Genetic Toolbox and Regulatory Circuits of Plant-Nematode Associations

In living cells Reactive Oxygen Species (ROS) participate in intra- and inter-cellular signaling and all cells contain specific systems that guard redox homeostasis. These systems contain both enzymes which may produce ROS such as NADPH-dependent and other oxidases or nitric oxide synthases, and ROS-neutralizing enzymes such as catalase, peroxiredoxins, thioredoxins, thioredoxin reductases, glutathione reductases, and many others. Most of the genes coding for these enzymes contain sequences targeted by micro RNAs (miRNAs), which are components of RNA-induced silencing complexes and play important roles in inhibiting translation of their targeted messenger RNAs (mRNAs). In this review we describe miRNAs that directly target and can influence enzymes responsible for scavenging of ROS and their possible role in cellular redox homeostasis. Regulation of antioxidant enzymes aims to adjust cells to survive in unstable oxidative environments; however, sometimes seemingly paradoxical phenomena appear where oxidative stress induces an increase in the levels of miRNAs which target genes which are supposed to neutralize ROS and therefore would be expected to decrease antioxidant levels. Here we show examples of such cellular behaviors and discuss the possible roles of miRNAs in redox regulatory circuits and further cell responses to stress.

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Plant–nematode interactions

Current Opinion in Plant Biology ◽

10.1016/s1369-5266(03)00059-1 ◽

2003 ◽

Vol 6 (4) ◽

pp. 327-333 ◽

Cited By ~ 178

Author(s):

Valerie M Williamson ◽

Cynthia A Gleason

Keyword(s):

Plant Nematode

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Regulation of CAMP (cathelicidin antimicrobial peptide) expression in adipocytes by TLR 2 and 4

Innate Immunity ◽

10.1177/1753425920988167 ◽

2021 ◽

Vol 27 (2) ◽

pp. 184-191

Author(s):

Alexandra Höpfinger ◽

Thomas Karrasch ◽

Andreas Schäffler ◽

Andreas Schmid

Keyword(s):

Signal Transduction ◽

Antimicrobial Peptide ◽

Drug Targets ◽

Specific Effect ◽

Potent Inducer ◽

Regulatory Circuits ◽

Signal Transduction Inhibitors ◽

Tlr4 Agonist ◽

Future Drug ◽

Regulatory Effects

Recent data argue for a pro-inflammatory role of CAMP (cathelicidin antimicrobial peptide) in adipocytes and adipose tissue (AT) and for regulatory circuits involving TLRs. In order to investigate regulatory effects of TLR2 and TLR4, 3T3-L1 adipocytes were stimulated with TLR2 agonistic lipopeptide MALP-2 and with TLR4 agonist LPS in presence or absence of signal transduction inhibitors. CAMP gene expression was analysed by quantitative real-time PCR in adipocytes and in murine AT compartments and cellular subfractions. CAMP expression was higher in gonadal than in subcutaneous AT and there was a gender-specific effect with higher levels in males. Adipocytes had higher CAMP expression than the stroma-vascular cell (SVC) fraction. MALP-2 up-regulated CAMP expression significantly, mediated by STAT3 and PI3K and potentially (non-significant trend) by NF-κB and MAPK, but not by raf-activated MEK-1/-2. Moreover, LPS proved to act as a potent inducer of CAMP via NF-κB, PI3K and STAT3, whereas specific inhibition of MAPK and MEK-1/-2 had no effect. In conclusion, activation of TLR2 and TLR4 by classical ligands up-regulates adipocyte CAMP expression involving classical signal transduction elements. These might represent future drug targets for pharmacological modulation of CAMP expression in adipocytes, especially in the context of metabolic and infectious diseases.

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Transcriptome Analysis of Eggplant Root in Response to Root-Knot Nematode Infection

Pathogens ◽

10.3390/pathogens10040470 ◽

2021 ◽

Vol 10 (4) ◽

pp. 470

Author(s):

Min Zhang ◽

Hongyuan Zhang ◽

Jie Tan ◽

Shuping Huang ◽

Xia Chen ◽

...

Keyword(s):

Defense Mechanisms ◽

Expression Profiles ◽

Resistance Mechanism ◽

Solanum Melongena ◽

Enrichment Analysis ◽

Nematode Resistance ◽

Differentially Expressed ◽

Root Knot Nematode ◽

Solanum Torvum ◽

Plant Nematode

Eggplant (Solanum melongena L.), which belongs to the Solanaceae family, is an important vegetable crop. However, its production is severely threatened by root-knot nematodes (RKNs) in many countries. Solanum torvum, a wild relative of eggplant, is employed worldwide as rootstock for eggplant cultivation due to its resistance to soil-borne diseases such as RKNs. In this study, to identify the RKN defense mechanisms, the transcriptomic profiles of eggplant and Solanum torvum were compared. A total of 5360 differentially expressed genes (DEGs) were identified for the response to RKN infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs are mainly involved in the processes of response to stimulus, protein phosphorylation, hormone signal transduction, and plant-pathogen interaction pathways. Many phytohormone-related genes and transcription factors (MYB, WRKY, and NAC) were differentially expressed at the four time points (ck, 7, 14, and 28 days post-infection). The abscisic acid signaling pathway might be involved in plant-nematode interactions. qRT-PCR validated the expression levels of some of the DEGs in eggplant. These findings demonstrate the nematode-induced expression profiles and provide some insights into the nematode resistance mechanism in eggplant.

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Spatial organization enhances versatility and specificity in cyclic di-GMP signaling

Biological Chemistry ◽

10.1515/hsz-2020-0202 ◽

2020 ◽

Vol 401 (12) ◽

pp. 1323-1334

Author(s):

Sandra Kunz ◽

Peter L. Graumann

Keyword(s):

Protein Interactions ◽

Cell Cycle Progression ◽

Spatial Organization ◽

Caulobacter Crescentus ◽

Second Messenger ◽

Protein Protein Interactions ◽

Spatial Cues ◽

Signaling Specificity ◽

Regulatory Circuits ◽

Second Messenger Signaling

AbstractThe second messenger cyclic di-GMP regulates a variety of processes in bacteria, many of which are centered around the decision whether to adopt a sessile or a motile life style. Regulatory circuits include pathogenicity, biofilm formation, and motility in a wide variety of bacteria, and play a key role in cell cycle progression in Caulobacter crescentus. Interestingly, multiple, seemingly independent c-di-GMP pathways have been found in several species, where deletions of individual c-di-GMP synthetases (DGCs) or hydrolases (PDEs) have resulted in distinct phenotypes that would not be expected based on a freely diffusible second messenger. Several recent studies have shown that individual signaling nodes exist, and additionally, that protein/protein interactions between DGCs, PDEs and c-di-GMP receptors play an important role in signaling specificity. Additionally, subcellular clustering has been shown to be employed by bacteria to likely generate local signaling of second messenger, and/or to increase signaling specificity. This review highlights recent findings that reveal how bacteria employ spatial cues to increase the versatility of second messenger signaling.

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Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp.

International Journal of Molecular Sciences ◽

10.3390/ijms21062096 ◽

2020 ◽

Vol 21 (6) ◽

pp. 2096

Author(s):

Przemyslaw Decewicz ◽

Piotr Golec ◽

Mateusz Szymczak ◽

Monika Radlinska ◽

Lukasz Dziewit

Keyword(s):

Dna Methyltransferase ◽

Wastewater Treatment Plants ◽

Biogas Production ◽

Genome Mining ◽

Sewage Sample ◽

Bacterial Strains ◽

Regulatory Circuits ◽

A Genome ◽

Insightful Analysis

The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.

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Studies on the Role of the are a Gene in the Regulation of Nitrogen Catabolism in Aspergillus nidulans

Australian Journal of Biological Sciences ◽

10.1071/bi9750301 ◽

1975 ◽

Vol 28 (3) ◽

pp. 301 ◽

Cited By ~ 84

Author(s):

MJ Hynes

Keyword(s):

Nitrogen Source ◽

Aspergillus Nidulans ◽

Carbon Sources ◽

Nitrogen Sources ◽

Selection Methods ◽

Growth Responses ◽

Dominance Relationships ◽

Regulatory Circuits ◽

Specific Activities

Mutants of Apergillus nidulanswith lesions in a gene, areA (formerly called amdT), have been isolated by a variety of different selection methods. The areA mutants show a range of pleiotropic growth responses to a number of compounds as sole nitrogen sources, but are normal in utilization of carbon sources. The levels of two amidase enzymes as well as urease have been investigated in the mutants and have been shown to be affected by this gene. Most of the areA mutants have much lower amidase-specific activities when grown in ammonium-containing medium, compared with mycelium incubated in medium la9king a nitrogen source. Some of the areA. mutants do not show derepression of urease upon relief of ammonium repression. The dominance relationships of areA alleles have been investigated in� heterozygous diploids, and these studies lend support to the proposal that areA codes for a positively acting regulatory product. One of the new areA alleles is partially dominant to areA + and areA102. This may be a result of negative complementation or indicate that areA has an additional negative reiuIatory function. Investigation.of various amdR; areA double mutants has led to the conclusion that amdR and areA participate in independent regulatory circuits in the control of acetamide utilizatiol1. Studies on an amdRc; areA.double mutant indicate that areA is involved in derepression of acetamidase upon relief of ammo.nium repression.

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MicroRNA-Mediated Regulation in Biological Systems with Oscillatory Behavior

BioMed Research International ◽

10.1155/2013/285063 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Zhiyong Zhang ◽

Fengdan Xu ◽

Zengrong Liu ◽

Ruiqi Wang ◽

Tieqiao Wen

Keyword(s):

Cell Cycle ◽

Biological Systems ◽

Noncoding Rnas ◽

Oscillatory Behavior ◽

Fine Tuning ◽

Base Pairing ◽

Periodic Behavior ◽

Small Noncoding Rnas ◽

Regulatory Circuits ◽

Mrna Transcripts

As a class of small noncoding RNAs, microRNAs (miRNAs) regulate stability or translation of mRNA transcripts. Some reports bring new insights into possible roles of microRNAs in modulating cell cycle. In this paper, we focus on the mechanism and effectiveness of microRNA-mediated regulation in the cell cycle. We first describe two specific regulatory circuits that incorporate base-pairing microRNAs and show their fine-tuning roles in the modulation of periodic behavior. Furthermore, we analyze the effects ofmiR369-3on the modulation of the cell cycle, confirming thatmiR369-3plays a role in shortening the period of the cell cycle. These results are consistent with experimental observations.

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