scholarly journals LuxR-Type Regulator AclR1 of Azorhizobium caulinodans Regulates Cyclic di-GMP and Numerous Phenotypes in Free-Living and Symbiotic States

2020 ◽  
Vol 33 (3) ◽  
pp. 528-538
Author(s):  
Wei Liu ◽  
Yan Li ◽  
Xue Bai ◽  
Haiguang Wu ◽  
Lanxing Bian ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Host Plants ◽  
Biological Processes ◽  
Azorhizobium Caulinodans ◽  
Free Living ◽  
A Genome ◽  
Living State ◽  
And Control ◽  
Functional Mechanisms ◽  
Azorhizobium Caulinodans Ors571

LuxR-type regulators play important roles in transcriptional regulation in bacteria and control various biological processes. A genome sequence analysis showed the existence of seven LuxR-type regulators in Azorhizobium caulinodans ORS571, an important nitrogen-fixing bacterium in both its free-living state and in symbiosis with its host, Sesbania rostrata. However, the functional mechanisms of these regulators remain unclear. In this study, we identified a LuxR-type regulator that contains a cheY-homologous receiver (REC) domain in its N terminus and designated it AclR1. Interestingly, phylogenetic analysis revealed that AclR1 exhibited relatively close evolutionary relationships with MalT/GerE/FixJ/NarL family proteins. Functional analysis of an aclR1 deletion mutant (ΔaclR1) in the free-living state showed that AclR1 positively regulated cell motility and flocculation but negatively regulated exopolysaccharide production, biofilm formation, and second messenger cyclic diguanylate (c-di-GMP)-related gene expression. In the symbiotic state, the ΔaclR1 mutant was defective in competitive colonization and nodulation on host plants. These results suggested that AclR1 could provide bacteria with the ability to compete effectively for symbiotic nodulation. Overall, our results show that the REC-LuxR-type regulator AclR1 regulates numerous phenotypes both in the free-living state and during host plant symbiosis.

scholarly journals Poly-β-Hydroxybutyrate Turnover inAzorhizobium caulinodans Is Required for Growth and AffectsnifA Expression

1998 ◽  
Vol 180 (19) ◽  
pp. 5070-5076 ◽  
Author(s):  
Karine Mandon ◽  
Nathalie Michel-Reydellet ◽  
Sergio Encarnación ◽  
P. Alexandre Kaminski ◽  
Alfonso Leija ◽  
...  
Keyword(s):  
Nitrogenase Activity ◽  
Constitutive Expression ◽  
Reducing Power ◽  
Azorhizobium Caulinodans ◽  
Free Living ◽  
Nucleotide Pools ◽  
Living State ◽  
Mutant Strains ◽  
Growth Properties ◽  
Phb Synthase

ABSTRACT Azorhizobium caulinodans is able to fix nitrogen in the free-living state and in symbiosis with the tropical legumeSesbania rostrata. The bacteria accumulate poly-β-hydroxybutyrate (PHB) under both conditions. The structural gene for PHB synthase, phbC, was inactivated by insertion of an interposon. The mutant strains obtained were devoid of PHB, impaired in their growth properties, totally devoid of nitrogenase activity ex planta (Nif−), and affected in nucleotide pools and induced Fix− nodules devoid of bacteria. The Nif− phenotype was the consequence of the lack ofnifA transcription. Nitrogenase activity was partially restored to a phbC mutant by constitutive expression of thenifA gene. However, this constitutive nifAexpression had no effect on the nucleotide content or on growth of thephbC mutant. It is suggested that PHB is required for maintaining the reducing power of the cell and therefore the bacterial growth. These observations also suggest a new control ofnifA expression to adapt nitrogen fixation to the availability of carbon and reducing equivalents.

scholarly journals The FtcR-Like Protein ActR in Azorhizobium caulinodans ORS571 Is Involved in Bacterial Motility and Symbiosis With the Host Plant

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Sun ◽  
Dandan Wang ◽  
Zhiqiu Yin ◽  
Chengsheng Zhang ◽  
Amber Bible ◽  
...  
Keyword(s):  
Host Plant ◽  
Brucella Melitensis ◽  
Transcriptional Regulator ◽  
Adaptive Responses ◽  
Azorhizobium Caulinodans ◽  
Free Living ◽  
Bacterial Flagellum ◽  
Flagellar Biosynthesis ◽  
Living State ◽  
Two Component Systems

Bacterial signal transduction pathways are important for a variety of adaptive responses to environment, such as two-component systems (TCSs). In this paper, we reported the characterization of a transcriptional regulator in Azorhizobium caulinodans ORS571, ActR, with an N-terminal receiver domain and one C-terminal OmpR/PhoB-type DNA binding domain. Sequence analysis showed that ActR shared a high similarity with FtcR regulator of Brucella melitensis 16M known to be involved in flagellar regulation. The structural gene of this regulator was largely distributed in Alphaproteobacteria, in particular in Rhizobiales and Rhodobacterales, and was located within clusters of genes related to motility functions. Furthermore, we studied the biological function of ActR in A. caulinodans grown at the free-living state or in association with Sesbania rostrata by constructing actR gene deletion mutant. In the free-living state, the bacterial flagellum and motility ability were entirely deleted, the expression of flagellar genes was downregulated; and the exopolysaccharide production, biofilm formation, and cell flocculation decreased significantly compared with those of the wild-type strain. In the symbiotic state, ΔactR mutant strain showed weakly competitive colonization and nodulation on the host plant. These results illustrated that FtcR-like regulator in A. caulinodans is involved in flagellar biosynthesis and provide bacteria with an effective competitive nodulation for symbiosis. These findings improved our knowledge of FtcR-like transcriptional regulator in A. caulinodans.

scholarly journals Azorhizobium caulinodans PIIand GlnK Proteins Control Nitrogen Fixation and Ammonia Assimilation

1999 ◽  
Vol 181 (8) ◽  
pp. 2655-2658 ◽  
Author(s):  
Nathalie Michel-Reydellet ◽  
P. Alexandre Kaminski
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Nitrogenase Activity ◽  
Ammonia Assimilation ◽  
Ammonium Excretion ◽  
Azorhizobium Caulinodans ◽  
Wild Type ◽  
Free Living ◽  
Living State ◽  
High Level

ABSTRACT We herein report that Azorhizobium caulinodansPII and GlnK are not necessary for glutamine synthetase (GS) adenylylation whereas both proteins are required for complete GS deadenylylation. The disruption of both glnB andglnK resulted in a high level of GS adenylylation under the condition of nitrogen fixation, leading to ammonium excretion in the free-living state. PII and GlnK also controllednif gene expression because NifA activated nifHtranscription and nitrogenase activity was derepressed in glnB glnK double mutants, but not in wild-type bacteria, grown in the presence of ammonia.

scholarly journals A Novel Regulatory Pathway for K+ Uptake in the Legume Symbiont Azorhizobium caulinodans in Which TrkJ Represses the kdpFABC Operon at High Extracellular K+ Concentrations

2017 ◽  
Vol 83 (19) ◽  
Author(s):  
Lowela Siarot ◽  
Hiroki Toyazaki ◽  
Makoto Hidaka ◽  
Keigo Kurumisawa ◽  
Tomoki Hirakawa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Uptake System ◽  
Azorhizobium Caulinodans ◽  
Free Living ◽  
Content Type ◽  
High K ◽  
Living State ◽  
In The Wild ◽  
Low K ◽  
Distinct Locus

ABSTRACT Bacteria have multiple K+ uptake systems. Escherichia coli, for example, has three types of K+ uptake systems, which include the low-K+-inducible KdpFABC system and two constitutive systems, Trk (TrkAG and TrkAH) and Kup. Azorhizobium caulinodans ORS571, a rhizobium that forms nitrogen-fixing nodules on the stems and roots of Sesbania rostrata, also has three types of K+ uptake systems. Through phylogenetic analysis, we found that A. caulinodans has two genes homologous to trkG and trkH, designated trkI and trkJ. We also found that trkI is adjacent to trkA in the genome and these two genes are transcribed as an operon; however, trkJ is present at a distinct locus. Our results demonstrated that trkAI, trkJ, and kup were expressed in the wild-type stem nodules, whereas kdpFABC was not. Interestingly, Δkup and Δkup ΔkdpA mutants formed Fix– nodules, while the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant formed Fix+ nodules, suggesting that with the additional deletion of Trk system genes in the Δkup mutant, Fix+ nodule phenotypes were recovered. kdpFABC of the Δkup ΔtrkJ mutant was expressed in stem nodules, but not in the free-living state, under high-K+ conditions. However, kdpFABC of the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant was highly expressed even under high-K+ conditions. The cytoplasmic K+ levels in the Δkup ΔtrkA ΔtrkI mutant, which did not express kdpFABC under high-K+ conditions, were markedly lower than those in the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant. Taking all these results into consideration, we propose that TrkJ is involved in the repression of kdpFABC in response to high external K+ concentrations and that the TrkAI system is unable to function in stem nodules. IMPORTANCE K+ is a major cytoplasmic cation in prokaryotic and eukaryotic cells. Bacteria have multiple K+ uptake systems to control the cytoplasmic K+ levels. In many bacteria, the K+ uptake system KdpFABC is expressed under low-K+ conditions. For years, many researchers have argued over how bacteria sense K+ concentrations. Although KdpD of Escherichia coli is known to sense both cytoplasmic and extracellular K+ concentrations, the detailed mechanism of K+ sensing is still unclear. In this study, we propose that the transmembrane TrkJ protein of Azorhizobium caulinodans acts as a sensor for the extracellular K+ concentration and that high extracellular K+ concentrations repress the expression of KdpFABC via TrkJ.

scholarly journals A Chemotaxis-Like Pathway of Azorhizobium caulinodans Controls Flagella-Driven Motility, Which Regulates Biofilm Formation, Exopolysaccharide Biosynthesis, and Competitive Nodulation

2018 ◽  
Vol 31 (7) ◽  
pp. 737-749 ◽  
Author(s):  
Wei Liu ◽  
Yu Sun ◽  
Rimin Shen ◽  
Xiaoxiao Dang ◽  
Xiaolin Liu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Biofilm Formation ◽  
Competitive Adsorption ◽  
Root Surface ◽  
Extracellular Polysaccharides ◽  
Azorhizobium Caulinodans ◽  
Mutant Strains ◽  
Exopolysaccharide Biosynthesis ◽  
Azorhizobium Caulinodans Ors571

The genome of the Azorhizobium caulinodans ORS571 contains a unique chemotaxis gene cluster (che) including five chemotaxis genes: cheA, cheW, cheY1, cheB, and cheR. Analysis of the role of the chemotaxis cluster of A. caulinodans using deletion mutant strains revealed that CheA or the Che signaling pathway controls chemotaxis behavior and flagella-driven motility and plays important roles in formation of biofilms and production of extracellular polysaccharides (EPS). Furthermore, the deletion mutants (ΔcheA and ΔcheA-R) were defective in competitive adsorption and colonization on the root surface of host plants. In addition, a functional CheA or Che pathway promoted competitive nodulation on roots and stems. Interestingly, a nonflagellated mutant, ΔfliM, displayed a phenotype highly similar to that of the ΔcheA or ΔcheA-R mutant strains. These findings suggest that through controlling flagella-driven motility behavior, the chemotaxis signaling pathway in A. caulinodans coordinates biofilm formation, EPS, and competitive colonization and nodulation.

scholarly journals bCNN-Methylpred: Feature-Based Prediction of RNA Sequence Modification Using Branch Convolutional Neural Network

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1155
Author(s):  
Naeem Islam ◽  
Jaebyung Park
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Domain Knowledge ◽  
Feature Space ◽  
Experimental Methods ◽  
Machine Learning Techniques ◽  
Rna Modification ◽  
Biological Processes ◽  
Rna Sequence ◽  
Functional Mechanisms

RNA modification is vital to various cellular and biological processes. Among the existing RNA modifications, N6-methyladenosine (m6A) is considered the most important modification owing to its involvement in many biological processes. The prediction of m6A sites is crucial because it can provide a better understanding of their functional mechanisms. In this regard, although experimental methods are useful, they are time consuming. Previously, researchers have attempted to predict m6A sites using computational methods to overcome the limitations of experimental methods. Some of these approaches are based on classical machine-learning techniques that rely on handcrafted features and require domain knowledge, whereas other methods are based on deep learning. However, both methods lack robustness and yield low accuracy. Hence, we develop a branch-based convolutional neural network and a novel RNA sequence representation. The proposed network automatically extracts features from each branch of the designated inputs. Subsequently, these features are concatenated in the feature space to predict the m6A sites. Finally, we conduct experiments using four different species. The proposed approach outperforms existing state-of-the-art methods, achieving accuracies of 94.91%, 94.28%, 88.46%, and 94.8% for the H. sapiens, M. musculus, S. cerevisiae, and A. thaliana datasets, respectively.

scholarly journals FixJ family regulator AcfR of Azorhizobium caulinodans is involved in symbiosis with the host plant

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wei Liu ◽  
Xue Bai ◽  
Yan Li ◽  
Haikun Zhang ◽  
Xiaoke Hu
Keyword(s):  
Signal Transduction ◽  
Host Plant ◽  
Type Strain ◽  
Wild Type Strain ◽  
Response Regulator ◽  
Azorhizobium Caulinodans ◽  
Wild Type ◽  
Response Regulators ◽  
Free Living ◽  
Two Component

Abstract Background A wide variety of bacterial adaptative responses to environmental conditions are mediated by signal transduction pathways. Two-component signal transduction systems are one of the predominant means used by bacteria to sense the signals of the host plant and adjust their interaction behaviour. A total of seven open reading frames have been identified as putative two-component response regulators in the gram-negative nitrogen-fixing bacteria Azorhizobium caulinodans ORS571. However, the biological functions of these response regulators in the symbiotic interactions between A. caulinodans ORS571 and the host plant Sesbania rostrata have not been elucidated to date. Results In this study, we identified and investigated a two-component response regulator, AcfR, with a phosphorylatable N-terminal REC (receiver) domain and a C-terminal HTH (helix-turn-helix) LuxR DNA-binding domain in A. caulinodans ORS571. Phylogenetic analysis showed that AcfR possessed close evolutionary relationships with NarL/FixJ family regulators. In addition, six histidine kinases containing HATPase_c and HisKA domains were predicted to interact with AcfR. Furthermore, the biological function of AcfR in free-living and symbiotic conditions was elucidated by comparing the wild-type strain and the ΔacfR mutant strain. In the free-living state, the cell motility behaviour and exopolysaccharide production of the ΔacfR mutant were significantly reduced compared to those of the wild-type strain. In the symbiotic state, the ΔacfR mutant showed a competitive nodule defect on the stems and roots of the host plant, suggesting that AcfR can provide A. caulinodans with an effective competitive ability for symbiotic nodulation. Conclusions Our results showed that AcfR, as a response regulator, regulates numerous phenotypes of A. caulinodans under the free-living conditions and in symbiosis with the host plant. The results of this study help to elucidate the involvement of a REC + HTH_LuxR two-component response regulator in the Rhizobium-host plant interaction.

scholarly journals Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

2021 ◽  
Author(s):  
Xiaoping Huang ◽  
Hongyu Zhang ◽  
Qiang Wang ◽  
Rong Guo ◽  
Lingxia Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Flag Leaf ◽  
Reduction Process ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Systematic Identification

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. Abstract LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation–reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

scholarly journals Risk factors and biofilm formation analyses of hospital-acquired infection of Candida pelliculosa in a neonatal intensive care unit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhijie Zhang ◽  
Yu Cao ◽  
Yanjian Li ◽  
Xufang Chen ◽  
Chen Ding ◽  
...  
Keyword(s):  
Risk Factors ◽  
Intensive Care Unit ◽  
Biofilm Formation ◽  
Prevention And Control ◽  
Neonatal Intensive Care ◽  
Infection Prevention ◽  
Infection Prevention And Control ◽  
Anti Fungal ◽  
Hospital Acquired ◽  
And Control

Abstract Background Candida pelliculosa is an ecological fungal species that can cause infections in immunocompromised individuals. Numerous studies globally have shown that C. pelliculosa infects neonates. An outbreak recently occurred in our neonatal intensive care unit; therefore, we aimed to evaluate the risk factors in this hospital-acquired fungal infection. Methods We performed a case-control study, analysing the potential risk factors for neonatal infections of C. pelliculosa so that infection prevention and control could be implemented in our units. Isolated strains were tested for drug resistance and biofilm formation, important factors for fungal transmission that give rise to hospital-acquired infections. Results The use of three or more broad-spectrum antimicrobials or long hospital stays were associated with higher likelihoods of infection with C. pelliculosa. The fungus was not identified on the hands of healthcare workers or in the environment. All fungal isolates were susceptible to anti-fungal medications, and after anti-fungal treatment, all infected patients recovered. Strict infection prevention and control procedures efficiently suppressed infection transmission. Intact adhesin-encoding genes, shown by genome analysis, indicated possible routes for fungal transmission. Conclusions The use of three or more broad-spectrum antimicrobials or a lengthy hospital stay is theoretically associated with the risk of infection with C. pelliculosa. Strains that we isolated are susceptible to anti-fungal medications, and these were eliminated by treating all patients with an antifungal. Transmission is likely via adhesion to the cell surface and biofilm formation.

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