Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function.

ABSTRACT: Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. Here we report a novel, widespread cyanophage AMG, encoding a fatty acid desaturase (FAD), found in two genotypes with distinct geographical distribution. FADs are capable of modulating the fluidity of the host's membrane, a fundamental stress response in living cells. We show that both viral FAD (vFAD) families are Δ9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present a comprehensive fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of medium- to long-chain fatty acids no longer than C16, in accordance with the vFAD activity. Our findings suggest that cyanophages are capable of fiddling with the infected host's membranes, possibly leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.

SUBMITTER: Roitman S

PROVIDER: S-EPMC5776448 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Structure and function of a cyanophage-encoded peptide deformylase.

Project description:Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal ?-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 Å resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.

| S-EPMC3660681 | biostudies-literature

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters.

Project description:Prasinophytes clade VII is a group of pico/nano-planktonic green algae (division Chlorophyta) for which numerous ribosomal RNA (rRNA) sequences have been retrieved from the marine environment in the last 15 years. A large number of strains have also been isolated but have not yet received a formal taxonomic description. A phylogenetic analysis of available strains using both the nuclear 18S and plastidial 16S rRNA genes demonstrates that this group composes at least 10 different clades: A1-A7 and B1-B3. Analysis of sequences from the variable V9 region of the 18S rRNA gene collected during the Tara Oceans expedition and in the frame of the Ocean Sampling Day consortium reveal that clade VII is the dominant Chlorophyta group in oceanic waters, replacing Mamiellophyceae, which have this role in coastal waters. At some location, prasinophytes clade VII can even be the dominant photosynthetic eukaryote representing up to 80% of photosynthetic metabarcodes overall. B1 and A4 are the overall dominant clades and different clades seem to occupy distinct niches, for example, A6 is dominant in surface Mediterranean Sea waters, whereas A4 extend to high temperate latitudes. Our work demonstrates that prasinophytes clade VII constitute a highly diversified group, which is a key component of phytoplankton in open oceanic waters but has been neglected in the conceptualization of marine microbial diversity and carbon cycle.

| S-EPMC5270561 | biostudies-literature

Phytoplankton size diversity and ecosystem function relationships across oceanic regions.

Project description:Trait diversity, a key component of biodiversity, mediates many essential ecosystem functions and services. However, the mechanisms behind such relationships at large spatial scales are not fully understood. Here we adopt the functional biogeography approach to investigate how the size composition of phytoplankton communities relates to primary production and export production along a broad latitudinal gradient. Using in situ phytoplankton size distribution data and a trait-based model, we find an increase in the average phytoplankton size, size diversity, primary production and export when moving from low to high latitudes. Our analysis indicates that the interplay between spatio-temporal heterogeneities in environmental conditions and a trade-off between the high affinity for nutrients of smaller cells and the ability to avoid predation by larger cells are the main mechanisms driving the observed patterns. Our results also suggest that variations in size diversity alone do not directly lead to changes in primary production and export. The trade-off thus introduces a feedback that influences the relationship between size diversity and ecosystem functions. These findings support the importance of environmentally mediated trade-offs as crucial mechanisms shaping biodiversity and ecosystem function relationships at large spatial scales.

| S-EPMC5998115 | biostudies-literature

Diversity and Function of Phage Encoded Depolymerases.

Project description:Bacteriophages of the Podoviridae family often exhibit so-called depolymerases as structural components of the virion. These enzymes appear as tail spike proteins (TSPs). After specific binding to capsular polysaccharides (CPS), exopolysaccharides (EPS) or lipopolysaccharide (LPS) of the host bacteria, polysaccharide-repeating units are specifically cleaved. Finally, the phage reaches the last barrier, the cell wall, injects its DNA, and infects the cell. Recently, similar enzymes from bacteriophages of the Ackermannviridae, Myoviridae, and Siphoviridae families were also described. In this mini-review the diversity and function of phage encoded CPS-, EPS-, and LPS-degrading depolymerases is summarized. The function of the enzymes is described in terms of substrate specificity and applications in biotechnology.

| S-EPMC6966330 | biostudies-literature

Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene.

Project description:BackgroundPhages infecting marine picocyanobacteria often carry a psbA gene, which encodes a homolog to the photosynthetic reaction center protein, D1. Host encoded D1 decays during phage infection in the light. Phage encoded D1 may help to maintain photosynthesis during the lytic cycle, which in turn could bolster the production of deoxynucleoside triphosphates (dNTPs) for phage genome replication.Methodology/principal findingsTo explore the consequences to a phage of encoding and expressing psbA, we derive a simple model of infection for a cyanophage/host pair--cyanophage P-SSP7 and Prochlorococcus MED4--for which pertinent laboratory data are available. We first use the model to describe phage genome replication and the kinetics of psbA expression by host and phage. We then examine the contribution of phage psbA expression to phage genome replication under constant low irradiance (25 microE m(-2) s(-1)). We predict that while phage psbA expression could lead to an increase in the number of phage genomes produced during a lytic cycle of between 2.5 and 4.5% (depending on parameter values), this advantage can be nearly negated by the cost of psbA in elongating the phage genome. Under higher irradiance conditions that promote D1 degradation, however, phage psbA confers a greater advantage to phage genome replication.Conclusions/significanceThese analyses illustrate how psbA may benefit phage in the dynamic ocean surface mixed layer.

| S-EPMC2570332 | biostudies-literature

Structural determinant of functionality in acyl lipid desaturases.

Project description:Little is known about the structure-function relationship of membrane-bound lipid desaturases. Using a domain-swapping strategy, we found that the N terminus (comprising the two first transmembrane segments) region of Bacillus cereus DesA desaturase improves Bacillus subtilis Des activity. In addition, the replacement of the first two transmembrane domains from Bacillus licheniformis inactive open reading frame (ORF) BL02692 with the corresponding domain from DesA was sufficient to resurrect this enzyme. Unexpectedly, we were able to restore the activity of ORF BL02692 with a single substitution (Cys40Tyr) of a cysteine localized in the first transmembrane domain close to the lipid-water interface. Substitution of eight residues (Gly90, Trp104, Lys172, His228, Pro257, Leu275, Tyr282, and Leu284) by site-directed mutagenesis produced inactive variants of DesA. Homology modeling of DesA revealed that His228 is part of the metal binding center, together with the canonical His boxes. Trp104 shapes the hydrophobic tunnel, whereas Gly90 and Lys172 are probably involved in substrate binding/recognition. Pro257, Leu275, Tyr282, and Leu284 might be relevant for the structural arrangement of the active site or interaction with electron donors. This study reveals the role of the N-terminal region of Δ5 phospholipid desaturases and the individual residues necessary for the activity of this class of enzymes.

| S-EPMC6168307 | biostudies-literature

Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts.

Project description:Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic prokaryotes in oceanic environments, and are key contributors to global CO(2) fixation, chlorophyll biomass and primary production. Cyanophages, viruses infecting cyanobacteria, are a major force in the ecology of their hosts. These phages contribute greatly to cyanobacterial mortality, therefore acting as a powerful selective force upon their hosts. Phage reproduction is based on utilization of the host transcription and translation mechanisms; therefore, differences in the G+C genomic content between cyanophages and their hosts could be a limiting factor for the translation of cyanophage genes. On the basis of comprehensive genomic analyses conducted in this study, we suggest that cyanophages of the Myoviridae family, which can infect both Prochlorococcus and Synechococcus, overcome this limitation by carrying additional sets of tRNAs in their genomes accommodating AT-rich codons. Whereas the tRNA genes are less needed when infecting their Prochlorococcus hosts, which possess a similar G+C content to the cyanophage, the additional tRNAs may increase the overall translational efficiency of their genes when infecting a Synechococcus host (with high G+C content), therefore potentially enabling the infection of multiple hosts.

| S-EPMC3280135 | biostudies-literature

Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms.

Project description:Bolidomonas is a genus of picoplanktonic flagellated algae that is closely related to diatoms. Triparma laevis, a species belonging to the Parmales, which are small cells with a siliceous covering, has been shown to form a monophyletic group with Bolidomonas. We isolated several novel strains of Bolidophyceae that have permitted further exploration of the diversity of this group using nuclear, plastidial and mitochondrial genes. The resulting phylogenetic data led us to formally emend the taxonomy of this group to include the Parmales within the Bolidophyceae, to combine Bolidomonas within Triparma and to define a novel species, Triparma eleuthera sp. nov. The global distribution of Bolidophyceae was then assessed using environmental sequences available in public databases, as well as a large 18S rRNA V9 metabarcode data set from the Tara Oceans expedition. Bolidophyceans appear ubiquitous throughout the sampled oceans but always constitute a minor component of the phytoplankton community, corresponding to at most ~4% of the metabarcodes from photosynthetic groups (excluding dinoflagellates). They are ~10 times more abundant in the small size fraction (0.8-5 μm) than in larger size fractions. T. eleuthera sp. nov. constitutes the most abundant and most widespread operational taxonomic unit (OTU) followed by T. pacifica, T. mediterranea and the T. laevis clade. The T. mediterranea OTU is characteristic of Mediterranean Sea surface waters and the T. laevis clade OTU is most prevalent in colder waters, in particular off Antarctica.

| S-EPMC5030691 | biostudies-literature

Efficient Broad-Spectrum Cyanophage Function Module Mining.

Project description:Cyanobacterial harmful algal blooms (CyanoHABs) cause health and environmental effects worldwide. Cyanophage is a virus that exclusively infects cyanobacteria. Using cyanophages to control blooms is the latest biological control method. However, little research on the genomics of cyanophages and the presence of numerous proteins with unidentified functions in cyanophage genomes pose challenges for their practical application and comprehensive investigation. We selected the broad-spectrum and efficient cyanophage YongM for our study. On the one hand, through rational analysis, we analyze essential genes, establish the minimal cyanophage genome and single essential gene modules, and examine the impact of essential modules on growth. Additionally, we conducted ultraviolet mutagenesis on YongM to generate more efficient cyanophages' critical modules through random mutagenesis. Then, we sequenced and analyzed the functionality of the mutational gene modules. These findings highlight several gene modules that contribute to a deeper understanding of the functional components within cyanophage genomes.

| S-EPMC11356776 | biostudies-literature

Characterization and genomic analysis of an oceanic cyanophage infecting marine <i>Synechococcus</i> reveal a novel genus.

Project description:Cyanophages play a crucial role in the biogeochemical cycles of aquatic ecosystems by affecting the population dynamics and community structure of cyanobacteria. In this study, a novel cyanophage, Nanhaivirus ms29, that infects Synechococcus sp. MW02 was isolated from the ocean basin in the South China Sea. It was identified as a T4-like phage using transmission electron microscopy. Phylogenetic analysis demonstrated that this cyanophage is distinct from other known T4-like cyanophage, belonging to a novel genus named Nanhaivirus within the family Kyanoviridae, according to the most recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV). The genome of this novel cyanophage is composed of 178,866 bp of double-stranded DNA with a G + C content of 42.5%. It contains 217 potential open reading frames (ORFs) and 6 tRNAs. As many as 30 auxiliary metabolic genes (AMGs) were identified in the genome, which related to photosynthesis, carbon metabolism, nutrient uptake and stress tolerance, possibly reflecting a genomic adaption to the oligotrophic environment. Read-mapping analysis showed that Nanhaivirus ms29 mainly distributed in temperate and tropical epipelagic waters. This study enriches of the virus gene database of cyanophages and provides valuable insights into the phylogeny of cyanophages and their interactions with their hosts.

| S-EPMC10436341 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data