Investigating the native functions of [NiFe]-CODH through genomic context analysis
- Molecular Biomimetics, Department of Chemistry – Ångström Laboratory, Uppsala University, Sweden
Figures
Figure 1
Schematic phylogenetic tree of [NiFe]-CODH, with selected CODHs marked with their respective positions.
Tree was built using IQ-TREE, 1000 ultrafast bootstrap, containing 5508 putative CODH sequences and one outgroup (MBE6442607.1 hydroxylamine reductase [Desulfovibrio desulfuricans]) for rooting. A detailed searchable tree with bootstrap values can be found in Supplementary file 5.
Figure 2
Operons of selected [NiFe]-CODH.
* NtCODH, formally known as MtCODH, formerly known as CtCODH due to renaming of host organism (Gtari and Ventura, 2025). ** NvCODH, formerly known as DvCODH due to renaming of host organism (Waite et al., 2020).
Figure 3 with 1 supplement
CODH co-occurence within organisms.
(A) Frequency of X amounts of [NiFe]-CODH from the same clade co-occurring in the same organism. (B) Probability matrix of [NiFe]-CODH from different clades co-occurring in the same organism. The equation for probability can be found in the Methods section. A long table format of the matrix can be found in Supplementary file 2. Additional raw data can also be found in Supplementary file 1.
Figure 3—figure supplement 1
Count of organisms that contain multiple HCP genes.
Raw data can be found in Supplementary file 1.
Figure 4 with 1 supplement
Operon content of CODH encoding operons in different clades.
(A) Phylogenetic tree of putative [NiFe]-CODH unrooted with 1376 sequences. The colored rings mark if the operon from a protein/leaf contains one or more of a certain type of protein using the same coloring as in C. The types of proteins are from center to outer ring: one carbon pool, CooC, CooT, CooJ, ferredoxin, FeS, hydrogenase, hydrogenase-maturase, NAD(P)/FAD-dependent oxidoreductase, regulation, ABC transporter, and transporter. A detailed searchable tree with bootstrap values can be found in Supplementary files 6 and 7. (B) Distribution of operon size for CODH and HCP genes. (C) Proportion of [NiFe]-CODH from one clade being coded near a certain type of protein. The dotted line marks a proportion of 10%, which we set as our significance cutoff. Raw data can be found in Supplementary file 1.
Figure 4—figure supplement 1
Selected neighbors of HCP genes and their proportion in regard to all HCP from one subclass.
Raw data can be found in Supplementary file 1.
Appendix 1—figure 1
Flowchart for the data collection and refinement process.
Numbers in braces refer to the number of sequences in each step, the first number referring to putative CODH sequences, the second number refers to putative HCP sequences. Custom scripts are available online (see Böhm, 2025a; Böhm, 2025b; Böhm, 2025c; Böhm, 2025d).
Additional files
-
Supplementary file 1
Contains information regarding neighbor analysis.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp1-v1.xlsx
-
Supplementary file 2
Contains data on the co-occurrence of CODH/HCP in one organism.
This data was used to create heatmaps in Supplementary files 10 and 11.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp2-v1.csv
-
Supplementary file 3
Contains initial sorting of CODH accession numbers based on their source.
Only sources that were classified as organisms passed and were further used for neighbor analysis.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp3-v1.csv
-
Supplementary file 4
Contains initial sorting of HCP accession numbers based on their source.
Only sources that were classified as organisms passed and were further used for neighbor analysis.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp4-v1.csv
-
Supplementary file 5
CODH phylogenetic tree with 5808 leaves.
Nodes supported with bootstrap values above 0.90 are marked with an orange dot. Ultrafast bootstrapping was performed using 1000 resamplings. Rooted using Desulfovibrio desulfuricans’ HCP (MBE6442607.1).
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp5-v1.zip
-
Supplementary file 6
CODH phylogenetic tree with 1376 leaves.
Nodes supported with bootstrap values above 0.90 are marked with an orange dot. Ultrafast bootstrapping was performed using 1000 resamplings. Unrooted.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp6-v1.zip
-
Supplementary file 7
Same tree as Tree1 with additional operon information.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp7-v1.zip
-
Supplementary file 8
HCP phylogenetic tree with 1476 leaves.
Nodes supported with bootstrap values above 0.90 are marked with an orange dot. Ultrafast bootstrapping was performed using 1000 resamplings. Unrooted.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp8-v1.zip
-
Supplementary file 9
Same tree as Tree3 with additional operon information.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp9-v1.zip
-
Supplementary file 10
Tree based on taxid using ete3 (Huerta-Cepas et al., 2016) from organism with heatmap indicating occurrence of CODH or HCP in an organism.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp10-v1.zip
-
Supplementary file 11
Tree based on tree generated by WoL (Zhu, 2023) from organism with heatmap indicating occurrence of CODH or HCP in an organism.
- https://cdn.elifesciences.org/articles/108780/elife-108780-supp11-v1.zip
-
MDAR checklist
- https://cdn.elifesciences.org/articles/108780/elife-108780-mdarchecklist1-v1.pdf
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Investigating the native functions of [NiFe]-CODH through genomic context analysis
eLife 15:RP108780.
https://doi.org/10.7554/eLife.108780.3
