Exploring the protein–protein interaction landscape in plants

Protein–protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.     

Reversal of Abscisic Acid-Induced Stomatal Closure by trans-Cinnamic and p-Coumaric Acid

Abscisic acid (ABA)-induced increase in stomatal diffusive resistance (SDR) in excised leaves of bean (Phaseolus vulgaris L. cv Pencil Pod) and maize (Zea mays L. cv Golden Bantam) is inhibited by low concentrations of trans-cinnamic acid (TCA) (1 micromolar) and p-coumaric acid (PCA) (10 micromolar) when given together with ABA (10 micromolar) in the transpiration stream through the cut end of the petiole or leaf blade. A concentration effect is observed both in the ABA action and its reversal by phenolic acids. Leaves having attained a high diffusive resistance in ABA solution recover rapidly when transferred to water. ABA (10 micromolar) induced closure of the stomata in onion, Allium cepa L. and Vicia faba epidermal peels. This is associated with loss of K⁺ from guard cells. In the presence of TCA (10 micromolar) and PCA (10 micromolar) K⁺ is retained in the guard cells with open stomata. The dark closure of stomata is also inhibited by TCA and PCA. It is suggested that these phenolic acids may inhibit the ABA effect by competing with or acting on some ABA-specific site, probably located on the plasma membrane, regulating flux of K⁺ ions. A weak association of ABA with the plasma membrane is envisaged because of the rapid recovery obtained upon transferral of the leaves to water.     

Conservative N cycling despite high atmospheric deposition in early successional African tropical lowland forests

Plant and Soil - Many applied disciplines have recognized problems related to the practice of data analysis within their own communities. Some of them have even declared the existence of a...     

Antiviral activity and synthesis of quaternized promazine derivatives against HSV-1

N-(4-chlorobenzyl)triflupromazinium chloride, a known antitubercular agent, has been found to also be active against HSV-1. A preliminary structure-activity relation has been explored to determine which groups are crucial to viral inhibition. Antiviral assessments such as GFP reduction, plaque reduction, treatment timing and wash-out studies have also been probed to determine a mode of action for QPD-1. Based on this preliminary data, it appears that QPD-1 is a reversible inhibitor, suspected to inhibit early stages of viral replication of HSV-1 at 50μM, equipotent to acyclovir.     

Incremental sampling methodology for petroleum hydrocarbon contaminated soils: volume estimates and remediation strategies

Current environmental assessments for petroleum hydrocarbon (PHC) contaminated sites are dependent on discrete soil sampling to estimate the degree and extent of contamination, leading to unreliable and non-reproducible results. Incremental sampling methodology (ISM) involves collecting and combining samples within a targeted area and holds promise for being a cost-effective, representative, and reproducible sampling strategy for contaminated site characterization. We hypothesized that traditional Phase II Environmental Site Assessments (ESA) discrete and ISM sampling protocols were not mutually exclusive, and the two approaches can be used to formulate a responsible land management strategy. Results gathered through ISM were compared to those from Phase II ESA for two PHC contaminated sites in Canada. Both methods indicated the sites were impacted with PHC beyond Saskatchewan Tier I guidance, however, the delineation of the PHC plume differed by as much as 75% for the heavier hydrocarbons. The Phase II ESA methods had higher incidences of false positive results and an overestimation of contamination at depth. A laboratory experiment confirmed that ISM does not “dilute” the samples as to cause underestimation, whereby the hydrocarbon concentrations for a single combined sample was equivalent to the mean of 30 discrete samples. Based on our results, sites should undergo risk assessment based on the estimates of the Phase II ESA results using vapor phase logs to estimate contaminant extent. If exposure pathways cannot be eliminated through the risk assessment process, remediation planning based on the ISM results is justified given the demonstrated cost-effectiveness, representativeness, and reproducibility.     

Diversity and polymorphism in AHL-lactonase gene (aiiA) of Bacillus

To explore bacterial diversity for elucidating genetic variability in acylhomoserine lactone (AHL) lactonase structure, we screened 800 bacterial strains. It revealed the presence of a quorum quenching (QQ) AHL-lactonase gene (aiiA) in 42 strains. These 42 strains were identified using rrs (16S rDNA) sequencing as Bacillus strains, predominantly B. cereus. An in silico restriction endonuclease (RE) digestion of 22 AHL lactonase gene (aiiA) sequences (from NCBI database) belonging to 9 different genera, along with 42 aiiA gene sequences from different Bacillus spp. (isolated here) with 14 type II REs, revealed distinct patterns of fragments (nucleotide length and order) with four REs; AluI, DpnII, RsaI, and Tru9I. Our study reflects on the biodiversity of aiiA among Bacillus species. Bacillus sp. strain MBG11 with polymorphism (115Alanine > Valine) may confer increased stability to AHL lactonase, and can be a potential candidate for heterologous expression and mass production. Microbes with ability to produce AHL-lactonases degrade quorum sensing signals such as AHL by opening of the lactone ring. The naturally occurring diversity of QQ molecules provides opportunities to use them for preventing bacterial infections, spoilage of food, and bioremediation.