Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production

Abstract

The variability and phylogeny among TRI5, TRI8 and TRI11 nucleotide and translated protein sequences of isolates from Trinidad belonging to Fusarium incarnatum-equiseti species complex (FIESC) were compared with FIESC reference sequences. Taxa appeared to be more divergent when DNA sequences were analyzed compared to protein sequences. Neutral and non-neutral mutations in TRI protein sequences that may correspond to variability in the function and structure of the selected TRI proteins were identified. TRI5p had the lowest amino acid diversity with zero predicted non-neutral mutations. TRI5p had potentially three protein disorder regions compared to TRI8p with five protein disorder regions. The deduced TRI11p was more conserved than TRI8p of the same strains. Amino acid substitutions that may be non-neutral to protein function were only detected in diacetoxyscirpenol (DAS) and fusarenon-X (FUS-X) producers of the reference sequence subset for TRI8p and TRI11p. The deduced TRI5 and TRI8 amino acid sequences were mapped to known 3D-structure models and indicated that variations in specific protein order/disorder regions exist in these sequences which affect the overall structural conservation of TRI proteins. Assigning single or combination non-neutral mutations to a particular toxicogenic phenotype may be more representative of potential compared to using genotypic data alone, especially in the absence of wet-lab, experimental validation.

Keywords: Fusarium; non-neutral mutations; sequence diversity; trichothecene.

Figure 1

TRI5 gene and protein phylogenetic trees. The trees were constructed using the maximum likelihood (ML) method. All positions containing gaps and missing data were eliminated and the trees are drawn to scale. The tree with the highest log likelihood is shown. Bootstrap support after 1000 replicates of associated taxa is shown next to the branches. The 75% majority consensus trees are shown; (A): phylogenetic tree for TRI5 gene sequences was based on the Kimura 2-parameter model; (B): phylogenetic tree for TRI5 protein sequences was constructed based on the maximum likelihood method using on the JTT + G matrix-based model.

Figure 2

TRI8 gene and protein phylogenetic trees constructed using the maximum likelihood method. All positions containing gaps and missing data were eliminated and the trees are drawn to scale. The tree with the highest log likelihood is shown. Bootstrap support after 1000 replicates of associated taxa is shown next to the branches; (A): phylogenetic tree for TRI8 gene sequences was based on the Kimura 2-parameter model; (B): phylogenetic tree for TRI8 protein sequences was constructed based on the maximum likelihood method using on the JTT matrix-based model.

Figure 3

TRI11 gene and protein phylogenetic trees constructed using the maximum likelihood method. All positions containing gaps and missing data were eliminated and the trees are drawn to scale. The tree with the highest log likelihood is shown. Bootstrap support after 1000 replicates of associated taxa is shown next to the branches; (A): phylogenetic tree for TRI11 gene sequences was based on the Kimura 2-parameter model; (B): phylogenetic tree for TRI11 protein sequences was constructed based on the maximum likelihood method using on the JTT + G matrix-based model.

Figure 4

Sequence display for secondary structure entities in PDB model 2PS5 (https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=2PS5) with TRI5 protein sequence amplified mapped onto the model sequence.

Figure 5

A sequence logo of the TRI5 amino acid sequence alignment generated by WebLogo v.3.

Figure 6

The protein features of PDB model 2PS5 (https://www.rcsb.org/pdb/protein/P13513) showing regions of protein order and predicted disorder that correspond to the TRI5 amino acid sequence alignment.

Figure 7

Sequence display for secondary structure entities in PDB model 3GUU (https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=3GUU) with TRI8 protein sequence amplified mapped onto the model sequence.

Figure 8

Sequence display for secondary structure entities in PDB model 3ZPX (https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=3ZPX) with TRI8 protein sequence mapped onto the model sequence.

Figure 9

A sequence logo of the TRI8 amino acid sequence alignment generated by WebLogo v.3.

Figure 10

The protein features of PDB model 3GUU (https://www.rcsb.org/pdb/protein/W3VKA4) showing regions of protein order and predicted disorder that correspond to the TRI8 amino acid sequence alignment.