선진국 생물산업 혁신체제의 구조변화에 관한 연구

송위진,김석관,박범순 과학기술정책연구원 2000 정책연구 Vol.- No.-

연구의 목적 및 필요성 □ 생물산업은 혁명적인 변화의 시기를 맞고 있다. 정보통신기술과 생명공학기술의 결합은 생물에 대한 기본 인식을 변화시키고 있으며, 생명현상을 연구하고 그것을 이용하여 유용한 제품을 개발하는 방식에 단절적인 변화를 낳고 있다. ○ 많은 생물학자들은 이제 생물산업을 문화적, 경제적 요구와 수요에 부응하도록 생물의 유전암호를 다시 프로그램하는 것 이라고 규정하면서 생물을 정보시스템의 관점에서 접근하고 있다. ○ 이는 유전자 정보의 확보와 활용과 관련된 Genomics, 생물정보학 (Bioinformatics)이 생물산업의 핵심 분야로 부상하고 있기 때문에 나타난 결과라고 할 수 있다. 최근 인간게놈프로젝트가 완료되면서 이와 같은 경향은 더욱 강화될 전망으로 보인다. □ Genomics의 등장과 확산에 따른 이와 같은 변화는 생물산업에서 기술개발이 이루어지는 전반적인 방식과 틀을 규정하는 생물산업 기술패러다임의 변화라고 이야기할 수 있다. 그리고 이와 같은 기술패러다임의 변화는 생물산업 기술 혁신체제에 전반에 새로운 틀을 모색하도록 하는 힘으로 작용한다. ○ 일반적으로 새로운 기술패러다임이 등장하게 되면 기술적 지식의 원천이 바뀌고, 기술개발이 이루어지는 방식을 변화하게 되며, 기술혁신에 참여하는 혁신주체들도 새로운 방식으로 조직화된다. 혁신체제가 변화하게 되는 것이다. ○ 그러나 혁신체제의 변화는 자동적으로 이루어지는 것이 아니다. 기존에 작동 되고 있는 혁신체제는 상당한 안정성을 가지고 있으며 계속 그 패턴을 유지 하고자 하는 경로의존성(path dependency)을 가지고 있다. ○ 또 혁신체제의 변화가 반드시 좋은 성과를 수반하는 것도 아니다. 새롭게 등 장하고 있는 기술패러다임의 특성과 부합되는 기술개발방식과 조직방식이 갖추어져야만 바람직한 성과를 얻을 수 있는 것이다. □ 본 연구의 목적은 우선 생물산업에서 나타나고 있는 기술패러다임의 변화의 내용이 무엇이고, 그것에 대응해서 선진국 혁신체제에서 어떠한 구조전환 노력들이 나타나고 있는가를 검토하는 데 있다. 생물산업에서 Genomics의 등장과 확산이라는 기술변화가 기술개발이 이루어지는 패턴에 어떠한 변화를 가져오고 있고 이에 대해 선진국의 정부와 기업, 그리고 혁신체제는 어떤 대응을 보여주고 있는지를 살펴보는 것이다. □ 다음으로는 선진국 혁신체제 구조변화의 양상을 파악하여 우리 나라 생물산업 혁신체제 구축과 관련된 교훈을 얻는 것이 본 연구의 목적이다. 선진국들이 자 신들이 처한 독특한 조건과 제도화된 국가혁신체제의 틀 속에서 대응하는 모습들을 검토하여 우리 나라의 기술개발에 도움이 될 수 있는 교훈을 이끌어 내어, 우리 나라 생물산업 혁신체제를 고도화하는 데 일조할 수 있는 기술개발전략을 도출하는 데 본 연구의 목적이 있다. □ 한편 본격적으로 논의에 들어가기 앞서 본 연구에서 사용하는 Genomics에 대한 개념 정의를 내려보기로 하자. ○ Genome은 유전자(Gene)와 염색체(Chromosome)의 합성어로 한 생물체가 가지는 유전정보의 총체를 뜻한다. Genomics는 생물체가 가지고 있는 개개 의 유전자를 넘어서 유전정보 전부를 총체적으로 연구하여 유전정보의 구조 와 기능, 그것이 생명현상의 발현에 미치는 효과들을 살펴보는 것으로 정의 할 수 있다. 연구의 내용 및 범위 □ 본 보고서에서는 Genomics의 등장과 확산으로 인해 생물산업에서 나타난 기술패러다임 변화와 그것에 대응하는 선진국 혁신체제의 변화에 초점을 맞추어 논의를 전개한다. □ 제2장에서는 생물산업의 특성과 발전 과정에 대해서 살펴본다. 생물산업의 산업적기술적 특성과 함께 생물산업이 어떻게 발전되어 왔는가를 정리한다. □ 제3장에서는 새로운 기술패러다임의 등장과 그 효과를 살펴본다. Genomics에 기반한 생물산업의 등장과 함께 나타난 새로운 기술패러다임의 성격은 무엇이며 그것이 의미하는 바를 정리한다. 그리고 새로운 기술패러다임의 등장이 기술개발이 이루어지는 방식에 미치는 영향을 살펴본다. □ 제4장에서는 새로운 기술패러다임의 등장에 대해서 선진국이 어떻게 대응하고 있는가를 살펴본다. 미국과 독일, 일본이 새로운 기술패러다임의 등장과 함께 재편되는 기술환경에 대응하여 어떤 노력들을 하고 있는지를 다룬다. □ 제5장에서는 우리 나라 생물산업 혁신체제 발전방안에 대한 제언을 다룬다. 새로운 기술패러다임의 등장에 대해서 효과적으로 대응할 수 있는 기술개발전략과 혁신체제의 발전 방향에 대해 논의한다. □ 부록에서는 미국의 생물산업 기술개발에서 핵심적 역할을 하고 수행하고 있는 NIH의 역사와 운영 방식 등을 인간게놈프로젝트를 중심으로 살펴본다. 미국의 생물산업 과학지식 기반이 오늘날과 같이 형성될 수 있었던 배경을 이해하는 데 도움이 될 것이다. ○ 협의의 개념으로 쓸 경우 genomics는 proteomics, bioinformatics와 구별되기도 하는데, 광의의 개념으로 사용할 때에는 Genomics내에 proteomics, bioinformatics 등이 포함되는 것으로 본다. 본 연구에서는 광의의 개념으로 Genomics를 사용하기로 한다.

The Insect Genomics in Future Pest Management

Woojin Kim,Yeon Ho Je 한국응용곤충학회 2012 한국응용곤충학회 학술대회논문집 Vol.2012 No.10

In 1990, the human genome project had begun with three billion dollars of budget, and the sequencing and analysis result of the three billion base pairs of human genome was finally published in 2000 to open a new era of genomics. Since the human genome project, many other genomes of eukaryotic model organisms, such as mouse, Drosophila, Arabidopsis, C. elegance, etc., became available, and this led the development of computational biology and comparative genomics. Also, during the last decade, the speed of the nucleotide sequencing increased significantly with lower cost by next generation sequencing technology, and the computational power to handle sequence information also has grown exponentially to make possible that a genomics approach is an affordable tool for many of the biological studies. In the entomology area, the 5000 insect genome project was launched in 2011 for understanding of the biology of insects in a new dimension. Based on the recent studies of functional genomics and the new discoveries in the biological sciences, such as innate immune system, RNAi technique, insect pathogens, etc., the information from the insect genomics study will make possible to improve our capability to manage insect pests in the future.

Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens

이규민,Zoe K. Scott-Nevros,이상목,김동혁 한국생물공학회 2023 Biotechnology and Bioprocess Engineering Vol.28 No.6

Methylobacterium is a genus belonging to the pink-pigmented facultative methylotrophs, which can use C1 substrates as a sole carbon source. Methylorubrum extorquens (formerly Methylobacterium extorquens) is a potentially valuable bacteria in methanol-based bioindustry producing high-value-added chemicals. Thus, it is critical to understand the core metabolic pathways of M. extorquens strains for further advancement as a platform bacterium in the bioindustry. However, there are no reported systems biological approaches comparing different M. extorquens strains. This paper focuses on comparing the genomic properties of seven completely sequenced M. extorquens strains, including M. extorquens PA1, which was re-sequenced, and M. extorquens ATCC 55366, which was newly sequenced in this study. Pan-genome analysis indicated that a total of 10,431 ortholog clusters composed the pan-genome of these M. extorquens strains, including 3,507 core genome, 1,860 accessory genome, and 5,064 unique genome clusters. The functional annotation discovered that genes related to signal transduction were the most abundant in the pan-genome. Pan-genome analysis of two different habitat-specific groups revealed that the strains isolated from various soil environments had a higher percentage of genes involved in mobilome in their core genome. Subsequent exploration for secondary metabolite biosynthesis clusters denoted the unique ability of M. extorquens AM1 to produce various toblerols. M. extorquens PA1 could be a strong candidate for industrial strain development because of its minimal genome size with fully conserved central metabolism. This study provides the first inclusive insight into the differences in genomic characteristics of central metabolic networks of M. extorquens.

Genomic and Proteomic Analysis of Microbial Function in the Gastrointestinal Tract of Ruminants - Review -

White, Bryan A.,Morrison, Mark Asian Australasian Association of Animal Productio 2001 Animal Bioscience Vol.14 No.6

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

개인유전체 시대의 유전정보의 이용과 법적 문제

박종화 ( Jong Bhak ) 한남대학교 과학기술법연구원 2006 과학기술법연구 Vol.11 No.1

Before 2010, human societies will meet the personal genomics era. Each individual will have his/her own genome sequences completely sequenced. The use of such massive private information has several legal implications. One is the patents of genes. Who can own the patents right while every human being has such genes in his/her genome? Another issue is how much intervention a nation can have over individual genome information. Can a nation own and manage her people`s genome information? For science and technology to develop fast, it will be necessary for public organizations maintain the databases and tools for handling genome information. Other issues are ethics in the use of such genome information. The past and present trend clearly show that the main driving force of enhancing science is money. The financial gains from scientific and technological knowledge will dominate the future direction of genome research and legal issues will be of economy problems in the society. The best approach of handling legal issues related to genomic and genetic information is to segregate the inherent social problems from inefficient management from the technical and scientific problems. Most social conflicts are not from the technology itself, but the management and distribution system of the resource and knowledge. Genomic data can bring social and legal problems but the essence is not in science but in the management of the society. A progressive and proactive bills should be forwarded to the society if there have to be restrictions and regulations on the use of genome information. This is because the idea of private genetic data is false. Individuals share nearly the same information with other social members in terms of genome. Genome information can not be personal, therefore, the concept of protecting private genetic information is not practical. Compared to social inequality found among disabled and different ethnic groups, genetic inequality is a minor problem in the next decades.

식물 유전자 연구의 최근 동향

조용구,우희종,윤웅한,김홍식,우선희 한국식물생명공학회 2010 JOURNAL OF PLANT BIOTECHNOLOGY Vol.37 No.2

As the completion of genome sequencing, large collection of expression data and the great efforts in annotating plant genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. Functional genome analysis of plants has entered the highthroughput stage. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. However, to identify the exact function of unknown genes it is necessary to understand each gene’s role in the complex orchestration of all gene activities in the plant cell. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns. The most conclusive information about changes in gene expression levels can be gained from analysis of the varying qualitative and quantitative changes of messenger RNAs, proteins and metabolites. New technologies have been developed to allow fast and highly parallel measurements of these constituents of the cell that make up gene activity. We have reviewed currently employed technologies to identify unknown functions of predicted genes including map-based cloning, insertional mutagenesis, reverse genetics, chemical mutagenesis, microarray analysis, FOX-hunting system, gene silencing mutagenesis, proteomics and chemical genomics. Recent improvements in technologies for functional genomics enable whole-genome functional analysis, and thus open new avenues for studies of the regulations and functions of unknown genes in plants.

식물 유전자 연구의 최근 동향

조용구,우희종,윤웅한,김홍식,우선희,Cho, Yong-Gu,Woo, Hee-Jong,Yoon, Ung-Han,Kim, Hong-Sig,Woo, Sun-Hee 한국식물생명공학회 2010 식물생명공학회지 Vol.37 No.2

As the completion of genome sequencing, large collection of expression data and the great efforts in annotating plant genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. Functional genome analysis of plants has entered the high-throughput stage. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. However, to identify the exact function of unknown genes it is necessary to understand each gene's role in the complex orchestration of all gene activities in the plant cell. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns. The most conclusive information about changes in gene expression levels can be gained from analysis of the varying qualitative and quantitative changes of messenger RNAs, proteins and metabolites. New technologies have been developed to allow fast and highly parallel measurements of these constituents of the cell that make up gene activity. We have reviewed currently employed technologies to identify unknown functions of predicted genes including map-based cloning, insertional mutagenesis, reverse genetics, chemical mutagenesis, microarray analysis, FOX-hunting system, gene silencing mutagenesis, proteomics and chemical genomics. Recent improvements in technologies for functional genomics enable whole-genome functional analysis, and thus open new avenues for studies of the regulations and functions of unknown genes in plants.

mySyntenyPortal: an application package to construct websites for synteny block analysis

Lee, Jongin,Lee, Daehwan,Sim, Mikang,Kwon, Daehong,Kim, Juyeon,Ko, Younhee,Kim, Jaebum BioMed Central 2018 BMC bioinformatics Vol.19 No.-

<P><B>Background</B></P><P>Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks.</P><P><B>Results</B></P><P>To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users’ own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements.</P><P><B>Conclusions</B></P><P>mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user’s own genome data.</P>

Perspectives on the genomics research of important crops in the tribe Andropogoneae: Focusing on the Saccharum complex

Choi, Sang Chul,Chung, Yong Suk,Kim, Changsoo Institute of Agricultural Science 2016 Korean Journal of Agricultural Science Vol.41 No.2

Climate changes are shifting the perception of C4 photosynthetic crops due to their superior adaptability to harsh conditions. The tribe Andropogoneae includes some economically important grasses, such as Zea mays, Sorghum bicolor, Miscanthus spp., and Saccharum spp., representing C4 photosynthetic grasses. Although the Andropogoneae grasses diverged fairly recently, their genomic structures are remarkably different from each other. As previously reported, the family Poaceae shares the pan-cereal duplication event occurring ca. 65 MYA. Since this event, Sorghum bicolor has never experienced any additional duplication event. However, some lineage-specific duplication events were reported in Z. mays and Saccharum spp., and, more recently, it was revealed that a shared allotetraploidization event occurred before the divergence between Miscanthus and Saccharum (but after the divergence from S. bicolor), which provided important clues to those two species having large genome sizes with complicated ploidy numbers. The complex genomic structures of sugarcane and Miscanthus (defined as the Saccharum complex along with some other taxa) have had a limiting effect on the use of their molecular information in breeding programs. For the last decade, genomics-associated technologies have become an important tool for molecular crop breeding (genomics-assisted breeding, GAB), but it has not been directly applied to sugarcane and Miscanthus due to their complicated genome structures. As genomics research advances, molecular breeding of those crops can take advantage of technical improvements at a reasonable cost through comparative genomic approaches. Active genomic research of non-model species using closely related model species will facilitate the improvement of those crops in the future.

Algal genomics perspective: the pangenome concept beyond traditional molecular phylogeny and taxonomy

이준모 국립생물자원관 2021 Journal of species research Vol.10 No.2

Algal genomics approaches provide a massive number of genome/transcriptome sequences and reveal the evolutionary history vis-à-vis primary and serial endosymbiosis events that contributed to the biodiversity of photosynthetic eukaryotes in the eukaryote tree of life. In particular, phylogenomic methods using several hundred or thousands of genes have provided new insights into algal taxonomy and systematics. Using this method, many novel insights into algal species diversity and systematics occurred, leading to taxonomic revisions. In addition, horizontal gene transfers (HGTs) of functional genes have been identified in algal genomes that played essential roles in environmental adaptation and genomic diversification. Finally, algal genomics data can be used to address the pangenome, including core genes shared among all isolates and partially shared strain-specific genes. However, some aspects of the pangenome concept (genome variability of intraspecies level) conflict with population genomics concepts, and the issue is closely related to defining species boundaries using genome variability. This review suggests a desirable future direction to merge algal pangenomics and population genomics beyond traditional molecular phylogeny and taxonomy.