Abstract
Diatoms are one of the major and most diverse groups of phytoplankton, with chimeric genomes harbouring a combination of genes of bacterial, animal and plant origin. They have developed sophisticated mechanisms to face environmental variations. In marine environments, nutrients concentration shows significant temporal and spatial variability, influencing phytoplankton growth. Among nutrients, nitrogen, present at micromolar levels, is often a limiting resource. Here, we report a comprehensive characterization of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in diatoms, diNPFs. NPFs are well characterized in many organisms where they recognize a broad range of substrates, ranging from short-chained di- and tri-peptides in bacteria, fungi and mammals to a wide variety of molecules including nitrate in higher plants. Scarce information is available for diNPFs. We integrated-omics, phylogenetic, structural and expression analyses, to infer information on their role in diatoms. diNPF genes diverged to produce two distinct clades with strong sequence and structural homology with either bacterial or plant NPFs, with different predicted sub-cellular localization, suggesting that the divergence resulted in functional diversification. Moreover, transcription analysis of diNPF genes under different laboratory and environmental growth conditions suggests that diNPF diversification led to genetic adaptations that might contribute to diatoms ability to flourish in diverse environmental conditions.
Highlights
Together with light availability, nutrient supply governs the life and distribution of photosynthetic organisms
Plant Nitrate Transporter 1/Peptide Transporter Family (NPF) are phylogenetically related to a family of peptide transporters (PTRs) or proton-coupled oligopeptide transporters (POTs) that are evolutionarily conserved in archaea, bacteria, fungi and animals [6]
We report the first characterization of the NPF family members in diatoms through a multilevel approach which integrated data coming from fully sequenced diatom genomes [34] with the TARA Oceans datasets [35,36,37], that provide a unique combination of environmental, metagenomic and metatranscriptomic data, and the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) dataset, which provides over 650 protist transcriptomes [38]
Summary
Nutrient supply governs the life and distribution of photosynthetic organisms. We report the first characterization of the NPF family members in diatoms (diNPFs) through a multilevel approach which integrated data coming from fully sequenced diatom genomes [34] with the TARA Oceans datasets [35,36,37], that provide a unique combination of environmental, metagenomic and metatranscriptomic data, and the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) dataset, which provides over 650 protist transcriptomes [38] These data, in combination with phylogenetic and expression analyses and structural predictions, uncover an unexpected evolutionary complexity of NPF transporters and offer the foundation for the genetic dissection of the extra- and intracellular transport system in diatoms, revealing once again the chimeric nature and the complex physiology of these successful microalgae
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