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Rice (New York, N.Y.) May 2024Rice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major...
Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping.
BACKGROUND
Rice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major factor limiting its growth.
RESULTS
In this experiment, we tested the tolerance to anaerobic germination of rice varieties NIP and HD84, and they were used as parents to construct a DH (doubled-haploid) population. The transcriptomes of NIP (highly tolerant) and HD86 (intolerant), and their progeny HR (highly tolerant) and NHR (intolerant) were sequenced from normal and anaerobic environments. The differentially-expressed genes (DEGs) were subjected to GO (Gene ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and WGCNA analyses. QTL mapping of the DH population identified tolerance to anaerobic germination-related chromosomal segments. The transcriptome results from 24 samples were combined with the anaerobic stress QTL results for 159 DH population lines to construct a metabolic network to identify key pathways and a gene interaction network to study the key genes. Essential genes were initially subjected to rigorous functional validation, followed by a comprehensive analysis aimed at elucidating their potential utility in domestication and breeding practices, particularly focusing on the exploitation of dominant haplotypes.
CONCLUSION
The results show that pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are the starting signals of energy metabolism for coleoptile length growth, the auxin transporter EXPA is the determining signal for coleoptile length growth. The pivotal genes Os05g0498700 and Os01g0866100 exert a negative regulatory influence on coleoptile length, ultimately enhancing tolerance to anaerobic germination in rice. Analyses of breeding potential underscore the additional value of Os05g0498700-hyp2 and Os01g0866100-hyp2, highlighting their potential utility in further improving rice through breeding programs. The results of our study will provide a theoretical basis for breeding anaerobic-tolerant rice varieties.
PubMed: 38819744
DOI: 10.1186/s12284-024-00714-y -
International Journal of Molecular... May 2024Floods induce hypoxic stress and reduce wheat growth. On the other hand, rice is a semi-aquatic plant and usually grows even when partially submerged. To clarify the...
Floods induce hypoxic stress and reduce wheat growth. On the other hand, rice is a semi-aquatic plant and usually grows even when partially submerged. To clarify the dynamic differences in the cellular mechanism between rice and wheat under flooding stress, morphological and biochemical analyses were performed. Although the growth of wheat in the early stage was significantly suppressed due to flooding stress, rice was hardly affected. Amino-acid analysis revealed significant changes in amino acids involved in the gamma-aminobutyric acid (GABA) shunt and anaerobic/aerobic metabolism. Flood stress significantly increased the contents of GABA and glutamate in wheat compared with rice, though the abundances of glutamate decarboxylase and succinyl semialdehyde dehydrogenase did not change. The abundance of alcohol dehydrogenase and pyruvate carboxylase increased in wheat and rice, respectively. The contents of aspartic acid and pyruvic acid increased in rice root but remained unchanged in wheat; however, the abundance of aspartate aminotransferase increased in wheat root. These results suggest that flooding stress significantly inhibits wheat growth through upregulating amino-acid metabolism and increasing the alcohol-fermentation system compared to rice. When plant growth is inhibited by flooding stress and the aerobic-metabolic system is activated, GABA content increases.
Topics: Triticum; Oryza; Floods; Stress, Physiological; Amino Acids; gamma-Aminobutyric Acid; Plant Roots; Plant Proteins
PubMed: 38791268
DOI: 10.3390/ijms25105229 -
Microbial Cell Factories May 2024Zymomonas mobilis is well known for its outstanding ability to produce ethanol with both high specific productivity and with high yield close to the theoretical maximum....
BACKGROUND
Zymomonas mobilis is well known for its outstanding ability to produce ethanol with both high specific productivity and with high yield close to the theoretical maximum. The key enzyme in the ethanol production pathway is the pyruvate decarboxylase (PDC) which is converting pyruvate to acetaldehyde. Since it is widely considered that its gene pdc is essential, metabolic engineering strategies aiming to produce other compounds derived from pyruvate need to find ways to reduce PDC activity.
RESULTS
Here, we present a new platform strain (sGB027) of Z. mobilis in which the native promoter of pdc was replaced with the IPTG-inducible P allowing for a controllable expression of pdc. Expression of lactate dehydrogenase from E. coli in sGB027 allowed the production of D-lactate with, to the best of our knowledge, the highest reported specific productivity of any microbial lactate producer as well as with the highest reported lactate yield for Z. mobilis so far. Additionally, by expressing the L-alanine dehydrogenase of Geobacillus stearothermophilus in sGB027 we produced L-alanine, further demonstrating the potential of sGB027 as a base for the production of compounds other than ethanol.
CONCLUSION
We demonstrated that our new platform strain can be an excellent starting point for the efficient production of various compounds derived from pyruvate with Z. mobilis and can thus enhance the establishment of this organism as a workhorse for biotechnological production processes.
Topics: Zymomonas; Pyruvate Decarboxylase; Metabolic Engineering; Ethanol; Lactic Acid; Escherichia coli; L-Lactate Dehydrogenase; Alanine; Pyruvic Acid; Fermentation
PubMed: 38773442
DOI: 10.1186/s12934-024-02419-9 -
The Journal of Clinical Investigation Apr 2024Carbohydrates and lipids provide the majority of substrates to fuel mitochondrial oxidative phosphorylation. Metabolic inflexibility, defined as an impaired ability to...
Carbohydrates and lipids provide the majority of substrates to fuel mitochondrial oxidative phosphorylation. Metabolic inflexibility, defined as an impaired ability to switch between these fuels, is implicated in a number of metabolic diseases. Here, we explore the mechanism by which physical inactivity promotes metabolic inflexibility in skeletal muscle. We developed a mouse model of sedentariness, small mouse cage (SMC), that, unlike other classic models of disuse in mice, faithfully recapitulated metabolic responses that occur in humans. Bioenergetic phenotyping of skeletal muscle mitochondria displayed metabolic inflexibility induced by physical inactivity, demonstrated by a reduction in pyruvate-stimulated respiration (JO2) in the absence of a change in palmitate-stimulated JO2. Pyruvate resistance in these mitochondria was likely driven by a decrease in phosphatidylethanolamine (PE) abundance in the mitochondrial membrane. Reduction in mitochondrial PE by heterozygous deletion of phosphatidylserine decarboxylase (PSD) was sufficient to induce metabolic inflexibility measured at the whole-body level, as well as at the level of skeletal muscle mitochondria. Low mitochondrial PE in C2C12 myotubes was sufficient to increase glucose flux toward lactate. We further implicate that resistance to pyruvate metabolism is due to attenuated mitochondrial entry via mitochondrial pyruvate carrier (MPC). These findings suggest a mechanism by which mitochondrial PE directly regulates MPC activity to modulate metabolic flexibility in mice.
Topics: Animals; Mice; Muscle, Skeletal; Pyruvic Acid; Mitochondria, Muscle; Phosphatidylethanolamines; Sedentary Behavior; Male; Carboxy-Lyases; Mice, Knockout; Stearoyl-CoA Desaturase
PubMed: 38652544
DOI: 10.1172/JCI167371 -
Plants (Basel, Switzerland) Mar 2024Soil compaction is one of the crucial factors that restrains the root respiration, energy metabolism and growth of peanut ( L.) due to hypoxia, which can be alleviated...
Soil compaction is one of the crucial factors that restrains the root respiration, energy metabolism and growth of peanut ( L.) due to hypoxia, which can be alleviated by ventilation. We therefore carried out a pot experiment with three treatments: no ventilation control (CK), (2) ventilation volumes at 1.2 (T1), and 1.5 (T2) times of the standard ventilation volume (2.02 L/pot). Compared to no-ventilation in compacted soil, ventilation T1 significantly increased total root length, root surface area, root volume and tips at the peanut anthesis stage (62 days after sowing), while T2 showed a negative impact on the above-mentioned root morphological characteristics. At the podding stage (S2, 95 days after sowing), both ventilation treatments improved root morphology, especially under T1. Compared to CK, both ventilation T1 and T2 decreased the activities of enzymes involving the anaerobic respiration, including root lactate dehydrogenase, pyruvate decarboxylase and alcohol dehydrogenase. The activities of antioxidant enzymes of root superoxide dismutase, peroxidase and catalase also decreased at S1, while superoxide dismutase and peroxidase significantly increased under T1 at S2. The ventilation of compacted soil changed soil nitrogen-fixing bacterial communities, with highest bacterial alpha diversity indices under T1. The Pearson correlation analyses indicated a positive relationship between the relative abundance of and root activity, and between unclassified_family of and the root surface area, while had a negative impact on the root nodule number. The Pearson correlation test showed that the root surface, tips and activity positively correlated with root superoxide dismutase and peroxidase activities. These results demonstrate that soil ventilation could enhance plant root growth, the diversity and function of soil nitrogen-fixing bacterial communities. The generated results from this present study could serve as important evidence in alleviating soil hypoxia caused by compaction.
PubMed: 38592790
DOI: 10.3390/plants13060790 -
Metabolic Engineering May 2024Precise control of gene expression is critical for optimizing cellular metabolism and improving the production of valuable biochemicals. However, hard-wired approaches...
Precise control of gene expression is critical for optimizing cellular metabolism and improving the production of valuable biochemicals. However, hard-wired approaches to pathway engineering, such as optimizing promoters, can take time and effort. Moreover, limited tools exist for controlling gene regulation in non-conventional hosts. Here, we develop a two-channel chemically-regulated gene expression system for the multi-stress tolerant yeast Kluyveromyces marxianus and use it to tune ethyl acetate production, a native metabolite produced at high titers in this yeast. To achieve this, we repurposed the plant hormone sensing modules (PYR1/HAB1 and PYR1*/HAB1*) for high dynamic-range gene activation and repression controlled by either abscisic acid (ABA) or mandipropamid (mandi). To redirect metabolic flux towards ethyl acetate biosynthesis, we simultaneously repress pyruvate dehydrogenase (PDA1) and activate pyruvate decarboxylase (PDC1) to enhance ethyl acetate titers. Thus, we have developed new tools for chemically tuning gene expression in K. marxianus and S. cerevisiae that should be deployable across many non-conventional eukaryotic hosts.
Topics: Kluyveromyces; Acetates; Plant Growth Regulators; Metabolic Engineering; Gene Expression Regulation, Fungal; Abscisic Acid
PubMed: 38554744
DOI: 10.1016/j.ymben.2024.03.006 -
Polish Journal of Microbiology Mar 2024Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects...
Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects on human health and the ecosystem. Bioaugmentation with microorganisms like bacteria is an emerging approach that can mitigate the toxins from environmental sources. The present study was initiated to target the petroleum-contaminated soil of gasoline stations situated in Lahore. Petroleum degrading bacteria were isolated by serial dilution method followed by growth analysis, biochemical and molecular characterization, removal efficiency estimation, metabolites extraction, and GC-MS of the metabolites. Molecular analysis identified the bacterium as Bacillus cereus, which exhibited maximum growth at 72 hours and removed 75% petroleum. Biochemical characterization via the Remel RapID ONE panel system showed positive results for arginine dehydrolase (ADH), ornithine decarboxylase (ODC), lysine decarboxylase (LDC), -nitrophenyl-β-D-galactosidase (ONPG), -nitrophenyl-β-D-glucosidase (βGLU), -nitrophenyl-N-acetyl-β-D-glucosaminidase (NAG), malonate (MAL), adonitol fermentation (ADON), and tryptophane utilization (IND). GC-MS-based metabolic profiling identified alcohols (methyl alcohol, -, - and -cresols, catechol, and 3-methyl catechol), aldehydes (methanone, acetaldehyde, and -tolualdehyde), carboxylic acid (methanoic acid, -muconic acid, cyclohexane carboxylic acid and benzoic acid), conjugate bases of carboxylic acids (benzoate, -muconate, 4-hydroxybenzoate, and pyruvate) and cycloalkane (cyclohexene). It suggested the presence of methane, methylcyclohexane, toluene, xylene, and benzene degradation pathways in .
Topics: Humans; Bacillus cereus; Ecosystem; Hydrocarbons; Methane; Carboxylic Acids
PubMed: 38437466
DOI: 10.33073/pjm-2024-012 -
Biology Feb 2024Ammonium (NH) toxicity is ubiquitous in plants. To investigate the underlying mechanisms of this toxicity and bicarbonate (HCO)-dependent alleviation, wheat plants were...
Ammonium (NH) toxicity is ubiquitous in plants. To investigate the underlying mechanisms of this toxicity and bicarbonate (HCO)-dependent alleviation, wheat plants were hydroponically cultivated in half-strength Hoagland nutrient solution containing 7.5 mM NO (CK), 7.5 mM NH (SA), or 7.5 mM NH + 3 mM HCO (AC). Transcriptomic analysis revealed that compared to CK, SA treatment at 48 h significantly upregulated the expression of genes encoding fermentation enzymes (pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH), and lactate dehydrogenase (LDH)) and oxygen consumption enzymes (respiratory burst oxidase homologs, dioxygenases, and alternative oxidases), downregulated the expression of genes encoding oxygen transporters (PIP-type aquaporins, non-symbiotic hemoglobins), and those involved in energy metabolism, including tricarboxylic acid (TCA) cycle enzymes and ATP synthases, but upregulated the glycolytic enzymes in the roots and downregulated the expression of genes involved in the cell cycle and elongation. The physiological assay showed that SA treatment significantly increased PDC, ADH, and LDH activity by 36.69%, 43.66%, and 61.60%, respectively; root ethanol concentration by 62.95%; and lactate efflux by 23.20%, and significantly decreased the concentrations of pyruvate and most TCA cycle intermediates, the complex V activity, ATP content, and ATP/ADP ratio. As a consequence, SA significantly inhibited root growth. AC treatment reversed the changes caused by SA and alleviated the inhibition of root growth. In conclusion, NH treatment alone may cause hypoxic stress in the roots, inhibit energy generation, suppress cell division and elongation, and ultimately inhibit root growth, and adding HCO remarkably alleviates the NH-induced inhibitory effects on root growth largely by attenuating the hypoxic stress.
PubMed: 38392319
DOI: 10.3390/biology13020101 -
Biotech (Basel (Switzerland)) Jan 2024Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be...
Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered . First, we evaluated five types of phenylalanine ammonia lyases (PALs) from (AtPAL) and (BdPAL) for their ability to produce -cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an strain that co-expressed AtPAL2 and ferulic acid decarboxylase from . After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large-scale industrial production of styrene.
PubMed: 38247732
DOI: 10.3390/biotech13010002 -
International Journal of Molecular... Dec 2023A cell population characterized by the release of glucose repression and known as [] emerges spontaneously in the yeast . This study revealed that the [] variants...
A cell population characterized by the release of glucose repression and known as [] emerges spontaneously in the yeast . This study revealed that the [] variants exhibit retarded alcoholic fermentation when glucose is the sole carbon source. To identify the key to the altered glucose response, the gene expression profile of [] cells was examined. Based on RNA-seq data, the [] status was linked to impaired function of the Cyc8p-Tup1p complex. Loss of Cyc8p led to a decrease in the initial rate of alcoholic fermentation under glucose-rich conditions via the inactivation of pyruvate decarboxylase, an enzyme unique to alcoholic fermentation. These results suggest that Cyc8p can become inactive to attenuate alcoholic fermentation. These findings may contribute to the elucidation of the mechanism of non-genetic heterogeneity in yeast alcoholic fermentation.
Topics: Carbon; Fermentation; Glucose; Pyruvate Decarboxylase; Saccharomyces cerevisiae
PubMed: 38203474
DOI: 10.3390/ijms25010304