Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea

<p>Abstract</p> <p>Background</p> <p>Hydrophobins are proteins containing eight conserved cysteine residues that occur uniquely in mycelial fungi. Their main function is to confer hydrophobicity to fungal surfaces in contact with air or during attachment of hyphae to hydrophobic surfaces of hosts, symbiotic partners or themselves resulting in morphogenetic signals. Based on their hydropathy patterns and solubility characteristics, hydrophobins are divided into two classes (I and II), the latter being found only in ascomycetes.</p> <p>Results</p> <p>We have investigated the mechanisms driving the evolution of the class II hydrophobins in nine species of the mycoparasitic ascomycetous genus <it>Trichoderma/Hypocrea</it>, using three draft sequenced genomes (<it>H. jecorina = T. reesei, H. atroviridis = T. atroviride; H. virens = T. virens</it>) an additional 14,000 ESTs from six other Trichoderma spp. (<it>T. asperellum, H. lixii = T. harzianum, T. aggressivum </it>var. <it>europeae, T. longibrachiatum</it>, <it>T</it>. cf. <it>viride</it>). The former three contained six, ten and nine members, respectively. Ten is the highest number found in any ascomycete so far. All the hydrophobins we examined had the conserved four beta-strands/one helix structure, which is stabilized by four disulfide bonds. In addition, a small number of these hydrophobins (HFBs)contained an extended N-terminus rich in either proline and aspartate, or glycine-asparagine. Phylogenetic analysis reveals a mosaic of terminal clades containing duplicated genes and shows only three reasonably supported clades. Calculation of the ratio of differences in synonymous vs. non-synonymous nucleotide substitutions provides evidence for strong purifying selection (<it>K</it>_<it>S</it>/<it>K</it>_{<it>a </it>}>> 1). A genome database search for class II HFBs from other ascomycetes retrieved a much smaller number of hydrophobins (2–4) from each species, and most were from Sordariomycetes. A combined phylogeny of these sequences with those of <it>Trichoderma </it>showed that the <it>Trichoderma </it>HFBs mostly formed their own clades, whereas those of other Sordariomycetes occurred in shared clades.</p> <p>Conclusion</p> <p>Our study shows that the genus <it>Trichoderma/Hypocrea </it>has a proliferated arsenal of class II hydrophobins which arose by birth-and-death evolution followed by purifying selection.</p

The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome

<p>Abstract</p> <p>Background</p> <p>The hypercellulolytic mutant <it>Hypocrea jecorina </it>(anamorph <it>Trichoderma reesei</it>) RUT C30 is the <it>H. jecorina </it>strain most frequently used for cellulase fermentations and has also often been employed for basic research on cellulase regulation. This strain has been reported to contain a truncated carbon catabolite repressor gene <it>cre1 </it>and is consequently carbon catabolite derepressed. To date this and an additional frame-shift mutation in the glycoprotein-processing β-glucosidase II encoding gene are the only known genetic differences in strain RUT C30.</p> <p>Results</p> <p>In the present paper we show that <it>H. jecorina </it>RUT C30 lacks an 85 kb genomic fragment, and consequently misses additional 29 genes comprising transcription factors, enzymes of the primary metabolism and transport proteins. This loss is already present in the ancestor of RUT C30 – NG 14 – and seems to have occurred in a palindromic AT-rich repeat (PATRR) typically inducing chromosomal translocations, and is not linked to the <it>cre1 </it>locus. The mutation of the <it>cre1 </it>locus has specifically occurred in RUT C30. Some of the genes that are lacking in RUT C30 could be correlated with pronounced alterations in its phenotype, such as poor growth on α-linked oligo- and polyglucosides (loss of maltose permease), or disturbance of osmotic homeostasis.</p> <p>Conclusion</p> <p>Our data place a general caveat on the use of <it>H. jecorina </it>RUT C30 for further basic research.</p

NJ analysis of amino acid sequences of class II hydrophobins from and other ascomycetes

<p><b>Copyright information:</b></p><p>Taken from "Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete "</p><p></p><p> 2008;8():4-4.</p><p>Published online 10 Jan 2008</p><p>PMCID:PMC2253510.</p><p></p> Conditions and design of figure are similar as for Fig. 3. Accession numbers and/or genome database entries for the non-sequences are provided in Table 2. The inset on the right bottom shows the topology of an unrooted Bayesian tree (the three clades being highlightened in grey)

Phylogenetic tree of the nucleotide sequences of class II hydrophobin genes by the split decomposition method

<p><b>Copyright information:</b></p><p>Taken from "Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete "</p><p></p><p> 2008;8():4-4.</p><p>Published online 10 Jan 2008</p><p>PMCID:PMC2253510.</p><p></p> The "HFB4" clade, whose branch shows the least reticulate network, is highlightened in grey

Amino acid alignment of the class II hydrophobins of used in this study

<p><b>Copyright information:</b></p><p>Taken from "Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete "</p><p></p><p> 2008;8():4-4.</p><p>Published online 10 Jan 2008</p><p>PMCID:PMC2253510.</p><p></p> The aa sequences were trimmed to show only the area from the first to the eight cysteine. Absolutely conserved aa's are within a black background, and functionally conserved aa's highlighted in grey. The symbols and letters over the alignment show the position of the four beta-strands (S1–S4) and the single helix (indicated by a horizontal cylinder). The sequence below the alignment proposes an updated consensus sequence for the class II HFBs, as derived from this study: therein, the cysteines are in red and numbered in order of their appearance in the sequence; X denotes any amino acid, and the subscript the number of them; "al" denotes any aliphatic, hydrophobic amino acid (A, V, L, I,

Only carbon sources where a difference to the parent strain QM6a was found are shown, and given in a color code

The ODrefers to measurements at 48 hrs of growth, at which time the value is proportional to the growth rate (OD/h) of the fungus on the respective carbon source. Carbon sources which are highlighted by a grey background are those which result in higher growth rates in RUT C30.<p><b>Copyright information:</b></p><p>Taken from "The hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome"</p><p>http://www.biomedcentral.com/1471-2164/9/327</p><p>BMC Genomics 2008;9():327-327.</p><p>Published online 11 Jul 2008</p><p>PMCID:PMC2483294.</p><p></p