Abstract
Incorrectly or simply not annotated data is largely increasing in most public databases, undoubtedly caused by the rise in sequence data and the more recent boom of genomic projects. Molecular biologists and bioinformaticists should join efforts to tackle this issue. Practical challenges have been experienced when studying the alternative oxidase (AOX) gene family, and hence the motivation for the present work. Commonly used databases were screened for their capacity to distinguish AOX from the plastid terminal oxidase (also called plastoquinol terminal oxidase; PTOX) and we put forward a simple approach, based on amino acids signatures, that unequivocally distinguishes these gene families. Further, available sequence data on the AOX family in plants was carefully revised to: (1) confirm the classification as AOX and (2) identify to which AOX family member they belong to. We bring forward the urgent need of misannotation awareness and re-annotation of public AOX sequences by highlighting different types of misclassifications and the large under-estimation of data availability.
Highlights
Reviewed by: Patrick Finnegan, University of Western Australia, Australia Nicolas L
Used databases were screened for their capacity to distinguish alternative oxidase (AOX) from the plastid terminal oxidase and we put forward a simple approach, based on amino acids signatures, that unequivocally distinguishes these gene families
But the first is located in the mitochondrial inner membrane at the mitochondria, is involved in the respiratory electron transport and interacts with ubiquinol; the second locates in the stroma, is active in the photosynthetic electron transport and it catalyzes the oxidation with plastoquinol
Summary
It has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. But the first is located in the mitochondrial inner membrane at the mitochondria, is involved in the respiratory electron transport and interacts with ubiquinol; the second locates in the stroma, is active in the photosynthetic electron transport and it catalyzes the oxidation with plastoquinol (on AOX role see Vanlerberghe, 2013; on PTOX role see Nawrocki et al, 2015; KriegerLiszkay and Feilke, 2016) Often, these two family members are mis-annotated in sequence databases. We have found two sites that seem to show a specific conservation of amino acids related to the subfamily members–fingerprints–and we propose their use as a quick and efficient way to distinguish plant AOX from PTOX sequences These signatures may serve as identification motifs specific for the two subfamilies, and when scanned against the GenBank database, retrieved only members of each subfamily. The general structure of both AOX and PTOX is different and on itself might represent an extra way to verify gene affiliation of already published sequences to either AOX or PTOX family member (Figure 1B)
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