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. 2016 Apr 6;28(4):911–929. doi: 10.1105/tpc.15.00879

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
a

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).

b

1 = nearly white, 2 = yellowish cream-colored, 3 = light green, and 4 = nearly green.

c

Potentially phenotypically neutral second site mutation. For details, see text.

d

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).

e

This mutant was originally obtained under the name II-beta, but redesignated in this work. For details, see Supplemental Table 1.

f

Second-site mutation isolated based on a phenotypic change in the primary mutant. For details, see text.

g

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.

h

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.

i

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.