Confronting the catalytic dark matter encoded by sequenced genomes

Newly-discovered enzymes that function in metabolite damage-control

Enzymes of unknown function are estimated to make up around 25% of the sequenced proteome. In the past decade, over 20 conserved families have been shown to function in the metabolism of 'damaged' or abnormal metabolites that are wasteful and often toxic. These newly discovered damage-control enzymes either repair or inactivate the offending metabolites, or pre-empt their formation in the first place. Comparative genomics has been of prime importance in predicting the functions of damage-control enzymes and in guiding the biochemical and genetic tests required to validate these functions.

Respiratory chain Complex I of unparalleled divergence in diplonemids

Mitochondrial genes of Euglenozoa (Kinetoplastida, Diplonemea, and Euglenida) are notorious for being barely recognizable, raising the question of whether such divergent genes actually code for functional proteins. Here we demonstrate the translation and identify the function of five previously unassigned y genes encoded by mitochondrial DNA (mtDNA) of diplonemids. As is the rule in diplonemid mitochondria, y genes are fragmented, with gene pieces transcribed separately and then trans-spliced to form contiguous mRNAs. Further, y transcripts undergo massive RNA editing, including uridine insertions that generate up to 16-residue-long phenylalanine tracts, a feature otherwise absent from conserved mitochondrial proteins. By protein sequence analyses, MS, and enzymatic assays in Diplonema papillatum, we show that these y genes encode the subunits Nad2, -3, -4L, -6, and -9 of the respiratory chain Complex I (CI; NADH:ubiquinone oxidoreductase). The few conserved residues of these proteins are essentially those involved in proton pumping across the inner mitochondrial membrane and in coupling ubiquinone reduction to proton pumping (Nad2, -3, -4L, and -6) and in interactions with subunits containing electron-transporting Fe-S clusters (Nad9). Thus, in diplonemids, 10 CI subunits are mtDNA-encoded. Further, MS of D. papillatum CI allowed identification of 26 conventional and 15 putative diplonemid-specific nucleus-encoded components. Most conventional accessory subunits are well-conserved but unusually long, possibly compensating for the streamlined mtDNA-encoded components and for missing, otherwise widely distributed, conventional subunits. Finally, D. papillatum CI predominantly exists as a supercomplex I:III:IV that is exceptionally stable, making this protist an organism of choice for structural studies.

Challenges, progress and promises of metabolite annotation for LC-MS-based metabolomics

Accurate annotation is vital for data interpretation; however, metabolite identification is a major bottleneck in untargeted metabolomics. Although community guidelines for metabolite identification were published over a decade ago, adaptation of the recommended standards has been limited. The complexity of LC-MS data due to combinations of various chromatographic and mass spectrometric acquisition methods has resulted in the advent of diverse workflows, which often involve non-standardized manual curation. Herein, we review the parameters involved in metabolite reporting and provide a workflow to estimate the level of confidence in reported metabolite annotation. The future of metabolite identification will be heavily based upon the use of metabolome data repositories and associated data analysis tools, which will enable data to be shared, re-analyzed and re-annotated in an automated fashion.