scholarly journals Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops

2021 ◽  
Author(s):  
Adina Chuang Howe ◽  
Nejc Stopnisek ◽  
Shane K Dooley ◽  
Fan Michelle Yang ◽  
Keara L Grady ◽  
...  
Keyword(s):  
Thioredoxin Reductase ◽  
Crop Productivity ◽  
Oxygen Species ◽  
Pyruvate Metabolism ◽  
Crop Phenology ◽  
Bacterial Populations ◽  
A Genome ◽  
Focus Analysis ◽  
Serine Biosynthesis ◽  
Phyllosphere Bacteria

Plants and microbes form beneficial associations. It is expected that understanding these interactions will allow for microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify key leaf microbiome members and quantify their activities on field-grown switchgrass and miscanthus. We integrate metagenome and metatranscriptome sequencing from 237 leaf samples collected over key time points in crop phenology. We curate metagenome-assembled-genomes (MAGs), and conservatively focus analysis on the highest quality MAGs that were <15.5% contaminated, >70% complete, and detected in a minimum of 10% of samples for each crop. Populations represented by these MAGs were actively transcribing genes, and exhibited seasonal dynamics in key functions, including pyruvate metabolism, threonine, homoserine and serine biosynthesis, and stress response. Notably, we detected enrichment in transcripts annotated to nonmavalonate isoprene biosynthesis in the late season, prior to and during host senescence, concurrent with when plants are expected to decrease their isoprene biosynthesis. We also detected groups of MAGs that had coherent transcript dynamics in thioredoxin reductase, which suggests a response to reactive oxygen species, potentially released by plant hosts experiencing abiotic stress. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptomes analysis to direct to some of the key activities of phyllosphere bacteria. These activities collectively support that leaf-associated bacterial populations can be seasonally dynamic, responsive to host cues, and, likely, interactively engage in feedbacks with the plant.

scholarly journals Acetylated Thioredoxin Reductase 1 Resists Oxidative Inactivation

2021 ◽  
Vol 9 ◽  
Author(s):  
David. E. Wright ◽  
Nikolaus Panaseiko ◽  
Patrick O’Donoghue
Keyword(s):  
Oxidative Stress ◽  
Thioredoxin Reductase ◽  
Oxygen Species ◽  
Site Specific ◽  
Oxidative Inactivation ◽  
Thioredoxin Reductase 1 ◽  
Lysine Residues ◽  
Canonical Amino Acid ◽  
Genetic Code Expansion ◽  
Low Activity

Thioredoxin Reductase 1 (TrxR1) is an enzyme that protects human cells against reactive oxygen species generated during oxidative stress or in response to chemotherapies. Acetylation of TrxR1 is associated with oxidative stress, but the function of TrxR1 acetylation in oxidizing conditions is unknown. Using genetic code expansion, we produced recombinant and site-specifically acetylated variants of TrxR1 that also contain the non-canonical amino acid, selenocysteine, which is essential for TrxR1 activity. We previously showed site-specific acetylation at three different lysine residues increases TrxR1 activity by reducing the levels of linked dimers and low activity TrxR1 tetramers. Here we use enzymological studies to show that acetylated TrxR1 is resistant to both oxidative inactivation and peroxide-induced multimer formation. To compare the effect of programmed acetylation at specific lysine residues to non-specific acetylation, we produced acetylated TrxR1 using aspirin as a model non-enzymatic acetyl donor. Mass spectrometry confirmed aspirin-induced acetylation at multiple lysine residues in TrxR1. In contrast to unmodified TrxR1, the non-specifically acetylated enzyme showed no loss of activity under increasing and strongly oxidating conditions. Our data suggest that both site-specific and general acetylation of TrxR1 regulate the enzyme’s ability to resist oxidative damage.

Future global crop production increases by adapting crop phenology to local climate change

2021 ◽  
Author(s):  
Sara Minoli ◽  
Jonas Jägermeyr ◽  
Senthold Asseng ◽  
Christoph Müller
Keyword(s):  
Climate Change ◽  
Crop Production ◽  
Management Practices ◽  
Crop Yields ◽  
Crop Productivity ◽  
Global Scale ◽  
Adaptation Strategies ◽  
Systematic Evaluation ◽  
Management Scenarios ◽  
Crop Phenology

&lt;p&gt;Broad evidence is pointing at possible adverse impacts of climate change on crop yields. Due to scarce information about farming management practices, most global-scale studies, however, do not consider adaptation strategies.&lt;/p&gt;&lt;p&gt;Here we integrate models of farmers' decision making with crop biophysical modeling at the global scale to investigate how accounting for adaptation of crop phenology affects projections of future crop productivity under climate change. Farmers in each simulation unit are assumed to adapt crop growing periods by continuously selecting sowing dates and cultivars that match climatic conditions best. We compare counterfactual management scenarios, assuming crop calendars and cultivars to be either the same as in the reference climate &amp;#8211; as often assumed in previous climate impact assessments &amp;#8211; or adapted to future climate.&lt;/p&gt;&lt;p&gt;Based on crop model simulations, we find that the implementation of adapted growing periods can substantially increase (+15%) total crop production in 2080-2099 (RCP6.0). In general, summer crops are responsive to both sowing and harvest date adjustments, which result in overall longer growing periods and improved yields, compared to production systems without adaptation of growing periods. Winter wheat presents challenges in adapting to a warming climate and requires region-specific adjustments to pre and post winter conditions. We present a systematic evaluation of how local and climate-scenario specific adaptation strategies can enhance global crop productivity on current cropland. Our findings highlight the importance of further research on the readiness of required crop varieties.&lt;/p&gt;

scholarly journals Genome-Wide Association Study for Maize Leaf Cuticular Conductance Identifies Candidate Genes Involved in the Regulation of Cuticle Development

2020 ◽  
Vol 10 (5) ◽  
pp. 1671-1683 ◽  
Author(s):  
Meng Lin ◽  
Susanne Matschi ◽  
Miguel Vasquez ◽  
James Chamness ◽  
Nicholas Kaczmar ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Crop Productivity ◽  
Genome Wide Association ◽  
Cell Wall Modification ◽  
Major Barrier ◽  
Maize Leaf ◽  
Genome Wide ◽  
A Genome

The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA, in 2016 and 2017). Five genomic regions significantly associated with gc were resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction of gc in locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control of gc and have the potential to help breeders more effectively develop drought-tolerant maize for target environments.

Effects of Reactive Oxygen Species on Crop Productivity

2017 ◽  
pp. 117-136 ◽  
Author(s):  
Marisha Sharma ◽  
Sunil K. Gupta ◽  
Farah Deeba ◽  
Vivek Pandey
Keyword(s):  
Reactive Oxygen Species ◽  
Reactive Oxygen ◽  
Crop Productivity ◽  
Oxygen Species

The production of reactive oxygen species enhanced with the reduction of menadione by active thioredoxin reductase

Metallomics ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1490-1497 ◽  
Author(s):  
Jing Li ◽  
Xin Zuo ◽  
Ping Cheng ◽  
Xiaoyuan Ren ◽  
Shibo Sun ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Molecular Oxygen ◽  
Thioredoxin Reductase ◽  
Reactive Oxygen ◽  
Semiquinone Radical ◽  
Ros Production ◽  
Oxygen Species ◽  
Reduction Mechanism ◽  
Radical Intermediate ◽  
Electron Reduction

TXNRD1 participates in the ROS production with menadione by a one-electron reduction mechanism. TXNRD1 transfers electrons from NADPH to menadione to yield a semiquinone radical intermediate, which reacts with molecular oxygen to generate ROS.

scholarly journals Auranofin resistance in Toxoplasma gondii decreases the accumulation of reactive oxygen species but does not target parasite thioredoxin reductase

2020 ◽  
Author(s):  
Christopher I. Ma ◽  
James A. Tirtorahardjo ◽  
Sharon Jan ◽  
Sakura S. Schweizer ◽  
Shawn A. C. Rosario ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Toxoplasma Gondii ◽  
Point Mutations ◽  
Thioredoxin Reductase ◽  
Reactive Oxygen ◽  
Chemical Mutagenesis ◽  
Resistance Locus ◽  
Sequencing Analysis ◽  
Oxygen Species ◽  
Wild Type

ABSTRACTAuranofin, a reprofiled FDA-approved drug originally designed to treat rheumatoid arthritis, has emerged as a promising anti-parasitic drug. It induces the accumulation of reactive oxygen species (ROS) in parasites, including Toxoplasma gondii. We generated auranofin resistant T. gondii lines through chemical mutagenesis in order to identify the molecular target of this drug. Resistant clones were confirmed with a competition assay using wild-type T. gondii expressing yellow fluorescence protein (YFP) as a reference strain. The predicted auranofin target, thioredoxin reductase, was not mutated in any of our resistant lines. Subsequent whole genomic sequencing analysis (WGS) did not reveal a consensus resistance locus, although many have point mutations in genes encoding redox-relevant proteins such as superoxide dismutase (TgSOD2) and ribonucleotide reductase. We investigated the SOD2 L201P mutation and found that it was not sufficient to confer resistance when introduced into wild-type parasites. Resistant clones accumulated less ROS than their wild type counterparts. Our results demonstrate that resistance to auranofin in T. gondii enhances its ability to abate oxidative stress through diverse mechanisms. This evidence supports a hypothesized mechanism of auranofin anti-parasitic activity as disruption of redox homeostasis.

scholarly journals Activating silent glycolysis bypasses in Escherichia coli

2021 ◽  
Author(s):  
Camillo Iacometti ◽  
Katharina Marx ◽  
Maria Hoenick ◽  
Viktoria Biletskaia ◽  
Helena Schulz-Mirbach ◽  
...  
Keyword(s):  
Triosephosphate Isomerase ◽  
Building Blocks ◽  
Scale Model ◽  
Deletion Strain ◽  
Central Metabolism ◽  
Adaptive Laboratory Evolution ◽  
Laboratory Evolution ◽  
E Coli ◽  
A Genome ◽  
Serine Biosynthesis

All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal, the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal immediately operated in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary for implementing a functional methylglyoxal pathway. Furthermore, we engineered the serine shunt which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection we performed an adaptive laboratory evolution study using an enolase deletion strain. The evolved mutants were shown to use the serine shunt. Our study reveals the flexible redesignation of metabolic pathways to create new metabolite links and rewire central metabolism.

scholarly journals Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton

2019 ◽  
Vol 20 (8) ◽  
pp. 1863 ◽  
Author(s):  
Xu ◽  
Magwanga ◽  
Cai ◽  
Zhou ◽  
Wang ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Abiotic Stress ◽  
Reactive Oxygen ◽  
Orthologous Gene ◽  
Network Evolution ◽  
Fiber Development ◽  
Oxygen Species ◽  
Transcription Analysis ◽  
Gene Pairs ◽  
A Genome

Reactive oxygen species (ROS) are important molecules in the plant, which are involved in many biological processes, including fiber development and adaptation to abiotic stress in cotton. We carried out transcription analysis to determine the evolution of the ROS genes and analyzed their expression levels in various tissues of cotton plant under abiotic stress conditions. There were 515, 260, and 261 genes of ROS network that were identified in Gossypium hirsutum (AD1 genome), G. arboreum (A genome), and G. raimondii (D genome), respectively. The ROS network genes were found to be distributed in all the cotton chromosomes, but with a tendency of aggregating on either the lower or upper arms of the chromosomes. Moreover, all the cotton ROS network genes were grouped into 17 families as per the phylogenetic tress analysis. A total of 243 gene pairs were orthologous in G. arboreum and G. raimondii. There were 240 gene pairs that were orthologous in G. arboreum, G. raimondii, and G. hirsutum. The synonymous substitution value (Ks) peaks of orthologous gene pairs between the At subgenome and the A progenitor genome (G. arboreum), D subgenome and D progenitor genome (G. raimondii) were 0.004 and 0.015, respectively. The Ks peaks of ROS network orthologous gene pairs between the two progenitor genomes (A and D genomes) and two subgenomes (At and Dt subgenome) were 0.045. The majority of Ka/Ks value of orthologous gene pairs between the A, D genomes and two subgenomes of TM-1 were lower than 1.0. RNA seq. analysis and RT-qPCR validation, showed that, CSD1,2,3,5,6; FSD1,2; MSD1,2; APX3,11; FRO5.6; and RBOH6 played a major role in fiber development while CSD1, APX1, APX2, MDAR1, GPX4-6-7, FER2, RBOH6, RBOH11, and FRO5 were integral for enhancing salt stress in cotton. ROS network-mediated signal pathway enhances the mechanism of fiber development and regulation of abiotic stress in Gossypium. This study will enhance the understanding of ROS network and form the basic foundation in exploring the mechanism of ROS network-involving the fiber development and regulation of abiotic stress in cotton.

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