Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus

Abstract

Background: The marine cyanobacterium Prochlorococcus marinus, having multiple ecotypes of distinct genotypic/phenotypic traits and being the first documented example of genome shrinkage in free-living organisms, offers an ideal system for studying niche-driven molecular micro-diversity in closely related microbes. The present study, through an extensive comparative analysis of various genomic/proteomic features of 6 high light (HL) and 6 low light (LL) adapted strains, makes an attempt to identify molecular determinants associated with their vertical niche partitioning.

Results: Pronounced strand-specific asymmetry in synonymous codon usage is observed exclusively in LL strains. Distinct dinucleotide abundance profiles are exhibited by 2 LL strains with larger genomes and G+C-content approximately 50% (group LLa), 4 LL strains having reduced genomes and G+C-content approximately 35-37% (group LLb), and 6 HL strains. Taking into account the emergence of LLa, LLb and HL strains (based on 16S rRNA phylogeny), a gradual increase in average aromaticity, pI values and beta- & coil-forming propensities and a decrease in mean hydrophobicity, instability indices and helix-forming propensities of core proteins are observed. Greater variations in orthologous gene repertoire are found between LLa and LLb strains, while higher number of positively selected genes exist between LL and HL strains.

Conclusion: Strains of different Prochlorococcus groups are characterized by distinct compositional, physicochemical and structural traits that are not mere remnants of a continuous genetic drift, but are potential outcomes of a grand scheme of niche-oriented stepwise diversification, that might have driven them chronologically towards greater stability/fidelity and invoked upon them a special ability to inhabit diverse oceanic environments.

Figure 1

Position of genes on the planes defined by the first (horizontal Axis1) and second (vertical Axis2) major axes generated by COA on RSCU values of coding sequences for each of the 12 Prochlorococcus strains (a to l). Genes transcribed from the leading and lagging strands are represented by red and blue coloured dots respectively.

Figure 2

Order of arrangement of 519 orthologs on chromosomes of 5 representative Prochlorococcus strains (LL1, LL3, LL6, HL3 and HL4). The red and blue lines join the locations of pair of orthologs on the linearly depicted chromosomes. Red lines indicate presence of the orthologous pairs on the same strand (either +/+ or -/-) of the two chromosomes they join, while the blue colour indicates the presence of the orthologs on different strands (+/- or -/+). Chromosomal scales are shown in megabase pairs (MB) and 0 MB represents the predicted origins of replication for the 5 strains.

Figure 3

Plot of dinucleotide abundance profiles of E. coli and 12 Prochlorococcus strains. Differently coloured lines join the abundance values of dinucleotide pairs for each of the organisms. Abundance values ≥ 1.23 or ≤ 0.78 are significantly over or underrepresented (as described by Karlin et al., Theoretical population biology, 61, 367-390, 2002).

Figure 4

Single linkage (Euclidean distances) clustering based on standardized amino acid usages (with respect to E. coli) of 12 Prochlorococcus strains and 4 other microbes, accompanied by a heatmap representation of the standardized amino acid usage values. The overrepresentation or underrepresentation of amino acid residues in the organisms are shown in green and red colored blocks of varying colour intensities, respectively. [Abbreviations, EC → E. coli; CJ → C. jejuni; GF → G. foresetii and CTH → Cyanothece sp.]

Figure 5

Venn diagram depicting the number of positively selected (d_N/d_S > 1) orthologs between pairs of different Prochlorococcus strains. The 519 core proteins of 3 representative organisms (LL1, LL6 & HL3) were considered for the analysis. d_N/d_S could be calculated for 414 × 3 pairs out of the 519 × 3 pairs considered.

Figure 6

Trends in genome/proteome evolution of Prochlorococcus, suggesting a stepwise diversification of the ecotypes. The model is based on the 16S rRNA phylogeny of the 12 strains, inferred from a bootstrap consensus tree (500 replicates) generated using the Minimum Evolution method (CNI algorithm), with the software MEGA (version 4).