Profiling the orphan enzymes

Abstract

The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called “orphan enzymes”. The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to “local orphan enzymes” that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new activities.ReviewersThis article was reviewed by Michael Galperin, Daniel Haft and Daniel Kahn.

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

“…Information about these genes can be easily obtained from KEGG database using the identified KEGG-reaction number of the steps involved in a pathway ( Figure 7B). Notably, MEG6 includes 2 steps for which the KEGG reaction number is known, but the gene information is unknown because they are orphan enzymes (Shearer et al, 2014;Sorokina et al, 2014;Watschinger and Werner, 2013).…”

“…Both reactions/steps of the only 2-step long MEG-producing pathway ( Table S3 in the supplementary data) belonged to KEGG, but the 1 st reaction (R05351) is an orphan enzyme, i.e., the gene information for the reaction is unknown (Shearer et al, 2014;Sorokina et al, 2014;Watschinger and Werner, 2013). A closer look at the accepted 3 and 4-step pathways (Figure 3) revealed that at least one novel reaction existed in each pathway, while no pathway was found in which all reactions/steps were known to be biological ( Figures 3A and 3B), i.e., belonged to the KEGG database with a KEGG-reaction number.…”

Accurate Microbial Genome Annotation Using an Integrated and User-Friendly Environment for Community Expertise of Gene Functions: The MicroScope Platform

“…In addition, large-scale sequencing projects have revealed that 30-40% of the proteins encoded in prokaryotic genomes have no clearly known function, and the vast majority belong to thousands of unknown orthologue families that continue to grow as more genomes are sequenced [8]. On the other hand, it is also estimated that about 1,000 of the >5,500 enzymatic activities described by the International Union of Biochemistry and Molecular Biology in the EC classification system lack an associated nucleic or protein sequence in the public databanks, a situation known as the 'orphan enzyme problem' [9][10][11][12].…”

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae

“…Focused analyses of new sequences for members of 37 protein families deposited in 2005 have shown that about 40% of these proteins remain misannotated (7,8). Our knowledge gap also includes over 1,000 of the known enzyme activities in the Enzyme Classification (of the 4,997 EC numbers) that have no associated gene sequence (orphan enzymes) (9,10).…”