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Search Results: 1 - 10 of 145137 matches for " Helge B. Bode "
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LuxR solos in Photorhabdus species
Sophie Brameyer,Helge B. Bode,Ralf Heermann
Frontiers in Cellular and Infection Microbiology , 2014, DOI: 10.3389/fcimb.2014.00166
Abstract: Bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. The basic molecular quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase producing acyl-homoserine lactones (AHLs) as signaling molecules, and a LuxR-type receptor detecting the AHLs to control expression of specific genes. However, many proteobacteria possess one or more unpaired LuxR-type receptors that lack a cognate LuxI-like synthase, referred to as LuxR solos. The enteric and insect pathogenic bacteria of the genus Photorhabdus harbor an extraordinarily high number of LuxR solos, more than any other known bacteria, and all lack a LuxI-like synthase. Here, we focus on the presence and the different types of LuxR solos in the three known Photorhabdus species using bioinformatics analyses. Generally, the N-terminal signal-binding domain (SBD) of LuxR-type receptors sensing AHLs have a motif of six conserved amino acids that is important for binding and specificity of the signaling molecule. However, this motif is altered in the majority of the Photorhabdus-specific LuxR solos, suggesting the use of other signaling molecules than AHLs. Furthermore, all Photorhabdus species contain at least one LuxR solo with an intact AHL-binding motif, which might allow the ability to sense AHLs of other bacteria. Moreover, all three species have high AHL-degrading activity caused by the presence of different AHL-lactonases and AHL-acylases, revealing a high quorum quenching activity against other bacteria. However, the majority of the other LuxR solos in Photorhabdus have a N-terminal so-called PAS4-domain instead of an AHL-binding domain, containing different amino acid motifs than the AHL-sensors, which potentially allows the recognition of a highly variable range of signaling molecules that can be sensed apart from AHLs. These PAS4-LuxR solos are proposed to be involved in host sensing, and therefore in inter-kingdom signaling. Overall, Photorhabdus species are perfect model organisms to study bacterial communication via LuxR solos and their role for a symbiotic and pathogenic life style.
Cytosolic re-localization and optimization of valine synthesis and catabolism enables inseased isobutanol production with the yeast Saccharomyces cerevisiae
Brat Dawid,Weber Christian,Lorenzen Wolfram,Bode Helge B
Biotechnology for Biofuels , 2012, DOI: 10.1186/1754-6834-5-65
Abstract: Background The branched chain alcohol isobutanol exhibits superior physicochemical properties as an alternative biofuel. The yeast Saccharomyces cerevisiae naturally produces low amounts of isobutanol as a by-product during fermentations, resulting from the catabolism of valine. As S. cerevisiae is widely used in industrial applications and can easily be modified by genetic engineering, this microorganism is a promising host for the fermentative production of higher amounts of isobutanol. Results Isobutanol production could be improved by re-locating the valine biosynthesis enzymes Ilv2, Ilv5 and Ilv3 from the mitochondrial matrix into the cytosol. To prevent the import of the three enzymes into yeast mitochondria, N-terminally shortened Ilv2, Ilv5 and Ilv3 versions were constructed lacking their mitochondrial targeting sequences. SDS-PAGE and immunofluorescence analyses confirmed expression and re-localization of the truncated enzymes. Growth tests or enzyme assays confirmed enzymatic activities. Isobutanol production was only increased in the absence of valine and the simultaneous blockage of the mitochondrial valine synthesis pathway. Isobutanol production could be even more enhanced after adapting the codon usage of the truncated valine biosynthesis genes to the codon usage of highly expressed glycolytic genes. Finally, a suitable ketoisovalerate decarboxylase, Aro10, and alcohol dehydrogenase, Adh2, were selected and overexpressed. The highest isobutanol titer was 0.63 g/L at a yield of nearly 15 mg per g glucose. Conclusion A cytosolic isobutanol production pathway was successfully established in yeast by re-localization and optimization of mitochondrial valine synthesis enzymes together with overexpression of Aro10 decarboxylase and Adh2 alcohol dehydrogenase. Driving forces were generated by blocking competition with the mitochondrial valine pathway and by omitting valine from the fermentation medium. Additional deletion of pyruvate decarboxylase genes and engineering of co-factor imbalances should lead to even higher isobutanol production.
The Expression of stlA in Photorhabdus luminescens Is Controlled by Nutrient Limitation
Lea Lango-Scholey, Alexander O. Brachmann, Helge B. Bode, David J. Clarke
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0082152
Abstract: Photorhabdus is a genus of Gram-negative entomopathogenic bacteria that also maintain a mutualistic association with nematodes from the family Heterorhabditis. Photorhabdus has an extensive secondary metabolism that is required for the interaction between the bacteria and the nematode. A major component of this secondary metabolism is a stilbene molecule, called ST. The first step in ST biosynthesis is the non-oxidative deamination of phenylalanine resulting in the production of cinnamic acid. This reaction is catalyzed by phenylalanine-ammonium lyase, an enzyme encoded by the stlA gene. In this study we show, using a stlA-gfp transcriptional fusion, that the expression of stlA is regulated by nutrient limitation through a regulatory network that involves at least 3 regulators. We show that TyrR, a LysR-type transcriptional regulator that regulates gene expression in response to aromatic amino acids in E. coli, is absolutely required for stlA expression. We also show that stlA expression is modulated by σS and Lrp, regulators that are implicated in the regulation of the response to nutrient limitation in other bacteria. This work is the first that describes pathway-specific regulation of secondary metabolism in Photorhabdus and, therefore, our study provides an initial insight into the complex regulatory network that controls secondary metabolism, and therefore mutualism, in this model organism.
Identification and Biosynthesis of a Novel Xanthomonadin-Dialkylresorcinol-Hybrid from Azoarcus sp. BH72
Tim A. Sch?ner, Sebastian W. Fuchs, Barbara Reinhold-Hurek, Helge B. Bode
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090922
Abstract: A novel xanthomonadin-dialkylresorcinol hybrid named arcuflavin was identified in Azoarcus sp. BH72 by a combination of feeding experiments, HPLC-MS and MALDI-MS and gene clusters encoding the biosynthesis of this non-isoprenoid aryl-polyene containing pigment are reported. A chorismate-utilizing enzyme from the XanB2-type producing 3- and 4-hydroxybenzoic acid and an AMP-ligase encoded by these gene clusters were characterized, that might perform the first two steps of the polyene biosynthesis. Furthermore, a detailed analysis of the already known or novel biosynthesis gene clusters involved in the biosynthesis of polyene containing pigments like arcuflavin, flexirubin and xanthomonadin revealed the presence of similar gene clusters in a wide range of bacterial taxa, suggesting that polyene and polyene-dialkylresorcinol pigments are more widespread than previously realized.
Diversity of Xenorhabdus and Photorhabdus spp. and Their Symbiotic Entomopathogenic Nematodes from Thailand
Aunchalee Thanwisai,Sarunporn Tandhavanant,Natnaree Saiprom,Nick R. Waterfield,Phan Ke Long,Helge B. Bode,Sharon J. Peacock,Narisara Chantratita
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0043835
Abstract: Xenorhabdus and Photorhabdus spp. are bacterial symbionts of entomopathogenic nematodes (EPNs). In this study, we isolated and characterized Xenorhabdus and Photorhabdus spp. from across Thailand together with their associated nematode symbionts, and characterized their phylogenetic diversity. EPNs were isolated from soil samples using a Galleria-baiting technique. Bacteria from EPNs were cultured and genotyped based on recA sequence. The nematodes were identified based on sequences of 28S rDNA and internal transcribed spacer regions. A total of 795 soil samples were collected from 159 sites in 13 provinces across Thailand. A total of 126 EPNs isolated from samples taken from 10 provinces were positive for Xenorhabdus (n = 69) or Photorhabdus spp. (n = 57). Phylogenetic analysis separated the 69 Xenorhabdus isolates into 4 groups. Groups 1, 2 and 3 consisting of 52, 13 and 1 isolates related to X. stockiae, and group 4 consisting of 3 isolates related to X. miraniensis. The EPN host for isolates related to X. stockiae was S. websteri, and for X. miraniensis was S. khoisanae. The Photorhabdus species were identified as P. luminescens (n = 56) and P. asymbiotica (n = 1). Phylogenenic analysis divided P. luminescens into five groups. Groups 1 and 2 consisted of 45 and 8 isolates defined as subspecies hainanensis and akhurstii, respectively. One isolate was related to hainanensis and akhurstii, two isolates were related to laumondii, and one isolate was the pathogenic species P. asymbiotica subsp. australis. H. indica was the major EPN host for Photorhabdus. This study reveals the genetic diversity of Xenorhabdus and Photorhabdus spp. and describes new associations between EPNs and their bacterial symbionts in Thailand.
Optical mapping as a routine tool for bacterial genome sequence finishing
Phil Latreille, Stacie Norton, Barry S Goldman, John Henkhaus, Nancy Miller, Brad Barbazuk, Helge B Bode, Creg Darby, Zijin Du, Steve Forst, Sophie Gaudriault, Brad Goodner, Heidi Goodrich-Blair, Steven Slater
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-321
Abstract: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished.Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.Xenorhabdus species are symbiotic bacteria associated with insectivorous nematodes of the genus Steinernema (for review see [1]) They reside in a specialized segment of the nematode gut [2,3], and provide insecticidal proteins [4,5] and small molecules [6-10] that help to kill the insect larvae that are the prey of the nematode. Both organisms reproduce in the dead larvae, the Xenorhabdus colonize the young nematodes, and the cycle repeats [11]. Xenorhabdus are closely related to the enteric gamma proteobacteria such as Escherichia coli [12], and are an emerging model for both mutualism and pathogenicity in invertebrate hosts. To better understand the genetic basis of these relationships, we are sequencing the genomes of two Xenorhabdus species: X. nematophila ATCC 19061 and an X. bovienii strain from Monsanto's collection.In the course of this work, we found that the X. nematophila genome contained large numbers of highly repetitive DNA regions, and efforts to finish the genome stalled. We sought a means to produce whole-genome maps for comparison with the genomic DNA sequence, and identified optical mapping as a useful means to align and orient the genome sections in silico. In addition, we produced an optical map of a second genome that we had considered finished, and identified a large sequence inversion that would have otherwise been unnoticed.Eight-fold
The Janthinobacterium sp. HH01 Genome Encodes a Homologue of the V. cholerae CqsA and L. pneumophila LqsA Autoinducer Synthases
Claudia Hornung, Anja Poehlein, Frederike S. Haack, Martina Schmidt, Katja Dierking, Andrea Pohlen, Hinrich Schulenburg, Melanie Blokesch, Laure Plener, Kirsten Jung, Andreas Bonge, Ines Krohn-Molt, Christian Utpatel, Gabriele Timmermann, Eva Spieck, Andreas Pommerening-R?ser, Edna Bode, Helge B. Bode, Rolf Daniel, Christel Schmeisser, Wolfgang R. Streit
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0055045
Abstract: Janthinobacteria commonly form biofilms on eukaryotic hosts and are known to synthesize antibacterial and antifungal compounds. Janthinobacterium sp. HH01 was recently isolated from an aquatic environment and its genome sequence was established. The genome consists of a single chromosome and reveals a size of 7.10 Mb, being the largest janthinobacterial genome so far known. Approximately 80% of the 5,980 coding sequences (CDSs) present in the HH01 genome could be assigned putative functions. The genome encodes a wealth of secretory functions and several large clusters for polyketide biosynthesis. HH01 also encodes a remarkable number of proteins involved in resistance to drugs or heavy metals. Interestingly, the genome of HH01 apparently lacks the N-acylhomoserine lactone (AHL)-dependent signaling system and the AI-2-dependent quorum sensing regulatory circuit. Instead it encodes a homologue of the Legionella- and Vibrio-like autoinducer (lqsA/cqsA) synthase gene which we designated jqsA. The jqsA gene is linked to a cognate sensor kinase (jqsS) which is flanked by the response regulator jqsR. Here we show that a jqsA deletion has strong impact on the violacein biosynthesis in Janthinobacterium sp. HH01 and that a jqsA deletion mutant can be functionally complemented with the V. cholerae cqsA and the L. pneumophila lqsA genes.
Regulation of nasal heat exchange in reindeer
Helge Kreützer Johnsen,James B. Mercer
Rangifer , 1986,
Abstract:
The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes
John M. Chaston, Garret Suen, Sarah L. Tucker, Aaron W. Andersen, Archna Bhasin, Edna Bode, Helge B. Bode, Alexander O. Brachmann, Charles E. Cowles, Kimberly N. Cowles, Creg Darby, Limaris de Léon, Kevin Drace, Zijin Du, Alain Givaudan, Erin E. Herbert Tran, Kelsea A. Jewell, Jennifer J. Knack, Karina C. Krasomil-Osterfeld, Ryan Kukor, Anne Lanois, Phil Latreille, Nancy K. Leimgruber, Carolyn M. Lipke, Renyi Liu, Xiaojun Lu, Eric C. Martens, Pradeep R. Marri, Claudine Médigue, Megan L. Menard, Nancy M. Miller, Nydia Morales-Soto, Stacie Norton, Jean-Claude Ogier, Samantha S. Orchard, Dongjin Park, Youngjin Park, Barbara A. Qurollo, Darby Renneckar Sugar, Gregory R. Richards, Zoé Rouy, Brad Slominski, Kathryn Slominski, Holly Snyder, Brian C. Tjaden, Ransome van der Hoeven, Roy D. Welch, Cathy Wheeler, Bosong Xiang, Brad Barbazuk, Sophie Gaudriault, Brad Goodner, Steven C. Slater, Steven Forst, Barry S. Goldman, Heidi Goodrich-Blair
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027909
Abstract: Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.
3D Conceptual Modelling and Direct Utilization Calculations of The Albanian Geothermal Resources  [PDF]
Nevton Kodhelaj, Aida Bode
Engineering (ENG) , 2013, DOI: 10.4236/eng.2013.51B037
Abstract: Balneological use of the Albanian Geothermal springs and waters dates back centuries, but the first modern use started in 1937. Unfortunately they had not been used for its energetic values yet. The temperature of the water is above 60 °C and the flow above 16 l/s, thus direct utilization is possible, in particular for space heating. Three-dimensional temperature field calculations and engineering calculations on a heating system with heat exchangers are presented here. The results show that the water temperature is expected to be stable and considerably higher temperature is expected through deep well drilling. The University’s Campus of Tirana is composed of 29 buildings, which are partially heated through a coal heater. The installed capacity is 2558kW while the coal consumption is about 920 kg/h. The University’s Campus of Tirana is one of the most important areas and with the highest density of population in Tirana, so it is the best area to show the heat exchanger efficiency. The economic analyses prove that the borehole heat exchangers are more convenient than the coal heating systems.
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