TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes

Generation and validation of a versatile inducible multiplex CRISPRi system to examine bacterial regulation in the Euprymna-Vibrio fischeri symbiosis

The Vibrio fischeri-Euprymna scolopes symbiosis has become a powerful animal-microbe model system to examine the genetic underpinnings of symbiont development and regulation. Although there has been a number of elegant bacterial genetic technologies developed to examine this symbiosis, there is still a need to develop more sophisticated methodologies to better understand complex regulatory pathways that lie within the association. Therefore, we have developed a suite of CRISPR interference (CRISPRi) vectors for inducible repression of specific V. fischeri genes associated with symbiotic competence. The suite utilizes both Tn7-integrating and shuttle vector plasmids that allow for inducible expression of CRISPRi dCas9 protein along with single-guide RNAs (sgRNA) modules. We validated this CRISPRi tool suite by targeting both exogenous (an introduced mRFP reporter) and endogenous genes (luxC in the bioluminescence producing lux operon, and flrA, the major regulatory gene controlling flagella production). The suite includes shuttle vectors expressing both single and multiple sgRNAs complementary to the non-template strand of multiple targeted genetic loci, which were effective in inducible gene repression, with significant reductions in targeted gene expression levels. V. fischeri cells harboring a version of this system targeting the luxC gene and suppressing the production of luminescence were used to experimentally validate the hypothesis that continuous luminescence must be produced by the symbiont in order to maintain the symbiosis at time points longer than the known 24-h limit. This robust new CRISPRi genetic toolset has broad utility and will enhance the study of V. fischeri genes, bypassing the need for gene disruptions by standard techniques of allelic knockout-complementation-exchange and the ability to visualize symbiotic regulation in vivo.

Development of a multi-epitope vaccine from outer membrane proteins and identification of novel drug targets against Francisella tularensis: an In Silico approach

Background

Francisella tularensis is a category A potential thread agent, making the development of vaccines and countermeasures a high priority. Therefore, identifying new vaccine candidates and novel drug targets is essential for addressing this significant public health concern.

Methods

This study presents an in silico analysis of two strategies against F. tularensis infection: the development of a multi-epitope vaccine (MEV) and the identification of novel drug targets. Outer membrane proteins (OMPs) were predicted using subcellular localization tools and immunogenicity was evaluated using a reverse vaccinology pipeline. Epitopes from these OMPs were combined to create candidate MEV for prophylactic protection. Concurrently, cytoplasmic proteins were subjected to rigorous analysis to identify potential novel drug targets.

Results

Of 1,921 proteins, we identified 12 promising protein vaccine candidates from F. tularensis OMPs and proposed a multi-epitope vaccine (MEV) designed using seven immunodominant epitopes derived from four of these OMPs, including two hypothetical proteins (WP_003026145.1 and WP_003029346.1), an OmpA family protein (WP_003020808.1), and PD40 (WP_003021546.1). In addition, we proposed 10 novel drug targets for F. tularensis: Asp-tRNA (Asn)/Glu-tRNA (Gln) amidotransferase subunit GatC (WP_003017413.1), NAD(P)-binding protein (WP_042522581.1), 30S ribosomal protein S16 (WP_003023081.1), Class I SAM-dependent methyltransferase (WP_003022345.1), haloacid dehalogenase (WP_003014157.1), uroporphyrinogen-III synthase (WP_003022220.1), and four hypothetical proteins (WP_003017784.1, WP_003020080.1, WP_003020066.1, and WP_003022350.1).

Conclusion

This study designed an MEV and proposed novel drug targets to address tularemia, offering broad protection against various F. tularensis strains. MEV, with favorable physicochemical properties, showed strong potential through molecular docking and dynamic simulations. Immune simulations suggest that it may elicit robust responses against pathogens. The identification of novel drug targets can lead to the discovery of new antimicrobial agents. However, further in vitro and in vivo studies are required to validate their efficacy and capability.

AcrAB Efflux Pump Plays a Crucial Role in Bile Salts Resistance and Pathogenesis of Klebsiella pneumoniae

Bile salts possess innate antibacterial properties and can cause significant damage to bacteria. To survive in the mammalian gut, Klebsiella pneumoniae has developed mechanisms to tolerate bile salts; however, the specific mechanisms remain unclear. Transposon library screening revealed that the efflux pump AcrAB is involved in bile salt resistance. acrA and acrB mutants exhibited high sensitivity not only to bile salts but also to SDS and various antibiotics, with a switch-loop, comprising residues G615, F616, A617, and G618, proving to be crucial in this process. A colonization defect of acrA and acrB mutants was demonstrated to be located in the mouse small intestine, where the bile salt concentration is higher compared to the large intestine. Additionally, both acrA and acrB mutants displayed reduced virulence in the Galleria mellonella model. In conclusion, our results suggest that the Resistance-Nodulation-Cell Division efflux pump serves as a critical determinant in the pathogenesis of K. pneumoniae through various aspects.

Essential Genes Discovery in Microorganisms by Transposon-Directed Sequencing (Tn-Seq): Experimental Approaches, Major Goals, and Future Perspectives

Essential genes are crucial for microbial viability, playing key roles in both the primary and secondary metabolism. Since mutations in these genes can threaten organism viability, identifying them is challenging. Conditionally essential genes are required only under specific conditions and are important for functions such as virulence, immunity, stress survival, and antibiotic resistance. Transposon-directed sequencing (Tn-Seq) has emerged as a powerful method for identifying both essential and conditionally essential genes. In this review, we explored Tn-Seq workflows, focusing on eubacterial species and some yeast species. A comparison of 14 eubacteria species revealed 133 conserved essential genes, including those involved in cell division (e.g., ftsA, ftsZ), DNA replication (e.g., dnaA, dnaE), ribosomal function, cell wall synthesis (e.g., murB, murC), and amino acid synthesis (e.g., alaS, argS). Many other essential genes lack clear orthologues across different microorganisms, making them specific to each organism studied. Conditionally essential genes were identified in 18 bacterial species grown under various conditions, but their conservation was low, reflecting dependence on specific environments and microorganisms. Advances in Tn-Seq are expected to reveal more essential genes in the near future, deepening our understanding of microbial biology and enhancing our ability to manipulate microbial growth, as well as both the primary and secondary metabolism.

New drug target identification in Vibrio vulnificus by subtractive genome analysis and their inhibitors through molecular docking and molecular dynamics simulations

Vibrio vulnificus is a rod shape, Gram-negative bacterium that causes sepsis (with a greater than 50% mortality rate), necrotizing fasciitis, gastroenteritis, skin, and soft tissue infection, wound infection, peritonitis, meningitis, pneumonia, keratitis, and arthritis. Based on pathogenicity V. vulnificus is categorized into three biotypes. Type 1 and type 3 cause diseases in humans while biotype 2 causes diseases in eel and fish. Due to indiscriminate use of antibiotics V. vulnificus has developed resistance to many antibiotics so curing is dramatically a challenge. V. vulnificus is resistant to cefazolin, streptomycin, tetracycline, aztreonam, tobramycin, cefepime, and gentamycin. Subtractive genome analysis is the most effective method for drug target identification. The method is based on the subtraction of homologous proteins from both pathogen and host. By this process set of proteins present only in the pathogen and perform essential functions in the pathogen can be identified. The entire proteome of Vibrio vulnificus strain ATCC 27562 was reduced step by step to a single protein predicted as the drug target. AlphaFold2 is one of the applications of deep learning algorithms in biomedicine and is correctly considered the game changer in the field of structural biology. Accuracy and speed are the major strength of AlphaFold2. In the PDB database, the crystal structure of the predicted drug target was not present, therefore the Colab notebook was used to predict the 3D structure by the AlphaFold2, and subsequently, the predicted model was validated. Potent inhibitors against the new target were predicted by virtual screening and molecular docking study. The most stable compound ZINC01318774 tightly attaches to the binding pocket of bisphosphoglycerate-independent phosphoglycerate mutase. The time-dependent molecular dynamics simulation revealed compound ZINC01318774 was superior as compared to the standard drug tetracycline in terms of stability. The availability of V. vulnificus strain ATCC 27562 has allowed in silico identification of drug target which will provide a base for the discovery of specific therapeutic targets against Vibrio vulnificus.

Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

Legionella pneumophila is the causative agent of a severe type of pneumonia (lung infection) called Legionnaires' disease. It is emerging as an antibiotic-resistant strain day by day. Hence, identifying novel drug targets and vaccine candidates is essential to fight against this pathogen. Here, attempts were taken through a subtractive genomics approach on the complete proteome of L. pneumophila to address the challenges of multidrug resistance. A total of 2,930 proteins from L. pneumophila proteome were investigated through diverse subtractive proteomics approaches, e.g., identification of human nonhomologous and pathogen-specific essential proteins, druggability and "anti-target" analysis, subcellular localization prediction, human microbiome nonhomology screening, and protein-protein interaction studies to find out effective drug and vaccine targets. Only three fulfilled these criteria and were proposed as novel drug targets against L. pneumophila. Furthermore, outer membrane protein TolB was identified as a potential vaccine target with a better antigenicity score. Antigenicity and transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis, and a molecular docking approach were adopted to generate the most potent epitopes. The final vaccine was constructed by the combination of highly immunogenic epitopes, along with suitable adjuvant and linkers. The designed vaccine construct showed higher binding interaction with different major histocompatibility complex (MHC) molecules and human immune TLR-2 receptors with minimum deformability at the molecular level. The present study aids the development of novel therapeutics and vaccine candidates for efficient treatment and prevention of L. pneumophila infections. However, further wet-lab-based phenotypic and genomic investigations and in vivo trials are highly recommended to validate our prediction experimentally. IMPORTANCE Legionella pneumophila is a human pathogen distributed worldwide, causing Legionnaires' disease (LD), a severe form of pneumonia and respiratory tract infection. L. pneumophila is emerging as an antibiotic-resistant strain, and controlling LD is now difficult. Hence, developing novel drugs and vaccines against L. pneumophila is a major research priority. Here, the complete proteome of L. pneumophila was considered for subtractive genomics approaches to address the challenge of antimicrobial resistance. Our subtractive proteomics approach identified three potential drug targets that are promising for future application. Furthermore, a possible vaccine candidate, "outer membrane protein TolB," was proposed using reverse vaccinology analysis. The constructed vaccine candidate showed higher binding interaction with MHC molecules and human immune TLR-2 receptors at the molecular level. Overall, the present study aids in developing novel therapeutics and vaccine candidates for efficient treatment of the infections caused by L. pneumophila.

Gradients in gene essentiality reshape antibacterial research

Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.

Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales

Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.

Essential Protein Recognition via Community Significance

Essential protein plays a vital role in understanding the cellular life. With the advance in high-throughput technologies, a number of protein-protein interaction (PPI) networks have been constructed such that essential proteins can be identified from a system biology perspective. Although a series of network-based essential protein discovery methods have been proposed, these existing methods still have some drawbacks. Recently, it has been shown that the significance-based method SigEP is promising on overcoming the defects that are inherent in currently available essential protein identification methods. However, the SigEP method is developed under the unrealistic Erdös-Rényi (E-R) model and its time complexity is very high. Hence, we propose a new significance-based essential protein recognition method named EPCS in which the essential protein discovery problem is formulated as a community significance testing problem. Experimental results on four PPI networks show that EPCS performs better than nine state-of-the-art essential protein identification methods and the only significance-based essential protein identification method SigEP.

Bacteriophage SRD2021 Recognizing Capsular Polysaccharide Shows Therapeutic Potential in Serotype K47 Klebsiella pneumoniae Infections

Klebsiella pneumoniae is an opportunistic pathogen posing an urgent threat to global public health, and the capsule is necessary for K. pneumoniae infection and virulence. Phage-derived capsule depolymerases have shown great potential as antivirulence agents in treating carbapenem-resistant K. pneumoniae (CRKP) infections. However, the therapeutic potential of phages encoding depolymerases against CRKP remains poorly understood. In this study, we identified a long-tailed phage SRD2021 specific for mucoid CRKP with capsular K47 serotype, which is the predominant infectious K-type in Asia. Genome sequencing revealed that ΦSRD2021 belonged to the Drulisvirus genus and exhibited a capsular depolymerase domain in its tail fiber protein. A transposon-insertion library of host bacteria was constructed to identify the receptor for ΦSRD2021. We found that most phage-resistant mutants converted to a nonmucoid phenotype, including the mutant in wza gene essential for capsular polysaccharides export. Further knockout and complementation experiments confirmed that the Δwza mutant avoided adsorption by ΦSRD2021, indicating that the K47 capsular polysaccharide is the necessary receptor for phage infection. ΦSRD2021 lysed the bacteria mature biofilms and showed a therapeutic effect on the prevention and treatment of CRKP infection in the Galleria mellonella model. Furthermore, ΦSRD2021 also reduced the colonized CRKP in mouse intestines significantly. By recognizing the host capsule as a receptor, our results showed that ΦSRD2021 may be used as a potential antibacterial agent for K47 serotype K. pneumoniae infections.

O-antigen serves as a two-faced host factor for bacteriophage NJS1 infecting nonmucoid Klebsiella pneumoniae

Klebsiella pneumoniae is an opportunistic pathogen commonly associated with nosocomial infections. In our previous study, we have demonstrated that colistin-resistant K. pneumoniae is more susceptible to killing by lytic tailed phages than the colistin-sensitive parent strain, including T1-like ФNJS1. This fitness cost associated with colistin resistance is due to the alteration of the surface charge that promotes phage adherence and infection. However, the receptor for phage adsorption has not been identified. In this study, we found that ФNJS1 specifically infected nonmucoid K. pneumoniae isolates, and the accelerated phage adsorption to colistin-resistant nonmucoid K. pneumoniae cells is reversible. Further research suggested that bacteria lipopolysaccharide may be involved in phage reversible adsorption, while capsule polysaccharide may block the receptors on cell surface from phage attachment. Transposon mutagenesis of colistin-resistant K. pneumoniae revealed that mutation in wecA and wecG, two genes involved in lipopolysaccharide O-antigen biosynthesis, significantly deceased phage adsorption capacity and infection efficiency. Inactivation of wzyE, which leaded to the shorten of O-antigen chain length, enhanced phage infectivity. Moreover, mutation of the outer membrane protein FepA slowed the phage lysis rate, suggesting that FepA may be an irreversible receptor for ФNJS1. In summary, our results show a delicate balance between ФNJS1 and its hosts, where the lipopolysaccharide O-antigen may serve as an essential reversible receptor for phage NJS1, while the long O-antigen chain hinders the bacteriophage infection.

The Type II Secretory System Mediates Phage Infection in Vibrio cholerae

Attachment and specific binding to the receptor on the host cell surface is the first step in the process of bacteriophage infection. The lytic phage VP2 is used in phage subtyping of the Vibrio cholerae biotype El Tor of the O1 serogroup; however, its infection mechanism is poorly understood. In this study, we aimed to identify its receptor on V. cholerae. The outer membrane protein EpsD in the type II secretory system (T2SS) was found to be related to VP2-specific adsorption to V. cholerae, and the T2SS inner membrane protein EpsM had a role in successful VP2 infection, although it was not related to adsorption of VP2. The tail fiber protein gp20 of VP2 directly interacts with EpsD. Therefore, we found that in V. cholerae, in addition to the roles of the T2SS as the transport apparatus of cholera toxin secretion and filamentous phage release, the T2SS is also used as the receptor for phage infection and probably as the channel for phage DNA injection. Our study expands the understanding of the roles of the T2SS in bacteria.

Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome

When the JCVI-syn3.0 genome was designed and implemented in 2016 as the minimal genome of a free-living organism, approximately one-third of the 438 protein-coding genes had no known function. Subsequent refinement into JCVI-syn3A led to inclusion of 16 additional protein-coding genes, including several unknown functions, resulting in an improved growth phenotype. Here, we seek to unveil the biological roles and protein-protein interaction (PPI) networks for these poorly characterized proteins using state-of-the-art deep learning contact-assisted structure prediction, followed by structure-based annotation of functions and PPI predictions. Our pipeline is able to confidently assign functions for many previously unannotated proteins such as putative vitamin transporters, which suggest the importance of nutrient uptake even in a minimized genome. Remarkably, despite the artificial selection of genes in the minimal syn3 genome, our reconstructed PPI network still shows a power law distribution of node degrees typical of naturally evolved bacterial PPI networks. Making use of our framework for combined structure/function/interaction modeling, we are able to identify both fundamental aspects of network biology that are retained in a minimal proteome and additional essential functions not yet recognized among the poorly annotated components of the syn3.0 and syn3A proteomes.

Suppressor Mutations in Type II Secretion Mutants of Vibrio cholerae: Inactivation of the VesC Protease

Genome-wide transposon mutagenesis has identified the genes encoding the T2SS in Vibrio cholerae as essential for viability, but the reason for this is unclear. Mutants with deletions or insertions in these genes can be isolated, suggesting that they have acquired secondary mutations that suppress their growth defect.

The type II secretion system (T2SS) is a conserved transport pathway responsible for the secretion of a range of virulence factors by many pathogens, including Vibrio cholerae. Disruption of the T2SS genes in V. cholerae results in loss of secretion, changes in cell envelope function, and growth defects. While T2SS mutants are viable, high-throughput genomic analyses have listed these genes among essential genes. To investigate whether secondary mutations arise as a consequence of T2SS inactivation, we sequenced the genomes of six V. cholerae T2SS mutants with deletions or insertions in either the epsG, epsL, or epsM genes and identified secondary mutations in all mutants. Two of the six T2SS mutants contain distinct mutations in the gene encoding the T2SS-secreted protease VesC. Other mutations were found in genes coding for V. cholerae cell envelope proteins. Subsequent sequence analysis of the vesC gene in 92 additional T2SS mutant isolates identified another 19 unique mutations including insertions or deletions, sequence duplications, and single-nucleotide changes resulting in amino acid substitutions in the VesC protein. Analysis of VesC variants and the X-ray crystallographic structure of wild-type VesC suggested that all mutations lead to loss of VesC production and/or function. One possible mechanism by which V. cholerae T2SS mutagenesis can be tolerated is through selection of vesC-inactivating mutations, which may, in part, suppress cell envelope damage, establishing permissive conditions for the disruption of the T2SS. Other mutations may have been acquired in genes encoding essential cell envelope proteins to prevent proteolysis by VesC.

IMPORTANCE Genome-wide transposon mutagenesis has identified the genes encoding the T2SS in Vibrio cholerae as essential for viability, but the reason for this is unclear. Mutants with deletions or insertions in these genes can be isolated, suggesting that they have acquired secondary mutations that suppress their growth defect. Through whole-genome sequencing and phenotypic analysis of T2SS mutants, we show that one means by which the growth defect can be suppressed is through mutations in the gene encoding the T2SS substrate VesC. VesC homologues are present in other Vibrio species and close relatives, and this may be why inactivation of the T2SS in species such as Vibrio vulnificus, Vibrio sp. strain 60, and Aeromonas hydrophila also results in a pleiotropic effect on their outer membrane assembly and integrity.

A modular chromosomally integrated toolkit for ectopic gene expression in Vibrio cholerae

The ability to express genes ectopically in bacteria is essential for diverse academic and industrial applications. Two major considerations when utilizing regulated promoter systems for ectopic gene expression are (1) the ability to titrate gene expression by addition of an exogenous inducer and (2) the leakiness of the promoter element in the absence of the inducer. Here, we describe a modular chromosomally integrated platform for ectopic gene expression in Vibrio cholerae. We compare the broadly used promoter elements P_tac and P_BAD to versions that have an additional theophylline-responsive riboswitch (P_tac-riboswitch and P_BAD-riboswitch). These constructs all exhibited unimodal titratable induction of gene expression, however, max induction varied with P_tac > P_BAD > P_BAD-riboswitch > P_tac-riboswitch. We also developed a sensitive reporter system to quantify promoter leakiness and show that leakiness for P_tac > P_tac-riboswitch > P_BAD; while the newly developed P_BAD-riboswitch exhibited no detectable leakiness. We demonstrate the utility of the tightly inducible P_BAD-riboswitch construct using the dynamic activity of type IV competence pili in V. cholerae as a model system. The modular chromosomally integrated toolkit for ectopic gene expression described here should be valuable for the genetic study of V. cholerae and could be adapted for use in other species.

A decade of advances in transposon-insertion sequencing

It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications.

In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.

Vibrio cholerae Virulence Activator ToxR Regulates Manganese Transport and Resistance to Reactive Oxygen Species

Like many other pathogens, Vibrio cholerae, the causative agent of cholera, can modulate its gene expression to combat stresses encountered in both aquatic and host environments, including stress posed by reactive oxygen species (ROS). We previously reported that the virulence activator AphB in V. cholerae is involved in ROS resistance. In this study, we found that another key virulence regulator, ToxR, was important for V. cholerae resistance to hydrogen peroxide. Through a genome-wide transposon screen, we discovered that a deletion in mneA, which encodes a manganese exporter, restored ROS resistance of the toxR mutant. We then showed that ToxR did not affect mneA transcription but that the ToxR-regulated major porin OmpU was critical for ROS resistance. The addition of manganese in culture medium restored ROS resistance in both the toxR and ompU mutants. Furthermore, elemental analysis indicated that the intracellular concentration of manganese in both the toxR and ompU mutants was reduced. This may result in intracellular ROS accumulation in these mutants. Our data suggest that ToxR plays an important role in the resistance to reactive oxygen species through the regulation of manganese transport.

Construction and Use of Transposon MycoTetOP 2 for Isolation of Conditional Mycobacteria Mutants

Mycobacteria are unique in many aspects of their biology. The development of genetic tools to identify genes critical for their growth by forward genetic analysis holds great promises to advance our understanding of their cellular, physiological and biochemical processes. Here we report the development of a novel transposon, MycoTetOP 2, to aid the identification of such genes by direct transposon mutagenesis. This mariner-based transposon contains nested anhydrotetracycline (ATc)-inducible promoters to drive transcription outward from both of its ends. In addition, it includes the Escherichia coli R6Kγ origin to facilitate the identification of insertion sites. MycoTetOP 2 was placed in a shuttle plasmid with a temperature-sensitive DNA replication origin in mycobacteria. This allows propagation of mycobacteria harboring the plasmid at a permissive temperature. The resulting population of cells can then be subjected to a temperature shift to select for transposon mutants. This transposon and its delivery system, once constructed, were tested in the fast-growing model Mycobacterium smegmatis and 13 mutants with ATc-dependent growth were isolated. The identification of the insertion sites in these mutants led to nine unique genetic loci with genes critical for essential processes in both M. smegmatis and Mycobacterium tuberculosis. These results demonstrate that MycoTetOP 2 and its delivery vector provide valuable tools for the studies of mycobacteria by forward genetics.

A Broad-Host-Range CRISPRi Toolkit for Silencing Gene Expression in Burkholderia

Genetic tools are critical to dissecting the mechanisms governing cellular processes, from fundamental physiology to pathogenesis. Members of the genus Burkholderia have potential for biotechnological applications but can also cause disease in humans with a debilitated immune system. The lack of suitable genetic tools to edit Burkholderia GC-rich genomes has hampered the exploration of useful capacities and the understanding of pathogenic features. To address this, we have developed CRISPR interference (CRISPRi) technology for gene silencing in Burkholderia, testing it in B. cenocepacia, B. multivorans, and B. thailandensis. Tunable expression was provided by placing a codon-optimized dcas9 from Streptococcus pyogenes under control of a rhamnose-inducible promoter. As a proof of concept, the paaABCDE operon controlling genes necessary for phenylacetic acid degradation was targeted by plasmid-borne gRNAs, resulting in near complete inhibition of growth on phenylacetic acid as the sole carbon source. This was supported by reductions in paaA mRNA expression. The utility of CRISPRi to probe other functions at the single cell level was demonstrated by knocking down phbC and fliF, which dramatically reduces polyhydroxybutyrate granule accumulation and motility, respectively. As a hallmark of the mini-CTX system is the broad host-range of integration, we putatively identified 67 genera of Proteobacteria that might be amenable to modification with our CRISPRi toolkit. Our CRISPRi toolkit provides a simple and rapid way to silence gene expression to produce an observable phenotype. Linking genes to functions with CRISPRi will facilitate genome editing with the goal of enhancing biotechnological capabilities while reducing Burkholderia's pathogenic arsenal.

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

A major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.

Gain of function methods based on gene overexpression are not easily applied to high-throughput screening across different experimental conditions. Here, the authors present Dub-seq, which separates overexpression library characterization from functional screening and uses random DNA barcodes to increase the experimental throughput.

The outer-membrane protein TolC of Vibrio cholerae serves as a second cell-surface receptor for the VP3 phage

Receptor recognition is a key step in the initiation of phage infection. Previously, we found that VP3, the T7 family phage of the Vibrio cholerae serogroup O1 biotype El Tor, can adsorb the core oligosaccharide (OS) of lipopolysaccharides of V. cholerae However, some wildtype strains of V. cholerae possessing the intact OS gene cluster still have VP3 binding but are resistant to VP3 infection. Moreover, an OS gene-deletion mutant still exhibits weak VP3 binding, suggesting multiple factors are possibly involved in VP3 binding to V. cholerae Here, we report that the outer-membrane protein TolC of V. cholerae is involved in the host adsorption of VP3. We observed that TolC directly interacts with the VP3 tail fiber protein gp44 and its C-terminal domains, and we also found that three amino acid residues in the outside loops of TolC, at positions 78, 290, and 291, are critical for binding to gp44. Among the VP3-resistant wildtype V. cholerae strains, frequent amino acid residue mutations were observed in the loops around the sites 78, 290, and 291, which were predicted to be exposed to the cell surface. These findings reveal a co-receptor-binding mechanism for VP3 infection of V. cholerae and that both outer-membrane TolC and OS are necessary for successful VP3 infection of V. cholerae We conclude that mutations on the outside loops of the receptor may confer V. cholerae strains with VP3 phage resistance, enabling these strains to survive in environments containing VP3 or related phages.

Prediction of essential proteins based on subcellular localization and gene expression correlation

Background

Essential proteins are indispensable to the survival and development process of living organisms. To understand the functional mechanisms of essential proteins, which can be applied to the analysis of disease and design of drugs, it is important to identify essential proteins from a set of proteins first. As traditional experimental methods designed to test out essential proteins are usually expensive and laborious, computational methods, which utilize biological and topological features of proteins, have attracted more attention in recent years. Protein-protein interaction networks, together with other biological data, have been explored to improve the performance of essential protein prediction.

Results

The proposed method SCP is evaluated on Saccharomyces cerevisiae datasets and compared with five other methods. The results show that our method SCP outperforms the other five methods in terms of accuracy of essential protein prediction.

Conclusions

In this paper, we propose a novel algorithm named SCP, which combines the ranking by a modified PageRank algorithm based on subcellular compartments information, with the ranking by Pearson correlation coefficient (PCC) calculated from gene expression data. Experiments show that subcellular localization information is promising in boosting essential protein prediction.

The Ribosomal Protein RplY Is Required for Pectobacterium carotovorum Virulence and Is Induced by Zantedeschia elliotiana Extract

Pectobacterium carotovorum subsp. carotovorum strain PccS1, a bacterial pathogen causing soft rot disease of Zantedeschia elliotiana (colored calla), was investigated for virulence genes induced by the host plant. Using a promoter-trap transposon (mariner), we obtained 500 transposon mutants showing kanamycin resistance dependent on extract of Z. elliotiana. One of these mutants, PM86, exhibited attenuated virulence on both Z. elliotiana and Brassica rapa subsp. pekinensis. The growth of PM86 was also reduced in minimal medium (MM), and the reduction was restored by adding plant extract to the MM. The gene containing the insertion site was identified as rplY. The deletion mutant ΔrplY, exhibited reduced virulence, motility and plant cell wall-degrading enzyme production but not biofilm formation. Analysis of gene expression and reporter fusions revealed that the rplY gene in PccS1 is up-regulated at both the transcriptional and the translational levels in the presence of plant extract. Our results suggest that rplY is induced by Z. elliotiana extract and is crucial for virulence in P. carotovorum subsp. carotovorum.

Ubiquitination and degradation of GBPs by a Shigella effector to suppress host defence

Interferon-inducible guanylate-binding proteins (GBPs) mediate cell-autonomous antimicrobial defences. Shigella flexneri, a Gram-negative cytoplasmic free-living bacterium that causes bacillary dysentery, encodes a repertoire of highly similar type III secretion system effectors called invasion plasmid antigen Hs (IpaHs). IpaHs represent a large family of bacterial ubiquitin-ligases, but their function is poorly understood. Here we show that S. flexneri infection induces rapid proteasomal degradation of human guanylate binding protein-1 (hGBP1). We performed a transposon screen to identify a mutation in the S. flexneri gene ipaH9.8 that prevented hGBP1 degradation. IpaH9.8 targets hGBP1 for degradation via Lys48-linked ubiquitination. IpaH9.8 targets multiple GBPs in the cytoplasm independently of their nucleotide-bound states and their differential function in antibacterial defence, promoting S. flexneri replication and resulting in the death of infected mice. In the absence of IpaH9.8, or when binding of GBPs to IpaH9.8 was disrupted, GBPs such as hGBP1 and mouse GBP2 (mGBP2) translocated to intracellular S. flexneri and inhibited bacterial replication. Like wild-type mice, mutant mice deficient in GBP1-3, 5 and 7 succumbed to S. flexneri infection, but unlike wild-type mice, mice deficient in these GBPs were also susceptible to S. flexneri lacking ipaH9.8. The mode of IpaH9.8 action highlights the functional importance of GBPs in antibacterial defences. IpaH9.8 and S. flexneri provide a unique system for dissecting GBP-mediated immunity.

The Vibrio cholerae VexGH RND Efflux System Maintains Cellular Homeostasis by Effluxing Vibriobactin

Resistance-nodulation-division (RND) superfamily efflux systems have been widely studied for their role in antibiotic resistance, but their native biological functions remain poorly understood. We previously showed that loss of RND-mediated efflux in Vibrio cholerae resulted in activation of the Cpx two-component regulatory system, which mediates adaptation to stress resulting from misfolded membrane proteins. Here, we investigated the mechanism linking RND-mediated efflux to the Cpx response. We performed transposon mutagenesis screening of RND-deficient V. cholerae to identify Cpx suppressors. Suppressor mutations mapped to genes involved in the biosynthesis of the catechol siderophore vibriobactin. We subsequently demonstrated that vibriobactin secretion is impaired in mutants lacking the VexGH RND efflux system and that impaired vibriobactin secretion is responsible for Cpx system activation, suggesting that VexGH secretes vibriobactin. This conclusion was bolstered by results showing that vexGH expression is induced by iron limitation and that vexH-deficient cells exhibit reduced fitness during growth under iron-limiting conditions. Our results support a model where VexGH contributes to cellular homeostasis by effluxing vibriobactin. In the absence of vexGH, retained vibriobactin appears to chelate iron from iron-rich components of the respiratory chain, with the deferrated proteins functioning to activate the Cpx response. Our collective results demonstrate that a native function of the V. cholerae VexGH RND efflux system is in vibriobactin secretion and that vibriobactin efflux is critical for maintenance of cellular homeostasis.IMPORTANCE RND efflux systems are ubiquitous Gram-negative transporters that play critical roles in antimicrobial resistance. In addition to antimicrobial resistance, RND transporters also affect the expression of diverse phenotypes, including virulence, cell metabolism, and stress responses. The latter observations suggest that RND transporters fulfill unknown physiological functions in the cell independently of their role in antimicrobial resistance. Vibrio cholerae is representative of many Gram-negative bacteria in encoding multiple RND transporters that are redundant in antimicrobial resistance and affect multiple phenotypes. Here we describe a novel function of the V. cholerae VexGH RND transporter in vibriobactin secretion. We show that vibriobactin production in VexGH-deficient cells impacts cell homeostasis, leading to activation of the Cpx stress response and reduced fitness under iron-limiting conditions. Our results highlight a native physiological function of an RND transporter and provide insight into the selective forces that maintain what was thought to be a redundant multidrug transporter.

Mining the Proteome of Fusobacterium nucleatum subsp. nucleatum ATCC 25586 for Potential Therapeutics Discovery: An In Silico Approach

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.

Competitive Growth Enhances Conditional Growth Mutant Sensitivity to Antibiotics and Exposes a Two-Component System as an Emerging Antibacterial Target in Burkholderia cenocepacia

Chemogenetic approaches to profile an antibiotic mode of action are based on detecting differential sensitivities of engineered bacterial strains in which the antibacterial target (usually encoded by an essential gene) or an associated process is regulated. We previously developed an essential-gene knockdown mutant library in the multidrug-resistant Burkholderia cenocepacia by transposon delivery of a rhamnose-inducible promoter. In this work, we used Illumina sequencing of multiplex-PCR-amplified transposon junctions to track individual mutants during pooled growth in the presence of antibiotics. We found that competition from nontarget mutants magnified the hypersensitivity of a clone underexpressing gyrB to novobiocin by 8-fold compared with hypersensitivity measured during clonal growth. Additional profiling of various antibiotics against a pilot library representing most categories of essential genes revealed a two-component system with unknown function, which, upon depletion of the response regulator, sensitized B. cenocepacia to novobiocin, ciprofloxacin, tetracycline, chloramphenicol, kanamycin, meropenem, and carbonyl cyanide 3-chlorophenylhydrazone, but not to colistin, hydrogen peroxide, and dimethyl sulfoxide. We named the gene cluster esaSR for enhanced sensitivity to antibiotics sensor and response regulator. Mutational analysis and efflux activity assays revealed that while esaS is not essential and is involved in antibiotic-induced efflux, esaR is an essential gene and regulates efflux independently of antibiotic-mediated induction. Furthermore, microscopic analysis of cells stained with propidium iodide provided evidence that depletion of EsaR has a profound effect on the integrity of cell membranes. In summary, we unraveled a previously uncharacterized two-component system that can be targeted to reduce antibiotic resistance in B. cenocepacia.

Genetic Strategies for Identifying New Drug Targets

Genetic strategies have yet to come into their own as tools for antibiotic development. While holding a lot of initial promise, they have only recently started to bear fruit in the quest for new drug targets. An ever-increasing body of knowledge is showing that genetics can lead to significant improvements in the success and efficiency of drug discovery. Techniques such as high-frequency transposon mutagenesis and expression modulation have matured and have been applied successfully not only to the identification and characterization of new targets, but also to their validation as tractable weaknesses of bacteria. Past experience shows that choosing targets must not rely on gene essentiality alone, but rather needs to incorporate knowledge of the system as a whole. The ability to manipulate genes and their expression is key to ensuring that we understand the entire set of processes that are affected by drug treatment. Focusing on exacerbating these perturbations, together with the identification of new targets to which resistance has not yet occurred--both enabled by genetic approaches--may point us toward the successful development of new combination therapies engineered based on underlying biology.

Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability

Gene essentiality is typically determined by assessing the viability of the corresponding mutant cells, but this definition fails to account for the ability of cells to adaptively evolve to genetic perturbations. Here, we performed a stringent screen to assess the degree to which Saccharomyces cerevisiae cells can survive the deletion of ~1,000 individual "essential" genes and found that ~9% of these genetic perturbations could in fact be overcome by adaptive evolution. Our analyses uncovered a genome-wide gradient of gene essentiality, with certain essential cellular functions being more "evolvable" than others. Ploidy changes were prevalent among the evolved mutant strains, and aneuploidy of a specific chromosome was adaptive for a class of evolvable nucleoporin mutants. These data justify a quantitative redefinition of gene essentiality that incorporates both viability and evolvability of the corresponding mutant cells and will enable selection of therapeutic targets associated with lower risk of emergence of drug resistance.

An integrated machine-learning model to predict prokaryotic essential genes

Essential genes are indispensable for the target organism's survival. Large-scale identification and characterization of essential genes has shown to be beneficial in both fundamental biology and medicine fields. Current existing genome-scale experimental screenings of essential genes are time consuming and costly, also sometimes confer erroneous essential gene annotations. To circumvent these difficulties, many research groups turn to computational approaches as the alternative to identify essential genes. Here, we developed an integrative machine-learning based statistical framework to accurately predict essential genes in microorganisms. First we extracted a variety of relevant features derived from different aspects of an organism's genomic sequences. Then we selected a subset of features have high predictive power of gene essentiality through a carefully designed feature selection system. Using the selected features as input, we constructed an ensemble classifier and trained the model on a well-studied microorganism. After fine-tuning the model parameters in cross-validation, we tested the model on the other microorganism. We found that the tenfold cross-validation results within the same organism achieves a high predictive accuracy (AUC ~0.9), and cross-organism predictions between distant related organisms yield the AUC scores from 0.69 to 0.89, which significantly outperformed homology mapping.

Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes

Streptococcus pyogenes (Group A Streptococcus, GAS) remains a major public health burden worldwide, infecting over 750 million people leading to over 500,000 deaths annually. GAS pathogenesis is complex, involving genetically distinct GAS strains and multiple infection sites. To overcome fastidious genetic manipulations and accelerate pathogenesis investigations in GAS, we developed a mariner-based system (Krmit) for en masse monitoring of complex mutant pools by transposon sequencing (Tn-seq). Highly saturated transposant libraries (Krmit insertions in ca. every 25 nucleotides) were generated in two distinct GAS clinical isolates, a serotype M1T1 invasive strain 5448 and a nephritogenic serotype M49 strain NZ131, and analyzed using a Bayesian statistical model to predict GAS essential genes, identifying sets of 227 and 241 of those genes in 5448 and NZ131, respectively. A large proportion of GAS essential genes corresponded to key cellular processes and metabolic pathways, and 177 were found conserved within the GAS core genome established from 20 available GAS genomes. Selected essential genes were validated using conditional-expression mutants. Finally, comparison to previous essentiality analyses in S. sanguinis and S. pneumoniae revealed significant overlaps, providing valuable insights for the development of new antimicrobials to treat infections by GAS and other pathogenic streptococci.

Genetic tools for manipulating Acinetobacter baumannii genome: an overview

Acinetobacter baumannii is an emerging nosocomial pathogen involved in a variety of infections ranging from minor soft-tissue infections to more severe infections such as ventilator-associated pneumonia and bacteraemia. A. baumannii has become resistant to most of the commonly used antibiotics and multidrug-resistant isolates are becoming a severe problem in the healthcare setting. In the past few years, whole-genome sequences of >200 A. baumannii isolates have been generated. Several methods and molecular tools have been used for genetic manipulation of various Acinetobacter spp. Here, we review recent developments of various genetic tools used for modification of the A. baumannii genome, including various ways to inactivate gene function, chromosomal integration and transposon mutagenesis.

Identifying essential proteins from active PPI networks constructed with dynamic gene expression

Essential proteins are vitally important for cellular survival and development, and identifying essential proteins is very meaningful research work in the post-genome era. Rapid increase of available protein-protein interaction (PPI) data has made it possible to detect protein essentiality at the network level. A series of centrality measures have been proposed to discover essential proteins based on the PPI networks. However, the PPI data obtained from large scale, high-throughput experiments generally contain false positives. It is insufficient to use original PPI data to identify essential proteins. How to improve the accuracy, has become the focus of identifying essential proteins. In this paper, we proposed a framework for identifying essential proteins from active PPI networks constructed with dynamic gene expression. Firstly, we process the dynamic gene expression profiles by using time-dependent model and time-independent model. Secondly, we construct an active PPI network based on co-expressed genes. Lastly, we apply six classical centrality measures in the active PPI network. For the purpose of comparison, other prediction methods are also performed to identify essential proteins based on the active PPI network. The experimental results on yeast network show that identifying essential proteins based on the active PPI network can improve the performance of centrality measures considerably in terms of the number of identified essential proteins and identification accuracy. At the same time, the results also indicate that most of essential proteins are active.

Harnessing the power of transposon mutagenesis for antibacterial target identification and evaluation

Determining the mechanism of action of bacterial growth inhibitors can be a formidable challenge in the progression of small molecules into antibacterial therapies. To help address this bottleneck, we have developed a robust transposon mutagenesis system using a suite of outward facing promoters in order to generate a comprehensive range of expression genotypes in Staphylococcus aureus from which to select defined compound-resistant transposon insertion mutants. Resistance stemming from either gene or operon over/under-expression, in addition to deletion, provides insight into multiple factors that contribute to a compound's observed activity, including means of cell envelope penetration and susceptibility to efflux. By profiling the entire resistome, the suitability of an antibacterial target itself is also evaluated, sometimes with unanticipated results. We herein show that for the staphylococcal signal peptidase (SpsB) inhibitors, modulating expression of lipoteichoic acid synthase (LtaS) confers up to a 100-fold increase in the minimal inhibitory concentration. As similarly efficient transposition systems are or will become established in other bacteria and cell types, we discuss the utility, limitations and future promise of Tnp mutagenesis for determining both a compound's mechanism of action and in the evaluation of novel targets.

Genomic tools to profile antibiotic mode of action

The increasing emergence of antimicrobial multiresistant bacteria is of great concern to public health. While these bacteria are becoming an ever more prominent cause of nosocomial and community-acquired infections worldwide, the antibiotic discovery pipeline has been stalled in the last few years with very few efforts in the research and development of novel antibacterial therapies. Some of the root causes that have hampered current antibiotic drug development are the lack of understanding of the mode of action (MOA) of novel antibiotic molecules and the poor characterization of the bacterial physiological response to antibiotics that ultimately causes resistance. Here, we review how bacterial genetic tools can be applied at the genomic level with the goal of profiling resistance to antibiotics and elucidating antibiotic MOAs. Specifically, we highlight how chemical genomic detection of the MOA of novel antibiotic molecules and antibiotic profiling by next-generation sequencing are leveraging basic antibiotic research to unprecedented levels with great opportunities for knowledge translation.

Predicting Essential Proteins Based on Weighted Degree Centrality

Essential proteins are vital for an organism's viability under a variety of conditions. There are many experimental and computational methods developed to identify essential proteins. Computational prediction of essential proteins based on the global protein-protein interaction (PPI) network is severely restricted because of the insufficiency of the PPI data, but fortunately the gene expression profiles help to make up the deficiency. In this work, Pearson correlation coefficient (PCC) is used to bridge the gap between PPI and gene expression data. Based on PCC and edge clustering coefficient (ECC), a new centrality measure, i.e., the weighted degree centrality (WDC), is developed to achieve the reliable prediction of essential proteins. WDC is employed to identify essential proteins in the yeast PPI and e-Coli networks in order to estimate its performance. For comparison, other prediction technologies are also performed to identify essential proteins. Some evaluation methods are used to analyze the results from various prediction approaches. The prediction results and comparative analyses are shown in the paper. Furthermore, the parameter λ in the method WDC will be analyzed in detail and an optimal λ value will be found. Based on the optimal λ value, the differentiation of WDC and another prediction method PeC is discussed. The analyses prove that WDC outperforms other methods including DC, BC, CC, SC, EC, IC, NC, and PeC. At the same time, the analyses also mean that it is an effective way to predict essential proteins by means of integrating different data sources.

A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa

Background

Antibiotics in current use target a surprisingly small number of cellular functions: cell wall, DNA, RNA, and protein biosynthesis. Targeting of novel essential pathways is expected to play an important role in the discovery of new antibacterial agents against bacterial pathogens, such as Pseudomonas aeruginosa, that are difficult to control because of their ability to develop resistance, often multiple, to all current classes of clinical antibiotics.

Results

We aimed to identify novel essential genes in P. aeruginosa by shotgun antisense screening. This technique was developed in Staphylococcus aureus and, following a period of limited success in Gram-negative bacteria, has recently been used effectively in Escherichia coli. To also target low expressed essential genes, we included some variant steps that were expected to overcome the non-stringent regulation of the promoter carried by the expression vector used for the shotgun antisense libraries. Our antisense screenings identified 33 growth-impairing single-locus genomic inserts that allowed us to generate a list of 28 “essential-for-growth” genes: five were “classical” essential genes involved in DNA replication, transcription, translation, and cell division; seven were already reported as essential in other bacteria; and 16 were “novel” essential genes with no homologs reported to have an essential role in other bacterial species. Interestingly, the essential genes in our panel were suggested to take part in a broader range of cellular functions than those currently targeted by extant antibiotics, namely protein secretion, biosynthesis of cofactors, prosthetic groups and carriers, energy metabolism, central intermediary metabolism, transport of small molecules, translation, post-translational modification, non-ribosomal peptide synthesis, lipopolysaccharide synthesis/modification, and transcription regulation. This study also identified 43 growth-impairing inserts carrying multiple loci targeting 105 genes, of which 25 have homologs reported as essential in other bacteria. Finally, four multigenic growth-impairing inserts belonged to operons that have never been reported to play an essential role.

Conclusions

For the first time in P. aeruginosa, we applied regulated antisense RNA expression and showed the feasibility of this technology for the identification of novel essential genes.

Construction and analysis of a modified transposable element carrying an outward directed inducible promoter for Bacillus subtilis

Transposons are important tools to inactivate chromosomal genes followed by a correlation with a particular phenotype or genotype. Here we demonstrated the development of a special type of genetically engineered transposon carrying an outward-directed inducible promoter in order to allow transcription of nearby genes. We have modified the mariner transposon TnYLB able to transpose in B. subtilis. This modified TnYLB carries an expression unit consisting of the xylose repressor xylR and an outward-directed promoter negatively controlled by this repressor. This TnYLB-XylOut transposon is able to turn on gene expression if insertion occurs close to a promoter-less gene. It will be an important tool to identify the function of genes either by turning on their expression or by enhanced expression depending on the xylose concentration.

Burkholderia cenocepacia conditional growth mutant library created by random promoter replacement of essential genes

Identification of essential genes by construction of conditional knockouts with inducible promoters allows the identification of essential genes and creation of conditional growth (CG) mutants that are then available as genetic tools for further studies. We used large-scale transposon delivery of the rhamnose-inducible promoter, PrhaB followed by robotic screening of rhamnose-dependent growth to construct a genomic library of 106 Burkholderia cenocepacia CG mutants. Transposon insertions were found where PrhaB was in the same orientation of widely conserved, well-characterized essential genes as well as genes with no previous records of essentiality in other microorganisms. Using previously reported global gene-expression analyses, we demonstrate that PrhaB can achieve the wide dynamic range of expression levels required for essential genes when the promoter is delivered randomly and mutants with rhamnose-dependent growth are selected. We also show specific detection of the target of an antibiotic, novobiocin, by enhanced sensitivity of the corresponding CG mutant (PrhaB controlling gyrB expression) within the library. Modulation of gene expression to achieve 30-60% of wild-type growth created conditions for specific hypersensitivity demonstrating the value of the CG mutant library for chemogenomic experiments. In summary, CG mutants can be obtained on a large scale by random delivery of a tightly regulated inducible promoter into the bacterial chromosome followed by a simple screening for the CG phenotype, without previous information on gene essentiality.

Overexpression of the tcp gene cluster using the T7 RNA polymerase/promoter system and natural transformation-mediated genetic engineering of Vibrio cholerae

The human pathogen and aquatic bacterium Vibrio cholerae belongs to the group of naturally competent bacteria. This developmental program allows the bacterium to take up free DNA from its surrounding followed by a homologous recombination event, which allows integration of the transforming DNA into the chromosome. Taking advantage of this phenomenon we genetically engineered V. cholerae using natural transformation and FLP recombination. More precisely, we adapted the T7 RNA polymerase/promoter system in this organism allowing expression of genes in a T7 RNA polymerase-dependent manner. We naturally transformed V. cholerae by adding a T7-specific promoter sequence upstream the toxin-coregulated pilus (tcp) gene cluster. In a V. cholerae strain, which concomitantly produced the T7 RNA polymerase, this genetic manipulation resulted in the overexpression of downstream genes. The phenotypes of the strain were also in line with the successful production of TCP pili. This provides a proof-of-principle that the T7 RNA polymerase/promoter system is functional in V. cholerae and that genetic engineering of this organism by natural transformation is a straightforward and efficient approach.

O antigen is the receptor of Vibrio cholerae serogroup O1 El Tor typing phage VP4

Bacteriophage VP4 is a lytic phage of the Vibrio cholerae serogroup O1, and it is used in phage subtyping of V. cholerae biotype El Tor. Studies of phage infection mechanisms will promote the understanding of the basis of phage subtyping as well as the genetic differences between sensitive and resistant strains. In this study, we investigated the receptor that phage VP4 uses to bind to El Tor strains of V. cholerae and found that it infects strains through adsorbing the O antigen of V. cholerae O1. In some natural isolates that are resistant to VP4 infection, mutations were identified in the wb* cluster (O-antigen gene cluster), which is responsible for the biosynthesis of O antigen. Mutations in the manB, wbeE, and wbeU genes caused failure of adsorption of VP4 to these strains, whereas the observed amino acid residue mutations within wbeW and manC have no effect on VP4 infection. Additionally, although mutations in two resistant strains were found only in manB and wbeW, complementing both genes did not restore sensitivity to VP4 infection, suggesting that other resistance mechanisms may exist. Therefore, the mechanism of VP4 infection may provide a basis for subtyping the phage. Elaborate mutations of the O antigen may imbue V. cholerae strains with resistance to phage infection.

Selective Capture of Transcribed Sequences: A Promising Approach for Investigating Bacterium-Insect Interactions

Bacterial interactions with eukaryotic hosts are complex processes which vary from pathogenic to mutualistic. Identification of bacterial genes differentially expressed in the host, promises to unravel molecular mechanisms driving and maintaining such interactions. Several techniques have been developed in the past 20 years to investigate bacterial gene expression within their hosts. The most commonly used techniques include in-vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays. However, the limitations of these techniques in analyzing bacterial in-vivo gene expression indicate the need to develop alternative tools. With many advantages over the other methods for analyzing bacterial in-vivo gene expression, selective capture of transcribed sequences (SCOTS) technique has the prospect of becoming an elegant tool for discovery of genes involved in the bacterium-host interaction. Here, we summarize the advances in SCOTS technique, including its current and potential applications in bacterial gene expression studies under a variety of conditions from in-vitro to in-vivo and from mammals to insects.

Comparative study of differential gene expression in closely related bacterial species by comparative hybridization

The ability to profile bacterial gene expression has markedly advanced the capacity to understand the molecular mechanisms of pathogenesis, epidemiology, and therapeutics. This advance has been coupled with the development of techniques that enable investigators to identify bacterial specifically expressed genes and promise to open new avenues of functional genomics by allowing researchers to focus on the identified differentially expressed genes. During the past two decades, a number of approaches have been developed to investigate bacterial genes differentially expressed in response to the changing environment, particularly during interaction with their hosts. The most commonly used techniques include in vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays, which fall into two broad classes: mutagenesis-based technologies and hybridization-based technologies. Selective capture of transcribed sequences, a recently emerging method, is a hybridization-based technique. This technique is powerful in analyzing differential gene expression of the bacteria, with the superb ability to investigate the bacterial species with unknown genomic information. Herein, we describe the application of this technique in a comparative study of the gene expression between two closely related bacteria induced or repressed under a variety of conditions.

Transposable elements as tools for reshaping the genome: it is a huge world after all!

Transposable elements (TEs) are discrete pieces of DNA that can move from one site to another within genomes and sometime between genomes. They are found in all major branches of life. Because of their wide distribution and considerable diversity, they are a considerable source of genomic variation and as such, they constitute powerful drivers of genome evolution. Moreover, it is becoming clear that the epigenetic regulation of certain genes is derived from defense mechanisms against the activity of ancestral transposable elements. TEs now tend to be viewed as natural molecular tools that can reshape the genome, which challenges the idea that TEs are natural tools used to answer biological questions. In the first part of this chapter, we review the classification and distribution of TEs, and look at how they have contributed to the structural and transcriptional reshaping of genomes. In the second part, we describe methodological innovations that have modified their contribution as molecular tools.

In silico prediction of drug targets in Vibrio cholerae

Identification of potential drug targets is the first step in the process of modern drug discovery, subjected to their validation and drug development. Whole genome sequences of a number of organisms allow prediction of potential drug targets using sequence comparison approaches. Here, we present a subtractive approach exploiting the knowledge of global gene expression along with sequence comparisons to predict the potential drug targets more efficiently. Based on the knowledge of 155 known virulence and their coexpressed genes mined from microarray database in the public domain, 357 coexpressed probable virulence genes for Vibrio cholerae were predicted. Based on screening of Database of Essential Genes using blastn, a total of 102 genes out of these 357 were enlisted as vitally essential genes, and hence good putative drug targets. As the effective drug target is a protein which is only present in the pathogen, similarity search of these 102 essential genes against human genome sequence led to subtraction of 66 genes, thus leaving behind a subset of 36 genes whose products have been called as potential drug targets. The gene ontology analysis using Blast2GO of these 36 genes revealed their roles in important metabolic pathways of V. cholerae or on the surface of the pathogen. Thus, we propose that the products of these genes be evaluated as target sites of drugs against V. cholerae in future investigations.