Abstract
BackgroundThe 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.ResultsPronounced 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 ≈ 50% (group LLa), 4 LL strains having reduced genomes and G+C-content ≈ 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.ConclusionStrains 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.
Highlights
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
On the basis of vertical niche partitioning, these 12 strains are classified into two major Prochlorococcus ecotypes: high light adapted (HL) ecotype being most abundant in surface waters and low light adapted (LL) ecotype dominating deeper waters [19,20]. 6 of the sequenced strains have been identified to belong to the LL group and the other 6 have been found to survive at HL conditions [19]
We have attempted to identify novel niche-specific molecular signatures in the genome and proteome compositions of 12 different Prochlorococcus strains, and investigated the adaptive strategies of different Prochlorococcus strains for their survival in diverse oceanic environments
Summary
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. A variety of Prochlorococcus strains, each specialized to dwell in different conditions of light, temperature and nutrient abundances [14,16,17,18] dominate the euphotic zones of the ocean - mostly between latitudes 40°S and 40°N, and sometimes beyond. We have attempted to identify novel niche-specific molecular signatures in the genome and proteome compositions of 12 different Prochlorococcus strains, and investigated the adaptive strategies of different Prochlorococcus strains for their survival in diverse oceanic environments
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