Genome-wide survey and expression analysis of NIN-like Protein (NLP) genes reveals its potential roles in the response to nitrate signaling in tomato

Abstract

Background Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference for nitrate as an inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. Results In this study, genome-wide analysis identified six NLP members in tomato genome. These members were clustered into three clades in a phylogenetic tree. Comparative genomic analysis showed that SlNLP genes exhibited collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in the tomato genome. Tissue-specific expression analysis showed that one of the close homologs of AtNLP6/7, SlNLP3, was strongly expressed in roots during both the seedling and flowering stages, that SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves and that SlNLP6 was expressed at high levels in fruits. Furthermore, the nitrate uptake in tomato roots and the expression patterns of SlNLP genes were measured under nitrogen deficiency and nitrate resupply conditions. Four SlNLPs, SlNLP1, SlNLP2, SlNLP4 and SlNLP6, were upregulated after nitrogen starvation. And SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions These results provide significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.

Genome-wide investigation of NLP gene family members in alfalfa (Medicago sativa L.): Evolution and expression profiles during development and stress

“…According to our collinearity analysis of the MsNLP genes, we observed all pairs of four groups of fragment duplications (Fig. 3and Additional le 5), in which similar events have been found to have occurred in many species, including Arabidopsis thaliana, rice [5], tomato [32] and others. Therefore, the presence of duplication events implied that segmental duplications was the major evolutionary mechanisms that drove alfalfa NLP expansion in our research.…”

Genome-wide investigation of NLP gene family members in alfalfa (Medicago sativa L.): evolution and expression profiles during development and stress

“…According to our collinearity analysis of the MsNLP genes, we observed all pairs of four groups of fragment duplications (Fig. 3 and Additional file 5 ), in which similar events have been found to have occurred in many species, including Arabidopsis thaliana, rice [ 5 ], tomato [ 32 ] and others. Therefore, the presence of duplication events implied that segmental duplications were the major evolutionary mechanisms that drove alfalfa NLP expansion in our research.…”

NLP2-NR Module Associated NO Is Involved in Regulating Seed Germination in Rice under Salt Stress

“…NIN-like protein (NLP) belongs to the transcript factor family which act as master regulator in nitrate response by binding to nitrate responsive cis-element (NRE) in many nitrogen responding genes in Arabidopsis [ 58 , 59 ]. In rice, 6 NLP genes has been identified based on in silico analysis [ 21 ]. OsNLP1 , OsNLP3 and OsNLP4 were reported to play key role in improving yield and nitrogen use efficiency.…”

“…Double mutation of two NR encoding genes, nia1/nia2 , resulted in reduced content of both NO and nitrite in Arabidopsis [ 19 ]. Numerous studies have proved that NO is critical in promoting salt tolerance of plant at different developmental stage [ 20 , 21 ]. In salt-affected plants, NO was found to significantly improve seed vigor and germination [ 22 ], while priming or pretreatment with SNP, a donor of NO, will significantly promote seed germination and early seedling growth under salt stress [ 23 , 24 ].…”