Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria

Abstract

Synechococcus cyanobacteria are ubiquitous and abundant in the marine environment and contribute to an estimated 16% of the ocean net primary productivity. Their light-harvesting complexes, called phycobilisomes (PBS), are composed of a conserved allophycocyanin core, from which radiates six to eight rods with variable phycobiliprotein and chromophore content. This variability allows Synechococcus cells to optimally exploit the wide variety of spectral niches existing in marine ecosystems. Seven distinct pigment types or subtypes have been identified so far in this taxon based on the phycobiliprotein composition and/or the proportion of the different chromophores in PBS rods. Most genes involved in their biosynthesis and regulation are located in a dedicated genomic region called the PBS rod region. Here, we examine the variability of gene content and organization of this genomic region in a large set of sequenced isolates and natural populations of Synechococcus representative of all known pigment types. All regions start with a tRNA-PheGAA and some possess mobile elements for DNA integration and site-specific recombination, suggesting that their genomic variability relies in part on a "tycheposon"-like mechanism. Comparison of the phylogenies obtained for PBS and core genes revealed that the evolutionary history of PBS rod genes differs from the core genome and is characterized by the co-existence of different alleles and frequent allelic exchange. We propose a scenario for the evolution of the different pigment types and highlight the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in different Synechococcus lineages despite multiple speciation events.

Keywords: cyanobacteria; genomic island; lateral gene transfer; phycobiliprotein; phycobilisome; tycheposon.

Fig. 1.

PBS rod region for strains of different pigment types. Regions are oriented from the phenylalanine tRNA (left) to the conserved low molecular weight tyrosine phosphatase ptpA (right). Genes are colored according to their inferred function (as indicated in the inset). Their length is proportional to the gene size and their thickness to the protein identity between strains of the same pigment type. The strains represented here are WH5701 (PT 1), WH7805 (PT 2A), RS9907 (PT 3a), KORDI-100 (PT 3f), RS9916 (PT 3dA), WH8102 (PT 3c), and A15-62 (PT 3dB).

Fig. 2.

Examples of tycheposons at 5′-end of PBS regions. Regions are oriented from the phenylalanine tRNA (tRNA-Phe) to unk1, the first coding gene of the PBS region per se. Genes putatively involved in DNA rearrangements (recombination, transposition, etc.) are colored and their orthologs in different regions are shown with the same color. Coding sequences with no gene name are hypothetical, conserved hypothetical, or pseudogenes. Gene length is proportional to the gene size. Abbreviations: TR, tyrosine recombinase; TPR, tetratricopeptide. The number after a gene name corresponds to its CLOG number in the Cyanorak database (Garczarek et al. 2021).

Fig. 3.

Location and genetic characterization of the samples used to retrieve the PBS rod regions from field populations of Synechococcus shown in figure 4. (A) Location of sampling sites used for fosmid library construction. (B) Synechococcus genetic diversity at each station, as assessed with the phylogenetic marker petB. (C) mpeBA phylogeny for isolates (black) and fosmids (gray). Squares and circles on the right-hand side correspond to reference strains and fosmids, respectively. Within PT 3dA, symbols with a blue center and a red contour correspond to PT 3aA (the reference 3aA strain, MVIR-18-1, exhibits a constitutive low Exc_495:545) and those with a blue center and a yellow contour to PT 3cA (the reference 3cA strain, BIOS-E4-1, exhibits a constitutive high Exc_495:545; see the text as well as Humily et al. 2013 and Grébert et al. 2018). Bootstrap values higher or equal to 90% are indicated by black circles, those comprised between 70% and <90% by empty circles, and no circles indicate values lower than 70%.

Fig. 4.

Partial or complete PBS rod region retrieved from natural Synechococcus populations. (A) Description of a new genomic organization related to 3dA pigment type with the CA4-A genomic island inserted at the 5′-end of the PBS rod genomic region. The PBS rod and CA4-A genomic regions of strain BL107 (3dA/clade IV) are shown as a reference. (B) Contigs other than those in (A) and longer than 10 kb sorted according to their organization and inferred corresponding pigment type. Colors represent the clade of the strain giving the best BlastX hit within the given pigment type. The highly conserved mpeBA operon is shaded in gray.

Fig. 5.

Correspondence between phylogenies for the mpeBA operon and the marker gene petB, which reproduces the core genome phylogeny. The pigment type for each strain is indicated by a colored square in the mpeBA phylogeny, and its clade is similarly indicated in the petB phylogeny. Bootstrap values higher or equal to 90% are indicated by black circles, those comprised between 70% and <90% by empty circles, and no circles indicate values lower than 70%.

Fig. 6.

Evolutionary events affecting genes present in more than half of the analyzed genomes inferred by reconciling gene trees with the species tree. Genes were classified either as belonging to the PBS rod region (“PBS genes”) or as other genes (“Other”). P values for the Wilcoxon rank sum exact test are shown.

Fig. 7

Putative evolutionary scenario for the occurrence of the different Synechococcus PT 3 subtypes. This scenario is globally congruent with individual phylogenies of genes in the PBS rod region. Note that the 5′- and 3′- ends of the PBS rod region are cropped for better visualization of the PE-I/PE-II subregions. Genes that changed between two consecutive PT precursor steps are highlighted by black contours (instead of blue-grey for the other genes).