From green to red: horizontal gene transfer of the phycoerythrin gene cluster between Planktothrix strains

Abstract

Horizontal gene transfer is common in cyanobacteria, and transfer of large gene clusters may lead to acquisition of new functions and conceivably niche adaption. In the present study, we demonstrate that horizontal gene transfer between closely related Planktothrix strains can explain the production of the same oligopeptide isoforms by strains of different colors. Comparison of the genomes of eight Planktothrix strains revealed that strains producing the same oligopeptide isoforms are closely related, regardless of color. We have investigated genes involved in the synthesis of the photosynthetic pigments phycocyanin and phycoerythrin, which are responsible for green and red appearance, respectively. Sequence comparisons suggest the transfer of a functional phycoerythrin gene cluster generating a red phenotype in a strain that is otherwise more closely related to green strains. Our data show that the insertion of a DNA fragment containing the 19.7-kb phycoerythrin gene cluster has been facilitated by homologous recombination, also replacing a region of the phycocyanin operon. These findings demonstrate that large DNA fragments spanning entire functional gene clusters can be effectively transferred between closely related cyanobacterial strains and result in a changed phenotype. Further, the results shed new light on the discussion of the role of horizontal gene transfer in the sporadic distribution of large gene clusters in cyanobacteria, as well as the appearance of red and green strains.

Fig 1

Comparison of eight Planktothrix genomes. Strains are color coded according to red (red font) and green (green font) phenotypes. (A) Correlation matrix of pairwise comparison of COG profiles. Pearson correlation coefficients range from 1.00 (highest correlation, dark blue) to 0.97 (dark red). (B) Hierarchical clustering of strains based on COG profiles and maximum likelihood phylogeny of 200 randomly selected core genes (see Materials and Methods). The proximity of grouping in the hierarchical tree indicates the relative degree of similarity of genomes to each other. ML bootstrap values at all branches are shown. (C) Percentage of homologous protein-coding genes in pairwise analyses. Values range from 100% (dark blue) to 82.2% (red). Homologous genes were detected using BLASTP and a minimum of 80% sequence identity.

Fig 2

Phycocyanin and phycoerythrin operons in Planktothrix. (A) The figure shows organization of the phycocyanin (green) gene cluster with individual gene names, the phycoerythrin gene cluster (red) with individual gene names, and flanking genes downstream of the cpeZ/cpcB gene. Flanking open reading frames are indicated as follows: SMC protein, SMC chromosome segregation protein; DUF88, protein of unknown function DUF88; SC, short-chain alcohol dehydrogenase; HPP, 4-hydroxyphenylpyruvate dioxygenase; CHAP, CHAP domain. (B) Alignment of informative sites in cpcA. Areas marked with a gold/yellow shade indicate identical regions between NIVA-CYA 540 and other Planktothrix strains. (C) Alignment of informative sites of the gene encoding the CHAP domain. Areas marked with a gold shade indicate identical regions between NIVA-CYA 540 and other Planktothrix strains. (D) Recombination breakpoints detected by RDP in NIVA-CYA 540. Strain NIVA-CYA 34 (green) was detected as major parent, and NIVA-CYA 98 (red) was detected as minor parent. Positions of recombination breakpoints in both genes are shown.

Fig 3

Maximum likelihood phylogenies of cpcA and cpcB versus cpcC1 and cpcC2, all concatenated. ML bootstrap values on all branches are shown. Planktothrix strains are color coded according to red (red font) and green (green font) phenotypes.