Table of Contents

Volume 7, Issue 2

  February 2012

  Pages 151 - 299

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PERSPECTIVES

The root as a drill: An ethylene-auxin interaction facilitates root penetration in soil

Parankusam Santisree, Sapana Nongmaithem, Yellamaraju Sreelakshmi, Maria Ivanchenko and Rameshwar Sharma
Pages 151 - 156
http://dx.doi.org/10.4161/psb.18936
Abstract | Full Text | PDF

Plant roots forage the soil for water and nutrients and overcome the soil’s physical compactness. Roots are endowed with a mechanism that allows them to penetrate and grow in dense media such as soil. However, the molecular mechanisms underlying this process are still poorly understood. The nature of the media in which roots grow adds to the difficulty to in situ analyze the mechanisms underlying root penetration. Inhibition of ethylene perception by application of 1-methylccyclopropene (1-MCP) to tomato seedlings nearly abolished the root penetration in Soilrite. The reversal of this process by auxin indicated operation of an auxin-ethylene signaling pathway in the regulation of root penetration. The tomato pct1–2 mutant that exhibits an enhanced polar transport of auxin required higher doses of 1-MCP to inhibit root penetration, indicating a pivotal role of auxin transport in this process. In this update we provide a brief review of our current understanding of molecular processes underlying root penetration in higher plants.




SHORT COMMUNICATIONS

A role for mechanosensitive channels in chloroplast and bacterial fission

Margaret Wilson and Elizabeth Haswell
Pages 157 - 160
http://dx.doi.org/10.4161/psb.18735
Abstract | Full Text | PDF

The division site in both chloroplasts and bacteria is established by the medial placement of the FtsZ ring, a process that is in part regulated by the evolutionarily conserved components of the Min system. We recently showed that mechanosensitive ion channels influence FtsZ ring assembly in both Arabidopsis thaliana chloroplasts and in Escherichia coli; in chloroplasts they do so through the same genetic pathway as the Min system. Here we describe the effect of heterologous expression of the Arabidopsis MS channel homolog MSL2 on FtsZ ring placement in E. coli. We also discuss possible molecular mechanisms by which MS channels might influence chloroplast or bacterial division.

Neofunctionalization within the Omp85 protein superfamily during chloroplast evolution

Mats Töpel, Qihua Ling and Paul Jarvis
Pages 161 - 164
http://dx.doi.org/10.4161/psb.18677
Abstract | Full Text | PDF

The Toc75 and OEP80 proteins reside in the chloroplast outer envelope membrane. Both are members of the Omp85 superfamily of β-barrel proteins, and both are essential in Arabidopsis plants with important roles throughout development. Toc75 forms the translocation channel of the TOC complex, which is responsible for importing nucleus-encoded proteins into chloroplasts, while the function of OEP80 remains uncertain. Deficiency of Toc75 in plants that have artificially reduced OEP80 levels suggests that the latter may be involved in the biogenesis of β-barrel proteins, in similar fashion to Omp85-related proteins in other systems. To elucidate the evolutionary relationship between the two proteins, we conducted a phylogenetic analysis using 48 sequences from diverse species. This indicated that Toc75 and OEP80 belong to sister groups in the Omp85 superfamily, and originate from a gene duplication in an ancient eukaryotic organism > 1.2 billion years ago. Our analysis also supports the notion that the Toc75 family has undergone a phase of neofunctionalization to accommodate the organelle’s newly acquired need to import proteins.

Metabolism and roles of phosphatidylinositol 3-phosphate in pollen development and pollen tube growth in Arabidopsis

Xin-Qi Gao and Xian Sheng Zhang
Pages 165 - 169
http://dx.doi.org/10.4161/psb.18743
Abstract | Full Text | PDF

Phosphoinositides play important roles in eukaryotic cells, although they constitute a minor fraction of total cellular lipids. Specific kinases and phosphatases function on the regulation of phosphoinositide levels. Phosphatidylinositol 3-phosphate (PtdIns3P), a molecule of phosphoinositides regulates multiple aspects of plant growth and development. In this mini-review, we introduce and discuss the kinases and phosphatases involved in PtdIns3P metabolism and their roles in pollen development and pollen tube growth in Arabidopsis.

ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock

Brenda Y. Chow, Anne Helfer, Dmitri A. Nusinow and Steve A. Kay
Pages 170 - 173
http://dx.doi.org/10.4161/psb.18766
Abstract | Full Text | PDF

Biological timekeeping is essential for proper growth and development. Organisms such as the model plant Arabidopsis use the circadian clock to coordinate biological processes with the environment so that changes in conditions are anticipated and processes favorably phased. Despite the identification of numerous clock genes, knowledge of their molecular connectivity and influence on output programs remains limited. We recently showed LUX encodes a sequence-specific DNA-binding protein that directly regulates expression of the morning clock gene PRR9. We also showed that LUX interacts with the evening-phased proteins ELF3 and ELF4 to form a complex called the Evening Complex (EC). The EC binds the PIF4 and PIF5 promoters to control hypocotyl growth as a clock output. Here we provide evidence that LUX also recruits ELF3 to the PRR9 promoter. As with the PIF4 and PIF5 promoters, both LUX and its close homolog NOX are required for recruitment. Hence the entire EC likely functions together as part of the core clock oscillator to optimize plant fitness.

NO serves as a signaling intermediate downstream of H₂O₂ to modulate dynamic microtubule cytoskeleton during responses to VD-toxins in Arabidopsis

Lin-Lin Yao, Bao-Lei Pei, Qun Zhou and Ying-Zhang Li
Pages 174 - 177
http://dx.doi.org/10.4161/psb.18768
Abstract | Full Text | PDF

Although hydrogen peroxide (H₂O₂) and nitric oxide (NO) can act as an upstream signaling molecule to modulate the dynamic microtubule cytoskeleton during the defense responses to Verticillium dahliae (VD) toxins in Arabidopsis, it is not known the relationship between these two signaling molecules. Here, we show that VD-toxin-induced NO accumulation was dependent on prior H₂O₂ production, NO is downstream of H₂O₂ in the signaling process, and that H₂O₂ acted synergistically with NO to modulate the dynamic microtubule cytoskeleton responses to VD-toxins in Arabidopsis.

Arabidopsis growth and defense are modulated by bacterial quorum sensing molecules

Sebastian T. Schenk, Elke Stein, Karl-Heinz Kogel and Adam Schikora
Pages 178 - 181
http://dx.doi.org/10.4161/psb.18789
Abstract | Full Text | PDF

N-acyl-homoserine lactones (AHLs) play an important role in the communication within the rhizosphere; they serve as a chemical base for interactions within and between different species of Gram-negative bacteria. Not only bacteria, also plants perceive and react to AHLs with diverse responses. Here we describe a negative correlation between the length of AHLs’ lipid chains and the observed growth promotion in Arabidopsis thaliana. Moreover, we speculate on a positive correlation between the reinforcement of defense mechanisms and the length of the lipid moieties. Observation presented here may be of great importance for understanding of the complex interplay between plants and their environment, as well as for agronomic applications.

The Mediator complex subunit 8 regulates organ size in Arabidopsis thaliana

Ran Xu and Yunhai Li
Pages 182 - 183
http://dx.doi.org/10.4161/psb.18803
Abstract | Full Text | PDF

Control of final organ size is a fundamental and core process of development of all multicellular organisms, but the mechanisms that set the final size of determinate organs are largely unknown. In a recent study, we demonstrated that the Mediator complex subunit 25 (MED25/PFT1), which is involved in the transcriptional regulation of gene expression, controls the final size of determinate organs by restricting both cell proliferation and cell expansion. med25 mutants formed large organs with larger and slightly more cells, whereas plants overexpressing MED25 produced small organs due to a reduction in both cell number and cell size. Here, we show that a loss-of-function mutation in the Mediator complex subunit 8 (MED8) causes small flowers as a result of reduced cell expansion. Analysis of the med8 med25–2 double mutant reveals that MED8 acts independently of MED25 to regulate cell expansion and organ growth. Taken together, our findings show that MED8 and MED25 play an important role in regulating organ size. Further identification of upstream and downstream components of MED8 and MED25 will help understand how the Mediator complex is involved in organ size control in plants.

Identification of the protein sequence of the type III effector XopD from the B100 strain of Xanthomonas campestris pv campestris

Joanne Canonne, Carole Pichereaux, Daniel Marino, Dominique Roby, Michel Rossignol and Susana Rivas
Pages 184 - 187
http://dx.doi.org/10.4161/psb.18828
Abstract | Full Text | PDF

During evolution, pathogens have developed sophisticated strategies to suppress plant defense responses and promote successful colonization of their hosts. In their attempt to quell host resistance, Gram-negative phytopathogenic bacteria inject type III effectors (T3Es) into plant cells, where they typically target plant components essential for the establishment of defense responses. We have recently shown that the XopD T3E from the strain B100 of Xanthomonas campestris pathovar campestris (XopDXccB100) is able to target AtMYB30, a positive regulator of Arabidopsis defense responses. This protein interaction leads to inhibition of AtMYB30 transcriptional activity and promotion of bacterial virulence. Here, we describe the identification of the complete protein sequence of XopDXccB100, which presents an N-terminal extension of 40 amino acids with respect to the protein annotated in public databases. The implications of this finding are discussed.

MBF1s regulate ABA-dependent germination of Arabidopsis seeds

María Florencia Di Mauro, María José Iglesias, Débora Pamela Arce, Estela Marta Valle, Roberto Benech Arnold, Kenichi Tsuda, Ken-ichi Yamazaki, Claudia Anahí Casalongué and Andrea Verónica Godoy
Pages 188 - 192
http://dx.doi.org/10.4161/psb.18843
Abstract | Full Text | PDF

Transcriptional co-activators of the multiprotein bridging factor 1 (MBF1) controls gene expression by connecting transcription factors and the basal transcription machinery. In Arabidopsis thaliana functions of MBF1 genes have been related to stress tolerance and developmental alterations. Endogenous ABA plays a major role in the regulation of Arabidopsis seed dormancy and germination. Seed dormancy and ABA sensitivity are enhanced in ethylene insensitive mutants suggesting that ethylene signal transduction pathway is necessary to fully develop ABA-dependent germination. In this report we showed that a triple knock-down mutant for Arabidopsis MBF1 genes (abc-) has enhanced seed dormancy and displays hypersensitivity to exogenous ABA. In addition, higher ABA contents were detected in abc- seeds after imbibition. These evidences suggest a negative role of MBF1s genes in ABA-dependent inhibition of germination. The participation of MBF1s in ethylene signal transduction pathway is also discussed.

Role of H₂O₂ in pea seed germination

Gregorio Barba-Espi´n, Jose´ Antonio Hern´ndez and Pedro Diaz-Vivancos
Pages 193 - 195
http://dx.doi.org/10.4161/psb.18881
Abstract | Full Text | PDF

The imbibition of pea seeds with hydrogen peroxide (H₂O₂) increased the germination as well as the seedling growth, producing an invigoration of the seeds. We propose that H₂O₂ could acts as signaling molecule in the beginning of seed germination involving specific changes at proteomic, transcriptomic and hormonal levels. These findings have practical implication in the context of seed priming technologies to invigorate low vigour seeds.

Nitric oxide: An emerging regulator of cell elongation during primary root growth

María Fernández-Marcos, Luis Sanz and Óscar Lorenzo
Pages 196 - 200
http://dx.doi.org/10.4161/psb.18895
Abstract | Full Text | PDF

Nitric oxide (NO) is a highly inducible molecule and overaccumulated during stress responses, such as drought, cold and pathogen infection. Several key developmental processes within a plant life cycle have been reported to be signaled by this gaseous molecule, and among them seed germination, de-etiolation, gravitropic response or root growth are well-characterized. The importance of NO as a plant growth and stress regulator is emerging considerably, despite the current knowledge about its signaling pathway is still limited. Therefore, the identification and characterization at the molecular level of NO targets is essential to get a deeper insight into this pathway. Here we characterize the effect of NO on root development in Arabidopsis and found that NO application reduces cell lengths in differentiation zone. Additionally, the contribution of the gibberellin (GA) signaling pathway to the NO root-related phenotypes, mainly through DELLA repressors, is also depicted.

Moonlighting kinases with guanylate cyclase activity can tune regulatory signal networks

Helen R. Irving, Lusisizwe Kwezi, Janet Wheeler and Chris Gehring
Pages 201 - 204
http://dx.doi.org/10.4161/psb.18891
Abstract | Full Text | PDF

Guanylate cyclase (GC) catalyzes the formation of cGMP and it is only recently that such enzymes have been characterized in plants. One family of plant GCs contains the GC catalytic center encapsulated within the intracellular kinase domain of leucine rich repeat receptor like kinases such as the phytosulfokine and brassinosteroid receptors. In vitro studies show that both the kinase and GC domain have catalytic activity indicating that these kinase-GCs are examples of moonlighting proteins with dual catalytic function. The natural ligands for both receptors increase intracellular cGMP levels in isolated mesophyll protoplast assays suggesting that the GC activity is functionally relevant. cGMP production may have an autoregulatory role on receptor kinase activity and / or contribute to downstream cell expansion responses. We postulate that the receptors are members of a novel class of receptor kinases that contain functional moonlighting GC domains essential for complex signaling roles.

Is there a role for trihelix transcription factors in embryo maturation?

Melissa S. Barr, Matthew R. Willmann and Pablo D. Jenik
Pages 205 - 209
http://dx.doi.org/10.4161/psb.18893
Abstract | Full Text | PDF

The development of the angiosperm seed includes the accumulation of storage products, the loss of most of its water and the establishment of dormancy. While much is known about the pathways that initiate maturation during mid-embryogenesis or repress it after germination, only recently has it been shown that other mechanisms repress the program during early embryogenesis.Two recent reports have shown that microRNAs are critical regulators of maturation in Arabidopsis early embryogenesis. Two closely related trihelix transcription factors, ASIL1 and ASIL2, were identified as probable partially redundant repressors of early maturation downstream of the microRNA-synthesizing enzyme DICER-LIKE1. An overlap between the genes upregulated in asil1–1 and dcl1–15 mutants support this conclusion. ASIL2 orthologs are found across seed plants, indicating that their role in maturation might be conserved. ASIL1 arose from the ancestral ASIL2 clade by a gene duplication event in the Brassicaceae, although it is not clear whether its function has diverged.




MINI-REVIEWS

Role of glutathione in plant signaling under biotic stress

Carole Dubreuil-Maurizi and Benoît Poinssot
Pages 210 - 212
http://dx.doi.org/10.4161/psb.18831
Abstract | Full Text | PDF

Glutathione (GSH) is a non-protein thiol compound which has been repeatedly reported to play an important role in plant responses during biotic stresses. However, our knowledge of glutathione-related molecular mechanisms underlying plant defense responses still remains limited. We first discovered that the Arabidopsis thaliana phytoalexin deficient 2–1 (pad2–1) mutant was linked to glutathione deficiency since the mutation was identified in the GSH1 gene encoding the first enzyme of glutathione biosynthesis: Glutamate Cysteine Ligase (GCL). Interestingly, this glutathione-deficient mutant pad2–1 also displays a high susceptibility to a wide range of invaders. We recently reported that the glutathione deficiency in pad2–1 is directly related to a low content of GCL protein. In parallel, we highlighted that the altered redox potential in pad2–1 upregulates the oxidative-stress marker genes GR1, GSTF6 and RbohD during infection with the hemibiotrophic oomycete Phytophthora brassicae. Moreover, the impairment of early signaling events such as plasma membrane depolarization, production of nitric oxide and reactive oxygen species also correlates with the reduced hypersensitive response (HR) observed during P. brassicae infection. Concerning the impaired salicylic acid (SA)-dependent pathway in pad2–1, our results indicated that transcripts of IsoChorismate Synthase1 (ICS1, a main enzyme of SA biosynthesis) do not accumulate in response to pathogen. In this review, we integrate previous knowledge and recent discoveries about pad2–1 to better understand the involvement of glutathione in the pad2–1 pleiotropic phenotype observed during biotic stresses.

Complex regulation of an R gene SNC1 revealed by auto-immune mutants

Mingyue Gou and Jian Hua
Pages 213 - 216
http://dx.doi.org/10.4161/psb.18884
Abstract | Full Text | PDF

Plants have evolved resistance (R) proteins to detect pathogen effectors and trigger plant defense responses in the so named effector-triggered immunity (ETI). R proteins are under negative regulation in plants as upregulated activation of R protein is detrimental to plant growth. Autoimmune mutants have been instrumental in understanding the fine tuning of plant defense responses. Recently, a number of such mutants have been molecularly characterized, and some of them result from over-activation of SNC1, a TIR-NBS-LRR type of R protein. Studies of these mutants revealed a complex negative regulation of SNC1 activity from transcriptional to post-translational regulation. Here, we summarize studies on these SNC1-dependent auto-immune mutants and discuss the fine regulation of R proteins in plant immunity.

Bacterial effectors target the plant cell nucleus to subvert host transcription

Joanne Canonne and Susana Rivas
Pages 217 - 221
http://dx.doi.org/10.4161/psb.18885
Abstract | Full Text | PDF

In order to promote virulence, Gram-negative bacteria have evolved the ability to inject so-called type III effector proteins into host cells. The plant cell nucleus appears to be a subcellular compartment repeatedly targeted by bacterial effectors. In agreement with this observation, mounting evidence suggests that manipulation of host transcription is a major strategy developed by bacteria to counteract plant defense responses. It has been suggested that bacterial effectors may adopt at least three alternative, although not mutually exclusive, strategies to subvert host transcription. T3Es may (1) act as transcription factors that directly activate transcription in host cells, (2) affect histone packing and chromatin configuration, and/or (3) target host transcription factor activity. Here, we provide an overview on how all these strategies may lead to host transcriptional re-programming and, as a result, to improved bacterial multiplication inside plant cells.




REVIEWS

Plant communication: Mediated by individual or blended VOCs?

Hirokazu Ueda, Yukio Kikuta and Kazuhiko Matsuda
Pages 222 - 226
http://dx.doi.org/10.4161/psb.18765
Abstract | Full Text | PDF

Plants emit volatile organic compounds (VOCs) as a means to warn other plants of impending danger. Nearby plants exposed to the induced VOCs prepare their own defense weapons in response. Accumulated data supports this assertion, yet much of the evidence has been obtained in laboratories under artificial conditions where, for example, a single VOC might be applied at a concentration that plants do not actually experience in nature. Experiments conducted outdoors suggest that communication occurs only within a limited distance from the damaged plants. Thus, the question remains as to whether VOCs work as a single component or a specific blend, and at which concentrations VOCs elicit insect and pathogen defenses in undamaged plants. We discuss these issues based on available literature and our recent work, and propose future directions in this field.

Open Access Article

HAM proteins promote organ indeterminacy: But how?

Eric M. Engstrom
Pages 227 - 234
http://dx.doi.org/10.4161/psb.18958
Abstract | Full Text | PDF

HAIRY MERISTEM (HAM) proteins, members of the GRAS family of transcriptional regulators, are essential for maintenance of indeterminate growth in flowering plant shoots, loss-of-function ham mutants exhibiting a strikingly novel phenotype of shoot meristem arrest and differentiation. Specific cellular/molecular functions of HAM proteins underlying meristem maintenance are unknown. In this review, I highlight findings from recent analyses of Arabidopsis ham (Atham) loss-of-function phenotypes, including that HAM function limits the generation of clonally-derived meristem layers and that HAM function regulates CLAVATA3 expression. I consider how this new information both refines our understanding of the role of HAM proteins in regulating meristem structure and function, and may also suggest possible downstream HAM protein transcriptional targets. Finally, I note the significant phenotypic overlap between Atham phenotypes, and aintegumenta/anintegumenta-like6 double mutant phenotypes, suggesting meristem regulatory functions common to, and possible genetic interactions between, HAM and AINTEGUMENTA.




RESEARCH PAPERS

Gene expression profiling through microarray analysis in Arabidopsis thaliana colonized by Pseudomonas putida MTCC5279, a plant growth promoting rhizobacterium

Suchi Srivastava, Vasvi Chaudhry, Aradhana Mishra, Puneet Singh Chauhan, Ateequr Rehman, Archana Yadav, Narendra Tuteja and Chandra S. Nautiyal
Pages 235 - 245
http://dx.doi.org/10.4161/psb.18957
Abstract | PDF

Plant growth promotion is a multigenic process under the influence of many factors; therefore an understanding of these processes and the functions regulated may have profound implications. Present study reports microarray analysis of Arabidopsis thaliana plants inoculated with Pseudomonas putida MTCC5279 (MTCC5279) which resulted in significant increase in growth traits as compared with non-inoculated control. The gene expression changes, represented by oligonucleotide array (24652 genes) have been studied to gain insight into MTCC5279 assisted plant growth promotion in Arabidopsis thaliana. MTCC5279 induced upregulated Arabidopsis thaliana genes were found to be involved in maintenance of genome integrity (At5g20850), growth hormone (At3g23890 and At4g36110), amino acid synthesis (At5g63890), abcissic acid (ABA) signaling and ethylene suppression (At2g29090, At5g17850), Ca⁺² dependent signaling (At3g57530) and induction of induced systemic resistance (At2g46370, At2g44840). The genes At3g32920 and At2g15890 which are suggested to act early in petal, stamen and embryonic development are among the downregulated genes. We report for the first time MTCC5279 assisted repression of At3g32920, a putative DNA repair protein involved in recombination and DNA strand transfer in a process of rapid meiotic and mitotic division.

Identification of miRNAs in sorghum by using bioinformatics approach

Amit Katiyar, Shuchi Smita, Viswanathan Chinnusamy, Dev Mani Pandey and Kailash Bansal
Pages 246 - 259
http://dx.doi.org/10.4161/psb.18914
Abstract | PDF

MicroRNAs (miRNAs) regulate gene expression mainly by post-transcriptional gene silencing (PTGS) and in some cases by transcriptional genes silencing (TGS). miRNAs play critical roles in developmental processes, nutrient homeostasis, abiotic stress and pathogen responses of plants. In contrast to the large number of miRNAs predicted in cereal model plant rice, only 148 miRNAs were predicted in sorghum till date (miRBase release 17). This suggested that miRNAs identified in sorghum is far from saturation. Hence, we developed a bioinformatics pipeline using an in-house PERL script and publicly available structure prediction tools to identify miRNAs and their target genes from publically available Expressed Sequence Tags (EST) and Genomic Survey Sequence (GSS). About 1379 known and unique plant miRNAs from 33 different crops were used to predict new miRNAs in sorghum. We identified 31 new miRNAs belonging to 10 different miRNA families. We predicted 72 potential target genes for 31 miRNAs, and most of these target genes are predicted to be involved in plant growth and development.These newly identified miRNAs add to the growing database of miRNA and lay the foundation for further understanding of miRNA function in sorghum plant development.




ARTICLE ADDENDA

From systems biology to photosynthesis and whole-plant physiology: A conceptual model for integrating multi-scale networks

David J. Weston, Paul J. Hanson, Richard J. Norby, Gerald A. Tuskan and Stan D. Wullschleger
Pages 260 - 262
http://dx.doi.org/10.4161/psb.18802
Abstract | Full Text | PDF

Network analysis is now a common statistical tool for molecular biologists. Network algorithms are readily used to model gene, protein and metabolic correlations providing insight into pathways driving biological phenomenon. One output from such an analysis is a candidate gene list that can be responsible, in part, for the biological process of interest. The question remains, however, as to whether molecular network analysis can be used to inform process models at higher levels of biological organization. In our previous work, transcriptional networks derived from three plant species were constructed, interrogated for orthology and then correlated with photosynthetic inhibition at elevated temperature. One unique aspect of that study was the link from co-expression networks to net photosynthesis. In this addendum, we propose a conceptual model where traditional network analysis can be linked to whole-plant models thereby informing predictions on key processes such as photosynthesis, nutrient uptake and assimilation, and C partitioning.

Experimental and statistical post-validation of positive example EST sequences carrying peroxisome targeting signals type 1 (PTS1)

Thomas Lingner, Amr R. A. Kataya and Sigrun Reumann
Pages 263 - 268
http://dx.doi.org/10.4161/psb.18720
Abstract | Full Text | PDF

We recently developed the first algorithms specifically for plants to predict proteins carrying peroxisome targeting signals type 1 (PTS1) from genome sequences.¹ As validated experimentally, the prediction methods are able to correctly predict unknown peroxisomal Arabidopsis proteins and to infer novel PTS1 tripeptides. The high prediction performance is primarily determined by the large number and sequence diversity of the underlying positive example sequences, which mainly derived from EST databases. However, a few constructs remained cytosolic in experimental validation studies, indicating sequencing errors in some ESTs. To identify erroneous sequences, we validated subcellular targeting of additional positive example sequences in the present study. Moreover, we analyzed the distribution of prediction scores separately for each orthologous group of PTS1 proteins, which generally resembled normal distributions with group-specific mean values. The cytosolic sequences commonly represented outliers of low prediction scores and were located at the very tail of a fitted normal distribution. Three statistical methods for identifying outliers were compared in terms of sensitivity and specificity.” Their combined application allows elimination of erroneous ESTs from positive example data sets. This new post-validation method will further improve the prediction accuracy of both PTS1 and PTS2 protein prediction models for plants, fungi, and mammals.

Plastid DNA in the nucleus: New genes for old

Mathieu Rousseau-Gueutin, Michael A. Ayliffe and Jeremy N. Timmis
Pages 269 - 272
http://dx.doi.org/10.4161/psb.18762
Abstract | Full Text | PDF

Nuclear genomes of eukaryotes are bombarded by a continuous deluge of organellar DNA which contributes significantly to eukaryote evolution. Here, we present a new PCR-based method that allows the specific amplification of nuclear integrants of organellar DNA (norgs) by exploiting recent deletions present in organellar genome sequences. We have used this method to amplify nuclear integrants of plastid DNA (nupts) from the nuclear genomes of several Nicotiana species and to study the evolutionary forces acting upon these sequences. The role of nupts in endosymbiotic evolution and the different genetic factors influencing the time available for a chloroplastic gene to be functionally relocated in the nucleus are discussed.

BiP links TOR signaling to ER stress in Chlamydomonas

José L. Crespo
Pages 273 - 275
http://dx.doi.org/10.4161/psb.18767
Abstract | Full Text | PDF

The highly conserved target of rapamycin (TOR) Ser/Thr kinase promotes protein synthesis under favorable growth conditions in all eukaryotes. Downregulation of TOR signaling in the model unicellular green alga Chlamydomonas reinhardtii has recently revealed a link between control of protein synthesis, endoplasmic reticulum (ER) stress and the reversible modification of the BiP chaperone by phosphorylation. Inhibition of protein synthesis by rapamycin or cycloheximide resulted in the phosphorylation of BiP on threonine residues while ER stress induced by tunicamycin or heat shock caused the fast dephosphorylation of the protein. Regulation of BiP function by phosphorylation/dephosphorylation events was proposed in early studies in mammalian cells although no connection to TOR signaling has been established so far. Here I will discuss about the coordinated regulation of BiP modification by TOR and ER stress signals in Chlamydomonas.

The ABA-INSENSITIVE-4 (ABI4) transcription factor links redox, hormone and sugar signaling pathways

Christine H. Foyer, Pavel I Kerchev and Robert D. Hancock
Pages 276 - 281
http://dx.doi.org/10.4161/psb.18770
Abstract | Full Text | PDF

The cellular reduction-oxidation (redox) hub processes information from metabolism and the environment and so regulates plant growth and defense through integration with the hormone signaling network. One key pathway of redox control involves interactions with ABSCISIC ACID (ABA). Accumulating evidence suggests that the ABA-INSENSITIVE-4 (ABI4) transcription factor plays a key role in transmitting information concerning the abundance of ascorbate and hence the ability of cells to buffer oxidative challenges. ABI4 is required for the ascorbate-dependent control of growth, a process that involves enhancement of salicylic acid (SA) signaling and inhibition of jasmonic acid (JA) signaling pathways. Low redox buffering capacity reinforces SA- JA- interactions through the mediation of ABA and ABI4 to fine-tune plant growth and defense in relation to metabolic cues and environmental challenges. Moreover, ABI4-mediated pathways of sugar sensitivity are also responsive to the abundance of ascorbate, providing evidence of overlap between redox and sugar signaling pathways.

Circadian rhythms in biologically closed electrical circuits of plants

Alexander Volkov, Astian J. Waite, Joseph D. Wooten and Vladislav S. Markin
Pages 282 - 284
http://dx.doi.org/10.4161/psb.18798
Abstract | Full Text | PDF

The circadian clock regulates a wide range of electrophysiological and developmental processes in plants. Here, we discuss the direct influence of a circadian clock on biologically closed electrochemical circuits in vivo. The biologically closed electrochemical circuits in the leaves of C. miniata (Kaffir lily), Aloe vera and Mimosa pudica, which regulate their physiology, were analyzed using the charge stimulation method. Plants are able to memorize daytime and nighttime. Even at continuous light or darkness, plants recognize nighttime or daytime and change the input resistance. The circadian clock can be maintained endogenously and has electrochemical oscillators, which can activate ion channels in biologically closed electrochemical circuits. The activation of voltage gated channels depends on the applied voltage, electrical charge, and the speed of transmission of electrical energy from the electrostimulator to plants.

The FEI2-SOS5 pathway and CELLULOSE SYNTHASE 5 are required for cellulose biosynthesis in the Arabidopsis seed coat and affect pectin mucilage structure

Smadar Harpaz-Saad, Tamara L. Western and Joseph J. Kieber
Pages 285 - 288
http://dx.doi.org/10.4161/psb.18819
Abstract | Full Text | PDF

A common adaptation in angiosperms is the deposition of hydrophilic mucilage into the apoplast of seed coat epidermal cells during the course of their differentiation. Upon imbibition, seed mucilage, composed mainly of carbohydrates (i.e. pectins, hemicelluloses and glycans) expands rapidly, encapsulating the seed and aiding in seed dispersal and germination. The FEI1/FEI2 receptor-like kinases and the SOS5 extracellular GPI-anchored protein were previously shown to act on a pathway regulating cellulose biosynthesis during Arabidopsis root elongation. In the highlighted study, we demonstrated that FEI2 and SOS5 regulate the production of the cellulosic rays deposited across the inner adherent-layer of seed mucilage. Mutations in either fei2 or sos5 disrupted the formation of rays, which was associated with an increase in the soluble, outer layer of pectin mucilage and accompanied by a reduction in the inner adherent-layer. Mutations in CELLULOSE SYNTHASE 5 also led to reduced rays and mal-partitioning of the pectic component of seed mucilage, further establishing a structural role for cellulose in seed mucilage. Here, we show that FEI2 expressed from a CaMV 35S promoter complemented both root and seed mucilage defects of the fei1 fei2 double mutant. In contrast, expression of FEI1 from a 35S promoter complemented the root, but not the seed phenotype of the fei1 fei2 double mutant, suggesting that unlike in the root, FEI2 plays a unique and non-redundant role in the regulation of cellulose synthesis in seed mucilage. Altogether, these data suggest a novel role for cellulose in anchoring the pectic component of seed mucilage to the seed surface and indicate that the FEI2 protein has a function distinct from that of FEI1, despite the high sequence similarity of these RLKs.

Mechanisms for calcium sensing receptor-regulated stomatal closure in response to the extracellular calcium signal

Wen-Hua Wang and Hai-Lei Zheng
Pages 289 - 291
http://dx.doi.org/10.4161/psb.18882
Abstract | Full Text | PDF

In Arabidopsis, extracellular calcium (Ca²⁺_o) promotes intracellular calcium (Ca²⁺_i) transients and stomatal closure, which has been found to be regulated by the calcium sensing receptor (CAS). However, the detailed pathways for transducting the Ca²⁺_o signal by CAS are still unclear. We found that nitric oxide (NO) and the hydrogen peroxide (H₂O₂) accumulated in the guard cell chloroplast were the two elements that act downstream of the CAS signaling and trigger the stomatal closure by prolonging Ca²⁺_i transients.¹ Here we provide more commentary on CAS-regulated H₂O₂ generation from chloroplast and Ca²⁺_i transients in response to Ca²⁺_o, as well as other potential mechanisms that may be involved in the CAS signaling pathway.

Does CK2 affect flowering time by modulating the autonomous pathway in Arabidopsis?

Jidnyasa Jayant Mulekar and Enamul Huq
Pages 292 - 294
http://dx.doi.org/10.4161/psb.18883
Abstract | Full Text | PDF

CK2 (Casein Kinase II), a ubiquitous Ser/Thr kinase, affects multiple developmental and stress response pathways in Arabidopsis, including flowering time under both long- and short-day conditions through the photoperiod and autonomous pathways. CK2 phosphorylates central clock components, CCA1 and LHY, to modulate circadian clock that regulates flowering time through the photoperiod pathway. However, how CK2 regulates flowering time through the autonomous pathway is still unknown. Analyses of phosphorylation sites using several prediction softwares show that most of the autonomous pathway components have multiple CK2 phosphorylation sites. CK2 might phosphorylate any or all of these components to modulate their activity/stability resulting in altered expression of FLC that drives flowering time through the autonomous pathway.

Adaptive radiation with regard to nutrient sequestration strategies in the carnivorous plants of the genus Nepenthes

Andrej Pavlovič
Pages 295 - 297
http://dx.doi.org/10.4161/psb.18842
Abstract | Full Text | PDF

Carnivorous pitcher plants of the genus Nepenthes have evolved a great diversity of pitcher morphologies. Selective pressures for maximizing nutrient uptake have driven speciation and diversification of the genus in a process known as adaptive radiation. This leads to the evolution of pitchers adapted to specific and often bizarre source of nutrients, which are not strictly animal-derived. One example is Nepenthes ampullaria with unusual growth pattern and pitcher morphology what enables the plant to capture a leaf litter from the canopy above. We showed that the plant benefits from nitrogen uptake by increased rate of photosynthesis and growth what may provide competitive advantage over others co-habiting plants. A possible impact of such specialization toward hybridization, an important mechanism in speciation, is discussed.

An emerging role of pectic rhamnogalacturonanII for cell wall integrity

Rebecca Reboul and Raimund Tenhaken
Pages 298 - 299
http://dx.doi.org/10.4161/psb.18894
Abstract | Full Text | PDF

The plant cell wall is a complex network of different polysaccharides and glycoproteins, showing high diversity in nature. The essential components, tethering cell wall are under debate, as novel mutants challenge established models. The mutant ugd2,3 with a reduced supply of the important wall precursor UDP-glucuronic acid reveals the critical role of the pectic compound rhamnogalacturonanII for cell wall stability. This polymer seems to be more important for cell wall integrity than the previously favored xyloglucan.