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- Crystal structure of the bacterial type VI secretion system component TssL from Vibrio cholerae
- Jeong Ho Chang , Yeon-Gil Kim
- J. Microbiol. 2015;53(1):32-37. Published online December 4, 2014
- DOI: https://doi.org/10.1007/s12275-015-4539-0
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- 12 Citations
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Abstract
- The type VI secretion system (T6SS), commonly found in Gram-negative bacteria, is responsible for exporting effector proteins. The T6SS has been reported to be cytotoxic to host cells. While the components and assembly of the T6SS complex have been largely assessed, structural data on T6SS components from virulent bacteria is remarkably insufficient. Here, we report the crystal structure of Vibrio cholerae TssL (VcTssL), a core component of T6SS. In spite of a relatively low sequence identity, the overall structure of VcTssL is largely similar to those from other bacterial homologs except for several differences found in local structural elements. A unique feature attributed to the C-terminal fragment of Vc- TssL is a crystallographic artifact. This incidental feature of VcTssL may provide insights into screening of molecular partners for the cytoplasmic domain of TssL. Additionally, our results may help in the design of molecular probes for a detailed understanding of the functional relationship between TssL and other T6SS components.
Journal Article
- Computational Detection of Prokaryotic Core Promoters in Genomic Sequences
- Ki-Bong Kim , Jeong Seop Sim
- J. Microbiol. 2005;43(5):411-416.
- DOI: https://doi.org/2282 [pii]
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Abstract
- The high-throughput sequencing of microbial genomes has resulted in the relatively rapid accumulation of an enormous amount of genomic sequence data. In this context, the problem posed by the detection of promoters in genomic DNA sequences via computational methods has attracted considerable research attention in recent years. This paper addresses the development of a predictive model, known as the dependence decomposition weight matrix model (DDWMM), which was designed to detect the core promoter region, including the -10 region and the transcription start sites (TSSs), in prokaryotic genomic DNA sequences. This is an issue of some importance with regard to genome annotation efforts. Our predictive model captures the most significant dependencies between positions (allowing for non-adjacent as well as adjacent dependencies) via the maximal dependence decomposition (MDD) procedure, which iteratively decomposes data sets into subsets, based on the significant dependence between positions in the promoter region to be modeled. Such dependencies may be intimately related to biological and structural concerns, since promoter elements are present in a variety of combinations, which are separated by various distances. In this respect, the DDWMM may prove to be appropriate with regard to the detection of core promoter regions and TSSs in long microbial genomic contigs. In order to demonstrate the effectiveness of our predictive model, we applied 10-fold cross-validation experiments on the 607 experimentally-verified promoter sequences, which evidenced good performance in terms of sensitivity.
- Phylofenetic relationships of Amanita species based on ITS1-5.8S rDNA-ITS2 region sequences
- Lim, Young Woon , Jung, Hack Sung
- J. Microbiol. 1998;36(3):203-207.
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Abstract
- To determine the phylogenetic relatedness of Amanita species, internal transcribed spacers (ITSs) and the 5.8S ribosomal RNA gene were amplified by polymerase chain reaction and then sequenced according to the dideoxy chain termination method using an automatic DNA sequencer. The ITS region provided sufficient variability for phylogenetic analyses within the species. Analyses of the ITS sequence data by distance and parsimony methods revealed that the Amanita species are composed of three distinct groups whose main branch is strongly supported by bootstrap analysis. The Singerian system did not fully correspond to present phylogenetic results based on molecuar data. The amyloidd nature of the spores was still phylogenetically significant and the type of volva as well as the cap color were proved to be additional important characters in Amanita phylogenetics.
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