Mutations in MetG (methionyl-tRNA synthetase) and TrmD [tRNA (guanine-N1)-methyltransferase] conferring meropenem tolerance in Burkholderia thailandensis

Yi, Hyojeong,Lee, Hyeri,Cho, Kwang-Hwi,Kim, Heenam Stanley Oxford University Press 2018 The Journal of antimicrobial chemotherapy Vol.73 No.2

Substrate Spectrum Extension of PenA in Burkholderia thailandensis with a Single Amino Acid Deletion, Glu168del

Yi, Hyojeong,Kim, Karan,Cho, Kwang-Hwi,Jung, Oksung,Kim, Heenam Stanley American Society for Microbiology 2012 Antimicrobial Agents and Chemotherapy Vol.56 No.7

<B>ABSTRACT</B><P>We describe a deletion mutation in a class A β-lactamase, PenA, ofBurkholderia thailandensisthat extended the substrate spectrum of the enzyme to include ceftazidime. Glu168del was located in a functional domain called the omega loop causing expansion of the space in the loop, which in turn increased flexibility at the active site. This deletion mutation represents a rare but significant alternative mechanical path to substrate spectrum extension in PenA besides more common substitution mutations.</P>

The Tandem Repeats Enabling Reversible Switching between the Two Phases of β-Lactamase Substrate Spectrum

Yi, Hyojeong,Song, Han,Hwang, Junghyun,Kim, Karan,Nierman, William C.,Kim, Heenam Stanley Public Library of Science 2014 PLoS genetics Vol.10 No.9

<P>Expansion or shrinkage of existing tandem repeats (TRs) associated with various biological processes has been actively studied in both prokaryotic and eukaryotic genomes, while their origin and biological implications remain mostly unknown. Here we describe various duplications (<I>de novo</I> TRs) that occurred in the coding region of a β-lactamase gene, where a conserved structure called the omega loop is encoded. These duplications that occurred under selection using ceftazidime conferred substrate spectrum extension to include the antibiotic. Under selective pressure with one of the original substrates (amoxicillin), a high level of reversion occurred in the mutant β-lactamase genes completing a cycle back to the original substrate spectrum. The <I>de novo</I> TRs coupled with reversion makes a genetic toggling mechanism enabling reversible switching between the two phases of the substrate spectrum of β-lactamases. This toggle exemplifies the effective adaptation of <I>de novo</I> TRs for enhanced bacterial survival. We found pairs of direct repeats that mediated the DNA duplication (TR formation). In addition, we found different duos of sequences that mediated the DNA duplication. These novel elements—that we named SCSs (same-strand complementary sequences)—were also found associated with β-lactamase TR mutations from clinical isolates. Both direct repeats and SCSs had a high correlation with TRs in diverse bacterial genomes throughout the major phylogenetic lineages, suggesting that they comprise a fundamental mechanism shaping the bacterial evolution.</P><P><B>Author Summary</B></P><P>β-lactamases can adapt to new antibiotics by mutations in their genes. The original and the extended substrate spectrums of β-lactamases define two phases of catalytic activity, and the conversion by point mutations is unidirectional from the initial to the new spectrum. We describe duplication mutations that enable reversible switching between the substrate spectrums, increasing the adaptability of the bacterium. We provide evidence supporting that two distinct groups of short sequences mediated the formation of DNA duplications in β-lactamases: direct repeats and novel elements that we named, SCSs (same-strand complementary sequences). Our study suggests that DNA duplication processes mediated by both direct repeats and SCSs are not just limited to the β-lactamase genes but comprise a fundamental mechanism in bacterial genome evolution.</P>

On the evolution of satellite galaxies around Milky Way-like hosts in the NewHorizon simulation

Hyojeong Kim,Sukyoung K. Yi 한국천문학회 2023 天文學會報 Vol.48 No.1

선조외 신체 영역에서 도구 행동유도성과 행위 주체감의 상호작용

김효정(Hyojeong Kim),박정호(Jeongho Park),이도준(Do-Joon Yi) 한국인지과학회 2013 인지과학 Vol.24 No.1

Opine-Based Agrobacterium Competitiveness: Dual Expression Control of the Agrocinopine Catabolism (acc) Operon by Agrocinopines and Phosphate Levels

Kim, H. Stanley,Yi, Hyojeong,Myung, Jaehee,Piper, Kevin R.,Farrand, Stephen K. American Society for Microbiology 2008 Journal of Bacteriology Vol.190 No.10

<B>ABSTRACT</B><P><I>Agrobacterium tumefaciens</I> strain C58 can transform plant cells to produce and secrete the sugar-phosphate conjugate opines agrocinopines A and B. The bacterium then moves in response to the opines and utilizes them as exclusive sources of carbon, energy, and phosphate via the functions encoded by the <I>acc</I> operon. These privileged opine-involved activities contribute to the formation of agrobacterial niches in the environment. We found that the expression of the <I>acc</I> operon is induced by agrocinopines and also by limitation of phosphate. The main promoter is present in front of the first gene, <I>accR</I>, which codes for a repressor. This operon structure enables efficient repression when opine levels are low. The promoter contains two putative operators, one overlapping the −10 sequence and the other in the further upstream from it; two partly overlapped putative <I>pho</I> boxes between the two operators; and two consecutive transcription start sites. DNA fragments containing either of the operators bound purified repressor AccR in the absence of agrocinopines but not in the presence of the opines, demonstrating the on-off switch of the promoter. Induction of the <I>acc</I> operon can occur under low-phosphate conditions in the absence of agrocinopines and further increases when the opines also are present. Such opine-phosphate dual regulatory system of the operon may ensure maximum utilization of agrocinopines when available and thereby increase the chances of agrobacterial survival in the highly competitive environment with limited general food sources.</P>

The Early Stage of Bacterial Genome-Reductive Evolution in the Host

Song, Han,Hwang, Junghyun,Yi, Hyojeong,Ulrich, Ricky L.,Yu, Yan,Nierman, William C.,Kim, Heenam Stanley Public Library of Science 2010 PLoS pathogens Vol.6 No.5

<▼1><P>The equine-associated obligate pathogen <I>Burkholderia mallei</I> was developed by reductive evolution involving a substantial portion of the genome from <I>Burkholderia pseudomallei</I>, a free-living opportunistic pathogen. With its short history of divergence (∼3.5 myr), <I>B. mallei</I> provides an excellent resource to study the early steps in bacterial genome reductive evolution in the host. By examining 20 genomes of <I>B. mallei</I> and <I>B. pseudomallei</I>, we found that stepwise massive expansion of IS (insertion sequence) elements IS<I>Bma</I>1, IS<I>Bma</I>2, and IS<I>407</I>A occurred during the evolution of <I>B. mallei</I>. Each element proliferated through the sites where its target selection preference was met. Then, IS<I>Bma</I>1 and IS<I>Bma</I>2 contributed to the further spread of IS<I>407</I>A by providing secondary insertion sites. This spread increased genomic deletions and rearrangements, which were predominantly mediated by IS<I>407</I>A. There were also nucleotide-level disruptions in a large number of genes. However, no significant signs of erosion were yet noted in these genes. Intriguingly, all these genomic modifications did not seriously alter the gene expression patterns inherited from <I>B. pseudomallei</I>. This efficient and elaborate genomic transition was enabled largely through the formation of the highly flexible IS-blended genome and the guidance by selective forces in the host. The detailed IS intervention, unveiled for the first time in this study, may represent the key component of a general mechanism for early bacterial evolution in the host.</P></▼1><▼2><P><B>Author Summary</B></P><P>It has been known for some time that bacteria undergo genome-reduction when they transition from a free-living state to a constantly host-restricted state. High levels of IS element expansion were also found in these bacteria, and the IS elements were suggested to play a role in genome reductive evolution. Here we provide evidence for stepwise IS actions as the exclusive mechanism that mediates bacterial genomic changes during the early stage of constant host-bacterial association, by unveiling the processes that resulted in the development of <I>B. mallei</I> genome. We show the details of the multi-level interplay of IS elements, which facilitate the wide spread of the IS copies, and the overall mechanics in genome reduction and rearrangement. These processes appeared to operate as chain reactions mediating elaborate genomic transition, without seriously affecting the original gene expression patterns. The absence of differential gene expression in the resulting genome suggests that changes in transcriptional regulation that are often observed in other old bacterial genomes may take place subsequent to the IS-mediated steps, along with gradual nucleotide-level changes.</P></▼2>

Simple Sequence Repeat (SSR)-Based Gene Diversity in Burkholderia pseudomallei and Burkholderia mallei

송한,황정현,Jaehee Myung,Hyoseok Seo,Hyojeong Yi,Hee-Sun Sim,Bong-Su Kim,William C. Nierman,김희남 한국분자세포생물학회 2009 Molecules and cells Vol.27 No.2

Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.

Deletion Mutations Conferring Substrate Spectrum Extension in the Class A β-Lactamase

Hwang, Junghyun,Cho, Kwang-Hwi,Song, Han,Yi, Hyojeong,Kim, Heenam Stanley American Society for Microbiology 2014 Antimicrobial Agents and Chemotherapy Vol.58 No.10

<P>We describe four new deletion mutations in a class A β-lactamase PenA in <I>Burkholderia thailandensis</I>, each conferring an extended substrate spectrum. Single-amino-acid deletions T171del, I173del, and P174del and a two-amino-acid deletion, R165_T167delinsP, occurred in the omega loop, increasing the flexibility of the binding cavity. This rare collection of mutations has significance, allowing exploration of the diverse evolutionary trajectories of β-lactamases and as potential future mutations conferring high-level ceftazidime resistance on isolates from clinical settings, compared with amino acid substitution mutations.</P>

한국 재래계의 HNF4α 유전자 내 SNP와 성장과의 연관성 분석

양송이,최소영,홍민욱,김훈,곽경록,이효정,정동기,손시환,홍영호,이성진,Yang, Song-Yi,Choi, So-Young,Hong, Min-Wook,Kim, Hun,Kwak, Kyeongrok,Lee, Hyojeong,Jeong, Dong Kee,Sohn, Sea Hwan,Hong, Yeong Ho,Lee, Sung-Jin 한국가금학회 2018 韓國家禽學會誌 Vol.45 No.4

$HNF4{\alpha}$ 유전자는 인간의 지질 수송 및 대사에 관여하는 간 전사인자로써, 닭의 지방 축적에 관련된 잠재적 후보유전자로 선정하였다. 선행연구에서 보고된 $HNF4{\alpha}$ 유전자 내 A543G SNP은 외래 육계뿐만 아니라, 외래 육계와 유전적 차이를 가지는 한국 재래계의 생시체중과 생체중에 유의적 연관성을 보인 바 있으나, 해당 SNP의 정확한 위치는 보고된 바 없다. 따라서 본 연구에서는 sequencing을 통하여 A543G SNP의 정확한 위치를 파악하고, A543G SNP의 주변 부위의 한국 재래계의 산육형질에 유의적 연관성이 있는 SNP을 파악하고자 하였다. Genomic DNA는 128수의 한국재래계의 혈액을 이용하여 추출하였으며, PCR 뒤 sequencing에 사용되었다. Sequencing 결과, 증폭범위 내에서 총 14개의 SNP가 탐색되었으며, 이 중 $HNF4{\alpha}$ 유전자의 intron 4 상에서 기존에 보고되지 않은 1개의 새로운 SNP를 발견하였다. 확인된 14개의 SNP 중 rs731246957과 rs736159604가 재래계의 생시체중 및 생체중에 유의적 연관성(P<0.001)을 보였다. rs731246957은 닭의 20번 염색체의 5,566,970번째에 위치하며, 선행논문에서 체중과의 연관성이 보고된 A543G SNP인 것으로 확인되었으며, 기존의 연구결과와 유사한 결과를 얻을 수 있었다. 반면에 선행논문에서 닭의 성장형질과의 연관성이 보고된 적 없는 rs736159604 SNP는 GG 유전자형 그룹이 GA, AA 유전자형 그룹에 비해 꾸준히 높은 체중 관측치를 보였으며, 특히 40주령의 체중은 다른 유전자형 그룹에 비해 약 1.8배 높게 관측되었다. 뿐만 아니라 신규 발견한 SNP의 T allele을 가지는 계군이 G allele을 가지는 계군보다 성장면에서 고능력을 보이는 것을 확인하였다. 따라서 본 연구결과는 한국재래계의 산육형질과 연관된 후보유전자로써 $HNF4{\alpha}$ 유전자의 기초정보를 제공하며, 해당 유전자내 특정 단일염기의 변이가 재래계의 체중 관련 유전자 마커로 유용하게 활용 가능할 것을 시사한다. The hepatocyte nuclear factor 4 alpha ($HNF4{\alpha}$) gene is related to lipid transport, including abdominal fat and growth, in chickens. Interestingly, the A543G SNP within the $HNF4{\alpha}$ gene has previously been reported to be associated with body weight in both broilers and Korean native chickens (KNCs). However, its exact position within the HNF4 is not yet reported. This study aimed to identify the position of the A543G SNP and to identify additional SNPs that can be used as genetic markers in KNCs. A total of 128 KNCs were used for the sequencing and analysis of these genetic associations. As a result, A543G SNP was located in intron 4 of the $HNF4{\alpha}$ gene; it is reported as rs731246957 in the NCBI database. Fourteen SNPs were detected in the sequenced portion of the $HNF4{\alpha}$ gene; three of these, rs731246957, rs736159604 and new SNP, intron 6 (249), were significantly related with growth in the chickens. In this study, the TT genotype of rs731246957, previously reported as A543G SNP, the GG genotype of rs736159604 and GT of new SNP have are highly associated with body weight from birth to 40 weeks of age in KNCs (P<0.01). These results suggest that rs736159604, rs731246957 and intron 6 (249) SNPs within the $HNF4{\alpha}$ gene could function as growth-related markers in the selective breeding of KNCs.