Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits

The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.

Putative spermine synthases fromThalassiosira pseudonanaandArabidopsis thalianasynthesize thermospermine rather than spermine

Polyamines are involved in many fundamental cellular processes. Common polyamines are putrescine, spermidine and spermine. Spermine is synthesized by transfer of an aminopropyl residue derived from decarboxylated S-adenosylmethionine to spermidine. Thermospermine is an isomer of spermine and assumed to be synthesized by an analogous mechanism. However, none of the recently described spermine synthases was investigated for their possible activity as thermospermine synthases. In this work, putative spermine synthases from the diatom Thalassiosira pseudonana and from Arabidopsis thaliana could be identified as thermospermine synthases. These findings may explain the previous result that two putative spermine synthase genes in Arabidopsis produce completely different phenotypes in knock-out experiments. Likely, part of putative spermine synthases identifiable by sequence comparisons represents in fact thermospermine synthases.

Polyamines as a chemotaxonomic marker in bacterial systematics

Aliphatic linear polyamines, from diamines to hexaamines, tertiary branched tetraamines, and quaternary branched pentaamines are widely distributed in eubacteria, archaebacteria, and cyanobacteria. Twenty-four linear types and four branched types are acid extractable from bacterial cells and can be chromatographically analyzed and identified. The varieties of polyamines are due to the combination of amino acid decarboxylase activities to form diamines, aminopropyl- and aminobutyl-transfer activities mediated by aminopropyltransferases or Schiff-base complex formation, and hydroxylation activity. The absence or presence of spermidine, norspermidine or homospermidine and the occurrence of 2-hydroxyputrescine and diaminopropane are related to grouping into the alpha, beta, gamma, and delta subclasses within Proteobacteria. Flavobacterium complex and green bacteria contain putrescine and homospermidine. Gram-negative thermophiles contain long linear and branched polyamines; however, their distribution profiles are species specific. Gram-positive eubacteria, which comprise Bacillus cluster, anaerobes, and actinomycetes, ubiquitously contain putrescine and spermidine, while the occurrence of spermine is limited to thermophiles. Archaebacteria are separated into polyamine-absent methanogens and halophiles, homospermidine-dominant methanogens, spermidine-dominant methanogens, and spermidine- and norspermidine-containing thermophiles. Cyanobacteria comprise two types; one group contains homospermidine and the other spermidine. The polyamine distribution pattern can serve as a chemotaxonomic marker in bacterial classification and is associated with bacterial systematics on the level of order, family, or genus.

Increase in spermine content coordinated with siderophore production in Paracoccus denitrificans

Spermine is present in relatively low amounts in Paracoccus denitrificans cultured aerobically in an ammonium succinate minimal salts medium supplemented with 50 microM iron(III). However, in iron-deprived cultures [minimal salts medium containing 0.5 microM iron(III)], spermine content increases by an order of magnitude in coordination with the well-known responses to iron derivation, e.g., derepression of siderophore synthesis and siderophore excretion. When iron-deprived cultures exhibiting both high spermine content and strong siderophore production are reseeded into fresh minimal salts medium containing 50 microM iron[III], both siderophore production and spermine content fall rapidly. Five hours after iron supplementation, spermine is below limits of detection. These results suggest a specific role for spermine in the response of P. denitrificans to low-iron stress.