DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family

EbfC/YbaB: A Widely Distributed Nucleoid-Associated Protein in Prokaryotes

Genomic compaction is an essential characteristic of living organisms. Nucleoid-associated proteins (NAPs) are a group of small proteins that play crucial roles in chromosome architecture and affect DNA replication, transcription, and recombination by imposing topological alterations in genomic DNA, thereby modulating global gene expression. EbfC/YbaB was first described as a DNA-binding protein of Borrelia burgdorferi that regulates the expression of surface lipoproteins with roles in virulence. Further studies indicated that this protein binds specifically and non-specifically to DNA and colocalises with nucleoids in this bacterium. The data showed that this protein binds to DNA as a homodimer, although it can form other organised structures. Crystallography analysis indicated that the protein possesses domains responsible for protein–protein interactions and forms a “tweezer” structure probably involved in DNA binding. Moreover, sequence analysis revealed conserved motifs that may be associated with dimerisation. Structural analysis also showed that the tridimensional structure of EbfC/YbaB is highly conserved within the bacterial domain. The DNA-binding activity was observed in different bacterial species, suggesting that this protein can protect DNA during stress conditions. These findings indicate that EbfC/YbaB is a broadly distributed NAP. Here, we present a review of the existing data on this NAP.

The Consistent Tick-Vertebrate Infectious Cycle of the Lyme Disease Spirochete Enables Borrelia burgdorferi To Control Protein Expression by Monitoring Its Physiological Status

The Lyme disease spirochete, Borrelia burgdorferi, persists in nature by alternatingly cycling between ticks and vertebrates. During each stage of the infectious cycle, B. burgdorferi produces surface proteins that are necessary for interactions with the tick or vertebrate tissues it encounters while also repressing the synthesis of unnecessary proteins. Among these are the Erp surface proteins, which are produced during vertebrate infection for interactions with host plasmin, laminin, glycosaminoglycans, and components of the complement system. Erp proteins are not expressed during tick colonization but are induced when the tick begins to ingest blood from a vertebrate host, a time when the bacteria undergo rapid growth and division. Using the erp genes as a model of borrelial gene regulation, our research group has identified three novel DNA-binding proteins that interact with DNA to control erp transcription. At least two of those regulators are, in turn, affected by DnaA, the master regulator of chromosome replication. Our data indicate that B. burgdorferi has evolved to detect the change from slow to rapid replication during tick feeding as a signal to begin expression of Erp and other vertebrate-specific proteins. The majority of other known regulatory factors of B. burgdorferi also respond to metabolic cues. These observations lead to a model in which the Lyme spirochete recognizes unique environmental conditions encountered during the infectious cycle to "know" where they are and adapt accordingly.

DNA-Binding Properties of YbaB, a Putative Nucleoid-Associated Protein From Caulobacter crescentus

Nucleoid-associated proteins (NAPs) or histone-like proteins (HLPs) are DNA-binding proteins present in bacteria that play an important role in nucleoid architecture and gene regulation. NAPs affect bacterial nucleoid organization via DNA bending, bridging, or forming aggregates. EbfC is a nucleoid-associated protein identified first in Borrelia burgdorferi, belonging to YbaB/EbfC family of NAPs capable of binding and altering DNA conformation. YbaB, an ortholog of EbfC found in Escherichia coli and Haemophilus influenzae, also acts as a transcriptional regulator. YbaB has a novel tweezer-like structure and binds DNA as homodimers. The homologs of YbaB are found in almost all bacterial species, suggesting a conserved function, yet the physiological role of YbaB protein in many bacteria is not well understood. In this study, we characterized the YbaB/EbfC family DNA-binding protein in Caulobacter crescentus. C. crescentus has one YbaB/EbfC family gene annotated in the genome (YbaB_Cc) and it shares 41% sequence identity with YbaB/EbfC family NAPs. Computational modeling revealed tweezer-like structure of YbaB_Cc, a characteristic of YbaB/EbfC family of NAPs. N-terminal–CFP tagged YbaB_Cc localized with the nucleoid and is able to compact DNA. Unlike B. burgdorferi EbfC protein, YbaB_Cc protein is a non-specific DNA-binding protein in C. crescentus. Moreover, YbaB_Cc shields DNA against enzymatic degradation. Collectively, our findings reveal that YbaB_Cc is a small histone-like protein and may play a role in bacterial chromosome structuring and gene regulation in C. crescentus.

LAZY2 controls rice tiller angle through regulating starch biosynthesis in gravity-sensing cells

Rice (Oryza sativa) tiller angle is a key component for achieving ideal plant architecture and higher grain yield. However, the molecular mechanism underlying rice tiller angle remains elusive. We characterized a novel rice tiller angle mutant lazy2 (la2) and isolated the causative gene LA2 through map-based cloning. Biochemical, molecular and genetic studies were conducted to elucidate the LA2-involved tiller angle regulatory mechanism. The la2 mutant shows large tiller angle with impaired shoot gravitropism and defective asymmetric distribution of auxin. We found that starch granules in amyloplasts are completely lost in the gravity-sensing leaf sheath base cells of la2, whereas the seed development is not affected. LA2 encodes a novel chloroplastic protein that can interact with the starch biosynthetic enzyme Oryza sativa plastidic phosphoglucomutase (OspPGM) to regulate starch biosynthesis in rice shoot gravity-sensing cells. Genetic analysis showed that LA2 regulates shoot gravitropism and tiller angle by acting upstream of LA1 to mediate lateral auxin transport. Our studies revealed that LA2 acts as a novel regulator of rice tiller angle by specifically regulating starch biosynthesis in gravity-sensing cells, and established the framework of the starch-statolith-dependent rice tiller angle regulatory pathway, providing new insights into the rice tiller angle regulatory network.

Gene Regulation and Transcriptomics

Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma factor cascade, the Hk1/Rrp1 two-component system and its product c-di-GMP, and the stringent response mediated by Rel_Bbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or fine- tuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by high-throughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each.

Bacterial secretion chaperones: the mycobacterial type VII case

Chaperones are central players in maintaining the proteostasis in all living cells. Besides highly conserved generic chaperones that assist protein folding and assembly in the cytosol, additional more specific chaperones have evolved to ensure the successful trafficking of proteins with extra-cytoplasmic locations. Associated with the distinctive secretion systems present in bacteria, different dedicated chaperones have been described that not only keep secretory proteins in a translocation competent state, but often are also involved in substrate targeting to the specific translocation channel. Recently, a new class of such chaperones has been identified that are involved in the specific recognition of substrates transported via the type VII secretion pathway in mycobacteria. In this minireview, we provide an overview of the different bacterial chaperones with a focus on their roles in protein secretion and will discuss in detail the roles of mycobacterial type VII secretion chaperones in substrate recognition and targeting.

EspL is essential for virulence and stabilizes EspE, EspF and EspH levels in Mycobacterium tuberculosis

The ESX-1, type VII, secretion system represents the major virulence determinant of Mycobacterium tuberculosis, one of the most successful intracellular pathogens. Here, by combining genetic and high-throughput approaches, we show that EspL, a protein of 115 amino acids, is essential for mediating ESX-1-dependent virulence and for stabilization of EspE, EspF and EspH protein levels. Indeed, an espL knock-out mutant was unable to replicate intracellularly, secrete ESX-1 substrates or stimulate innate cytokine production. Moreover, proteomic studies detected greatly reduced amounts of EspE, EspF and EspH in the espL mutant as compared to the wild type strain, suggesting a role for EspL as a chaperone. The latter conclusion was further supported by discovering that EspL interacts with EspD, which was previously demonstrated to stabilize the ESX-1 substrates and effector proteins, EspA and EspC. Loss of EspL also leads to downregulation in M. tuberculosis of WhiB6, a redox-sensitive transcriptional activator of ESX-1 genes. Overall, our data highlight the importance of a so-far overlooked, though conserved, component of the ESX-1 secretion system and begin to delineate the role played by EspE, EspF and EspH in virulence and host-pathogen interaction.

Mycobacterium tuberculosis is the etiological agent of human tuberculosis, a life-threatening disease which has seen a recrudescence in the last decades due to the spread of drug-resistant bacterial strains and to co-morbidities such as HIV and diabetes. To develop effective treatment and limit bacterial dissemination within and outside the host, it is pivotal to improve our understanding of the strategies used by the pathogen to colonize the host and subvert the immune defenses. The ESX-1 secretion system represents a key player in these processes. Here we show that the EspL protein, encoded by the ESX-1 gene cluster, is essential for bacterial virulence and for stabilizing the abundance of the EspE, EspF and EspH components of the ESX-1 system. Tubercle bacilli lacking EspL cannot multiply inside macrophages, do not secrete the major virulence factor EsxA and fail to trigger the ESX-1 dependent innate immune response. EspL is thus an important but so-far neglected contributor to ESX-1 function.

Structural and biophysical characterization of Rv3716c, a hypothetical protein from Mycobacterium tuberculosis

Latent tuberculosis (TB) is the main hurdle in reaching the goal of "Stop TB 2050". Tuberculin skin and Interferon-gamma release assay tests used currently for the diagnosis of TB infection cannot distinguish between active disease and latent tuberculosis infection (LTBI) and hence new and sensitive protein markers need to be identified for the diagnosis. A protein Rv3716c from Mycobacterium tuberculosis (MtbRv3716c) has been identified as a potential surrogate marker for the diagnosis of LTBI. Here, we present characterization of MtbRv3716c (∼13 kDa) using both biophysical and X-Ray crystallographic methods. EMSA study showed that MtbRv3716c binds to double stranded DNA. X-ray diffraction data collected on a crystal of MtbRv3716c at 1.9 Å resolution was used for structure determination using the molecular replacement method. Significant electron density was not observed for the N-terminal 21 and C-terminal 41 residues in the final electron density map. The C- terminal disordered region is proline rich and displays characteristics of intrinsically disordered proteins. Although the crystal asymmetric unit contained a protomer, a tight dimer could be generated by the application of the crystal two-fold symmetry parallel to the b axis. Packing of dimers in the crystal is mediated by a cadmium ion (Cd²⁺) occurring at the interface of two dimers. Molecular packing analysis reveals large cavities that are probably occupied by the disordered segments of the N- and C-termini. Structural comparison with other homologous hypothetical DNA binding proteins (PDB codes: 1PUG, 1YBX) highlights structural features that might be significant for DNA binding.

Functional assignment for essential hypothetical proteins of Staphylococcus aureus N315

Staphylococcus aureus, the causative agent of nosocomial infections worldwide, has acquired resistance to almost all antibiotics stressing the need to develop novel drugs against this pathogen. In S. aureus N315, 302 genes have been identified as essential genes, indispensable for growth and survival of the pathogen. The functions of 40 proteins encoded by S. aureus essential genes were found to be hypothetical and thus referred as essential hypothetical proteins (EHPs). The present study aims to carry out functional characterization of EHPs using bioinformatics tools/databases, whose performance was assessed by Receiver operating characteristic curve analysis. Evaluation of physicochemical parameters, homology search against known proteins, domain analysis, subcellular localization analysis and virulence prediction assisted us to characterize EHPs. Functional assignment for 35 EHPs was made with high confidence. They belong to different functional classes like enzymes, binding proteins, miscellaneous proteins, helicases, transporters and virulence factors. Around 35% of EHPs were from hydrolases family. A group of EHPs (32.5%) were predicted as virulence factors. Of 35, 19 essential pathogen-specific proteins were considered as probable drug targets. Two targets were found to be druggable and others were novel targets. Outcome of the study could aid to identify novel drugs for better treatment of S. aureus infections.

Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis

To extend our understanding of chloroplast protein import and the role played by the import machinery component Tic40, we performed a genetic screen for suppressors of chlorotic tic40 knockout mutant Arabidopsis thaliana plants. As a result, two suppressor of tic40 loci, stic1 and stic2, were identified and characterized. The stic1 locus corresponds to the gene ALBINO4 (ALB4), which encodes a paralog of the well-known thylakoid protein targeting factor ALB3. The stic2 locus identified a previously unknown stromal protein that interacts physically with both ALB4 and ALB3. Genetic studies showed that ALB4 and STIC2 act together in a common pathway that also involves cpSRP54 and cpFtsY. Thus, we conclude that ALB4 and STIC2 both participate in thylakoid protein targeting, potentially for a specific subset of thylakoidal proteins, and that this targeting pathway becomes disadvantageous to the plant in the absence of Tic40. As the stic1 and stic2 mutants both suppressed tic40 specifically (other TIC-related mutants were not suppressed), we hypothesize that Tic40 is a multifunctional protein that, in addition to its originally described role in protein import, is able to influence downstream processes leading to thylakoid biogenesis.

Modes of antibacterial action of curcumin under dark and light conditions: A toxicoproteomics approach

Curcumin is a potent natural food-grade antimicrobial compound. Exposure to light further enhances its antimicrobial capacity. Proteomic methods were used in this study for investigating the mechanistic aspects of the antibacterial curcumin effects in the dark and upon illumination. Escherichia coli cells exposed to water-dispersible curcumin-methyl-β-cyclodextrin inclusion complex under dark and light conditions were compared with the non-treated cells kept under the same illumination regimes. Curcumin treatment in the dark evoked adaptive responses aimed at mitigation of oxidative stress, DNA protection, proteostasis, modulation of redox state via changing NADH level, and gasotransmitter (H₂S and NH₃) biosynthesis. Although part of these phenomena were also present in E. coli treated under light, the light-induced curcumin toxicity was prevailed by maladaptive responses. The ROS burst induced upon curcumin treatment under light overrode the cellular adaptive mechanisms disrupting the iron metabolism, deregulating the iron-sulfur cluster biosynthesis and eventually leading to cell death. The toxicoproteomic findings were validated by transcriptomic analysis and by assessment of intracellular ROS, NADH, NADPH and iron levels.

SIGNIFICANCE

The results of this study elucidate putative mechanistic basis of antibacterial effects of curcumin, suggesting ways towards more efficient contamination control. In particular, the antimicrobial efficacy of curcumin can be potentiated by targeting bacterial systems that remediate its dark toxicity by free radical detoxification and modulation of cell redox status. To the best of the authors' knowledge, this is the first proteomic study differentiating between the dark and light-induced antimicrobial activity of curcumin.

Regulation of Gene and Protein Expression in the Lyme Disease Spirochete

The infectious cycle of Borrelia burgdorferi necessitates persistent infection of both vertebrates and ticks, and efficient means of transmission between those two very different types of hosts. The Lyme disease spirochete has evolved mechanisms to sense its location in the infectious cycle, and use that information to control production of the proteins and other factors required for each step. Numerous components of borrelial regulatory pathways have been characterized to date. Their effects are being pieced together, thereby providing glimpses into a complex web of cooperative and antagonistic interactions. In this chapter, we present a broad overview of B. burgdorferi gene and protein regulation during the natural infectious cycle, discussions of culture-based methods for elucidating regulatory mechanisms, and summaries of many of the known regulatory proteins and small molecules. We also highlight areas that are in need of substantially more research.

Escherichia coli Proteome Microarrays Identified the Substrates of ClpYQ Protease

Proteolysis is a vital mechanism to regulate the cellular proteome in all kingdoms of life, and ATP-dependent proteases play a crucial role within this process. In Escherichia coli, ClpYQ is one of the primary ATP-dependent proteases. In addition to function with removals of abnormal peptides in the cells, ClpYQ degrades regulatory proteins if necessary and thus let cells adjust to various environmental conditions. In E. coli, SulA, RcsA, RpoH and TraJ as well as RNase R, have been identified as natural protein substrates of ClpYQ. ClpYQ contains ClpY and ClpQ. The ATPase ClpY is responsible for protein recognition, unfolding, and translocation into the catalytic core of ClpQ. In this study, we use an indirect identification strategy to screen possible ClpY targets with E. coli K12 proteome chips. The chip assay results showed that YbaB strongly bound to ClpY. We used yeast two-hybrid assay to confirm the interactions between ClpY and YbaB protein and determined the K_d between ClpY and YbaB by quartz crystal microbalance. Furthermore, we validated that YbaB was successfully degraded by ClpYQ protease activity using ClpYQ in vitro and in vivo degradation assay. These findings demonstrated the YbaB is a novel substrate of ClpYQ protease. This work also successfully demonstrated that with the use of recognition element of a protease can successfully screen its substrates by indirect proteome chip screening assay.

Expression, purification and characterization of Esx-1 secretion-associated protein EspL from Mycobacterium tuberculosis

The Esx-1 cluster encodes a special secretion system that is important for granuloma formation and virulence when Mycobacterium tuberculosis infects the host. As one of the 'core' genes in the cluster, Rv3880c gene codes an Esx-1 secretion-associated protein EspL from Mycobacterium tuberculosis (MtEspL). It has been reported that EspL had a strong influence on the secretion of other two virulence factors, EsxA and EspE. However, so far little is known about the tertiary structure and specific function of MtEspL due to the difficulty in preparing the high-quality protein. In this study, we tried several fusion tags and various expression conditions to recombinantly express MtEspL. Through a four-step purification procedure, ultimately, we successfully prepared the full-length MtEspL in Escherichia coli BL21 (DE3) with a purity of 98%. The yields of the purified MtEspL protein were 14 mg/L in Luria Bertani medium and 5.6 mg/L in M9 minimal medium, respectively. Biophysical experiments showed that MtEspL existed in a dimeric form. Moreover, the (1)H-(15)N HSQC spectrum recorded on MtEspL illustrates a favorable dispersion of the resonance peaks, indicating that the symmetric dimeric MtEspL adopted a well-folded structure and might be feasible to determine its solution structure by NMR spectroscopy. Moreover, we identified a strong DNA-binding ability of MtEspL with fluorescence quenching experiments. Our work lays the basis for further structural determination and functional exploration of MtEspL.

Iron deficiency resistance mechanisms enlightened by gene expression analysis in Paenibacillus riograndensis SBR5

Despite its importance in growth and cell division, iron metabolism is still poorly understood in microorganisms, especially in Gram-positive bacteria. In this work, we used RNA sequencing technology to elucidate global mechanisms involved in iron starvation resistance in Paenibacillus riograndensis SBR5, a potential plant growth-promoting bacterium. Iron deficiency caused several changes in gene expression, and 150 differentially expressed genes were found: 71 genes were overexpressed and 79 genes were underexpressed. Eight genes for which expression was at least twice as high or twice as low in iron-limited condition compared with iron-sufficient condition were chosen for RT-qPCR analysis to validate the RNA seq data. In general, most genes exhibited the same pattern of expression after 24 h of P. riograndensis growth under iron-limiting condition. Our results suggest that, during iron deficiency, bacteria express several genes related to nutrient uptake when they start to grow to obtain all of the molecules necessary for maintaining major cellular processes. However, once iron becomes highly limiting and is no longer able to sustain exponential growth, bacteria begin to express genes related to several processes, like sporulation and DNA protection, as a way of resisting this stress.

Expanded microbial genome coverage and improved protein family annotation in the COG database

Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the COGs is expected to become an important tool for microbial genomics.

Crystal structure of Pyrococcus furiosus PF2050, a member of the DUF2666 protein family

Pyrococcus furiosus PF2050 is an uncharacterized putative protein that contains two DUF2666 domains. Functional and structural studies of PF2050 have not previously been performed. In this study, we determined the crystal structure of PF2050. The structure of PF2050 showed that the two DUF2666 domains interact tightly, forming a globular structure. Each DUF2666 domain comprises an antiparallel β-sheet and an α-helical bundle. One side of the PF2050 structure has a positively charged basic cleft, which may have a DNA-binding function. Furthermore, we confirmed that PF2050 interacts with circular and linear dsDNA.

EbfC (YbaB) is a new type of bacterial nucleoid-associated protein and a global regulator of gene expression in the Lyme disease spirochete

Nearly every known species of Eubacteria encodes a homolog of the Borrelia burgdorferi EbfC DNA-binding protein. We now demonstrate that fluorescently tagged EbfC associates with B. burgdorferi nucleoids in vivo and that chromatin immunoprecipitation (ChIP) of wild-type EbfC showed it to bind in vivo to sites throughout the genome, two hallmarks of nucleoid-associated proteins. Comparative RNA sequencing (RNA-Seq) of a mutant B. burgdorferi strain that overexpresses EbfC indicated that approximately 4.5% of borrelial genes are significantly impacted by EbfC. The ebfC gene was highly expressed in rapidly growing bacteria, but ebfC mRNA was undetectable in stationary phase. Combined with previous data showing that EbfC induces bends in DNA, these results demonstrate that EbfC is a nucleoid-associated protein and lead to the hypothesis that B. burgdorferi utilizes cellular fluctuations in EbfC levels to globally control transcription of numerous genes. The ubiquity of EbfC proteins in Eubacteria suggests that these results apply to a wide range of pathogens and other bacteria.

Genetic and biochemical characteristics of the histone-like protein DR0199 in Deinococcus radiodurans

Bacterial histone-like proteins are important for nucleoid structure, cell growth, DNA replication, recombination and gene regulation. In this study, we focused on the role of DR0199 (the EbfC orthologue), a newly identified member of the nucleoid-associated protein family in Deinococcus radiodurans. The survival fraction of DR0199-null mutant decreased by tenfold after treatment with 50 mM H(2)O(2), nearly sixfold at a 10 kGy dose of gamma ray and nearly eightfold at a UV exposure of 1000 J m(-2) compared with wild-type cells. The results of fluorescence labelling assays indicated that DR0199 protein localized in the nucleoid area of cells. Electrophoretic mobility shift assays demonstrated that D. radiodurans DR0199 is a DNA-binding protein. Furthermore, DNA protection assays suggested that DR0199 shields DNA from hydroxyl radical- and DNase I-mediated cleavage. The supercoiling of relaxed plasmid DNA in the presence of topoisomerase I revealed that DR0199 constrains DNA supercoils in vitro. Collectively, these findings suggest that DR0199 is a protein with DNA-protective properties and histone-like features that are involved in protecting D. radiodurans DNA from damage.

BpaB and EbfC DNA-binding proteins regulate production of the Lyme disease spirochete's infection-associated Erp surface proteins

Vector-borne pathogens regulate their protein expression profiles, producing factors during host infection that differ from those produced during vector colonization. The Lyme disease agent, Borrelia burgdorferi, produces Erp surface proteins throughout mammalian infection and represses their synthesis during colonization of vector ticks. Known functions of Erp proteins include binding of host laminin, plasmin(ogen), and regulators of complement activation. A DNA region immediately 5' of erp operons, the erp operator, is required for transcriptional regulation. The B. burgdorferi BpaB and EbfC proteins exhibit high in vitro affinities for erp operator DNA. In the present studies, chromatin immunoprecipitation (ChIP) demonstrated that both proteins bind erp operator DNA in vivo. Additionally, a combination of in vivo and in vitro methods demonstrated that BpaB functions as a repressor of erp transcription, while EbfC functions as an antirepressor.

Biofilms can be dispersed by focusing the immune system on a common family of bacterial nucleoid-associated proteins

Bacteria that cause chronic and/or recurrent diseases often rely on a biofilm lifestyle. The foundation of the biofilm structure is the extracellular polymeric substance (EPS) that acts as a barrier to both effectors of the immune system and antimicrobial agents. Recent work has highlighted extracellular DNA (eDNA) as a key component common to many pathogenic biofilms. Here, we show that the DNABII family of proteins, well known for their strong structural influences on intracellular DNA, was also critical for the integrity of the EPS matrix of biofilms that contain eDNA. In fact, antisera derived against a purified Escherichia coli DNABII family member rapidly disrupts the biofilm EPS formed by multiple human pathogens in vitro. In addition, when a member of this family of proteins was used as an immunogen in an animal model in which the bacteria had already formed a robust biofilm at the site of infection, the resultant targeted immune response strongly ameliorated this biofilm disease in vivo. Finally, this methodology to debulk the biofilm of EPS was shown to work synergistically with otherwise ineffective traditional anti-microbial approaches in vitro. We discuss the prospects for targeting DNABII family members as a potential universal strategy for treating biofilm diseases.

Simple genetic selection protocol for isolation of overexpressed genes that enhance accumulation of membrane-integrated human G protein-coupled receptors in Escherichia coli

The efficient production of membrane proteins in bacteria remains a major challenge. In this work, we sought to identify overexpressed genes that enhance the yields of recombinant membrane proteins in Escherichia coli. We developed a genetic selection system for bacterial membrane protein production, consisting of membrane protein fusions with the enzyme beta-lactamase and facile selection of high-production strains on ampicillin-containing media. This system was used to screen the ASKA library, an ordered library of plasmids encoding all the known E. coli open reading frames (ORFs), and several clones with the ability to accumulate enhanced amounts of recombinant membrane proteins were selected. Notably, coexpression of ybaB, a gene encoding a putative DNA-binding protein of unknown function, was found to enhance the accumulation of a variety of membrane-integrated human G protein-coupled receptors and other integral membrane proteins in E. coli by up to 10-fold. The results of this study highlight the power of genetic approaches for identifying factors that impact membrane protein biogenesis and for generating engineered microbial hosts for membrane protein production.