Identification of transporter genes from the fungal endophyte Neotyphodium lolii : this thesis is presented in partial fulfilment of the requirements for the degree of Master of Science (MSc) in Plant Biology at Massey University, Palmerston North, New Zealand /

Neotyphodium lolii is an endophytic fungus that lives in the pasture grass, Lolium perenne. They share a mutualistic symbiotic relationship. N. lolii lives out its life cycle within the plant and produces secondary metabolites, including alkaloids peramine, ergovaline and lolitrem which protect the grass from insect and animal herbivory. In fungi the biosynthetic genes of secondary metabolites are often located in gene clusters. These clusters frequently contain one or more genes that code for transporter proteins responsible for the removal of toxic products from the fungal cells. Plants produce defence compounds, including antifungals to protect themselves from colonising fungi. However endophytes are able to neutralise these host toxins, one mechanism for this is possibly by efflux through transporter channels. The goal of this study was to identify ABC and MFS genes from N. lolii. These two families are the largest and most diverse of transporter families, which transport a variety of substrates, including peptides, toxins, ions and sugars across membranes. Using degenerate PCR primers designed from fungal multi-drug transporter sequences, four unique ABC gene fragments were amplified from N. lolii. A further two ABC sequences and two MFS gene fragments were identified in a database of N. lolii EST sequences. RT-PCR was used to compare expression of isolated ABC and MFS genes in N. lolii, growing in culture and in infected plants. Up-regulation of transporter transcripts in planta could suggest a role in symbiosis. Some genes were seen to have a visibly different expression pattern from others, although all genes were strongly expressed in cultured mycelia. Gene expression in the plant host was most evident in tissues more heavily infected with endophyte. To discover possible roles for the isolated transporter genes in transporting endophyte secondary metabolites a strain distribution study was completed. Five of the putative ABC and MFS genes were compared against 12 Epichloë and Neotyphodium endophytes. Amplified PCR products in the genotypes screened produced a unique pattern of gene occurrence for each of the five transporters. This added to the characterisation of the transporter genes and showed that one gene, gABC 4e, was the most diverse in its distribution, while another ABC gene gABC 4g was present across all genotypes. One ABC gene (gABC 4e) plus flanking DNA was sequenced in full. Bioinformatic analyses suggested that gABC 4c may be a half sized ABC transporter gene of 2 kb with four exons. An orotate phosphoribosyltransferase was identified 2 kb upstream of the ABC transporter. Further work will be needed to confirm that the start and stop codons of this ABC transporter have been accurately predicted, as well as to verify the putative intron/ exon boundaries identified by gene prediction programmes. The role of N. lolii ABC transporter gABC 4c has not been determined, however future research could focus on the nature of the substrate(s) transported, the sub-cellular location of the channel, and the effects of gene knockout or over-expression on the symbiosis between N. lolii and perennial ryegrass

The Varied Role of Efflux Pumps of the MFS Family in the Interplay of Bacteria with Animal and Plant Cells

Efflux pumps represent an important and large group of transporter proteins found in all organisms. The importance of efflux pumps resides in their ability to extrude a wide range of antibiotics, resulting in the emergence of multidrug resistance in many bacteria. Besides antibiotics, multidrug efflux pumps can also extrude a large variety of compounds: Bacterial metabolites, plant-produced compounds, quorum-sensing molecules, and virulence factors. This versatility makes efflux pumps relevant players in interactions not only with other bacteria, but also with plant or animal cells. The multidrug efflux pumps belonging to the major facilitator superfamily (MFS) are widely distributed in microbial genomes and exhibit a large spectrum of substrate specificities. Multidrug MFS efflux pumps are present either as single-component transporters or as tripartite complexes. In this review, we will summarize how the multidrug MFS efflux pumps contribute to the interplay between bacteria and targeted host cells, with emphasis on their role in bacterial virulence, in the colonization of plant and animal host cells and in biofilm formation. We will also address the complexity of these interactions in the light of the underlying regulatory networks required for the effective activation of efflux pump genes

Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE.

The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins

The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus.

Filamentous fungi, such as Neurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling of N. crassa on 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors in N. crassa and characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level

Using cellular fitness to map the structure and function of a major facilitator superfamily effluxer.

The major facilitator superfamily (MFS) effluxers are prominent mediators of antimicrobial resistance. The biochemical characterization of MFS proteins is hindered by their complex membrane environment that makes in vitro biochemical analysis challenging. Since the physicochemical properties of proteins drive the fitness of an organism, we posed the question of whether we could reverse that relationship and derive meaningful biochemical parameters for a single protein simply from fitness changes it confers under varying strengths of selection. Here, we present a physiological model that uses cellular fitness as a proxy to predict the biochemical properties of the MFS tetracycline efflux pump, TetB, and a family of single amino acid variants. We determined two lumped biochemical parameters roughly describing Km and Vmax for TetB and variants. Including in vivo protein levels into our model allowed for more specified prediction of pump parameters relating to substrate binding affinity and pumping efficiency for TetB and variants. We further demonstrated the general utility of our model by solely using fitness to assay a library of tet(B) variants and estimate their biochemical properties

Further studies of dothistromin toxin genes in the fungal forest pathogen Dothistroma septosporum : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Biochemistry at Massey University, Palmerston North, New Zealand

The fungal pathogen Dothistroma septosporum is the main causal agent of Dothistroma (red-hand) needle blight, which is a devastating foliar disease of a wide range of pine species. Dothistromin is a difuranoanthraquinone toxin produced by D. septosporum and is considered as a possible virulence factor for the disease. Based on the similarity of chemical structure between dothistromin and aflatoxin (AF) /sterigmatocystin (ST) precursors, nine putative dothistromin biosynthetic genes have been identified, which are homologous to their corresponding genes in the AF/ST gene clusters. However, in contrast to all 25 AF biosynthetic genes tightly clustered in one region (70-Kb) of the genome, the dothistromin gene clusters are located on a 1.3-Mb chromosome and separated into three mini-clusters along with non-dothistromin genes. The dotC gene, located in the mini-cluster 1, is predicted to encode a major facilitator superfamily (MFS) membrane transporter involved in secretion of dothistromin. In this work, by constructing DotC-eGFP fusion protein containing mutants, the subcellular localization of the DotC protein was determined to be mainly targeted to the plasma membrane. The biological function of the dotC gene was characterized by targeted gene disruption. The dotC gene disrupted mutants showed a significant reduction of dothistromin production in both the medium and mycelium. In addition, the exponential growth of dotC null mutants was inhibited when exogenous dothistromin was presented and these mutants also displayed more sensitivity than the wild type strain to exogenous dothistromin. The results indicated that the DotC protein is a membrane associated protein and might have a role in dothistromin production and be involved in secretion of exogenously supplied dothistromin toxin. Two novel dothistromin biosynthetic genes, norA/B and verB (partial sequence), were identified by using degenerate PCR and D. septosporum genomic library screening. The putative NorA/B and VerB are postulated to encode a dehydrogenase and a desaturase, respectively and are similar to AF/ST genes. These findings further confirmed that the dothistromin shares biosynthetic pathway steps with AF/ST

Genome-Wide Transposon Screen of a Pseudomonas syringae mexB Mutant Reveals the Substrates of Efflux Transporters.

Bacteria express numerous efflux transporters that confer resistance to diverse toxicants present in their environment. Due to a high level of functional redundancy of these transporters, it is difficult to identify those that are of most importance in conferring resistance to specific compounds. The resistance-nodulation-division (RND) protein family is one such example of redundant transporters that are widespread among Gram-negative bacteria. Within this family, the MexAB-OprM protein complex is highly expressed and conserved among Pseudomonas species. We exposed barcoded transposon mutant libraries in isogenic wild-type and ΔmexB backgrounds in P. syringae B728a to diverse toxic compounds in vitro to identify mutants with increased susceptibility to these compounds. Mutants with mutations in genes encoding both known and novel redundant transporters but with partially overlapping substrate specificities were observed in a ΔmexB background. Psyr_0228, an uncharacterized member of the major facilitator superfamily of transporters, preferentially contributes to tolerance of acridine orange and acriflavine. Another transporter located in the inner membrane, Psyr_0541, contributes to tolerance of acriflavine and berberine. The presence of multiple redundant, genomically encoded efflux transporters appears to enable bacterial strains to tolerate a diversity of environmental toxins. This genome-wide screen performed in a hypersusceptible mutant strain revealed numerous transporters that would otherwise be dispensable under these conditions. Bacterial strains such as P. syringae that likely encounter diverse toxins in their environment, such as in association with many different plant species, probably benefit from possessing multiple redundant transporters that enable versatility with respect to toleration of novel toxicants.IMPORTANCE Bacteria use protein pumps to remove toxic compounds from the cell interior, enabling survival in diverse environments. These protein pumps can be highly redundant, making their targeted examination difficult. In this study, we exposed mutant populations of Pseudomonas syringae to diverse toxicants to identify pumps that contributed to survival in those conditions. In parallel, we examined pump redundancy by testing mutants of a population lacking the primary efflux transporter responsible for toxin tolerance. We identified partial substrate overlap for redundant transporters, as well as several pumps that appeared more substrate specific. For bacteria that are found in diverse environments, having multiple, partially redundant efflux pumps likely allows flexibility in habitat colonization

Cyanate Assimilation by the Alkaliphilic Cyanide-Degrading Bacterium Pseudomonas pseudoalcaligenes CECT5344: Mutational Analysis of the cyn Gene Cluster

The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 can grow with cyanate, cyanide, or cyanide-containing industrial residues as the sole nitrogen source, but the assimilation of cyanide and cyanate takes place through independent pathways. Therefore, cyanide degradation involves a chemical reaction between cyanide and oxaloacetate to form a nitrile that is hydrolyzed to ammonium by the nitrilase NitC, whereas cyanate assimilation requires a cyanase that catalyzes cyanate decomposition to ammonium and carbon dioxide. The P. pseudoalcaligenes CECT5344 cynFABDS gene cluster codes for the putative transcriptional regulator CynF, the ABC-type cyanate transporter CynABD, and the cyanase CynS. In this study, transcriptional analysis revealed that the structural cynABDS genes constitute a single transcriptional unit, which was induced by cyanate and repressed by ammonium. Mutational characterization of the cyn genes indicated that CynF was essential for cynABDS gene expression and that nitrate/nitrite transporters may be involved in cyanate uptake, in addition to the CynABD transport system. Biodegradation of hazardous jewelry wastewater containing high amounts of cyanide and metals was achieved in a batch reactor operating at an alkaline pH after chemical treatment with hydrogen peroxide to oxidize cyanide to cyanate

An MFS Transporter-Like ORF from MDR Acinetobacter baumannii AIIMS 7 Is Associated with Adherence and Biofilm Formation on Biotic/Abiotic Surface

A major facilitator superfamily (MFS) transporter-like open reading frame (ORF) of 453 bp was identified in a pathogenic strain Acinetobacter baumannii AIIMS 7, and its association with adherence and biofilm formation was investigated. Reverse transcription PCR (RT-PCR) showed differential expression in surface-attached biofilm cells than nonadherent cells. In vitro translation showed synthesis of a ~17 kDa protein, further confirmed by cloning and heterologous expression in E. coli DH5α. Up to 2.1-, 3.1-, and 4.1- fold biofilm augmentation was observed on abiotic (polystyrene) and biotic (S. cerevisiae/HeLa) surface, respectively. Scanning electron microscopy (SEM) and gfp-tagged fluorescence microscopy revealed increased adherence to abiotic (glass) and biotic (S. cerevisiae) surface. Extracellular DNA(eDNA) was found significantly during active growth; due to probable involvement of the protein in DNA export, strong sequence homology with MFS transporter proteins, and presence of transmembrane helices. In summary, our findings show that the putative MFS transporter-like ORF (pmt) is associated with adherence, biofilm formation, and probable eDNA release in A. baumannii AIIMS 7