Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction

BACKGROUND

The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype.

RESULTS

Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions.

CONCLUSION

We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

Sm2, a paralog of the Trichoderma cerato-platanin elicitor Sm1, is also highly important for plant protection conferred by the fungal-root interaction of Trichoderma with maize

Background

The proteins Sm1 and Sm2 from the biocontrol fungus Trichoderma virens belong to the cerato-platanin protein family. Members of this family are small, secreted proteins that are abundantly produced by filamentous fungi with all types of life-styles. Some species of the fungal genus Trichoderma are considered as biocontrol fungi because they are mycoparasites and are also able to directly interact with plants, thereby stimulating plant defense responses. It was previously shown that the cerato-platanin protein Sm1 from T. virens - and to a lesser extent its homologue Epl1 from Trichoderma atroviride - induce plant defense responses. The plant protection potential of other members of the cerato-platanin protein family in Trichoderma, however, has not yet been investigated.

Results

In order to analyze the function of the cerato-platanin protein Sm2, sm1 and sm2 knockout strains were generated and characterized. The effect of the lack of Sm1 and Sm2 in T. virens on inducing systemic resistance in maize seedlings, challenged with the plant pathogen Cochliobolus heterostrophus, was tested. These plant experiments were also performed with T. atroviride epl1 and epl2 knockout strains. In our plant-pathogen system T. virens was a more effective plant protectant than T. atroviride and the results with both Trichoderma species showed concordantly that the level of plant protection was more strongly reduced in plants treated with the sm2/epl2 knockout strains than with sm1/epl1 knockout strains.

Conclusions

Although the cerato-platanin genes sm1/epl1 are more abundantly expressed than sm2/epl2 during fungal growth, Sm2/Epl2 are, interestingly, more important than Sm1/Epl1 for the promotion of plant protection conferred by Trichoderma in the maize-C. heterostrophus pathosystem.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0333-0) contains supplementary material, which is available to authorized users.

Spore germination of Trichoderma atroviride is inhibited by its LysM protein TAL6

LysM motifs are carbohydrate-binding modules found in prokaryotes and eukaryotes. They have general N-acetylglucosamine binding properties and therefore bind to chitin and related carbohydrates. In plants, plasma-membrane-bound proteins containing LysM motifs are involved in plant defence responses, but also in symbiotic interactions between plants and microorganisms. Filamentous fungi secrete LysM proteins that contain several LysM motifs but no enzymatic modules. In plant pathogenic fungi, for LysM proteins roles in dampening of plant defence responses and protection from plant chitinases were shown. In this study, the carbohydrate-binding specificities and biological function of the LysM protein TAL6 from the plant-beneficial fungus Trichoderma atroviride were investigated. TAL6 contains seven LysM motifs and the sequences of its LysM motifs are very different from other fungal LysM proteins investigated so far. The results showed that TAL6 bound to some forms of polymeric chitin, but not to chito-oligosaccharides. Further, no binding to fungal cell wall preparations was detected. Despite these rather weak carbohydrate-binding properties, a strong inhibitory effect of TAL6 on spore germination was found. TAL6 was shown to specifically inhibit germination of Trichoderma spp., but interestingly not of other fungi. Thus, this protein is involved in self-signalling processes during fungal growth rather than fungal-plant interactions. These data expand the functional repertoire of fungal LysM proteins beyond effectors in plant defence responses and show that fungal LysM proteins are also involved in the self-regulation of fungal growth and development.

Self-assembly at air/water interfaces and carbohydrate binding properties of the small secreted protein EPL1 from the fungus Trichoderma atroviride

The protein EPL1 from the fungus Trichoderma atroviride belongs to the cerato-platanin protein family. These proteins occur only in filamentous fungi and are associated with the induction of defense responses in plants and allergic reactions in humans. However, fungi with other lifestyles also express cerato-platanin proteins, and the primary function of this protein family has not yet been elucidated. In this study, we investigated the biochemical properties of the cerato-platanin protein EPL1 from T. atroviride. Our results showed that EPL1 readily self-assembles at air/water interfaces and forms protein layers that can be redissolved in water. These properties are reminiscent of hydrophobins, which are amphiphilic fungal proteins that accumulate at interfaces. Atomic force microscopy imaging showed that EPL1 assembles into irregular meshwork-like substructures. Furthermore, surface activity measurements with EPL1 revealed that, in contrast to hydrophobins, EPL1 increases the polarity of aqueous solutions and surfaces. In addition, EPL1 was found to bind to various forms of polymeric chitin. The T. atroviride genome contains three epl genes. epl1 was predominantly expressed during hyphal growth, whereas epl2 was mainly expressed during spore formation, suggesting that the respective proteins are involved in different biological processes. For epl3, no gene expression was detected under most growth conditions. Single and double gene knock-out strains of epl1 and epl2 did not reveal a detectable phenotype, showing that these proteins are not essential for fungal growth and development despite their abundant expression.

Stappia taiwanensis sp. nov., isolated from a coastal thermal spring

A beige-coloured, Gram-stain-negative, aerobic, non-motile moderately thermotolerant, rod-shaped organism, strain CC-SPIO-10-1(T), was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on Marine Agar 2216. Based on 16S rRNA gene sequence analysis, this organism was grouped into the genus Stappia, showing 98.3 % sequence similarity to Stappia indica B106(T) and 98.2 % gene sequence similarity to Stappia stellulata IAM 12621(T). Ubiquinone Q-10 was the major respiratory quinone and C18 : 1ω7c and C18 : 1ω7c 11-methyl were detected as the major fatty acids. The hydroxylated fatty acid C18 : 0 3-OH was detected as well. Predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid AL1 and unidentified phospholipid PL1. Minor amounts of several unidentified lipids (PL2 and L1-L7) were present as well. The polyamine pattern contained the major compounds spermidine and spermine. Strain CC-SPIO-10-1(T) could be differentiated from the type strains of S. stellulata and S. indica by a set of biochemical tests. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain CC-SPIO-10(T) represents a novel species of the genus Stappia for which the name Stappia taiwanensis sp. nov. is proposed. The type strain is CC-SPIO-10 (T) ( = CCUG 59208(T) = LMG 25538 (T) = CCM 7757(T)).

Corynebacterium epidermidicanis sp. nov., isolated from skin of a dog

A Gram-stain-positive, pleomorphic, oxidase-negative, non-motile isolate from the skin of a dog, designated strain 410(T), was subjected to comprehensive taxonomic characterization. Comparison of the 16S rRNA gene sequences revealed that the novel isolate showed highest similarities to the type strains of Corynebacterium humireducens, Corynebacterium diphtheriae, Corynebacterium pseudotuberculosis and Corynebacterium ulcerans (96.1-96.8 %). The quinone system consisted predominantly of MK-8(H(2)) and MK-9(H(2)). The polar lipid profile of strain 410(T) contained the major compounds diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids and four unidentified glycolipids. The polyamine pattern was composed of the major amines spermidine and spermine. In the fatty acid profile, predominantly straight-chain, saturated and mono-unsaturated fatty acids were detected (C(18 : 1)ω9c, C(16 : 1)ω7c, C(16 : 0)). These chemotaxonomic traits are in agreement with those reported for representatives of the genus Corynebacterium. Strain 410(T) tested negative for diphtheria toxin. Physiological properties as well as unique traits in the polar lipid profile could be used to distinguish strain 410(T) from the most closely related species. These data suggest that strain 410(T) represents a novel species of the genus Corynebacterium, for which we propose the name Corynebacterium epidermidicanis sp. nov. The type strain is 410(T) (= DSM 45586(T) = LMG 26322(T) = CCUG 60915(T)).

Gordonia humi sp. nov., isolated from soil

A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301T) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301T was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6 % similarity), Gordonia terrae (97.5 %), Gordonia amarae (97.5 %) and Gordonia malaquae (97.4 %). The quinone system was determined to consist predominantly of menaquinone MK-9(H2), minor amounts of MK-8(H2) and MK-7(H2). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis9, C16 : 0, C18 : 1 and tuberculostearic acid (10-methyl C18 : 0), supported the affiliation of strain CC-12301T to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301T from the most closely related Gordonia species. Strain CC-12301T therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301T (=DSM 45298T =CCM 7727T).

Fontibacter flavus gen. nov., sp. nov., a member of the family ‘Cyclobacteriaceae’, isolated from a hot spring

The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130T, isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25–40 °C and in the presence of 1–3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130T, B. baltica and Aquiflexum balticum were similar, with iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130T (=CCUG 57694T=CCM 7650T) as the type strain of the type species.

Jeotgalicoccus coquinae sp. nov. and Jeotgalicoccus aerolatus sp. nov., isolated from poultry houses

Two Gram-stain-positive, non-motile, non-spore-forming cocci (strains MK-7(T) and MPA-33(T)) were isolated from poultry houses. Strain MK-7(T) was isolated on marine broth agar from coquina, a food supplement for female ducks used in a duck-fattening farm. Strain MPA-33(T) was isolated from the air of a turkey house on TSA after filter sampling. On the basis of 16S rRNA gene sequence similarity studies, both strains were shown to belong to the genus Jeotgalicoccus; MK-7(T) was most closely related to Jeotgalicoccus psychrophilus YKJ-115(T) (99.3 % similarity) and MPA-33(T) was most closely related to Jeotgalicoccus halotolerans YKJ-101(T) (98.8 %). The quinone system of MK-7(T) was composed of equal amounts of menaquinones MK-7 and MK-6 and that of MPA-33(T) contained 76 % MK-7 and 24 % MK-6. The polar lipid profile of strain MK-7(T) consisted of the major compounds diphosphatidylglycerol and phosphatidylglycerol and six unidentified lipids present in minor to moderate amounts. In strain MPA-33(T), diphosphatidylglycerol was the single predominant lipid, whereas phosphatidylglycerol was detected in moderate amounts. In addition, one unidentified phospholipid and four unidentified lipids were detected. Fatty acid profiles with iso-15 : 0 and anteiso-15 : 0 as major fatty acids supported the affiliation of the strains to the genus Jeotgalicoccus. The results of physiological and biochemical tests as well as DNA-DNA hybridizations allowed clear phenotypic differentiation of strains MK-7(T) and MPA-33(T) from the most closely related species. Strains MK-7(T) and MPA-33(T) therefore represent novel species, for which the names Jeotgalicoccus coquinae sp. nov. (type strain MK-7(T) =DSM 22419(T) =CCM 7682(T) =CCUG 57956(T)) and Jeotgalicoccus aerolatus sp. nov. (type strain MPA-33(T) =DSM 22420(T) =CCM 7679(T) =CCUG 57953(T)) are proposed.