Exploring the diversification of Plant PIP aquaporin by sequence similarity network analysis

BUSSOLINI LIZUNDIA, ROCIO; ALLEVA, KARINA; TESAN, FIORELLA C; VITALI, VICTORIA ANDREA; SOTO, GABRIELA

Conferencia; 2nd Women in Bioinformatics & Data Science LA Conference; 2021

The PIP (plasma membrane intrinsic proteins) subfamily is the largest of the seven MIP (Major intrinsic proteins) subfamilies found in plants. Interestingly, not all isoforms exhibit the same functional properties in terms of solute permeability or capability to form heterotetramers. The two Asn-Pro-Ala (NPA) motives and the aromatic/arginine (Ar/R) selectivity filter regulate transport specificity and the larger loopD is crucial for the open-closed transition found in PIP channels. PIP1 and PIP2 are the biggest of the four PIP paralogues, have a high amino acid identity (> 70%), and predominate in vascular plants. Both PIP1 and PIP2 are present even in plant ancient lineages such as Selaginella moellendorffii and Physcomitrella patens showing that PIP diversification was already established when land plant evolution began. For years, efforts have been focused on elucidating whether this great multiplicity of isoforms implies diversity or functional overlap. Here, we analyze extensively the PIP subfamily. The PF00230 Pfam database entry (MIP) was selected as a starting point of 26169 sequences (release Pfam 34.0, March 2021). Employing the NPA motif and the consensus Loop D sequence, we selected only PIP1 and PIP2 isoforms by using the bioseq Package in R Software and obtained a PIP dataset of 2034 sequences. Then, a sequence similarity network (SSN) for the PIP subfamily was built using the EFI-EST online tool and visualized in Cytoscape 3.8.2.Based on neighborhood connectivity, we characterized the topology of the PIP subfamily within SSN clusters. This approach provides a clear picture of how the PIP2 subfamily is organized in smaller clusters and points out outsider sequences distributed among different species. In contrast, PIP1 is a homogeneous cluster with high connectivity. This approach allows us to get insights regarding their structure-functions relationships, and generate testable hypotheses about the uncharacterized isoforms in the PIP subfamily.