Table 1.
List of mutations derived in the Modern AM1 lineage
|
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 (AG
G
→ AG
C
) |
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 (AC
C
→ AC
G
) |
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 (C
A
G → C
G
G) |
rpoB |
RNA polymerase, beta subunit |
| META1 |
4,498,413 |
A → G |
Q1081R (C
A
G → C
G
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 | ||||
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.