Article Figures & Data
Figures
- Fig 1
Unrooted maximum-likelihood phylogenetic tree of Der1-like proteins and subcellular localizations of B. natans Der1-like proteins. (A) B. natans sequences are shown in green, and Der1 sequences of putative translocons at the second plastid membrane are indicated in red. The numbers next to the species names indicate GenBank, JGI, or C. merolae genome identifiers. The values at nodes are the bootstrap support values and are indicated only when they are higher than 50%. The scale bar represents the estimated number of amino acid substitutions per site. (B) GFP localization of a transformed cell expressing BnDer1-49642-GFP, BnDer1-92850-GFP, and control GFP, respectively. The pictures labeled “GFP” and “Plastids” show GFP fluorescence (green) and chlorophyll autofluorescence (red), respectively. DIC, differential interference contrast image; SP, signal peptide; ER, endoplasmic reticulum; Cy, cytoplasm. Scale bar, 5 μm.
- Fig 2
Alignment of BnTOC75-Nm, BnOMP85, P. sativum TOC75, and Bordetella pertussis FhaC. Amino acids identical in at least two of the sequences are shaded in black, and conserved substitutions are shaded in gray. The putative signal peptide, transit peptide, and polyglycine stretch are highlighted with pink, blue, and yellow, respectively. POTRA1, POTRA2, and 16 β-strands (β-1 to -16) of FhaC that have been reported previously (18) are indicated below the sequence.
- Fig 3
Reconstructed translocons in a chlorarachniophyte plastid. (A) Predicted localization of B. natans TOC and TIC homologs. Nucleus-encoded components are highlighted with blue, and nucleomorph-encoded ones are red. Arrows indicate the transport pathway of plastid precursor proteins. (B) Schematic illustration of putative B. natans TOC and TIC proteins. Predicted signals, motifs, and domains are plotted in each sequence. Abbreviations: SP, signal peptide; Ag, antigen; TPL, transit peptide-like sequence; G-stretch, polyglycine stretch; TMD, transmembrane domain; POTRA, polypeptide transport-associated domain; CaM, calmodulin-binding site; TPR, tetratricopeptide repeat; PAO, pheophorbide a oxygenase; [2Fe-2S], 2Fe-2S binding site; [Fe2+], mononuclear-iron-binding site.
- Fig 4
Protein structures of BnTIC22, BnTIC40, BnTIC32, BnTIC55, and BnTIC62. Sequence conservations among TIC homologs of land plants (Pisum sativum, Arabidopsis thaliana, Oryza sativa, and Physcomitrella patens) and green algae (Chlamydomonas reinhardtii, Chlorella variabilis, Micromonas pusilla, Ostreococcus tauri, O. lucimarinus, and/or Volvox carteri) are shown as logo plots generating by WebLogo v. 2.8.2. B. natans TIC sequences are shown above the logo plots, and conserved amino acids are indicated by asterisks.
Tables
- Table 1
Putative TOC and TIC components in the Bigelowiella natans genomea
Component P. sativum accession no. B. natans accession no.b No. of aa Presence of: TPL net charge (no. of aa) E value SP sequence (probability score) TPL sequence (probability score) TOC34 Q41009 — TOC64 AAF62870 (JGI 89506) 784 Yes (0.998) No (0.493) 4 (50) 7.00E−20 TOC75 Q43715 ABA27321(Nm) 818 No No (0.427) −2.9 (50) 9.00E−24 OMP85 Q43715 JGI 79166 899 Yes (0.786) No (0.435) 10 (50) 0.002 TOC159 AF75761 — TIC20 AAC64607 ABA27416 (Nm) 207 No No (0.458) 9 (50) 5.00E−5 JGI 115241 322 Yes (1.000) Yes (0.549) 3.1 (32) 1.00E−5 TIC21 ABG00264 JGI 66755 272 Yes (1.000) Yes (0.518) 7.1 (36) 2.00E−4 TIC22 AAC64606 JGI 127449 341 Yes (0.996) Yes (0.530) 8 (32) 0.001 JGI 66754 330 Yes (0.948) Yes (0.538) 9.1 (53) 0.15 TIC32 AAS38575 JGI 91380 527 Yes (0.329) Yes (0.521) 0 (9) 3.00E−32 TIC40 CAB50925 JGI 82201 569 Yes (0.574) Yes (0.556) 11.2 (58) 2.00E−22 TIC55 CAA04157 JGI 77479 648 Yes (0.600) Yes (0.514) 6.2 (26) 7.00E−59 TIC62 CAC87810 JGI 86815 339 Yes (0.835) Yes (0.560) 12.3 (53) 3.00E−46 TIC110 CAA92823 — ↵a The GenBank accession or JGI protein identification number of each TOC/TIC component is recorded. “SP sequence” indicates the result of signal peptide prediction by the HMM method of SignalP, and the probability scores are shown in parentheses. “TPL sequence” is the result of transit peptide prediction by ChloroP. “TPL net charge” shows the net charge of the predicted TPL sequence, with the predicted length of the TPL sequence in parentheses (the N-terminal 50 aa of TOC64, TOC75, and TIC20 were used for the net charge calculation, since their TPL regions could not be predicted by ChloroP). The BLASTP E values against P. sativum TOC/TIC components are in the rightmost column.
↵b —, no component present. The parentheses around JGI 89506 indicate that it is a paralog of TOC64. ABA27321 and ABA27416 are nucleomorph (Nm)-containing genes.
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
ML phylogenetic tree for OMP85 homologs of plants, green algae, cyanobacteria, and chlorarachniophytes (Fig. S1); ML phylogenetic
tree for TIC20 homologs of plants, green algae, cyanobacteria, and chlorarachniophytes (Fig. S2); PCR primers used for 5'
and 3' RACE of TOC and TIC genes (Table S1); PCR primers used to amplify cDNA of Der1-like proteins (Table S2).
PDF file, 784K.
- Supplemental file 1 -
ML phylogenetic tree for OMP85 homologs of plants, green algae, cyanobacteria, and chlorarachniophytes (Fig. S1); ML phylogenetic
tree for TIC20 homologs of plants, green algae, cyanobacteria, and chlorarachniophytes (Fig. S2); PCR primers used for 5'
and 3' RACE of TOC and TIC genes (Table S1); PCR primers used to amplify cDNA of Der1-like proteins (Table S2).
