Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

Clutterbuck, A. J.

doi:10.1016/j.fgb.2010.09.002

Cited by 119 publications

(146 citation statements)

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“…Like the other fungi examined, the 7 two thermophiles harbor large numbers (>210) of glycoside hydrolases and polysaccharide 8 lyases covering most of the recognized families, albeit with important differences Tables 5, 6). For instance T. terrestris is poor 10 in pectin and pectate lyases (no PL1, PL3, PL9 and PL11) and relatively rich in 11 polygalacturonases (seven GH28).…”

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“…Only a subset of genes encoding a given enzyme 6 activity is upregulated. Moreover, the same subset of genes is upregulated in different growth 7 conditions. For example, the orthologs in Clades A, B, E, G and P of GH61 are upregulated 8 under growth in complex substrates for both thermophiles (Fig.…”

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confidence: 99%

“…Genome analyses and 2 experimental data suggest that both thermophiles are capable of hydrolyzing all major 3 polysaccharides found in biomass. Examination of transcriptome data and secreted 4 proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose 5 and xylan but distinct mechanisms in pectin degradation s. Characterization of the 6 biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are 7 highly efficient in biomass decomposition at both moderate and high temperatures. 8 Furthermore, we present evidence suggesting that aside from representing a potential 9 reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using 10 classical and molecular genetics.…”

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“…In addition, extensive translocation is observed between Ch1/Ch6 of M. 17 thermophila and Ch2/Ch5 of T. terrestris. The protein coding fractions of the genomes include 18 9,110 genes in M. thermophila and 9,813 genes in T. terrestris ( Table 1); both are smaller than 19 average proteomes of other fungi in the class Sordariomycetes, and substantially smaller than the 20 closely related mesophile Chaetomium globosum 7 , which has 11,124 predicted genes in a 34. [9][10][11][12][13][14][15][16][17][18][19][20][21] Mbp genome.…”

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“…In this context, we evaluated genes involved in mating 6 and the potential for outcrossing, particularly in M. thermophila. 7 Nearly all thermophilic Chaetomiaceae are either homothallic (self-fertile), as is the case 8 for C. globosum and T. terrestris, or have been observed only in the asexual state, as is the case 9 for M. thermophila. We examined these genomes for homologs of the mating-type genes of 10 Neurospora crassa.…”

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Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

et al. 2011

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Thermostable enzymes and thermophilic cell factories may afford economic advantages inFurthermore, we present evidence suggesting that aside from representing a potential 9 reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using 10 classical and molecular genetics. 11Rapid, efficient and robust enzymatic degradation of biomass-derived polysaccharides is 12 currently a major challenge for biofuel production. A prerequisite is the availability of enzymes 13 that hydrolyze cellulose, hemicellulose and other polysaccharides into fermentable sugars at 14 conditions suitable for industrial use. The best studied and most widely used cellulases and to overcome these obstacles is to raise the reaction temperature, thereby increasing hydrolytic 20 rates and reducing contamination risks. AT-rich repetitive regions (Fig. 1) To examine the strategy used by these thermophiles for decomposition of plant cell wall 9 polysaccharides, we used RNA-Seq to compare transcript profiles during growth on barley straw 10 or alfalfa straw to growth on glucose. Alfalfa was chosen to represent dicotyledonous plants, 11 whereas barley was used to represent monocotyledon plants. The major difference between these 12 materials is that the carbohydrates from barley cell wall are mainly cellulose and hemicellulose 13 with a negligible amount of pectin 11 , whereas alfalfa cell wall contains pectin and xylan in 14 roughly similar proportions, each consisting of 15-20% of total carbohydrates 12, . 15 We observed notable differences between the transcriptional profiles of genes encoding conditions. For example, the orthologs in Clades A, B, E, G and P of GH61 are upregulated 8 under growth in complex substrates for both thermophiles (Fig. 2b). An even more striking 9 correlation between transcript levels and orthologs is evident for the GH6 and GH7 cellulases 10 ( Supplementary Fig. 7) where the transcript profiles for the orthologs of the two organisms are Table 7). Thermophilic fungi are major components of the microflora in self-heating composts. They 9 break down cellulose at a faster rate than prodigious, mesophilic cellulase producers such as T. Tables 11-14). On the basis of 24 our comparative analyses of the genomes from two thermophilic fungi, we conclude that their 25 nucleotide and protein features are different from those observed in thermophilic prokaryotes. 26 We also investigated the possibility that thermophilic fungi possess major differences in 27 processes mediating thermophily including heat shock, oxidative stress, membrane biosynthesis, 28 chromatin structure and modification, and fungal cell wall metabolism. We compared the 29 proteins predicted to be involved in these processes in C. globosum, M. thermophila and T. 30 terrestris, but were unable to find differences that can convincingly be interpreted as the Fig. 9). Within the Sordiariales, thermophily 6 is restricted to subgroups of the family Chaetomiaceae. Among fungi more broadly, thermophily 7 also exists in the Zygomycota, but it ...

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confidence: 99%

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confidence: 99%

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confidence: 99%