Table 1. Phenotypes, Major Defects, and Mutated Loci of the Mutant Lines in the Oenothera Plastome Mutant Collection.
| Mutanta | Defect in | Gene or Locus | Leaf Phenotypeb |
Description | Mutation and Predicted Molecular Consequence | ||||
|---|---|---|---|---|---|---|---|---|---|
| Young | Medium | Old | |||||||
| M1/M4 | I-alpha/I-delta | PSII | psbD | 4 | 3-4 | 4 | Very old leaves with narrow whitish zones, older leaves sometimes darker green | 5-bp duplication (CTTGG), +18 to +22 psbD, truncated PsbD, alternative start codon [?] | |
| M2 | I-beta | Cyt b6f | petD | 4 | 3 | 1 | Old leaves often with small green spots | 4-bp duplication (ATTT), +998 to +1001 petD, truncated PetD | |
| M2 | I-beta | – | SSC-IRA junction | 4 | 3 | 1 | Old leaves often with small green spots | 66-bp deletion (AATTT…TATGG), −258 to −323 ycf1 (tic214)c | |
| M3/M5 | I-gamma/I-epsilon | PSII | psbA | 3 | 2-3 | 1 | Older leaves with enhanced greening close to vascular tissue | 2-bp duplication (GT), +82 to +83 psbA, truncated PsbA | |
| M6 | I-zeta | PSI | psaA | 1-2 | 1 | 1 | – | 5-bp duplication (GTTTT), +1350 to +1354 psbA, truncated PsaA | |
| M7 | I-eta | PSI | psaA | 2 | 1-2 | 1 | – | 4-bp duplication (GATT), +1088 to +1090 psaA, truncated PsaA | |
| M8 | I-theta | PSI | psaB | 2 | 1-2 | 1 | – | 32-bp duplication (TTCCA…ATTAG), +2132 to +2163 psaB, truncated PsaB | |
| M9 | I-iota | ATP synthase | atpB | (1) | (1-4) | (4) | Mottled, young leaves white, old leaves nearly green | 1-bp insertion (A), +58 atpB, truncated AtpB [?] | |
| M10/M15 | I-kappa/I-omikron | PSI | psaA | 1-2 | 1-2 | 1-2 | – | 70-bp duplication (ACGAT…CCCGT), +1437 to +1506 psaA, truncated PsaA | |
| M11 | I-lambda | PSII | psbA | 3-4 | 1-2 | 1 | – | 4-bp deletion (GCTT), +859 to +862 psbA, truncated PsbA | |
| M12 | I-my | Cyt b6f | ccsA | 4 | 3-4 | 1 | Old leaves often with small green spots | 31-bp duplication (GAATT…TTAAA), +540 to +570 ccsA; truncated CcsA | |
| M13 | I-ny | PSI | psaB | 2 | 1-2 | 1 | – | 4-bp deletion (AGAT), +399 to +402 psaB, truncated PsaB | |
| M14 | I-xi | PSII | psbD | 4 | 3-4 | 1 | – | 5-bp deletion (CAGCT), +530 to +534 psbD, truncated PsbD | |
| M16 | I-pi | PSII | psbA | 3-4 | 2-3 | 1 | – | 5-bp deletion (TCTCT), +208 to +212 psbA, truncated PsbA | |
| M17 | I-rho | PSII | psbA | 3-4 | 2 | 1 | Greening declining from leaf base to tip | 5-bp deletion (ACAAC), +797 to +801 psbA, truncated PsbA | |
| M17 | I-rho | – | Upstream accD | 3-4 | 2 | 1 | Greening declining from leaf base to tip | 30-bp deletion (CCTTT…CTTTA), −30 to −1 accDc | |
| M18d | I-sigma | Rubisco | rbcL | 4 | 4 | 4 | – | 5-bp deletion (TTAAC), +808 to +812 rbcL, truncated RbcL | |
| M19 | I-tau | Translation | rps7 | (1-4) | (1-4) | (1-4) | Periodical bleaching/regreening (virescent), viable on soil at homoplasmic state, retarded in cell growth | 4-bp duplication (ATTT), +462 to +465 rps7, last 2 aa of Rps7 modified and 2 aa added | |
| M20 | I-ypsilon | ATP synthase | atpB | (1) | (1) | (1) | Mottled, but spots very rare | 34-bp duplication (GATAC…AATTA), +461 to +494 atpB, truncated AtpB | |
| M20 | I-ypsilon | – | ycf1 (tic214) | (1) | (1) | (1) | Mottled, but spots very rare | 21-bp deletion (AAAAG…ACGTC), +2404 to +2424 ycf1 (tic 214), 21-bp duplication (TCAAA…CGAAA), +2486 to +2406 ycf1 (tic214), 3 aa exchanges in the variable part of Ycf1 (Tic214)c | |
| M21 | I-phi | Cyt b6f | ccsA | 3-4 | 2 | 2 | – | 4-bp duplication (ATTT), +10 to +13 ccsA, truncated CcsA | |
| M22 | I-chi | PSI | psaA | 1-2 | 1 | 1 | – | 5-bp duplication (CCGCT), +1420 to +1424 psaA, truncated PsaA | |
| M23 | I-psi | PSI | ycf3 (intron) | 1-2 | 2 | 2 | – | 5-bp duplication (ATTGA), +316 to +320 ycf3 (intron), splicing deficiency | |
| M24 | I-omega | PSI | psaA | 1-2 | 1 | 1 | – | 4-bp duplication (TCTT), +2226 to +2229 psaA, changed/extended PsaA | |
| M25 | I-do | Cyt b6f | ccsA | 3 | 2 | 2 | – | 6-bp deletion (ACAATA), +298 to +303 ccsA, deletion of 2 aa in CcsA | |
| M26/M27 | I-re/I-mi | Cyt b6f | petA | 2-3 | 1-2 | 1-2 | – | 1-bp insertion (G), +667 petA, truncated PetA | |
| M28 | II-alpha | PSI | ycf4 | 3 | 2-3 | 1 | Old leaves of field grown plants with characteristic yellowish/whitish tip | 4-bp duplication (AAAA), +442 to +445 ycf4; truncated Ycf4 | |
| M29 | III-epsilone | PSI | ycf3 | 2 | 1 | 1 | – | 29-bp duplication (ACAAG…GCTTT), +996 to +1024 ycf3, truncated Ycf3 | |
| M30d | II-gamma | PSII | psbE | 4 | 2-3 | 1-2 | Old leaves often with small green spots | 5-bp duplication (ATTAT), +42 to +46 psbE, truncated PsbE | |
| M31 | II-delta | – | ndhE-psaC spacer | 4 | 4 | 4 | No change during development | 24-bp deletion (TATAT…AATCA), −60 to −83 psaC, transcript processing affected | |
| M32 | II-epsilon | PSI | psaA | 2 | 1 | 1 | – | 4-bp duplication (TGAG), +124 to +127 psaA, truncated PsaA | |
| M33 | II-zeta | PSII | psbB | 4 | 2-3 | 1 | Old leaves with enhanced greening close to vascular tissue | 4-bp duplication (CTTT), +117 to +120 psbB, truncated PsbB | |
| M34 | II-eta | Cyt b6f | petB | 4 | 3 | 1 | Old leaves often with small green spots | 5-bp duplication (ATTAC), +1346 to +1350 petB, truncated PetB, transcript processing/stability affected | |
| M35d | II-theta | Cyt b6f | petB (intron) | 4 | 3 | 1 | Old leaves often with small green spots | 2-bp deletion (AC), +430 to +431 petB (intron), splicing deficiency | |
| M36/M47 | II-iota/IV-delta | PSI | psaA | 2 | 2 | 2 | – | 5-bp duplication (TTAAC), +667 to +671 psaA, truncated PsaA | |
| M37 | II-kappa | PSI | ycf3 (intron) | 3-4 | 3-4 | 4 | Old leaves in parts darker than younger leaves, viable on soil at homoplasmic state | transversion G/T, +1438 ycf3 (intron), splicing deficiency | |
| M37 | II-kappa | – | ndhF-rpl32 spacer | 3-4 | 3-4 | 4 | Old leaves in parts darker than younger leaves, viable on soil at homoplasmic state | Single-bp insertion/deletion, results in a transversion (C/T), −511 rpl32c | |
| M38 | II-lambda | Cyt b6f | petA | 4 | 3-4 | 2-3 | – | 39-bp deletion (GGTTT...CCGAG), +337 to +375 petA, 13 aa deleted in PetA | |
| M39 | II-my | Cyt b6f | petA | 3-4 | 3-4 | 1-2 | – | 5-bp duplication (TAGCC), +352 to +356 petA, truncated PetA | |
| M39 | II-my | – | ndhG-ndhI spacer | 3-4 | 3-4 | 1-2 | – | Single-bp deletion (A), −310 ndhGc | |
| M40 | II-ny | PSI | ycf4 | Mutation of M28 (II-alpha) | |||||
| M40 | II-ny | PSII | psbB | 2 | 1-2 | 1 | – | 2-bp deletion (CT), +791 to +792 psbB, truncated PsbBf | |
| M41g | III-alpha | PSII | psbD | 4 | 3-4 | 1 | – | 6-bp duplication (TATATT), +540 to +545 psbD, 2 additional aa in PsbD | |
| M42 | III-beta | PSI | psaB | 1-3 | 1-3 | 1-3 | Bleaches under higher light conditions, sometimes inhomogeneous | 5-bp duplication (ATAAA), +1246 to +1250 psaB, truncated PsaB | |
| M43 | III-gamma | PSI | psaA | 1-2h | 1-2 | 1 | – | 8-bp duplication (AATTTAGT), +1540 to +1547 psaA, truncated PsaA | |
| M43 | III-gamma | – | trnQ-UUG-accD spacer | 1-2h | 1-2 | 1 | – | 12-bp deletion (CTCGGCTGATGA), −689 to −678 accDc | |
| M44 | III-delta | PSI | psaB | 1 | 1 | 1 | – | Mutation of M42 (III-beta) | |
| M44 | III-delta | ATP synthase | atpB | 1 | 1 | 1 | – | 1-bp deletion (A), +57 atpB, truncated AtpBf | |
| M45 | IV-alpha | PSI | psaA | 3 | 1-2 | 1 | – | 5-bp duplication (GTACT), +2173 to +2177 psaA, truncated PsaA | |
| M464) | IV-beta | Rubisco | rbcL | 4 | 4 | 3-4 | – | Transversion (G/C), +337 rbcL, single aa exchange | |
| M48 | IV-epsilon | PSII | psbA | 3 | 2-3 | 1-2 | Greening declining from leaf base to tip | 8-bp deletion (AGTGGGAA), +389 to +396 psbA, truncated PsbA | |
| M49 | V-alpha | Rubisco (tentative)i | rbcL (tentative)i | 4 | 4 | 4 | Grayish green phenotype, older leaves in parts darker | 6-bp deletion (GATGAA), +750 to +755 rbcL, deletion of 2 aa in RbcL | |
| M50 | V-delta | PSI | ycf3 | 4 | 3 | 1 | – | 1364-bp deletion in ycf3 affecting 11 bp of the 3′-end of exon 1, the full intron 1, the full exon 2, and 403 bp of the 5′-end of intron 2 | |
| M50 | V-delta | – | accD | 4 | 3 | 1 | – | 153-bp deletion +208 to +360 accD, deletion of 51 aa in the variable part of AccDc | |
| M51 | I-fa | Cyt b6f | ccsA | 3 | 2-3 | 1-2 | – | 5-bp duplication (TTAAC), +702 to +705 ccsA, truncated CcsA | |
Mutants are designated according to their basic plastome genotype (I to V) with Greek letters indicating the sequence of mutant isolation (with alpha representing the first mutant isolated). In the case of plastome I, for which more mutants have been isolated than letters exist in the Greek alphabet, additional mutants are designated by the seven tone syllables. For details, see Kutzelnigg and Stubbe (1974) and Stubbe (1989).
1 = nearly white, 2 = yellowish cream-colored, 3 = light green, and 4 = nearly green.
Potentially phenotypically neutral second site mutation. For details, see text.
Mutations in the mutants M18 (I-sigma), M30 (II-gamma), M35 (II-theta), and M46 (IV-beta) were determined previously and could be verified in this study. For summary and references, see Greiner (2012).
This mutant was originally obtained under the name II-beta, but redesignated in this work. For details, see Supplemental Table 1.
Second-site mutation isolated based on a phenotypic change in the primary mutant. For details, see text.
With respect to its reference plastome (deserens de Vries; GenBank accession number KT881172.1), the mutant M41 (III-alpha) carries a 6-bp deletion (TAATCA) in the rbcL-atpB intergenic spacer, −113 to −118 of rbcL. However, this mutation must have arisen in the wild-type reference after the isolation of M41 (III-alpha). Hence, it is not treated as second site mutation in M41 (III-alpha). For details, see text.
The phenotype of the mutant M43 (III-gamma) was described as “lighter green (3)” in young tissue by W. Stubbe. However, in our hands, the mutant appeared to be nearly white to yellowish (1-2) at most developmental stages. It is possible that this phenotypic change is due to a second site mutation upstream of accD which was not present when W. Stubbe initially assessed the phenotypes. For details, see text.
The corresponding wild-type strain (argillicola Douthat 4b) of the mutant M50 (V-alpha) is no longer present in our genetic stocks. For mutant allele identification, the two available O. argillicola plastomes (EU262887.2 and KT881177.1) were used. See Stubbe and Herrmann (1982) for assignment of this mutant to a physiological defect in Rubisco.