Identification of genes regulated by the two-component system response regulator NarP of Actinobacillus pleuropneumoniae via DNA-affinity-purified sequencing

Zhang, Liqun; Huang, Qi; Fang, Qiong; Li, Haotian; Tang, Hao; Zou, Geng; Wang, Dong; Li, Siqi; Bei, Weicheng; Chen, Huanchun; Li, Lü; Zhou, Rui

doi:10.1016/j.micres.2019.126343

Cited by 12 publications

(17 citation statements)

References 55 publications

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“…Two‐component systems are the major signal transduction system for sensing environmental signals and responding to them by regulating the expression of downstream genes (Zhang et al ., 2020a, 2020b). As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Figure 4c shows that in the amino acid metabolism, the extracellular amino acids were transported into the cell by amino acid transporter (0.95‐fold). Amino acid transporters play a vital role in transporting amino acids for cellular biosynthesis (Zhang et al ., 2020). The result also showed that the amino acid metabolism in L .…”

Section: Resultsmentioning

confidence: 99%

“…First, the changes in the levels of nutrients and nitrites in the environment were detected and transported into the cell (Liu et al ., 2020). Second, extracellular glucose was transported into the cell by PTS glucose transporter subunit IIA (Kalbermatter et al ., 2017), while amino acids were transported into the cell by amino acid transporter (Zhang et al ., 2020). Glucose was converted into pyruvate, producing NADH through glycolysis; amino acids were also converted into pyruvate.…”

Section: Resultsmentioning

confidence: 99%

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Detection of nitrite degradation by Lactobacillus plantarum DMDL9010 through the anaerobic respiration electron transport chain using proteomic analysis

Yao

Liu

Liang

et al. 2020

Int J of Food Sci Tech

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This study aimed to investigate the mechanism of nitrite degradation by Lactobacillus plantarum DMDL9010 using the proteomic technology. The results showed that 0.276 g L−1 nitrite was degraded completely by L. plantarum DMDL9010 in 24 h. Nitrite was transported into the pericytoplasm by a two‐component system. Reduced nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide‐2 (FADH2) were produced during metabolism via these pathways of phosphotransferase system, glycolysis/gluconeogenesis and citrate cycle. NADH and FADH2 produced electrons catalysed by dehydrogenase. The electrons were transferred through the electron transport chain eventually to nitrite. Some molecules of nitrites gained electrons and were reduced to NH3 by nitrite reductase. Then NH3 from nitrite was converted into l‐glutamine catalysed by glutamine synthetase, which was one of the ways to generate l‐glutamine. This study can provide theoretical guidance to the research on the biological technique to reduce nitrite in food products.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Detection of nitrite degradation by Lactobacillus plantarum DMDL9010 through the anaerobic respiration electron transport chain using proteomic analysis

Yao

Liu

Liang

et al. 2020

Int J of Food Sci Tech

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“…In some of these studies, the challenges associated with heterologous expression and purification of the TF protein have been addressed by employing in vitro translations, which further assists in the automation of this approach. Among bacterial TCSs, DAP‐seq has been applied to map the target genes for metal‐responsive TCSs in Pseudomonas stutzeri , enabling the discovery of co‐regulated networks (Garber et al ., ), and to determine the targets for the RR NarP of Actinobacillus pleuropneumoniae (Zhang et al ., ). Application of DAP‐seq to more than one RR often reveals aspects of signal integration.…”

Section: Binding Site Mapping Techniquesmentioning

confidence: 97%

Tools to map target genes of bacterial two‐component system response regulators

Rajeev

Garber

Mukhopadhyay

2020

Environ Microbiol Rep

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Studies on bacterial physiology are incomplete without knowledge of the signalling and regulatory systems that a bacterium uses to sense and respond to its environment. Two-component systems (TCSs) are among the most prevalent bacterial signalling systems, and they control essential and secondary physiological processes; however, even in model organisms, we lack a complete understanding of the signals sensed, the phosphotransfer partners and the functions regulated by these systems. In this review, we discuss several tools to map the genes targeted by transcriptionally acting TCSs. Many of these tools have been used for studying individual TCSs across diverse species, but systematic approaches to delineate entire signalling networks have been very few. Since genome sequences and high-throughput technologies are now readily available, the methods presented here can be applied to characterize the entire DNA-binding TCS signalling network in any bacterial species and are especially useful for non-model environmental bacteria.

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“…Recently, a new in vitro cistromic approach called DAP-seq was developed for the in vitro large-scale analysis of TFs binding sites (TFBSs) and notably allowed the characterization of hundreds of TFs in the plant model organism Arabidopsis thaliana due to its high scalability when used in combination with cell-free protein expression (Bartlett et al, 2017;O'Malley et al, 2016). Since then, DAPseq has been used by us and others to analyze the TFBS landscapes of different bacterial regulators and showed high sensitivity, allowing the delineation of key regulatory features (Garber et al, 2018;Trouillon et al, 2020Trouillon et al, , 2021Zhang et al, 2020). Although it is believed that transcription regulatory network are highly versatile and adaptable (Lozada-Chavez, 2006;Perez and Groisman, 2009;Price et al, 2008), as shown by in silico analyses revealing potential inter-and intra-species TF functional variability (Galardini et al, 2015), the vast majority of TF studies still focus on a single strain to assess a particular TF function.…”

Section: Introductionmentioning

confidence: 99%

Determination of the Two-Component Systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages

Trouillon

Imbert

Villard

et al. 2021

Preprint

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Pseudomonas aeruginosa possesses one of the most complex bacterial regulatory networks, which largely contributes to its success as a human opportunistic pathogen. However, most of its transcription factors (TFs) are still uncharacterized and the potential intra-species variability in regulatory networks has been mostly ignored so far. Here, to provide a first global view of the two-component systems (TCSs) regulatory network in P. aeruginosa, we produced and purified all DNA-binding TCS response regulators (RRs) and used DAP-seq to map the genome-wide binding sites of these 55 TFs across the three major P. aeruginosa lineages. The resulting networks encompass about 40% of all genes in each strain and contain numerous new important regulatory interactions across most major physiological processes, including virulence and antibiotic resistance. Strikingly, the comparison between the three representative strains shows that about half of the detected targets are specific to only one or two of the tested strains, revealing a previously unknown large functional diversity of TFs within a single species. Three main mechanisms were found to drive this diversity, including differences in accessory genome content, as exemplified by the strain-specific plasmid in the IHMA87 outlier strain which harbors numerous binding sites of chromosomally-encoded RRs. Additionally, most RRs display potential auto-regulation or RR-RR cross-regulation, bringing to light the vast complexity of this network. Overall, we provide the first complete delineation of the TCS regulatory network in P. aeruginosa that will represent an important resource for future studies on this pathogen.

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Identification of genes regulated by the two-component system response regulator NarP of Actinobacillus pleuropneumoniae via DNA-affinity-purified sequencing

Cited by 12 publications

References 55 publications

Detection of nitrite degradation by Lactobacillus plantarum DMDL9010 through the anaerobic respiration electron transport chain using proteomic analysis

Detection of nitrite degradation by Lactobacillus plantarum DMDL9010 through the anaerobic respiration electron transport chain using proteomic analysis

Tools to map target genes of bacterial two‐component system response regulators

Determination of the Two-Component Systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages

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