Feeling the heat at the millennium: Thermosensors playing with fire

Direct RNA sequencing of the Escherichia coli epitranscriptome uncovers alterations under heat stress

Modifications of RNA, known as the epitranscriptome, affect gene expression, translation, and splicing in eukaryotes, with implications for developmental processes, cancer, and viral infections. In prokaryotes, regulation at the level of the epitranscriptome is still poorly understood. Here, we used nanopore direct RNA sequencing of Escherichia coli to study RNA modifications and their changes under heat stress. With a single sequencing reaction, we detected most known modification types in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA). RNA sequencing was complemented by a multifaceted approach that included mass spectrometry, deletion mutants, single-nucleotide polymerase chain reaction, and in vitro methylation. Known 5-methylcytidine (m5C) and N6-methyladenosine (m6A) sites in the rRNA were confirmed, but these types of modifications could not be localized in the mRNA. In response to heat stress, levels of m5C, m6A, and N6,N6-dimethyladenosine increased in the 16S rRNA. Sequencing and mass spectrometry data demonstrated a decrease in tRNA modification abundance in the anticodon loop at 45°C. In general, mRNA modifications at 37°C were enriched in the coding regions of genes associated with general metabolism and RNA processing, which shifted to genes involved in cell wall synthesis and membrane transport under heat stress. This study provides new insights into the complexity of post-transcriptional regulation in bacteria.

RNase R vs. PNPase: selecting the best-suited exoribonuclease for environmental adaptation

3' → 5' exoribonucleases play a critical role in many aspects of RNA metabolism. RNase R, PNPase, and RNase II are the major contributors to RNA processing, maturation, and quality control in bacteria. Bacteria don't seem to have dedicated RNA degradation machineries to process different classes of RNAs. Under different environmental and physiological conditions, their roles can be redundant and sometimes overlapping. Here, I discuss why PNPase and RNase R may have switched their physiological roles in some bacterial species to adapt to environmental conditions, despite being biochemically distinct exoribonucleases.

Temperatures above 37°C increase virulence of a convergent Klebsiella pneumoniae sequence type 307 strain

Background

Convergence of Klebsiella pneumoniae (KP) pathotypes has been increasingly reported in recent years. These pathogens combine features of both multidrug-resistant and hypervirulent KP. However, clinically used indicators for hypervirulent KP identification, such as hypermucoviscosity, appear to be differentially expressed in convergent KP, potential outbreak clones are difficult to identify. We aimed to fill such knowledge gaps by investigating the temperature dependence of hypermucoviscosity and virulence in a convergent KP strain isolated during a clonal outbreak and belonging to the high-risk sequence type (ST)307.

Methods

Hypermucoviscosity, biofilm formation, and mortality rates in Galleria mellonella larvae were examined at different temperatures (room temperature, 28°C, 37°C, 40°C and 42°C) and with various phenotypic experiments including electron microscopy. The underlying mechanisms of the phenotypic changes were explored via qPCR analysis to evaluate plasmid copy numbers, and transcriptomics.

Results

Our results show a temperature-dependent switch above 37°C towards a hypermucoviscous phenotype, consistent with increased biofilm formation and in vivo mortality, possibly reflecting a bacterial response to fever-like conditions. Furthermore, we observed an increase in plasmid copy number for a hybrid plasmid harboring carbapenemase and rmpA genes. However, transcriptomic analysis revealed no changes in rmpA expression at higher temperatures, suggesting alternative regulatory pathways.

Conclusion

This study not only elucidates the impact of elevated temperatures on hypermucoviscosity and virulence in convergent KP but also sheds light on previously unrecognized aspects of its adaptive behavior, underscoring its resilience to changing environments.

Split Proteins and Reassembly Modules for Biological Applications

Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.

Flipping the script: Understanding riboswitches from an alternative perspective

Riboswitches are broadly distributed regulatory elements most frequently found in the 5'-leader sequence of bacterial mRNAs that regulate gene expression in response to the binding of a small molecule effector. The occupancy status of the ligand-binding aptamer domain manipulates downstream information in the message that instructs the expression machinery. Currently, there are over 55 validated riboswitch classes, where each class is defined based on the identity of the ligand it binds and/or sequence and structure conservation patterns within the aptamer domain. This classification reflects an "aptamer-centric" perspective that dominates our understanding of riboswitches. In this review, we propose a conceptual framework that groups riboswitches based on the mechanism by which RNA manipulates information directly instructing the expression machinery. This scheme does not replace the established aptamer domain-based classification of riboswitches but rather serves to facilitate hypothesis-driven investigation of riboswitch regulatory mechanisms. Based on current bioinformatic, structural, and biochemical studies of a broad spectrum of riboswitches, we propose three major mechanistic groups: (1) "direct occlusion", (2) "interdomain docking", and (3) "strand exchange". We discuss the defining features of each group, present representative examples of riboswitches from each group, and illustrate how these RNAs couple small molecule binding to gene regulation. While mechanistic studies of the occlusion and docking groups have yielded compelling models for how these riboswitches function, much less is known about strand exchange processes. To conclude, we outline the limitations of our mechanism-based conceptual framework and discuss how critical information within riboswitch expression platforms can inform gene regulation.

Temperature-sensing riboceptors

Understanding how cells sense temperature is a fundamental question in biology and is pivotal for the evolution of life. In numerous organisms, temperature is not only sensed but also generated due to cellular processes. Consequently, the mechanisms governing temperature sensation in various organisms have been experimentally elucidated. Extending upon others' proposals and demonstration of protein- and nucleic acid-based thermosensors, and utilizing a colonial India 'punkah-wallahs' analogy, I present my rationale for the necessity of temperature sensing in every organelle in a cell. Finally, I propose temperature-sensing riboceptors (ribonucleic acid receptors) to integrate all the RNA molecules (mRNA, non-coding RNA, and so forth) capable of sensing temperature and triggering a signaling event, which I call as thermocrine signaling. This approach could enable the identification of riboceptors in every cell of almost every organism, not only for temperature but also for other classes of ligands, including gaseous solutes, and water.

The plant noncoding transcriptome: a versatile environmental sensor

Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.

The oxidative stress response, in particular the katY gene, is temperature-regulated in Yersinia pseudotuberculosis

Pathogenic bacteria, such as Yersinia pseudotuberculosis encounter reactive oxygen species (ROS) as one of the first lines of defense in the mammalian host. In return, the bacteria react by mounting an oxidative stress response. Previous global RNA structure probing studies provided evidence for temperature-modulated RNA structures in the 5'-untranslated region (5'-UTR) of various oxidative stress response transcripts, suggesting that opening of these RNA thermometer (RNAT) structures at host-body temperature relieves translational repression. Here, we systematically analyzed the transcriptional and translational regulation of ROS defense genes by RNA-sequencing, qRT-PCR, translational reporter gene fusions, enzymatic RNA structure probing and toeprinting assays. Transcription of four ROS defense genes was upregulated at 37°C. The trxA gene is transcribed into two mRNA isoforms, of which the most abundant short one contains a functional RNAT. Biochemical assays validated temperature-responsive RNAT-like structures in the 5'-UTRs of sodB, sodC and katA. However, they barely conferred translational repression in Y. pseudotuberculosis at 25°C suggesting partially open structures available to the ribosome in the living cell. Around the translation initiation region of katY we discovered a novel, highly efficient RNAT that was primarily responsible for massive induction of KatY at 37°C. By phenotypic characterization of catalase mutants and through fluorometric real-time measurements of the redox-sensitive roGFP2-Orp1 reporter in these strains, we revealed KatA as the primary H2O2 scavenger. Consistent with the upregulation of katY, we observed an improved protection of Y. pseudotuberculosis at 37°C. Our findings suggest a multilayered regulation of the oxidative stress response in Yersinia and an important role of RNAT-controlled katY expression at host body temperature.

Robust network topologies for temperature-inducible bioswitches

BACKGROUND

Thermoinducible bioswitches are unique in that the all-or-none switch response is triggered by temperature, which is a global factor that impacts all biochemical reaction processes. To date, temperature-inducible bioswitches rely exclusively on special thermal sensing biomolecules of DNA, RNA, proteins and lipids whose conformations are critically temperature dependent.

METHOD

This paper extends the traditional thermal switch by utilizing purposely designed network topologies of biomolecular interactions to achieve the switching function. By assuming the general Arrhenius law for biochemical reactions, we explore the full space of all three-node genetic interaction networks to screen topologies capable of thermal bioswitches. Three target bioswitches, i.e., thermal-inducible Off-On, cold-inducible On-Off, and hybrid Off-On-Off double switches, are considered separately.

CONCLUSIONS

We identify the minimal and core network skeletons that are basic and essential for building robust high-performance bioswitches: three Off-On motifs, three On-Off motifs, and an incoherent feedforward motif for an Off-On-Off double switch. Functional topologies are implicitly preferential in choosing parameter values to achieve the target functions. The scenario of the topology-based bioswitch we propose here is an extension of molecule-based bioswitches and would be valuable in aiding the rational design and synthesis of efficient high-performance thermal bioswitches.

Microbial Mechanisms of Heat Sensing

Temperature is one of the ubiquitous signals that control both the development as well as virulence of various microbial species. Therefore their survival is dependent upon initiating appropriate response upon temperature fluctuations. In particular, pathogenic microbes exploit host-temperature sensing mechanisms for triggering the expression of virulence genes. Many studies have revealed that the biomolecules within a cell such as DNA, RNA, lipids and proteins help in sensing change in temperature, thereby acting as thermosensors. This review shall provide an insight into the different mechanisms of thermosensing and how they aid pathogenic microbes in host invasion.

Thermogenetics: Applications come of age

Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.

Design of a Toolbox of RNA Thermometers

RNA thermometers are RNA regulatory elements that convert temperature into a functional biological response through a temperature-induced conformational change. These regulatory elements have been investigated in numerous natural contexts and have been designed for synthetic biology as well. A basic challenge has been the design of an RNA thermometer whose final activity in response to temperature matches a prespecified response, in terms of its sensitivity, threshold, and leakiness. This chapter provides a methodology for the design of a toolbox of RNA thermometers. We describe considerations for the conceptual design, a computational assessment, and strategies for experimental synthesis and measurement.

The life and death of RNA across temperatures

Temperature is an environmental condition that has a pervasive effect on cells along with all the molecules and reactions in them. The mechanisms by which prototypical RNA molecules sense and withstand heat have been identified mostly in bacteria and archaea. The relevance of these phenomena is, however, broader, and similar mechanisms have been recently found throughout the tree of life, from sex determination in reptiles to adaptation of viral RNA polymerases, to genetic disorders in humans. We illustrate the temperature dependence of RNA metabolism with examples from the synthesis to the degradation of mRNAs, and review recently emerged questions. Are cells exposed to greater temperature variations and gradients than previously surmised? How do cells reconcile the conflicting thermal stability requirements of primary and tertiary structures of RNAs? To what extent do enzymes contribute to the temperature compensation of the reaction rates in mRNA turnover by lowering the energy barrier of the catalyzed reactions? We conclude with the ecological, forensic applications of the temperature-dependence of RNA degradation and the biotechnological aspects of mRNA vaccine production.

Genetically Encoded Protein Thermometer Enables Precise Electrothermal Control of Transgene Expression

Body temperature is maintained at around 37 °C in humans, but may rise to 40 °C or more during high-grade fever, which occurs in most adults who are seriously ill. However, endogenous temperature sensors, such as ion channels and heat-shock promoters, are fully activated only at noxious temperatures above this range, making them unsuitable for medical applications. Here, a genetically encoded protein thermometer (human enhanced gene activation thermometer; HEAT) is designed that can trigger transgene expression in the range of 37-40 °C by linking a mutant coiled-coil temperature-responsive protein sensor to a synthetic transcription factor. To validate the construct, a HEAT-transgenic monoclonal human cell line, FeverSense, is generated and it is confirmed that it works as a fever sensor that can temperature- and exposure-time-dependently trigger reporter gene expression in vitro and in vivo. For translational proof of concept, microencapsulated designer cells stably expressing a HEAT-controlled insulin production cassette in a mouse model of type-1 diabetes are subcutaneously implanted and topical heating patches are used to apply heat corresponding to a warm sensation in humans. Insulin release is induced, restoring normoglycemia. Thus, HEAT appears to be suitable for practical electrothermal control of cell-based therapy, and may also have potential for next-generation treatment of fever-associated medical conditions.

Precision of Protein Thermometry

Temperature sensing is a ubiquitous cell behavior, but the fundamental limits to the precision of temperature sensing are poorly understood. Unlike in chemical concentration sensing, the precision of temperature sensing is not limited by extrinsic fluctuations in the temperature field itself. Instead, we find that precision is limited by the intrinsic copy number, turnover, and binding kinetics of temperature-sensitive proteins. Developing a model based on the canonical TlpA protein, we find that a cell can estimate temperature to within 2%. We compare this prediction with in vivo data on temperature sensing in bacteria.

Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa

The ability to fine tune global gene expression in response to host environment is critical for the virulence of pathogenic bacteria. The host temperature is exploited by the bacteria as a cue for triggering virulence gene expression. However, little is known about the mechanism employed by Pseudomonas aeruginosa to response to host body temperature. CspA family proteins are RNA chaperones that modulate gene expression. Here we explored the functions of P. aeruginosa CspA family proteins and found that CspC (PA0456) controls the bacterial virulence. Combining transcriptomic analyses, RNA-immunoprecipitation and high-throughput sequencing (RIP-Seq), we demonstrated that CspC represses the type III secretion system (T3SS) by binding to the 5' untranslated region of the mRNA of exsA, which encodes the T3SS master regulatory protein. We further demonstrated that acetylation at K41 of the CspC reduces its affinity to nucleic acids. Shifting the culture temperature from 25°C to 37°C or infection of mouse lung increased the CspC acetylation, which derepressed the expression of the T3SS genes, resulting in elevated virulence. Overall, our results identified the regulatory targets of CspC and revealed a regulatory mechanism of the T3SS in response to temperature shift and host in vivo environment.

OmpA, a Common Virulence Factor, Is Under RNA Thermometer Control in Yersinia pseudotuberculosis

The outer membrane protein OmpA is a virulence factor in many mammalian pathogens. In previous global RNA structure probing studies, we found evidence for a temperature-modulated RNA structure in the 5'-untranslated region (5'-UTR) of the Yersinia pseudotuberculosis ompA transcript suggesting that opening of the structure at host-body temperature might relieve translational repression. Here, we support this hypothesis by quantitative reverse transcription PCR, translational reporter gene fusions, enzymatic RNA structure probing, and toeprinting assays. While ompA transcript levels decreased at 37°C compared to 25°C, translation of the transcript increased with increasing temperature. Biochemical experiments show that this is due to melting of the RNA structure, which permits ribosome binding to the 5'-UTR. A point mutation that locks the RNA structure in a closed conformation prevents translation by impairing ribosome access. Our findings add another common virulence factor to the growing list of pathogen-associated genes that are under RNA thermometer control.

Trans-Acting Effectors Versus RNA Cis-Elements: A Tightly Knit Regulatory Mesh

Prokaryotic organisms often react instantly to environmental variations to ensure their survival. They can achieve this by rapidly and specifically modulating translation, the critical step of protein synthesis. The translation machinery responds to an array of cis-acting elements, located on the RNA transcript, which dictate the fate of mRNAs. These cis-encoded elements, such as RNA structures or sequence motifs, interact with a variety of regulators, among them small regulatory RNAs. These small regulatory RNAs (sRNAs) are especially effective at modulating translation initiation through their interaction with cis-encoded mRNA elements. Here, through selected examples of canonical and non-canonical regulatory events, we demonstrate the intimate connection between mRNA cis-encoded features and sRNA-dependent translation regulation. We also address how sRNA-based mechanistic studies can drive the discovery of new roles for cis-elements. Finally, we briefly overview the challenges of using translation regulation by synthetic regulators as a tool.

Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas

Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).