Rong Long Pan

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

BackgroundThe elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as A. thaliana, O. sativa and Z. mays. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands) in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs) is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required.ResultsThis study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator), for recognizing combinatorial cis-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0), AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented.ConclusionIn addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at http://PlantPAN.mbc.nctu.edu.tw.

EMF Genes Maintain Vegetative Development by Repressing the Flower Program in Arabidopsis

The EMBRYONIC FLOWER (EMF) genes EMF1 and EMF2 are required to maintain vegetative development and repress flower development. EMF1 encodes a putative transcriptional regulator, and EMF2 encodes a Polycomb group protein homolog. We examined expression profiles of emf mutants using GeneChip technology. The high degree of overlap in expression changes from the wild type among the emf1 and emf2 mutants was consistent with the functional similarity between the two genes. Expression profiles of emf seedlings before flower development were similar to that of Arabidopsis flowers, indicating the commitment of germinating emf seedlings to the reproductive fate. The germinating emf seedlings ectopically expressed flower organ genes, suggesting that vegetative development in wild-type plants results from EMF repression of the flower program, directly or indirectly. In addition, the seed development program is derepressed in the emf1 mutants. Gene expression analysis showed no clear regulation of CONSTANS (CO), FLOWERING LOCUS T (FT), LEAFY (LFY), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 by EMF1. Consistent with epistasis results that co, lfy, or ft cannot rescue rosette development in emf mutants, these data show that the mechanism of EMF-mediated repression of flower organ genes is independent of these flowering genes. Based on these findings, a new mechanism of EMF-mediated floral repression is proposed.

Crystal structure of a membrane-embedded H+-translocating pyrophosphatase

H+-translocating pyrophosphatases (H+-PPases) are active proton transporters that establish a proton gradient across the endomembrane by means of pyrophosphate (PPi) hydrolysis. H+-PPases are found primarily as homodimers in the vacuolar membrane of plants and the plasma membrane of several protozoa and prokaryotes. The three-dimensional structure and detailed mechanisms underlying the enzymatic and proton translocation reactions of H+-PPases are unclear. Here we report the crystal structure of a Vigna radiata H+-PPase (VrH+-PPase) in complex with a non-hydrolysable substrate analogue, imidodiphosphate (IDP), at 2.35 Å resolution. Each VrH+-PPase subunit consists of an integral membrane domain formed by 16 transmembrane helices. IDP is bound in the cytosolic region of each subunit and trapped by numerous charged residues and five Mg2+ ions. A previously undescribed proton translocation pathway is formed by six core transmembrane helices. Proton pumping can be initialized by PPi hydrolysis, and H+ is then transported into the vacuolar lumen through a pathway consisting of Arg 242, Asp 294, Lys 742 and Glu 301. We propose a working model of the mechanism for the coupling between proton pumping and PPi hydrolysis by H+-PPases.

Photosystem I electron transport and phosphorylation supported by electron donation to the plastoquinone region.

Abstract In chloroplasts, tetramethyl-p-hydroquinone supports high rates of phosphorylation-coupled, noncyclic electron flow through Photosystem I to methylviologen. The reaction is totally sensitive to dibromothymoquinone, indicating an electron donation to the plastoquinone region of the photosynthetic chain. The uncoupled electron flow rate exceeds 1000 μequivalents per hour per mg chlorophyll. The phosphorylation efficiency ( P e 2 ) at the optimal pH of 8 is 0.6–0.65. Presumably this ratio represents the efficiency of energy coupling in the electron transfer step plastoquinone → cytochrome f.

HYDROXYL RADICAL-INDUCED DECLINE IN MOTILITY AND INCREASE IN LIPID PEROXIDATION AND DNA MODIFICATION IN HUMAN SPERM

We employed the xanthine‐xanthine oxidase system to produce H2O2 or simply used commercially available H2O2 solution to investigate the effects of exogenous hydroxyl radicals on the motility characteristics and on lipid peroxidation and DNA modification of human sperm. The functional parameters of sperm motility declined concomitantly upon incubation of sperm with hydroxyl radicals. After incubation of freshly ejaculated human sperm with 0.23 mM H2O2 in the presence of 1.8 mM ADP and 2.7 mM FeSO4 for 1 hr at 37°C, 90% reduction of motility was observed. Effect of hydroxyl radicals on sperm motility was dependent on the concentrations of FeSO4 and H2O2, respectively. The remaining motility of sperm after 1 hr incubation showed negative linear correlation with FeSO4 concentration. The response of sperm motility to FeSO4 was also dependent on the concentration of H2O2. Except for the amplitude of lateral head displacement, functional parameters of sperm declined with the increase of H2O2 concentration. Moreover, we found that lipid peroxidation measured as malondialdehyde (MDA) and accumulation of modified DNA indicated by 8‐hydroxy‐2′‐deoxyguanosine (8‐OH‐dG) in human sperm were significantly accelerated by exogenous hydroxyl radicals. The contents of lipid peroxides and 8‐OH‐dG in the spermatozoa were increased from 24.6±2.4 nmol MDA/1×107 sperm and 0.17±0.02% in the untreated group to 30.6±1.2 nmol MDA/1×107 sperm and 1.9±0.47%, respectively, in the sperm treated at 37°C for 1 hr with 2.03 mM H2O2, 1.8 mM ADP and 4.5 mM FeSO4. Taken together, these results suggest that the detrimental effects of hydroxyl radicals on human sperm functions may be mediated, at least partly, through lipid peroxidation and DNA modification.

Incorporating Support Vector Machine for Identifying Protein Tyrosine Sulfation Sites

Tyrosine sulfation is a post‐translational modification of many secreted and membrane‐bound proteins. It governs protein‐protein interactions that are involved in leukocyte adhesion, hemostasis, and chemokine signaling. However, the intrinsic feature of sulfated protein remains elusive and remains to be delineated. This investigation presents SulfoSite, which is a computational method based on a support vector machine (SVM) for predicting protein sulfotyrosine sites. The approach was developed to consider structural information such as concerning the secondary structure and solvent accessibility of amino acids that surround the sulfotyrosine sites. One hundred sixty‐two experimentally verified tyrosine sulfation sites were identified using UniProtKB/SwissProt release 53.0. The results of a five‐fold cross‐validation evaluation suggest that the accessibility of the solvent around the sulfotyrosine sites contributes substantially to predictive accuracy. The SVM classifier can achieve an accuracy of 94.2% in five‐fold cross validation when sequence positional weighted matrix (PWM) is coupled with values of the accessible surface area (ASA). The proposed method significantly outperforms previous methods for accurately predicting the location of tyrosine sulfation sites.

Infection-induced intestinal oxidative stress triggers organ-to-organ immunological communication in drosophila

Local infections can trigger immune responses in distant organs, and this interorgan immunological crosstalk helps maintain immune homeostasis. We find that enterobacterial infection or chemically and genetically stimulating reactive oxygen species (ROS)-induced stress responses in the Drosophila gut triggers global antimicrobial peptide (AMP) responses in the fat body, a major immune organ in flies. ROS stress induces nitric oxide (NO) production in the gut, which triggers production of the AMP Diptericin, but not Drosomycin, in the fat body. Hemocytes serve as a signaling relay for communication between intestinal ROS/NO signaling and fat body AMP responses. The induction of AMP responses requires Rel/NF-κB activation within the fat body. Although Rel-mediated Drosomycin induction is repressed by the AP-1 transcription factor, this repressor activity is inhibited by intestinal ROS. Thus, intestinal ROS signaling plays an important role in initiating gut-to-fat body immunological communication in Drosophila.

The high-affinity binding site for manganese on the oxidizing side of Photosystem II

Abstract Electron donation to Photosystem II (PS II) by diphenylcarbazide (DPC) is interrupted by the presence of endogenous Mn in PS II particles. Removal of this Mn by Tris treatment greatly stimulates the electron transport with DPC as donor. Binding of low concentration of exogenous Mn(II) to Tris-treated PS II particles inhibits DPC photooxidation competitively with DPC. This phenomenon was used to locate a highly specific Mn(II) binding site on the oxidizing side of Photosystem II with dissociation constant about 0.15 μM. The binding of Mn(II) is electrostatic in nature. Its affinity depends not only on the ionic strength, but also on the anion species of the salt in the medium. The effectiveness in decreasing the affinity follows the order F− > SO2−4 > CH3COO− > CI− > Br− > NO3−. This observation is interpreted as follows: smaller ions, like F−, CH3COO−, and larger ions, like SO2−4, have inhibitory effects on Mn(II) binding, whereas ions with optimal size, like Cl−, Br− and NO3−, can stabilize the binding, resembling the anion requirement for reactivation of Cl−-depleted chloroplasts. We suggest that the binding site for Mn(II) we observed is the site for the endogenous Mn in the O2-evolving complex of PS II. This site remains after Tris treatment, which removes all the endogenous Mn as well as the three extrinsic proteins, indicating that it is on the intrinsic component(s) of PS II reaction centers. Furthermore, the Cl− requirement for O2 evolution may be attributed, at least partly to its stabilizing effect on Mn binding.

An anti-IgE monoclonal antibody that binds to IgE on CD23 but not on high-affinity IgE.Fc receptors

A new monoclonal antibody (mAb), specific for human IgE, the central mediator of immediate-type hypersensitivity reactions, has been shown to possess a unique set of binding specificities. The mAb, 8D6, binds to a conformational epitope on the CH3 domain of human e immunoglobulin and can compete with omalizumab for binding to IgE. Like omalizumab, it does not bind to IgE bound by the high-affinity IgE.Fc receptor (FcɛRI) on basophils and mast cells. It also does not cause activation and degranulation of IgE-pulsed, human FcɛRI-expressing rat basophilic leukemic cells (RBL SX-38). The mAb can inhibit IgE binding to recombinant α chain of human FcɛRI in ELISA and to human FcɛRI-expressing RBL SX38 cells in fluorescence flow cytometric analysis. However, unlike omalizumab, 8D6 can bind to IgE already bound by the low-affinity IgE.Fc receptors (FcɛRII, or CD23), as revealed in ELISA with recombinant CD23 and in flow cytometric analysis with human B cells. Since earlier investigators have shown that anti-CD23 mAbs can inhibit the synthesis of IgE in lymphocyte culture in vitro and can down-regulate IgE production in treated patients, 8D6 may offer pharmacological mechanisms in addition to those mediated by omalizumab, for controlling IgE in patients with allergic diseases.

Leptospiral Outer Membrane Lipoprotein LipL32 Binding on Toll-like Receptor 2 of Renal Cells As Determined with an Atomic Force Microscope

Leptopirosis is a renal disease caused by pathogenic Leptospira that primarily infects the renal proximal tubules, consequently resulting in severe tubular injuries and malfunctions. The protein extracted from the outer membrane of this pathogenic strain contains a major component of a 32 kDa lipoprotein (LipL32), which is absent in the counter membrane of nonpathogenic strains and has been identified as a crucial factor for host cell infection. Previous studies showed that LipL32 induced inflammatory responses and interacted with the extracellular matrix (ECM) of the host cell. However, the exact relationship between LipL32-mediated inflammatory responses and ECM binding is still unknown. In this study, an atomic force microscope with its tip modified by purified LipL32 was used to assess the interaction between LipL32 and cell surface receptors. Furthermore, an antibody neutralization technique was employed to identify Toll-like receptor 2 (TLR2) but not TLR4 as the major target of LipL32 attack. The interaction force between LipL32 and TLR2 was measured as approximately 59.5 +/- 8.7 pN, concurring with the theoretical value for a single-pair molecular interaction. Moreover, transformation of a TLR deficient cell line with human TLR2 brought the interaction force from the basal level to approximately 60.4 +/- 11.5 pN, confirming unambiguously TLR2 as counter receptor for LipL32. The stimulation of CXCL8/IL-8 expression by full-length LipL32 as compared to that without the N-terminal signal peptide domain suggests a significant role of the signal peptide of the protein in the inflammatory responses. This study provides direct evidence that LipL32 binds to TLR2, but not TLR4, on the cell surface, and a possible mechanism for the virulence of leptospirosis is accordingly proposed.