Donghyuk Kim

Genome-wide transcription start site (TSS) profiles of the enterobacteria Escherichia coli and Klebsiella pneumoniae were experimentally determined through modified 5' RACE followed by deep sequencing of intact primary mRNA. This identified 3,746 and 3,143 TSSs for E. coli and K. pneumoniae, respectively. Experimentally determined TSSs were then used to define promoter regions and 5' UTRs upstream of coding genes. Comparative analysis of these regulatory elements revealed the use of multiple TSS

Among CO 2 -fixing metabolic pathways in nature, the linear Wood–Ljungdahl pathway (WLP) in phylogenetically diverse acetate-forming acetogens comprises the most energetically efficient pathway, requires the least number of reactions, and converts CO 2 to formate and then into acetyl-CoA. Despite two genes encoding glycine synthase being well-conserved in WLP gene clusters, the functional role of glycine synthase under autotrophic growth conditions has remained uncertain. Here, using the reconst

Transcriptional regulation enables cells to respond to environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods have been used to fully characterize only a few dozen. Identifying these remaining TFs is key to improving our knowledge of the E. coli transcriptional regulatory network (TRN). Here, we developed an integrated workflow for the computational prediction and comprehensive e

Two major transcriptional regulators of carbon metabolism in bacteria are Cra and CRP. CRP is considered to be the main mediator of catabolite repression. Unlike for CRP, in vivo DNA binding information of Cra is scarce. Here we generate and integrate ChIP-exo and RNA-seq data to identify 39 binding sites for Cra and 97 regulon genes that are regulated by Cra in Escherichia coli. An integrated metabolic-regulatory network was formed by including experimentally-derived regulatory information and

While a range of artificial biochemical circuits is likely to play a significant role in biological engineering, one of the challenges in the field is the design of circuits that can transduce between biomolecule classes (e.g., moving beyond nucleic acid only circuits). Herein, we design a transduction mechanism whereby a protein signal is transduced into an amplified nucleic acid output using DNA nanotechnology. In this system, a protein is recognized by nucleic acid bound recognition elements

This study provides insights into the transcriptomic profile of Methylomonas sp. DH-1 grown on major carbon sources for C1 assimilation, providing in-depth knowledge on the metabolic pathways of this strain. These observations and analyses can contribute to future metabolic engineering with the newly isolated, yet under-characterized, Methylomonas sp. DH-1 to enhance its biochemical application in relevant industries.

Plant growth-promoting rhizobacteria play vital roles not only in plant growth, but also in reducing biotic/abiotic stress. Sphingomonas panacis DCY99T is isolated from soil and root of Panax ginseng with rusty root disease, characterized by raised reddish-brown root and this is seriously affects ginseng cultivation. To investigate the relationship between 159 sequenced Sphingomonas strains, pan-genome analysis was carried out, which suggested genomic diversity of the Sphingomonas genus. Compara

Equol is a nonsteroidal estrogen that is produced by intestinal bacterial metabolism. Equol and equol-producing bacteria have been extensively investigated with soybean-based materials under anaerobic condition. In this study, an under-appreciated plant material, Pueraria lobata, was used to find new bacterial strains that produce equol under aerobic conditions. Three new intestinal bacteria, CS1, CS2, and CS3, were isolated, and internal transcribed spacer analysis revealed that belonging to ge

Nucleic acids, DNA and RNA, provide important fingerprint information for various pathogens and have significant diagnostic value; however, improved approaches are urgently needed to enable rapid detection of nucleic acids in simple point-of-care formats with high sensitivity and specificity. Here, we present a system that utilizes a series of toehold-triggered hybridization/displacement reactions that are designed to convert a given amount of RNA molecules (i.e., the analyte) into an amplified

Previously, we have reported that 3-hydroxypropionate (3-HP) tolerance in Escherichia coli W is improved by deletion of yieP, a less-studied transcription factor. Here, through systems analyses along with physiological and functional studies, we suggest that the yieP deletion improves 3-HP tolerance by upregulation of yohJK, encoding putative 3-HP transporter(s). The tolerance improvement by yieP deletion was highly specific to 3-HP, among various C2-C4 organic acids. Mapping of YieP binding sit

Concerns over Klebsiella pneumoniae resistance to the last-line antibiotic treatment have prompted a reconsideration of bacteriophage therapy in public health. Biotechnological application of phages and their gene products as an alternative to antibiotics necessitates the understanding of their genomic context. This study sequenced, annotated, characterized, and compared two Klebsiella phages, KP1 and KP12. Physiological validations identified KP1 and KP12 as members of Myoviridae family. Both p

Neutrophils are always surrounded by/interacting with other components of the immune system; however, the current mechanistic understanding of neutrophil function is largely based on how neutrophils respond to a single chemical signal in a simplified environment. Such approaches are unable to recapitulate the in vivo microenvironment; thus, cell behavior may not fully represent the physiological behavior. Herein, we exploit a microfluidic model of the complex in vivo milieu to investigate how ce

BACKGROUND: Equol is a major isoflavone metabolite, and equol-producing bacteria have been isolated and characterized; however, fermentation has been performed with soybean-based products as substrates. Pueraria lobata has been reported as a plant with higher content of isoflavones. RESULTS: The genome of new equol-producing bacteria, Lactobacillus paracasei JS1, was analyzed. Also, the effect of P. lobata extract fermented with L. paracasei JS1 (FPE) on the skin and intestinal immune response w

It is fundamental to understand the relationship between genotype and phenotype in biology. This requires comprehensive knowledge of metabolic pathways, genetic information and well-defined mathematic modeling. Integration of knowledge on metabolism with mathematical modeling results in genome-scale metabolic models which have proven useful to investigate bacterial metabolism and to engineer bacterial strains capable of producing value-added biochemical. Single carbon substrates such as methane