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1 Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
2 Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
Correspondence
Nemat O. Keyhani
keyhani{at}ufl.edu
| ABSTRACT |
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The GenBank/EMBL/DDBJ accession numbers for the EST sequences reported in this paper are shown in the Supplementary Tables.
A figure and tables with further details about the EST data are available as supplementary data with the online version of this paper.
| INTRODUCTION |
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Aside from their use in biological control regimes, Beauveria sp. are the second most widely used whole-cell eukaryotic biocatalysts, and are responsible for a range of biological transformations and remediations that remain elusive via chemical and synthetic methods (Grogan & Holland, 2000
). Beauveria sp. produce an array of secondary metabolites, including oosporein, a red dibenzoquinone, which can oxidize proteins and amino acids (El Basyouni & Vining, 1966
; Kucera & Samsinakova, 1968
; Seger et al., 2005
). Oosporein displays antibiotic activity towards Gram-positive (but not Gram-negative) bacteria, and appears to cause avian gout in chickens and turkeys (Pegram et al., 1982
). Other important metabolites produced by Beauveria sp. include bassianin and tenellin, yellow pigments that affect membrane ATPases, various antimicrobial hexadepsipeptides known as beauvericins, as well as small molecular mass organic compounds, such as oxalic acid, that play important roles in pathogenesis (Isaka et al., 2005
; Jeffs & Khachatourians, 1997
; Kagamizono et al., 1995
; Kirkland et al., 2005
; Takahashi et al., 1998
).
Despite this interest, the molecular mechanisms of entomopathogenicity, endophyte establishment or rhizosphere competence, and B. bassiana-mediated biochemical transformations, are largely unknown. Few of the genes encoding proteins involved in any of these processes have been described, leaving a wealth of potential for the characterization of novel natural products derived from this organism. Analysis of expressed sequence tag (EST) transcripts expressed during discrete developmental and growth conditions represents an efficient means of characterizing the genome potential of an organism. Large numbers of genes can be rapidly examined in systems where little or no genetic information is available, and this information can be used to develop models regarding virulence factors and pathways important for the insectfungus association, as well as give insights into biochemical pathways that lead to the many interesting metabolites produced by B. bassiana. In the accompanying paper (Cho et al., 2006
), we analysed ESTs derived from homogeneous distinct single cell populations derived from B. bassiana, namely, aerial conidia, in vitro blastospores and submerged conidia. In an effort to maximize the diversity of transcripts isolated, two additional cDNA libraries were constructed from fungi sporulating on chitin, the major carbohydrate constituent of arthropod cuticles, and from cultures grown under conditions that lead to the production of oosporein. An overall comparative analysis between all five libraries is discussed.
| METHODS |
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Construction, characterization and sequencing of the cDNA libraries.
RNA isolation, construction of the cDNA libraries in the unidirectional pBluescript II XR system (Stratagene), and subsequent plasmid isolation and DNA sequencing were performed as previously described (Cho et al., 2006
). Approximately 2500 clones were picked at random from each library and subjected to single pass 5' end sequencing. The mean insert size of the cDNA libraries was 1.1 and 0.85 kb for the oosporein and chitin libraries, respectively, with an overall range of between 0.3 and 3.0 kb. After editing the mean length of the single read sequences ranged from 0.4 to 0.5 kb.
Sequence analysis.
EST sequence clustering, assembly and gene ontology (GO) mappings were performed as described previously (Cho et al., 2006
).
| RESULTS AND DISCUSSION |
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104 identified contigs with amino acid sequence similarity to previously characterized proteins deposited in the GenBank non-redundant and/or Swissprot databases (as of September 2005) and were used to extract gene annotation terms for grouping sequences into functional classifications. The complete search results and GenBank submission numbers for each EST are available as supplementary data with the online journal (Supplementary Table S1). Annotation and analyses were performed using all valid ESTs (in total 2030 and 2134 from the oosporein- and chitin-derived libraries, respectively) and on the best redundant ESTs from the contigs (1370 and 1346 from the oosporein- and chitin-derived libraries, respectively). Similarity matches (e value <104) to proteins in the GenBank/Swissprot databases were identified for 648 out of 1346 ESTs (48 %) and 566 out of 1370 ESTs (41 %) for the chitin and oosporein libraries, respectively. Approximately 7585 % of sequences displaying matches were mapped to GO categories. Most hits were detected among ascomycete sequences (7080 %), with only 2 % of the hits detected among the basidiomycete sequences. Approximately 10 % of the sequences were most similar to sequences from animals or prokaryotes, with a smaller set showing similarity to plant, archaeal or protist sequences.
ESTs derived from the unigene set with BLASTX e values <104 were parsed into one or more subcategories within the biological processes (containing 12 major subcategories), cellular components (containing 8 subcategories), and molecular functions (containing 12 subcategories) hierarchies of GO representations (Farmerie et al., 2005
; Harris et al., 2004
). The distribution of ESTs within each subcategory is presented for the oosporein (Fig. 2
) and the chitin (Fig. 3
) libraries. A table of these results is available as supplementary data with the online journal (Supplementary Table S2).
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Broad functional categorization of the ESTs isolated from the oosporein and chitin libraries revealed similar expression representation of catabolic pathways, carbohydrate metabolism and other metabolism categories, including protein, nucleic acid and amino acid catabolism, and biosynthesis. A twofold difference in the representation of phosphorus metabolism ESTs was noted in the oosporein as compared to the chitin library (see Supplementary Fig. S1 available with the online journal). The distribution of sequences within ribosomal and mitochondrial intracellular categories was similar between the two libraries, although some variation in cytoskeletal, nuclear and membrane subcategories could be seen. The oosporein library contained a slightly greater proportion of transferases (12 %, versus 9 % for the chitin library), with both libraries displaying very similar patterns of representation with respect to hydrolases, oxidoreductases, lyases, ligases and isomerases. Helicase transcripts were identified in the oosporein but not in the chitin library. Little variation was observed in the annotated sequences sorted by ligand-binding categories between the two libraries.
The top two most abundant ESTs found in both the oosporein and chitin libraries did not display any significant hits to any sequences currently in the databases (Table 2
, see Supplementary Table S3 available with the online journal, for the 25 most represented transcripts). Indeed, 13 of the top 25 most abundant ESTs found in the chitin library, representing approximately 10 % of the total transcripts sequenced, displayed no significant hits to sequences in the databases. In contrast, only 9 of the top 25, representing less than 5 % of the total dataset in the oosporein library, had no significant hits. Abundant ESTs shared between the two libraries included elongation factor 1-
, histone H3, an ATP synthase component, ADP/ATP translocase, transaldolase, a putative clock-controlled protein, a hydrophobin (see the accompanying paper, Cho et al., 2006
) and a number of ESTs with no significant hits in the searched databases (e.g. oosporein.033.c1 and chitin.032.c1).
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-glucoside (maltose) and lactose permeases (Chang & Dickson, 1988
The oosporein library also contained a range of hydrolases, including proteases, phosphatases, lipases and nucleases, but in contrast to the chitin library, no chitinases. A number of different ESTs were similar to a class of unique proteases relatively insensitive to specific inhibitors of ordinary acid or aspartic proteinases, such as pepstatin, and other compounds. In one instance, two different oosporein EST contigs were similar to the same protein, namely, the Aspergillus niger var. macrosporus endopeptidase or aspergillopepsin (Inoue et al., 1991
). One such contig (oosporein.167.C1, e value <10100) was represented moderately (seven times), whereas the other (oosporein.240.C1, e value=3.25x1039) comprised two sequences. Although the sequences of these two contigs could not be aligned into a single contig and have been scored as representing separate transcripts (and hence genes), they were approximately 80 % identical. A third EST was similar to the skin disease-causing dermatiaceous coelomycete Scytalidium dimidiatum (lignocolum) scytalidopepsin B, which also belongs to the pepstatin-insensitive acid protease family (Oda et al., 1998
). In addition, the oosporein collection contained an EST with similarity to an S. cerevisiae prenylmetalloprotease required for proper processing and secretion of yeast mating factors (Fujimura-Kamada et al., 1997
). Other hydrolases included ESTs similar to carboxypeptidase, two tripeptidyl peptidases (which could not be aligned into a single EST contig), acid phosphatase, endonuclease and cellobiase.
Although the production of toxic metabolites by B. bassiana is well known, to date, none of the genes that encode enzymes involved in the biosynthesis of these compounds has been reported. The synthesis of enniatins and cyclosporins, both N-methylated cyclohexadepsipeptides produced by Fusarium and Beauveria species (Kamyar et al., 2004
; Lawen, 1996
), are catalysed by large single polypeptide multifunctional enzymes that belong to the class of nonribosomal peptide synthases (Glinski et al., 2002
; Haese et al., 1993
; Herrmann et al., 1996
). We have identified ESTs in both the oosporein and chitin libraries similar to the Fusarium enniatin synthetase (oosporein_10-H08.e, e value=7.6x107, chitin_8-D06.e, e value=4x1042). These two ESTs did not contain any overlapping sequences (and hence did not cluster into a contig) but in this case due to the length of the ennitain gene (
10 kb) they could represent different regions of the same transcript.
In addition to the production of toxic metabolites, entomopathogenic fungi are able to persist within the insect haemolymph as freely circulating hyphal bodies where they interface with the host innate immune responses (Pendland et al., 1993
). These reactions rely upon recognition and targeting of foreign cells, and successful pathogens have developed a range of mechanisms for masking their presence, mostly involving alterations in cell wall composition. This can involve modifications of cell-surface carbohydrates and/or proteins (Brown & Gordon, 2005
; Gillespie et al., 2000
; Pendland & Boucias, 1998
). Mucins form a protective coat surrounding many epithelial cells, and are very hydrophilic glycoproteins that provide a scaffold for the attachment of oligosaccharides (Gum et al., 1994
). Interestingly, the oosporein library contained an EST (oosporein_24-C12.e, e value=4.4x107) similar to human mucin 2 (Gum et al., 1994
).
The cDNA library derived from chitin-grown cells contained a number of unique ESTs, including three chitinases: two similar to the Coccidioides immitis complement-fixation antigen endochitinase (Zimmermann et al., 1996
) (again these sequences could not be aligned into a single contig, but may still represent transcripts of the same gene), and another similar to C. albicans chitinase 3 (McCreath et al., 1995
). A number of other glycosidases were found including a melibiase, and two ESTs similar to 1,3-
-glucanases most likely involved in cell wall remodelling.
Comparative analysis between the aerial conidia, in vitro blastospore, submerged conidia, oosporein and chitin libraries
Subtilisin proteases and other pathogenicity factors.
Characterization of EST libraries from aerial conidia, in vitro blastospores and submerged conidia are presented in the accompanying paper (Cho et al., 2006
). Along with the EST libraries presented in this report, approximately 4360 different transcripts were identified between the five libraries. Subtilisins represent an important class of pathogenicity factors extensively studied within the context of fungal-mediated insect pathogenesis (Bagga et al., 2004
). In this regard, one of the best-studied model systems is the entomopathogenic fungus Metarhizium anisopliae (Bagga et al., 2004
; Freimoser et al., 2003a
, 2005
; Wang & St Leger, 2005
; Wang et al., 2005
). Indeed, in M. anisopliae overexpression of a subtilisin has been demonstrated to lead to enhanced virulence (St Leger et al., 1996
); therefore, a comparative analysis between the B. bassiana and M. anisopliae subtilisins was performed (Table 3
). Depending upon the strain, M. anisopliae can produce up to 11 different subtilisins, many of which are upregulated during growth on insect cuticle. These enzymes have been grouped into four groups: class I (bacterial) subtilisin (Pr1C), and three groups of proteinase K-like class II subtilisins, extracellular subfamily 1 (Pr1A, Pr1B, Pr1G, Pr1I and Pr1K), extracellular subfamily 2 (Pr1D, Pr1E, Pr1F and Pr1J) and an endocellular subtilisin (Pr1H) (Bagga et al., 2004
). Our B. bassiana EST collection contained eight different subtilisins displaying various levels of similarity to the M. anisopliae enzymes (Table 3
). The aerial conidia library contained seven of these enzymes, four of which were not found in the other EST sets (conidia_11-D01.e, conidia_22-C04.e, conidia_08-G10.e and conidia_12-H11.e, see Table 3
). The chitin-grown library also contained an enzyme not found in any of the other libraries (chitin_8-G09.e). It should be noted that these sequences represent only a part of the gene; therefore, any conclusions should be taken with some caution. Two of the B. bassiana subtilisins (each represented by two contigs, conidia_22-B05.e/oosporein_9-D06.e and conidia.60.C1/chitin_24-D01.e) were most similar to the class II extracellular subfamily 1 enzymes (Pr1A/B/G/I/K) of M. anisopliae [note that it was overexpression of Pr1A that led to enhanced virulence in M. anisopliae (St Leger et al., 1996
)]. A distinct B. bassiana class I subtilisin was also noted, and the other three enzymes appeared to represent class II endocellular proteins.
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Shared and unique sequences.
An overall analysis of unique and shared sequences between all five libraries was performed and is presented in a non-simple Venn diagram (Fig. 4
). A table containing (1) the number of times each sequence was found in each library and (2) the identities of the sequences belonging to each set delineated in Fig. 4
is available as supplementary data with the online journal (Supplementary Table S6). In the figure, the dataset derived from each library is bound by a colour coded line. The outermost ring represents those sequences unique to each library, the second ring sequences uniquely shared between two libraries, the third ring sequences unique to any given three libraries, the fourth ring sequences unique to any four libraries, and the innermost ring ESTs found in all five libraries. To find the full complement of shared sequences several levels need to added, e.g. the unique set of shared sequences between aerial conidia and the oosporein library (ac+o) is 66 ESTs; however, the total shared sequences would include (ac+o=66)+(ac+o+ch=25)+(b+ac+o=19)+(sc+ac+o=24)+(ac+ch+sc+o=25)+(b+ac+o+ch=17)+(sc+ac+o+b=26)+(ac+b+sc+ch+o=60)=66+25+19+24+25+17+26+60=262 ESTs. An interesting insight gained from the Venn diagram analysis was the high degree of unique sequences present in each library. These results indicate the robust nature of the cDNA libraries and suggest that production of cDNA libraries from distinct developmental conditions can maximize gene diversity in EST data collection. No distinct patterns of gene expression could be surmised from the sorted gene datasets, although the small number of transcripts (<2 %) shared by all libraries suggest that further sequencing of the libraries is likely to yield additional new transcripts (until this number grows large enough to be considered saturated).
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| ACKNOWLEDGEMENTS |
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Received 13 January 2006;
revised 22 May 2006;
accepted 24 May 2006.
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