Genome-Wide Identification, In Silico Characterization, and Evolutionary Significance of NIN-LIKE PROTEINS (NLP) Gene Family in 20 Spermatophyte Plants

Abstract

Nodule-Inception-Like Proteins (NLPs) are plant specific transcription factors that play significant role in orchestrating nitrogen response. NLPs have been widely studied in vascular plants, but they are not explicitly reported in many spermatophytes. In current study, in silico tools were employed for genome wide identification and characterization of NLPs in 20 different spermatophyte plants. The physico-chemical properties, protein motifs, conserved protein domains and phylogenetic properties of NLPs were assessed and compared to model plant, Arabidopsis thaliana’s NLPs (AtNLPs). The gene length, protein length and molecular weight of identified NLPs were greater than AtNLPs. The comparison of iso-electric point of selected NLPs showed slightly acidic range, which is close to that of AtNLPs. Online tools employed that all identified NLPs were hydrophilic, and they were found to be localised in the nucleus, except PpNLPs and AhNLPs which were found to be localized in periplasmic space and extracellular regions, respectively. Characteristic conserved domains of NLPs, including PB1 and RWP-RK were found in all the selected NLPs. Gene location analysis results yielded that chromosome number of many NLPs in the selected plants have not yet been identified. Protein motifs already identified in AtNLPs were also found in the selected NLPs. Gene structure analysis showed that both exons and introns were present in majority of NLPs. But CsNLPs, MgNLPs, MaNLPs and BrNLPs showed lack of introns. Phylogenetic analysis of the identified NLPs classified them into 5 distinct groups. Group I, II and III were classified based on previous studies done on NLPs from different plants. Group IV contained NLPs from Amborella trichopoda and Brachypodium stacei. Group V was recognised as the most evolutionary diverged group.