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Table 1 List of mutations derived in the Modern AM1 lineage

From: Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance

Single nucleotide polymorphisms   
Chromosome Position Mutation Annotation Gene/Locus Description
META1 611,700 G → A Intergenic (+342/-18) META1_0578/META1_0579 Transcriptional accessory protein/hypothetical protein
META1 2,050,899 G → C S359R (AGG → AGC) META1_1984 Putative catecholate siderophore receptor fiu precursor (TonB-dependent receptor fiu)
META1 2,511,236 C → T L8004F (C TC → T TC) META1_2412 Hypothetical protein
META1 3,795,848 C → T L264F (C TC → T TC) aldB Aldehyde dehydrogenase; chloroacetaldehyde dehydrogenase
META1 4,123,848 C → T Intergenic (-1754/+2180) META1_4038/rffH Fragment of transposase related to IS701 family/glucose-1-phosphate thymidylyltransferase
META1 4,382,526 C → G T160T (ACC → ACG) META1_4292 Plasmid replication protein RepA
META1 4,494,119 A → G N55D (A AC → G AC) rplJ 50S ribosomal subunit protein L10
META1 4,496,733 A → G Q521R (CA G → CG G) rpoB RNA polymerase, beta subunit
META1 4,498,413 A → G Q1081R (CA G → CG G) rpoB RNA polymerase, beta subunit
META1 4,665,003 C → A L300M (C TG → A TG) recG DNA helicase, ATP-dependent resolution of Holliday junctions, branch migration
META1 5,187,175 G → A A260T (G CC → A CC) META1_5044 Putative o-succinylbenzoate--CoA ligase
Small insertions & deletions   
Chromosome Position Mutation Annotation Gene/Locus Description
META1 1,083,921 +1 bp Intergenic (-299/+188) META1_1041/META1_1042 Putative CoxB/conserved hypothetical protein
META1 2,012,135 +5 bp Coding (126-130/228 nt) META1_1939 Hypothetical protein
META1 5,018,430 Δ1 bp Intergenic (-120/+218) META1_4900/META1_4901 Putative hydrolase of beta-lactamase superfamily/conserved hypothetical protein DUF949
META2 821,910 +1 bp Intergenic (+133/-26) META2_0863/META2_0864 AAA superfamily ATPase/hypothetical protein
IS elements    
Chromosome Position Mutation Annotation Gene/Locus Description
META1 772,350 +1408 bp Gain ISMex3; coding META1_0742–META1_0743 META1_0742, META1_0743
META1 929,023 +1390 bp Gain ISMex14; intergenic META1_0895-META1_0898 Transposase of ISMex1, IS3 family (ORF 1)/transposase of ISMex14, IS256 family
META1 3,730,805 +1408 bp Gain ISMex3; coding META1_3592–META1_CDS3732187D META1_3592, META1_3593, META1_CDS3732187D
META1 4,143,329 +1620 bp Gain ISMex4; intergenic META1_4059-META1_4061 Hypothetical protein/transposase of ISMex4, IS1380 family
META1 4,149,803 +1408 bp Gain ISMex3; coding META1_4069 META1_4069
META1 4,702,223 +1620 bp Gain ISMex4; intergenic META1_4586-META1_CDS4704205D Transposase of ISMex4, IS1380 family/hypothetical protein; RMQ08497
META1 4,909,262 +1620 bp Gain ISMex4; coding META1_4801-META1_4803 Hypothetical protein///transposase of ISMex4, IS1380 family/conserved hypothetical protein
META2 426,304 +1205 bp Gain ISMex1; coding META2_0472-META2_0475 Transposase of ISMex1, IS3 family (ORF 1)/conserved hypothetical protein
META2 1,153,967 +1620 bp Gain ISMex4; intergenic META2_1243-META2_1245 Transposase of ISMex10, ISL3 family/transposase of ISMex4, IS1380 family
Unmapped Archival AM1 DNA   
Size (bp) Location(s) Composition   
11908 ? Porin protein, transcriptional regulator (AraC) protein, conjugative relaxase domain protein, sodium/hydrogen exchanger, TraG homolog
8419 META1_4345/META2_0137 TonB-dependent receptor/siderophore receptor protein, hypothetical proteins
8000 META1_1083 Sodium/calcium exchanger, hypothetical proteins
5207 META2_0137 Cold shock protein A (cspA), metallophosphoesterase, plasmid stabilization system, addiction module antidote protein, cobyrinic acid ac-diamide synthase, stability/partitioning determinant, hypothetical proteins
2423 p2META_0017 Oxidoreductase molybdopterin binding protein, sulfite:cytochrome c oxidase subunit B, hypothetical proteins
35957 Total bp  
  1. Mutations were identified by comparing the Archival genome to a previously sequenced Modern reference [21]. By comparing the mutational state (Archival or Modern) at each site to other previously sequenced strains of M. extorquens (see Methods), all but two mutations can be unambiguously traced as having occurred on the branch from the Ancestral to Modern AM1 (Figure 1). The effect of nonsynonymous mutations on coding regions are highlighted in bold and italic.