ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms.

Kim, Kangseok,Kim, Wonil,Kim, Sunshin Oxford University Press 2011 Bioinformatics Vol.27 No.12

<P>ReMark is a fully automatic tool for clustering orthologs by combining a Recursive and a Markov clustering (MCL) algorithms. The ReMark detects and recursively clusters ortholog pairs through reciprocal BLAST best hits between multiple genomes running software program (RecursiveClustering.java) in the first step. Then, it employs MCL algorithm to compute the clusters (score matrices generated from the previous step) and refines the clusters by adjusting an inflation factor running software program (MarkovClustering.java). This method has two key features. One utilizes, to get more reliable results, the diagonal scores in the matrix of the initial ortholog clusters. Another clusters orthologs flexibly through being controlled naturally by MCL with a selected inflation factor. Users can therefore select the fitting state of orthologous protein clusters by regulating the inflation factor according to their research interests.</P>

Structural and Mechanistic Insights into the <i>Pseudomonas fluorescens</i> 2-Nitrobenzoate 2-Nitroreductase NbaA

Kim, Yong-Hak,Song, Wooseok,Kim, Jin-Sik,Jiao, Li,Lee, Kangseok,Ha, Nam-Chul American Society for Microbiology 2015 Applied and environmental microbiology Vol.81 No.15

<P>The bacterial 2-nitroreductase NbaA is the primary enzyme initiating the degradation of 2-nitrobenzoate (2-NBA), and its activity is controlled by posttranslational modifications. To date, the structure of NbaA remains to be elucidated. In this study, the crystal structure of a Cys194Ala NbaA mutant was determined to a 1.7-Å resolution. The substrate analog 2-NBA methyl ester was used to decipher the substrate binding site by inhibition of the wild-type NbaA protein. Tandem mass spectrometry showed that 2-NBA methyl ester produced a 2-NBA ester bond at the Tyr193 residue in the wild-type NbaA but not residues in the Tyr193Phe mutant. Moreover, covalent binding of the 2-NBA methyl ester to Tyr193 reduced the reactivity of the Cys194 residue on the peptide link. The Tyr193 hydroxyl group was shown to be essential for enzyme catalysis, as a Tyr193Phe mutant resulted in fast dissociation of flavin mononucleotide (FMN) from the protein with the reduced reactivity of Cys194. FMN binding to NbaA varied with solution NaCl concentration, which was related to the catalytic activity but not to cysteine reactivity. These observations suggest that the Cys194 reactivity is negatively affected by a posttranslational modification of the adjacent Tyr193 residue, which interacts with FMN and the substrate in the NbaA catalytic site.</P>

Functional Analysis of Vibrio vulnificus Orthologs of Escherichia coli RraA and RNase E

Kim, Daeyoung,Kim, Yong-Hak,Jang, Jinyang,Yeom, Ji-Hyun,Jun, Jong Woo,Hyun, Seogang,Lee, Kangseok Springer-Verlag 2016 Current microbiology Vol.72 No.6

<P>RNase E plays an important role in the degradation and processing of RNA in Escherichia coli. The enzymatic activity of RNase E is controlled by the protein inhibitors RraA and RraB. The marine pathogenic bacterium Vibrio vulnificus also contains homologs of RNase E and RraA, designated as RNase EV, RraAV1, and RraAV2. Here, we report that RraAV1 actively inhibits the enzymatic activity of RNase EV in vivo and in vitro by interacting with the C-terminal domain of RNase EV. Coexpression of RraAV1 reduced ribonucleolytic activity in the cells overproducing RNase EV and consequently restored normal growth of these cells. An in vitro cleavage assay further demonstrated that RraAV1 efficiently inhibits the ribonucleolytic activity of RNase EV on BR10 + hpT, a synthetic oligonucleotide containing the RNase E cleavage site of RNA I. Our findings suggest that RraAV1 plays an active role in RNase EV-mediated RNA cleavage in V. vulnificus.</P>

Fluorescence Enhancement from Nitro-Compound-Sensitive Bacteria within Spherical Hydrogel Scaffolds

Kim, Soohyun,Kim, Hyunji,Qiao, Tian,Cha, Chaenyung,Lee, Sung Kuk,Lee, Kangseok,Ro, Hyun Ji,Kim, Youngkyun,Lee, Wonmok,Lee, Hyunjung American Chemical Society 2019 ACS APPLIED MATERIALS & INTERFACES Vol.11 No.15

<P>For the safety of both production and life, it is a very significant issue to detect explosive nitro compounds in a remote way or over a long distance. Here, we report that nitro compounds were detected by the bacterial sensor based on hydrogel microbeads as a platform. Green fluorescent protein-producing <I>Escherichia coli</I>, which was genetically engineered to be sensitive to nitro compounds, was loaded within poly(2-hydroxyethyl methacrylate) [poly(HEMA)]-based hydrogel beads, in which fluorescent signals from bacteria were concentrated and strong enough to be easily detected. For efficient loading of negatively charged bacteria, the surface charge of poly(HEMA)-based beads was controlled by copolymerization with 2-(methacryloyloxy)ethyltrimethylammonium chloride (MAETC) as a cationic monomer. With the addition of MAETC, the cell affinity was nine times enhanced by the interaction between the positively charged poly(HEMA-<I>co</I>-MAETC) beads and negatively charged bacteria. The increased cell affinity resulted in an enhancement of a sensing signal. After exposure to 2,4,6-trinitrotoluene, a typical explosive nitro compound, the fluorescence intensity of bacterial sensors using poly(HEMA-<I>co</I>-MAETC) beads having 80 wt % MAETC was five times increased compared to those based on poly(HEMA) beads. This amplification of the fluorescent signal enables easier detection of explosives efficiently by a remote detection, even over a long distance.</P> [FIG OMISSION]</BR>

Heterogeneous rRNAs are differentially expressed during the morphological development of Streptomyces coelicolor.

Kim, Hyun-Lee,Shin, Eun-Kyoung,Kim, Hong-Man,Ryou, Sang-Mi,Kim, Sanggoo,Cha, Chang-Jun,Bae, Jeehyeon,Lee, Kangseok Published by Elsevier/North Holland on behalf of t 2007 FEMS microbiology letters Vol.275 No.1

<P>It is generally assumed that all mature rRNA molecules assembled into ribosomes within a single cell are identical. However, sequence analysis of Streptomyces coelicolor genome revealed that it harbors six copies of divergent rRNA operons that may express and constitute three and five different kinds of small subunit (SSU) and large subunit (LSU) rRNA molecules, respectively, in a single cell. Phylogenetic analyses of the LSU rRNA genes and the internal transcribed spacer between SSU and LSU genes indicated that the LSU gene of rrnA and rrnE operons might be the result of interspecies recombination between rRNA genes in closely related streptomycetes. Profiling of rRNA species using primer extension analysis showed that heterogeneous rRNA transcripts are expressed and assembled into ribosomes in the cell. As the cells developed from germination to sporulation, the relative amount of LSU rRNA molecules derived from three rRNA operons (rrnA, D, and E) gradually decreased from approximately 85% to approximately 60%, whereas the distribution of LSU rRNA molecules from two other operons (rrnB and F) and rrnC operon gradually increased from approximately 10% to approximately 20% of the total LSU rRNA. These findings indicate that heterogeneous rRNA molecules are differentially expressed during the life cycle of this developmentally complex microorganism.</P>

Genetic Analysis of the Invariant Residue G791 in Escherichia coli 16S rRNA Implicates RelA in Ribosome Function

Kim, Hong-Man,Ryou, Sang-Mi,Song, Woo-Seok,Sim, Se-Hoon,Cha, Chang-Jun,Han, Seung Hyun,Ha, Nam-Chul,Kim, Jae-Hong,Bae, Jeehyeon,Cunningham, Philip R.,Lee, Kangseok American Society for Microbiology 2009 Journal of Bacteriology Vol.191 No.7

<B>ABSTRACT</B><P>Previous studies identified G791 in <I>Escherichia coli</I> 16S rRNA as an invariant residue for ribosome function. In order to establish the functional role of this residue in protein synthesis, we searched for multicopy suppressors of the mutant ribosomes that bear a G-to-U substitution at position 791. We identified <I>relA</I>, a gene whose product has been known to interact with ribosomes and trigger a stringent response. Overexpression of RelA resulted in the synthesis of approximately 1.5 times more chloramphenicol acetyltransferase (CAT) protein than could be synthesized by the mutant ribosomes in the absence of RelA overexpression. The ratio of mutant rRNA to the total ribosome pool was not changed, and the steady-state level of CAT mRNA was decreased by RelA overexpression. These data confirmed that the phenotype of RelA as a multicopy suppressor of the mutant ribosome did not result from the enhanced synthesis of mutant rRNA or CAT mRNA from the plasmid. To test whether the phenotype of RelA was related to the stringent response induced by the increased cellular level of (p)ppGpp, we screened for mutant RelA proteins whose overexpression enhances CAT protein synthesis by the mutant ribosomes as effectively as wild-type RelA overexpression and then screened for those whose overexpression does not produce sufficiently high levels of (p)ppGpp to trigger the stringent response under the condition of amino acid starvation. Overexpression of the isolated mutant RelA proteins resulted in the accumulation of (p)ppGpp in cells, which was amounted to approximately 18.2 to 38.9% of the level of (p)ppGpp found in cells that overexpress the wild-type RelA. These findings suggest that the function of RelA as a multicopy suppressor of the mutant ribosome does not result from its (p)ppGpp synthetic activity. We conclude that RelA has a previously unrecognized role in ribosome function.</P>

Functional Role of bdm During Flagella Biogenesis in Escherichia coli

Kim, Ji-Sun,Kim, Yu Jin,Seo, Sojin,Seong, Maeng-Je,Lee, Kangseok Springer-Verlag 2015 Current microbiology Vol.70 No.3

<P>The biofilm-dependent modulation gene (bdm) has recently been shown to play a role in osmotic-induced formation of biofilm in Escherichia coli. In this study, we demonstrated that deletion of bdm results in down-regulation of flagella biosynthesis genes and, consequently, a defect in E. coli motility. In addition, we employed atomic force microscopy to confirm the absence of flagella-like structures on the surface of bdm-null cells. These findings indicate that bdm plays a key role in regulatory pathway for the formation of flagella.</P>

Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Suggests an Alternative Assembly Mode

Kim, Jin-Sik,Jeong, Hyeongseop,Song, Saemee,Kim, Hye-Yeon,Lee, Kangseok,Hyun, Jaekyung,Ha, Nam-Chul Korean Society for Molecular and Cellular Biology 2015 Molecules and cells Vol.38 No.2

Escherichia coli AcrAB-TolC is a multidrug efflux pump that expels a wide range of toxic substrates. The dynamic nature of the binding or low affinity between the components has impeded elucidation of how the three components assemble in the functional state. Here, we created fusion proteins composed of AcrB, a transmembrane linker, and two copies of AcrA. The fusion protein exhibited acridine pumping activity, suggesting that the protein reflects the functional structure in vivo. To discern the assembling mode with TolC, the AcrBA fusion protein was incubated with TolC or a chimeric protein containing the TolC aperture tip region. Three-dimensional structures of the complex proteins were determined through transmission electron microscopy. The overall structure exemplifies the adaptor bridging model, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel interaction with the ${\alpha}$-barrel tip region of TolC, and a direct interaction between AcrB and TolC is not allowed. These observations provide a structural blueprint for understanding multidrug resistance in pathogenic Gram-negative bacteria.

Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds

Kim, HyoYoung,Caetano-Anolles, Kelsey,Seo, Minseok,Kwon, Young-jun,Cho, Seoae,Seo, Kangseok,Kim, Heebal Korea Genome Organization 2015 Genomics & informatics Vol.13 No.4

Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5), Landrace (n = 13), and Duroc (n = 6). An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc. These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs) related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718) in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.

Guidelines for the Design of Solid CO2 Adsorbents for Mobile Carbon Capture in Heavy-Duty Vehicles: A Review

Kim Taenam,Kim Kangseok,이기욱,Seo Minhye,황종국 한국화학공학회 2024 Korean Journal of Chemical Engineering Vol.41 No.1

The transportation sector is the largest contributor to carbon dioxide (CO 2 ) emissions, largely due to heavy-duty vehicles (HDVs) that inevitably rely on internal combustion engines. Electrifi cation is a promising technology for decarbonizing light-duty vehicles but it is diffi cult to apply to HDVs with long driving ranges and signifi cant weights. One possible solution is a mobile carbon capture (MCC) system that adapts onboard CO 2 capture and storage to the HDV. Although conceptual designs have been presented for MCC systems that use adsorbents and temperature-swing adsorption (TSA), the development of the adsorbent-based MCC remains in its infancy. Since adsorbents play a critical role in determining the overall weight, volume, and energy consumption of the MCC, the development of a high performance adsorbent is a key factor in the successful MCC design. In this review, we aim to provide guidelines for the design of CO 2 adsorbents for MCC in HDVs. First, we briefl y introduce the adsorbent selection criteria for TSA in MCC, including the CO 2 working capacity, purity, stability, and regeneration energy. Then, we summarize recent progress in the development of adsorbents tested under MCC-relevant conditions. Finally, the current challenges and future prospects of MCC are discussed.