Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology

The centrality of RNA for engineering gene expression

(2013) James Chappell et al.   Biotechnology Journal

Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks

(2013) Yun Chen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Sigma factors in a thousandE. coligenomes

(2013) Helen Cook et al.   ENVIRONMENTAL MICROBIOLOGY

Dual function of the McaS small RNA in controlling biofilm formation

(2013) M. G. Jorgensen et al.   GENES & DEVELOPMENT

Bacterial sRNAs: Regulation in stress

(2013) Chee-Hock Hoe et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Deciphering the Interplay between Two Independent Functions of the Small RNA Regulator SgrS in Salmonella

(2013) D. Balasubramanian et al.   JOURNAL OF BACTERIOLOGY

Mapping the Spatial Neighborhood of the Regulatory 6S RNA Bound to Escherichia coli RNA Polymerase Holoenzyme

(2013) Benedikt Steuten et al.   JOURNAL OF MOLECULAR BIOLOGY

New options to engineer biofuel microbes: Development and application of a high-throughput screening system

(2013) Michael Scheel et al.   METABOLIC ENGINEERING

Engineering dynamic pathway regulation using stress-response promoters

(2013) Robert H Dahl et al.   NATURE BIOTECHNOLOGY

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli

(2013) Seung Min Yoo et al.   Nature Protocols

Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress

(2013) S. M. Gaida et al.   NUCLEIC ACIDS RESEARCH

miRmap web: comprehensive microRNA target prediction online

(2013) Charles E. Vejnar et al.   NUCLEIC ACIDS RESEARCH

Alternative Sigma Factor Over-Expression Enables Heterologous Expression of a Type II Polyketide Biosynthetic Pathway in Escherichia coli

(2013) David Cole Stevens et al.   PLoS One

A new frontier in synthetic biology: automated design of small RNA devices in bacteria

(2013) Guillermo Rodrigo et al.   TRENDS IN GENETICS

Synthetic RNA devices to expedite the evolution of metabolite-producing microbes

(2013) Jina Yang et al.   Nature Communications

Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices

(2013) Pablo Ceres et al.   ACS Synthetic Biology

Development of a 2,4-Dinitrotoluene-Responsive Synthetic Riboswitch in E. coli Cells

(2012) Molly E. Davidson et al.   ACS Chemical Biology

Metabolite Recognition Principles and Molecular Mechanisms Underlying Riboswitch Function

(2012) Alexander Serganov et al.   Annual Review of Biophysics

Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery

(2012) Thomas Neusser et al.   BMC GENOMICS

Synthetic biology with RNA: progress report

(2012) Yaakov Benenson   CURRENT OPINION IN CHEMICAL BIOLOGY

Synthetic biology and the development of tools for metabolic engineering

(2012) Jay D. Keasling   METABOLIC ENGINEERING

The csgD mRNA as a hub for signal integration via multiple small RNAs

(2012) Alex Boehm et al.   MOLECULAR MICROBIOLOGY

A global sampling approach to designing and reengineering RNA secondary structures

(2012) Alex Levin et al.   NUCLEIC ACIDS RESEARCH

De novo design of a synthetic riboswitch that regulates transcription termination

(2012) M. Wachsmuth et al.   NUCLEIC ACIDS RESEARCH

Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals

(2012) Lei Qi et al.   NUCLEIC ACIDS RESEARCH

BSRD: a repository for bacterial small regulatory RNA

(2012) Lei Li et al.   NUCLEIC ACIDS RESEARCH

De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells

(2012) G. Rodrigo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small regulatory RNAs inPseudomonas aeruginosa

(2012) Elisabeth Sonnleitner et al.   RNA Biology

Automated and fast building of three-dimensional RNA structures

(2012) Yunjie Zhao et al.   Scientific Reports

Small RNA RyhB as a potential tool used for metabolic engineering in Escherichia coli

(2011) Zhen Kang et al.   BIOTECHNOLOGY LETTERS

Metabolic engineering, synthetic biology and systems biology

(2011) Jens Nielsen et al.   FEMS YEAST RESEARCH

Engineering Escherichia coli for efficient production of 5-aminolevulinic acid from glucose

(2011) Zhen Kang et al.   METABOLIC ENGINEERING

Engineering Biological Systems with Synthetic RNA Molecules

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

Reducing acetate excretion from E. coli K-12 by over-expressing the small RNA SgrS

(2011) Alejandro Negrete et al.   New Biotechnology

Artificial trans -encoded small non-coding RNAs specifically silence the selected gene expression in bacteria

(2011) Shuai Man et al.   NUCLEIC ACIDS RESEARCH

Engineered riboswitches: Overview, problems and trends

(2011) Beatrix Suess et al.   RNA Biology

E. coli6S RNA: A universal transcriptional regulator within the centre of growth adaptation

(2011) René Geißen et al.   RNA Biology

Bacterial aptamers that selectively bind glutamine

(2011) Tyler D. Ames et al.   RNA Biology

Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors

(2011) A. Ogawa   RNA

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli

(2011) Vandana Sharma et al.   ACS Synthetic Biology

High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection

(2010) Jeffrey A. Dietrich et al.   Annual Review of Biochemistry

Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species

(2010) S. Topp et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Construction of stress-induced metabolic pathway from glucose to 1,3-propanediol in Escherichia coli

(2010) Quanfeng Liang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metabolic fluxes and beyond—systems biology understanding and engineering of microbial metabolism

(2010) Michael Kohlstedt et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Using a Riboswitch Sensor to Examine Coenzyme B12 Metabolism and Transport in E. coli

(2010) Casey C. Fowler et al.   CHEMISTRY & BIOLOGY

Systems biology of microbial metabolism

(2010) Matthias Heinemann et al.   CURRENT OPINION IN MICROBIOLOGY

MicA sRNA links the PhoP regulon to cell envelope stress

(2010) Audrey Coornaert et al.   MOLECULAR MICROBIOLOGY

Reprogramming bacteria to seek and destroy an herbicide

(2010) Joy Sinha et al.   Nature Chemical Biology

Identification of regulatory RNAs in Bacillus subtilis

(2010) Irnov Irnov et al.   NUCLEIC ACIDS RESEARCH

Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development

(2010) Zhen Chen et al.   TRENDS IN BIOTECHNOLOGY

6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products

(2009) Reinhild Wurm et al.   BIOLOGICAL CHEMISTRY

Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects

(2009) Francis Repoila et al.   BIOLOGY OF THE CELL

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

An overview of RNAs with regulatory functions in gram-positive bacteria

(2009) Pascale Romby et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Experimental approaches for the discovery and characterization of regulatory small RNA

(2009) Cynthia Mira Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

Expanding roles for metabolite-sensing regulatory RNAs

(2009) Michael D Dambach et al.   CURRENT OPINION IN MICROBIOLOGY

The long and the short of riboswitches

(2009) Alexander Serganov   CURRENT OPINION IN STRUCTURAL BIOLOGY

Engineering Escherichia coli for an efficient aerobic fermentation platform

(2009) Zhen Kang et al.   JOURNAL OF BIOTECHNOLOGY

The secret to 6S: regulating RNA polymerase by ribo-sequestration

(2009) Kimberly B. Decker et al.   MOLECULAR MICROBIOLOGY

6S RNA binding to Eσ70requires a positively charged surface of σ70region 4.2

(2009) Andrew D. Klocko et al.   MOLECULAR MICROBIOLOGY

Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

(2009) Kai Papenfort et al.   MOLECULAR MICROBIOLOGY

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

An efficient platform for genetic selection and screening of gene switches in Escherichia coli

(2009) Norihito Muranaka et al.   NUCLEIC ACIDS RESEARCH

Characterization of homologs of the small RNA SgrS reveals diversity in function

(2009) Caryn S. Wadler et al.   NUCLEIC ACIDS RESEARCH

Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli

(2009) Nobutaka Nakashima et al.   NUCLEIC ACIDS RESEARCH

A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

(2009) Thomas Geissmann et al.   NUCLEIC ACIDS RESEARCH

Construction of a stress-induced system in Escherichia coli for efficient polyhydroxyalkanoates production

(2008) Zhen Kang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Small RNA gene identification and mRNA target predictions in bacteria

(2008) C. Pichon et al.   BIOINFORMATICS

RNA interference: The story of gene silencing in plants and humans

(2008) Mahmood-ur-Rahman et al.   BIOTECHNOLOGY ADVANCES

Riboswitches: Ancient and Promising Genetic Regulators

(2008) Simon Blouin et al.   CHEMBIOCHEM

Combinatorial engineering of microbes for optimizing cellular phenotype

(2008) Christine Nicole S Santos et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Riboswitch RNAs: using RNA to sense cellular metabolism

(2008) T. M. Henkin   GENES & DEVELOPMENT

Screening of Bacillus subtilis transposon mutants with altered riboflavin production

(2008) Simon Tännler et al.   METABOLIC ENGINEERING

Riboswitches that Sense S-adenosylhomocysteine and Activate Genes Involved in Coenzyme Recycling

(2008) Joy Xin Wang et al.   MOLECULAR CELL

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

(2008) Elizabeth E. Regulski et al.   MOLECULAR MICROBIOLOGY

The expanding world of small RNAs

(2008) Helge Großhans et al.   NATURE

Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

(2008) N. Sudarsan et al.   SCIENCE

Complex Riboswitches

(2008) R. R. Breaker   SCIENCE