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Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [ChIP-chip]

ABSTRACT: Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) experiments were carried out for all 8 FFRPs in H. salinarum NRC-1.

ORGANISM(S): Halobacterium salinarum NRC-1

PROVIDER: GSE62051 | GEO | 2014/10/03

SECONDARY ACCESSION(S): PRJNA263042

REPOSITORIES: GEO

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Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [ChIP-chip]

Project description:Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) experiments were carried out for all 8 FFRPs in H. salinarum NRC-1. To study the FFRP localization in both nutrient-replete and -deplete conditions, all strains were grown in CDM and genomic DNA of samples was harvested in both early log phase and late log phase. DNA from FFRP-bound regions was collected through c-Myc-tagged protein complexes and unenriched non-IP DNA were each labeled and hybridized to the whole genome tiling array.

2014-10-03 | E-GEOD-62051 | biostudies-arrayexpress

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.

Project description:BackgroundExpansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment.ResultsWe mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions that mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively.ConclusionsThis study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism.

| S-EPMC4236453 | biostudies-literature

Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-03 | E-GEOD-62052 | biostudies-arrayexpress

Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins

Project description:We validated context dependent regulation by two FFRPs AsnC and VNG1237C by deleting the FFRP and testing the effect on downstream target genes. For validtion of AsnC condition specific regulation we grew wild-type and delta-AsnC in the presence of 4mM paraquat (PQ) and samples at 1 and 160 minutes post addition of this sub-lethal dose of PQ. For validation of VNG1237C we grew wild-type and delta-VNG1237C in a standard growth curve sampling at OD 0.18 and 1.15. The asnC deletion strain (M-bM-^HM-^FasnC) and the control M-bM-^HM-^Fura3 strain were grown in 4mM paraquat (PQ) and were sampled at 1 and 160 minutes after PQ addition. Sampling timing for M-bM-^HM-^FVNG1237C was designed such that the starting ODs were as similar as possible and once an OD of 1.17 was reached for M-bM-^HM-^Fura3 the M-bM-^HM-^FVNG1237C was sampled at this same time point.

2014-10-02 | E-GEOD-61975 | biostudies-arrayexpress

Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-10-03 | GSE62052 | GEO

Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [expression]

2014-10-02 | GSE61975 | GEO

Prevalence of transcription promoters within archaeal operons and coding sequences

Project description:This SuperSeries is composed of the following subset Series: GSE12923: Halobacterium salinarum NRC-1 growth curve, tiling arrays. GSE12977: Halobacterium salinarum NRC-1 growth curve GSE13108: Halobacterium salinarum NRC-1 conditional ChIP-chip for transcription initiation factor IIB 4 (TFBd) GSE7045: ChIP-Chip of General Transcription factors in Halobacterium NRC-1 GSE15786: Halobacterium sp. NRC-1 ChIP-chip for TFBa, TFBd and TFBf, high resolution array GSE15788: Halobacterium salinarum NRC-1 total RNA hybridization of TFBd overexpression versus Reference sample Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction datasets revealed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes - events usually considered spurious or non-functional. With experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements Refer to individual Series

2010-05-17 | E-GEOD-13150 | biostudies-arrayexpress

DIA/SWATH-MS analysis of Halobacterium salinarum NRC-1 collected at four time points of batch culture growth

Project description:Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon.

2023-09-21 | PXD042774 | Pride

A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

2023-09-21 | PXD042770 | Pride

RNA-seq on rRNA depleted libraries from exponentially growing Halobacterium salinarum NRC-1 strains Δura3 and Δhlx2

Project description:RNA-seq on rRNA depleted libraries from exponentially growing Halobacterium salinarum NRC-1 strains Δura3 and Δhlx2

2017-06-07 | GSE99730 | GEO