Release of apical dominance in potato tuber is accompanied by programmed cell death in the apical bud meristem

Involvement of Vacuolar Processing Enzyme CgVPE1 in Vacuole Rupture in the Programmed Cell Death during the Development of the Secretory Cavity in Citrus grandis 'Tomentosa' Fruits

Vacuolar processing enzymes (VPEs) with caspase-1-like activity are closely associated with vacuole rupture. The destruction of vacuoles is one of the characteristics of programmed cell death (PCD) in plants. However, whether VPE is involved in the vacuole destruction of cells during secretory cavity formation in Citrus plants remains unclear. This research identified a CgVPE1 gene that encoded the VPE and utilized cytology and molecular biology techniques to explore its temporal and spatial expression characteristics during the PCD process of secretory cavity cells in the Citrus grandis 'Tomentosa' fruit. The results showed that CgVPE1 is an enzyme with VPE and caspase-1-like activity that can self-cleave into a mature enzyme in an acidic environment. CgVPE1 is specifically expressed in the epithelial cells of secretory cavities. In addition, it mainly accumulates in vacuoles before it is ruptured in the secretory cavity cells. The spatial and temporal immunolocalization of CgVPE1 showed a strong relationship with the change in vacuole structure during PCD in secretory cavity cells. In addition, the change in the two types of VPE proteins from proenzymes to mature enzymes was closely related to the change in CgVPE1 localization. Our results indicate that CgVPE1 plays a vital role in PCD, causing vacuole rupture in cells during the development of the secretory cavity in C. grandis 'Tomentosa' fruits.

The protein phosphatase 2A catalytic subunit StPP2Ac2b is involved in the control of potato tuber sprouting and source-sink balance in tubers and sprouts

Sprouting negatively affects the quality of stored potato tubers. Understanding the molecular mechanisms that control this process is important for the development of potato varieties with desired sprouting characteristics. Serine/threonine protein phosphatase type 2A (PP2A) has been implicated in several developmental programs and stress responses in plants. PP2A comprises a catalytic (PP2Ac), a scaffolding (A), and a regulatory (B) subunit. In cultivated potato, six PP2Ac isoforms were identified, named StPP2Ac1, 2a, 2b, 3, 4, and 5. In this study we evaluated the sprouting behavior of potato tubers overexpressing the catalytic subunit 2b (StPP2Ac2b-OE). The onset of sprouting and initial sprout elongation is significantly delayed in StPP2Ac2b-OE tubers; however, sprout growth is accelerated during the late stages of development, due to a high degree of branching. StPP2Ac2b-OE tubers also exhibit a pronounced loss of apical dominance. These developmental characteristics are accompanied by changes in carbohydrate metabolism and response to gibberellic acid, and a differential balance between abscisic acid, gibberellic acid, cytokinins, and auxin. Overexpression of StPP2Ac2b alters the source-sink balance, increasing the source capacity of the tuber, and the sink strength of the sprout to support its accelerated growth.

A high trans-zeatin nucleoside concentration in corms may promote the multileaf growth of Amorphophallus muelleri

Amorphophallus muelleri has a multileaf growth pattern different from that of other konjacs; however, the hormonal mechanism underlying this phenomenon is not clear. In this study, the levels of hormones closely related to the sprouting of the axillary bud, including five types of cytokinins, indole-3-acetic acid (IAA) and abscisic acid (ABA) were measured. In the second leaf sprouting stage, the content of trans-zeatin riboside (tZR) in corms increased more than 5000-fold over that in the dormancy period. Surprisingly, although the expression of CYP735A1 and CYP735A2, which synthesize the precursors for tZR was elevated at the second leaf sprouting stage, the expression of IPTs, which have key roles in cytokinin biosynthesis, did not change significantly. In addition, most cytokinin contents in leaves during the same period were significantly lower than those in corms. We speculate that the high cytokinin contents in the corms may not biosynthesized de novo in corms. In addition, the IAA content in the corms also considerably increased during the second leaf sprouting stage. Indole-3-acetaldehyde oxidase (AO1) and auxin efflux carrier PIN1A, presented relatively high expression levels in the same period. In contrast, ABA content, and the expression of NCED1, a rate-limiting enzyme in ABA biosynthesis, were suppressed at the second leaf sprouting stage. It is worth mentioning that N6-(Δ2-isopentenyl) adenosine (iP)-type cytokinins have a high content in corms in the dormant period that significantly decreases after the first leaf sprouting stage, which is completely different from the trend of tZR. By treating dormant corms with iP, the percentage of multibud plants increased, and the growth performance in terms of bud and root length was significantly higher than those of the control. This implies that iP-type cytokinins tend to play a role in promoting first seedling sprouting. Furthermore, there was a remarkable increase of the IAA content in both corms and roots under iP treatment but an inhibitory effect in buds. We speculate that the increase in the IAA content induced by iP is tissue specific. These results will assist in the understanding of the role of hormones, especially cytokinins, in the multileaf growth type of konjac.

Comparative Proteomics of Potato Cultivars with a Variable Dormancy Period

The control of the duration of the dormancy phase is a significant challenge in the potato industry and for seed producers. However, the proteome landscape involved in the regulation of the length of the dormancy period over potato cultivars remains largely unexplored. In this study, we performed for the first time a comparative proteome profiling of potato cultivars with differential duration of tuber dormancy. More specifically, the proteome profiling of Agata, Kennebec and Agria commercial potato varieties with short, medium and medium-long dormancy, respectively, was assessed at the endodormancy stage using high-resolution two-dimensional electrophoresis (2-DE) coupled to reversed-phase liquid chromatography–tandem mass spectrometry (LC-TripleTOF MS/MS). A total of 11 proteins/isoforms with statistically significant differential abundance among cultivars were detected on 2-DE gels and confidently identified by LC-TripleTOF MS/MS. Identified proteins have known functions related to tuber development, sprouting and the oxylipins biosynthesis pathway. Fructokinase, a mitochondrial ADP/ATP carrier, catalase isozyme 2 and heat shock 70 kDa were the proteins with the strongest response to dormancy variations. To the best of our knowledge, this study reports the first candidate proteins underlying variable dormancy length in potato cultivars.

Sucrose promotes stem branching through cytokinin

Shoot branching is an important aspect of plant architecture because it substantially affects plant biology and agricultural performance. Sugars play an important role in the induction of shoot branching in several species, including potato (Solanum tuberosum L.). However, the mechanism by which sugars affect shoot branching remains mostly unknown. In the present study, we addressed this question using sugar-mediated induction of bud outgrowth in potato stems under etiolated conditions. Our results indicate that sucrose feeding to detached stems promotes the accumulation of cytokinin (CK), as well as the expression of vacuolar invertase (VInv), an enzyme that contributes to sugar sink strength. These effects of sucrose were suppressed by CK synthesis and perception inhibitors, while CK supplied to detached stems induced bud outgrowth and VInv activity in the absence of sucrose. CK-induced bud outgrowth was suppressed in vinv mutants, which we generated by genome editing. Altogether, our results identify a branching-promoting module, and suggest that sugar-induced lateral bud outgrowth is in part promoted by the induction of CK-mediated VInv activity.

Vacuolar processing enzyme translocates to the vacuole through the autophagy pathway to induce programmed cell death

The caspase-like vacuolar processing enzyme (VPE) is a key factor in programmed cell death (PCD) associated with plant stress responses. Growth medium lacking a carbon source and dark conditions caused punctate labeling of 35S::VPE1-GFP (StVPE1-GFP) in potato leaves. Under conditions of carbon starvation, VPE activity and PCD symptoms strongly increased in BY-2 cells, but to a much lesser extent in VPE-RNAi BY-2 cells. During extended exposure to carbon starvation, VPE expression and activity levels peaked, with a gradual increase in BY-2 cell death. Histological analysis of StVPE1-GFP in BY-2 cells showed that carbon starvation induces its translocation from the endoplasmic reticulum to the central vacuole through tonoplast engulfment. Exposure of BY-2 culture to the macroautophagy/autophagy inhibitor concanamycin A led to, along with an accumulation of autophagic bodies, accumulation of StVPE1-GFP in the cell vacuole. This accumulation did not occur in the presence of 3-methyladenine, an inhibitor of early-stage autophagy. BY-2 cells constitutively expressing RFP-StATG8IL, an autophagosome marker, showed colocalization with the StVPE1-GFP protein in the cytoplasm and vacuole. RNAi silencing of the core autophagy component ATG4 in BY-2 cells reduced VPE activity and cell death. These results are the first to suggest that VPE translocates to the cell vacuole through the autophagy pathway, leading to PCD.Abbreviations: ATG: autophagy related; CLP: caspase-like protease; HR: hypersensitive response; PCD: programmed cell death; St: Solanum tuberosum; VPE: vacuolar processing enzyme.

Assessment of physiological age and antioxidant status of new somatic hybrid potato seeds during extended cold storage

Yield components of potato are largely affected by the physiology age of the tuber seeds at planting. The current study focuses on monitoring seed tuber aging in two CN1 and CN2 somatic hybrid lines and Spunta (Sp) variety during 270 days of storage at 4 °C. Aging rate was monitored based on sprouting, emergence and tissue oxidation rates. Investigation of sprouting parameters such as physiological age index (PAI) considering physiological and chronological age and the incubation period (IP) indicated lower physiological age in hybrids than in Sp during the storage. Moreover, these analyses showed that off-seasonal growing conditions increased the aging, more clearly, in Sp tubers than in hybrid ones. However, dormancy periods (endodormancy and after storage dormancy) were equivalent in the different tuber lots. PAI and IP data when combined with those from emergence parameters (duration until emergence and stem number) seem more efficient for the characterization of the different potato lines. However, emergence indicators, when considered separately, were not able to distinguish clearly between seasonal and off-seasonal tubers. Data suggest that hybrid seeds exhibited high performances since they produced higher stem number per plant than Sp. The high aging rate in Sp tubers seems to be associated with the few developed stems. Biochemical analyses supported in part morphophysiological differences between hybrids and Sp seeds although these indicators seem more sensitive to aging. Indeed data showed that the dormancy break, and then, the development were associated with some level of tissue oxidation. Antioxidants such as superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX) and carotenoids seem more enhanced after the release of dormancy. However, induction of these activities started earlier in off-seasonal tubers than in seasonal ones, this was consistent with their advanced aging level revealed by PAI and IP data. Activation of these antioxidants appears to respond effectively to the increase of ROS suggesting a better control of postharvest development and tissue deterioration especially in CN2 off-seasonal tubers. This study suggests that CN2 followed by CN1 exhibited the best performance compared to Sp variety.

NO and ABA Interaction Regulates Tuber Dormancy and Sprouting in Potato

In plants, nitric oxide synthase (NOS)-like or nitrate reductase (NR) produces nitric oxide (NO), which is involved in releasing seed dormancy. However, its mechanism of effect in potato remains unclear. In this study, spraying 40 μM sodium nitroprusside (SNP), an exogenous NO donor, quickly broke tuber dormancy and efficiently promoted tuber sprouting, whereas 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (c-PTIO), an NO scavenger, repressed the influence of NO on tuber sprouting. Compared with the control (distilled water), SNP treatment led to a rapid increase in NO content after 6 h and a decreased abscisic acid (ABA) content at 12 and 24 h. c-PTIO treatment significantly inhibited increase of NO levels and increased ABA production. In addition, N ^G -nitro-L-arginine methyl ester, an NOS inhibitor, clearly inhibited the NOS-like activity, whereas tungstate, an NR inhibitor, inhibited the NR activity. Furthermore, NO promoted the expression of a gene involved in ABA catabolism (StCYP707A1, encoding ABA 8'-hydroxylase) and inhibited the expression of a gene involved in ABA biosynthesis (StNCED1, encoding 9-cis-epoxycarotenoid dioxygenase), thereby decreasing the ABA content, disrupting the balance between ABA and gibberellin acid (GA), and ultimately inducing dormancy release and tuber sprouting. The results demonstrated that NOS-like or NR-generated NO controlled potato tuber dormancy release and sprouting via ABA metabolism and signaling in tuber buds.

Genome-Wide Identification and Characterization of Vacuolar Processing Enzyme Gene Family and Diverse Expression Under Stress in Apple (Malus × Domestic)

Vacuolar processing enzymes (VPEs) play an important role in stress resistance and development of plants. Despite their diverse roles, little information is available in apple (Malus × domestic). This study firstly presents the genome-wide identification of VPE family genes in apple, resulting in 20 family members those are unevenly distributed across six out of the 17 chromosomes. Phylogenetic analysis assigned these genes into four groups. Analysis of exon-intron junctions and motifs of each candidate gene revealed high levels of conservation within and between phylogenetic groups. Cis-element including w box, ABRE, LTR, and TC-rich repeats were found in promoters of MdVPEs. NCBI-GEO database shown that the expression of MdVPEs exhibited diverse patterns in different tissues as well as the infection of Pythium ultimum and Apple Stem Grooving Virus. Furthermore, qRT-PCR showed that MdVPE genes were responsive to salt, cadmium, low-temperature, and drought. Overexpression of MDP0000172014, which was strongly induced by salt and drought stress, significantly decreased Arabidopsis tolerance to salt stress. The genome-wide identification and characterization of MdVPEs in apple provided basic information for the potential utilization of MdVPEs in stress resistance.

Rapeseed calcium-dependent protein kinase CPK6L modulates reactive oxygen species and cell death through interacting and phosphorylating RBOHD

Reactive oxygen species (ROS) play important roles in plant growth, development, responses to abiotic and biotic stresses. Hypersensitive response (HR)-like cell death is often associated with excess ROS. However, how a calcium-dependent protein kinase (CPK) modulates this process remains elusive in rapeseed (Brassica napus L.). In the present study, we identified and characterized CPK6L from rapeseed as a novel regulator of ROS and cell death. The subcellular localization of BnaCPK6L was investigated through GFP and was found to be located at the endoplasmic reticulum membrane. Overexpression of the constitutively active BnaCPK6LCA resulted in significant accumulation of ROS and HR-like cell death than the full-length. A quantitative RT-PCR survey identified that the expression levels of a few ROS, cell death and defense-related marker genes were up-regulated upon BnaCPK6LCA expression. Mating-based split ubiquitin system (mbSUS) screening revealed that BnaCPK6L interacted with BnaRBOHD (Respiratory Burst Oxidase Homolog D), which was validated by bimolecular fluorescence complementation (BiFC). An in vitro phosphorylation assay indicated that BnaCPK6L phosphorylated BnaRBOHD. Lastly, we also found that three 2C type protein phosphatases (PP2Cs) interacted with BnaCPK6L. Taken together, this study indicates that BnaCPK6L plays an important role in ROS and HR-like cell death through interacting with and phosphorylating RBOHD.

Effect of wet storage conditions on potato tuber transcriptome, phytohormones and growth

BACKGROUND

Stored potato (Solanum tuberosum L.) tubers are sensitive to wet conditions that can cause rotting in long-term storage. To study the effect of water on the tuber surface during storage, microarray analysis, RNA-Seq profiling, qRT-PCR and phytohormone measurements were performed to study gene expression and hormone content in wet tubers incubated at two temperatures: 4 °C and 15 °C. The growth of the plants was also observed in a greenhouse after the incubation of tubers in wet conditions.

RESULTS

Wet conditions induced a low-oxygen response, suggesting reduced oxygen availability in wet tubers at both temperatures when compared to that in the corresponding dry samples. Wet conditions induced genes coding for heat shock proteins, as well as proteins involved in fermentative energy production and defense against reactive oxygen species (ROS), which are transcripts that have been previously associated with low-oxygen stress in hypoxic or anoxic conditions. Wet treatment also induced senescence-related gene expression and genes involved in cell wall loosening, but downregulated genes encoding protease inhibitors and proteins involved in chloroplast functions and in the biosynthesis of secondary metabolites. Many genes involved in the production of phytohormones and signaling were also affected by wet conditions, suggesting altered regulation of growth by wet conditions. Hormone measurements after incubation showed increased salicylic acid (SA), abscisic acid (ABA) and auxin (IAA) concentrations as well as reduced production of jasmonate 12-oxo-phytodienoic acid (OPDA) in wet tubers. After incubation in wet conditions, the tubers produced fewer stems and more roots compared to controls incubated in dry conditions.

CONCLUSIONS

In wet conditions, tubers invest in ROS protection and defense against the abiotic stress caused by reduced oxygen due to excessive water. Changes in ABA, SA and IAA that are antagonistic to jasmonates affect growth and defenses, causing induction of root growth and rendering tubers susceptible to necrotrophic pathogens. Water on the tuber surface may function as a signal for growth, similar to germination of seeds.

Plant Vacuolar Processing Enzymes

Plant proteomes contain hundreds of proteases divided into different families based on evolutionary and functional relationship. In particular, plant cysteine proteases of the C1 (papain-like) and C13 (legumain-like) families play key roles in many physiological processes. The legumain-like proteases, also called vacuolar processing enzymes (VPEs), perform a multifunctional role in different plant organs and during different stages of plant development and death. VPEs are similar to animal caspases, and although caspase activity was identified in plants almost 40 years ago, there still remains much research to be done to gain a complete understanding of their various roles and functions in plants. Here we not only summarize the current existing knowledge of plant VPEs, including recent developments in the field, but also highlight the future prospective areas to be investigated to obtain a more detailed understanding of the role of VPEs in plants.

Functional characterization of calcium-dependent protein kinase (CPK) 2 gene from oilseed rape (Brassica napus L.) in regulating reactive oxygen species signaling and cell death control

Calcium-dependent protein kinases (CPKs), being Ser/Thr protein kinases found only in plants and some protozoans are calcium sensors that regulate diverse biological processes. However, the function and mode of CPKs in oilseed rape (Brassica napus) remain elusive. In this study, we identified CPK2 from oilseed rape as a novel regulator of reactive oxygen species (ROS) and cell death. BnaCPK2 was identified to be located at the endoplasmic reticulum membrane. Expression of BnaCPK2 was induced during Bax-induced cell death. Overexpression of the constitutively active form of BnaCPK2 led to significantly more accumulation of ROS and cell death than the full-length CPK2, which is supported by various measurements of physiological data. In addition, a quantitative RT-PCR survey revealed that the expression levels of a few marker genes are significantly changed as a result of CPK2 expression. Mating-based split ubiquitin system (mbSUS) and bimolecular fluorescence complementation (BiFC) were used to screen and confirm the BnaCPK2 interacting proteins. We identified and confirmed that CPK2 interacted with NADPH oxidase-like respiratory burst oxidase homolog D (RbohD), but not with RbohF. Based on its function and interacting partners, we propose that BnaCPK2 plays an important role in ROS and cell death control through interacting with RbohD.

A Novel NAC-Type Transcription Factor, NAC87, from Oilseed Rape Modulates Reactive Oxygen Species Accumulation and Cell Death

Reactive oxygen species (ROS) are thought to play a dual role in plants by functioning as signaling molecules and toxic by-products of aerobic metabolism. The hypersensitive response (HR) is a typical feature of immune responses in plants and also a type of programmed cell death (PCD). How these two processes are regulated in oilseed rape (Brassica napus L.) at the transcriptional level remains largely unknown. In this study, we report that an oilseed rape (Brassica napus L.) NAM-ATAF-CUC (NAC)-type transcription factor NAC87 modulates ROS and cell death accompanied by typical changes at the morphological and cellular levels. The BnaNAC87 gene was induced by multiple stress and hormone treatments and was highly expressed in senescent leaves by quantitative reverse transcription-PCR (qRT-PCR). BnaNAC87 is located in nuclei and has transcriptional activation activity. Expression of BnaNAC87 promoted significant ROS production, cell death as well as death of protoplasts, as indicated by histological staining. In addition, putative downstream target genes of NAC87 were identified through both qRT-PCR and dual luciferase reporter assays. We found that genes implicated in ROS generation (RbohB), cell death (VPE1a, ZEN1), leaf senescence (WRKY6, ZAT12) and defense (PR2, PR5 and HIN1) were significantly induced. Through an electrophoretic mobility shift assay (EMSA), we confirmed that BnaNAC87 directly binds to the NACRS-containing promoter fragments of ZEN1, ZAT12, HIN1 and PR5 genes. From these results, we conclude that oilseed rape NAC87 is a novel NAC transcription factor that acts as a positive regulator of ROS metabolism and cell death.

Genome-Wide Analysis of Long Non-Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process

Sprouting is a key factor affecting the quality of potato tubers. The present study aimed to compare the differential expression of long non-coding RNAs (lncRNAs) in the apical meristem during the dormancy release and sprouting stages by using lncRNA sequencing. Microscopic observations and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed the changes in the morphology and expression of lncRNAs in potato tubers during sprouting. Meristematic cells of potato tuber apical buds divided continuously and exhibited vegetative cone bulging and vascularisation. In all, 3175 lncRNAs were identified from the apical buds of potato tubers, among which 383 lncRNAs were up-regulated and 340 were down-regulated during sprouting. The GO enrichment analysis revealed that sprouting mainly influenced the expression of lncRNAs related to the cellular components of potato apical buds (e.g., cytoplasm and organelles) and cellular metabolic processes. The KEGG enrichment analysis also showed significant enrichment of specific metabolic pathways. In addition, 386 differentially expressed lncRNAs during sprouting were identified as putative targets of 235 potato miRNAs. Quantitative real-time polymerase chain reaction results agreed with the sequencing data. Our study provides the first systematic study of numerous lncRNAs involved in the potato tuber sprouting process and lays the foundation for further studies to elucidate their precise functions.

Cytosolic glyceraldehyde-3-phosphate dehydrogenases play crucial roles in controlling cold-induced sweetening and apical dominance of potato (Solanum tuberosum L.) tubers

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme that functions in producing energy and supplying intermediates for cellular metabolism. Recent researches indicate that GAPDHs have multiple functions beside glycolysis. However, little information is available for functions of GAPDHs in potato. Here, we identified 4 putative cytosolic GAPDH genes in potato genome and demonstrated that the StGAPC1, StGAPC2, and StGAPC3, which are constitutively expressed in potato tissues and cold inducible in tubers, encode active cytosolic GAPDHs. Cosuppression of these 3 GAPC genes resulted in low tuber GAPDH activity, consequently the accumulation of reducing sugars in cold stored tubers by altering the tuber metabolite pool sizes favoring the sucrose pathway. Furthermore, GAPCs-silenced tubers exhibited a loss of apical dominance dependent on cell death of tuber apical bud meristem (TAB-meristem). It was also confirmed that StGAPC1, StGAPC2, and StGAPC3 interacted with the autophagy-related protein 3 (ATG3), implying that the occurrence of cell death in TAB-meristem could be induced by ATG3 associated events. Collectively, the present research evidences first that the GAPC genes play crucial roles in diverse physiological and developmental processes in potato tubers.

Vacuolar processing enzyme activates programmed cell death in the apical meristem inducing loss of apical dominance

The potato (Solanum tuberosum L.) tuber is a swollen underground stem that can sprout in an apical dominance (AD) pattern. Bromoethane (BE) induces loss of AD and the accumulation of vegetative vacuolar processing enzyme (S. tuberosum vacuolar processing enzyme [StVPE]) in the tuber apical meristem (TAM). Vacuolar processing enzyme activity, induced by BE, is followed by programmed cell death in the TAM. In this study, we found that the mature StVPE1 (mVPE) protein exhibits specific activity for caspase 1, but not caspase 3 substrates. Optimal activity of mVPE was achieved at acidic pH, consistent with localization of StVPE1 to the vacuole, at the edge of the TAM. Downregulation of StVPE1 by RNA interference resulted in reduced stem branching and retained AD in tubers treated with BE. Overexpression of StVPE1 fused to green fluorescent protein showed enhanced stem branching after BE treatment. Our data suggest that, following stress, induction of StVPE1 in the TAM induces AD loss and stem branching.

Etiolated Stem Branching Is a Result of Systemic Signaling Associated with Sucrose Level

The potato (Solanum tuberosum) tuber is a swollen stem. Sprouts growing from the tuber nodes represent loss of apical dominance and branching. Long cold storage induces loss of tuber apical dominance and results in secondary branching. Here, we show that a similar branching pattern can be induced by short heat treatment of the tubers. Detached sprouts were induced to branch by the heat treatment only when attached to a parenchyma cylinder. Grafting experiments showed that the scion branches only when grafted onto heat- or cold-treated tuber parenchyma, suggesting that the branching signal is transmitted systemically from the bud-base parenchyma to the grafted stem. Exogenous supply of sucrose (Suc), glucose, or fructose solution to detached sprouts induced branching in a dose-responsive manner, and an increase in Suc level was observed in tuber parenchyma upon branching induction, suggesting a role for elevated parenchyma sugars in the regulation of branching. However, sugar analysis of the apex and node after grafting showed no distinct differences in sugar levels between branching and nonbranching stems. Vacuolar invertase is a key enzyme in determining the level of Suc and its cleavage products, glucose and fructose, in potato parenchyma. Silencing of the vacuolar invertase-encoding gene led to increased tuber branching in combination with branching-inducing treatments. These results suggest that Suc in the parenchyma induces branching through signaling and not by excess mobilization from the parenchyma to the stem.

Stronger sink demand for metabolites supports dominance of the apical bud in etiolated growth

The potato tuber is a swollen underground stem that can sprout under dark conditions. Sprouting initiates in the tuber apical bud (AP), while lateral buds (LTs) are repressed by apical dominance (AD). Under conditions of lost AD, removal of tuber LTs showed that they partially inhibit AP growth only at the AD stage. Detached buds were inhibited by exogenous application of naphthaleneacetic acid (NAA), whereas 6-benzyladenine (6-BA) and gibberellic acid (GA₃) induced bud burst and elongation, respectively. NAA, applied after 6-BA or GA₃, nullified the latters' growth-stimulating effect in both the AP and LTs. GA₃ applied to the fifth-position LT was transported mainly to the tuber's AP. GA₃ treatment also resulted in increased indole-3-acetic acid (IAA) concentration and cis-zeatin O-glucoside in the AP. In a tuber tissue strip that included two or three buds connected by the peripheral vascular system, treatment of a LT with GA₃ affected only the AP side of the strip, suggesting that the AP is the strongest sink for GA₃, which induces its etiolated elongation. Dipping etiolated sprouts in labeled GA₃ showed specific accumulation of the signal in the AP. Transcriptome analysis of GA₃'s effect showed that genes related to the cell cycle, cell proliferation, and hormone transport are up-regulated in the AP as compared to the LT. Sink demand for metabolites is suggested to support AD in etiolated stem growth by inducing differential gene expression in the AP.

Cellular and Molecular Changes Associated with Onion Skin Formation Suggest Involvement of Programmed Cell Death

Skin formation of onion (Allium cepa L.) bulb involves scale desiccation accompanied by scale senescence, resulting in cell death and tissue browning. Understanding the mechanism of skin formation is essential to improving onion skin and bulb qualities. Although onion skin plays a crucial role in postharvest onion storage and shelf life, its formation is poorly understood. We investigated the mode of cell death in the outermost scales that are destined to form the onion skin. Surprisingly, fluorescein diacetate staining and scanning electron microscopy indicated that the outer scale desiccates from the inside out. This striking observation suggests that cell death in the outer scales, during skin formation, is an internal and organized process that does not derive only from air desiccation. DNA fragmentation, a known hallmark of programmed cell death (PCD), was revealed in the outer scales and gradually decreased toward the inner scales of the bulb. Transmission electron microscopy further revealed PCD-related structural alterations in the outer scales which were absent from the inner scales. De novo transcriptome assembly for three different scales: 1st (outer), 5th (intermediate) and 8th (inner) fleshy scales identified 2,542 differentially expressed genes among them. GO enrichment for cluster analysis revealed increasing metabolic processes in the outer senescent scale related to defense response, PCD processes, carbohydrate metabolism and flavonoid biosynthesis, whereas increased metabolism and developmental growth processes were identified in the inner scales. High expression levels of PCD-related genes were identified in the outer scale compared to the inner ones, highlighting the involvement of PCD in outer-skin development. These findings suggest that a program to form the dry protective skin exists and functions only in the outer scales of onion.

Proteomic changes during tuber dormancy release process revealed by iTRAQ quantitative proteomics in potato

Given that limited information is available with regard to tuber dormancy release related proteome, we conducted proteome analysis of tuber dormancy release process at dormant tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) using the iTRAQ technology. A total of 1,752 proteins were identified. Among them, a subset of 316 proteins was screened as significant up- (137) and down regulated (179) between DT vs DRT. A subset of 120 proteins experienced significant up- (40) or down-regulation (80) between DRT vs ST. The differentially expressed proteins were grouped into 11 functional categories. Proteins enriched in functional categories of major carbohydrate (CHO) metabolism, glycolysis, fermentation, amino acid metabolism, protein and transport were highly up-regulated, while functional categories of photosynthesis and RNA were down-regulated between DT vs DRT. Proteins enriched in functional groups of protein, cell wall, lipid metabolism, miscellaneous, and signaling were strongly up-regulated, while functional categories of photosynthesis, hormone metabolism and protein were down-regulated between DRT vs ST. Consistent with previous documented differentially expressed genes, most of differentially expressed proteins were also identified between DT and DRT, indicating the metabolism shift from growth suspension to growth activation as tubers dormancy breaking. The changes in protein profiles showed lower concordance with corresponding alterations in transcript levels, indicating possible transcriptional and posttranscriptional regulation. Furthermore, the possible mechanism of tuber dormancy release was discussed in relation to what was known in transcripts change and other plant models from carbohydrate metabolism, protein metabolism, stress response, redox regulation, transcription regulation, DNA metabolism, amino acid metabolism, development, signaling as well as hormone metabolism.

Vacuolar processing enzyme in plant programmed cell death

Vacuolar processing enzyme (VPE) is a cysteine proteinase originally identified as the proteinase responsible for the maturation and activation of vacuolar proteins in plants, and it is known to be an ortholog of animal asparaginyl endopeptidase (AEP/VPE/legumain). VPE has been shown to exhibit enzymatic properties similar to that of caspase 1, which is a cysteine protease that mediates the programmed cell death (PCD) pathway in animals. Although there is limited sequence identity between VPE and caspase 1, their predicted three-dimensional structures revealed that the essential amino-acid residues for these enzymes form similar pockets for the substrate peptide YVAD. In contrast to the cytosolic localization of caspases, VPE is localized in vacuoles. VPE provokes vacuolar rupture, initiating the proteolytic cascade leading to PCD in the plant immune response. It has become apparent that the VPE-dependent PCD pathway is involved not only in the immune response, but also in the responses to a variety of stress inducers and in the development of various tissues. This review summarizes the current knowledge on the contribution of VPE to plant PCD and its role in vacuole-mediated cell death, and it also compares VPE with the animal cell death executor caspase 1.

Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis)

Background

Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looked into the morphological aspects of self-pruning process, the underlying molecular mechanisms remain unknown.

Results

In this study, the hallmarks of programmed cell death (PCD) were identified by TUNEL experiments, transmission electron microscopy (TEM) and histochemical staining for reactive oxygen species (ROS) during self-pruning of the spring shoots in sweet orange. Our results indicated that PCD occurred systematically and progressively and may play an important role in the control of self-pruning of citrus. Microarray analysis was used to examine transcriptome changes at three stages of self-pruning, and 1,378 differentially expressed genes were identified. Some genes were related to PCD, while others were associated with cell wall biosynthesis or metabolism. These results strongly suggest that abscission layers activate both catabolic and anabolic wall modification pathways during the self-pruning process. In addition, a strong correlation was observed between self-pruning and the expression of hormone-related genes. Self-pruning plays an important role in citrus floral bud initiation. Therefore, several key flowering homologs of Arabidopsis and tomato shoot apical meristem (SAM) activity genes were investigated in sweet orange by real-time PCR and in situ hybridization, and the results indicated that these genes were preferentially expressed in SAM as well as axillary meristem.

Conclusion

Based on these findings, a model for sweet orange spring shoot self-pruning is proposed, which will enable us to better understand the mechanism of self-pruning and abscission.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-892) contains supplementary material, which is available to authorized users.

Regulation of potato tuber sprouting

Following tuber induction, potato tubers undergo a period of dormancy during which visible bud growth is inhibited. The length of the dormancy period is under environmental, physiological and hormonal control. Sucrose availability is one prerequisite for bud break. In the absence of sucrose, no bud break occurs. Thus, sucrose is likely to serve as nutrient and signal molecule at the same time. The mode of sucrose sensing is only vaguely understood, but most likely involves trehalose-6-phosphate and SnRK1 signalling networks. This conclusion is supported by the observation that ectopically manipulation of trehalose-6-phosphate levels influences the length of the dormancy period. Once physiological competence is achieved, sprouting is controlled by the level of phytohormones. Two phytohormones, ABA and ethylene, are supposed to suppress tuber sprouting; however, the exact role of ethylene remains to be elucidated. Cytokinins and gibberellins are required for bud break and sprout growth, respectively. The fifth classical phytohormone, auxin, seems to play a role in vascular development. During the dormancy period, buds are symplastically isolated, which changes during bud break. In parallel to the establishment of symplastic connectivity, vascular tissue develops below the growing bud most likely to support the outgrowing sprout with assimilates mobilised in parenchyma cells. Sprouting leads to major quality losses of stored potato tubers. Therefore, control of tuber sprouting is a major objective in potato breeding. Although comparative transcriptome analysis revealed a large number of genes differentially expressed in growing versus dormant buds, no master-regulator of potato tuber sprouting has been identified so far.

Phylogenetically distant barley legumains have a role in both seed and vegetative tissues

Legumains or vacuolar processing enzymes are cysteine peptidases (C13 family, clan CD) with increasingly recognized physiological significance in plants. They have previously been classified as seed and vegetative legumains. In this work, the entire barley legumain family is described. The eight members of this family belong to the two phylogenetic clades in which the angiosperm legumains are distributed. An in-depth molecular and functional characterization of a barley legumain from each group, HvLeg-2 and HvLeg-4, was performed. Both legumains contained a signal peptide and were located in the endoplasmic reticulum, were expressed in seeds and vegetative tissues, and when expressed as recombinant proteins showed legumain and caspase proteolytic activities. However, the role of each protein seemed to be different in their target tissues. HvLeg-2 responded in leaves to biotic and abiotic stimuli, such as salicylic acid, jasmonic acid, nitric oxide, abscisic acid, and aphid infestation, and was induced by gibberellic acid in seeds, where the protein is able to degrade storage globulins. HvLeg-4 responded in leaves to wounding, nitric oxide, and abscisic acid treatments, and had an unknown role in the germinating seed. From these results, a multifunctional role was assumed for these two phylogenetically distant legumains, achieving different physiological functions in both seed and vegetative tissues.

The role of the potato (Solanum tuberosum) CCD8 gene in stolon and tuber development

· Strigolactones (SLs) are a class of phytohormones controlling shoot branching. In potato (Solanum tuberosum), tubers develop from underground stolons, diageotropic stems which originate from basal stem nodes. As the degree of stolon branching influences the number and size distribution of tubers, it was considered timely to investigate the effects of SL production on potato development and tuber life cycle. · Transgenic potato plants were generated in which the CAROTENOID CLEAVAGE DIOXYGENASE8 (CCD8) gene, key in the SL biosynthetic pathway, was silenced by RNA interference (RNAi). · The resulting CCD8-RNAi potato plants showed significantly more lateral and main branches than control plants, reduced stolon formation, together with a dwarfing phenotype and a lack of flowering in the most severely affected lines. New tubers were formed from sessile buds of the mother tubers. The apical buds of newly formed transgenic tubers grew out as shoots when exposed to light. In addition, we found that CCD8 transcript levels were rapidly downregulated in tuber buds by the application of sprout-inducing treatments. · These results suggest that SLs could have an effect, solely or in combination with other phytohormones, in the morphology of potato plants and also in controlling stolon development and maintaining tuber dormancy.

Can loss of apical dominance in potato tuber serve as a marker of physiological age?

The potato tuber constitutes a model system for the study of dormancy release and sprouting, suggested to be regulated by endogenous plant hormones and their balance inside the tuber. During dormancy, potato tubers cannot be induced to sprout without some form of stress or exogenous hormone treatment. When dormancy is released, sprouting of the apical bud may be inhibited by sprout control agents or cold temperature. Dominance of the growing apical bud over other lateral buds decreases during storage and is one of the earliest morphophysiological indicators of the tuber's physiological age. Three main types of loss of apical dominance (AD) affect sprouting shape. Hallmarks of programmed cell death (PCD) have been identified in the tuber apical bud meristem (TAB-meristem) during normal growth, and are more extensive when AD is lost following extended cold storage or chemical stress. Nevertheless, the role of hormonal regulation in TAB-meristem PCD remains unclear.