Article Figures & Data
- FIG 1
The distribution of complex I across bacteria. The distribution of predicted complex I enzymes in sequenced bacterial genomes. (A) The number of bacterial genomes predicted to encode 0, 1, or 2 complex I enzymes, organized by phylum or class. The x axis phylogeny was modeled using data from Ciccarelli et al. (77). (B) The percentage of bacterial genomes predicted to encode 0, 1, or 2 complex I enzymes, organized by trait. An asterisk (*) indicates that the distribution of complex I (0, 1, or 2 or more enzymes) for a specific trait is significantly different from the distribution of complex I in all bacteria (fist bar) at P values of <0.0005 (chi-square test). “N/A” indicates there were not enough genomes in the category to perform the statistical analysis.
- FIG 2
Phylogeny of bacterial complex I. A phylogeny of predicted complex I enzymes from 508 sequenced bacterial genomes was generated using amino acid sequences from all 14 concatenated complex I subunits. There are five main clades of bacterial complex I (clades A to E), which can be distinguished by specific subunit features. Genome names and most of the support values were omitted for clarity.
- FIG 3
The extended C terminus of clade A NuoE is poorly conserved. Protein alignment of the first 300 amino acids of the complex I subunit NuoE from clade E E. coli and clade A R. sphaeroides, R. capsulatus, and Agrobacterium tumefaciens. The first ~170 amino acids of NuoE are well conserved between all organisms. Most clade A NuoE subunits have an extended C terminus, which is poorly conserved even between closely related bacteria.
- FIG 4
Inheritance pattern of complex I in specific bacterial groups. A species phylogeny of representative members of Bacteroidetes, Actinobacteria, Deltaproteobacteria, and Gammaproteobacteria was generated using the amino acid sequences of 9 highly conserved housekeeping genes. The absence or presence of complex I (by complex I clade) was mapped onto the phylogeny to show the patchwork inheritance pattern of complex I within specific groups of bacteria. For visualization purposes, Bacillus cereus was used to root the tree, as the Firmicutes phylum represents a distantly related phylum in which no complex I enzymes were identified. Support values were omitted for clarity, but the full phylogeny is available in Fig. S8 in the supplemental material. Abbreviations: C. Amoebophilus asiaticus, “Candidatus Amoebophilus asiaticus”; Blattabacterium sp. B. germ, Blattabacterium sp. Blattella germanica; Anaeromyxo. sp. Fw109-5, Anaeromyxobacter sp. Fw109-5; Syntrophobact. fumaroxidans, Syntrophobacter fumaroxidans; Pseudoxanthomonas s., Pseudoxanthomonas suwonensis; Pseuodoaltero. sp. SM9913, Pseudoalteromonas sp. SM9913; Actinobacillus pleuro., Actinobacillus pleuropneumoniae.
- FIG 5
Biochemical pathways enriched in bacterial genomes that encode complex I. (A) Heat map showing the biochemical pathways (KEGG modules) that are enriched in bacterial genomes predicted to encode complex I compared to members of the same class/phylum that are predicted to lack complex I. We present pathways that show significant enrichment with a P value of <0.01 (see Data Set S2 in the supplemental materials for full results). Pathways are colored according to their level of significance, which was calculated by −log10(P value), so that the most significantly enriched pathways have a higher value on the color key and are darker shades of blue. For visual purposes, the value of the most significant pathway (“NADH:quinone oxidoreductase, prokaryotes” in Actinobacteria) was adjusted from 44 to 25, which still represents the upper limit of the scale, while improving the resolution of other enriched pathways found in the analysis. Pathway names highlighted in pink produce NADH as a byproduct (72). (B) Schematic of biochemical pathways that are enriched across different groups of bacteria predicted to encode complex I. Beta-oxidation produces NADH and acetyl-CoA, the latter of which feeds into the TCA cycle to produce additional NADH. The glyoxylate cycle and ethylmalonyl pathway (not shown) assimilate acetyl-CoA by bypassing the CO2-generating reactions of the TCA cycle.
- TABLE 1
Genomes predicted to encode two or more complex I isozymes
Phylum or class (no. of strains) Strain Enzyme clades Alphaproteobacteria (18) Acidiphilium cryptum JF-5 A, E Gluconacetobacter diazotrophicus PAl 5 A, E Rhizobium etli (2 strains) A, other Rhodobacter sphaeroides (4 strains) A, E Rhodopseudomonas palustris (7 strains) A, E Sinorhizobium fredii NGR234 A, other Sinorhizobium medicae WSM419 A, other Sinorhizobium meliloti 1021 A, other Bacteroidetes (1) Chitinophaga pinensis DSM 2588 C, E Betaproteobacteria (1) Nitrosospira multiformis ATCC 25196 B, E Deltaproteobacteria (9) Geobacter bemidjiensis Bem E, other Geobacter metallireducens GS-15 E, other Geobacter sp. FRC-32 E, other Geobacter sp. M18 E, other Geobacter sp. M21 E, other Geobacter sulfurreducens PCA E, other Geobacter uraniireducens Rf4 E, other Pelobacter propionicus DSM 2379a C, C, C Syntrophobacter fumaroxidans MPOBb E, E Gammaproteobacteria (4) Gammaproteobacterium HdN1 E, E Nitrosococcus halophilus Nc4 B, E Nitrosococcus oceani ATCC 19707 B, E Nitrosococcus watsoni C-113 B, E Gemmatimonadetes (1) Gemmatimonas aurantiaca T-27 C, C - TABLE 2
Most significantly enriched biochemical pathways when comparing clade B- to clade E-containing gammaproteobacteria
Pathways enriched in clade B-containing gammaproteobacteria, P < 0.05 Pathways enriched in clade E-containing gammaproteobacteria, P < 0.05 Cytochrome bc1 complex respiratory unit Fumarate reductase, prokaryotes Cytochrome bc1 complex Dissimilatory nitrate reduction, nitrate → ammonia Cytochrome c oxidase Malonate semialdehyde pathway, propionyl-CoA → acetyl-CoA Cytochrome c oxidase, prokaryotes Valine/isoleucine biosynthesis, pyruvate → valine/2-oxobutanoate → isoleucine RaxAB-RaxC type I secretion system Isoleucine biosynthesis, threonine → 2-oxobutanoate → isoleucine Type IV secretion system Ascorbate degradation, ascorbate → d-xylulose-5P Helicobacter pylori pathogenicity signature, cagA pathogenicity island Catechol ortho-cleavage, catechol → 3-oxoadipate HydH-HydG (metal tolerance) two-component regulatory system Type III secretion system CheA-CheYBV (chemotaxis) two-component regulatory system Enterohemorrhagic/enteropathogenic E. coli pathogenicity signature, T3SS and effectors Cph1-Rcp1 (light response) two-component regulatory system RstB-RstA two-component regulatory system PleC-PleD (cell fate control) two-component regulatory system Sulfate transport system Cysteine biosynthesis, homocysteine and serine → cysteine Iron(III) transport system Putative ABC transport system Thiamine transport system ABC-2-type transport system Putative spermidine/putrescine transport system Fatty acid biosynthesis, elongation Glycine betaine/proline transport system Ribosome, bacteria l-Arabinose transport system NADH:quinone oxidoreductase, prokaryotesa Lysine/arginine/ornithine transport system Histidine transport system Glutamate/aspartate transport system General l-amino acid transport system Cystine transport system Branched-chain amino acid transport system Peptides/nickel transport system Iron complex transport system PTS system, glucose-specific II component PTS system, cellobiose-specific II component PTS system, ascorbate-specific II component Dipeptide transport system Microcin C transport system Taurine transport system Sulfonate transport system Oligopeptide transport system ↵a Only 2 of the 14 genes encoding complex I (nuoC and nuoD) were enriched in clade B-containing gammaproteobacteria. This is because these genes are separate in clade B operons (counted as 2 genes) and fused in clade E operons (counted as 0 genes). Thus, clade B-containing gammaproteobacteria appear to be enriched for complex I (NADH:quinone oxidoreductase, prokaryotes).
Supplemental Material
Figure S1
Phylogeny of concatenated complex I subunits NuoBCD. A concatenated phylogeny of predicted NuoBCD complex I subunits from sequenced bacterial genomes. Download Figure S1, PDF file, 2.4 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S2
Phylogeny of complex I subunit NuoF. A phylogeny of predicted NuoF complex I subunits from sequenced bacterial genomes. Download Figure S2, PDF file, 2.3 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S3
Phylogeny of complex I subunit NuoG. A phylogeny of predicted NuoG complex I subunits from sequenced bacterial genomes. Download Figure S3, PDF file, 2.1 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S4
Phylogeny of complex I subunit NuoH. A phylogeny of predicted NuoH complex I subunits from sequenced bacterial genomes. Download Figure S4, PDF file, 2.4 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S5
Phylogeny of complex I subunit NuoL. A phylogeny of predicted NuoL complex I subunits from sequenced bacterial genomes. Download Figure S5, PDF file, 2.3 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S6
Phylogeny of complex I subunit NuoM. A phylogeny of predicted NuoM complex I subunits from sequenced bacterial genomes. Download Figure S6, PDF file, 2.1 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S7
Phylogeny of complex I subunit NuoN. A phylogeny of predicted NuoN complex I subunits from sequenced bacterial genomes. Download Figure S7, PDF file, 2.5 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S8
Inheritance pattern of complex I in specific bacterial groups with support values. An identical phylogeny as depicted in Fig. 4 with SH-like support values provided for each node. Specifically, a species phylogeny of representative members of Bacteroidetes, Actinobacteria, Deltaproteobacteria, and Gammaproteobacteria was generated using the amino acid sequences of 9 highly conserved housekeeping genes. The absence or presence of complex I (by complex I clade) was mapped onto the phylogeny to show the patchwork inheritance pattern of complex I within specific groups of bacteria. For visualization purposes, Bacillus cereus was used to root the tree, as the Firmicutes phylum represents a distantly related phylum in which no complex I enzymes were identified. Abbreviations: C. Amoebophilus asiaticus, “Candidatus Amoebophilus asiaticus”; Blattabacterium sp. B. germ, Blattabacterium sp. Blattella germanica; Anaeromyxo. sp. Fw109-5; Anaeromyxobacter sp. Fw109-5; Syntrophobact. fumaroxidans, Syntrophobacter fumaroxidans; Pseudoxanthomonas s., Pseudoxanthomonas suwonensis; Pseuodoaltero. sp. SM9913, Pseudoalteromonas sp. SM9913; Actinobacillus pleuro., Actinobacillus pleuropneumoniae. Download Figure S8, PDF file, 1.7 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Set S2
KEGG modules enriched in Actinobacteria, Bacteroidetes, Chloroflexi, Deltaproteobacteria, and Spirochaetes with complex I or in clade B-containing, clade E-containing Gammaproteobacteria. Download Data Set S2, XLSX file, 0.1 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Set S1
Genomes used in the study and their associated metadata. Download Data Set S1, XLSX file, 0.1 MB.
Copyright © 2015 Spero et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Additional Files
Supplementary Data
Supplementary Data
Files in this Data Supplement:
- Figure sf1, PDF - Figure sf1, PDF
- Figure sf2, PDF - Figure sf2, PDF
- Figure sf3, PDF - Figure sf3, PDF
- Figure sf4, PDF - Figure sf4, PDF
- Figure sf5, PDF - Figure sf5, PDF
- Figure sf6, PDF - Figure sf6, PDF
- Figure sf7, PDF - Figure sf7, PDF
- Figure sf8, PDF - Figure sf8, PDF
- Dataset sd1, XLSX - Dataset sd1, XLSX
- Dataset sd2, XLSX - Dataset sd2, XLSX
