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1. Advancing Crop Transformation in the Era of Genome Editing

   https://doi.org/10.1105/tpc.16.00196  

   Altpeter, F.; Springer, N.M.; Bartley, L.E.; Blechl, A.E.; Brutnell, T.P.; Citovsky, V.; Conrad, L.J.; Gelvin, S.B.; Jackson, D.P.; Kausch, A.P.; et al (July 2016, The Plant cell)

   Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than thirty years of technological advances. Genome editing provides new opportunities to enhance crop productivity, but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Herein we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimize time in culture. Currently, specialized facilities exist for crop transformation. Single cell and robotic techniques should be developed for high throughput genomic screens. Utilization of plant genes involved in developmental reprogramming, wound response, and/or homologous recombination could boost recovery of transformed plants. Engineering universal Agrobacterium strains and recruitment of other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. 

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2. Nanotechnology Approaches for Chloroplast Biotechnology Advancements

   https://doi.org/10.3389/fpls.2021.691295  

   Newkirk, Gregory M.; de Allende, Pedro; Jinkerson, Robert E.; Giraldo, Juan Pablo (July 2021, Frontiers in Plant Science)

   Photosynthetic organisms are sources of sustainable foods, renewable biofuels, novel biopharmaceuticals, and next-generation biomaterials essential for modern society. Efforts to improve the yield, variety, and sustainability of products dependent on chloroplasts are limited by the need for biotechnological approaches for high-throughput chloroplast transformation, monitoring chloroplast function, and engineering photosynthesis across diverse plant species. The use of nanotechnology has emerged as a novel approach to overcome some of these limitations. Nanotechnology is enabling advances in the targeted delivery of chemicals and genetic elements to chloroplasts, nanosensors for chloroplast biomolecules, and nanotherapeutics for enhancing chloroplast performance. Nanotechnology-mediated delivery of DNA to the chloroplast has the potential to revolutionize chloroplast synthetic biology by allowing transgenes, or even synthesized DNA libraries, to be delivered to a variety of photosynthetic species. Crop yield improvements could be enabled by nanomaterials that enhance photosynthesis, increase tolerance to stresses, and act as nanosensors for biomolecules associated with chloroplast function. Engineering isolated chloroplasts through nanotechnology and synthetic biology approaches are leading to a new generation of plant-based biomaterials able to self-repair using abundant CO 2 and water sources and are powered by renewable sunlight energy. Current knowledge gaps of nanotechnology-enabled approaches for chloroplast biotechnology include precise mechanisms for entry into plant cells and organelles, limited understanding about nanoparticle-based chloroplast transformations, and the translation of lab-based nanotechnology tools to the agricultural field with crop plants. Future research in chloroplast biotechnology mediated by the merging of synthetic biology and nanotechnology approaches can yield tools for precise control and monitoring of chloroplast function in vivo and ex vivo across diverse plant species, allowing increased plant productivity and turning plants into widely available sustainable technologies. 

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3. Systems Biology Applications in Revealing Plant Defense Mechanisms in Disease Triangle

   https://doi.org/10.3390/ijms26157318  

   Akter, Tahmina; Maqsood, Hajra; Castilla, Nicholas; Song, Wenyuan; Chen, Sixue (August 2025, International Journal of Molecular Sciences)

   Plant diseases resulting from pathogens and pests constitute a persistent threat to global food security. Pathogenic infections of plants are influenced by environmental factors; a concept encapsulated in the “disease triangle” model. It is important to elucidate the complex molecular mechanisms underlying the interactions among plants, their pathogens and various environmental factors in the disease triangle. This review aims to highlight recent advancements in the application of systems biology to enhance understanding of the plant disease triangle within the context of microbiome rising to become the 4th dimension. Recent progress in microbiome research utilizing model plant species has begun to illuminate the roles of specific microorganisms and the mechanisms of plant–microbial interactions. We will examine (1) microbiome-mediated functions related to plant growth and protection, (2) advancements in systems biology, (3) current -omics methodologies and new approaches, and (4) challenges and future perspectives regarding the exploitation of plant defense mechanisms via microbiomes. It is posited that systems biology approaches such as single-cell RNA sequencing and mass spectrometry-based multi-omics can decode plant defense mechanisms. Progress in this significant area of plant biology has the potential to inform rational crop engineering and breeding strategies aimed at enhancing disease resistance without compromising other pathways that affect crop yield. 

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4. Biosystems Design to Accelerate C ₃ -to-CAM Progression

   https://doi.org/10.34133/2020/3686791  

   Yuan, Guoliang; Hassan, Md. Mahmudul; Liu, Degao; Lim, Sung Don; Yim, Won Cheol; Cushman, John C.; Markel, Kasey; Shih, Patrick M.; Lu, Haiwei; Weston, David J.; et al (October 2020, BioDesign Research)

   Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C 3 or C 4 photosynthesis. CAM plants are derived from C 3 photosynthesis ancestors. However, it is extremely unlikely that the C 3 or C 4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C 3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C 3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C 3 -to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C 3 -to-CAM transition in plants using synthetic biology toolboxes. 

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5. Evolutionary History of Plant Metabolism

   https://doi.org/10.1146/annurev-arplant-080620-031054  

   Maeda, Hiroshi A.; Fernie, Alisdair R. (May 2021, Annual Review of Plant Biology)

   null (Ed.)

   Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO 2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore underlying evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. 

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