• Journal of Microbiology and Biotechnology
• /
• v.25 no.10
• /
• pp.1599-1605
• /
• 2015

The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique genome. The core genome was converged to a smaller number of genes than reported previously, with 3,096 gene families. Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome. Finally, we investigated core genes for the sigma factors, mycothiol biosynthesis pathway, and secondary metabolism pathways; our data showed that many genes involved in stress response and morphological differentiation were commonly expressed in Streptomyces species. Elucidation of the core genome offers a basis for understanding the functional evolution of Streptomyces species and provides insights into target selection for the construction of industrial strains.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.7
• /
• pp.903-911
• /
• 2021

Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.

• BMB Reports
• /
• v.54 no.1
• /
• pp.59-69
• /
• 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.

• Journal of Animal Reproduction and Biotechnology
• /
• v.38 no.4
• /
• pp.247-253
• /
• 2023

Revolutionary advancements, such as the reduction in DNA sequencing costs and genome editing, have transformed biotechnology, fostering progress in manipulating biomolecules, engineering cells, and computational biology. Agriculture and food production have significantly benefited from tools like high-throughput microarrays, accelerating the selection of desired traits. Genetic engineering, especially utilizing genome editing, facilitates precise alterations in plants and animals, harnessing microbiomes and fostering lab-grown meat production to alleviate environmental pressures. The emergence of new biotechnologies, notably genome editing, underscores the necessity for regulatory frameworks governing LM (living modified) organisms. Global regulations overseeing genetically engineered or genome-edited (GE) organisms, encompassing animals, exhibit considerable diversity. Nonetheless, prevailing international regulatory trends typically exclude genomeedited plants and animals, employing novel biotechnological techniques, from GMO/ LMO classification if they lack foreign genes and originate through natural mutations or traditional breeding programs. This comprehensive review scrutinizes ongoing risk and safety assessment cases, such as genome-edited beef cattle and fish in the USA and Japan. Furthermore, it investigates the limitations of existing regulations related to genome editing in Korea and evaluates newly proposed legislation, offering insights into the future trajectory of regulatory frameworks.

• Genomics & Informatics
• /
• v.2 no.1
• /
• pp.1-6
• /
• 2004

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.5 no.5
• /
• pp.307-312
• /
• 2000

As the first assembly of the human genome was announced on June 26, 2000, we have entered post genome era. The genome sequence represents a new starting point for science and medicine with possible impact on research across the life sciences. In this review I tried to offer brief summaries of history and progress of the Human Genome Project and two major challenges ahead, functional genomics and DNA sequence variation research.

• Horticultural Science & Technology
• /
• v.35 no.2
• /
• pp.149-164
• /
• 2017

Next generation sequencing (NGS) technologies have led to the rapid accumulation of genome sequences through whole-genome sequencing and re-sequencing of crop species. Genomic resources provide the opportunity for a new revolution in plant breeding by facilitating the dissection of complex traits. Among vegetable crops, reference genomes have been sequenced and assembled for several species in the Solanaceae and Cucurbitaceae families, including tomato, pepper, cucumber, watermelon, and melon. These reference genomes have been leveraged for re-sequencing of diverse germplasm collections to explore genome-wide sequence variations, especially single nucleotide polymorphisms (SNPs). The use of genome-wide SNPs and high-throughput genotyping methods has led to the development of new strategies for dissecting complex quantitative traits, such as genome-wide association study (GWAS). In addition, the use of multi-parent populations, including nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) populations, has helped increase the accuracy of quantitative trait loci (QTL) detection. Consequently, a number of QTL have been discovered for agronomically important traits, such as disease resistance and fruit traits, with high mapping resolution. The molecular markers for these QTL represent a useful resource for enhancing selection efficiency via marker-assisted selection (MAS) in vegetable breeding programs. In this review, we discuss current genomic resources and marker-trait association analysis to facilitate genome-assisted breeding in vegetable species in the Solanaceae and Cucurbitaceae families.

• Genomics & Informatics
• /
• v.7 no.1
• /
• pp.38-40
• /
• 2009

The EST Knowledge Integrated System, EKIS (http://ekis.kribb.re.kr), was established as a part of Korea's Ministry of Education, Science and Technology initiative for genome sequencing and application research of the biological model organisms (GEAR) project. The goals of the EKIS are to collect EST information from GEAR projects and make an integrated database to provide transcriptomic and metabolomic information for biological scientists. The EKIS constitutes five independent categories and several retrieval systems in each category for incorporating massive EST data from high-throughput sequencing of 65 different species. Through the EKIS database, scientists can freely access information including BLAST functional annotation as well as Genechip and pathway information for KEGG. By integrating complex data into a framework of existing EST knowledge information, the EKIS provides new insights into specialized metabolic pathway information for an applied industrial material.

• Molecules and Cells
• /
• v.38 no.6
• /
• pp.475-481
• /
• 2015

Programmable nucleases, which include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and RNA-guided engineered nucleases (RGENs) repurposed from the type II clustered, regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system are now widely used for genome editing in higher eukaryotic cells and whole organisms, revolutionising almost every discipline in biological research, medicine, and biotechnology. All of these nucleases, however, induce off-target mutations at sites homologous in sequence with on-target sites, limiting their utility in many applications including gene or cell therapy. In this review, we compare methods for detecting nuclease off-target mutations. We also review methods for profiling genome-wide off-target effects and discuss how to reduce or avoid off-target mutations.

• Genomics & Informatics
• /
• v.5 no.4
• /
• pp.194-195
• /
• 2007

We have constructed the Rice Genome Information Service System (RGISS), which is an information service system of the Oryza sativa L. ssp. japonica (rice) genome, using the released version of rice Build 3.0 pseudomolecules based on the Ensembl architecture. The nonredundant library, composed of 3,360 clones of BACs, PACs, and fosmids, was used to construct supercontigs. RGISS contains 50,717 annotated genes from GenBank, 56,161 predicted genes from FgeneSH, and information on 9,587 markers, which includes STS, SSR, and EST-based RFLP. The 20,180 ESTs sequenced by the Korea National Institute of Agricultural Biotechnology (NIAB) were aligned and mapped into 168,792 exons. By gene ontology analysis, the classified protein numbers in the rice genome were 6158, 4531, and 12,364 proteins, which were mapped to molecular function, cellular component, and biological process, respectively.