scholarly journals Interactions among Redox Regulators and the CtrA Phosphorelay in Dinoroseobacter shibae and Rhodobacter capsulatus

2020 ◽  
Vol 8 (4) ◽  
pp. 562
Author(s):  
Sonja Koppenhöfer ◽  
Andrew S. Lang
Keyword(s):  
Regulatory Networks ◽  
Rhodobacter Capsulatus ◽  
Environmental Changes ◽  
Environmental Signals ◽  
Complex Interactions ◽  
Regulatory Systems ◽  
Dinoroseobacter Shibae ◽  
Transcriptional Effect ◽  
First Time ◽  
Encoding Genes

Bacteria employ regulatory networks to detect environmental signals and respond appropriately, often by adjusting gene expression. Some regulatory networks influence many genes, and many genes are affected by multiple regulatory networks. Here, we investigate the extent to which regulatory systems controlling aerobic–anaerobic energetics overlap with the CtrA phosphorelay, an important system that controls a variety of behavioral processes, in two metabolically versatile alphaproteobacteria, Dinoroseobacter shibae and Rhodobacter capsulatus. We analyzed ten available transcriptomic datasets from relevant regulator deletion strains and environmental changes. We found that in D. shibae, the CtrA phosphorelay represses three of the four aerobic–anaerobic Crp/Fnr superfamily regulator-encoding genes (fnrL, dnrD, and especially dnrF). At the same time, all four Crp/Fnr regulators repress all three phosphorelay genes. Loss of dnrD or dnrF resulted in activation of the entire examined CtrA regulon, regardless of oxygen tension. In R. capsulatus FnrL, in silico and ChIP-seq data also suggested regulation of the CtrA regulon, but it was only with loss of the redox regulator RegA where an actual transcriptional effect on the CtrA regulon was observed. For the first time, we show that there are complex interactions between redox regulators and the CtrA phosphorelays in these bacteria and we present several models for how these interactions might occur.

scholarly journals Achieving similar root microbiota composition in neighbouring plants through airborne signalling

2020 ◽  
Author(s):  
Hyun Gi Kong ◽  
Geun Cheol Song ◽  
Hee-Jung Sim ◽  
Choong-Min Ryu
Keyword(s):  
Microbial Community ◽  
Environmental Changes ◽  
Tomato Seedling ◽  
Environmental Signals ◽  
Plant Volatile ◽  
The Status ◽  
Plant Growth Promoting ◽  
The Impact ◽  
First Time ◽  
Rhizosphere Microbial Community

Abstract The ability to recognize and respond to environmental signals is essential for plants. In response to environmental changes, the status of a plant is transmitted to other plants in the form of signals such as volatiles. Root-associated bacteria trigger the release of plant volatile organic compounds (VOCs). However, the impact of VOCs on the rhizosphere microbial community of neighbouring plants is not well understood. Here, we investigated the effect of VOCs on the rhizosphere microbial community of tomato plants inoculated with a plant growth-promoting rhizobacterium Bacillus amyloliquefaciens strain GB03 and that of their neighbouring plants. Interestingly, high similarity (up to 69%) was detected in the rhizosphere microbial communities of the inoculated and neighbouring plants. Leaves of the tomato plant treated with strain GB03-released β-caryophyllene as a signature VOC, which elicited the release of a large amount of salicylic acid (SA) in the root exudates of a neighbouring tomato seedling. The exposure of tomato leaves to β-caryophyllene resulted in the secretion of SA from the root. Our results demonstrate for the first time that the composition of the rhizosphere microbiota in surrounding plants is synchronized through aerial signals from plants.

scholarly journals The Role of Light and Circadian Clock in Regulation of Leaf Senescence

2021 ◽  
Vol 12 ◽  
Author(s):  
Juhyeon Lee ◽  
Myeong Hoon Kang ◽  
Jung Yeon Kim ◽  
Pyung Ok Lim
Keyword(s):  
Circadian Clock ◽  
Leaf Senescence ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Environmental Changes ◽  
Control Plant ◽  
Structural Features ◽  
Clock Period ◽  
Environmental Signals

Leaf senescence is an integrated response of the cells to develop age information and various environmental signals. Thus, some of the genes involved in the response to environmental changes are expected to regulate leaf senescence. Light acts not only as the primary source of energy for photosynthesis but also as an essential environmental cue that directly control plant growth and development including leaf senescence. The molecular mechanisms linking light signaling to leaf senescence have recently emerged, exploring the role of Phytochrome-Interacting Factors (PIFs) as a central player leading to diverse senescence responses, senescence-promoting gene regulatory networks (GRNs) involving PIFs, and structural features of transcription modules in GRNs. The circadian clock is an endogenous time-keeping system for the adaptation of organisms to changing environmental signals and coordinates developmental events throughout the life of the plant. Circadian rhythms can be reset by environmental signals, such as light-dark or temperature cycles, to match the environmental cycle. Research advances have led to the discovery of the role of core clock components as senescence regulators and their underlying signaling pathways, as well as the age-dependent shortening of the circadian clock period. These discoveries highlight the close relationship between the circadian system and leaf senescence. Key issues remain to be elucidated, including the effect of light on leaf senescence in relation to the circadian clock, and the identification of key molecules linking aging, light, and the circadian clock, and integration mechanisms of various senescence-affecting signals at the multi-regulation levels in dynamics point of view.

Anaerobic regulation of hydrogenase transcription in different bacteria

2005 ◽  
Vol 33 (1) ◽  
pp. 36-38 ◽  
Author(s):  
Á.T. Kovács ◽  
G. Rákhely ◽  
J. Balogh ◽  
G. Maróti ◽  
A. Fülöp ◽  
...  
Keyword(s):  
Rhizobium Leguminosarum ◽  
Rhodobacter Capsulatus ◽  
Environmental Changes ◽  
Anaerobic Respiration ◽  
Respiratory Control ◽  
Bacterial Cells ◽  
Hydrogen Metabolism ◽  
Regulatory Systems ◽  
Reducing Conditions ◽  
Anaerobic Regulation

Hydrogen metabolism is closely related to other important metabolic and energetic processes of bacterial cells, such as photosynthesis, anaerobic respiration and sulphur metabolism. Even small environmental changes influence these networks through different regulatory systems. The presence or absence of oxygen is one of the most important signals; how the cascades evolved to transmit this signal in different bacteria is summarized. In many instances, hydrogen is released only under anoxic conditions, because of bioenergetic considerations. Most [NiFe] hydrogenases are inactivated by oxygen, but many of them can be re-activated under reducing conditions. In addition to direct inactivation of the hydrogenases, oxygen can also regulate their expression. The global regulatory systems [FNR (fumarate and nitrate reduction regulator), ArcAB (aerobic respiratory control) and RegAB], which respond to alterations in oxygen content and redox conditions of the environment, have an important role in hydrogenase regulation of several bacteria. FNR-like proteins were shown to be important for the regulation of hydrogenases in Escherichia coli, Thiocapsa roseopersicina and Rhizobium leguminosarum, whereas RegA protein modulates the expression of hupSL genes in Rhodobacter capsulatus.

scholarly journals The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa

2021 ◽  
Vol 22 (8) ◽  
pp. 3982
Author(s):  
Karolina Kotecka ◽  
Adam Kawalek ◽  
Kamil Kobylecki ◽  
Aneta Agnieszka Bartosik
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Binding Sites ◽  
Transcriptional Profiling ◽  
Mrna Level ◽  
Transcriptional Regulators ◽  
Resistance Mechanisms ◽  
Chronic Infections ◽  
Environmental Signals ◽  
Regulatory Systems

Pseudomonas aeruginosa is a facultative human pathogen, causing acute and chronic infections that are especially dangerous for immunocompromised patients. The eradication of P. aeruginosa is difficult due to its intrinsic antibiotic resistance mechanisms, high adaptability, and genetic plasticity. The bacterium possesses multilevel regulatory systems engaging a huge repertoire of transcriptional regulators (TRs). Among these, the MarR family encompasses a number of proteins, mainly acting as repressors, which are involved in response to various environmental signals. In this work, we aimed to decipher the role of PA3458, a putative MarR-type TR from P. aeruginosa. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3458 showed changes in the mRNA level of 133 genes; among them, 100 were down-regulated, suggesting the repressor function of PA3458. Concomitantly, ChIP-seq analysis identified more than 300 PA3458 binding sites in P. aeruginosa. The PA3458 regulon encompasses genes involved in stress response, including the PA3459–PA3461 operon, which is divergent to PA3458. This operon encodes an asparagine synthase, a GNAT-family acetyltransferase, and a glutamyl aminopeptidase engaged in the production of N-acetylglutaminylglutamine amide (NAGGN), which is a potent bacterial osmoprotectant. We showed that PA3458-mediated control of PA3459–PA3461 expression is required for the adaptation of P. aeruginosa growth in high osmolarity. Overall, our data indicate that PA3458 plays a role in osmoadaptation control in P. aeruginosa.

scholarly journals Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dilara Uzuner ◽  
Yunus Akkoç ◽  
Nesibe Peker ◽  
Pınar Pir ◽  
Devrim Gözüaçık ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Regulatory Networks ◽  
Metastatic Cancer ◽  
Interaction Network ◽  
Current Treatment ◽  
Cellular Mechanisms ◽  
Protein Protein Interaction ◽  
Cancer Dormancy ◽  
Protein Protein Interaction Networks ◽  
First Time

AbstractPrimary cancer cells exert unique capacity to disseminate and nestle in distant organs. Once seeded in secondary sites, cancer cells may enter a dormant state, becoming resistant to current treatment approaches, and they remain silent until they reactivate and cause overt metastases. To illuminate the complex mechanisms of cancer dormancy, 10 transcriptomic datasets from the literature enabling 21 dormancy–cancer comparisons were mapped on protein–protein interaction networks and gene-regulatory networks to extract subnetworks that are enriched in significantly deregulated genes. The genes appearing in the subnetworks and significantly upregulated in dormancy with respect to proliferative state were scored and filtered across all comparisons, leading to a dormancy–interaction network for the first time in the literature, which includes 139 genes and 1974 interactions. The dormancy interaction network will contribute to the elucidation of cellular mechanisms orchestrating cancer dormancy, paving the way for improvements in the diagnosis and treatment of metastatic cancer.

scholarly journals First Report of blaNDM-1 Bearing IncX3 Plasmid in Clinically Isolated ST11 Klebsiella pneumoniae from Pakistan

2021 ◽  
Vol 9 (5) ◽  
pp. 951
Author(s):  
Hazrat Bilal ◽  
Gaojian Zhang ◽  
Tayyab Rehman ◽  
Jianxion Han ◽  
Sabir Khan ◽  
...  
Keyword(s):  
Sequence Type ◽  
The Other ◽  
High Rate ◽  
Antibiotics Resistance ◽  
New Delhi ◽  
Molecular Type ◽  
Plasmid Analysis ◽  
First Time ◽  
Encoding Genes ◽  
Sequence Types

The New Delhi Metallo-β-lactamase (NDM) is among the most threatening forms of carbapenemases produced by K. pneumoniae, well-known to cause severe worldwide infections. The molecular epidemiology of blaNDM-1-harboring K. pneumoniae is not well elucidated in Pakistan. Herein, we aim to determine the antibiotics-resistance profile, genes type, molecular type, and plasmid analysis of 125 clinically isolated K. pneumoniae strains from urine samples during July 2018 to January 2019 in Pakistan. A total of 34 (27.2%) K. pneumoniae isolates were carbapenemases producers, and 23 (18.4%) harbored the blaNDM-1 gene. The other carbapenemases encoding genes, i.e., blaIMP-1 (7.2%), blaVIM-1 (3.2%), and blaOXA-48 (2.4%) were also detected. The Multi Locus Sequence Typing (MLST) results revealed that all blaNDM-1-harboring isolates were ST11. The other sequence types detected were ST1, ST37, and ST105. The cluster analysis of Xbal Pulsed Field Gel Electrophoresis (PFGE) revealed variation amongst the clusters of the identical sequence type isolates. The blaNDM-1 gene in all of the isolates was located on a 45-kb IncX3 plasmid, successfully transconjugated. For the first time, blaNDM-1-bearing IncX3 plasmids were identified from Pakistan, and this might be a new primary vehicle for disseminating blaNDM-1 in Enterobacteriaceae as it has a high rate of transferability.

scholarly journals Variability in larval gut pH regulation defines sensitivity to ocean acidification in six species of the Ambulacraria superphylum

2017 ◽  
Vol 284 (1864) ◽  
pp. 20171066 ◽  
Author(s):  
Marian Hu ◽  
Yung-Che Tseng ◽  
Yi-Hsien Su ◽  
Etienne Lein ◽  
Hae-Gyeong Lee ◽  
...  
Keyword(s):  
Ocean Acidification ◽  
Large Scale ◽  
Environmental Changes ◽  
Ph Regulation ◽  
Gastric Ph ◽  
Differential Sensitivity ◽  
Larval Stages ◽  
Regulatory Systems ◽  
Alkaline Conditions ◽  
Gut Ph

The unusual rate and extent of environmental changes due to human activities may exceed the capacity of marine organisms to deal with this phenomenon. The identification of physiological systems that set the tolerance limits and their potential for phenotypic buffering in the most vulnerable ontogenetic stages become increasingly important to make large-scale projections. Here, we demonstrate that the differential sensitivity of non-calcifying Ambulacraria (echinoderms and hemichordates) larvae towards simulated ocean acidification is dictated by the physiology of their digestive systems. Gastric pH regulation upon experimental ocean acidification was compared in six species of the superphylum Ambulacraria. We observed a strong correlation between sensitivity to ocean acidification and the ability to regulate gut pH. Surprisingly, species with tightly regulated gastric pH were more sensitive to ocean acidification. This study provides evidence that strict maintenance of highly alkaline conditions in the larval gut of Ambulacraria early life stages may dictate their sensitivity to decreases in seawater pH. These findings highlight the importance of identifying and understanding pH regulatory systems in marine larval stages that may contribute to substantial energetic challenges under near-future ocean acidification scenarios.

scholarly journals Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors

2012 ◽  
Vol 367 (1593) ◽  
pp. 1213-1225 ◽  
Author(s):  
Stephen Spiro
Keyword(s):  
Nitrous Oxide ◽  
Transcription Initiation ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Environmental Signals ◽  
Production And Consumption ◽  
Genes Encoding ◽  
Nitrous Oxide Production ◽  
Biochemical Mechanisms ◽  
Nitrate And Nitrite

Several biochemical mechanisms contribute to the biological generation of nitrous oxide (N 2 O). N 2 O generating enzymes include the respiratory nitric oxide (NO) reductase, an enzyme from the flavo-diiron family, and flavohaemoglobin. On the other hand, there is only one enzyme that is known to use N 2 O as a substrate, which is the respiratory N 2 O reductase typically found in bacteria capable of denitrification (the respiratory reduction of nitrate and nitrite to dinitrogen). This article will briefly review the properties of the enzymes that make and consume N 2 O, together with the accessory proteins that have roles in the assembly and maturation of those enzymes. The expression of the genes encoding the enzymes that produce and consume N 2 O is regulated by environmental signals (typically oxygen and NO) acting through regulatory proteins, which, either directly or indirectly, control the frequency of transcription initiation. The roles and mechanisms of these proteins, and the structures of the regulatory networks in which they participate will also be reviewed.

scholarly journals The Protease ClpXP and the PAS Domain Protein DivL Regulate CtrA and Gene Transfer Agent Production inRhodobacter capsulatus

2018 ◽  
Vol 84 (11) ◽  
Author(s):  
Alexander B. Westbye ◽  
Lukas Kater ◽  
Christina Wiesmann ◽  
Hao Ding ◽  
Calvin K. Yip ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Rhodobacter Capsulatus ◽  
Caulobacter Crescentus ◽  
Response Regulator ◽  
Pas Domain ◽  
Content Type ◽  
Regulatory Systems ◽  
Gene Transfer Agent ◽  
Domain Protein

ABSTRACTSeveral members of theRhodobacterales(Alphaproteobacteria) produce a conserved horizontal gene transfer vector, called the gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system used to study GTA biology is theRhodobacter capsulatusGTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in theAlphaproteobacteriaand is an essential regulator of RcGTA production: it controls the production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that dysregulation of the CckA-ChpT-CtrA phosphorelay either by the loss of the PAS domain protein DivL or by substitution of the autophosphorylation residue of the hybrid histidine kinase CckA decreased CtrA phosphorylation and greatly increased RcGTA protein production inR. capsulatus. We show that the loss of the ClpXP protease or the three C-terminal residues of CtrA results in increased CtrA levels inR. capsulatusand identify ClpX(P) to be essential for the maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in theRhodobacterales.IMPORTANCEMembers of theRhodobacteralesare abundant in ocean and freshwater environments. The conserved GTA produced by manyRhodobacteralesmay have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay; however, several questions about GTA regulation remain. Our identification that a short DivL homologue and ClpXP regulate CtrA inR. capsulatusextends the model of CtrA regulation fromCaulobacter crescentusto a member of theRhodobacterales. We found that the magnitude of RcGTA production greatly depends on DivL and CckA kinase activity, adding yet another layer of regulatory complexity to RcGTA. RcGTA is known to undergo CckA-dependent maturation, and we extend the understanding of this process by showing that the ClpX chaperone is required for formation of tailed, DNA-containing particles.

Investigating cave responses to regional climate change: an approach to calibrate speleothem proxies in Madagascar

2021 ◽  
Author(s):  
Ny Riavo G. Voarintsoa ◽  
Antsa Lal’Aina J. Ratovonanahary ◽  
Avotriniaina Z. M. Rakotovao ◽  
Steven Bouillon
Keyword(s):  
Environmental Changes ◽  
Regional Climate ◽  
Winter Season ◽  
Regional Climate Change ◽  
Environmental Signals ◽  
Drip Water ◽  
Internal Parameters ◽  
Monitoring Study ◽  
Water Ph ◽  
Specific Factors

<p>Caves are an excellent natural laboratory for understanding the transfer processes of the region’s environmental signals to speleothems. At least eight speleothems have produced high resolution paleoclimate and paleoenvironment records from Anjohibe Cave, NW Madagascar. However, due to the remote and difficult access to many caves in Madagascar, no studies have yet been done to understand the transfer of climate and environmental changes of the region to the cave. This is the first monitoring study to understand the linkage between regional climatology and various responses in Anjohibe Cave. We monitored (1) the drip water pH, TDS, EC, temperature, δ<sup>13</sup>C<sub>DIC</sub>, δ<sup>18</sup>O<sub>w</sub>, δ<sup>2</sup>H<sub>w</sub>, and elemental (Ca, Mg, Sr) composition, and (2) the cave atmosphere <em>p</em>CO<sub>2</sub>, relative humidity and temperature. Results show that air-to-air transfer is fast, and the internal parameters closely vary with the regional climatology. In contrast, rainfall to drip signal transfer is not immediate, and it can take few months to one season for the signals to be detected in the drip water due to the “epikarst storage effect”. The deposition of CaCO<sub>3</sub> is inferred to occur late in the dry austral winter season, during which prior carbonate precipitation was also detected. Since the growth of speleothems is influenced by numerous cave-specific factors, this study, although preliminary, indicates that Anjohibe Cave drip waters are capable of registering changes in its surrounding environment. A longer monitoring study is expected in the future to constrain the timing and the mode of transfer.</p>

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