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

Abstract

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.

A Native Threonine Coordinates Ordered Water to Tune Light-Oxygen-Voltage (LOV) Domain Photocycle Kinetics and Osmotic Stress Signaling in Trichoderma reesei ENVOY

“…Casein kinases are well known to be involved in light response and circadian rhythms (37) in N. crassa. In Trichoderma spp., the group of CKII kinases shows an expansion compared with N. crassa (38). N. crassa PRD-3 was found to be sensitive to sodium chloride, which suggests relevance for dealing with osmotic stress.…”

A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi

“…Much of what we know about histone modification enzymes, RNA interference and cell cycle control was first addressed in S. cerevisiae and S. pombe [4, 5]. Thus fungi have been at the cutting edge of this emerging discipline and there are many recent reviews available to dive into the details of yeast chromatin and epigenetics [4–13], or chromatin of other, mostly filamentous, fungi [14–26]. One important purpose of this contribution is to suggest where additional data are necessary to better define the structure and function of chromatin and chromosomes in the fungi.…”

Histone Deacetylase HDA-2 Regulates Trichoderma atroviride Growth, Conidiation, Blue Light Perception, and Oxidative Stress Responses

“…In fungi, transcription of genes encoding pathogenicity factors, stress response, and secondary metabolism have been related to histone acetylation and deacetylation (24)(25)(26)(27). T. atroviride contains the classical HDAC classes I, II, and III (28). A connection between light responses and histone acetylation in filamentous fungi has been demonstrated in N. crassa, in which both WC-1 and NGF-1 (orthologous to Gcn5p) physically interact to promote light-induced acetylation of residue K14 of histone H3 associated with the promoter of the al-3 gene (29,30).…”