Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Abstract

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

“…Recent bioinformatic study on the genotypes of cob subunits in prokaryotic genomes revealed that cobS and cobT are absent in most prokaryotic genomes, whereas cobN is present [ 65 ]. Many such prokaryotes, including haloarchaea, were suggested to employ a mosaic cobaltochelatase consisting of CobN and magnesium chelatase subunits [ 65 , 67 ]. Our finding of the broad distribution of the cobST gene cluster in tailed viruses, both bacterial and archaeal, suggests that viral CobST likely hijacks the host CobN (from the mosaic cobaltochelatase in the absence of the host encoded CobST), to increase the production of cobalamin, thereby promoting the virus replication.…”

A crowdsourcing open platform for literature curation in UniProt

“…Dr. Pfeiffer (Max Planck Institute, Germany) has actively provided feedback to UniProt on the annotation of prokaryotic proteins. Since the community annotation functionality started, he has now contributed over 250 submissions, especially adding publications and annotation to proteins from haloarchaeal genomes while developing a strategy for curation of their corresponding genomes [ 7 , 8 ].…”

Comparative Analysis of rRNA removal methods for RNA-seq Differential Expression in Halophilic Archaea

“…In this work, we have studied four species of halophilic archaea that have been widely used as model organisms in the archaeal research community: Halobacteium salinarum (HBT) and Haloarcula hispanica (HAH) of the family Halobacteriaceae require salt concentrations close to saturation, whereas Haloferax volcanii (HVO) and Haloferax mediterranei (HFX) of the family Haloferacales colonize lower salinity environments. These four species are highly tractable models for extremophilic microorganisms given their relatively fast generation time (2-6 hours in rich medium), facile genetic tools [23][24][25], and highly curated genomic annotations and databases [26][27][28][29]. Establishing a set of tools and best practices for transcriptomics methods would therefore greatly facilitate advances in this field.…”