scholarly journals Defensins of Grasses: A Systematic Review

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1029 ◽  
Author(s):  
Tatyana I. Odintsova ◽  
Marina P. Slezina ◽  
Ekaterina A. Istomina

The grass family (Poaceae) is one of the largest families of flowering plants, growing in all climatic zones of all continents, which includes species of exceptional economic importance. The high adaptability of grasses to adverse environmental factors implies the existence of efficient resistance mechanisms that involve the production of antimicrobial peptides (AMPs). Of plant AMPs, defensins represent one of the largest and best-studied families. Although wheat and barley seed γ-thionins were the first defensins isolated from plants, the functional characterization of grass defensins is still in its infancy. In this review, we summarize the current knowledge of the characterized defensins from cultivated and selected wild-growing grasses. For each species, isolation of defensins or production by heterologous expression, peptide structure, biological activity, and structure–function relationship are described, along with the gene expression data. We also provide our results on in silico mining of defensin-like sequences in the genomes of all described grass species and discuss their potential functions. The data presented will form the basis for elucidation of the mode of action of grass defensins and high adaptability of grasses to environmental stress and will provide novel potent molecules for practical use in medicine and agriculture.

Author(s):  
Yuna Blum ◽  
Magalie Houée-Bigot ◽  
David Causeur

AbstractInference on gene regulatory networks from high-throughput expression data turns out to be one of the main current challenges in systems biology. Such networks can be very insightful for the deep understanding of interactions between genes. Because genes-gene interactions is often viewed as joint contributions to known biological mechanisms, inference on the dependence among gene expressions is expected to be consistent to some extent with the functional characterization of genes which can be derived from ontologies (GO, KEGG, …). The present paper introduces a sparse factor model as a general framework either to account for a prior knowledge on joint contributions of modules of genes to latent biological processes or to infer on the corresponding co-expression network. We propose an


2013 ◽  
Vol 92 (1) ◽  
pp. 126-130 ◽  
Author(s):  
Lucia Conde ◽  
Paige M. Bracci ◽  
Rhea Richardson ◽  
Stephen B. Montgomery ◽  
Christine F. Skibola

2021 ◽  
Vol 22 (10) ◽  
pp. 5366
Author(s):  
Ornella Urzì ◽  
Stefania Raimondo ◽  
Riccardo Alessandro

The scientific interest in the beneficial properties of natural substances has been recognized for decades, as well as the growing attention in extracellular vesicles (EVs) released by different organisms, in particular from animal cells. However, there is increasing interest in the isolation and biological and functional characterization of these lipoproteic structures in the plant kingdom. Similar to animal vesicles, these plant-derived extracellular vesicles (PDEVs) exhibit a complex content of small RNAs, proteins, lipids, and other metabolites. This sophisticated composition enables PDEVs to be therapeutically attractive. In this review, we report and discuss current knowledge on PDEVs in terms of isolation, characterization of their content, biological properties, and potential use as drug delivery systems. In conclusion, we outline controversial issues on which the scientific community shall focus the attention shortly.


2021 ◽  
Vol 9 (4) ◽  
pp. 407-416
Author(s):  
Satyabrata Nanda ◽  
◽  
Gagan Kumar ◽  
Sudheer Kumar Yadav ◽  
Sajid Hussain ◽  
...  

The GATA transcription factors (TFs) play a crucial role in regulating various physiological processes in plants. Identification and characterization of the GATA TF family has been carried out in several important grass species, including rice, maize, and bamboo. However, no information is available on the GATA TFs in the C3 grass species Dichanthelium oligosanthes. In the current study, 31 GATA genes have been identified in the D. oligosanthes genome by stringent bioinformatics analysis. The exon-intron arrangement analysis of the DoGATAs via the Gene Structure Display Server (GSDS 2.0) revealed the redundancy and differences in their gene structural organization. In addition, the sequence comparisons within the DoGATAs via BLAST revealed 11 numbers of putative paralogs. Similarly, the BLAST comparisons among the OsGATAs and DoGATAs resulted in the identification of 21 orthologs. Structural analysis of the identified DoGATAs through Simple Modular Architecture Research Tool (SMART), Conserved Domain Database (CDD), and Multiple Expectation Maximization for Motif Elicitation (MEME) revealed that all of them possess the signature GATA domain and the C-X2-C-X18-C-X2-C consensus sequence. The phylogenetic analysis via MEGA divided the DoGATAs into four groups along with rice and Arabidopsis GATAs. In addition, the subcellular localization, gene ontology, and other peptide functional prediction results further supported the DoGATAs to be putative GATA genes. Moreover, the findings of this study can serve as a basic framework for the isolation and functional characterization of GATA genes in D. oligosanthes.


2018 ◽  
Vol 16 (11) ◽  
pp. 1825-1835 ◽  
Author(s):  
Zixiang Wen ◽  
Ruijuan Tan ◽  
Shichen Zhang ◽  
Paul J. Collins ◽  
Jiazheng Yuan ◽  
...  

2016 ◽  
Author(s):  
Μαρία Ρήγα

Ο τετράνυχος, Tetranychus urticae Koch, αποτελεί σημαντικό εχθρό των καλλιεργειών. Καταπολεμάται κυρίως με εντομοκτόνα που σε συνδυασμό με τα ιδιαίτερα χαρακτηριστικά του οργανισμού, εμφανίζει υψηλά επίπεδα ανθεκτικότητας σε μεγάλο αριθμό ουσιών, όπως αβερμεκτίνες, METIs και πυρεθροειδή. Η ανθεκτικότητα του τετρανύχου στα εντομοκτόνα είναι πιθανότατα αποτέλεσμα της μεταβολικής ανθεκτικότητας ή/ και αλλαγών στο στόχο του εντομοκτόνου.Ανάλυση δεδομένων γονιδιακής έκφρασης από ανθεκτικούς πληθυσμούς στις ουσίες αυτές δείχνουν υψηλά επίπεδα έκφρασης γονιδίων αποτοξικοποίησης και κυρίως P450s. Οι P450s CYP392A16 και CYP392A11 εκφράστηκαν επιτυχώς σε βακτηριακό σύστημα. Φάνηκε πως η CYP392A16 μεταβολίζει το εντομοκτόνο abamectin παράγοντας έναν μη τοξικό υδροξυλιωμένο μεταβολίτη, όπως επιβεβαιώθηκε και από πειράματα βιοδοκιμών. Επίσης, αναπτύχθηκε αντίσωμα για το συγκεκριμένο ένζυμο με υψηλή εκξειδίκευση για την CYP392A16 σύμφωνα με πειράματα ανοσοαποτύπωσης. Επιπρόσθετα, βρέθηκε πως η CYP392A11 μεταβολίζει δύο δραστικές ουσίες που ανήκουν στα METI ακαρεοκτόνα, τα fenpyroximate και cyenopyrafen. Ο μεταβολισμός του fenpyroximate οδηγεί στη δημιουργία ενός μη τοξικού μεταβολίτη και ο μεταβολίτης του cyenopyrafen είναι ένα υδροξυλιωμένο προϊόν.Με τη χρήση του GAL4/UAS συστήματος δημιουργήθηκαν διαγονιδιακά στελέχη δροσόφιλας στα οποία συνεκφράζονται οι CYP392A16 ή CYP392A11 με τη CPR του τετρανύχου και αξιολογήθηκε η δράση αυτών σε σχέση με τον φαινότυπο της ανθεκτικότητας. Το στέλεχος που εκφράζει την CYP392A16 και TuCPR εμφανίζει ανθεκτικότητα στο εντομοκτόνο abamectin σε σύγκριση με το στέλεχος αναφοράς. Επίσης, δημιουργήθηκε το στέλεχος TuCPR; CYP392A11 που εμφανίζει ανθεκτικότητα στο fenpyroximate. Μελετήθηκε η σχετική επίδραση γνωστών μεταλλαγών (G314D, G326E στα κανάλια χλωρίου και οι L1024V, F1538I στο κανάλι νατρίου) στον φαινότυπο της ανθεκτικότητας του τετρανύχου και η κάθε μεταλλαγή εισήχθησε σε ευαίσθητο γενετικό υπόβαθρο μέσω πολλαπλών διασταυρώσεων. Φάνηκε πως οι μεμονωμένες μεταλλαγές 314D και 326E προσδίδουν χαμηλά επίπεδα ανθεκτικότητας στις μακροκυκλικές λακτόνες. Ωστόσο, ο συνδυασμός τους προσδίδει υψηλότερη ανθεκτικότητα, αλλά χαμηλότερη σε σχέση με αυτή του ανθεκτικού πληθυσμού. Συνεπώς οι μεταλλαγές αυτές δεν αποτελούν τον μοναδικό μηχανισμό που συνεισφέρει ανθεκτικότητα στις ουσίες αυτές. Η ανθεκτικότητα στα πυρεθροειδή μελετήθηκε σε ομόζυγα στελέχη που φέρουν τις μεταλλαγές 1024V και 1538I. Τα στελέχη αυτά εμφανίζουν υψηλά επίπεδα ανθεκτικότητας στο bifenthrin, χαμηλότερα από αυτά των πατρικών στελεχών. Πιθανότατα και άλλοι μηχανισμοί να παίζουν ρόλο στην ανθεκτικότητα στο bifenthrin. Επίσης, τα fenpropathrin και fluvalinate χρησιμοποιήθηκαν στα ίδια στελέχη. Φαίνεται πως οι μεταλλαγές αυτές προσδίδουν υψηλά επίπεδα προστασίας και παίζουν σημαντικό ρόλο στην ανθεκτικότητα σε αυτά τα εντομοκτόνα.


2019 ◽  
Vol 17 (04) ◽  
pp. 1950025 ◽  
Author(s):  
Sovan Saha ◽  
Abhimanyu Prasad ◽  
Piyali Chatterjee ◽  
Subhadip Basu ◽  
Mita Nasipuri

Computational prediction of functional annotation of proteins is an uphill task. There is an ever increasing gap between functional characterization of protein sequences and deluge of protein sequences generated by large-scale sequencing projects. The dynamic nature of protein interactions is frequently observed which is mostly influenced by any new change of state or change in stimuli. Functional characterization of proteins can be inferred from their interactions with each other, which is dynamic in nature. In this work, we have used a dynamic protein–protein interaction network (PPIN), time course gene expression data and protein sequence information for prediction of functional annotation of proteins. During progression of a particular function, it has also been observed that not all the proteins are active at all time points. For unannotated active proteins, our proposed methodology explores the dynamic PPIN consisting of level-1 and level-2 neighboring proteins at different time points, filtered by Damerau–Levenshtein edit distance to estimate the similarity between two protein sequences and coefficient variation methods to assess the strength of an edge in a network. Finally, from the filtered dynamic PPIN, at each time point, functional annotations of the level-2 proteins are assigned to the unknown and unannotated active proteins through the level-1 neighbor, following a bottom-up strategy. Our proposed methodology achieves an average precision, recall and F-Score of 0.59, 0.76 and 0.61 respectively, which is significantly higher than the reported state-of-the-art methods.


PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0069533 ◽  
Author(s):  
Gabriel G. Perron ◽  
Lyle Whyte ◽  
Peter J. Turnbaugh ◽  
Jacqueline Goordial ◽  
William P. Hanage ◽  
...  

2020 ◽  
Vol 477 (7) ◽  
pp. 1261-1286 ◽  
Author(s):  
Marie Anne Richard ◽  
Hannah Pallubinsky ◽  
Denis P. Blondin

Brown adipose tissue (BAT) has long been described according to its histological features as a multilocular, lipid-containing tissue, light brown in color, that is also responsive to the cold and found especially in hibernating mammals and human infants. Its presence in both hibernators and human infants, combined with its function as a heat-generating organ, raised many questions about its role in humans. Early characterizations of the tissue in humans focused on its progressive atrophy with age and its apparent importance for cold-exposed workers. However, the use of positron emission tomography (PET) with the glucose tracer [18F]fluorodeoxyglucose ([18F]FDG) made it possible to begin characterizing the possible function of BAT in adult humans, and whether it could play a role in the prevention or treatment of obesity and type 2 diabetes (T2D). This review focuses on the in vivo functional characterization of human BAT, the methodological approaches applied to examine these features and addresses critical gaps that remain in moving the field forward. Specifically, we describe the anatomical and biomolecular features of human BAT, the modalities and applications of non-invasive tools such as PET and magnetic resonance imaging coupled with spectroscopy (MRI/MRS) to study BAT morphology and function in vivo, and finally describe the functional characteristics of human BAT that have only been possible through the development and application of such tools.


2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.


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