Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem
Bogert, B. van den; Boekhorst, J. te; Herrmann, R. ; Smid, E.J. ; Zoetendal, E.G. ; Kleerebezem, M. - \ 2013
PLoS ONE 8 (2013)12. - ISSN 1932-6203
human gastrointestinal-tract - group-b streptococcus - prokaryotic genomes - lactococcus-lactis - bacterial samples - transport-system - microbiota - pneumoniae - competence - sequences
The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine
Woudenberg, J.H.C. ; Groenewald, J.Z. ; Binder, M. ; Crous, P.W. - \ 2013
Studies in Mycology 75 (2013)1. - ISSN 0166-0616 - p. 171 - 212.
ribosomal dna - phylogenetic-relationships - species-group - ulocladium - embellisia - genus - identification - sequences - taxonomy - nuclear
Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species associated with a wide variety of substrates. In recent years, DNA-based studies revealed multiple non-monophyletic genera within the Alternaria complex, and Alternaria species clades that do not always correlate to species-groups based on morphological characteristics. The Alternaria complex currently comprises nine genera and eight Alternaria sections. The aim of this study was to delineate phylogenetic lineages within Alternaria and allied genera based on nucleotide sequence data of parts of the 18S nrDNA, 28S nrDNA, ITS, GAPDH, RPB2 and TEF1-alpha gene regions. Our data reveal a Pleospora/Stemphylium clade sister to Embellisia annulata, and a well-supported Alternaria clade. The Alternaria clade contains 24 internal clades and six monotypic lineages, the assemblage of which we recognise as Alternaria. This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria. In this study, we treat the 24 internal clades in the Alternaria complex as sections, which is a continuation of a recent proposal for the taxonomic treatment of lineages in Alternaria. Embellisia annulata is synonymised with Dendryphiella salina, and together with Dendryphiella arenariae, are placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, which were previously associated with Alternaria, cluster within the Pleosporaceae, outside Alternaria s. str., whereas Alternariaster, a genus formerly seen as part of Alternaria, clusters within the Leptosphaeriaceae. Paradendryphiella is newly described, the generic circumscription of Alternaria is emended, and 32 new combinations and 10 new names are proposed. A further 10 names are resurrected, while descriptions are provided for 16 new Alternaria sections
Habitat- and host-related variation in sponge bacterial symbiont communities in Indonesian waters
Cleary, D.F.R. ; Becking, L.E. ; Voogd, N.J. de; Pires, A.C.C. ; Polonia, A. ; Egas, C. ; Gomes, N. - \ 2013
FEMS microbiology ecology 85 (2013)3. - ISSN 0168-6496 - p. 465 - 482.
enso-induced fires - marine sponges - vertical transmission - east kalimantan - kakaban-island - suberites-domuncula - butterfly diversity - microbial community - sp nov. - sequences
Marine lakes are unique ecosystems that contain isolated populations of marine organisms. Isolated from the surrounding marine habitat, many lakes house numerous endemic species. In this study, microbial communities of sponges inhabiting these lakes were investigated for the first time using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of two sponge species (Suberites diversicolor and Cinachyrella australiensis) inhabiting both marine lakes and adjacent open coastal systems. Host species and habitat explained almost 59% of the variation in bacterial composition. There was a significant difference in composition between both host species. Within S. diversicolor, there was little discernible difference between bacterial communities inside and outside lakes. The bacterial community of this species was, furthermore, dominated (63% of all sequences) by three very closely related alphaproteobacterial taxa identified as belonging to the recently described order Kiloniellales. Cinachyrella australiensis, in contrast, hosted markedly different bacterial communities inside and outside lakes with very few shared abundant taxa. Cinachyrella australiensis in open habitat only shared 9.4% of OTUs with C. australiensis in lake habitat. Bacteria were thus both highly species specific and, in the case of C. australiensis, habitat specific.
Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet
Suarez Diez, M. ; Pujol, M. ; Matzapetakis, M. ; Jaramillo, A. ; Iranzo, O. - \ 2013
Biotechnology Journal 8 (2013)7. - ISSN 1860-6768 - p. 855 - 864.
solution nmr structure - structural basis - peptides - recognition - prediction - sequences - dynamics - energy - trifluoroethanol - optimization
Automated methodologies to design synthetic proteins from first principles use energy computations to estimate the ability of the sequences to adopt a targeted structure. This approach is still far from systematically producing native-like sequences, due, most likely, to inaccuracies when modeling the interactions between the protein and its aqueous environment. This is particularly challenging when engineering small protein domains (with less polar pair interactions than with the solvent). We have re-designed a three-helix bundle, domain B, using a fixed backbone and a four amino acid alphabet. We have enlarged the rotamer library with conformers that increase the weight of electrostatic interactions within the design process without altering the energy function used to compute the folding free energy. Our synthetic sequences show less than 15% similarity to any Swissprot sequence. We have characterized our sequences in different solvents using circular dichroism and nuclear magnetic resonance. The targeted structure achieved is dependent on the solvent used. This method can be readily extended to larger domains. Our method will be useful for the engineering of proteins that become active only in a given solvent and for designing proteins in the context of hydrophobic solvents, an important fraction of the situations in the cell
Detection and Quantification of Leveillula taurica Growth in Pepper Leaves
Zheng, Z. ; Nonomura, T. ; Bóka, K. ; Matsuda, Y. ; Visser, R.G.F. ; Toyoda, H. ; Kiss, L. ; Bai, Y. - \ 2013
Phytopathology 103 (2013)6. - ISSN 0031-949X - p. 623 - 632.
internal transcribed spacer - powdery-mildew - genus leveillula - capsicum-annuum - resistance - pcr - infections - sequences - fungi - dna
Leveillula taurica is an obligate fungal pathogen that causes powdery mildew disease on a broad range of plants, including important crops such as pepper, tomato, eggplant, onion, cotton, and so on. The early stage of this disease is difficult to diagnose and the disease can easily spread unobserved; for example, in pepper and tomato production fields and greenhouses. The objective of this study was to develop a detection and quantification method of L. taurica biomass in pepper leaves with special regard to the early stages of infection. We monitored the development of the disease to time the infection process on the leaf surface as well as inside the pepper leaves. The initial and final steps of the infection taking place on the leaf surface were consecutively observed using a dissecting microscope and a scanning electron microscope. The development of the intercellular mycelium in the mesophyll was followed by light and transmission electron microscopy. A pair of L. taurica-specific primers was designed based on the internal transcribed spacer sequence of L. taurica and used in real-time polymerase chain reaction (PCR) assay to quantify the fungal DNA during infection. The specificity of this assay was confirmed by testing the primer pair with DNA from host plants and also from another powdery mildew species, Oidium neolycopersici, infecting tomato. A standard curve was obtained for absolute quantification of L. taurica biomass. In addition, we tested a relative quantification method by using a plant gene as reference and the obtained results were compared with the visual disease index scoring. The real-time PCR assay for L. taurica provides a valuable tool for detection and quantification of this pathogen in breeding activities as well in plant-microbe interaction studies.
Multi-locus phylogenies of the genus Barteria (Passifloraceae) protray complex patterns in the evolution of myrmecophytism.
Peccoud, J. ; Piatscheck, F. ; Yockteng, R. ; Garcia, M. ; Sauve, M. ; Djieto-Lordon, C. ; Harris, D.J. ; Wieringa, J.J. ; Breteler, F.J. ; Born, C. ; McKey, D. ; Blatrix, R. - \ 2013
Molecular Phylogenetics and Evolution 66 (2013)3. - ISSN 1055-7903 - p. 824 - 832.
chloroplast dna - rain-forest - population - sequences - ants - pseudomyrmecinae - euphorbiaceae - divergence - protection - mutualism
The four species of the central African genus Barteria show variation in habitat and in degree of association with ants. Whereas B. solida, restricted to submontane forests, attracts opportunistic ants to extrafloral nectar, the three other species, found in lowland rainforests (B. fistulosa, B. dewevrei) and in littoral scrub (B. nigritana), possess stem domatia of varying shapes and degrees of specialisation, hosting either non-specific arboreal ants (B. nigritana, some B. dewevrei) or two large species of ants of the genus Tetraponera Smith, 1852 that are specific to some species of Barteria (B. fistulosa, some B. dewevrei). We aimed to investigate whether this variation represents an evolutionary trend toward increasing specialisation of mutualism or the reduction or loss of myrmecophytic traits. For this, we determined phylogenetic relationships within the genus using DNA sequences (primarily nuclear ITS) and microsatellite genotypes (11 loci) on a large sample of individuals, mostly from Cameroon and Gabon. The two types of markers support an initial dichotomy that groups B. dewevrei with B. nigritana and B. fistulosa with B. solida respectively. Within these pairs, species do not appear reciprocally monophyletic. At microsatellite loci, B. nigritana forms a clade embedded within B. dewevrei; and within both B. solida and B. fistulosa, geographical populations show levels of differentiation similar to that observed between populations of B. solida and B. fistulosa. Geographic distance alone does not account for genetic differentiation between species, which indicates reproductive isolation. Divergence in each of the two pairs implies evolutionary transitions in habitat and in myrmecophytism. Specialised mutualism with specific ant species of the genus Tetraponera has been lost in species found in more marginal habitats.
Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units
Vettraino, A.M. ; Bonants, P.J.M. ; Tomassini, A. ; Bruni, N. ; Vannini, A. - \ 2012
Letters in Applied Microbiology 55 (2012)5. - ISSN 0266-8254 - p. 390 - 396.
fungal communities - identification - phylogeny - diversity - sequences - reveals
Aims: To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). Methods and Results: Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was used to describe the structure of a DNA mixture comprising eight Phytophthora spp. and Pythium vexans. Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTUs. The total error rate was 0_63% and comprised mainly mismatches (0_25%) Conclusions: Pyrosequencing of ITS1 region is an efficient and accurate technique for the detection and identification of Phytophthora spp. In environmental samples. However, the risk of allocating false MOTUs, even when demonstrated to be low, may require additional validation with alternative detection methods. Significance and Impact of the Study: Phytophthora spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of Phytophthora complexes in environmental samples offers an unique opportunity for the interception of known and unknown species along pathways of introduction, along with the identification of these organisms in invaded environments.
Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1
Todt, T.J. ; Wels, M. ; Bongers, R.S. ; Siezen, R.J. ; Hijum, S.A.F.T. van; Kleerebezem, M. - \ 2012
PLoS ONE 7 (2012)9. - ISSN 1932-6203
transcription start sites - escherichia-coli - rna-polymerase - sequences - identification - dna - conservation - compilation - metabolism - initiation
Background - In prokaryotes, sigma factors are essential for directing the transcription machinery towards promoters. Various sigma factors have been described that recognize, and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor s70 is commonly involved in transcription of the cell's housekeeping genes, which is mediated by the conserved s70 promoter sequence motifs. In this study the s70-promoter sequences in Lactobacillus plantarum WCFS1 were predicted using a genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with transcription start sites inferred from the 5'-ends of transcripts detected by high-resolution tiling array transcriptome datasets. Results - To identify s70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focussing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved s70-promoter consensus. Position weight matrices-based models of the recovered s70-promoter sequence motif were employed to identify 3874 motifs with significant similarity (p-value
Stagonosporopsis spp. associated with ray blight disease of Asteraceae
Vaghefi, N. ; Pethybridge, S.J. ; Ford, R. ; Nicolas, M.E. ; Crous, P.W. ; Taylor, P.W.J. - \ 2012
Australasian Plant Pathology 41 (2012)6. - ISSN 0815-3191 - p. 675 - 686.
phoma-ligulicola - phylogenetic analyses - ribosomal dna - mixed models - host-range - pyrethrum - sequences - complex - genera - taxa
Ray blight disease of pyrethrum (Tanacetum cinerariifolium) is shown to be caused by more than one species of Stagonosporopsis. The Australian pathogen, previously identified as Phoma ligulicola var. inoxydabilis, represents a new species described as Stagonosporopsis tanaceti based on morphological characters and a five-gene phylogeny employing partial sequences of the actin, translation elongation factor 1-alpha, internal transcribed spacers and 5.8S of the nrDNA, 28S large subunit and beta-tubulin 2 gene sequences. Furthermore, the two varieties of Stagonosporopsis ligulicola are elevated to species level as S. chrysanthemi and S. inoxydabilis based on their DNA phylogeny and morphology.
Prediction of Altered 3'- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region
Endale, M.L. ; Fritz, E.R. ; Estelle, J. ; Hu, Z.L. ; Madsen, O. ; Groenen, M.A.M. - \ 2012
PLoS ONE 7 (2012)11. - ISSN 1932-6203
microrna target recognition - mediated gene-regulation - phenotypic variation - expression - accessibility - principles - sequences - evolution - disease - genome
The SLA (swine leukocyte antigen, MHC: SLA) genes are the most important determinants of immune, infectious disease and vaccine response in pigs; several genetic associations with immunity and swine production traits have been reported. However, most of the current knowledge on SLA is limited to gene coding regions. MicroRNAs (miRNAs) are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation. We explored the impact of variants in the 3'-UTR miRNA target sites of genes within the whole SLA region. The combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, empowered the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs). Predictions for three SLA genes characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues. Twenty-four novel SNPs were predicted to affect miRNA-binding sites in 19 genes of the SLA region. Seven of these genes (SLA-1, SLA-6, SLA-DQA, SLA-DQB1, SLA-DOA, SLA-DOB and TAP1) are linked to antigen processing and presentation functions, which is reminiscent of associations with disease traits reported for altered miRNA binding to MHC genes in humans. An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq) of three porcine tissues. Our results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered miRNA regulation patterns.
Cloning and characterization of a tuberous root-specific promoter from cassava (Manihot esculenta Crantz)
Koehorst-van Putten, H.J.J. ; Wolters, A.M.A. ; Pereira-Bertram, I.J. ; Berg, H. ; Krol, A.R. van der; Visser, R.G.F. - \ 2012
Planta 236 (2012)6. - ISSN 0032-0935 - p. 1955 - 1965.
bound-starch-synthase - storage roots - transformation - expression - gene - agrobacterium - elements - sequences - database - program
In order to obtain a tuberous root-specific promoter to be used in the transformation of cassava, a 1,728 bp sequence containing the cassava granule-bound starch synthase (GBSSI) promoter was isolated. The sequence proved to contain light- and sugar-responsive cis elements. Part of this sequence (1,167 bp) was cloned into binary vectors to drive expression of the firefly luciferase gene. Cassava cultivar Adira 4 was transformed with this construct or a control construct in which the luciferase gene was cloned behind the 35S promoter. Luciferase activity was measured in leaves, stems, roots and tuberous roots. As expected, the 35S promoter induced luciferase activity in all organs at similar levels, whereas the GBSSI promoter showed very low expression in leaves, stems and roots, but very high expression in tuberous roots. These results show that the cassava GBSSI promoter is an excellent candidate to achieve tuberous root-specific expression in cassava.
Phyllosticta species associated with freckle disease of banana
Wong, M.H. ; Crous, P.W. ; Henderson, J. ; Groenewald, J.Z. ; Drenth, A. - \ 2012
Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 173 - 187.
citrus black spot - ribosomal dna - mycosphaerella - sequences - musarum - plants
The identity of the casual agent of freckle disease of banana was investigated. The pathogen is generally referred to in literature under its teleomorphic name, Guignardia musae, or that of its purported anamorph, Phyllosticta musarum. Based on morphological and molecular data from a global set of banana specimens, several species were found associated with freckle disease. Phyllosticta maculata (from Southeast Asia and Oceania) is introduced as a new name for Guignardia musae, and an epitype is designated from Australia. Phyllosticta musarum (from India and Thailand) is shown to represent a distinct species, and the name is fixed by designation of an epitype from India. Guignardia stevensii is confirmed as distinct species from Hawaii, while Guignardia musicola from northern Thailand is shown to contain different taxa and is regarded as nomen confusum. Phyllosticta cavendishii is described as a new, widely distributed species, appearing primarily on Cavendish, but also on non-Cavendish banana cultivars.
A phylogenetic and taxonomic re-evaluation of the Bipolaris - Cochliobolus - Curvularia Complex
Manamgoda, D.S. ; Cai, L. ; McKenzie, E.H.C. ; Crous, P.W. ; Madrid, H. ; Chukeatirote, E. ; Shivas, R.G. ; Tan, Y.P. ; Hyde, K.D. - \ 2012
Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 131 - 144.
species concepts - sequences - pseudocochliobolus - helminthosporium - pathogens - alignment - genes - fungi - genus - rdna
Three genera, Cochliobolus, Bipolaris and Curvularia form a complex that contains many plant pathogens, mostly on grasses (Poaceae) with a worldwide distribution. The taxonomy of this complex is confusing as frequent nomenclatural changes and refinements have occurred. There is no clear morphological boundary between the asexual genera Bipolaris and Curvularia, and some species show intermediate morphology. We investigated this complex based on a set of ex-type cultures and collections from northern Thailand. Combined gene analysis of rDNA ITS (internal transcribed spacer), GPDH (glyceraldehyde 3-phosphate dehydrogenase), LSU (large subunit) and EF1-a (translation elongation factor 1-a) shows that this generic complex divides into two groups. Bipolaris and Cochliobolus species clustered in Group 1 along with their type species, whereas Curvularia species (including species named as Bipolaris, Cochliobolus and Curvularia) clustered in Group 2, with its generic type. The nomenclatural conflict in this complex is resolved giving priority to the more commonly used established generic names Bipolaris and Curvularia. Modern descriptions of the genera Bipolaris and Curvularia are provided and species resolved in this study are transferred to one of these genera based on their phylogeny.
The development of a validated real-time (TaqMan) PCR for detection of Stagonosporopsis andigena and S. crystalliniformis in infected leaves of potato and tomato
Gruyter, J. de; Gent-Pelzer, M.P.E. van; Woudenberg, J.H.C. ; Rijswick, P.C.J. van; Meekes, E.T.M. ; Crous, P.W. ; Bonants, P.J.M. - \ 2012
European Journal of Plant Pathology 134 (2012)2. - ISSN 0929-1873 - p. 301 - 313.
polymerase-chain-reaction - phoma-tracheiphila - didymella-bryoniae - complex - foveata - differentiation - phylogeny - multiplex - sequences - disease
Stagonosporopsis andigena and S. crystalliniformis are serious foliage pathogens on potato (Solanum tuberosum) and tomato (Solanum lycopersicum). As both species have been recorded only in the Andes area, S. andigena is listed as an A1 quarantine organism in Europe. The actin region of isolates of Stagonosporopsis and allied species of Boeremia, Didymella, Peyronellaea and Phoma was amplified using generic primers. DNA sequence differences of the actin gene were utilised to develop species-specific real-time (TaqMan) PCR assays for the detection of S. andigena and S. crystalliniformis in leaves of potato or tomato. The specificity of the TaqMan PCR assays was determined on genomic DNA extracted from two S. andigena and two S. crystalliniformis isolates and 16 selected isolates of Stagonosporopsis, Phoma and Boeremia, which are the closest relatives. The validation of the methods developed included the DNA extraction and the TaqMan PCR assays. The performance criteria specificity, analytical sensitivity, reproducibility, repeatability and robustness of the TaqMan PCR assays demonstrated the reliability of both methods for the detection of S. andigena and S. crystalliniformis in leaf material. The TaqMan PCR assays were tested on symptomatic leaves of potato and tomato that were obtained after artificial inoculation of detached leaves with both pathogens under quarantine conditions. In the artificial inoculation experiments both S. andigena and S. crystalliniformis caused leaf infections on potato and tomato.
Characterization of Hubera (Annonaceae), a new genus segregated from Polyalthia and allied to Miliusa.
Chaowasku, T. ; Johnson, D.M. ; Ham, R.W.J.M. van der; Chatrou, L.W. - \ 2012
Phytotaxa 69 (2012). - ISSN 1179-3155 - p. 33 - 56.
molecular phylogenetics - uvaria annonaceae - pollen morphology - chloroplast dna - evolution - genera - reconstruction - hypotheses - sequences - revision
On the basis of molecular phylogenetics, pollen morphology and macromorphology, a new genus of the tribe Miliuseae, Hubera, segregrated from Polyalthia and allied to Miliusa, is established and described. It is characterized by the combination of reticulate tertiary venation of the leaves, axillary inflorescences, a single ovule per ovary and therefore single-seeded monocarps, seeds with a flat to slightly raised raphe, spiniform(-flattened peg) ruminations of the endosperm, and pollen with a finely and densely granular infratectum. Twenty-seven species are accordingly transferred to this new genus.
Efficiency of Agrobacterium rhizogenes-mediated root transformation of Parasponia and Trema is temperature dependent
Cao, Q. ; Camp, R. Op den; Seifi Kalhor, M. ; Bisseling, T. ; Geurts, R. - \ 2012
Plant Growth Regulation 68 (2012)3. - ISSN 0167-6903 - p. 459 - 465.
medicago-truncatula - gene-transfer - non-legume - plants - nitrogen - andersonii - nodulation - rhizobium - phaseolus - sequences
Parasponia trees are the only non-legume species that form nitrogen-fixing root nodules with rhizobium. Based on its taxonomic position in relation to legumes (Fabaceae), it is most likely that both lineages have gained this symbiotic capacity independently. Therefore, Parasponia forms a bridging species to understand the evolutionary constraints underlying this symbiosis. However, absence of key technologies to genetically modify Parasponia seriously impeded studies on these species. We employed Agrobacterium rhizogenes to create composite Parasponia andersonii plants that harbour transgenic roots. Here, we provide an optimized protocol to infect P. andersonii as well as its non-symbiotic sister species Trema tomentosa with A. rhizogenes. We show that the transformation efficiency is temperature dependent. Whereas the optimal growth temperature for both these species is 28 °C, the transformation is most efficient when co-cultivation with A. rhizogenes occurs at 21 °C. Using this optimized protocol up to 80 % transformation efficiency can be obtained. These robust transformation platforms will provide a strong tool to unravel the Parasponia–rhizobium symbiosis
Scenario Analysis of Nutrient Removal from Municipal Wastewater by Microalgal Biofilms
Boelee, N.C. ; Temmink, H. ; Janssen, M. ; Buisman, C.J.N. ; Wijffels, R.H. - \ 2012
Water 4 (2012)2. - ISSN 2073-4441 - p. 460 - 473.
afvalwaterbehandeling - biofilms - algen - biologische waterzuiveringsinstallaties - vergelijkend onderzoek - volgorden - haalbaarheidsstudies - heterotrofe micro-organismen - stikstof - fosfor - verwijdering - biomassa productie - biobased economy - waste water treatment - biofilms - algae - biological water treatment plants - comparative research - sequences - feasibility studies - heterotrophic microorganisms - nitrogen - phosphorus - removal - biomass production - biobased economy - marine-phytoplankton - chemical-composition - chlorella-vulgaris - nitrate uptake - algal biofilm - growth - photobioreactor - photosynthesis
Microalgae can be used for the treatment of municipal wastewater. The application of microalgal biofilms in wastewater treatment systems seems attractive, being able to remove nitrogen, phosphorus and COD from wastewater at a short hydraulic retention time. This study therefore investigates the area requirement, achieved effluent concentrations and biomass production of a hypothetical large-scale microalgal biofilm system treating municipal wastewater. Three scenarios were defined: using microalgal biofilms: (1) as a post-treatment; (2) as a second stage of wastewater treatment, after a first stage in which COD is removed by activated sludge; and (3) in a symbiotic microalgal/heterotrophic system. The analysis showed that in the Netherlands, the area requirements for these three scenarios range from 0.32 to 2.1 m2 per person equivalent. Moreover, it was found that it was not possible to simultaneously remove all nitrogen and phosphorus from the wastewater, because of the nitrogen:phosphorus ratio in the wastewater. Phosphorus was limiting in the post-treatment scenario, while nitrogen was limiting in the two other scenarios. Furthermore, a substantial amount of microalgal biomass was produced, ranging from 13 to 59 g per person equivalent per day. These findings show that microalgal biofilm systems hold large potential as seasonal wastewater treatment systems and that it is worthwhile to investigate these systems further
Promoter propagation in prokaryotes
Matus-Garcia, M. ; Nijveen, H. ; Passel, M.W.J. van - \ 2012
Nucleic acids research 40 (2012)20. - ISSN 0305-1048 - p. 10032 - 10040.
horizontal gene-transfer - escherichia-coli - adaptive evolution - lactococcus-lactis - sequences - genomes - networks - identification - mutations - families
Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. In many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large impact on rapid adaptation of novel or cryptic functions. Querying all publicly available prokaryotic genomes (1362) uncovered >4000 families of highly conserved PMPs (50 to 100 long with =80% nt identity) in 1043 genomes from 424 different genera. The genomes with the largest number of PMP families are Anabaena variabilis (28 families), Geobacter uraniireducens (27 families) and Cyanothece PCC7424 (25 families). Family size varied from 2 to 93 homologous promoters (in Desulfurivibrio alkaliphilus). Some PMPs are present in particular species, but some are conserved across distant genera. The identified PMPs represent a conservative dataset of very recent or conserved events of mobilization of non-coding DNA and thus they constitute evidence of an extensive reservoir of recyclable regulatory sequences for rapid transcriptional rewiring
Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
Bohlin, J. ; Passel, M.W.J. van - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164 - 35 p.
usage patterns - sequences - prokaryotes - communication - reduction - diversity - ancestor
Background: We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure. Results: Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes >GI>phage>plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes. Conclusions: We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids
Analysis of the mating-type loci of co-occurring and phylogenetically related species of Ascochyta and Phoma
Woudenberg, J.H.C. ; Gruyter, J. de; Crous, P.W. ; Zwiers, L.H. - \ 2012
Molecular Plant Pathology 13 (2012)4. - ISSN 1464-6722 - p. 350 - 362.
evolutionary relationships - sexual development - pyrenophora-teres - pisum-sativum - complex - genes - teleomorph - phylogeny - sequences - cloning
Ascochyta and Phoma are fungal genera containing several important plant pathogenic species. These genera are morphologically similar, and recent molecular studies performed to unravel their phylogeny have resulted in the establishment of several new genera within the newly erected Didymellaceae family. An analysis of the structure of fungal mating-type genes can contribute to a better understanding of the taxonomic relationships of these plant pathogens, and may shed some light on their evolution and on differences in sexual strategy and pathogenicity. We analysed the mating-type loci of phylogenetically closely related Ascochyta and Phoma species (Phoma clematidina, Didymella vitalbina, Didymella clematidis, Peyronellaea pinodes and Peyronellaea pinodella) that co-occur on the same hosts, either on Clematis or Pisum. The results confirm that the mating-type genes provide the information to distinguish between the homothallic Pey. pinodes (formerly Ascochyta pinodes) and the heterothallic Pey. pinodella (formerly Phoma pinodella), and indicate the close phylogenetic relationship between these two species that are part of the disease complex responsible for Ascochyta blight on pea. Furthermore, our analysis of the mating-type genes of the fungal species responsible for causing wilt of Clematis sp. revealed that the heterothallic D. vitalbina (Phoma anamorph) is more closely related to the homothallic D. clematidis (Ascochyta anamorph) than to the heterothallic P. clematidina. Finally, our results indicate that homothallism in D. clematidis resulted from a single crossover between MAT1-1 and MAT1-2 sequences of heterothallic ancestors, whereas a single crossover event followed by an inversion of a fused MAT1/2 locus resulted in homothallism in Pey. pinodes.