Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Lactobacillus plantarum strains can enhance human mucosal and systemic immunity and prevent non-steroidal anti-inflammatory drug induced reduction in T regulatory Cells
Vos, Paul de; Mujagic, Zlatan ; Haan, Bart J. de; Siezen, Roland J. ; Bron, Peter A. ; Meijerink, Marjolein ; Wells, Jerry M. ; Masclee, Ad A.M. ; Boekschoten, Mark V. ; Faas, Marijke M. ; Troost, Freddy J. - \ 2017
Frontiers in Immunology 8 (2017). - ISSN 1664-3224 - 18 p.
Adaptive immunity - Indomethacin - Intestinal mucosal immunity - Lactobacillus plantarum - Non-steroidal anti-inflammatory drug - Probiotics

Orally ingested bacteria interact with intestinal mucosa and may impact immunity. However, insights in mechanisms involved are limited. In this randomized placebo-controlled cross-over trial, healthy human subjects were given Lactobacillus plantarum supplementation (strain TIFN101, CIP104448, or WCFS1) or placebo for 7 days. To determine whether L. plantarum can enhance immune response, we compared the effects of three stains on systemic and gut mucosal immunity, by among others assessing memory responses against tetanus toxoid (TT)-antigen, and mucosal gene transcription, in human volunteers during induction of mild immune stressor in the intestine, by giving a commonly used enteropathic drug, indomethacin [non-steroidal anti-inflammatory drug (NSAID)]. Systemic effects of the interventions were studies in peripheral blood samples. NSAID was found to induce a reduction in serum CD4+ /Foxp3 regulatory cells, which was prevented by L. plantarum TIFN101. T-cell polarization experiments showed L. plantarum TIFN101 to enhance responses against TT-antigen, which indicates stimulation of memory responses by this strain. Cell extracts of the specific L. plantarum strains provoked responses after WCFS1 and TIFN101 consumption, indicating stimulation of immune responses against the specific bacteria. Mucosal immunomodulatory effects were studied in duodenal biopsies. In small intestinal mucosa, TIFN101 upregulated genes associated with maintenance of T- and B-cell function and antigen presentation. Furthermore, L. plantarum TIFN101 and WCFS1 downregulated immunological pathways involved in antigen presentation and shared downregulation of snoRNAs, which may suggest cellular destabilization, but may also be an indicator of tissue repair. Full sequencing of the L. plantarum strains revealed possible gene clusters that mightbe responsible for the differential biological effects of the bacteria on host immunity. In conclusion, the impact of oral consumption L. plantarum on host immunity is strain dependent and involves responses against bacterial cell components. Some strains may enhance specific responses against pathogens by enhancing antigen presentation and leukocyte maintenance in mucosa. In future studies and clinical settings, caution should be taken in selecting beneficial bacteria as closely related strains can have different effects. Our data show that specific bacterial strains can prevent immune stress induced by commonly consumed painkillers such as NSAID and can have enhancing beneficial effects on immunity of consumers by stimulating antigen presentation and memory responses.

Plasmid Complement of Lactococcus lactis NCDO712 Reveals a Novel Pilus Gene Cluster
Tarazanova, Mariya ; Beerthuyzen, M. ; Siezen, Roland ; Fernandez Gutierrez, Maria ; Jong, Anne de; Meulen, Sjoerd van der; Kok, Jan ; Bachmann, Herwig - \ 2016
PLoS One 11 (2016)12. - ISSN 1932-6203

Lactococcus lactis MG1363 is an important gram-positive model organism. It is a plasmidfree and phage-cured derivative of strain NCDO712. Plasmid-cured strains facilitate studies on molecular biological aspects, but many properties which make L. lactis an important organism in the dairy industry are plasmid encoded. We sequenced the total DNA of strain NCDO712 and, contrary to earlier reports, revealed that the strain carries 6 rather than 5 plasmids. A new 50-kb plasmid, designated pNZ712, encodes functional nisin immunity (nisCIP) and copper resistance (lcoRSABC). The copper resistance could be used as a marker for the conjugation of pNZ712 to L. lactis MG1614. A genome comparison with the plasmid cured daughter strain MG1363 showed that the number of single nucleotide polymorphisms that accumulated in the laboratory since the strains diverted more than 30 years ago is limited to 11 of which only 5 lead to amino acid changes. The 16-kb plasmid pSH74 was found to contain a novel 8-kb pilus gene cluster spaCB-spaA-srtC1-srtC2, which is predicted to encode a pilin tip protein SpaC, a pilus basal subunit SpaB, and a pilus backbone protein SpaA. The sortases SrtC1/SrtC2 are most likely involved in pilus polymerization while the chromosomally encoded SrtA could act to anchor the pilus to peptidoglycan in the cell wall. Overexpression of the pilus gene cluster from a multi-copy plasmid in L. lactis MG1363 resulted in cell chaining, aggregation, rapid sedimentation and increased conjugation efficiency of the cells. Electron microscopy showed that the over-expression of the pilus gene cluster leads to appendices on the cell surfaces. A deletion of the gene encoding the putative basal protein spaB, by truncating spaCB, led to more pilus-like structures on the cell surface, but cell aggregation and cell chaining were no longer observed. This is consistent with the prediction that spaB is involved in the anchoring of the pili to the cell.

Comparative genomics of iron-transporting systems in Bacillus cereus strains and impact of iron sources on growth and biofilm formation
Hayrapetyan, Hasmik ; Siezen, Roland ; Abee, Tjakko ; Nierop Groot, Masja - \ 2016
Frontiers in Microbiology 7 (2016)JUN. - ISSN 1664-302X
Bacillus cereus - Biofilm formation - Complex iron sources - Genotypes - Growth - Iron transport

Iron is an important element for bacterial viability, however it is not readily available in most environments. We studied the ability of 20 undomesticated food isolates of Bacillus cereus and two reference strains for capacity to use different (complex) iron sources for growth and biofilm formation. Studies were performed in media containing the iron scavenger 2,2-Bipyridine. Transcriptome analysis using B. cereus ATCC 10987 indeed showed upregulation of predicted iron transporters in the presence of 2,2-Bipyridine, confirming that iron was depleted upon its addition. Next, the impact of iron sources on growth performance of the 22 strains was assessed and correlations between growth stimulation and presence of putative iron transporter systems in the genome sequences were analyzed. All 22 strains effectively used Fe citrate and FeCl3 for growth, and possessed genes for biosynthesis of the siderophore bacillibactin, whereas seven strains lacked genes for synthesis of petrobactin. Hemoglobin could be used by all strains with the exception of one strain that lacked functional petrobactin and IlsA systems. Hemin could be used by the majority of the tested strains (19 of 22). Notably, transferrin, ferritin, and lactoferrin were not commonly used by B. cereus for growth, as these iron sources could be used by 6, 3, and 2 strains, respectively. Furthermore, biofilm formation was found to be affected by the type of iron source used, including stimulation of biofilms at liquid-air interphase (FeCl3 and Fe citrate) and formation of submerged type biofilms (hemin and lactoferrin). Our results show strain variability in the genome-encoded repertoire of iron-transporting systems and differences in efficacy to use complex iron sources for growth and biofilm formation. These features may affect B. cereus survival and persistence in specific niches.

Linking Bacillus cereus genotypes and carbohydrate utilization capacity
Warda, Alicja K. ; Siezen, Roland J. ; Boekhorst, Jos ; Wells-Bennik, Marjon H.J. ; Jong, Anne de; Kuipers, Oscar P. ; Nierop Groot, Masja N. ; Abee, Tjakko - \ 2016
PLoS One 11 (2016)6. - ISSN 1932-6203

We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.

Complete genome sequence of Anoxybacillus flavithermus TNO-09.006, a thermophilic sporeformer associated with a dairy-processing environment
Caspers, M.P.M. ; Boekhorst, J. te; Abee, T. ; Siezen, R.J. ; Kort, R. - \ 2013
Genome announcements 1 (2013)1. - ISSN 2169-8287
Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain Anoxybacillus flavithermus TNO-09.006 from a milk-processing plant, and we report the complete genome of this isolate consisting of a single chromosome of 2.65 Mb.
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data
Bryant, J.M. ; Schürch, A.C. ; Deutekom, H. van; Harris, S.R. ; Beer, J.L. de; Jager, V.C.L. de; Kremer, K. ; Hijum, S.A.F.T. van; Siezen, R.J. ; Borgdorff, M. ; Bentley, S.D. ; Parkhill, J. ; Soolingen, D. van - \ 2013
Bmc Infectious Diseases 13 (2013)1. - ISSN 1471-2334
resistance - strains - mutations - evolution - epidemiology - complex - gene
BACKGROUND: Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required. METHODS: We attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years. RESULTS: Multiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links. CONCLUSIONS: This in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing
Contribution of bi-allelic germline MUTYH mutations to early-onset and familial colorectal cancer and to low number of adenomatous polyps: case-series and literature review
Knopperts, A.P. ; Nielsen, M. ; Niessen, R.C. ; Tops, C.M.J. ; Jorritsma, B. ; Varkevisser, J. ; Wijnen, J. ; Siezen, C.L.E. ; Heine-Bröring, R.C. ; Kranen, H.J. ; Vos, Y.J. ; Westers, H. ; Kampman, E. - \ 2013
Familial Cancer 12 (2013)1. - ISSN 1389-9600 - p. 43 - 50.
lynch-syndrome - microsatellite instability - gene-mutations - myh mutations - frequency - identification - feasibility - consumption - carriers - colon
In the absence of a polyposis phenotype, colorectal cancer (CRC) patients referred for genetic testing because of early-onset disease and/or a positive family history, typically undergo testing for molecular signs of Lynch syndrome in their tumors. In the absence of these signs, DNA testing for germline mutations associated with other known tumor syndromes is usually not performed. However, a few studies in large series of CRC patients suggest that in a small percentage of CRC cases, bi-allelic MUTYH germline mutations can be found in the absence of the MUTYH-associated polyposis phenotype. This has not been studied in the Dutch population. Therefore, we analyzed the MUTYH gene for mutations in 89 patients with microsatellite-low or stable CRC cancer diagnosed before the age of 40 years or otherwise meeting the Bethesda criteria, all of them without a polyposis phenotype. In addition, we studied a series of 693 non-CRC patients with 1-13 adenomatous colorectal polyps for the MUTYH hotspot mutations Y179C, G396D and P405L. No bi-allelic MUTYH mutations were observed. Our data suggest that the contribution of bi-allelic MUTYH mutations to the development of CRC in Dutch non-polyposis patients that meet clinical genetic referral criteria, and to the development of low number of colorectal adenomas in non-CRC patients, is likely to be low.
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
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome
Siezen, R.J. ; Francke, C. ; Renckens, B. ; Boekhorst, L.J.S. ; Wels, M. ; Kleerebezem, M. ; Hijum, S.A.F.T. van - \ 2012
Journal of Bacteriology 194 (2012)1. - ISSN 0021-9193 - p. 195 - 196.
lactic-acid bacteria - gastrointestinal-tract - identification - fermentation - database - artemis - growth - genes - mice - carbohydrate
There is growing interest in the beneficial effects of Lactobacillus plantarum on human health. The genome of L. plantarum WCFS1, first sequenced in 2001, was resequenced using Solexa technology. We identified 116 nucleotide corrections and improved function prediction for nearly 1,200 proteins, with a focus on metabolic functions and cell surface-associated proteins.
Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730)
Axelsson, L. ; Rud, I. ; Naterstad, K. ; Blom, H. ; Renckens, B. ; Boekhorst, L.J.S. ; Kleerebezem, M. ; Hijum, S.A.F.T. van; Siezen, R.J. - \ 2012
Journal of Bacteriology 194 (2012)9. - ISSN 0021-9193 - p. 2391 - 2392.
inducible gene-expression - lactic-acid bacteria - sakei - fermentations - diversity - vectors - healthy - mucosa - wcfs1
Lactobacillus plantarum is a highly versatile lactic acid bacterium found in various ecological niches, such as fermented vegetable, meat, and dairy products and the gastrointestinal tract. We sequenced the genome of L. plantarum NC8, a naturally plasmid-free strain, which has been used as a model strain in many laboratories worldwide.
Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment
Zhao, Y. ; Caspers, M.P. ; Abee, T. ; Siezen, R.J. ; Kort, R. - \ 2012
Journal of Bacteriology 194 (2012)15. - ISSN 0021-9193 - p. 4118 - 4118.
database - artemis - act
Thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain Geobacillus thermoglucosidans TNO-09.020 from a milk processing plant and report the complete genome of a dairy plant isolate consisting of a single chromosome of 3.75 Mb.
Toward pectin fermentation by Saccharomyces cerevisiae: Expression of the first two steps of a bacterial pathway for d-galacturonate metabolism.
Huisjes, E.H. ; Luttik, M.A. ; Almering, M.J. ; Bisschops, M.M. ; Dang, D.H. ; Kleerebezem, M. ; Siezen, R.J. ; Maris, A.J. van; Pronk, J.T. - \ 2012
Journal of Biotechnology 162 (2012)2-3. - ISSN 0168-1656 - p. 303 - 310.
uronic acid metabolism - limited chemostat cultures - neighbor-joining method - mold hypocrea-jecorina - xylose isomerase gene - d-altronic acid - escherichia-coli - l-arabinose - alcoholic fermentation - shuttle vectors
Saccharomyces cerevisiae cannot metabolize d-galacturonate, an important monomer of pectin. Use of S. cerevisiae for production of ethanol or other compounds of interest from pectin-rich feedstocks therefore requires introduction of a heterologous pathway for d-galacturonate metabolism. Bacterial d-galacturonate pathways involve d-galacturonate isomerase, d-tagaturonate reductase and three additional enzymes. This study focuses on functional expression of bacterial d-galacturonate isomerases in S. cerevisiae. After demonstrating high-level functional expression of a d-tagaturonate reductase gene (uxaB from Lactococcus lactis), the resulting yeast strain was used to screen for functional expression of six codon-optimized bacterial d-galacturonate isomerase (uxaC) genes. The L. lactis uxaC gene stood out, yielding a tenfold higher enzyme activity than the other uxaC genes. Efficient expression of d-galacturonate isomerase and d-tagaturonate reductase represents an important step toward metabolic engineering of S. cerevisiae for bioethanol production from d-galacturonate. To investigate in vivo activity of the first steps of the d-galacturonate pathway, the L. lactis uxaB and uxaC genes were expressed in a gpd1¿ gpd2¿ S. cerevisiae strain. Although d-tagaturonate reductase could, in principle, provide an alternative means for re-oxidizing cytosolic NADH, addition of d-galacturonate did not restore anaerobic growth, possibly due to absence of a functional d-altronate exporter in S. cerevisiae.
Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli
Kormelink, T.G. ; Koenders, E. ; Hagemeijer, Y. ; Overmars, L. ; Siezen, R.J. ; Vos, W.M. de; Francke, C. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164
glutamine-synthetase gene - transcription factor tnra - subtilis ureabc operon - streptococcus-mutans - nucleotide-sequence - escherichia-coli - lactococcus-lactis - reductase/2,3-butanediol dehydrogenase - lactobacillus-plantarum - asparagine synthetase
BACKGROUND: The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR. RESULTS: Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase (glnRA operon), and the transport of ammonium (amtB-glnK) and glutamine/glutamate (i.e. via glnQHMP, glnPHQ, gltT, alsT). In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae. CONCLUSIONS: Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling
Monitoring strain diversity and dynamics in metagenomics data using meta-MLST SNP profiling
Jager, V.C.L. de; Hazelwood, L.A. ; Kutahya, O. ; Kleerebezem, M. ; Smid, E.J. ; Siezen, R.J. ; Hijum, S.A.F.T. van - \ 2012
Nederlands Tijdschrift voor Medische Microbiologie 20 (2012)Supplement. - ISSN 0929-0176 - p. S142 - S142.
Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs
Wels, M. ; Overmars, L. ; Francke, C. ; Kleerebezem, M. ; Siezen, R.J. - \ 2011
Microbial Biotechnology 4 (2011)3. - ISSN 1751-7907 - p. 333 - 344.
bacillus-subtilis - comparative genomics - transcriptional regulation - negative regulator - escherichia-coli - ctsr - regulon - identification - discovery - bacteria
P>Gene regulatory networks can be reconstructed by combining transcriptome data from many different experiments to elucidate relations between the activity of certain transcription factors and the genes they control. To obtain insight in the regulatory network of Lactobacillus plantarum, microarray transcriptome data from more than 70 different experimental conditions were combined and the expression profiles of the transcriptional units (TUs) were compared. The TUs that displayed correlated expression were used to identify putative cis-regulatory elements by searching the upstream regions of the TUs for conserved motifs. Predicted motifs were extended and refined by searching for motifs in the upstream regions of additional TUs with correlated expression. In this way, cis-acting elements were identified for 41 regulons consisting of at least four TUs (correlation > 0.7). This set of regulons included the known regulons of CtsR and LexA, but also several novel ones encompassing genes with coherent biological functions. Visualization of the regulons and their connections revealed a highly interconnected regulatory network. This network contains several subnetworks that encompass genes of correlated biological function, such as sugar and energy metabolism, nitrogen metabolism and stress response.
Single-cell genomics: unravelling the genomes of unculturable microorganisms
Jager, V.C.L. de; Siezen, R.J. - \ 2011
Microbial Biotechnology 4 (2011)4. - ISSN 1751-7907 - p. 431 - 437.
genetic-analysis - marine sponges - flow-cytometry - amplification - heterogeneity - communities - polymerase
The human gut microbiome: are we our enterotypes?
Siezen, R.J. ; Kleerebezem, M. - \ 2011
Microbial Biotechnology 4 (2011)5. - ISSN 1751-7907 - p. 550 - 553.
gastrointestinal-tract microbiota - 16s ribosomal-rna - diversity - functionality - metagenomics - communities - intestine - bacteria - catalog - obesity
Monitoring strain diversity in metagenomics data using meta-MLST SNP profiling
Jager, V.C.L. de; Sijde, M.R. van der; Hazelwood, L.A. ; Kutahya, O. ; Kleerebezem, M. ; Smid, E.J. ; Siezen, R.J. ; Hijum, S.A.F.T. van - \ 2011
In: 8th Symposium Kluyver Centre for Genomics of Industrial Fermentation, Noordwijkerhout, The Netherlands, 25-27 January 2011. - Kluyver Centre - p. P48 - P48.
Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
Francke, C. ; Groot Kormelink, T. ; Hagemeijer, Y. ; Overmars, L. ; Sluijter, V. ; Moezelaar, R. ; Siezen, R.J. - \ 2011
BMC Genomics 12 (2011). - ISSN 1471-2164 - 21 p.
enhancer-binding proteins - gram-positive bacteria - termite group 1 - escherichia-coli - bacillus-subtilis - phosphotransferase-system - gene-expression - transcription-factor - signal-transduction - listeria-monocytogenes
Background - Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. Results - We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. Conclusion - Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm
Comparative genomics of Lactobacillus
Kant, R. ; Siezen, R.J. ; Vos, W.M. de - \ 2011
Microbial Biotechnology 4 (2011)3. - ISSN 1751-7907 - p. 323 - 332.
lactic-acid bacteria - genus lactobacillus - sequence - plantarum - diversity - protein - tract
The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3 Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14 000 protein-encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group-specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes
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