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

Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates

BackgroundThe ancestral dinoflagellate most likely established a peridinin-containing plastid, which have been inherited in the extant photosynthetic descendants. However, kareniacean dinoflagellates and Lepidodinium species were known to bear “non-canonical” plastids lacking peridinin, which were established through haptophyte and green algal endosymbioses, respectively. For plastid function and maintenance, the aforementioned dinoflagellates were known to use nucleus-encoded proteins vertically inherited from the ancestral dinoflagellates (vertically inherited- or VI-type), and those acquired from non-dinoflagellate organisms (including the endosymbiont). These observations indicated that the proteomes of the non-canonical plastids derived from a haptophyte and a green alga were modified by “exogenous” genes acquired from non-dinoflagellate organisms. However, there was no systematic evaluation addressing how “exogenous” genes reshaped individual metabolic pathways localized in a non-canonical plastid.ResultsIn this study, we surveyed transcriptomic data from two kareniacean species (Karenia brevis and Karlodinium veneficum) and Lepidodinium chlorophorum, and identified proteins involved in three plastid metabolic pathways synthesizing chlorophyll a (Chl a), heme and isoprene. The origins of the individual proteins of our interest were investigated, and we assessed how the three pathways were modified before and after the algal endosymbioses, which gave rise to the current non-canonical plastids. We observed a clear difference in the contribution of VI-type proteins across the three pathways. In both Karenia/Karlodinium and Lepidodinium, we observed a substantial contribution of VI-type proteins to the isoprene and heme biosynthesises. In sharp contrast, VI-type protein was barely detected in the Chl a biosynthesis in the three dinoflagellates.DiscussionPioneering works hypothesized that the ancestral kareniacean species had lost the photosynthetic activity prior to haptophyte endosymbiosis. The absence of VI-type proteins in the Chl a biosynthetic pathway in Karenia or Karlodinium is in good agreement with the putative non-photosynthetic nature proposed for their ancestor. The dominance of proteins with haptophyte origin in the Karenia/Karlodinium pathway suggests that their ancestor rebuilt the particular pathway by genes acquired from the endosymbiont. Likewise, we here propose that the ancestral Lepidodinium likely experienced a non-photosynthetic period and discarded the entire Chl a biosynthetic pathway prior to the green algal endosymbiosis. Nevertheless, Lepidodinium rebuilt the pathway by genes transferred from phylogenetically diverse organisms, rather than the green algal endosymbiont. We explore the reasons why green algal genes were barely utilized to reconstruct the Lepidodinium pathway

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

Analysis of Reactive Oxygen Metabolites (ROMs) after Cardiovascular Surgery as a Marker of Oxidative Stress

The transient systemic low perfusion that occurs during cardiovascular surgery leads to oxidative stress and the production of free radicals. A systemic increase of various markers of oxidative stress has been shown to occur during cardiopulmonary bypass (CPB). However, these markers have not been adequately evaluated because they seem to be reactive and short-lived. Here, oxidative stress was measured using the free radical analytical system (FRAS 4) assessing the derivatives of reactive oxygen metabolites (d-ROMs) and biological antioxidant potential (BAP). Blood samples were taken from 21 patients undergoing elective cardiovascular surgery. CPB was used in 15 patients, and abdominal aortic aneurysm (AAA) surgery without CPB was performed in 6. Measurements of d-ROMs and BAP were taken before surgery, 1 day, 1 week, and 2 weeks after surgery, and oxidative stress was evaluated. The d-ROM level increased gradually after cardiovascular surgery up to 2 weeks. Over time, the d-ROM level after surgery involving CPB became higher than that after AAA surgery. This difference reached statistical significance at 1 week and lasted to 2 weeks. The prolongation of CPB was prone to elevate the d-ROM level whereas the duration of the aortic clamp in AAA surgery had no relation to the d-ROM level. The BAP was also elevated after surgery, and was positively correlated with the level of d-ROMs. In this study, patients who underwent cardiovascular surgery involving CPB had significant oxidative damage. The production of ROMs was shown to depend on the duration of CPB. Damage can be reduced if CPB is avoided. When CPB must be used, shortening the CPB time may be effective in reducing oxidative stress

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

Effect Of Epa Ethyl Ester On Fatty Acid Profile In Hemodialysis Patients With Low Epa/Aa Ratio

BackgroundLarge amounts of n-3 polyunsaturated fatty acids are known to lower the risk of cardiovascular events (CVE). Serum eicosapentaenoic acid (EPA) / arachidonic acid (AA) ratio may potentially be a predictor of CVE which is the most common cause of death in hemodialysis (HD) patients. Therefore, we estimated the effect of EPA ethyl ester on fatty acid profile in HD patients.Subjects & MethodsFatty acid profile and high sensitivity CRP (hs-CRP) were measured in 131 patients receiving maintenance HD. Among these, 64 patients (F:M=25:39) with both low EPA/AA ratio (≦0.4) and negative CRP were enrolled in this randomized study (Group A, EPA administrated group, n=30; Group B, EPA non-administrated group, n=34). The mean age of the patients was 66.5 ± 11.9 years old and the duration of HD was 8.4 ± 7.9 years. The serum levels of EPA, AA, docosahexaenoic acid (DHA), and dihomogammalinolenic acid (DHL-A) were measured by gas chromatography (SRL, Tokyo, Japan).ResultsThe mean levels of EPA/AA ratio, DHA/AA ratio, DHL-A, non HDL-C and GNRI (Geriatric Nutritional Risk Index) were 0.28±0.13, 0.62±0.15, 22.7±8.4 μg/ml, 112.2±31.0 mg/dl and 93.6±5.5, respectively. After one month of treatment with EPA in group A, EPA/AA ratio was significantly increased (0.30±0.15 vs. 0.95±0.45, p<0.0001) and DHL-A significantly decreased (22.7±7.4 vs. 15.7±6.8, p= 0.0003), but DHA/AA ratio, serum non HDL-C and phosphate levels did not change. EPA/AA ratio was significantly higher and DHL-A lower in group A compared with group B after one month of the start of study.ConclusionsMedication of EPA for one month increases EPA/AA ratio, and decreases DHL-A level without the change of serum phosphate level in HD patients with low EPA/AA ratio