Isolation of cold-responsive genes from garlic, Allium sativum

손재한,박경철,이성일,김행훈,김종화,김선형,김남수 한국유전학회 2012 Genes & Genomics Vol.34 No.1

Cold stress discourages development of the full genetic potential of plants and results in serious adverse effects on plant growth and limits agricultural productivity. Garlic (Allium sativum) requires low temperatures for the induction of flowering and bulb development. However, low or freezing temperatures can often cause physiological damage. Cold-responsive genes were isolated from a Korean garlic variety through systematic analyses using differential display (DD)-PCR, reverse transcription (RT)-PCR, and quantitative (Q)-PCR. Of the 2470 transcripts observed, 76 transcripts were up-regulated and 20 transcripts were down-regulated in response to cold temperatures (4°C)as determined by DD-PCR analysis. The differentially-expressed genes were further narrowed to 15 up-regulated and four down-regulated genes through subsequent RT-PCR and Q-PCR analyses. Of the 15 up-regulated genes, 11 genes were homologous to previously-reported abiotic-stress regulated genes in other species, and four genes did not match any known genes. Of the four down-regulated genes, three genes matched function-annotated genes and one gene did not match any genein the BLAST analysis. While most of the up-regulated poly-peptides were hydrophilic, the down-regulated polypeptides were neutral or hydrophobic. Of the 19 differentially-regulated genes, four genes showed different expression profiles in different tissues upon cold stress. Genetic manipulation of the CR genes obtained may provide molecular tool for overcoming frost damage of the garlic plants during hibernation.

Endoplasmic recticulum stress와 관련된 유전자기능과 전사조절인자의 in silico 분석

김태민(Tae-Min Kim),여지영(Jiyoung Yeo),박찬선(Chan Sun Park),이문수(Moon Soo Rhee),정명호(Myeong Ho Jung) 한국생명과학회 2009 생명과학회지 Vol.19 No.8

ER stress에 관련된 유전자의 기능변화와 전사조절인자 분석하기 위해 ER stress를 유도한 간세포에서 expression microarray로 유전자 발현을 확보한 후 GSECA로 분석하였다. ER stress가 유도되면, ER에 주어지는 과도한 부하를 감소시키는 기능들이 증가하는 반면, ER stress가 더 증가함에 따라 ATP 생성이나 DNA repair, 더 나아가 세포분열의 기능이 감소하는 등 세포가 damage을 받음을 알 수 있었다. ER stress에 관련된 전사조절인자로는 FOXO4, AP-1, FOXO3, HNF4, IRF-1, GATA 등의 전사조절인자들이 ER stress에 의해 발현이 증가하는 유전자들의 promoter에 공통적으로 존재하였으며, E2F, Nrf-1, Elk-1, YY1, CREB, MTF-1, STAT-1, ATF 등의 전사인자 들이 발현이 감소하는 유전자들의 promoter에서 공통적으로 존재하여, 이들의 전사인자들이 ER stress에 의한 유전자의 발현조절에 중요한 역할을 하는 전사조절인자임을 알 수 있었다. It has been postulated that endoplasmic (ER) stress is involved in the development of several diseases. However, the detailed molecular mechanisms have not been fully understood. Therefore, we characterized a genetic network of genes induced by ER stress using cDNA microarray and gene set expression coherence analysis (GSECA), and identified gene function as well as several transcription regulators associated with ER stress. We analyzed time-dependent gene expression profiles in thapsigargin-treated Sk-Hep1 using an oligonucleotide expression chip, and then selected functional gene sets with significantly high expression coherence which was processed into functional clusters according to the expression similarities. The functions related to sugar binding, lysosome, ribosomal protein, ER lumen, and ER to golgi transport increased, whereas the functions with mRNA processing, DNA replication, DNA repair, cell cycle, electron transport chain and helicase activity decreased. Furthermore, functional clusters were investigated for the enrichment of regulatory motifs using GSECA, and several transcriptional regulators associated with regulation of ER-induced gene expression were found.

Development of Stress-tolerant Crop Plants

Park, Hyung-In,Kang, Jung-Youn,Sohn, Hee-Kyung,Kim, Soo-Young The Korean Society of Plant Biotechnology 2002 Plant molecular biology and biotechnology research Vol.4 No.2

Adverse environmental conditions such as drought, high salt and cold/freezing are major factors that reduces crop productivity worldwide. According to a survey, 50-80% of the maximum potential yield is lost by these "environmental or abiotic stresses", which is approximately ten times higher than the loss by biotic stresses. Thus, improving stress-tolerance of crop plants is an important way to improve agricultural productivity, In order to develop such stress-tolerant crop plants, we set out to identify key stress signaling components that can be used to develop commercially viable crop varieties with enhanced stress tolerance. Our primary focus so far has been on the identification of transcription factors that regulate stress responsive gene expression, especially those involved in ABA-mediated stress response. Be sessile, plants have the unique capability to adapt themselves to the abiotic stresses. This adaptive capability is largely dependent on the plant hormone abscisic acid (ABA), whose level increases under various stress conditions, triggering adaptive response. Central to the response is ABA-regulated gene expression, which ultimately leads to physiological changes at the whole plant level. Thus, once identified, it would be possible to enhance stress tolerance of crop plants by manipulating the expression of the factors that mediate ABA-dependent stress response. Here, we present our work on the isolation and functional characterization of the transcription factors.n factors.

Regulation of polyubiquitin genes to meet cellular ubiquitin requirement

( Seung-woo Han ),( Byung-kwon Jung ),( Kwon-yul Ryu ) 생화학분자생물학회 2021 BMB Reports Vol.54 No.4

Ubiquitin (Ub) is one of the proteins that are highly conserved from yeast to humans. It is an essential core unit of the welldefined post-translational modification, called ubiquitination, which is involved in a variety of biological processes. In metazoans, Ub is encoded by two monoubiquitin genes and two polyubiquitin genes, in which a single Ub is fused to a ribosomal protein or Ub coding units are arranged in tandem repeats. In mice, polyubiquitin genes (Ubb and Ubc) play a pivotal role to meet the requirement of cellular Ub pools during embryonic development. In addition, expression levels of polyubiquitin genes are increased to adapt to environmental stimuli such as oxidative, heat-shock, and proteotoxic stress. Several researchers have reported about the perturbation of Ub pools through genetic alteration or exogenous Ub delivery using diverse model systems. To study Ub pool changes in a physiologically relevant manner, changing Ub pools via the regulation of endogenous polyubiquitin gene expression has recently been introduced. Furthermore, to understand the regulation of polyubiquitin gene expression more precisely, cis-acting elements and trans-acting factors, which are regulatory components of polyubiquitin genes, have been analyzed. In this review, we discuss how the role of polyubiquitin genes has been studied during the past decade, especially focusing on their regulation. [BMB Reports 2021; 54(4): 189-195]

아동기 외상에서 FK506 Binding Protein 5의 유전자 환경 상호작용과 후생유전적 조절

주열(Yeol Joo) 대한생물치료정신의학회 2014 생물치료정신의학 Vol.20 No.1

It is well known that trauma during childhood significantly increases risk for posttraumatic stress disorder(PTSD), other mood and anxiety disorder in adulthood. Childhood trauma is known as altered regulations of the HPA axis in adulthood. Considering the importance of the HPA system in the etiology of PTSD, the effect of childhhood trauma on adult with PTSD and other psychiatric disorders may be mediated by dysregulation of the HPA axis. Recently, it has been recognized that for the development of PTSD, complex interplay between genetic predisposition and environmental factors plays crucial roles. FKBP5, which is a HSP90-associated co-chaperone, regulates sensitivity of glucocorticoid receptor. Multiple studies replicated the findings that interaction of FKBP5 genetic variants and childhood trauma significantly increased the risk of adult PTSD, suicide attempt and aggressive behaviour. Recent studies suggest that in specific risk allele of FKBP5 single nucleotide polymorphism(SNP), 3D conformational change of intron increases the expression of FKBP5 in response to stress. In addition, the model which explains the difference of epigenetic modulation of FKBP5 between risk allele and protective allele has been proposed. The findings that in FKBP5 SNP risk allele, relative irreversibility of cytosine demethylation by environmental factor occurs only in developmentally vulnerable period, may shed light on molecular underpinnings of long lasting effect of childhood trauma.

Increased Abiotic Stress Tolerance by Over-expressing OsABF2 in Transgenic Arabidopsis thaliana

Phun Bum Park(박훤범) 한국생명과학회 2012 생명과학회지 Vol.22 No.11

식물호르몬인 abscisic acid (ABA)는 식물의 비생물학적 스트레스의 적응과정에서 중요한 역할을 수행하고 있다. 또한 ABA는 종자휴면, 발아, 세포분열의 저해, 기공개폐와 같은 중요한 과정에 관여하고 있다. OsABF2 (Oryza sativa ABRE Binding Factor2)는 벼에서 비생물학적 스트레스와 ABA 신호전달 과정에 양성적으로 관여하는 bZIP 형태의 전사인자이다. OsABF2 유전자의 발현은 ABA와 다양한 스트레스 처리에 의해 유도된다. 본 논문에서는 OsABF2 유전자를 과발현한 애기장대가 가뭄, 고염, 고온 상태에서의 생존율이 야생형보다 증가하는 것을 확인하였다. 또한 ABA가 존재하는 상황에서 OsABF2 유전자를 과발현한 애기장대의 발아율이 감소하는 것을 확인하였다. 이러한 결과로 미루어 OsABF2 유전자를 과발현한 애기장대는 비생물학적 스트레스에 대한 내성이 증가하고 ABA 감수성은 증가하는 것으로 확인되었다. The phytohormone abscisic acid (ABA) plays an important role in the adaptive response of plants to abiotic stresses. ABA also regulates many important processes, including seed dormancy, germination, inhibition of cell division, and stomatal closure. OsABF2 (Oryza sativa ABRE binding factor2) is one of the bZIP type transcription factors, which are involved in abiotic stress response and ABA signaling in rice. Expression of OsABF2 is induced by ABA and various stress treatments. Findings show that survival rates of OsABF2 over-expressing Arabidopsis lines were increased under drought, salt, and heat stress conditions. The germination ratio of OsABF2 over-expressing Arabidopsis lines was decreased in the presence of ABA. Results indicate that OsABF2 over-expressing Arabidopsis lines have enhanced abiotic stress tolerance and have increased ABA sensitivity.

ER Stress-driven BCL-2 Overexpression Inhibits Cell Death in CHO Cells

Minji KYEONG,Jae Seong LEE 한국생물공학회 2020 한국생물공학회 학술대회 Vol.2020 No.10

Construction and Application of Functional Gene Modules to Regulatory Pathways in Rice

홍우종,Anil Kumar Nalini Chandran,전종성,정기홍 한국식물학회 2017 Journal of Plant Biology Vol.60 No.4

Signal transduction and transcriptional regulationpathways are key elements in the control of diverse physiologicalresponses and agronomic traits in plants. The regulatory rolesof more than 1,000 known genes have been functionallycharacterized in rice, a model crop plant, and many of themare associated with transcriptional regulation and signaltransduction pathways. In this study, we collected andanalyzed 417 known genes associated with regulatorypathways, about 40% of the known genes, using the regulationoverview installed in the MapMan toolkit. Connecting novelgenes to current knowledge about regulatory pathways canelucidate their molecular functions and inspire ideas forfurther applications. We have summarized the functions ofknown regulatory genes in the areas of transcriptional regulation,epigenetic regulation, protein modification, protein degradation,signaling and hormone metabolism, also we have emphasizedthe unique features of several gene families in these classes,including MADS box families, which are strongly associatedwith the regulation of floral organ identity and floweringtime. In addition, our construction of functional modules infour agronomic categories, morphological, physiological,biotic stress and abiotic stress, suggests a basic frameworkfor expanding current knowledge about regulatory pathwaysto enhance agronomic traits in rice. We also provide a quickillustration of the positive and negative regulatory relationshipsof the target gene to manipulate agronomic trait by usinggenome-wide transcriptome data of knockout or overexpressionmutations of genes of interest in each functional module.

Expression of stress regulator and virulence genes of Cronobacter sakazakii strain Yrt2a as a response to acid stress

Maerani Maerani,Ratih Dewanti-Hariyadi,Siti Nurjanah 한국식품과학회 2020 Food Science and Biotechnology Vol.29 No.9

This research aimed to evaluate the effect of acidstress on the expression of stress regulator (grxB and rpoS)and virulence (ompA, hfq, and cpa) genes of Cronobactersakazakii Yrt2a. The results showed that C. sakazakii Yrt2aexperienced decrease in number during acid stress and wasno longer culturable 90 min post exposure to pH 3.0. During acid stress, the expression of grxB, rpoS, ompA, cpaand hfq was upregulated by 2.15; 2.19; 1.55; 1.1 and 1.41log, respectively. However, all genes expression wasdownregulated when the bacteria entered the unculturablestate. The expression of gene grxB, rpoS, ompA, cpadecreased to 1.04; 0.37; 0.84 and 1.71 log, respectively;while hfq gene expression reached a level lower than thatof control. This research implies a supposition that duringacid stress, C. sakazakii was capable of maintaining itsculturability and pathogenicity until they are no longerculturable.

Discovery of Stress Responsive TATA-box Binding Protein Associated Factor6 (TAF6) from Finger Millet (Eleusine coracana (L.) Gaertn)

M. S. Parvathi,Karaba N. Nataraja 한국식물학회 2017 Journal of Plant Biology Vol.60 No.4

Drought is one of the major abiotic factors affectingplant growth mainly in the tropical regions. During stressacclimation response, basal transcriptional process is criticalwhich is coordinated by several cofactors, among which TATAboxBinding Protein (TBP) - Associated Factors (TAFs) are themajor proteins involved in pre-initiation complex assembly. Insearch of novel transcriptional regulators, we identified one ofthe factors, TAF6, in a drought cDNA library generated from anadapted crop, finger millet (Eleusine coracana (L.) Gaertn). RTPCRanalysis in leaf tissues of finger millet experiencingdifferent levels of drought, revealed its stress responsiveness inthree different genotypes. The gene is also induced under salt,osmotic and oxidative stresses at seedling stage. Analysis of itspromoter in model plants indicated the presence of cis-elementsassociated with diverse stress responses. Down regulation ofNbTAF6 by virus induced gene silencing (VIGS) approachresulted in a developmentally defective and stress sensitivephenotype in Nicotiana benthamiana. This is the first report onthe up-regulation of EcTAF6 under abiotic stresses and the geneprobably has a crucial role in safeguarding the stress relatedtranscription process. The basal regulators like TAF6 can thus beconsidered as prospective candidates associated with stressacclimation in plants.