• IMMUNE NETWORK
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• 제12권6호
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• pp.230-239
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• 2012

Activation-induced cytidine deaminase (AID) is an enzyme that is predominantly expressed in germinal center B cells and plays a pivotal role in immunoglobulin class switch recombination and somatic hypermutation for antibody (Ab) maturation. These two genetic processes endow Abs with protective functions against a multitude of antigens (pathogens) during humoral immune responses. In B cells, AID expression is regulated at the level of either transcriptional activation on AID gene loci or post-transcriptional suppression of AID mRNA. Furthermore, AID stabilization and targeting are determined by post-translational modifications and interactions with other cellular/nuclear factors. On the other hand, aberrant expression of AID causes B cell leukemias and lymphomas, including Burkitt's lymphoma caused by c-myc/IgH translocation. AID is also ectopically expressed in T cells and non-immune cells, and triggers point mutations in relevant DNA loci, resulting in tumorigenesis. Here, I review the recent literatures on the function of AID, regulation of AID expression, stability and targeting in B cells, and AID-related tumor formation.

• 한국발생생물학회지:발생과생식
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• 제21권4호
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• pp.449-456
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• 2017

The germline stem cells of the Drosophila ovary continuously produce eggs throughout the life-span. Intricate regulation of stemness and differentiation is critical to this continuous production. The translational regulator Nos is an intrinsic factor that is required for maintenance of stemness in germline stem cells. Nos expression is reduced in differentiating cells at the post-transcriptional level by diverse translational regulators. However, molecular mechanisms underlying Nos repression are not completely understood. Through three distinct protein-protein interaction experiments, we identified specific molecular interactions between translational regulators involved in Nos repression. Our findings suggest a model in which protein complexes assemble on the 3' untranslated region of Nos mRNA in order to regulate Nos expression at the post-transcriptional level.

• Journal of Microbiology and Biotechnology
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• 제15권3호
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• pp.551-559
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• 2005

The recent rapid increase in genomic data related to many microorganisms and the development of computational tools to accurately analyze large amounts of data have enabled us to design several kinds of simulation approaches for the complex behaviors of cells. Among these approaches, dFBA (dynamic flux balance analysis), which utilizes FBA, differential equations, and regulatory events, has correctly predicted cellular behaviors under given environmental conditions. However, until now, dFBA has centered on substrate concentration, cell growth, and gene on/off, but a detailed hierarchical structure of a regulatory network has not been taken into account. The use of Boolean rules for regulatory events in dFBA has limited the representation of interactions between specific regulatory proteins and genes and the whole transcriptional regulation mechanism with environmental change. In this paper, we adopted the operon as the basic structure, constructed a hierarchical structure for a regulatory network with defined fundamental symbols, and introduced a weight between symbols in order to solve the above problems. Finally, the total control mechanism of regulatory elements (operons, genes, effectors, etc.) with time was simulated through the linkage of dFBA with regulatory network modeling. The lac operon, trp operon, and tna operon in the central metabolic network of E. coli were chosen as the basic models for control patterns. The suggested modeling method in this study can be adopted as a basic framework to describe other transcriptional regulations, and provide biologists and engineers with useful information on transcriptional regulation mechanisms under extracellular environmental change.

• 대한약학회:학술대회논문집
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• 대한약학회 2002년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2
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• pp.151-152
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• 2002

Bacterial infection is a very complex process in which both pathogenic microorganisms and host cells play crucial roles, and it is the outcome of interactions between the two participants. To elucidate the bacterial pathogenesis mechanisms, therefore, it is essential to understand the cellular and systemic responses of the host as well as the virulence factors of the pathogen. Infection of a host by pathogenic bacteria causes drastic changes in the physiology of host cells, leading to activation of a program of various gene expression. (omitted)

• Journal of Microbiology
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• 제38권3호
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• pp.176-179
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• 2000

A challenge phage system was used to study the DNA-protein interaction between C4-dicarboxylic acid transport protein D(DCTD) or $\sigma$54, and a $\sigma$54 -dependent promoter, dctAp. R. meliloti dctA promoter regulatory region replaced the Omnt site on the phage. S. typhimurium strains overproducing either DCTD or $\sigma$54 directed this challenge phage towards lysogency, indicating that DCTD or E$\sigma$54 recognized the dctA promoter on the phage and repressed transcription of the ant gene. These challenge phage constructs will be useful for examining interactions between DCTD(or $\sigma$54) and the dctA promoter region.

• 한국자기공명학회논문지
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• 제2권2호
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• pp.152-157
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• 1998

The diversity of RNA functions ranges from storage and propagation of genetic information to enzymatic activity during RNA processing and protein synthesis. This diversity of functions requires an equally diverse arrays of structures, and, very often, the formation of functional RNA-protein complexes. Recognition of specific RNA signals by RNA-binding proteins is central to all aspects of post-transcriptional regulation of gene expression. We will describe how NMR is being used to understand at the atomic level how these important biological processes occur.

• BMB Reports
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• 제42권1호
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• pp.41-46
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• 2009

Post-transcriptional regulation of mRNA stability by Hu proteins is an important mechanism for tumorigenesis. We focused on the molecular interactions between the HuC protein and AU-rich elements (AREs) to find chemical inhibitors of RNA-protein interactions using RNA electrophoretic mobility shift assay with non-radioactive probes. Screening of 52 natural compounds identified 14 candidate compounds that displayed potent inhibitory activity. Six (quercetin, myricetin, (-)-epigallocatechin gallate, ellagic acid, (-)-epicatechin gallate, and rhamnetin) were categorized as phytochemicals, and their $IC_{50}$ values were low ($0.2-1.8\;{\mu}M$).

• The Plant Pathology Journal
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• 제20권1호
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• pp.22-29
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• 2004

Many important horticultural and field crops are susceptible to virus infections or may possess a degree of resistance to some viruses, but become infected by others. Plant viruses enter cells through the presence of wounds, and replicate intracellularly small genomes that encode genes required for replication, cell-to-cell movement and encapsidation. There are numerous evidences from specific virus-host interactions to require the involvement of host factors and steps during viral replication cycle. However, viruses should deal with host defense responses either by general or specific mechanisms, targeting viral components or genome itself. On the other hand, the host plants have also adapted to defend themselves against viral attack by operating different lines of resistance responses. The defense-related interactions provide new insights into the complex molecular strategies for hosts for defense and counter-defense employed by viruses.

• 한국미생물·생명공학회지
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• 제49권4호
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• pp.478-484
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• 2021

Cellular resources including transcriptional and translational machineries in bacteria are limited, yet microorganisms depend upon them to maximize cellular fitness. Bacteria have evolved strategies for using resources economically. Regulatory networks for the gene expression system enable the cell to synthesize proteins only when necessary. At the same time, regulatory interactions enable the cell to limit losses when the system cannot make a cellular profit due to fake substrates. Also, the architecture of the gene expression flow can be advantageous for clustering functionally related products, thus resulting in effective interactions among molecules. In addition, cellular systems modulate the investment of proteomes, depending upon nutrient qualities, and fast-growing cells spend more resources on the synthesis of ribosomes, whereas nonribosomal proteins are synthesized in nutrient-limited conditions. A deeper understanding of cellular mechanisms underlying the optimal allocation of cellular resources can be used for biotechnological purposes, such as designing complex genetic circuits and constructing microbial cell factories.

• Molecules and Cells
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• 제39권5호
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• pp.375-381
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• 2016

MicroRNAs (miRNAs) are small non-coding RNAs (~22 nucleotides) regulating gene expression at the post-transcriptional level. By directing the RNA-induced silencing complex (RISC) to bind specific target mRNAs, miRNA can repress target genes and affect various biological phenotypes. Functional miRNA target recognition is known to majorly attribute specificity to consecutive pairing with seed region (position 2-8) of miRNA. Recent advances in a transcriptome-wide method of mapping miRNA binding sites (Ago HITS-CLIP) elucidated that a large portion of miRNA-target interactions in vivo are mediated not only through the canonical "seed sites" but also via non-canonical sites (~15-80%), setting the stage to expand and determine their properties. Here we focus on recent findings from transcriptome-wide non-canonical miRNA-target interactions, specifically regarding "nucleation bulges" and "seed-like motifs". We also discuss insights from Ago HITS-CLIP data alongside structural and biochemical studies, which highlight putative mechanisms of miRNA target recognition, and the biological significance of these non-canonical sites mediating marginal repression.