aBIOTECH最新文献

{"title":"Expanding the range of CRISPR/Cas9-directed genome editing in soybean","authors":"Reqing He,&nbsp;Pengxiang Zhang,&nbsp;Yuchuan Yan,&nbsp;Chen Yu,&nbsp;Liyun Jiang,&nbsp;Youlin Zhu,&nbsp;Dong Wang","doi":"10.1007/s42994-021-00051-4","DOIUrl":"10.1007/s42994-021-00051-4","url":null,"abstract":"<div><p>The CRISPR/Cas9 system has been widely applied for plant genome editing. The commonly used SpCas9 has been shown to rely on the protospacer adjacent motif (PAM) sequences in the canonical form NGG and non-canonical NAG. Although these PAM sequences are extensively distributed across plant genomes, a broader scope of PAM sequence is required to expand the range of genome editing. Here we report the adoption of three variant enzymes, xCas9, SpCas9-NG and XNG-Cas9, to produce targeted mutation in soybean. Sequencing results determined that xCas9 with the NGG and KGA (contains TGA and GGA) PAMs successfully induces genome editing in soybean genome. SpCas9-NG could recognize NGD (contains NGG, NGA and NGT), RGC (contains AGC and GGC), GAA and GAT PAM sites. In addition, XNG-Cas9 was observed to cleave soybean genomic regions with NGG, GAA and AGY (contains AGC and AGT) PAM. Moreover, off-target analyses on soybean editing events induced by SpCas9 and xCas9 indicated that two high-fidelity Cas9 variants including eSpCas9 (enhanced specificity SpCas9) and exCas9 (enhanced specificity xCas9) could improve the specificity of the GGA PAM sequence without reducing on-target editing efficiency. These findings significantly expand the scope of Cas9-mediated genome editing in soybean.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 2","pages":"89 - 98"},"PeriodicalIF":3.6,"publicationDate":"2021-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00051-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9549839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic engineering in woody plants: challenges, advances, and opportunities","authors":"Shu Yu,&nbsp;Cody S. Bekkering,&nbsp;Li Tian","doi":"10.1007/s42994-021-00054-1","DOIUrl":"10.1007/s42994-021-00054-1","url":null,"abstract":"<div><p>Woody plant species represent an invaluable reserve of biochemical diversity to which metabolic engineering can be applied to satisfy the need for commodity and specialty chemicals, pharmaceuticals, and renewable energy. Woody plants are particularly promising for this application due to their low input needs, high biomass, and immeasurable ecosystem services. However, existing challenges have hindered their widespread adoption in metabolic engineering efforts, such as long generation times, large and highly heterozygous genomes, and difficulties in transformation and regeneration. Recent advances in omics approaches, systems biology modeling, and plant transformation and regeneration methods provide effective approaches in overcoming these outstanding challenges. Promises brought by developments in this space are steadily opening the door to widespread metabolic engineering of woody plants to meet the global need for a wide range of sustainably sourced chemicals and materials.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 3","pages":"299 - 313"},"PeriodicalIF":3.6,"publicationDate":"2021-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00054-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9101582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution-aided engineering of plant specialized metabolism","authors":"Mohammad Irfan,&nbsp;Benjamin Chavez,&nbsp;Paride Rizzo,&nbsp;John C. D’Auria,&nbsp;Gaurav D. Moghe","doi":"10.1007/s42994-021-00052-3","DOIUrl":"10.1007/s42994-021-00052-3","url":null,"abstract":"<div><p>The evolution of new traits in living organisms occurs via the processes of mutation, recombination, genetic drift, and selection. These processes that have resulted in the immense biological diversity on our planet are also being employed in metabolic engineering to optimize enzymes and pathways, create new-to-nature reactions, and synthesize complex natural products in heterologous systems. In this review, we discuss two evolution-aided strategies for metabolic engineering—directed evolution, which improves upon existing genetic templates using the evolutionary process, and combinatorial pathway reconstruction, which brings together genes evolved in different organisms into a single heterologous host. We discuss the general principles of these strategies, describe the technologies involved and the molecular traits they influence, provide examples of their use, and discuss the roadblocks that need to be addressed for their wider adoption. A better understanding of these strategies can provide an impetus to research on gene function discovery and biochemical evolution, which is foundational for improved metabolic engineering. These evolution-aided approaches thus have a substantial potential for improving our understanding of plant metabolism in general, for enhancing the production of plant metabolites, and in sustainable agriculture.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 3","pages":"240 - 263"},"PeriodicalIF":3.6,"publicationDate":"2021-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00052-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9094534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reprogramming plant specialized metabolism by manipulating protein kinases","authors":"Ruiqing Lyu,&nbsp;Sanjay K. Singh,&nbsp;Yongliang Liu,&nbsp;Barunava Patra,&nbsp;Yan Zhou,&nbsp;Bingwu Wang,&nbsp;Sitakanta Pattanaik,&nbsp;Ling Yuan","doi":"10.1007/s42994-021-00053-2","DOIUrl":"10.1007/s42994-021-00053-2","url":null,"abstract":"<div><p>Being sessile, plants have evolved sophisticated mechanisms to balance between growth and defense to survive in the harsh environment. The transition from growth to defense is commonly achieved by factors, such as protein kinases (PKs) and transcription factors, that initiate signal transduction and regulate specialized metabolism. Plants produce an array of lineage-specific specialized metabolites for chemical defense and stress tolerance. Some of these molecules are also used by humans as drugs. However, many of these defense-responsive metabolites are toxic to plant cells and inhibitory to growth and development. Plants have, thus, evolved complex regulatory networks to balance the accumulation of the toxic metabolites. Perception of external stimuli is a vital part of the regulatory network. Protein kinase-mediated signaling activates a series of defense responses by phosphorylating the target proteins and translating the stimulus into downstream cellular signaling. As biosynthesis of specialized metabolites is triggered when plants perceive stimuli, a possible connection between PKs and specialized metabolism is well recognized. However, the roles of PKs in plant specialized metabolism have not received much attention until recently. Here, we summarize the recent advances in understanding PKs in plant specialized metabolism. We aim to highlight how the stimulatory signals are transduced, leading to the biosynthesis of corresponding metabolites. We discuss the post-translational regulation of specialized metabolism and provide insights into the mechanisms by which plants respond to the external signals. In addition, we propose possible strategies to increase the production of plant specialized metabolites in biotechnological applications using PKs.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 3","pages":"226 - 239"},"PeriodicalIF":3.6,"publicationDate":"2021-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00053-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9179308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Natural variation and artificial selection of photoperiodic flowering genes and their applications in crop adaptation","authors":"Xiaoya Lin,&nbsp;Chao Fang,&nbsp;Baohui Liu,&nbsp;Fanjiang Kong","doi":"10.1007/s42994-021-00039-0","DOIUrl":"10.1007/s42994-021-00039-0","url":null,"abstract":"<div><p>Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information. Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment. The domestication of plants into crops, and later crop expansion and improvement, has often involved selection for early flowering. In this review, we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species. The ancestors of rice (<i>Oryza sativa</i>), maize (<i>Zea mays</i>), soybean (<i>Glycine max</i>), and tomato (<i>Solanum lycopersicum</i>) are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas. Wheat (<i>Triticum aestivum</i>) and barley (<i>Hordeum vulgare</i>) are long-day crops whose photosensitivity is influenced by both latitude and vernalization type. Here, we summarize recent studies about where these crops were domesticated, how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions, and how allelic variants of photoperiodic flowering genes were selected during this process. A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 2","pages":"156 - 169"},"PeriodicalIF":3.6,"publicationDate":"2021-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00039-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9462833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CSCS: a chromatin state interface for Chinese Spring bread wheat","authors":"Xiaojuan Ran,&nbsp;Tengfei Tang,&nbsp;Meiyue Wang,&nbsp;Luhuan Ye,&nbsp;Yili Zhuang,&nbsp;Fei Zhao,&nbsp;Yijing Zhang","doi":"10.1007/s42994-021-00048-z","DOIUrl":"10.1007/s42994-021-00048-z","url":null,"abstract":"<div><p>A chromosome-level genome assembly of the bread wheat variety Chinese Spring (CS) has recently been published. Genome-wide identification of regulatory elements (REs) responsible for regulating gene activity is key to further mechanistic studies. Because epigenetic activity can reflect RE activity, defining chromatin states based on epigenomic features is an effective way to detect REs. Here, we present the web-based platform Chinese Spring chromatin state (CSCS), which provides CS chromatin signature information. CSCS includes 15 recently published epigenomic data sets including open chromatin and major chromatin marks, which are further partitioned into 15 distinct chromatin states. CSCS curates detailed information about these chromatin states, with trained self-organization mapping (SOM) for segments in all chromatin states and JBrowse visualization for genomic regions or genes. Motif analysis for genomic regions or genes, GO analysis for genes and SOM analysis for new epigenomic data sets are also integrated into CSCS. In summary, the CSCS database contains the combinatorial patterns of chromatin signatures in wheat and facilitates the detection of functional elements and further clarification of regulatory activities. We illustrate how CSCS enables biological insights using one example, demonstrating that CSCS is a highly useful resource for intensive data mining. CSCS is available at http://bioinfo.cemps.ac.cn/CSCS/.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 4","pages":"357 - 364"},"PeriodicalIF":3.6,"publicationDate":"2021-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00048-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9096199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant geranylgeranyl diphosphate synthases: every (gene) family has a story","authors":"M. Victoria Barja,&nbsp;Manuel Rodriguez-Concepcion","doi":"10.1007/s42994-021-00050-5","DOIUrl":"10.1007/s42994-021-00050-5","url":null,"abstract":"<div><p>Plant isoprenoids (also known as terpenes or terpenoids) are a wide family of primary and secondary metabolites with multiple functions. In particular, most photosynthesis-related isoprenoids (including carotenoids and chlorophylls) as well as diterpenes and polyterpenes derive from geranylgeranyl diphosphate (GGPP) produced by GGPP synthase (GGPPS) enzymes in several cell compartments. Plant genomes typically harbor multiple copies of differentially expressed genes encoding GGPPS-like proteins. While sequence comparisons allow to identify potential GGPPS candidates, experimental evidence is required to ascertain their enzymatic activity and biological function. Actually, functional analyses of the full set of potential GGPPS paralogs are only available for a handful of plant species. Here we review our current knowledge on the GGPPS families of the model plant <i>Arabidopsis thaliana</i> and the crop species rice (<i>Oryza sativa</i>), pepper (<i>Capsicum annuum</i>) and tomato (<i>Solanum lycopersicum</i>). The results indicate that a major determinant of the biological role of particular GGPPS paralogs is the expression profile of the corresponding genes even though specific interactions with other proteins (including GGPP-consuming enzymes) might also contribute to subfunctionalization. In some species, however, a single GGPPS isoforms appears to be responsible for the production of most if not all GGPP required for cell functions. Deciphering the mechanisms regulating GGPPS activity in particular cell compartments, tissues, organs and plant species will be very useful for future metabolic engineering approaches aimed to manipulate the accumulation of particular GGPP-derived products of interest without negatively impacting the levels of other isoprenoids required to sustain essential cell functions.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 3","pages":"289 - 298"},"PeriodicalIF":3.6,"publicationDate":"2021-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00050-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9096191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optogenetic tools controlled by ultraviolet-B light","authors":"Xinhao Ouyang,&nbsp;Hui Ren,&nbsp;Xi Huang","doi":"10.1007/s42994-021-00049-y","DOIUrl":"10.1007/s42994-021-00049-y","url":null,"abstract":"<div><p>Decades of genetic, molecular and biochemical studies in plants have provided foundational knowledge about light sensory proteins and led to their application in synthetic biology. Optogenetic tools take advantage of the light switchable activity of plant photoreceptors to control intracellular signaling pathways. The recent discovery of the UV-B photoreceptor UV RESISTANCE LOCUS 8 in the model plant <i>Arabidopsis thaliana</i> opens up new avenues for light-controllable methodologies. In this review, we discuss current developments in optogenetic control by UV-B light and its signaling components, as well as rational considerations in the design and applications of UV-B-based optogenetic tools.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 2","pages":"170 - 175"},"PeriodicalIF":3.6,"publicationDate":"2021-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00049-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9088391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Arabidopsis seeds","authors":"Tianhu Sun,&nbsp;Qinlong Zhu,&nbsp;Ziqing Wei,&nbsp;Lauren A. Owens,&nbsp;Tara Fish,&nbsp;Hyojin Kim,&nbsp;Theodore W. Thannhauser,&nbsp;Edgar B. Cahoon,&nbsp;Li Li","doi":"10.1007/s42994-021-00046-1","DOIUrl":"10.1007/s42994-021-00046-1","url":null,"abstract":"<div><p>Staple grains with low levels of provitamin A carotenoids contribute to the global prevalence of vitamin A deficiency and therefore are the main targets for provitamin A biofortification. However, carotenoid stability during both seed maturation and postharvest storage is a serious concern for the full benefits of carotenoid biofortified grains. In this study, we utilized Arabidopsis as a model to establish carotenoid biofortification strategies in seeds. We discovered that manipulation of carotenoid biosynthetic activity by seed-specific expression of <i>Phytoene synthase</i> (<i>PSY</i>) increases both provitamin A and total carotenoid levels but the increased carotenoids are prone to degradation during seed maturation and storage, consistent with previous studies of provitamin A biofortified grains. In contrast, stacking with <i>Orange</i> (<i>OR</i>^<i>His</i>), a gene that initiates chromoplast biogenesis, dramatically enhances provitamin A and total carotenoid content and stability. Up to 65- and 10-fold increases of β-carotene and total carotenoids, respectively, with provitamin A carotenoids composing over 63% were observed in the seeds containing <i>OR</i>^<i>His</i> and <i>PSY</i>. Co-expression of <i>Homogentisate geranylgeranyl transferase</i> (<i>HGGT</i>) with <i>OR</i>^<i>His</i> and <i>PSY</i> further increases carotenoid accumulation and stability during seed maturation and storage. Moreover, knocking-out of <i>β-carotene hydroxylase 2</i> (<i>BCH2</i>) by CRISPR/Cas9 not only potentially facilitates β-carotene accumulation but also minimizes the negative effect of carotenoid over production on seed germination. Our findings provide new insights into various processes on carotenoid accumulation and stability in seeds and establish a multiplexed strategy to simultaneously target carotenoid biosynthesis, turnover, and stable storage for carotenoid biofortification in crop seeds.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 3","pages":"191 - 214"},"PeriodicalIF":3.6,"publicationDate":"2021-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00046-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9096190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wheat speciation and adaptation: perspectives from reticulate evolution","authors":"Xuebo Zhao,&nbsp;Xiangdong Fu,&nbsp;Changbin Yin,&nbsp;Fei Lu","doi":"10.1007/s42994-021-00047-0","DOIUrl":"10.1007/s42994-021-00047-0","url":null,"abstract":"<div><p>Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (<i>Triticum aestivum</i> subsp. <i>aestivum</i>) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera <i>Triticum</i> and <i>Aegilops</i>. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of <i>Triticum</i> species should be beneficial to future genetic study and breeding of bread wheat.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"2 4","pages":"386 - 402"},"PeriodicalIF":3.6,"publicationDate":"2021-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42994-021-00047-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9101590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}