The transposable element-rich genome of the cereal pest Sitophilus oryzae

Abstract Background The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. Results We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. Conclusions Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

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The genome of the cereal pestSitophilus oryzae: a transposable element haven

10.1101/2021.03.03.408021 ◽

2021 ◽

Author(s):

Nicolas Parisot ◽

Carlos Vargas-Chavez ◽

Clément Goubert ◽

Patrice Baa-Puyoulet ◽

Séverine Balmand ◽

...

Keyword(s):

Amino Acids ◽

Transposable Element ◽

Metabolic Networks ◽

Sitophilus Oryzae ◽

Essential Amino Acids ◽

Gene Expansion ◽

Long Reads ◽

High Gene ◽

The Impact ◽

Eukaryotic Genomes

AbstractBackgroundAmong beetles, the rice weevilSitophilus oryzaeis one of the most important pests causing extensive damage to cereal in fields and to stored grains.S. oryzaehas an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacteriumSodalis pierantoniusand is a valuable model to decipher host-symbiont molecular interactions.ResultsWe sequenced theSitophilus oryzaegenome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show thatS. oryzaehas undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state.S. oryzaehas undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear),S. pierantoniusrelies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis.ConclusionsIn addition to being an agricultural pest and a valuable endosymbiotic system,S. oryzaecan be a remarkable model for studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

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The impact of delivery profile of essential amino acids upon skeletal muscle protein synthesis in older men: clinical efficacy of pulse vs. bolus supply

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00112.2015 ◽

2015 ◽

Vol 309 (5) ◽

pp. E450-E457 ◽

Cited By ~ 26

Author(s):

W. Kyle Mitchell ◽

Bethan E. Phillips ◽

John P. Williams ◽

Debbie Rankin ◽

Jonathan N. Lund ◽

...

Keyword(s):

Skeletal Muscle ◽

Amino Acids ◽

Blood Flow ◽

Protein Synthesis ◽

Muscle Protein ◽

Muscle Protein Synthesis ◽

Older Men ◽

Essential Amino Acids ◽

Low Amplitude ◽

The Impact

Essential amino acids (EAA) are responsible for skeletal muscle anabolic effects after nutrient intake. The pattern of appearance of EAA in blood, e.g., after intake of “slow” or “fast” protein sources or in response to grazing vs. bolus feeding patterns, may impact anabolism. However, the influence of this on muscle anabolism is poorly understood, particularly in older individuals. We determined the effects of divergent feeding profiles of EAA on blood flow, anabolic signaling, and muscle protein synthesis (MPS) in older men. Sixteen men (∼70 yr) consumed EAA either as a single dose (bolus, 15 g; n = 8) or as small repeated fractions (pulse, 4 × 3.75 g every 45 min; n = 8) during 13C6 phenylalanine infusion. Repeated blood samples and muscle biopsies permitted measurement of fasting and postprandial plasma EAA, insulin, anabolic signaling, and MPS. Muscle blood flow was assessed by contrast-enhanced ultrasound (Sonovue). Bolus achieved rapid insulinemia (12.7 μiU/ml 25-min postfeed), essential aminoacidemia (∼3,000 μM, 45–65 min postfeed), and mTORC1 activity; pulse achieved attenuated insulin responses, gradual low-amplitude aminoacidemia (∼1,800 μM 80–195 min after feeding), and undetectable mTORC1 signaling. Despite this, equivalent anabolic responses were observed: fasting FSRs of 0.051 and 0.047%/h (bolus and pulse, respectively) increased to 0.084 and 0.073%/h, respectively. Moreover, pulse led to sustainment of MPS beyond 180 min, when bolus MPS had returned to basal rates. We detected no benefit of rapid aminoacidemia in this older population despite enhanced anabolic signaling and greater overall EAA exposure. Rather, apparent delayed onset of the “muscle-full” effect permitted identical MPS following low-amplitude-sustained EAA exposure.

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Specification of the Impact of Socioeconomic Factors on Consumption of the Animal and Vegetable Sources of Protein

Journal of Agricultural and Applied Economics ◽

10.1017/s0081305200012656 ◽

1975 ◽

Vol 7 (2) ◽

pp. 141-147

Author(s):

John Adrian ◽

Raymond Daniel

Keyword(s):

Amino Acids ◽

Dairy Products ◽

Vegetable Protein ◽

Essential Amino Acids ◽

Recent Analysis ◽

Human Diet ◽

Legume Seeds ◽

The Individual ◽

Red Meats ◽

The Impact

Proteins are one of the basic and essential nutrients consumed by man. Both animal and vegetable sources provide proteins in the human diet. Many proteins derived from animal sources are nutritionally adequate because all essential amino acids are present. However, proteins from vegetable sources are often deficient in one or more essential amino acids. Therefore, vegetable protein must generally be supplemented with other proteins in order to provide good nutition. However, vegetable proteins can provide a satisfactory diet if the individual is judicious in selecting foods.A study of 1955 data indicated that approximately 55 percent of the protein component of the American diet came from animal sources. A recent analysis indicated that red meats contributed approximately 30 percent of the animal source to total protein. Dairy products, poultry, and fish contributed the balance. Similarly, wheat flour provided approximately 15 percent of total vegetable protein intake with other cereals (rice, corn, barley and rye), legume seeds (beans, peas and soybeans), and nuts constituting the balance.

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Biotransformation of flaxseed meal by effective microorganisms and possibility of application in aquaculture

BIO Web of Conferences ◽

10.1051/bioconf/20202303001 ◽

2020 ◽

Vol 23 ◽

pp. 03001

Author(s):

Irina A. Sazonova ◽

Tatyana S. Osina ◽

Petr V. Smutnev ◽

Elena G. Zhnichkova ◽

Sergey V. Shpul

Keyword(s):

Amino Acids ◽

Biochemical Parameters ◽

Essential Amino Acids ◽

Chemical Parameters ◽

Effective Microorganisms ◽

Flaxseed Meal ◽

Fish Blood ◽

Feed Value ◽

The Impact ◽

Fatty Acid Compositions

This article describes studies on the impact of effective microorganisms of the “Baikal EM-1” probiotic on the biotransformation of flaxseed meal, its organoleptic and chemical parameters, and changes in amino acid and fatty acid compositions. It has been established that after fermentation in flaxseed meal, the amount of fiber decreases, it saturates with protein, and the amount of essential and non-essential amino acids increases. We made an analysis of the feed value of biotransformed meal depending on the probiotic concentration for the purpose of further use in the feeding of carps – the most effective probiotic concentration for biotransformation was selected. The effect of replacing part of the feed with biotransformed flaxseed meal on the change in liveweight and biochemical parameters of fish blood was studied. Positive dynamics of fishes’ liveweight was noted. The inexpediency of feeding unfermented meal to carps is proved.

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Improving the levels of essential amino acids and sulfur metabolites in plants

Biological Chemistry ◽

10.1515/bc.2005.097 ◽

2005 ◽

Vol 386 (9) ◽

Cited By ~ 54

Author(s):

Gad Galili ◽

Rachel Amir ◽

Rainer Hoefgen ◽

Holger Hesse

Keyword(s):

Amino Acids ◽

Metabolic Engineering ◽

Amino Acid Metabolism ◽

Metabolic Networks ◽

Acid Metabolism ◽

Significant Proportion ◽

Essential Amino Acids ◽

Plant Foods ◽

Livestock Feeds ◽

Low Levels

AbstractPlants represent the major source of food for humans, either directly or indirectly through their use as livestock feeds. Plant foods are not nutritionally balanced because they contain low proportions of a number of essential metabolites, such as vitamins and amino acids, which humans and a significant proportion of their livestock cannot produce on their own. Among the essential amino acids needed in human diets, Lys, Met, Thr and Trp are considered as the most important because they are present in only low levels in plant foods. In the present review, we discuss approaches to improve the levels of the essential amino acids Lys and Met, as well as of sulfur metabolites, in plants using metabolic engineering approaches. We also focus on specific examples for which a deeper understanding of the regulation of metabolic networks in plants is needed for tailor-made improvements of amino acid metabolism with minimal interference in plant growth and productivity.

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Body Weight Loss, Tissue Wasting and Shortened Lifespan in Late Middle-aged Mice on Imbalanced Essential/Non-essential Amino Acids Diet

10.20944/preprints201802.0048.v1 ◽

2018 ◽

Author(s):

Giovanni Corsetti ◽

Evasio Pasini ◽

Claudia Romano ◽

Riccardo Calvani ◽

Anna Picca ◽

...

Keyword(s):

Amino Acids ◽

Weight Loss ◽

Adipose Tissue ◽

Essential Amino Acids ◽

Skeletal Muscle Atrophy ◽

Calorie Intake ◽

Middle Aged ◽

Brown Adipose ◽

Body Wasting ◽

The Impact

Inadequate protein intake can impair protein balance and lead to skeletal muscle atrophy, impaired body growth, and functional decline. Foods provide both non-essential (NEAAs) and essential amino acids (EAAs) that may convey different metabolic stimuli to specific organs and tissues. In this study, we sought to evaluate the impact of six diets with various EAA/NEAA blends on body composition and the risk of developing tissue wasting in late middle-aged male mice. Mice consuming NEAA-based diets, although showing increased food and calorie intake, suffered the most severe weight loss. Interestingly, even moderate NEAAs prevalence was able to induce inflammatory catabolic stimuli, generalized body wasting and systemic metabolic alterations. Complete depletion of retroperitoneal white adipose tissue and a severe loss (>75%) of brown adipose tissue were observed together with muscle wasting. Conversely, EAA-based diets induced significant decreases in weight by reducing primarily fat reserves, but improved clinical parameters. Tissue wasting was caused by altered AA quality, independent of reduced nitrogen or caloric intake. Our results indicate that an optimized balance of AA composition is necessary for preserving overall bodily energy status. These findings are particularly relevant in the context of aging and may be exploited for contrasting its negative correlates including body wasting.

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The impact of fixation method on the biochemical characteristics of hawk tea (Litsea coreana)

International Journal of Food Engineering ◽

10.1515/ijfe-2019-0290 ◽

2020 ◽

Vol 16 (8) ◽

Author(s):

Qing Xu ◽

Yuanjing Zhou ◽

Jihong Wang

Keyword(s):

Amino Acids ◽

Sensory Quality ◽

Radical Scavenging Activity ◽

Radical Scavenging ◽

Essential Amino Acids ◽

Boiling Water ◽

Fixation Method ◽

Biochemical Characteristics ◽

Fixation Techniques ◽

The Impact

AbstractFixation is one of the critical steps in tea processing and can cause various physico-chemical changes, thus affecting tea quality. There are many tea processing techniques, but their influence on quality remains unclear. Here, we studied the impact of different fixation methods, including for 6 or 10 min by machine, by iron pan, or by boiling water, on the biochemical characteristics of hawk tea. The results showed that tea fixation technique had a significant influence on the sensory quality, biochemical components, and antioxidant activity of the tea. Compared to other fixation techniques, fixation by boiling water produced a more nutritious hawk tea with stronger DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity (EC50 = 6.56 μg/mL). Processing with boiling water also resulted in a better sensory quality with a unique sweet aftertaste. This tea also contained more polyphenols (19.60%), total amino acids (21,219 mg/100 g), essential amino acids (10,564 mg/100 g), and trace elements (5873.13 mg/kg). These results can guide the development of hawk tea products.

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Food Products as Sources of Protein and Amino Acids—The Case of Poland

Nutrients ◽

10.3390/nu10121977 ◽

2018 ◽

Vol 10 (12) ◽

pp. 1977 ◽

Cited By ~ 18

Author(s):

Hanna Górska-Warsewicz ◽

Wacław Laskowski ◽

Olena Kulykovets ◽

Anna Kudlińska-Chylak ◽

Maksymilian Czeczotko ◽

...

Keyword(s):

Amino Acids ◽

Total Protein ◽

Agricultural Land ◽

Meat Products ◽

Food Products ◽

Essential Amino Acids ◽

Food Sources ◽

Grain Products ◽

Protein Supply ◽

The Impact

The aim of this study was to identify the food sources of protein and 18 amino acids (AAs) in the average Polish diet. The analysis was conducted based on the 2016 Household Budget Survey (HBS) on the consumption of food products from a representative sample of 38,886 households (n = 99,230). This survey was organized, conducted and controlled by the Central Statistical Office, Social Surveys and Living Conditions Statistics Department in cooperation with the Statistic Office in Łódź based on the recording of expenditures, quantitative consumption, and revenues in budget books for one month. 91 food products from 13 food categories (e.g., meat and meat products, grain products) consisting of 42 food groups (e.g., red meat, milk, cheese) were analyzed to determine protein and amino acid intake from these products. Three categories delivered 80.9% of total protein (meat and meat products: 38.9%; grain products: 23.9%; and milk and dairy products: 18.1%). The branched-chain amino acids (BCAAs: leucine, isoleucine and valine) were delivered mainly by meat and meat products (39.9%; 41.3% and 37.4%, respectively). Meat and meat products were also the most important source for other essential amino acids (EAAs: lysine 49.2%, histidine 46.6%, threonine 44.7%, tryptophan 41.4%, phenylalanine 35.3%, and methionine 44.2%). In terms of the contribution of the non-essential or conditionally essential amino acids to the average Polish diet, most important were grain products (for cysteine: 41.2%; glutamic acid: 33.8%; proline: 34.1%), and meat and meat products (for tyrosine: 38.3%; arginine: 46.1%; alanine: 48.7%; aspartic acid: 41.7%; glycine: 52.5%; serine: 33.6%). Five clusters were identified to assess the impact of socio-demographic and economic factors on the protein supply. The largest impact was observed for respondent education, degree of urbanization, study month, and usage of agricultural land. The shares of animal food in total protein supply amounted to 66.5% in total population and varied from 56.4% to 73.6% in different clusters.

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Newly Identified Essential Amino Acids Affecting Chlorella ellipsoidea DGAT1 Function Revealed by Site-Directed Mutagenesis

International Journal of Molecular Sciences ◽

10.3390/ijms19113462 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3462 ◽

Cited By ~ 1

Author(s):

Baocheng Sun ◽

Xuejie Guo ◽

Chengming Fan ◽

Yuhong Chen ◽

Jingqiao Wang ◽

...

Keyword(s):

Amino Acids ◽

Mutant Gene ◽

Essential Amino Acids ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Chlorella Ellipsoidea ◽

And Function ◽

The Impact ◽

Rate Limiting ◽

Important Form

Diacylglycerol acyltransferase (DGAT) is a rate-limiting enzyme in the synthesis of triacylglycerol (TAG), the most important form of energy storage in plants. Some residues have previously been proven to be crucial for DGAT1 activity. In this study, we used site-directed mutagenesis of the CeDGAT1 gene from Chlorella ellipsoidea to alter 16 amino acids to investigate effects on DGAT1 function. Of the 16 residues (L482R, E542R, Y553A, G577R, R579D, Y582R, R596D, H603D, H609D, A624R, F629R, S632A, W650R, A651R, Q658H, and P660R), we newly identified 5 (L482, R579, H603, A651, and P660) as being essential for DGAT1 function and 7 (E542, G577, R596, H609, A624, S632, and Q658) that significantly affect DGAT1 function to different degrees, as revealed by heterologous expression of the mutants in yeast strain INVSc1. Importantly, compared with CeDGAT1, expression of the mutant CeDGAT1Y553A significantly increased the total fatty acid and TAG contents of INVSc1. Comparison among CeDGAT1Y553A, GmDGAT1Y341A, AtDGAT1Y364A, BnDGAT1Y347A, and BoDGAT1Y352A, in which tyrosine at the position corresponding to the 553rd residue in CeDGAT1 is changed into alanine, indicated that the impact of changing Y to A at position 553 is specific for CeDGAT1. Overall, the results provide novel insight into the structure and function of DGAT1, as well as a mutant gene with high potential for lipid improvement in microalgae and plants.

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Metabolic cooperation among commensal bacteria supports Drosophila juvenile growth under nutritional stress

10.1101/2020.05.27.119370 ◽

2020 ◽

Author(s):

Jessika Consuegra ◽

Théodore Grenier ◽

Houssam Akherraz ◽

Isabelle Rahioui ◽

Hugo Gervais ◽

...

Keyword(s):

Amino Acids ◽

Gut Microbiota ◽

Metabolic Networks ◽

Molecular Mechanisms ◽

Larval Growth ◽

Essential Amino Acids ◽

Nutritional Stress ◽

List Type ◽

Juvenile Growth ◽

Metabolic Cooperation

SUMMARYThe gut microbiota shapes animal growth trajectory in stressful nutritional environments, but the molecular mechanisms behind such physiological benefits remain poorly understood. The gut microbiota is mostly composed of bacteria, which construct metabolic networks among themselves and with the host. Until now, how the metabolic activities of the microbiota contribute to host juvenile growth remains unknown. Here, using Drosophila as a host model, we report that two of its major bacterial partners, Lactobacillus plantarum and Acetobacter pomorum engage in a beneficial metabolic dialogue that boosts host juvenile growth despite nutritional stress. We pinpoint that lactate, produced by L. plantarum, is utilized by A. pomorum as an additional carbon source, and A. pomorum provides essential amino-acids and vitamins to L. plantarum. Such bacterial cross-feeding provisions a set of anabolic metabolites to the host, which may foster host systemic growth despite poor nutrition.GRAPHICAL ABSTRACTHIGHLIGHTSL. plantarum feeds lactate to A. pomorumA. pomorum supplies essential amino acids and vitamins to L. plantarumMicrobiota metabolic dialogue boosts Drosophila’s larval growthLactate utilization by Acetobacter releases anabolic metabolites to larvae

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