Arabidopsis heterotrimeric G protein β subunit interacts with a plasma membrane 2C-type protein phosphatase, PP2C52

AbstractHeterotrimeric G proteins (Gα, Gβ, Gγ) play important roles in signal transduction among various eukaryotic species. G proteins transmit signals by regulating the activities of effector proteins, but only a few Gβ-interacting effectors have been identified in plants. Here we show by a yeast two-hybrid screen that a putative myristoylated 2C-type protein phosphatase, PP2C52, is an Arabidopsis Gβ (AGB1)-interacting partner. The interaction between AGB1 and PP2C52 was confirmed by an in vitro pull-down assay and a bimolecular fluorescence complementation assay. PP2C52 transcripts were detected in many tissues. PP2C52 was localized to the plasma membrane and a mutation in the putative myristoylation site of PP2C52 disrupted its plasma membrane localization. Our results suggest that PP2C52 interacts with AGB1 on the plasma membrane and transmits signals via dephosphorylation of other proteins

Comprehensive Analysis of NAC Transcription Factor Family Uncovers Drought and Salinity Stress Response in Pearl Millet (\u3cem\u3ePennisetum glaucum\u3c/em\u3e)

BACKGROUND: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet. RESULTS: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (− 073, − 29, and − 151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet. CONCLUSION: The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet

Cafebr - Citation Amender/Formatter for Biological Research

A reference list is an essential part of a manuscript for an academic article. It is often necessary to reformat (i.e., change orders of pieces of article information such as authors, article title, publication year, and journal where the article was published) of a preformatted reference list when a manuscript is declined by one journal and submitted to another. EndNote, Zotero and Mendeley are examples of sophisticated reference management programs that help generate a reference list with less errors. However, their multifunctionality seems to have complicated the process of generating a reference list: they require many selection steps to obtain a final output, and also require to manually edit a file outside the execuiton program even to make small changes in the output. The author developed a program, Cafebr (Citation Amender/Formatter for Biological Research), to more simply generate a reference list for an article of biological research. It is written in HTML/JavaScript, and as such works on a web browser on any platform. On Cafebr, articles for a final reference list can be either given by a user or collected from PubMed. Pieces of article information are then extracted according to the format of these articles or to the delimiters designated by a user. Preset formats for output are currently only four, but all of them can be directly edited on the user interface, allowing to change output formats quickly and flexibly. All of the functions of Cafebr is available on its website (either http://stdtgm.itigo.jp/cafebr/cafebr.html (main) or http://studtsugama.s1006.xrea.com/cafebr/cafebr.xhtm (backup)) with aids of a CGI program. A stand-alone version of Cafebr is available at these websites or Zenodo (10.5281/zenodo.1404887)

VIP1 is very important/interesting protein 1 regulating touch responses of Arabidopsis

VIP1 (VIRE2-INTERACTING PROTEIN 1) is a bZIP transcription factor in Arabidopsis thaliana. VIP1 and its close homologs (i.e., Arabidopsis group I bZIP proteins) are present in the cytoplasm under steady conditions, but are transiently localized to the nucleus when cells are exposed to hypo-osmotic conditions, which mimic mechanical stimuli such as touch. Recently we have reported that overexpression of a repression domain-fused form of VIP1 represses the expression of some touch-responsive genes, changes structures and/or local auxin responses of the root cap cells, and enhances the touch-induced root waving. This raises the possibility that VIP1 suppresses touch-induced responses. VIP1 should be useful to further characterize touch responses of plants. Here we discuss 2 seemingly interesting perspectives about VIP1: (1) What factors are involved in regulating the nuclear localization of VIP1?; (2) What can be done to further characterize the physiological functions of VIP1 and other Arabidopsis group I bZIP proteins

Possible inhibition of Arabidopsis VIP1-mediated mechanosensory signaling by streptomycin

VIP1 (VIRE2-INTERACTING PROTEIN 1) and its close homologues are Arabidopsis thaliana bZIP proteins regulating stress responses and root tropisms. They are present in the cytoplasm under steady conditions, but transiently accumulate in the nucleus when cells are exposed to mechanical stress such as hypo-osmotic stress and touch. This pattern of changes in subcellular localization is unique to VIP1 and its close homologues, and can be useful to further characterize mechanical stress signaling in plants. A recent study showed that calcium signaling regulates this pattern of subcellular localization. Here, we show that a possible calcium channel inhibitor, streptomycin, also inhibits the nuclear accumulation of VIP1. Candidates for the specific regulators of the mechanosensitive calcium signaling are further discussed

Data of whole genome sequencing of five garden asparagus (Asparagus officinalis) individuals with the MinION nanopore sequencer

Garden asparagus (Asparagus officinalis) is a perennial, dioecious crop. Genomic DNA samples were prepared from five A. officinalis individuals that differ in sex and phenotypes, and sequenced with the MinION nanopore sequencer. The obtained data were 1.5-5 Gb/sample, and the average read length was larger than 1.4 kb for all the samples. The resulting reads were mapped to the existing A. officinalis genome sequence. The existing A. officinalis transcript sequences were mapped to the MinION-derived reads. On the basis of these mapping results, flanking sequences of five partial gene fragments that previously had not been mapped to any region of the existing genome were determined by genomic PCR followed by Sanger sequencing. These sequences enabled to estimate the genomic positions of those five partial gene fragments. The MinION-derived data and the flanking sequences of the five gene fragments were deposited in the NCBI (National Center for Biotechnology Information) SRA (Sequence Read Archive) database and the NCBI Nucleotide database, respectively. (C) 2019 The Author(s). Published by Elsevier Inc

A rapid chemical method for lysing <it>Arabidopsis </it>cells for protein analysis

Abstract Background Protein extraction is a frequent procedure in biological research. For preparation of plant cell extracts, plant materials usually have to be ground and homogenized to physically break the robust cell wall, but this step is laborious and time-consuming when a large number of samples are handled at once. Results We developed a chemical method for lysing Arabidopsis cells without grinding. In this method, plants are boiled for just 10 minutes in a solution containing a Ca2+ chelator and detergent. Cell extracts prepared by this method were suitable for SDS-PAGE and immunoblot analysis. This method was also applicable to genomic DNA extraction for PCR analysis. Our method was applied to many other plant species, and worked well for some of them. Conclusions Our method is rapid and economical, and allows many samples to be prepared simultaneously for protein analysis. Our method is useful not only for Arabidopsis research but also research on certain other species.</p