Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi

Abstract

Prior to the recent discovery of Ignavibacterium album (I. album), anaerobic photoautotrophic green sulfur bacteria (GSB) were the only members of the bacterial phylum Chlorobi that had been grown axenically. In contrast to GSB, sequence analysis of the 3.7-Mbp genome of I. album shows that this recently described member of the phylum Chlorobi is a chemoheterotroph with a versatile metabolism. I. album lacks genes for photosynthesis and sulfur oxidation but has a full set of genes for flagella and chemotaxis. The occurrence of genes for multiple electron transfer complexes suggests that I. album is capable of organoheterotrophy under both oxic and anoxic conditions. The occurrence of genes encoding enzymes for CO(2) fixation as well as other enzymes of the reductive TCA cycle suggests that mixotrophy may be possible under certain growth conditions. However, known biosynthetic pathways for several amino acids are incomplete; this suggests that I. album is dependent upon on exogenous sources of these metabolites or employs novel biosynthetic pathways. Comparisons of I. album and other members of the phylum Chlorobi suggest that the physiology of the ancestors of this phylum might have been quite different from that of modern GSB.

Keywords: Chlorobi; Ignavibacterium album; genome sequence.

Figure 1

Phylogenetic tree of 16S rRNA sequences of I. album and related species from the phylum Chlorobi. The tree was generated using neighbor-joining algorithm with Jukes–Cantor correction. Sequences of three Bacteroidetes species were used as the outgroup. Bootstrap support values based on 1000 bootstrap samplings were shown for each node. Bar denotes 0.02 changes per nucleotide site. The classes Chlorobia and Ignavibacteria only contain one order and brackets for those orders were omitted to simplify the figure.

Figure 2

Circular map of I. album genome. Circles from outside in: genes on the forward strand; genes on the reverse strand; G + C% plot; and GC skew plot. Baseline on the G + C% plot represents the average value of 34%. Gene colors indicate the COG categories to which they belong.

Figure 3

Phylogenetic distribution of BLASTP best hits of I. album proteins compared to proteins in the NCBI nr database. An e-value cut-off of 0.001 was used.

Figure 4

Proposed mixotrophy and a potential unconventional reverse TCA cycle in I. album. Fd, ferredoxin; red, reduced; ox, oxidized; Hyd, hydrogenase; MKH₂, menaquinol; Rnf, Na⁺-translocating ferredoxin:NAD⁺ oxidoreductase.

Figure 5

High-performance liquid chromatography elution profile of pigments produced in I. album. The in-line absorption spectra of the peaks are shown in the numbered boxes. (A) Elution profile monitoring absorbance at 270 nm. Peaks 1–4, menaquinones. (B) Elution profile monitoring absorbance at 491 nm. Peaks 1, 2, deoxyflexixanthin derivatives; peaks 3-10 1′-hydroxytorulene derivatives.

Figure 6

Cellular overview of I. album metabolism deduced from its genome sequence. Only selected pathways and enzymes discussed in the text are shown. Blue arrows indicate pathways of electron flow. NDH-1, type-1 NADH dehydrogenase; Fd, ferredoxin; MK, menaquinone; cyt, cytochrome; Mo complex, complexes containing a molybdopterin-guanine dinucleotide cofactor; ACIII, alternative complex III.

Figure 7

Gene clusters encoding type-1 NADH dehydrogenase (A) and alternative complex III and caa3-type cytochrome oxidase (B) of I. album.

Figure 8

Phylogenetic trees type-1 NADH dehydrogenase proteins (A), cytochrome bd-quinol oxidases (B), and molybdopterin-guanine dinucleotide cofactor-containing complexes (C) from I. album and other organisms. Concatenated NuoABCDHIJKLMN protein sequences were used for (A); concatenated CydAB protein sequences were used for (B); molybdopterin-guanine dinucleotide-containing subunit sequences were used for (C). Trees were created using the neighbor-joining algorithm from 100 bootstrap samplings. Bootstrap support values over 50% are shown. Scale bars denote X changes per amino acid where X is the number above bars. SU, subunits. (C) was adapted from Yanyushin et al. (2005) and was recreated by including I. album proteins.

Figure 9

Schematic representation of the predicted Fe/S cluster contents of two hydrogenases from I. album compared to two related and experimentally characterized hydrogenases from Thermotoga maritima and Thermoanaerobacter tengcongensis. H, H cluster; 2Fe, [2Fe-2S] cluster; 4Fe, [4Fe-4S] cluster; NuoF, FMN and NAD(P)(H) binding domain.