2022, Maier, Uwe G., Moog, Daniel, Flori, Serena, Jouneau, Pierre-Henri, Falconet, Denis, Heimerl, Thomas, Kroth, Peter G., Finazzi, Giovanni

Diatoms are phototrophic, unicellular, and eukaryotic organisms. They originate from secondary endosymbiosis, a specific evolutionary process. Accordingly, their cells and organelles have a typical organisation, as revealed by ultrastructural investigations. Diatoms possess specific compartments and structures, including a silica shell surrounding the diatom cell, the so-called silica deposition vesicles (SDVs), as well as complex plastids that are surrounded by four membranes. Here we provide an overview of diatom organelles, and recapitulate recent information obtained from 3D imaging of whole diatom cells, focusing on the subcellular topology of the model diatom Phaeodactylum tricornutum. This chapter will not discuss issues of the cell wall and the SDVs, which are covered in Chaps. “Structure and Morphogenesis of the Frustule” and “Biomolecules Involved in Frustule Biogenesis and Function”.

2018, Schober, Alexander, Flori, Serena, Finazzi, Giovanni, Kroth, Peter G., Río Bártulos, Carolina

The so-called "complex" plastids from diatoms possessing four envelope membranes are a typical feature of algae that arose from secondary endosymbiosis. Studying isolated plastids from these algae may allow answering a number of fundamental questions regarding diatom photosynthesis and plastid functionality. Due to their complex architecture and their integration into the cellular endoplasmic reticulum (ER) system, their isolation though is still challenging. In this work, we report a reliable isolation technique that is applicable for the two model diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. The resulting plastid-enriched fractions are of homogenous quality, almost free from cellular contaminants, and feature structurally intact thylakoids that are capable to perform oxygenic photosynthesis, though in most cases they seem to lack most of the stromal components as well as plastid envelopes.

2022, Kroth, Peter G., Matsuda, Yusuke

Diatoms are unicellular algae that perform photosynthesis, a process that comprises both the electron transport processes in the thylakoid membranes and the reactions involved in CO2 fixation. The latter process is the starting point for carbohydrate biosynthesis and numerous reactions and pathways in different cellular locations, including the generation, modification, conversion, subsequent storage, and degradation of carbohydrates. While there is vast knowledge of these processes available of land plants and green algae, much less is known of algae like diatoms that are derived from secondary endosymbiosis. Comparative studies on the localization and regulation of photosynthetic pathways in recent years revealed in principle a similarity of photosynthesis in land plants and diatoms, but also a number of peculiar differences, which may be due both to the general phylogenetic distance between these groups and the evolution of diatoms by secondary endosymbiosis, resulting in a different genetic background. This chapter describes the current knowledge of CO₂ acquisition and fixation processes in diatoms on the molecular, cellular, and physiological levels in diatoms. Additional focus is laid on photorespiration, as well as carbohydrate pathways, carbohydrate degradation, and carbohydrate storage.

2014, Matsuda, Yusuke, Kroth, Peter G.

Diatoms are unicellular photoautotrophic algae and very successful primary producers in the oceans. Their high primary productivity is probably sustained by their high adaptability and a uniquely arranged metabolism. Diatom belongs to the Chromista, a large eukaryotic group, which has evolved by multiple endosymbiotic steps. As a result, diatoms possess a plastids with four membranes together with complicated translocation systems to transport proteins and metabolites including inorganic substances into and out of the plastids. In addition to the occurrence of potential plasma-membrane transporters, there are numerous carbonic anhydrases (CAs) within the matrix of the layered plastidic membranes, strongly suggesting large interconversion activity between CO₂ and HCO₃ − within the chloroplast envelope as a part of a CO2-concentrating mechanism (CCM). In diatoms also the Calvin cycle and its adjacent metabolism reveal unique characteristics as, for instance, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activase, the plastidic sedoheptulose-1,7-bisphosphatase (SBPase), and the plastidic oxidative pentose phosphate pathway (OPP) are absent. Furthermore, the Calvin cycle metabolism in diatoms is not under the strict redox control by the thioredoxin (Trx) system. Instead, a CO₂-supplying system in the pyrenoid shows CA activities which are probably regulated by chloroplastic Trxs. Pyrenoidal CAs are also regulated on the transcriptional level by CO₂ concentrations via cAMP as a second messenger, suggesting an intense control system of CO₂ acquisition in response to CO₂ availability. The photorespiratory carbon oxidation cycle (PCOC) is the major pathway to recycle phosphoglycolate in diatoms although this process might not be involved in recycling of 3-phosphoglycerate but instead produces glycine and serine. In this review we focus on recent experimental data together with supportive genome information of CO₂ acquisition and fixation systems primarily in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana.

2022, Jaubert, Marianne, Duchêne, Carole, Kroth, Peter G., Rogato, Alessandra, Bouly, Jean-Pierre, Falciatore, Angela

Diatoms are prominent microalgae that proliferate in a wide range of aquatic environments. Still, fundamental questions regarding their biology, such as how diatoms sense and respond to environmental variations, remain largely unanswered. In recent years, advances in the molecular and cell biology of diatoms and the increasing availability of genomic data have made it possible to explore sensing and signalling pathways in these algae. Pivotal studies of photosensory perception have highlighted the great capacity of diatoms to accurately detect environmental variations by sensing differential light signals and adjust their physiology accordingly. The characterization of photoreceptors and light-dependent processes described in this review, such as plastid signalling and diel regulation, is unveiling sensing systems which are unique to these algae, reflecting their complex evolutionary history and adaptation to aquatic life. Here, we also describe putative sensing components involved in the responses to nutrient, osmotic changes, and fluid motions. Continued elucidation of the molecular systems processing endogenous and environmental cues and their interactions with other biotic and abiotic stress signalling pathways is expected to greatly increase our understanding of the mechanisms controlling the abundance and distribution of the highly diverse diatom communities in marine ecosystems.

2014, Gruber, Ansgar, Kroth, Peter G.

In the recent years, a large number of genomes from a variety of different organisms have been sequenced. Most of the sequence data has been publicly released and can be assessed by interested users. However, this wealth of information is currently underexploited by scientists not directly involved in genome annotation. This is partially because sequencing, assembly, and automated annotation can be done much faster than the identification, classification, and prediction of the intracellular localization of the gene products. This part of the annotation process still largely relies on manual curation and addition of contextual information. Users of genome databases who are unfamiliar with the types of data available from (whole) genomes might therefore find themselves either overwhelmed by the vast amount and multiple layers of data or dissatisfied with less-than-meaningful analyses of the data.
In this chapter we present procedures and approaches to identify and characterize gene models of enzymes involved in metabolic pathways based on their similarity to known sequences. Furthermore we describe how to predict the subcellular location of the proteins using publicly available prediction servers and how to interpret the obtained results. The strategies we describe are generally applicable to organisms with primary plastids such as land plants or green algae. Additionally, we describe strategies suitable for those groups of algae with secondary plastids (for instance diatoms), which are characterized by a different cellular topology and a larger number of intracellular compartments compared to plants.