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Article
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Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis
Transcriptional plasticity (TP) governs gene expression variability, yet remains unexplored in prokaryotes. This study examines Mycobacterium tuberculosis genes’ TP via RNA-seq meta-analysis, uncovering genetic and functional traits impacting mycobacterial TP.
- Cheng Bei
- , Junhao Zhu
- & Qingyun Liu
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Article
| Open Access
Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism
The mechanisms underlying adaptation of bacteria to changing environmental conditions remain poorly understood. Here, the authors show bacteria using lysine acetylation of transcriptional regulators to adjust gene expression to changing conditions.
- Magdalena Kremer
- , Sabrina Schulze
- & Michael Lammers
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Article
| Open Access
The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli
Here, the authors use the proVWXoperon of Escherichia coli as a model system to show how the nucleoid associated protein H-NS regulates gene expression in vivo by local chromatin remodelling.
- Fatema-Zahra M. Rashid
- , Frédéric G. E. Crémazy
- & Remus T. Dame
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| Open Access
Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi
Transcription termination can tune bacterial gene expression in response to diverse signals. Here, the authors use several RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi, providing insights into various modes of transcription termination and identifying potential RNA regulators in this pathogen.
- Emily Petroni
- , Caroline Esnault
- & Philip P. Adams
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| Open Access
Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift
Bacteria undergo nutrient fluctuations during repeated feast and famine cycles and need to metabolically adapt to these changes. Using quantitative proteomics, Zhu & Dai show that the stringent response of (p)ppGpp is crucial for the timely adaption of bacterial growth to both amino acid and carbon downshift.
- Manlu Zhu
- & Xiongfeng Dai
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Rho-dependent transcription termination proceeds via three routes
Rho is a general transcription termination factor in bacteria. Here, Song et al. use single-molecule fluorescence assays to provide evidence that Rho-mediated transcription termination can occur via three kinetically different routes.
- Eunho Song
- , Heesoo Uhm
- & Sungchul Hohng
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Article
| Open Access
Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity
Bacteria use specific silencing proteins to prevent spurious transcription of horizontally acquired DNA. Here, Forrest et al. describe differences in silencing strategies between E. coli and Bacillus subtilis, driven by the respective specificities of the silencing protein and the RNA polymerase in each organism.
- David Forrest
- , Emily A. Warman
- & David C. Grainger
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| Open Access
RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection
Bacterial stress responses are potential targets for new antimicrobials. Here, Avican et al. present global transcriptomes for 32 bacterial pathogens grown under 11 stress conditions, and identify common and unique regulatory responses, as well as processes participating in different stress responses.
- Kemal Avican
- , Jehad Aldahdooh
- & Maria Fällman
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| Open Access
Mycobacterium tuberculosis precursor rRNA as a measure of treatment-shortening activity of drugs and regimens
It is unclear why different antibiotics vary in their ability to shorten treatment of tuberculosis. Here, the authors show that a measure based on ribosomal RNA synthesis in Mycobacterium tuberculosis correlates with treatment shortening in culture, in mice and in human studies.
- Nicholas D. Walter
- , Sarah E. M. Born
- & Martin I. Voskuil
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| Open Access
Structural visualization of transcription activated by a multidrug-sensing MerR family regulator
The MerR family of transcriptional regulators, such as EcmrR, activate promoters with a structure that is suboptimal for recognition by RNA polymerase holoenzyme. Structural insights into the EcmrR-dependent transcription process elucidate the mechanisms enabling optimal promoter recognition and transition from initiation to elongation.
- Yang Yang
- , Chang Liu
- & Bin Liu
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| Open Access
Structural basis of ribosomal RNA transcription regulation
Ribosomal RNA (rRNA) expression is regulated at the initiation stage of RNA synthesis. Here, the authors report cryo-EM structures of E. coli RNA polymerase and rRNA promoter complex with DksA/ppGpp on the way to open complex formation, identifying key steps in promoter recognition and opening.
- Yeonoh Shin
- , M. Zuhaib Qayyum
- & Katsuhiko S. Murakami
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| Open Access
The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription
BmrR is a member of the bacterial MerR transcription factor family that regulates the expression of the bacterial efflux pump Bmr. Here, the authors present the cryo-EM structure of a B. subtilis transcription activation complex (TAC) containing the RNA Polymerase (RNAP) core enzyme, σA, promoter DNA and ligand-bound BmrR, which reveals that in contrast to most other transcription factors BmrR does not directly interact with RNAP and instead activates transcription by modulating the shape of the core promoter.
- Chengli Fang
- , Linyu Li
- & Yu Zhang
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Article
| Open Access
A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
The authors set out to identify binding motifs for all 301 transcription factors of a plant pathogenic bacterium, Pseudomonas syringae, using HT-SELEX. They successfully identify binding motifs for 100 transcription factors, infer their binding sites on the genome, and validate the predicted interactions and functions.
- Ligang Fan
- , Tingting Wang
- & Xin Deng
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| Open Access
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron
Bacteroides thetaiotaomicron is a human gut microbe and an emergent model organism. Here, Ryan et al. generate single-nucleotide resolution RNA-seq data for this bacterium and map transcription start sites and noncoding RNAs, one of which modulates expression of metabolic enzymes.
- Daniel Ryan
- , Laura Jenniches
- & Alexander J. Westermann
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An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3′-to-5′ exoRNases and RNase Y
Bacterial RNA degradation is typically initiated by endoribonucleases and followed by exoribonucleases. Here the authors report the targetome of endoRNase Y in Streptococcus pyogenes, revealing the interplay between RNase Y and 3′-to-5′ exoribonuclease PNPase and YhaM.
- Laura Broglia
- , Anne-Laure Lécrivain
- & Emmanuelle Charpentier
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| Open Access
Transcription and translation contribute to gene locus relocation to the nucleoid periphery in E. coli
Transcription and translation are coupled in bacteria. Here, the authors show that the movement of a gene locus to the nucleoid periphery correlates with transcription, and the effect is potentiated by translation.
- Sora Yang
- , Seunghyeon Kim
- & Nam Ki Lee
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Article
| Open Access
Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC
The transcriptional activator PafBC is a regulator of mycobacterial DNA damage response and upregulates genes involved in DNA repair. Here, the authors present the crystal structure of Arthrobacter aurescens PafBC and suggest that PafBC might be activated by binding of a nucleic acid ligand, and bioinformatics analysis shows that its central WYL domain is a widespread feature in bacterial transcription factors.
- Andreas U. Müller
- , Marc Leibundgut
- & Eilika Weber-Ban
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Article
| Open Access
High-throughput screen reveals sRNAs regulating crRNA biogenesis by targeting CRISPR leader to repress Rho termination
Small non-coding RNAs (sRNA) regulate bacterial functions by finding nucleic acids and proteins. Here the authors identify PhrS sRNA in Pseudomonas as a positive regulator of CRISPR, and show PhrS acts by binding to CRISPR leader, thereby preventing Rho-mediated transcription termination and promoting anti-bacteriophage immunity.
- Ping Lin
- , Qinqin Pu
- & Min Wu
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| Open Access
Structural basis for transcription antitermination at bacterial intrinsic terminator
Bacteriophages reprogram the host transcriptional machinery. Here the authors provide insights into the mechanism of how bacteriophages regulate host transcription by determining the cryo-EM structures of two bacterial transcription elongation complexes bound with the bacteriophage master host-transcription regulator protein P7.
- Linlin You
- , Jing Shi
- & Yu Zhang
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| Open Access
An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa
The virulence of Pseudomonas aeruginosa is regulated by many transcriptional factors (TFs). Here, the authors study the crosstalk between 20 key virulence-related TFs, validate 347 functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that is available as an online platform.
- Hao Huang
- , Xiaolong Shao
- & Xin Deng
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Article
| Open Access
Environmental pH and peptide signaling control virulence of Streptococcus pyogenes via a quorum-sensing pathway
The mechanism by which environmental pH controls the virulence of the pathogen Streptococcus pyogenes is unclear. Here, Do et al. show that changes in pH affect the activity of the virulence regulator RopB via its interaction with a quorum-sensing peptide signal.
- Hackwon Do
- , Nishanth Makthal
- & Muthiah Kumaraswami
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Article
| Open Access
Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
In bacteria, the Rho protein dislodges elongation complexes to terminate transcription, and the Mfd protein removes RNA polymerases (RNAPs) stalled at DNA lesions. Here, Jain et al. show that Rho also dissociates stalled RNAPs at DNA lesions, which may facilitate DNA repair and other DNA-dependent processes.
- Sriyans Jain
- , Richa Gupta
- & Ranjan Sen
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Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism
Resistance to rifamycin antibiotics, which target bacterial RNA polymerases, is a growing problem. Here, the authors identify gene clusters from soil metagenomes encoding production of rifamycin analogues that are active against rifampicin-resistant bacteria through a distinct mechanism.
- James Peek
- , Mirjana Lilic
- & Sean F. Brady
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| Open Access
SMRT-Cappable-seq reveals complex operon variants in bacteria
Fragmentation of transcripts can hide operon complexity in genome-wide transcriptome sequencing. Here the authors sequenced a prokaryotic transcriptome using PacBio and provide insights into operon structure and read-through at termination sites.
- Bo Yan
- , Matthew Boitano
- & Laurence Ettwiller
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Article
| Open Access
The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage
The bacterial transcription-repair coupling factor Mfd displaces stalled RNA polymerase (RNAP) by promoting transcription termination at sites of DNA lesions. Here the authors find—using single molecule imaging in live Escherichia coli—that RNAP stalls frequently during transcription, and needs to be rescued by Mfd during normal growth.
- Han N. Ho
- , Antoine M. van Oijen
- & Harshad Ghodke
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| Open Access
The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development
BldC regulates the onset of differentiation in Streptomycetes by a yet unknown molecular mechanism. Using a combination of structural, biochemical and in vivo approaches, the authors show that BldC controls the transcription of several developmental regulators and unravel its DNA binding mode.
- Maria A. Schumacher
- , Chris D. den Hengst
- & Mark J. Buttner
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| Open Access
Identification of regulatory targets for the bacterial Nus factor complex
The Nus factor complex regulates rRNA folding and prevents Rho-dependent transcription termination in bacteria. Here, Baniulyte et al. show that it also inhibits translation of one of the Nus factor-encoding genes, suhB, and probably regulates the expression of other genes in diverse bacterial species.
- Gabriele Baniulyte
- , Navjot Singh
- & Joseph T. Wade
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| Open Access
The metabolic enzyme fructose-1,6-bisphosphate aldolase acts as a transcriptional regulator in pathogenic Francisella
The enzyme fructose-bisphosphate aldolase (FBA) plays central roles in glycolysis and gluconeogenesis. Here, Ziveri et al. show that FBA of the pathogen Francisella novicida acts, in addition, as a transcriptional regulator and is important for bacterial multiplication in macrophages.
- Jason Ziveri
- , Fabiola Tros
- & Alain Charbit
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| Open Access
A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants
Quantitative analysis of how DNA sequence determines transcription and translation regulation is of interest to systems and synthetic biologists. Here the authors present ELM-seq, which uses Dam activity as reporter for high-throughput analysis of promoter and 5’-UTR regions.
- Eva Yus
- , Jae-Seong Yang
- & Luis Serrano
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Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death
The transcription termination factor Rho is essential for growth in some bacteria but not in others. Here, Botellaet al. show that Rho inactivation causes extensive pervasive transcription and loss of viability of the pathogen Mycobacterium tuberculosis both in vitroand in a mouse model of infection.
- Laure Botella
- , Julien Vaubourgeix
- & Dirk Schnappinger
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Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription
How DNA cytosine methylation affects gene expression inEscherichia coli is poorly understood. Here, the first genome-wide study of cytosine methylation in E. coliat single-base resolution reveals that cytosine methylation controls the expression of genes during the stationary growth phase.
- Christina Kahramanoglou
- , Ana I. Prieto
- & Aswin S.N. Seshasayee
A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program