Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

Modulation of lipocalin-type prostaglandin D2 synthase expression in catfish seminal vesicles by thyroid disrupting agents and hormones

Thyroid hormones play crucial role in several biological processes including reproduction. Disruption of normal thyroid status by environmental contaminants can cause severe impairment in reproductive functions. In our previous study, we reported down-regulation of a protein in seminal vesicular fluid of air-breathing catfish, Clarias gariepinus during experimentally induced hyperthyroidism. N-terminal amino acid sequence analysis followed by search in sequence database denoted it to be lipocalin-type prostaglandin D2 synthase (ptgds-b). In the present study, we cloned full-length cDNA of ptgds-b based on the N-terminal amino acid sequence. Surprisingly, Northern blot as well as RT-PCR analysis demonstrated the presence of ptgds-b transcript predominantly in seminal vesicles and developing testis. Further, ptgds-b mRNA significantly decreased in seminal vesicles following L-thyroxine overdose while there was an increased expression of ptgds-b after depletion of thyroid hormone by thiourea and withdrawal of the treatments reverted this effect. Treatment of catfish with human chorionic gonadotropin and estradiol significantly reduced ptgds-b expression. Taken together, we report ptgds-b as a thyroid hormone regulated protein in the seminal vesicles in addition to gonadotropin and estradiol. Further studies might explain the exclusive presence of ptgds-b in seminal vesicles and developing testis yet present data evaluated it as a putative biomarker for thyroid hormone disruption.