Article Figures & Data
Figures
- Fig. 1.
Maximum-likelihood (ML) phylogenetic trees of mitochondrial Hsp70 (A), cysteine desulfurase (IscS) (B), [FeFe]-hydrogenase (C), and pyruvate:ferredoxin oxidoreductase (D). Trees were constructed using RAxML with a WAG+Γ model of evolution. Bootstrap support values above 50 are shown over branches.
- Fig. 2.
Comparison of the N termini of several different protein homologues from Sawyeria and several representative eukaryote sequences, showing the putative targeting peptides. Aligned bacterial homologues, which do not contain targeting peptides, are also shown. Most of the putative targeting peptides of Sawyeria were not predicted by automated software (see Materials and Methods and the main text).
- Fig. 3.
Transmission electron micrographs of Sawyeria marylandensis. (A) Full view of a Sawyeria marylandensis cell. (B) Partial view of an S. marylandensis cell showing the three different shapes of the mitochondrion-related organelle. (C) S. marylandensis cell with several hydrogenosomes. (D) An inset view of picture C. (E) View of a hydrogenosome of S. marylandensis. (F) Close view showing double-membrane structure of the organelle.
- Fig. 4.
3D reconstruction of shape of Sawyeria hydrogenosomes derived from serial sectioning transmission electron microscopy. The bean-shaped MRO is about 1.8 μm tall, 1.5 μm long, and 0.840 μm wide. The cup-shaped MRO is 1.5 μm tall and 1.65 μm wide. See the main text for more details.
Tables
- Table 1.
Mitocondrial/hydrogenosomal proteins in Sawyeria marylandensis and comparison with N. gruberi, T. vaginalis, and G. intestinalisa
Category or S. marylandensis mitochondrial/hydrogenosomal protein Accession no.d N-terminal extensione Annotationf TBestDB NCBI Ng Tv Gi Energy metabolism [FeFe]-hydrogenaseb EF612752 (SmHydA) Yes + + + EF612753 (SmHydB) Pyruvate:ferredoxin oxidoreductase (PFO)b EF612751 Yes − + + Alpha-succinyl-CoA synthetaseb SML00000322 EF612760 Yes + + − Beta-succinyl-CoA synthetaseb SML00000048 EF612761 Yes + + − 2Fe-2S Ferredoxinc SML00003510 EC818301 ? + + + Putative glycerol kinasec SML00001707 EC823814 ? + − + Fe-hydrogenase assembly HydGb SML00000047 EF612762 Yes + + − HydFc SML00000703 EC826105 ? + + − Mitochondrial carrier family Putative ATP/ADP Carrier (AAC)b SML00000111 EC824912 No + + − SML00000209 EC825377 Mitochondrial import pathway Cpn60b EU233795 Yes + + + Hsp70b EF612755 Yes + + + Cpn10b EF612758 No + + − TOM34c SML00000787 EC825338 ? −/+ − − TIM 23c SML00000812 EC826107 ? + − − TIM 44c SML00000628 EC825535 ? + − − Mitochondrial respiratory complex I 51 kDa (NuoF)b EF612754 Yes + + − 24 kDa (NuoE)c SML00003413 EC824286 ? + + − ISC pathway IscSb EF612756 Yes + + + IscUb EF612757 ? + + + Frataxinc SML00000479 EC823663 ? + + + Fatty acid metabolism Propionyl-CoA carboxylase alpha chainc SML00000070 EC826322 ? + − − Propionyl-CoA carboxylase beta chainc SML00000244 EC825818 ? + − − 3-Ketoacyl-CoA thiolasec SML00000148 EC826272 + − − Amino acid metabolism Dihydrolipoamide dehydrogenase (L protein)b SML00002324 EF612759 Yes + − − Glycine cleavage system Hc SML00003411 EC819138 ? + + − Glycine cleavage system Pc SML00003181 EC821614 ? + + − 4-Aminobutyrate transaminasec SML00000492 EC825405 ? + − − Methylmalonyl-CoA mutasec SML00000635 EC825225 ? + − − Serine hydroxymethyltransferasec SML00001624 EC824484 ? + + − Branched chain ketoacid dehydrogenase E1, alpha polypeptidec SML00000388 EC826530 ? + − − SML00002275 EC817751 Branched-chain alpha-keto acid dehydrogenase E1-beta subunitc SML00001068 EC825728 ? + − − Lipoamide acyltransferase (branched-chain alpha-keto acid dehydrogenase complex) E2c SML00000474 EC826090 ? + − − Glutamate dehydrogenasec SML00000006 EC826618 ? + + + Alanine aminotransferasec SML00000316 EC825413 ? + − − Aspartate aminotransferasec SML00001965 EC817939 ? + + + Ornithine carbamoyltransferasec SML00001073 EC825834 ? −/+ + + Putative delta-1-pyrroline-5-carboxylate dehydrogenasec SML00000009 EC826523 ? + − − Putative glutaryl-CoA dehydrogenasec SML00001691 EC823693 ? + − − 2-Amino-3-ketobutyrate coenzyme A ligasec SML00000023 EC826214 ? + − − Other functions Thioredoxin reductase 2c SML00002472 EC820868 ? + + + NADH-cytochrome b5 reductasec SML00002452 EC819124 ? + − − Succinate semialdehyde dehydrogenasec SML00000871 EC822494 ? −/+ − − Dynamin like proteinc SML00000756 EC822881 ? + + + ↵a Hits confirmed by BLAST (E < 10−5) to NCBI and PFAM.
↵b Phylogeny shown in Fig. 1 or the supplemental material.
↵c Automatic annotation as obtained by the AnaBench pipeline (http://anabench.bcm.umontreal.ca/anabench/ ).
↵d For those genes fully sequenced, NCBI accession numbers are provided in bold. For the rest, TBestDB accession numbers are provided for the contigs plus an additional NCBI accession number for a representative EST of the contig.
↵e ? indicates an incomplete sequence at the N terminus.
↵f Ng, Naegleria gruberi; Tv, Trichomonas vaginalis; Gi, Giardia intestinalis. “−/+” indicates that a potential distant homolog of the protein was found but its assignment to the specific protein family named could not be confirmed by reciprocal BLAST.
Supplemental material
Files in this Data Supplement:
- Supplemental file 3 -
Nine supplemental figures depicting maximum likelihood phylogenetic trees of proteins mentioned in the manuscript.
PDF file, 576K. - Supplemental file 1
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Supplemental video 1 depicting 3D reconstruction of Sawyeria marylandensis hydrogenosomes from serial sectioning in transmission electron microscopy.
Zipped GIF file, 2.7MB. - Supplemental file 2
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Supplemental video 2 depicting Sawyeria marylandensis under fluorescence microscopy.
Zipped GIF file, 3.5MB. - Supplemental file 4
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Legends to supplemental figures and videos.
MS Word document, 29K.
- Supplemental file 3 -
Nine supplemental figures depicting maximum likelihood phylogenetic trees of proteins mentioned in the manuscript.
