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Mini Review : The art of reporter proteins in science: past, present and future applications
( Cheol Min Ghim ),( Sung Kuk Lee ),( Shuichi Takayama ),( Robert J. Mitchell ) 생화학분자생물학회 (구 한국생화학분자생물학회) 2010 BMB Reports Vol.43 No.7
Starting with the first publication of lacZ gene fusion in 1980, reporter genes have just entered their fourth decade. Initial studies relied on the simple fusion of a promoter or gene with a particular reporter gene of interest. Such constructs were then used to determine the promoter activity under specific conditions or within a given cell or organ. Although this protocol was, and still is, very effective, current research shows a paradigm shift has occurred in the use of reporter systems. With the advent of innovative cloning and synthetic biology techniques and microfluidic/nanodroplet systems, reporter genes and their proteins are now finding themselves used in increasingly intricate and novel applications. For example, researchers have used fluorescent proteins to study biofilm formation and discovered that microchannels develop within the biofilm. Furthermore, there has recently been a “fusion” of art and science; through the construction of genetic circuits and regulatory systems, researchers are using bacteria to “paint” pictures based upon external stimuli. As such, this review will discuss the past and current trends in reporter gene applications as well as some exciting potential applications and models that are being developed based upon these remarkable proteins. [BMB reports 2010; 43(7): 451-460]
Synthetic Biology for Biofuels: Building Designer Microbes from the Scratch
Ghim, Cheol-Min,Kim, Tae-Sung,Mitchell, Robert J.,Lee, Sung-Kuk 한국생물공학회 2010 Biotechnology and Bioprocess Engineering Vol.15 No.1
The ultimate goal in the production of biofuels is to produce fuels identical or similar to petroleum-derived transportation fuels more efficiently and in commercial quantities. Synthetic biologists have been engineering microbes to synthesize biofuels, such as butanol and fatty acid- or isoprenoid-based fuels, which are nearly identical to gasoline and diesel. One of the most urgent demands along this direction is to attain a solid framework for characterizing and standardizing the biological parts and devices. It seems quite promising because biotechnologies specially based on miniaturizations have been making a big contribution to this work. Therefore, in this review, recent advances and difficulties in the biofuel field are discussed, along with the advances of synthetic biology, which will make it possible to create designer microorganisms that produce economically viable next generation biofuels, aside from bioethanol, from corn or sugar cane, and biodiesel from plant or animal oils.
Rewiring carbon catabolite repression for microbial cell factory
( Parisutham Vinuselvi ),( Min Kyung Kim ),( Sung Kuk Lee ),( Cheol Min Ghim ) 생화학분자생물학회 (구 한국생화학분자생물학회) 2012 BMB Reports Vol.45 No.2
Carbon catabolite repression (CCR) is a key regulatory system found in most microorganisms that ensures preferential utilization of energy-efficient carbon sources. CCR helps microorganisms obtain a proper balance between their metabolic capacity and the maximum sugar uptake capability. It also constrains the deregulated utilization of a preferred cognate substrate, enabling microorganisms to survive and dominate in natural environments. On the other side of the same coin lies the tenacious bottleneck in microbial production of bioproducts that employs a combination of carbon sources in varied proportion, such as lignocellulose-derived sugar mixtures. Preferential sugar uptake combined with the transcriptional and/or enzymatic exclusion of less preferred sugars turns out one of the major barriers in increasing the yield and productivity of fermentation process. Accumulation of the unused substrate also complicates the downstream processes used to extract the desired product. To overcome this difficulty and to develop tailor-made strains for specific metabolic engineering goals, quantitative and systemic understanding of the molecular interaction map behind CCR is a prerequisite. Here we comparatively review the universal and strain-specific features of CCR circuitry and discuss the recent efforts in developing synthetic cell factories devoid of CCR particularly for lignocellulose- based biorefinery. [BMB reports 2012; 45(2): 59-70].
( Robert J. Mitchell ),( Sung Kuk Lee ),( Tae Sung Kim ),( Cheol Min Ghim ) 생화학분자생물학회(구 한국생화학분자생물학회) 2011 BMB Reports Vol.44 No.1
Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent “autoinducer” molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions. (BMB reports 2011; 44(1): 1-10)
Kim, Jihyun F.,Jeong, Haeyoung,Park, Soo-Young,Kim, Seong-Bin,Park, Yon Kyoung,Choi, Soo-Keun,Ryu, Choong-Min,Hur, Cheol-Goo,Ghim, Sa-Youl,Oh, Tae Kwang,Kim, Jae Jong,Park, Chang Seuk,Park, Seung-Hwan American Society for Microbiology 2010 Journal of Bacteriology Vol.192 No.22
<B>ABSTRACT</B><P><I>Paenibacillus polymyxa</I> E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of <I>P. polymyxa</I> E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes.</P>