Transcription of Bacterial Chromatin

Shen, Beth A.; Landick, Robert

doi:10.1016/j.jmb.2019.05.041

Cited by 67 publications

(67 citation statements)

References 276 publications

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“…5). "Combined" refers to the full set of motifs discovered after pooling all motifs across all conditions and redundancy filtering; a horizontal dashed line shows the total number of known motifs present in SwissRegulon.…”

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confidence: 99%

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

Freddolino

Goss

Amemiya

et al. 2020

Preprint

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Free living bacteria adapt to changes in the environment by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. Technologies such as ChIP-seq enable targeted characterization of regulatory interactions for individual DNA-binding proteins. However, in order to understand the cell's global regulatory logic, we need to simultaneously monitor all such interactions in response to diverse genetic and environmental perturbations. To address this challenge, we have developed high-resolution in vivo protein occupancy display (IPOD-HR), a technology that enables rapid, quantitative, and comprehensive monitoring of DNA-protein interactions across a bacterial chromosome. IPOD-HR enables simultaneous activity profiling of all known sequence specific transcription factors, discovery of novel condition-dependent DNA-binding proteins, and systematic inference of binding specificity models for all bound transcription factors. IPOD-HR also reveals many large domains of extended protein occupancy in Escherichia coli that define relatively stable, transcriptionally silent regions with unique sequence and gene functional features.

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confidence: 99%

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

Freddolino

Goss

Amemiya

et al. 2020

Preprint

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“…6B ). This result suggests that Z. mobilis may rely on positive supercoiling generated by opposing transcription units to enhance intrinsic termination between converging transcription units ( 51 , 52 ).…”

Section: Resultsmentioning

confidence: 97%

Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters

et al. 2020

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Zymomonas mobilis is an ethanologenic alphaproteobacterium with promise for the industrial conversion of renewable plant biomass into fuels and chemical bioproducts. Limited functional annotation of the Z. mobilis genome is a current barrier to both fundamental studies of Z. mobilis and its development as a synthetic biology chassis. To gain insight, we collected sample-matched multiomics data, including RNA sequencing (RNA-seq), transcription start site (TSS) sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry, across different growth conditions and used these data to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. We developed statistical methods for annotating transcript 5′ and 3′ ends, enabling the identification of 3,940 TSSs and their corresponding promoters and 2,091 transcription termination sites, which were distinguished from RNA processing sites by the lack of an adjacent RNA 5′ end. Our results revealed that Z. mobilis σA −35 and −10 promoter elements closely resemble canonical Escherichia coli −35 and −10 elements, with one notable exception: the Z. mobilis −10 element lacks the highly conserved −7 thymine observed in E. coli and other previously characterized σA promoters. The σA promoters of another alphaproteobacterium, Caulobacter crescentus, similarly lack the conservation of −7 thymine in their −10 elements. Our results anchor the development of Z. mobilis as a platform for synthetic biology and establish strategies for empirical genome annotation that can complement purely computational methods. IMPORTANCE Efforts to rationally engineer synthetic pathways in Zymomonas mobilis are impeded by a lack of knowledge and tools for predictable and quantitative programming of gene regulation at the transcriptional, posttranscriptional, and posttranslational levels. With the detailed functional characterization of the Z. mobilis genome presented in this work, we provide crucial knowledge for the development of synthetic genetic parts tailored to Z. mobilis. This information is vital as researchers continue to develop Z. mobilis for synthetic biology applications. Our methods and statistical analyses also provide ways to rapidly advance the understanding of poorly characterized bacteria via empirical data that enable the experimental validation of sequence-based prediction for genome characterization and annotation.

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“…Hydrogels (LLPS) appear to be incompletely characterized and somewhat difficult to analyze in prokaryotic systems [12][13][14]44,136]. We guess that hydrogel compartments are important for many bacterial processes including cell division, coupling of transcription and translation, nucleoid body maintenance and rearrangements, ion transport and signaling.…”

Section: Hydrogelsmentioning

confidence: 99%

“…Although not yet as extensively studied, hydrogels and LLPS are also becoming recognized in prokaryotic systems [12][13][14]. In this paper, we explore hydrogel and LLPS compartments as drivers of the establishment of the genetic code.…”

Section: Introductionmentioning

confidence: 99%

“…LLPS compartments are disordered with complex interactions and components, so disruption of LLPS compartments is associated with human diseases such as cancers and neurological impairments [6][7][8][9][10][11][45][46][47]. So far as we can ascertain, prokaryotes utilize LLPS probably utilizing short disordered protein regions, RNAs and DNA [12][13][14].…”

Section: Introductionmentioning

confidence: 99%

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Chaos, Order and Systematics in Evolution of the Genetic Code

Lei¹,

Burton²

2020

Preprint

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The genetic code evolved by parallel tracks of chaotic and ordered processes. Liquid-liquid phase separation (hydrogels), a chaotic process, constructs diverse membraneless compartments within cells, resulting in regulated hydration and sequestration and concentration of reaction components. Hydrogels relate to chaotic amyloid fiber production. We propose that polyglycine and related hydrogels (i.e. GADV; G is glycine), phase separations, membraneless droplets and amyloid accretions organized protocell domains to drive the earliest evolution of the genetic code and the pre-life to cellular life transition. By contrast, evolution of tRNA, tRNAomes, aminoacyl-tRNA synthetases and translation systems followed highly ordered and systematic pathways, described by well-defined mechanisms and rules. The pathway of evolution of aminoacyl-tRNA synthetases, which tracked evolution of the genetic code, is clarified. Hydrogels and amyloids form a chaotic component, therefore, that complemented otherwise systematic processes. We describe with detail a pre-life world in which hydrogels and amyloids provided the selections of the first life.

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Transcription of Bacterial Chromatin

Cited by 67 publications

References 276 publications

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters

Chaos, Order and Systematics in Evolution of the Genetic Code

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