Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation

Remmers, Ilse M.; D’Adamo, Sarah; Martens, Dirk E.; Vos, Ric C. H. de; Mumm, Roland; America, Twan; Cordewener, J.H.G.; Bakker, Linda V.; Peters, Sander; Wijffels, René H.; Lamers, Packo P.

doi:10.1016/j.algal.2018.08.012

Cited by 97 publications

(103 citation statements)

References 92 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Each nutrient stress condition results in different metabolic changes and hence, differences in lipid class profile, positional isomers and enantiomers [87]. The waning of the diurnal cycle and macronutrient deficiency have been shown to cause co-ordinated changes in transcriptional regulation, re-organization of metabolic flux and the reallocation of cellular carbon towards lipid production [83,85,[88][89][90][91]. Similar effects can be achieved by disrupting nutrient assimilation, such as knocking-out or knocking-down nitrate reductase [92,93].…”

Section: Biogenesismentioning

confidence: 99%

A Review of Diatom Lipid Droplets

Leyland

Boussiba

Khozin‐Goldberg

2020

Biology

View full text Add to dashboard Cite

The dynamic nutrient availability and photon flux density of diatom habitats necessitate buffering capabilities in order to maintain metabolic homeostasis. This is accomplished by the biosynthesis and turnover of storage lipids, which are sequestered in lipid droplets (LDs). LDs are an organelle conserved among eukaryotes, composed of a neutral lipid core surrounded by a polar lipid monolayer. LDs shield the intracellular environment from the accumulation of hydrophobic compounds and function as a carbon and electron sink. These functions are implemented by interconnections with other intracellular systems, including photosynthesis and autophagy. Since diatom lipid production may be a promising objective for biotechnological exploitation, a deeper understanding of LDs may offer targets for metabolic engineering. In this review, we provide an overview of diatom LD biology and biotechnological potential.

show abstract

Section: Biogenesismentioning

confidence: 99%

A Review of Diatom Lipid Droplets

Leyland

Boussiba

Khozin‐Goldberg

2020

Biology

View full text Add to dashboard Cite

show abstract

“…The transcriptome or RNA expression levels in these organisms are also being explored with the goal of understanding the timing of transcription, translation, and protein secretion as it pertains to the events occurring in the biomineralizing matrix . What has emerged from these studies…”

Section: Biomineral‐associated Secretomesmentioning

confidence: 99%

“…Within these genomes lurk mineralization‐associated genes. Since many biomineral‐associated proteins are extracellular and thus subjected to post‐translational modifications, these genomic studies have been augmented by proteomic studies that identify gene products that are phosphorylated, sulfated, glycosylated, enzymatically cleaved, or otherwise chemically modified at side‐chain groups . The challenge that we are now facing is to identify these mineralization‐associated proteins, their structure, synthesis, secretion, and temporal/regional localization, and most importantly, their purpose or function.…”

Section: Introductionmentioning

confidence: 99%

The Biomineralization Proteome: Protein Complexity for a Complex Bioceramic Assembly Process

Evans

2019

Proteomics

View full text Add to dashboard Cite

There are over 62 different biominerals on Earth and a diverse array of organisms that generate these biominerals for survival. This review will introduce the process of biomineralization and the current understanding of the molecular mechanisms of mineral formation, and then comparatively explore the representative secretomes of two well-documented skeletal systems: vertebrate bone (calcium phosphate) and invertebrate mollusk shell (calcium carbonate). It is found that both skeletal secretomes have gross similarities and possess proteins that fall into four functional categories: matrix formers, nucleation assisters, communicators, and remodelers. In many cases the mineral-associated matrix former and nucleation assister sequences in both skeletal systems are unique and possess interactive conserved globular domains, intrinsic disorder, post-translational modifications, sequence redundancy, and amyloid-like aggregation-prone sequences. Together, these molecular features create a protein-based environment that facilitates mineral formation and organization and argue in favor of conserved features that evolve from the mollusk shell to bone. Interestingly, the mollusk shell secretome appears to be more complex compared to that of bone tissue, in that there are numerous protein subcategories that are required for the nucleation and organization of inner (nacre) and outer (prismatic) calcium carbonate regions of the shell. This may reflect the organizational and material requirements of an exoskeletal protective system.

show abstract

“…1a), their relative expression levels were very low under various conditions (data obtained from published transcriptomes 30,31 , Supplementary Fig. 1), and the proteins were not detected (data obtained from published proteomes [32][33][34] ). In contrast, the type III MCs, PtMC2, PtMC4, and PtMC5 proteins were detected [32][33][34] , and had higher gene expression levels in all the examined conditions.…”

Section: Resultsmentioning

confidence: 99%

“…1), and the proteins were not detected (data obtained from published proteomes [32][33][34] ). In contrast, the type III MCs, PtMC2, PtMC4, and PtMC5 proteins were detected [32][33][34] , and had higher gene expression levels in all the examined conditions. The gene expression levels in steady state, and the protein abundance of all the type III MCs were similar.…”

Section: Resultsmentioning

confidence: 99%

A redox-regulated type III metacaspase controls cell death in a marine diatom

Creveld¹,

Ben‐Dor

Mizrachi³

et al. 2018

Preprint

View full text Add to dashboard Cite

Programmed cell death (PCD) in marine phytoplankton was suggested as one of the mechanisms that facilitates large scale bloom demise. Yet, the molecular basis for algal PCD machinery is rudimentary. Metacaspases are considered ancestral proteases that regulate cell death, but their activity and role in algae are still elusive. Here we biochemically characterized a recombinant metacaspase 5 from the model diatom Phaeodactylum tricornutum (PtMC5), revealing calcium-dependent protease activity. This activity includes auto-processing and cleavage following arginine. PtMC5 overexpressing cells exhibited higher metacaspase activity and were more sensitive to a diatom-specific infochemical compared to WT cells. Mutagenesis of potential disulfide-forming cysteines decreased PtMC5 activity, suggesting redox regulation. This cysteine pair is widespread in diatom type III metacaspases, but was not found in any other taxa. The characterization of a cell death associated protein in marine phytoplankton will enable deeper understanding of the ecological significance of PCD in bloom dynamics.

show abstract

Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation

Cited by 97 publications

References 92 publications

A Review of Diatom Lipid Droplets

A Review of Diatom Lipid Droplets

The Biomineralization Proteome: Protein Complexity for a Complex Bioceramic Assembly Process

A redox-regulated type III metacaspase controls cell death in a marine diatom

Contact Info

Product

Resources

About