Biology subjects

Grove, A.

Publications and source records attributed to Grove, A..

3 recordsLinked to original sources

bioRxiv2025

Transcriptome-proteome profiling in Burkholderia thailandensis during the transition from exponential to stationary phase

Bacterial cells commonly exist in stationary phase, for instance within a host cell. Burkholderia thailandensis is closely related to, and a surrogate for highly pathogenic Burkholderia species. Understanding the molecular mechanisms that characterize the transition of B. thailandensis from exponential to stationary phases is critical to understanding responses to stress or nutrient limitation. We present here an integrated transcriptomic and proteomic analysis of gene and protein expression changes during entry into stationary phase. We identified 928 differentially expressed genes and 832 differentially expressed proteins. Genes encoding proteins involved in benzoate degradation and O-antigen nucleotide sugar biosynthesis were among the most highly upregulated in stationary phase, whereas processes such as translation and flagellar biosynthesis were downregulated. Proteins related to fatty acid degradation and butanoate metabolism accumulated along with proteins involved in synthesis of secondary metabolites. Markedly downregulated proteins included ribosomal proteins as well as the house-keeping iron-sulfur biogenesis proteins. An only modest correlation between transcriptome and proteome changes was seen, and the RpoS sigma factor was not significantly increased during early stationary phase; RpoS is typically abundant during stationary phase and critical for expression of stress-response genes. Our data therefore point to distinct adaptive mechanisms in B. thailandensis, including post-translational regulation.

microbiology↗

bioRxiv2021

Identification of a MarR subfamily that regulates arsenic resistance genes

Members of the family of Multiple Antibiotic Resistance Regulators (MarR) often regulate genes that encode antibiotic resistance in bacteria. In this study, comprehensive analyses were performed to determine the function of an atypical MarR homolog in Achromobacter sp. As-55. Genomic analyses showed that this marR is located in an arsenic gene island in Achromobacter sp. As-55 adjacent to an arsV gene. ArsV is a flavin-dependent monooxygenase that confers resistance to the antibiotic methylarsenite (MAs(III)), the organoarsenic compound roxarsone(III) (Rox(III)), and the inorganic antimonite (Sb(III)). Similar marR genes are widely distributed in arsenic-resistant bacteria. Phylogenetic analyses showed that these MarRs are found in operons predicted to be involved in resistance to inorganic and organic arsenic species, so the subfamily was named MarRars. MarRars orthologs have three conserved cysteine residues, which are Cys36, Cys37 and Cys157 in Achromobacter sp. As-55, mutation of which compromises the response to MAs(III)/Sb(III). GFP-fluorescent biosensor assays show that AdMarRars (MarR protein of Achromobacter deleyi As-55) responds to trivalent As(III) and Sb(III) but not to pentavalent As(V) or Sb(V). The results of RT-qPCR assays show that arsV is expressed constitutively in a marR deletion mutant, indicating that marR represses transcription of arsV. Moreover, electrophoretic mobility shift assays (EMSA) demonstrate that AdMarRars binds to the promoters of both marR and arsV in the absence of ligands and that DNA binding is relieved upon binding of As(III) and Sb(III). Our results demonstrate that AdMarRars is a novel As(III)/Sb(III)-responsive transcriptional repressor that controls expression of arsV, which confers resistance to MAs(III), Roxarsone(III) and Sb(III). AdMarRars and its orthologs form a subfamily of MarR proteins that regulate genes conferring resistance to arsenic-containing antibiotics. IMPORTANCEIn this study, a MarR family member, AdMarRars was shown to regulate the arsV gene, which confers resistance to arsenic-containing antibiotics. It is a founding member of a distinct subfamily that we refer to as MarRars, regulating genes conferring resistance to arsenic and antimony antibiotic compounds. AdMarRars was shown to be a repressor containing conserved cysteine residues that are required to bind As(III) and Sb(III), leading to a conformational change and subsequent derepression. Here we show that members of the MarR family are involved in regulating arsenic-containing compounds.

microbiology↗

bioRxiv2021

Intricate regulation of ribosome biogenesis genes in response to mTORC1 signaling

Genes encoding ribosomal proteins are repressed in response to inhibition of mTORC1. In Saccharomyces cerevisiae, this involves dissociation of the activator Ifh1p in a process that depends on Utp22p, a protein that also functions in pre-rRNA processing. Ifh1p has a paralog, Crf1p, which can mediate mTORC1 inhibition by acting as a repressor. Ifh1p and Crf1p derive from a common ancestor, which may have acted as both an activator and a repressor. We report here that UTP22 and RRP7, which encodes another pre-rRNA processing factor, are controlled by mTORC1; both gene promoters are bound by Ifh1p, which dissociates on mTORC1 inhibition. Notably, Crf1p acts as an activator as evidenced by reduced expression in a crf1{Delta} strain. By contrast, Crf1p is required to repress expression of HMO1, which encodes a cofactor involved in communicating mTORC1 activity to target genes. Our data therefore indicate that Crf1p exhibits the dual repressor/activator functions of the Ifh1p-Crf1p ancestor.

molecular biology↗