Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri

Lv, Fanyang; Zhan, Yuhua; Lu, Wei; Xia, Ke; Shao, Yahui; Ma, Yiyuan; Zheng, Juan; Yang, Ziyin; Jiang, Shanshan; Shang, Lei; Ma, Yao; Cheng, Lei; Elmerich, Claudine; Yan, Yongliang; Lin, Min

doi:10.1016/j.isci.2022.105663

“…A total of 1,093 genes whose RNA abundance was significantly altered (Table S2) accounted for approximately 26% of P. stutzeri A1501 annotated open reading frames compared with those of the WT. The abundance of approximately 53% of the differentially accumulated transcripts was decreased in Δ hfq, including pslA and nifH , which had been reported previously (9), whereas the abundance of 47% of these transcripts was increased. Among the upregulated genes, translation initiation of benR , estA , and mupP was previously reported to be directly controlled by Hfq (34).…”

Section: Resultssupporting

confidence: 85%

“…In addition, A1501 is isolated from the rice rhizosphere and exists either in a free-living lifestyle in the soil or in root association with host plants. The successful transition from the free-living state to rhizosphere colonization involves massive reprogramming of gene expression by both regulatory proteins and ncRNAs, such as the regulatory network involving RpoS/RsmA/RsmZY for nitrogen-fixing biofilm formation and the Hfq/Crc/CrcZY regulatory system underlying hierarchical carbon substrate utilization (9,28). Random chemical mutagenesis screenings in Azorhizobium caulinodans identified Hfq as an activator for translation of NifA, one of the master regulators of nitrogen fixation (29).…”

Section: Introductionmentioning

confidence: 99%

“…Hfq is a ubiquitous RNA-binding protein (RBP), originally identified in Escherichia coli as a host factor essential for the in vitro synthesis of RNA bacteriophage Qβ-RNA(1), and has now been widely recognized as an RNA matchmaker (2). Due to its ability to bind a diverse array of RNAs, Hfq has been implicated in a multitude of complex phenotypes, including motility, carbon metabolism, host colonization, nitrogen fixation, fitness, and virulence of bacteria (5, 6, 7, 8, 9). The primary mode of action of Hfq is through acceleration of sRNA-mRNA annealing and subsequent RNA stabilization or degradation though alternative regulatory mechanisms(2, 3, 4).…”

Section: Introductionmentioning

confidence: 99%

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Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associatedPseudomonas stutzeriA1501

Lv,

Zhan,

Feng

et al. 2023

Preprint

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The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing (eCLIP-seq) to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these isnifM, encoding an isomerase necessary for nitrogenase reductase solubility;amtB,encoding an ammonium transporter;oprB,encoding a carbohydrate porin; andcheZ,encoding a chemotaxis protein. Furthermore, we identified more than one hundred genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with regulatory proteins (RsmA, AlgU, NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways.IMPORTANCENumerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing (eCLIP-seq) was employed to identify the Hfq-binding sites and potential targets in the root-associatedP. stutzeriA1501, and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown that Hfq interactions with various regulatory proteins and their potential targets at both the protein and RNA levels. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.

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“…3b). This can likely be attributed to the reverse carbon catabolite repression (rCCR) mechanism present in P. putida, which operates at the mRNA levelcontrary to transcriptional CCR in microorganisms like E. coli and B. subtilis [54][55][56] . This post-transcriptional regulation has evident physicochemical advantages, which allow for an extremely rapid and sensitive response to substrate availability.…”

Section: Discussionmentioning

confidence: 99%

Complex waste stream valorisation through combined enzymatic hydrolysis and catabolic assimilation byPseudomonas putida

Gonzalez

¹

,

Chacόn

²

,

Fisher

³

et al. 2023

Preprint

1

0

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Linear consumption models in combination with the poor waste management results in negative impact upon the climate and environment. Here we show an advanced biorefinery concept to produce biopolymers and recombinant therapeutic proteins from municipal solid waste. Careful selection and metabolic engineering of Pseudomonas putida was employed to permit efficient co-utilisation of complex, heterogenous substrate compositions derived from the most abundant municipal solid waste fractions. Enzymatic pre-treatment of the feedstock was performed, which afforded sufficient carbon for growth and bio-production of value-added products. Unlike current waste processing methods and supply of feedstocks for bio-based manufacturing, this biorefinery concept re-directs the carbon away from direct emissions and creates a land-use negative feedstock ideal for advanced biomanufacturing. We envisage this demonstration will lead to the creation of circular consumption solutions for waste and bio-production of a range of chemicals and materials in future resource finite scenarios.

show abstract

“…3b). This can likely be attributed to the reverse carbon catabolite repression (rCCR) mechanism present in P. putida, which operates at the mRNA levelcontrary to transcriptional CCR in microorganisms like E. coli and B. subtilis [54][55][56] . This post-transcriptional regulation has evident physicochemical advantages, which allow for an extremely rapid and sensitive response to substrate availability.…”

Section: Discussionmentioning

confidence: 99%

Degradation and bioconversion of complex municipal solid waste streams into human biotherapeutics and biopolymers

Gonzalez

¹

,

Chacόn

²

,

Berepiki

³

et al. 2023

Preprint

1

0

View full text Add to dashboard Cite

Linear consumption models in combination with the poor waste management results in negative impact upon the climate and environment. Here we show an advanced biorefinery concept to produce biopolymers and recombinant therapeutic proteins from municipal solid waste. Careful selection and metabolic engineering of Pseudomonas putida was employed to permit efficient co-utilisation of complex, heterogenous substrate compositions derived from the most abundant municipal solid waste fractions. Enzymatic pre-treatment of the feedstock was performed, which afforded sufficient carbon for growth and bio-production of value-added products. Unlike current waste processing methods and supply of feedstocks for bio-based manufacturing, this biorefinery concept re-directs the carbon away from direct emissions and creates a land-use negative feedstock ideal for advanced biomanufacturing. We envisage this demonstration will lead to the creation of circular consumption solutions for waste and bio-production of a range of chemicals and materials in future resource finite scenarios.

show abstract

Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri

Cited by 9 publications

References 97 publications

Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associatedPseudomonas stutzeriA1501

Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associatedPseudomonas stutzeriA1501

Complex waste stream valorisation through combined enzymatic hydrolysis and catabolic assimilation byPseudomonas putida

Degradation and bioconversion of complex municipal solid waste streams into human biotherapeutics and biopolymers

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