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author:("Lin, jiaxing")
1.  Salt stress triggers enhanced cycling of Arabidopsis root plasma-membrane aquaporins 
Plant Signaling & Behavior  2012;7(4):529-532.
Aquaporins of the plasma membrane intrinsic protein (PIP) subfamily are channels which facilitate the diffusion of water across the plant plasma membrane (PM). Although PIPs have been considered as canonical protein markers of this compartment, their endomembrane trafficking is still not well documented. We recently obtained insights into the constitutive cycling of PIPs in Arabidopsis root cells by means of fluorescence recovery after photobleaching (FRAP). This work also uncovered the behavior of the model isoform AtPIP2;1 in response to NaCl. The present addendum connects these findings to another recent work which describes the dynamic properties of AtPIP2;1 in the PM in normal and salt stress conditions by means of single particle tracking (SPT) and fluorescence correlation spectroscopy (FCS). The results suggest that membrane rafts play an important role in the partitioning of AtPIP2;1 in normal conditions and that clathrin-mediated endocytosis is predominant. In salt stress conditions, the rate of AtPIP2;1 cycling was enhanced and endocytosis was cooperated by a membrane raft-associated salt-induced pathway and a clathrin-dependent pathway.
doi:10.4161/psb.19350
PMCID: PMC3419046  PMID: 22499180
aquaporin; constitutive cycling; salt stress; fluorescence recovery after photobleaching; single particle tracking; fluorescence correlation spectroscopy
2.  Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing 
BMC Plant Biology  2012;12:146.
Background
Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date.
Results
To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated.
Conclusions
We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution.
doi:10.1186/1471-2229-12-146
PMCID: PMC3462689  PMID: 22894611
Chinese fir; miRNA; rasiRNA; tasiRNA; Cunninghamia lanceolata
3.  Transcriptome-wide identification and characterization of miRNAs from Pinus densata 
BMC Genomics  2012;13:132.
Background
MicroRNAs (miRNAs) play key roles in diverse developmental processes, nutrient homeostasis and responses to biotic and abiotic stresses. The biogenesis and regulatory functions of miRNAs have been intensively studied in model angiosperms, such as Arabidopsis thaliana, Oryza sativa and Populus trichocarpa. However, global identification of Pinus densata miRNAs has not been reported in previous research.
Results
Here, we report the identification of 34 conserved miRNAs belonging to 25 miRNA families from a P. densata mRNA transcriptome database using local BLAST and MIREAP programs. The primary and/or precursor sequences of 29 miRNAs were further confirmed by RT-PCR amplification and subsequent sequencing. The average value of the minimal folding free energy indexes of the 34 miRNA precursors was 0.92. Nineteen (58%) mature miRNAs began with a 5' terminal uridine residue. Analysis of miRNA precursors showed that 19 mature miRNAs were novel members of 14 conserved miRNA families, of which 17 miRNAs were further validated by subcloning and sequencing. Using real-time quantitative RT-PCR, we found that the expression levels of 7 miRNAs were more than 2-fold higher in needles than in stems. In addition, 72 P. densata mRNAs were predicted to be targets of 25 miRNA families. Four target genes, including a nodal modulator 1-like protein gene, two GRAS family transcription factor protein genes and one histone deacetylase gene, were experimentally verified to be the targets of 3 P. densata miRNAs, pde-miR162a, pde-miR171a and pde-miR482a, respectively.
Conclusions
This study led to the discovery of 34 conserved miRNAs comprising 25 miRNA families from Pinus densata. These results lay a solid foundation for further studying the regulative roles of miRNAs in the development, growth and responses to environmental stresses in P. densata.
doi:10.1186/1471-2164-13-132
PMCID: PMC3347991  PMID: 22480283
Pinus densata; miRNA; Transcriptome
4.  Casparian strip development and its potential function in salt tolerance 
Plant Signaling & Behavior  2011;6(10):1499-1502.
The root system is particularly affected by unfavorable conditions because it is in direct contact with the soil environment. Casparian strips, a specialized structure deposited in anticlinal walls, are characterized by the impregnation of the primary wall pores with lignin and suberin. The Casparian strips in the endo- and exodermis of vascular plant roots appear to play an important role in preventing the non-selective apoplastic bypass of salts into the stele along the apoplast under salt stress. However, only a few investigations have examined the deposition and function of these apoplastic barriers in response to salt stress in higher plants.
doi:10.4161/psb.6.10.17054
PMCID: PMC3256377  PMID: 21904117
Casparian strip; chemical components; development; root
5.  Mutation in SUMO E3 ligase, SIZ1, Disrupts the Mature Female Gametophyte in Arabidopsis 
PLoS ONE  2012;7(1):e29470.
Female gametophyte is the multicellular haploid structure that can produce embryo and endosperm after fertilization, which has become an attractive model system for investigating molecular mechanisms in nuclei migration, cell specification, cell-to-cell communication and many other processes. Previous reports found that the small ubiquitin-like modifier (SUMO) E3 ligase, SIZ1, participated in many processes depending on particular target substrates and suppression of salicylic acid (SA) accumulation. Here, we report that SIZ1 mediates the reproductive process. SIZ1 showed enhanced expression in female organs, but was not detected in the anther or pollen. A defect in the siz1-2 maternal source resulted in reduced seed-set regardless of high SA concentration within the plant. Moreover, aniline blue staining and scanning electron microscopy revealed that funicular and micropylar pollen tube guidance was arrested in siz1-2 plants. Some of the embryo sacs of ovules in siz1-2 were also disrupted quickly after stage FG7. There was no significant affects of the siz1-2 mutation on expression of genes involved in female gametophyte development- or pollen tube guidance in ovaries. Together, our results suggest that SIZ1 sustains the stability and normal function of the mature female gametophyte which is necessary for pollen tube guidance.
doi:10.1371/journal.pone.0029470
PMCID: PMC3253799  PMID: 22253727
6.  Golgi Apparatus-Localized Synaptotagmin 2 Is Required for Unconventional Secretion in Arabidopsis 
PLoS ONE  2011;6(11):e26477.
Background
Most secretory proteins contain signal peptides that direct their sorting to the ER and secreted via the conventional ER/Golgi transport pathway, while some signal-peptide-lacking proteins have been shown to export through ER/Golgi independent secretory pathways. Hygromycin B is an aminoglycoside antibiotic produced by Streptomyces hygroscopicus that is active against both prokaryotic and eukaryotic cells. The hygromycin phosphotransferase (HYGR) can phosphorylate and inactivate the hygromycin B, and has been widely used as a positive selective marker in the construction of transgenic plants. However, the localization and trafficking of HYGR in plant cells remain unknown. Synaptotagmins (SYTs) are involved in controlling vesicle endocytosis and exocytosis as calcium sensors in animal cells, while their functions in plant cells are largely unclear.
Methodology/Principal Findings
We found Arabidopsis synaptotagmin SYT2 was localized on the Golgi apparatus by immunofluorescence and immunogold labeling. Surprisingly, co-expression of SYT2 and HYGR caused hypersensitivity of the transgenic Arabidopsis plants to hygromycin B. HYGR, which lacks a signal sequence, was present in the cytoplasm as well as in the extracellular space in HYGR-GFP transgenic Arabidopsis plants and its secretion is not sensitive to brefeldin A treatment, suggesting it is not secreted via the conventional secretory pathway. Furthermore, we found that HYGR-GFP was truncated at carboxyl terminus of HYGR shortly after its synthesis, and the cells deficient SYT2 failed to efficiently truncate HYGR-GFP,resulting in HYGR-GFP accumulated in prevacuoles/vacuoles, indicating that SYT2 was involved in HYGR-GFP trafficking and secretion.
Conclusion/Significance
These findings reveal for the first time that SYT2 is localized on the Golgi apparatus and regulates HYGR-GFP secretion via the unconventional protein transport from the cytosol to the extracelluar matrix in plant cells.
doi:10.1371/journal.pone.0026477
PMCID: PMC3225361  PMID: 22140429
7.  Arabidopsis R-SNARE Proteins VAMP721 and VAMP722 Are Required for Cell Plate Formation 
PLoS ONE  2011;6(10):e26129.
Background
Cell plate formation during plant cytokinesis is facilitated by SNARE complex-mediated vesicle fusion at the cell-division plane. However, our knowledge regarding R-SNARE components of membrane fusion machinery for cell plate formation remains quite limited.
Methodology/Principal Findings
We report the in vivo function of Arabidopsis VAMP721 and VAMP722, two closely sequence-related R-SNAREs, in cell plate formation. Double homozygous vamp721vamp722 mutant seedlings showed lethal dwarf phenotypes and were characterized by rudimentary roots, cotyledons and hypocotyls. Furthermore, cell wall stubs and incomplete cytokinesis were frequently observed in vamp721vamp722 seedlings. Confocal images revealed that green fluorescent protein-tagged VAMP721 and VAMP722 were preferentially localized to the expanding cell plates in dividing cells. Drug treatments and co-localization analyses demonstrated that punctuate organelles labeled with VAMP721 and VAMP722 represented early endosomes overlapped with VHA-a1-labeled TGN, which were distinct from Golgi stacks and prevacuolar compartments. In addition, protein traffic to the plasma membrane, but not to the vacuole, was severely disrupted in vamp721vamp722 seedlings by subcellular localization of marker proteins.
Conclusion/Significance
These observations suggest that VAMP721 and VAMP722 are involved in secretory trafficking to the plasma membrane via TGN/early endosomal compartment, which contributes substantially to cell plate formation during plant cytokinesis.
doi:10.1371/journal.pone.0026129
PMCID: PMC3191180  PMID: 22022536
8.  Variable-angle total internal reflection fluorescence microscopy of intact cells of Arabidopsis thaliana 
Plant Methods  2011;7:27.
Background
Total internal reflection fluorescence microscopy (TIRFM) is a powerful tool for observing fluorescently labeled molecules on the plasma membrane surface of animal cells. However, the utility of TIRFM in plant cell studies has been limited by the fact that plants have cell walls, thick peripheral layers surrounding the plasma membrane. Recently, a new technique known as variable-angle epifluorescence microscopy (VAEM) was developed to circumvent this problem. However, the lack of a detailed analysis of the optical principles underlying VAEM has limited its applications in plant-cell biology.
Results
Here, we present theoretical and experimental evidence supporting the use of variable-angle TIRFM in observations of intact plant cells. We show that when total internal reflection occurs at the cell wall/cytosol interface with an appropriate angle of incidence, an evanescent wave field of constant depth is produced inside the cytosol. Results of experimental TIRFM observations of the dynamic behaviors of phototropin 1 (a membrane receptor protein) and clathrin light chain (a vesicle coat protein) support our theoretical analysis.
Conclusions
These findings demonstrate that variable-angle TIRFM is appropriate for quantitative live imaging of cells in intact tissues of Arabidopsis thaliana.
doi:10.1186/1746-4811-7-27
PMCID: PMC3219692  PMID: 21943324
Quantitative; VA-TIRFM; optical analysis; intact cell; cell wall
9.  Development of casparian strip in rice cultivars 
Plant Signaling & Behavior  2011;6(1):59-65.
The development of Casparian strips (CSs) on the endo- and exodermis and their chemical components in roots of three cultivars of rice (Oryza sativa) with different salt tolerance were compared using histochemistry and Fourier transform infrared (FTIR) spectroscopy. The development and deposition of suberin lamellae of CSs on the endo- and exodermis in the salt-tolerant cultivar Liaohan 109 was earlier than in the moderately tolerant cultivar Tianfeng 202 and the sensitive cultivar Nipponbare. The detection of chemical components indicated major contributions to the structure of the outer part from aliphatic suberin, lignin and cell wall proteins and carbohydrates to the rhizodermis, exodermis, sclerenchyma and one layer of cortical cells in series (OPR) and the endodermal Casparian strip. Moreover, the amounts of these major chemical components in the outer part of the Liaohan 109 root were higher than in Tianfeng 202 and Nipponbare, but there was no distinct difference in endodermal CSs among the three rice cultivars. The results suggest that the exodermis of the salt-tolerant cultivar Liaohan 109 functions as a barrier for resisting salt stress.
doi:10.4161/psb.6.1.13545
PMCID: PMC3122007  PMID: 21248477
casparian strip; chemical components; development; rice; root
10.  Multiple receptor complexes assembled for transmitting CLV3 signaling in Arabidopsis 
Plant Signaling & Behavior  2010;5(3):300-302.
In Arabidopsis, the feedback regulatory loop between CLAVATA3 (CLV3) signaling pathway and transcription factor, WUSCHEL (WUS) plays a significant role in shoot apical meristems (SAM) maintenance. Previously, CLV1/CLV2 heterodimers were supposed to perceive and transmit CLV3 signaling. Recent genetic analysis isolated a novel receptor kinase, CORYNE (CRN), which was found to be involved in the CLV3 pathway. Therefore, new hypothesis was put forward that CRN probably acts with CLV2 to transmit CLV3 in parallel with CLV1 based on genetic analysis. In our recent work, we took advantage of firefly luciferase complementation imaging (LCI) assay to analyze the interactions among CLV1, CLV2 and CRN in both Arabidopsis thaliana protoplasts and Nicotiana benthamiana leaves. We identified the physical interaction between CLV2 and CRN in the absence of CLV3 and found some interesting phenomenon such as CLV1, CLV2 and CRN may form a complex, and that CRN was able to form homodimers. These new observations make the relationships among these three proteins more complex than that indicated in two-parallel pathway model. Combining current genetic and our new biochemical evidence, a more possible and detailed model for CLV3 pathway was developed.
PMCID: PMC2881284  PMID: 20220313
CLAVATA3 (CLV3) signaling pathway; firefly luciferase complementation imaging (LCI) assay; Arabidopsis thaliana protoplasts; Nicotiana benthamiana leaves; homodimers
11.  Disruption of actin filaments induces mitochondrial Ca2+ release to the cytoplasm and [Ca2+]c changes in Arabidopsis root hairs 
BMC Plant Biology  2010;10:53.
Background
Mitochondria are dynamic organelles that move along actin filaments, and serve as calcium stores in plant cells. The positioning and dynamics of mitochondria depend on membrane-cytoskeleton interactions, but it is not clear whether microfilament cytoskeleton has a direct effect on mitochondrial function and Ca2+ storage. Therefore, we designed a series of experiments to clarify the effects of actin filaments on mitochondrial Ca2+ storage, cytoplasmic Ca2+ concentration ([Ca2+]c), and the interaction between mitochondrial Ca2+ and cytoplasmic Ca2+ in Arabidopsis root hairs.
Results
In this study, we found that treatments with latrunculin B (Lat-B) and jasplakinolide (Jas), which depolymerize and polymerize actin filaments respectively, decreased membrane potential and Ca2+ stores in the mitochondria of Arabidopsis root hairs. Simultaneously, these treatments induced an instantaneous increase of cytoplasmic Ca2+, followed by a continuous decrease. All of these effects were inhibited by pretreatment with cyclosporin A (Cs A), a representative blocker of the mitochondrial permeability transition pore (mPTP). Moreover, we found there was a Ca2+ concentration gradient in mitochondria from the tip to the base of the root hair, and this gradient could be disrupted by actin-acting drugs.
Conclusions
Based on these results, we concluded that the disruption of actin filaments caused by Lat-B or Jas promoted irreversible opening of the mPTP, resulting in mitochondrial Ca2+ release into the cytoplasm, and consequent changes in [Ca2+]c. We suggest that normal polymerization and depolymerization of actin filaments are essential for mitochondrial Ca2+ storage in root hairs.
doi:10.1186/1471-2229-10-53
PMCID: PMC2923527  PMID: 20334630
12.  No Detectable Maternal Effects of Elevated CO2 on Arabidopsis thaliana Over 15 Generations 
PLoS ONE  2009;4(6):e6035.
Maternal environment has been demonstrated to produce considerable impact on offspring growth. However, few studies have been carried out to investigate multi-generational maternal effects of elevated CO2 on plant growth and development. Here we present the first report on the responses of plant reproductive, photosynthetic, and cellular characteristics to elevated CO2 over 15 generations using Arabidopsis thaliana as a model system. We found that within an individual generation, elevated CO2 significantly advanced plant flowering, increased photosynthetic rate, increased the size and number of starch grains per chloroplast, reduced stomatal density, stomatal conductance, and transpiration rate, and resulted in a higher reproductive mass. Elevated CO2 did not significantly influence silique length and number of seeds per silique. Across 15 generations grown at elevated CO2 concentrations, however, there were no significant differences in these traits. In addition, a reciprocal sowing experiment demonstrated that elevated CO2 did not produce detectable maternal effects on the offspring after fifteen generations. Taken together, these results suggested that the maternal effects of elevated CO2 failed to extend to the offspring due to the potential lack of genetic variation for CO2 responsiveness, and future plants may not evolve specific adaptations to elevated CO2 concentrations.
doi:10.1371/journal.pone.0006035
PMCID: PMC2698214  PMID: 19557175
13.  Actin Turnover Is Required for Myosin-Dependent Mitochondrial Movements in Arabidopsis Root Hairs 
PLoS ONE  2009;4(6):e5961.
Background
Previous studies have shown that plant mitochondrial movements are myosin-based along actin filaments, which undergo continuous turnover by the exchange of actin subunits from existing filaments. Although earlier studies revealed that actin filament dynamics are essential for many functions of the actin cytoskeleton, there are little data connecting actin dynamics and mitochondrial movements.
Methodology/Principal Findings
We addressed the role of actin filament dynamics in the control of mitochondrial movements by treating cells with various pharmaceuticals that affect actin filament assembly and disassembly. Confocal microscopy of Arabidopsis thaliana root hairs expressing GFP-FABD2 as an actin filament reporter showed that mitochondrial distribution was in agreement with the arrangement of actin filaments in root hairs at different developmental stages. Analyses of mitochondrial trajectories and instantaneous velocities immediately following pharmacological perturbation of the cytoskeleton using variable-angle evanescent wave microscopy and/or spinning disk confocal microscopy revealed that mitochondrial velocities were regulated by myosin activity and actin filament dynamics. Furthermore, simultaneous visualization of mitochondria and actin filaments suggested that mitochondrial positioning might involve depolymerization of actin filaments on the surface of mitochondria.
Conclusions/Significance
Base on these results we propose a mechanism for the regulation of mitochondrial speed of movements, positioning, and direction of movements that combines the coordinated activity of myosin and the rate of actin turnover, together with microtubule dynamics, which directs the positioning of actin polymerization events.
doi:10.1371/journal.pone.0005961
PMCID: PMC2694364  PMID: 19536333
14.  Overexpression of PwTUA1, a pollen-specific tubulin gene, increases pollen tube elongation by altering the distribution of α-tubulin and promoting vesicle transport 
Journal of Experimental Botany  2009;60(9):2737-2749.
Tubulin genes are intimately associated with cell division and cell elongation, which are central to plant secondary cell wall development. However, their roles in pollen tube polar growth remain elusive. Here, a TUA1 gene from Picea wilsonii, which is specifically expressed in pollen, was isolated. Semi-quantitative RT-PCR analysis showed that the amount of PwTUA1 transcript varied at each stage of growth of the pollen tube and was induced by calcium ions and boron. Transient expression analysis in P. wilsonii pollen indicated that PwTUA1 improved pollen germination and pollen tube growth. The pollen of transgenic Arabidopsis overexpressing PwTUA1 also showed a higher percentage of germination and faster growth than wild-type plants not only in optimal germination medium, but also in medium supplemented with elevated levels of exogenous calcium ions or boron. Immunofluorescence and electron microscopy showed α-tubulin to be enriched and more vesicles accumulated in the apex region in germinating transgenic Arabidopsis pollen compared with wild-type plants. These results demonstrate that PwTUA1 up-regulated by calcium ions and boron contributes to pollen tube elongation by altering the distribution of α-tubulin and regulating the deposition of pollen cell wall components during the process of tube growth. The possible role of PwTUA1 in microtubule dynamics and organization was discussed.
doi:10.1093/jxb/erp143
PMCID: PMC2692020  PMID: 19454597
Microtubules; Picea wilsonii; pollen tube; PwTUA1; transgenic Arabidopsis; α-tubulin

Results 1-14 (14)