Exploiting the Natural Diversity of Microviridin Gene Clusters for Discovery of Novel Tricyclic Depsipeptides

Microviridins are ribosomally synthesized tricyclic depsipeptides produced by different genera of cyanobacteria. The prevalence of the microviridin gene clusters and the natural diversity of microviridin precursor sequences are currently unknown. Screening of laboratory strains and field samples of the bloom-forming freshwater cyanobacterium Microcystis via PCR revealed global occurrence of the microviridin pathway and an unexpected natural variety. We could detect 15 new variants of the precursor gene mdnA encoding microviridin backbones that differ in up to 4 amino acid positions from known isoforms of the peptide. The survey not only provides insights into the versatility of the biosynthetic enzymes in a closely related group of cyanobacteria, but also facilitates the discovery and characterization of cryptic microviridin variants. This is demonstrated for microviridin L in Microcystis aeruginosa strain NIES843 and heterologously produced variants.Bloom-forming freshwater cyanobacteria are a rich source of natural products (30). They flourish in lakes and ponds of different temperate zones, where they can eventually form thick scums at the surface. Microcystis is one of the predominant genera composing these blooms, particularly in lakes suffering from eutrophication (17). Like other bloom-forming species, it is infamous for the production of the hepatotoxin microcystin, a nonribosomal peptide toxin that inhibits protein phosphatases in a broad range of eukaryotes from zooplankton to humans (1, 9). Moreover, Microcystis is known to produce a multitude of other peptides that are considered to be potential drug leads (14, 30).Microviridins form one of the most intriguing classes of peptides, since they feature a cage-like structure (e.g., microviridin B) (Fig. ​(Fig.1A).1A). The highly unusual tricyclic architecture results from ω-ester and ω-amide bonds between amino acid side chains. The past few years have afforded 13 variants of the peptide from both field samples and laboratory strains (5, 8, 13, 15, 21, 22). Most of the variants show inhibitory activities against serine-type proteases, most notably against elastase, which is a target enzyme in the treatment of lung emphysema (28). One of the peptide isoforms, microviridin J, has been shown to inhibit the molting process of Daphnia, leading to death of the animals (23).Open in a separate windowFIG. 1.(A) Representative structure of microviridin B and three-dimensional model. (B) Schematic representation of the microviridin gene cluster of M. aeruginosa NIES298. The positions of primers for the amplification of mdnA, -B, and -C are indicated. GNAT, GCN5-related N-acetyltransferase. (C) PCR gel picture showing the amplification of mdnB from a selection of laboratory strains.Recent studies have revealed a unique biosynthetic mechanism for microviridins in Microcystis and the filamentous cyanobacterial genus Planktothrix (18, 31). The 14-amino-acid (aa) peptide sequence is encoded at the C terminus of the ribosomal precursor peptide MdnA (31). Macrocyclization of the peptide depends on the activities of two ATP grasp-type ligases, MdnB and -C, that are encoded downstream of the precursor gene. Further enzymes encoded by the cluster include the N-acetyltransferase MdnD and the putative transporter-peptidase MdnE (31) (Fig. ​(Fig.1B).1B). The activities of the enzymes MdnB, -C, and -D were confirmed by heterologous production of microviridins in Escherichia coli (31). The MdnB and -C orthologs of the filamentous cyanobacterial strain Planktothrix agardhii CYA126, MvdC and MvdD, were characterized using synthetic precursor peptides in vitro (18). Furthermore, Philmus et al. have shown limited flexibility of MvdD, catalyzing two rounds of microviridin lactonization to accept substrates with altered amino acid compositions and a stringent ring size requirement (19).Recent genome-sequencing projects with cyanobacteria have revealed widespread occurrence of microviridin-related gene clusters in various cyanobacterial genera, although the production of microviridins by these strains remains to be shown (18, 24, 31). Here, we present data showing an unprecedented natural diversity of microviridin precursor genes in a set of closely related Microcystis laboratory strains and field samples. The insights gained from our survey provide lessons about the flexibility of the microviridin ligases in a small group of cyanobacteria and an estimate of the size of the natural microviridin library that still awaits discovery. The detection of novel natural microviridin prepeptides from Microcystis can ultimately guide the heterologous production of novel microviridins in E. coli. As proof of principle, we have identified and characterized the new variant microviridin L from the strain Microcystis aeruginosa NIES843.     

Cyanobacterial Protease Inhibitor Microviridin J Causes a Lethal Molting Disruption in Daphnia pulicaria

Laboratory experiments identified microviridin J as the source of a fatal molting disruption in Daphnia species organisms feeding on Microcystis cells. The molting disruption was presumably linked to the inhibitory effect of microviridin J on daphnid proteases, suggesting that hundreds of further cyanobacterial protease inhibitors must be considered potentially toxic to zooplankton.     

Effects of nutrient and light availability on production of bioactive anabaenopeptins and microviridin by the cyanobacterium <Emphasis Type="Italic">Planktothrix agardhii</Emphasis>

Cyanobacteria produce a large number of bioactive oligopeptides with yet unknown functions. Here the effect of environmental factors on the production of two anabaenopeptins and a microviridin by Planktothrix agardhii was investigated. The results were compared with previous findings on the production of a third family of oligopeptides, the highly toxic microcystins, to test the hypothesis that environmental factors affect the production of different types of cyanobacterial bioactive oligopeptides in a similar manner. Despite marked changes in culture conditions, variations in the amount of cell-bound anabaenopeptins and microviridin I per biomass unit did not exceed a factor of 5. High amounts of cell-bound anabaenopeptins and microviridin I per Planktothrix biovolume were associated with a high availability of nitrogen and phosphorus. The production of anabaenopeptins and microviridin continued as long as the Planktothrix cultures grew. In all cases the oligopeptide net production rate was linearly correlated to the growth rate of Planktothrix, identifying the growth activity as a major regulator of anabaenopeptin and microviridin production. The concentration of anabaenopeptins and microviridins in nature may therefore be estimated from the biomass concentration of their producers. These findings are similar to those previously reported for microcystins and thus support the idea that different types of bioactive cyanobacterial oligopeptides may share common regulation patterns. This may be seen as a hint to a mutual function of cyanobacterial oligopeptides, although further studies are needed to draw final conclusions on this issue. Handling editor: J. Padisak     

A new clade of Mesorhizobium nodulating Alhagi sparsifolia

We isolated 33 nodule bacteria from the legume Alhagi sparsifolia growing in the desert of northwest China. They fell into three groups by restriction analysis of their rrs (small subunit ribosomal RNA) genes, and these, together with dnaK and dnaJ genes, were sequenced from representative isolates to assess their taxonomic position by phylogenetic analysis. The bacteria in each group belonged to different lineages that might represent three different new Mesorhizobium species, two of which form a novel clade very distinct from other species in the genus. Most A. sparsifolia symbionts harboured closely related nodA and nodC genes forming new lineages. The presence of these closely related symbiosis genes in various genomic backgrounds and the incongruence observed between the different gene phylogenies indicate a history of horizontal gene transfer of symbiosis genes between the A. sparsifolia symbionts.     

Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria

Background

Cyanobacteria are well known for the production of a range of secondary metabolites. Whilst recent genome sequencing projects has led to an increase in the number of publically available cyanobacterial genomes, the secondary metabolite potential of many of these organisms remains elusive. Our study focused on the 11 publically available Subsection V cyanobacterial genomes, together with the draft genomes of Westiella intricata UH strain HT-29-1 and Hapalosiphon welwitschii UH strain IC-52-3, for their genetic potential to produce secondary metabolites. The Subsection V cyanobacterial genomes analysed in this study are reported to produce a diverse range of natural products, including the hapalindole-family of compounds, microcystin, hapalosin, mycosporine-like amino acids and hydrocarbons.

Results

A putative gene cluster for the cyclic depsipeptide hapalosin, known to reverse P-glycoprotein multiple drug resistance, was identified within three Subsection V cyanobacterial genomes, including the producing cyanobacterium H. welwitschii UH strain IC-52-3. A number of orphan NRPS/PKS gene clusters and ribosomally-synthesised and post translationally-modified peptide gene clusters (including cyanobactin, microviridin and bacteriocin gene clusters) were identified. Furthermore, gene clusters encoding the biosynthesis of mycosporine-like amino acids, scytonemin, hydrocarbons and terpenes were also identified and compared.

Conclusions

Genome mining has revealed the diversity, abundance and complex nature of the secondary metabolite potential of the Subsection V cyanobacteria. This bioinformatic study has identified novel biosynthetic enzymes which have not been associated with gene clusters of known classes of natural products, suggesting that these cyanobacteria potentially produce structurally novel secondary metabolites.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1855-z) contains supplementary material, which is available to authorized users.     

A gene cluster for the synthesis of serotype g-specific polysaccharide antigen in Aggregatibacter actinomycetemcomitans

Aggregatibacter actinomycetemcomitans is an important pathogen related to aggressively progressive periodontal breakdown in adolescents and adults. The species can be divided into six serotypes (a–f) according to their surface carbohydrate antigens. Recently, a new serotype g of A. actinomycetemcomitans was proposed. The aim of the present study was to sequence the gene cluster associated with the biosynthesis of the serotype g-specific polysaccharide antigen and develop serotype-specific primers for PCR assay to identify serotype g strains of A. actinomycetemcomitans. The serotype-specific polysaccharide (SSPS) gene cluster of the NUM-Aa 4039 strain contained 21 genes in 21,842-bp nucleotides. The similarity of the SSPS gene cluster sequence was 96.7 % compared with that of the serotype e strain. Seventeen serotype g genes showed more than 90 % homology both in nucleotide and amino acids to the serotype e strain. Three additional genes with 1,579 bp in NUM-Aa 4039 were inserted into the corresponding ORF13 of the serotype e strain. The serotype g-specific primers were designed from the insertion region of NUM-Aa 4039. Serotypes of the a–f strains were not amplified by serotype-specific g primers; only NUM-Aa 4039 showed an amplicon band. The NUM-Aa 4039 strain was three genes in the SSPS gene cluster different from those of serotype e strain. The specific primers derived from these different regions are useful for identification and distribution of serotype g strain among A. actinomycetemcomitans from clinical samples.     

Microevolution of the Chromosomal Region of Acute Disease Antigen A (adaA) in the Query (Q) Fever Agent Coxiella burnetii

The acute disease antigen A (adaA) gene is believed to be associated with Coxiella burnetii strains causing acute Q fever. The detailed analysis of the adaA genomic region of 23 human- and 86 animal-derived C. burnetii isolates presented in this study reveals a much more polymorphic appearance and distribution of the adaA gene, resulting in a classification of C. burnetii strains of better differentiation than previously anticipated. Three different genomic variants of the adaA gene were identified which could be detected in isolates from acute and chronic patients, rendering the association of adaA positive strains with acute Q fever disease disputable. In addition, all adaA positive strains in humans and animals showed the occurrence of the QpH1 plasmid. All adaA positive isolates of acute human patients except one showed a distinct SNP variation at position 431, also predominant in sheep strains, which correlates well with the observation that sheep are a major source of human infection. Furthermore, the phylogenetic analysis of the adaA gene revealed three deletion events and supported the hypothesis that strain Dugway 5J108-111 might be the ancestor of all known C. burnetii strains. Based on our findings, we could confirm the QpDV group and we were able to define a new genotypic cluster. The adaA gene polymorphisms shown here improve molecular typing of Q fever, and give new insights into microevolutionary adaption processes in C. burnetii.     

Heritable Targeted Inactivation of the Rainbow Trout (Oncorhynchus mykiss) Master Sex-Determining Gene Using Zinc-Finger Nucleases

Gene targeting is a powerful tool for analyzing gene function. Recently, new technology for gene targeting using engineered zinc-finger nucleases (ZFNs) has been described in fish species. However, it has not yet been widely used for cold water and slow developing species, such as Salmonidae. Here, we present the results of successful ZFN-mediated disruption of the sex-determining gene sdY (sexually dimorphic on the Y chromosome) in rainbow trout (Oncorhynchus mykiss). Three pairs of ZFN mRNA targeted to different regions of the sdY gene were injected into fertilized rainbow trout eggs. Sperm from 1-year-old male founders (parental generation one or P1) carrying a ZFN-induced mutation in their germline were then used to produce F1 non-mosaic animals. In these F1 populations, we characterized 14 different mutations in the sdY gene, including one mutation leading to the deletion of leucine 43 (L43) and 13 mutations at other target sites that had different effects on the SdY protein, i.e., amino acid insertions, deletions, and frameshift mutations producing premature stop codons in the mRNA. The gonadal phenotype analysis of the F1-mutated animals revealed that the single L43 amino acid deletion did not lead to a male-to-female sex reversal, but all other mutations induced a clear ovarian phenotype. These results show that targeted gene disruption using ZFN is efficient in rainbow trout but depends on the ZFN design. We also characterized new sdY mutations resulting in male-to-female sex reversal, and we conclude that L43 seems dispensable for SdY function.     

On the Diversity of the Laccase Gene: A Phylogenetic Perspective from Botryosphaeria rhodina (Ascomycota: Fungi) and Other Related Taxa

The present study is the first describing the sequencing of a fragment of the copper-oxidase domain of a laccase gene in the family Botryosphaeriaceae. The aim of this work was to assess the degree of genetic and evolutionary relationships of a laccase gene from Botryosphaeria rhodina MAMB-05 with other ascomycete and basidiomycete laccase genes. The 193-amino acid sequences of the copper-oxidase domain from several different fungi, insects, a plant, and a bacterial species were retrieved from GenBank and aligned. Phylogenetic analyses were performed using neighbor-joining, maximum parsimony, and Bayesian inference methods. The organisms studied clustered into five gene clades: fungi (ascomycetes and basidiomycetes), insects, plants, and bacteria. Also, the topologies showed that fungal laccases of the ascomycetes and basidiomycetes are clearly separated into two distinct clusters. This evidence indicated that B. rhodina MAMB-05 and other closely related ascomycetes are a new biological resource given the biotechnological potential of their laccase genes.     

A cluster of cell division genes maps to the terC region of the chromosome of Escherichia coli K-12

Thirty-nine cell division mutants were isolated in Escherichia coli K-12 and were mapped in the terminus region of the chromosome, between 33.5 and 36 min. They were obtained by two different approaches involving specific mutagenesis of the terC region. The mutants could be divided into eight classes (I to VIII) based on their map position and phenotype at the restrictive temperature, and constitute a new cell division gene cluster.     

Construction of expression vectors for metabolic engineering of the vanillin-producing actinomycete Amycolatopsis sp. ATCC 39116

Amycolatopsis sp. ATCC 39116 is able to synthesize the important flavoring agent vanillin from cheap natural substrates. The bacterium is therefore of great interest for the industry and used for the fermentative production of vanillin. In order to improve the production of natural vanillin with Amycolatopsis sp. ATCC 39116, the strain has been genetically engineered to optimize the metabolic flux towards the desired product. Extensive metabolic engineering was hitherto hampered, due to the lack of genetic tools like functional promoters and expression vectors. In this study, we report the establishment of a plasmid-based gene expression system for Amycolatopsis sp. ATCC 39116 that allows a further manipulation of the genotype. Four new Escherichia coli–Amycolatopsis shuttle vectors harboring different promoter elements were constructed, and the functionality of these regulatory elements was proven by the expression of the reporter gene gusA, encoding a β-glucuronidase. Glucuronidase activity was detected in all plasmid-harboring strains, and remarkable differences in the expression strength of the reporter gene depending on the used promoter were observed. The new expression vectors will promote the further genetic engineering of Amycolatopsis sp. ATCC 39116 to get insight into the metabolic network and to improve the strain for a more efficient industrial use.     

Construction of Novel Bacillus thuringiensis Strains with Different Insecticidal Activities by Transduction and Transformation

The shuttle vector pHT3101 and its derivative pHT408, bearing a copy of a cryIA(a) δ-endotoxin gene, were transferred into several Bacillus thuringiensis subspecies through phage CP-54Ber-mediated transduction, with frequencies ranging from 5 × 10^-8 to 2 × 10^-6 transductant per CFU, depending on the strain and on the plasmid. In Cry^- and Cry⁺ native recipients, the introduction of the cryIA(a) gene resulted in the formation of large bipyramidal crystals that were active against the insect Plutella xylostella (order Lepidoptera). In both cases, high levels of gene expression were observed. Transductants displaying a dual specificity were constructed by using as recipients the new isolates LM63 and LM79, which have larvicidal activity against insects of the order Coleoptera. It was not possible, however, to introduce pHT7911 into B. thuringiensis subsp. entomocidus, aizawai, or israelensis by transduction. However, electrotransformation was successful, and transformants expressing the toxin gene cryIIIA, carried by pHT7911, were obtained. Again, high levels of expression of the cloned gene were observed. The results indicate that CP-54Ber-mediated transduction is a useful procedure for introducing cloned crystal protein genes into various B. thuringiensis recipients and thereby creating strains with new combinations of genes. Finally it was also shown that pHT3101 is a very good expression vector for the cloned δ-endotoxin genes in the different recipients.     

Molecular characterisation of the Wx-B1 allelic variants identified in cultivated emmer wheat and comparison with those of durum wheat

Emmer wheat is a neglected crop that could be used in the breeding of modern durum wheat for quality, one important aspect of which is the starch composition that is related to the waxy proteins. A collection of 87 accessions of Spanish emmer wheat was analysed for waxy protein composition by SDS?CPAGE. No polymorphism was found for the Wx-A1 gene. However, for the Wx-B1 gene, three alleles were detected, two of them new. The whole gene sequence of these alleles was amplified by PCR in three fragments, which were digested with several endonucleases to determine internal differences in the sequence. These variants were also compared with the Wx alleles present in durum wheat. Differences in size and restriction sites were detected. DNA sequence analysis confirmed that the alleles found in emmer wheat are different from those in durum wheat. The first data suggested that these alleles showed a different influence on the amylose content of these lines. The variation found could be used to enlarge the gene pool of durum and emmer wheat, and design new materials with different amylose content.     

A new O-antigen gene cluster has a key role in the virulence of the Escherichia coli meningitis clone O45:K1:H7

A new highly pathogenic clone of Escherichia coli meningitis strains harboring the unusual serogroup O45 has recently emerged in France. To gain insight into the pathogenicity of this new clone, we investigated the possible role of antigen O45 in the virulence of strain S88 (O45:K1:H7), representative of this emerging clone. We first showed that the S88 O-antigen gene cluster sequence differs from that of O45 in the reference strain E. coli 96-3285, suggesting that the two O45 polysaccharides, while probably sharing a community of epitopes, represent two different antigens. The unique functional organization of the two O-antigen gene clusters and the low DNA sequence homology of the orthologous genes suggest that the two loci originated from a common ancestor and have since undergone multiple recombination events. Phylogenetic analysis based on the flanking gene gnd sequences indicates that the S88 antigen O45 (O45_S88) gene cluster may have been acquired, at least in part, from another member of the Enterobacteriaceae. Mutagenesis of the O45_S88 antigen gene cluster was used for functional analysis of the loci and revealed the crucial role of the O polysaccharide in S88 virulence in a neonatal rat meningitis model. We also developed a PCR method to specifically identify the O45_S88 antigen gene cluster. Together, our findings suggest that horizontal acquisition of a new O-antigen gene cluster, at least partly from another species, may have been a key event in the emergence and virulence of the E. coli O45:K1:H7 clone in France.     

The ScAACT1 gene at the Q alt5 locus as a candidate for increased aluminum tolerance in rye (Secale cereale L.)

Soluble aluminum (Al³⁺) is a major constraint to plant growth in highly acidic soils, which comprise up to 50% of the world??s arable land. The primary mechanism of Al resistance described in plants is the chelation of Al³⁺ cations by release of organic acids into the rhizosphere. Candidate aluminum tolerance genes encoding organic acid transporter of the ALMT (aluminum-activated malate transporter) and MATE (multi-drug and toxic compound extrusion) families have been characterized in several plant species. In this study, we have isolated in five different cultivars the rye ScAACT1 gene, homolog to barley aluminum activated citrate transporter HvAACT1. This gene mapped to the 7RS chromosome arm, 25?cM away from the ScALMT1 aluminum tolerance gene. The gene consisted of 13 exons and 12 introns and encodes a predicted membrane protein that contains the MatE domain and at least seven putative transmembrane regions. Expression of the ScAACT1 gene is Al-induced, but there were differences in the levels of expression among the cultivars analyzed. A new quantitative trait locus for Al tolerance in rye that co-localizes with the ScAACT1 gene was detected in the 7RS chromosome arm. These results suggest that the ScAACT1 gene is a candidate gene for increased Al tolerance in rye. The phylogenetic relationships between different MATE proteins are discussed.     

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis.     

Bacterial and archaeal communities in the acid pit lake sediments of a chalcopyrite mine

Bacterial and archaeal community structures and diversity of three different sedimentary environments (BH1A, BH2A and BH3A) in the acid pit lake of a chalcopyrite mine at Touro (Spain) were determined by 16S rRNA gene PCR-DGGE and sequencing of clone libraries. DGGE of bacterial and archaeal amplicons showed that the sediments harbor different communities. Bacterial 16S rRNA gene sequences were assigned to Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, Proteobacteria, Chloroflexi and uncultured bacteria, after clustering into 42 operational taxonomic units (OTUs). OTU 2 represented approximately 37, 42 and 37 % of all sequences from sediments BH1A, BH2A and BH3A, respectively, and was phylogenetically related to uncultured Chloroflexi. Remaining OTUs were phylogenetically related to heterotrophic bacteria, including representatives of Ferrithrix and Acidobacterium genera. Archaeal 16S rRNA gene sequences were clustered into 54 OTUs. Most of the sequences from the BH1A sediment were assigned to Euryarchaeota, whereas those from BH2A sediment were assigned to Crenarchaeota. The majority of the sequences from BH3A sediment were assigned to unclassified Archaea, and showed similarities to uncultured and unclassified environmental clones. No sequences related to Acidithiobacillus and Leptospirillum, commonly associated with acid mine drainage, were detected in this study.