The nitrate transporter family protein LjNPF8.6 controls the N-fixing nodule activity

N-fixing nodules are new organs formed on legume roots as a result of the beneficial interaction with soil bacteria, rhizobia. The nodule functioning is still a poorly characterized step of the symbiotic interaction, as only a few of the genes induced in N-fixing nodules have been functionally characterized. We present here the characterization of a member of the Lotus japonicus nitrate transporter1/peptide transporter family, LjNPF8.6. The phenotypic characterization carried out in independent L. japonicus LORE1 insertion lines indicates a positive role of LjNPF8.6 on nodule functioning, as knockout mutants display N-fixation deficiency (25%) and increased nodular superoxide content. The partially compromised nodule functioning induces two striking phenotypes: anthocyanin accumulation already displayed 4 weeks after inoculation and shoot biomass deficiency, which is detected by long-term phenotyping. LjNPF8.6 achieves nitrate uptake in Xenopus laevis oocytes at both 0.5 and 30 mm external concentrations, and a possible role as a nitrate transporter in the control of N-fixing nodule activity is discussed

Multisignal control of expression of the LHCX protein family in the marine diatom Phaeodactylum tricornutum

Diatoms are phytoplanktonic organisms that grow successfully in the ocean where light conditions are highly variable. Studies of the molecular mechanisms of light acclimation in the marine diatom Phaeodactylum tricornutum show that carotenoid de-epoxidation enzymes and LHCX1, a member of the light-harvesting protein family, both contribute to dissipate excess light energy through non-photochemical quenching (NPQ). In this study, we investigate the role of the other members of the LHCX family in diatom stress responses. Our analysis of available genomic data shows that the presence of multiple LHCX genes is a conserved feature of diatom species living in different ecological niches. Moreover, an analysis of the levels of four P. tricornutum LHCX transcripts in relation to protein expression and photosynthetic activity indicates that LHCXs are differentially regulated under different light intensities and nutrient starvation, mostly modulating NPQ capacity. We conclude that multiple abiotic stress signals converge to regulate the LHCX content of cells, providing a way to fine-tune light harvesting and photoprotection. Moreover, our data indicate that the expansion of the LHCX gene family reflects functional diversification of its members which could benefit cells responding to highly variable ocean environments

Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes

Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment

Gene silencing in the marine diatom Phaeodactylum tricornutum

Diatoms are a major but poorly understood phytoplankton group. The recent completion of two whole genome sequences has revealed that they contain unique combinations of genes, likely recruited during their history as secondary endosymbionts, as well as by horizontal gene transfer from bacteria. A major limitation for the study of diatom biology and gene function is the lack of tools to generate targeted gene knockout or knockdown mutants. In this work, we have assessed the possibility of triggering gene silencing in Phaeodactylum tricornutum using constructs containing either anti-sense or inverted repeat sequences of selected target genes. We report the successful silencing of a GUS reporter gene expressed in transgenic lines, as well as the knockdown of endogenous phytochrome (DPH1) and cryptochrome (CPF1) genes. To highlight the utility of the approach we also report the first phenotypic characterization of a diatom mutant (cpf1). Our data open the way for reverse genetics in diatoms and represent a major advance for understanding their biology and ecology. Initial molecular analyses reveal that targeted downregulation likely occurs through transcriptional and post-transcriptional gene silencing mechanisms. Interestingly, molecular players involved in RNA silencing in other eukaryotes are only poorly conserved in diatoms

Physical, Chemical, and Genetic Techniques for Diatom Frustule Modification: Applications in Nanotechnology

Diatom frustules represent one of the most complex examples of micro- and nano-structured materials found in nature, being the result of a biomineralization process refined through tens of milions of years of evolution. They are constituted by an intricate, ordered porous silica matrix which recently found several applications in optoelectronics, sensing, solar light harvesting, filtering, and drug delivery, to name a few. The possibility to modify the composition and the structure of frustules can further broaden the range of potential applications, adding new functions and active features to the material. In the present work the most remarkable physical and chemical techniques aimed at frustule modification are reviewed, also examining the most recent genetic techniques developed for its controlled morphological mutation

Dynamics of mathematical models in biology: bringing mathematics to life

This volume focuses on contributions from both the mathematics and life science community surrounding the concepts of time and dynamicity of nature, two significant elements which are often overlooked in modeling process to avoid exponential computations. The book is divided into three distinct parts: dynamics of genomes and genetic variation, dynamics of motifs, and dynamics of biological networks. Chapters included in dynamics of genomes and genetic variation analyze the molecular mechanisms and evolutionary processes that shape the structure and function of genomes and those that govern genome dynamics. The dynamics of motifs portion of the volume provides an overview of current methods for motif searching in DNA, RNA and proteins, a key process to discover emergent properties of cells, tissues, and organisms. The part devoted to the dynamics of biological networks covers networks aptly discusses networks in complex biological functions and activities that interpret processes in cells. Moreover, chapters in this section examine several mathematical models and algorithms available for integration, analysis, and characterization. Once life scientists began to produce experimental data at an unprecedented pace, it become clear that mathematical models were necessary to interpret data, to structure information with the aim to unveil biological mechanisms, discover results, and make predictions. The second annual “Bringing Maths to Life” workshop held in Naples, Italy October 2015, enabled a bi-directional flow of ideas from and international group of mathematicians and biologists. The venue allowed mathematicians to introduce novel algorithms, methods, and software that may be useful to model aspects of life science, and life scientists posed new challenges for mathematicians

Physical, Chemical, and Genetic Techniques for Diatom Frustule Modification: Applications in Nanotechnology

Diatom frustules represent one of the most complex examples of micro- and nano-structured materials found in nature, being the result of a biomineralization process refined through tens of milions of years of evolution. They are constituted by an intricate, ordered porous silica matrix which recently found several applications in optoelectronics, sensing, solar light harvesting, filtering, and drug delivery, to name a few. The possibility to modify the composition and the structure of frustules can further broaden the range of potential applications, adding new functions and active features to the material. In the present work the most remarkable physical and chemical techniques aimed at frustule modification are reviewed, also examining the most recent genetic techniques developed for its controlled morphological mutation