Nitrate Signaling and Its Role in Regulating Flowering Time in Arabidopsis thaliana.

Plant growth is coordinated with the availability of nutrients that ensure its development. Nitrate is a major source of nitrogen (N), an essential macronutrient for plant growth. It also acts as a signaling molecule to modulate gene expression, metabolism, and a variety of physiological processes. Recently, it has become evident that the calcium signal appears to be part of the nitrate signaling pathway. New key players have been discovered and described in Arabidopsis thaliana (Arabidopsis). In addition, knowledge of the molecular mechanisms of how N signaling affects growth and development, such as the nitrate control of the flowering process, is increasing rapidly. Here, we review recent advances in the identification of new components involved in nitrate signal transduction, summarize newly identified mechanisms of nitrate signaling-modulated flowering time in Arabidopsis, and suggest emerging concepts and existing open questions that will hopefully be informative for further discoveries.

An Ultrastable Virus-Like Particle with a Carbon Dot Core and Expanded Sequence Plasticity.

Ordered bio-inorganic hybridization has evolved for the generation of high-performance materials in living organisms and inspires novel strategies to design artificial hybrid materials. Virus-like particles (VLPs) are attracting extensive interest as self-assembling systems and platforms in the fields of biotechnology and nanotechnology. However, as soft nanomaterials, their structural stability remains a general and fundamental problem in various applications. Here, an ultrastable VLP assembled from the major capsid protein (VP1) of simian virus 40 is reported, which contains a carbon dot (C-dot) core. Co-assembly of VP1 with C-dots led to homogeneous T = 1 VLPs with a fourfold increase in VLP yields. The resultant hybrid VLPs showed markedly enhanced structural stability and sequence plasticity. C-dots and a polyhistidine tag fused to the inner-protruding N-terminus of VP1 contributed synergistically to these enhancements, where extensive and strong noncovalent interactions on the C-dot/VP1 interfaces are responsible according to cryo-EM 3D reconstruction, molecular simulation, and affinity measurements. C-dot-enhanced ultrastable VLPs can serve as a new platform, enabling the fabrication of new architectures for bioimaging, theranostics, nanovaccines, etc. The hybridization strategy is simple and can easily be extended to other VLPs and protein nanoparticle systems.

Identification of miRNAs associated with dark-induced senescence in Arabidopsis.

BACKGROUND: microRNAs (miRNAs) are endogenous small (~21 nucleotide) single-stranded non-coding RNAs that typically function by guiding cleavage of target genes. To find the miRNAs that may be involved in dark-induced leaf senescence, we identified miRNAs by microarray platform using Arabidopsis thaliana leaves from both whole darkened plants (DPs) and individually darkened leaves (IDLs). RESULTS: We found that the expressions of 137 miRNAs (P < 0.01, signal intensity >0) were significantly changed both in DP and IDL leaves. Among them, the expression levels of 44 miRNAs were relative higher than others (P < 0.01, signal intensity > 500). Of these differentially expressed miRNAs, 6 miRNAs (miR319a, 319c, miR159, miR164a, miR164c and miR390a) have been previously reported to be involved in dark-induced leaf senescence, and the remaining 38 miRNAs have not been implicated in leaf senescence before. Target genes of all 44 miRNAs were predicted, and some of them, such as NAC1, At3g28690, At2g17640 and At2g45160, were found in the Leaf Senescence Database (LSD). GO and KEGG analysis of 137 miRNAs showed that the predicted target genes were significantly enriched in transcription regulation, development-related biological processes and metabolic pathways. Expression levels of some of the corresponding miRNA targets (At1g73440, At2g03220 and At5g54810) were analysed and found to be significantly different in DP/IDL than that in WT. CONCLUSIONS: A microarray analysis about dark-induced miRNAs involved in leaf senescence are present here. Further expression analysis revealed that some new founding miRNAs maybe regulate leaf senescence in Arabidopsis, and the findings highlight the important role of miRNAs in dark-induced leaf senescence.

Nitrate Transporter 1.1 is involved in regulating flowering time via transcriptional regulation of FLOWERING LOCUS C in Arabidopsis thaliana.

Nitrate Transporter 1.1 (NRT1.1) is a nitrate transporter and sensor that modulates plant metabolism and growth. It has previously been shown that NRT1.1 is involved in the regulation of flowering time in Arabidopsis thaliana. In this study, we mainly used genetic and molecular methods to reveal the key flowering pathway that NRT1.1 may be involved in. Mutant alleles of CO and FLC, two crucial components in the flowering pathway, were introduced into the NRT1.1 defective mutant background by crossing. When the CO mutation was introduced into chl1-5 plants, the double mutant had delayed flowering time, and the CO transcription levels did not change in the chl1-5 plants. These results indicate that the CO-dependent photoperiod may be not associated with the delayed flowering shown by chl1-5. However, FLC loss of function could rescue the late flowering phenotype of the chl1-5 mutant, and FLC expression levels significantly increased in the NRT1.1 defective mutant plants. The FT expression levels in the chl1-5flc-3 double mutant plants recovered when the FLC mutation was introduced into chl1-5 plants and the up-regulation of FLC transcripts in the chl1-5 mutant plants was not related to nitrate availability. Our findings suggest that NRT1.1 affects flowering time via interaction with the FLC-dependent flowering pathway to influence its target gene FT, and that NRT1.1 may be included in an additional signaling pathway that represses the expression of FLC in a nitrate-independent manner.

Genome-wide identification and analysis of MICU genes in land plants and their potential role in calcium stress.

Mitochondrial calcium uptake (MICU) plays a vital role in the regulation of mitochondrial calcium homeostasis, and, consequently, influences calcium signaling transduction. Although genes involved in mitochondrial calcium uptake have been well studied in animals, less is known about their ubiquity and function in plants. In this study, we identified 96 MICU genes in land plants. On the basis of phylogenetic analysis of MICU proteins, they were classified into three clades: MICU from eudicots (Clade I), from monocots (Clade II), and from a basal angiosperm, a bryophyte, and a lycophyte (Clade III). Pairwise identity analysis across all MICU proteins showed that they are highly conserved among land plants at the protein level. Conserved motif analysis showed that most MICU proteins contained three EF-hands, and an additional EF-hand motif first identified in the MICU of Arabidopsis thaliana but not mammals was found in all 96 putative MICU proteins. This suggests that a cellular pathway of calcium uptake and signaling that requires three EF-hand motifs is evolutionarily conserved in plants. In addition, we discovered that MICU-defective mutants of Arabidopsis thaliana exhibited longer roots than wild-type under high calcium stress. Concurrently, the mRNA transcription levels of MICU were decreased under high calcium conditions. These results suggest that loss-of-function mutations of MICU may have potential roles in helping plants resist high calcium stress. This study provides clues to the possible role of plant MICU in mitochondrial calcium uptake, as well as useful information to support further studies on MICU function in plants.

Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.

The circadian clock controls many metabolic, developmental and physiological processes in a time-of-day-specific manner in both plants and animals. The photoreceptors involved in the perception of light and entrainment of the circadian clock have been well characterized in plants. However, how light signals are transduced from the photoreceptors to the central circadian oscillator, and how the rhythmic expression pattern of a clock gene is generated and maintained by diurnal light signals remain unclear. Here, we show that in Arabidopsis thaliana, FHY3, FAR1 and HY5, three positive regulators of the phytochrome A signalling pathway, directly bind to the promoter of ELF4, a proposed component of the central oscillator, and activate its expression during the day, whereas the circadian-controlled CCA1 and LHY proteins directly suppress ELF4 expression periodically at dawn through physical interactions with these transcription-promoting factors. Our findings provide evidence that a set of light- and circadian-regulated transcription factors act directly and coordinately at the ELF4 promoter to regulate its cyclic expression, and establish a potential molecular link connecting the environmental light-dark cycle to the central oscillator.

Effect of CO2 enrichment on the glucosinolate contents under different nitrogen levels in bolting stem of Chinese kale (Brassica alboglabra L.).

The effects of CO(2) enrichment on the growth and glucosinolate (GS) concentrations in the bolting stem of Chinese kale (Brassica alboglabra L.) treated with three nitrogen (N) concentrations (5, 10, and 20 mmol/L) were investigated. Height, stem thickness, and dry weights of the total aerial parts, bolting stems, and roots, as well as the root to shoot ratio, significantly increased as CO(2) concentration was elevated from 350 to 800 microl/L at each N concentration. In the edible part of the bolting stem, 11 individual GSs were identified, including 7 aliphatic and 4 indolyl GSs. GS concentration was affected by the elevated CO(2) concentration, N concentration, and CO(2)xN interaction. At 5 and 10 mmol N/L, the concentrations of aliphatic GSs and total GSs significantly increased, whereas those of indolyl GSs were not affected, by elevated atmospheric CO(2). However, at 20 mmol N/L, elevated CO(2) had no significant effects on the concentrations of total GSs and total indolyl GSs, but the concentrations of total aliphatic GSs significantly increased. Moreover, the bolting stem carbon (C) content increased, whereas the N and sulfur (S) contents decreased under elevated CO(2) concentration in the three N treatments, resulting in changes in the C/N and N/S ratios. Also the C/N ratio is not a reliable predictor of change of GS concentration, while the changes in N and S contents and the N/S ratio at the elevated CO(2) concentration may influence the GS concentration in Chinese kale bolting stems. The results demonstrate that high nitrogen supply is beneficial for the growth of Chinese kale, but not for the GS concentration in bolting stems, under elevated CO(2) condition.

Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction.

Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. We recently showed that Arabidopsis (Arabidopsis thaliana) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), a pair of homologous proteins sharing significant sequence homology to Mutator-like transposases, act as novel transcription factors essential for activating the expression of FHY1 and FHL (for FHY1-like), whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses. FHY3, FAR1, and Mutator-like transposases also share a similar domain structure, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). In this study, we performed a promoter-swapping analysis of FHY3 and FAR1. Our results suggest that the partially overlapping functions of FHY3 and FAR1 entail divergence of their promoter activities and protein subfunctionalization. To gain a better understanding of the molecular mode of FHY3 function, we performed a structure-function analysis, using site-directed mutagenesis and transgenic approaches. We show that the conserved N-terminal C2H2 zinc finger domain is essential for direct DNA binding and biological function of FHY3 in mediating light signaling, whereas the central core transposase domain and C-terminal SWIM domain are essential for the transcriptional regulatory activity of FHY3 and its homodimerization or heterodimerization with FAR1. Furthermore, the ability to form homodimers or heterodimers largely correlates with the transcriptional regulatory activity of FHY3 in plant cells. Together, our results reveal discrete roles of the multiple domains of FHY3 and provide functional support for the proposition that FHY3 and FAR1 represent transcription factors derived from a Mutator-like transposase(s).