Littérature scientifique sur le sujet « Transcriptomic response to N-starvation »

Nitrogen (N) is probably the most important macronutrient and its scarcity limits plant growth, development and fitness. N starvation response has been largely studied by transcriptomic analyses, but little is known about the role of alternative polyadenylation (APA) in such response. In this work, we show that N starvation modifies poly(A) usage in a large number of transcripts, some of them mediated by FIP1, a component of the polyadenylation machinery. Interestingly, the number of mRNAs isoforms with poly(A) tags located in protein-coding regions or 5′-UTRs significantly increases in response to N starvation. The set of genes affected by APA in response to N deficiency is enriched in N-metabolism, oxidation-reduction processes, response to stresses, and hormone responses, among others. A hormone profile analysis shows that the levels of salicylic acid (SA), a phytohormone that reduces nitrate accumulation and root growth, increase significantly upon N starvation. Meta-analyses of APA-affected and fip1-2-deregulated genes indicate a connection between the nitrogen starvation response and salicylic acid (SA) signaling. Genetic analyses show that SA may be important for preventing the overgrowth of the root system in low N environments. This work provides new insights on how plants interconnect different pathways, such as defense-related hormonal signaling and the regulation of genomic information by APA, to fine-tune the response to low N availability.

In eukaryotes, autophagy, a catabolic mechanism for macromolecule and protein recycling, allows the maintenance of amino acid pools and nutrient remobilization. For a better understanding of the relationship between autophagy and nitrogen metabolism, we studied the transcriptional plasticity of autophagy genes (ATG) in nine Arabidopsis accessions grown under normal and nitrate starvation conditions. The status of the N metabolism in accessions was monitored by measuring the relative expression of 11 genes related to N metabolism in rosette leaves. The transcriptional variation of the genes coding for enzymes involved in ammonium assimilation characterize the genetic diversity of the response to nitrate starvation. Starvation enhanced the expression of most of the autophagy genes tested, suggesting a control of autophagy at transcriptomic level by nitrogen. The diversity of the gene responses among natural accessions revealed the genetic variation existing for autophagy independently of the nutritive condition, and the degree of response to nitrate starvation. We showed here that the genetic diversity of the expression of N metabolism genes correlates with that of the ATG genes in the two nutritive conditions, suggesting that the basal autophagy activity is part of the integral response of the N metabolism to nitrate availability.

Salvia miltiorrhiza is a model plant for Chinese herbal medicine with significant pharmacologic effects due to its tanshinone components. Our previous study indicated that nitrogen starvation stress increased its tanshinone content. However, the molecular mechanism of this low nitrogen-induced tanshinone biosynthesis is still unclear. Thus, this study aimed to elucidate the molecular mechanism of tanshinone biosynthesis in S. miltiorrhiza under different N conditions [N-free (N0), low-N (Nl), and full-N (Nf, as control) conditions] by using transcriptome and metabolome analyses. Our results showed 3,437 and 2,274 differentially expressed unigenes between N0 and Nf as well as Nl and Nf root samples, respectively. N starvation (N0 and Nl) promoted the expression of the genes involved in the MVA and MEP pathway of tanshinone and terpenoid backbone biosynthesis. Gene ontology and KEGG analyses revealed that terpenoid backbone biosynthesis, hormone signal transduction, and phenylpropanoid biosynthesis were promoted under N starvation conditions, whereas starch and sucrose metabolisms, nitrogen and phosphorus metabolisms, as well as membrane development were inhibited. Furthermore, metabolome analysis showed that metabolite compounds and biosynthesis of secondary metabolites were upregulated. This study provided a novel insight into the molecular mechanisms of tanshinone production in S. miltiorrhiza in response to nitrogen stress.

ABSTRACT Adaptation of Lactococcus lactis towards progressive carbon starvation is mediated by three different types of transcriptomic responses: (i) global responses, i.e., general decreases of functions linked to bacterial growth and lack of induction of the general stress response; (ii) specific responses functionally related to glucose exhaustion, i.e., underexpression of central metabolism genes, induction of alternative sugar transport and metabolism, and induction of the arginine deiminase pathway; and (iii) other responses never described previously during carbon starvation.

Bananas are an important part of the diets of millions of people around the globe. Low P absorption and use efficiency significantly restrict banana yields. To further explore the molecular mechanisms of P regulation in banana plants, we used RNA sequencing-based transcriptomic analysis for banana plants subjected to Pi deficit stress for 60 days. We detected 1900 significantly differentially expressed genes (DEGs) in aboveground plant parts and 7398 DEGs in root parts under low P stress. Gene ontology (GO) classification analysis showed that 156,291 GO terms belonging to molecular functions, 53,114 GO terms belonging to cellular components, and 228,544 GO terms belonging to biological processes were enriched in the aboveground and root components. A number of DEGs involved in energy metabolism-related processes, signal transduction, control of rhizosphere P activation, and Pi mobilization were found, which were confirmed by quantitative reverse-transcription Polymerase Chain Reaction (qRT-PCR) analysis. At the transcriptomic level, we detected 13 DEGs from different organs and with different functions in the time-course response to phosphorus deficiency stress. These DEGs may include some key genes that regulate the phosphorus network, increasing our understanding of the molecular mechanism of Pi homeostasis in banana. These findings will also help develop biotechnologies to create a variant of banana with more effective Pi absorption and utilization.

ABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that causes a number of infections in humans, but is best known for its association with cystic fibrosis. It is able to use a wide range of sulfur compounds as sources of sulfur for growth. Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as the sulfur source led not only to a sulfate starvation response but also to induction of genes involved with type III secretion systems.

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.

Bacterial adaptive responses to biotic and abiotic stresses often involve large-scale reprogramming of the transcriptome. Since nitrogen is an essential component of the bacterial cell, the transcriptional basis of the adaptive response to nitrogen starvation has been well studied. The adaptive response to N starvation in Escherichia coli is primarily a ‘scavenging response’, which results in the transcription of genes required for the transport and catabolism of nitrogenous compounds. However, recent genome-scale studies have begun to uncover and expand some of the intricate regulatory complexities that underpin the adaptive transcriptional response to nitrogen starvation in E. coli. The purpose of this review is to highlight some of these new developments.

Tea (Camellia sinensis (L.) O. Kuntze) is a widely consumed beverage. Lack of macronutrients is a major cause of tea yield and quality losses. Though the effects of macronutrient starvation on tea metabolism have been studied, little is known about their molecular mechanisms. Hence, we investigated changes in the gene expression of tea plants under nitrogen (N), phosphate (P), and potassium (K) deficient conditions by RNA-sequencing. A total of 9103 differentially expressed genes (DEG) were identified. Function enrichment analysis showed that many biological processes and pathways were common to N, P, and K starvation. In particular, cis-element analysis of promoter of genes uncovered that members of the WRKY, MYB, bHLH, NF-Y, NAC, Trihelix, and GATA families were more likely to regulate genes involved in catechins, l-theanine, and caffeine biosynthetic pathways. Our results provide a comprehensive insight into the mechanisms of responses to N, P, and K starvation, and a global basis for the improvement of tea quality and molecular breeding.

Candida glabrata est à la fois un commensal de l’homme et une levure pathogène dont la prévalence est en train d’exploser. Elle est souvent cause d’infections systémiques mortelles, notamment en raison de ses aptitudes à résister aux azoles, limiter sa détection par le système immunitaire et facilement coloniser l’hôte humain. Par ailleurs, elle possède une incroyable capacité à s’adapter et résister aux conditions de croissance défavorables. Cependant, on ne sait que très peu de choses sur les capacités d’adaptation de C. glabrata et les régulations qui les sous-tendent. Ce constat a mené à la création du projet Candihub, qui a pour but de décrire les mécanismes permettant à ce champignon de survivre et prospérer en tant que pathogène de l’homme. Candihub se focalise sur les réseaux de régulations transcriptionnelles favorisant la forte résistance au stress de Candida glabrata. Mon projet de thèse s’est déroulé dans le cadre de Candihub. J’ai étudié les réseaux de régulation associés à plusieurs facteurs de transcription. Ces facteurs ont été spécialement choisis en raison de leurs rôles clés dans le contrôle de diverses réponses au stress, telles que la carence en fer, l’excès de fer, stress oxydatif, stress osmotique... Dans ce but, j’ai réalisé des expériences haut-débit de transcriptomique (puces à ADN) et génomique (ChIP-seq). Cela a mené à la construction d’un vaste réseau d’interactions. Je me suis ensuite concentré sur des sous-ensembles de ce réseau. La première partie a abordé le rôle du CCAAT-Binding Complex dans la respiration et l’homéostasie du fer. Le CBC est très conservé parmi les champignons. Dans S. cerevisiae, il contrôle la respiration cellulaire tandis que dans les champignons pathogènes tels que C. albicans, il gère l’homéostasie du fer. Nous avons montré que le CBC a un double rôle dans C. glabrata : il interagit avec la sous-unité régulatrice Hap4 pour contrôler la respiration et il collabore avec Yap5 pour réguler l’homéostasie du fer. La deuxième partie est fondée sur l’utilisation de la transcriptomique comparative pour découvrir de nouvelles propriétés de la réponse à la carence en fer de C. glabrata. Nous avons démontré l’importance d’Aft2 dans la réponse à la carence en fer et identifié le réseau de régulation d’Aft2. Cela a révélé le rôle de gènes normalement impliqués dans le sauvetage des ribosomes dans la voie du No Go Decay, ce qui suggère l’existence d’un lien entre l’homéostasie du fer et le NGD
Candida glabrata is simultaneously a commensal of human gut and a pathogenic yeast with an increasing prevalence. It is often associated with fatal bloodstream infections, notably because of its ability to resist azole treatments, evade the immune system and easily colonize the human host. Also, it displays incredible abilities to adapt and resist adverse growth conditions. However, little is known about C. glabrata capacities to adapt and the underlying regulations. This assessment led to the implementation of the Candihub project. It aims to describe the mechanisms that allow C. glabrata to survive and thrive as a pathogen and has a focus on the transcriptional regulatory networks promoting the yeast strong resistance to stress. My PhD project was undertaken within the framework of Candihub. I tried to unravel the regulation networks associated to several transcription factors. These factors were chosen because of their key roles in controlling an array of stress responses : iron deprivation, iron excess, oxidative stress, osmotic stress... To achieve that goal, I performed high-throughput transcriptomic (microarrays) and genomic (ChIP -seq) analyses. This led to the construction of a wide network of interactions. Afterwards, I focused on smaller subparts of this network. The first part tackled the role of the CCAAT-Binding Complex in respiration and iron homeostasis. The CBC is very conserved across the fungi. In S. cerevisiae, it controls cellular respiration, while in pathogenic fungi such as C. albicans, it controls the iron homeostasis. We showed that the CBC has a dual role in C. glabrata : it interacts with the regulatory subunit Hap4 to control respiration and it collaborates with Yap5 to act on iron homeostasis. The second part was based on the use of comparative transcriptomics to uncover unknown features of the iron starvation response of C. glabrata. We demonstrated the significance of Aft2 in response to iron starvation and we identified the regulatory network of Aft2. This revealed the involvement of genes responsible for ribosome rescue in the No GO Decay pathway, thus suggesting a link between iron homeostasis and the NGD

L'azoto (N) è l'elemento richiesto in quantità maggiori dalle piante dopo il carbonio (C) ed è un costituente principale di acidi nucleici, proteine, coenzimi, fitormoni, clorofilla e metaboliti secondari. La biodisponibilità di questo elemento è quindi un fattore cruciale per la crescita delle piante e di conseguenza l'uso di fertilizzanti è necessario per la produttività dei sistemi agricoli. Nella maggior parte dei terreni, ammonio e nitrato sono le fonti principali di N disponibili per la nutrizione delle piante. Anche se le concentrazioni medie del primo nel suolo sono spesso 10-1000 volte inferiori a quelle del NO3-, questa differenza non riflette necessariamente il rapporto di assorbimento da parte delle radici. L'assorbimento del NO3- è stato ampiamente studiato, mentre meno informazioni sono invece disponibili per NH4+. Precedenti studi condotti su riso, abete rosso e Arabidopsis hanno rivelato l'esistenza di due sistemi di trasporto per NH4 + con alta (HATS) e bassa (LATS) affinità. Dal momento che le informazioni riguardanti gli aspetti molecolari dell'assorbimento dell' NH4+ in mais sono molto limitate, in questo lavoro ne abbiamo caratterizzato alcuni aspetti biochimici in due linee pure di mais (LO5 e T250). Queste due linee sono state studiate in esperimenti di campo, determinando la differente efficienza di uso dell'azoto (NUE), in particolare, una mostra una NUE alta (LO5), mentre l'altra bassa (T250). Queste due linee pure erano già state caratterizzate solamente per l'assorbimento del nitrato in un precedente lavoro, evidenziando l'esistenza di due distinti sistemi di trasporto anche per questa forma azotata. L'analisi dei parametri cinetici dell'assorbimento di ammonio determinate per la prima volta in questo lavoro mostrato una minore Km per la linea ad alta NUE. L'influenza del pH sulla velocità di assorbimento dei sistemi HATS e LATS è stata determinata evidenziando che la velocità di assorbimento non dipende dalla disponibilità di H+. Differenze tra le due linee nel tasso di assorbimento delle due diverse fonti inorganiche di azoto in piante cresciute in carenza dell'elemento sono state studiate. La velocità dell'assorbimento dell'ammonio aumenta in queste condizioni più velocemente nella linea Lo5 mentre la velocità di assorbimento del NO3- tendeva a diminuire in entrambe le linee. Quando i tassi di assorbimento sono stati analizzati quando le due forme (nitrato e ammonio) erano presenti contemporaneamente nella soluzione di assorbimento (rapporto 100: 1), i tassi di assorbimento di NH4 + mostravano livelli simili a quelli del NO3-. Le due linee sono state anche caratterizzate per le loro differenze nei profili trascrizioni della radice durante la crescita in risposta alla N carenza attraverso analisi microarray. I dati ottenuti hanno evidenziato che 112 trascritti erano differenzialmente espressi tra Lo5 e T250 dopo 0, 1 e 4 giorni dall'inizio del trattamento, mentre 85 e 646 trascritti erano differenzialmente espressi sia a 0 e 1 giorni e sia a 1 e 4 giorni, rispettivamente. L'annotazione manuale di questi trascritti differenzialmente espressi e lo studio del loro comportamento nei due linee ci permettono di sostenere l'ipotesi che la linea ad alta NUE (Lo5) risponde alla N carenza rispetto alla linea NUE basso (T250) attraverso una forte espressione di geni che sembrano essere coinvolti nei meccanismi molecolari che mediano la risposta all'assenza di macronutrienti nelle radici.
Nitrogen (N) is the element required in greatest amounts by plants after carbon (C) and it is a primary component of nucleic acids, proteins, co-enzymes, phytohormones, chlorophyll and also secondary metabolites which plays extremely important roles for plant life. The bioavailability this element to roots is therefore a crucial factor for plant growth and consequently the use of fertilizers is required to agricultural systems. In most soils, NH4+ and NO3- are the predominant sources of N that are available for plant nutrition. Although the average NH4+ concentrations in soils are often 10-1000 times lower than those of NO3-, this difference does not necessarily reflect the uptake ratio of each N source. The characteristics of root NO3- uptake have been extensively studied. Less information is on the contrary available for NH4+. Previous works performed in rice, spruce and Arabidopsis have revealed the existence of two transport systems for NH4+ with high (HATS) and low (LATS) affinity. Since information regarding molecular aspects of NH4+ uptake in maize is very limited, as a first purpose of this work we characterized some biochemical aspects of NH4+ uptake in seedlings of two maize inbred lines (Lo5 and T250). These two lines were identified in field experiments as a high (Lo5) and low (T250) nitrogen use efficiency (NUE), lines respectively. As far as, the uptake of N mineral forms, the two lines were previously characterized for the difference in HATS and LATS for NO3-. The analysis of kinetics parameters of NH4+ uptake here determined showed a lower Km for the high-NUE line. The influence of pH on the uptake rate on both HATS and LATS was also evaluated showing that the uptake rate is not dependent from H+ availability. Differences between Lo5 and T250 in the uptake rate of the two inorganic N-forms during the growth without N source were analyzed. NH4+ uptake rate increased during N deprivation with a steeper profile in Lo5 whilst NO3- uptake rate tended to decrease in both lines. When the uptake rates were analyzed in the contemporary presence of NO3- and NH4+ in the uptake solution with a 100:1 ratio, the NH4+ uptake rates showed similar levels to those of and NO3-. The two lines were also characterized for their differences in root transcriptional profile during N deprivation through microarray analysis. Data analysis highlighted that 112 transcripts were differentially expressed between Lo5 and T250 at 0, 1 and 4 days of N deprivation, while 85 and 646 transcripts were differentially expressed both at 0 and 1 days and both at 1 and 4 days, respectively. The annotation of these differentially expressed transcripts and the study of their behaviour in the two lines strongly support the idea that the high NUE line responds to N deprivation though a stronger expression of genes known as involved in the molecular mechanisms mediating the response to the absence of the macronutrient in roots relative to the low NUE line (T250).

The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.