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Insights into a dinoflagellate genome through expressed sequence tag analysis.

Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D - BMC Genomics (2005)

Bottom Line: We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X.We speculate this histone may be retained for its role in DNA double-strand break repair.These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA. jeremiah-hackett@uiowa.edu

ABSTRACT

Background: Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging.

Results: Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair.

Conclusion: This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

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Analysis of dinoflagellate HLPs. A) HLPs from dinoflagellates (red taxa names) and bacteria (blue) and HU proteins from bacteria (black). B) The predicted secondary structure of HLPs from A. tamarense and B. pertussis aligned with the known secondary structure of E. coli HU. Curled lines indicate α-helices and jagged lines indicate β-strands. The arrow indicates the position of a conserved lysine. The asterisk indicates the proline that intercalates into the DNA in HU proteins. C) An ML tree of HU and HLP proteins from bacteria and eukaryotes. The numbers above and below the branches result from ML and NJ bootstrap analyses, respectively. The thick branches indicate > 0.95 posterior probability from Bayesian inference. Only bootstrap values ≥ 50% are shown. Branch lengths are proportional to the number of substitutions per site (see scale bar).
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Figure 4: Analysis of dinoflagellate HLPs. A) HLPs from dinoflagellates (red taxa names) and bacteria (blue) and HU proteins from bacteria (black). B) The predicted secondary structure of HLPs from A. tamarense and B. pertussis aligned with the known secondary structure of E. coli HU. Curled lines indicate α-helices and jagged lines indicate β-strands. The arrow indicates the position of a conserved lysine. The asterisk indicates the proline that intercalates into the DNA in HU proteins. C) An ML tree of HU and HLP proteins from bacteria and eukaryotes. The numbers above and below the branches result from ML and NJ bootstrap analyses, respectively. The thick branches indicate > 0.95 posterior probability from Bayesian inference. Only bootstrap values ≥ 50% are shown. Branch lengths are proportional to the number of substitutions per site (see scale bar).

Mentions: Dinoflagellate chromosomes do not contain nucleosomes, instead the DNA is associated with HLPs [10,30,31]. The similarity between dinoflagellate HLPs and bacterial HU and HLPs has only recently been noted and these proteins have not yet been subjected to phylogenetic analysis with a broad taxon sampling [32]. In our A. tamarense EST data, HLPs were the most highly represented transcripts (45/11,171 ESTs) and encoded 5 closely related proteins. Alignment of the HLPs from A. tamarense and other dinoflagellates with HLPs and HU proteins from bacteria and eukaryotes showed moderate sequence similarity (a representative alignment is shown in Figure 4A). This alignment was constructed using information from secondary structure predictions (discussed below).


Insights into a dinoflagellate genome through expressed sequence tag analysis.

Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D - BMC Genomics (2005)

Analysis of dinoflagellate HLPs. A) HLPs from dinoflagellates (red taxa names) and bacteria (blue) and HU proteins from bacteria (black). B) The predicted secondary structure of HLPs from A. tamarense and B. pertussis aligned with the known secondary structure of E. coli HU. Curled lines indicate α-helices and jagged lines indicate β-strands. The arrow indicates the position of a conserved lysine. The asterisk indicates the proline that intercalates into the DNA in HU proteins. C) An ML tree of HU and HLP proteins from bacteria and eukaryotes. The numbers above and below the branches result from ML and NJ bootstrap analyses, respectively. The thick branches indicate > 0.95 posterior probability from Bayesian inference. Only bootstrap values ≥ 50% are shown. Branch lengths are proportional to the number of substitutions per site (see scale bar).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1173104&req=5

Figure 4: Analysis of dinoflagellate HLPs. A) HLPs from dinoflagellates (red taxa names) and bacteria (blue) and HU proteins from bacteria (black). B) The predicted secondary structure of HLPs from A. tamarense and B. pertussis aligned with the known secondary structure of E. coli HU. Curled lines indicate α-helices and jagged lines indicate β-strands. The arrow indicates the position of a conserved lysine. The asterisk indicates the proline that intercalates into the DNA in HU proteins. C) An ML tree of HU and HLP proteins from bacteria and eukaryotes. The numbers above and below the branches result from ML and NJ bootstrap analyses, respectively. The thick branches indicate > 0.95 posterior probability from Bayesian inference. Only bootstrap values ≥ 50% are shown. Branch lengths are proportional to the number of substitutions per site (see scale bar).
Mentions: Dinoflagellate chromosomes do not contain nucleosomes, instead the DNA is associated with HLPs [10,30,31]. The similarity between dinoflagellate HLPs and bacterial HU and HLPs has only recently been noted and these proteins have not yet been subjected to phylogenetic analysis with a broad taxon sampling [32]. In our A. tamarense EST data, HLPs were the most highly represented transcripts (45/11,171 ESTs) and encoded 5 closely related proteins. Alignment of the HLPs from A. tamarense and other dinoflagellates with HLPs and HU proteins from bacteria and eukaryotes showed moderate sequence similarity (a representative alignment is shown in Figure 4A). This alignment was constructed using information from secondary structure predictions (discussed below).

Bottom Line: We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X.We speculate this histone may be retained for its role in DNA double-strand break repair.These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA. jeremiah-hackett@uiowa.edu

ABSTRACT

Background: Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging.

Results: Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair.

Conclusion: This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

Show MeSH
Related in: MedlinePlus