Global analysis of the genetic network controlling a bacterial cell cycle

On the evolution of chromosomal regions with high gene strand bias in bacteria

On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.

MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein

MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α-proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone-like Nucleoid Structuring (H-NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H-NS-like protein, which binds AT-rich regions of genomic DNA and regulates gene expression.

Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing

Bacterial transcription is not monolithic. Microbes exist in a wide variety of cell states that help them adapt to their environment, acquire and produce essential nutrients, and engage in both competition and cooperation with their neighbors. While we typically think of bacterial adaptation as a group behavior, where all cells respond in unison, there is often a mixture of phenotypic responses within a bacterial population, where distinct cell types arise. A primary phenomenon driving these distinct cell states is transcriptional heterogeneity. Given that bacterial mRNA transcripts are extremely short-lived compared to eukaryotes, their transcriptional state is closely associated with their physiology, and thus the transcriptome of a bacterial cell acts as a snapshot of the behavior of that bacterium. Therefore, the application of single-cell transcriptomics to microbial populations will provide novel insight into cellular differentiation and bacterial ecology. In this review, we provide an overview of transcriptional heterogeneity in microbial systems, discuss the findings already provided by single-cell approaches, and plot new avenues of inquiry in transcriptional regulation, cellular biology, and mechanisms of heterogeneity that are made possible when microbial communities are analyzed at single-cell resolution.

Transcription-replication interactions reveal bacterial genome regulation

Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. In bacteria, the relationship between the regulatory architecture of a gene and its expression is well understood for individual model gene circuits2,3. However, a broader perspective of these dynamics at the genome scale is lacking, in part because bacterial transcriptomics has hitherto captured only a static snapshot of expression averaged across millions of cells4. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on the transcriptional response of each gene to its own replication, which we term the transcription-replication interaction profile (TRIP). Analysing single-bacterium RNA-sequencing data, we found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal the local regulatory context of a gene. Whereas the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, and this is shaped by factors such as intra-operon position and repression state. By revealing the underlying mechanistic drivers of gene expression heterogeneity, this work provides a quantitative, biophysical framework for modelling replication-dependent expression dynamics.

Competition and evolutionary selection among core regulatory motifs in gene expression control

Gene products that are beneficial in one environment may become burdensome in another, prompting the emergence of diverse regulatory schemes that carry their own bioenergetic cost. By ensuring that regulators are only expressed when needed, we demonstrate that autoregulation generally offers an advantage in an environment combining mutation and time-varying selection. Whether positive or negative feedback emerges as dominant depends primarily on the demand for the target gene product, typically to ensure that the detrimental impact of inevitable mutations is minimized. While self-repression of the regulator curbs the spread of these loss-of-function mutations, self-activation instead facilitates their propagation. By analyzing the transcription network of multiple model organisms, we reveal that reduced bioenergetic cost may contribute to the preferential selection of autoregulation among transcription factors. Our results not only uncover how seemingly equivalent regulatory motifs have fundamentally different impact on population structure, growth dynamics, and evolutionary outcomes, but they can also be leveraged to promote the design of evolutionarily robust synthetic gene circuits.

Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum

S-Adenosylmethionine (SAM) acts as a methyl donor in living organisms, and S-adenosylmethionine synthetase (MetK) is an essential enzyme for cells, as it synthesizes SAM from methionine and adenosine triphosphate (ATP). This study determined the crystal structures of the apo form and adenosine/triphosphate complex form of MetK from Corynebacterium glutamicum (CgMetK). Results showed that CgMetK has an allosteric inhibitor binding site for the SAM product in the vicinity of the active site and is inhibited by SAM both competitively and noncompetitively. Through structure-guided protein engineering, the CgMetKE68A variant was developed that exhibited an almost complete release of inhibition by SAM with rather enhanced enzyme activity. The crystal structure of the CgMetKE68A variant revealed that the formation of a new hydrogen bond between Tyr66 and Glu102 by the E68A mutation disrupted the allosteric SAM binding site and also improved the protein thermal stability by strengthening the tetramerization of the enzyme.

Extracellular transfer of a conserved polymerization factor for multi-flagellin filament assembly in Caulobacter

Unidirectional growth of filamentous protein assemblies including the bacterial flagellum relies on dedicated polymerization factors (PFs). The molecular determinants and structural transitions imposed by PFs on multi-subunit assembly are poorly understood. Here, we unveil FlaY from the polarized α-proteobacterium Caulobacter crescentus as a defining member of an alternative class of specialized flagellin PFs. Unlike the paradigmatic FliD capping protein, FlaY relies on a funnel-like β-propeller fold for flagellin polymerization. FlaY binds flagellin and is secreted by the flagellar secretion apparatus, yet it can also promote flagellin polymerization exogenously when donated from flagellin-deficient cells, serving as a transferable, extracellular public good. While the surge in FlaY abundance precedes bulk flagellin synthesis, FlaY-independent filament assembly is enhanced by mutation of a conserved region in multiple flagellin paralogs. We suggest that FlaYs are (multi-)flagellin PFs that evolved convergently to FliDs yet appropriated the versatile β-propeller fold implicated in human diseases for chaperone-assisted filament assembly.

Network medicine: an approach to complex kidney disease phenotypes

Scientific reductionism has been the basis of disease classification and understanding for more than a century. However, the reductionist approach of characterizing diseases from a limited set of clinical observations and laboratory evaluations has proven insufficient in the face of an exponential growth in data generated from transcriptomics, proteomics, metabolomics and deep phenotyping. A new systematic method is necessary to organize these datasets and build new definitions of what constitutes a disease that incorporates both biological and environmental factors to more precisely describe the ever-growing complexity of phenotypes and their underlying molecular determinants. Network medicine provides such a conceptual framework to bridge these vast quantities of data while providing an individualized understanding of disease. The modern application of network medicine principles is yielding new insights into the pathobiology of chronic kidney diseases and renovascular disorders by expanding the understanding of pathogenic mediators, novel biomarkers and new options for renal therapeutics. These efforts affirm network medicine as a robust paradigm for elucidating new advances in the diagnosis and treatment of kidney disorders.

Synchronized Swarmers and Sticky Stalks: Caulobacter crescentus as a Model for Bacterial Cell Biology

First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.

Transcriptome Dynamics of Pseudomonas aeruginosa during Transition from Overlapping To Non-Overlapping Cell Cycles

Bacteria either duplicate their chromosome once per cell division or a new round of replication is initiated before the cells divide, thus cell cycles overlap. Here, we show that the opportunistic pathogen Pseudomonas aeruginosa switches from fast growth with overlapping cell cycles to sustained slow growth with only one replication round per cell division when cultivated under standard laboratory conditions. The transition was characterized by fast-paced, sequential changes in transcriptional activity along the ori-ter axis of the chromosome reflecting adaptation to the metabolic needs during both growth phases. Quorum sensing (QS) activity was highest at the onset of the slow growth phase with non-overlapping cell cycles. RNA sequencing of subpopulations of these cultures sorted based on their DNA content, revealed a strong gene dosage effect as well as specific expression patterns for replicating and nonreplicating cells. Expression of flagella and mexE, involved in multidrug efflux was restricted to cells that did not replicate, while those that did showed a high activity of the cell division locus and recombination genes. A possible role of QS in the formation of these subpopulations upon switching to non-overlapping cell cycles could be a subject of further research. IMPORTANCE The coordination of gene expression with the cell cycle has so far been studied only in a few bacteria, the bottleneck being the need for synchronized cultures. Here, we determined replication-associated effects on transcription by comparing Pseudomonas aeruginosa cultures that differ in their growth mode and number of replicating chromosomes. We further show that cell cycle-specific gene regulation can be principally identified by RNA sequencing of subpopulations from cultures that replicate only once per cell division and that are sorted according to their DNA content. Our approach opens the possibility to study asynchronously growing bacteria from a wide phylogenetic range and thereby enhance our understanding of the evolution of cell cycle control on the transcriptional level.

NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity

A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for constructing core transcription factor regulatory networks using both transcriptomics data and literature-based transcription factor-target databases. NetAct robustly infers regulators' activity using target expression, constructs networks based on transcriptional activity, and integrates mathematical modeling for validation. Our in silico benchmark test shows that NetAct outperforms existing algorithms in inferring transcriptional activity and gene networks. We illustrate the application of NetAct to model networks driving TGF-β-induced epithelial-mesenchymal transition and macrophage polarization.

A Half Century Defining the Logic of Cellular Life

Over more than fifty years, I have studied how the logic that controls and integrates cell function is built into the dynamic architecture of living cells. I worked with a succession of exceptionally talented students and postdocs, and we discovered that the bacterial cell is controlled by an integrated genetic circuit in which transcriptional and translational controls are interwoven with the three-dimensional deployment of key regulatory and morphological proteins. Caulobacter's interconnected genetic regulatory network includes logic that regulates sets of genes expressed at specific times in the cell cycle and mechanisms that synchronize the advancement of the core cyclical circuit with chromosome replication and cytokinesis. Here, I have traced my journey from New York City art student to Stanford developmental biologist.

G1/S restriction point coordinates phasic gene expression and cell differentiation

Pluripotent embryonic stem cells have a unique cell cycle structure with a suppressed G1/S restriction point and little differential expression across the cell cycle phases. Here, we evaluate the link between G1/S restriction point activation, phasic gene expression, and cellular differentiation. Expression analysis reveals a gain in phasic gene expression across lineages between embryonic days E7.5 and E9.5. Genetic manipulation of the G1/S restriction point regulators miR-302 and P27 respectively accelerates or delays the onset of phasic gene expression in mouse embryos. Loss of miR-302-mediated p21 or p27 suppression expedites embryonic stem cell differentiation, while a constitutive Cyclin E mutant blocks it. Together, these findings uncover a causal relationship between emergence of the G1/S restriction point with a gain in phasic gene expression and cellular differentiation.

Transcription Regulation of Cell Cycle Regulatory Genes Mediated by NtrX to Affect Sinorhizobium meliloti Cell Division

The cell division of the alfalfa symbiont, Sinorhizobium meliloti, is dictated by a cell cycle regulatory pathway containing the key transcription factors CtrA, GcrA, and DnaA. In this study, we found that NtrX, one of the regulators of nitrogen metabolism, can directly regulate the expression of ctrA, gcrA, and dnaA from the cell cycle pathway. Three sets of S. meliloti ntrX mutants showed similar cell division defects, such as slow growth, abnormal morphology of some cells, and delayed DNA synthesis. Transcription of ctrA and gcrA was upregulated, whereas the transcription of dnaA and ftsZ1 was downregulated in the insertion mutant and the strain of Sm1021 expressing ntrXD53E. Correspondingly, the inducible transcription of ntrX activates the expression of dnaA and ftsZ1, but represses ctrA and gcrA in the depletion strain. The expression levels of CtrA and GcrA were confirmed by Western blotting. The transcription regulation of these genes requires phosphorylation of the conserved 53rd aspartate in the NtrX protein that binds directly to the promoter regions of ctrA, gcrA, dnaA, and ftsZ1 by recognizing the characteristic sequence CAAN2-5TTG. Our findings suggest that NtrX affects S. meliloti cell division by regulating the transcription of the key cell cycle regulatory genes.

System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks

Synthetic biology aims to apply engineering principles for the rational, systematical design and construction of biological systems displaying functions that do not exist in nature or even building a cell from scratch. Understanding how molecular entities interconnect, work, and evolve in an organism is pivotal to this aim. Here, we summarize and discuss some historical organizing principles identified in bacterial gene regulatory networks. We propose a new layer, the concilion, which is the group of structural genes and their local regulators responsible for a single function that, organized hierarchically, coordinate a response in a way reminiscent of the deliberation and negotiation that take place in a council. We then highlight the importance that the network structure has, and discuss that the natural decomposition approach has unveiled the system-level elements shaping a common functional architecture governing bacterial regulatory networks. We discuss the incompleteness of gene regulatory networks and the need for network inference and benchmarking standardization. We point out the importance that using the network structural properties showed to improve network inference. We discuss the advances and controversies regarding the consistency between reconstructions of regulatory networks and expression data. We then discuss some perspectives on the necessity of studying regulatory networks, considering the interactions’ strength distribution, the challenges to studying these interactions’ strength, and the corresponding effects on network structure and dynamics. Finally, we explore the ability of evolutionary systems biology studies to provide insights into how evolution shapes functional architecture despite the high evolutionary plasticity of regulatory networks.

RdsA Is a Global Regulator That Controls Cell Shape and Division in Rhizobium etli

Unlike other bacteria, cell growth in rhizobiales is unipolar and asymmetric. The regulation of cell division, and its coordination with metabolic processes is an active field of research. In Rhizobium etli, gene RHE_PE00024, located in a secondary chromosome, is essential for growth. This gene encodes a predicted hybrid histidine kinase sensor protein, participating in a, as yet undescribed, two-component signaling system. In this work, we show that a conditional knockdown mutant (cKD24) in RHE_PE00024 (hereby referred as rdsA, after rhizobium division and shape) generates a striking phenotype, where nearly 64% of the cells present a round shape, with stochastic and uncoordinated cell division. For rod-shaped cells, a large fraction (12 to 29%, depending on their origin) present growth from the old pole, a sector that is normally inactive for growth in a wild-type cell. A fraction of the cells (1 to 3%) showed also multiple ectopic polar growths. Homodimerization of RdsA appears to be required for normal function. RNAseq analysis of mutant cKD24 reveals global changes, with downregulated genes in at least five biological processes: cell division, wall biogenesis, respiration, translation, and motility. These modifications may affect proper structuring of the divisome, as well as peptidoglycan synthesis. Together, these results indicate that the hybrid histidine kinase RdsA is an essential global regulator influencing cell division and cell shape in R. etli.

Hybrid Histidine Kinase WelA of Sphingomonas sp. WG Contributes to WL Gum Biosynthesis and Motility

Sphingomonas sp. WG produced WL gum with commercial utility potential in many industries. A hybrid sensor histidine kinase/response regulator WelA was identified to regulate the WL gum biosynthesis, and its function was evaluated by gene deletion strategy. The WL gum production and broth viscosity of mutant ΔwelA was only 44% and 0.6% of wild type strain at 72 h. The transcriptomic analysis of differentially expressed genes showed that WelA was mapped to CckA; ChpT, and CtrA in the CckA-ChpT-CtrA pathway was up-regulated. One phosphodiesterase was up-regulated by CtrA, and the intracellular c-di-GMP was decreased. Most genes involved in WL gum biosynthesis pathway was not significantly changed in ΔwelA except the up-regulated atrB and atrD and the down-regulated pmm. Furthermore, the up-regulated regulators ctrA, flaEY, flbD, and flaF may participate in the regulation of flagellar biogenesis and influenced motility. These results suggested that CckA-ChpT-CtrA pathway and c-di-GMP were involved in WL gum biosynthesis regulation. This work provides useful information on the understanding of molecular mechanisms underlying WL gum biosynthesis regulation.

Plasmids Bring Additional Capabilities to Caulobacter Isolates

Caulobacter is a well-studied bacterial genus, but little is known about the plasmids that are found in some wild Caulobacter isolates. We used bioinformatic approaches to identify nine plasmids from seven different Caulobacter strains and grouped them based on their size and the similarity of their repABC, parAB, and mobAB genes. Protein pathway analysis of the genes on the K31p1 and K31p2 plasmids showed many metabolic pathways that would enhance the metabolic versatility of the host strain. In contrast, the CB4 plasmid contained 21 heavy metal resistance genes with the majority coding for proteins that enhance copper resistance. Growth assays of C. henricii CB4 demonstrated increased copper resistance and quantitative PCR showed an increase in the expression of eight heavy metal genes when induced with copper.

Computational modeling of unphosphorylated CtrA:Cori binding in the Caulobacter cell cycle

In the alphaproteobacterium, Caulobacter crescentus, phosphorylated CtrA (CtrA∼P), a master regulatory protein, binds directly to the chromosome origin (Cori) to inhibit DNA replication. Using a mathematical model of CtrA binding at Cori site [d], we provide computational evidence that CtrA_U can displace CtrA∼P from Cori at the G1-S transition. Investigation of this interaction within a detailed model of the C. crescentus cell cycle suggests that CckA phosphatase may clear Cori of CtrA∼P by altering the [CtrA_U]/[CtrA∼P] ratio rather than by completely depleting CtrA∼P. Model analysis reveals that the mechanism allows for a speedier transition into S phase, stabilizes the timing of chromosome replication under fluctuating rates of CtrA proteolysis, and may contribute to the viability of numerous mutant strains. Overall, these results suggest that CtrA_U enhances the robustness of chromosome replication. More generally, our proposed regulation of CtrA:Cori dynamics may represent a novel motif for molecular signaling in cell physiology.

The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle

The highly conserved protease Lon has important regulatory and protein quality control functions in cells from the three domains of life. Despite many years of research on Lon, only a few specific protein substrates are known in most organisms. Here, we used a quantitative proteomics approach to identify novel substrates of Lon in the dimorphic bacterium Caulobacter crescentus. We focused our study on proteins involved in polar cell differentiation and investigated the developmental regulator StaR and the flagella hook length regulator FliK as specific Lon substrates in detail. We show that Lon recognizes these proteins at their C-termini, and that Lon-dependent degradation ensures their temporally restricted accumulation in the cell cycle phase when their function is needed. Disruption of this precise temporal regulation of StaR and FliK levels in a Δlon mutant contributes to defects in stalk biogenesis and motility, respectively, revealing a critical role of Lon in coordinating developmental processes with cell cycle progression. Our work underscores the importance of Lon in the regulation of complex temporally controlled processes by adjusting the concentrations of critical regulatory proteins. Furthermore, this study includes the first characterization of FliK in C. crescentus and uncovers a dual role of the C-terminal amino acids of FliK in protein function and degradation.

Are There Biomimetic Lessons from Genetic Regulatory Networks for Developing a Lunar Industrial Ecology?

We examine the prospect for employing a bio-inspired architecture for a lunar industrial ecology based on genetic regulatory networks. The lunar industrial ecology resembles a metabolic system in that it comprises multiple chemical processes interlinked through waste recycling. Initially, we examine lessons from factory organisation which have evolved into a bio-inspired concept, the reconfigurable holonic architecture. We then examine genetic regulatory networks and their application in the biological cell cycle. There are numerous subtleties that would be challenging to implement in a lunar industrial ecology but much of the essence of biological circuitry (as implemented in synthetic biology, for example) is captured by traditional electrical engineering design with emphasis on feedforward and feedback loops to implement robustness.

Caulobacter crescentus: model system extraordinaire

In scientific research, we often rely on well-established model systems to tackle important questions. In this context, extensive characterization of specific bacterial species such as Escherichia coli and Bacillus subtilis has provided a vast amount of knowledge that extends well beyond the biology of these two organisms. However, the bacterial world is large and extremely diverse, necessitating the development of additional models that complement the classical rod-shaped and symmetrically dividing systems. Caulobacter crescentus is a species that has met this need effectively, as its dimorphic lifestyle showcases distinctive features, including cellular asymmetry and differentiation during the cell cycle. Studying C. crescentus has reformed our understanding of bacterial intracellular organization, cellular development, and cell-cycle regulation. These findings have, in turn, stimulated studies in other bacteria, shedding light on how protein function and cell morphology can evolve and diversify. Studies in C. crescentus have also deepened our knowledge of other topics (e.g. cell mechanosensing, motility, and bacterial aging), while opening the door to biotechnological innovations. In this Primer, we provide some general background to this peculiar bacterium and highlight specific features that have contributed to its rise as a versatile bacterial model. This Primer is not meant to be exhaustive on any topic and is instead intended to provide a taste of the power of C. crescentus as a model system to explore a diverse range of topics.

Activation of a signaling pathway by the physical translocation of a chromosome

In every organism, the cell cycle requires the execution of multiple processes in a strictly defined order. However, the mechanisms used to ensure such order remain poorly understood, particularly in bacteria. Here, we show that the activation of the essential CtrA signaling pathway that triggers cell division in Caulobacter crescentus is intrinsically coupled to the initiation of DNA replication via the physical translocation of a newly replicated chromosome, powered by the ParABS system. We demonstrate that ParA accumulation at the new cell pole during chromosome segregation recruits ChpT, an intermediate component of the CtrA signaling pathway. ChpT is normally restricted from accessing the selective PopZ polar microdomain until the new chromosome and ParA arrive. Consequently, any disruption to DNA replication initiation prevents ChpT polarization and, in turn, cell division. Collectively, our findings reveal how major cell-cycle events are coordinated in Caulobacter and, importantly, how chromosome translocation triggers an essential signaling pathway.

A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms

How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, contrary to previous reports, Caulobacter crescentus breaks with the E. coli paradigm.

Connection Between Chromosomal Location and Function of CtrA Phosphorelay Genes in Alphaproteobacteria

Most bacterial chromosomes are circular, with replication starting at one origin (ori) and proceeding on both replichores toward the terminus (ter). Several studies have shown that the location of genes relative to ori and ter can have profound effects on regulatory networks and physiological processes. The CtrA phosphorelay is a gene regulatory system conserved in most alphaproteobacteria. It was first discovered in Caulobacter crescentus where it controls replication and division into a stalked and a motile cell in coordination with other factors. The locations of the ctrA gene and targets of this response regulator on the chromosome affect their expression through replication-induced DNA hemi-methylation and specific positioning along a CtrA activity gradient in the dividing cell, respectively. Here we asked to what extent the location of CtrA regulatory network genes might be conserved in the alphaproteobacteria. We determined the locations of the CtrA phosphorelay and associated genes in closed genomes with unambiguously identifiable ori from members of five alphaproteobacterial orders. The location of the phosphorelay genes was the least conserved in the Rhodospirillales followed by the Sphingomonadales. In the Rhizobiales a trend toward certain chromosomal positions could be observed. Compared to the other orders, the CtrA phosphorelay genes were conserved closer to ori in the Caulobacterales. In contrast, the genes were highly conserved closer to ter in the Rhodobacterales. Our data suggest selection pressure results in differential positioning of CtrA phosphorelay and associated genes in alphaproteobacteria, particularly in the orders Rhodobacterales, Caulobacterales and Rhizobiales that is worth deeper investigation.

The DUF1013 protein TrcR tracks with RNA polymerase to control the bacterial cell cycle and protect against antibiotics

How DNA-dependent RNA polymerase (RNAP) acts on bacterial cell cycle progression during transcription elongation is poorly investigated. A forward genetic selection for Caulobacter crescentus cell cycle mutants unearthed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR promotes the accumulation of the essential cell cycle transcriptional activator CtrA in late S-phase but also affects transcription at a global level to protect cells from the quinolone antibiotic nalidixic acid that induces a multidrug efflux pump and from the RNAP inhibitor rifampicin that blocks transcription elongation. We show that TrcR associates with promoters and coding sequences in vivo in a rifampicin-dependent manner and that it interacts physically and genetically with RNAP. We show that TrcR function and its RNAP-dependent chromatin recruitment are conserved in symbiotic Sinorhizobium sp. and pathogenic Brucella spp Thus, TrcR represents a hitherto unknown antibiotic target and the founding member of the DUF1013 family, an uncharacterized class of transcriptional regulators that track with RNAP during the elongation phase to promote transcription during the cell cycle.

An organelle-tethering mechanism couples flagellation to cell division in bacteria

In some free-living and pathogenic bacteria, problems in the synthesis and assembly of early flagellar components can cause cell-division defects. However, the mechanism that couples cell division with the flagellar biogenesis has remained elusive. Herein, we discover the regulator MadA that controls transcription of flagellar and cell-division genes in Caulobacter crescentus. We demonstrate that MadA, a small soluble protein, binds the type III export component FlhA to promote activation of FliX, which in turn is required to license the conserved σ⁵⁴-dependent transcriptional activator FlbD. While in the absence of MadA, FliX and FlbD activation is crippled, bypass mutations in FlhA restore flagellar biogenesis and cell division. Furthermore, we demonstrate that MadA safeguards the divisome stoichiometry to license cell division. We propose that MadA has a sentinel-type function that senses an early flagellar biogenesis event and, through cell-division control, ensures that a flagellated offspring emerges.

Using optimal control to understand complex metabolic pathways

BACKGROUND

Optimality principles have been used to explain the structure and behavior of living matter at different levels of organization, from basic phenomena at the molecular level, up to complex dynamics in whole populations. Most of these studies have assumed a single-criteria approach. Such optimality principles have been justified from an evolutionary perspective. In the context of the cell, previous studies have shown how dynamics of gene expression in small metabolic models can be explained assuming that cells have developed optimal adaptation strategies. Most of these works have considered rather simplified representations, such as small linear pathways, or reduced networks with a single branching point, and a single objective for the optimality criteria.

RESULTS

Here we consider the extension of this approach to more realistic scenarios, i.e. biochemical pathways of arbitrary size and structure. We first show that exploiting optimality principles for these networks poses great challenges due to the complexity of the associated optimal control problems. Second, in order to surmount such challenges, we present a computational framework which has been designed with scalability and efficiency in mind, including mechanisms to avoid the most common pitfalls. Third, we illustrate its performance with several case studies considering the central carbon metabolism of S. cerevisiae and B. subtilis. In particular, we consider metabolic dynamics during nutrient shift experiments.

CONCLUSIONS

We show how multi-objective optimal control can be used to predict temporal profiles of enzyme activation and metabolite concentrations in complex metabolic pathways. Further, we also show how to consider general cost/benefit trade-offs. In this study we have considered metabolic pathways, but this computational framework can also be applied to analyze the dynamics of other complex pathways, such as signal transduction or gene regulatory networks.

Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria

Although the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly growing bacteria, DNA replication and cell division are temporally resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine whether cell-cycle-dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations of Mycobacterium tuberculosis (Mtb). By enriching for genes that display a sinusoidal expression pattern, we discover 485 genes that oscillate with a period consistent with the cell cycle. During cytokinesis, the timing of gene induction could be used to predict the timing of gene function, as mRNA abundance was found to correlate with the order in which proteins were recruited to the developing septum. Similarly, the expression pattern of primary metabolic genes could be used to predict the relative importance of these pathways for different cell cycle processes. Pyrimidine synthetic genes peaked during DNA replication, and their depletion caused a filamentation phenotype that phenocopied defects in this process. In contrast, the inosine monophasphate dehydrogenase dedicated to guanosine synthesis, GuaB2, displayed the opposite expression pattern and its depletion perturbed septation. Together, these data imply obligate coordination between primary metabolism and cell division and identify periodically regulated genes that can be related to specific cell biological functions.

Spectroscopic Identification of Peptide Chemistry in the Caulobacter crescentus Holdfast

The bacterium Caulobacter crescentus is known to attach irreversibly to underwater surfaces by utilizing an adhesive structure called the holdfast, which exhibits the greatest known adhesive strength of any organism. The very small size of the holdfast (∼400 nm wide and ∼40 nm high) has made direct chemical analysis difficult, and its structure remains poorly understood. In this study, we employ spectroscopic techniques, including attenuated total reflection infrared spectroscopy (ATR-IR) and X-ray photoelectron spectroscopy, to probe holdfast chemistry. The data indicate the presence of a peptide signal within the holdfast polymer. By comparing the ATR-IR spectrum of the holdfast to peptidoglycan spectra from other bacterial species, we demonstrate the similarity of the holdfast chemistry to that of peptidoglycan, suggesting peptide cross-linking may play a role in holdfast architecture. To probe the molecular groups at the interface, surface-sensitive sum frequency generation spectroscopy was used to show that aromatic and hydroxyl groups related to this protein content at the adhesive interface could be playing a crucial role in adhesion. On the basis of these results, we propose a model of the holdfast architecture with similarities to the peptide cross-linking observed in the peptidoglycan polymer of the bacterial cell wall. These results not only provide information about the development of adhesives that could be based on holdfast chemical architecture but also reveal a potentially yet unexplored biosynthetic pathway in holdfast synthesis that has not yet been revealed by genetic approaches, thereby opening up a potentially new avenue of research in holdfast synthesis.

Novel Divisome-Associated Protein Spatially Coupling the Z-Ring with the Chromosomal Replication Terminus in Caulobacter crescentus

Growing bacteria require careful tuning of cell division processes with dynamic organization of replicating chromosomes. In enteric bacteria, ZapA associates with the cytoskeletal Z-ring and establishes a physical linkage to the chromosomal replication terminus through its interaction with ZapB-MatP-DNA complexes. However, because ZapB and MatP are found only in enteric bacteria, it remains unclear how the Z-ring and the terminus are coordinated in the vast majority of bacteria. Here, we provide evidence that a novel conserved protein, termed ZapT, mediates colocalization of the Z-ring with the terminus in Caulobacter crescentus, a model organism that is phylogenetically distant from enteric bacteria. Given that ZapT facilitates cell division processes in C. crescentus, this study highlights the universal importance of the physical linkage between the Z-ring and the terminus in maintaining cell integrity.

Cell division requires proper spatial coordination with the chromosome, which undergoes dynamic changes during chromosome replication and segregation. FtsZ is a bacterial cytoskeletal protein that assembles into the Z-ring, providing a platform to build the cell division apparatus. In the model bacterium Caulobacter crescentus, the cellular localization of the Z-ring is controlled during the cell cycle in a chromosome replication-coupled manner. Although dynamic localization of the Z-ring at midcell is driven primarily by the replication origin-associated FtsZ inhibitor MipZ, the mechanism ensuring accurate positioning of the Z-ring remains unclear. In this study, we showed that the Z-ring colocalizes with the replication terminus region, located opposite the origin, throughout most of the C. crescentus cell cycle. Spatial organization of the two is mediated by ZapT, a previously uncharacterized protein that interacts with the terminus region and associates with ZapA and ZauP, both of which are part of the incipient division apparatus. While the Z-ring and the terminus region coincided with the presence of ZapT, colocalization of the two was perturbed in cells lacking zapT, which is accompanied by delayed midcellular positioning of the Z-ring. Moreover, cells overexpressing ZapT showed compromised positioning of the Z-ring and MipZ. These findings underscore the important role of ZapT in controlling cell division processes. We propose that ZapT acts as a molecular bridge that physically links the terminus region to the Z-ring, thereby ensuring accurate site selection for the Z-ring. Because ZapT is conserved in proteobacteria, these findings may define a general mechanism coordinating cell division with chromosome organization.

Chromosome Segregation Proteins as Coordinators of Cell Cycle in Response to Environmental Conditions

Chromosome segregation is a crucial stage of the cell cycle. In general, proteins involved in this process are DNA-binding proteins, and in most bacteria, ParA and ParB are the main players; however, some bacteria manage this process by employing other proteins, such as condensins. The dynamic interaction between ParA and ParB drives movement and exerts positioning of the chromosomal origin of replication (oriC) within the cell. In addition, both ParA and ParB were shown to interact with the other proteins, including those involved in cell division or cell elongation. The significance of these interactions for the progression of the cell cycle is currently under investigation. Remarkably, DNA binding by ParA and ParB as well as their interactions with protein partners conceivably may be modulated by intra- and extracellular conditions. This notion provokes the question of whether chromosome segregation can be regarded as a regulatory stage of the cell cycle. To address this question, we discuss how environmental conditions affect chromosome segregation and how segregation proteins influence other cell cycle processes.

Dynamic insights on transcription initiation and RNA processing during bacterial adaptation

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σ^E system in E. coli was coupled to our previously described tagRNA-seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5' RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity: (i) constant and independent of RNA levels, (ii) increased once RNA has accumulated, and (iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes and can serve as a blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control.

Bacterial cell cycle control by citrate synthase independent of enzymatic activity

Proliferating cells must coordinate central metabolism with the cell cycle. How central energy metabolism regulates bacterial cell cycle functions is not well understood. Our forward genetic selection unearthed the Krebs cycle enzyme citrate synthase (CitA) as a checkpoint regulator controlling the G₁→S transition in the polarized alpha-proteobacterium Caulobacter crescentus, a model for cell cycle regulation and asymmetric cell division. We find that loss of CitA promotes the accumulation of active CtrA, an essential cell cycle transcriptional regulator that maintains cells in G₁-phase, provided that the (p)ppGpp alarmone is present. The enzymatic activity of CitA is dispensable for CtrA control, and functional citrate synthase paralogs cannot replace CitA in promoting S-phase entry. Our evidence suggests that CitA was appropriated specifically to function as a moonlighting enzyme to link central energy metabolism with S-phase entry. Control of the G₁-phase by a central metabolic enzyme may be a common mechanism of cellular regulation.

Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus

Selective recruitment and concentration of signalling proteins within membraneless compartments is a ubiquitous mechanism for subcellular organization1-3. The dynamic flow of molecules into and out of these compartments occurs on faster timescales than for membrane-enclosed organelles, presenting a possible mechanism to control spatial patterning within cells. Here, we combine single-molecule tracking and super-resolution microscopy, light-induced subcellular localization, reaction-diffusion modelling and a spatially resolved promoter activation assay to study signal exchange in and out of the 200 nm cytoplasmic pole-organizing protein popZ (PopZ) microdomain at the cell pole of the asymmetrically dividing bacterium Caulobacter crescentus4-8. Two phospho-signalling proteins, the transmembrane histidine kinase CckA and the cytoplasmic phosphotransferase ChpT, provide the only phosphate source for the cell fate-determining transcription factor CtrA9-18. We find that all three proteins exhibit restricted rates of entry into and escape from the microdomain as well as enhanced phospho-signalling within, leading to a submicron gradient of activated CtrA-P19 that is stable and sublinear. Entry into the microdomain is selective for cytosolic proteins and requires a binding pathway to PopZ. Our work demonstrates how nanoscale protein assemblies can modulate signal propagation with fine spatial resolution, and that in Caulobacter, this modulation serves to reinforce asymmetry and differential cell fate of the two daughter cells.

Untargeted metabolomics links glutathione to bacterial cell cycle progression

Cell cycle progression requires the coordination of cell growth, chromosome replication, and division. Consequently, a functional cell cycle must be coupled with metabolism. However, direct measurements of metabolome dynamics remained scarce, in particular in bacteria. Here, we describe an untargeted metabolomics approach with synchronized Caulobacter crescentus cells to monitor the relative abundance changes of ~400 putative metabolites as a function of the cell cycle. While the majority of metabolite pools remains homeostatic, ~14% respond to cell cycle progression. In particular, sulfur metabolism is redirected during the G1-S transition, and glutathione levels periodically change over the cell cycle with a peak in late S phase. A lack of glutathione perturbs cell size by uncoupling cell growth and division through dysregulation of KefB, a K+/H+ antiporter. Overall, we here describe the impact of the C. crescentus cell cycle progression on metabolism, and in turn relate glutathione and potassium homeostasis to timely cell division.

Transcriptome dynamics of the Myxococcus xanthus multicellular developmental program

The bacterium Myxococcus xanthus exhibits a complex multicellular life cycle. In the presence of nutrients, cells prey cooperatively. Upon starvation, they enter a developmental cycle wherein cells aggregate to produce macroscopic fruiting bodies filled with resistant myxospores. We used RNA-Seq technology to examine the transcriptome of the 96 hr developmental program. These data revealed that 1415 genes were sequentially expressed in 10 discrete modules, with expression peaking during aggregation, in the transition from aggregation to sporulation, or during sporulation. Analysis of genes expressed at each specific time point provided insights as to how starving cells obtain energy and precursors necessary for assembly of fruiting bodies and into developmental production of secondary metabolites. This study offers the first global view of developmental transcriptional profiles and provides important tools and resources for future studies.

The Two Chemotaxis Clusters in Caulobacter crescentus Play Different Roles in Chemotaxis and Biofilm Regulation

The holdfast polysaccharide adhesin is crucial for irreversible cell adhesion and biofilm formation in Caulobacter crescentus Holdfast production is tightly controlled via developmental regulators, as well as via environmental and physical signals. Here, we identify a novel mode of regulation of holdfast synthesis that involves chemotaxis proteins. We characterized the two identified chemotaxis clusters of C. crescentus and showed that only the previously characterized major cluster is involved in the chemotactic response toward different carbon sources. However, both chemotaxis clusters encoded in the C. crescentus genome play a role in biofilm formation and holdfast production by regulating the expression of hfiA, the gene encoding the holdfast inhibitor HfiA. We show that CheA and CheB proteins act in an antagonistic manner, as follows: while the two CheA proteins negatively regulate hfiA expression, the CheB proteins are positive regulators, thus providing a modulation of holdfast synthesis and surface attachment.IMPORTANCE Chemosensory systems constitute major signal transduction pathways in bacteria. These systems are involved in chemotaxis and other cell responses to environment conditions, such as the production of adhesins to enable irreversible adhesion to a surface and surface colonization. The C. crescentus genome encodes two complete chemotaxis clusters. Here, we characterized the second novel chemotaxis-like cluster. While only the major chemotaxis cluster is involved in chemotaxis, both chemotaxis systems modulate C. crescentus adhesion by controlling expression of the holdfast synthesis inhibitor HfiA. Here, we identify a new level in holdfast regulation, providing new insights into the control of adhesin production that leads to the formation of biofilms in response to the environment.

Chromosome Dynamics in Bacteria: Triggering Replication at the Opposite Location and Segregation in the Opposite Direction

Maintaining the integrity of the genome is essential to cell survival. In the bacterium Caulobacter crescentus, the single circular chromosome exhibits a specific orientation in the cell, with the replication origin (ori) residing at the pole of the cell bearing a stalk. Upon initiation of replication, the duplicated centromere-like region parS and ori move rapidly to the opposite pole where parS is captured by a microdomain hosting a unique set of proteins that contribute to the identity of progeny cells. Many questions remain as to how this organization is maintained. In this study, we constructed strains of Caulobacter in which ori and the parS centromere can be induced to move to the opposite cell pole in the absence of chromosome replication, allowing us to ask whether once these chromosomal foci were positioned at the wrong pole, replication initiation and chromosome segregation can proceed in the opposite orientation. Our data reveal that DnaA can initiate replication and ParA can orchestrate segregation from either cell pole. The cell reconstructs the organization of its ParA gradient in the opposite orientation to segregate one replicated centromere from the new pole toward the stalked pole (i.e., opposite direction), while displaying no detectable viability defects. Thus, the unique polar microdomains exhibit remarkable flexibility in serving as a platform for directional chromosome segregation along the long axis of the cell.IMPORTANCE Bacteria can accomplish surprising levels of organization in the absence of membrane organelles by constructing subcellular asymmetric protein gradients. These gradients are composed of regulators that can either trigger or inhibit cell cycle events from distinct cell poles. In Caulobacter crescentus, the onset of chromosome replication and segregation from the stalked pole are regulated by asymmetric protein gradients. We show that the activators of chromosome replication and segregation are not restricted to the stalked pole and that their organization and directionality can be flipped in orientation. Our results also indicate that the subcellular location of key chromosomal loci play important roles in the establishment of the asymmetric organization of cell cycle regulators.

Recent Advances on Electrochemical Biosensing Strategies toward Universal Point-of-Care Systems

A number of very recently developed electrochemical biosensing strategies are promoting electrochemical biosensing systems into practical point-of-care applications. The focus of research endeavors has transferred from detection of a specific analyte to the development of general biosensing strategies that can be applied for a single category of analytes, such as nucleic acids, proteins, and cells. In this Minireview, recent cutting-edge research on electrochemical biosensing strategies are described. These developments resolved critical challenges regarding the application of electrochemical biosensors to practical point-of-care systems, such as rapid readout, simple biosensor fabrication method, ultra-high detection sensitivity, direct analysis in a complex biological matrix, and multiplexed target analysis. This Minireview provides general guidelines both for scientists in the biosensing research community and for the biosensor industry on development of point-of-care system, benefiting global healthcare.

Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B12 Scavenging

Caulobacter crescentus is a model system of the bacterial cell cycle culminating in asymmetric cell division, with each daughter cell inheriting a distinct set of proteins. While a genetic network of master transcription factors coordinates the cell cycle timing of transcription for nearly 20% of Caulobacter genes, we lack knowledge of how many of each protein “part” encoded in the genome are synthesized. Therefore, to determine the absolute production rates across the genome, we performed ribosome profiling, providing, for the first time, a quantitative resource with measurements of each protein “part” needed to generate daughter cells. This resource furthers the goal of a systems-level understanding of the genetic network controlling asymmetric cell division. To highlight the utility of this data set, we probe the protein synthesis cost of a B₁₂ utilization pathway and provide new insights into Caulobacter’s adaptation to its natural environments.

Caulobacter crescentus is a model for the bacterial cell cycle which culminates in asymmetric cell division, yet little is known about the absolute levels of protein synthesis of the cellular parts needed to complete the cell cycle. Here we utilize ribosome profiling to provide absolute measurements of mRNA translation in C. crescentus, providing an important resource with quantitative genome-wide measurements of protein output across individual genes. Analysis of protein synthesis rates revealed ∼4.5% of cellular protein synthesis is for genes related to vitamin B₁₂ import (btuB) and B₁₂-independent methionine biosynthesis (metE) when grown in common growth media lacking B₁₂. While its facultative B₁₂ lifestyle provides a fitness advantage in the absence of B₁₂, we find that it provides a fitness disadvantage of the cells in the presence of B₁₂, potentially explaining why many Caulobacter species have lost the metE gene and become obligates for B₁₂.

IMPORTANCECaulobacter crescentus is a model system of the bacterial cell cycle culminating in asymmetric cell division, with each daughter cell inheriting a distinct set of proteins. While a genetic network of master transcription factors coordinates the cell cycle timing of transcription for nearly 20% of Caulobacter genes, we lack knowledge of how many of each protein “part” encoded in the genome are synthesized. Therefore, to determine the absolute production rates across the genome, we performed ribosome profiling, providing, for the first time, a quantitative resource with measurements of each protein “part” needed to generate daughter cells. This resource furthers the goal of a systems-level understanding of the genetic network controlling asymmetric cell division. To highlight the utility of this data set, we probe the protein synthesis cost of a B₁₂ utilization pathway and provide new insights into Caulobacter’s adaptation to its natural environments.

Author Video: An author video summary of this article is available.

Microfluidic Synchronizer Using a Synthetic Nanoparticle-Capped Bacterium

Conventional techniques to synchronize bacterial cells often require manual manipulations and lengthy incubation lacking precise temporal control. An automated microfluidic device was recently developed to overcome these limitations. However, it exploits the stalk property of Caulobacter crescentus that undergoes asymmetric stalked and swarmer cell cycle stages and is therefore restricted to this species. To address this shortcoming, we have engineered Escherichia coli cells to adhere to microchannel walls via a synthetic and inducible "stalk". The pole of E. coli is capped by magnetic fluorescent nanoparticles via a polar-localized outer membrane protein. A mass of cells is immobilized in a microfluidic chamber by an externally applied magnetic field. Daughter cells are formed without the induced stalk and hence are flushed out, yielding a synchronous population of "baby" cells. The stalks can be tracked by GFP and nanoparticle fluorescence; no fluorescence signal is detected in the eluted cell population, indicating that it consists solely of daughters. The collected daughter cells display superb synchrony. The results demonstrate a new on-chip method to synchronize the model bacterium E. coli and likely other bacterial species, and also foster the application of synthetic biology to the study of the bacterial cell cycle.

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

The CRISPR-Cas9 system provides the ability to edit, repress, activate, or mark any gene (or DNA element) by pairing of a programmable single guide RNA (sgRNA) with a complementary sequence on the DNA target. Here we present a new method for small-molecule control of CRISPR-Cas9 function through insertion of RNA aptamers into the sgRNA. We show that CRISPR-Cas9-based gene repression (CRISPRi) can be either activated or deactivated in a dose-dependent fashion over a >10-fold dynamic range in response to two different small-molecule ligands. Since our system acts directly on each target-specific sgRNA, it enables new applications that require differential and opposing temporal control of multiple genes.

In Vitro Thermal and Ethanol Adaptations to Improve Vinegar Fermentation at High Temperature of Komagataeibacter oboediens MSKU 3

High temperature and high ethanol concentrations obviously affect vinegar fermentation. The thermotolerant and ethanol-resistant strains are expected to become one of the technologies for effective vinegar fermentation. This study aimed to further improve thermotolerant Komagataeibacter oboediens MSKU 3 through thermal and ethanol adaptations for acetic acid fermentation. The MSKU 3 strain was independently cultured by a repetitive cultivation in gradually increasing temperature from 37 to 39 °C for thermal adaptation, while adaptation to ethanol was carried out from concentrations of 3 to 5.5% (v/v) at 37 °C. Acetic acid fermentation revealed that the thermo-adapted T4 strain could produce 2.82% acidity with 3% ethanol at 39 °C, whereas the ethanol-adapted E3 strain could produce 3.54% acidity with 5.5% ethanol at 37 °C, in contrast to the parental strain, MSKU 3, in which no fermentation occurs at either 39 °C or 5.5% ethanol. Furthermore, genome mapping analysis of T4 and E3 strains against the genome of parental strain MSKU 3 revealed several mutated genes that are associated with thermotolerance or ethanol adaptation. The occurrence of these adaptation-associated mutations during adaptive evolution was also analyzed. Therefore, adapted strains T4 and E3 revealed the potential of Komagataeibacter oboediens strain improvement to further enhance vinegar fermentation with high ethanol concentration at high temperature.

Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens

A core regulatory pathway that directs developmental transitions and cellular asymmetries in Agrobacterium tumefaciens involves two overlapping, integrated phosphorelays. One of these phosphorelays putatively includes four histidine sensor kinase homologues, DivJ, PleC, PdhS1 and PdhS2, and two response regulators, DivK and PleD. In several different alphaproteobacteria, this pathway influences a conserved downstream phosphorelay that ultimately controls the phosphorylation state of the CtrA master response regulator. The PdhS2 sensor kinase reciprocally regulates biofilm formation and swimming motility. In the current study, the mechanisms by which the A. tumefaciens sensor kinase PdhS2 directs this regulation are delineated. PdhS2 lacking a key residue implicated in phosphatase activity is markedly deficient in proper control of attachment and motility phenotypes, whereas a kinase-deficient PdhS2 mutant is only modestly affected. A genetic interaction between DivK and PdhS2 is revealed, unmasking one of several connections between PdhS2-dependent phenotypes and transcriptional control by CtrA. Epistasis experiments suggest that PdhS2 may function independently of the CckA sensor kinase, the cognate sensor kinase for CtrA, which is inhibited by DivK. Global expression analysis of the pdhS2 mutant reveals a restricted regulon, most likely functioning through CtrA to separately control motility and regulate the levels of the intracellular signal cyclic diguanylate monophosphate (cdGMP), thereby affecting the production of adhesive polysaccharides and attachment. We hypothesize that in A. tumefaciens the CtrA regulatory circuit has expanded to include additional inputs through the addition of PdhS-type sensor kinases, likely fine-tuning the response of this organism to the soil microenvironment.

Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus

Molecular components of the Brucella abortus cell envelope play a major role in its ability to infect, colonize and survive inside mammalian host cells. In this study, we have defined a role for a conserved gene of unknown function in B. abortus envelope stress resistance and infection. Expression of this gene, which we name eipA, is directly activated by the essential cell cycle regulator, CtrA. eipA encodes a soluble periplasmic protein that adopts an unusual eight-stranded β-barrel fold. Deletion of eipA attenuates replication and survival in macrophage and mouse infection models, and results in sensitivity to treatments that compromise the cell envelope integrity. Transposon disruption of genes required for LPS O-polysaccharide biosynthesis is synthetically lethal with eipA deletion. This genetic connection between O-polysaccharide and eipA is corroborated by our discovery that eipA is essential in Brucella ovis, a naturally rough species that harbors mutations in several genes required for O-polysaccharide production. Conditional depletion of eipA expression in B. ovis results in a cell chaining phenotype, providing evidence that eipA directly or indirectly influences cell division in Brucella. We conclude that EipA is a molecular determinant of Brucella virulence that functions to maintain cell envelope integrity and influences cell division.

Learning from the master: targets and functions of the CtrA response regulator in Brucella abortus and other alpha-proteobacteria

The α-proteobacteria are a fascinating group of free-living, symbiotic and pathogenic organisms, including the Brucella genus, which is responsible for a worldwide zoonosis. One common feature of α-proteobacteria is the presence of a conserved response regulator called CtrA, first described in the model bacterium Caulobacter crescentus, where it controls gene expression at different stages of the cell cycle. Here, we focus on Brucella abortus and other intracellular α-proteobacteria in order to better assess the potential role of CtrA in the infectious context. Comparative genomic analyses of the CtrA control pathway revealed the conservation of specific modules, as well as the acquisition of new factors during evolution. The comparison of CtrA regulons also suggests that specific clades of α-proteobacteria acquired distinct functions under its control, depending on the essentiality of the transcription factor. Other CtrA-controlled functions, for instance motility and DNA repair, are proposed to be more ancestral. Altogether, these analyses provide an interesting example of the plasticity of a regulation network, subject to the constraints of inherent imperatives such as cell division and the adaptations to diversified environmental niches.