Structural and physiological analyses of the alkanesulphonate-binding protein (SsuA) of the citrus pathogen Xanthomonas citri

Rational design of a bacterial import system for new-to-nature molecules

Integration of novel compounds into biological processes holds significant potential for modifying or expanding existing cellular functions. However, the cellular uptake of these compounds is often hindered by selectively permeable membranes. We present a novel bacterial transport system that has been rationally designed to address this challenge. Our approach utilizes a highly promiscuous sulfonate membrane transporter, which allows the passage of cargo molecules attached as amides to a sulfobutanoate transport vector molecule into the cytoplasm of the cell. These cargoes can then be unloaded from the sulfobutanoyl amides using an engineered variant of the enzyme γ-glutamyl transferase, which hydrolyzes the amide bond and releases the cargo molecule within the cell. Here, we provide evidence for the broad substrate specificity of both components of the system by evaluating a panel of structurally diverse sulfobutanoyl amides. Furthermore, we successfully implement the synthetic uptake system in vivo and showcase its functionality by importing an impermeant non-canonical amino acid.

Curtobacterium allii sp. nov., the actinobacterial pathogen causing onion bulb rot

A Gram-stain-positive, aerobic, and non-spore-forming bacterial strain, 20TX0166^T, was isolated from a diseased onion bulb in Texas, USA. Upon testing its pathogenicity on onion bulb, it produced pathogenic response which makes it first species of pathogen belonging to the phylum actinobacteria detected in onion. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain belonged to the genus Curtobacterium and was most similar to Curtobacterium flaccumfaciens LMG 3645^T (100%), C. pusillum DSM 20527^T (99.5%), and C. oceanosedimentum ATCC 31317^T (99.5%). The estimated genome size of the novel species was 4.0 Mbp with a G + C content of 70.8%. The orthologous ANI (orthoANIu), ANI based on blast (ANIb), and dDDH values between the novel strain and the closest relative, C. flaccumfaciens LMG 3645^T, were 95.7%, 95.4%, and 63.3%, respectively. These values were below the recommended species cut-off threshold of 96% (ANI) and 70% (dDDH), suggesting the strain may be a novel species. Physiologic and phenotypic characters of this novel strain were also unique when compared with the closely related species. The major cellular fatty acids of this strain were anteiso-C_15:0 and anteiso-C_17:0. Using a polyphasic approach based on phenotypic and genotypic analyses, strain 20TX0166^T represents a novel species of the genus Curtobacterium, and the name Curtobacterium allii sp. nov. is proposed. The type strain is 20TX0166^T (= LMG 32517^T = CIP112023^T = NCIMB 15427^T).

Sparking a sulfur war between plants and pathogens

The biochemical versatility of sulfur (S) lends itself to myriad roles in plant-pathogen interactions. This review evaluates the current understanding of mechanisms by which pathogens acquire S from their plant hosts and highlights new evidence that plants can limit S availability during the immune responses. We discuss the discovery of host disease-susceptibility genes related to S that can be genetically manipulated to create new crop resistance. Finally, we summarize future research challenges and propose a research agenda that leverages systems biology approaches for a holistic understanding of this important element's diverse roles in plant disease resistance and susceptibility.

Complete Genome Sequences of One Salt-Tolerant and Petroleum Hydrocarbon-Emulsifying Terribacillus saccharophilus Strain ZY-1

Salt tolerance is one of the most important problems in the field of environmental governance and restoration. Among the various sources of factors, except temperature, salinity is a key factor that interrupts bacterial growth significantly. In this regard, constant efforts are made for the development of salt-tolerant strains, but few strains with salt tolerance, such as Terribacillus saccharophilus, were found, and there are still few relevant reports about their salt tolerance from complete genomic analysis. Furthermore, with the development of the economy, environmental pollution caused by oil exploitation has attracted much attention, so it is crucial to find the bacteria from T. saccharophilus which could degrade petroleum hydrocarbon even under high-salt conditions. Herein, one T. saccharophilus strain named ZY-1 with salt tolerance was isolated by increasing the salinity on LB medium step by step with reservoir water as the bacterial source. Its complete genome was sequenced, which was the first report of the complete genome for T. saccharophilus species with petroleum hydrocarbon degradation and emulsifying properties. In addition, its genome sequences were compared with the other five strains that are from the same genus level. The results indicated that there really exist some differences among them. In addition, some characteristics were studied. The salt-tolerant strain ZY-1 developed in this study and its emulsification and degradation performance of petroleum hydrocarbons were studied, which is expected to widely broaden the research scope of petroleum hydrocarbon-degrading bacteria in the oil field environment even in the extreme environment. The experiments verified that ZY-1 could significantly grow not only in the salt field but also in the oil field environment. It also demonstrated that the developed salt-tolerant strain can be applied in the petroleum hydrocarbon pollution field for bioremediation. In addition, we expect that the identified variants which occurred specifically in the high-salt strain will enhance the molecular biological understanding and be broadly applied to the biological engineering field.

The citrus plant pathogen Xanthomonas citri has a dual polyamine-binding protein

ATP-Binding Cassette transporters (ABC transporters) are protein complexes involved in the import and export of different molecules, including ions, sugars, peptides, drugs, and others. Due to the diversity of substrates, they have large relevance in physiological processes such as virulence, pathogenesis, and antimicrobial resistance. In Xanthomonas citri subsp. citri, the phytopathogen responsible for the citrus canker disease, 20% of ABC transporters components are expressed under infection conditions, including the putative putrescine/polyamine ABC transporter, PotFGHI. Polyamines are ubiquitous molecules that mediate cell growth and proliferation and play important role in bacterial infections. In this work, we characterized the X. citri periplasmic-binding protein PotF (XAC2476) using bioinformatics, biophysical and structural methods. PotF is highly conserved in Xanthomonas sp. genus, and we showed it is part of a set of proteins related to the import and assimilation of polyamines in X. citri. The interaction of PotF with putrescine and spermidine was direct and indirectly shown through fluorescence spectroscopy analyses, and experiments of circular dichroism (CD) and small-angle X-ray scattering (SAXS), respectively. The protein showed higher affinity for spermidine than putrescine, but both ligands induced structural changes that coincided with the closing of the domains and increasing of thermal stability.

Desolvation of the substrate-binding protein TauA dictates ligand specificity for the alkanesulfonate ABC importer TauABC

Under limiting sulfur availability, bacteria can assimilate sulfur from alkanesulfonates. Bacteria utilize ATP-binding cassette (ABC) transporters to internalise them for further processing to release sulfur. In gram-negative bacteria the TauABC and SsuABC ensure internalization, although, these two systems have common substrates, the former has been characterized as a taurine specific system. TauA and SsuA are substrate-binding proteins (SBPs) that bind and bring the alkanesulfonates to the ABC importer for transport. Here, we have determined the crystal structure of TauA and have characterized its thermodynamic binding parameters by isothermal titration calorimetry in complex with taurine and different alkanesulfonates. Our structures revealed that the coordination of the alkanesulfonates is conserved, with the exception of Asp205 that is absent from SsuA, but the thermodynamic parameters revealed a very high enthalpic penalty cost for binding of the other alkanesulfonates relative to taurine. Our molecular dynamic simulations indicated that the different levels of hydration of the binding site contributed to the selectivity for taurine over the other alkanesulfonates. Such selectivity mechanism is very likely to be employed by other SBPs of ABC transporters.

Roles of Efflux Pumps from Different Superfamilies in the Surface-Associated Motility and Virulence of Acinetobacter baumannii ATCC 17978

Although the relationship between Acinetobacter baumannii efflux pumps and antimicrobial resistance is well documented, less is known about the involvement of these proteins in the pathogenicity of this nosocomial pathogen. In previous work, we identified the AbaQ major facilitator superfamily (MFS) efflux pump and demonstrated its participation in the motility and virulence of A. baumannii In the present study, we examined the role in these processes of A. baumannii transporters belonging to different superfamilies of efflux pumps. Genes encoding known or putative permeases belonging to efflux pump superfamilies other than the MFS were selected, and the corresponding knockouts were constructed. The antimicrobial susceptibilities of these mutants were consistent with previously reported data. In mutants of A. baumannii strain ATCC 17978 carrying inactivated genes encoding the efflux pumps A1S_2736 (resistance nodulation division [RND]), A1S_3371 (multidrug and toxic compound extrusion [MATE]), and A1S_0710 (small multidrug resistance [SMR]), as well as the newly described ATP-binding cassette (ABC) permeases A1S_1242 and A1S_2622, both surface-associated motility and virulence were reduced compared to the parental strain. However, inactivation of the genes encoding the known ABC permeases A1S_0536 and A1S_1535, the newly identified putative ABC permeases A1S_0027 and A1S_1057, or the proteobacterial antimicrobial compound efflux (PACE) transporters A1S_1503 and A1S_2063 had no effects on bacterial motility or virulence. Our results demonstrate the involvement of antimicrobial transporters belonging at least to five of the six known efflux pump superfamilies in both surface-associated motility and virulence in A. baumannii ATCC 17978.

The periplasmic binding protein NrtT affects xantham gum production and pathogenesis in Xanthomonas citri

In Xanthomonas citri, the bacterium that causes citrus canker, three ATP-binding cassette (ABC) transporters are known to be dedicated to the uptake of sulfur compounds. In this work, using functional, biophysical and structural methods, we showed that NrtT, a periplasmic component of the ABC transporter NrtCB, is an alkanesulfonate-binding protein and that the deletion of the nrtT gene affected xantham gum synthesis, adhesion and biofilm production, similarly to the phenotype obtained in the X. citri ssuA-knockout strain, in which the alkanesulfonate-binding protein SsuA is absent. Although NrtA and SsuA share similar ligands, the function of these proteins is not complementary. These results emphasize that organic-sulfur sources are directly involved with bacterial infection in vivo and are needed for pathogenesis in X. citri.

Sulfate-Binding Protein (Sbp) from Xanthomonas citri: Structure and Functional Insights

The uptake and transport of sulfate in bacteria is mediated by an ATP-binding cassette transporter (ABC transporter) encoded by sbpcysUWA genes, whose importance has been widely demonstrated due to their relevance in cysteine synthesis and bacterial growth. In Xanthomonas citri, the causative agent of canker disease, the expression of components from this ABC transporter and others related to uptake of organic sulfur sources has been shown during in vitro growth cultures. In this work, based on gene reporter and proteomics analyses, we showed the activation of the promoter that controls the sbpcysUWA operon in vitro and in vivo and the expression of sulfate-binding protein (Sbp), a periplasmic-binding protein, indicating that this protein plays an important function during growth and that the transport system is active during Citrus sinensis infection. To characterize Sbp, we solved its three-dimensional structure bound to sulfate at 1.14 Å resolution and performed biochemical and functional characterization. The results revealed that Sbp interacts with sulfate without structural changes, but the interaction induces a significant increasing of protein thermal stability. Altogether, the results presented in this study show the evidence of the functionality of the ABC transporter for sulfate in X. citri and its relevance during infection.

The sulfur/sulfonates transport systems in Xanthomonas citri pv. citri

Background

The Xanthomonas citri pv. citri (X. citri) is a phytopathogenic bacterium that infects different species of citrus plants where it causes canker disease. The adaptation to different habitats is related to the ability of the cells to metabolize and to assimilate diverse compounds, including sulfur, an essential element for all organisms. In Escherichia coli, the necessary sulfur can be obtained by a set of proteins whose genes belong to the cys regulon. Although the cys regulon proteins and their importance have been described in many other bacteria, there are no data related to these proteins in X. citri or in the Xanthomonas genus. The study of the relevance of these systems in these phytopathogenic bacteria that have distinct mechanisms of infection is one essential step toward understanding their physiology. In this work, we used bioinformatics, molecular modeling and transcription analysis (RT-PCR) to identify and characterize the putative cys regulon genes in X. citri.

Results

We showed that the ATP Binding Cassette Transporter (ABC transporter) SbpCysUWA for sulfate uptake is conserved in X. citri and translated in presence of sulfate. On the other hand, differently from what is predicted in databases, according molecular modeling and phylogenetic analysis, X. citri does not show a proper taurine transporter, but two different ABC systems related to the alkanesulfonate/sulfonate transport that were recently acquired during evolution. RT-PCR analysis evidenced that these genes and their putative transcriptional regulator CysB are rather transcripted in XAM1, a medium with defined concentration of sulfate, than LB.

Conclusions

The presence of at least three distinct systems for sulfate and sulfonates  assimilation in X. citri evidenced the importance of these compounds for the bacterium. The transcription of genes involved with alkanesulfonate/sulfur compounds in XAM1 along to CysB suggests that despite the differences in the transporters, the regulation of these systems might be similar to the described for E. coli. Altogether, these results will serve as a foundation for further studies aimed to understanding the relevance of sulfur in growth, virulence and pathogenesis of X. citri and related bacteria.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1736-5) contains supplementary material, which is available to authorized users.

Crystallization and preliminary X-ray diffraction analysis of the phosphate-binding protein PhoX from Xanthomonas citri

Xanthomonas axonopodis pv. citri (X. citri) is an important bacterium that causes citrus canker disease in plants in Brazil and around the world, leading to significant economic losses. Determination of the physiology and mechanisms of pathogenesis of this bacterium is an important step in the development of strategies for its containment. Phosphate is an essential ion in all microrganisms owing its importance during the synthesis of macromolecules and in gene and protein regulation. Interestingly, X. citri has been identified to present two periplasmic binding proteins that have not been further characterized: PstS, from an ATP-binding cassette for high-affinity uptake and transport of phosphate, and PhoX, which is encoded by an operon that also contains a putative porin for the transport of phosphate. Here, the expression, purification and crystallization of the phosphate-binding protein PhoX and X-ray data collection at 3.0 Å resolution are described. Biochemical, biophysical and structural data for this protein will be helpful in the elucidation of its function in phosphate uptake and the physiology of the bacterium.

Structure determination of a sugar-binding protein from the phytopathogenic bacterium Xanthomonas citri

The uptake of maltose and related sugars in Gram-negative bacteria is mediated by an ABC transporter encompassing a periplasmic component (the maltose-binding protein or MalE), a pore-forming membrane protein (MalF and MalG) and a membrane-associated ATPase (MalK). In the present study, the structure determination of the apo form of the putative maltose/trehalose-binding protein (Xac-MalE) from the citrus pathogen Xanthomonas citri in space group P6522 is described. The crystals contained two protein molecules in the asymmetric unit and diffracted to 2.8 Å resolution. Xac-MalE conserves the structural and functional features of sugar-binding proteins and a ligand-binding pocket with similar characteristics to eight different orthologues, including the residues for maltose and trehalose interaction. This is the first structure of a sugar-binding protein from a phytopathogenic bacterium, which is highly conserved in all species from the Xanthomonas genus.