oa Structure, Function and Evolution of Y-Nucleoporins and Eukaryotic Coatomer Components Using Sequence Space Walks and Tissue-Specific Expression Patterns

We developed novel methodological approaches using multi-level data integration bioinformatics techniques to explore the structural, functional and evolutionary relationships of the Y-complex nucleoporins (Y-Nups), essential components of the eukaryotic nuclear pore. Previous evidence suggested that Y-Nups are involved in cellular processes beyond the nuclear pore Y-complex. We obtained all known (1813) and newly discovered (1149) homologs of Y-Nups from the public protein sequence databases and further delineated their complex superfamily relationships by extensive database queries, sequence clustering and iterative profile searches [1]. Protein domain decomposition has revealed novel composite architectures and previously unknown evolutionary relationships between Y-Nups and other functionally related neighbours [2]. Using tissue-specific gene expression patterns both as a filtering device and supporting evidence, we obtain strong indications that certain Y-Nups might be involved in new moonlighting functions such as DNA repair, RNA processing, cell signaling pathways and mitotic control. These functions appear to be under coordinated regulation across different cell types and tissues, as suggested by RNAseq information, both for human and mouse. During the process of functional inference, we have also discovered and further highlighted mis-annotation inconsistencies, encompassing various phylogenetic anomalies and artifactual genomic regions [3] – which are then excluded from our candidate lists. Ultimately, the newly detected functional relationships provide an expanded network of Y-Nup interactions, clearly extending the functional involvement of Y-Nups in the nuclear pore towards other cellular roles. Furthermore, protein superfamily delineation has also uncovered subtle sequence similarities between Y-Nup superfamilies. Adaptive, supervised sequence space walks across Y-Nups and other known coatomer superfamilies have been established, using highly specific patterns generated by iterative sequence profile searches. These sequence space walks unify for the first time all known eukaryotic coatomers beyond the nuclear pore, including transport vesicles and intraflagellar transport. Eukaryotic endomembrane coatomers, long suspected to be divergently related, are thus connected for the first time at the sequence level. A handful of converved residues in the derived sequence and structure alignments are shared by the currently available 3,502 sequences of coatomer elements in eukaryotes. These invariant sequence positions are mapped onto known protein structure representatives, further supporting the detection of sequence divergence patterns at very low, yet significant sequence similarity levels [4]. The sophisticated sequence space walk and RNAseq-based functional profiling connecting multiple coatomer superfamilies involved in cell physiology and human disease represents a complex, yet efficient methodological strategy, generally applicable for other functionally related superfamilies and associated cellular processes.

References

[1] Katsani KR, Irimia M, Karapiperis C, Scouras ZG, Blencowe BJ, Promponas VJ, Ouzounis CA (2014) Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins. Scientific Reports 4, 4655. http://www.nature.com/articles/srep04655

[2] Promponas, V. J., Ouzounis, C. A. & Iliopoulos, I. (2012) Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Brief Bioinform. 15, 443. http://www.ncbi.nlm.nih.gov/pubmed/23220349

[3] Promponas VJ, Iliopoulos I, Ouzounis CA (2015) Annotation errors beyond sequence similarity-based function prediction – phylogeny and genome structure. Standards Genomic Sci., in press.

[4] Promponas VJ, Katsani KR, Blencowe BJ, Ouzounis CA (2015) Sequence evidence for common ancestry of eukaryotic endomembrane coatomers. Submitted manuscript. http://biorxiv.org/content/early/2015/06/16/020990