Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis

海洋微生物も”密”ならウイルスに感染する --頻度依存的なウイルス感染を大阪湾で実証--. 京都大学プレスリリース. 2023-02-24.Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of their hosts. Model systems suggest that viral infection is frequency dependent and constrained by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection is pervasive among the abundant prokaryotic populations with different temporal dynamics. To address this question, we performed a comparison of prokaryotic and viral communities using 16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that the abundance of viruses correlated with that of their predicted host phyla (or classes). Cooccurrence network analysis between abundant prokaryotes and viruses revealed 6, 423 cooccurring pairs, suggesting a tight coupling of host and viral abundances and their “one-to-many” correspondence. Although stable dominant species, such as SAR11, showed few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these populations changed continuously. Our results suggest that frequency-dependent viral infection prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics

Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan

International audienceViruses infecting microorganisms are ubiquitous and abundant in the ocean. However, it is unclear when and where the numerous viral particles we observe in the sea are produced and whether they are active. To address these questions, we performed time-series analyses of viral metagenomes and microbial metatranscriptomes collected over a period of 24 h at a Japanese coastal site. Through mapping the metatranscriptomic reads on three sets of viral genomes ((i) 878 contigs of Osaka Bay viromes (OBV), (ii) 1766 environmental viral genomes from marine viromes, and (iii) 2429 reference viral genomes), we revealed that all the local OBV contigs were transcribed in the host fraction. This indicates that the majority of viral populations detected in viromes are active, and suggests that virions are rapidly diluted as a result of diffusion, currents, and mixing. Our data further revealed a peak of cyanophage gene expression in the afternoon/dusk followed by an increase of genomes from their virions at night and less-coherent infectious patterns for viruses putatively infecting various groups of heterotrophs. This suggests that cyanophages drive the diel release of cyanobacteria-derived organic matter into the environment and viruses of heterotrophic bacteria might have adapted to the population-specific life cycles of hosts

Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer

<div><p>Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the <i>TCRα</i> gene is enhanced by the cooperative binding of the Runx1–CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1–CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations. Consequently, we detected high flexibility of the loop region between the HI2 and H1 helices of Ets1. Upon Runx1–CBFβ heterodimer binding, this loop transiently adopts various sub-stable conformations in its interactions with the DNA. In addition, a network analysis suggested an allosteric pathway in the molecular assembly and identified some key residues that coincide with previous experimental studies. Our simulations suggest that the cooperative binding of Ets1 and the Runx1–CBFβ heterodimer alters the DNA conformation and induces sub-stable conformations of the HI2–H1 loop of Ets1. This phenomenon increases the flexibility of the regulatory module, including the HI2 helix, and destabilizes the inhibitory form of this module. Thus, we hypothesize that this effect facilitates Ets1–DNA binding and prevents the phosphorylation-dependent DNA binding autoinhibition.</p></div

The mDCC correlation maps.

<p>(A) The correlation map of the quaternary complex. The horizontal and vertical axes indicate each residue from the N- to C-termini of Runx1, CBFβ, and Ets1, and the 5’- to 3’-termini of the DNA chains. The colored bars along the axes indicate the secondary structures of each residue: green, red, and blue indicate α-helix, β-strand, and others, respectively; and nucleotides are colored purple. In the heatmap, the graduation from blue to red corresponds to mDCC values from -1.0 to 1.0. The grid drawn with cyan lines highlights the checkered pattern on the map. It divides the residues into the two groups colored green and purple in the color bar at the top of the map, and in the 3D structure of the molecular complex overlaid on the lower triangle of the map. The grey arrows indicate the flexible loops discussed in the main text. The region corresponding to these loops on the heatmap are marked as grey dashed lines. (B) The correlation maps focusing on Ets1 and DNA in the quaternary complex (the upper-triangle) and in the Ets1–DNA complex (the lower-triangle). The upper-triangle of panel B is identical to part of the map in panel (A). The grey dashed lines highlight the HI2–H1 loop, discussed in the main text.</p

Changes in DNA conformations around the G4–C112 base-pair.

<p>(A) 3D structures of the G4–C112 base-pair taken from the three simulations: the wild-type quaternary complex (red), the quaternary complex with the Runx1 K167A mutant (green), and the isolated DNA (purple). The snapshots were taken at the times when the X-displacement parameter was near the average value for each model. The three structures are superimposed, based on the adjacent base-pair (A3–T113; the thin lines). (B) The averages and standard deviations of the X-displacement parameter in the wild-type quaternary complex (red), the Ets1–DNA complex (blue), the isolated DNA (purple), the quaternary complex with Runx1 K167A mutant (green), and the quaternary complex with Ets1 Y329A mutant (cyan).</p

The correlation network of the wild-type quaternary complex.

<p>Each node indicates each residue, labeled with the one-letter codes for amino acids and nucleotides. An asterisk “*” denotes the termini of polypeptides, <i>i</i>.<i>e</i>., N-methyl and acetyl groups. The circles correspond to DNA (upper-left circle), Ets1 (upper-right), Runx1 (lower-left), and CBFβ (lower-right). Nodes are aligned in the sequence order for each molecule in the counter-clockwise direction, starting from the bottom of each circle. The colors of the nodes indicate the betweenness values: higher values are darker. In particular, the top 15 highest betweenness residues in each molecule are shown as large squares. The colors of the node borders indicate the secondary structures of the residues: green, red, and blue represent α-helix, β-strand, and others, respectively; nodes in DNA are shown as a purple border. Edges are drawn between nodes with highly positive correlations (mDCC ≥0.5) with contact (distance between the centers <5Å). Edges between the top 15 betweenness residues are colored black, and other edges are grey. Zigzag edges indicate transient interactions, meaning that DCC <0.5 but mDCC ≥0.5. Some edges that are particularly discussed in the main text are highlighted with a colored background.</p

The RMSF value of each residue.

<p>(A) The RMSF values of the Cα atoms in Ets1. (B) The RMSF values of the phosphorus atoms in DNA. The horizontal axes represent each residue of the molecule from the N-terminus to the C-terminus for Ets1, and from 5’ to 3’ for the DNA. The grey solid line, black solid line, grey dashed line, black dashed line, and black dotted line indicate the results from (i) the quaternary complex, (ii) the Ets1–DNA complex, (iii) the isolated DNA, (iv) the K176A model, and (v) the Y329A model, respectively. The bar below the plot in panel (A) is a secondary structure guide of Ets1: grey, black and white indicate α-helix, β-strand, and others, respectively. For the RMSF calculations of each molecule, the trajectories were superimposed only on the backbone atoms of the molecule, and the other molecules in the model were ignored.</p