RNA localization in prokaryotes: Where, when, how, and why

Dynamic Membrane Localization of RNase Y in Bacillus subtilis

(2020) Lina Hamouche et al.   mBio

An RNA biology perspective on species‐specific programmable RNA antibiotics

(2020) Jörg Vogel   MOLECULAR MICROBIOLOGY

Noncontiguous operon is a genetic organization for coordinating bacterial gene expression

(2019) S. Sáenz-Lahoya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detachment of the RNA degradosome from the inner membrane of Escherichia coli results in a global slowdown of mRNA degradation, proteolysis of RN ase E and increased turnover of ribosome‐free transcripts

(2019) Lydia Hadjeras et al.   MOLECULAR MICROBIOLOGY

Spatial organization of the gene expression hardware in Pseudomonas putida

(2019) Juhyun Kim et al.   ENVIRONMENTAL MICROBIOLOGY

Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

(2019) William T. Gray et al.   CELL

Phase separation and clustering of an ABC transporter in Mycobacterium tuberculosis

(2019) Florian Heinkel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

(2019) Charlotte Soneson et al.   Nature Communications

A secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis

(2019) Osnat Cohen-Zontag et al.   PLoS Genetics

Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation

(2019) Shanmugapriya Kannaiah et al.   MOLECULAR CELL

Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

(2019) Alejandro Padrón et al.   MOLECULAR CELL

Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli

(2019) Xiaoli Weng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality

(2019) Mengyu Wang et al.   Nature Microbiology

RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles

(2019) Sahar Melamed et al.   MOLECULAR CELL

Transcription and translation contribute to gene locus relocation to the nucleoid periphery in E. coli

(2019) Sora Yang et al.   Nature Communications

Subcellular Organization: A Critical Feature of Bacterial Cell Replication

(2018) Ivan V. Surovtsev et al.   CELL

tRNA tracking for direct measurements of protein synthesis kinetics in live cells

(2018) Ivan L. Volkov et al.   Nature Chemical Biology

Simultaneous Binding of Multiple EF-Tu Copies to Translating Ribosomes in Live Escherichia coli

(2018) Mainak Mustafi et al.   mBio

A New Lens for RNA Localization: Liquid-Liquid Phase Separation

(2018) Erin M. Langdon et al.   Annual Review of Microbiology

α-Proteobacterial RNA Degradosomes Assemble Liquid-Liquid Phase-Separated RNP Bodies

(2018) Nadra Al-Husini et al.   MOLECULAR CELL

Ribosome Profiling: Global Views of Translation

(2018) Nicholas T. Ingolia et al.   Cold Spring Harbor Perspectives in Biology

SMRT-Cappable-seq reveals complex operon variants in bacteria

(2018) Bo Yan et al.   Nature Communications

Biochemical Methods To Image and Analyze RNA Localization: From One to Many

(2018) Ying Li et al.   BIOCHEMISTRY

RNAs, Phase Separation, and Membrane-Less Organelles: Are Post-Transcriptional Modifications Modulating Organelle Dynamics?

(2018) Aleksej Drino et al.   BIOESSAYS

Bacterial FtsZ protein forms phase‐separated condensates with its nucleoid‐associated inhibitor SlmA

(2018) Begoña Monterroso et al.   EMBO REPORTS

Measures of single- versus multiple-round translation argue against a mechanism to ensure coupling of transcription and translation

(2018) Menglin Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure and dynamics of bacterial ribosome biogenesis

(2017) Joseph H. Davis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Escherichia coliresponds to environmental changes using enolasic degradosomes and stabilized DicF sRNA to alter cellular morphology

(2017) Oleg N. Murashko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA–RNA interactions are critical for chromosome condensation inEscherichia coli

(2017) Zhong Qian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

(2017) Jordi Carreras-Puigvert et al.   Nature Communications

Evidence for a cytoplasmic pool of ribosome-free mRNAs encoding inner membrane proteins in Escherichia coli

(2017) Daniel Benhalevy et al.   PLoS One

Membrane association of the bacterial riboregulator Hfq and functional perspectives

(2017) Antoine Malabirade et al.   Scientific Reports

sRNA-Mediated Control of Transcription Termination in E. coli

(2016) Nadezda Sedlyarova et al.   CELL

Modular Assembly of the Bacterial Large Ribosomal Subunit

(2016) Joseph H. Davis et al.   CELL

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

In vivo compaction dynamics of bacterial DNA: A fingerprint of DNA/RNA demixing?

(2016) Marc Joyeux   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Where are things inside a bacterial cell?

(2016) Sutharsan Govindarajan et al.   CURRENT OPINION IN MICROBIOLOGY

Emerging roles of RNA modifications in bacteria

(2016) Carmelita Nora Marbaniang et al.   CURRENT OPINION IN MICROBIOLOGY

Colocalization of distant chromosomal loci in space in E. coli : a bacterial nucleolus

(2016) Tamas Gaal et al.   GENES & DEVELOPMENT

Methods for studying RNA localization in bacteria

(2016) Shanmugapriya Kannaiah et al.   METHODS

Global Mapping of Small RNA-Target Interactions in Bacteria

(2016) Sahar Melamed et al.   MOLECULAR CELL

Global profiling of SRP interaction with nascent polypeptides

(2016) Daniela Schibich et al.   NATURE

In vivosingle-RNA tracking shows that most tRNA diffuses freely in live bacteria

(2016) Anne Plochowietz et al.   NUCLEIC ACIDS RESEARCH

Silencing of natural transformation by an RNA chaperone and a multitarget small RNA

(2016) Laetitia Attaiech et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ubiquitous accumulation of 3′ mRNA decay fragments inSaccharomyces cerevisiaemRNAs with chromosomally integrated MS2 arrays

(2016) Jennifer F. Garcia et al.   RNA

The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni

(2016) Gaurav Dugar et al.   Nature Communications

On the Spatial Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host Overexpressing Membrane Proteins

(2016) Lieke A. van Gijtenbeek et al.   PLoS Genetics

Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea

(2016) Daniel Dar et al.   Nature Microbiology

Chromosome-Membrane Interactions in Bacteria

(2015) Manuela Roggiani et al.   Annual Review of Genetics

Chromosomal Arrangement of Phosphorelay Genes Couples Sporulation and DNA Replication

(2015) Jatin Narula et al.   CELL

RNA Controls PolyQ Protein Phase Transitions

(2015) Huaiying Zhang et al.   MOLECULAR CELL

Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II

(2015) Kathleen A. Burke et al.   MOLECULAR CELL

Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate

(2015) Rob W. van Nues et al.   NUCLEIC ACIDS RESEARCH

Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code

(2015) Thomas Philipp Hoernes et al.   NUCLEIC ACIDS RESEARCH

Model Uracil-Rich RNAs and Membrane Protein mRNAs Interact Specifically with Cold Shock Proteins in Escherichia coli

(2015) Daniel Benhalevy et al.   PLoS One

Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid

(2015) Mathew Stracy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system

(2015) J. F. Garcia et al.   RNA

Determination of in vivo target search kinetics of regulatory noncoding RNA

(2015) J. Fei et al.   SCIENCE

A New Noncoding RNA Arranges Bacterial Chromosome Organization

(2015) Zhong Qian et al.   mBio

Membrane Recognition and Dynamics of the RNA Degradosome

(2015) Henrik Strahl et al.   PLoS Genetics

The membrane: transertion as an organizing principle in membrane heterogeneity

(2015) Kouji Matsumoto et al.   Frontiers in Microbiology

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Labeling native bacterial RNA in live cells

(2014) Paul Toran et al.   CELL RESEARCH

Organization of Ribosomes and Nucleoids inEscherichia coliCells during Growth and in Quiescence

(2014) Qian Chai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparative analysis of the secretion capability of early and late flagellar type III secretion substrates

(2014) Hanna M. Singer et al.   MOLECULAR MICROBIOLOGY

Time-dependent effects of transcription- and translation-halting drugs on the spatial distributions of theEscherichia colichromosome and ribosomes

(2014) Somenath Bakshi et al.   MOLECULAR MICROBIOLOGY

The RNA World: molecular cooperation at the origins of life

(2014) Paul G. Higgs et al.   NATURE REVIEWS GENETICS

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromosome position effects on gene expression in Escherichia coli K-12

(2014) Jack A. Bryant et al.   NUCLEIC ACIDS RESEARCH

Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli

(2014) Justin E. Clarke et al.   NUCLEIC ACIDS RESEARCH

Spatially segregated transcription and translation in cells of the endomembrane-containing bacterium Gemmata obscuriglobus

(2014) E. Y. Gottshall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid

(2014) A. Sanamrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA localization in bacteria

(2014) Avi-ad Avraam Buskila et al.   RNA Biology

Single  -Actin mRNA Detection in Neurons Reveals a Mechanism for Regulating Its Translatability

(2014) A. R. Buxbaum et al.   SCIENCE

Ultrastructure and complex polar architecture of the human pathogenCampylobacter jejuni

(2014) Axel Müller et al.   MicrobiologyOpen

TheEscherichia coliRNA processing and degradation machinery is compartmentalized within an organized cellular network

(2013) Aziz Taghbalout et al.   BIOCHEMICAL JOURNAL

Protein targeting via mRNA in bacteria

(2013) Shanmugapriya Kannaiah et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

The centrality of RNA for engineering gene expression

(2013) James Chappell et al.   Biotechnology Journal

Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells

(2013) Jay K. Fisher et al.   CELL

The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity

(2013) Bradley R. Parry et al.   CELL

How do bacteria localize proteins to the cell pole?

(2013) G. Laloux et al.   JOURNAL OF CELL SCIENCE

Extracting intracellular diffusive states and transition rates from single-molecule tracking data

(2013) Fredrik Persson et al.   NATURE METHODS

Genome architecture and global gene regulation in bacteria: making progress towards a unified model?

(2013) Charles J. Dorman   NATURE REVIEWS MICROBIOLOGY

Effect of ribosome shielding on mRNA stability

(2013) Carlus Deneke et al.   PHYSICAL BIOLOGY

Analysis and Expansion of the Role of the Escherichia coli Protein ProQ

(2013) Daniel T. Sheidy et al.   PLoS One

In Vivo Biochemistry in Bacterial Cells Using FRAP: Insight into the Translation Cycle

(2012) Paula Montero Llopis et al.   BIOPHYSICAL JOURNAL

DivIVA-Mediated Polar Localization of ComN, a Posttranscriptional Regulator of Bacillus subtilis

(2012) V. T. dos Santos et al.   JOURNAL OF BACTERIOLOGY

Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis inEscherichia coli

(2012) Mikhail Bubunenko et al.   MOLECULAR MICROBIOLOGY

Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells

(2012) Somenath Bakshi et al.   MOLECULAR MICROBIOLOGY

Gene location and DNA density determine transcription factor distributions in Escherichia coli

(2012) Thomas E Kuhlman et al.   Molecular Systems Biology

Membrane protein expression triggers chromosomal locus repositioning in bacteria

(2012) E. A. Libby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

2011: Signaling Breakthroughs of the Year

(2012) E. M. Adler   Science Signaling

ProQ Is an RNA Chaperone that Controls ProP Levels inEscherichia coli

(2011) Steven G. Chaulk et al.   BIOCHEMISTRY

Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells

(2011) Jagannath Mondal et al.   BIOPHYSICAL JOURNAL

RNase Y in Bacillus subtilis: a Natively Disordered Protein That Is the Functional Equivalent of RNase E from Escherichia coli

(2011) M. Lehnik-Habrink et al.   JOURNAL OF BACTERIOLOGY

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

Isolation of small RNA-binding proteins fromE. coli: Evidence for frequent interaction of RNAs with RNA polymerase

(2011) Nikolai Windbichler et al.   RNA Biology

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

(2011) W. Wang et al.   SCIENCE

Translation-Independent Localization of mRNA in E. coli

(2011) K. Nevo-Dinur et al.   SCIENCE

Is there a twist in the Escherichia coli signal recognition particle pathway?

(2011) Eitan Bibi   TRENDS IN BIOCHEMICAL SCIENCES

The archaeal exosome localizes to the membrane

(2010) Verena Roppelt et al.   FEBS LETTERS

CaulobacterPopZ forms a polar subdomain dictating sequential changes in pole composition and function

(2010) Grant R. Bowman et al.   MOLECULAR MICROBIOLOGY

Spatial organization of the flow of genetic information in bacteria

(2010) Paula Montero Llopis et al.   NATURE

Membrane Protein Biogenesis in Ffh- or FtsY-Depleted Escherichia coli

(2010) Ido Yosef et al.   PLoS One

Poles Apart: Prokaryotic Polar Organelles and Their Spatial Regulation

(2010) C. L. Kirkpatrick et al.   Cold Spring Harbor Perspectives in Biology

Protein Subcellular Localization in Bacteria

(2010) D. Z. Rudner et al.   Cold Spring Harbor Perspectives in Biology

Cellular Electron Microscopy Imaging Reveals the Localization of the Hfq Protein Close to the Bacterial Membrane

(2009) Elia Diestra et al.   PLoS One

Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs

(2009) J. Prilusky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells

(2009) M. Valencia-Burton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subcellular localization of a bacterial regulatory RNA

(2009) J. H. Russell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorescence in situ hybridization for intracellular localization of nifH mRNA

(2009) Martin Pilhofer et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Three-Dimensional Imaging of the Highly Bent Architecture of Bdellovibrio bacteriovorus by Using Cryo-Electron Tomography

(2008) M. J. Borgnia et al.   JOURNAL OF BACTERIOLOGY

The Control of mRNA Decapping and P-Body Formation

(2008) Tobias M. Franks et al.   MOLECULAR CELL

The RNase E ofEscherichia coliis a membrane-binding protein

(2008) Vanessa Khemici et al.   MOLECULAR MICROBIOLOGY

The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

(2008) Atilio Deana et al.   NATURE

Protein Translocation Across the Bacterial Cytoplasmic Membrane

(2007) Arnold J.M. Driessen et al.   Annual Review of Biochemistry