Nature Plants，NBT同一天发表5篇中国学者在植物科学领域取得的重要进展

植物科学最前沿

6月29日，著名Nature子刊Nature Biotechnology 和Nature Plants在线发表6篇植物科学领域的重要研究进展，值得一提的是其中5篇由中国学者完成。6篇文章中3篇为基因组编辑领域的新突破。具体内容如下：

1.中国科学院遗传与发育研究所高彩霞团队发表在Nature Biotechnology的题为“Precise, predictable multi-nucleotide deletions in rice and wheat using APOBEC–Cas9”的研究论文，建立新型可预测多核苷酸删除基因组编辑系统。

该研究组基于胞嘧啶脱氨以及碱基切除修复（Base Excision Repair, BER）原理，首次将野生型SpCas9与胞嘧啶脱氨酶APOBEC、尿嘧啶糖基化酶(UDG)以及无嘌呤嘧啶位点裂合酶（AP lyase）组合，建立了新型的多核苷酸靶向删除系统（APOBEC-Cas9 fusion-induced deletion systems, AFIDs），并成功在水稻和小麦基因组中实现了精准、可预测的多核苷酸删除。考虑植物细胞本身存在BER体系，该研究组首先利用高脱氨活性的APOBEC3A脱氨酶构建出3种形式的AFID系统（AFID-1~3），并在水稻和小麦细胞中对多个内源DNA靶点进行测试，结果显示AFID-3介导的删除效率高达33.1%, 且产生从不同的5’-胞嘧啶到Cas9切割位点间的多核苷酸删除，可预测的删除比例高达30%以上。研究人员进一步对不同胞嘧啶脱氨酶进行筛选，发现截断的APOBEC3B脱氨酶（A3Bctd）不仅有较高的脱氨活性，同时还具有一个更窄的脱氨窗口。将A3Bctd替换AFID-3系统中的A3A，从而开发出eAFID-3系统。eAFID-3更高效地介导从偏好TC基序的脱氨位点到Cas9 切割位点之间的可预测删除，效率是AFID-3的1.5倍。此外，研究组利用AFID-3系统靶向水稻OsSWEET14基因启动子上的效应子结合元件，获得了多核苷酸删除的突变体植株，经白叶枯病接种试验发现：相较于1~2 bp的插入缺失，该系统产生的多核苷酸删除水稻突变体对白叶枯病菌的抗性更强。

第二篇为浙江大学李正和教授团队题为“Highly efficient DNA-free plant genome editing using virally delivered CRISPR–Cas9”，在病毒介导的基因组编辑技术领域取得重要突破。

Here we report the engineering of a plant negative-strand RNA virus-based vector for DNA-free in planta delivery of the entire CRISPR–Cas9 cassette to achieve single, multiplex mutagenesis and chromosome deletions at high frequency in a model allotetraploid tobacco host. Over 90% of plants regenerated from virus-infected tissues without selection contained targeted mutations, among which up to 57% carried tetra-allelic, inheritable mutations. The viral vector remained stable even after mechanical transmission, and can readily be eliminated from mutated plants during regeneration or after seed setting. Despite high on-target activities, off-target effects, if any, are minimal. Our study provides a convenient, highly efficient and cost-effective approach for CRISPR–Cas9 gene editing in plants through virus infection.

第三篇为芬兰赫尔辛基大学Ari Pekka Mähönen团队题为“An inducible genome editing system for plants”的研究论文，发布了一种可诱导的基因组编辑系统，值得一提的是该论文的第一作者为中国学者。

Here, we present a new tool with which target genes can efficiently and conditionally be knocked out by genome editing at any developmental stage. Target genes can also be knocked out in a cell-type-specific manner. Our tool is easy to construct and will be particularly useful for studying genes having null alleles that are non-viable or show pleiotropic developmental defects.

第四篇和第五篇分别来自加州大学Yangnan Gu团队发表的题为“Global profiling of plant nuclear membrane proteome in Arabidopsis”的研究论文和Sheng Luan团队题为“Calcium spikes, waves and oscillations in plant development and biotic interactions”的综述性论文。

Abstract

The nuclear envelope (NE) is structurally and functionally vital for eukaryotic cells, yet its protein constituents and their functions are poorly understood in plants. Here, we combined subtractive proteomics and proximity-labelling technology coupled with quantitative mass spectrometry to understand the landscape of NE membrane proteins in Arabidopsis. We identified ~200 potential candidates for plant NE transmembrane (PNET) proteins, which unravelled the compositional diversity and uniqueness of the plant NE. One of the candidates, named PNET1, is a homologue of human TMEM209, a critical driver for lung cancer. A functional investigation revealed that PNET1 is a bona fide nucleoporin in plants. It displays both physical and genetic interactions with the nuclear pore complex (NPC) and is essential for embryo development and reproduction in different NPC contexts. Our study substantially enlarges the plant NE proteome and sheds new light on the membrane composition and function of the NPC.

Abstract

The calcium ion (Ca2+) is a universal signal in all eukaryotic cells. A fundamental question is how Ca2+, a simple cation, encodes complex information with high specificity. Extensive research has established a two-step process (encoding and decoding) that governs the specificity of Ca2+ signals. While the encoding mechanism entails a complex array of channels and transporters, the decoding process features a number of Ca2+ sensors and effectors that convert Ca2+ signals into cellular effects. Along this general paradigm, some signalling components may be highly conserved, but others are divergent among different organisms. In plant cells, Ca2+ participates in numerous signalling processes, and here we focus on the latest discoveries on Ca2+-encoding mechanisms in development and biotic interactions. In particular, we use examples such as polarized cell growth of pollen tube and root hair in which tip-focused Ca2+ oscillations specify the signalling events for rapid cell elongation. In plant–microbe interactions, Ca2+ spiking and oscillations hold the key to signalling specificity: while pathogens elicit cytoplasmic spiking, symbiotic microorganisms trigger nuclear Ca2+ oscillations. Herbivore attacks or mechanical wounding can trigger Ca2+ waves traveling a long distance to transmit and convert the local signal to a systemic defence program in the whole plant. What channels and transporters work together to carve out the spatial and temporal patterns of the Ca2+ fluctuations? This question has remained enigmatic for decades until recent studies uncovered Ca2+ channels that orchestrate specific Ca2+ signatures in each of these processes. Future work will further expand the toolkit for Ca2+-encoding mechanisms and place Ca2+ signalling steps into larger signalling networks.

第六篇论文为法国蒙彼利埃大学Christophe Maurel发表的观点文章，题为“Root architecture and hydraulics converge for acclimation to changing water availability”

Abstract

Because of intense transpiration and growth, the needs of plants for water can be immense. Yet water in the soil is most often heterogeneous if not scarce due to more and more frequent and intense drought episodes. The converse context, flooding, is often associated with marked oxygen deficiency and can also challenge the plant water status. Under our feet, roots achieve an incredible challenge to meet the water demand of the plant’s aerial parts under such dramatically different environmental conditions. For this, they continuously explore the soil, building a highly complex, branched architecture. On shorter time scales, roots keep adjusting their water transport capacity (their so-called hydraulics) locally or globally. While the mechanisms that directly underlie root growth and development as well as tissue hydraulics are being uncovered, the signalling mechanisms that govern their local and systemic adjustments as a function of water availability remain largely unknown. A comprehensive understanding of root architecture and hydraulics as a whole (in other terms, root hydraulic architecture) is needed to apprehend the strategies used by plants to optimize water uptake and possibly improve crops regarding this crucial trait.

链接：

https://www.nature.com/nplants/

https://www.nature.com/nbt/

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