Technologies developed over the past decade have made Saccharomyces cerevisiae a promising platform for producing various natural products. Balancing multi-enzyme expression, while maintaining robust microbial growth, remains a limiting factor for engineering long biosynthetic pathways in yeast. Here, we improved the transcriptional capacity of our previously developed IPTG-inducible synthetic transcription factors (synTFs) derived from the plant JUB1 DNA-binding domain. To this end, at cysteine positions within surface-exposed loop regions of a JUB1-derived DNA-binding scaffold, we introduced a short peptide to enhance loop flexibility while providing local stability and orientation. The generated synTFs, so-called JUB1-X synTFs, varying in strength, have been successfully used to improve the synthesis of 3′-phosphoadenosine 5′-phosphosulfate (PAPS), a universal sulfate donor necessary for the synthesis of bioactive molecules, including therapeutic glycosaminoglycans and sulfolipids. Using only this engineered yeast strain in simple batch culture, PAPS accumulation of 21.4 ± 5.8 mg/g cdw was achieved after only 5 hours of inducing the expression of JUB1-X synTFs. Beyond PAPS production, the design principle demonstrated here provides a generalizable strategy to fine-tune other plant-derived synTFs, expanding the regulatory capabilities of existing synTF collections. Together, this work offers a modular, scalable approach to constructing high-performance gene circuits and supports the development of yeast cell factories for complex metabolic and synthetic biology applications.

Despite the fact that microbes in natural environments spend most of their time in growth arrest, we understand little about how this physiological state affects the performance of engineered genetic circuits. Here, we measure repression curves from a library of genetic NOT gates at single-cell resolution in Escherichia coli under both active growth and growth arrest to systematically investigate how growth arrest affects circuit behavior. We find that the impact of growth arrest on circuit performance is almost entirely dominated by a single effect: a >100-fold reduction in unrepressed expression levels. Growth arrest caused gene expression noise to increase moderately and had only minimal impacts on the sensitivity and sharpness of the repression curves. Our work shows both that conventional genetic circuit design paradigms are currently insufficient to develop circuits that can function properly under growth arrest, but also that addressing the reduction in just a single performance parameter would be sufficient to resolve this problem. This work expands our understanding of bacterial gene regulation under growth arrest and lays the groundwork for new design paradigms that will be essential in ensuring the safe and reliable performance of synthetic biology systems in real-world environments.

Riboglow probes are small molecules where a synthetic fluorophore is connected to an RNA-binding moiety via a chemical linker. Upon binding a short RNA sequence, probe fluorescence intensity and lifetime increase. The fluorescence change is modulated by the architecture of the chemical linker. Here, we systematically interrogated the linker composition in a series of Riboglow probes and assessed fluorescence properties. We found that glycine linkers result in higher fluorescence turn-on compared to a polyethylene glycol linker of similar length. When varying the length of the polyglycine linker, we found that increasing the number of glycine residues led to more substantial fluorescence turn-on upon RNA-ligand binding. Surprisingly, the composition of the Riboglow chemical linker influences fluorescence lifetime contrast when comparing probe binding to two different RNA ligands, a quality necessary for RNA multiplexing. Finally, evaluating probe fluorescence lifetimes in live mammalian cells demonstrated the ability of new Riboglow probes to visualize RNAs live. Insights gained from the systematic assessment of the linker’s architecture will dictate the rational design of future fluorophore-quencher probe designs.

Plant roots are usually ground organs that perform essential roles, mostly associated with the anchoring of plants to the soil and absorption of nutrients and water. However, they are also exposed to a wide variety of microorganisms and may develop various symbiotic relationships, such as mutualism, which benefits both organisms. For instance, arbuscular mycorrhizal AMF symbiosis is likely the oldest and most widespread mutualistic association, that occurs between plants and fungi. Another relevant example is the root nodule symbiosis, established between nitrogen-fixing bacteria and nodulating legumes, actinorhizal plants and Parasponia species. In both cases, microbial colonization of plant roots culminates in the formation of specialized symbiotic structures. In this regard, microbial infection is a critical step for the mutualistic relationship, where altering the cell wall biomechanics is necessary to facilitate microbial entry, which can be modulated by various cell wall protein families. This review examines the current knowledge on cell wall modifications occurring in plants roots during the symbiotic entry of microorganisms, focusing on the role of cell wall-remodeling proteins involved in these processes.

Diverse bacterial sensory domains detect intracellular and extracellular cues and relay this information to downstream signaling pathways. PAS domains are well known to bind cofactors such as heme for intracellular sensing, whereas Cache domains, the largest family of bacterial extracytoplasmic sensor modules, are thought to function exclusively as cofactor independent ligand binding domains. Here, we identify and characterize a large family of Cache domains that contain a covalently bound c type heme. Systematic sequence analysis of the DUF3365/Tll0287 family of unknown function reveals exceptional conservation of a canonical CXXCH heme-binding motif, establishing c-type heme binding as a defining feature of this domain family. Structure- and sequence-based comparisons demonstrate that, despite prior annotation as PAS, these domains belong to the Cache superfamily and share a conserved Cache fold augmented by a distinct structural element harboring the heme-binding motif. Heme containing Cache domains are widely distributed across bacterial phyla, with strong enrichment in Gracilicutes, and frequently occur as stand-alone modules, an atypical presentation of Cache domains. Phylogenetic analyses support insertion of a short cytochrome c derived fragment containing the heme-binding motif into a preexisting Cache scaffold, representing a previously unrecognized mode of sensor domain evolution. Spectral and ligand binding analyses indicate that heme containing Cache domains fused to signal-transduction modules have properties typical of nitric oxide, but not oxygen, sensors; whereas stand-alone domains likely have redox-related roles. Our findings expand the functional repertoire of Cache domains to include covalently bound cofactors and reveal fragment-level recruitment of enzymatic motifs as a route for the emergence of bacterial sensory systems.

Single-cell phenotypic diversity underlies fundamental bacterial behaviors. Resolving this heterogeneity at scale while maintaining sensitive detection remains a central challenge. Here, we address this gap by combining the strengths of single-molecule fluorescence in situ hybridization (smFISH) and transcriptome-wide sequencing. We present par2FISH, a framework for discovering transcriptionally defined subpopulations across conditions by multiplexing tens of thousands of smFISH reactions. Through comparative single-cell transcriptomics in E. coli and Salmonella, we uncover conserved and species-specific patterns of heterogeneity, including mutually exclusive states, coordinated metabolic specialization, and differential activation of virulence programs. We further obtain complete transcriptomes for selected subpopulations using marker-based cell sorting and RNA-sequencing (FACS-RNA-seq). This integrated strategy paves the way for exposing bacterial phenotypic landscapes and the environmental, physiological, and evolutionary factors that shape them.

Dopamine deficiency resulting from nigrostriatal dopaminergic neuronal damage manifests as extrapyramidal motor symptoms of Parkinson’s disease (PD). Oral tablet dosing of levodopa, administered 3–4 times a day, remains the standard of care due to its tolerability and effectiveness; however, it is prone to deleterious side effects, including off-periods and levodopa-induced dyskinesia after long-term use. Herein, using synthetic biology approaches, we developed and systematically evaluated the feasibility of a probiotic-based live-biotherapeutic system to continuously deliver L-DOPA stably, thereby relieving motor symptoms. Our data demonstrate that our engineered plasmid-based L-DOPA-expressing E. coli Nissle 1917 probiotic strain (EcN2LDOPA-P3) efficiently produced up to 12,000 ng/mL L-DOPA in vitro. In mouse model systems, EcN2LDOPA-P3 readily colonized for up to 48 h, achieved steady-state plasma L-DOPA concentrations, and increased brain L-DOPA and dopamine levels by 1- to 2-fold. Lastly, EcN2LDOPA-P3 significantly diminished motor and nonmotor behavioral deficits in a mouse model of PD compared to traditional chemical L-DOPA therapy. These findings support the therapeutic feasibility of a noninvasive, orally administered bioengineered bacterial therapy for the chronic delivery of L-DOPA, which may address limitations associated with current treatment alternatives.

Fusarium oxysporum plays crucial roles as both a damaging plant pathogen and a model for studying host-pathogen interactions. It is well established that systematic functional genomics approaches are vital for advancing agricultural biotechnology and developing biological agents. Creating efficient gene-editing systems can help elucidate virulence mechanisms and enable rapid production of modified strains for practical use. However, current transformation methods face major challenges, such as high enzyme costs, and CRISPR/Cas9 systems are limited by PAM sequence availability and by blunt-end DNA cleavage, which hampers homologous recombination. Furthermore, complex guide RNA scaffolds complicate large-scale functional studies with traditional methods. To address these challenges, we have developed a streamlined CRISPR/Cpf1 (Cas12a) platform that combines small-scale protoplast preparation with significantly reduced enzyme use, exploiting Cpf1's unique features, such as flexible PAM recognition, staggered DNA cuts that promote recombination, improved target specificity, and simpler guide RNA design. This platform can also accelerate the development of biological agents and support high-throughput screening applications essential to the progress of agricultural biotechnology.

RNA function is governed by RNA folding, but strategies for measuring RNA folding thermodynamics are limited, and fundamental questions such as the energy of base pair opening remain debated. Here we introduce Probing-Resolved Inference of Molecular Energetics (PRIME) to extract nucleotide-resolution RNA structural energetics from scalable chemical probing experiments. Applying PRIME to diverse RNAs, we find that RNA base pairs and tertiary interactions dynamically open with free energies of 0.5-3 kcal/mol, revealing that RNA nucleotides ubiquitously sample open conformations at biologically accessible energies. PRIME further resolves energetic coupling across RNAs, providing an energetic understanding of RNA structural dynamics and long-range coordination in RNA folding. PRIME represents a widely accessible strategy for interrogating RNA thermodynamics, enabling mechanistic understanding and engineering of RNA biology.