Type I interferon-activated microglia are critical for neuromyelitis optica pathology

Neuromyelitis optica (NMO) is an inflammatory disease of the central nervous system (CNS) most frequently mediated by serum autoantibodies against the water channel aquaporin 4, expressed on CNS astrocytes, resulting in primary astrocytopathy. There is no cure for NMO, and treatment with Type I interferon (IFNI)-IFN beta is ineffective or even detrimental. We have previously shown that both NMO lesions and associated microglial activation were reduced in mice lacking the receptor for IFN beta. However, the role of microglia in NMO is not well understood. In this study, we clarify the pathomechanism for IFNI dependence of and the role of microglia in experimental NMO. Transcriptome analysis showed a strong IFNI footprint in affected CNS tissue as well as in microglial subpopulations. Treatment with IFN beta led to exacerbated pathology and further microglial activation as evidenced by expansion of a CD11c(+) subset of microglia. Importantly, depletion of microglia led to suppression of pathology and decrease of IFNI signature genes. Our data show a pro-pathologic role for IFNI-activated microglia in NMO and open new perspectives for microglia-targeted therapies

Using shotgun sequence data to find active restriction enzyme genes

Whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a biological experiment. It determines which segments of the genome can be cloned into Escherichia coli and which cannot. By analyzing the complete set of sequences from such an experiment, it is possible to identify genes lethal to E. coli. Among this set are genes encoding restriction enzymes which, when active in E. coli, lead to cell death by cleaving the E. coli genome at the restriction enzyme recognition sites. By analyzing shotgun sequence data sets we show that this is a reliable method to detect active restriction enzyme genes in newly sequenced genomes, thereby facilitating functional annotation. Active restriction enzyme genes have been identified, and their activity demonstrated biochemically, in the sequenced genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus

Group II Intron-Anchored Gene Deletion in Clostridium

Clostridium plays an important role in commercial and medical use, for which targeted gene deletion is difficult. We proposed an intron-anchored gene deletion approach for Clostridium, which combines the advantage of the group II intron “ClosTron” system and homologous recombination. In this approach, an intron carrying a fragment homologous to upstream or downstream of the target site was first inserted into the genome by retrotransposition, followed by homologous recombination, resulting in gene deletion. A functional unknown operon CAC1493–1494 located in the chromosome, and an operon ctfAB located in the megaplasmid of C. acetobutylicum DSM1731 were successfully deleted by using this approach, without leaving antibiotic marker in the genome. We therefore propose this approach can be used for targeted gene deletion in Clostridium. This approach might also be applicable for gene deletion in other bacterial species if group II intron retrotransposition system is established

Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018

<p>Abstract</p> <p>Background</p> <p><it>Clostridium acetobutylicum</it>, a gram-positive and spore-forming anaerobe, is a major strain for the fermentative production of acetone, butanol and ethanol. But a previously isolated hyper-butanol producing strain <it>C. acetobutylicum </it>EA 2018 does not produce spores and has greater capability of solvent production, especially for butanol, than the type strain <it>C. acetobutylicum </it>ATCC 824.</p> <p>Results</p> <p>Complete genome of <it>C. acetobutylicum </it>EA 2018 was sequenced using Roche 454 pyrosequencing. Genomic comparison with ATCC 824 identified many variations which may contribute to the hyper-butanol producing characteristics in the EA 2018 strain, including a total of 46 deletion sites and 26 insertion sites. In addition, transcriptomic profiling of gene expression in EA 2018 relative to that of ATCC824 revealed expression-level changes of several key genes related to solvent formation. For example, <it>spo0A </it>and <it>adhEII </it>have higher expression level, and most of the acid formation related genes have lower expression level in EA 2018. Interestingly, the results also showed that the variation in CEA_G2622 (CAC2613 in ATCC 824), a putative transcriptional regulator involved in xylose utilization, might accelerate utilization of substrate xylose.</p> <p>Conclusions</p> <p>Comparative analysis of <it>C. acetobutylicum </it>hyper-butanol producing strain EA 2018 and type strain ATCC 824 at both genomic and transcriptomic levels, for the first time, provides molecular-level understanding of non-sporulation, higher solvent production and enhanced xylose utilization in the mutant EA 2018. The information could be valuable for further genetic modification of <it>C. acetobutylicum </it>for more effective butanol production.</p

ΦF1 and ΦF3, two novel virulent, archaeal phages infecting different thermophilic strains of the genus Methanobacterium

Two virulent, archaeal phages, ΦF1 and ΦF3, were isolated that were capable of infecting different thermophilic members of the genus Methanobacterium. Both phages exhibited a similar morphology consisting of a polyhedral head and a tail but differed considerably in their host specificities and the size and topology of their genomes. Phage ΦF1 contained a linear, double-stranded DNA genome of 85 ± 5 kb in size and showed a broad host range including M. thermoformicicum strains Z-245, FTF, FF1, FF3 and CSM3, and M. thermoautotrophicum strain ΔH. In contrast, ΦF3 phage particles contained a circular or terminally redundant linear genome, comprising approximately 36 ± 2 kb double-stranded DNA, and could only be propagated on M. thermoformicicum strain FF3. Hybridization experiments did not reveal similarity between the genomes of ΦF1 and ΦF3 nor between both phages and genomic DNA from different thermophilic members of the genus Methanobacterium or DNA from phage ΨM1 of M. thermoautotrophicum Marburg. A physical map of both phage genomes was constructed. The DNA of phage ΦF1 was found to contain multiple GGCC sites which form the target for the restriction-modification (R/M) system MthT1 of M. thermoformicicum THF. In contrast, the DNA of ΦF1 contained only a single CTAG site recognized by the R/M systems MthZI and MthFI of M. thermoformicicum Z-245 and FTF, respectively. The distribution of these sites correlates well with the capacity of ΦF1 to infect M. thermoformicicum strains Z-245 and FTF but not strain THF