scholarly journals Proteomic and Transcriptomic Analyses of “Candidatus Pelagibacter ubique” Describe the First PII-Independent Response to Nitrogen Limitation in a Free-Living Alphaproteobacterium

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Daniel P. Smith ◽  
J. Cameron Thrash ◽  
Carrie D. Nicora ◽  
Mary S. Lipton ◽  
Kristin E. Burnum-Johnson ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Stress Responses ◽  
Nitrogen Limitation ◽  
Nitrogen Assimilation ◽  
Field Studies ◽  
Nitrogen Stress ◽  
Marine Microorganisms ◽  
Geochemical Cycles ◽  
Major Nutrients ◽  
Microbial Productivity

ABSTRACTNitrogen is one of the major nutrients limiting microbial productivity in the ocean, and as a result, most marine microorganisms have evolved systems for responding to nitrogen stress. The highly abundant alphaproteobacterium “CandidatusPelagibacter ubique,” a cultured member of the orderPelagibacterales(SAR11), lacks the canonical GlnB, GlnD, GlnK, and NtrB/NtrC genes for regulating nitrogen assimilation, raising questions about how these organisms respond to nitrogen limitation. A survey of 266Alphaproteobacteriagenomes found these five regulatory genes nearly universally conserved, absent only in intracellular parasites and members of the orderPelagibacterales, including “Ca. Pelagibacter ubique.” Global differences in mRNA and protein expression between nitrogen-limited and nitrogen-replete cultures were measured to identify nitrogen stress responses in “Ca.Pelagibacter ubique” strain HTCC1062. Transporters for ammonium (AmtB), taurine (TauA), amino acids (YhdW), and opines (OccT) were all elevated in nitrogen-limited cells, indicating that they devote increased resources to the assimilation of nitrogenous organic compounds. Enzymes for assimilating amine into glutamine (GlnA), glutamate (GltBD), and glycine (AspC) were similarly upregulated. Differential regulation of the transcriptional regulator NtrX in the two-component signaling system NtrY/NtrX was also observed, implicating it in control of the nitrogen starvation response. Comparisons of the transcriptome and proteome supported previous observations of uncoupling between transcription and translation in nutrient-deprived “Ca.Pelagibacter ubique” cells. Overall, these data reveal a streamlined, PII-independent response to nitrogen stress in “Ca.Pelagibacter ubique,” and likely otherPelagibacterales, and show that they respond to nitrogen stress by allocating more resources to the assimilation of nitrogen-rich organic compounds.IMPORTANCEPelagibacteralesare extraordinarily abundant and play a pivotal role in marine geochemical cycles, as one of the major recyclers of labile dissolved organic matter. They are also models for understanding how streamlining selection can reshape chemoheterotroph metabolism. Streamlining and its broad importance to environmental microbiology are emerging slowly from studies that reveal the complete genomes of uncultured organisms. Here, we report another remarkable example of streamlined metabolism inPelagibacterales, this time in systems that control nitrogen assimilation.Pelagibacteralesare major contributors to metatranscriptomes and metaproteomes from ocean systems, where patterns of gene expression are used to gain insight into ocean conditions and geochemical cycles. The data presented here supply background that is essential to interpreting data from field studies.

scholarly journals Expanded Role for the Nitrogen Assimilation Control Protein in the Response of Klebsiella pneumoniae to Nitrogen Stress

2010 ◽  
Vol 192 (19) ◽  
pp. 4812-4820 ◽  
Author(s):  
Ryan L. Frisch ◽  
Robert A. Bender
Keyword(s):  
Growth Rate ◽  
Stress Response ◽  
Klebsiella Pneumoniae ◽  
Nitrogen Metabolism ◽  
Nitrogen Limitation ◽  
Nitrogen Assimilation ◽  
Nitrogen Sources ◽  
Nitrogen Stress ◽  
A Genome ◽  
Regulated Promoters

ABSTRACT Klebsiella pneumoniae is able to utilize many nitrogen sources, and the utilization of some of these nitrogen sources is dependent on the nitrogen assimilation control (NAC) protein. Seven NAC-regulated promoters have been characterized in K. pneumoniae, and nine NAC-regulated promoters have been found by microarray analysis in Escherichia coli. So far, all characterized NAC-regulated promoters have been directly related to nitrogen metabolism. We have used a genome-wide analysis of NAC binding under nitrogen limitation to identify the regions of the chromosome associated with NAC in K. pneumoniae. We found NAC associated with 99 unique regions of the chromosome under nitrogen limitation. In vitro, 84 of the 99 regions associate strongly enough with purified NAC to produce a shifted band by electrophoretic mobility shift assay. Primer extension analysis of the mRNA from genes associated with 17 of the fragments demonstrated that at least one gene associated with each fragment was NAC regulated under nitrogen limitation. The large size of the NAC regulon in K. pneumoniae indicates that NAC plays a larger role in the nitrogen stress response than it does in E. coli. Although a majority of the genes with identifiable functions that associated with NAC under nitrogen limitation are involved in nitrogen metabolism, smaller subsets are associated with carbon and energy acquisition (18 genes), and growth rate control (10 genes). This suggests an expanded role for NAC regulation during the nitrogen stress response, where NAC not only regulates genes involved in nitrogen metabolism but also regulates genes involved in balancing carbon and nitrogen pools and growth rate.

scholarly journals Heatwave frequency and seedling death alter stress-specific emissions of volatile organic compounds in Aleppo pine

Oecologia ◽  
2021 ◽  
Author(s):  
Benjamin Birami ◽  
Ines Bamberger ◽  
Andrea Ghirardo ◽  
Rüdiger Grote ◽  
Almut Arneth ◽  
...  
Keyword(s):  
Volatile Organic Compounds ◽  
Gas Exchange ◽  
Organic Compounds ◽  
Stress Responses ◽  
Methyl Salicylate ◽  
Environmental Changes ◽  
Pinus Halepensis ◽  
Dark Respiration ◽  
Seedling Mortality ◽  
Volatile Organic

AbstractBiogenic volatile organic compounds (BVOC) play important roles in plant stress responses and can serve as stress indicators. While the impacts of gradual environmental changes on BVOCs have been studied extensively, insights in emission responses to repeated stress and recovery are widely absent. Therefore, we studied the dynamics of shoot gas exchange and BVOC emissions in Pinus halepensis seedlings during an induced moderate drought, two four-day-long heatwaves, and the combination of drought and heatwaves. We found clear stress-specific responses of BVOC emissions. Reductions in acetone emissions with declining soil water content and transpiration stood out as a clear drought indicator. All other measured BVOC emissions responded exponentially to rising temperatures during heat stress (maximum of 43 °C), but monoterpenes and methyl salicylate showed a reduced temperature sensitivity during the second heatwave. We found that these decreases in monoterpene emissions between heatwaves were not reflected by similar declines in their internal storage pools. Because stress intensity was extremely severe, most of the seedlings in the heat-drought treatment died at the end of the second heatwave (dark respiration ceased). Interestingly, BVOC emissions (methanol, monoterpenes, methyl salicylate, and acetaldehyde) differed between dying and surviving seedlings, already well before indications of a reduced vitality became visible in gas exchange dynamics. In summary, we could clearly show that the dynamics of BVOC emissions are sensitive to stress type, stress frequency, and stress severity. Moreover, we found indications that stress-induced seedling mortality was preceded by altered methanol, monoterpene, and acetaldehyde emission dynamics.

Pathogen suppression by microbial volatile organic compounds in soils

2019 ◽  
Vol 95 (8) ◽  
Author(s):  
Wietse de Boer ◽  
Xiaogang Li ◽  
Annelein Meisner ◽  
Paolina Garbeva
Keyword(s):  
Volatile Organic Compounds ◽  
Organic Compounds ◽  
Abiotic Factors ◽  
Management Strategies ◽  
Field Studies ◽  
Growth Media ◽  
Soil Borne Pathogens ◽  
Volatile Organic ◽  
Microbial Volatile Organic Compounds ◽  
Pathogen Suppression

ABSTRACT There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of soil-borne pathogens are discussed.

scholarly journals RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

2019 ◽  
Author(s):  
Vinay K Nagarajan ◽  
Patrick M Kukulich ◽  
Bryan von Hagel ◽  
Pamela J Green
Keyword(s):  
Stress Responses ◽  
Lateral Root ◽  
Nitrogen Stress ◽  
Degradome Analysis ◽  
Nonsense Mediated Decay ◽  
Whole Plant ◽  
Major Player ◽  
Plant Level ◽  
The Impact ◽  
Dark Stress

Abstract XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5′ end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among these XRN4 substrates that have 5′ ends precisely at cap sites, those associated with photosynthesis, nitrogen responses and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during N resupply, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3′ fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level.

Novel aspects for management of xenobiotic compounds in wastewater treatment plants – linking theory, field studies, regulation, engineering, and experience

2000 ◽  
Vol 42 (7-8) ◽  
pp. 315-322 ◽  
Author(s):  
B. N. Jacobsen ◽  
T. Guildal
Keyword(s):  
Heavy Metals ◽  
Antibiotic Resistance ◽  
Organic Compounds ◽  
Endocrine Disruption ◽  
Wastewater Treatment Plants ◽  
Environmental Contaminants ◽  
Environmental Issues ◽  
Field Studies ◽  
Future Research ◽  
Order Of Magnitude

Management aspects for control of environmental contaminants has widened from being focussed on heavy metals to a broader approach including specific organic compounds, inhibition of sensitive bacteria or algae, and newly identified environmental issues, e.g., endocrine disruption and antibiotic resistance. Studies conducted at the Avedøre WWTP confirm the relevance of such newly discovered environmental problems, however, the order of magnitude of the effects do not seem alarming. It is recommended in future research to establish links between occurrence of specific organic compounds and heavy metals to various measures of toxicity and bioaccumulation. Also data for specific biodegradation rates in WWTPs represent a bottleneck for simulating fate of specific organic compounds in the plants.

scholarly journals Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress

2014 ◽  
Vol 112 (2) ◽  
pp. 412-417 ◽  
Author(s):  
Orly Levitan ◽  
Jorge Dinamarca ◽  
Ehud Zelzion ◽  
Desmond S. Lun ◽  
L. Tiago Guerra ◽  
...  
Keyword(s):  
Phaeodactylum Tricornutum ◽  
Nitrogen Assimilation ◽  
Nitrogen Availability ◽  
Carbon Fixation ◽  
De Novo ◽  
Nitrogen Stress ◽  
Gene Encoding ◽  
Storage Lipids ◽  
Intermediate Metabolism ◽  
Key Enzyme

Diatoms are unicellular algae that accumulate significant amounts of triacylglycerols as storage lipids when their growth is limited by nutrients. Using biochemical, physiological, bioinformatics, and reverse genetic approaches, we analyzed how the flux of carbon into lipids is influenced by nitrogen stress in a model diatom, Phaeodactylum tricornutum. Our results reveal that the accumulation of lipids is a consequence of remodeling of intermediate metabolism, especially reactions in the tricarboxylic acid and the urea cycles. Specifically, approximately one-half of the cellular proteins are cannibalized; whereas the nitrogen is scavenged by the urea and glutamine synthetase/glutamine 2-oxoglutarate aminotransferase pathways and redirected to the de novo synthesis of nitrogen assimilation machinery, simultaneously, the photobiological flux of carbon and reductants is used to synthesize lipids. To further examine how nitrogen stress triggers the remodeling process, we knocked down the gene encoding for nitrate reductase, a key enzyme required for the assimilation of nitrate. The strain exhibits 40–50% of the mRNA copy numbers, protein content, and enzymatic activity of the wild type, concomitant with a 43% increase in cellular lipid content. We suggest a negative feedback sensor that couples photosynthetic carbon fixation to lipid biosynthesis and is regulated by the nitrogen assimilation pathway. This metabolic feedback enables diatoms to rapidly respond to fluctuations in environmental nitrogen availability.

Interactions of endocrine-disrupting chemicals with stress responses in wildlife

2003 ◽  
Vol 75 (11-12) ◽  
pp. 2321-2333 ◽  
Author(s):  
T. G. Pottinger
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Environmental Contaminants ◽  
Endocrine Disrupting Chemicals ◽  
Endocrine System ◽  
Field Studies ◽  
Peripheral Tissues ◽  
Endocrine Disrupting ◽  
The Individual ◽  
Corticosteroid Response

The extent to which nonreproductive aspects of the endocrine system are affected by environmental contaminants is to a large extent unknown. However, an emerging body of data demonstrates that the neuroendocrine stress response is a sensitive target for disruption by a range of environmental contaminants, at a number of discrete loci. Several mechanisms are responsible for generating and sustaining the corticosteroid response to a stressor, including synthesis of the steroid, negative feedback at the pituitary and hypothalamus, and clearance via metabolism and conjugation in peripheral tissues and the liver. Laboratory and field studies provide evidence that these elements of the stress response are susceptible to interference by EAS. The functional significance to the individual of interference with this important adaptive mechanism remains to be established.

scholarly journals Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds

2002 ◽  
Vol 2 (6) ◽  
pp. 1847-1903 ◽  
Author(s):  
S. M. Saunders ◽  
M. E. Jenkin ◽  
R. G. Derwent ◽  
M. J. Pilling
Keyword(s):  
Volatile Organic Compounds ◽  
Organic Compounds ◽  
Good Description ◽  
Field Studies ◽  
Companion Paper ◽  
Chemical Mechanism ◽  
North West ◽  
Radical Intermediates ◽  
Volatile Organic ◽  
Master Chemical Mechanism

Abstract. Kinetic and mechanistic data relevant to the tropospheric degradation of volatile organic compounds (VOC), and the production of secondary pollutants, have previously been used to define a protocol which underpinned the construction of a near-explicit Master Chemical Mechanism. In this paper, an update to the previous protocol is presented, which has been used to define degradation schemes for 107 non-aromatic VOC as part of version 3 of the Master Chemical Mechanism (MCM v3). The treatment of 18 aromatic VOC is described in a companion paper. The protocol is divided into a series of subsections describing initiation reactions, the reactions of the radical intermediates and the further degradation of first and subsequent generation products. Emphasis is placed on updating the previous information, and outlining the methodology which is specifically applicable to VOC not considered previously (e.g. a- and b-pinene). The present protocol aims to take into consideration work available in the open literature up to the beginning of 2001, and some other studies known by the authors which were under review at the time. Application of MCM v3 in appropriate box models indicates that the representation of isoprene degradation provides a good description of the speciated distribution of oxygenated organic products observed in reported field studies where isoprene was the dominant emitted hydrocarbon, and that the a-pinene degradation chemistry provides a good description of the time dependence of key gas phase species in a-pinene/NOX photo-oxidation experiments carried out in the European Photoreactor (EUPHORE). Photochemical Ozone Creation Potentials (POCP) have been calculated for the 106 non-aromatic non-methane VOC in MCM v3 for idealised conditions appropriate to north-west Europe, using a photochemical trajectory model. The POCP values provide a measure of the relative ozone forming abilities of the VOC. Where applicable, the values are compared with those calculated with previous versions of the MCM.

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