Allelic Variation in the Chloroplast Division Gene FtsZ2-2 Leads to Natural Variation in Chloroplast Size

Abstract

Chloroplast size varies considerably in nature, but the underlying mechanisms are unknown. By exploiting a near-isogenic line population derived from a cross between the Arabidopsis (Arabidopsis thaliana) accessions Cape Verde Islands (Cvi-1), which has larger chloroplasts, and Landsberg erecta (Ler-0), with smaller chloroplasts, we determined that the large-chloroplast phenotype in Cvi-1 is associated with allelic variation in the gene encoding the chloroplast-division protein FtsZ2-2, a tubulin-related cytoskeletal component of the contractile FtsZ ring inside chloroplasts. Sequencing revealed that the Cvi-1 FtsZ2-2 allele encodes a C-terminally truncated protein lacking a region required for FtsZ2-2 interaction with inner-envelope proteins, and functional complementation experiments in a Columbia-0 ftsZ2-2 null mutant confirmed this allele as causal for the increased chloroplast size in Cvi-1. Comparison of FtsZ2-2 coding sequences in the 1001 Genomes database showed that the Cvi-1 allele is rare and identified additional rare loss-of-function alleles, including a natural null allele, in three other accessions, all of which had enlarged-chloroplast phenotypes. The ratio of nonsynonymous to synonymous substitutions was higher among the FtsZ2-2 genes than among the two other FtsZ family members in Arabidopsis, FtsZ2-1, a close paralog of FtsZ2-2, and the functionally distinct FtsZ1-1, indicating more relaxed constraint on the FtsZ2-2 coding sequence than on those of FtsZ2-1 or FtsZ1-1. Our results establish that allelic variation in FtsZ2-2 contributes to natural variation in chloroplast size in Arabidopsis, and they also demonstrate that natural variation in Arabidopsis can be used to decipher the genetic basis of differences in fundamental cell biological traits, such as organelle size. to K.W.O.) and by the National Science Foundation (grant no.

Decoding Natural Variation in Chloroplast Size

“…However, FtsZ2-2 protein levels were much lower in these two accessions compared with Cvi-1 and Ler-0, without differences in transcript levels, suggesting instability of the FtsZ2-2 protein (Kadirjan-Kalbach et al, 2019).…”

“…Most protein-coding genes fall into this category. FtsZ1, FtsZ2-1, and FtsZ2-2 all had dN/dS , 1, suggesting negative selection against nonsynonymous polymorphisms (Kadirjan-Kalbach et al, 2019). However, the authors point out that the relatively high dN/ dS of FtsZ2-2 compared with that of FtsZ1 and FtsZ2-1 may indicate a more relaxed tolerance of FtsZ2-2 for variation.…”

“…In nature, chloroplast number or size can vary between species (Honda et al, 1971) and also between cell types of the same species (Ahmadabadi and Bock, 2012); however, the genes/alleles responsible for this variation are unknown. In this issue of Plant Physiology, Kadirjan-Kalbach et al (2019) explored the molecular mechanisms underlying natural variation in chloroplast size using different accessions of Arabidopsis (Arabidopsis thaliana).…”

“…FtsZ2-1 and FtsZ2-2 appear to be functionally interchangeable: it is the overall level of FtsZ2 protein that is critical for proper Z-ring function (Schmitz et al, 2009). Kadirjan-Kalbach et al (2019) began by taking advantage of existing near-isogenic lines (NILs) originating from parents that exhibit notable differences in chloroplast size. In an initial screen, the chloroplast area per mesophyll cell was measured in 22 Arabidopsis accessions, with the largest difference in chloroplast size occurring between Cvi-1 (large) and Ler-2 or Ler-0 (small).…”

“…Both of these accessions had large chloroplasts. A third accession, ANH-1, had an amino acid deletion within the chloroplast targeting signal of FtsZ2-2, which had no effect on the localization of FtsZ2-2 or chloroplast size relative to Ler-0 (Kadirjan-Kalbach et al, 2019). Thirteen accessions contained one or more amino acid polymorphisms in FtsZ2-2.…”