Diversification of Ferredoxins across Living Organisms
Abstract
:1. Introduction
2. Methodology
2.1. Species and Database
2.2. Genome Data Mining and Annotation of Ferredoxins
2.3. Ferredoxins Subtype Classification and Nomenclature
2.4. Assigning Fe-S Cluster Subtypes to the Ferredoxins Retrieved from the Literature
2.5. Phylogenetic Analysis of Ferredoxins
2.6. Generation of Ferredoxin Subtype Profile Heat Maps
3. Results and Discussion
3.1. Alphaproteobacterial and Firmicutes Species Have Different Fe-S Cluster Type Ferredoxins in Their Genomes
3.2. Highly Diverse and Common Ancestral Origin of Ferredoxins between Alphaproteobacteria and Firmicutes
3.2.1. 2Fe-2S
3.2.2. 3Fe-4S
3.2.3. 4Fe-4S
3.2.4. 7Fe-8S
3.2.5. 2[4Fe-4S]
3.2.6. 2[4Fe-4S]Alv
3.3. Ferredoxin Fe-S Cluster Types Canonical Motifs
3.4. Evolutionary Linkage of Ferredoxins Subtype Classification
3.5. LGT of Ferredoxins
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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2Fe-2S. | ||
---|---|---|
GenBank Accession Number or PDB Code | Species Name | Reference |
NP_004100.1 (Adrenodoxin) | Homo sapiens | [22] |
1PDX (Putidaredoxin) | Pseudomonas putida | [24] |
ABB56370.1 | Synechococcus elongatus PCC 7942 = FACHB-805 | [50] |
ABB56928.1 | Synechococcus elongatus PCC 7942 = FACHB-805 | [50] |
WP_013424358.1 (FraEuI1c_3227) | Frankia sp. EuI1c (Frankia inefficax sp.) | [51] |
WP_012394830.1 (mmi:MMAR_3155) | Mycobacterium marinum | [52] |
3Fe-4S/4Fe-4S | ||
CAB59502.1 | Streptomyces coelicolor A3(2) | [53] |
WP_013425251.1 (FraEuI1c_4132) | Frankia sp. EuI1c (Frankia inefficax sp.) | [51] |
WP_013426476.1 (FraEuI1c_5370) | Frankia sp. EuI1c (Frankia inefficax sp.) | [51] |
WP_011740769.1 (Mmar_2879) | Mycobacterium marinum | [52] |
WP_012395565.1 (Mmar_3973) | Mycobacterium marinum | [52] |
WP_012396301.1 (Mmar_4763) | Mycobacterium marinum | [52] |
NP_215277.1 (FdX-Rv0763c) | Mycobacterium tuberculosis H37Rv | [17,54] |
NP_216302.1 (FdxE-Rv1786) | Mycobacterium tuberculosis H37Rv | [17,54] |
ABB57779.1 | Synechococcus elongatus PCC 7942 = FACHB-805 | [50] |
7Fe-8S | ||
NP_215693 (FdxC-Rv1177), | Mycobacterium tuberculosis H37Rv | [17] |
NP_216523.1 (FdxA-Rv2007c) | Mycobacterium tuberculosis H37Rv | [17] |
2VKR | Acidianus ambivalens | [55] |
1H98 | Thermus thermophilus | [56] |
ABB56846.1 | Synechococcus elongatus PCC 7942 = FACHB-805 | [50] |
2[4Fe-4S] | ||
2ZVS | Escherichia coli K-12 | [27] |
2FDN | Clostridium acidurici | [57] |
WP_013068980.1 (FDI) | Rhodobacter capsulatus | [58] |
2[4Fe-4S]Alv | ||
1BLU | Allochromatium vinosum | [59] |
2FGO | Pseudomonas aeruginosa | [57] |
WP_023923722.1 (FDIII) | Rhodobacter capsulatus | [58] |
1RGV | Thauera aromatica K172 | [60] |
Subtypes | Cysteine Spacing Signature | No. AA | No of Ferredoxins | ||||
---|---|---|---|---|---|---|---|
Alphaproteobacteria | Firmicutes | From Literature | |||||
Archaea | Bacteria | Eukarya | |||||
2Fe-2S | |||||||
Subtype 1 | CX5CX2CX36C | 47 | 296 | 2 | 64 | ||
Subtype 2 | CX5CX2CX37C | 48 | 81 | 1 | 4 | 22 | |
Subtype 3 | CX4CX2CX29C | 39 | 11 | 1 | 7 | 11 | 55 |
Subtype 4 | CX5CX2CX35C | 46 | 12 | 3 | 2 | ||
Subtype 5 | CX5CX2CX38C | 49 | 12 | 1 | |||
Subtype 6 | CX4CX2CX34C | 44 | 11 | 11 | 7 | 1 | |
Subtype 7 | CX4CX2CX51C | 61 | 8 | 1 | |||
Subtype 8 | CX4CX2CX31C | 41 | 7 | 6 | 1 | 1 | |
Subtype 9 | CX4CX2CX33C | 43 | 2 | 3 | 19 | 2 | |
Subtype 10 | CX5CX2CX39C | 50 | 2 | 1 | |||
Subtype 11 | CX4CX2CX35C | 46 | 1 | ||||
Subtype 12 | CX4CX2CX25C | 35 | 1 | ||||
Subtype 13 | CX7CX34CX3C | 48 | 1 | ||||
Subtype 14 | CX4CX29C | 36 | 1 | ||||
Subtype 15 | CX7CX29C | 39 | 1 | ||||
Subtype 16 | CX7CX35C | 45 | 1 | ||||
Subtype 17 | CX5CX2CX33C | 44 | 1 | ||||
Subtype 18 | CX5CX2CX34C | 45 | 2 | 20 | 2 | 1 | 1 |
Subtype 19 | CX5CX2CX35C | 46 | 1 | ||||
Subtype 20 | CX5CX2CX32C | 43 | 44 | 1 | 5 | ||
Subtype 21 | CX4CX31CX3C | 42 | 5 | ||||
Subtype 22 | CX2CX41CX3C | 50 | 2 | ||||
Subtype 23 | CX7CX38CX3C | 52 | 1 | ||||
Subtype 24 | CX4CX2CX30C | 40 | 70 | 1 | |||
Subtype 25 | CX5CX2CX30C | 41 | 1 | ||||
Subtype 26 | CX12CX30CX3C | 49 | 21 | ||||
Subtype 27 | CX12CX31CX3C | 50 | 4 | ||||
Subtype 28 | CX8CX44CX3C | 59 | 3 | ||||
Subtype 29 | CX8CX33CX3C | 48 | 3 | ||||
Subtype 30 | CX8CX32CX3C | 47 | 2 | ||||
Subtype 31 | CX4CX36CX3C | 47 | 1 | 1 | |||
Subtype 32 | CX8CX38CX3C | 53 | 1 | ||||
Subtype 33 | CX8CX39CX3C | 54 | 1 | ||||
Subtype 34 | CX9CX33CX3C | 49 | 1 | ||||
Subtype 35 | CX12CX33CX3C | 52 | 1 | ||||
Subtype 36 | CX3CX1CX38C | 46 | 1 | ||||
Subtype 37 | CX12CX32CX3C | 51 | 1 | ||||
Subtype 38 | CX4CX2CX28C | 38 | 40 | 3 | |||
Subtype 39 | CX4CX2CX46C | 56 | 2 | ||||
Subtype 40 | CX4CX2CX49C | 59 | 3 | ||||
Subtype 41 | CX4CX2CX45C | 55 | 2 | ||||
Subtype 42 | CX4CX2CX65C | 75 | 1 | ||||
Subtype 43 | CX4CX2CX50C | 60 | 2 | ||||
Subtype 44 | CX4CX2CX47C | 57 | 2 | ||||
Subtype 45 | CX4CX2CX48C | 58 | 1 | ||||
Subtype 46 | CX5CX2CX52C | 63 | 2 | ||||
Subtype 47 | CX5CX2CX31C | 42 | 1 | ||||
Subtype 48 | CX5CX2CX28C | 39 | 2 | ||||
Subtype 49 | CX5CX2CX27C | 38 | 10 | ||||
Subtype 50 | CX5CX2CX82C | 93 | 2 | ||||
Subtype 51 | CX5CX2CX29C | 40 | 1 | ||||
Subtype 52 | CX4CX2CX32C | 42 | 1 | ||||
Subtype 53 | CX5CX2CX42C | 53 | 1 | ||||
Subtype 54 | CX4CX2CX22C | 32 | 2 | ||||
Subtype 55 | CX4CX2CX29C | 39 | 2 | ||||
3Fe-4S | |||||||
Subtype 1 | CX5CX38CP | 47 | 26 | 2 | 7 | ||
Subtype 2 | CX5CX37CP | 46 | 16 | 13 | |||
Subtype 3 | CX5CX36CP | 45 | 14 | 2 | |||
Subtype 4 | CX5CX40CP | 49 | 3 | ||||
Subtype 5 | CX5CX36CP | 45 | 1 | ||||
Subtype 6 | CX5CX35CP | 44 | 5 | ||||
Subtype 7 | CX5CX49CP | 58 | 2 | ||||
4Fe-4S | |||||||
Subtype 1 | CX5CX3CX33CP | 46 | 2 | ||||
Subtype 2 | CX2CX2CX43CP | 52 | 107 | ||||
Subtype 3 | CX2CX2CX45CP | 54 | 24 | 1 | |||
Subtype 4 | CX2CX2CX37CP | 46 | 6 | ||||
Subtype 5 | CX2CX2CX44CP | 53 | 2 | ||||
Subtype 6 | CX2CX2CX39CP | 48 | 1 | ||||
Subtype 7 | CX2CX2CX36CP | 45 | 2 | ||||
Subtype 8 | CX2CX2CX34CP | 43 | 1 | ||||
Subtype 9 | CX2CX2CX38CP | 47 | 1 | 1 | |||
Subtype 10 | CX5CX3CX32CP | 45 | 1 | ||||
Subtype 11 | CX5CX3CX30CP | 43 | 12 | ||||
Subtype 12 | CX5CX3CX31CP | 44 | 2 | ||||
7Fe-8S | |||||||
Subtype 1 | CX7CX3CPX17CX2CX2CX3CP * | 43 | 6 | 32 | 13 | ||
Subtype 2 | CX5CX3CPX40CX2CX2CX3CP | 64 | 4 | ||||
Subtype 3 | CX5CX3CPX20CX2CX2CX3CP | 44 | 1 | ||||
Subtype 4 | CX10CX3CPX22CX2CX2CX3CP | 51 | 1 | ||||
Subtype 5 | CX5CX3CPX26CX2CX2CX3CP | 50 | 1 | ||||
Subtype 6 | CX5CX3CPX24CX2CX2CX3CP | 48 | 1 | 1 | |||
Subtype 7 | CX10CX3CPX17CX2CX2CX3CP | 46 | 1 | ||||
Subtype 8 | CX5CX3CPX22CX2CX2CX3CP | 46 | 9 | ||||
Subtype 9 | CX5CX3CPX18CX2CX2CX3C | 42 | 1 | ||||
Subtype 10 | CX3CX3CPX22CX2CX2CX3CP | 44 | 2 | ||||
2[4Fe-4S] | |||||||
Subtype 1 | CX2CX4CX3CX18CX2CX2CX3C | 42 | 267 | ||||
Subtype 2 | CX2CX2CX3CX18CX2CX8CX3C | 46 | 90 | 4 | |||
Subtype 3 | CX2CX2CX3CX20CX2CX2CX3C | 42 | 33 | 2 | 52 | 1 | |
Subtype 4 | CX7CX2CX3CX23CX2CX2CX3C | 50 | 5 | ||||
Subtype 5 | CX2CX2CX3CX42CX2CX2CX3C | 64 | 3 | ||||
Subtype 6 | CX2CX2CX3CX18CX2CX7CX3C | 45 | 2 | ||||
Subtype 7 | CX2CX2CX3CX18CX2CX6CX3C | 44 | 2 | ||||
Subtype 8 | CX2CX2CX3CX24CX2CX2CX3C | 46 | 2 | 2 | |||
Subtype 9 | CX2CX2CX3CX18CX2CX2CX3C | 40 | 1 | 6 | 78 | 3 | 1 |
Subtype 10 | CX2CX2CX3CX21CX2CX2CX3C | 43 | 6 | 2 | |||
Subtype 11 | CX2CX2CX3CX18CX3CX2CX3C | 42 | 2 | ||||
Subtype 12 | CX2CX2CX3CX28CX2CX2CX3C | 50 | 132 | 1 | 2 | ||
Subtype 13 | CX2CX2CX3CX27CX2CX2CX3C | 49 | 2 | ||||
Subtype 14 | CX5CX2CX3CX20CX2CX2CX3C | 45 | 21 | ||||
Subtype 15 | CX2CX2CX3CX19CX2CX2CX3C | 41 | 1 | 4 | 58 | ||
Subtype 16 | CX2CX2CX3CX40CX2CX2CX3C | 50 | 1 | ||||
Subtype 17 | CX2CX2CX3CX29CX2CX2CX3C | 51 | 144 | 2 | |||
Subtype18 | CX4CX2CX3CX18CX2CX2CX3C | 42 | 1 | 1 | |||
Subtype 19 | CX3CX2CX3CX20CX2CX2CX3C | 43 | 2 | ||||
Subtype 20 | CX2CX2CX3CX17CX2CX2CX3C | 39 | 24 | 1 | |||
Subtype 21 | CX3CX3CX3CX37CX1CX3CX3C | 61 | 1 | ||||
Subtype 22 | CX2CX2CX3CX26CX2CX2CX3C | 48 | 6 | ||||
Subtype 23 | CX2CX2CX3CX30CX2CX2CX3C | 52 | 1 | ||||
Subtype 24 | CX2CX2CX3CX33CX2CX2CX3C | 55 | 22 | ||||
Subtype 25 | CX2CX2CX3CX32CX2CX2CX3C | 54 | 23 | ||||
Subtype 26 | CX2CX2CX3CX23CX2CX2CX3C | 45 | 2 | ||||
Subtype 27 | CX2CX2CX3CX34CX2CX2CX3C | 56 | 1 | ||||
Subtype 28 | CX2CX2CX3CX14CX2CX2CX3C | 36 | 2 | ||||
Subtype 29 | CX2CX2CX3CX22CX2CX2CX3C | 44 | 2 | ||||
Subtype 30 | CX2CX2CX2CX38CX2CX2CX3C | 59 | 1 | ||||
Subtype 31 | CX4CX2CX3CX19CX2CX2CX3C | 43 | 24 | ||||
Subtype 32 | CX5CX2CX3CX19CX2CX2CX3C | 44 | 3 | ||||
Subtype 33 | CX2CX2CX3CX16CX2CX2CX3C | 38 | 16 | ||||
2[4Fe-4S]Alv | |||||||
Subtype 1 | CX2CX2CX3CX18CX2CX8CX3CX3C | 50 | 10 | 5 | |||
Subtype 2 | CX2CX2CX3CX39CX2CX2CX3CX3C | 65 | 9 | ||||
Subtype 3 | CX2CX2CX3CX43CX2CX2CX3CX3C | 69 | 5 | 1 | |||
Subtype 4 | CX2CX2CX3CX42CX2CX2CX3CX3C | 68 | 1 | ||||
Subtype 5 | CX2CX2CX3CX40CX2CX2CX3CX3C | 66 | 2 | ||||
Subtype 6 | CX2CX2CX3CX38CX2CX2CX3CX3C | 64 | 1 | ||||
Subtype 7 | CX2CX2CX3CX46CX2CX2CX3CX3C | 72 | 2 | ||||
Subtype 8 | CX2CX2CX3CX44CX2CX2CX3CX3C | 70 | 1 | ||||
Subtype 9 | CX2CX2CX3CX30CX2CX2CX3CX3C | 56 | 2 | ||||
Subtype 10 | CX2CX2CX3CX19CX2CX2CX3CX3C | 45 | 8 |
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Nzuza, N.; Padayachee, T.; Chen, W.; Gront, D.; Nelson, D.R.; Syed, K. Diversification of Ferredoxins across Living Organisms. Curr. Issues Mol. Biol. 2021, 43, 1374-1390. https://doi.org/10.3390/cimb43030098
Nzuza N, Padayachee T, Chen W, Gront D, Nelson DR, Syed K. Diversification of Ferredoxins across Living Organisms. Current Issues in Molecular Biology. 2021; 43(3):1374-1390. https://doi.org/10.3390/cimb43030098
Chicago/Turabian StyleNzuza, Nomfundo, Tiara Padayachee, Wanping Chen, Dominik Gront, David R. Nelson, and Khajamohiddin Syed. 2021. "Diversification of Ferredoxins across Living Organisms" Current Issues in Molecular Biology 43, no. 3: 1374-1390. https://doi.org/10.3390/cimb43030098