Present address: Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT 59101, USA.
Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria
Article first published online: 27 SEP 2011
© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: OMICS Driven Microbial Ecology
Volume 14, Issue 1, pages 177–190, January 2012
How to Cite
Garcia Costas, A. M., Liu, Z., Tomsho, L. P., Schuster, S. C., Ward, D. M. and Bryant, D. A. (2012), Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria. Environmental Microbiology, 14: 177–190. doi: 10.1111/j.1462-2920.2011.02592.x
- Issue published online: 2 JAN 2012
- Article first published online: 27 SEP 2011
- Received 23 April, 2011; revised 31 July, 2011; accepted 5 August, 2011.
Fig. S1. Distribution of CDS belonging to different Cluster of Orthologous Groups on the two chromosomes of Ca. C. thermophilum. Key to individual columns: Information storage and processing: (i) translation, ribosomal structure and biogenesis, (ii) transcription and (iii) replication, recombination and repair. Cellular processes and signalling: (i) cell cycle control, cell division, chromosome partitioning, (ii) defence mechanisms, (iii) signal transduction mechanisms, (iv) cell wall/membrane/envelope biogenesis, (v) cell motility, (vi) intracellular trafficking, secretion and (vii) post-translational modification, protein turnover, chaperones. Metabolism: (i) energy production and conversion, (ii) transport and metabolism of carbohydrates, (iii) amino acids, (iv) nucleotides, (v) coenzymes, (vi) lipids, (vii) inorganic ions and (viii) secondary metabolites. Poorly characterized: (i) general function prediction only and (ii) function unknown.
Fig. S2. Neighbour-joining phylogenetic tree of concatenated PetA and PetB sequences. The Sulfolobus islandicus PetA-PetB sequence was used to root the tree. Bootstrap values after 1000 iterations are shown. Cabther_0913 and Cabther_0914 were concatenated and Cabther_0771 and Cabther_0772 were concatenated and used to build the tree seen below. The former sequences were more closely related to those of Chlorobi and Deltaproteobacteria and the latter were more closely related to other members of the Acidobacteria.
Fig. S3. Neighbour-joining phylogenetic tree of B(Chl) synthases rooted with the Escherichia coli ubiA gene. Bootstrap values after 100 iterations are shown.
Fig. S4. Predicted carotenoid biosynthesis pathway in Ca. C. thermophilum. The genome of Ca. C. thermophilum contains carotenoid biosynthesis genes that suggest that it synthesizes lycopene via the multi-step crtP-crtQ-crtH pathway. In addition it contains genes coding for two different types of lycopene cyclases (cruA and YcYd), which introduce rings to the Ψ-ends of lycopene generating γ-carotene and β-carotene as well as a ketolase (crtO) that introduces a keto group to these rings producing echinenone and canthaxanthin. The presence of crtC and crtD and biochemical analyses (Garcia Costas, 2010) suggest that Ca. C. thermophilum also produces monocyclic hydroxylated carotenoids with an as yet unidentified structure.
Table S1. Genes involved in carotenoid and (B)Chl biosynthesis.
Table S2. Genes involved in electron transport in Ca. C. thermophilum.
Table S3. Predicted auxotrophies and carbon-related biochemical pathways in Ca. C. thermophilum.
Table S4. Menaquinone biosynthesis genes in Ca. C. thermophilum and their homology to those in Streptomyces coelicolor A3(2), in which this pathway was first identified.
Table S5. Genes in Ca. C. thermophilum that are predicted to code for subunits of type-I NADH dehydrogenase.
Table S6. Properties and homology of transposase genes found in Ca. C. thermophilum.
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