Genomic identification and expression analysis of nuclear pore proteins in Malus domestica

Abstract

The nuclear pore complex (NPC), comprised of individual nucleoporin (Nup) proteins, controls nucleo-cytoplasmic transport of RNA and protein, and is important for regulating plant growth and development. However, there are no reports on this complex in fruit tree species. In this study, we identified 38 apple Nups and named them based on the known Arabidopsis thaliana homologs. We also completed bioinformatics analyses of the intron and exon structural data for apple Nups. The proteins encoded by the apple Nups lacked a universally conserved domain. Moreover, a phylogenetic analysis separated the apple and A. thaliana Nups into three groups. The phylogenetic tree indicated that MdNup54 and MdNup62 are most closely related to genes in other Rosaceae species. To characterize the 38 candidate Malus domestica Nups, we measured their stage-specific expression levels. Our tests revealed these proteins were differentially expressed among diverse tissues. We analyzed the expression levels of seven apple Nups in response to an indole-3-acetic acid (IAA) treatment. The phytohormone treatment significantly inhibited apple flowering. A qRT-PCR analysis proved that an IAA treatment significantly inhibited the expression of these seven genes. A preliminary study regarding two members of the Nup62 subcomplex, MdNup54 and MdNup62, confirmed these two proteins can interact with each other. A yeast two-hybrid assay verified that MdNup54 can interact with MdKNAT4 and MdKNAT6. On the basis of the study results, we identified apple NPC and predicted its structure and function. The data generated in this investigation provide important reference material for follow-up research.

Evolution and diversification of the nuclear pore complex

“…ELYS mediates post-mitotic NPC assembly/anchoring, chromatin compaction and NPC/lamina associations, but most of these functions are metazoan and/or open mitosis-specific [31,32]. Paradoxically ELYS is present in most taxa, except excavates or TSAR, suggesting a probable ancient origin [12,[17][18][19][20][21]. As neither plants nor fungi share a lamina with metazoa, ELYS functions are unclear [33,34].…”

“… Data collated for H. Sapiens [ 8 ], S. cerevisiae [ 10 ], S. pombe [ 12 ], C. thermophilum [ 14 ], C. reinhardtii [ 17 ], A. thaliana [ 18 ], M. domestica [ 19 ], T. thermophila [ 20 ], T. brucei [ 21 ] species and Chlorarachniophytes and Cryptophyceae species clades [ 125 ]. Nucleoporins are listed according to their complex and ring disposition in NPC compartments: the inner ring (IR), outer cytoplasmic and nucleoplasmic rings (CR and NR), membrane ring (Mem.…”

“…Whether this is related to the transcriptional activity differences is yet to be explored. M. domestica (apple) differs from Arabidopsis as it possesses multiple Y-complex subunit paralogs (albeit likely results of genome duplication) [ 18 , 19 ] ( Figure 2 ), while T. brucei acquired an additional complex of three FG-Nups, symmetrically positioned on both sides of the NE [ 21 ]; the exact symmetry and stoichiometry of the outer ring in plants and excavates remains to be established.…”

“…Molecular data are available for NPCs from many lineages, including metazoa (Homo sapiens) [5][6][7][8], fungi (S. cerevisiae, Schizosaccharomyces pombe, Chaetomium thermophilum) [9][10][11][12][13][14][15][16], algae (Chlamydomonas reinhardtii) [17], higher plants (Arabidopsis thaliana, Malus domestica) [18,19], alveolates (Tetrahymena thermophila) [20] and excavates (Trypanosoma brucei) [21]. While not particularly deep in taxon coverage, these data span a considerable proportion of eukaryotic diversity.…”

MdNup62 interactions with MdHSFs involved in flowering and heat-stress tolerance in apple

“…A nuclear pore complex (NPC) is composed of a class of nucleoporins (Nups ) located in the nuclear pore (Tamura, Fukao, Iwamoto, Haraguchi & Hara-Nishimura, 2010). More than 30 Nups have been identified in Arabidopsis and 38 members have been identified in apple (Tamuraet al , 2010, Zhang, An, Jia, Zhang, Liang, Zhang, Zhou, Ma, Han, Xing & Ren, 2020. Some Nups interact and form three subcomplexes:Nup62 , Nup93 , and Nup107-160 (Tamura et al , 2010, Zhu, Wang, Tang, Hsu, Xie, Du H, Yang, Tao & Zhu, 2017.Nups control the transport of substances, such as RNA and proteins, between the nucleus and cytoplasm (Parry, 2013, Zhang, Wang, Kim, Yan, Yan, Pang & Hua, 2020.…”