Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90
© Wang et al.; licensee BioMed Central Ltd. 2012
Received: 14 May 2012
Accepted: 5 November 2012
Published: 13 November 2012
Cyanobacteria can form massive toxic blooms in fresh and brackish bodies of water and are frequently responsible for the poisoning of animals and pose a health risk for humans. Anabaena is a genus of filamentous diazotrophic cyanobacteria commonly implicated as a toxin producer in blooms in aquatic ecosystems throughout the world. The biology of bloom-forming cyanobacteria is poorly understood at the genome level.
Here, we report the complete sequence and comprehensive annotation of the bloom-forming Anabaena sp. strain 90 genome. It comprises two circular chromosomes and three plasmids with a total size of 5.3 Mb, encoding a total of 4,738 genes. The genome is replete with mobile genetic elements. Detailed manual annotation demonstrated that almost 5% of the gene repertoire consists of pseudogenes. A further 5% of the genome is dedicated to the synthesis of small peptides that are the products of both ribosomal and nonribosomal biosynthetic pathways. Inactivation of the hassallidin (an antifungal cyclic peptide) biosynthetic gene cluster through a deletion event and a natural mutation of the buoyancy-permitting gvpG gas vesicle gene were documented. The genome contains a large number of genes encoding restriction-modification systems. Two novel excision elements were found in the nifH gene that is required for nitrogen fixation.
Genome analysis demonstrated that this strain invests heavily in the production of bioactive compounds and restriction-modification systems. This well-annotated genome provides a platform for future studies on the ecology and biology of these important bloom-forming cyanobacteria.
KeywordsCyanobacteria Anabaena Mobile genetic elements Insertion sequences Biosynthetic gene clusters Restriction-modification system nifH excision element
Cyanobacteria are evolutionarily important prokaryotic organisms that created the oxygenic atmosphere on Earth via oxygenic photosynthesis and were the progenitors of chloroplasts in eukaryotic algae and plants. Cyanobacteria often dominate phytoplankton as surface scum in freshwater lakes and brackish water during the summer months. A small number of cyanobacterial genera are typically involved in bloom formation. Gas vesicles are common in planktonic cyanobacteria and allow the organisms to regulate their buoyancy. Bloom-forming cyanobacteria produce an array of potent hepatotoxins and neurotoxins. Microcystins are commonly reported hepatotoxic heptapeptides that inhibit eukaryotic protein phosphatases 1 and 2A. Toxic blooms are responsible for the toxicoses of wild and domestic animals and are a health risk for humans through the consumption or recreational use of water.
Anabaena is a genus of filamentous nitrogen-fixing cyanobacteria that is especially common in aquatic environments, both in fresh and brackish waters worldwide[8, 9]. Nitrogen fixation occurs in specialized cells called heterocysts that differentiate from the vegetative cells. This property combined with photosynthesis makes Anabaena cyanobacteria autotrophic organisms that are able to live in a wide range of environments. Strains of the planktonic Anabaena genus are some of the most common cyanobacteria capable of forming blooms. Blooms of Anabaena are a serious health risk, due to the production of a range of toxins such as microcystins, anatoxins and saxitoxins[4, 11].
Cyanobacteria, including Anabaena, are prolific sources of natural products, many of which have biotechnological and biomedical importance. In recent years, many new compounds and their biosynthetic pathways have been discovered[11, 12]. The cyanobacterial hepatotoxins, microcystins and nodularins, are the end products of nonribosomal biosynthetic pathways. Recently, it has been shown that cyanobacteria also use diverse ribosomally encoded pathways for the production of small linear and cyclic peptides[14, 15]. To understand the role of these bioactive compounds in cyanobacteria, as well as the biotechnological exploitation of the biosynthetic machinery used to assemble them, more information on the regulation and association of these biosynthetic pathways with other metabolic processes is needed.
Only a small number of genomes for planktonic bloom-forming cyanobacteria are known, including Microcystis aeruginosa PCC 7806 and NIES-843[16, 17], Planktothrix rubescens NIVA CYA 98, Cylindrospermopsis raciborskii CS-505 and Raphidiopsis brookii D9, which produce microcystins, cylindrospermopsin or saxitoxin. Here, we present the complete genome of Anabaena sp. strain 90, a bloom-forming, microcystin-producing strain originating from a freshwater lake in Finland.
Summary of the Anabaena sp. 90 genome
Gene composition between the chromosomes and plasmids is highly biased. All enzymes of essential biological pathways, such as photosynthesis, are encoded in the two chromosomes. The three plasmids mostly encode integrases, recombinases, transposases, phage-related proteins and a high percentage of hypothetical proteins (Table1).
Pseudogenes and transposable elements
Categorized IS subfamilies in the Anabaena sp. 90 genome
Family and Subgroup
IS4 ssgr ISPepr1
IS4 ssgr IS10
IS200/IS605 ssgr IS1341
IS200/IS605 ssgr IS1341
IS200/IS605 ssgr IS1341
IS200/IS605 ssgr IS1341
IS200/IS605 ssgr IS608
IS200/IS605 ssgr IS200
IS5 ssgr IS5
IS5 ssgr IS1031
Bioactive peptide synthesis
The photosynthetic gene clusters in the genome retain the conserved organizational pattern found in other cyanobacteria. A quarter of the photosynthetic genes are distributed in chromosome II, such as psbA, psbB, and operons of atpIHGFDAC encoding ATP synthase, petBD cytochrome b6/f complex and apcABC light antenna. The rest of the photosynthetic genes were found in chromosome I.
The genome shows a remarkable density of genes encoding transporter proteins. There are four porin genes that encode channels for passive nutrient diffusion. A variety of ATP transport systems, often in operons, are present in both chromosomes (see Additional file1: Table S6) for active uptake of various substrates, such as cations and anions, nucleosides, amino acids, sugars, glycolipids and polyamines. Six copies (three complete, two partial and one disrupted) of the ABC transporter operon devBCA, which encode essential exporters for heterocyst envelope formation, are present. Two of these are encoded in chromosome II.
Signal transduction and gene regulation
In all, 153 ORFs, including those carrying insertions, were annotated for signal transduction and regulation. A total of 69 ORFs (see Additional file1: Table S7), scattered over both chromosomes, were predicted to be involved in two-component signal transduction systems. They include 19 histidine kinases (of which three were pseudogenes), 31 response regulators and 19 hybrid kinases according to their domain composition. These also include five pseudogenes. There are 32 Ser/Thr type protein kinases, six protein phosphatases and other regulation or sensor domain-containing proteins that form the one-component systems that coordinate with the two-component systems. Moreover, all group 1 (sigA) and group 2 (sigB, sigC, sigD, sigE) sigma factors are present in the Anabaena sp. 90 genome. The common group 3 (sigF, sigG) and one extracytoplasmic function sigma factors were found as well. Four proteins with anti-sigma-factor antagonist domain were also identified. They work together with the sigma factors in regulating various cell processes at the transcriptional level.
Gas vesicle gene cluster
Metabolic pathway analysis
We annotated 206 putative metabolic pathways in the genome of Anabaena sp. 90 (see Additional file1: Table S8), in addition to those for bioactive peptide biosynthesis. These pathways are composed of 777 enzymes that catalyse 1,211 enzymatic reactions. However, nearly half of these pathways are incomplete, because 227 (29%) enzyme-encoding genes are missing or were not found. Many of the incomplete pathways are responsible for catabolic processes, such as nutrient degradation, utilization and assimilation, whereas the essential pathways are complete, e.g. amino acid metabolism, photosynthesis and glycolysis. The energy-related pathways have fewer missing enzymes than others. Nearly 40% of the genes in this genome are hypothetical or with unknown functions, due most likely to their low homology to counterparts in model organisms. This may leave some of the enzymes in annotated pathways unrecognized. Moreover, our analysis revealed that some enzyme-encoding genes are pseudogenes with disrupted ORF. For instance, one (ANA_C20606) of the two deoxycytidine triphosphate deaminases, which catalyse the conversion of dCTP to dUTP in the pyrimidine deoxyribonucleotide de novo biosynthesis pathway, was interrupted by an inserted DNA recombinase. In addition, an alcohol dehydrogenase-encoding gene (ANA_C20081) was found with a deletion. This enzyme catalyses the reduction of acetaldehyde to ethanol in fermentation pathways. Three copies of alcohol dehydrogenases were found in this genome in an intact form.
Here, we report the complete genome of Anabaena sp. 90, an ecologically important hepatotoxic bloom-forming cyanobacterium. The genome has a multichromosome composition with essential metabolic core genes encoded in the two circular chromosomes. This study was the first to report such a multichromosome composition in the order of Nostocales. Previously, the strain of Cyanothece sp. ATCC 51142 was known with two chromosomes, one circular and one linear. We succeeded in completing the genome with high sequence quality, even though it contains a plethora of repetitive mobile genetic elements with diverse sizes (prophage remnants: ~11 kb, ISs: 1–3 kb, MITEs: 100–300 bp) and five nearly identical rRNA operons. A large number of repeats makes genome assembly difficult and cannot be resolved simply by increasing the sequencing depth e.g. using the next-generation low-cost sequencing platforms, due in large part to their short read lengths. As a result, the majority of genomes remain in the ‘draft’ state, including a number of bloom-forming cyanobacteria[17–19]. In this study, we tackled this problem by including data from mate-pair libraries with large inserts. This strategy could be used in sequencing bloom-forming cyanobacterial genomes that are rich in mobile genetic element-derived repeats[16, 17, 19]. Complete and high quality genomes are crucial to comparative genomics and genome evolution studies, pathway reconstruction for metabolic engineering and postgenomic analysis[39–41].
The Anabaena sp. 90 genome contains various types of mobile genetic elements, including plasmids, prophage remnants, ISs and MITEs. They are collectively termed as mobile genetic elements, since they are capable of moving within genomes (duplication) and between prokaryotic organisms (horizontal gene transfer). These elements may have contributed to genome plasticity, genomic rearrangements and most likely the multichromosome composition. ISs are mobile genetic elements transferred within and between species through a cut-and-paste mechanism, which is driven by the internally encoded transposases[43, 44]. The percentage of IS elements in Anabaena sp. 90 (~2%) was comparable to that in other cyanobacteria, but less than in the bloom-forming hepatotoxin-producing Microcystis aeruginosa strains, in which IS elements comprised about 10% of the genomes. Recent genome studies showed that the planktonic cyanobacteria Cylindrospermopsis raciborskii CS505 and Crocosphaera watsonii WH8501 also contain high numbers of repetitive elements, partly contributed by ISs. MITEs are small mobile sequences that have only terminal inverted repeats. The MITEs found in this study were classified as type II, because there is no evident similarity found with inverted repeats of the ISs in this genome. The mobilization of type I MITEs was hypothesized to be mediated by the transposase of IS that holds the same terminal inverted repeats. This may imply an autonomous mechanism for the movement and duplication of type II MITEs.
Surprisingly, we found that nearly 5% of the gene repertoires are pseudogenes that include not only disrupted transposases but also disrupted ORFs from many other different functional categories (Figure3). However, the pseudogenes found in the Anabaena sp. 90 genome were most likely derived from the transposition activities of ISs and MITEs. Mutations and genome rearrangements induced by transposable elements have also been described in Microcystis aeruginosa strains[16, 17]. However, an abundance of pseudogenes has rarely been reported in genomes of cyanobacteria, except the endosymbiotic strain ‘Nostoc azollae’ 0708, which has an extremely high number (31.2%) of pseudogenes that were attributed to the genome erosion process. Here, we accurately labelled a number of disrupted ORFs, many of which could be associated with the transpositions of mobile genetic elements, through detailed manual annotation (Figures1 and4). Recent metagenomic data analysis also demonstrated the incidence of genes inactivated by IS transposition, including some with essential functions, within the population of Synechococcus strains in hot spring mats. High frequencies of mobile genetic element-derived pseudogenes are likely to be common among transposable element-rich cyanobacteria, especially in strains of bloom-forming genera, but as yet remain undocumented.
Anabaena sp. 90 dedicates 5% of its genome to biosynthesis of small peptides, such as hepatotoxic microcystins and the protease inhibitors anabaenopeptins and anabaenopeptilides. Between 3% and 4% of the genomes is typically devoted to the biosynthesis of secondary metabolites among sequenced cyanobacterial genomes[17, 18, 49]. However, previous works only counted nonribosomal gene clusters and missed the ribosomal biosynthesis pathways. Here, we took into account both ribosomal and nonribosomal gene clusters. Considering the widespread occurrences of ribosomal pathways in cyanobacteria[14, 15] and that nonribosomal gene clusters also amount to 3.5% of Anabaena sp. 90 genome, it appears that about 5% of the genome is commonly assigned to natural product biosynthesis in cyanobacteria. An additional nonribosomal gene cluster responsible for production of the antifungal compounds hassallidins was discovered during genome assembly, mainly because the gene cluster was inactivated by a deletion event. Moreover, the genome sequence led us to discover the ribosomal production pathway for cyanobactins and their common occurrence in Anabaena as well as in other planktonic cyanobacteria. We also identified seven putative bacteriocin gene clusters in the genome. Their end products are presently unknown, but the high number of these types of gene clusters in cyanobacterial genomes suggests that yet new compound families from cyanobacteria await identification and structural determination. To date, bacteriocins have only been identified in Prochlorococcus marinus MIT9313.
The toxin microcystin synthetase (mcy) gene cluster was shown to be of ancient origin. Previous environmental studies showed the stable presence of mutant cyanobacterial mcy gene clusters, which were inactivated both in freshwater samples by ISs and in brackish water by MITEs. Note that the intact hassallidin gene cluster is still retained in parallel cultures of mutant Anabaena sp. 90, which has an inactivated anabaenopeptilide synthetase gene cluster. Our results showed that those mutants with an inactive hassallidin biosynthetic pathway prevailed over cells with functional genes in the culture. This may indicate a growth advantage for cells with mutated bioactive compound synthetase gene clusters under laboratory conditions, perhaps due to a lower metabolic burden.
Similarly, we detected a loss of gas vesicles, the subcellular structures responsible for buoyancy, which are essential for bloom-forming planktonic cyanobacteria. This phenotype is derived from the truncated gvpG gene in the gvp operon (Figure10). The truncation most probably was selected when the strain was purified (axenic) on solid media. Loss of buoyancy due to rearranged gas vesicle gene clusters by IS transpositions was also previously described in Microcystis strains kept in laboratory culture.
Anabaena sp. 90 has been under continuous culture since 1986 and was introduced into pure culture in 1992. The mobile genetic elements were probably acquired by the strain prior to this time. Some metabolic properties of Anabaena sp. 90 were altered by the activities of these mobile genetic elements. We found mobile element-derived pseudogenes among the genes encoding enzymes for the metabolic pathways of the strain. This may indicate that Anabaena sp. 90 has lost genes for metabolic pathways with nonessential functions under laboratory conditions, where optimal, nutrient-rich and competitor-free environments are provided. Our analysis revealed that the laterally acquired mobile genetic elements may have played a role in the process. Perhaps growing cyanobacteria under conditions that reflect those found in nature would reduce genetic changes.
The Anabaena sp. 90 genome contains 31 RM systems, which function as microbial defence systems against foreign DNAs. Type I, II, III and IV RM systems were annotated from the Anabaena sp. 90 genome, type II restriction enzymes being the most numerous RMs (22). Previously, restriction enzyme activities, such as AflIII, in Anabaena sp. 90 were experimentally confirmed. An RM system usually contains a restriction endonuclease that recognizes a specific sequence for cleavage and a DNA methyltransferase that modifies the same sequence and protects it from cleavage. Bacteria that possess multiple RM systems are thought to be virtually impregnable. This seems to hold true for Anabaena sp. 90 since it is resistant to genetic manipulation. Over the years we have succeeded in producing only one mutant of this strain. This is a familiar feature with many filamentous cyanobacteria, which were proposed more intensively protected by RM systems than unicellular strains. However, this has been contradicted by the frequent occurrence of RM systems in genomes of unicellular toxic bloom-forming Microcystis aeruginosa strains[16, 17]. To date the two highest numbers of restriction enzymes are found in two planktonic microcystin-producing cyanobacteria, Anabaena sp. 90 (this study) and Microcystis aeruginosa NIES-843 (Figure8). This perhaps is a reflection of the ecological or evolutionary pressures exerted on planktonic cyanobacteria. The Anabaena sp. 90 genome also contains abundant mobile genetic elements. The question that naturally arises is how these mobile elements have invaded the planktonic cyanobacterial genomes with the presence of pronounced RM systems. The mobile genetic elements are, however, relatively short sequences (see Additional file1: Tables S3 and S4) and may lack many restriction cleavage sites of restriction endonucleases. For Anabaena sp. 90, this may be partly explained by the disrupted genes encoding enzymes in RM systems (see Additional file1: Table S5). In addition, it is known that RM systems may be inefficient in blocking single-stranded or modified foreign DNA and work only temporarily. However, it was suggested that RM systems may also be mobile genetic elements that cause genome rearrangements.
In filamentous cyanobacteria, the cellular processes of photosynthesis and nitrogen fixation are spatially separated and compartmentalized into vegetative cells and heterocysts, respectively. Anabaena strains have long been used as model organisms for studying heterocyst development and nitrogen fixation in cyanobacteria[1, 64]. The differentiation processes from vegetative cells to heterocysts involve programmed DNA rearrangements at multiple sites in Anabaena genomes[65–67]. To date, three known elements, ranging from 11 to 55 kb, have been reported in nifD, fdxN and hupL genes in heterocystous cyanobacteria. Here, for the first time we report the simultaneous presence of four excision elements in the genome of Anabaena sp. 90. Moreover, two novel elements for the nifH gene were found and one of these is the largest known in size (80 kb) (Figure9). The nifH gene is commonly used to detect nitrogen-fixing organisms in environmental samples. The presence of excision elements is likely to cause problems with detection of nifH genes if they occur commonly among heterocystous cyanobacteria. Our results showed that the heterocyst differentiation process in cyanobacteria involves precise genomic splicing over distances as long as 122 kb. The excision elements interrupting nif genes in heterocystous cyanobacteria appear to play a role in protecting nitrogenase and hydrogenase from the effects of oxygen during heterocyst development. A compact and conserved nif operon was recently discovered without any excision elements in a symbiotic strain ‘Nostoc azollae’ 0708 (Figure9). This evidence supports the proposed loss of photosynthetic activity in cells of ‘Nostoc azollae’ 0708, which may have differentiated only to perform nitrogen fixation for the hosts. A similar nif operon without excision elements was presented in the heterocyst-forming cyanobacterium Cylindrospermopsis raciborskii CS-505, but lost in its closely related strain Raphidiopsis brookii D9. This may suggest that the growth of these strains is less dependent on the nitrogen fixation process. The presence of multiple copies of devBCA operons in Anabaena sp. 90 may increase the efficiency of nitrogen fixation, whereas lack of the patS and hetN genes in Anabaena sp. 90 (this study) and Cylindrospermopsis raciborskii CS-505 may suggest a new pattern of heterocyst spatial development. Simultaneous inactivation of patS and hetN genes in Nostoc sp. PCC 7120 is known to be lethal, due to overproduction of HetR and heterocysts. Genome mining of Cylindrospermopsis raciborskii CS-505 suggested that a protein with the C-terminal pentapeptide RGSGR may take over the function of PatS. Similarly, we also identified an ORF (ANA_C10293) with the C-terminal pentapeptide in Anabaena sp. 90, which may play a role as a HetR suppressor.
The 5.3-Mb Anabaena sp. 90 genome contains a lower number of genes for signal transduction than the 7.2 Mb-genome of Nostoc PCC 7120 and nearly 10-Mb genome of Nostoc punctiforme. However, the number of signal transduction pathways is positively correlated with genome size. It is also well known that soil microbes such as Nostoc punctiforme invest more heavily in sensing changes in environmental conditions than organisms living in more stable aquatic environments. Usually, a one-to-one relationship exists between the cyanobacterial sensors (histidine kinases) and response regulators, but in Anabaena sp. 90 the ratio is lower, indicating either integration of multiple signalling pathways or perhaps loss of sensoring systems when grown in protected laboratory environments.
This study gives a snapshot of the Anabaena sp. 90 genome. It shows a high potential of genetic variation by virtue of the occupation of a wide range of mobile genetic elements. Our results indicated that mobile genetic element-imposed selective pressure led to genome adaption to the strain by trimming nonessential genes and pathways during cultivation in the laboratory. In addition, due to the array of biosynthesis gene clusters for multiple peptides in Anabaena sp. 90, the complete sequence provides a valuable research subject in studying the regulation of natural product biosynthesis, which may have potential pharmaceutical and biotechnology applications.
Strain isolation and culture
Anabaena sp. 90 was isolated as a microcystin producer in 1986 from Lake Vesijärvi, Finland. The axenic culture was originally purified from a single filament that was placed over a solid medium and then has been continuously maintained at the University of Helsinki cyanobacterial culture collection in Z8 nitrogen-free medium at room temperature (20–23°C) with continuous illumination of 10–20 μmol m-2 s-1. The phylogeny of this strain was previously published.
DNA extraction and genomic library construction
The DNA extraction was described earlier. Three sizes of genomic libraries were utilized for end sequencing. The large insert library was a cosmid library with an insert size of approximately 40 kb. Two shotgun libraries with 2-kb and 6-kb inserts ligated into the pUC18 plasmid vector were constructed using standard protocols.
Genome sequencing, assembly and finishing
All reads were generated from clone ends sequencing by the Sanger sequencing platforms Megabase 1000 (GE Healthcare, Buckinghamshire, UK) and ABI 3730 (Applied Biosystems, CA, USA). An initial 9.9X sequencing data was sequenced from a combination of 2%, 8% and 90% of the reads from the 40-kb, 6-kb and 2-kb libraries, respectively. The Phred/Phrap/Consed software package was used for genome assembly and gap closure according to the paired ends from the large-insert (6 and 40 kb) libraries. The remaining physical gaps that were derived from the unclonable regions were linked through combinatorial multiplex PCR screening of primers designed from the contig ends. Autofinish was used for guiding, either by clone-end resequencing or primer walking over the clones or PCR products to attain the standard that each base was covered by at least two independent high-quality reads and with a Phred[76, 77] quality value ≥ Q40. Large repetitive regions (i.e. RNA operons, prophage remnants) were resolved by primer-walking over long PCR products amplified from the corresponding regions. In all, 119316 reads were produced, which amounted to a final sequencing depth of 12.5X.
Genome annotation and analysis
Gene finding and function assignment
ORFs were initially predicted by Glimmer 3.02 with a threshold of 100 bp. The intergenic regions were subjected to blastx searching against the nonredundant database for unrecognized ORFs. All predicted genes were translated into amino acid sequences for homologue searches with the InterPro, Cluster of Orthologous Groups and nonredundant databases. Functional assignments and start sites for each ORF were determined manually by combining the search results from these sources. Transfer RNA genes were predicted with tRNAscan-SE and rRNA genes were located through homologue searches. The annotated proteins were further assigned to functional groups according to the Comprehensive Microbial Resource role category. The putative bacteriocin gene clusters were classified, according to methods described previously. Hypothetical proteins were defined as conserved if they had at least 30 homologues with full-length matching in other genomes, while unique hypothetical proteins had no full-length matching in other genomes.
The pseudogenes (see Additional file1: Table S2) were examined manually using Artemis for frameshift and premature stop codons, as well as the boundaries of the truncation, deletion and insertion. The boundaries of truncated pseudogenes were determined through iterative BLAST searches for the surrounding regions. The pseudogenes were assigned a function according to the hits of the homologue search with significant similarity.
IS and MITE
The ISs were identified and classified using the ISfinder database. Fifteen MITEs were originally discovered as insertions from interrupted pseudogenes. Additional MITEs were found by blastn searching the 15 insertions against the complete genome sequence (E < 1e-5). Fragmented MITEs with over 50% coverage were counted as partial. The secondary structures of the MITEs were predicted using the RNAfold webserver.
A protein database of RM system genes was locally prepared by collecting data from the REBASE. All annotated proteins initially searched against this database, and protein hits of blastP (E < 1e-4) were chosen as candidates for manual checking. RM systems were confirmed with the associated presence of restriction enzymes, DNA methylase and other RM genes or domains. Separate RM genes were kept while the E value was 1e-10 or less. The disrupted RM genes were reconfirmed by manually inspecting the alignment of the remaining parts.
Metabolic pathway analysis
DNA extraction and PCR
Both Anabaena sp. 90 and a knockout mutant constructed in 1999 were grown as previously described. Genomic DNA from the two Anabaena strains was extracted using either the DNeasy® Plant Mini Kit (Qiagen Gmbh, Hilden, Germany) or the E.Z.N.A™ SP Plant DNA Mini Kit (Omega Bio-Tek Inc., Norcross, GA, USA). PCR amplifications of DNA from Anabaena were performed in iCycler (Bio-Rad, Hercules, CA, USA) using the primers hasV-fw (5-TCTAGATGGTTGGAGTGTGGC-3) and hasV-rev (5-AGGATGCGGTAGCTTTGAGGAGGCG-3), which were designed to amplify across the site of deletion in the hasV gene. The primer pairs a1 (5-TGGTAACAGGTAACGTAATTAAAAC-3) and hasV-rev, and y1 (5-ATCAGTAGTTTCGGGTCTGG-3) and hasV-fw were designed to allow specific detection of deletion and full-length versions of hasV, respectively. Each PCR was carried out in 1 × DyNAzymeTM buffer (Tris–HCl, MgCl2, KCl, Triton® X-100) (Finnzymes, Espoo, Finland) with 100 μM of each dNTP (dNTP mix, 10 mM, Finnzymes), 0.25 μM of each primer (Sigma Genosys, Sigma-Aldrich, St. Louis, MO, USA), 0.4 U DyNAzyme II DNA polymerase (F-501S, 2 U/μl, Finnzymes) and 10–170 ng of template DNA in a final volume of 20 μl. The following PCR thermocycle was used to amplify the hasV gene: initial denaturation at 94°C for 3 min, 32 cycles of 94°C for 30 s, 57°C for 30 s and 72°C for 1.5 min, and a final extension at 72°C for 10 min. For detection of the deletion, a similar PCR programme was used, with the exception of annealing at 64°C for 30 s and elongation at 72°C for 1 min.
Cells of the cyanobacterial strains were collected from the 20–40-ml cultures by centrifugation at 7000 × g for 7 min and freeze-dried (Maxi dry plus, Heto-Holten A/S, Allerød, Denmark). The dried cells were extracted with 1 ml of methanol in 2-ml plastic tubes containing glass beads (Cell Disruption Media, 0.5-mm glass beads, Scientific Industries Inc., Bohemia, NY, USA) using a FastPrep cell disrupter (FP120, Bio101, Thermo Electron Corporation, Qbiogene, Inc., CA, USA) for 10 s at a speed of 6.5 m s-1. The extracts were centrifuged at 10 000 × g 5 min prior to LC/MS analysis. The LC/MS analyses of extracts were carried out in an Agilent 1100 Series LC/MSD Trap XCT Plus System (Agilent Technologies, CA, USA) using a Phenomenex Luna C18(2) LC column (100 mm × 4.6 mm, particle size 5 μm, 100 Å; Phenomenex, CA, USA). The column was protected with a C18 precolumn (4 mm × 2 mm; Phenomenex). The LC/MS parameters were optimized with hassallidin ion m/z 1862 with negative mode of polarity. The mobile phase consisted of 0.1% aqueous formic acid (50% solution in water; Fluka, Sigma Aldrich, Steinheim, Germany) (solvent A) and acetonitrile (Chromasolv® for LC/MS, Fluka, Sigma-Aldrich, Steinheim) (solvent B). A gradient (solvent B) from 10% to 100% was run over 30 min at a flow rate of 0.15 ml min-1 with 5-μl injection at 40°C. Hassallidins were detected with MS using electrospray ionization set in the positive ion mode. The nebulizer gas (N2) pressure was 35.0 pounds per square inch (psi), the drying gas flow rate was 8.0 l min-1 and the temperature was 350°C. The capillary voltage was set to 3650 V, and the capillary offset value was 250 V. A skimmer potential of 58.0 V and a trap drive value of 112.0 was used. The spectra were recorded at a scanning range of 100–2200 m/z on average of three spectra using an ion charge control (ICC). Identification of hassallidins was based on the similarities between the spectra of the extracts analysed and known hassallidins A and B (Alexis Biochemicals, Ezno Life Science Inc., Lausen, Switzerland). The structures of the hassallidins were identified by fragmentation analysis MSn (n = 1–3) using the SmartFrag function.
The complete annotated genome sequence was submitted to GenBank under accession number [GenBank: CP003284 (ChromosomeI), CP003285 (ChromosomeII), CP003286 (PlasmidA), CP003287 (PlasmidB), CP003288 (PlasmidC)].
Open reading frame
Miniature inverted-repeat transposable element
Clustered regularly interspaced short palindromic repeat.
We thank Dr. Elina Roine for her helpful advice concerning prophage elements and Lyudmila Saari for maintaining and growing the organism. This work was financially supported by the Academy of Finland and the University of Helsinki to KS (Research Centre of Excellence grants 53305 and 118637), to ARY (128480), and by the Viikki Doctoral Programme in Molecular Biosciences to HW.
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