting in its dissociation from the DNA template. Bacteria have a number of pathways for overriding termination, one of which is the formation of mutually exclusive RNA motifs. ANTAR domains are a class of antiterminator that bind and stabilize dual hexaloop RNA motifs within the nascent RNA chain to prevent terminator loop formation. We have determined the structures of the dimeric ANTAR domain protein EutV, from Enterococcus faecialis, in the absence of and in complex with the dual hexaloop RNA target. The structures illustrate conformational changes that occur upon RNA binding and reveal that the molecular interactions between the ANTAR domains and RNA are restricted to a single hexaloop of the motif. An ANTAR domain dimer must contact each hexaloop of the dual hexaloop motif individually to prevent termination in eubacteria. Our findings thereby redefine the minimal ANTAR domain binding motif to a single hexaloop and revise the current model for ANTAR-mediated antitermination. These insights will inform and facilitate the discovery of novel ANTAR domain RNA targets.

Resolving the activation mechanism of the D99N antiterminator LicT protein

LicT is an antiterminator protein of the BglG family whose members are key players in the control of carbohydrate catabolism in bacteria. These antiterminators are generally composed of three modules, an N-terminal RNA-binding domain (CAT) followed by two homologous regulation modules (PRD1 and PRD2) that control the RNA binding activity of the effector domain via phosphorylation on conserved histidines. Although several structures of isolated domains of BglG-like proteins have been described, no structure containing CAT and at least one PRD simultaneously has yet been reported in an active state, precluding detailed understanding of signal transduction between modules. To fulfill this gap, we recently reported the complete NMR sequence assignment of a constitutively active mutant (D99N) CAT-PRD1*, which contains the effector domain and the first regulation domain of LicT. As a follow-up, we have determined and report here the 3D solution structure of this active, dimeric LicT construct (40 kDa). The structure reveals how the mutation constrains the PRD1 regulation domain into an active conformation which is transduced to CAT via a network of negatively charged residues belonging to PRD1 dimeric interface and to the linker region. In addition, our data support a model where BglG-type antitermination regulatory modules can only adopt a single conformation compatible with the active structure of the effector domain, regardless of whether activation is mediated by mutation on the first or second PRD. The linker between the effector and regulation modules appears to function as an adaptable hinge tuning the position of the functional modules.

The mannose phosphotransferase system (Man-PTS) - Mannose transporter and receptor for bacteriocins and bacteriophages

Mannose transporters constitute a superfamily (Man-PTS) of the Phosphoenolpyruvate Carbohydrate Phosphotransferase System (PTS). The membrane complexes are homotrimers of protomers consisting of two subunits, IIC and IID. The two subunits without recognizable sequence similarity assume the same fold, and in the protomer are structurally related by a two fold pseudosymmetry axis parallel to membrane-plane (Liu et al. (2019) Cell Research 29 680). Two reentrant loops and two transmembrane helices of each subunit together form the N-terminal transport domain. Two three-helix bundles, one of each subunit, form the scaffold domain. The protomer is stabilized by a helix swap between these bundles. The two C-terminal helices of IIC mediate the interprotomer contacts. PTS occur in bacteria and archaea but not in eukaryotes. Man-PTS are abundant in Gram-positive bacteria living on carbohydrate rich mucosal surfaces. A subgroup of IICIID complexes serve as receptors for class IIa bacteriocins and as channel for the penetration of bacteriophage lambda DNA across the inner membrane. Some Man-PTS are associated with host-pathogen and -symbiont processes.

NMR chemical shift assignment of a constitutively active fragment of the antitermination protein LicT

LicT belongs to an essential family of bacterial antitermination proteins which bind to nascent mRNAs in order to stimulate transcription of sugar-metabolizing operons. As most of other antitermination proteins involved in carbohydrate metabolism, LicT is composed of a N-terminal RNA-binding module (CAT) and two homologous regulatory modules (PRD1 and PRD2). The activity of the CAT effector module is controlled by antagonist phosphorylations by the phosphotransferase system on conserved histidines of the two C-terminal PRDs in response to available carbon sources. Previous studies on truncated and mutant constructs have provided partial structural insight into the mechanism of signal transduction between the N-terminal RNA-binding domain and the two regulation modules. However, no structure at atomic resolution has been ever solved that contain the RNA-binding domain and a regulation module. We report the NMR assignment of a constitutively active fragment of LicT, named D99A-CAT-PRD1 or CAT-PRD1*. This fragment is composed of the RNA-binding module and the first N-terminal regulation module which bears the mutation of Asp99 to an asparagine. It is dimeric as the native protein, with a 40 kD molecular weight. The D99N mutation is sufficient to endow this fragment with a high RNA-binding constitutive activity, in a phosphorylation-free context. The assignment reported here should set the base of future NMR investigation of signal transduction between the regulatory module and the effector module in the active state of the protein, and in the long term enable the structural study of the full length protein structure in interaction with its target RNA.

Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis

The anthrax toxin is a virulence factor produced by the bacterium Bacillus anthracis. Transcription of anthrax toxin genes is controlled by the transcription factor AtxA. Thus, AtxA is thought to be a key factor for the pathogenicity of B. anthracis. Despite its important role in B. anthracis infection, the molecular mechanism by which AtxA controls expression of anthrax toxin remains unclear. This study aimed to characterize the molecular mechanism of AtxA-mediated regulation of protective antigen (PA), a component of anthrax toxin encoded by the pagA gene. First, the interaction between the upstream region of pagA and AtxA was evaluated in vivo by constructing a transcriptional fusion of the upstream region with an auxotrophic marker. The results showed that (i) the upstream region of pagA suppressed transcription of the downstream gene and (ii) AtxA recovered suppressed transcription. Second, in vitro analysis using a gel mobility shift assay was performed to evaluate binding specificity of the AtxA–DNA interaction. The result showed sequence-independent binding of AtxA to DNA. Taken together, our findings suggest that the expression of PA was suppressed by the upstream region of pagA and that an interaction of AtxA and the upstream region releases the suppression.

Interplay of self-association and conformational flexibility in regulating protein function

Many functional roles have been attributed to homodimers, the most common mode of protein self-association, notably in the regulation of enzymes, ion channels, transporters and transcription factors. Here we review findings that offer new insights into the different roles conformational flexibility plays in regulating homodimer function. Intertwined homodimers of two-domain proteins and their related family members display significant conformational flexibility, which translates into concerted motion between structural domains. This flexibility enables the corresponding proteins to regulate function across family members by modulating the spatial positions of key recognition surfaces of individual domains, to either maintain subunit interfaces, alter them or break them altogether, leading to a variety of functional consequences. Many proteins may exist as monomers but carry out their biological function as homodimers or higher-order oligomers. We present early evidence that in such systems homodimer formation primes the protein for its functional role. It does so by inducing elevated mobility in protein regions corresponding to the binding epitopes of functionally important ligands. In some systems this process acts as an allosteric response elicited by the self-association reaction itself. Our analysis furthermore suggests that the induced extra mobility likely facilitates ligand binding through the mechanism of conformational selection.This article is part of a discussion meeting issue 'Allostery and molecular machines'.

Regulons and protein-protein interactions of PRD-containing Bacillus anthracis virulence regulators reveal overlapping but distinct functions

Bacillus anthracis produces three regulators, AtxA, AcpA and AcpB, which control virulence gene transcription and belong to an emerging class of regulators termed 'PCVRs' (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA, named for its control of toxin gene expression, is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. Reports of PCVR activity suggest overlapping function. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA level or activity result in capBCADE transcription in strains lacking acpA and acpB. We used RNA-Seq to assess the regulons of the paralogous regulators in strains constructed to express individual PCVRs at native levels. Plasmid and chromosome-borne genes were PCVR controlled, with AtxA, AcpA and AcpB having a ≥ 4-fold effect on transcript levels of 145, 130 and 49 genes respectively. Several genes were coregulated by two or three PCVRs. We determined that AcpA and AcpB form homomultimers, as shown previously for AtxA, and we detected AtxA-AcpA heteromultimers. In co-expression experiments, AcpA activity was reduced by increased levels of AtxA. Our data show that the PCVRs have specific and overlapping activity and that PCVR stoichiometry and potential heteromultimerization can influence target gene expression.

Competitive folding of RNA structures at a termination-antitermination site

Antitermination is a regulatory process based on the competitive folding of terminator-antiterminator structures that can form in the leader region of nascent transcripts. In the case of the Bacillus subtilis licS gene involved in β-glucosides utilization, the binding of the antitermination protein LicT to a short RNA hairpin (RAT) prevents the formation of an overlapping terminator and thereby allows transcription to proceed. Here, we monitored in vitro the competition between termination and antitermination by combining bulk and single-molecule fluorescence-based assays using labeled RNA oligonucleotide constructs of increasing length that mimic the progressive transcription of the terminator invading the antiterminator hairpin. Although high affinity binding is abolished as soon as the antiterminator basal stem is disrupted by the invading terminator, LicT can still bind and promote closing of the partially unfolded RAT hairpin. However, binding no longer occurs once the antiterminator structure has been disrupted by the full-length terminator. Based on these findings, we propose a kinetic competition model for the sequential events taking place at the termination-antitermination site, where LicT needs to capture its RAT target before completion of the terminator to remain tightly bound during RNAP pausing, before finally dissociating irreversibly from the elongated licS transcript.

The Landscape of Intertwined Associations in Homooligomeric Proteins

We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. Furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers, with a particular focus on the mechanistic aspects that underpin intertwined self-association processes in proteins. Insights gained from this integrated overview into the physical and biological roles of intertwining are highlighted.

The bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system: regulation by protein phosphorylation and phosphorylation-dependent protein-protein interactions

The bacterial phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) carries out both catalytic and regulatory functions. It catalyzes the transport and phosphorylation of a variety of sugars and sugar derivatives but also carries out numerous regulatory functions related to carbon, nitrogen, and phosphate metabolism, to chemotaxis, to potassium transport, and to the virulence of certain pathogens. For these different regulatory processes, the signal is provided by the phosphorylation state of the PTS components, which varies according to the availability of PTS substrates and the metabolic state of the cell. PEP acts as phosphoryl donor for enzyme I (EI), which, together with HPr and one of several EIIA and EIIB pairs, forms a phosphorylation cascade which allows phosphorylation of the cognate carbohydrate bound to the membrane-spanning EIIC. HPr of firmicutes and numerous proteobacteria is also phosphorylated in an ATP-dependent reaction catalyzed by the bifunctional HPr kinase/phosphorylase. PTS-mediated regulatory mechanisms are based either on direct phosphorylation of the target protein or on phosphorylation-dependent interactions. For regulation by PTS-mediated phosphorylation, the target proteins either acquired a PTS domain by fusing it to their N or C termini or integrated a specific, conserved PTS regulation domain (PRD) or, alternatively, developed their own specific sites for PTS-mediated phosphorylation. Protein-protein interactions can occur with either phosphorylated or unphosphorylated PTS components and can either stimulate or inhibit the function of the target proteins. This large variety of signal transduction mechanisms allows the PTS to regulate numerous proteins and to form a vast regulatory network responding to the phosphorylation state of various PTS components.

Single-molecule FRET characterization of RNA remodeling induced by an antitermination protein

Single-molecule Förster Resonance Energy Transfer (smFRET) is a useful technique to probe conformational changes within bio-macromolecules. Here, we introduce how to perform smFRET measurements in solution to investigate RNA remodeling and RNA-protein interactions. In particular, we focus on how the close-to-open transition of an antiterminator hairpin is influenced by the binding of the antitermination protein and the competition by oligonucleotides.

Crystal structure of Bacillus anthracis virulence regulator AtxA and effects of phosphorylated histidines on multimerization and activity

The Bacillus anthracis virulence regulator AtxA controls transcription of the anthrax toxin genes and capsule biosynthetic operon. AtxA activity is elevated during growth in media containing glucose and CO(2)/bicarbonate, and there is a positive correlation between the CO(2)/bicarbonate signal, AtxA activity and homomultimerization. AtxA activity is also affected by phosphorylation at specific histidines. We show that AtxA crystallizes as a dimer. Distinct folds associated with predicted DNA-binding domains (HTH1 and HTH2) and phosphoenolpyruvate: carbohydrate phosphotransferase system-regulated domains (PRD1 and PRD2) are apparent. We tested AtxA variants containing single and double phosphomimetic (His→Asp) and phosphoablative (His→Ala) amino acid changes for activity in B. anthracis cultures and for protein-protein interactions in cell lysates. Reduced activity of AtxA H199A, lack of multimerization and activity of AtxAH379D variants, and predicted structural changes associated with phosphorylation support a model for control of AtxA function. We propose that (i) in the AtxA dimer, phosphorylation of H199 in PRD1 affects HTH2 positioning, influencing DNA-binding; and (ii) phosphorylation of H379 in PRD2 disrupts dimer formation. The AtxA structure is the first reported high-resolution full-length structure of a PRD-containing regulator, and can serve as a model for proteins of this family, especially those that link virulence to bacterial metabolism.

Landscape of intertwined associations in multi-domain homo-oligomeric proteins

This study charts the landscape of multi-domain protein structures that form intertwined homodimers by exchanging structural domains between subunits. A representative dataset of such homodimers was derived from the Protein Data Bank, and their structural and topological properties were compared to those of a representative set of non-intertwined homodimers. Most of the intertwined dimers form closed assemblies with head-to-tail arrangements, where the subunit interface involves contacts between dissimilar domains. In contrast, the non-intertwined dimers form preferentially head-to-head arrangements, where the subunit interface involves contacts between identical domains. Most of these contacts engage only one structural domain from each subunit, leaving the remaining domains free to form other associations. Remarkably, we find that multi-domain proteins closely related to the intertwined homodimers are significantly more likely than relatives of the non-intertwined versions to adopt alternative intramolecular domain arrangements. In ~40% of the intertwined dimers, the plasticity in domain arrangements among relatives affords maintenance of the head-to-head or head-to-tail topology and conservation of the corresponding subunit interface. This property seems to be exploited in several systems to regulate DNA binding. In ~58%, however, intramolecular domain re-arrangements are associated with changes in oligomeric states and poorly conserved interfaces among relatives. This time, the corresponding structural plasticity appears to be exploited by evolution to modulate function by switching between active and inactive states of the protein. Surprisingly, in total, only three systems were found to undergo the classical monomer to intertwined dimer conversion associated with three-dimensional domain swapping.

Dynamic localization of a transcription factor in Bacillus subtilis: the LicT antiterminator relocalizes in response to inducer availability

Bacillus subtilis transports β-glucosides such as salicin by a dedicated phosphotransferase system (PTS). The expression of the β-glucoside permease BglP is induced in the presence of the substrate salicin, and this induction requires the binding of the antiterminator protein LicT to a specific RNA target in the 5' region of the bglP mRNA to prevent the formation of a transcription terminator. LicT is composed of an N-terminal RNA-binding domain and two consecutive PTS regulation domains, PRD1 and PRD2. In the absence of salicin, LicT is phosphorylated on PRD1 by BglP and thereby inactivated. In the presence of the inducer, the phosphate group from PRD1 is transferred back to BglP and consequently to the incoming substrate, resulting in the activation of LicT. In this study, we have investigated the intracellular localization of LicT. While the protein was evenly distributed in the cell in the absence of the inducer, we observed a subpolar localization of LicT if salicin was present in the medium. Upon addition or removal of the inducer, LicT rapidly relocalized in the cells. This dynamic relocalization did not depend on the binding of LicT to its RNA target sites, since the localization pattern was not affected by deletion of all LicT binding sites. In contrast, experiments with mutants affected in the PTS components as well as mutations of the LicT phosphorylation sites revealed that phosphorylation of LicT by the PTS components plays a major role in the control of the subcellular localization of this RNA-binding transcription factor.

Transcription regulators controlled by interaction with enzyme IIB components of the phosphoenolpyruvate: sugar phosphotransferase system

Numerous bacteria possess transcription activators and antiterminators composed of regulatory domains phosphorylated by components of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). These domains, called PTS regulation domains (PRDs), usually contain two conserved histidines as potential phosphorylation sites. While antiterminators possess two PRDs with four phosphorylation sites, transcription activators contain two PRDs plus two regulatory domains resembling PTS components (EIIA and EIIB). The activity of these transcription regulators is controlled by up to five phosphorylations catalyzed by PTS proteins. Phosphorylation by the general PTS components EI and HPr is usually essential for the activity of PRD-containing transcription regulators, whereas phosphorylation by the sugar-specific components EIIA or EIIB lowers their activity. For a specific regulator, for example the Bacillus subtilis mtl operon activator MtlR, the functional phosphorylation sites can be different in other bacteria and consequently the detailed mode of regulation varies. Some of these transcription regulators are also controlled by an interaction with a sugar-specific EIIB PTS component. The EIIBs are frequently fused to the membrane-spanning EIIC and EIIB-mediated membrane sequestration is sometimes crucial for the control of a transcription regulator. This is also true for the Escherichia coli repressor Mlc, which does not contain a PRD but nevertheless interacts with the EIIB domain of the glucose-specific PTS. In addition, some PRD-containing transcription activators interact with a distinct EIIB protein located in the cytoplasm. The phosphorylation state of the EIIB components, which changes in response to the presence or absence of the corresponding carbon source, affects their interaction with transcription regulators. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).

Competitive folding of anti-terminator/terminator hairpins monitored by single molecule FRET

The control of transcription termination by RNA-binding proteins that modulate RNA-structures is an important regulatory mechanism in bacteria. LicT and SacY from Bacillus subtilis prevent the premature arrest of transcription by binding to an anti-terminator RNA hairpin that overlaps an intrinsic terminator located in the 5'-mRNA leader region of the gene to be regulated. In order to investigate the molecular determinants of this anti-termination/termination balance, we have developed a fluorescence-based nucleic acids system that mimics the competition between the LicT or SacY anti-terminator targets and the overlapping terminators. Using Förster Resonance Energy Transfer on single diffusing RNA hairpins, we could monitor directly their opening or closing state, and thus investigate the effects on this equilibrium of the binding of anti-termination proteins or terminator-mimicking oligonucleotides. We show that the anti-terminator hairpins adopt spontaneously a closed structure and that their structural dynamics is mainly governed by the length of their basal stem. The induced stability of the anti-terminator hairpins determines both the affinity and specificity of the anti-termination protein binding. Finally, we show that stabilization of the anti-terminator hairpin, by an extended basal stem or anti-termination protein binding can efficiently counteract the competing effect of the terminator-mimic.

Structure of the RBD-PRDI fragment of the antiterminator protein GlcT

GlcT is a transcriptional antiterminator protein that is involved in regulation of glucose metabolism in Bacillus subtilis. Antiterminator proteins bind specific RNA sequences, thus preventing the formation of overlapping terminator stem-loops. The structure of a fragment (residues 3-170) comprising the RNA-binding domain (RBD) and the first regulatory domain (PRDI) of GlcT was solved at 2.0 Å resolution with one molecule in the asymmetric unit. The two domains are connected by a helical linker. Their interface is mostly constituted by hydrophobic interactions.

Bacillus anthracis virulence regulator AtxA: oligomeric state, function and CO(2) -signalling

AtxA, a unique regulatory protein of unknown molecular function, positively controls expression of the major virulence genes of Bacillus anthracis. The 475 amino acid sequence of AtxA reveals DNA binding motifs and regions similar to proteins associated with the phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS). We used strains producing native and functional epitope-tagged AtxA proteins to examine protein-protein interactions in cell lysates and in solutions of purified protein. Co-affinity purification, non-denaturing polyacrylamide gel electrophoresis and bis(maleimido)hexane (BMH) cross-linking experiments revealed AtxA homo-multimers. Dimers were the most abundant species. BMH cross-links available cysteines within 13 Å. To localize interaction sites, six AtxA mutants containing distinct Cys→Ser substitutions were tested for multimerization and cross-linking. All mutants multimerized, but one mutation, C402S, prevented cross-linking. Thus, BMH uses C402 to make the inter-molecular bond between AtxA proteins, but C402 is not required for protein-protein interaction. C402 is in a region bearing amino acid similarity to Enzyme IIB proteins of the PTS. The AtxA EIIB motif may function in protein oligomerization. Finally, cultures grown with elevated CO(2) /bicarbonate exhibited increased AtxA dimer/monomer ratios and increased AtxA activity, relative to cultures grown without added CO(2) /bicarbonate, suggesting that this host-associated signal enhances AtxA function by shifting the dimer/monomer equilibrium towards the dimeric state.

Insight into bacterial phosphotransferase system-mediated signaling by interspecies transplantation of a transcriptional regulator

The bacterial sugar:phosphotransferase system (PTS) delivers phosphoryl groups via proteins EI and HPr to the EII sugar transporters. The antitermination protein LicT controls β-glucoside utilization in Bacillus subtilis and belongs to a family of bacterial transcriptional regulators that are antagonistically controlled by PTS-catalyzed phosphorylations at two homologous PTS regulation domains (PRDs). LicT is inhibited by phosphorylation of PRD1, which is mediated by the β-glucoside transporter EII(Bgl). Phosphorylation of PRD2 is catalyzed by HPr and stimulates LicT activity. Here, we report that LicT, when artificially expressed in the nonrelated bacterium Escherichia coli, is likewise phosphorylated at both PRDs, but the phosphoryl group donors differ. Surprisingly, E. coli HPr phosphorylates PRD1 rather than PRD2, while the stimulatory phosphorylation of PRD2 is carried out by the HPr homolog NPr. This demonstrates that subtle differences in the interaction surface of HPr can switch its affinities toward the PRDs. NPr transfers phosphoryl groups from EI(Ntr) to EIIA(Ntr). Together these proteins form the paralogous PTS(Ntr), which controls the activity of K(+) transporters in response to unknown signals. This is achieved by binding of dephosphorylated EIIA(Ntr) to other proteins. We generated LicT mutants that were controlled either negatively by HPr or positively by NPr and were suitable bio-bricks, in order to monitor or to couple gene expression to the phosphorylation states of these two proteins. With the aid of these tools, we identified the stringent starvation protein SspA as a regulator of EIIA(Ntr) phosphorylation, indicating that PTS(Ntr) represents a stress-related system in E. coli.

Structural mechanism of signal transduction between the RNA-binding domain and the phosphotransferase system regulation domain of the LicT antiterminator

LicT belongs to a family of bacterial transcriptional antiterminators, which control the expression of sugar-metabolizing operons in response to phosphorylations by the phosphoenolpyruvate:sugar phosphotransferase system (PTS). Previous studies of LicT have revealed the structural basis of RNA recognition by the dimeric N-terminal co-antiterminator (CAT) domain on the one hand and the conformational changes undergone by the duplicated regulation domain (PRD1 and PRD2) upon activation on the other hand. To investigate the mechanism of signal transduction between the effector and regulation modules, we have undertaken the characterization of a fragment, including the CAT and PRD1 domains and the linker in-between. Comparative experiments, including RNA binding assays, NMR spectroscopy, limited proteolysis, analytical ultracentrifugation, and circular dichroism, were conducted on native CAT-PRD1 and on a constitutively active CAT-PRD1 mutant carrying a D99N substitution in PRD1. We show that in the native state, CAT-PRD1 behaves as a rather unstable RNA-binding deficient dimer, in which the CAT dimer interface is significantly altered and the linker region is folded as a trypsin-resistant helix. In the activated mutant form, the CAT-PRD1 linker becomes protease-sensitive, and the helix content decreases, and the CAT module adopts the same dimeric conformation as in isolated CAT, thereby restoring the affinity for RNA. From these results, we propose that a helix-to-coil transition in the linker acts as the structural relay triggered by the regulatory domain for remodeling the effector dimer interface. In essence, the structural mechanism modulating the LicT RNA antitermination activity is thus similar to that controlling the DNA binding activity of dimeric transcriptional regulators.

Genetic dissection of the divergent activities of the multifunctional membrane sensor BglF

BglF catalyzes beta-glucoside phosphotransfer across the cytoplasmic membrane in Escherichia coli. In addition, BglF acts as a sugar sensor that controls expression of beta-glucoside utilization genes by reversibly phosphorylating the transcriptional antiterminator BglG. Thus, BglF can exist in two opposed states: a nonstimulated state that inactivates BglG by phosphorylation and a sugar-stimulated state that activates BglG by dephosphorylation and phosphorylates the incoming sugar. Sugar phosphorylation and BglG (de)phosphorylation are both catalyzed by the same residue, Cys24. To investigate the coordination and the structural requirements of the opposing activities of BglF, we conducted a genetic screen that led to the isolation of mutations that shift the balance toward BglG phosphorylation. We show that some of the mutants that are impaired in dephosphorylation of BglG retained the ability to catalyze the concurrent activity of sugar phosphotransfer. These mutations map to two regions in the BglF membrane domain that, based on their predicted topology, were suggested to be implicated in activity. Using in vivo cross-linking, we show that a glycine in the membrane domain, whose substitution impaired the ability of BglF to dephosphorylate BglG, is spatially close to the active-site cysteine located in a hydrophilic domain. This residue is part of a newly identified motif conserved among beta-glucoside permeases associated with RNA-binding transcriptional antiterminators. The phenotype of the BglF mutants could be suppressed by BglG mutants that were isolated by a second genetic screen. In summary, we identified distinct sites in BglF that are involved in regulating phosphate flow via the common active-site residue in response to environmental cues.

Regulation of sugar catabolism in Lactococcus lactis

The increasing number of genomic and post-genomic studies on Gram-positive organisms and especially on lactic acid bacteria brings a lot of information on sugar catabolism in these bacteria. Like for many other bacteria, glucose is the most preferred source of carbon and energy for Lactococcus lactis. Other carbon sources can induce their own utilization in the absence of well-metabolized sugar. These processes engage numbers of genes and undergo complex mechanisms of regulation. In this review, we discuss various biochemical and genetic control mechanisms involved in sugar catabolism, like regulation by repressors, activators, antiterminators or carbon catabolite repression control.

Regulation of the mpt operon in Listeria innocua by the ManR protein

The phosphotransferase system regulation domain (PRD)-containing activator, ManR, is required for glucose-controlled transcription of the mannose permease two (mpt) operon in Listeria innocua. His-871 in ManR PRD-II is needed for mpt repression in glucose-free media. His-506 in PRD-I is needed for mpt induction by glucose.

How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria

The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.

Opposing effects of histidine phosphorylation regulate the AtxA virulence transcription factor in Bacillus anthracis

Expression of genes for Bacillus anthracis toxin and capsule virulence factors are dependent upon the AtxA transcription factor. The mechanism by which AtxA regulates the transcription of its target genes is unknown. Here we report that bioinformatic analyses suggested the presence in AtxA of two PTS (phosphenolpyruvate : sugar phosphotransferase system) regulation domains (PRD) generally regulated by phosphorylation/dephosphorylation at conserved histidine residues. By means of amino acid substitutions that mimic the phosphorylated (H to D) or the unphosphorylated (H to A) state of the protein, we showed that phosphorylation of H199 of PRD1 is likely to be necessary for AtxA activation while phosphorylation of H379 in PRD2 is inhibitory to toxin gene transcription. In vivo labelling experiments with radioactive phosphate allowed us to propose that H199 and H379 are AtxA residues subject to regulated phosphorylation. In support to these notions, we also show that deletion of ptsHI, encoding the HPr intermediate and the EI enzymes of PTS, or growth in the presence of glucose affect positively and negatively, respectively, the activity of AtxA. Our results link virulence factor production in B. anthracis to carbohydrate metabolism and, for the first time, provide a mechanistic explanation for AtxA transcriptional activity.

Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues

In CAPRI Rounds 1 and 2, we assumed that because there are many ionic charges that weaken electrostatic interaction forces in living cells, the hydrophobic interaction force might be important entropically. As a result of Rounds 1 and 2, the predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor, because only the largest benzene cluster was used for generating the initial docking structures. These were generated by fitting of benzene clusters formed on the surface of receptor and ligand. In CAPRI Rounds 3-5, the grid-scoring sum on the protein-protein interaction surface and the pairwise potential of the amino acid residues, which were indicated as coming easily into the protein-protein interaction regions, were used as the calculation methods, along with the smaller benzene clusters that participated in benzene cluster fitting. Good predicted models were obtained for Targets 11 and 12. When the modeled receptor proteins were superimposed on the experimental structures, the smallest ligand root-mean-square deviation (RMSD) values corresponding to the RMSD between the model and experimental structures were 6.2 A and 7.3 A, respectively.

Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI

In rounds 3-5 of CAPRI, the community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction, we applied the 3D-Dock software package to predict the atomic structures of nine biophysical interactions. This approach starts with an initial grid-based shape complementarity search. The product of this is a large number of potential interacting conformations that are subsequently ranked by interface residue propensities and interaction energies. Refinement through detailed energetics and optimization of side-chain positions using a rotamer library is also performed. For rounds 3, 4, and 5 of the CAPRI evaluation, where possible, we clustered functional residues on the surfaces of the monomers as an indication of binding sites, using sequence based evolutionary conservations. In certain targets this provided a very useful tool for identifying the areas of interaction. During round 5, we also applied the techniques of side-chain trimming and geometrical clustering described in the literature. Of the nine target complexes in rounds 3-5, we predicted conformations that contained at least some correct contact residues for seven of these systems. For two of the targets, we submitted predictions that were considered as medium-quality. These were a nidogen-laminin complex for target 8 (T08) and a serine-threonine phosphatase bound to a targeting subunit (T14). For a further three target systems, we produced models that were rated as acceptable predictions.

Approaching the CAPRI challenge with an efficient geometry-based docking

The last 3 rounds (3-5) of CAPRI included a wide range of docking targets. Several targets were especially challenging, since they involved large-scale movements and symmetric rearrangement, while others were based on homology models. We have approached the targets with a variety of geometry-based docking algorithms that include rigid docking, symmetric docking, and flexible docking with symmetry constraints. For all but 1 docking target, we were able to submit at least 1 acceptable quality prediction. Here, we detail for each target the prediction methods used and the specific biological data employed, and supply a retrospective analysis of the results. We highlight the advantages of our techniques, which efficiently exploit the geometric shape complementarity properties of the interaction. These enable them to run only few minutes on a standard PC even for flexible docking, thus proving their scalability toward computational genomic scale experiments. We also outline the major required enhancements, such as the introduction of side-chain position refinement and the introduction of flexibility for both docking partners.

Hexose/Pentose and Hexitol/Pentitol Metabolism

Escherichia coli and Salmonella enterica serovar Typhimurium exhibit a remarkable versatility in the usage of different sugars as the sole source of carbon and energy, reflecting their ability to make use of the digested meals of mammalia and of the ample offerings in the wild. Degradation of sugars starts with their energy-dependent uptake through the cytoplasmic membrane and is carried on further by specific enzymes in the cytoplasm, destined finally for degradation in central metabolic pathways. As variant as the different sugars are, the biochemical strategies to act on them are few. They include phosphorylation, keto-enol isomerization, oxido/reductions, and aldol cleavage. The catabolic repertoire for using carbohydrate sources is largely the same in E. coli and in serovar Typhimurium. Nonetheless, significant differences are found, even among the strains and substrains of each species. We have grouped the sugars to be discussed according to their first step in metabolism, which is their active transport, and follow their path to glycolysis, catalyzed by the sugar-specific enzymes. We will first discuss the phosphotransferase system (PTS) sugars, then the sugars transported by ATP-binding cassette (ABC) transporters, followed by those that are taken up via proton motive force (PMF)-dependent transporters. We have focused on the catabolism and pathway regulation of hexose and pentose monosaccharides as well as the corresponding sugar alcohols but have also included disaccharides and simple glycosides while excluding polysaccharide catabolism, except for maltodextrins.

ATTRACT: Protein-protein docking in CAPRI using a reduced protein model

Protein-protein complex structures have been predicted for CAPRI Rounds 3 and 5 using a reduced protein model. Proteins are represented by up to 3 pseudoatoms per amino acid. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to another protein. The reduced protein model allows one to perform systematic docking minimization of many thousand start structures in reasonable computer time. Flexibility of critical surface side-chains can be accounted for by a multiple conformational copy approach. The multicopy approach allows simultaneous adjustment of side-chain conformations and optimization of translational and rotational degrees of freedom of one protein with respect to the partner during docking. For 3 (Targets 8, 14, and 19) out of 5 CAPRI targets, the approach resulted in predictions in close agreement with experiment [root-mean-square deviation (RMSD) of backbone atoms within 10 A of the protein-protein interface < 1.8 A]. The comparison of predicted and experimental structures of the CAPRI targets indicates that besides local conformational changes (e.g., changes in side-chain conformations), global conformational changes of the protein backbone can be critical for complex formation. These conformational changes not accounted for during docking are a likely reason for the unrealistic predictions in 2 cases (Targets 9 and 18).

Docking to single-domain and multiple-domain proteins: Old and new challenges

The diverse selection of targets in the CAPRI experiments provides grounds for determining the limits of our rigid-body docking program MolFit, and for extending it. We find that the sensitivity of MolFit is high, enabling it to produce reasonably accurate docking solutions when the structures undergo moderate local conformation changes upon complex formation or when the docked molecules are modeled. Yet the ranks of these solutions are sometimes too low to meet the requirements of CAPRI assessment. This indicates that the selectivity of MolFit, which was optimized for docking of unbound X-ray structures, and which relies on the availability of external data from biochemical and bioinformatic sources, needs readjustment in order to meet the challenges presented by NMR or modeled structures. A different challenge is presented by large global conformation changes such as movements of domains. We show that such changes can be accommodated within the rigid-body approximation by employing rigid multibody multistage docking procedures. We also address the difficulty of ranking results from 2-body and multibody docking scans in cases in which there are no external data favoring one option over the other.

The bgl sensory system: a transmembrane signaling pathway controlling transcriptional antitermination

The bgl system represents a family of sensory systems composed of membrane-bound sugar-sensors and transcriptional antiterminators, which regulate expression of genes involved in sugar utilization in response to the presence of the corresponding sugar in the growth medium. The BglF sensor catalyzes different activities depending on its stimulation state: in its non-stimulated state, it phosphorylates the BglG transcriptional regulator, thus inactivating it; in the presence of the stimulating sugar, it transports the sugar and phosphorylates it and also activates BglG by dephosphorylation, leading to bgl operon expression. The sugar stimulates BglF by inducing a change in its membrane topology. BglG exists in several conformations: a dimer, which is active, and compact and non-compact monomers, which are inactive. BglF modulates the transition of BglG from one conformation to another, depending on sugar availability. The two Bgl proteins form a pre-complex at the membrane that dissociates upon stimulation, enabling BglG to exert its effect on transcription.

Experimental and Computational Characterization of the Dimerization of the PTS-regulation Domains of BglG from Escherichia coli

BglG and LicT are transcriptional antiterminators from Escherichia coli and Bacillus subtilis, respectively, that control the expression of genes and operons involved in transport and catabolism of carbohydrates. Both proteins contain a duplicate conserved domain, the PTS-regulation domain (PRD), and they are regulated by phosphorylation on specific, highly conserved histidine residues located in the PRDs. However, despite their similar function and the high sequence identity, experimental evidence implies different modes of regulation. Thus, BglG must be de-phosphorylated on PRD2 in order to form active dimers, whereas activation of LicT requires de-phosphorylation on PRD1 and phosphorylation on PRD2. Here we address two goals. First, we test in vivo and in silico the effect of point mutations in the PRDs of BglG on the PRD-PRD dimerization. Second, we explore computationally the effect of histidine phosphorylation on PRD dimerization in BglG and LicT. We find excellent correspondence between the experimental and computational measures of the influence of mutations on PRD dimerization in BglG. This establishes that the geometric-electrostatic complementarity scores computed with the program MolFit provide a good measure of the effects of mutations in this system. In addition, it indicates that the dimerization mode of the separately expressed PRDs of BglG is similar to the dimers formed by activated LicT. The computations also show that phosphorylation of the histidine residues in PRD1 of either BglG or LicT leads to a strong electrostatic repulsion. Conversely, the phosphorylation of one histidine residue in PRD2 of LicT leads to improved electrostatic complementarity at the PRD2-PRD2 interface, whereas the corresponding phosphorylation in BglG has negligible contribution. This different conduct may be attributed to a single replacement in the sequence of PRD2 in BglG compared to LicT, Ala262 versus Asp261, respectively.

Activation of the LicT Transcriptional Antiterminator Involves a Domain Swing/Lock Mechanism Provoking Massive Structural Changes

The transcriptional antiterminator protein LicT regulates the expression of Bacillus subtilis operons involved in beta-glucoside metabolism. It consists of an N-terminal RNA-binding domain (co-antiterminator (CAT)) and two phosphorylatable phosphotransferase system regulation domains (PRD1 and PRD2). In the activated state, each PRD forms a dimeric unit with the phosphorylation sites totally buried at the dimer interface. Here we present the 1.95 A resolution structure of the inactive LicT PRDs as well as the molecular solution structure of the full-length protein deduced from small angle x-ray scattering. Comparison of native (inactive) and mutant (constitutively active) PRD crystal structures shows massive tertiary and quaternary rearrangements of the entire regulatory domain. In the inactive state, a wide swing movement of PRD2 results in dimer opening and brings the phosphorylation sites to the protein surface. This movement is accompanied by additional structural rearrangements of both the PRD1-PRD1 ' interface and the CAT-PRD1 linker. Small angle x-ray scattering experiments indicate that the amplitude of the PRD2 swing might even be wider in solution than in the crystals. Our results suggest that PRD2 is highly mobile in the native protein, whereas it is locked upon activation by phosphorylation.

Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis

HutP is an L-histidine-activated RNA binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on the hut mRNA. The crystal structure of HutP complexed with an L-histidine analog showed a novel fold; there are four antiparallel beta strands in the central region of each monomer, with two alpha helices each on the front and back. Two HutP monomers form a dimer, and three dimers are arranged in crystallographic 3-fold symmetry to form a hexamer. A histidine analog was located in between the two monomers of HutP, with the imidazole group of L-histidine hydrogen bonded to Glu81. An activation mechanism is proposed based on the identification of key residues of HutP. The HutP binding region in hut mRNA was defined: it consists of three UAG trinucleotide motifs separated by four spacer nucleotides. Residues of HutP potentially important for RNA binding were identified.

Crystallization and preliminary X-ray diffraction studies of the metal-ion-mediated ternary complex of the HutP protein with L-histidine and its cognate RNA

HutP is an RNA-binding protein that regulates the expression of the Bacillus subtilis hut operon by binding to cis-acting regulatory sequences within hut mRNA, exclusively in the presence of L-histidine. We recently solved the crystal structure of a binary complex (HutP with an L-histidine analog) that revealed a novel RNA-binding fold, and identified the important residues that interact with the L-histidine analog. In addition, we have defined the minimal RNA binding segment that is required for HutP recognition. Interestingly, we showed that ternary complex formation depends on the availability of not only L-histidine but also divalent metal ions. Here we report the crystallization and preliminary X-ray diffraction analysis of the HutP ternary complex. The ternary complex was crystallized in the presence of Mg2+ along with L-histidine and hut mRNA, using the hanging drop vapor diffusion method. The crystal belongs to the R3 space group, with unit cell parameters a=b=75.30 A, c=133.8 A. A complete data set at 1.60 A was collected.

Modulation of monomer conformation of the BglG transcriptional antiterminator from Escherichia coli

The BglG protein positively regulates expression of the bgl operon in Escherichia coli by binding as a dimer to the bgl transcript and preventing premature termination of transcription in the presence of beta-glucosides. BglG activity is negatively controlled by BglF, the beta-glucoside phosphotransferase, which reversibly phosphorylates BglG according to beta-glucoside availability, thus modulating its dimeric state. BglG consists of an RNA-binding domain and two homologous domains, PRD1 and PRD2. Based on structural studies of a BglG homologue, the two PRDs fold similarly, and the interactions within the dimer are PRD1-PRD1 and PRD2-PRD2. We have recently shown that the affinity between PRD1 and PRD2 of BglG is high, and a fraction of the BglG monomers folds in the cell into a compact conformation, in which PRD1 and PRD2 are in close proximity. We show here that both BglG forms, the compact and noncompact, bind to the active site-containing domain of BglF, IIB(bgl), in vitro. The interaction of BglG with IIB(bgl) or BglF is mediated by PRD2. Both BglG forms are detected as phosphorylated proteins after in vitro phosphorylation with IIB(bgl) and are dephosphorylated by BglF in vitro in the presence of beta-glucosides. Nevertheless, genetic evidence indicates that the interaction of IIB(bgl) and BglF with the compact form is seemingly less favorable. Using in vivo cross-linking, we show that BglF enhances folding of BglG into a compact conformation, whereas the addition of beta-glucosides reduces the amount of this form. Based on these results we suggest a model for the modulation of BglG conformation and activity by BglF.

Prediction of protein–protein interactions: the CAPRI experiment, its evaluation and implications

Given the increasing interest in protein-protein interactions, the prediction of these interactions from sequence and structural information has become a booming activity. CAPRI, the community-wide experiment for assessing blind predictions of protein-protein interactions, is playing an important role in fostering progress in docking procedures. At the same time, novel methods are being derived for predicting regions of a protein that are likely to interact and for characterizing putative intermolecular contacts from sequence and structural data. Together with docking procedures, these methods provide an integrated computational approach that should be a valuable complement to genome-scale experimental studies of protein-protein interactions.

Control of the Bacillus subtilis Antiterminator Protein GlcT by Phosphorylation

Bacillus subtilis transports glucose by the phosphotransferase system (PTS). The genes for this system are encoded in the ptsGHI operon, which is induced by glucose and depends on a termination/antitermination mechanism involving a riboswitch and the RNA-binding antitermination protein GlcT. In the absence of glucose, GlcT is inactive, and a terminator is formed in the leader region of the ptsG mRNA. If glucose is present, GlcT can bind to its RNA target and prevent transcription termination. The GlcT protein is composed of three domains, an N-terminal RNA binding domain and two PTS regulation domains, PTS regulation domain (PRD) I and PRD-II. In this work, we demonstrate that GlcT can be phosphorylated by two PTS proteins, HPr and the glucose-specific enzyme II (EIIGlc). HPr-dependent phosphorylation occurs on PRD-II and has a slight stimulatory effect on GlcT activity. In contrast, EIIGlc phosphorylates the PRD-I of GlcT, and this phosphorylation inactivates GlcT. This latter phosphorylation event links the availability of glucose to the expression of the ptsGHI operon via the phosphorylation state of EIIGlc and GlcT. This is the first in vitro demonstration of a direct phosphorylation of an antiterminator of the BglG family by the corresponding PTS permease.

Interactions between the PTS regulation domains of the BglG transcriptional antiterminator from Escherichia coli

The E. coli BglG protein inhibits transcription termination within the bgl operon in the presence of beta-glucosides. BglG represents a family of transcriptional antiterminators that bind to RNA sequences, which partially overlap rho-independent terminators, and prevent termination by stabilizing an alternative structure of the transcript. The activity of BglG is determined by its dimeric state, which is modulated by reversible phosphorylation catalyzed by BglF, a PTS permease. Only the non-phosphorylated BglG dimer binds to RNA and allows read-through of transcription. BglG is composed of three domains: an RNA-binding domain followed by two domains, PRD1 and PRD2 (PTS regulation domains), which are similar in their sequence and folding. Based on the three-dimensional structure of dimeric LicT, a BglG homologue from Bacillus subtilis, the interactions within the dimer are PRD1-PRD1 and PRD2-PRD2. We have shown before that PRD2 mediates homodimerization very efficiently. Using genetic systems and in vitro techniques that assay and characterize protein-protein interactions, we show here that the PRD1 dimerizes very slowly, but once it does, the homodimers are stable. These results support our model that formation of BglG dimers initiates with PRD2 dimerization followed by zipping up of two BglG monomers to create the active RNA-binding domain. Moreover, our results demonstrate that PRD1 and PRD2 heterodimerize efficiently in vitro and in vivo. The affinity among the PRDs is in the following order: PRD2-PRD2 > PRD1-PRD2 > PRD1-PRD1. The interaction between PRD1 and PRD2 offers an explanation for the requirement of conserved residues in PRD1 for the phosphorylation of PRD2 by BglF.

Regulation of the Escherichia coli antiterminator protein BglG by phosphorylation at multiple sites and evidence for transfer of phosphoryl groups between monomers

Activity of antiterminator protein BglG regulating the beta-glucoside operon in Escherichia coli is controlled by the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) in a dual manner. It requires HPr phosphorylation to be active, whereas phosphorylation by the beta-glucoside-specific transport protein EIIBgl inhibits its activity. BglG and its relatives carry two PTS regulation domains (PRD1 and PRD2), each containing two conserved histidines. For BglG, histidine 208 in PRD2 was reported to be the negative phosphorylation site. In contrast, other antiterminators of this family are negatively regulated by phosphorylation of the first histidine in PRD1, and presumably activated by phosphorylation of the histidines in PRD2. In this work, a screen for mutant BglG proteins that escape repression by EIIBgl yielded exchanges of nine residues within PRD1, including conserved histidines His-101 and His-160, and C-terminally truncated proteins. Genetic and phosphorylation analyses indicate that His-101 in PRD1 is phosphorylated by EIIBgl and that His-160 contributes to negative regulation. His-208 in PRD2 is essential for BglG activity, suggesting that it is phosphorylated by HPr. Surprisingly, phosphorylation by HPr is not fully abolished by exchanges of His-208. However, phosphorylation by HPr is inhibited by exchanges in PRD1 and the phosphorylation of these mutants is restored in the presence of wild-type BglG. These results suggest that the activating phosphoryl group is transiently donated from HPr to PRD1 and subsequently transferred to His-208 of a second BglG monomer. The active His-208-phosphorylated BglG dimer can subsequently be inhibited in its activity by EIIBgl-catalyzed phosphorylation at His-101.

A fraction of the BglG transcriptional antiterminator from Escherichia coli exists as a compact monomer

Expression of the bgl operon in Escherichia coli, induced by beta-glucosides, is positively regulated by BglG, a transcriptional antiterminator. In the presence of inducer, BglG dimerizes and binds to the bgl transcript to prevent premature termination of transcription. The dimeric state of BglG is determined by BglF, a membrane-bound enzyme II of the phosphoenolpyruvate-dependent phosphotransferase system (PTS), which reversibly phosphorylates BglG according to beta-glucoside availability. BglG is composed of an RNA-binding domain followed by two homologous PTS regulation domains (PRD1 and PRD2). The predicted structure of dimeric LicT, a BglG homologue from Bacillus subtilis, suggests that the two PRDs adopt a similar structure and that the interactions within the dimer are PRD1-PRD1 and PRD2-PRD2. We have shown recently that the PRD1 and PRD2 domains of BglG can form a stable heterodimer. We report here, based on in vitro and in vivo cross-linking experiments, that a fraction of BglG is present in the cell in a compact form in which PRD1 and PRD2 are in close proximity. The compact form is present mainly in the BglG monomers. Our results imply that the monomer-dimer transition involves a conformational change. The possible role of the compact form in preventing untimely induction of the bgl operon is discussed.

Domain analysis of transcriptional regulators bearing PTS regulatory domains

Multidomain transcriptional activators and antiterminators that include PTS regulatory domains (PRDs) were subjected to sequence analyses. All of these transcriptional regulators exhibit one or more N-terminal nucleic acid binding site(s) and two PRD regions. Additionally, we show that the activators contain C-terminal PTS IIB and IIA domains with fully conserved phosphorylation sites (cysteine and histidine, respectively). One activator, LevR has a different domain order than all other activators with a truncated IIA domain preceding (rather than following) the IIB domain, and it has a C-terminal PRD, rather than two adjacent PRDs. Our analyses suggest that the activators and antiterminators arose early, and that domain shuffling either within or between proteins has occurred rarely. The results allow us to propose an evolutionary pathway for the appearance of these transcription factors and to suggest functional significance for these domains and specific residues within them.

Transcription attenuation

In this review, we describe a variety of mechanisms that bacteria use to regulate transcription elongation in order to control gene expression in response to changes in their environment. Together, these mechanisms are known as attenuation and antitermination, and both involve controlling the formation of a transcription terminator structure in the RNA transcript prior to a structural gene or operon. We examine attenuation and antitermination from the point of view of the different biomolecules that are used to influence the RNA structure. Attenuation of many amino acid biosynthetic operons, particularly in enteric bacteria, is controlled by ribosomes translating leader peptides. RNA-binding proteins regulate attenuation, particularly in gram-positive bacteria such as Bacillus subtilis. Transfer RNA is also used to bind to leader RNAs and influence transcription antitermination in a large number of amino acyl tRNA synthetase genes and several biosynthetic genes in gram-positive bacteria. Finally, antisense RNA is involved in mediating transcription attenuation to control copy number of several plasmids.

Bacillus subtilis mutant LicT antiterminators exhibiting enzyme I- and HPr-independent antitermination affect catabolite repression of the bglPH operon

The Bacillus subtilis antiterminator LicT regulates the expression of bglPH and bglS, which encode the enzymes for the metabolism of aryl-beta-glucosides and the beta-glucanase BglS. The N-terminal domain of LicT (first 55 amino acids) prevents the formation of rho-independent terminators on the respective transcripts by binding to target sites overlapping these terminators. Proteins of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) regulate the antitermination activity of LicT by phosphorylating histidines in its two PTS regulation domains (PRDs). Phosphorylation at His-100 in PRD-1 requires the PTS proteins enzyme I and HPr and the phosphorylated permease BglP and inactivates LicT. During transport and phosphorylation of aryl-beta-glucosides, BglP is dephosphorylated, which renders LicT active and thus leads to bglPH and bglS induction. In contrast, phosphorylation at His-207 and/or His-269 in PRD-2, which requires only enzyme I and HPr, is absolutely necessary for LicT activity and bglPH and bglS expression. We isolated spontaneous licT mutants expressing bglPH even when enzyme I and HPr were absent (as indicated by the designation "Pia" [PTS-independent antitermination]). Introduced in a ptsHI(+) strain, two classes of licT(Pia) mutations could be distinguished. Mutants synthesizing LicT(Pia) antiterminators altered in PRD-2 still required induction by aryl-beta-glucosides, whereas mutations affecting PRD-1 caused constitutive bglPH expression. One of the two carbon catabolite repression (CCR) mechanisms operative for bglPH requires the rho-independent terminator and is probably prevented when LicT is activated by P approximately His-HPr-dependent phosphorylation in PRD-2 (where the prefix "P approximately " stands for "phospho"). During CCR, the small amount of P approximately His-HPr present in cells growing on repressing PTS sugars probably leads to insufficient phosphorylation at PRD-2 of LicT and therefore to reduced bglPH expression. In agreement with this concept, mutants synthesizing a P approximately His-HPr-independent LicT(Pia) had lost LicT-modulated CCR.