NommPred: Prediction of Mitochondrial and Mitochondrion-Related Organelle Proteins of Nonmodel Organisms

Abstract

To estimate the functions of mitochondria of diverse eukaryotic nonmodel organisms in which the mitochondrial proteomes are not available, it is necessary to predict the protein sequence features of the mitochondrial proteins computationally. Various prediction methods that are trained using the proteins of model organisms belonging particularly to animals, plants, and fungi exist. However, such methods may not be suitable for predicting the proteins derived from nonmodel organisms because the sequence features of the mitochondrial proteins of diversified nonmodel organisms can differ from those of model organisms that are present only in restricted parts of the tree of eukaryotes. Here, we proposed NommPred, which predicts the mitochondrial proteins of nonmodel organisms that are widely distributed over eukaryotes. We used a gradient boosting machine to develop 2 predictors—one for predicting the proteins of mitochondria and the other for predicting the proteins of mitochondrion-related organelles that are highly reduced mitochondria. The performance of both predictors was found to be better than that of the best method available.

Barthelonids represent a deep-branching Metamonad clade with mitochondrion-related organelles generating no ATP

“…Reconstructed metabolic pathways in the MRO of strain PAP020. Dark purple ellipses indicate that the transcripts encoding hydrogenosomal/MRO proteins were detected in the Barthelona RNA-seq data, and their N-termini were predicted as transit peptides for mitochondria/MRO by MitoFates (Fukasawa et al 2015) and/or NommPred (Kume et al 2018). Pale purple ellipses indicate putative hydrogenosomal/MRO proteins lacking N-terminal sequence information or those with N-terminal extensions that were not predicted as mitochondria/MRO localizing by MitoFates and NommPred.…”

“…The domain structures of the putative MRO proteins were examined using hmmscan 3.1 (http://hmmer.org). We inspected each of the putative MRO proteins for potential mitochondrial targeting sequences using MitoFates (Fukasawa et al 2015) with default parameters for the fungal sequences, and NommPred (Kume et al 2018) with parameters for canonical mitochondria and MRO.…”

Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa

“…The dashes and crosses represent the absences of homologs in transcriptome and those in both transcriptome and genome, respectively. The sequences with the complete N-termini were subjected to in silico prediction of the mitochondrial targeted signal (MTS) at their N-termini by using TargetP [29], NommPred [30], PredSL [31], and MitoFates [32]. In the case of the MTS being predicted, a subset (or all) of the quarters is filled (upper-right, TargetP The precise function of PolIA of Trypanosoma brucei has yet to be clarified experimentally [3].…”

“…The mitochondrial localization of the family A DNA polymerases identified in this study were predicted based on their N-terminal sequences by the four different programs, TargetP 1.1 [29], NommPred [30], PredSL [31] and MitoFates [32]. In addition, the Euglena gracilis POP_e1 and POP_e2 sequences were subjected to SignalP v3.0 [40] and TMHMM v2.0 [41] to evaluate their plastid localization.…”

Catalase and Ascorbate Peroxidase in Euglenozoan Protists

“…To assess a putative subcellular localization of all studied euglenozoan proteins, PrediSi [68], NommPred (in kinetoplastid setting; [69]), TargetP v.2.0 [70], and MultiLoc2 (in fungal and animal settings; [71]) tools were employed. Glycosomal predictions were determined by an in-house python script based on previously identified targeting signals in kinetoplastids [28].…”