Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms

Organelle acquisitions via endosymbioses with prokaryotes were milestones in the evolution of eukaryotes. Still, quite a few uncertainties have remained for the evolution in the early stage of organellogenesis. In this respect, rhopalodiacean diatoms and their obligate cyanobacterial endosymbionts, called spheroid bodies, are emerging as new models for the study of organellogenesis. The genome for the spheroid body of Epithemia turgida, a rhopalodiacean diatom, has unveiled its unique metabolic nature lacking the photosynthetic ability. Nevertheless, the genome sequence of a spheroid body from a single lineage may not be sufficient to depict the evolution of these cyanobacterium-derived intracellular structures as a whole. Here, we report on the complete genome for the spheroid body of Rhopalodia gibberula, a lineage distinct from E. turgida, of which genome has been fully determined. Overall, features in genome structure and metabolic capacity, including a lack of photosynthetic ability, were highly conserved between the two spheroid bodies. However, our comparative genomic analyses revealed that the genome of the R. gibberula spheroid body exhibits a lower non-synonymous substitution rate and a slower progression of pseudogenisation than those of E. turgida, suggesting that a certain degree of diversity exists amongst the genomes of obligate endosymbionts in unicellular eukaryotes

Evolving genetic code

In 1985, we reported that a bacterium, Mycoplasma capricolum, used a deviant genetic code, namely UGA, a “universal” stop codon, was read as tryptophan. This finding, together with the deviant nuclear genetic codes in not a few organisms and a number of mitochondria, shows that the genetic code is not universal, and is in a state of evolution. To account for the changes in codon meanings, we proposed the codon capture theory stating that all the code changes are non-disruptive without accompanied changes of amino acid sequences of proteins. Supporting evidence for the theory is presented in this review. A possible evolutionary process from the ancient to the present-day genetic code is also discussed

Unique genome evolution in an intracellular N2-fixing symbiont of a rhopalodiacean diatom

Cyanobacteria, the major photosynthetic prokaryotic lineage, are also known as a major nitrogen fixer in nature. N2-fixing cyanobacteria are frequently found in symbioses with various types of eukaryotes and supply fixed nitrogen compounds to their eukaryotic hosts, which congenitally lack N2-fixing abilities. Diatom species belonging to the family Rhopalodiaceae also possess cyanobacterial symbionts called spheroid bodies. Unlike other cyanobacterial N2-fixing symbionts, the spheroid bodies reside in the cytoplasm of the diatoms and are inseparable from their hosts. Recently, the first spheroid body genome from a rhopalodiacean diatom has been completely sequenced. Overall features of the genome sequence showed significant reductive genome evolution resulting in a diminution of metabolic capacity. Notably, despite its cyanobacterial origin, the spheroid body was shown to be truly incapable of photosynthesis implying that the symbiont energetically depends on the host diatom. The comparative genome analysis between the spheroid body and another N2-fixing symbiotic cyanobacterial group corresponding to the UCYN-A phylotypes – both were derived from cyanobacteria closely related to genus Cyanothece – revealed that the two symbionts are on similar, but explicitly distinct tracks of reductive evolution. Intimate symbiotic relationships linked by nitrogen fixation as seen in rhopalodiacean diatoms may help us better understand the evolution and mechanisms of bacterium-eukaryote endosymbioses

Multiple ferromagnetic transitions and structural distortion in the van der Waals ferromagnet VI3 at ambient and finite pressures

We present a combined study of zero-field (51) V and I-127 NMR at ambient pressure and specific heat and magnetization measurements under pressure up to 2.08 GPa on bulk single crystals of the van der Waals ferromagnet VI3. At ambient pressure, our results consistently demonstrate that VI3 undergoes a structural transition at T-s approximate to 78 K, followed by two subsequent ferromagnetic transitions at T-FM1 approximate to 50 K and T-FM2 approximate to 36 K upon cooling. At lowest temperature (T \u3c T-FM2), two magnetically ordered V sites exist, whereas only one magnetically ordered V site is observed for T-FM1 \u3c T \u3c T-FM2. Whereas T-FM1 is almost unaffected by external pressure, T-FM2 is highly responsive to pressure and merges with the T-FM1 line at p 0.6 GPa. At even higher pressures (p approximate to 1.25 GPa), the T-FM2 line merges with the structural transition at T-s which becomes moderately suppressed with p for p \u3c 1.25 GPa. Taken together, our data point toward a complex magnetic structure and an interesting interplay of magnetic and structural degrees of freedom in VI3

Lateral Transfer of an EF-1α Gene Origin and Evolution of the Large Subunit of ATP Sulfurylase in Eubacteria

AbstractIt is generally accepted that new genes arise via duplication and functional divergence of existing genes, in accordance with Ohno's model [1], now called “Mutation During Redundancy,” or MDR [2]. In this model, one of the two gene copies is free to acquire novel (although likely related) activities through mutation, since only one copy is required for its original function. However, duplication within a genome is not the only process that might give rise to this situation: acquisition of a functionally redundant gene by lateral gene transfer (LGT) could also initiate the MDR process. Here we describe a probable instance, involving LGT of an archaeal or eukaryotic elongation factor 1α (EF-1α) gene. The large subunit of ATP sulfurylase (CysN or the N-terminal portion of NodQ), found mainly in proteobacteria, is clearly related to translation elongation factors [3, 4]. However, our analyses show that cysN arose from an EF-1α gene initially acquired by LGT, not from a within-genome duplication of the resident EF-Tu gene. To our knowledge, this is the first unequivocal case of LGT followed by functional modification to be described; this mechanism could be a potentially important force in establishing genes with novel functions in genomes

Multiple conversion between the genes encoding bacterial class-I release factors

Bacteria require two class-I release factors, RF1 and RF2, that recognize stop codons and promote peptide release from the ribosome. RF1 and RF2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. This scenario expects that the two RF gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. However, we here report two independent cases of conversion between RF1 and RF2 genes (RF1-RF2 gene conversion), which were severely examined by procedures incorporating the maximum-likelihood phylogenetic method. In both cases, RF1-RF2 gene conversion was predicted to occur in the region encoding nearly entire domain 3, of which functions are common between RF paralogues. Nevertheless, the direction of gene conversion appeared to be opposite from one another - from RF2 gene to RF1 gene in one case, while from RF1 gene to RF2 gene in the other. The two cases of RF1-RF2 gene conversion prompt us to propose two novel aspects in the evolution of bacterial class-I release factors: (i) domain 3 is interchangeable between RF paralogues, and (ii) RF1-RF2 gene conversion have occurred frequently in bacterial genome evolution