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Jiří Neustupa - One of the best experts on this subject based on the ideXlab platform.
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Splitting of Micrasterias fimbriata (Desmidiales, Viridiplantae) into two monophyletic species and description of Micrasterias compereana sp. nov.
2016Co-Authors: Jiří Neustupa, Jan Šťastný, Pavel ŠkaloudAbstract:The freshwater microalgal genus Micrasterias C.Agardh ex Ralfs represents a monophyletic lineage of the Desmi-diaceae (Škaloud et al. 2011). Besides the species tradition-ally included in this genus on the basis of the morphologi
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Splitting of Micrasterias fimbriata (Desmidiales, Viridiplantae) into two monophyletic species and description of Micrasterias compereana sp. nov.
Plant Ecology and Evolution, 2014Co-Authors: Jiří NeustupaAbstract:The freshwater microalgal genus Micrasterias C.Agardh ex Ralfs represents a monophyletic lineage of the Desmidiaceae (Skaloud et al. 2011). Besides the species traditionally included in this genus on the basis of the morphological data (see e.g. Prescott et al. 1977, Růžicka 1981, Coesel & Meesters 2007), the Micrasterias lineage also includes several morphologically dissimilar taxa, such as Micrasterias ralfsii (Brebisson ex Ralfs) Skaloud, Nemjova, Vesela, Cerna & Neustupa and M. dickiei (Ralfs) Skaloud, Nemjova, Vesela, Cerna & Neustupa. These species were previously classified into other desmid genera, but proved to be included within the phylogenetically defined genus Micrasterias on the basis of the multigenic molecular data (Gontcharov 2008, Hall et al. 2008, Gontcharov & Melkonian 2011, Skaloud et al. 2011). The morphological species concepts within the genus turned out to be relatively well supported by molecular data (Nemjova et al. 2011, Neustupa et al. 2010, 2011). While different populations of individual traditional species, such as M. rotata, typically formed monophyletic or closely related lineages (Neustupa et al. 2011), the phylogenetic species diversity of several other taxa, such as M. truncata Brebisson ex Ralfs, M. crux-melitensis Ralfs, or M. fimbriata Ralfs, proved to be higher than what was expected solely from the morphological data (Nemjova et al. 2011, Neustupa et al. 2010). The infraspecific phylogenetic clades of traditional M. crux-melitensis and M. truncata often could not be unambiguously delimited by morphological methods, and their separate species status remains uncertain. On the contrary, phylogenetic structure of the traditional M. fimbriata proved to be considerably less complicated (Neustupa et al. 2011). The natural populations and strains of this species, originating from various European and North American localities, turned out to belong to two well delimited and homogenous phylogenetic lineages on the basis of the group II intron sequences of the plastid encoded trnGUCC gene. Both lineages were firmly placed into the clade C of the genus Micrasterias sensu Skaloud et al. (2011). Interestingly, the members of the M. fimbriata lineages were clearly morphologically delimited and could be unambiguously recognized, either
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patterns of symmetric and asymmetric morphological variation in unicellular green microalgae of the genus micrasterias desmidiales Viridiplantae
Fottea, 2013Co-Authors: Jiří NeustupaAbstract:Morphological symmetry and asymmetry in three clonal populations of Micrasterias cells was decomposed using a new geometric morphometric method specifically developed for shape analysis of complex symmetric structures. Micrasterias cells are symmetric relative to two perpendicular axes of symmetry: a left-right axis and a juvenile-adult axis. Shape variation is decomposed into a component of symmetric variation and other components of asymmetry. Principal component analysis suggested that symmetric variation and juvenile-adult asymmetry were dominant in describing morphological differences among objects in all three datasets. The left-right asymmetric variation among adjacent quadrants of the same semicells was consistently more pronounced than the asymmetric variation with respect to the transversal axis. The strains of Micrasterias radians var. bogoriensis (SVCK 389) and M. radians var. evoluta (SVCK 518) were consistently more variable than the population of M. semiradiata (CAUP K606), with respect to both symmetric and different aspects of asymmetric variation. The shape differences among cell quadrants from opposite semicells were statistically not different from shape differences among cell quadrants from different cells of clonal populations.
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Geometric morphometrics of symmetry and allometry in Micrasterias rotata (Zygnemophyceae, Viridiplantae)
Nova Hedwigia Beihefte, 2010Co-Authors: Yoland Savriama, Jiří Neustupa, Christian Peter KlingenbergAbstract:Algal cells show many types of complex symmetry. For instance, Micrasterias rotata cells are symmetric relative to two perpendicular axes of symmetry. Due to the mode of cell division of Micrasterias rotata cells, the symmetry axes can be interpreted as a left-right axis and a juvenile-adult axis. Here, we analyze symmetry and allometry in Micrasterias rotata cells. We apply a new general approach for shape analysis of structures with any type of symmetry. Our method can separate a component of symmetric variation among individuals from one or more components of asymmetry, depending on the type of sym- metry under study, and thus is appropriate for the study of symmetry in these cells. Our results suggest that almost two-thirds of the shape variation in our example (62.3 % of the total variance) is explained by the asymmetric component relative to the juvenile-adult axis. Therefore, most morphological variation occurs between juvenile and adult semicells. Given that these shape changes are associated with the size of the semicells, they indicate a type of allometry between semicells. We also compared these patterns of allometry within cells to allometry among cells by using a multivariate regression of shape averaged by individuals onto size of the whole cells. A permutation test shows a highly signifi cant association between size and shape of the whole cells.
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in Micrasterias rotata (Zygnemophyceae, Viridiplantae)
2010Co-Authors: Jiří Neustupa, Christian Peter KlingenbergAbstract:Abstract; Algal cells show many types of complex symmetry. For instance, Micrasterias rotata cells are symmetric relative to two perpendicular axes of symmetry. Due to the mode of cell division of Micrasterias rotata cells, the symmetry axes can be interpreted as a left-right axis and a juvenile-adult axis. Here, we analyze symmetry and allometry in Micrasterias rotata cells. We apply a new general approach for shape analysis of structures with any type of symmetry. Our method can separate a component of symmetric variation among individuals from one or more components of asymmetry, depending on the type of sym-metry under study, and thus is appropriate for the study of symmetry in these cells. Our results suggest that almost two-thirds of the shape variation in our example (62.3 % of the total variance) is explained by the asymmetric component relative to the juvenile-adult axis. Therefore, most morphological variation occurs between juvenile and adult semicells. Given that these shape changes are associated with the size of the semicells, they indicate a type of allometry between semicells. We also compared these patterns of allometry within cells to allometry among cells by using a multivariate regression of shape averaged by individuals onto size of the whole cells. A permutation test shows a highly signifi cant association between size and shape of the whole cells. Key words: Micrasterias rotata, geometric morphometrics, Procrustes superimposition, shape analysis, symmetry, morphological variation, allometr
Helgi B Schioth - One of the best experts on this subject based on the ideXlab platform.
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functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster eama duf6 before the radiation of Viridiplantae
BMC Evolutionary Biology, 2011Co-Authors: Ake Vastermark, Markus Sallman Almen, Martin W Simmen, Robert Fredriksson, Helgi B SchiothAbstract:Background: The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. Results: We present evidence that the triose-phosphate transporters, domain unknown function 914, uracildiphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6). We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the “35C/E” branch of EamA, which formed in the lineage of T. adhaerens (Animalia). We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6)-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. Conclusions: The nucleotide sugar transporters families were formed through differentiation of the gene cluster EamA (domain unknown function 6) before Viridiplantae, showing for the first time the significance of EamA.
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functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster eama duf6 before the radiation of Viridiplantae
BMC Evolutionary Biology, 2011Co-Authors: Ake Vastermark, Markus Sallman Almen, Martin W Simmen, Robert Fredriksson, Helgi B SchiothAbstract:The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. We present evidence that the triose-phosphate transporters, domain unknown function 914, uracil-diphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6). We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the "35C/E" branch of EamA, which formed in the lineage of T. adhaerens (Animalia). We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6)-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. The nucleotide sugar transporters families were formed through differentiation of the gene cluster EamA (domain unknown function 6) before Viridiplantae, showing for the first time the significance of EamA.
Michael Melkonian - One of the best experts on this subject based on the ideXlab platform.
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genome wide analyses across Viridiplantae reveal the origin and diversification of small rna pathway related genes
Communications Biology, 2021Co-Authors: Michael Melkonian, Sibo Wang, Hongli Wang, Hongping Liang, Durgesh Nandini Sahu, Morten Petersen, Sunil Kumar SahuAbstract:Small RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment.
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The Origin and Evolution of the Plant Cell Surface: Algal Integrin-Associated Proteins and a New Family of Integrin-Like Cytoskeleton-ECM Linker Proteins.
Genome Biology and Evolution, 2015Co-Authors: Burkhard Becker, Gane Ka-shu Wong, Jean Michel Doan, Brandon A. Wustman, Eric J. Carpenter, Yong Zhang, Li Chen, Michael MelkonianAbstract:The extracellular matrix of scaly green flagellates consists of small organic scales consisting of polysaccharides and scale-associated proteins (SAPs). Molecular phylogenies have shown that these organisms represent the ancestral stock of flagellates from which all green plants (Viridiplantae) evolved. The molecular characterization of four different SAPs is presented. Three SAPs are type-2 membrane proteins with an arginine/alanine-rich short cytoplasmic tail and an extracellular domain that is most likely of bacterial origin. The fourth protein is a filamin-like protein. In addition, we report the presence of proteins similar to the integrin-associated proteins α-actinin (in transcriptomes of glaucophytes and some viridiplants), LIM-domain proteins, and integrin-associated kinase in transcriptomes of viridiplants, glaucophytes, and rhodophytes. We propose that the membrane proteins identified are the predicted linkers between scales and the cytoskeleton. These proteins are present in many green algae but are apparently absent from embryophytes. These proteins represent a new protein family we have termed gralins for green algal integrins. Gralins are absent from embryophytes. A model for the evolution of the cell surface proteins in Plantae is discussed.
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the mystery of clade x orciraptor gen nov and viridiraptor gen nov are highly specialised algivorous amoeboflagellates glissomonadida cercozoa
Protist, 2013Co-Authors: Sebastian Hess, Michael MelkonianAbstract:In freshwater ecosystems a vast diversity of elusive protists exists that specifically feed on microalgae. Due to difficulties in isolation and long-term maintenance, most of these are still poorly known. In this study stable, bacteria-free cultures of several limnetic, algivorous amoeboflagellates were investigated by light microscopy and molecular phylogenetic analyses. All strains represent naked, biflagellate cells, either occurring as rigid flagellates or as surface-attached amoebae. They perforate cell walls of certain Zygnematophyceae and Chlorophyceae (Viridiplantae) and phagocytose algal cell contents. Time-lapse microscopy revealed the feeding behaviour, locomotional processes and life histories of the amoeboflagellates. Clear differences in cell morphology and food range specificity led to the description of two new, monotypic genera Orciraptor and Viridiraptor, which occupy similar, but distinct ecological niches in aquatic ecosystems as ‘necrophytophagous’ and ‘parasitoid’ protists, respectively. Molecular phylogenetic analyses based on 18S rDNA sequence data demonstrated that Orciraptor and Viridiraptor belonged to ‘clade X’ within the order Glissomonadida (Cercozoa, Rhizaria). In conclusion, we established the phenotypic identity of a clade, which until now was exclusively known from environmental sequences, and erect the new family Viridiraptoridae for ‘clade X’. Its algivorous members are compared with other glissomonads and nomenclatural, methodological and ecological aspects of these novel ‘raptorial’ amoeboflagellates are discussed.
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RESEARCH ARTICLE Open Access Origin of land plants: Do conjugating green algae hold the key?
2013Co-Authors: Sabina Wodniok, Michael Melkonian, Henner Brinkmann, Gernot Glöckner, Andrew J. Heidel, Burkhard BeckerAbstract:Background: The terrestrial habitat was colonized by the ancestors of modern land plants about 500 to 470 million years ago. Today it is widely accepted that land plants (embryophytes) evolved from streptophyte algae, also referred to as charophycean algae. The streptophyte algae are a paraphyletic group of green algae, ranging from unicellular flagellates to morphologically complex forms such as the stoneworts (Charales). For a better understanding of the evolution of land plants, it is of prime importance to identify the streptophyte algae that are the sister-group to the embryophytes. The Charales, the Coleochaetales or more recently the Zygnematales have been considered to be the sister group of the embryophytes However, despite many years of phylogenetic studies, this question has not been resolved and remains controversial. Results: Here, we use a large data set of nuclear-encoded genes (129 proteins) from 40 green plant taxa (Viridiplantae) including 21 embryophytes and six streptophyte algae, representing all major streptophyte algal lineages, to investigate the phylogenetic relationships of streptophyte algae and embryophytes. Our phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zygnematales and the Coleochaetales are the sister group to embryophytes. Conclusions: Our analyses support the notion that the Charales are not the closest living relatives o
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a close up view on its2 evolution and speciation a case study in the ulvophyceae chlorophyta Viridiplantae
BMC Evolutionary Biology, 2011Co-Authors: Lenka Caisova, Birger Marin, Michael MelkonianAbstract:The second Internal Transcriber Spacer (ITS2) is a fast evolving part of the nuclear-encoded rRNA operon located between the 5.8S and 28S rRNA genes. Based on crossing experiments it has been proposed that even a single Compensatory Base Change (CBC) in helices 2 and 3 of the ITS2 indicates sexual incompatibility and thus separates biological species. Taxa without any CBC in these ITS2 regions were designated as a 'CBC clade'. However, in depth comparative analyses of ITS2 secondary structures, ITS2 phylogeny, the origin of CBCs, and their relationship to biological species have rarely been performed. To gain 'close-up' insights into ITS2 evolution, (1) 86 sequences of ITS2 including secondary structures have been investigated in the green algal order Ulvales (Chlorophyta, Viridiplantae), (2) after recording all existing substitutions, CBCs and hemi-CBCs (hCBCs) were mapped upon the ITS2 phylogeny, rather than merely comparing ITS2 characters among pairs of taxa, and (3) the relation between CBCs, hCBCs, CBC clades, and the taxonomic level of organisms was investigated in detail. High sequence and length conservation allowed the generation of an ITS2 consensus secondary structure, and introduction of a novel numbering system of ITS2 nucleotides and base pairs. Alignments and analyses were based on this structural information, leading to the following results: (1) in the Ulvales, the presence of a CBC is not linked to any particular taxonomic level, (2) most CBC 'clades' sensu Coleman are paraphyletic, and should rather be termed CBC grades. (3) the phenetic approach of pairwise comparison of sequences can be misleading, and thus, CBCs/hCBCs must be investigated in their evolutionary context, including homoplasy events (4) CBCs and hCBCs in ITS2 helices evolved independently, and we found no evidence for a CBC that originated via a two-fold hCBC substitution. Our case study revealed several discrepancies between ITS2 evolution in the Ulvales and generally accepted assumptions underlying ITS2 evolution as e.g. the CBC clade concept. Therefore, we developed a suite of methods providing a critical 'close-up' view into ITS2 evolution by directly tracing the evolutionary history of individual positions, and we caution against a non-critical use of the ITS2 CBC clade concept for species delimitation.
Ake Vastermark - One of the best experts on this subject based on the ideXlab platform.
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functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster eama duf6 before the radiation of Viridiplantae
BMC Evolutionary Biology, 2011Co-Authors: Ake Vastermark, Markus Sallman Almen, Martin W Simmen, Robert Fredriksson, Helgi B SchiothAbstract:Background: The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. Results: We present evidence that the triose-phosphate transporters, domain unknown function 914, uracildiphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6). We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the “35C/E” branch of EamA, which formed in the lineage of T. adhaerens (Animalia). We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6)-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. Conclusions: The nucleotide sugar transporters families were formed through differentiation of the gene cluster EamA (domain unknown function 6) before Viridiplantae, showing for the first time the significance of EamA.
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functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster eama duf6 before the radiation of Viridiplantae
BMC Evolutionary Biology, 2011Co-Authors: Ake Vastermark, Markus Sallman Almen, Martin W Simmen, Robert Fredriksson, Helgi B SchiothAbstract:The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. We present evidence that the triose-phosphate transporters, domain unknown function 914, uracil-diphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6). We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the "35C/E" branch of EamA, which formed in the lineage of T. adhaerens (Animalia). We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6)-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. The nucleotide sugar transporters families were formed through differentiation of the gene cluster EamA (domain unknown function 6) before Viridiplantae, showing for the first time the significance of EamA.
Neil P Schultes - One of the best experts on this subject based on the ideXlab platform.
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the solute specificity profiles of nucleobase cation symporter 1 ncs1 from zea mays and setaria viridis illustrate functional flexibility
Protoplasma, 2016Co-Authors: Micah Rapp, Jessica Schein, Kevin A Hunt, Vamsi J Nalam, George Mourad, Neil P SchultesAbstract:The solute specificity profiles (transport and binding) for the nucleobase cation symporter 1 (NCS1) proteins, from the closely related C4 grasses Zea mays and Setaria viridis, differ from that of Arabidopsis thaliana and Chlamydomonas reinhardtii NCS1. Solute specificity profiles for NCS1 from Z. mays (ZmNCS1) and S. viridis (SvNCS1) were determined through heterologous complementation studies in NCS1-deficient Saccharomyces cerevisiae strains. The four Viridiplantae NCS1 proteins transport the purines adenine and guanine, but unlike the dicot and algal NCS1, grass NCS1 proteins fail to transport the pyrimidine uracil. Despite the high level of amino acid sequence similarity, ZmNCS1 and SvNCS1 display distinct solute transport and recognition profiles. SvNCS1 transports adenine, guanine, hypoxanthine, cytosine, and allantoin and competitively binds xanthine and uric acid. ZmNCS1 transports adenine, guanine, and cytosine and competitively binds, 5-fluorocytosine, hypoxanthine, xanthine, and uric acid. The differences in grass NCS1 profiles are due to a limited number of amino acid alterations. These amino acid residues do not correspond to amino acids essential for overall solute and cation binding or solute transport, as previously identified in bacterial and fungal NCS1, but rather may represent residues involved in subtle solute discrimination. The data presented here reveal that within Viridiplantae, NCS1 proteins transport a broad range of nucleobase compounds and that the solute specificity profile varies with species.
