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

Genome-wide investigation of SQUAMOSA promoter binding protein-like transcription factor family in pearl millet (Pennisetum glaucum (L) R. Br.)

Abiotic stress negatively affects the yield of many crops. The SQUAMOSA promoter binding protein-like proteins (SBPs) represent a family of plant-specific transcription factors which play essential roles in plant growth, development, and stress responsiveness. In this study, 18 putative SBPs (PgSBPs) were identified in the genome of pearl millet on the basis of the SBP domain. One or two zinc finger-like structure(s) and a nuclear localization signal (NLS) were found in the SBP domains of all the PgSBPs. Fourteen PgSBPs were distributed on 7 chromosomes unevenly, while the other 4 were located on the scaffolds (i.e., non-chromosomal genomic sequences). Moreover, all the PgSBPs were clustered into seven groups (I-VII) based on the phylogenetic analysis. The intron/ exon structures and the motif composition were similar between PgSBPs within the same groups. PgSBPs in groups V and VII were predicted as the targets of two microRNAs, PgmiR156q and PgmiR529b. Some PgSBPs have abscisic acid (ABA)-responsive elements and stress-responsive elements in their promoters. Expression levels of these PgSBPs were upregulated by abiotic stresses and downregulated by ABA. Together, this study shows a comprehensive overview of PgSBPs and provides vital information for elucidating the biological functions of PgSBPs

Small RNA sequencing reveals the role of pearl millet miRNAs and their targets in salinity stress responses

Pearl millet [Pennisetum glaucum (L.) R. Br.] is an important crop in arid and semi-arid areas of India and Africa. It is well known for its tolerance to abiotic stresses, but it lags behind other cereals in terms of research and development. MicroRNAs (miRNAs) are a versatile group of small regulatory RNAs of 20�22 bases that play important roles in plant growth, development, and stress responses. However, the regulatory mechanisms underlying miRNA-mediated responses to salinity stress in pearl millet are still unclear. In this study, we performed small RNA sequencing to identify conserved and novel miRNAs from the salinity tolerant pearl millet genotype. In total, 130 million sequence reads were generated, and 81 conserved and 14 novel miRNAs were identified as salinity stress responsive microRNAs. We also performed target prediction for these miRNAs, and a total of 448 pearl millet mRNAs were identified as the targets. Among these target mRNAs, 122 (~25%) encode transcription factors. A pathway analysis showed that differentially expressed miRNAs and their target genes can regulate the auxin response pathway. Quantitative real-time PCR analysis of miRNAs and their targets showed consistent expression patterns. These results suggest that miRNAs play a role in salinity stress tolerance in pearl millet

Comparative de novo transcriptomic profiling of the salinity stress responsiveness in contrasting pearl millet lines

Pearl millet (Pennisetum glaucum (L) R. Br.) is a staple crop for more than 90 million poor farmers. It is known for its tolerance against drought, salinity, and high temperature. To understand the molecular mechanisms underlying its salinity tolerance, physiological analyses and a comparative transcriptome analysis between salinity tolerant (ICMB 01222) and salinity susceptible (ICMB 081) lines were conducted under control and salinity conditions. The physiological studies revealed that the tolerant line ICMB 01222 had a higher growth rate and accumulated higher amount of sugar in leaves under salinity stress. Sequencing using the Illumina HiSeq 2500 system generated a total of 977 million reads, and these reads were assembled de novo into contigs corresponding to gene products. A total of 11,627 differentially expressed genes (DEGs) were identified in both lines. These DEGs are involved in various metabolic pathways such as plant hormone signal transduction, mitogen-activated protein kinase signaling pathways, and so on. Genes involved in ubiquitin-mediated proteolysis and phenylpropanoid biosynthesis pathways were upregulated in the tolerant line. In contrast, unigenes involved in glycolysis/gluconeogenesis and genes for ribosomes were downregulated in the susceptible line. Genes encoding SBPs (SQUAMOSA promoter binding proteins), which are plant-specific transcription factors, were differentially expressed only in the tolerant line. Functional unigenes and pathways that are identified can provide useful clues for improving salinity stress tolerance in pearl millet

Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber

Monoecious species provide a comprehensive system to study the developmental programs underlying the establishment of female and male organs in unisexual flowers. However, molecular resources for most monoecious non-model species are limited, hampering our ability to study the molecular mechanisms involved in flower development of these species. The objective of this study was to identify differentially expressed genes during the development of male and female flowers of the monoecious species Quercus suber, an economically important Mediterranean tree. Total RNA was extracted from different developmental stages of Q. suber flowers. Non-normalized cDNA libraries of male and female flowers were generated using 454 pyrosequencing technology producing a total of 962,172 high-quality reads with an average length of 264 nucleotides. The assembly of the reads resulted in 14,488 contigs for female libraries and 10,438 contigs for male libraries. Comparative analysis of the transcriptomes revealed genes differentially expressed in early and late stages of development of female and male flowers, some of which have been shown to be involved in pollen development, in ovule formation and in flower development of other species with a monoecious, dioecious, or hermaphroditic sexual system. Moreover, we found differentially expressed genes that have not yet been characterized and others that have not been previously shown to be implicated in flower development. This transcriptomic analysis constitutes a major step toward the characterization of the molecular mechanisms involved in flower development in a monoecious tree with a potential contribution toward the knowledge of conserved developmental mechanisms in other species.This work was funded by FEDER funds through the Operational Competitiveness Programme-COMPETE and by National Funds through FCT-Fundacao para a Ciencia e a Tecnologia under the project FCOMP-01-0124-FEDER-019461 (PTDC/AGR-GPL/118508/2010) and the sub-project SOBREIRO/0019/2009 within the National Consortium (COEC-Cork Oak ESTs Consortium). Romulo Sobral was supported by funding from FCT with a PhD grant (ref. SFRH/BD/84365/2012). Margarida Rocheta was supported by funding from FCT with a Post-Doc grant (ref. SFRH/BPD/64905/2009). Teresa Ribeiro was supported by funding from FCT with a Post-Doc grant (SFRH/BPD/64618/2009). We are grateful to Alexandre Magalhaes for the kind help given in bioinformatic analysis

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

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)

Study on Cardiovascular and Respiratory Responses Relevant to Tactile Softness Evaluation : Based on ECG and PPG Analysis

The main purpose of this study is to explore physiological parameters that are usable for tactile softness differentiation. Two pillows and a cushion which were different in tactile softness (perceived compressibility and resilience) were chosen as the samples. 10 healthy students participated in the physiological test. Each of them was tested on three days, twice a day with the same sample involved. Each subject was required to keep quiet, compress the sample and keep quiet again in succession during a whole test. ECG (electrocardiography), PPG (photoplethysmography) and RSP (respiration) signals were recorded simultaneously during each physiological test. Several parameters indicating cardiovascular and respiratory reactions were calculated based on these signals. The statistical analysis results revealed that, HFnorm (normalized power of high-frequency components) calculated from the power spectrum of PWTT (pulse wave transmitting time) might be a very promising parameter which can be used for tactile softness differentiation.ArticleInternational Journal of Affective Engineering.13(4):269-277(2014)journal articl