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Bragg JG, Chisholm SW. Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene. PLoS One 2008; 3:e3550. [PMID: 18958282 PMCID: PMC2570332 DOI: 10.1371/journal.pone.0003550] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/03/2008] [Indexed: 11/20/2022] Open
Abstract
Background Phages 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 Findings To 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 µE 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 / Significance These analyses illustrate how psbA may benefit phage in the dynamic ocean surface mixed layer.
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Bryan MJ, Burroughs NJ, Spence EM, Clokie MRJ, Mann NH, Bryan SJ. Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer. PLoS One 2008; 3:e2048. [PMID: 18431505 PMCID: PMC2297514 DOI: 10.1371/journal.pone.0002048] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 03/11/2008] [Indexed: 11/21/2022] Open
Abstract
Background S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage. Methodology/Principal Findings This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces. Conclusions/Significance This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene.
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Liu X, Shi M, Kong S, Gao Y, An C. Cyanophage Pf-WMP4, a T7-like phage infecting the freshwater cyanobacterium Phormidium foveolarum: complete genome sequence and DNA translocation. Virology 2007; 366:28-39. [PMID: 17499329 DOI: 10.1016/j.virol.2007.04.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 04/05/2007] [Accepted: 04/10/2007] [Indexed: 11/27/2022]
Abstract
We report the complete 40,938-bp genome sequence of a cyanophage, Pf-WMP4, which infects the freshwater cyanobacterium Phormidium foveolarum Gom. Nine of the forty-five potential open reading frames in the Pf-WMP4 genome share similarities with the genes found in T7-like phages. Using in vitro transcription, we found that seven promoters at the leftmost end of the genome can be recognized by the host RNA polymerase. By blocking transcriptional and translational inhibitors, we found that Pf-WMP4 DNA translocation, with an average translocation rate of 19.8+/-2.7 bp s(-1) at 28 degrees C, requires both host transcription and protein synthesis of an unknown factor. Therefore the mechanism of cyanophage Pf-WMP4 DNA injection may be driven both by a T7-like internalization mechanism as well as an additional unknown mechanism requiring de novo protein synthesis. Our analysis of the Pf-WMP4 genome sheds new light on the translocation strategies and evolutionary traces of phages belonging to the T7 supergroup.
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Abstract
In contrast to the phages of heterotrophic hosts, light can play a key role in all aspects of the life cycle of phages infecting ecologically important marine unicellular cyanobacteria of the genera Synechococcus and Prochlorococcus. Phage adsorption, replication, modulation of the host cell metabolism, and survival in the environment following lysis, all exhibit light-dependent components. The analysis of cyanophage genomes has revealed the acquisition of key photosynthetic genes during the course of evolution, such as those encoding central components of the light harvesting apparatus. These discoveries are beginning to reveal novel features of the interactions between parasite and host that shape the biology of both.
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Baker AC, Goddard VJ, Davy J, Schroeder DC, Adams DG, Wilson WH. Identification of a diagnostic marker to detect freshwater cyanophages of filamentous cyanobacteria. Appl Environ Microbiol 2006; 72:5713-9. [PMID: 16957185 PMCID: PMC1563665 DOI: 10.1128/aem.00270-06] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanophages are viruses that infect the cyanobacteria, globally important photosynthetic microorganisms. Cyanophages are considered significant components of microbial communities, playing major roles in influencing host community diversity and primary productivity, terminating cyanobacterial water blooms, and influencing biogeochemical cycles. Cyanophages are ubiquitous in both marine and freshwater systems; however, the majority of molecular research has been biased toward the study of marine cyanophages. In this study, a diagnostic probe was developed to detect freshwater cyanophages in natural waters. Oligonucleotide PCR-based primers were designed to specifically amplify the major capsid protein gene from previously characterized freshwater cyanomyoviruses that are infectious to the filamentous, nitrogen-fixing cyanobacterial genera Anabaena and Nostoc. The primers were also successful in yielding PCR products from mixed virus communities concentrated from water samples collected from freshwater lakes in the United Kingdom. The probes are thought to provide a useful tool for the investigation of cyanophage diversity in freshwater environments.
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Clokie MRJ, Shan J, Bailey S, Jia Y, Krisch HM, West S, Mann NH. Transcription of a 'photosynthetic' T4-type phage during infection of a marine cyanobacterium. Environ Microbiol 2006; 8:827-35. [PMID: 16623740 DOI: 10.1111/j.1462-2920.2005.00969.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transcription of S-PM2 phage following infection of Synechococcus sp. WH7803, a marine cyanobacterium, was analysed by quantitative real-time PCR. Unlike the distantly related coliphage T4, there were only two (early and late) instead of three (early, middle and late) classes of transcripts during the developmental cycle of the phage. This difference is consistent with the absence from the S-PM2 genome of T4-like middle mode promoter sequences and the transcription factors associated with their recognition. Phage S-PM2 carries the 'photosynthetic' genes psbA and psbD that encode homologues of the host photosystem II proteins D1 and D2. Transcripts of the phage psbA gene appeared soon after infection and remained at high levels until lysis. Throughout the course of infection, the photosynthetic capacity of the cells remained constant. A considerable transient increase in the abundance of the host psbA transcripts occurred shortly after infection, suggesting that the host responds to the trauma of phage infection in a similar way as it does to a variety of other environmental stresses. The very substantial transcription of the phage psbA gene during the latter phase of phage infection suggests that S-PM2 has acquired this cellular gene to ensure that D1 levels and thus photosynthesis are fully maintained until the infected cell finally lyses. Unexpectedly, transcripts of a phage-encoded S-layer protein gene were among the earliest and most abundant detected, suggesting that this partial homologue of a host protein plays an important role in the S-PM2 infection process.
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Lee LH, Lui D, Platner PJ, Hsu SF, Chu TC, Gaynor JJ, Vega QC, Lustigman BK. Induction of temperate cyanophage AS-1 by heavy metal--copper. BMC Microbiol 2006; 6:17. [PMID: 16504132 PMCID: PMC1397841 DOI: 10.1186/1471-2180-6-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Accepted: 02/24/2006] [Indexed: 11/21/2022] Open
Abstract
Background It has been reported that some marine cyanophage are temperate and can be induced from a lysogenic phase to a lytic phase by different agents such as heavy metals. However, to date no significant reports have focused on the temperate nature of freshwater cyanophage/cyanobacteria. Previous experiments with cyanophage AS-1 and cyanobacteria Anacystis nidulans have provided some evidence that AS-1 may have a lysogenic life cycle in addition to the characterized lytic cycle. Results In this study, the possible temperate A. nidulans was treated with different concentrations of heavy metal-copper. CuSO4 with concentrations of 3.1 × 10-3 M, 3.1 × 10-4 M, 3.1 × 10-5 M and 3.1 × 10-6 M were used to detect the induction of AS-1 from A. nidulans. The population of the host, unicellular cyanobacteria Anacystis nidulans, was monitored by direct count and turbidity while the amount of virus produced was derived from plaque forming units (PFU) by a direct plating method. The ratio of AS-1 release from A. nidulans was also determined. From these results it appears that AS-1 lysogenic phage can be induced by copper at concentrations from 3.1 × 10-6 M to 3.1 × 10-4 M. Maximal phage induction occurred at 6 hours after addition of copper, with an optimal concentration of 3.1 × 10-6 M. Conclusion Cu2+ is a significant inducer for lysogenic cyanobacterial cells and consequently would be a potential control agent in the cyanobacteria population in fresh water ecosystems.
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Hambly E, Suttle CA. The viriosphere, diversity, and genetic exchange within phage communities. Curr Opin Microbiol 2005; 8:444-50. [PMID: 15979387 DOI: 10.1016/j.mib.2005.06.005] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Accepted: 06/13/2005] [Indexed: 01/25/2023]
Abstract
Natural phage communities are reservoirs of the greatest uncharacterized genetic diversity on Earth. Yet, identical phage sequences can be found in extremely different environments, which implies that there is wide circulation of viral genes among distantly related host populations. Further evidence of genetic exchange among phage and host communities is the presence in phage of genes coding for proteins that are essential for photosynthesis. These observations support the idea that a primary role of host populations in phage ecology and evolution is to serve as vectors for genetic exchange.
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Tan G, Gao Y, Shi M, Zhang X, He S, Chen Z, An C. SiteFinding-PCR: a simple and efficient PCR method for chromosome walking. Nucleic Acids Res 2005; 33:e122. [PMID: 16077029 PMCID: PMC1182332 DOI: 10.1093/nar/gni124] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In this paper, we present a novel PCR method, termed SiteFinding-PCR, for gene or chromosome walking. The PCR was primed by a SiteFinder at a low temperature, and then the target molecules were amplified exponentially with gene-specific and SiteFinder primers, and screened out by another gene-specific primer and a vector primer. However, non-target molecules could not be amplified exponentially owing to the suppression effect of stem–loop structure and could not be screened out. This simple method proved to be efficient, reliable, inexpensive and time-saving, and may be suitable for the molecules for which gene-specific primers are available. More importantly, large DNA fragments can be obtained easily using this method. To demonstrate the feasibility and efficiency of SiteFinding-PCR, we employed this method to do chromosome walking and obtained 16 positive results from 17 samples.
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Short CM, Suttle CA. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 2005; 71:480-6. [PMID: 15640224 PMCID: PMC544240 DOI: 10.1128/aem.71.1.480-486.2005] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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Millard A, Clokie MRJ, Shub DA, Mann NH. Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proc Natl Acad Sci U S A 2004; 101:11007-12. [PMID: 15263091 PMCID: PMC503734 DOI: 10.1073/pnas.0401478101] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The discovery of the genes psbA and psbD, encoding the D1 and D2 core components of the photosynthetic reaction center PSII (photosystem II), in the genome of the bacteriophage S-PM2 (a cyanomyovirus) that infects marine cyanobacteria begs the question as to how these genes were acquired. In an attempt to answer this question, it was established that the occurrence of the genes is widespread among marine cyanomyovirus isolates and may even extend to podoviruses. The phage psbA genes fall into a clade that includes the psbA genes from their potential Synechococcus and Prochlorococcus hosts, and thus, this phylogenetic analysis provides evidence to support the idea of the acquisition of these genes by horizontal gene transfer from their cyanobacterial hosts. However, the phage psbA genes form distinct subclades within this lineage, which suggests that their acquisition was not very recent. The psbA genes of two phages contain identical 212-bp insertions that exhibit all of the canonical structural features of a group I self-splicing intron. The different patterns of genetic organization of the psbAD region are consistent with the idea that the psbA and psbD genes were acquired more than once by cyanomyoviruses and that their horizontal transfer between phages via a common phage gene pool, as part of mobile genetic modules, may be a continuing process. In addition, genes were discovered encoding a high-light inducible protein and a putative key enzyme of dark metabolism, transaldolase, extending the areas of host-cell metabolism that may be affected by phage infection.
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Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, Chisholm SW. Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci U S A 2004; 101:11013-8. [PMID: 15256601 PMCID: PMC503735 DOI: 10.1073/pnas.0401526101] [Citation(s) in RCA: 354] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomics gives us a new window into phage-host interactions and their evolutionary implications. Here we report the presence of genes central to oxygenic photosynthesis in the genomes of three phages from two viral families (Myoviridae and Podoviridae) that infect the marine cyanobacterium Prochlorococcus. The genes that encode the photosystem II core reaction center protein D1 (psbA), and a high-light-inducible protein (HLIP) (hli) are present in all three genomes. Both myoviruses contain additional hli gene types, and one of them encodes the second photosystem II core reaction center protein D2 (psbD), whereas the other encodes the photosynthetic electron transport proteins plastocyanin (petE) and ferredoxin (petF). These uninterrupted, full-length genes are conserved in their amino acid sequence, suggesting that they encode functional proteins that may help maintain photosynthetic activity during infection. Phylogenetic analyses show that phage D1, D2, and HLIP proteins cluster with those from Prochlorococcus, indicating that they are of cyanobacterial origin. Their distribution among several Prochlorococcus clades further suggests that the genes encoding these proteins were transferred from host to phage multiple times. Phage HLIPs cluster with multicopy types found exclusively in Prochlorocococus, suggesting that phage may be mediating the expansion of the hli gene family by transferring these genes back to their hosts after a period of evolution in the phage. These gene transfers are likely to play a role in the fitness landscape of hosts and phages in the surface oceans.
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Reva ON, Tümmler B. Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics 2004; 5:90. [PMID: 15239845 PMCID: PMC487896 DOI: 10.1186/1471-2105-5-90] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Accepted: 07/07/2004] [Indexed: 11/29/2022] Open
Abstract
Background Oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail. In this paper we analyzed oligonucleotide usage (OU) biases in a comprehensive collection of 155 completely sequenced bacterial chromosomes, 316 plasmids and 104 phages. Results Two global features were analyzed: pattern skew (PS) and variance of OU deviations normalized by mononucleotide content of the sequence (OUV). OUV reflects the strength of OU biases and taxonomic signals. PS denotes asymmetry of OU in direct and reverse DNA strands. A trend towards minimal PS was observed for almost all complete sequences of bacterial chromosomes and plasmids, however, PS was substantially higher in separate genomic loci and several types of plasmids and phages characterized by long stretches of non-coding DNA and/or asymmetric gene distribution on the two DNA strands. Five of the 155 bacterial chromosomes have anomalously high PS, of which the chromosomes of Xylella fastidiosa 9a5c and Prochlorococcus marinus MIT9313 exhibit extreme PS values suggesting an intermediate unstable state of these two genomes. Conclusions Strand symmetry as indicated by minimal PS is a universally conserved feature of complete bacterial genomes that results from the matching mutual compensation of local OU biases on both replichors while OUV is more a taxon specific feature. Local events such as inversions or the incorporation of genome islands are balanced by global changes in genome organization to minimize PS that may represent one of the leading evolutionary forces driving bacterial genome diversification.
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Dorigo U, Jacquet S, Humbert JF. Cyanophage diversity, inferred from g20 gene analyses, in the largest natural lake in France, Lake Bourget. Appl Environ Microbiol 2004; 70:1017-22. [PMID: 14766584 PMCID: PMC348939 DOI: 10.1128/aem.70.2.1017-1022.2004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic diversity of the natural freshwater community of cyanophages and its variations over time have been investigated for the first time in the surface waters of the largest natural lake in France. This was done by random screening of clone libraries for the g20 gene and by denaturing gradient gel electrophoresis (DGGE). Nucleotide sequence analysis revealed 35 distinct cyanomyovirus g20 genotypes among the 47 sequences analyzed. Phylogenetic analyses showed that these sequences fell into seven genetically distinct operational taxonomic units (OTUs). The distances between these OTUs were comparable to those reported between marine clusters. Moreover, some of these freshwater cyanophage sequences were genetically more closely related to marine cyanophage sequences than to other freshwater sequences. Both approaches for the g20 gene (sequencing and DGGE analysis) showed that there was a clear seasonal pattern of variation in the composition of the cyanophage community that could reflect changes in its biological, chemical, and/or physical environment.
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Mendzhul MI, Lysenko TG, Busakhina IV, Shainskaia OA. [Phagoresistance of filamentous cyanobacteria clones]. MIKROBIOLOHICHNYI ZHURNAL (KIEV, UKRAINE : 1993) 2004; 66:48-56. [PMID: 15104055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The paper deals with formation regularities of phagoresistant clones of cyanobacteria in two productive virus-cell systems: heterocyst cyanobacterium Nostoc linckia--cyanophage N-2, and mutant in heterocysts strain of Anabaena variabilis--cyanophage A-1. Frequency of spontaneous formation of phagoresistant clones of cyanobacterium N. linckia varies within 1.0-8.0 x 10(-6) per a cell, A. variabilis--5.0 x 10(-6)-7.0 x 10(-7) per cell. All the studied phagoresistant clones of N. linckia have identical morpho-cultural properties and do not differ from those of the initial culture. Phagoresistant clones of A. variabilis are presented by two groups. One of them, as to its properties, does not practically differ from the wild type culture. The second group differs considerably from the initial culture A. variabilis as to a number of characteristics--time of colonies appearance, their amount, length of trichomas, specific rate of growth and biomass accumulation. Spontaneous transfer of cyanophages to the culture liquid of clones resistant forms of cyanobacteria has not been revealed. Lysis of cells of the studied clones also was not induced under the effect of mytomycin C, thermal treatment and UV-irradiation. Cyanophage N-2 is not adsorbed by the cells of resistant cloned forms of cyanobacteria N. linckia. Only nonspecific adsorption takes place on the cells of phage-resistant clones of A. variabilis of both groups: about 20% of virions introduced in the adsorption mixture. Basing on the data obtained, it is supposed that phage-resistance of stable clones of filamentous cyanobacteria under the conditions of the given experiment is determined by the structure modification of cells receptors.
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Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J. The genome of a motile marine Synechococcus. Nature 2003; 424:1037-42. [PMID: 12917641 DOI: 10.1038/nature01943] [Citation(s) in RCA: 386] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2003] [Accepted: 07/28/2003] [Indexed: 11/08/2022]
Abstract
Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria.
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Sullivan MB, Waterbury JB, Chisholm SW. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 2003; 424:1047-51. [PMID: 12944965 DOI: 10.1038/nature01929] [Citation(s) in RCA: 346] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2003] [Accepted: 07/15/2003] [Indexed: 11/08/2022]
Abstract
Prochlorococcus is the numerically dominant phototroph in the tropical and subtropical oceans, accounting for half of the photosynthetic biomass in some areas. Here we report the isolation of cyanophages that infect Prochlorococcus, and show that although some are host-strain-specific, others cross-infect with closely related marine Synechococcus as well as between high-light- and low-light-adapted Prochlorococcus isolates, suggesting a mechanism for horizontal gene transfer. High-light-adapted Prochlorococcus hosts yielded Podoviridae exclusively, which were extremely host-specific, whereas low-light-adapted Prochlorococcus and all strains of Synechococcus yielded primarily Myoviridae, which has a broad host range. Finally, both Prochlorococcus and Synechococcus strain-specific cyanophage titres were low (< 10(3) ml(-1)) in stratified oligotrophic waters even where total cyanobacterial abundances were high (> 10(5) cells x ml(-1)). These low titres in areas of high total host cell abundance seem to be a feature of open ocean ecosystems. We hypothesize that gradients in cyanobacterial population diversity, growth rates, and/or the incidence of lysogeny underlie these trends.
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Mann NH, Cook A, Millard A, Bailey S, Clokie M. Marine ecosystems: bacterial photosynthesis genes in a virus. Nature 2003; 424:741. [PMID: 12917674 DOI: 10.1038/424741a] [Citation(s) in RCA: 292] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Marston MF, Sallee JL. Genetic diversity and temporal variation in the cyanophage community infecting marine Synechococcus species in Rhode Island's coastal waters. Appl Environ Microbiol 2003; 69:4639-47. [PMID: 12902252 PMCID: PMC169111 DOI: 10.1128/aem.69.8.4639-4647.2003] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cyanophage community in Rhode Island's coastal waters is genetically diverse and dynamic. Cyanophage abundance ranged from over 10(4) phage ml(-1) in the summer months to less then 10(2) phage ml(-1) during the winter months. Thirty-six distinct cyanomyovirus g20 genotypes were identified over a 3-year sampling period; however, only one to nine g20 genotypes were detected at any one sampling date. Phylogenetic analyses of g20 sequences revealed that the Rhode Island cyanomyoviral isolates fall into three main clades and are closely related to other known viral isolates of Synechococcus spp. Extinction dilution enrichment followed by host range tests and PCR restriction fragment length polymorphism analysis was used to detect changes in the relative abundance of cyanophage types in June, July, and August 2002. Temporal changes in both the overall composition of the cyanophage community and the relative abundance of specific cyanophage g20 genotypes were observed. In some seawater samples, the g20 gene from over 50% of isolated cyanophages could not be amplified by using the PCR primer pairs specific for cyanomyoviruses, which suggested that cyanophages in other viral families (e.g., Podoviridae or Siphoviridae) may be important components of the Rhode Island cyanophage community.
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Mendzhul MI, Perepelytsia SI. [Comparative characteristics of native proteinases of the cyanobacteria Plectonema boryanum and Anabaena variabilis and those induced by cyanophages]. MIKROBIOLOHICHNYI ZHURNAL (KIEV, UKRAINE : 1993) 2003; 65:21-8. [PMID: 12945190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Physico-chemical and catalytic properties of proteinases of native and induced cells of cyanobacteria Plectonema boryanum have been comparatively studied. It has been established that at early stages of reproduction of cyanophage LPP-3 in cyanobacteria P. boryanum is formed de novo proteinase complex consisting at least of five enzymes. Proteinases induced by the virus are distinguished from those of native cells by a series of physico-chemical characteristics and possess higher catalytic activity. Analogous virus-induced changes in proteinase complex also occur in the system cyanobacterium Anabaena variabilis--cyanophage A-1. Possible functions of certain enzymes of proteinase complex in the virus pathology of cyanobacteria cells are discussed in the paper.
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Abstract
Cyanobacteria of the genera Synechococcus and Prochlorococcus dominate the prokaryotic component of the picophytoplankton in the oceans. It is still less than 10 years since the discovery of phages that infect marine Synechococcus and the beginning of the characterisation of these phages and assessment of their ecological impact. Estimations of the contribution of phages to Synechococcus mortality are highly variable, but there is clear evidence that phages exert a significant selection pressure on Synechococcus community structure. In turn, there are strong selection pressures on the phage community, in terms of both abundance and composition. This review focuses on the factors affecting the diversity of cyanophages in the marine environment, cyanophage interactions with their hosts, and the selective pressures in the marine environment that affect cyanophage evolutionary biology.
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47
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Mendzhul MI, Lysenko TG, Syrchin SA. [Development of cyanobacterial phages at the Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine (History and perspectives)]. MIKROBIOLOHICHNYI ZHURNAL (KIEV, UKRAINE : 1993) 2003; 65:133-40. [PMID: 12774505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The paper deals with the basic trends of fundamental investigations of the Department of Algae Viruses in the field of cyanophagia-ecology, biological and physico-chemical properties of cyanophages as well as interrelation with the host cells. Such problems as a possibility to use the system cyanophage-cyanobacteria as the experimental model for development of the unified functional model of productive infection, efficient methods of prophylaxis and therapy of virus infections as well as the solution of various biotechnological problems are discussed.
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48
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Gorobets OB, Blinkova LP, Baturo AP. [Action of Spirulina platensis on bacterial viruses]. ZHURNAL MIKROBIOLOGII, EPIDEMIOLOGII I IMMUNOBIOLOGII 2002:18-21. [PMID: 12506621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The impact of the biomass of the blue-green microalga (cyanobacterium) S. platensis on bacteriophage T4 (bacterial virus) has been evaluated. The study revealed that the addition of S. platensis biomass into the agar nutrient medium, followed by sterilization with 2% chloroform and thermal treatment, produced an inhibiting or stimulating effect on the reproduction of the bacteriophage in Escherichia coli B cells, depending on the concentration of S. platensis and the multiplicity of phage infection, as well as on the fact whether the microalgae were added during the first cycle of the development of the virus. The reproduction of the bacteriophage in E. coli B was influenced by the method and duration of the sterilization of the nutrient medium with S. platensis.
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Gons HJ, Ebert J, Hoogveld HL, van den Hove L, Pel R, Takkenberg W, Woldringh CJ. Observations on cyanobacterial population collapse in eutrophic lake water. Antonie Van Leeuwenhoek 2002; 81:319-26. [PMID: 12448730 DOI: 10.1023/a:1020595408169] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In two laboratory-scale enclosures of water from the shallow, eutrophic Lake Loosdrecht (the Netherlands), the predominating filamentous cyanobacteria grew vigorously for 2 weeks, but then their populations simultaneously collapsed, whereas coccoid cyanobacteria and algae persisted. The collapse coincided with a short peak in the counts of virus-like particles. Transmission electron microscopy showed the morphotype Myoviridae phages, with isometric heads of about 90 nm outer diameter and > 100-nm long tails, that occurred free, attached to and emerging from cyanobacterial cells. Also observed were other virus-like particles of various morphology. Similar mass mortality of the filamentous cyanobacteria occurred in later experiments, but not in Lake Loosdrecht. As applies to lakes in general, this lake exhibits high abundance of virus-like particles. The share and dynamics of infectious cyanophages remain to be established, and it is as yet unknown which factors primarily stabilize the host-cyanophage relationship. Observations on shallow, eutrophic lakes elsewhere indicate that the cyanophage control may also fail in natural water bodies exhibiting predominance of filamentous cyanobacteria. Rapid supply of nutrients appeared to be a common history of mass mortality of cyanobacteria and algae in laboratory and outdoor enclosures as well as in highly eutrophic lakes.
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50
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Syrchin SA, Mendzhul MI. [Physical mapping of DNA of cyanophage LPP-3]. MIKROBIOLOHICHNYI ZHURNAL (KIEV, UKRAINE : 1993) 2002; 64:24-30. [PMID: 12436868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Restrictases fit for the purposes of physical mapping of cyanophage LPP-3 DNA have been selected as a result of the restriction analysis. The use of the methods of mutual hydrolysis, restriction of the fragment isolated from gel and terminal labeling allowed formation a physical map of LPP-3 cyanophage DNA with the complete scheme of allocation of 14 sites for 8 restrictases: Alw44I, Bsp1191, BsuRI, Eco147I, EheI, NcoI, Kpn2I and PvuI as well as the position of certain sites for restrictases HindIII, KpnI and Sau3A.
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