PredAlgo: A New Subcellular Localization Prediction Tool Dedicated to Green Algae

Abstract

The unicellular green alga Chlamydomonas reinhardtii is a prime model for deciphering processes occurring in the intracellular compartments of the photosynthetic cell. Organelle-specific proteomic studies have started to delineate its various subproteomes, but sequence-based prediction software is necessary to assign proteins subcellular localizations at whole genome scale. Unfortunately, existing tools are oriented toward land plants and tend to mispredict the localization of nuclear-encoded algal proteins, predicting many chloroplast proteins as mitochondrion targeted. We thus developed a new tool called PredAlgo that predicts intracellular localization of those proteins to one of three intracellular compartments in green algae: the mitochondrion, the chloroplast, and the secretory pathway. At its core, a neural network, trained using carefully curated sets of C. reinhardtii proteins, divides the N-terminal sequence into overlapping 19-residue windows and scores the probability that they belong to a cleavable targeting sequence for one of the aforementioned organelles. A targeting prediction is then deduced for the protein, and a likely cleavage site is predicted based on the shape of the scoring function along the N-terminal sequence. When assessed on an independent benchmarking set of C. reinhardtii sequences, PredAlgo showed a highly improved discrimination capacity between chloroplast- and mitochondrion-localized proteins. Its predictions matched well the results of chloroplast proteomics studies. When tested on other green algae, it gave good results with Chlorophyceae and Trebouxiophyceae but tended to underpredict mitochondrial proteins in Prasinophyceae. Approximately 18% of the nuclear-encoded C. reinhardtii proteome was predicted to be targeted to the chloroplast and 15% to the mitochondrion.

Two Glycerol-3-Phosphate Dehydrogenases from Chlamydomonas Have Distinct Roles in Lipid Metabolism

“…S2), which otherwise have very high amino acid sequence identity (89% identity and 91% similarity), while GPD4 shows much lower sequence identity to GPD2 and GPD3 (64% and 62% identity, respectively). Subcellular localization prediction using PredAlgo (Tardif et al, 2012) also predicted plastidic localization for GPD2 and GPD4 and nonplastidic localization for the other C. reinhardtii GPDH proteins. GPD2, GPD3, and GPD4 are bidomain proteins and, in addition to the GPDH domain, contain an N-terminal domain with unknown function but with similarity to a haloacid dehalogenase (HAD)-like hydrolase and to a SerB phosphoserine phosphatase (He et al, 2007).…”

Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control

“…A list of 348 proteins was obtained whose change in abundance appears to be specifically linked to the depletion of ClpP1 in the DCH16 strain (Table 2; Supplemental Data Set 6). Of these proteins 27 and 11% are predicted to be targeted to the chloroplast and mitochondria, respectively, by PredAlgo, an algorithm specifically designed for predicting the cellular localization of C. reinhardtii proteins that is based on a neural network trained to recognize transit peptide sequences (Tardif et al, 2012). The number of proteins differentially expressed increased at each time point (Supplemental Figure 5).…”

PHOTOSYSTEM II SUBUNIT R Is Required for Efficient Binding of LIGHT-HARVESTING COMPLEX STRESS-RELATED PROTEIN3 to Photosystem II-Light-Harvesting Supercomplexes in Chlamydomonas reinhardtii

“…Protein sequences were taken from the National Center for Biotechnology Information (reference sequences XP_001696588.1, XP_002945815.1, XP_005847921.1, XP_001760191.1, and NP_178025.1). Transit peptide cleavage sites were deduced by Emanuelsson et al (2000) and PredAlgo (Tardif et al, 2012). Arrows indicate identified phosphorylation sites.…”