Plastids of diatoms and related algae with complex plastids of red algal origin are surrounded by four membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. Metabolic reactions as well as cell biological processes take place in the PPC; however, genome-wide predictions of the proteins targeted to this compartment were so far based on manual annotation work. Using published experimental protein localizations as reference data, we developed the first automatic prediction method for PPC proteins, which we included as a new feature in an updated version of the plastid protein predictor ASAFind. With our method, at least a subset of the PPC proteins can be predicted with high specificity, with an estimate of at least 81 proteins (0.7% of the predicted proteome) targeted to the PPC in the model diatom Phaeodactylum tricornutum. The proportion of PPC proteins varies, since 180 PPC proteins (1.3% of the predicted proteome) were predicted in the genome of the diatom Thalassiosira pseudonana. The new ASAFind version can also generate a newly designed graphical output that visualizes the contribution of each position in the sequence to the score and accepts the output of the recent versions of SignalP (5.0) and TargetP (2.0) as input data. Furthermore, we release a script to calculate custom scoring matrices that can be used for predictions in a simplified score cut-off mode. This allows for adjustments of the method to other groups of algae.

• Klíčová slova
• chloroplast, diatoms, evolution, gene transfer, genome annotation, mitochondria, organelle, periplastidic compartment, protein transport, secretory pathway, technical advance,
• MeSH
• bílkoviny řas * metabolismus   MeSH
• plastidy * metabolismus   MeSH
• proteom MeSH
• Rhodophyta metabolismus   MeSH
• rozsivky * metabolismus   genetika   MeSH
• software * MeSH
• výpočetní biologie * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bílkoviny řas * MeSH
• proteom MeSH

A considerable part of the diversity of eukaryotic phototrophs consists of algae with plastids that evolved from endosymbioses between two eukaryotes. These complex plastids are characterized by a high number of envelope membranes (more than two) and some of them contain a residual nucleus of the endosymbiotic alga called a nucleomorph. Complex plastid-bearing algae are thus chimeric cell assemblies, eukaryotic symbionts living in a eukaryotic host. In contrast, the primary plastids of the Archaeplastida (plants, green algae, red algae, and glaucophytes) possibly evolved from a single endosymbiosis with a cyanobacterium and are surrounded by two membranes. Complex plastids have been acquired several times by unrelated groups of eukaryotic heterotrophic hosts, suggesting that complex plastids are somewhat easier to obtain than primary plastids. Evidence suggests that complex plastids arose twice independently in the green lineage (euglenophytes and chlorarachniophytes) through secondary endosymbiosis, and four times in the red lineage, first through secondary endosymbiosis in cryptophytes, then by higher-order events in stramenopiles, alveolates, and haptophytes. Engulfment of primary and complex plastid-containing algae by eukaryotic hosts (secondary, tertiary, and higher-order endosymbioses) is also responsible for numerous plastid replacements in dinoflagellates. Plastid endosymbiosis is accompanied by massive gene transfer from the endosymbiont to the host nucleus and cell adaptation of both endosymbiotic partners, which is related to the trophic switch to phototrophy and loss of autonomy of the endosymbiont. Such a process is essential for the metabolic integration and division control of the endosymbiont in the host. Although photosynthesis is the main advantage of acquiring plastids, loss of photosynthesis often occurs in algae with complex plastids. This chapter summarizes the essential knowledge of the acquisition, evolution, and function of complex plastids.

• Klíčová slova
• Complex endosymbiosis, Plastid replacement, Reductive evolution,
• MeSH
• biologická evoluce * MeSH
• fylogeneze MeSH
• plastidy genetika   metabolismus   MeSH
• Rhodophyta * genetika   MeSH
• rostliny genetika   MeSH
• symbióza MeSH
• Publikační typ
• časopisecké články MeSH

Eukaryotic organelles supposedly evolved from their bacterial ancestors because of their benefits to host cells. However, organelles are quite often retained, even when the beneficial metabolic pathway is lost, due to something other than the original beneficial function. The organellar function essential for cell survival is, in the end, the result of organellar evolution, particularly losses of redundant metabolic pathways present in both the host and endosymbiont, followed by a gradual distribution of metabolic functions between the organelle and host. Such biological division of metabolic labor leads to mutual dependence of the endosymbiont and host. Changing environmental conditions, such as the gradual shift of an organism from aerobic to anaerobic conditions or light to dark, can make the original benefit useless. Therefore, it can be challenging to deduce the original beneficial function, if there is any, underlying organellar acquisition. However, it is also possible that the organelle is retained because it simply resists being eliminated or digested untill it becomes indispensable.

• Klíčová slova
• benefit, endosymbiosis, essential function, mitochondrion, organelle, plastid,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

• Klíčová slova
• endosymbiosis, evolution, loss, photosynthesis, plastid,
• Publikační typ
• úvodníky MeSH

Plastids are membrane-bound organelles that bestow phototrophic abilities to eukaryotes [...].

• MeSH
• biologická evoluce MeSH
• plastidy * metabolismus   genetika   MeSH
• symbióza * MeSH
• Publikační typ
• úvodní články MeSH
• úvodníky MeSH

Heme biosynthesis is essential for almost all living organisms. Despite its conserved function, the pathway's enzymes can be located in a remarkable diversity of cellular compartments in different organisms. This location does not always reflect their evolutionary origins, as might be expected from the history of their acquisition through endosymbiosis. Instead, the final subcellular localization of the enzyme reflects multiple factors, including evolutionary origin, demand for the product, availability of the substrate, and mechanism of pathway regulation. The biosynthesis of heme in the apicomonad Chromera velia follows a chimeric pathway combining heme elements from the ancient algal symbiont and the host. Computational analyses using different algorithms predict complex targeting patterns, placing enzymes in the mitochondrion, plastid, endoplasmic reticulum, or the cytoplasm. We employed heterologous reporter gene expression in the apicomplexan parasite Toxoplasma gondii and the diatom Phaeodactylum tricornutum to experimentally test these predictions. 5-aminolevulinate synthase was located in the mitochondria in both transfection systems. In T. gondii, the two 5-aminolevulinate dehydratases were located in the cytosol, uroporphyrinogen synthase in the mitochondrion, and the two ferrochelatases in the plastid. In P. tricornutum, all remaining enzymes, from ALA-dehydratase to ferrochelatase, were placed either in the endoplasmic reticulum or in the periplastidial space.

• Klíčová slova
• Chromera velia, heterologous expression, predictions, tetrapyrrole biosynthesis,
• MeSH
• Alveolata fyziologie   MeSH
• Apicomplexa metabolismus   MeSH
• biologický transport MeSH
• hem metabolismus   MeSH
• metabolické sítě a dráhy * MeSH
• mitochondrie genetika   metabolismus   ultrastruktura   MeSH
• molekulární evoluce MeSH
• protozoální proteiny chemie   genetika   metabolismus   MeSH
• regulace genové exprese enzymů MeSH
• rozsivky metabolismus   MeSH
• sekvence aminokyselin MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• hem MeSH
• protozoální proteiny MeSH

Fatty acids are essential components of biological membranes, important for the maintenance of cellular structures, especially in organisms with complex life cycles like protozoan parasites. Apicomplexans are obligate parasites responsible for various deadly diseases of humans and livestock. We analyzed the fatty acids produced by the closest phototrophic relatives of parasitic apicomplexans, the chromerids Chromera velia and Vitrella brassicaformis, and investigated the genes coding for enzymes involved in fatty acids biosynthesis in chromerids, in comparison to their parasitic relatives. Based on evidence from genomic and metabolomic data, we propose a model of fatty acid synthesis in chromerids: the plastid-localized FAS-II pathway is responsible for the de novo synthesis of fatty acids reaching the maximum length of 18 carbon units. Short saturated fatty acids (C14:0-C18:0) originate from the plastid are then elongated and desaturated in the cytosol and the endoplasmic reticulum. We identified giant FAS I-like multi-modular enzymes in both chromerids, which seem to be involved in polyketide synthesis and fatty acid elongation. This full-scale description of the biosynthesis of fatty acids and their derivatives provides important insights into the reductive evolutionary transition of a phototropic algal ancestor to obligate parasites.

• Klíčová slova
• Chromera velia, Vitrella brassicaformis, de novo biosynthesis, desaturation, elongation, evolution, fatty acids,
• MeSH
• Apicomplexa klasifikace   genetika   metabolismus   MeSH
• biosyntetické dráhy genetika   MeSH
• desaturasy mastných kyselin klasifikace   genetika   metabolismus   MeSH
• druhová specificita MeSH
• elongasy mastných kyselin klasifikace   genetika   metabolismus   MeSH
• fylogeneze MeSH
• lidé MeSH
• mastné kyseliny biosyntéza   MeSH
• molekulární evoluce MeSH
• protozoální infekce parazitologie   MeSH
• protozoální proteiny klasifikace   genetika   metabolismus   MeSH
• synthasa mastných kyselin, typ 2 klasifikace   genetika   metabolismus   MeSH
• synthasa mastných kyselin, typ I klasifikace   genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• desaturasy mastných kyselin MeSH
• elongasy mastných kyselin MeSH
• mastné kyseliny MeSH
• protozoální proteiny MeSH
• synthasa mastných kyselin, typ 2 MeSH
• synthasa mastných kyselin, typ I MeSH

Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic tissues, or during the dark, depend on external supply of ATP. A dedicated antiporter that exchanges ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) takes over this function in most photosynthetic eukaryotes. Additional forms of such nucleotide transporters (NTTs), with deviating activities, are found in intracellular bacteria, and, surprisingly, also in diatoms, a group of algae that acquired their plastids from other eukaryotes via one (or even several) additional endosymbioses compared to algae with primary plastids and higher plants. In this review, we summarize what is known about the nucleotide synthesis and transport pathways in diatom cells, and discuss the evolutionary implications of the presence of the additional NTTs in diatoms, as well as their applications in biotechnology.

• Klíčová slova
• adenosine triphosphate (ATP), endosymbiosis, evolution, photosynthesis, plastid, synthetic biology, transport,
• MeSH
• biologická evoluce MeSH
• biologický transport MeSH
• biotechnologie MeSH
• membránové transportní proteiny chemie   metabolismus   MeSH
• nukleotidy biosyntéza   metabolismus   MeSH
• rozsivky metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• membránové transportní proteiny MeSH
• nukleotidy MeSH