LETTER LETTER REPLY TO ZHOU AND LI: Plasticity of the genomic haplotype of Synechococcus elongatus leads to rapid strain adaptation under laboratory conditions Justin Ungerera, Kristen E. Wendta, John I. Hendryb, Costas D. Maranasb, and Himadri B. Pakrasia,1

Zhou and Li (1) describe a classic phenomenon in mi- Considering the sequencing results reported by crobiology in which the genotypes of bacteria rapidly Zhou and Li (1), we find their report and that of Lou evolve to optimize growth under selective conditions. et al. (3) to be consistent with our original work (4). In the original paper describing the fast-growing cya- Zhou and Li report that the Synechococcus 2973 hap- nobacterium Synechococcus elongatus UTEX 2973, lotype (obtained from UTEX) lacks the atpA SNP, Yu et al. (2) described the genome sequence that de- whereas the premise of Lou et al.’s. report is that Syn- fines the strain. Since 2015, several colleagues who echococcus 7942 with only the atpA SNP grows at the obtained the strain directly from the original Pakrasi same rate as the Synechococcus 2973 strain. In our laboratory stock successfully replicated the 2-h dou- work, we show that Synechococcus 2973 with the bling time of the strain. Seemingly, specific loci affect- atpA SNP removed does grow at the same rate as ing growth rate and light tolerance rapidly interconvert Synechococcus 7942 with only the atpA SNP in- between alternative haplotypes based on the growth cluded (figure 1 of ref. 4). Sequencing results by Zhou conditions. This is confirmed by the sequencing results and Li show that Synechococcus 2973 in their labora- of Zhou and Li (1) who report that the sample in their tory has reverted the atpA SNP; thus, as our data laboratory has mutated toward the Synechococcus show, it grows at the same rate as Synechococcus 7942 haplotype via SNP conversion. In fact, this is sim- 7942-C252Y. ilar to the HL-1 strain of Synechococcus 7942, which Both groups (1, 3) argue that their strains grow they describe as a mutant strain. similarly to Synechococcus 2973; however, neither re- Both Zhou and Li (1) and Lou et al. (3) report that port specific growth rates nor compare their data Synechococcus 7942-C252Y grows similarly to the against a positive control (i.e., haplotype with all three sample of Synechococcus 2973 obtained from UTEX. relevant SNPs). The discrepancy reported by Zhou and However, neither group reports specific growth rates Li (1) clearly arises from the fact that neither they nor or doubling times for direct comparison. Furthermore, Lou et al. (3) seem to have obtained a haplotype iden- Lou et al. (3) reported that the atpA SNP imparts only tical to the “original” Synechococcus 2973. Based on light tolerance similar to that of Synechococcus 2973, the sequencing results, both groups are working with not growth rate. In the course of our work (4), we reg- intermediate haplotypes with intermediate growth ularly verify the complement of SNPs in both wild types rates. We are confident that if Zhou and Li (1) had and mutants thereof. Moreover, we make reciprocal Synechococcus 2973 with the full complement of mutations that demonstrate that removal of individual SNPs, they would find that it grows faster than the SNPs decreases the growth rate of Synechococcus Synechococcus 2973 currently available in their labo- 2973, while adding any individual SNP increases the ratory and the fast Synechococcus 7942-C252Y from growth rate of Synechococcus 7942 (4). Lou et al. (3).

1 Zhou J, Li Y (2018) SNPs deciding the rapid growth of cyanobacteria are alterable. Proc Natl Acad Sci USA 116:3945.

2 Yu J, et al. (2015) Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2. Sci Rep 5:8132.

aDepartment of Biology, Washington University in St. Louis, St. Louis, MO 63130; and bDepartment of Chemical Engineering, Pennsylvania State University, University Park, PA 16802 Author contributions: J.U., K.E.W., J.I.H., C.D.M., and H.B.P. wrote the paper. The authors declare no conflict of interest. Published under the PNAS license. 1To whom correspondence should be addressed. Email: [email protected]. Published online February 12, 2019.

3946–3947 | PNAS | March 5, 2019 | vol. 116 | no. 10 www.pnas.org/cgi/doi/10.1073/pnas.1900792116 Downloaded by guest on October 2, 2021 3 Lou W, et al. (2018) A specific single nucleotide polymorphism in the ATP synthase gene significantly improves environmental stress tolerance of Synechococcus elongatus PCC 7942. Appl Environ Microbiol 84:e01222–e01218. 4 Ungerer J, Wendt KE, Hendry JI, Maranas CD, Pakrasi HB (2018) Comparative genomics reveals the molecular determinants of rapid growth of the cyanobacterium Synechococcus elongatus UTEX 2973. Proc Natl Acad Sci USA 115:E11761–E11770.

Ungerer et al. PNAS | March 5, 2019 | vol. 116 | no. 10 | 3947 Downloaded by guest on October 2, 2021