Conserved Immunoglobulin Domain Similarities of Higher Plant Proteins

Jaroslav Kubrycht,Karel Sigler

doi:10.4236/cmb.2020.101002

Abstract

The traces of immunoglobulin domain similarities were searched in sequences of higher plants using bioinformatic tools to look for possible early phylogenic structural relationships. 280 thousand sequence IDs, obtained by sixteen types of primary BLAST searches, were differently processed by seventeen selection procedures and an anti-redundant sequence-related approach using JavaScript, PHP, Windows programs and conserved domain searches by means CDD. The resulting seventeen sets of records describing conserved domain similarities of 1323 different sequence IDs yielded a set of next generation (final set) comprising forty-nine records containing superior (“non-refutable”) conserved immunoglobulin domain similarities. The selected sets and their subsets were mapped and subsequently statistically compared with respect to immunoglobulin-related as well as other reciprocal domain linkages. The list of frequently occurring conserved domain similarities concerned first of all domains important for plant and metazoan immunity, e.g. tyrosine kinases accompanying variable immunoglobulin domains in early Metazoa, toll-like receptors, lectin and leucine-rich repeat domains. Detailed description of immunoglobulin domain similarities occurring in the final set was completed by fold analysis of the restricted segments. The data were then discussed with respect to i) immunoglobulin fold evolution, ii) possible structural importance of domains cd14066 (IRAK) and PLN00113 (LRR-associated kinase) for deep evolution of catalytic serine/threonine/tyrosine kinase domains, iii) interatomic, structural and specificity standpoints and iv) traces of antibody-like phosphorylation sites described in our previous paper.

Highlights

In accordance with recent opinions, we distinguish two main layers of plant immunity, i.e. pathogenic pattern-triggered immunity (PTI) and effector-triggered immunity (ETI)
The traces of immunoglobulin domain similarities were searched in sequences of higher plants using bioinformatic tools to look for possible early phylogenic structural relationships. 280 thousand sequence IDs, obtained by sixteen types of primary BLAST searches, were differently processed by seventeen selection procedures and an anti-redundant sequence-related approach using JavaScript, PHP, Windows programs and conserved domain searches by means CDD
The data were discussed with respect to i) immunoglobulin fold evolution, ii) possible structural importance of domains cd14066 (IRAK) and PLN00113 (LRR-associated kinase) for deep evolution of catalytic serine/threonine/tyrosine kinase domains, iii) interatomic, structural and specificity standpoints and iv) traces of antibody-like phosphorylation sites described in our previous paper

Summary

Introduction

In accordance with recent opinions, we distinguish two main layers of plant immunity, i.e. pathogenic pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). These layers are frequently accompanied by activation of kinase cascades, Ca2+ influxes, generation of reactive oxygen species, transcriptional reprogramming, phytohormone signalling, proteasome degradation pathways and (i.e. in special cases of virus infections) RNA silencing machinery [1] [2]. Among familiar groups of RLK, serine/threonine kinases receptor-like kinases (STRK) are frequent In addition to their specific catalytic domains, these STRK can contain binding sites formed by e.g. lectin or leucine-rich repeat (LRR) domains [7] [8] [9] [10]. Molecules of NLR are composed of i) nucleotide-binding LRR domain and ii) alternatively of either coiled-coil (CC) or Toll-like/interleukin 1 receptor (TIR) domain [11] [12] [13]

Methods

Results

Discussion

Conclusion