Over the past twenty years, nitric oxide (NO) has emerged as an important player in various plant physiological processes. Although many advances in the understanding of NO functions have been made, ...the question of how NO is produced in plants is still challenging. It is now generally accepted that the endogenous production of NO is mainly accomplished through the reduction of nitrite via both enzymatic and non-enzymatic mechanisms which remain to be fully characterized. Furthermore, experimental arguments in favour of the existence of plant nitric oxide synthase (NOS)-like enzymes have been reported. However, recent investigations revealed that land plants do not possess animal NOS-like enzymes while few algal species do. Phylogenetic and structural analyses reveals interesting features specific to algal NOS-like proteins.
•Plants use nitrite as main substrate for NO synthesis.•Land plants do not possess nitric oxide synthase-like enzymes.•A nitric oxide synthase-like synthase is conserved in few algal species.•Algal NOSs display specific structural features.
The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation. In this ...work a broad phylogenetic study has been undertaken which, considered in the context of the functional characteristics of some fully characterised CDF transporters, has aimed at identifying molecular determinants of substrate selectivity and at suggesting metal specificity for newly identified CDF transporters.
Representative CDF members from all three kingdoms of life (Archaea, Eubacteria, Eukaryotes) were retrieved from genomic databases. Protein sequence alignment has allowed detection of a modified signature that can be used to identify new hypothetical CDF members. Phylogenetic reconstruction has classified the majority of CDF family members into three groups, each containing characterised members that share the same specificity towards the principally-transported metal, i.e. Zn, Fe/Zn or Mn. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The function of some conserved amino acids was assessed by site-directed mutagenesis in the poplar Zn2+ transporter PtdMTP1 and compared with similar experiments performed in prokaryotic members. An essential structural role can be assigned to a widely conserved glycine residue, while aspartate and histidine residues, highly conserved in putative transmembrane domains, might be involved in metal transport. The potential role of group-conserved amino acid residues in metal specificity is discussed.
In the present study phylogenetic and functional analyses have allowed the identification of three major substrate-specific CDF groups. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The modified signature sequence proposed in this work can be used to identify new hypothetical CDF members.
Nitric oxide (NO) signaling regulates various physiological processes in both animals and plants. In animals, NO synthesis is mainly catalyzed by NO synthase (NOS) enzymes. Although NOS-like ...activities that are sensitive to mammalian NOS inhibitors have been detected in plant extracts, few bona fide plant NOS enzymes have been identified. We searched the data set produced by the 1000 Plants (1KP) international consortium for the presence of transcripts encoding NOS-like proteins in over 1000 species of land plants and algae. We also searched for genes encoding NOS-like enzymes in 24 publicly available algal genomes. We identified no typical NOS sequences in 1087 sequenced transcriptomes of land plants. In contrast, we identified NOS-like sequences in 15 of the 265 algal species analyzed. Even if the presence of NOS enzymes assembled from multipolypeptides in plants cannot be conclusively discarded, the emerging data suggest that, instead of generating NO with evolutionarily conserved NOS enzymes, land plants have evolved finely regulated nitrate assimilation and reduction processes to synthesize NO through a mechanism different than that in animals.
In animals, NO is synthesized from L-arginine by three isoforms of nitric oxide synthase (NOS) enzyme. NO production and effects have also been reported in plants but the identification of its ...sources, especially the enzymatic ones, remains one of the critical issues in the field. NOS-like activities have been reported, although there are no homologs of mammalian NOS in the land plant genomes sequenced so far. However, several NOS homologs have been found in algal genomes and transcriptomes. A first study has characterized a functional NOS in the chlorophyte
and the presence of NOS homologs was later confirmed in a dozen algae. These results raise the questions of the significance of the presence of NOS and their molecular diversity in algae. We hypothesize that comparisons among protein structures of the two KnNOS, together with the identification of their interacting partner proteins, might allow a better understanding of the molecular diversification and functioning of NOS in different physiological contexts and, more generally, new insights into NO signaling in photosynthetic organisms. We recently identified two NOS homologs sequences in the genome of the streptophyte
, a model alga in the study of plant adaptation to terrestrial life. The first sequence, named KnNOS1, contains canonical NOS signatures while the second, named KnNOS2, presents a large C-ter extension including a globin domain. In order to identify putative candidates for KnNOSs partner proteins, we draw the protein-protein interaction networks of the three human NOS using the BioGRID database and hypothesized on the biological role of
orthologs. Some of these conserved partners are known to be involved in mammalian NOSs regulation and functioning. In parallel, our methodological strategy for the identification of partner proteins of KnNOS1 and KnNOS2 by
pull-down assay is presented.
Microalgae have recently emerged as a key research topic, especially as biological models. Among them, the green alga Klebsormidium nitens, thanks to its particular adaptation to environmental ...stresses, represents an interesting photosynthetic eukaryote for studying the transition stages leading to the colonization of terrestrial life. The tolerance to different stresses is manifested by changes in gene expression, which can be monitored by quantifying the amounts of transcripts by RT-qPCR. The identification of optimal reference genes for experiment normalization was therefore necessary. In this study, using four statistical algorithms followed by the RankAggreg package, we determined the best reference gene pairs suitable for normalizing RT-qPCR data in K. nitens in response to three abiotic stresses: high salinity, PEG-induced dehydration and heat shock. Based on these reference genes, we were able to identify marker genes in response to the three abiotic stresses in K. nitens.
Listeria monocytogenes is a human pathogen. It is the causative agent of listeriosis, the leading cause of bacterial‐linked foodborne mortality in Europe and elsewhere. Outbreaks of listeriosis have ...been associated with the consumption of fresh produce including vegetables and fruits. In this review we summarize current data providing direct or indirect evidence that plants can serve as habitat for L. monocytogenes, enabling this human pathogen to survive and grow. The current knowledge of the mechanisms involved in the interaction of this bacterium with plants is addressed, and whether this foodborne pathogen elicits an immune response in plants is discussed.
In this review, we summarize current data providing direct or indirect evidence that plants can serve as habitats for Listeria monocytogenes, the causative agent of the food‐borne life‐threatening disease listeriosis. The mechanisms involved in the complex interplay between plants and this bacterium are addressed, and whether this pathogen elicits an immune response in plants is discussed. The combination of plant intrinsic factors, extrinsic biotic factors, and abiotic environmental factors draws the boundaries of plant habitat colonization by L. monocytogenes.
Significant efforts have been directed towards the identification of genes differentially regulated through nitric oxide (NO)-dependent processes. These efforts comprise the use of medium- and ...large-scale transcriptomic analyses including microarray and cDNA-amplification fragment length polymorphism (AFLP) approaches. Numerous putative NO-responsive genes have been identified in plant tissues and cell suspensions with transcript levels altered by artificially released NO, or endogenously produced. Comparative analysis of the data from such transcriptomic analyses in
Arabidopsis reveals that a significant part of these genes encode proteins related to plant adaptive responses to biotic and abiotic stresses. Putative common transcription factor-binding sites in the promoter of NO-regulated genes have been defined. The current challenge remains to validate the interpretations deduced from the transcriptomic analyses and to understand the molecular mechanisms underlying the NO-dependent modulation of the genes of interest.
Facing stressful conditions imposed by their environment and affecting their growth and their development throughout their life cycle, plants must be able to perceive, to process and to translate ...different stimuli into adaptive responses. Understanding the organism-coordinated responses involves a fine description of the mechanisms occurring at the cellular and molecular level. A major challenge is also to understand how the large diversity of molecules identified as signals, sensors or effectors could drive a cell to the appropriate plant response and to finally cope with various environmental cues. In this Research Topic we aim to provide an overview of various signaling mechanisms or to present new molecular signals involved in stress response and to demonstrate how basic/fundamental research on cell signaling will help to understand stress responses at the whole plant level.
Various data sets and methods of analysis were combined to produce the first comprehensive molecular phylogeny of the genus Tuber and to analyse its biogeography. Europe, North Africa, China, Asia, ...North America. Phylogenetic relationships among Tuber species were reconstructed based on a data set of internal-transcribed spacer (ITS) sequences and various phylogenetic inference methods, specifically maximum parsimony, Bayesian analysis and neighbour joining. Tajima's relative rate test showed that Tuber 18S rRNA, 5.8S rRNA, 5.8S-ITS2 rRNA and β-tubulin sequences evolved in a clock-like manner. These genes, combined or not, were employed for molecular clock estimates after construction of linearized trees using mega 3.1. We reconstructed ancestral areas in the Northern Hemisphere by means of a dispersal-vicariance analysis ( diva 1.1) based on current distribution patterns of the genus Tuber determined from the literature. The resulting molecular phylogeny divided the genus Tuber into five distinct clades, in agreement with our previously published studies. The Puberulum, Melanosporum and Rufum groups were diversified in terms of species and geographical distribution. In contrast, the Aestivum and Excavatum groups were less diversified and were located only in Europe or North Africa. Using a global molecular clock analysis, we estimated the divergence times for the origin of the genus and for the origin of several groups. diva inferred nine dispersal events and suggested that the ancestor of Tuber was originally present in Europe or was widespread in Eurasia. Equally optimal distributions were obtained for several nodes, suggesting different possible biogeographical patterns. Our analyses identified several discrepancies with the classical taxonomy of the genus, and we propose a new phylogenetic classification. According to molecular clocks, the radiation of the genus Tuber could have started between 271 and 140 Ma. Used in combination with the results obtained from time divergence estimates, this allows us to propose two equally probable scenarios of intra- and inter-continental diversification of the genus according to the geographic distribution of the most recent common ancestor in Europe or Eurasia. The biogeographical patterns imply intra-continental dispersal events between Europe and Asia and inter-continental dispersal events between North America and Europe or Asia, which are compatible with land connections during the Tertiary.
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