Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins

cAMP-independent Crp homolog adds to the multi-layer regulatory network in Porphyromonas gingivalis

Introduction

Porphyromonas gingivalis encodes three CRP/FNR superfamily proteins: HcpR, PgRsp, and CrpPg, with CrpPg similar to cAMP-sensing proteins but not classified into known families. This study investigates the role of CrpPg in regulating the expression of factors essential for P. gingivalis virulence in A7436 and ATCC 33277 strains.

Methods

The role of CrpPg protein in P. gingivalis was determined using the ΔcrpPg mutant strains to characterize their phenotype and to assess the impact of crpPg inactivation on gene expression using RNA-seq and RT-qPCR. Additionally, the CrpPg protein was purified and characterized.

Results

Key findings in the ΔcrpPg mutant strain include up-regulated mfa1-5 and rgpA genes and down-regulated trxA, soxR, and ustA genes. While crpPg inactivation does not affect growth in liquid culture media, it impairs biofilm formation and enhances adhesion to and invasion of gingival keratinocytes. CrpPg binds directly to its own and mfa promoters without interacting with cyclic nucleotides or di-nucleotides. Its three-dimensional structure, resembling E. coli Crp in complex with cAMP and DNA, suggests that CrpPg functions as a global regulator independently of cAMP binding. The highest crpPg expression in the early exponential growth phase declines as cell density and metabolic conditions change over time, suggesting a regulatory function depending on the CrpPg protein amount.

Conclusions

By controlling the shift from planktonic to biofilm lifestyle, CrpPg may play a role in pathogenicity. Regulating the expression of virulence factors required for host cell invasion and intracellular replication, CrpPg may help P. gingivalis evade immune responses.

Rapid adaptation of Bacillus thuringiensis to alkaline environments via the L-lactate metabolism pathway regulated by the CRP/FNR family regulator LtmR

Bacillus thuringiensis (Bt) is an entomopathogenic bacterium. During infection, Bt often encounters alkaline conditions in the insect midgut and adaptation to this alkaline environment is crucial for its survival and establishment. Here, we investigated the mechanisms of rapid adaptation of Bt to an alkaline environment. DNA microarray revealed 739 downregulated genes and 662 upregulated genes in the presence of 28 mM NaOH for 10 min relative to the condition without alkaline treatment. The activities of some primary metabolic pathways of Bt were enhanced under alkaline conditions, and many genes related to synthesis and transportation of amino acids, nucleic acids, and cell surfaces were significantly induced. In particular, ldh2 (HD73_5189) and lpm1 (HD73_0686), which encode lactate dehydrogenase and lactate permease, respectively, were significantly upregulated. Transcription of ldh2 and lpm1 was directly regulated by the CRP/FNR family transcriptional regulator, LtmR (L-lactate transport and metabolism regulator), through binding between LtmR and their promoters. The intracellular concentration of pyruvate increased and that of lactate decreased under alkaline conditions. Following deletion of ldh2, the concentration of pyruvate decreased, and that of lactate increased, suggesting that ldh2 catalyzes the conversion of lactate to pyruvate. ltmR, ldh2, and lpm1 were shown to contribute to Bt virulence in Ostrinia furnacalis. Collectively, these data indicate that the pyruvate-L-lactate metabolic pathway is important for Bt adaptation and virulence in alkaline environments. Homologues of LtmR are highly conserved in B. cereus group, suggesting that they share a similar strategy for pH adaptation.

Identifying Allosteric Hotspots in Mycobacterium tuberculosis cAMP Receptor Protein through Structural Homology

Understanding the mechanisms of allosteric regulation in response to second messengers is crucial for advancing basic and applied research. This study focuses on the differential allosteric regulation by the ubiquitous signaling molecule, cAMP, in the cAMP receptor protein from Escherichia coli (CRPEcoli) and from Mycobacterium tuberculosis (CRPMTB). By introducing structurally homologous mutations from allosteric hotspots previously identified in CRPEcoli into CRPMTB and examining their effects on protein solution structure, stability and function, we aimed to determine the factors contributing to their differential allosteric regulation. Our results demonstrate that the mutations did not significantly alter the overall fold, assembly and thermodynamic stability of CRPMTB, but had varying effects on cAMP binding affinity and cooperativity. Interestingly, the mutations had minimal impact on the specific binding of CRPMTB to DNA promoter sites. However, we found that cAMP primarily reduces nonspecific CRPMTB-DNA complexes and that the mutants largely lose this ability. Furthermore, our experiments revealed that CRPMTB-DNA complexes serve as a nucleation point for additional binding of CRPMTB proteins to form high-order oligomers with the DNA. Overall, our findings highlight the importance of both cAMP and DNA interactions in modulating the allosteric regulation of CRPMTB and provide insights into the differential responses of CRPEcoli and CRPMTB to cAMP.

Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase

The CRP-FNR (cAMP receptor protein-fumarate/nitrate reductase regulator) superfamily of transcriptional regulators includes the cyanobacterial master regulator NtcA, which orchestrates large responses of cyanobacteria to nitrogen scarcity. NtcA uses as allosteric activator 2-oxoglutarate (2OG), a signal of nitrogen poorness and carbon richness, and binds a co-activating protein (PipX) that shuttles between the signaling protein PII and NtcA depending on nitrogen richness, thus connecting PII signaling and gene expression regulation. Here, combining structural (X-ray crystallography of six types of crystals including NtcA complexes with DNA, 2OG, and PipX), modeling, and functional [electrophoretic mobility shift assays and bacterial two-hybrid (BACTH)] studies, we clarify the reasons for the exquisite specificity for the binding of NtcA to its target DNA, its mechanisms of activation by 2OG, and its co-activation by PipX. Our crystal structures of PipX-NtcA-DNA complexes prove that PipX does not interact with DNA, although it increases NtcA-DNA contacts, and that it stabilizes the active, DNA-binding-competent conformation of NtcA. Superimposition of this complex on a very recently reported cryo-electron microscopy structure of NtcA in a transcription activity complex with RNA polymerase (RNAP), shows that PipX binding helps recruit RNAP by PipX interaction with RNAP, particularly with its gamma and sigma (region 4) subunits, a structural prediction supported here by BACTH experiments.

Targeting bacterial transcription factors for infection control: opportunities and challenges

The rising threat of antibiotic resistance in pathogenic bacteria emphasizes the need for new therapeutic strategies. This review focuses on bacterial transcription factors (TFs), which play crucial roles in bacterial pathogenesis. We discuss the regulatory roles of these factors through examples, and we outline potential therapeutic strategies targeting bacterial TFs. Specifically, we discuss the use of small molecules to interfere with TF function and the development of transcription factor decoys, oligonucleotides that compete with promoters for TF binding. We also cover peptides that target the interaction between the bacterial TF and other factors, such as RNA polymerase, and the targeting of sigma factors. These strategies, while promising, come with challenges, from identifying targets to designing interventions, managing side effects, and accounting for changing bacterial resistance patterns. We also delve into how Artificial Intelligence contributes to these efforts and how it may be exploited in the future, and we touch on the roles of multidisciplinary collaboration and policy to advance this research domain.Abbreviations: AI, artificial intelligence; CNN, convolutional neural networks; DTI: drug-target interaction; HTH, helix-turn-helix; IHF, integration host factor; LTTRs, LysR-type transcriptional regulators; MarR, multiple antibiotic resistance regulator; MRSA, methicillin resistant Staphylococcus aureus; MSA: multiple sequence alignment; NAP, nucleoid-associated protein; PROTACs, proteolysis targeting chimeras; RNAP, RNA polymerase; TF, transcription factor; TFD, transcription factor decoying; TFTRs, TetR-family transcriptional regulators; wHTH, winged helix-turn-helix.

Synergy of native mass spectrometry and other biophysical techniques in studies of iron‑sulfur cluster proteins and their assembly

The application of mass spectrometric methodologies has revolutionised biological chemistry, from identification through to structural and conformational studies of proteins and other macromolecules. Native mass spectrometry (MS), in which proteins retain their native structure, is a rapidly growing field. This is particularly the case for studies of metalloproteins, where non-covalently bound cofactors remain bound following ionisation. Such metalloproteins include those that contain an iron‑sulfur (FeS) cluster and, despite their fragility and O2 sensitivity, they have been a particular focus for applications of native MS because of its capacity to accurately monitor mass changes that reveal chemical changes at the cluster. Here we review recent advances in these applications of native MS, which, together with data from more traditionally applied biophysical methods, have yielded a remarkable breadth of information about the FeS species present, and provided key mechanistic insight not only for FeS cluster proteins themselves, but also their assembly.

Identification of a cellular role of hemolysin co-regulatory protein (Hcp) in Vibrio alginolyticus modulating substrate metabolism and biofilm formation by cAMP-CRP

Cyclic AMP (cAMP) and cAMP receptor protein (CRP) system controls catabolic enzyme expression based on metabolite concentrations in bacteria. Hemolysin co-regulatory protein (Hcp) is well known as a molecular chaperone for virulence factor secretion of the type VI secretion system (T6SS). However, the intracellular role of Hcp involving in bacterial physiological processes remains unknown. To clarify that, we constructed a single hcp mutant strain and analyzed their effects on the physiological processes of Vibrio alginolyticus. The omics results revealed the extensive involvement of Hcp in the catabolic metabolism in bacteria. Simultaneously, Hcp1 and Hcp2 played opposing regulatory roles on the bacterial growth, biofilm formation, and intracellular cAMP-CRP levels during cultivation in a glucose medium. Furthermore, the interacting protein screening and co-immunoprecipitation (Co-IP) assays confirmed that the glucose-specific phosphoenolpyruvate (PEP)-phosphotransferase system (PTS) enzyme IIA component (EIIAglc) was a key interacting partner with Hcp proteins as well as class I adenylyl cyclase (AC-I) in Vibrio alginolyticus. These results indicated that, to achieve cellular homeostasis, Hcp1 and Hcp2 might exert antagonistic and synergistic effects, respectively, on the interaction between EIIAglc and AC thus cooperatively regulating intracellular cAMP-CRP production.

Mechanisms underlying the low-temperature adaptation of 17β-estradiol-degrading bacterial strain Rhodococcus sp. RCBS9: insights from physiological and transcriptomic analyses

The 17β-estradiol (E2)-degrading bacterium Rhodococcus sp.RCBS9 previously showed remarkable resistance to the combined stresses of low temperature and E2. In this study, physiological experiments and transcriptomic analysis were performed to investigate the mechanisms underlying the strain's low-temperature adaptation and briefly analyze how it maintains its ability to degrade E2 at low temperature. The results showed that the strain's signal transduction functions, adaptive changes in cell membrane and cell wall structure, gene repair functions, and synthesis of antioxidants and compatible solutes are key to its ability to adapt to low temperature. In addition, its stress proteins in response to low temperature were not typical cold shock proteins, but rather universal stress proteins (USPs) and heat shock proteins (HSPs), among others. The strain also upregulated biofilm production, transporter proteins for carbon source uptake, and proteins for fatty acid degradation to ensure energy generation. The strain's multiple stress responses work synergistically to resist low-temperature stress, ensuring its adaptability to low-temperature environments and ability to degrade E2. Finally, six genes related to survival at low temperature (identified in the transcriptome analysis) were expressed in E. coli BL21, and they were found to contribute to recombinant E. coli growth at low temperature.

The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell

Terpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacterium Streptomyces griseus. Here, we revise the function of EshA, now referred to as Sg Enc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find that Sg Enc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein. Sg Enc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show that Sg Enc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity and Sg Enc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.

cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans

The cAMP receptor proteins (CRPs) play a critical role in bacterial environmental adaptation by regulating global gene expression levels via cAMP binding. Here, we report the structure of DdrI, a CRP family protein from Deinococcus radiodurans. Combined with biochemical, kinetic, and molecular dynamics simulations analyses, our results indicate that DdrI adopts a DNA-binding conformation in the absence of cAMP and can form stable complexes with the target DNA sequence of classical CRPs. Further analysis revealed that the high-affinity cAMP binding pocket of DdrI is partially filled with Tyr113-Arg55-Glu65 sidechains, mimicking the anti-cAMP-mediated allosteric transition. Moreover, the second syn-cAMP binding site of DdrI at the protein-DNA interface is more negatively charged compared to that of classical CRPs, and manganese ions can enhance its DNA binding affinity. DdrI can also bind to a target sequence that mimics another transcription factor, DdrO, suggesting potential cross-talk between these two transcription factors. These findings reveal a class of CRPs that are independent of cAMP activation and provide valuable insights into the environmental adaptation mechanisms of D. radiodurans.IMPORTANCEBacteria need to respond to environmental changes at the gene transcriptional level, which is critical for their evolution, virulence, and industrial applications. The cAMP receptor protein (CRP) of Escherichia coli (ecCRP) senses changes in intracellular cAMP levels and is a classic example of allosteric effects in textbooks. However, the structures and biochemical activities of CRPs are not generally conserved and there exist different mechanisms. In this study, we found that the proposed CRP from Deinococcus radiodurans, DdrI, exhibited DNA binding ability independent of cAMP binding and adopted an apo structure resembling the activated CRP. Manganese can enhance the DNA binding of DdrI while allowing some degree of freedom for its target sequence. These results suggest that CRPs can evolve to become a class of cAMP-independent global regulators, enabling bacteria to adapt to different environments according to their characteristics. The first-discovered CRP family member, ecCRP (or CAP) may well not be typical of the family and be very different to the ancestral CRP-family transcription factor.

The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell

Terpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacterium Streptomyces griseus. Here, we revise the function of EshA, now referred to as Sg Enc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find that Sg Enc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein. Sg Enc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show that Sg Enc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity and Sg Enc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.

Structure and molecular mechanism of bacterial transcription activation

Transcription activation is an important checkpoint of regulation of gene expression which occurs in response to different intracellular and extracellular signals. The key elements in this signal transduction process are transcription activators, which determine when and how gene expression is activated. Recent structural studies on a considerable number of new transcription activation complexes (TACs) revealed the remarkable mechanistic diversity of transcription activation mediated by different factors, necessitating a review and re-evaluation of the transcription activation mechanisms. In this review, we present a comprehensive summary of transcription activation mechanisms and propose a new, elaborate, and systematic classification of transcription activation mechanisms, primarily based on the structural features of diverse TAC components.

Catabolic Network of the Fermentative Gut Bacterium Phocaeicola vulgatus (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective

INTRODUCTION

Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary-fiber-fueled, fermentative metabolism the microbial community as well as the host health. Moreover, the fermentative metabolism of P. vulgatus bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the P. vulgatus physiology.

METHODS

P. vulgatus was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics.

RESULTS

The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (gCDW/mmolS) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (mMATP/mMC) from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one sided (with rhamnose or fucose: mainly propane-1,2-diol). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to d-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, Sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected.

CONCLUSIONS

The present study provides insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols.

Aminoglycoside uptake, stress, and potentiation in Gram-negative bacteria: new therapies with old molecules

SUMMARYAminoglycosides (AGs) are long-known molecules successfully used against Gram-negative pathogens. While their use declined with the discovery of new antibiotics, they are now classified as critically important molecules because of their effectiveness against multidrug-resistant bacteria. While they can efficiently cross the Gram-negative envelope, the mechanism of AG entry is still incompletely understood, although this comprehension is essential for the development of new therapies in the face of the alarming increase in antibiotic resistance. Increasing antibiotic uptake in bacteria is one strategy to enhance effective treatments. This review aims, first, to consolidate old and recent knowledge about AG uptake; second, to explore the connection between AG-dependent bacterial stress and drug uptake; and finally, to present new strategies of potentiation of AG uptake for more efficient antibiotic therapies. In particular, we emphasize on the connection between sugar transport and AG potentiation.

New progress in the identifying regulatory factors of exopolysaccharide synthesis in lactic acid bacteria

The exopolysaccharides (EPSs) of lactic acid bacteria (LAB) have presented various bioactivities and beneficial characteristics, rendering their vast commercial value and attracting a broad interest of researchers. The diversity of EPS structures contributes to the changes of EPS functions. However, the low yield of EPS of LAB has severely limited these biopolymers' comprehensive studies and applications in different areas, such as functional food, health and medicine fields. The clarification of biosynthesis mechanism of EPS will accelerate the synthesis and reconstruction of EPS. In recent years, with the development of new genetic manipulation techniques, there has been significant progress in the EPS biosynthesis mechanisms in LAB. In this review, the structure of LAB-derived EPSs, the EPS biosynthesis basic pathways in LAB, the EPS biosynthetic gene cluster, and the regulation mechanism of EPS biosynthesis will be summarized. It will focus on the latest progress in EPS biosynthesis regulation of LAB and provide prospects for future related developments.