Biosynthesis of Tetrapyrrole Cofactors by Bacterial Community Inhabiting Porphyrine-Containing Shale Rock (Fore-Sudetic Monocline)
Abstract
:1. Introduction
2. Results
2.1. Taxonomic Diversity of BC Inhabiting Black Shale
2.2. General Characteristics of the Metagenome and Metaproteome of BC
2.3. Biosynthesis of Cofactors Detected in the Studied BC
2.3.1. Uroporphyrinogen III Biosynthesis
2.3.2. Siroheme Biosynthesis
2.3.3. Heme Biosynthesis
Protoporphyrin-Dependent Heme Biosynthetic Pathway
Coproporphyrin-Dependent Heme Biosynthetic Pathway
Siroheme-Dependent Heme Biosynthetic Pathway
2.3.4. Cobalamin Biosynthesis
Biosynthesis of Anaerobic and Aerobic Cob(II)yrinate a,c-Diamide
Biosynthesis of Cobalamin from Cob(II)yrinate a,c-Diamide
2.3.5. Transport of Exogenous Porphyrins
2.3.6. Tetrapyrrole Cofactor-Containing Enzymes Produced by BC
3. Discussion
4. Materials and Methods
4.1. Site and Sample Description
4.2. Isolation of DNA
4.3. Sequencing and Analysis of DNA
4.4. Isolation of Proteins
4.5. Identification of Proteins
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Organic Compound | Name | Reference |
---|---|---|
Primary geoporphyrins | Iron aetioporphyrins (octaethyl porphyrins), | [8] |
Iron cycloalkanoporphyrins | ||
Iron di-cycloalkanoporphyrins | ||
Iron benz-cycloalkanoporphyrins | ||
Vanadyl-cycloalkano-porphyrins | [9] | |
Etio and DPEP iron porphyrins | [10] | |
Etio,DPEP benzo-etio and benzo-DPEP vanadyl porphyrins | ||
Vanadyl porphyrins of series etio/DPEP | [11] | |
Octaethyl nickel porphyrin | [12] | |
Octaethyl vanadyl porphyrin | ||
Meso-tetraphenyl vanadyl porphyrin | ||
Meso-tetraphenyl nickel porphyrin | ||
Protoporphyrin IX cobalt | ||
Modified geoporphyrins | Diphenyl vanadyl porphyrin | [12] |
Tetraethyl vanadyl porphyrin | ||
Vanadyl porphyrin | ||
Tetraethyl nickel porphyrin | ||
Nickel porphyrin | ||
Organic compounds containing 3 pyrrole rings | 3-[2-[[3-(2-Carboxyethyl)-5-[(3.4-dimethyl-5-oxopyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl]methylidene]-4-methyl-5-oxopyrrol-3-yl]propanoic acid | [12] |
3-[(5Z)-5-[[4-Ethenyl-5-[(Z)-(4-ethenyl-3-methyl-5-oxopyrrol-2-ylidene)methyl]-3-methyl-1H-pyrrol-2-yl]methylidene]-4-methyl-2-oxopyrrol-3-yl]propanoate | ||
Organic compounds containing 2 pyrrole rings | 3,3′-Bipyrrole | |
2,2′-Bipyrrole | ||
1,1′-Bipyrrole-2,2′,5,5′-tetraone | ||
3,3′,4,4′-Tetramethyl-1H,1′H-2,2′-bipyrrole-5,5′-dicarboxylic acid | ||
Organic compounds containing 1 pyrrole ring | 1H-Pyrrole | |
1H-Pyrrole-2-carboxylic acid | ||
2H-Pyrrol-2-one, 5-[[2-[(4-aminophenyl)methylene]-3,4-dimethyll]methylene]-3-ethyl-1,5-dihydro-4-methyl | ||
Indole acetic acid | ||
1H-Indole-2-carboxylic acid | ||
Indole carbaldehyde | ||
1H-pyrrole-2,5-diones | [13] |
Enzyme | Accession | Score | Seq(sig) | emPAI | Genus/Species |
---|---|---|---|---|---|
Heme-Containing Cytochromes | |||||
cbb3-type cytochrome c oxidase subunit ii | gi|653251020 | 62 | 1 | 0.19 | Dechloromonas agitata |
cb-type cytochrome c oxidase ccoo subunit | gi|4519209 | 55 | 1 | 0.12 | Magnetospirillum magnetotacticum |
cytochrome b6 | gi|499245897 | 128 | 2 | 0.13 | Geobacter sulfurreducens |
cytochrome b6 | gi|493924522 | 117 | 2 | 0.13 | Legionella drancourtii |
cytochrome bd-type quinol oxidase, subunit 1 | gi|493975388 | 67 | 1 | 0.07 | Desulfovibrio magneticus |
cytochrome c | gi|504001995 | 71 | 2 | 0.1 | Azospira oryzae |
cytochrome c oxidase cbb3-type, subunit iii | gi|330949201 | 56 | 1 | 0.77 | Pseudomonas syringa. 1704B |
cytochrome c1 | gi|268584477 | 58 | 1 | 0.11 | Neisseria gonorrhoeae PID18 |
cytochrome cbb3 | gi|499630345 | 55 | 1 | 0.27 | Thiobacillus denitrificans |
cytochrome d ubiquinol oxidase | gi|498185039 | 55 | 1 | 0.06 | Lactobacillus acidipiscis |
cytochrome o ubiquinol oxidase | gi|657198419 | 40 | 1 | 0.12 | Aeromonas caviae |
cytochrome p450 | gi|503190589 | 20 | 1 | 0.1 | Frankia sp. EuI1c |
cytochrome p450 | gi|664433299 | 44 | 1 | 0.07 | Streptomyces sp. NRRL F-5140 |
cytochrome soxa | gi|499630342 | 44 | 1 | 0.11 | Thiobacillus denitrificans |
cytochrome soxa | gi|517333069 | 74 | 1 | 0.11 | Thiobacillus thioparu |
multispecies: cytochrome c | gi|494962102 | 68 | 1 | 0.25 | Sphingobium sp. |
flavocytochrome c sulfide dehydrogenase | gi|519012058 | 39 | 1 | 0.07 | Methylotenera sp. |
succinate dehydrogenase cytochrome b-556 subunit | gi|254672872 | 66 | 1 | 0.39 | Neisseria meningitidis alpha275 |
thiosulfate reductase cytochrome b subunit | gi|488713780 | 61 | 1 | 0.15 | Myxococcus sp. |
Heme-Containing Catalases | |||||
catalase | gi|491324047 | 515 | 11 | 0.84 | Acinetobacter sp.CIP 53.82 |
catalase | gi|3927890 | 86 | 1 | 0.06 | Desulfovibrio vulgaris |
catalase | gi|520401 | 60 | 1 | 0.06 | Haemophilus influenzae |
catalase | gi|500251659 | 103 | 2 | 0.13 | Pseudomonas stutzeri |
catalase | gi|504938131 | 67 | 1 | 0.09 | Synechococcus sp. PCC 6312 |
Heme-Containing Peroxidases | |||||
hydroperoxidase | gi|647531474 | 46 | 1 | 0.04 | Shewanella marina |
hydroperoxidase II | gi|489375670 | 84 | 2 | 0.09 | Pseudomonas stutzeri |
hydroperoxidase II | gi|515815228 | 105 | 2 | 0.09 | Pseudomonas stutzeri |
peroxidase | gi|491142120 | 58 | 1 | 0.14 | Nitrococcus mobilis |
Sirroheme-Containing Enzymes | |||||
nitrite reductase (NAD(P)H) large subunit | gi|159882975 | 62 | 1 | 0.04 | Hydrogenivirga sp. 128-5-R1-1 |
nitrite reductase | gi|491129994 | 58 | 1 | 0.08 | Streptomyces ghanaensis |
nitrite reductase | gi|23392987 | 65 | 1 | 0.14 | uncultured bacterium |
sulfite reductase | gi|521065095 | 689 | 6 | 0.47 | Thiothrix disciformis |
sulfite reductase | gi|655041650 | 53 | 1 | 0.08 | Thiothrix lacustris |
sulfite reductase | gi|488797739 | 2076 | 7 | 1.18 | Thiothrix nivea |
sulfite reductase | gi|488797740 | 251 | 3 | 0.27 | Thiothrix nivea |
dissimilatory sulfite reductase alpha subunit | gi|30525497 | 52 | 1 | 0.08 | uncultured sulfate-reducing bacterium |
reverse-type dissimilatory siroheme sulfite reductase subunit A | gi|162072844 | 2187 | 7 | 1.3 | Thiothrix nivea DSM 5205 |
reverse-type dissimilatory sulfite reductase (rDSR), alpha subunit (DsrA) | gi|385763698 | 48 | 1 | 0.07 | uncultured bacterium 172H5 |
Cobalamin-Containing Enzymes | |||||
methylcrotonoyl-CoA carboxylase | gi|648618195 | 36 | 1 | 0.06 | Niabella aurantiaca |
methylmalonyl-CoA carboxyltransferase | gi|587641191 | 40 | 1 | 0.06 | Skermanella stibiiresistens SB22 |
methionyl-tRNA synthetase | gi|516410008 | 68 | 1 | 0.04 | Erwinia toletana |
methionyl-tRNA synthetase | gi|588476233 | 35 | 1 | 0.04 | Lactobacillus composti JCM 14202 |
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Stasiuk, R.; Krucoń, T.; Matlakowska, R. Biosynthesis of Tetrapyrrole Cofactors by Bacterial Community Inhabiting Porphyrine-Containing Shale Rock (Fore-Sudetic Monocline). Molecules 2021, 26, 6746. https://doi.org/10.3390/molecules26216746
Stasiuk R, Krucoń T, Matlakowska R. Biosynthesis of Tetrapyrrole Cofactors by Bacterial Community Inhabiting Porphyrine-Containing Shale Rock (Fore-Sudetic Monocline). Molecules. 2021; 26(21):6746. https://doi.org/10.3390/molecules26216746
Chicago/Turabian StyleStasiuk, Robert, Tomasz Krucoń, and Renata Matlakowska. 2021. "Biosynthesis of Tetrapyrrole Cofactors by Bacterial Community Inhabiting Porphyrine-Containing Shale Rock (Fore-Sudetic Monocline)" Molecules 26, no. 21: 6746. https://doi.org/10.3390/molecules26216746