Nature of selection varies on different domains of IFI16-like PYHIN genes in ruminants

Abstract

Background: ALRs (AIM2-like Receptors) are germline encoded PRRs that belong to PYHIN gene family of cytokines, which are having signature N-terminal PYD (Pyrin, PAAD or DAPIN) domain and C-terminal HIN-200 (hematopoietic, interferon-inducible nuclear protein with 200 amino acid repeat) domain joined by a linker region. The positively charged HIN-200 domain senses and binds with negatively charged phosphate groups of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) purely through electrostatic attractions. On the other hand, PYD domain interacts homotypically with a PYD domain of other mediators to pass the signals to effector molecules downwards the pathways for inflammatory responses. There is remarkable inter-specific diversity in the numbers of functional PYHIN genes e.g. one in cow, five in human, thirteen in mice etc., while there is a unique loss of PYHIN genes in the bat genomes which was revealed by Ahn et al. (2016) by studying genomes of ten different bat species belonging to sub-orders yinpterochiroptera and yangochiroptera. The conflicts between host and pathogen interfaces are compared with "Red queen's arms race" which is also described as binding seeking dynamics and binding avoidance dynamics. As a result of this never-ending rivalry, eukaryotes developed PRRs as antiviral mechanism while viruses developed counter mechanisms to evade host immune defense. The PYHIN receptors are directly engaged with pathogenic molecules, so these should have evolved under the influence of selection pressures. In the current study, we investigated the nature of selection pressure on different domain types of IFI16-like (IFI16-L) PYHIN genes in ruminants.

Results: Three transcript variants of the IFI16-like gene were found in PBMCs of ruminant animals-water buffalo, zebu cattle, goat, and sheep. The IFI16-like gene has one N-terminal PYD domain and one C-terminal HIN-200 domain, separated by an inter-domain linker region. HIN domain and inter-domain region are positively selected while the PYD domain is under the influence of purifying selection.

Conclusion: Herein, we conclude that the nature of selection pressure varies on different parts (PYD domain, HIN domain, and inter-domain linker region) of IFI16-like PYHIN genes in the ruminants. This data can be useful to predict the molecular determinants of pathogen interactions.

Keywords: DAMP; HIN; IFI16; IFI16-like; Inter-domain; PAMP; PRR; PYD; PYHIN; Selection.

Fig. 1

Exon skipping of different transcript variants of IFI16-like PYHIN genes. The three transcript variants of different lengths of IFI16-like genes in buffalo, zebu cattle, sheep and goat were studied. The illustration depicts exon skipping among transcript variants of IFI16-like genes. In case of buffalo and cow, there are eight exons while in the case of sheep and goat, 8th exon is fused with 7th exon

Fig. 2

Intra-cellular localization of ruminant IFI16-L proteins. Immuno-cytochemistry was carried out for IFI16-L proteins in the cultured buffalo fetal fibroblast cells (a) Green fluorescence showing the localization of IFI16-L protein; (b) Fluorescence showing nuclei of the fetal fibroblast cells stained with DAPI; (c) Image formed by merging A and B. The IFI16-L protein was found to co-localize in both, the nucleus as well as the cytoplasm

Fig. 3

ML phylogenetic tree of HIN domains from different mammalian orders rooted with marsupial sequence. ML phylogenetic tree is rooted on marsupial Sarcophilus harrisii, which is taken as the outgroup. All nodes having bootstrap values of < 50% were collapsed. Tree was visualized using iTOL. Names of the animals belonging to the same mammalian order have same color. The color-strip represent the type of HIN domain of corresponding PYHIN gene- HINa (turquoise) HINb (yellow), HINc (violet) and HINd (black)

Fig. 4

ML phylogenetic tree of PYD domains from different mammalian orders rooted with marsupial sequence. ML phylogenetic tree is rooted on marsupial Sarcophilus harrisii, which is taken as the outgroup. All nodes having bootstrap values of < 50% were collapsed. Tree was visualized using iTOL. Names of the animals belonging to the same mammalian order have same color. The color-strip represent the type of PYD domain of corresponding PYHIN gene- IFI (non-AIM2) PYD domain (turquoise), AIM2 PYD (Yellow) and marsupial PYD (black)

Fig. 5

ML phylogenetic tree of inter-domains (ID) from ruminants IFI16-L gene, rooted with whale sequence. ML phylogenetic tree is rooted on cetacean Orcinus orca (whale), which is taken as the outgroup. All nodes having bootstrap values of < 50% were collapsed. Tree was visualized using iTOL. Names of the animals belonging to the same mammalian order (Artiodactyla) have same color. The color-strip represent the type of inter-domain of corresponding ruminant ID (turquoise), and whale ID (black)