Fig 1.
The presence of C. tuberculosum sequence candidates in the monolignol pathway.
Red indicates presence of a putative homolog in C. tuberculosum; blue indicates no significant hits; green indicates ambiguous presence. Note how the PTAL/PAL/TAL sequences obtained from the HMMER search were indicated as absent as all sequences found were too short, 1/4-1/3 in length relative to those in land plants. All sequences identified have genomic support except for PTAL/PAL/TAL.
Fig 2.
4CL candidates from C. tuberculosum in relation to plants and other taxa.
(A) Partial alignment of C. tuberculosum candidates (bolded) and embryophyte 4CL sequences. Residues involved in hydroxycinnamate binding are indicated with black triangles [47, 48]. Phenylalanine substrate binding pocket [49] is indicated with Box I and Box II. (B) Maximum likelihood acyl-activating enzyme (AAE) gene tree showing relationships between Calliarthron sequences (magenta dots) and other taxa (Embryophyta–dark green, Chlorophyta–light green, Rhodophyta–red, Animalia and Opisthokonta–purple, Bacteria and Cyanobacteria–blue, Oomycota, Mycetozoa and Fungi–yellow, Ochrophyta–brown). Functionally demonstrated plant 4CLs are labelled (+). Additional functional groups are labelled [50, 51]. Ultrafast bootstrap values > 95 are marked by *. Model = WAG+F+G4. Sites with ≤ 80% occupancy were removed. Accession numbers can be found in S1 Appendix.
Fig 3.
CCR candidates from C. tuberculosum in relation to plants and other taxa.
(A) Partial alignment C. tuberculosum candidates (bolded) and land plant CCR sequences. Catalytic residues are labelled with NWYCY [52] and additional residues are indicated above with a black box. NADPH binding pocket residues are indicated with black triangles [53] and the GXXGXX[A/G] motif is underlined [54]. Hydroxycinnamonyl binding pocket residues are indicated with a gray triangle [53]. (B) CCR maximum likelihood gene tree showing relationships between C. tuberculosum (magenta dots) and other taxa (Embryophyta–dark green, Chlorophyta–light green, Rhodophyta–red, Animalia and Opisthokonta–purple, Bacteria and Cyanobacteria–blue, Oomycota, Mycetozoa and Fungi–yellow, Ochrophyta–brown). Functionally demonstrated plant CCRs are labelled (+). Additional functional groups are labelled. Ultrafast bootstrap values >95 are marked by *. Model = LG+G4. Sites with ≤ 80% occupancy were removed. Accession numbers can be found in S1 Appendix.
Fig 4.
CAD candidates from C. tuberculosum in relation to plants and other taxa.
(A) Partial alignment of C. tuberculosum CAD sequence candidates (bolded) with land plant CAD sequences. Zn+2 ion coordinating and proton shuttling residues are indicated with the black triangle, NADPH or NADH interacting residues are boxed. Hydrostatic interaction forming residues are indicated with a black box. Putative substrate-binding residues are indicated with grey boxes [55–57]. (B) CAD maximum likelihood gene tree showing relationships between C. tuberculosum (magenta dots) and other taxa (Embryophyta–dark green, Chlorophyta–light green, Rhodophyta–red, Animalia and Opisthokonta–purple, Bacteria and Cyanobacteria–blue, Oomycota, Mycetozoa and Fungi–yellow, Ochrophyta–brown). Alcohol dehydrogenase (ADH) sequences from yeast, and aldehyde reductase (YAHK and AHR) sequences from E. coli were used as the ADH family is closely related to that of CAD [58, 59]. Functionally demonstrated plant CADs are labelled (+). Additional functional groups are labelled. Ultrafast bootstrap values >95 are marked by *. Model = LG+G4. Sites with ≤ 80% occupancy were removed. Accession numbers can be found in S1 Appendix.