In Silico Identification of Type III PKS Chalcone and Stilbene Synthase Homologs in Marine Photosynthetic Organisms

Cloning and Molecular Characterization of the phlD Gene Involved in the Biosynthesis of "Phloroglucinol", a Compound with Antibiotic Properties from Plant Growth Promoting Bacteria Pseudomonas spp

phlD is a novel kind of polyketide synthase involved in the biosynthesis of non-volatile metabolite phloroglucinol by iteratively condensing and cyclizing three molecules of malonyl-CoA as substrate. Phloroglucinol or 2,4-diacetylphloroglucinol (DAPG) is an ecologically important rhizospheric antibiotic produced by pseudomonads; it exhibits broad spectrum anti-bacterial and anti-fungal properties, leading to disease suppression in the rhizosphere. Additionally, DAPG triggers systemic resistance in plants, stimulates root exudation, as well as induces phyto-enhancing activities in other rhizobacteria. Here, we report the cloning and analysis of the phlD gene from soil-borne gram-negative bacteria-Pseudomonas. The full-length phlD gene (from 1078 nucleotides) was successfully cloned and the structural details of the PHLD protein were analyzed in-depth via a three-dimensional topology and a refined three-dimensional model for the PHLD protein was predicted. Additionally, the stereochemical properties of the PHLD protein were analyzed by the Ramachandran plot, based on which, 94.3% of residues fell in the favored region and 5.7% in the allowed region. The generated model was validated by secondary structure prediction using PDBsum. The present study aimed to clone and characterize the DAPG-producing phlD gene to be deployed in the development of broad-spectrum biopesticides for the biocontrol of rhizospheric pathogens.

The type III polyketide synthase supergene family in plants: complex evolutionary history and functional divergence

Type III polyketide synthases (PKSs) are key enzymes involved in the biosynthesis of a variety of plant specialized metabolites, including flavonoids, stilbenes, and sporopollenin, to name a few. These enzymes likely played vital roles in plant adaptation during their transition from aquatic to terrestrial habitats and their colonization of specific ecological environments. Members of this supergene family have diverse functions, but how type III PKSs and their functions have evolved remains poorly understood. Here, we conducted comprehensive phylogenomics analysis of the type III PKS supergene family in 60 species representing the major plant lineages and elucidated the classification, origin, and evolutionary history of each class. Molecular evolutionary analysis of the typical chalcone synthase and stilbene synthase types revealed evidence for strong positive natural selection in both the Pinaceae and Fabaceae lineages. The positively selected sites of these proteins include residues at the catalytic tunnel entrance and homodimer interface, which might have driven the functional divergence between the two types. Our results also suggest that convergent evolution of enzymes involved in plant flavonoid biosynthesis is quite common. The results of this study provide new insights into the origin, evolution, and functional diversity of plant type III PKSs. In addition, they serve as a guide for the enzymatic engineering of plant polyketides.

Transcriptome Mining to Identify Genes of Interest: From Local Databases to Phylogenetic Inference

The advancement in next-generation sequencing technologies and the dropping of sequencing costs have seen an increase in the amount of transcriptome data generated each year. These data are of big potential for identifying genes and molecular pathways of interest across a plethora of organisms. However, navigating these resources requires some bioinformatics and evolutionary skills. Here, we describe a protocol of transcriptome data mining for genes of interest, from the creation of a protein database to the inference of phylogenetic trees, which was used for marine protists, but can be used as general pipeline across different taxa.

Chalcone Derivatives: Role in Anticancer Therapy

Chalcones (1,3-diaryl-2-propen-1-ones) are precursors for flavonoids and isoflavonoids, which are common simple chemical scaffolds found in many naturally occurring compounds. Many chalcone derivatives were also prepared due to their convenient synthesis. Chalcones as weandhetic analogues have attracted much interest due to their broad biological activities with clinical potentials against various diseases, particularly for antitumor activity. The chalcone family has demonstrated potential in vitro and in vivo activity against cancers via multiple mechanisms, including cell cycle disruption, autophagy regulation, apoptosis induction, and immunomodulatory and inflammatory mediators. It represents a promising strategy to develop chalcones as novel anticancer agents. In addition, the combination of chalcones and other therapies is expected to be an effective way to improve anticancer therapeutic efficacy. However, despite the encouraging results for their response to cancers observed in clinical studies, a full description of toxicity is required for their clinical use as safe drugs for the treatment of cancer. In this review, we will summarize the recent advances of the chalcone family as potential anticancer agents and the mechanisms of action. Besides, future applications and scope of the chalcone family toward the treatment and prevention of cancer are brought out.

Physiological and Molecular Responses to Main Environmental Stressors of Microalgae and Bacteria in Polar Marine Environments

The Arctic and Antarctic regions constitute 14% of the total biosphere. Although they differ in their physiographic characteristics, both are strongly affected by snow and ice cover changes, extreme photoperiods and low temperatures, and are still largely unexplored compared to more accessible sites. This review focuses on microalgae and bacteria from polar marine environments and, in particular, on their physiological and molecular responses to harsh environmental conditions. The data reported in this manuscript show that exposure to cold, increase in CO₂ concentration and salinity, high/low light, and/or combination of stressors induce variations in species abundance and distribution for both polar bacteria and microalgae, as well as changes in growth rate and increase in cryoprotective compounds. The use of -omics techniques also allowed to identify specific gene losses and gains which could have contributed to polar environmental adaptation, and metabolic shifts, especially related to lipid metabolism and defence systems, such as the up-regulation of ice binding proteins, chaperones and antioxidant enzymes. However, this review also provides evidence that -omics resources for polar species are still few and several sequences still have unknown functions, highlighting the need to further explore polar environments, the biology and ecology of the inhabiting bacteria and microalgae, and their interactions.

De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates

Many dinoflagellates species, especially of the Alexandrium genus, produce a series of toxins with tremendous impacts on human and environmental health, and tourism economies. Alexandrium tamutum was discovered for the first time in the Gulf of Naples, and it is not known to produce saxitoxins. However, a clone of A. tamutum from the same Gulf showed copepod reproduction impairment and antiproliferative activity. In this study, the full transcriptome of the dinoflagellate A. tamutum is presented in both control and phosphate starvation conditions. RNA-seq approach was used for in silico identification of transcripts that can be involved in the synthesis of toxic compounds. Phosphate starvation was selected because it is known to induce toxin production for other Alexandrium spp. Results showed the presence of three transcripts related to saxitoxin synthesis (sxtA, sxtG and sxtU), and others potentially related to the synthesis of additional toxic compounds (e.g., 44 transcripts annotated as "polyketide synthase"). These data suggest that even if this A. tamutum clone does not produce saxitoxins, it has the potential to produce toxic metabolites, in line with the previously observed activity. These data give new insights into toxic microalgae, toxin production and their potential applications for the treatment of human pathologies.