Abscisic acid (ABA) regulates numerous developmental processes and adaptive stress responses in plants. Many ABA signaling components have been identified, but their interconnections and a consensus on the structure of the ABA signaling network have eluded researchers. Recently, several advances have led to the identification of ABA receptors and their three-dimensional structures, and an understanding of how key regulatory phosphatase and kinase activities are controlled by ABA. A new model for ABA action has been proposed and validated, in which the soluble PYR/PYL/RCAR receptors function at the apex of a negative regulatory pathway to directly regulate PP2C phosphatases, which in turn directly regulate SnRK2 kinases. This model unifies many previously defined signaling components and highlights the importance of future work focused on defining the direct targets of SnRK2s and PP2Cs, dissecting the mechanisms of hormone interactions (i.e., cross talk) and defining connections between this new negative regulatory pathway and other factors implicated in ABA signaling.

/pdf/abscisic-acid-emergence-of-a-core-signaling-network-1o69szbfnn.pdf

Abscisic Acid: Emergence of a Core Signaling Network

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Plants respond to survive under water-deficit conditions via a series of physiological, cellular, and molecular processes culminating in stress tolerance. Many drought-inducible genes with various functions have been identified by molecular and genomic analyses in Arabidopsis, rice, and other plants, including a number of transcription factors that regulate stress-inducible gene expression. The products of stress-inducible genes function both in the initial stress response and in establishing plant stress tolerance. In this short review, recent progress resulting from analysis of gene expression during the drought-stress response in plants as well as in elucidating the functions of genes implicated in the stress response and/or stress tolerance are summarized. A description is also provided of how various genes involved in stress tolerance were applied in genetic engineering of dehydration stress tolerance in transgenic Arabidopsis plants.

Gene networks involved in drought stress response and tolerance

Reverse genetics in model organisms such as Drosophila melanogaster, Arabidopsis thaliana, zebrafish and rats, efficient genome engineering in human embryonic stem and induced pluripotent stem cells, targeted integration in crop plants, and HIV resistance in immune cells - this broad range of outcomes has resulted from the application of the same core technology: targeted genome cleavage by engineered, sequence-specific zinc finger nucleases followed by gene modification during subsequent repair. Such 'genome editing' is now established in human cells and a number of model organisms, thus opening the door to a range of new experimental and therapeutic possibilities.

/pdf/genome-editing-with-engineered-zinc-finger-nucleases-3i1sf7uaja.pdf

Genome editing with engineered zinc finger nucleases

Plants respond to survive under water-deficit conditions via a series of physiological, cellular, and molecular processes culminating in stress tolerance. Many drought-inducible genes with various functions have been identified by molecular and genomic analyses in Arabidopsis, rice, and other plants, including a number of transcription factors that regulate stress-inducible gene expression. The products of stress-inducible genes function both in the initial stress response and in establishing plant stress tolerance. In this short review, recent progress resulting from analysis of gene expression during the drought-stress response in plants as well as in elucidating the functions of genes implicated in the stress response and/or stress toler ance are summarized. A description is also provided of how various genes involved in stress tolerance were applied in genetic engineering of dehydration stress tolerance in transgenic Arabidopsis plants.

Gene networks involved in drought stress response and

シロイヌナズナの初期応答脱水ストレス1(erd1)の乾燥誘導発現におけるzfhd1およびnac転写因子の役割

Genome editing has revolutionized plant research and plant breeding by enabling precise genome manipulation. In particular, the application of type II CRISPR-Cas9 systems to genome editing has proved an important milestone, accelerating genetic engineering and the analysis of gene function. On the other hand, the potential of other types of CRISPR-Cas systems, especially many of the most abundant type I CRISPR-Cas systems, remains unexplored. We recently developed a novel genome editing tool, TiD, based on the type I-D CRISPR-Cas system. In this chapter, we describe a protocol for genome editing of plant cells using TiD. This protocol allows the application of TiD to induce short insertion and deletions (indels) or long-range deletions at target sites with high specificity in tomato cells. 

Type I-D CRISPR System-Mediated Genome Editing in Plants.

표적 뉴클레오타이드 서열을 표적화하는 방법으로서, 세포 중에, (i) CRISPR 타입 I-D 관련 단백질 Cas5d, Cas6d 및 Cas7d, 또는 이들 단백질을 인코딩하는 핵산, 및 (ii) 상기 표적 뉴클레오타이드 서열에 상보적인 서열 및 해당 서열의 전후에 CRISPR 유전자자리에서 유래하는 공통 반복 서열을 포함하는 가이드 RNA, 또는 해당 가이드 RNA를 인코딩하는 DNA를 도입하는 것을 포함하는 방법 등이 제공된다.

뉴클레오타이드 표적 인식을 이용한 표적 서열 특이적 개변 기술

Cytokinins (CKs), a class of phytohormones with vital roles in growth and development, occur naturally with various side-chain structures, including N6-(Δ2-isopentenyl)adenine-, cis-zeatin- and trans-zeatin (tZ)-types. Recent studies in a model dicot plant Arabidopsis demonstrated that tZ-type CKs are biosynthesized via cytochrome P450 monooxygenase (P450) CYP735A, and have a specific function in shoot growth promotion. Although the function of some of these CKs has been demonstrated in a few dicotyledonous plant species, the significance of these variations and their biosynthetic mechanism and function in monocots and in plants with distinctive side-chain profiles than Arabidopsis, such as Oryza sativa (rice), remain elusive. In this study, we characterized CYP735A3 and CYP735A4 to investigate the role of tZ-type CKs in rice. Complementation test of the Arabidopsis CYP735A-deficient mutant and CK profiling of loss-of-function rice mutant, cyp735a3 cyp735a4, demonstrated that CYP735A3 and CYP735A4 encode P450s required for tZ-type side-chain modification in rice. CYP735As are expressed in both roots and shoots. The cyp735a3 cyp735a4 mutants exhibited growth retardation concomitant with reduction in CK activity in both roots and shoots, indicating that tZ-type CKs function in growth promotion of both organs. Expression analysis revealed that tZ-type CK biosynthesis is negatively regulated by auxin, abscisic acid, and cytokinin and positively by dual nitrogen nutrient signals, namely glutamine-related and nitrate-specific signals. These results suggest that the physiological role of tZ-type CKs in rice is different from that in Arabidopsis and they control growth of both roots and shoots in response to internal and environmental cues in rice.

/pdf/the-trans-zeatin-type-side-chain-modification-of-cytokinins-18joyfy0.pdf

The trans-zeatin-type side-chain modification of cytokinins controls rice growth

[] Potassium is an essential element in plant growth and has an important role in regulating cell water potential and turgor in osmotic regulation. Potassium content in plants is high compared to trace elements, however, it is difficult to measure a relatively small change of potassium content in the large total. Here, we describe a procedure for measuring potassium in Arabidopsis that is easy to handle in preparative scale and avoids contamination.

/pdf/measurement-of-potassium-content-in-arabidopsis-3v6hzferq9.pdf

Yuriko Osakabe

Papers

シロイヌナズナの初期応答脱水ストレス1(erd1)の乾燥誘導発現におけるzfhd1およびnac転写因子の役割

Type I-D CRISPR System-Mediated Genome Editing in Plants.

뉴클레오타이드 표적 인식을 이용한 표적 서열 특이적 개변 기술

The trans-zeatin-type side-chain modification of cytokinins controls rice growth

Measurement of Potassium Content in Arabidopsis