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Open accessJournal ArticleDOI: 10.1038/S41467-021-21282-5

A molecular switch in sulfur metabolism to reduce arsenic and enrich selenium in rice grain.

02 Mar 2021-Nature Communications (Springer Science and Business Media LLC)-Vol. 12, Iss: 1, pp 1392-1392
Abstract: Rice grains typically contain high levels of toxic arsenic but low levels of the essential micronutrient selenium. Anthropogenic arsenic contamination of paddy soils exacerbates arsenic toxicity in rice crops resulting in substantial yield losses. Here, we report the identification of the gain-of-function arsenite tolerant 1 (astol1) mutant of rice that benefits from enhanced sulfur and selenium assimilation, arsenic tolerance, and decreased arsenic accumulation in grains. The astol1 mutation promotes the physical interaction of the chloroplast-localized O-acetylserine (thiol) lyase protein with its interaction partner serine-acetyltransferase in the cysteine synthase complex. Activation of the serine-acetyltransferase in this complex promotes the uptake of sulfate and selenium and enhances the production of cysteine, glutathione, and phytochelatins, resulting in increased tolerance and decreased translocation of arsenic to grains. Our findings uncover the pivotal sensing-function of the cysteine synthase complex in plastids for optimizing stress resilience and grain quality by regulating a fundamental macronutrient assimilation pathway.

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Journal ArticleDOI: 10.1071/CP21033
Abstract: Widespread distribution, toxicity and exposure through rice and rice-based food products make arsenic (As) contamination of environment a serious issue. This review discusses various strategies that can be utilised to tackle the As problem in rice, and the socioeconomic impacts of the As problem. The countries of south and south-east Asia are renowned as hotspots of As contamination owing to occurrence and enrichment of As in soil and groundwater via natural biogeochemical weathering of rocks and As-enriched sediment. The irrigation of rice is mostly applied through the use of contaminated groundwater leading to high As accumulation in rice grains. The intensification of research to address the problem of As in rice has been seen in the past two decades. It has been realised that appropriate irrigation water management, which acts as a major driver of As chemistry in soil and As uptake and transport in plants, can be an easy and affordable solution. Further, balanced supplement of various nutrient elements like selenium (Se), silicon (Si), sulfur (S), nitrogen (N), iron (Fe) and zinc (Zn) has been found to impart dual benefits in terms of reduced As toxicity as well as enhance the nutritional quality of rice grains. Several other agronomic and biotechnological approaches, processing, and cooking methods of rice were found to have profound impacts on rice As and its speciation from farms to table.

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3 Citations


Open accessJournal ArticleDOI: 10.3390/IJMS22084206
Qier Liu, Fan Yang1, Jingjuan Zhang1, Hang Liu1  +4 moreInstitutions (1)
Abstract: The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.

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3 Citations


Journal ArticleDOI: 10.1016/J.ENVPOL.2021.117987
Jie Zhang1, Ameer Hamza2, Zuoming Xie, Sajad Hussain3  +7 moreInstitutions (7)
Abstract: Arsenic (As) is a ubiquitous metalloid that is highly toxic to all living organisms. When grown in As-contaminated soils, plants may accumulate significant amounts of As in the grains or edible shoot parts which then enter a food chain. Plant growth and development per se are also both affected by arsenic. These effects are traditionally attributed to As-induced accumulation of reactive oxygen species (ROS) and a consequent lipid peroxidation and damage to cellular membranes. However, this view is oversimplified, as As exposure have a major impact on many metabolic processes in plants, including availability of essential nutrients, photosynthesis, carbohydrate metabolism, lipid metabolism, protein metabolism, and sulfur metabolism. This review is aimed to fill this gap in the knowledge. In addition, the molecular basis of arsenic uptake and transport in plants and prospects of creating low As-accumulating crop species, for both agricultural productivity and food safety, are discussed.

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2 Citations


Open accessJournal ArticleDOI: 10.1073/PNAS.2113071118
Abstract: As a postdoc exploring rice paddies in Cambodia in 2011, Angelia Seyfferth was struck by the towering mounds of husks piling up outside rice mills. Rice husks, the hard outer layer that encloses each grain, are a byproduct of rice production. “It is often considered a waste product that farmers are trying to get rid of,” explains Seyfferth, now a soil biogeochemist at the University of Delaware in Newark. Maybe, she thought at the time, she could use a key nutrient in these discarded husks to help address a global health problem: arsenic contamination in the rice itself. Working as a postdoc in Cambodia in 2011, soil biogeochemist Angelia Seyfferth wondered whether the towering mounds of husks piling up outside rice mills could help mitigate arsenic contamination in rice. Image credit: Angelia Seyfferth. Arsenic, a pollutant stemming from industrial processes and pesticides, also naturally occurs in soil and groundwater in regions across the globe. In its inorganic form, it’s highly toxic, with chronic exposure raising the risk for a host of health conditions, including diabetes, cardiovascular diseases, and cancers (1). Drinking water is often a major exposure route. But in the early 2000s, researchers discovered that rice, a staple food for more than half the global population, can also contain arsenic (2). In 2012, a Consumer Reports analysis raised public awareness of the issue by showing that nearly all of 65 types of rice and rice products tested contained arsenic—many of them at concerning levels (3). In 2020, a team of researchers in the United Kingdom found that of 55 samples of commercial rice sold in the UK, more than half exceeded the European Commission’s limit for inorganic arsenic levels suitable for infant food or direct feeding to infants (4). Although the US Food and Drug Administration (FDA) has …

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2 Citations


Journal ArticleDOI: 10.1016/J.ENVPOL.2021.118029
Aarifa Nabi1, M. Naeem1, Tariq Aftab1, M. Masroor A. Khan1  +1 moreInstitutions (2)
Abstract: Arsenic (As) is recognized as a toxic metalloid and a severe threat to biodiversity due to its contamination. Soil and groundwater contamination with this metalloid has become a major concern. Large fractions of cultivable lands are becoming infertile gradually due to the irrigation of As contaminated water released from various sources. The toxicity of As causes the generation of free radicals, which are harmful to cellular metabolism and functions of plants. It alters the growth, metabolic, physiological, and molecular functions of the plants due to oxidative burst. Plants employ different signaling mechanisms to face the As toxicity like phosphate cascade, MAPK (Mitogen-Activated Protein Kinase), Ca-calmodulin, hormones, and ROS-signaling. The toxicity of As may significantly be reduced through various remediation techniques. Among them, the microbial-assisted remediation technique is cost-effective and eco-friendly. It breaks down the metalloid into less harmful species through various processes viz. biovolatilization, biomethylation, and transformation. Moreover, the adaptation strategies towards As toxicity are vacuolar sequestration, involvement of plant defense mechanism, and restricting its uptake from plant roots to above-ground parts. The speciation, uptake, transport, metabolism, ion dynamics, signaling pathways, crosstalk with phytohormones and gaseous molecules, as well as harmful impacts of the As on physiological processes, overall development of plants and remediation techniques are summarized in this review.

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Topics: Arsenic toxicity (52%)

2 Citations


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66 results found


Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTP324
Heng Li1, Richard Durbin1Institutions (1)
01 Jul 2009-Bioinformatics
Abstract: Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: [email protected]

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Topics: Hybrid genome assembly (54%), Sequence assembly (53%), 2 base encoding (52%) ... read more

35,234 Citations


Open accessJournal ArticleDOI: 10.1101/GR.107524.110
Aaron McKenna1, Matthew Hanna, Eric Banks, Andrey Sivachenko  +7 moreInstitutions (1)
01 Sep 2010-Genome Research
Abstract: Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

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Topics: Variant Call Format (52%), Software framework (50%)

16,404 Citations


Open accessJournal ArticleDOI: 10.1110/PS.8.5.978
01 Jan 1999-Protein Science
Abstract: We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross-validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif-finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within +/-2 residues from the cleavage sites given in SWISS-PROT. An analysis of 715 Arabidopsis thaliana sequences from SWISS-PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome-wide sequence data. The ChloroP predictor is available as a web-server at http://www.cbs.dtu.dk/services/ChloroP/.

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1,800 Citations


Journal ArticleDOI: 10.1038/NPROT.2006.286
01 Jan 2006-Nature Protocols
Abstract: Expression and tracking of fluorescent fusion proteins has revolutionized our understanding of basic concepts in cell biology. The protocol presented here has underpinned much of the in vivo results highlighting the dynamic nature of the plant secretory pathway. Transient transformation of tobacco leaf epidermal cells is a relatively fast technique to assess expression of genes of interest. These cells can be used to generate stable plant lines using a more time-consuming, cell culture technique. Transient expression takes from 2 to 4 days whereas stable lines are generated after approximately 2 to 4 months.

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Topics: Fusion protein (52%)

1,167 Citations


Open accessJournal ArticleDOI: 10.1073/PNAS.0802361105
Jian Feng Ma1, Naoki Yamaji, Namiki Mitani, Xiao-Yan Xu1  +3 moreInstitutions (2)
Abstract: Arsenic poisoning affects millions of people worldwide. Human arsenic intake from rice consumption can be substantial because rice is particularly efficient in assimilating arsenic from paddy soils, although the mechanism has not been elucidated. Here we report that two different types of transporters mediate transport of arsenite, the predominant form of arsenic in paddy soil, from the external medium to the xylem. Transporters belonging to the NIP subfamily of aquaporins in rice are permeable to arsenite but not to arsenate. Mutation in OsNIP2;1 (Lsi1, a silicon influx transporter) significantly decreases arsenite uptake. Furthermore, in the rice mutants defective in the silicon efflux transporter Lsi2, arsenite transport to the xylem and accumulation in shoots and grain decreased greatly. Mutation in Lsi2 had a much greater impact on arsenic accumulation in shoots and grain in field-grown rice than Lsi1. Arsenite transport in rice roots therefore shares the same highly efficient pathway as silicon, which explains why rice is efficient in arsenic accumulation. Our results provide insight into the uptake mechanism of arsenite in rice and strategies for reducing arsenic accumulation in grain for enhanced food safety.

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Topics: Arsenite transport (72%), Arsenite (64%), Arsenic contamination of groundwater (56%) ... read more

996 Citations


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202112