• Interdisciplinary Bio Central
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• 제5권2호
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• pp.5.1-5.3
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• 2013

Introduced were two biological investigations in which information biology played a significant role. In the first case independent findings in cancer research over a long period were united and organized by information biology and led to the outcome that was subject to a Nobel Prize. The outcome has revealed that the cause of human cancer is located in the genome in a dormant condition. The second case shows how to elucidate the function of an unknown DNA sequence or ORF in prokaryotes by a large - scale computer homology search and analyses. For the elucidation the International DNA Databases and a large - scale computer were two key factors.

• BMB Reports
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• 제43권1호
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• pp.1-8
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• 2010

The cold shock domain (CSD) is among the most ancient and well conserved nucleic acid binding domains from bacteria to higher animals and plants. The CSD facilitates binding to RNA, ssDNA and dsDNA and most functions attributed to cold shock domain proteins are mediated by this nucleic acid binding activity. In prokaryotes, cold shock domain proteins only contain a single CSD and are termed cold shock proteins (Csps). In animal model systems, various auxiliary domains are present in addition to the CSD and are commonly named Y-box proteins. Similar to animal CSPs, plant CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. Cold shock domain proteins have been shown to play important roles in development and stress adaptation in wide variety of organisms. In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal CSPs.

• 약학회지
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• 제48권1호
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• pp.47-54
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• 2004

ClpP is a stress-inducible protein and proteolytic subunit of the ATP-dependent Clp protease in prokaryotes and eukaryotes. Although its physiological roles in bacterial virulence were widely studied in various organsims, including Streptococcus pneumoniae, until now the immunological effect has not been investigated. Here, we have examined the cross reactivity of S. pneumoniae ClpP antibody with other organisms's cell lysate proteins. Although the protein sequence of S. pneumoniae ClpP was highly conserved among various organisms including human, the antibody rasised by S. pneumoniae ClpP was not cross-reacted with other organism's cell lysates, which were Saccharomyces cerevisiae , human lung A549 cell, Bacillus subtilis, Pseuomonas aeruginosa, E. coli, and Salmonella typhi. It was only reacted with S. pneumoniae and Lato-bacillus thermophilus. Thus we examined the immunoprotective effect of ClpP by immunizing mice with the purified ClpP. The mean survival time of mouse was significantly increased with the ClpP immunization. These results suggest that S. pneumoniae ClpP could be used as a vaccine candidate for prevention of S. pneumoniae infection.

• Genomics & Informatics
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• 제7권2호
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• pp.111-121
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• 2009

Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.71-71
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• 2003

The quinolinic acid(QA) phosphoribosyltransferase (PRTase) (EC 2.4.2.19), is a key enzyme involved in NAD$\^$+/ biosynthesis in prokaryotes and eukaryotes, The QAPRTase produces nicotinic acid mononucleotide (NAMN) from QA and 5-phosphoribosyl-1-pyrophosphate (PRPP). For this reaction, the QA is decarboxylated (Fig.1). Produced NAMN is used to a synthesis of nicotinate adenine dinucleotide(NAD$\^$+/).

• BMB Reports
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• 제41권8호
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• pp.568-574
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• 2008

Antisense RNA molecules are powerful tools for controlling the expression of specific genes but their use in prokaryotes has been limited by their unpredictable antisense effectiveness. Moreover, appreciation of the molecular mechanisms associated with silencing in bacteria is still restricted. Here we report our attempts to define an effective antisense strategy in E. coli, and to dissect the observed silencing process. Antisense constructs complementary to different regions of lacZ were investigated, and silencing was observed exclusively upon expression of antisense RNA hybridising the 5'UTR of lac messenger. The level of lacZ mRNA was reduced upon expression of this antisense construct, and the silencing competence was found to be closely associated with its stability. These observations may help in the design of antisense molecules directed against prokaryotic genes.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1999년도 학술발표회 진행표 및 논문초록
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• pp.13-13
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• 1999

"Two-component" phosphorelay signal transduction systems constitute a potential target for antibacterial and antifungal agents, since they are found exclusively in prokaryotes and lower eukaryotes (yeast, fungi, slime mold, and plants) but not in mammalian organisms.(omitted)

• Genomics & Informatics
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• 제7권4호
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• pp.217-219
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• 2009

The primary clue for locating protein-coding regions is the open reading frame and the determination of ORFs (Open Reading Frames) is the first step toward the gene prediction, especially for prokaryotes. In this respect, we have developed a web-based ORF search tool called ORF Miner. The ORF Miner is a graphical analysis utility which determines all possible open reading frames of a selectable minimum size in an input sequence. This tool identifies all open reading frames using alternative genetic codes as well as the standard one and reports a list of ORFs with corresponding deduced amino acid sequences. The ORF Miner can be employed for sequence annotation and give a crucial clue to determination of actual protein-coding regions.

• Journal of Microbiology and Biotechnology
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• 제29권7호
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• pp.1014-1021
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• 2019

In the bacterial community, unicellular organisms act together as a multicellular being. Bacteria interact within the community and programmed cell death (PCD) in prokaryotes is a sort of altruistic action that enables the whole population to thrive. Genetically, encoded cell death pathways are triggered by DNA damage or nutrient starvation. Given the environmental and bacterial diversity, different PCD mechanisms are operated. Still, their biochemical and physiological aspects remain unrevealed. There are three main pathways; thymineless death, apoptosis-like death, and toxin-antitoxin systems. The discovery of PCD in bacteria has revealed the possibility of developing new antibiotics. In this review, the molecular and physiological characteristics of the three types of PCD and their development potential as antibacterial agents are addressed.

• BMB Reports
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• 제54권1호
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• pp.59-69
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• 2021

The ability to read, write, and edit genomic information in living organisms can have a profound impact on research, health, economic, and environmental issues. The CRISPR/Cas system, recently discovered as an adaptive immune system in prokaryotes, has revolutionized the ease and throughput of genome editing in mammalian cells and has proved itself indispensable to the engineering of immune cells and identification of novel immune mechanisms. In this review, we summarize the CRISPR/Cas9 system and the history of its discovery and optimization. We then focus on engineering T cells and other types of immune cells, with emphasis on therapeutic applications. Last, we describe the different modifications of Cas9 and their recent applications in the genome-wide screening of immune cells.