YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family of Prokaryotic DNA-binding Proteins

Schneider, Daniel; Kaiser, W.; Stutz, Cian; Holinski, Alexandra; Mayans, Olga; Babinger, Patrick

doi:10.1074/jbc.m114.620575

Cited by 7 publications

(19 citation statements)

References 44 publications

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“…However, the GN contains two domains of a DNA unwinding helicase (PF00271, PF06733) suggesting DNA interaction for these 452 sequences. Indeed, one representative, YbiB, has recently been characterized as a DNA-binding protein [ 12 ]. Altogether, this retrospective test case demonstrates the predictive power of GNNs, because the GNs are indicative of putative functions for all three clusters of homologs.…”

Section: Resultsmentioning

confidence: 99%

AGeNNT: annotation of enzyme families by means of refined neighborhood networks

2017

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BackgroundLarge enzyme families may contain functionally diverse members that give rise to clusters in a sequence similarity network (SSN). In prokaryotes, the genome neighborhood of a gene-product is indicative of its function and thus, a genome neighborhood network (GNN) deduced for an SSN provides strong clues to the specific function of enzymes constituting the different clusters. The Enzyme Function Initiative (http://enzymefunction.org/) offers services that compute SSNs and GNNs.ResultsWe have implemented AGeNNT that utilizes these services, albeit with datasets purged with respect to unspecific protein functions and overrepresented species. AGeNNT generates refined GNNs (rGNNs) that consist of cluster-nodes representing the sequences under study and Pfam-nodes representing enzyme functions encoded in the respective neighborhoods. For cluster-nodes, AGeNNT summarizes the phylogenetic relationships of the contributing species and a statistic indicates how unique nodes and GNs are within this rGNN. Pfam-nodes are annotated with additional features like GO terms describing protein function. For edges, the coverage is given, which is the relative number of neighborhoods containing the considered enzyme function (Pfam-node). AGeNNT is available at https://github.com/kandlinf/agennt.ConclusionsAn rGNN is easier to interpret than a conventional GNN, which commonly contains proteins without enzymatic function and overly specific neighborhoods due to phylogenetic bias. The implemented filter routines and the statistic allow the user to identify those neighborhoods that are most indicative of a specific metabolic capacity. Thus, AGeNNT facilitates to distinguish and annotate functionally different members of enzyme families.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1689-6) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

AGeNNT: annotation of enzyme families by means of refined neighborhood networks

2017

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“…It was concluded that the cells maintained a consistent intracellular concentration of reduced thiols, and that oxidation of the thiols by CrO 4 2only had the observable effect of decreasing growth(24). Hence, the metabolomics analysis reported herein of the samples both exposed and not exposed to CrO 4 2allow us to further test the(28)(29)(30)(31). No DNA repair and/or division genes had large negative gene fitness changes…”

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confidence: 82%

Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics

Thorgersen

Xue

Majumder

et al. 2021

Appl Environ Microbiol

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To uncover metal toxicity targets and defense mechanisms of the facultative anaerobe Pantoea strain sp. MT58 (MT58), we used a multi-omic strategy combining two global techniques, random bar code transposon-site sequencing (RB-TnSeq) and activity-based metabolomics. MT58 is a metal-tolerant Oak Ridge Reservation (ORR) environmental isolate that was enriched in the presence of metals at concentrations measured in contaminated groundwater at an ORR nuclear waste site. The effects of three chemically-different metals found at elevated concentrations in the ORR contaminated environment were investigated: the cation Al 3+ , the oxyanion CrO 4 2- , and the oxycation UO 2 2+ . Both global techniques were applied using all three metals under both aerobic and anaerobic cultures to elucidate metal interactions mediated through the activity of metabolites and key genes/proteins. These revealed that Al 3+ binds intracellular arginine, CrO 4 2- enters the cell through sulfate transporters and oxidizes intracellular reduced thiols, and membrane-bound lipopolysaccharides protect the cell from UO 2 2+ toxicity. In addition, the Tol outer membrane system contributed to the protection of cellular integrity from the toxic effects of all three metals. Likewise, we found evidence of regulation of lipid content in membranes under metal stress. Individually, RB-TnSeq and metabolomics are powerful tools to explore the impact various stresses have on biological systems. Herein we show that together they can be used synergistically to identify the molecular actors and mechanisms of these pertubations to an organism furthering our understanding of how living systems interact with their environment. Importance Studying microbial interactions with their environment can lead to a deeper understanding of biological molecular mechanisms. In this manuscript, two global techniques, RB-TnSeq and activity metabolomics, were successfully used to probe the interactions between a metal resistant microorganism, Pantoea strain sp. MT58, and metals contaminating a site where the organism can be located. A number of novel metal to microbe interactions were uncovered including Al 3+ toxicity targeting arginine synthesis, which could lead to a deeper understanding of the impact Al 3+ contamination has on microbial communities as well as its impact on higher level organisms including plants for whom Al 3+ contamination is an issue. Using multi-omic approaches as the one described here is a way to further our understanding of microbial interactions and their impacts on the environment overall.

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“…The motif-based ClusPro-PeptiDock peptide docking protocol was used for unbiased global peptide docking ( 56 ). A model of YbiB containing all loop regions was taken from the AlphaFold Protein Structure Database ( 57 , 58 ) and converted into the biological dimer by superposition on the available experimental YbiB structure (PDB: 4MUO) ( 41 ). This model was provided as receptor structure to ClusPro.…”

Section: Methodsmentioning

confidence: 99%

“…Interestingly, in E. coli , the ybiB gene is part of a LexA-regulated operon, together with the dinG helicase gene. As LexA is the main suppressor of the SOS stress response, this suggests that YbiB may play a so far unknown role in the SOS stress response, which is activated upon DNA damage ( 41 ).…”

Section: Introductionmentioning

confidence: 99%

YbiB: a novel interactor of the GTPase ObgE

Deckers

Vercauteren

Kock

et al. 2023

Nucleic Acids Research

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Obg is a widely conserved and essential GTPase in bacteria, which plays a central role in a large range of important cellular processes, such as ribosome biogenesis, DNA replication, cell division and bacterial persistence. Nevertheless, the exact function of Obg in these processes and the interactions it makes within the associated pathways remain largely unknown. Here, we identify the DNA-binding TrpD2 protein YbiB as an interactor of the Escherichia coli Obg (ObgE). We show that both proteins interact with high affinity in a peculiar biphasic fashion, and pinpoint the intrinsically disordered and highly negatively charged C-terminal domain of ObgE as a main driver for this interaction. Molecular docking and X-ray crystallography, together with site-directed mutagenesis, are used to map the binding site of this ObgE C-terminal domain within a highly positively charged groove on the surface of the YbiB homodimer. Correspondingly, ObgE efficiently inhibits the binding of DNA to YbiB, indicating that ObgE competes with DNA for binding in the positive clefts of YbiB. This study thus forms an important step for the further elucidation of the interactome and cellular role of the essential bacterial protein Obg.

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YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family of Prokaryotic DNA-binding Proteins

Cited by 7 publications

References 44 publications

AGeNNT: annotation of enzyme families by means of refined neighborhood networks

AGeNNT: annotation of enzyme families by means of refined neighborhood networks

Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics

YbiB: a novel interactor of the GTPase ObgE

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