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Table 2 List of FPase activities produced by T. reesei RUT-C30 mutants for genes affected by SNPs and indels in T. reesei SS-II

From: Enhancement of cellulase production in Trichoderma reesei RUT-C30 by comparative genomic screening

No. Trire2: protein ID Mutation (element: amino acid change) Annotation/function FPase activity (U/mL) of KO strainsa Increased vs RUT-C30 (%)b t-testc
1 108642 A → G (exon: synonymous variant) Unknown protein 3.05 ± 0.16 + 83.7% ***
2 56839 T → A (promoter) Zinc-dependent alcohol dehydrogenase 2.82 ± 0.14 + 70.1 ***
3 108784 − 1: A (intron) Alcohol dehydrogenase GroES 2.55 ± 0.13 + 53.4 ***
4 66256 T → C (terminator) NAD(P)-binding protein 2.45 ± .15 + 47.3 **
5 74622 − 16: GATGACGA TGATTTTC (terminator) P-loop containing nucleoside triphosphate hydrolase protein 1.95 ± 0.078 + 17.3 *
6 108914 T → C (exon: Cys193 → Arg) Methyltransferase type 11 1.88 ± 0.11 + 13.3
7 109925 A → G (promoter) Unknown protein 1.81 ± 0.11 + 9.1
8 67504 A → T (terminator) Conidiospore surface protein 1.80 ± 0.14 + 8.8
9 123441 A → T (promoter) Unknown protein 1.78 ± 0.11 + 7.3
10 45598 T → C (terminator) Unknown protein 1.75 ± 0.15 + 5.3
11 23171 T → A (exon: Phe14759 → Leu) AMP-dependent synthetase and ligase 1.75 ± 0.09 + 5.2
12 63558 − 1: A (terminator) PLC-like phosphodiesterase 1.70 ± 0.13 + 2.5
13 75568 A → T (terminator) Thioredoxin 1.70 ± 0.12 + 2.3
14 55105 − 12: ACAATGACATG (promoter) Amylolytic gene expression activator 1.68 ± 0.12 + 1.3
15 109305 G → A (promoter) Unknown protein 1.64 ± 0.098 − 1.2
16 109304 G → A (promoter) Unknown protein 1.62 ± 0.11 − 2.2
17 104898 A → T (exon: Asp227 → Val); A → T (exon: Gln229 → Leu); G → T (exon: Gly230 → Val)
A → T (exon: Gln233 → Leu)
Unknown protein 1.62 ± 0.12 − 2.3
18 67806 A → T (exon: Ile120 → Asn) Amino acid transporter 1.61 ± 0.086 − 2.8
19 120806 − 1: C (intron); − 2: AG (terminator); − 1: T (terminator) Pkinase-domain-containing protein 1.60 ± 0.095 − 3.5
20 120044 T → G (promoter) GDP dissociation inhibitor 1.59 ± 0.10 − 4.3
21 56934 T → G (promoter) Carbohydrate kinase 1.58 ± 0.095 − 4.6
22 43161 C → G (terminator) Unknown protein 1.58 ± 0.094 − 4.8
23 62053 + 1: T (promoter) YVTN repeat-like/Quino protein amine dehydrogenase 1.58 ± 0.11 − 5.2
24 110688 − 1: G (intron) Unknown protein 1.56 ± 0.13 − 5.8
25 76453 A → G (exon: Met867 → Thr) ABC transporter 1.54 ± 0.096 − 7.3
26 70973 − 3: TAC (terminator) Acyl-CoA N-acyltransferase 1.52 ± 0.075 − 8.3
27 66888 − 6: GCAGCA (terminator) Glycosyltransferase 1.51 ± 0.078 − 8.7
28 107297 T → C (promoter) Unknown protein 1.50 ± 0.088 − 9.2
29 107743 T → G (promoter) Unknown protein 1.48 ± 0.096 − 11.0
30 70859 A → G (terminator) Amidase signature enzyme 1.44 ± 0.098 − 13.1
31 75012 G → C (promoter) Root hair defective 3 GTP-binding protein 1.43 ± 0.094 − 13.8
32 63464 − 1: A (intron) Unknown protein 1.34 ± 0.067 − 19.5 **
33 59381 C → T (promoter) Class I S-adenosyl-l-methionine-dependent methyltransferase 1.28 ± 0.055 − 22.6 **
34 73678 A → C (promoter) Calnexin 1.20 ± 0.071 − 27.7 **
35 120661 T → C (intron) Adaptor protein complex AP-1 small subunit 1.17 ± 0.058 − 29.3 **
36 122630 G → A (exon: Ser140 → Asn) Unknown protein 1.16 ± 0.065 − 30.1 **
37 112034 A → G (exon: Phe122 → Ser) MFS general substrate transporter 1.15 ± 0.058 − 30.8 ***
38 53811 G → A (exon: Ser73 → Leu) Clathrin adaptor complex 1.15 ± 0.047 − 31.0 ***
39 76505 A → T (promoter) Stress response element binding protein 0.94 ± 0.045 − 43.6 ***
40 121915 T → A (intron) Translationally controlled tumor protein 0.92 ± 0.054 − 44.3 ***
41 60887 C → G (exon: His438 → Asp) Unknown protein 0.91 ± 0.038 − 45.4 ***
42 81043 G → A (intron) Zinc finger, TFIIS-type 0.76 ± 0.040 − 54.5 ***
43 80339 T → A (terminator); T → G (terminator); T → G (terminator); − 1: T (terminator) Apolipophorin-III and similar insect proteins 0.72 ± 0.038 − 56.5 ***
44 3529 − 1: T (promoter) Alpha and gamma adaptin binding protein p34 0.68 ± 0.041 − 59.3 ***
45 111216 C → T (promoter) Class II Histone H3 methyltransferase 0.58 ± 0.033 − 65.2 ***
46 55868 + 1: C (terminator) serine/threonine phosphatase 0.56 ± 0.025 − 66.3 ***
47 58191 C → T (promoter) RAM signaling pathway protein n.t.
48 120794 A → G (promoter) ubiquitin n.t.
49 80956 A → C (promoter) unknown protein n.t.
50 124205 G → T (terminator) RNA polymerase III transcription initiation factor complex n.t.
51 74162 + 3: TCT (terminator) rRNA helicase RRP3 n.t.
52 74624 − 16: GATGACGATGATTTTC (terminator) unknown protein n.t.
53 108697 T → G (exon: Ile49 → Arg) Calcium-responsive transcription coactivator n.t.
54 102973 + 3: TCT (exon) Transcriptional corepressor n.t.
55 57217 C → T (exon: synonymous variant) WD40 repeat-like protein n.t.
56 71304 T → C (intron) Ribosomal protein L39e n.t.
57 2125 A → T (intron) RuvB-like helicase 2 n.t.
  1. “—” indicates no significant difference
  2. n.t. not detected for gene knockout, leading to death
  3. aSupernatant of mutant cultures 5 days from cultivation was used to measure FPase activity
  4. bThe increased percentage of FPase activity relative to the parent strain RUT-C30
  5. cAsterisks indicate significant differences (*p < 0.05, **p < 0.01, ***p < 0.001, Student’s t-test)