Marine Viruses Exploit Their Host's Two-Component Regulatory System in Response to Resource Limitation

Phosphorus (P) availability, which often limits productivity in marine ecosystems, shapes the P-acquisition gene content of the marine cyanobacteria Prochlorococcus [ [1], [2], [3] and [4]] and its viruses (cyanophages) [ [5] and [6]]. As in other bacteria, in Prochlorococcus these genes are regulated by the PhoR/PhoB two-component regulatory system that is used to sense and respond to P availability and is typical of signal transduction systems found in diverse organisms [7]. Replication of cyanophage genomes requires a significant amount of P, and therefore these phages could gain a fitness advantage by influencing host P acquisition in P-limited environments. Here we show that the transcription of a phage-encoded high-affinity phosphate-binding protein gene (pstS) and alkaline phosphatase gene (phoA)—both of which have host orthologs—is elevated when the phages are infecting host cells that are P starved, relative to P-replete control cells. We further show that the phage versions of these genes are regulated by the host's PhoR/PhoB system. This not only extends this fundamental signaling mechanism to viruses but is also the first example of regulation of lytic phage genes by nutrient limitation in the host. As such, it reveals an important new dimension of the intimate coevolution of phage, host, and environment in the world's oceans.Gordon and Betty Moore FoundationCenter for Microbial Oceanography: Research and EducationCenter for Microbial Oceanography: Research and Education and Biological Oceanography ProgramsUnited States. Dept. of Energ

Picocyanobacteria and deep-ocean fluorescent dissolved organic matter share similar optical properties

Marine chromophoric dissolved organic matter (CDOM) and its related fluorescent components (FDOM), which are widely distributed but highly photobleached in the surface ocean, are critical in regulating light attenuation in the ocean. However, the origins of marine FDOM are still under investigation. Here we show that cultured picocyanobacteria, Synechococcus and Prochlorococcus, release FDOM that closely match the typical fluorescent signals found in oceanic environments. Picocyanobacterial FDOM also shows comparable apparent fluorescent quantum yields and undergoes similar photo-degradation behaviour when compared with deep-ocean FDOM, further strengthening the similarity between them. Ultrahigh-resolution mass spectrometry (MS) and nuclear magnetic resonance spectroscopy reveal abundant nitrogen-containing compounds in Synechococcus DOM, which may originate from degradation products of the fluorescent phycobilin pigments. Given the importance of picocyanobacteria in the global carbon cycle, our results indicate that picocyanobacteria are likely to be important sources of marine autochthonous FDOM, which may accumulate in the deep ocean

Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage.

Cyanophage infecting the marine cyanobacteria Prochlorococcus and Synechococcus require light and host photosystem activity for optimal reproduction. Many cyanophages encode multiple photosynthetic electron transport (PET) proteins, which are presumed to maintain electron flow and produce ATP and NADPH for nucleotide biosynthesis and phage genome replication. However, evidence suggests phage augment NADPH production via the pentose phosphate pathway (PPP), thus calling into question the need for NADPH production by PET. Genes implicated in cyclic PET have since been identified in cyanophage genomes. It remains an open question which mode of PET, cyclic or linear, predominates in infected cyanobacteria, and thus whether the balance is towards producing ATP or NADPH. We sequenced transcriptomes of a cyanophage (P-HM2) and its host (Prochlorococcus MED4) throughout infection in the light or in the dark, and analyzed these data in the context of phage replication and metabolite measurements. Infection was robust in the light, but phage were not produced in the dark. Host gene transcripts encoding high-light inducible proteins and two terminal oxidases (plastoquinol terminal oxidase and cytochrome c oxidase)-implicated in protecting the photosynthetic membrane from light stress-were the most enriched in light but not dark infection. Among the most diminished transcripts in both light and dark infection was ferredoxin-NADP+ reductase (FNR), which uses the electron acceptor NADP+ to generate NADPH in linear photosynthesis. The phage gene for CP12, which putatively inhibits the Calvin cycle enzyme that receives NADPH from FNR, was highly expressed in light infection. Therefore, both PET production of NADPH and its consumption by carbon fixation are putatively repressed during phage infection in light. Transcriptomic evidence is thus consistent with cyclic photophosphorylation using oxygen as the terminal electron acceptor as the dominant mode of PET under infection, with ATP from PET and NADPH from the PPP producing the energy and reducing equivalents for phage nucleotide biosynthesis and replication

F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif

Abstract Background There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does not resemble any characterized homing endonucleases. Instead, the C-terminus of F-CphI aligns well with the N-terminal catalytic domain of a Holliday junction DNA resolvase, phage T4 endonuclease VII (Endo VII). Results A PSI-BLAST search resulted in a total of 313 Endo VII motif–containing sequences in sequenced genomes. Multiple sequence alignment showed that the catalytically important residues of T4 Endo VII were all well conserved in these proteins. Our site-directed mutagenesis studies further confirmed that the catalytically important residues of T4 Endo VII were also essential for F-CphI activity, and thus F-CphI might use a similar protein fold as Endo VII for DNA cleavage. A phylogenetic tree of the Endo VII motif–containing sequences showed that putative resolvases grouped into one clade while putative homing endonucleases and restriction endonucleases grouped into another clade. Conclusions Based on the unique conserved residues, we proposed that F-CphI represents a new homing endonuclease family, which was named the DHHRN family. Our phylogenetic analysis could be used to predict the functions of many previously unknown proteins

Results summary.

<p>Results summary.</p

Phage gene expression in early, middle, and late temporal clusters during light and dark infection.

<p>Relative expression of phage mRNA is in units of reads per kbp gene length per million (RPKM) of host and phage reads (see methods). Phage auxiliary metabolic genes (AMGs) are labeled: <i>cp12</i>, Calvin cycle inhibitor CP12; <i>talC</i>, transaldolase; <i>psbA</i> and <i>psbD</i>, photosystem II D1 and D2 proteins; <i>nrdA</i> and <i>nrdB</i>, ribonucleotide reductase alpha and beta subunits; and <i>hli</i>, high-light inducible proteins.</p

Sedimentary microfacies and palaeogeomorphology as well as their controls on gas accumulation within the deep-buried Cretaceous in Kuqa Depression, Tarim Basin, China

The gas and oil exploration in Kuqa Depression has entered the deep-buried and ultra-deep areas below 5000 m. This paper represents the systematic research accomplished which included microfacies observation and sandstone modeling in the outcrop, the lithofacies interpretation with imaging logging data, and the recovery of nappe tectonics as well as the folding analysis based on the single sedimentary factors in order to define the characteristics of lithofacies and microfacies, the background of paleography and their effects on gas accumulation. This study illustrated that the climate was mainly hot and dry during the sedimentary period of Bashijiqike within the deep-buried Cretaceous, and the deposited water was characterized by low to medium salinity. The deep-buried areas were controlled by three provenances, namely, the Kapushaliang River, the Kelasuhe River, and the Kuqa River. The Dabei-Bozi area was mainly the proximal deposit, the silty-fine sandstone with subrounded and well-sorting features developed in the main channel areas of underwater distributary channel which was constructed in the braided (or fan) delta front. The Keshen area, on the other hand was the distal deposit, the medium-fine sandstone with subangular-subrounded and medium-well sorting features developed in the main channel areas of underwater distributary channel which was constructed also in the braided (or fan) delta front. In the latter stage of the Yanshanian Period, the silty-fine sandstone of the underwater distributary channel had developed with the background of residual palaeohigh and drought climate in Dabei-Bozi area-meanwhile the medium-fine sandstone of the underwater distributary channel had developed with the background of residual palaeohigh slopes and humid climate in Keshen area. In addition, the gas accumulation within the deep zone was evidently controlled by the lithofacies paleography. The gas in the medium-fine sandstone lithofacies of paleoslope was significantly richer than the silty-fine sandstone lithofacies of the paleohigh; the silty lithofacies in the paleohigh was relatively poor. It was supposed that systematic studies would accelerate the oil and gas exploration and development in the deep zones, not to mention provide guidance for the trillion cubic prospects of gas reserves in the deep zones

Tectonic Factors Restricting Differences among Layers in Microstructure of Ultradeep Clastic Rock Reservoir: A Case Study on Cretaceous Bashijiqike Formation in Kuqa Depression

AbstractThe Cretaceous Bashijiqike Formation in the Kelasu structural belt of Kuqa Depression is an ultradeep reservoir with burial depth of more than 6 km. Due to the influence of strong thrust nappe from the South Tianshan in the north, the burial depth gradually deepened from north to south in the Kelasu tectonic belt. With the increase of the burial depth, the influence of tectonic compression relatively weakens, and the formation mechanism that affects the microstructure of ultradeep clastic reservoir is changed. Comprehensive analysis of thin section and quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN), scanning electron microscope (SEM), and micro-CT scanning are used to investigate the characteristics of the Cretaceous Bashijiqike Formation at the depth of 8000 m (TVD) in various stress sections. The result shows that, for the ultradeep reservoir with burial depth up to 8000 m, its reservoir characteristics and interlayer differences are not completely restricted by the neutral surface effect. (1) The porosity and permeability of various stress sections are different, and the reservoir physical properties of the tensile section are higher than that in the compressive section. (2) The pore types, pore radius, and pore throat connectivity of various stress sections are different, and the development of pores and throats in the tensile section is better than that in the compressive section. (3) As an ultradeep clastic rock reservoir, the vertical fracture development characteristics of Well Bozi9 at the depth of 8000 m differ from that in Kela-Keshen area at the depth of 6000 m in the model of strain neutral surface. The interlayer difference in the microstructure of ultradeep clastic rock reservoir is clarified, which has a positive effect to evaluate and predict the distribution of favorable deep reservoir