scholarly journals d-Amino Acids in Plants: Sources, Metabolism, and Functions

2020 ◽  
Vol 21 (15) ◽  
pp. 5421
Author(s):  
Üner Kolukisaoglu
Keyword(s):  
Amino Acids ◽  
Side Reactions ◽  
Inhibitory Effects ◽  
Physiological Processes ◽  
Long Time ◽  
Critical Revision ◽  
Metabolizing Enzyme ◽  
First Time ◽  
Identification And Characterization

Although plants are permanently exposed to d-amino acids (d-AAs) in the rhizosphere, these compounds were for a long time regarded as generally detrimental, due to their inhibitory effects on plant growth. Recent studies showed that this statement needs a critical revision. There were several reports of active uptake by and transport of d-AAs in plants, leading to the question whether these processes happened just as side reactions or even on purpose. The identification and characterization of various transporter proteins and enzymes in plants with considerable affinities or specificities for d-AAs also pointed in the direction of their targeted uptake and utilization. This attracted more interest, as d-AAs were shown to be involved in different physiological processes in plants. Especially, the recent characterization of d-AA stimulated ethylene production in Arabidopsis thaliana revealed for the first time a physiological function for a specific d-AA and its metabolizing enzyme in plants. This finding opened the question regarding the physiological or developmental contexts in which d-AA stimulated ethylene synthesis are involved in. This question and the ones about the transport characteristics of d-AAs, their metabolism, and their different physiological effects, are the focus of this review.

scholarly journals Identification and Characterization of Mutations Conferring Resistance to d-Amino Acids in Bacillus subtilis

2015 ◽  
Vol 197 (9) ◽  
pp. 1632-1639 ◽  
Author(s):  
Sara A. Leiman ◽  
Charles Richardson ◽  
Lucy Foulston ◽  
Alexander K. W. Elsholz ◽  
Eric A. First ◽  
...  
Keyword(s):  
Amino Acids ◽  
Bacillus Subtilis ◽  
Protein Biosynthesis ◽  
Trna Synthetase ◽  
Inhibitory Effects ◽  
Content Type ◽  
Growth Inhibitory ◽  
Spontaneous Mutants ◽  
Identification And Characterization

ABSTRACTBacteria produced-amino acids for incorporation into the peptidoglycan and certain nonribosomally produced peptides. However,d-amino acids are toxic if mischarged on tRNAs or misincorporated into protein. Common strains of the Gram-positive bacteriumBacillus subtilisare particularly sensitive to the growth-inhibitory effects ofd-tyrosine due to the absence ofd-aminoacyl-tRNA deacylase, an enzyme that prevents misincorporation ofd-tyrosine and otherd-amino acids into nascent proteins. We isolated spontaneous mutants ofB. subtilisthat survive in the presence of a mixture ofd-leucine,d-methionine,d-tryptophan, andd-tyrosine. Whole-genome sequencing revealed that these strains harbored mutations affecting tRNATyrcharging. Three of the most potent mutations enhanced the expression of the gene (tyrS) for tyrosyl-tRNA synthetase. In particular, resistance was conferred by mutations that destabilized the terminator hairpin of thetyrSriboswitch, as well as by a mutation that transformed a tRNAPheinto atyrSriboswitch ligand. The most potent mutation, a substitution near the tyrosine recognition site of tyrosyl-tRNA synthetase, improved enzyme stereoselectivity. We conclude that these mutations promote the proper charging of tRNATyr, thus facilitating the exclusion ofd-tyrosine from protein biosynthesis in cells that lackd-aminoacyl-tRNA deacylase.IMPORTANCEProteins are composed ofl-amino acids. Mischarging of tRNAs withd-amino acids or the misincorporation ofd-amino acids into proteins causes toxicity. This work reports on mutations that confer resistance tod-amino acids and their mechanisms of action.

scholarly journals Identification and Characterization of α-Glucosidase Inhibition Flavonol Glycosides from Jack Bean (Canavalia ensiformis (L.) DC

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2481
Author(s):  
Anita M. Sutedja ◽  
Emiko Yanase ◽  
Irmanida Batubara ◽  
Dedi Fardiaz ◽  
Hanifah N. Lioe
Keyword(s):  
2D Nmr ◽  
The Other ◽  
Inhibition Activity ◽  
Jack Bean ◽  
Canavalia Ensiformis ◽  
Kaempferol Glycosides ◽  
Uv Visible ◽  
First Time ◽  
Identification And Characterization

Although the intake of jack bean (Canavalia ensiformis (L.) DC.), an underutilized tropical legume, can potentially decrease the risk of several chronic diseases, not much effort has been directed at profiling the polyphenolics contained therein. Hence, this work aimed to identify and quantify the dominant jack bean polyphenolics, which are believed to have antioxidant and other bioactivities. Four major compounds were detected and identified as kaempferol glycosides with three or four glycoside units. Their structures were established based on UV-visible, 1D, 2D NMR, and HR-ESI-MS analyses. Specifically, kaempferol 3-O-α-l-rhamnopyranosyl (1→6)- β-d-glucopyranosyl (1→2)-β-d-galactopyranosyl-7-O-[3-O-o-anisoyl]-α-l-rhamnopyranoside was detected for the first time, while the other three compounds have already been described in plants other than jack bean. This new compound was found to have a higher α-glucosidase inhibition activity compared to acarbose.

scholarly journals Chromatin accessibility is dynamically regulated across C. elegans development and ageing

2018 ◽  
Author(s):  
Jürgen Jänes ◽  
Yan Dong ◽  
Michael Schoof ◽  
Jacques Serizay ◽  
Alex Appert ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Protein Coding ◽  
C Elegans ◽  
Transcription Profiles ◽  
Physiological Processes ◽  
Global Identification ◽  
Identification And Characterization

AbstractAn essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, hundreds of promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements is regulated during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

Dispersal of linezolid-resistant enterococci carrying poxtA or optrA in retail meat and food-producing animals from Tunisia

2019 ◽  
Vol 74 (10) ◽  
pp. 2865-2869 ◽  
Author(s):  
Houyem Elghaieb ◽  
Ana R Freitas ◽  
Mohamed Salah Abbassi ◽  
Carla Novais ◽  
Mohamed Zouari ◽  
...  
Keyword(s):  
Developed Countries ◽  
Cow Milk ◽  
Urban Wastewater ◽  
Virulence Markers ◽  
Linezolid Resistance ◽  
Alternative Measures ◽  
Retail Meat ◽  
First Time ◽  
Identification And Characterization

Abstract Objectives The epidemiology of Enterococcus resistant to priority antibiotics including linezolid has mainly been investigated in developed countries and especially in hospitals. We aimed to evaluate the contribution of different non-human reservoirs for the burden of MDR enterococci in Tunisia, where scarce data are available. Methods Samples (n = 287) were collected from urban wastewater (n = 57), retail meat (n = 29; poultry/bovine/ovine), milk (n = 89; bovine/ovine), farm animal faeces (n = 80; poultry/bovine/ovine) and pets (n = 32; rabbit/dogs/cats/birds) in different Tunisian regions (2014–17). They were plated onto Slanetz–Bartley agar after pre-enrichment without antibiotics. Standard methods were used for bacterial identification and characterization of antibiotic resistance and virulence genes (PCR), antibiotic susceptibility testing (disc diffusion/broth microdilution; EUCAST/CLSI) and clonality (SmaI-PFGE/MLST). Results All samples carried Enterococcus (n = 377 isolates) resistant to antibiotics considered to be critical or highly important by WHO. Even without antibiotic selection, 38% of Enterococcus faecalis (Efs) and 22% of Enterococcus faecium (Efm) were identified as MDR. Linezolid-resistant isolates (5%; MIC = 8 mg/L) comprised six poxtA-carrying Efm (cow milk), seven optrA-carrying Efs (chicken faeces/meat) and five Efm lacking cfr/optrA/poxtA (poultry/bovine/ovine/wastewater). Clinically relevant Efm clones (clade A1) were identified in animal/meat sources. Ampicillin resistance (1%) was confined to ST18/ST78-like MDR Efm clones from bovine meat/milk samples carrying relevant virulence markers (e.g. ptsD/IS16). Conclusions This study provides evidence of the contribution of livestock and foodstuffs to the dispersal of acquired linezolid resistance genes including poxtA and optrA. We report the first poxtA-carrying Efm in Tunisia, and for the first time in bovine samples, stressing the urgent need for alternative measures to counteract the spread of linezolid-resistant enterococci globally.

scholarly journals The Quest for Phenolic Compounds from Macroalgae: A Review of Extraction and Identification Methodologies

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 847 ◽  
Author(s):  
Sónia A. O. Santos ◽  
Rafael Félix ◽  
Adriana C. S. Pais ◽  
Sílvia M. Rocha ◽  
Armando J. D. Silvestre
Keyword(s):  
Phenolic Compounds ◽  
Biological Activities ◽  
Mass Spectrometry Data ◽  
Brown Macroalgae ◽  
Isolation And Characterization ◽  
Analytical Strategies ◽  
Critical Revision ◽  
Identification Techniques ◽  
First Time

The current interest of the scientific community for the exploitation of high-value compounds from macroalgae is related to the increasing knowledge of their biological activities and health benefits. Macroalgae phenolic compounds, particularly phlorotannins, have gained particular attention due to their specific bioactivities, including antioxidant, antiproliferative, or antidiabetic. Notwithstanding, the characterization of macroalgae phenolic compounds is a multi-step task, with high challenges associated with their isolation and characterization, due to the highly complex and polysaccharide-rich matrix of macroalgae. Therefore, this fraction is far from being fully explored. In fact, a critical revision of the extraction and characterization methodologies already used in the analysis of phenolic compounds from macroalgae is lacking in the literature, and it is of uttermost importance to compile validated methodologies and discourage misleading practices. The aim of this review is to discuss the state-of-the-art of phenolic compounds already identified in green, red, and brown macroalgae, reviewing their structural classification, as well as critically discussing extraction methodologies, chromatographic separation techniques, and the analytical strategies for their characterization, including information about structural identification techniques and key spectroscopic profiles. For the first time, mass spectrometry data of phlorotannins, a chemical family quite exclusive of macroalgae, is compiled and discussed.

scholarly journals A small mitochondrial protein present in myzozoans is essential for malaria transmission

Open Biology ◽  
2016 ◽  
Vol 6 (4) ◽  
pp. 160034 ◽  
Author(s):  
Dennis Klug ◽  
Gunnar R. Mair ◽  
Friedrich Frischknecht ◽  
Ross G. Douglas
Keyword(s):  
Drug Targets ◽  
Mitochondrial Protein ◽  
Sister Group ◽  
Developmental Defect ◽  
Mitochondrial Mass ◽  
First Time ◽  
Potential Drug Targets ◽  
Identification And Characterization

Myzozoans (which include dinoflagellates, chromerids and apicomplexans) display notable divergence from their ciliate sister group, including a reduced mitochondrial genome and divergent metabolic processes. The factors contributing to these divergent processes are still poorly understood and could serve as potential drug targets in disease-causing protists. Here, we report the identification and characterization of a small mitochondrial protein from the rodent-infecting apicomplexan parasite Plasmodium berghei that is essential for development in its mosquito host. Parasites lacking the gene mitochondrial protein ookinete developmental defect ( mpodd ) showed malformed parasites that were unable to transmit to mosquitoes. Knockout parasites displayed reduced mitochondrial mass without affecting organelle integrity, indicating no role of the protein in mitochondrial biogenesis or morphology maintenance but a likely role in mitochondrial import or metabolism. Using genetic complementation experiments, we identified a previously unrecognized Plasmodium falciparum homologue that can rescue the mpodd(−) phenotype, thereby showing that the gene is functionally conserved. As far as can be detected, mpodd is found in myzozoans, has homologues in the phylum Apicomplexa and appears to have arisen in free-living dinoflagellates. This suggests that the MPODD protein has a conserved mitochondrial role that is important for myzozoans. While previous studies identified a number of essential proteins which are generally highly conserved evolutionarily, our study identifies, for the first time, a non-canonical protein fulfilling a crucial function in the mitochondrion during parasite transmission.

scholarly journals Bakerian lecture - Amino-acid analysis and the structure of proteins

1942 ◽  
Vol 131 (863) ◽  
pp. 136-160 ◽  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Analysis ◽  
Nutritive Value ◽  
Analytical Data ◽  
Seed Proteins ◽  
Decomposition Products ◽  
First Time ◽  
Structure Of Proteins

In recent years the X-ray crystallographers have made remarkable advances in the interpretation of protein structure, and it is becoming more and more evident that a stage has been reached when their views need to be reconciled with data obtained from accurate amino-acid analysis of the proteins concerned. In all too many cases these data are, unfortunately, not yet available, and the reason why the analyst cannot supply them at short notice is due not so much to the com­plexity of the problem—which he has never sought to minimize—but to the fact that many of the more important methods of analysis in current use are an inheritance from an earlier period when such accuracy as is now demanded would have been considered almost impossible of achievement. From about 1840 until 1900, following the lead given by Liebig and later by Ritthausen, the attention of protein chemists was centred chiefly on the prepara­tion and characterization of various animal and seed proteins; as substances of physiological interest their enzymic digestion products were studied in elaborate detail by Kühne, but little attention was paid to the ultimate decomposition products, the amino-acids, in spite of the fact that Ritthausen as early as 1872 had pointed out that the proportions in which these occur might be characteristic of the protein concerned. The enunciation by Hofmeister and Fischer of the peptide hypothesis in 1901 emphasized for the first time the fundamental importance of the amino-acids, and a most fruitful period followed in which attention became almost exclusively focused on these products. Under the inspiring leadership of Fischer himself great improvements were effected in the separation and identification of the amino-acids, so that by about 1915 reasonably good analyses were available for most of the better-known proteins. Though far from complete, the analytical data showed quite clearly that proteins could differ widely in composition, and in many cases it was possible to correlate composition with nutritive value. Such an aim was, indeed, the incentive behind much of the work of this period.

scholarly journals Identification and Characterization of a Rhodopsin Kinase Gene in the Suckers of Octopus vulgaris: Looking around Using Arms?

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 936
Author(s):  
Al-Sayed Al-Soudy ◽  
Valeria Maselli ◽  
Stefania Galdiero ◽  
Michael J. Kuba ◽  
Gianluca Polese ◽  
...  
Keyword(s):  
3D Structure ◽  
Complete Characterization ◽  
Octopus Vulgaris ◽  
Kinase Gene ◽  
Light Sensing ◽  
Rhodopsin Kinase ◽  
First Time ◽  
Identification And Characterization

In their foraging behavior octopuses rely on arm search movements outside the visual field of the eyes. In these movements the environment is explored primarily by the suckers that line the entire length of the octopus arm. In this study, for the first time, we report the complete characterization of a light-sensing molecule, Ov-GRK1, in the suckers, skin and retina of Octopus vulgaris. We sequenced the O. vulgaris GRK1 gene, defining a phylogenetic tree and performing a 3D structure model prediction. Furthermore, we found differences in relative mRNA expression in different sucker types at several arm levels, and localized it through in situ hybridization. Our findings suggest that the suckers in octopus arms are much more multimodal than was previously shown, adding the potential for light sensing to the already known mechanical and chemical sensing abilities.

scholarly journals Identification and Characterization of Circular RNA as a Novel Regulator and Biomarker in Preterm Birth

2020 ◽  
Vol 8 ◽  
Author(s):  
Yuxin Ran ◽  
Nanlin Yin ◽  
Dongni Huang ◽  
Yangyu Zhao ◽  
Jing Yang ◽  
...  
Keyword(s):  
Preterm Birth ◽  
Roc Analysis ◽  
Underlying Mechanism ◽  
Circular Rna ◽  
Diagnosis And Treatment ◽  
Rna Seq ◽  
Discrimination Ability ◽  
First Time ◽  
Identification And Characterization

Preterm birth (PTB), as the leading cause of neonatal death, is a severe threat to maternal–fetal health. The diagnosis and treatment of PTB are difficult as its underlying mechanism still unknown. Circular RNA (circRNA) is an emerging molecule that plays an essential role in the pathological processes of various diseases. However, it is still unclear whether circRNAs are abnormal or involves in the PTB pathology. In this study, we analyzed RNA-seq data of peripheral blood from preterm and term pregnant women and verified with microarray data. There were 211 circRNA expression disorders in PTB, of which 68 increased and 143 decreased. Bioinformatics analysis revealed that the top 20 circRNAs competitively bind 68 miRNAs, thereby regulating 622 mRNAs mainly related to immunity, inflammation, and nerve activity, which may ultimately contribute to the occurrence of PTB. Moreover, 6 regulatory pairs, including hsa-MORC3_0001–hsa-miR-1248–CHRM2 were the core parts of this mechanism network, which might be therapeutic targets for PTB. Besides, ROC analysis indicated that hsa-ANKFY1_0025, hsa-FAM13B_0019, and hsa-NUSAP1_0010 (AUC = 0.7138, 0.9589, 1.000) have an excellent discrimination ability for PTB. Taken together, we explored for the first time the circRNA expression profile of PTB, and preliminarily analyzed its regulatory mechanism and predictive value for PTB, thus bringing new light to the diagnosis and treatment of PTB.

scholarly journals Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803

2020 ◽  
Vol 40 (4) ◽  
Author(s):  
Lauren A. Mills ◽  
Alistair J. McCormick ◽  
David J. Lea-Smith
Keyword(s):  
Amino Acids ◽  
Heterotrophic Bacteria ◽  
Membrane Lipids ◽  
Current Knowledge ◽  
Oxygenic Photosynthesis ◽  
Photosynthetic Organisms ◽  
Physiological Processes ◽  
Synechocystis Sp ◽  
Pcc 6803

Abstract Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.

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