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  • 1
    Electronic Resource
    Electronic Resource
    Molecular Evolution of Calmodulin and Calmodulin-Like Genes in the Cephalochordate Branchiostoma (2000)
    Springer
    Journal of molecular evolution 51 (2000), S. 141-148 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Branchiostoma— Calmodulin — Chordate evolution — EF-hand — Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Calmodulin is a calcium-binding EF-hand protein that is an activator of many enzymes as well as ion pumps and channels. Due to its multiple targets and its central role in the cell, understanding the evolutionary history of calmodulin genes should provide insights into the origin of genetic complexity in eukaryotes. We have previously isolated and characterized a calmodulin gene from the early-diverging chordate Branchiostoma lanceolatum (CaM1). In this paper, we report the existence of a second calmodulin gene (CaM2) as well as two CaM-like genomic fragments (CaML-2, CaML-3) in B. lanceolatum and a CaM2 and three CaM-like genes (CaML-1, CaML-2, CaML-3) in B. floridae. The CaM-like genes were isolated using low-stringency PCR. Surprisingly, the nucleotide sequences of the B. lanceolatum CaM1 and CaM2 cDNAs differ by 19.3%. Moreover, the CaM2 protein differs at two positions from the amino acid sequence of CaM1; the latter is identical to calmodulins in Drosophila melanogaster, the mollusc Aplysia californica, and the tunicate Halocynthia roretzi. The two B. lanceolatum CaM-like genes are more closely related to the CaM2 than to the CaM1 gene. This relationship is supported by the phylogenetic analyses and the identical exon/intron organization of these three genes, a relationship unique among animal CaM sequences. These data demonstrate the existence of a CaM multigene family in the cephalochordate Branchiostoma, which may have evolved independently from the multigene family in vertebrates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002390010074
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  • 2
    Electronic Resource
    Electronic Resource
    Sequence analysis of duplicated actin genes in Lagenidium giganteum and Pythium irregulare (Oomycota) (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 56-61 
    Details
    ISSN: 1432-1432
    Keywords: Actin ; Gene family ; Lagenidium giganteum ; Oomycetes ; Phylogenetic analysis ; Pythium irregulare
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Southern analysis of genomic DNA identified multiple-copy actin gene families in Lagenidium giganteum and Pythium irregulare (Oomycota). Polymerase chain reaction (PCR) protocols were used to amplify members of these actin gene families. Sequence analysis of genomic coding regions demonstrated five unique actin sequences in L. giganteum (Lg-Ac 1, 2, 3, 4, 5) and four unique actin sequences in P. irregulare (Pi-Acl, 2, 3, 4); none were interrupted by introns. Maximum parsimony analysis of the coding regions demonstrated a close phylogenetic relationship between oomycetes and the chromophyte alga Costaria costata. Three types of actin coding regions were identified in the chromophyte/oomycete lineage. The type 1 actin is the single-copy coding region found in C. costata. The type 2 and type 3 actins are found in the oomycetes and are the result of a gene duplication which occurred soon after the divergence of the oomycetes from the chromophyte algae. The type 2 coding regions are the single-copy sequence of Phytophthora megasperma, the Phytophthora infestans actB gene, Lg-Ac5 and Pi-Ac2. The type 3 coding regions are the single-copy sequence of Achlya bisexualis, the P. infestans actA gene, Lg-Ac1, 2, 3, 4 and Pi-Acl, 3, 4.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178249
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular phylogenetic analysis of actin genic regions fromAchlya bisexualis (Oomycota) andCostaria costata (Chromophyta) (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 525-536 
    Details
    ISSN: 1432-1432
    Keywords: Actin ; Chromophytes ; Phylogenetic analysis ; Small subunit RNA ; Monophyly ; Molecular evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Actin genic regions were isolated and characterized from the heterokont-flagellated protists,Achlya bisexualis (Oomycota) andCostaria costata (Chromophyta). Restriction enzyme and cloning experiments suggested that the genes are present in a single copy and sequence determinations revealed the existence of two introns in theC. costata actin genic region. Phylogenetic analyses of actin genic regions using distance matrix and maximum parsimony methods confirmed the close evolutionary relationship ofA. bisexualis andC. costata suggested by ribosomal DNA (rDNA) sequence comparisons and reproductive cell ultrastructure. The higher fungi, green plants, and animals were seen as monophyletic groups; however, a precise order of branching for these assemblages could not be determined. Phylogenetic frameworks inferred from comparisons of rRNAs were used to assess rates of evolution in actin genic regions of diverse eukaryotes. Actin genic regions had nonuniform rates of nucleotide substitution in different lineages. Comparison of rates of actin and rDNA sequence divergence indicated that actin genic regions evolve 2.0 and 5.3 times faster in higher fungi and flowering plants, respectively, than their rDNA sequences. Conversely, animal actins evolve at approximately one-fifth the rate of their rDNA sequences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102805
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  • 4
    Electronic Resource
    Electronic Resource
    The Family of Major Royal Jelly Proteins and Its Evolution (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 290-297 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Apis mellifera— Gene duplication — Nitrogen content — Royal jelly — Nutrition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. A cDNA encoding a new member of the gene family of major royal jelly proteins (MRJPs) from the honeybee, Apis mellifera, was isolated and sequenced. Royal jelly (RJ) is a secretion of the cephalic glands of nurse bees. The origin and biological function of the protein component (12.5%, w/w) of RJ is unknown. We show that the MRJP gene family encodes a group of closely related proteins that share a common evolutionary origin with the yellow protein of Drosophila melanogaster. Yellow protein functions in cuticle pigmentation in D. melanogaster. The MRJPs appear to have evolved a novel nutritional function in the honeybee.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006551
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  • 5
    Electronic Resource
    Electronic Resource
    Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 203-210 
    Details
    ISSN: 1432-1432
    Keywords: Cyanelles ; Cyanophora paradoxa ; Endosymbiosis ; Evolution ; Glaucocystophyta ; Glaucophyta ; Phylogeny ; Plastid ; 16S ribosomal RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyanobacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are “primitive” plastids that may represent undeveloped associations between heterotrophic “host” cells (i.e., glaucocystophytes) and cyanobacteria. To test the monophyly of glaucocystophyte cyanelles and to determine their evolutionary relationship to other plastids, complete 16S ribosomal RNA sequences were determined for Cyanophora paradoxa, Glaucocystis nostochinearum, Glaucosphaera vacuolata, and Gloeochaete wittrockiana. Plastid rRNAs were analyzed with the maximum-likelihood, maximumparsimony, and neighbor joining methods. The phylogenetic analyses show that the cyanelles of C. paradoxa, G. nostochinearum, and G. wittrockiana form a distinct evolutionary lineage; these cyanelles presumably share a monophyletic origin. The rDNA sequence of G. vacuolata was positioned within the nongreen plastid lineage. This result is consistent with analyses of nuclear-encoded rRNAs that identify G. vacuolata as a rhodophyte and support its removal from the Glaucocystophyta. Results of a global search with the maximumlikelihood method suggest that cyanelles are the first divergence among all plastids; this result is consistent with a single loss of the peptidoglycan wall in plastids after the divergence of the cyanelles. User-defined tree analyses with the maximum-likelihood method indicate, however, that the position of the cyanelles is not stable within the rRNA phylogenies. Both maximumparsimony and neighbor-joining analyses showed a close evolutionary relationship between cyanelles and nongreen plastids; these phylogenetic methods were sensitive to inclusion/exclusion of the G. wittrockiana cyanelle sequence. Base compositional bias within the G. wittrockiana 16S rRNA may explain this result. Taken together the phylogenetic analyses are interpreted as supporting a near-simultaneous radiation of cyanelles and green and nongreen plastids; these organelles are all rooted within the cyanobacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00170674
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  • 6
    Electronic Resource
    Electronic Resource
    Origin of the NEFA and Nuc Signal Sequences (1998)
    Springer
    Journal of molecular evolution 46 (1998), S. 327-333 
    Details
    ISSN: 1432-1432
    Keywords: Key words: EF-hand — Gene duplication — Molecular evolution — Nuc — Secretory proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The human protein NEFA binds calcium, contains a leucine zipper repeat that does not form a homodimer, and is proposed (along with the homologous Nuc protein) to have a common evolutionary history with an EF-hand ancestor. We have isolated and characterized the N-terminal domain of NEFA that contains a signal sequence inferred from both endoproteinase Asp-N (Asp-N) and tryptic digests. Analysis of this N-terminal sequence shows significant similarity to the conserved multiple domains of the mitochondrial carrier family (MCF) proteins. The leader sequence of Nuc is, however, most similar to the signal sequences of membrane and/or secreted proteins (e.g., mouse insulin-like growth factor receptor). We suggest that the divergent NEFA and Nuc N-terminal sequences may have independent origins and that the common high hydrophobicity governs their targeting to the ER. These results provide insights into signal sequence evolution and the multiple origins of protein targeting.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006309
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  • 7
    Electronic Resource
    Electronic Resource
    Primary and secondary structure analyses of the rDNA group-I introns of the Zygnematales (Charophyta) (1996)
    Springer
    Current genetics 29 (1996), S. 282-286 
    Details
    ISSN: 1432-0983
    Keywords: Group-I introns ; Secondary structure ; Small subunit ribosomal DNA ; Zygnematales
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Zygnematales (Charophyta) contain a group-I intron (subgroup ICl) within their nuclear-encoded small subunit ribosomal DNA (SSU rDNA) coding region. This intron, which is inserted after position 1506 (relative to the SSU rDNA ofEscherichia coli), is proposed to have been vertically inherited since the origin of the Zygnematales approximately 350–400 million years ago. Primary and secondary structure analyses were carried out to model group-I intron evolution in the Zygnematales. Secondary structure analyses support genetic data regarding sequence conservation within regions known to be functionally important for in vitro self-splicing of group-I introns. Comparisons of zygnematalean group-I intron secondary structures also provided some new insights into sequences that may have important roles in in vivo RNA splicing. Sequence analyses showed that sequence divergence rates and the nucleotide compositions of introns and coding regions within any one taxon varied widely, suggesting that the “1506” group-I introns and rDNA coding regions in the Zygnematales evolve independently.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02221559
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  • 8
    Electronic Resource
    Electronic Resource
    The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I intron (2000)
    Springer
    Current genetics 37 (2000), S. 12-23 
    Details
    ISSN: 1432-0983
    Keywords: Key words Group-I intron ; Phylogeny ; Plastids ; tRNALeu
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have surveyed the distribution and reconstructed the phylogeny of the group-I intron that is positioned in the anticodon loop of the tRNALeu gene in cyanobacteria and several plastid genomes. Southern-blot and PCR analyses showed that the tRNALeu intron is found in all 330 land plants that were examined. The intron was also found, and sequenced, in all but one of nine charophycean algae examined. Conversely, PCR analyses showed that the tRNALeu group-I intron is absent from the red, cryptophyte and haptophyte algae, although it is present in three members of the heterokont lineage. Phylogenetic analyses of the intron indicate that it was present in the cyanobacterial ancestor of the three primary plastid lineages, the Rhodophyta, Chlorophyta, and Glaucocystophyta. Its present-day distribution in plastids is consistent with a history of strictly vertical transmission, with no losses in land plants, several losses among green algae, and nearly pervasive loss in the Rhodophyta and its secondary derivatives.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002940050002
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  • 9
    Electronic Resource
    Electronic Resource
    Frontiers in Genomics: Insights into Protist Evolutionary Biology, University of Iowa, May 19–21, 2004 (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract. Protists constitute the bulk of eukaryotic diversity yet their genomes remain relatively unexplored. To address this issue, a workshop entitled, “Frontiers in Genomics: Insights into Protist Evolutionary Biology”, was convened at the University of Iowa on June 19–21, 2004. The specific aims of the workshop were to define the role of genomics in the eukaryotic tree of life, to identify challenges in characterizing protist (i.e. microbial eukaryote) genomes, and in proposing specific solutions to these challenges. The findings of the workshop are presented here and in a white paper that provide a set of guidelines for organizing the protist community and for planning and executing a protist genome project.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05-3355.x
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  • 10
    Electronic Resource
    Electronic Resource
    Molecular Evolutionary Analyses of Nuclear-Encoded Small Subunit Ribosomal RNA Identify an Independent Rhizopod Lineage Containing the Euglyphina and the Chlorarachniophyta (1995)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 42 (1995), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The Rhizopoda comprise a diverse assemblage of protists which depend on lobose or filose pseudopodia for locomotion. The biochemical and morphological diversity of rhizopods has led to an uncertain taxonomy. Ribosomal RNA sequence comparisons offer a measure of evolutionary relatedness that is independent of morphology and has been used to demonstrate a polyphyletic origin of the Lobosea. We sequenced complete small subunit ribosomal RNA coding regions from the filose amoebae, Euglypha rotunda and Paulinella chromatophora (Euglyphina) to position these taxa in the eukaryote phylogeny. The neighbor-joining analyses show that E. rotunda and P. chromatophora share a monophyletic origin and are not closely related to any lobose amoebae in our analyses. Instead, the Euglyphina form a robust sister group to the Chlorarachniophyta. These results provide further evidence for the polyphyly of the Rhizopoda and support the creation of a new amoeboid lineage which includes the Euglyphina and the chlorarachniophyte algae; taxa with tubular mitochondrial cristae and filose or reticulate pseudopodia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1995.tb01541.x
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