Skip to main content

Table 4 Ancient metabolic pathways

From: Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

Species Pathways Status Enzymes Genes Starting molecule Final product
Clostridium sp. CADE PreQ0 biosynthesis Complete GTP cyclohydrolase I folE guanosine 5′-triphosphate (GTP) 7-cyano-7-deazaguanine (preQ0)
6-carboxy-5,6,7,8-tetrahydropterin synthase queD
7-carboxy-7-deazaguanine synthase queE
7-cyano-7-deazaguanine synthase queC
β-d-glucuronide and d-glucuronate degradation Complete β-d-glucuronidase uidA β-d-glucuronoside d-fructuronate
d-glucuronate isomerase uxaC
d-mannonate oxidoreductase uxuB
d-mannonate dehydratase uxuA
2-keto-3-deoxygluconokinase kdgK
2-keto-3-deoxygluconate 6-phosphate aldolase eda
Flavin biosynthesis I Partial bifunctional riboflavin kinase/FMN adenylyltransferase ribF Guanosine 5′-triphosphate (GTP) Flavin adenine dinucleotide (FAD)
5-amino-6-(5-phospho-d-ribitylamino) uracil phosphatase ybjI
3,4-dihydroxy-2-butanone 4-phosphate synthase ribB
Biotin biosynthesis from 8-amino-7-oxononanoate I Partial Biotin synthase bioB 8-amino-7-oxononanoate (KAPA) Vitamin H (biotin)
Biotin biosynthesis from 8-amino-7-oxononanoate II Partial Biotin synthase bioB 8-amino-7-oxononanoate (KAPA) Vitamin H (biotin)
Sucrose degradation I (sucrose phosphotransferase) Absent Sucrose β-d-fructofuranose 6-phosphate (F6P)
C. algidicarnis CALG Myo-, chiro- and scillo-inositol degradation Partial (methyl) malonate-semialdehyde dehydrogenase gene mmsA Inositol Glycerone phosphate (DHAP) + acetyl-CoA
Myo-inositol degradation Partial (methyl) malonate-semialdehyde dehydrogenase gene mmsA Inositol Glycerone phosphate (DHAP) + acetyl-CoA
P. fluorescens PFLU KDO transfer to lipid IVA I Absent CMP-3-deoxy-β-d-manno-octulosonate α-Kdo-(2- > 4)-α-Kdo-(2- > 6)-lipid IVA
KDO transfer to lipid IVA II Absent CMP-3-deoxy-β-d-manno-octulosonate 4-O-phospho-α-Kdo-(2 → 6)-lipid IVA
P. veronii PVER Pyochelin biosynthesis Absent l-cysteine Pyochelin
4-hydroxyphenylacetate degradation Complete 4-coumarate 3-monooxygenase hpaB 4-hydroxyphenylacetate Succinate