A Role for Phosphoinositides in Regulating Plant Nuclear Functions

Nuclear localized inositol phospholipids and inositol phosphates are important for regulating many essential processes in animal and yeast cells such as DNA replication, recombination, RNA processing, mRNA export and cell cycle progression. An overview of the current literature indicates the presence of a plant nuclear phosphoinositide (PI) pathway. Inositol phospholipids, inositol phosphates, and enzymes of the PI pathway have been identified in plant nuclei and are implicated in DNA replication, chromatin remodeling, stress responses and hormone signaling. In this review, the potential functions of the nuclear PI pathway in plants are discussed within the context of the animal and yeast literature. It is anticipated that future research will help shed light on the functional significance of the nuclear PI pathway in plants

PII: S1360-1385(00)01652-6

T he challenge for today's scientists is to maintain a broad perspective of interactive signaling pathways, while dissecting their parts sufficiently to render them understandable. Our goal is to stimulate the reader to consider the phosphoinositide (PI) pathway as a functional component of a complex growth response and to move beyond the reductionist's perspective of confining PI signaling to the generation of a transient, Ins(1,4,5)P 3 -induced Ca 2ϩ oscillation. (For additional coverage of plant PIs and the enzymes involved in their metabolism see Refs 1,2.) Inositol phospholipids as regulators of growth Most plant responses to external stimuli involve a change in growth and therefore membrane biogenesis. Membrane trafficking and signaling are inexorably linked in regulating cellular metabolism and controlling growth. To coordinate these processes, evolution appears to have capitalized on the stereospecificity of the PIs. During membrane trafficking, individual inositol phospholipids on the vesicle surface specify functional information like cogs on a wheel. As vesicles traffic from the endoplasmic reticulum (ER) to the plasma membrane, and from the ER to the vacuole and retrograde pathways, inositol phospholipids attract specific proteins necessary for budding, docking and fusion Biosynthesis and function of PtdIns(3) P The first evidence for the exacting requirements for stereospecific isomers of phosphatidylinositol (PtdIns) phosphate in membrane trafficking was revealed when the gene for yeast PtdIns-3-kinase, VPS34, was shown to be essential for trafficking of hydrolytic enzymes to the vacuole 5 . The plant PtdIns-3-kinase is related to the yeast Vps34p, which uses only PtdIns as a substrate. In plants, PtdIns-3-kinase activity is associated with nodule formation during symbiotic nitrogen fixation Exploiting yeast genetics to demonstrate the necessity of PtdIns(4)P in membrane trafficking and to elucidate the physiological roles of the distinct PtdIns-4-kinase isoforms has corroborated these findings. In an elegant mutant screen, yeast mutants were identified that were compromised in various steps of intracellular lipid transpor

Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome

15 p.-8 fig.-2 tab.Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure. To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration’s GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets. Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments. Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware. Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.This work was coordinated through the GeneLab Plant Analysis Working Group and was supported by NASA grants 80NSSC19K0126, 80NSSC18K0132 and 80NSSC21K0577 to S.G. and R.B., through NASA 80NSSC19K1481 to S.W., NNX15AG55G to C.W., and NNX15AG56G to L.D. and N.L., from the Spanish Agencia Estatal de Investigación grant RTI2018-099309-B-I00 and ESA 1340112 4000131202/20/NL/PG/pt to R.H. Contributions from P.J. and P.G. were partially supported by funds from the Oregon State University, NSF awards 1127112 and 1340112 and the United States Department of Agriculture, Agriculture Research Service. The Qlik software used in this work is provided under a free-to-use educational license from Qlik Technologies Inc. GeneLab datasets were obtained from https://genelab-data.ndc.nasa.gov/genelab/projects/, maintained by NASA GeneLab, NASA Ames Research Center, Moffett Field, CA 94035.Peer reviewe

Isolation, characterization and expression of calmodulin genes from carrot and Arabidopsis

Calmodulin is a highly conserved calcium-binding protein universally distributed among eukaryotes. Although the role of calmodulin in regulatory pathways in animals is well characterized, information on similar pathways in plants is limited. To better understand the role of calmodulin in plant systems, the structure and expression of calmodulin genes from carrot suspension cells and Arabidopsis was studied.A full-length calmodulin cDNA clone was isolated from a $\lambda$gt10 library and this cDNA was used as a probe to measure steady state calmodulin mRNA levels during the growth cycle of carrot cells. During the exponential phase of culture growth, when mitotic activity and oxidative respiration rates of the culture were maximal, calmodulin mRNA levels were four to five-fold higher than they were during the later stages of culture growth. Net calmodulin polypeptide synthesis paralleled the changes in steady state calmodulin mRNA levels during the growth cycle. Calmodulin polypeptide levels, in contrast, remained constant throughout the growth cycle. The data suggest that the calmodulin polypeptide is turned over more rapidly during periods of high mitotic activity and respiration.A 2.3-kb genomic sequence and its corresponding cDNA of 755 bp, encoding Arabidopsis calmodulin were isolated. These sequences represent a third Arabidopsis calmodulin gene (Acam 3), distinct from the two previously isolated cDNAs Acam 1 and Acam 2 (Ling, V., Perera, I., and Zielinski, R. E., 1991. Plant Physiol. 96, 1196-1202). Genomic Southern blots confirmed the presence of a calmodulin multi-gene family in Arabidopsis. The three cDNAs share 83-87% nucleotide sequence identity within their coding regions. Acam 2 and 3 encode identical calmodulin polypeptides. The relative levels of expression of the three genes varied in different plant organs. Both Acam 1 and 3 mRNAs were two to three-fold more abundant than Acam 2 mRNA in Arabidopsis leaves, flowers and developing siliques. Acam 2 and 3 mRNAs were not expressed at detectable levels in Arabidopsis roots. There were detectable differences in the relative levels of transcription and the kinetics of touch induction of Acam 1, 2, and 3, suggesting that the three genes may serve different functions in the plant.U of I OnlyETDs are only available to UIUC Users without author permissio