Structure, function and microbial ecology of diverse MarR bacterial regulators of auxin catabolism
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA868387 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21008845.fastq.gz | Fastqsanger.gz | |||
| SRR21008846.fastq.gz | Fastqsanger.gz | |||
| SRR21008847.fastq.gz | Fastqsanger.gz | |||
| SRR21008848.fastq.gz | Fastqsanger.gz | |||
| SRR21008849.fastq.gz | Fastqsanger.gz |
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Project description:Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. We identify auxin-degradation operons across the bacterial tree of life and define two distinct types based on gene content and metabolic products: iac-like and iad-like. We solve the structures of MarRs from representatives of each auxin degradation operon type, establishing that each have distinct IAA binding pockets. Comparison of representative IAA degrading strains from diverse bacterial genera show that while all degrade IAA, only strains containing iad-like auxin degrading operons interfere with auxin signaling in a complex synthetic community context. This suggests that iad-like operon containing strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
2022-08-11 | GSE210968 | GEO
Project description:Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon's MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
| S-EPMC9613470 | biostudies-literature
Project description:Structure, function and microbial ecology of diverse MarR bacterial regulators of auxin catabolism
| PRJNA768850 | ENA
Project description:SlyA and its homologs are conserved essential transcription factors in enteric bacteria, including Salmonella enterica and Yersinia pestis, in which they upregulate horizontally-acquired virulence genes. As members of the MarR family of transcription factors, they possess a small molecule binding pocket that allows the protein to undergo a conformational change upon ligand interaction that abrogates DNA binding. Although the original discovery of MarR was based on its ability to recognize xenobiotic compounds and promote their efflux, the conservation of the MarR family throughout Bacteria and Archaea suggests a more general function. Because SlyA is known to bind xenobiotic aromatic carboxylates, we performed a targeted analysis of aromatic metabolic genes in S. Typhimurium to identify potential endogenous ligands, including genes involved in essential cellular processes including iron metabolism, respiration, and aromatic amino acid and folate biosynthesis. We found that SlyA is promiscuously inhibited by multiple aromatic carboxylates including 2,3-dihydroxybenzoate, a precursor of iron-scavenging catecholate siderophores, and 4-hydroxybenzoate, a precursor of quinone-based electron-carriers, which allows it to sense changes in iron availability, respiration and growth on succinate. We suggest that SlyA and other MarR proteins sense bacterial metabolic status via the flux of aromatic carboxylates in biosynthetic pathways, allowing SlyA to function as a counter-silencer of horizontally-acquired genes that is exquisitely responsive to the metabolic state of the cell.
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Project description:Canonical auxin signalling starts with auxin binding to the receptor complex, followed by modulation of gene transcription and protein abundance (Tan et al., 2007; Chapman and Estelle, 2009; Slade et al., 2017). However, recent studies also showed an alternative mechanism in roots involving intra-cellular auxin perception, but not transcriptional reprogramming (Fendrych et al., 2018). Despite knowledge on effects of auxin on Arabidopsis root growth at the protein and phosphorylation level is increasing (Zhang et al., 2013; Mattei et al., 2013; Slade et al., 2017), it still remains incomplete. To address this gap in our knowledge, we explored the impact of auxin on the root tip proteome and phosphoproteome.
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Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmids pAMNF (encoding an N-terminal MarR-3xFLAG fusion) or pAMNM (encoding an N-terminal MarR-8xmyc fusion). The cells was cultured at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using an anti-FLAG antibody (i.e. the strain encoding the MarR-8xmyc fusion was used as a control). Libraries were prepared using DNA remaining after immunoprecipitation.
2017-12-01 | E-MTAB-5591 | biostudies-arrayexpress
Project description:The marine picocyanobacterium Prochlorococcus contributes significantly to global primary production, and its abundance and diversity is shaped in part by viral infection. Here, we identified a cyanophage-encoded MarR-type transcription factor that induces gene expression of host Prochlorococcus MED4 endoribonuclease (RNase) E during phage infection. The increase in rne transcript levels relies on the phage (p)MarR-mediated activation of an alternative promoter that gives rise to a truncated, yet, enzymatically fully functional RNase E isoform. In this study, we demonstrate that pMarR binds to an atypical activator site downstream of the transcriptional start site and that binding is enhanced in the presence of Ca2+ ions. Furthermore, we show that dimeric pMaR interacts with the α subunit of RNA polymerase, and we identified amino acid residues S66, R67 and G106, which are important for Ca2+ binding, DNA binding and dimerization of pMarR, respectively.
2023-03-11 | PXD035458 | Pride
Project description:The phytohormone auxin triggers transcriptional reprograming utilizing a well-characterized nuclear perception machinery. In contrast, mechanisms underlying other auxin effects, such as auxin feed-back on its transport, rapid regulation of ion fluxes or ultrafast global phospho-response, remain enigmatic. Auxin Binding Protein 1 (ABP1) has been contested as an auxin receptor candidate since decades. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at the acidic pH typical for the apoplast. ABP1 and its plasma membrane-localized partner, Transmembrane Kinase 1 (TMK1) are required for auxin-induced phosphorylation of about thousand proteins. Loss-of-function abp1 alleles but not complemented lines show defects in in vitro shoot regeneration and formation of auxin-transporting channels for vasculature formation and regeneration. These results support a role of ABP1-TMK1 in cell surface auxin perception mediating global auxin phospho-response and regenerative development.
2022-08-25 | PXD031063 | Pride
Project description:Single-cell transcriptome-based strategy to determine the evolutionary trajectories of longitudinal tumor biopsies from liver cancer patients by measuring cellular lineage and ecology. Our study provides a framework for monitoring tumor evolution in response to therapeutic intervention.
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