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. 2003 May;185(10):2980–2987. doi: 10.1128/JB.185.10.2980-2987.2003

TABLE 1.

Methylotrophy genes in M. extorquens AM1

Gene Function Cluster Essential for C1 growtha Metabolic moduleb Previous name Accession no. Source or reference
Primary oxidation
    mxaW Unknown 1 − MOX moxW M31108 41
    mxaF Methanol dehydrogenase large subunit 1 + MOX moxF M31108 1, 2, 26
    mxaJ Unknown 1 + MOX moxJ M31108 1, 2, 26
    mxaG Cytochrome c1 1 + MOX moxG X07856 1, 2, 26, 30
    mxaI Methanol dehydrogenase small subunit 1 + MOX moxI X15792 1, 26, 30, 31
    mxaR Unknown 1 + MOX moxR Y07864 1, 26, 44
    mxaS Unknown 1 + MOX moxS L41608 1, 26, 44
    mxaA Essential for Ca2+ insertion into MDH 1 + MOX moxA L41608 1, 26, 29
    mxaC Essential for Ca2+ insertion into MDH 1 + MOX moxC L41608 1, 26, 29, 44
    mxaK Essential for Ca2+ insertion into MDH 1 + MOX moxK L41608 1, 26, 29
    mxaL Essential for Ca2+ insertion into MDH 1 + MOX moxL L41608 1, 26, 29
    mxaD Essential for Ca2+ insertion into MDH 1 − MOX L41608 1, 26, 29, 44
    mxaE Unknown 1 + MOX AF017434 41
    mxaH Unknown 1 NM MOX AF017434 41
    mxaB Transcriptional regulator 1 + MOX moxB AF017434 41
    mxbD Sensor kinase 2 + MOX moxD AF032114 42
    mxbM Transcriptional regulator 2 + MOX moxM AF032114 42
    pqqA PQQ synthesis 2 − PQQ-S pqqD, moxT L25889 26, 45, 46
    pqqB PQQ synthesis 2 + PQQ-S pqqG, moxO U72662 26, 45
    pqqC/D PQQ synthesis 2 + PQQ-S pqqB, pqqC, moxV, moxT L25889/U72662 26, 45
    pqqE PQQ synthesis 2 + PQQ-S pqqA, moxC U72662 26, 45
    mxcQ Sensor kinase 3 + MOX moxQ 26, 42
    mxcE Transcriptional regulator 3 + MOX moxE 26, 42
    pqqF PQQ synthesis 4 + PQQ-S pqqE, moxH L43135 26, 43
    pqqG PQQ synthesis 4 + PQQ-S pqqF, moxU L43135 26, 43
    mauF Unknown 5 + MAU L26406 5
    mauB Methylamine dehydrogenase large subunit 5 + MAU L26406 5
    mauE Essential for small subunit maturation 5 + MAU L26406 5
    mauD Essential for small subunit maturation 5 + MAU L26406 5
    mauA Methylamine dehydrogenase small subunit 5 + MAU L26406 5
    mauC Amicyanin 5 + MAU L26406 5
    mauJ Unknown 5 − MAU L26406 5
    mauG Unknown 5 + MAU L26406 5
    mauI Unknown 5 + MAU L26406 5
    mauM Unknown 5 − MAU L26406 5
    mauN Unknown 5 − MAU L26406 5
Formate oxidation
    fdh1A Tungsten-dependent formate dehydrogenase, α subunit 6 − FOX1 AF489516 25
    fdh1B Tungsten-dependent formate dehydrogenase, β subunit 6 − FOX1 AF489516 25
    fdh2A Molybdenum-dependent formate dehydrogenase, α subunit 7 − FOX2 AY183757 Unpublished
    fdh2B Molybdenum-dependent formate dehydrogenase, β subunit 7 − FOX2 AY183757 Unpublished
    fdh2C Molybdenum-dependent formate dehydrogenase, γ subunit 7 − FOX2 AY183757 Unpublished
    fdh2D Molybdenum-dependent formate dehydrogenase, δ subunit 7 − FOX2 AY183757 Unpublished
    fdh3A Cytochrome-linked formate dehydrogenase, α subunit 8 − FOX3 AY181035 Unpublished
    fdh3B Cytochrome-linked formate dehydrogenase, β subunit 8 − FOX3 AY181035 Unpublished
    fdh3C Cytochrome-linked formate dehydrogenase, γ subunit 8 − FOX3 AY181035 Unpublished
C1 transfer
    dmrA Dihydromethanopterin reductase 9 + H4MPT-T AY093431 28
    fae Formaldehyde activating enzyme 2 + H4MPT-T orf18 AF032114 52
    mtdB Methylene-H4MPT dehydrogenase 2 + H4MPT-T orfX AF032114 15, 18
    mch Methenyl-H4MPT cyclohydrolase 2 + H4MPT-T orfZ AF032114 15, 36
    fhcA Formyltransferase/hydrolase complex, α subunit 2 + H4MPT-T orf1 AF032114 15, 34, 35
    fhcB Formyltransferase/hydrolase complex, β subunit 2 + H4MPT-T orf2 AF032114 15, 34, 35
    fhcC Formyltransferase/hydrolase complex, γ subunit 2 + H4MPT-T orf3 AF032114 15, 34, 35
    fhcD Formyltransferase/hydrolase complex, δ subunit 2 + H4MPT-T ffsA AF032114 15, 34, 35
    orf4 H4MPT biosynthesis 2 + H4MPT-T AF032114 15, 38
    orf5 Unknown 2 − H4MPT-T AF032114 15
    orf7 Cofactor biosynthesis 2 + H4MPT-T AF032114 15
    orf9 Cofactor biosynthesis 2 + H4MPT-T AF032114 15
    orf17 Cofactor biosynthesis 2 + H4MPT-T AF032114 15
    orf19 Cofactor biosynthesis 2 + H4MPT-T AY117134 Unpublished
    orf20 Cofactor biosynthesis 2 + H4MPT-T AY117134 Unpublished
    orf21 Cofactor biosynthesis 2 + H4MPT-T AY117134 Unpublished
    orf22 Cofactor biosynthesis 2 + H4MPT-T AY117134 Unpublished
    orfY Unknown 2 − H4MPT-T AF032114 15
    mtdA Methylene-H4MPT/Methylene-H4F dehydrogenase 2 + H4F-T/H4MPT-T L27235 9, 16, 17, 51
    fch Methenyl-H4F cyclohydrolase 2 + H4F-T orf4 L33465 36
    ftfL Formyl-H4F ligase 10 + H4F-T 28
    folK 2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase 2 E H4F-S folA U72662 13
    folB Dihydroneopterin aldolase 2 E H4F-S folB U72662 13
    folP Dihydropteroate synthase 2 E H4F-S folC U72662 13
    folE GTP cyclohydrolase 11 E H4F-S AY183759 Unpublished
    folC Dihydrofolate synthase 12 E H4F-S AY183760 Unpublished
    dyr Dihydrofolate reductase 13 NM H4F-S dfrA AY093432 28
C1 assimilation
    sga Serine glyoxylate aminotransferase 2 + QSC sgaA L27235 9
    hpr Hydroxupyruvate reductase 2 + QSC hprA L27235 7, 8, 9
    ppc PEP carboxylase 2 + QSC ppcA U72662 4
    mtkA Malate thiokinase, α subunit 2 + QSC/GRC L33465 10
    mtkB Malate thiokinase, β subunit 2 + QSC/GRC L33465 10
    mcl Malyl-CoA lyase 2 + QSC/GRC mclA U72662 4, 13
    glyA Serine hydroxymethyltrasferase 14 + QSC L33463 11
    gck Glycerate kinase 15 + QSC gckA U87316 14
    eno Enolase 16 E QSC/GNG AY181039 Unpublished
    mdh Malate dehydrogenase 17 E QSC/TCAC AY181040 Unpublished
    qscR Serine cycle transcriptional regulator 18 + QSC AF516903 20
    phaA β-ketothiolase 19 + GRC/PHBC AF287907 22, 23, 24
    phaB Acetoacetyl-CoA reductase 19 + GRC/PHBC AF287907 22, 23, 24
    phaR Regulator of PHB synthesis and acetyl-CoA flux 19 + GRC/PHBC orf3 AF287907 23, 24
    croR Crotonase 20 + GRC AF416777 22
    pccA Propionyl-CoA carboxylase, α subunit 21 + GRC AY181038 22
    pccB Propionyl-CoA carboxylase, β subunit 22 + GRC pccA L48340 12, 22
    crr Crotonyl-CoA reductase 22 + GRC adhA L48340 12, 22
    meaA A mutase 22 + GRC U28335 12, 22, 40
    meaB Essential for methylmalonyl-CoA mutase reaction 22 + GRC AF416776 22
    meaC Unknown 23 + GRC 28
    meaD Unknown 24 + GRC 28
    ibd2 Isobutyryl-CoA dehydrogenase 25 + GRC AY054980 22
    mcmA Methylmalonyl-CoA mutase, α subunit 26 + GRC AY181037 22
    mcmB Methylmalonyl-CoA mutase, β subunit 27 + GRC 22
    epm Epimerase 28 + GRC AY183758 Unpublished
    sdhA Succinate dehydrogenase flavoprotein subunit 29 EG GRC/TCAC AY181036 48, 49
    sdhB Succinate dehydrogenase iron-sulfur binding subunit 29 NM GRC/TCAC AY181036 48, 49
    sdhC Succinate dehydrogenase cytochrome B556 subunit 29 NM GRC/TCAC AY181036 48, 49
    sdhD Succinate dehydrogenase membrane anchor subunit 29 NM GRC/TCAC AY181036 48, 49
    fumA Fumarase 13 EG GRC/TCAC AF497854 49
a

+, mutation impairs growth on a C1 compound; −, mutation does not impair growth on a C1 compound; NM, no mutant available: involvement in methylotrophy implicated by regulation, location, or phenotype of mutant in other subunit(s); E, essential for both methylotrophic and heterotrophic growth; EG, growth on C1 compounds rescued by glyoxylate.

b

Metabolic module designations: MOX, methanol oxidation; PQQ-S, PQQ biosynthesis; MAU, methylamine utilization; H4F-T, H4F-linked C1 transfer; H4F-S, H4F biosynthesis; H4MPT-TS, H4MPT-linked C1 transfer and H4MPT biosynthesis; FOX1, FOX2, and FOX3, three nonhomologous formate dehydrogenases; QSC, (Quayle) serine cycle; PHBC, PHB cycle; TCAC, TCA cycle.