The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Oded Beja - One of the best experts on this subject based on the ideXlab platform.
-
an uncultured marine Cyanophage encodes an active phycobilisome proteolysis adaptor protein nbla
Environmental Microbiology Reports, 2019Co-Authors: Omer Nadel, Jose Floresuribe, Shirley Larom, Andrey Rozenberg, Rakefet Schwarz, Oded BejaAbstract:Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as light-harvesting antennae for the photosynthetic apparatus. When deplete of nitrogen or sulphur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish these vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (∼6 kDa), which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater Cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine Cyanophage lineage, representatives of which contain genes coding for the PBS degradation protein. Here, we examined the functionality of nblA-like genes from these marine Cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine Cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and Cyanophages.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
Environmental Microbiology Reports, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
bioRxiv, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Summary Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, the genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment. Originality-Significance Statement Marine cyanobacteria are major contributors to primary production in the ocean. Despite reports of lysogeny in marine cyanobacteria, genomes from lysogenic marine Cyanophages have not been reported yet. Using metagenomics assemblies, we recovered complete genomes of a novel uncultured marine Cyanophage lineage. Remarkably, the DNA polymerase of these uncultured phages forms a monophyletic clade with the DNA polymerase from a genomic island in Synechococcus WH8016. The genomic island contains a putative relic prophage that does not resemble any known cultured Cyanophage but shares several genes with the newly identified Cyanophage family. These findings provide both phylogenomic and abundance estimates that are missing from current ecological models of this important group of marine viruses.
-
uncultured marine Cyanophages encode for active nbla phycobilisome proteolysis adaptor protein
bioRxiv, 2018Co-Authors: Omer Nadel, Jose Floresuribe, Shirley Larom, Andrey Rozenberg, Rakefet Schwarz, Oded BejaAbstract:Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as a light-harvesting antennas for the photosynthetic apparatus. When short of nitrogen or sulfur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish the vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (~6 kDa) which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater Cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine Cyanophage lineage which contain genes coding for the PBS degradation protein. Here, we examine the functionality of nblA-like genes from these marine Cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine Cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and Cyanophages.
-
a novel oceanic uncultured temperate Cyanophage lineage
bioRxiv, 2018Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Oded BejaAbstract:Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, isolation of lysogenic marine Cyanophages has not been reported yet. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain genes coding for common Cyanophage proteins, as well as the phycobilisome degradation protein NblA, an integrase, and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a putative prophage in Synechococcus WH8016. The putative prophage does not resemble any known Cyanophage but shares several genes with the newly identified Cyanophages. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. This is the first report of a putative prophage in a cultured marine Synechococcus and the genomic characterization of its Cyanophage relatives.
Jose Floresuribe - One of the best experts on this subject based on the ideXlab platform.
-
an uncultured marine Cyanophage encodes an active phycobilisome proteolysis adaptor protein nbla
Environmental Microbiology Reports, 2019Co-Authors: Omer Nadel, Jose Floresuribe, Shirley Larom, Andrey Rozenberg, Rakefet Schwarz, Oded BejaAbstract:Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as light-harvesting antennae for the photosynthetic apparatus. When deplete of nitrogen or sulphur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish these vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (∼6 kDa), which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater Cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine Cyanophage lineage, representatives of which contain genes coding for the PBS degradation protein. Here, we examined the functionality of nblA-like genes from these marine Cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine Cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and Cyanophages.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
Environmental Microbiology Reports, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
bioRxiv, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Summary Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, the genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment. Originality-Significance Statement Marine cyanobacteria are major contributors to primary production in the ocean. Despite reports of lysogeny in marine cyanobacteria, genomes from lysogenic marine Cyanophages have not been reported yet. Using metagenomics assemblies, we recovered complete genomes of a novel uncultured marine Cyanophage lineage. Remarkably, the DNA polymerase of these uncultured phages forms a monophyletic clade with the DNA polymerase from a genomic island in Synechococcus WH8016. The genomic island contains a putative relic prophage that does not resemble any known cultured Cyanophage but shares several genes with the newly identified Cyanophage family. These findings provide both phylogenomic and abundance estimates that are missing from current ecological models of this important group of marine viruses.
-
uncultured marine Cyanophages encode for active nbla phycobilisome proteolysis adaptor protein
bioRxiv, 2018Co-Authors: Omer Nadel, Jose Floresuribe, Shirley Larom, Andrey Rozenberg, Rakefet Schwarz, Oded BejaAbstract:Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as a light-harvesting antennas for the photosynthetic apparatus. When short of nitrogen or sulfur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish the vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (~6 kDa) which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater Cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine Cyanophage lineage which contain genes coding for the PBS degradation protein. Here, we examine the functionality of nblA-like genes from these marine Cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine Cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and Cyanophages.
-
a novel oceanic uncultured temperate Cyanophage lineage
bioRxiv, 2018Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Oded BejaAbstract:Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, isolation of lysogenic marine Cyanophages has not been reported yet. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain genes coding for common Cyanophage proteins, as well as the phycobilisome degradation protein NblA, an integrase, and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a putative prophage in Synechococcus WH8016. The putative prophage does not resemble any known Cyanophage but shares several genes with the newly identified Cyanophages. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. This is the first report of a putative prophage in a cultured marine Synechococcus and the genomic characterization of its Cyanophage relatives.
Curtis A Suttle - One of the best experts on this subject based on the ideXlab platform.
-
The Environment and Cyanophage Diversity: Insights From Environmental Sequencing of DNA Polymerase
Frontiers Media S.A., 2019Co-Authors: Jan F. Finke, Curtis A SuttleAbstract:Globally distributed and abundant Cyanophages in the family Myoviridae have dsDNA genomes with variable gene content, including host-derived auxiliary metabolic genes (AMGs) that potentially can facilitate viral replication. However, it is not well understood how this variation in gene content interacts with environmental variables to shape cyanomyovirus communities. This project correlated the genetic repertoire of cyanomyoviruses with their phyologeny, and investigated cyanomyovirus ecotype distribution as a function of environmental conditions across locations and seasons. Reference cyanomyovirus genomes were compared for their overlap in gene content to infer phyologenetic distances, and these distances were compared to distances calculated based on DNA polymerase (gp43) gene sequences. In turn, gp43 partial gene sequences amplified from natural Cyanophage communities were used to describe cyanomyovirus community composition and to assess the relationship between environmental variables. The results showed the following: (1) DNA polymerase gene phylogeny generally correlated with the similarity in gene content among reference cyanomyoviruses, and thus can be used to describe environmental cyanomyovirus communities; (2) spatial and seasonal patterns in cyanomyovirus communities were related to environmental variables; (3) salinity and temperature, combined with nutrient concentration were predictors of cyanomyovirus richness, diversity and community composition. This study shows that environmental variables shape viral communities by drawing on a diverse seed bank of viral genotypes. From these results it is evident that that viral ecotypes with their corresponding genetic repertoires underlie selection pressures. However, the mechanisms involved in selecting for specific viral genotypes remain to be fully understood
-
viruses infecting a freshwater filamentous cyanobacterium nostoc sp encode a functional crispr array and a proteobacterial dna polymerase b
Mbio, 2016Co-Authors: Caroline Chenard, Jennifer F Wirth, Curtis A SuttleAbstract:ABSTRACT Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced Cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a Cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc Cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages. IMPORTANCE Filamentous cyanobacteria belonging to the genus Nostoc are widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of Cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other Cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, Cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these Cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.
-
phylogenetic diversity of sequences of Cyanophage photosynthetic gene psba in marine and freshwaters
Applied and Environmental Microbiology, 2008Co-Authors: Caroline Chenard, Curtis A SuttleAbstract:Many Cyanophage isolates which infect the marine cyanobacteria Synechococcus spp. and Prochlorococcus spp. contain a gene homologous to psbA, which codes for the D1 protein involved in photosynthesis. In the present study, Cyanophage psbA gene fragments were readily amplified from freshwater and marine samples, confirming their widespread occurrence in aquatic communities. Phylogenetic analyses demonstrated that sequences from freshwaters have an evolutionary history that is distinct from that of their marine counterparts. Similarly, sequences from Cyanophages infecting Prochlorococcus and Synechococcus spp. were readily discriminated, as were sequences from podoviruses and myoviruses. Viral psbA sequences from the same geographic origins clustered within different clades. For example, Cyanophage psbA sequences from the Arctic Ocean fell within the Synechococcus as well as Prochlorococcus phage groups. Moreover, as psbA sequences are not confined to a single family of phages, they provide an additional genetic marker that can be used to explore the diversity and evolutionary history of Cyanophages in aquatic environments.
-
nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments
Applied and Environmental Microbiology, 2005Co-Authors: Cindy M Short, Curtis A SuttleAbstract:Primers were designed to amplify a 592-bp region within a conserved structural gene (g20) found in some Cyanophages. The goal was to use this gene as a proxy to infer genetic richness in natural Cyanophage communities and to determine if sequences were more similar in similar environments. Gene products were amplified from samples from the Gulf of Mexico, the Arctic, Southern, and Northeast and Southeast Pacific Oceans, an Arctic cyanobacterial mat, a catfish production pond, lakes in Canada and Germany, and a depth of ca. 3,246 m in the Chuckchi Sea. Amplicons were separated by denaturing gradient gel electrophoresis, and selected bands were sequenced. Phylogenetic analysis revealed four previously unknown groups of g20 clusters, two of which were entirely found in freshwater. Also, sequences with >99% identities were recovered from environments that differed greatly in temperature and salinity. For example, nearly identical sequences were recovered from the Gulf of Mexico, the Southern Pacific Ocean, an Arctic freshwater cyanobacterial mat, and Lake Constance, Germany. These results imply that closely related hosts and the viruses infecting them are distributed widely across environments or that horizontal gene exchange occurs among phage communities from very different environments. Moreover, the amplification of g20 products from deep in the cyanobacterium-sparse Chuckchi Sea suggests that this primer set targets bacteriophages other than those infecting cyanobacteria.
-
lysogeny and lytic viral production during a bloom of the cyanobacterium synechococcus spp
Microbial Ecology, 2002Co-Authors: Alice C Ortmann, Janice E Lawrence, Curtis A SuttleAbstract:Lytic viral production and lysogeny were investigated in cyanobacteria and heterotrophic bacteria during a bloom of Synechococcus spp. in a pristine fjord in British Columbia, Canada. Triplicate seawater samples were incubated with and without mitomycin C and the abundances of heterotrophic bacteria, cyanobacteria, total viruses and infectious Cyanophage were followed over 24 h. Addition of mitomycin C led to increases in total viral abundance as well as the abundance of Cyanophages infecting Synechococcus strain DC2. Given typical estimates of burst size, these increases were consistent with 80% of the heterotrophic bacteria and 0.6% of Synechococcus cells being inducible by the addition of mitomycin C. This is the highest percentage of lysogens reported for a natural microbial community and demonstrates induction in a marine Synechococcus population. It is likely that the Cyanophage production following the addition of mitomycin C was much higher than that titered against a single strain of Synechococcus; hence this estimate is a minimum. In untreated seawater samples, lytic viral production was estimated to remove ca. 27% of the gross heterotrophic bacterial production, and a minimum of 1.0% of the gross cyanobacterial production. Our results demonstrate very high levels of lysogeny in the heterotrophic bacterial community, outside of an oligotrophic environment, and the presence of inducible lysogens in Synechococcus spp. during a naturally occurring bloom. These data emphasize the need for further examination of the factors influencing lytic and lysogenic viral infection in natural microbial communities.
Itai Sharon - One of the best experts on this subject based on the ideXlab platform.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
Environmental Microbiology Reports, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
bioRxiv, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Summary Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, the genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment. Originality-Significance Statement Marine cyanobacteria are major contributors to primary production in the ocean. Despite reports of lysogeny in marine cyanobacteria, genomes from lysogenic marine Cyanophages have not been reported yet. Using metagenomics assemblies, we recovered complete genomes of a novel uncultured marine Cyanophage lineage. Remarkably, the DNA polymerase of these uncultured phages forms a monophyletic clade with the DNA polymerase from a genomic island in Synechococcus WH8016. The genomic island contains a putative relic prophage that does not resemble any known cultured Cyanophage but shares several genes with the newly identified Cyanophage family. These findings provide both phylogenomic and abundance estimates that are missing from current ecological models of this important group of marine viruses.
-
a novel oceanic uncultured temperate Cyanophage lineage
bioRxiv, 2018Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Oded BejaAbstract:Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, isolation of lysogenic marine Cyanophages has not been reported yet. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain genes coding for common Cyanophage proteins, as well as the phycobilisome degradation protein NblA, an integrase, and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a putative prophage in Synechococcus WH8016. The putative prophage does not resemble any known Cyanophage but shares several genes with the newly identified Cyanophages. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. This is the first report of a putative prophage in a cultured marine Synechococcus and the genomic characterization of its Cyanophage relatives.
-
Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function
The ISME Journal, 2018Co-Authors: Sheila Roitman, Itai Sharon, Ellen Hornung, José Flores-uribe, Ivo Feussner, Oded BejaAbstract: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.
-
Cyanophage encoded lipid desaturases oceanic distribution diversity and function
bioRxiv, 2017Co-Authors: Sheila Roitman, Itai Sharon, Jose Floresuribe, Ellen Hornung, Ivo Feussner, Oded BejaAbstract: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 host9s membrane, a fundamental stress response in living cells. We show that both viral fatty acid desaturases (vFADs) families are Δ9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present the first 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 to the vFADs activity. Our findings suggest that Cyanophages fiddle with the infected host9s cell, leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.
Shirley Larom - One of the best experts on this subject based on the ideXlab platform.
-
an uncultured marine Cyanophage encodes an active phycobilisome proteolysis adaptor protein nbla
Environmental Microbiology Reports, 2019Co-Authors: Omer Nadel, Jose Floresuribe, Shirley Larom, Andrey Rozenberg, Rakefet Schwarz, Oded BejaAbstract:Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as light-harvesting antennae for the photosynthetic apparatus. When deplete of nitrogen or sulphur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish these vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (∼6 kDa), which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater Cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine Cyanophage lineage, representatives of which contain genes coding for the PBS degradation protein. Here, we examined the functionality of nblA-like genes from these marine Cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine Cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and Cyanophages.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
Environmental Microbiology Reports, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment.
-
a novel uncultured marine Cyanophage lineage with lysogenic potential linked to a putative marine synechococcus relic prophage
bioRxiv, 2019Co-Authors: Jose Floresuribe, Itai Sharon, Alon Philosof, Svetlana Fridman, Shirley Larom, Oded BejaAbstract:Summary Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (Cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, the genome sequence of such temperate Cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine Cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine Cyanophage lineage, which contain, in addition to common Cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported Cyanophage but shares several genes with the newly identified Cyanophages reported here. Metagenomic recruitment indicates that the novel Cyanophages are widespread, albeit at low abundance. Here we describe a novel potentially lysogenic Cyanophage family, their abundance and distribution in the marine environment. Originality-Significance Statement Marine cyanobacteria are major contributors to primary production in the ocean. Despite reports of lysogeny in marine cyanobacteria, genomes from lysogenic marine Cyanophages have not been reported yet. Using metagenomics assemblies, we recovered complete genomes of a novel uncultured marine Cyanophage lineage. Remarkably, the DNA polymerase of these uncultured phages forms a monophyletic clade with the DNA polymerase from a genomic island in Synechococcus WH8016. The genomic island contains a putative relic prophage that does not resemble any known cultured Cyanophage but shares several genes with the newly identified Cyanophage family. These findings provide both phylogenomic and abundance estimates that are missing from current ecological models of this important group of marine viruses.
-
uncultured marine Cyanophages encode for active nbla phycobilisome proteolysis adaptor protein
bioRxiv, 2018Co-Authors: Omer Nadel, Jose Floresuribe, Shirley Larom, Andrey Rozenberg, Rakefet Schwarz, Oded BejaAbstract:Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as a light-harvesting antennas for the photosynthetic apparatus. When short of nitrogen or sulfur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish the vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (~6 kDa) which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater Cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine Cyanophage lineage which contain genes coding for the PBS degradation protein. Here, we examine the functionality of nblA-like genes from these marine Cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine Cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and Cyanophages.
-
a myovirus encoding both photosystem i and ii proteins enhances cyclic electron flow in infected prochlorococcus cells
Nature microbiology, 2017Co-Authors: Svetlana Fridman, Jose Floresuribe, Shirley Larom, Onit Alalouf, Oded Liran, Iftach Yacoby, Faris Salama, Benjamin Bailleul, Fabrice Rappaport, Tamar ZivAbstract:Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (Cyanophages). Although photosystem II (PSII) genes are common in both cultured Cyanophages and environmental samples 1–4 , viral photosystem I (vPSI) genes have so far only been detected in environmental samples 5,6 . Here, we have used a targeted strategy to isolate a Cyanophage from the tropical Pacific Ocean that carries a PSI gene cassette with seven distinct PSI genes (psaJF, C, A, B, K, E, D) as well as two PSII genes (psbA, D). This Cyanophage, P-TIM68, belongs to the T4-like myoviruses, has a prolate capsid, a long contractile tail and infects Prochlorococcus sp. strain MIT9515. Phage photosynthesis genes from both photosystems are expressed during infection, and the resultant proteins are incorporated into membranes of the infected host. Moreover, photosynthetic capacity in the cell is maintained throughout the infection cycle with enhancement of cyclic electron flow around PSI. Analysis of metagenomic data from the Tara Oceans expedition 7 shows that phages carrying PSI gene cassettes are abundant in the tropical Pacific Ocean, composing up to 28% of T4-like cyanomyophages. They are also present in the tropical Indian and Atlantic Oceans. P-TIM68 populations, specifically, compose on average 22% of the PSI-gene-cassette carrying phages. Our results suggest that Cyanophages carrying PSI and PSII genes are likely to maintain and even manipulate photosynthesis during infection of their Prochlorococcus hosts in the tropical oceans. Isolation of a Cyanophage encoding photosystem I genes reveals that these are expressed during infection and inserted into host membranes, resulting in enhanced electron flow, and that phage carrying these genes are abundant in marine environments.
