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  • 1
    Electronic Resource
    Electronic Resource
    The evolutionary origin of red algae as deduced from the nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases from Chondrus crispus (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 319-327 
    Details
    ISSN: 1432-1432
    Keywords: Molecular phylogeny of plastids and mitochondria ; Endosymbiotic origin ; Monophylesis ; Cyanobacteria ; Purple bacteria ; Transit peptide ; Neighbor joining method ; Bootstrapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Algae are a heterogeneous group of photosynthetic eukaryotes traditionally separated into three major subdivisions: rhodophytes, chlorophytes, and chromophytes. The evolutionary origin of rhodophytes or red algae and their links to other photosynthetic and nonphotosynthetic eukaryotes have been a matter of much controversy and speculation. Here we present the first cDNAs of nuclear protein genes from red algae: Those encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from Chondrus crispus. A phylogenetic analysis including GAPDH gene sequences from a number of eukaryotic taxa, cyanobacteria, and purple bacteria suggests that chloroplasts and rhodoplasts together form a monophyletic group of cyanobacterial descent and that rhodophytes separated from chlorophytes at about the same time as animals and fungi. The composite GAPDH tree further demonstrates that chloroplast and cytosolic GAPDH genes are closely related to their homologs in cyanobacteria and purple bacteria, respectively, the presumptive ancestors of chloroplasts and mitochondria, thereby firmly establishing the endosymbiotic origin of these nuclear genes and their fixation in eukaryotic cells before the rhodophyte/chlorophyte separation. The present data are in conflict with phylogenetic inferences based on plastid-encoded rbcL sequences supporting a polyphyletic origin of rhodoplasts and chloroplasts. Comparison of rbcL to GAPDH phylogenies suggests that rbcL trees may be misleading because they are composed of branches representing ancient duplicated (paralogous) genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163149
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  • 2
    Electronic Resource
    Electronic Resource
    Evolutionary Origin of Cryptomonad Microalgae: Two Novel Chloroplast/Cytosol-Specific GAPDH Genes as Potential Markers of Ancestral Endosymbiont and Host Cell Components (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S028 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Pyrenomonas salina, Guillardia theta— Glyceraldehyde-3-phosphate dehydrogenase — Endosymbiotic gene transfer — Signal peptide — Enzyme engineering — Cell evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Cryptomonads are complex microalgae which share characteristics of chromophytes (chlorophyll c, extra pair of membranes surrounding the plastids) and rhodophytes (phycobiliproteins). Unlike chromophytes, however, they contain a small nucleus-like organelle, the nucleomorph, in the periplastidial space between the inner and outer plastid membrane pairs. These cellular characteristics led to the suggestion that cryptomonads may have originated via a eukaryote–eukaryote endosymbiosis between a phagotrophic host cell and a unicellular red alga, a hypothesis supported by rRNA phylogenies. Here we characterized cDNAs of the nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from the two cryptomonads Pyrenomonas salina and Guillardia theta. Our results suggest that in cryptomonads the classic Calvin cycle GAPDH enzyme of cyanobacterial origin, GapAB, is absent and functionally replaced by a photosynthetic GapC enzyme of proteobacterial descent, GapC1. The derived GapC1 precursor contains a typical signal/transit peptide of complex structure and sequence signatures diagnostic for dual cosubstrate specificity with NADP and NAD. In addition to this novel GapC1 gene a cytosol-specific GapC2 gene of glycolytic function has been found in both cryptomonads showing conspicuous sequence similarities to animal GAPDH. The present findings support the hypothesis that the host cell component of cryptomonads may be derived from a phototrophic rather than a organotrophic cell which lost its primary plastid after receiving a secondary one. Hence, cellular compartments of endosymbiotic origin may have been lost or replaced several times in eukaryote cell evolution, while the corresponding endosymbiotic genes (e.g., GapC1) were retained, thereby increasing the chimeric potential of the nuclear genome.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000050
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  • 3
    Electronic Resource
    Electronic Resource
    Five identical intron positions in ancient duplicated genes of eubacterial origin (1994)
    [s.l.] : Nature Publishing Group
    Nature 367 (1994), S. 387-389 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Two introns strictly conserved in nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPDH; Gap A/Gap B and GapC, respectively) have been generally regarded as strong evidence in favour of the 'introns early' hypothesis10, although the identity of intron ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/367387a0
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  • 4
    Electronic Resource
    Electronic Resource
    Structural features and phylogeny of the actin gene of Chondrus crispus (Gigartinales, Rhodophyta) (1995)
    Springer
    Current genetics 28 (1995), S. 164-172 
    Details
    ISSN: 1432-0983
    Keywords: Chondrus crispus ; Actin ; Promoter region Intron
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have characterized the cDNA and genomic sequences that encode actin from the multicellular red alga Chondrus crispus. Southern-blot analysis indicates that the C. crispus actin gene (ChAc) is present as a single copy. Northern analysis shows that, like the GapA gene, the actin gene is well expressed in gametophytes but weakly in protoplasts. Compared to actin genes of animals, fungi, green plants and oomycetes, that of C. crispus displays a higher evolutionary rate and does not show any of the amino-acid signatures characteristic of the other lineages. As previously described for GapA, ChAc is interrupted by a single intron at the beginning of the coding region. The site of initiation of transcription was characterized by RNAse protection. The promoter region displays a CAAT box but lacks a canonical TATA motif. Other noticeable features, such as a high content of pyrimidines as well as a 14-nt motif found in both the 5′-untranslated region and the intron, were observed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00315783
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  • 5
    Electronic Resource
    Electronic Resource
    The marine red alga Chondrus crispus has a highly divergent β-tubulin gene with a characteristic 5′ intron: functional and evolutionary implications (1995)
    Springer
    Plant molecular biology 28 (1995), S. 313-325 
    Details
    ISSN: 1573-5028
    Keywords: red algae ; Chondrus crispus ; β-tubulin ; gene families ; isoform diversity ; intron loss
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We characterized a nuclear gene and its corresponding cDNA encoding β-tubulin (gene TubB1) of the marine red alga Chondrus crispus. The deduced TubB1 protein is the most divergent β-tubulin so far reported with only 64 to 69% amino acid identity relative to other β-tubulins from higher and lower eukaryotes. Our analysis reveals that TubB1 has an accelerated evolutionary rate probably due to a release of functional constraints in connexion with a specialization of microtubular structures in rhodophytes. It further indicates that isoform diversity and functional differentiation of tubulins in eukaryotic cells may be controlled by independent selective constraints. TubB1 has a short spliceosomal intron at its 5′ end which seems to be a characteristic feature of nuclear protein-coding genes from rhodophytes. The splice junctions of the four known rhodophyte introns comply well with the corresponding consensus sequences of higher plants in agreement with previous suggestions from phylogenetic inference that red algae and green plants may be sister groups. The paucity and asymmetrical location of introns in rhodophyte genes can be explained by differential intron loss due to conversion of genes by homologous recombination with cDNAs corresponding to reverse transcribed mRNAs or partially spliced pre-mRNAs, respectively. The identification of an intron containing TubB1 cDNA in C. crispus confirms that pre-mRNAs can escape both splicing and degradation in the nucleus prior to transport into the cytoplasm. Differential Southern hybridizations under non-stringent conditions with homologous and heterologous probes suggest that C. crispus contains a second degenerate β-tubulin gene (or pseudogene?) which, however, is only distantly related to TubB1 as it is to the more conserved homologues of other organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00020250
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  • 6
    Electronic Resource
    Electronic Resource
    The β-tubulin gene family of pea: Primary structures, genomic organization and intron-dependent evolution of genes (1992)
    Springer
    Plant molecular biology 18 (1992), S. 639-651 
    Details
    ISSN: 1573-5028
    Keywords: dispensable proteins ; evolutionary rates ; exon theory of genes ; homologous recombination ; intron shift ; multigene family
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract One gene and two cDNAs encoding three different β-tubulins (TUB1, TUB2, TUB3) of pea have been cloned and sequenced. The derived amino acid sequences show between 92% and 96% identity relative to one another and to most other β-tubulins of higher plants and green algae. Two notable extremes are the high similarity of 98% between pea TUB3 and maize β-tubulin 2 and the relatively low similarity (90%) of the hypocotyl-specific β-tubulin 1 of soybean to the pea sequences. These similarities do not reflect the molecular phylogeny but rather differences in evolutionary rate of β-tubulins which are differentially regulated during plant development. Genomic Southern blots reveal a β-tubulin gene family in pea with at least four separate members including two TUB1 genes, one TUB2 gene and one TUB3 gene. This contradicts an earlier report by Rahaet al. (Plant Mol Biol 9: 565–571, 1987) suggesting a tandem repeat organization of tubulin genes in pea. The pea TUB1 gene has two introns in identical positions compared to the β-tubulin genes fromArabidopsis and soybean. In an attempt to reconstruct the universal ancestor of all present-day tubulin genes the intron positions in 38 different α- and β-tubulin genes from plants, animals, fungi and protozoa were compared. This comparison shows that the primordial gene probably had many introns (more than 20) separating ‘protoexons’ of 15 to 20 codons in agreement with the ‘exon theory of genes’. It also supports the view that, during the course of evolutions introns have shifted and were deleted preferentially in the 3′ part of the genes. Similar observations have been made previously for other genes. They can be interpreted in terms of a homologous recombination of genes with their modified (incorrectly spliced) and reverse-transcribed pre-mRNAs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00020007
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  • 7
    Electronic Resource
    Electronic Resource
    The maize GapC4 promoter confers anaerobic reporter gene expression and shows homology to the maize anthocyanin regulatory locus C1 (1995)
    Springer
    Plant molecular biology 29 (1995), S. 1293-1298 
    Details
    ISSN: 1573-5028
    Keywords: anaerobiosis ; BMS cells ; glyceraldehyde-3-phosphate dehydrogenase ; transient gene expression ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The cytosolic glyceraldehyde-3-phosphate dehydrogenase (GapC) gene family of maize is differentially expressed in response to anaerobic stress. While GapC1 and GapC2 are downregulated, GapC3 and GapC4 are anaerobically induced. We have sequenced and analyzed a 3073 bp promoter fragment of GapC4. The promoter confers anaerobic induction of a reporter gene construct in a transient gene expression system in maize. Deletion analysis of the GapC4 promoter revealed a 270 bp long DNA region required for anaerobic induction. This region contains sequence motifs resembling the cis-acting sequences of the anaerobically induced maize Adh1 and Adh2 genes. Furthermore, the 3073 bp GapC4 promoter fragment displays homology to long terminal repeats of maize retrotransposons and to the 3′ region of the maize anthocyanin regulatory locus C1.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00020469
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  • 8
    Electronic Resource
    Electronic Resource
    The GAPDH gene system of the red alga Chondrus crispus: promotor structures, intron/exon organization, genomic complexity and differential expression of genes (1993)
    Springer
    Plant molecular biology 23 (1993), S. 981-994 
    Details
    ISSN: 1573-5028
    Keywords: cis-acting elements ; intron conservation ; intron secondary structure ; pre-mRNA splicing ; CpG suppression ; protoplasts ; transcript levels
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Our previous phylogenetic analysis based on cDNA sequences of chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPDH; genes GapA and GapC, respectively) of the red alga Chondrus crispus suggested that rhodophytes and green plants are sister groups with respect to plastids and mitochondria and diverged at about the same time or somewhat later than animals and fungi. Here we characterize the genomic sequences of genes GapC and GapA of C. crispus with respect to promotor structures, intron/exon organization, genomic complexity, G+C content, CpG suppression and their transcript levels in gametophytes and protoplasts, respectively. To our knowledge this is the first report on nuclear protein genes of red algae. The GapC gene is G+C-rich, contains no introns and displays a number of classic sequence motifs within its promotor region, such as TATA, CAAT, GC boxes and several elements resembling the plant-specific G-box palindrome. The GapA gene has a moderate G+C content, a single CAAT box motif in its promotor region and a single intron of 115 bp near its 5′ end. This intron occupies a conserved position corresponding to that of intron 1 in the transit peptide region of chloroplast GAPDH genes (GapA and GapB) of higher plants. It has consensus sequences similar to those of yeast introns and folds into a conspicuous secondary structure of - 61.3 kJ. CpG profiles of genes GapC and GapA and their flanking sequences show no significant CpG depletion suggesting that these genomic sequences are not methylated. Genomic Southern blots hybridized with generic and gene specific probes indicate that both genes are encoded by single loci composed of multiple polymorphic alleles. Northern hybridizations demonstrate that both genes are expressed in gametophytes but not in protoplasts where appreciable amounts of transcripts can only be detected for GapC.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00021813
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  • 9
    Electronic Resource
    Electronic Resource
    Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species (1998)
    Springer
    Plant molecular biology 37 (1998), S. 363-375 
    Details
    ISSN: 1573-5028
    Keywords: Ty3/Gypsy ; gene transduction ; genome mapping ; horizontal transmission ; Pisum sativum ; retrotransposon ; reverse transcriptase ; tRNA-priming
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We characterized a novel giant Gypsy-like retrotransposon, Cyclops, present in about 5000 copies in the genome of Pisum sativum. The individual element Cyclops-2 measures 12 314 bp including long terminal repeats (LTRs) of 1504 bp and 1594 bp, respectively, showing 4.1% sequence divergence between one another. Cyclops-2 carries a polypurine tract (PPT) and an unusual primer binding site (PBS) complementary to tRNA-Glu. The element is bounded by 5 bp target site duplications and harbors three successive internal regions with homology to retroviral genes gag (424 codons) and pol (1382 codons) and an additional open reading frame (423 codons) of unknown function indicating the element's potential capacity for gene transduction. The pol region contains sequence motifs related to the enzymes protease, reverse transcriptase, RNAse H and integrase in the same typical order (5′-PR-RT-RH-IN-3′) known for retroviruses and Gypsy-like retrotransposons. The reading frame of the pol region is disrupted by several mutations suggesting that Cyclops-2 does not encode functional enzymes. A phylogenetic analysis of the reverse transcriptase domain confirms our differential genetic assessment that Cyclops from pea is a novel element with no specific relationship to the previously described Gypsy-like elements from plants. Genomic Southern hybridizations show that Cyclops is abundant not only in pea but also in common bean, mung bean, broad bean, soybean and the pea nut suggesting that Cyclops may be an useful genetic tool for analyzing the genomes of agronomically important legumes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1005969626142
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