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Phylogenetic tree of TPPPs of Chytridiomycetes constructed by Maximum Parsimony (MP) analysis. Full circle at a node indicates that the branch was supported by MP bootstrap !85 %. All the other branches were supported by MP bootstrap !50 %. The box with full lines indicates the "animal-type" TPPPs (see the text). The box with dotted lines indicates the same group of TPPPs as the dotted lined box in Fig. 4 (Blue background in color figure online.) C. stands for Chytriomyces. Outgroup: Spizellomyces punctatus XP_016604112. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
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TPPP-like proteins, exhibiting microtubule stabilizing function, constitute a eukaryotic superfamily, characterized by the presence of the p25alpha domain. TPPPs in the strict sense are present in animals except Trichoplax adhaerens, which instead contains apicortin where a part of the p25alpha domain is combined with a DCX domain. Apicortin is abs...
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... were submitted to the IUPRED server freely available at http://iupred.elte.hu/ (Doszt anyi et al., 2005a, 2005b). ...
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... (Fig. 4), in accordance with earlier results (James et al., 2006b; Longcore et al., 2011), it was included in the analysis since other species of the genus Entophlyctis are considered to belong to Chytridiomycetes ( James et al., 2006b). The trees show clearly that E. helioformis does not belong to the class Chytridiomycetes, indeed. Both the MP (Fig. 5) and the Bayesian (Fig. S5) trees show with high statistical support that these species contain 3 kinds of TPPPs, an "animal-type" and two "fungal-types". Within the clades, they are more similar to each other than to TPPPs occurring in the same species. They can be considered as "outparalogs" (Sonnhammer and Koonin, 2002) since the ...
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... earlier results (James et al., 2006b; Longcore et al., 2011), it was included in the analysis since other species of the genus Entophlyctis are considered to belong to Chytridiomycetes ( James et al., 2006b). The trees show clearly that E. helioformis does not belong to the class Chytridiomycetes, indeed. Both the MP (Fig. 5) and the Bayesian (Fig. S5) trees show with high statistical support that these species contain 3 kinds of TPPPs, an "animal-type" and two "fungal-types". Within the clades, they are more similar to each other than to TPPPs occurring in the same species. They can be considered as "outparalogs" (Sonnhammer and Koonin, 2002) since the duplication events happened ...
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... assemblies of the MycoCosm webpage, which contains the results of completed projects, were analyzed (Table 2). Occasionally, data from other web sites were also used for refinement of the analysis. Fungi of Dikarya, which compose the vast majority of the available genomes, do not possess either flagellum or p25alpha-containing proteins (Cf. also Fig. 5). In the case of basal fungi, far less data are available. Fungi of Zoopagomycota (22 genomes listed) miss also both the flagellum and the TPPP/ apicortin. Fungi of Mucoromycota (86 genomes listed) are nonflagellated but the four genomes of Endogonomycetes ( Chang et al., 2019) listed on the webpage contain apicortin. Other classes of ...
Citations
... TPPP orthologs are also present in some protists and algae [17]. A strong correlation was suggested between the incidence of tppp/TPPP genes/proteins and that of the eukaryotic flagellum [18,19]. ...
... The eukaryotic flagellum is a microtubule-based organelle; thus, the connection is self-evident. The correlation between the occurrence of a flagellum and TPPPs, based on bioinformatic analysis of genomic and proteomic data, is strong: in general, with very few exceptions, flagellated organisms do contain TPPP proteins; on the other hand, in non-flagellated species, TPPPs usually do not occur [18,19]. Thus, TPPP is absent in prokaryotes and archaea, as well as in terrestrial plants. ...
Tubulin polymerization-promoting protein2 (TPPP2) is one of the three paralogs of mammalian TPPP proteins. Its possible role in spermatogenesis is described in this narrative review. TPPP2 is expressed specifically in the male reproductive system, mainly in testes and sperm, and also in the epididymis. In testes, TPPP2 is exclusively expressed in elongating spermatids; in the epididymis, it is located in the middle piece of the sperm tail. TPPP2 is involved in spermiogenesis, in steps which are determinative for the formation and morphology of spermatids. The inhibition of TPPP2 decreases sperm motility (the curvilinear velocity of sperms), probably due to influencing mitochondrial energy production since TPPP2 knockout mice possess an impaired mitochondrial structure. There are data on the role of TPPP2 in various mammalian species: human, mouse, swine, and various ruminants; there is a significant homology among TPPP2s from different species. Experiments with Tppp2−/−-mice show that the absence of TPPP2 results in decreased sperm count and serious dysfunction of sperm, including decreased motility; however, the in vitro capacitation and acrosome reaction are not influenced. The symptoms show that Tppp2−/−-mice may be considered as a model for oligoasthenozoospermia.
... (For example, apicortins contain a partial (C-terminal) p25alpha domain and a doublecortin (DCX) domain [21].) 'Long' TPPP ( Figure 1) is present in Opisthokonta (animals, flagellated fungi, and Choanoflagellata [12,17]), and contains a 'long' (full length) p25alpha domain. There is only long TPPP in animals thus long TPPP is also named 'animal-type' TPPP [12,22]. ...
... 'Long' TPPP ( Figure 1) is present in Opisthokonta (animals, flagellated fungi, and Choanoflagellata [12,17]), and contains a 'long' (full length) p25alpha domain. There is only long TPPP in animals thus long TPPP is also named 'animal-type' TPPP [12,22]. A special, 'fungal-type' TPPP, which contains both a full and a partial p25alpha domain (Figure 1), is present only in certain fungi [12,22,23]. ...
... There is only long TPPP in animals thus long TPPP is also named 'animal-type' TPPP [12,22]. A special, 'fungal-type' TPPP, which contains both a full and a partial p25alpha domain (Figure 1), is present only in certain fungi [12,22,23]. In general, there is high homology between the C-terminus of the full-length domain and the partial domain [23]. ...
The unicellular, parasitic fungi of the phylum Sanchytriomycota (sanchytrids) were discovered a few years ago. These unusual chytrid-like fungi parasitize algae. The zoospores of the species of the phylum contain an extremely long kinetosome composed of microtubular singlets or doublets and a non-motile pseudocilium (i.e., a reduced posterior flagellum). Fungi provide an ideal opportunity to test and confirm the correlation between the occurrence of flagellar proteins (the ciliome) and that of the eukaryotic cilium/flagellum since the flagellum occurs in the early-branching phyla and not in terrestrial fungi. Tubulin polymerization promoting protein (TPPP)-like proteins, which contain a p25alpha domain, were also suggested to belong to the ciliome and are present in flagellated fungi. Although sanchytrids have lost many of the flagellar proteins, here it is shown that they possess a DNA sequence possibly encoding long (animal-type) TPPP, but not the fungal-type one characteristic of chytrid fungi. Phylogenetic analysis of p25alpha domains placed sanchytrids into a sister position to Blastocladiomycota, similarly to species phylogeny, with maximal support.
... The long (animaltype) TPPP is specific for Opisthokonta and is found in almost all animals, some flagellated fungi, and Choanoflagellate Monosiga brevicollis [10]. Some flagellated fungi contain fungaltype TPPPs (single copy or two paralogs) that have both a full domain and a partial domain (the C-terminal part), so that the Rossmann-like motif can be found twice in them [14]. The short TPPP is found in algae and protists (Alveolata, Euglenozoa), the C-terminal part of which is incomplete, while Rossmann-like motif is also absent [10]. ...
... The tree follows the species phylogeny; the fungal phyla, Aphelidiomycota, Blastocladiomycota, Chytridiomycota, and Olpidiomycota form separate clades; within Chytridiomycota, the classes Chytridiomycetes, Rhizophydiomycetes, and Spizellomycetes are also separated. Species in Chytridiomycetes have two paralogous fungal-type TPPPs [14], thus forming two clades. The plant sequences are within the fungal clades. ...
... The study of apicortins seems to represent another scenario. This protein has been found in the placozoan animal T. adhaerens [25], in flagellated fungi [14], and in myzozoans (Apicomplexa [25], chromerids [16], Perkinsozoa [26], and dinoflagellates [17]). In the present study, it was found at nucleotide level, as TSA or EST. ...
Genome and transcriptome assembly data often contain DNA and RNA contaminations from external organisms, introduced during nucleotide extraction or sequencing. In this study, contamination of seed plant (Spermatophyta) transcriptomes/genomes with p25alpha domain encoding RNA/DNA was systematically investigated. This domain only occurs in organisms possessing a eukaryotic flagellum (cilium), which seed plants usually do not have. Nucleotide sequences available at the National Center for Biotechnology Information website, including transcriptome shotgun assemblies (TSAs), whole-genome shotgun contigs (WGSs), and expressed sequence tags (ESTs), were searched for sequences containing a p25alpha domain in Spermatophyta. Despite the lack of proteins containing the p25alpha domain, such fragments or complete mRNAs in some EST and TSA databases were found. A phylogenetic analysis showed that these were contaminations whose possible sources were microorganisms (flagellated fungi, protists) and arthropods/worms; however, there were cases where it cannot be excluded that the sequences found were genuine hits and not of external origin.
... As an exception in the fungal kingdom, zoospores of the Chytridiomycota are powered by flagella that due to their diverse ultrastructure are used for phylogenetic classification [92]. A recent study highlights the strong correlation between the occurrence of the p25-alpha domain of tubulin polymerization promoting protein-like proteins in eukaryotic cilia/ flagella of animals and fungi [147]. In animals, a second type of cilia, immobile or primary cilia, are found as antennalike protrusions on many excitatory and non-excitatory cells [192]. ...
Many cell biological facts that can be found in dedicated scientific textbooks are based on findings originally made in humans and/or other mammals, including respective tissue culture systems. They are often presented as if they were universally valid, neglecting that many aspects differ—in part considerably—between the three major kingdoms of multicellular eukaryotic life, comprising animals, plants and fungi. Here, we provide a comparative cross-kingdom view on the basic cell biology across these lineages, highlighting in particular essential differences in cellular structures and processes between phyla. We focus on key dissimilarities in cellular organization, e.g. regarding cell size and shape, the composition of the extracellular matrix, the types of cell–cell junctions, the presence of specific membrane-bound organelles and the organization of the cytoskeleton. We further highlight essential disparities in important cellular processes such as signal transduction, intracellular transport, cell cycle regulation, apoptosis and cytokinesis. Our comprehensive cross-kingdom comparison emphasizes overlaps but also marked differences between the major lineages of the three kingdoms and, thus, adds to a more holistic view of multicellular eukaryotic cell biology.
... P25alpha (Pfam05517; IPR008907) is not a structural domain but is derived from a sequence alignment (https://bioinf.umbc.edu/DMDM/generatelogo. php?accession=pfam05517 (accessed on 5 March 2023)). The p25alpha domain is exclusive to eukaryotes and there is a strong correlation between its presence and the presence of the eukaryotic flagellum/cilium [5,6]. TPPP-like proteins occur in different types, such as long-, short-and truncated (the C-terminal third is completely missing) TPPPs, depending on the length of the p25alpha domain (about 160, 140, and 120 amino acids, respectively) ( Figure 1). ...
... For example, animals contain only long-type TPPPs, except for the placozoan Trichoplax adhaerens, which contains apicortin instead [7]. Truncatedand fungal-type TPPPs occur only in Endopterygota (Holometabola) [16] and in fungi [6], respectively. In this article, the occurrence, and the possible role of TPPP-like proteins in Myzozoa, which include apicomplexans and related taxa, chrompodellids (chromerids plus colpodellids), dinoflagellates, and perkinsids, is reviewed ( Figure 2). ...
... Apicortin was originally thought to occur only in apicomplexans and in the placozoan animal T. adhaerens [7]. Later, it was found that its occurrence is broader than thought earlier: it is present in chromerids (Chromera velia and Vitrella brassicaformis) [30] and in flagellated fungi [6,31,32]. The presence of apicortin in chromerids was not surprising, given the phylogenetic proximity and the structural similarity of chromerids and apicomplexans. ...
TPPP (tubulin polymerization promoting protein)-like proteins contain one or more p25alpha (Pfam05517) domains. TPPP-like proteins occur in different types as determined by their length (e.g., long-, short-, truncated-, and fungal-type TPPP) and include the protein apicortin, which possesses another domain, doublecortin (DCX, Pfam 03607). These various TPPP-like proteins are found in various phylogenomic groups. In particular, short-type TPPPs and apicortin are well-represented in the Myzozoa, which include apicomplexans and related taxa, chrompodellids, dinoflagellates, and perkinsids. The long-, truncated-, and fungal-type TPPPs are not found in the myzozoans. Apicortins are found in all apicomplexans except one piroplasmid species, present in several other myzozoans, and seem to be correlated with the conoid and apical complex. Short-type TPPPs are predominantly found in myzozoans that have flagella, suggesting a role in flagellum assembly or structure.
... The members of the family of TPPP-like proteins differ from each other in the completeness of the p25alpha domain (long, short, truncated, partial) and in the presence or absence of other domains (e.g., DCX or EF-hand) [5]. A distinct 'fungal-type' TPPP, which is found in some flagellated fungi, contains both a complete and a partial p25alpha domain [6] (Figure 1). An essential role of TPPP in the formation of flagella was demonstrated in Chlamydomonas reinhardtii, biflagellated green algae, through the use of null mutant of FAP265, its TPPP ortholog [7]. ...
... Very recently, it has also been shown that TPPP (Py05543) is required for male gametocyte exflagellation in Plasmodium yoelli [8]. [6,9] and this paper). Black and dashed line squares indicate highly conservative sequence motifs. ...
... Thus, only the Aphelidiomycota phylum lacked data regarding proteins with a p25alpha domain. [6,9] and this paper). Black and dashed line squares indicate highly conservative sequence motifs. ...
The seven most early diverging lineages of the 18 phyla of fungi are the non-terrestrial fungi, which reproduce through motile flagellated zoospores. There are genes/proteins that are present only in organisms with flagellum or cilium. It was suggested that TPPP-like proteins (proteins containing at least one complete or partial p25alpha domain) are among them, and a correlation between the incidence of the p25alpha domain and the eukaryotic flagellum was hypothesized. Of the seven phyla of flagellated fungi, six have been known to contain TPPP-like proteins. Aphelidiomycota, one of the early-branching phyla, has some species (e.g., Paraphelidium tribonematis) that retain the flagellum, whereas the Amoeboaphelidium genus has lost the flagellum. The first two Aphelidiomycota genomes (Amoeboaphelidium protococcorum and Amoeboaphelidium occidentale) were sequenced and published last year. A BLASTP search revealed that A. occidentale does not have a TPPP, but A. protococcorum, which possesses pseudocilium, does have a TPPP. This TPPP is the ‘long-type’ which occurs mostly in animals as well as other Opisthokonta. P. tribonematis has a ‘fungal-type’ TPPP, which is found only in some flagellated fungi. These data on Aphelidiomycota TPPP proteins strengthen the correlation between the incidence of p25alpha domain-containing proteins and that of the eukaryotic flagellum/cilium.
... (For example, apicortin contains both partial p25alpha and DCX domains [15].) Recently, a TPPP-form present only in Fungi has also been identified [16]. (See later). ...
... These proteins can be grouped on the basis of the length and completeness of the p25alpha domain and the presence of another kind of domain(s) [10]. A special, "fungal-type" TPPP, which contains both a full and a partial (C-terminal) p25alpha domain, is present only in certain Fungi (Figure 1) [16]. ...
... apicortin contains both partial p25alpha and DCX domains [15].) Recently, a TPPP-form present only in Fungi has also been identified [16]. (See later.) ...
Loss of the flagellum was an important step in the evolution of fungi. The flagellated fungi of the phylum Olpidiomycota are the closest relative of the non-flagellated terrestrial fungi. There are genes encoding proteins, the occurrence of which shows a strong correlation with the incidence of the flagellum. One of these gene/protein families is “TPPP-like proteins” whose main feature is the presence of the p25alpha domain. The functional link between TPPP and flagellum has also been shown. Most of the phyla of flagellated fungi have been known to contain TPPP-like proteins but Olpidiomycota was an exception. This study demonstrates that Olpidium bornovanus, similarly to some fungi of Chytridiomycota and Blastocladiomycota, has a “fungal-type” TPPP characterized by the presence of two (a complete and an incomplete) p25alpha domains.
... It has also been revealed that some primitive fungi also possess this protein; first it was shown in the cases of Spizellomyces punctatus [6] and Rozella allomycis [5]. Later, a systematic examination of fungal genomes showed that the flagellated fungi contain apicortin almost without exception; and it is present even in a non-flagellated but also deeper branching clade (Endogonomycetes) [8]. ...
... Animal draft genomes and transcriptomes contain sometimes nucleotide sequences, contigs and TSAs (transcriptome shot-gun assemblies), homologous to apicortin, but they have been shown to be contaminations from parasitizing apicomplexans, based on sequence similarities and GC ratios [11,12]. In the case of T. adhaerens, this option was excluded by phylogenetic analysis [8]. Several authors suggested that the presence of frequent contaminants could serve as a basis for the identification of hitherto unknown apicomplexans and, in general, parasites [13][14][15]. ...
... Strong correlation between the presence of the p25alpha domain and that of the eukaryotic flagellum was suggested before the identification of apicortin [16]. With very few exceptions, each flagellated organism contains p25alpha domain-containing proteins; on the other side, in non-flagellated species, the p25alpha domain generally does not occur [8,10]. The protein that contains the p25alpha domain varies depending on the phylum; e.g., it is the so called "long-type" TPPP in animals (except T. adhaerens) [10,17], a fungal-type TPPP and apicortin in flagellated fungi [8], while the "short-type" TPPP and apicortin are found in apicomplexan species [10]. ...
In 2009, apicortin was identified in silico as a characteristic protein of apicomplexans that also occurs in the placozoa, Trichoplax adhaerens. Since then, it has been found that apicortin also occurs in free-living cousins of apicomplexans (chromerids) and in flagellated fungi. It contains a partial p25-α domain and a doublecortin (DCX) domain, both of which have tubulin/microtubule binding properties. Apicortin has been studied experimentally in two very important apicomplexan pathogens, Toxoplasma gondii and Plasmodium falciparum. It is localized in the apical complex in both parasites. In T. gondii, apicortin plays a key role in shaping the structure of a special tubulin polymer, conoid. In both parasites, its absence or downregulation has been shown to impair pathogen–host interactions. Based on these facts, it has been suggested as a therapeutic target for treatment of malaria and toxoplasmosis.
... As an exception in the fungal kingdom, zoospores of the Chytridiomycota are powered by flagella that due to their diverse ultrastructure are used for phylogenetic classification [92]. A recent study highlights the strong correlation between the occurrence of the p25-alpha domain of tubulin polymerization promoting protein-like proteins in eukaryotic cilia/ flagella of animals and fungi [147]. In animals, a second type of cilia, immobile or primary cilia, are found as antennalike protrusions on many excitatory and non-excitatory cells [192]. ...
Twenty year ago, Trichoderma was among the first filamentous fungi that successfully utilized the green fluorescent protein, sGFP, for cell biological research. Since then, several fluorescent proteins (FPs) have been applied as visual reporters of fungal biomass, gene expression, and subcellular protein localization. This chapter reviews the live-cell imaging applications of FPs established in various Trichoderma species so far and highlights key advances achieved with this technology. Furthermore, the practical aspects regarding the application of fluorescent dyes, the choice of microscopy technology, and the optimization of cultivation and sample preparation methods for live-cell imaging are discussed. The complexity and quality of live-cell imaging analyses conducted with Trichoderma is at state-of-the-art level. The impact of previous and recent hallmark studies is an encouragement to further advance live-cell imaging analysis in this exciting and diverse fungal genus operating in biotechnologically and agriculturally highly relevant areas.
