Nup98 mutation results in early senescence in Arabidopsis thaliana
Nup98 is a highly conserved nuclear pore protein in eukaryotes. In Arabidopsis thaliana, there are two homologs of the mammalian Nucleoporin98 in Arabidopsis, Nup98a (At1g10390) and Nup98b (At1g59660), and they share highly conserved amino acid sequences in the Phe-Gly (FG)-repeats and autoproteolytic domain (APD, Supplementary Fig. 1) [3, 6]. Nup98a was previously reported as DRACULA2 (DRA2), a regulator of the shade avoidance syndrome (SAS) in Arabidopsis  and immune responses to a rice fungal pathogen . To investigate Nup98 functions in plant development, we screened mutants of nup98a (SALK_080083, SALK_090744, SALK_023493, SALK_103803, SALK_015016) and nup98b (CS803848 and GABI_288A08) ordered from ABRC and GABI T-DNA mutant center, respectively. Homozygous lines were isolated for the following insertional mutants of SALK_103803, SALK_015016, GABI_288A08, and among them SALK_103803 and GABI_288A08 were the mutants reported by Parry . The T-DNAs in these homozygous mutants are inserted in coding regions (Fig. 1A) and RT-PCR results demonstrated that these mutants were null alleles (Fig. 1B), consistent with the Parry’s results . We did not observe any obvious phenotypes in flowering and senescence in either the nup98a or nup98b single mutants compared to wild type plants under long-day photoperiod conditions (Fig. 1C), as previous studies showed . As Nup98a and Nup98b share high conserved amino acid sequences (Supplementary Fig. 1), we tested the hypothesis that Nup98a and Nup98b functioned redundantly within the nup98a nup98b double mutants, which made by crossing the nup98a to nup98b single mutants. Strikingly, both double mutants, nup98a-1 nup98b-1 and nup98a-2 nup98b-1, displayed similar early senescence phenotypes compared to wild type plants (Fig. 1C and 1D). The senescence phenotype appeared not only on leaves, but also in the whole plant. Also, the double mutant plants had additional phenotypes, such as smaller inflorescences, flowers and siliques, short stature, and severe sterility compared to wild type plants (Supplementary Fig. 2 and 3). We recently reported that the nup98a-1 nup98b-1 double mutants has early flowering phenotype . When expressing the Nup98b gene in the double mutant, the senescence phenotypes were rescued (Fig. 1E). Our results demonstrate that Nup98a and Nup98b act redundantly.
To investigate the senescence phenotype is specific to the nup98a-1 nup98b-1 mutant, we selected another three nucleoporin mutants, nup96-1, nup160-1, and nup107-1, which show flowering phenotypes in our previous report , to analyze the effect of other nuclear pore components on senescence. To our surprise, there is no early senescence phenotypes observed in these mutants (Supplementary Fig. 4), suggesting that some of nucleoporins may not be involved in the regulation of senescence and that Nup98 likely has specific functions on senescence regulation.
Nup98 gene involves in multiple pathways of senescence initiation
Because the early senescence observed in the nup98a-1 nup98b-1 double mutant could be a secondary effect of altered development, we further explored the role of Nup98a and Nup98b in senescence regulation. To date, at least 200 genes have been identified to participate in senescence regulation in plants . We summarized main literatures as shown in Supplementary Fig. 5, which shows that various endogenous and environmental cues, such as hormones, sugar, light and photoperiod, and stresses, trigger plant senescence in multiple cross-talking patterns. To identify the potential link to early senescence, we measured mRNA abundance of important senescence-associated genes in the nup98a-1 nup98b-1 double mutant plants (Supplementary Fig. 5) at ZT0 (Zeitgeber 0, the time when light turned on) and ZT16 (the time when light turned off) in plants grown under long day conditions by real time quantitative PCR (RT-qPCR). As shown in Fig. 2, the transcript abundance of many genes tested in the nup98a-1 nup98b-1 mutant was obviously different from that in wild type plants. In the first category, WRKY53 (WRKY DNA-BINDING PROTEIN53), SAG13 (SENESCENCE-ASSOCIATED GENE13), WRKY6, NAC1 (NAM, ATAF, and CUC) and NAC2 displayed higher transcript abundances at both ZT0 and ZT16 (Fig. 2A), suggesting that genes in stress pathway (WRKY53, WRKY6, and NAC1) and SA pathway (WRKY53, WRKY6, and NAC2) were related to the senescence phenotypes of the nup98a-1 nup98b-1 double mutant. In the second category, SAG12, NAP (NAC DOMAIN CONTAINING PROTEIN), SAG2 and CAT1 (CATALASE1), also genes in stress and SA pathways, were only increased at either ZT0 or ZT16 (Fig. 2B). In contrast, in the third category, SAUR36 (SMALL AUXIN UPREGULATED36), WRKY70, ARP4 (ACTIN-RELATED PROTEIN4), SEN1 (SPLICING ENDONUCLEASE1), and COI1 (CORONATINE INSENSITIVE1) were decreased in abundance at either ZT0 and/or ZT16 (Fig. 2C), indicating that auxin (SAUR36) and jasmonate (COI1) signalling may be negatively related to the nup98 senescence phenotypes. The abundance of AGL15 (AGAMOUS-LIKE15), EBP1 (ERBB-3 BINDING PROTEIN1), RPS6a (RIBOSOMAL PROTEIN6a), and NPR1 (NONEXPRESSOR OF PR-GENES1) had opposite changes at ZT0 and ZT16 (Fig. 2D), suggesting that the function of these genes on Nup98 senescence regulation may be dependent on circadian clock.
This expression profile suggests that there are at least three characteristics of senescence processes in the nup98 double mutant. Firstly, several pathways, mainly stress and SA pathways, were involved in regulation of senescence processes in the nup98a-1 nup98b-1 double mutant. Secondly, different genes functioned in their own special modes, positively or negatively at different phases (morning or afternoon phases). Thirdly, some of genes, such as WRKY53, WRKY6, NAP1, and SAG2, may play roles in multiple pathways. The results indicate that the senescence phenotypes of the nup98 double mutant resulted from multiple pathways. Many genes showed circadian expression patterns, consistent with our previous report that Nup98 genes participate in regulation circadian clock .
Starch metabolism is impaired in the nup98a-1 nup98b-1 double mutant
During photosynthesis, starch is synthesized and stored in chloroplast, and then degraded at night. A number of genes are involved in starch degradation in plants (Supplementary Fig. 6) [17, 18]. Firstly, we checked starch homeostasis in leaves of the nup98a-1 nup98b-1 double mutant plants grown under 12 h light/12 h dark conditions (at ZT0, dawn, and ZT12, dusk) (Fig. 3). Leaves of all plants accumulated starch at dusk, however, double mutant plants had much more starch than wild type plants as determined by both iodine staining (Fig. 3A) and starch quantitative assay (Fig. 3B). The more intense signals in older, 21 and 28-day, leaves in the double mutant may be a consequence of accumulating starch over time. Therefore, the double mutant displayed much more starch not only at dawn but also at dusk than wild type plants, and this phenotype was much clearer in 14 and 21-day old seedlings (Fig. 3A and 3B). Together, these results suggest that starch metabolism is impaired in the nup98a-1 nup98b-1 double mutant.
We measured the transcript abundance of genes involved in starch metabolism  by RT-qPCR (Fig. 4) and found that many genes had significantly lower abundance in the double mutant at least at one time point compared to wild type plants. These genes encode enzymes for the degrading process of starch not only in the early steps in chloroplasts , such as GWD1 (α-GLUCAN WATER, DIKINASE1; or STARCH EXCESS1, SEX1), β-BAM1 (β-AMYLASE1), BAM3, BAM5, BAM6, BAM7, BAM8, SEX4, and LSF1 (LIKE SEX FOUR1), but also in the later steps, such as LDA (LIMIT-DEXTRINASE), AMY1 (α-AMYLASE) and AMY2, DPE1 (DISPROPORTIONING ENZYME) and DPE2, PHS1 (α-GLUCAN PHOSPHORYLASE) and PHS2. Time-dependent low-expression of these genes suggest that they are under the control of circadian clock, since Nup98 is involved in circadian regulation in Arabidopsis . These genes function at different steps of starch degradation . GWD1 is α-glucan water dikinase, which phosphorylates glucosyl residues of amylopectin at the C-6 position. BAMs are a family of β-amylase breaking down the α-1,4-linked glucose chains. LSF1 and SEX4 release the phosphate bound at C-6 and C-3 of glucosyl residues. Both ISA (ISOAMYLASE 3) and LDA (LIMIT-DEXTRINASE) hydrolyze α-1,6 branch points but have different substrates. AMYs act on α-1,4-linkages releasing linear α-1,4-linked oligosaccharides and branching α-1,4- and α-1,6-linked oligosaccharides. DPEs (DISPROPORTIONATING ENZYMEs) transfer glucose/α-1,4-linked glucan moiety from a donor glucan to an acceptor, releasing the non-reducing end of glucose/glucan moiety. PHSs (α--GLUCAN PHOSPHORYLASEs) act on the non-reducing end of α-1,4-linked glucose. Lower abundance of these genes resulted in a starch-excess phenotype in the nup98a-1 nup98b-1 double mutant (Fig. 3) as these gene mutants . The mRNA abundance of some other genes involved in starch metabolism, including GWD2, GWD3, ISA3 (ISOAMYLASE3) and AMY3, was not significantly affected, suggesting the effect of Nup98a/b on starch metabolism was limited to some specific enzymes.
We also measured the mRNA abundance of genes related to photosynthesis and sugar metabolism by RT-qPCR in the nup98a-1 nup98b-1 double mutant and wild type plants (Supplementary Fig. 7). In terms of photosynthesis related genes, the decrease of mRNA abundance of LHCA (PHOTOSYSTEM I LIGHT HARVESTING COMPLEX GENE A) and LHCB (PHOTOSYSTEM I LIGHT HARVESTING COMPLEX GENE B) was observed in the nup98a-1 nup98b-1 double mutant at different time points, e.g., LHCA1/2 and LHCB1.1 at ZT0 and LHCA1 and LHCB1.4 genes at ZT16. We also observed the decrease of mRNA abundances of KIN10 and KIN11, which is expected since both of genes are sugar signaling genes, in the double mutant compared to wild type plants. Both genes are involved in delaying plant senescence [21, 26, 27], therefore the reduced mRNA abundance may be associated with earlier senescence (Supplementary Fig. 5). We also observed slightly-increased mRNA abundance of HXK1 at dusk (ZT16), that may contribute to earlier senescence via the cytokinin signaling pathway . Unexpectedly, mRNA abundance of TPS1, a senescence activator , was reduced in the nup98a-1 nup98b-1 double mutant compared to wild type plants, suggesting that T6P (trehalose-6-phosphate) was not related to senescence of the nup98a-1 nup98b-1 double mutant. The results indicate that starch synthesis and sugar signalling are impaired in the double mutant.
Exogenous sugar rescues the early senescence in the nup98a-1 nup98b-1 double mutant
Based on our results, we interpreted that the carbon or energy supply was impaired in nup98a-1 nup98b-1 double mutant plants. We tested the idea by supplying exogenous carbon in the form of sucrose in growing medium to see if the early senescence phenotype in the nup98a-1 nup98b-1 double mutant plants could be rescued. Our results showed that sucrose and MS basal nutrients could support the double mutant plants growing well even though they were weak compared to wild type plants (Fig. 5). Both plants completed their life cycles on medium containing agarose supplement with sucrose and basal nutrients. Then, we allowed double mutant and control plants to grow in MS medium until inflorescence emergence and then transferred them to soil. As expected, the double mutant grew well as wild type plants did on MS medium before transplanting (Supplementary Fig. 8). However, after transferring to soil, senescence symptoms on mutant plants’ leaves quickly appeared at day 6, and the mutant plants wilted at day 30 (Supplementary Fig. 8). If seeds were sown on agarose medium plus either MS basal nutrients or sucrose, both wild type plants and the nup98 double mutant would not survive as plants growing on agarose medium without any supplements (Supplementary Fig. 9).
To rule out the potential effect of soil on senescence phenotypes observed above, we carried out another experiment to test if exogenous macro and micronutrients would complement the phenotypes observed in the mutant by continuously growing plants on medium at different strengths of sucrose and macro- and micro-nutrients (Supplementary Fig. 9). To our surprise, not only did sucrose suppress the early senescence phenotype in the double mutant but also macro- and micro-nutrients in the presence of sucrose. The lower strength basal nutrients (½ MS) enhanced the lower sucrose (1.5%) effect on suppressing senescence, suggesting that both energy supply and basal nutrients metabolism are impaired in the nup98a-1 nup98b-1 double mutant.
Starvation and senescence marker genes express highly in the nup98a-1 nup98b-1 double mutant
Results above imply that the nup98a-1 nup98b-1 double mutant may suffer from sugar starvation and senescence. Next, we asked if markers genes of starvation or senescence expressed highly in the nup98a-1 nup98b-1 double mutant. DORMANCY-ASSOCIATED PROTEIN-LIKE 1 (DRM1/DYL1, At1g28330) and DARK INDUCIBLE 6 (DIN6, At3g47340) [38, 39] are two well-studied sugar starvation marker genes, whereas SAG12 (At5g45890) and WRKY53 (At4g23810) are well-characterized senescence markers [40-42]. Autophagy is an important event occurring during sugar starvation and senescence [38, 43, 44], and AUTOPHAGY8a (ATG8a, At4g21980) and ATG8e (At2g45170) are two typical molecular indicators for autophagy in plants . Therefore, we investigated expression changes of these genes in the nup98a-1 nup98b-1 double mutant compared to that in wild type plants, and the results showed that they had different changes in a time- and developmental-dependent mode (Fig. 6). In the double mutant, DRM1 had significantly higher expression at ZT0, but lower at ZT12 from very early stage (day 5 after germination) (Fig. 6A). DIN is a light-repressed and dark-induced gene , and its high level of expression at ZT0 in the nup98a-1 nup98b-1 double mutant became obvious at day 15, but at ZT12 higher abundancy appeared earlier from day 10 (Fig. 6A). Compared to wild type plants, the senescence marker WARKY53 in the nup98a-1 nup98b-1 double mutant expressed higher at the early stage when DRM1 expression was in disorder (day 5) (Fig. 6B). SAG12 is a developmentally-controlled indicator for the later stage of senescence [47, 48]. We found that there was no much difference of SAG12 expression in the early stage (day 5) between the nup98a-1 nup98b-1 double mutant and wild type plants. However, SAG12 had a higher expression level in the nup98a-1 nup98b-1 double mutant at both ZT0 and ZT12 from day 10 (Fig. 6B). In the meanwhile, the two markers of autophagy, ATG8a and ATG8e, also had higher abundancy of mRNA in most of samples of the double mutant from day 10. Token together, our results showed that the nup98a-1 nup98b-1 double mutant appeared the sign of energy starvation, at least at molecular level, in early developmental stage when plants did not display visible senescence phenotypes. And these expression changes had circadian and developmental characters. A previous report shows that different sugars (such as sucrose, glucose, and fructose) have different effects on the regulation of senescence . Therefore, these earlier and higher expression levels of these marker genes were consistent with the senescence phenotype of the nup98a-1 nup98b-1 double mutant.
Nup98 proteins mainly localize to both the nuclear membrane and nucleoplasm
Nup98 is one of the mobile and peripheral FG (Phe-Gly domain) nucleoporins and locates at both the nuclear and cytoplasmic sides of the NPC central channel [4, 5]. Arabidopsis Nup98a (also known as DRA2) is also found distributing in different subcellular compartments . We constructed transgenic Arabidopsis plants expressing 35S::GFP:Nup98a and 35S::GFP:Nup98b and analyzed the subcellular localization of both translation fusion proteins. Not surprisingly, both proteins were distributed in the cytoplasm, the nucleoplasm and at the nuclear periphery (Fig. 7). We also observed no significant difference in the subcellular distribution of Nup98a and Nup98b and this is consistent with our observations of their genetic redundancy. In conclusion, our combined results demonstrate that Nup98b proteins localize at both the nucleus and cytoplasm as Nup98a proteins  and their homologs in other organisms do [4, 5].