|Yoshizumi Ishino||Last modified date：2019.06.14|
Professor / Molecular Biosciences / Department of Bioscience and Biotechnology / Faculty of Agriculture
|Yoshizumi Ishino||Last modified date：2019.06.14|
|1.||Ishino, Y., Krupovic, M., Forterre, P. , History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology. , Journal of Bacteriology, doi: 10.1128/JB.00580-17., 2018.03, Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in the Escherichia coli genome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparative genomics, structural biology, and advanced biochemistry could then work hand in hand, not only culminating in the explosion of genome editing tools based on CRISPR-Cas9 and other class II CRISPR-Cas systems but also providing insights into the origin and evolution of this system from mobile genetic elements denoted casposons. To celebrate the 30th anniversary of the discovery of CRISPR, this minireview briefly discusses the fascinating history of CRISPR-Cas systems, from the original observation of an enigmatic sequence in E. coli to genome editing in humans.
|2.||Yoshizumi Ishino, Sonoko Iahino, DNA polymerases as useful reagents for biotechnology - the history of developmental research in the field. , 2014.08, DNA polymerase is a ubiquitous enzyme that synthesizes complementary DNA strands according to the template DNA in the living cells. Multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. In addition to their fundamental role in maintaining genome integrity during replication and repair, DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, labeling, mutagenesis, and other experiments. The fundamental ability of DNA polymerases to synthesize a deoxyribonucleotide chain is conserved. However, the more specific properties, including processivity, fidelity (synthesis accuracy), and substrate nucleotide selectivity, differ among the enzymes. The distinctive properties of each DNA polymerase may lead to the potential development of unique reagents, and therefore searching for novel DNA polymerase has been one of the major focuses in this research field. In addition, protein engineering techniques to create mutant or artificial DNA polymerases have been successfully developing powerful DNA polymerases, suitable for specific purposes among the many kinds of DNA manipulations. Thermostable DNA polymerases are especially important for PCR-related techniques in molecular biology. In this review, we summarize the history of the research on developing thermostable DNA polymerases as reagents for genetic manipulation and discuss the future of this research field..|
|3.||Yoshizumi Ishino, Sonoko Iahino, The archaeal DNA replication machinery: past, present and future. , Genes and Genetic Systems, 2013.12, Living organisms are divided into three domains: Bacteria, Archaea, and Eukarya. Whereas Bacteria and Archaea are both prokaryotes, proteins involved in information processes; replication, transcription, and translation, are more similar in Archaea and Eukarya. Here the history of the research on archaeal DNA replication is summarized and the future of the field is discussed..|
|4.||Yoshizumi Ishino, Sonoko Iahino, Molecular evolution of DNA replication machinery approached from the viewpoints of archaea. – Evolutional discussion from the distribution of DNA polymerase –, Viva Origino , 2013.11, DNA replication is a fundamental phenomenon to maintain and transfer of the genetic information in the living organisms. Elucidation of the molecular mechanism of DNA replication has been one of the main subjects since molecular biology started. Most of the research results in the field were obtained from Escherichia coli and its phages in an early stage. Then, research was expanded to the eukaryotic cells, including yeast and mammalian cells. It is now wellrecognized that living organisms are divided into three domains. Archaea, the third domain, different from Bacteria and Eukarya, was joined to the field of DNA replication after two other domains and the research has been active since late 1990’s to present. Comparative studies in the three domains of life provide much useful information to understand the evolution of DNA replication machinery. In this
mini-review article, we will discuss mainly the molecular evolution of DNA polymerase in the living organisms. .
|5.||Ishino, Y. and Ishino, S., Rapid progress of DNA replication studies in Archaea, the third domain of life. , Sci. China, Ser-C Life Sci. , 2012.05, Archaea, the third domain of life, is a very interesting living organism to study from the aspects of molecular and evolutional biology. Archaeal cells have a unicellular ultrastructure without a nucleus, resembling bacterial cells, but the, proteins involved in the genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of Eukaryota. Therefore, the archaeal processes provide useful model systems to understand the more complex mechanisms of genetic information processing in the eukaryotic cells. Moreover, the hyperthermophilic archaea provide very stable proteins, which are especially useful for the isolation of replisomal multicomplexes, to analyze their structures and functions. This review focuses on the history, current status, and future directions of archaeal DNA replication studies..|
|6.||Ishino, S and Ishino, Y., Application of environmental DNA resources to create useful DNA polymerases with different properties., Microorganisms in Sustainable Agriculture and Biotechnology. (Springer Science+Business Media), 2012.01, DNA polymerases use deoxynucleotide triphosphates to synthesize new DNA strands according to the template DNA during DNA replication and repair, and are essential to maintain genome integrity in DNA metabolism. In addition, these enzymes are widely used for genetic engineering techniques, including dideoxy-sequencing, PCR, DNA labeling, mutagenesis, and other in vitro gene manipulations. Thermostable DNA polymerases are especially useful for PCR and cycle-sequencing. We describe in this chapter a powerful strategy to use environmental DNA as a genetic resource to create useful DNA polymerases. The region corresponding to the active center of the DNA polymerizing reaction in the structural gene of well known DNA polymerases, such as Pfu DNA polymerase and Taq DNA polymerase, can be substituted with gene fragments amplified by PCR from DNAs within soil samples from various world-wide locations. The constructed chimeric pol genes can be expressed in E. coli, and the produced chimeric enzymes, possessing DNA polymerase activities with different properties, can be evaluated in terms of their processivity, fidelity, and efficiency of primer usage, to select valuable DNA polymerases for genetic engineering techniques..|
|7.||Nishino, T., Ishino Y., Morikawa, K., Structure-specific DNA nucleases: structural basis for 3D-scissors., Curr. Opin. Struct. Biol., 16巻 1-8ページ, 2006.01.|
|8.||Ishino, Y., Nishino, T., Morikawa, K., Mechanisms of Maintaining Genetic Stability by Homologous Recombination., Chem Rev., 106巻 324-339ページ, 2006.01.|