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Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
Correspondence
Nemat O. Keyhani
keyhani{at}ufl.edu
| ABSTRACT |
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10 kDa protein found in boiling SDS-insoluble, trifluoroacetic acid-soluble extracts from aerial conidia identified the major component of the B. bassiana rodlet layer to be the hyd2 gene product. These results reveal the differential regulation of the isolated hydrophobins and indicate that phage display represents a novel approach to cDNA cloning of hydrophobins.
The GenBank/EMBL/DDBJ accession numbers for the hyd1 and hyd2 sequences of B. bassiana are EF452344 and EF520285, respectively.
Figures showing the sequences of hydrophobin genes used in phylogenetic analysis, atomic force micrographs and SDS-PAGE results obtained during rodlet extraction, MS results for a peptide fragment resulting from in-gel tryptic digestion, and BLAST matches of peptide fragment data are available with the online version of this paper.
| INTRODUCTION |
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Beauveria bassiana is an important entomopathogenic fungus that displays a broad host range, and is able to target a diverse range of arthropod species (Clarkson & Charnley, 1996
; Leathers et al., 1993
; Maurer et al., 1997
). Strains of B. bassiana have been selected for the control of insects and other arthropods that act as disease vectors, including mosquitoes and ticks, crop pests such as whiteflies and borers, and even ecologically hazardous, invading pests such as fire ants and termites (Blanford et al., 2005
; Brownbridge et al., 2001
; Cruz et al., 2006
; Kirkland et al., 2004
; Klinger et al., 2006
; Marti et al., 2005
; McCoy, 1990
).
Phage display technology is based upon the expression of protein or peptide sequences on the surface of phage particles by genetic fusion with phage capsid proteins. Applications include biopanning for antibody-, protein-, peptide-, DNA-, RNA- and oligonucleotide-binding phage-fusion particles (particularly using peptide libraries), as well as cDNA cloning of proteins that act as allergens (Danner & Belasco, 2001
; Mullen et al., 2006
; Paschke, 2006
; Rhyner et al., 2004
; Sergeeva et al., 2006
). Phage display has also been used to clone a protein with carbohydrate affinity, namely galectin-3 from a HeLa cell display library by mucin affinity selection (Yamamoto et al., 1999
).
In this report, we describe the successful use of phage display for the isolation of hydrophobins. A phage display cDNA library was constructed using RNA from B. bassiana grown in the presence of insect cuticle. Biopanning experiments were performed using a number of carbohydrate affinity resins, including N,N'-diacetylchitobiose–, fucose–, lactose–, maltose– and melibiose–agarose beads. Hydrophobins appeared to be selectively enriched by melibiose–agarose beads, which yielded two different hydrophobin proteins highly represented in the final library enrichment, and to a lesser extent by lactose–agarose beads, which yielded one of the hydrophobins. Expression studies were performed using RNA isolated from a variety of fungal developmental stages, including: (i) single-cell types such as aerial conidia, in vitro blastospores and submerged conidia; (ii) during fungal mycelial growth; and (iii) during sporulation on chitin and insect cuticle. Additionally, extraction and mass spectrometric analysis of the major protein constituent of the hydrophobic aerial conidia rodlet layer revealed it to be composed of the hyd2 gene product.
| METHODS |
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Biopanning protocol.
N,N'-Diacetylchitobiose-, fucose-, lactose-, maltose- and melibiose-coupled agarose beads were obtained from Seigakagu (Tokyo). Beads were washed three times with PBS (50 mM sodium phosphate, pH 7.4, 0.15 M NaCl) before being resuspended in PBS+1 % BSA before use. The phage stock (10 ml of 1010 p.f.u. ml–1) was precipitated using PEG-8000 (4 % final concentration) and NaCl (3 % final concentration) and resuspended in 1 ml PBS+1 % BSA. Beads (200 µl) were mixed with 0.5 ml precipitated phage and incubated at 4 °C for 2 h with gentle shaking, before being washed five times with 1 ml PBS containing 0.5 M NaCl. Bound phage was eluted (twice) with a 0.2 M solution (300 µl total volume, incubated at room temperature for 30 min) of the carbohydrate moiety bound to each respective agarose-coupled bead. The titre of the eluted phage was amplified by passage through an Escherichia coli host, and the resultant phage stock was used for the next round of biopanning. Five rounds of the biopanning procedure were performed successively with each affinity resin.
Molecular manipulations.
cDNA inserts of phage plaques were analysed by PCR amplification and sequencing (ICBR Sequencing Facility, University of Florida) using vector primers (T7Up and T7Down). Genomic DNA was extracted from fungal mycelium using hexamethyltrimethyl ammonium bromide (CTAB), as described by Talbot (2001
). DNA hybridization probes were labelled using the BioPrime chemiluminescent DNA labelling system (Invitrogen). Plasmid preparation, restriction enzyme digestion, agarose gel electrophoresis and Southern blotting were performed using standard procedures (Ausubel et al., 1996
).
RNA extraction.
Total RNA was extracted from B. bassiana cells using either RNAwiz or TRI Reagent (Ambion) according to the manufacturer's recommendations, including the high-salt precipitation step for removal of proteoglycans and polysaccharides. Culture conditions for RNA extraction were as follows: B. bassiana was grown on PD agar (PDA) or on Sabouraud dextrose+1 % yeast extract either on agar plates (SDAY) or in liquid broth (SDY). Plates were incubated at 26 °C for 10–12 days and aerial conidia were harvested by flooding the plate with sterile dH2O. Conidial suspensions were filtered through Miracloth and final spore concentrations were determined by direct counting using a haemocytometer. Liquid broth cultures were inoculated (1 : 50, v/v) with conidia harvested from plates to a final concentration of 0.5–5x105 conidia ml–1. Cultures were grown for 3–4 days at 26 °C with aeration. Cultures were filtered through glass wool or Mira cloth to remove mycelia, and the concentration of blastospores was determined by direct counting. Submerged conidia were isolated from TKI broth (per litre: 50.0 g fructose, 10.0 g KNO3, 5.0 g KH2PO4, 2.0 g MgSO4 . 7H20, 50.0 mg CaCl2, 50.0 mg yeast extract), as previously described (Cho et al., 2006b
). A time course of growing mycelia was prepared by growing B. bassiana on PDA. At the desired time points (3, 5, 10, 18 and 28 days), conidia were removed by washing the plates by flooding two to three times with dH2O, and the mycelium was obtained by lightly scraping off the fungal biomass from the resultant agar plates. Mycelia were examined by light microscopy for the presence of conidia, and samples containing less than 1 % conidia were used for further experimentation. Chitin and insect cuticle liquid broth cultures (50–100 ml), consisting of 1 : 4 diluted Sabouraud dextrose broth supplemented with 1 % (w/v) chitin, 1 % powdered, sterilized Manduca sexta cuticle (kind gift of D. Boucias, Department of Entomology and Nematology, University of Florida), or 1 % chitin+1 % M. sexta culticle, were inoculated with conidia harvested from plates to a final concentration of 0.5–5x105 conidia ml–1 and were grown for 3 days at 26 °C with aeration, after which the total fungal cell culture was harvested by centrifugation (10 000 g, 10 min), washed twice with dH2O, flash-frozen in liquid nitrogen, and stored at –70 °C.
Semi-quantitative RT-PCR analysis.
Total RNA isolated as described above was precipitated once with LiCl before being DNase-treated using the DNA-free reagent (Ambion). RNA samples were then treated with SUPERase-In (RNase inhibitor, Ambion) and stored at –70 °C until use. Total RNA concentration was quantified for each sample preparation using the Ribogreen RNA quantification kit (Molecular Probes). cDNA for each sample was synthesized using 1.0 µg of total RNA plus Superscript III reverse transcriptase with oligo dT18 priming, following the manufacturer's protocol (Invitrogen). PCR reactions were as follows: 1.0 µl of a twofold dilution of the cDNA sample was PCR-amplified using 6.0 µl DNA polymerase MasterMix (Eppendorf), 0.3 µl of 0.01 mM of each primer, and dH2O to a final volume of 17.0 µl. PCR amplification was performed at 94 °C for 30 s, 64 °C for 30 s, and 72 °C for 35 s. Samples (10 µl) were taken and analysed by agarose gel electrophoresis after 15, 20, 25 and 30 PCR cycles. Amplifications of portions of the B. bassiana actin and β-tubulin genes (see Table 2
) were performed as controls during all reactions, and were used as internal standards to normalize the expression levels of the hyd1 and hyd2 genes in the various RNA samples. The relative intensity of the bands was determined after densitometric scanning using Adobe Photoshop. Primer sets used for the amplification of hyd1, hyd2, actin and β-tubulin are presented in Table 2
. In all experiments, controls containing no template or no enzyme were performed. Each PCR reaction was performed in duplicate with duplicate biological samples and duplicate cDNA preparations for each sample.
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Rodlet layer extracts were electrophoresed on SDS-PAGE and electroblotted onto Immobilon-P PVDF membranes. After transfer, the blot was stained with Coomassie Blue, an
10 kDa protein band was cut out, and the N-terminal sequence determined using an Applied Biosystems Procise Sequencer (Protein CORE Facility, University of Florida).
Phylogenetic analysis.
A phylogenetic analysis was performed using nearest-neighbour joining analysis of 56 hydrophobin sequences found in GenBank, along with the B. bassiana sequences using the CLUSTALW (EMBL-EBI, 1000 bootstrap trails, 500 random number generator) multiple sequence alignment program. The resultant tree was visualized using the online program Phylodendron phylogenetic tree printer (http://iubio.bio.indiana.edu/treeapp/treeprint-form.html).
| RESULTS |
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After five rounds of enrichment, inserts from 20 plaques of each library selected by biopanning were amplified by PCR and examined by agarose gel electrophoresis, revealing that >95 % of the plaques tested had inserts ranging in size from 0.4 to 1.5 kb. Using heat-denatured phage lysate from each cycle of the biopanning procedures, cDNA inserts were amplified by PCR, and enrichment of certain phages was observed, as judged by the increased band intensity through the rounds of selections (data not shown). Sixteen plaques from each library were randomly selected and their insert nucleotide sequences determined. Sequencing reads averaged
450 bp per read, and their translated amino acid sequences were analysed by BLAST searches of the National Center for Biotechnology Information (NCBI) database (http://www.ncbi.nlm.nih.gov/blast/). Sequences derived from enrichment using two of the five affinity resins, lactose–agarose and melibiose–agarose, corresponded to cDNAs encoding two different B. bassiana hydrophobins. Four cDNA clones contained almost identical sequence inserts, which were used to construct a full-length unambiguous cDNA sequence termed hyd1. Three additional phage-display-enriched cDNA sequences that shared no homology to hyd1 clustered to yield hyd2.
In order to obtain the positions of possible introns within the coding sequences of the B. bassiana genes, primer oligonucleotides covering the start and stop codons of each hydrophobin gene were used in PCR reactions performed on genomic DNA. A summary of the gene and deduced protein characteristics is listed in Table 1
. Based upon the genomic sequence, hyd1 contained two small (53 and 56 nt) introns, whereas hyd2 contained a single intron (64 nt). Putative promoters and polyadenylation signals were also detected in the isolated gene sequences. The ORFs corresponding to hyd1 and hyd2 coded for proteins of 136 and 116 aa, respectively, with both proteins containing putative export signal peptides. Southern blot analysis using the cloned genes as probes indicated that only one allele of each gene was present in the genome (data not shown).
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The relative expression level of the two genes was assessed in RNA pools derived from aerial conidia, blastospores, submerged conidia, growing mycelia, and from cells grown on insect cuticle, chitin (the main carbohydrate constituent of insect cuticles), and insect cuticle+chitin (Fig. 3
). The data presented were determined to be within the linear portion of the PCR analysis (25 cycles), with the actin concentration closely correlating to the amount of RNA quantified for each sample under test. Hydrophobin expression was normalized to the quantification of the actin band. B. bassiana hyd1 expression was detected in all developmental stages and media conditions tested. Hyd1 levels appeared to increase during mycelial growth, with the highest level of expression observed after 28 days of growth on agar plates, although caution should be taken in any interpretation of these results, as they derived from semi-quantitative measurements. On agar plates, cells began sporulating (i.e. producing aerial conidia) after
14 days; however, conidia were washed from the plates of all the mycelial samples before RNA isolation. This was confirmed by microscopic visualization of the mycelial samples, in which <1 % of contaminating aerial conidia were visible in the mycelial preparations. Thus, the observed hyd1 expression appears to be derived from the mycelia. Expression in aerial conidia was similar to that observed in either blastospores or submerged conidia, and was equivalent to that observed in 18 day mycelia. Cells growing in the presence of 1 % chitin, 1 % cuticle, and 1 % chitin+1 % cuticle also showed robust expression of hyd1, similar to levels seen in blastospores and submerged conidia, and 5–10 day mycelia. In contrast to hyd1, hyd2 appeared to be constitutively expressed and at about the same level as actin throughout the growing mycelia stages (3–28 days). Little or no hyd2 was observed in either blastospores or aerial conidia. Some hyd2 transcript was detected in submerged conidia, which corresponded to about 5–10 % of the levels seen in the mycelial samples. Intriguingly, hyd2 was expressed (at approximately the same levels as actin) in fungal cells growing on 1 % chitin or 1 % cuticle, but almost no transcript could be detected when the cells were grown on 1 % chitin+1 % cuticle.
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10 kda band resulted in the sequence (P/H)-GPSHGPXVKTGDI, where (P/H) represents poorly identified residues and X an unresolved residue. The amino acid fingerprints were consistent with the translated ORF of the hyd2 sequence cloned by phage display, and the N-terminal amino acid sequence matched the sequence of the putative mature Hyd2 sequence: (APH)GPSHGP(S)VKTGDI. These data indicate that the hyd2 gene product constitutes the rodlet layer hydrophobin that surrounds B. bassiana conidia. | DISCUSSION |
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Phage display technologies represent a method for isolating proteins and/or peptides that bind molecules of interest. (Danner & Belasco, 2001
; Mullen et al., 2006
; Paschke, 2006
; Rhyner et al., 2004
; Sergeeva et al., 2006
). Phage display has been used to isolate human galectin-3, a galactose/lactose-specific lectin and member of the S-type lectin family, using blood group glycoproteins during a biopanning selection (Yamamoto et al., 1999
). In this report, we demonstrate the feasibility of phage display to isolate cDNAs coding for hydrophobins. Initial attempts using hydrophobic substrata for biopanning were unsuccessful, due to non-specific adsorption of the phage. However, it may be possible to alter the conditions to minimize this background. Using various carbohydrate-derivatized beads, cDNAs encoding two hydrophobins were enriched from a B. bassiana phage display library constructed using mRNA isolated from fungal cells grown in vitro in the presence of insect cuticle. The interaction between the hydrophobins and the carbohydrate-derivatized beads appeared to be specific, since (1) not all carbohydrate-derivatized beads tested enriched for the B. bassiana hydrophobins, and (2) the elution step during each round of enrichment was competitive, using 0.2 M of the cognate carbohydrate. Further experiments, using the purified hydrophobin preparations, are however needed to conclusively demonstrate lectin-like activity for the isolated proteins.
The translated amino acid sequences of hyd1 and hyd2 did not match the 16 aa N-terminal sequence of a putative hydrophobin isolated from B. bassiana reported elsewhere, although the N terminus of mature hyd2 did show some homology (
50 %) to the reported protein (Bidochka et al., 1995b
). Similarly, although not an exact match, the N terminus of mature Hyd1 showed homology (
40 %) to the N terminus (as determined by amino acid sequencing) of what was termed an inner cell wall protein (cwp1) of B. bassiana (Bidochka et al., 1995a
). Although our results indicate that Hyd2 is a major constituent of the spore rodlet layer, additional experiments are needed to determine the cellular localization of Hyd1. Expression analysis indicated that hyd1 was highly expressed under almost all conditions. These results are consistent with our previous EST analyses of B. bassiana grown under different developmental conditions (Cho et al., 2006a
, b
). Notably, hyd1 transcript was abundant in all the single-cell spore types (aerial conidia, in vitro blastospores and submerged conidia), whereas hyd2 transcripts were essentially absent from these cells. Thus, even though the spore coat of aerial conidia is composed of the Hyd2 protein, no hyd2 transcript was detected in these cells. This is perhaps not too surprising, since it is the conidiogenic cells that need to make hyd2 and its protein product (in order to make the aerial conidia), and therefore one would not expect to see hyd2 transcript in the final product of this process, namely the aerial conidia themselves. Transcripts corresponding to hyd2 were also detected in cells grown in 1 % chitin or 1 % insect cuticle, but were not detected in cultures containing chitin+cuticle, each at 1 % concentration. This result was observed in two separate biological samples in which actin was used as a control. Altough it is unclear why hyd2 transcript was not detected under the latter growth conditions, it could be due to the relative nutrient levels in the cultures. Cells growing under 1 % chitin or 1 % cuticle conditions may be nutrient-limited, which would result in sporulation (i.e. conidiogenesis and hence hyd2 transcript production), whereas cultures containing both nutrient sources may grow in a vegetative state for a longer period of time. Further experiments delineating the expression of hyd1 and hyd2, especially during growth on insect hosts, i.e. during pathogenesis, as well as gene knockouts, are likely to give important insights into the role of these hydrophobins in fungal development and virulence.
Edited by: S. D. Harris
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Received 28 March 2007;
revised 14 May 2007;
accepted 30 May 2007.
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