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Yang, Xiaohan

Publications and source records attributed to Yang, Xiaohan.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Phylogeny and Expression Atlas of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Agave

Agave species are widely cultivated crassulacean acid metabolism (CAM) plants for alcoholic beverages, food and fiber production. Among these, the Agave hybrid H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for sisal fiber in the tropical areas of Brazil, China, and African countries. The plants of Agave hybrid H11648 have a long life cycle and large leaves, which require a huge amount of nitrogen nutrient. However, the molecular basis of nitrogen transport and allocation has not been well understood in agave. In this study, we identified 19 NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY(NPF) genes (called AhNPFs) with full-length coding sequences in Agave hybrid H11648. Our analysis of gene expression in various types of tissues revealed the tissue-specific expression pattern of AhNPFs. We further examined their expression patterns at different leaf developmental stages, under abiotic/biotic stresses and nutrient deficiency. The results reveal several candidate regulators in the agave NPF family, including AhNPF4.3/5.2/7.1. We first characterized the NPF genes in agave based on published leaf transcriptome datasets and emphasized their potential functions. The study will benefit future studies related to nitrogen nutrient in agave.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Editorial: Wood Development and Physiology in a Changing Climate

Wood of forest trees is a renewable, sustainable and easily workable material and has been widely used in construction, paper making, furniture, and as a feedstock for biofuels. Wood formation is the result of a highly ordered and finely regulated process. Secondary xylem (wood) and phloem are the inner and outer derivative products of the vascular cambium, respectively. Xylem is mainly composed of dead cells with thickened cell walls rich in cellulose, hemicelluloses, and lignin, which are responsible for providing mechanical support and conducting water and minerals for the trees. Phloem transports photoassimilates and signaling molecules, including phytohormones and peptides. Wood structure varies greatly between, and within, tree species. A thorough understanding of developmental processes and metabolic pathways during wood formation would provide a basis for improving wood biomass and modifying properties in forest trees.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Reporter genes confer new-to-nature ornamental traits in plants

Ornamental plants (trees, shrubs, and herbs) beautify our urban and rural environments, enrich the quality of human life, and represent a vital component of the horticultural industry. The introduction of novel plant varieties and cultivars is critical to the ornamental horticultural industry [1]. To develop ornamental plants with desirable traits, different approaches, such as ploidy manipulation, interspecific hybridization, and physical/chemical mutagenesis, have been used for decades [2, 3]. However, the breeding of new ornamental varieties of trees and shrubs is a time- and labor-consuming process, because these plants may have a long juvenile growth period, large physical size, or altered floral structures, and consequently require long-term observations, large areas for progeny testing, and/or special equipment for pollination and/or seed collection [4].

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

A grand challenge facing society is climate change caused mainly by rising CO 2 concentration in Earth’s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO 2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO 2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO 2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Biological Carbon Sequestration for Climate and Soil Health

The United States recently launched the Net Zero World Initiative on decarbonization. As temperatures and sea levels rise, strong action is needed to mitigate high atmospheric CO2 levels. In response to this need, a joint workshop between the US Department of Energy’s Oak Ridge National Laboratory (ORNL) and Lawrence Berkeley National Laboratory (LBNL) was convened to assess the challenges and opportunities within biological carbon (C) capture.

58 GEOSCIENCES↗
DOE OSTI2021

Biological Carbon Sequestration for Climate and Soil Health

The United States recently launched the Net Zero World Initiative on decarbonization. As temperatures and sea levels rise, strong action is needed to mitigate high atmospheric CO 2 levels. In response to this need, a joint workshop between the US Department of Energy’s Oak Ridge National Laboratory (ORNL) and Lawrence Berkeley National Laboratory (LBNL) was convened to assess the challenges and opportunities within biological carbon (C) capture. The virtual workshop on Biological Carbon Sequestration for Climate and Soil Health focused on three aspects of biological C capture research: natural systems, engineered systems, and modeling. For this workshop, the scope of natural systems included unmanaged (e.g., grasslands, wetlands, natural forests) and managed (e.g., agricultural lands, commercial forests, forest biofuels) ecosystems. The engineered systems group covered topics in genetically modified plants and microbes, synthetic microbiomes, and altered plant–microbe interactions for enhancing C capture, storage, and utilization. The modeling group focused on computational tools and data collection to predict and assess the effectiveness of new biocarbon sequestration advances. Participant expertise included plant and microbial systems biology, synthetic biology, soil biogeochemistry, and techno-economic analysis. Together, participants outlined key scientific advances in support of biological C capture and storage. Among the major findings of the meeting were the need to better measure C flux within natural, agricultural, and fabricated ecosystems for experimentation; better understand the role of soil composition, plant roots, and the rhizosphere (i.e., the soil surrounding the plant root) in the underground storage of organic C; and design plant–microbe systems for maximal C storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Temporal dynamics of protein and post-translational modification abundances in Populus leaf across a diurnal period

Populus spp. are dedicated woody biomass feedstocks for advanced biofuels and bioproducts. Proper growth and fitness of poplar as a sustainable feedstock depends on timely perception and response to environmental signals (e.g., light, temperature, water). Poplar leaves, like other C3 photosynthesis plants, have evolved oscillating or circadian rhythms that play important roles in synchronizing biological processes with external cues. To characterize this phenomenon at a molecular level, we employed bottom-up proteomics using high-resolution mass spectrometry and de novo-assisted database searching to identify abundance changes in proteins and post-translational modifications in poplar leaf tissue sampled across a 12/12-hour light/dark diurnal period.

09 BIOMASS FUELS↗
DOE OSTI2021

Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi

The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Construct design for CRISPR/Cas-based genome editing in plants

CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Recent Advances in the Roles of HSFs and HSPs in Heat Stress Response in Woody Plants

A continuous increase in ambient temperature caused by global warming has been considered a worldwide threat. As sessile organisms, plants have evolved sophisticated heat shock response (HSR) to respond to elevated temperatures and other abiotic stresses, thereby minimizing damage and ensuring the protection of cellular homeostasis. In particular, for perennial trees, HSR is crucial for their long life cycle and development. HSR is a cell stress response that increases the number of chaperones including heat shock proteins (HSPs) to counter the negative effects on proteins caused by heat and other stresses. There are a large number of HSPs in plants, and their expression is directly regulated by a series of heat shock transcription factors (HSFs). Therefore, understanding the detailed molecular mechanisms of woody plants in response to extreme temperature is critical for exploring how woody species will be affected by climate changes. In this review article, we summarize the latest findings of the role of HSFs and HSPs in the HSR of woody species and discuss their regulatory networks and cross talk in HSR. In addition, strategies and programs for future research studies on the functions of HSFs and HSPs in the HSR of woody species are also proposed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genes for enhancing drought and heat tolerance in plants and methods of use

The present disclosure provides methods for increasing drought resistance and heat resistance of a plant. The methods encompass expression of at least one heat shock protein (HSP) from the group consisting of HSP40, HSP60 or HSP70 together with a phosphoenolpyruvate carboxylase (PEPC) comprising an aspartic acid (D) at a position that corresponds to the position 509 of SEQ ID NO: 4, in the plant. In comparison to a plant not manipulated in this manner, the disclosed, genetically-modified, plants display improved drought resistance and heat resistance. Also provided are plants that can be obtained by the method according to the invention, and nucleic acid vectors to be used in the described methods.

Yang, Xiaohan↗
DOE OSTI2021

Transcriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnieriana

Crassulacean acid metabolism (CAM) is an important photosynthetic pathway for plant adaptation to dry environments. CAM plants feature a coordinated interaction between mesophyll and epidermis functions that involves refined regulations of gene expression. Plant microRNAs (miRNAs) are crucial post-transcription regulators of gene expression, however, their roles underlying the CAM pathway remain poorly investigated. Here, we present a study characterizing the expression of miRNAs in an obligate CAM species Kalanchoë marnieriana. Through sequencing of transcriptome and degradome in mesophyll and epidermal tissues under the drought treatments, we identified differentially expressed miRNAs that were potentially involved in the regulation of CAM. In total, we obtained 84 miRNA genes, and eight of them were determined to be Kalanchoë-specific miRNAs. It is widely accepted that CAM pathway is regulated by circadian clock. We showed that miR530 was substantially downregulated in epidermal peels under drought conditions; miR530 targeted two tandem zinc knuckle/PLU3 domain encoding genes (TZPs) that were potentially involved in light signaling and circadian clock pathways. Our work suggests that the miR530-TZPs module might play a role of regulating CAM-related gene expression in Kalanchoë.

Kalanchoë↗
DOE OSTI2021

Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant–microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biosystems Design to Accelerate C 3 -to-CAM Progression

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.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Reconfiguring Plant Metabolism for Biodegradable Plastic Production

For decades, plants have been the subject of genetic engineering to synthesize novel, value-added compounds. Polyhydroxyalkanoates (PHAs), a large class of biodegradable biopolymers naturally synthesized in eubacteria, are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic pathways. It was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic wastes. However, after three decades of effort synthesizing PHAs, and in particular the simplest form polyhydroxybutyrate (PHB), and seeking to improve their production in plants, it has proven very difficult to reach a commercially profitable rate in a normally growing plant. This seems to be due to the growth defects associated with PHA production and accumulation in plant cells. Here, we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been encountered. Then, from the point of view of plant synthetic biology, we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production, with the goal of maximizing PHA yield while minimizing growth inhibition. Specifically, we suggest genetic elements that can be considered in genetic circuit design, approaches for nuclear genome and plastome modification, and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.

59 BASIC BIOLOGICAL SCIENCES↗