Proteomics

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Mycoplasma pneumoniae Gene Regulatory Network II

ABSTRACT: Determining the gene regulatory network of an organism is fundamental to achieving a global understanding of cell behavior. In general, studies of transcription regulation are limited to the annotated transcription factors, not considering other non-canonical regulators. Here we describe the first systematic analysis of the DNA-interactome of a bacterium with a minimal proteome (Mycoplasma pneumoniae). We first determined by DNA affinity chromatography and intact chromatin isolation all potential DNA binding proteins. We then mapped the DNA binding of these factors by ChIP-seq, as well as their functionality by gain- and loss-of-function experiments, by transcriptomics and proteomics. This identified new DNA binding proteins and novel regulators with moonlighting properties like proteases and metabolic enzymes and allowed to reconstruct the gene regulatory network.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mycoplasma Pneumoniae (strain Atcc 29342 / M129)

SUBMITTER: Eva Yus  

LAB HEAD: Luis Serrano

PROVIDER: PXD007545 | Pride | 2019-11-12

REPOSITORIES: Pride

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010611_Eva_Yus_Luis_Serrano_TF_11_a.msf Msf
010611_Eva_Yus_Luis_Serrano_TF_11_b.msf Msf
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Publications

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.

Yus Eva E   Lloréns-Rico Verónica V   Martínez Sira S   Gallo Carolina C   Eilers Hinnerk H   Blötz Cedric C   Stülke Jörg J   Lluch-Senar Maria M   Serrano Luis L  

Cell systems 20190821 2

Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium's annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome,  ...[more]

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