Abstract:SummaryThe RNAi machinery is generally involved in genome protection in filamentous fungi; however, the physiological role of RNAi has been poorly studied in fungal models. Here, we report that in the filamentous fungus Trichoderma atroviride, the products of the dcr2 and rdr3 genes control reproductive development, because mutations in these genes affect conidiation. In addition, Dcr1 together with Dcr2 control vegetative growth since Δdcr1, Δdcr2 and Δdcr1Δdcr2 present morphological alterations. Whole-genome… Show more
“…In T. reesei, however, lack of the cp2 homolog causes no discernible phenotype (1034). The cp2 gene is regulated by light in A. nidulans and T. atroviride (50,1035), and so it may be a good candidate in future studies of developmental processes in fungi.…”
“…Sequencing of sRNAs from many species of fungi has led to the discovery of many classes of them, e.g., siRNAs in Schizosaccharomyces pombe, Saccharomyces castellii, Candida albicans, Cryptococcus neoformans, and Magnaporthe oryzae; qiRNAs (QDE-2-interacting RNAs) in N. crassa; priRNAs (primal small RNAs) in S. pombe; ex-siRNAs (exonic-siRNAs) in Mucor circinelloides and T. atroviride; disiRNAs (Dicer-independent small interfering RNAs) in N. crassa, and milRNAs (miRNAslike small RNAs) in N. crassa, Sclerotinia sclerotiorum, Metharizium anisopliae, C. neoformans, and T. reesei. The functional role of some of these classes of sRNAs has been proven, but for many others it still remains to be shown (50,(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67). For T. atroviride, however, a functional characterization of the components of the RNAi machinery is already available.…”
“…The functions of these proteins are unknown, so we cannot infer the role of Trichoderma RDR3 in any mechanism of gene silencing for protecting genome integrity. However, in T. atroviride, RDR3 is involved in asexual development (50), suggesting its role in regulation of gene expression (see Fig. S3 in the supplemental material).…”
“…For T. atroviride, however, a functional characterization of the components of the RNAi machinery is already available. This mechanism was shown to control growth and asexual development (50), opening the possibility of the participation of the RNAi machinery of Trichoderma in both posttranscriptional and transcriptional gene regulation.…”
SUMMARYThe genusTrichodermacontains 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 inT. reesei,T. atroviride, andT. 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 eachTrichodermaspecies 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 inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.
“…In T. reesei, however, lack of the cp2 homolog causes no discernible phenotype (1034). The cp2 gene is regulated by light in A. nidulans and T. atroviride (50,1035), and so it may be a good candidate in future studies of developmental processes in fungi.…”
“…Sequencing of sRNAs from many species of fungi has led to the discovery of many classes of them, e.g., siRNAs in Schizosaccharomyces pombe, Saccharomyces castellii, Candida albicans, Cryptococcus neoformans, and Magnaporthe oryzae; qiRNAs (QDE-2-interacting RNAs) in N. crassa; priRNAs (primal small RNAs) in S. pombe; ex-siRNAs (exonic-siRNAs) in Mucor circinelloides and T. atroviride; disiRNAs (Dicer-independent small interfering RNAs) in N. crassa, and milRNAs (miRNAslike small RNAs) in N. crassa, Sclerotinia sclerotiorum, Metharizium anisopliae, C. neoformans, and T. reesei. The functional role of some of these classes of sRNAs has been proven, but for many others it still remains to be shown (50,(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67). For T. atroviride, however, a functional characterization of the components of the RNAi machinery is already available.…”
“…The functions of these proteins are unknown, so we cannot infer the role of Trichoderma RDR3 in any mechanism of gene silencing for protecting genome integrity. However, in T. atroviride, RDR3 is involved in asexual development (50), suggesting its role in regulation of gene expression (see Fig. S3 in the supplemental material).…”
“…For T. atroviride, however, a functional characterization of the components of the RNAi machinery is already available. This mechanism was shown to control growth and asexual development (50), opening the possibility of the participation of the RNAi machinery of Trichoderma in both posttranscriptional and transcriptional gene regulation.…”
SUMMARYThe genusTrichodermacontains 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 inT. reesei,T. atroviride, andT. 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 eachTrichodermaspecies 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 inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.
“…In M. circinelloides, Ago-1 was involved in the response to environmental signals in vegetative development (Cervantes et al 2013). Two Dcr genes are involved in vegetative growth, and the dcr2 and rdr3 genes control reproductive development in Trichoderma atroviride (Carreras-Villaseñor et al 2013). These data indicated that the Qip gene, together with other RNA-silencing genes, regulates the process of normal hyphal growth and development.10.1080/21501203.2015.1027313-F0004Figure 4.Phenotypic comparison between wild-type Fusarium oxysporum strain A8 and its Δ Qip mutant; (a), (c), (e), (g) wild-type Fusarium oxysporum strain A8; (b), (d), (f), (h) Δ Qip mutant; (a), (b) colonial morphology of the wild-type A8 and Δ Qip mutant; (c), (d) colonial margin of the wild-type A8 and Δ Qip mutant; (e), (f) mycelial morphology of the wild-type A8 and Δ Qip mutant; (g), (h) conidial morphology of the wild-type A8 and Δ Qip mutant.…”
Ribonucleic acid (RNA)-silencing mechanisms exist in many eukaryotes to regulate a variety of biological processes. The known molecular components are related to Dicers, Argonautes and RNA-dependent RNA polymerases. Previous biochemical studies have also suggested that Qip, with an exonuclease domain, facilitates the conversion of duplex small interfering RNAs into single strands. In our study, the Qip gene in Fusarium oxysporum was disrupted using homologous recombination technology. The deletion of the Qip gene resulted in a decrease in colony growth rates but increased the number of branches. Additionally, the ΔQip mutant had a reduced pathogenicity in cabbage. Our results show Qip gene in F. oxysporum is required for normal hyphae morphology and virulence. The mutant will be useful for elucidating the relationship between the RNA-silencing mechanism and hyphal growth and development in F. oxysporum.
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