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Open Access Research article

The unique evolution of the programmed cell death 4 protein in plants

Shijun Cheng1, Renyi Liu2 and Daniel R Gallie1*

Author Affiliations

1 Department of Biochemistry, University of California, Riverside, CA 92521-0129, USA

2 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0129, USA

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BMC Evolutionary Biology 2013, 13:199  doi:10.1186/1471-2148-13-199

Published: 16 September 2013

Additional files

Additional file 1:

Sequence comparison of the MA3 domains in A. thaliana eIF4G and PDCD4 proteins. Comparison of the amino acid sequence of the MA3 domains of eIF4G and PDCD4 proteins is shown with amino acid identity highlighted in yellow amino acid and similarity highlighted in green. Conserved residues for MAT5-8 proteins (MAT consensus) are indicated below the sequence alignment as are the conserved residues for eIF4G and eIFiso4G (4G/iso4G consensus). The eIFiso4G-like sequence is MAT4 (At4g30680). Those residues absolutely conserved among all MA3 domain proteins are indicated as bold residues in both consensus sequences.

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Additional file 2:

Domain organization of PDCD4 homologs in algae and algal relatives. The domain organization of PDCD4 homologs is shown for green algae and algal relatives with the MA3 domains indicated in blue. PDCD4 proteins for green marine algae (Chlamydomonas reinhardtii, Volvox carteri, Micromonas species, and Ostreococcus species), fresh water alga (Chaetosphaeridium globosum), and stramenopiles or algal relatives (Ectocarpus siliculosus, Aureococcus anophagefferens, Phaeodactylum tricornutum, Thalassiisira pseudoonana, Phytophthora species, and Albugo laibachii) are shown. The additional sequence interrupting the fourth MA3 domain of the C. reinhardtii and V. carteri homologs is indicated by a gap. The first MA3 domain is missing from the partial C. globosum cDNA but is proposed.

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Additional file 3:

Sequence analysis of the MA3 domains of PDCD4 homologs in algae and algal relatives suggests domain duplication in at least some chlorophytes. A phylogenetic tree was generated using the sequences comprising MA3 domains 1–2 and MA3 domains 3–4 of the four MA3 domain PDCD4 homologs of chlorophytes Chlamydomonas reinhardtii and Volvox carteri, and MA3 domains 1–2 and MA3 domain 3 from the partial cDNA of the Chlorella variabilis PDCD4 homolog, MA3 domains 1–2 of the two MA3 domain PDCD4 homologs of prasinophyte Micromonas species and Ostreococcus species, and those of the stramenopiles Ectocarpus siliculosus, Aureococcus anophagefferens, Phaeodactylum tricornutum, Thalassiisira pseudoonana, Phytophthora species, and Albugo laibachii. The phylogenetic tree was constructed using the maximum-likelihood method. Numbers on each branch denote percentages of bootstrap support. Chlorophytes are shaded dark green, species of the Mamiellales are shaded light green, and the stramenopiles are shaded tan.

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Additional file 4:

Aligned sequences used for the phylogenetic analysis of Figure2.

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Additional file 5:

Aligned sequences used for the phylogenetic analysis of Additional file3.

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Additional file 6:

Aligned sequences used for the phylogenetic analysis of Figure6.

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