TABLE 5.
Features deduced from genomic analysis of LCP-89 genomes assembled from Zodletone Spring sediment in comparison to genomes of sister phyla SM23-31, AABM5-125-24, KSB1, and Calditrichota
| Featureb | Presence ina: |
||||
|---|---|---|---|---|---|
| LCP-89 | SM23-31 | KSB1 | AABM5-125-24 | Calditrichota | |
| Structural features | |||||
| Cell wall | |||||
| LPS biosynthesis | ✓ | ✓ | ✓ | ✓ | ✓ |
| Peptidoglycan (Gram negative) | ✗ | ✓ | ✓ | ✓ | ✓ |
| S-layer homology domain protein | ✓ | ✓ | ✓ | ✗ | ✓ |
| CMP-legionaminate biosynthesis from UDP-N, N'-diacetylbacillosamine | ✓ | ✗ | ✗ | ✗ | Partial (1 genome) |
| Cell membrane glycerophospholipid | |||||
| Phosphatidyl glycerol | ✓ | ✓ | ✓ | ✓ | ✓ |
| Cardiolipin | ✗ | ✗ | ✓ | ✓ | ✓ |
| Phosphatidylserine | ✓ | ✓ | ✓ | ✓ | ✓ |
| Phosphatidyl ethanolamine | ✓ | ✓ | ✓ | ✓ | ✓ |
| Flagellar motility | ✗ | ✓ | ✓ | ✓ | ✓ |
| Type IV pilus assembly | ✓ | ✓ | ✗ | ✓ | ✓ |
| Chemotaxis | ✓ | ✓ | ✓ | ✓ | ✓ |
| Cell shape | |||||
| Rod-shape determining RodA/MreBCD | ✓ | ✓ | ✓ | ✓ | ✓ |
| Bacterial microcompartments (BMC) | ✓ | ✓ | ✓ | ✓ | ✓ |
| Defense mechanisms | |||||
| CRISPR-Cas system | ✓ | ✓ | ✓ | ✓ | ✓ |
| Restriction endonucleases | |||||
| Type I | ✓ | ✓ | ✓ | ✓ | ✓ |
| Type II | ✓ | ✓ | ✓ | ✓ | ✓ |
| Type III | ✓ | ✓ | ✓ | ✓ | ✓ |
| Oxidative stress | |||||
| Superoxide dismutase | |||||
| Fe/Mn family | ✓ | ✓ | ✓ | ✗ | ✓ |
| Ni family | ✓ | ✗ | ✓ | ✗ | ✓ |
| Cu/Zn family | ✓ | ✗ | ✗ | ✗ | ✓ |
| Catalase | ✗ | ✓ | ✓ | ✓ | ✓ |
| Peroxidase | ✗ | ✗ | ✓ | ✗ | ✗ |
| Rubrerythrin | ✓ | ✓ | ✓ | ✓ | ✓ |
| Rubredoxin | ✓ | ✓ | ✓ | ✗ | ✓ |
| Alkylhydroperoxide reductase | ✓ | ✗ | ✓ | ✓ | ✓ |
| Superoxide reductase | ✓ | ✓ | ✗ | ✓ | ✓ |
| Biosynthesis | |||||
| Gluconeogenesis | |||||
| Glyceraldehyde-3-P dehydrogenase | |||||
| NAD-dependent (EC 1.2.1.12) | ✓ | ✓ | ✓ | ✓ | ✓ |
| NADP-dependent (EC 1.2.1.9) | ✓ | ✓ | ✗ | ✓ | ✗ |
| NAD(P)-dependent (EC 1.2.1.59) | ✗ | ✗ | ✗ | ✓ | ✗ |
| Phosphoglycerate mutase | |||||
| 2,3-diphosphoglycerate-dependent (EC 5.4.2.11) | ✗ | ✓ | ✗ | ✓ | ✗ |
| 2,3-diphosphoglycerate-independent (EC 5.4.2.12) | ✓ | ✓ | ✓ | ✓ | ✓ |
| Reversal of pyruvate kinase via: | |||||
| Pyruvate phosphate dikinase (EC 2.7.9.1) | ✓ | ✓ | ✓ | ✓ | ✓ |
| Pyruvate water dikinase (EC 2.7.9.2) | ✓ | ✗ | ✗ | ✓ | ✗ |
| Pyruvate carboxylase (EC 6.4.1.1) and PEP carboxykinase (ATP) (EC 4.1.1.49) | ✗ | ✗ | ✓ | ✓ | ✗ |
| Pentose phosphate pathway | |||||
| Oxidative branch | ✓ | ✗ | ✓ | ✗ | ✓ |
| Nonoxidative branch | ✓ | ✓ | ✓ | ✓ | ✓ |
| Amino acids | |||||
| Asp from oxaloacetate | ✓ | ✓ | ✓ | ✓ | ✓ |
| Asn from Asp | ✓ | ✗ | ✓ | ✓ | ✓ |
| Glu from alpha-ketoglutarate | ✓ | ✓ | ✓ | ✓ | ✓ |
| Gln from Glu | ✓ | ✓ | ✓ | ✓ | ✓ |
| Cys from Ser | ✓ | ✓ | ✓ | ✗ | ✓ |
| Ser from Gly | ✓ | ✓ | ✓ | ✓ | ✓ |
| Thr from Gly | ✓ | ✓ | ✓ | ✓ | ✓ |
| Gly from Ser | ✓ | ✓ | ✓ | ✓ | ✓ |
| Met from Cys | ✓ | ✓ | ✓ | ✗ | ✓ |
| Lys (diaminopimelate intermediates) | ✓ | ✓ | ✓ | ✓ | ✓ |
| Arg from Glu | ✗ | ✗ | ✓ | ✗ | ✓ |
| Val | ✓ | ✓ | ✓ | ✗ | ✓ |
| Leu | ✓ | ✓ | ✓ | ✓ | ✓ |
| Ile | ✓ | ✓ | ✓ | ✗ | ✓ |
| Tyr | ✓ | ✓ | ✓ | ✓ | ✓ |
| Phe | ✓ | ✓ | ✓ | ✓ | ✓ |
| Trp | ✗ | ✓ | ✓ | ✗ | ✓ |
| Ala | ✓ | ✓ | ✗ | ✓ | ✓ |
| His | ✓ | ✓ | ✓ | ✗ | ✓ |
| Pro | ✓ | ✓ | ✓ | ✓ | ✓ |
| Cofactor biosynthesis | |||||
| Thiamine biosynthesis | ✗ | ✗ | ✓ | ✗ | ✗ |
| Thiamine salvage | ✓ | ✓ | ✓ | ✓ | ✓ |
| Riboflavin | ✓ | ✓ | ✓ | ✓ | ✓ |
| Pyridoxal-phosphate | ✓ | ✓ | ✓ | ✓ | ✓ |
| NAD/NADP | ✓ | ✓ | ✓ | ✓ | ✓ |
| Pantothenate | ✓ | ✓ | ✓ | ✓ | ✓ |
| Coenzyme A | ✓ | ✓ | ✓ | ✓ | ✓ |
| Acyl-carrier protein | ✓ | ✓ | ✓ | ✓ | ✓ |
| Biotin biosynthesis from pimelate | ✗ | ✗ | ✗ | ✗ | ✗ |
| Biotin import (via energy coupling factor transport system) and then ligation to enzymes | ✓ | ✓ | ✓ | ✓ | ✓ |
| Lipoic acid biosynthesis from octanoyl-ACP | ✓ | ✗ | ✓ | ✗ | ✗ |
| Lipoic acid salvage | ✗ | ✗ | ✓ | ✓ | ✓ |
| Folate biosynthesis from GTP | ✓ | ✓ | Partial | Partial | ✓ |
| Molybdenum cofactor from GTP | ✓ | ✗ | ✗ | ✗ | ✗ |
| Heme biosynthesis from Glu | ✗ | ✓ | ✗ | Partial | ✓ |
| MEP/DOXP pathway for terpenoid backbone biosynthesis | ✓ | ✓ | ✓ | ✓ | ✓ |
| Mevalonate pathway for terpenoid backbone biosynthesis | ✗ | ✗ | ✓ | ✗ | ✓ |
| Menaquinone biosynthesis from terpenoids and chorismate | ✗ | ✗ | ✗ | ✗ | ✓ |
| Menaquinone biosynthesis from terpenoids and isochorismate | ✗ | ✗ | ✓ | ✓ | ✗ |
| Catabolism | |||||
| Sugar catabolism to central metabolites | |||||
| Glucose (EMP) | ✓ | ✓ | ✓ | ✓ | ✓ |
| Glucose (Entner-Doudoroff pathway) | ✓ | ✓ | ✗ | ✗ | Partial |
| Mannose | ✓ | ✓ | ✓ | ✓ | ✓ |
| Galactose | Partial | ✓ | ✓ | ✗ | ✓ |
| Fructose | ✓ | ✓ | ✓ | ✗ | ✓ |
| Mannitol-1-P | ✗ | ✓ | ✗ | ✗ | ✗ |
| Fucose | ✗ | ✓ | ✓ | ✗ | ✓ |
| Sorbitol | ✓ | ✗ | ✓ | ✗ | ✓ |
| Rhamnose | ✓ | ✗ | ✓ | ✗ | ✗ |
| Xylose | ✓ | ✓ | ✓ | ✗ | ✓ |
| Xylitol | ✓ | ✓ | ✓ | ✗ | ✓ |
| Arabinose | ✗ | ✓ | ✓ | ✗ | ✗ |
| Lactose | ✓ | ✓ | ✓ | ✓ | ✓ |
| Amino acid catabolism | |||||
| Ala | ✓ | ✓ | ✗ | ✓ | ✓ |
| Asp | ✓ | ✓ | ✓ | ✓ | ✓ |
| Asn | ✗ | ✓ | ✓ | ✗ | ✓ |
| Glu | ✓ | ✓ | ✓ | ✓ | ✓ |
| Gln | ✗ | ✗ | ✗ | ✓ | ✗ |
| His | ✗ | ✓ | ✓ | ✓ | ✓ |
| Met | ✗ | ✓ | ✓ | ✓ | ✓ |
| Cys | ✗ | ✓ | ✓ | ✓ | ✓ |
| Ser | ✗ | ✓ | ✓ | ✓ | ✓ |
| Thr | ✓ | ✓ | ✓ | ✓ | ✓ |
| Gly | ✓ | ✓ | ✓ | ✓ | ✗ |
| Val | ✗ | Partial | Partial | ✓ | ✓ |
| Leu | ✗ | Partial | Partial | Partial | ✓ |
| Ile | ✗ | Partial | Partial | Partial | ✓ |
| Lys | ✗ | ✗ | ✗ | ✗ | ✓ |
| Pro | ✓ | ✓ | ✓ | ✓ | ✓ |
| Products of metabolism | |||||
| Fate of pyruvate | |||||
| Pyruvate to acetyl-CoA | |||||
| Pyruvate:ferredoxin oxidoreductase | ✓ | ✓ | ✓ | ✓ | ✓ |
| Pyruvate dehydrogenase | ✓ | ✓ | ✓ | ✓ | ✓ |
| Acetyl-CoA to acetate | |||||
| Acetyl-CoA synthetase (EC 6.2.1.1) | ✗ | ✓ | ✓ | ✓ | ✓ |
| Phosphate acetyltransferase and acetate kinase (EC 2.3.1.8 and EC 2.7.2.1) | ✓ | ✓ | ✓ | ✓ | ✓ |
| Ethanol production from acetyl-CoA | ✓ | ✓ | ✗ | ✓ | ✓ |
| Formate production from pyruvate | ✗ | ✓ | ✓ | ✗ | ✓ |
| l-Lactate production from pyruvate | ✗ | ✓ | ✓ | ✗ | ✗ |
| d-Lactate production from pyruvate | ✓ | ✗ | ✗ | ✗ | ✓ |
| Acetoin production from pyruvate (via acetolactate) | ✓ | ✓ | ✓ | ✗ | ✗ |
| Butanediol production from acetoin | ✓ | ✓ | ✓ | ✗ | ✗ |
| Propanol production from fucose/rhamnose degradation | ✓ | ✓ | ✓ | ✗ | ✓ |
| Propionate production from fucose/rhamnose degradation | ✓ | ✓ | ✓ | ✗ | ✓ |
| TCA cycle | ✓ | ✓ | ✓ | ✓ | ✓ |
| Respiration | |||||
| NADH dehydrogenase (complex I) | Partial | ✓ | Partial | ✓ | ✓ |
| Succinate dehydrogenase (complex II) | Partial | ✓ | ✓ | ✓ | ✓ |
| Cytochrome c reductase (complex III) | ✗ | ✓ | ✓ | ✓ | ✓ |
| Cytochrome bd respiratory O2 reductase (high O2 affinity, complex IV) | ✗ | ✓ | ✗ | ✓ | ✓ |
| Cytochrome c oxidase (complex IV) | |||||
| aa3 (low O2 affinity) | ✗ | ✗ | ✓ | ✗ | ✓ |
| cbb3 (high O2 affinity) | ✗ | ✗ | ✗ | ✓ | ✗ |
| ATP synthase (complex V) | Both F and V type | F type | Both F and V type | F type | F type |
| Dissimilatory nitrite reduction to ammonia | |||||
| Periplasmic nitrate reductase NapAB (EC 1.7.99.4) | ✗ | ✗ | ✗ | ✗ | ✓ |
| Nitrite reductase NADH (EC 1.7.1.15) | ✗ | ✗ | ✗ | ✗ | ✓ |
| Nitrite reductase (cytochrome; ammonia forming) (EC 1.7.2.2) | ✓ | ✗ | ✗ | ✓ | ✗ |
| Sulfur reduction via polysulfide (EC 1.12.98.4) | ✓ | ✓ | ✗ | ✗ | ✓ |
| Thiosulfate reductase/polysulfide reductase | ✗ | ✓ | ✗ | ✗ | ✓ |
| Thiosulfate/tetrathionate interconversion | |||||
| Thiosulfate dehydrogenase | ✗ | ✗ | ✓ | ✗ | ✓ |
| Tetrathionate reductase | ✗ | ✗ | ✗ | ✗ | ✓ |
| Dissimilatory sulfate reduction | |||||
| Dissimilatory sulfite reductase | ✗ | ✗ | ✗ | ✓ | ✗ |
| Sulfate adenylyltransferase | ✗ | ✗ | ✗ | ✓ | ✗ |
| Adenylylsulfate reductase | ✗ | ✗ | ✗ | ✓ | ✗ |
| Quinone-interacting, membrane-bound oxidoreductase complex (QmoABC) | ✗ | ✗ | ✗ | ✓ | ✗ |
a
Information in this table is based on genomic analysis of incomplete genomes, and care should be taken in interpreting the results on auxotrophies or the partial presence of certain pathways, as these could be due to the incompleteness of the genomes. However, a check mark (✓) denotes that a complete set of genes mediating a specific pathway were identified in the genomes. An ✗ denotes the complete absence of the pathway.
b
CRISPR-Cas, clustered regularly interspaced short palindromic repeat–CRISPR-associated protein; MEP/DOXP pathway, 2-C-methyl-d-erythritol 4-phosphate/1-deoxy-d-xylulose 5-phosphate pathway; EMP, Embden-Meyerhof pathway.