Identification of Egr1 Direct Target Genes in the Uterus by In Silico Analyses with Expression Profiles from mRNA Microarray Data

서봉정,손지원,김혜련,홍석호,송행석 한국발생생물학회 2014 발생과 생식 Vol.18 No.1

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(–/–) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within –500 bp of DEG’s promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

Identification of Egr1 Direct Target Genes in the Uterus by In Silico Analyses with Expression Profiles from mRNA Microarray Data

Seo, Bong-Jong,Son, Ji Won,Kim, Hye-Ryun,Hong, Seok-Ho,Song, Haengseok The Korean Society of Developmental Biology 2014 발생과 생식 Vol.18 No.1

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(-/-) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within -500 bp of DEG's promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

Prediction of Maximum Yields of Metabolites and Optimal Pathways for Their Production by Metabolic Flux Analysis

( Hong Soon Ho ),( Soo Yun Moon ),( Sang Yup Lee ) 한국미생물생명공학회 2003 Journal of microbiology and biotechnology Vol.13 No.4

Identification of Egr1 Direct Target Genes in the Uterus by In Silico Analyses with Expression Profiles from mRNA Microarray Data

Bong-jong Seo,Ji Won Son,Hye-Ryun Kim,Seok-Ho Hong,Haengseok Song 한국발생생물학회 2014 발생과 생식 Vol.18 No.1

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(-/-) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within -500 bp of DEG’s promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

Genetic Profiles of Korean Patients With Glucose-6-Phosphate Dehydrogenase Deficiency

이재웅,박준홍,최하영,김지연,권아름,장우리,채효진,김명신,김용구,이재욱,정낙균,조빈 대한진단검사의학회 2017 Annals of Laboratory Medicine Vol.37 No.2

Background: We describe the genetic profiles of Korean patients with glucose-6-phosphate dehydrogenase (G6PD) deficiencies and the effects of G6PD mutations on protein stability and enzyme activity on the basis of in silico analysis. Methods: In parallel with a genetic analysis, the pathogenicity of G6PD mutations detected in Korean patients was predicted in silico. The simulated effects of G6PD mutations were compared to the WHO classes based on G6PD enzyme activity. Four previously reported mutations and three newly diagnosed patients with missense mutations were estimated. Results: One novel mutation (p.Cys385Gly, labeled G6PD Kangnam) and two known mutations [p.Ile220Met (G6PD São Paulo) and p.Glu416Lys (G6PD Tokyo)] were identified in this study. G6PD mutations identified in Koreans were also found in Brazil (G6PD São Paulo), Poland (G6PD Seoul), United States of America (G6PD Riley), Mexico (G6PD Guadalajara), and Japan (G6PD Tokyo). Several mutations occurred at the same nucleotide, but resulted in different amino acid residue changes in different ethnic populations (p.Ile380 variant, G6PD Calvo Mackenna; p.Cys385 variants, Tomah, Madrid, Lynwood; p.Arg387 variant, Beverly Hills; p.Pro396 variant, Bari; and p.Pro396Ala in India). On the basis of the in silico analysis, Class I or II mutations were predicted to be highly deleterious, and the effects of one Class IV mutation were equivocal. Conclusions: The genetic profiles of Korean individuals with G6PD mutations indicated that the same mutations may have arisen by independent mutational events, and were not derived from shared ancestral mutations. The in silico analysis provided insight into the role of G6PD mutations in enzyme function and stability.

미생물 유전체의 in silico분석에 의한 보존적 유전자 탐색

강호영,신창진,강병철,박준형,신동훈,최정현,조환규,차재호,이동근 한국생명과학회 2002 생명과학회지 Vol.12 No.5

미생물 유전체(genome)들 사이의 보존된 유전자 (con-served gene)를 밝히는 것은 생명의 본질을 이해하는데 있어 다양한 의미를 갖는다고 할 수 있을 것이다. 본 연구에서는 보존적 유전자를 찾아내고, distance value를 이용하여 구한 보존성의 정도 C(conservation score)를 이용하여 종간의 유전자 변이의 정도를 단백질 관점에서 분석하였다. 분석에 사용된 자료는 COGs 데이티베이스의 총 43종의 미생물 유전체들이며, 이들은 총 n,009개의 유전자들을 포함하는 3,852 개의 ortholog들로 구성되어있었다. 분석 결과 43종의 미생물 유전체에 대하여 총 $\ulcorner$2개의 유전자들이 보존적인 것으로 나타났으며, 이들 중 72.2%인 52종의 유전자가 단백질 합성에 관련되는 것으로 나타났다. 이들 보존적 유전자들에 대하여 보존성의 정도 C를 계산하여 보존성의 순위를 얻었으며, 가장 잘 보존된 유전자는 CTPase-trans-lation elogation factor (COG0050)로 나타났다. 그리고 72개의 보존적 유전자가 나타내는 CU 모두를 이용한 분석결과 고세균(archaea)과 진정세균(bacteria)이 각각 독자적인 그룹을 형성하는 것을 관찰하였다. 본 연구의 결과에서 도출한 72개의 보존적 유전자는 생명체의 본질적 기능에 중요한 역할을 담당하는 것으로 사료되었고, 생명체의 진화 과정에서 이 유전자들이 보존된 이유와 기능적 연계에 대한 생물학적 연구에 기초 자료를 제공할 것으로 판단되어 진다. Conserved genes are importantly used to understand the major function in survival and replication of living organism. This study was focused on identification of conserved genes in microbial species and measuring the degree of conservation. For this purpose, in silico analysis was performed to search conserved genes based on the conservation level within microbial species. The ortholog list of COGs (Clusters of Orthologous Groups of proteins) in NCBI was used and whole genomes of 43 microbial species were included in that list. The distance value, derived from CLUSTALW multiple alignment program, was used as a descriptor of the conservation level of orthologs. It was revealed that 43 microbial genomes hold 72 conserved orthologs in common. The majority(72.2%) of the conserved genes was related to "translation, ribosomal structure and biogenesis" functional category. A GTPase-translation elogation factor(COG0050) was the best conserved gene from the distance value analysis. The 72 conserved genes, found in this research, would be useful not only to study minimal function genes but also new drug target among pathogens and to make a model of the virtual cell.tual cell.

Understanding of real alternative redox partner of <i>Streptomyces peucetius</i> DoxA: Prediction and validation using <i>in silico</i> and <i>in vitro</i> analyses

Rimal, Hemraj,Lee, Seung-Won,Lee, Joo-Ho,Oh, Tae-Jin Elsevier 2015 Archives of biochemistry and biophysics Vol.585 No.-

<P><B>Abstract</B></P> <P> <I>Streptomyces peucetius</I> ATCC27952 contains the cytochrome P450 monoxygenase DoxA that is responsible for the hydroxylation of daunorubicin into doxorubicin. Although <I>S. peucetius</I> ATCC27952 contains several potential redox partners, the most suitable endogenous electron-transport system is still unclear; therefore, we conducted a study of potential redox partners using Accelrys Discovery Studio 3.5. Recombinant DoxA along with its redox partners from <I>S. peucetius</I> FDX1, FDR2, and FDX3, and the putidaredoxin and putidaredoxin reductase from <I>Pseudomonas putida</I> that are essential equivalents of the class I type of bacterial electron-transport system were over-expressed and purified. The successful development of an efficient redox system was achieved by an <I>in vitro</I> enzymatic catalysis reaction with DoxA. The optimal pH for the activation of the heme was 7.6 and the optimal temperature was 30 °C. Our findings suggest a two-fold increase of DoxA activity via the NADH → FDR2 → FDX1 → DoxA pathway for the hydroxylation of the daunorubicin, and indicate that the usage of a native redox partner may increase daunorubicin-derived doxorubicin production due to the inclusion of DoxA.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Endogenous redox partner system of DoxA for the production of doxorubicin is purposed. </LI> <LI> <I>In silico</I> study show FDR2 and FDX1 as a best electron transfer partners. </LI> <LI> The optimum temperature and pH are 7.6 and 30 °C respectively for the catalytic activity of enzyme. </LI> </UL> </P>

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

Aditya Banerjee,Aryadeep Roychoudhury,S. Krishnamoorthi 한국식물생명공학회 2016 Plant biotechnology reports Vol.10 No.4

MicroRNAs (miRNAs) are a distinct class of non-coding, small regulatory RNAs which have evolved significantly in generating abiotic stress tolerance across a variety of model plants and crop species. These miRNAs, while undergoing post-transcriptional modifications, have often been found to be linked with epigenetic regulations of stress-responsive gene expression. The discovery of isomers of miRNAs (isomiRs) is also a remarkable event, as some schools of scientists believe them to be regulatory molecules distinct from the conventional miRNAs. The link between isomiRs and abiotic stress responses in plants is now a field of intense research. In this review, we have highlighted the mechanism of various tools and techniques which are essential to visualize high-throughput data analysis. Such data are required for generating large-scale libraries of small RNAs, from which stress-responsive miRNAs are conventionally screened. The concluding part of the review especially contains an exhaustive discussion on the recent developments of miRNA-mediated tolerance towards multiple stresses, such as nutrient deficiency, salinity, drought, oxidative stress, hypoxia, temperature stress, radiation, and heavy metal toxicity. Both transgenic as well as miRNAome approaches have been focussed in this section of the review.

Systems-Level Analysis of Genome-Scale In Silico Metabolic Models Using MetaFluxNet

Lee, Sang-Yup,Woo, Han-Min,Lee, Dong-Yup,Choi, Hyun-Seok,Kim, Tae-Yong,Yun, Hong-Seok The Korean Society for Biotechnology and Bioengine 2005 Biotechnology and Bioprocess Engineering Vol.10 No.5

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.

Characterizing Escherichia coli DH5α growth and metabolism in a complex medium using genome-scale flux analysis

Selvarasu, Suresh,Ow, Dave Siak-Wei,Lee, Sang Yup,Lee, May May,Oh, Steve Kah-Weng,Karimi, Iftekhar A.,Lee, Dong-Yup Wiley Subscription Services, Inc., A Wiley Company 2009 Biotechnology and Bioengineering Vol.102 No.3

<P>Genome-scale flux analysis of Escherichia coli DH5α growth in a complex medium was performed to investigate the relationship between the uptake of various nutrients and their metabolic outcomes. During the exponential growth phase, we observed a sequential consumption order of serine, aspartate and glutamate in the complex medium as well as the complete consumption of key carbohydrate nutrients, glucose and trehalose. Based on the consumption and production rates of the measured metabolites, constraints-based flux analysis of a genome-scale E. coli model was then conducted to elucidate their utilization in the metabolism. The in silico analysis revealed that the cell exploited biosynthetic precursors taken up directly from the complex medium, through growth-related anabolic pathways. This suggests that the cell could be functioning in an energetically more efficient manner by reducing the energy needed to produce amino acids. The in silico simulation also allowed us to explain the observed rapid consumption of serine: excessively consumed external serine from the complex medium was mainly converted into pyruvate and glycine, which in turn, led to the acetate accumulation. The present work demonstrates the application of an in silico modeling approach to characterizing microbial metabolism under complex medium condition. This work further illustrates the use of in silico genome-scale analysis for developing better strategies related to improving microbial growth and enhancing the productivity of desirable metabolites. Biotechnol. Bioeng. 2009; 102: 923–934. © 2008 Wiley Periodicals, Inc.</P>