Cellular polarity in prokaryotic organisms

Origin of homochirality in peptides: The first milestone at the origin of life

Living organisms have some common structures, chemical reactions and molecular structures. The organisms consist of cells with cell division, they have homochirality of protein and carbohydrate units, metabolism, and genetics, and they are mortal. The molecular structures and chemical reactions underlying these features are common to all, from the simplest bacteria to human beings. The origin of life is evolutionary with the emergence of a network of spontaneous biochemical reactions, and the evolution has taken place over a very long time. The evolution contains, however, some "landmarks" and bottlenecks, which in a revolutionary manner directed the evolution, and the article establishes an order of some of these events. Recent articles show that peptides in living organisms are long-time unstable with loss of their secondary homochiral conformations and with D-amino acids. Based on these observations and an extensive scientific literature on Abiogenesis, we argue that the first milestone in the prebiotic evolution is at the emergence of homochiral peptides in an aqueous solution with a high concentration of amino acids and a lower water activity than in the cytosol in living organisms. The homochiral peptides in cytosol are unstable, and the long-time aging of peptides in the cytosol causes mortality of living organisms. The metabolism and genetics are established in an environment with homochiral peptides in the Earth's crust for ≈ 4 Gyr ago at a lower water activity than in the cytosol in living organisms. Finally, the cells with cell division are established in the Hot Springs environment at the interface between the crust and the Hadean Ocean.

Global quantitative understanding of non-equilibrium cell fate decision-making in response to pheromone

Cell-cycle arrest and polarized growth are commonly used to characterize the response of yeast to pheromone. However, the quantitative decision-making processes underlying time-dependent changes in cell fate remain unclear. In this study, we conducted single-cell level experiments to observe multidimensional responses, uncovering diverse fates of yeast cells. Multiple states are revealed, along with the kinetic switching rates and pathways among them, giving rise to a quantitative landscape of mating response. To quantify the experimentally observed cell fates, we developed a theoretical framework based on non-equilibrium landscape and flux theory. Additionally, we performed stochastic simulations of biochemical reactions to elucidate signal transduction and cell growth. Notably, our experimental findings have provided the first global quantitative evidence of the real-time synchronization between intracellular signaling, physiological growth, and morphological functions. These results validate the proposed underlying mechanism governing the emergence of multiple cell fate states. This study introduces an emerging mechanistic approach to understand non-equilibrium cell fate decision-making in response to pheromone.

Biofilm Formation by Listeria monocytogenes 15G01, a Persistent Isolate from a Seafood-Processing Plant, Is Influenced by Inactivation of Multiple Genes Belonging to Different Functional Groups

Listeria monocytogenes is a ubiquitous foodborne pathogen that results in a high rate of mortality in sensitive and immunocompromised people. Contamination of food with L. monocytogenes is thought to occur during food processing, most often as a result of the pathogen producing a biofilm that persists in the environment and acting as the source for subsequent dispersal of cells onto food. A survey of seafood-processing plants in New Zealand identified the persistent strain 15G01, which has a high capacity to form biofilms. In this study, a transposon library of L. monocytogenes 15G01 was screened for mutants with altered biofilm formation, assessed by a crystal violet assay, to identify genes involved in biofilm formation. This screen identified 36 transposants that showed a significant change in biofilm formation compared to the wild type. The insertion sites were in 27 genes, 20 of which led to decreased biofilm formation and seven to an increase. Two insertions were in intergenic regions. Annotation of the genes suggested that they are involved in diverse cellular processes, including stress response, autolysis, transporter systems, and cell wall/membrane synthesis. Analysis of the biofilms produced by the transposants using scanning electron microscopy and fluorescence microscopy showed notable differences in the structure of the biofilms compared to the wild type. In particular, inactivation of uvrB and mltD produced coccoid-shaped cells and elongated cells in long chains, respectively, and the mgtB mutant produced a unique biofilm with a sandwich structure which was reversed to the wild-type level upon magnesium addition. The mltD transposant was successfully complemented with the wild-type gene, whereas the phenotypes were not or only partially restored for the remaining mutants.IMPORTANCE The major source of contamination of food with Listeria monocytogenes is thought to be due to biofilm formation and/or persistence in food-processing plants. By establishing as a biofilm, L. monocytogenes cells become harder to eradicate due to their increased resistance to environmental threats. Understanding the genes involved in biofilm formation and their influence on biofilm structure will help identify new ways to eliminate harmful biofilms in food processing environments. To date, multiple genes have been identified as being involved in biofilm formation by L. monocytogenes; however, the exact mechanism remains unclear. This study identified four genes associated with biofilm formation by a persistent strain. Extensive microscopic analysis illustrated the effect of the disruption of mgtB, clsA, uvrB, and mltD and the influence of magnesium on the biofilm structure. The results strongly suggest an involvement in biofilm formation for the four genes and provide a basis for further studies to analyze gene regulation to assess the specific role of these biofilm-associated genes.

The Emergence of the Bilateral Symmetry in Animals: A Review and a New Hypothesis

Most biological organisms exhibit different kinds of symmetry; an Animal (Metazoa), which is our Darwinist ancestor, has bilateral symmetry, and many plants exhibit rotational symmetry. It raises some questions: I. How can the evolution from an undifferentiated cell without bilateral symmetry to a complex biological organism with symmetry, which is based on asymmetric DNA and enzymes, lead to the bilateral symmetry? II. Is this evolution to an organism with bilateral symmetry obtained by other factors than DNA and enzymatic reactions? The existing literature about the evolution of the bilateral symmetry has been reviewed, and a new hypothesis has been formulated based on these reviews. The hypothesis is that the morphogenesis of biosystems is connected with the metabolism and that the oscillating kinetics in the Glycolysis have played a role in the polarity of the biological cells and in the establishment of the bilateral symmetry in Animals.

Four different mechanisms for switching cell polarity

The mechanisms and design principles of regulatory systems establishing stable polarized protein patterns within cells are well studied. However, cells can also dynamically control their cell polarity. Here, we ask how an upstream signaling system can switch the orientation of a polarized pattern. We use a mathematical model of a core polarity system based on three proteins as the basis to study different mechanisms of signal-induced polarity switching. The analysis of this model reveals four general classes of switching mechanisms with qualitatively distinct behaviors: the transient oscillator switch, the reset switch, the prime-release switch, and the push switch. Each of these regulatory mechanisms effectively implements the function of a spatial toggle switch, however with different characteristics in their nonlinear and stochastic dynamics. We identify these characteristics and also discuss experimental signatures of each type of switching mechanism.

Polarity, planes of cell division, and the evolution of plant multicellularity

Organisms as diverse as bacteria, fungi, plants, and animals manifest a property called "polarity." The literature shows that polarity emerges as a consequence of different mechanisms in different lineages. However, across all unicellular and multicellular organisms, polarity is evident when cells, organs, or organisms manifest one or more of the following: orientation, axiation, and asymmetry. Here, we review the relationships among these three features in the context of cell division and the evolution of multicellular polarity primarily in plants (defined here to include the algae). Data from unicellular and unbranched filamentous organisms (e.g., Chlamydomonas and Ulothrix) show that cell orientation and axiation are marked by cytoplasmic asymmetries. Branched filamentous organisms (e.g., Cladophora and moss protonema) require an orthogonal reorientation of axiation, or a localized cell asymmetry (e.g., "tip" growth in pollen tubes and fungal hyphae). The evolution of complex multicellular meristematic polarity required a third reorientation of axiation. These transitions show that polarity and the orientation of the future plane(s) of cell division are dyadic dynamical patterning modules that were critical for multicellular eukaryotic organisms.

End-in-Sight: Cell Polarization by the Polygamic Organizer PopZ

Understanding how asymmetries in cellular constituents are achieved and how such positional information directs the construction of structures in a nonrandom fashion is a fundamental problem in cell biology. The recent identification of determinants that self-assemble into macromolecular complexes at the bacterial cell pole provides new insight into the underlying organizational principles in bacterial cells. Specifically, polarity studies in host-associated or free-living α-proteobacteria, a lineage of Gram-negative (diderm) bacteria, reveals that functional and cytological mono- and bipolarity is often conferred by the multivalent polar organizer PopZ, originally identified as a component of a polar chromosome anchor in the cell cycle model system Caulobacter crescentus. PopZ-dependent polarization appears to be widespread and also functional in obligate intracellular pathogens. Here, we discuss how PopZ polarization and the establishment of polar complexes occurs, and we detail the physiological roles of these complexes.

Functional dichotomy and distinct nanoscale assemblies of a cell cycle-controlled bipolar zinc-finger regulator

Protein polarization underlies differentiation in metazoans and in bacteria. How symmetric polarization can instate functional asymmetry remains elusive. Here, we show by super-resolution photo-activated localization microscopy and edgetic mutations that the bitopic zinc-finger protein ZitP implements specialized developmental functions – pilus biogenesis and multifactorial swarming motility – while shaping distinct nanoscale (bi)polar architectures in the asymmetric model bacterium Caulobacter crescentus. Polar assemblage and accumulation of ZitP and its effector protein CpaM are orchestrated in time and space by conserved components of the cell cycle circuitry that coordinate polar morphogenesis with cell cycle progression, and also act on the master cell cycle regulator CtrA. Thus, this novel class of potentially widespread multifunctional polarity regulators is deeply embedded in the cell cycle circuitry.

DOI:http://dx.doi.org/10.7554/eLife.18647.001

Living cells become asymmetric for many different reasons and how they do so has been a long-standing question in biology. In some cells, the asymmetry arises because a given protein accumulates at one side of the cell. In particular, this process happens before some cells divide to produce two non-identical daughter cells that then go on to develop in very different ways – which is vital for the development of almost all multicellular organisms. The single-celled bacterium Caulobacter crescentus also undergoes this type of asymmetric division. The polarized Caulobacter cell produces two very different offsprings – a stationary cell and a nomadic cell that swims using a propeller-like structure, called a flagellum, and has projections called pili on its surface.

Before it divides asymmetrically, the Caulobacter cell must accumulate specific proteins at its extremities, or poles. Two such proteins are ZitP and CpaM, which appear to have multiple roles and are thought to interact with other factors that regulate cell division. However, little is known about how ZitP and CpaM become organized at the poles at the right time and how they interact with these regulators of cell division.

Mignolet et al. explored how ZitP becomes polarized in Caulobacter crescentus using a combination of approaches including biochemical and genetic analyses and very high-resolution microscopy. This revealed that ZitP accumulated via different pathways at the two poles and that it formed distinct structures at each pole. These structures were associated with different roles for ZitP. While ZitP recruited proteins, including CpaM, required for assembly of pili to one of the poles, it acted differently at the opposite pole.

By mutating regions of ZitP, Mignolet et al. went on to show that different regions of the protein carry out these roles. Further experiments demonstrated that regulators of the cell division cycle influenced how ZitP and CpaM accumulated and behaved in cells, ensuring that the proteins carry out their roles at the correct time during division. These findings provide more evidence that proteins can have different roles at distinct sites within a cell, in this case at opposite poles of a cell. Future studies will be needed to determine whether this is seen in cells other than Caulobacter including more complex, non-bacterial cells.

DOI:http://dx.doi.org/10.7554/eLife.18647.002

Modulation of the Lytic Activity of the Dedicated Autolysin for Flagellum Formation SltF by Flagellar Rod Proteins FlgB and FlgF

SltF was identified previously as an autolysin required for the assembly of flagella in the alphaproteobacteria, but the nature of its peptidoglycan lytic activity remained unknown. Sequence alignment analyses suggest that it could function as either a muramidase, lytic transglycosylase, or β-N-acetylglucosaminidase. Recombinant SltF from Rhodobacter sphaeroides was purified to apparent homogeneity, and it was demonstrated to function as a lytic transglycosylase based on enzymatic assays involving mass spectrometric analyses. Circular dichroism (CD) analysis determined that it is composed of 83.4% α-structure and 1.48% β-structure and thus is similar to family 1A lytic transglycosylases. However, alignment of apparent SltF homologs identified in the genome database defined a new subfamily of the family 1 lytic transglycosylases. SltF was demonstrated to be endo-acting, cleaving within chains of peptidoglycan, with optimal activity at pH 7.0. Its activity is modulated by two flagellar rod proteins, FlgB and FlgF: FlgB both stabilizes and stimulates SltF activity, while FlgF inhibits it. Invariant Glu57 was confirmed as the sole catalytic acid/base residue of SltF.

IMPORTANCE

The bacterial flagellum is comprised of a basal body, hook, and helical filament, which are connected by a rod structure. With a diameter of approximately 4 nm, the rod is larger than the estimated pore size within the peptidoglycan sacculus, and hence its insertion requires the localized and controlled lysis of this essential cell wall component. In many beta- and gammaproteobacteria, this lysis is catalyzed by the β-N-acetylglucosaminidase domain of FlgJ. However, FlgJ of the alphaproteobacteria lacks this activity and instead it recruits a separate enzyme, SltF, for this purpose. In this study, we demonstrate that SltF functions as a newly identified class of lytic transglycosylases and that its autolytic activity is uniquely modulated by two rod proteins, FlgB and FlgF.

Protein Targeting during Bacillus subtilis Sporulation

The Gram-positive bacterium Bacillus subtilis initiates the formation of an endospore in response to conditions of nutrient limitation. The morphological differentiation that spores undergo initiates with the formation of an asymmetric septum near to one pole of the cell, forming a smaller compartment, the forespore, and a larger compartment, the mother cell. This process continues with the complex morphogenesis of the spore as governed by an intricate series of interactions between forespore and mother cell proteins across the inner and outer forespore membranes. Given that these interactions occur at a particular place in the cell, a critical question is how the proteins involved in these processes get properly targeted, and we discuss recent progress in identifying mechanisms responsible for this targeting.

Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models

Cell-fate asymmetry in the predivisional cell of Caulobacter crescentus requires that the regulatory protein DivL localizes to the new pole of the cell where it up-regulates CckA kinase, resulting in a gradient of CtrA~P across the cell. In the preceding stage of the cell cycle (the "stalked" cell), DivL is localized uniformly along the cell membrane and maintained in an inactive form by DivK~P. It is unclear how DivL overcomes inhibition by DivK~P in the predivisional cell simply by changing its location to the new pole. It has been suggested that co-localization of DivL with PleC phosphatase at the new pole is essential to DivL's activity there. However, there are contrasting views on whether the bifunctional enzyme, PleC, acts as a kinase or phosphatase at the new pole. To explore these ambiguities, we formulated a mathematical model of the spatiotemporal distributions of DivL, PleC and associated proteins (DivJ, DivK, CckA, and CtrA) during the asymmetric division cycle of a Caulobacter cell. By varying localization profiles of DivL and PleC in our model, we show how the physiologically observed spatial distributions of these proteins are essential for the transition from a stalked cell to a predivisional cell. Our simulations suggest that PleC is a kinase in predivisional cells, and that, by sequestering DivK~P, the kinase form of PleC enables DivL to be reactivated at the new pole. Hence, co-localization of PleC kinase and DivL is essential to establishing cellular asymmetry. Our simulations reproduce the experimentally observed spatial distribution and phosphorylation status of CtrA in wild-type and mutant cells. Based on the model, we explore novel combinations of mutant alleles, making predictions that can be tested experimentally.

A new suite of tnaA mutants suggests that Escherichia coli tryptophanase is regulated by intracellular sequestration and by occlusion of its active site

Background

The Escherichia coli enzyme tryptophanase (TnaA) converts tryptophan to indole, which triggers physiological changes and regulates interactions between bacteria and their mammalian hosts. Tryptophanase production is induced by external tryptophan, but the activity of TnaA is also regulated by other, more poorly understood mechanisms. For example, the enzyme accumulates as a spherical inclusion (focus) at midcell or at one pole, but how or why this localization occurs is unknown.

Results

TnaA activity is low when the protein forms foci during mid-logarithmic growth but its activity increases as the protein becomes more diffuse, suggesting that foci may represent clusters of inactive (or less active) enzyme. To determine what protein characteristics might mediate these localization effects, we constructed 42 TnaA variants: 6 truncated forms and 36 missense mutants in which different combinations of 83 surface-exposed residues were converted to alanine. A truncated TnaA protein containing only domains D1 and D3 (D1D3) localized to the pole. Mutations affecting the D1D3-to-D1D3 interface did not affect polar localization of D1D3 but did delay assembly of wild type TnaA foci. In contrast, alterations to the D1D3-to-D2 domain interface produced diffuse localization of the D1D3 variant but did not affect the wild type protein. Altering several surface-exposed residues decreased TnaA activity, implying that tetramer assembly may depend on interactions involving these sites. Interestingly, changing any of three amino acids at the base of a loop near the catalytic pocket decreased TnaA activity and caused it to form elongated ovoid foci in vivo, indicating that the alterations affect focus formation and may regulate how frequently tryptophan reaches the active site.

Conclusions

The results suggest that TnaA activity is regulated by subcellular localization and by a loop-associated occlusion of its active site. Equally important, these new TnaA variants are immediately available to the research community and should be useful for investigating how tryptophanase is localized and assembled, how substrate accesses its active site, the functional role of acetylation, and other structural and functional questions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0346-3) contains supplementary material, which is available to authorized users.

Phytoplasma infection in tomato is associated with re-organization of plasma membrane, ER stacks, and actin filaments in sieve elements

Phytoplasmas, biotrophic wall-less prokaryotes, only reside in sieve elements of their host plants. The essentials of the intimate interaction between phytoplasmas and their hosts are poorly understood, which calls for research on potential ultrastructural modifications. We investigated modifications of the sieve-element ultrastructure induced in tomato plants by 'Candidatus Phytoplasma solani,' the pathogen associated with the stolbur disease. Phytoplasma infection induces a drastic re-organization of sieve-element substructures including changes in plasma membrane surface and distortion of the sieve-element reticulum. Observations of healthy and stolbur-diseased plants provided evidence for the emergence of structural links between sieve-element plasma membrane and phytoplasmas. One-sided actin aggregates on the phytoplasma surface also inferred a connection between phytoplasma and sieve-element cytoskeleton. Actin filaments displaced from the sieve-element mictoplasm to the surface of the phytoplasmas in infected sieve elements. Western blot analysis revealed a decrease of actin and an increase of ER-resident chaperone luminal binding protein (BiP) in midribs of phytoplasma-infected plants. Collectively, the studies provided novel insights into ultrastructural responses of host sieve elements to phloem-restricted prokaryotes.

A memory system of negative polarity cues prevents replicative aging

Cdc42 is a highly conserved master regulator of cell polarity. Here, we investigated the mechanism by which yeast cells never re-establish polarity at cortical sites (cytokinesis remnants [CRMs]) that have previously supported Cdc42-mediated growth as a paradigm to mechanistically understand how Cdc42-inhibitory polarity cues are established. We revealed a two-step mechanism of loading the Cdc42 antagonist Nba1 into CRMs to mark these compartments as refractory for a second round of Cdc42 activation. Our data indicate that Nba1 together with a cortically tethered adaptor protein confers memory of previous polarization events to translate this spatial legacy into a biochemical signal that ensures the local singularity of Cdc42 activation. "Memory loss" mutants that repeatedly use the same polarity site over multiple generations display nuclear segregation defects and a shorter lifespan. Our work thus established CRMs as negative polarity cues that prevent Cdc42 reactivation to sustain the fitness of replicating cells.

RNA localization in bacteria

One of the most important discoveries in the field of microbiology in the last two decades is that bacterial cells have intricate subcellular organization. This understanding has emerged mainly from the depiction of spatial and temporal organization of proteins in specific domains within bacterial cells, e.g., midcell, cell poles, membrane and periplasm. Because translation of bacterial RNA molecules was considered to be strictly coupled to their synthesis, they were not thought to specifically localize to regions outside the nucleoid. However, the increasing interest in RNAs, including non-coding RNAs, encouraged researchers to explore the spatial and temporal localization of RNAs in bacteria. The recent technological improvements in the field of fluorescence microscopy allowed subcellular imaging of RNAs even in the tiny bacterial cells. It has been reported by several groups, including ours that transcripts may specifically localize in such cells. Here we review what is known about localization of RNA and of the pathways that determine RNA fate in bacteria, and discuss the possible cues and mechanisms underlying these distribution patterns.

Delineation of polar localization domains of Agrobacterium tumefaciens type IV secretion apparatus proteins VirB4 and VirB11

Agrobacterium tumefaciens transfers DNA and proteins to a plant cell through a type IV secretion apparatus assembled by the VirB proteins. All VirB proteins localized to a cell pole, although these conclusions are in dispute. To study subcellular location of the VirB proteins and to identify determinants of their subcellular location, we tagged two proteins, VirB4 and VirB11, with the visual marker green fluorescent protein (GFP) and studied localization of the fusion proteins by epifluorescence microscopy. Both GFP-VirB4 and GFP-VirB11 fusions localized to a single cell pole. GFP-VirB11 was also functional in DNA transfer. To identify the polar localization domains (PLDs) of VirB4 and VirB11, we analyzed fusions of GFP with smaller segments of the two proteins. Two noncontiguous regions in VirB4, residues 236–470 and 592–789, contain PLDs. The VirB11 PLD mapped to a 69 amino acid segment, residues 149–217, in the central region of the protein. These domains are probably involved in interactions that target the two proteins to a cell pole.

Intracellular locations of replication proteins and the origin of replication during chromosome duplication in the slowly growing human pathogen Helicobacter pylori

We followed the position of the replication complex in the pathogenic bacterium Helicobacter pylori using antibodies raised against the single-stranded DNA binding protein (HpSSB) and the replicative helicase (HpDnaB). The position of the replication origin, oriC, was also localized in growing cells by fluorescence in situ hybridization (FISH) with fluorescence-labeled DNA sequences adjacent to the origin. The replisome assembled at oriC near one of the cell poles, and the two forks moved together toward the cell center as replication progressed in the growing cell. Termination and resolution of the forks occurred near midcell, on one side of the septal membrane. The duplicated copies of oriC did not separate until late in elongation, when the daughter chromosomes segregated into bilobed nucleoids, suggesting sister chromatid cohesion at or near the oriC region. Components of the replication machinery, viz., HpDnaB and HpDnaG (DNA primase), were found associated with the cell membrane. A model for the assembly and location of the H. pylori replication machinery during chromosomal duplication is presented.

c-di-GMP heterogeneity is generated by the chemotaxis machinery to regulate flagellar motility

Individual cell heterogeneity is commonly observed within populations, although its molecular basis is largely unknown. Previously, using FRET-based microscopy, we observed heterogeneity in cellular c-di-GMP levels. In this study, we show that c-di-GMP heterogeneity in Pseudomonas aeruginosa is promoted by a specific phosphodiesterase partitioned after cell division. We found that subcellular localization and reduction of c-di-GMP levels by this phosphodiesterase is dependent on the histidine kinase component of the chemotaxis machinery, CheA, and its phosphorylation state. Therefore, individual cell heterogeneity in c-di-GMP concentrations is regulated by the activity and the asymmetrical inheritance of the chemotaxis organelle after cell division. c-di-GMP heterogeneity results in a diversity of motility behaviors. The generation of diverse intracellular concentrations of c-di-GMP by asymmetric partitioning is likely important to the success and survival of bacterial populations within the environment by allowing a variety of motility behaviors.

DOI:http://dx.doi.org/10.7554/eLife.01402.001

Bacterial populations have traditionally been assumed to be made up of identical cells. However, while the bacteria within a population may be genetically identical, individual cells have different growth rates, metabolisms and motilities, among other things. This ‘phenotypic heterogeneity’ has been observed in many different species of bacteria, and in some cases it can be attributed to changes in the concentration of molecules called second messengers that help to relay signals from the external environment to targets within the cell.

It can be challenging to monitor changes in the concentration of specific molecules inside cells, but researchers recently developed a form of microscopy based on FRET (short for Forster resonance energy transfer) that can measure the levels of a second messenger molecule called cyclic di-guanylate (c-di-GMP) inside individual cells. This technique was used to study P. aeruginosa, a bacterium that has a single corkscrew-shaped propeller that enables it to swim through liquid. P. aeruginosa divides to form two daughter cells—one with a propeller and one without.

Although the daughter cell that does not have a propeller quickly grows one, FRET-based microscopy revealed that the daughter cell with a propeller had less c-di-GMP than the daughter without a propeller, but the reasons underlying this difference and its effects on bacterial behavior were not clear.

Now Kulasekara et al. show that the cell that inherits the propeller contains an enzyme that degrades c-di-GMP, and that the low levels of this second messenger molecule—caused by the enzyme being concentrated near the base of the propeller, and the presence of a protein (CheA) that enables the bacteria to swim towards sources of nutrients—result in faster swimming speeds and increased responsiveness to nutrients. In other words, although the two daughter cells are genetically identical, they behave quite differently because of the different levels of this second messenger molecule.

The existence of heterogeneity within a bacterial population likely leads to increased success and survival within changing diverse environments, and this work sets the stage for similar investigations into what establishes heterogeneity in other bacterial populations.

DOI:http://dx.doi.org/10.7554/eLife.01402.002

How do bacteria localize proteins to the cell pole?

It is now well appreciated that bacterial cells are highly organized, which is far from the initial concept that they are merely bags of randomly distributed macromolecules and chemicals. Central to their spatial organization is the precise positioning of certain proteins in subcellular domains of the cell. In particular, the cell poles - the ends of rod-shaped cells - constitute important platforms for cellular regulation that underlie processes as essential as cell cycle progression, cellular differentiation, virulence, chemotaxis and growth of appendages. Thus, understanding how the polar localization of specific proteins is achieved and regulated is a crucial question in bacterial cell biology. Often, polarly localized proteins are recruited to the poles through their interaction with other proteins or protein complexes that were already located there, in a so-called diffusion-and-capture mechanism. Bacteria are also starting to reveal their secrets on how the initial pole 'recognition' can occur and how this event can be regulated to generate dynamic, reproducible patterns in time (for example, during the cell cycle) and space (for example, at a specific cell pole). Here, we review the major mechanisms that have been described in the literature, with an emphasis on the self-organizing principles. We also present regulation strategies adopted by bacterial cells to obtain complex spatiotemporal patterns of protein localization.

LPS unmasking of Shigella flexneri reveals preferential localisation of tagged outer membrane protease IcsP to septa and new poles

The Shigella flexneri outer membrane (OM) protease IcsP (SopA) is a member of the enterobacterial Omptin family of proteases which cleaves the polarly localised OM protein IcsA that is essential for Shigella virulence. Unlike IcsA however, the specific localisation of IcsP on the cell surface is unknown. To determine the distribution of IcsP, a haemagglutinin (HA) epitope was inserted into the non-essential IcsP OM loop 5 using Splicing by Overlap Extension (SOE) PCR, and IcsP(HA) was characterised. Quantum Dot (QD) immunofluorescence (IF) surface labelling of IcsP(HA) was then undertaken. Quantitative fluorescence analysis of S. flexneri 2a 2457T treated with and without tunicaymcin to deplete lipopolysaccharide (LPS) O antigen (Oag) showed that IcsP(HA) was asymmetrically distributed on the surface of septating and non-septating cells, and that this distribution was masked by LPS Oag in untreated cells. Double QD IF labelling of IcsP(HA) and IcsA showed that IcsP(HA) preferentially localised to the new pole of non-septating cells and to the septum of septating cells. The localisation of IcsP(HA) in a rough LPS S. flexneri 2457T strain (with no Oag) was also investigated and a similar distribution of IcsP(HA) was observed. Complementation of the rough LPS strain with rmlD resulted in restored LPS Oag chain expression and loss of IcsP(HA) detection, providing further support for LPS Oag masking of surface proteins. Our data presents for the first time the distribution for the Omptin OM protease IcsP, relative to IcsA, and the effect of LPS Oag masking on its detection.

Tiny cells meet big questions: a closer look at bacterial cell biology

While studying actin assembly as a graduate student with Matt Welch at the University of California at Berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. Curiosity about these phenomena drew me to Lucy Shapiro's lab at Stanford University for my postdoctoral research. In the Shapiro lab, and now in my lab at Johns Hopkins, I have focused on investigating the mechanisms of bacterial cytokinesis. Spending time as both a eukaryotic cell biologist and a bacterial cell biologist has convinced me that bacterial cells present the same questions as eukaryotic cells: How are chromosomes organized and accurately segregated? How is force generated for cytokinesis? How is polarity established? How are signals transduced within and between cells? These problems are conceptually similar between eukaryotes and bacteria, although their solutions can differ significantly in specifics. In this Perspective, I provide a broad view of cell biological phenomena in bacteria, the technical challenges facing those of us who peer into bacterial cells, and areas of common ground as research in eukaryotic and bacterial cell biology moves forward.

Coordination of division and development influences complex multicellular behavior in Agrobacterium tumefaciens

The α-Proteobacterium Agrobacterium tumefaciens has proteins homologous to known regulators that govern cell division and development in Caulobacter crescentus, many of which are also conserved among diverse α-Proteobacteria. In light of recent work demonstrating similarity between the division cycle of C. crescentus and that of A. tumefaciens, the functional conservation for this presumptive control pathway was examined. In C. crescentus the CtrA response regulator serves as the master regulator of cell cycle progression and cell division. CtrA activity is controlled by an integrated pair of multi-component phosphorelays: PleC/DivJ-DivK and CckA-ChpT-CtrA. Although several of the conserved orthologues appear to be essential in A. tumefaciens, deletions in pleC or divK were isolated and resulted in cell division defects, diminished swimming motility, and a decrease in biofilm formation. A. tumefaciens also has two additional pleC/divJhomologue sensor kinases called pdhS1 and pdhS2, absent in C. crescentus. Deletion of pdhS1 phenocopied the ΔpleC and ΔdivK mutants. Cells lacking pdhS2 morphologically resembled wild-type bacteria, but were decreased in swimming motility and elevated for biofilm formation, suggesting that pdhS2 may serve to regulate the motile to non-motile switch in A. tumefaciens. Genetic analysis suggests that the PleC/DivJ-DivK and CckA-ChpT-CtrA phosphorelays in A. tumefaciens are vertically-integrated, as in C. crescentus. A gain-of-function mutation in CckA (Y674D) was identified as a spontaneous suppressor of the ΔpleC motility phenotype. Thus, although the core architecture of the A. tumefaciens pathway resembles that of C. crescentus there are specific differences including additional regulators, divergent pathway architecture, and distinct target functions.

Localization of new peptidoglycan at poles in Bacillus mycoides, a member of the Bacillus cereus group

Bacillus mycoides is a sporogenic Gram-positive soil bacillus of the B. cereus group. This bacillus, which forms hyphal colonies, is composed of cells connected in filaments that make up bundles and turn clock- or counterclockwise depending on the strain. A thick peptidoglycan wall gives the rod cells of these bacilli strength and shape. One approach used to study peptidoglycan neoformation in Gram positives exploits the binding properties of antibiotics such as vancomycin and ramoplanin to nascent peptidoglycan, whose localization in the cell is monitored by means of a fluorescent tag. When we treated B. mycoides strains with BODIPY-vancomycin, we found the expected accumulation of fluorescence at the midcell septa and localization along the cell sidewall in small foci distributed quite uniformly. Intense fluorescence was also observed at the poles of many cells, more clearly visible at the outer edges of the cell chains. The unusual abundance of peptidoglycan intermediates at the cell poles after cell separation suggests that the construction process of this structure is different from that of B. subtilis, in which the free poles are rarely reactive to vancomycin.

DivIVA-mediated polar localization of ComN, a posttranscriptional regulator of Bacillus subtilis

ComN (YrzD) is a small, 98-amino-acid protein recently shown to be involved in the posttranscriptional control of the late competence comE operon in Bacillus subtilis. We show here that ComN localizes to the division site and cell poles in a DivIVA-dependent fashion. Yeast two-hybrid and glutathione S-transferase pulldown experiments showed that ComN interacts directly with DivIVA. ComN is not essential for the polar assembly of the core competence DNA uptake machinery. Nevertheless, polar localization of ComN should play some role in competence acquisition because delocalization of ComN leads to a small reduction in competence efficiency. We found that ComN promotes the accumulation of its target comE mRNA to septal and polar sites. Thus, we speculate that localized translation of ComE proteins may be required for efficient competence development. Our results underscore the versatility of DivIVA as a promoter of the differentiation of bacterial poles and demonstrate that the repertoire of polarly localized molecules in B. subtilis is broad, including a regulator of gene expression and its target mRNA. Moreover, our findings suggest that mRNA localization may play a role in the subcellular organization of bacteria.

The conserved polarity factor podJ1 impacts multiple cell envelope-associated functions in Sinorhizobium meliloti

Although diminutive in size, bacteria possess highly diverse and spatially confined cellular structures. Two related alphaproteobacteria, Sinorhizobium meliloti and Caulobacter crescentus, serve as models for investigating the genetic basis of morphological variations. S. meliloti, a symbiont of leguminous plants, synthesizes multiple flagella and no prosthecae, whereas C. crescentus, a freshwater bacterium, has a single polar flagellum and stalk. The podJ gene, originally identified in C. crescentus for its role in polar organelle development, is split into two adjacent open reading frames, podJ1 and podJ2, in S. meliloti. Deletion of podJ1 interferes with flagellar motility, exopolysaccharide production, cell envelope integrity, cell division and normal morphology, but not symbiosis. As in C. crescentus, the S. meliloti PodJ1 protein appears to act as a polarity beacon and localizes to the newer cell pole. Microarray analysis indicates that podJ1 affects the expression of at least 129 genes, the majority of which correspond to observed mutant phenotypes. Together, phenotypic characterization, microarray analysis and suppressor identification suggest that PodJ1 controls a core set of conserved elements, including flagellar and pili genes, the signalling proteins PleC and DivK, and the transcriptional activator TacA, while alternative downstream targets have evolved to suit the distinct lifestyles of individual species.

Membrane protein expression triggers chromosomal locus repositioning in bacteria

It has long been hypothesized that subcellular positioning of chromosomal loci in bacteria may be influenced by gene function and expression state. Here we provide direct evidence that membrane protein expression affects the position of chromosomal loci in Escherichia coli. For two different membrane proteins, we observed a dramatic shift of their genetic loci toward the membrane upon induction. In related systems in which a cytoplasmic protein was produced, or translation was eliminated by mutating the start codon, a shift was not observed. Antibiotics that block transcription and translation similarly prevented locus repositioning toward the membrane. We also found that repositioning is relatively rapid and can be detected at positions that are a considerable distance on the chromosome from the gene encoding the membrane protein (>90 kb). Given that membrane protein-encoding genes are distributed throughout the chromosome, their expression may be an important mechanism for maintaining the bacterial chromosome in an expanded and dynamic state.

High cellular organization of pyoverdine biosynthesis in Pseudomonas aeruginosa: clustering of PvdA at the old cell pole

Pyoverdine I (PVDI) is the major siderophore produced by Pseudomonas aeruginosa PAO1 to import iron. Its biosynthesis requires the coordinated action of cytoplasmic, periplasmic and membrane proteins. The individual enzymatic activities of these proteins are well known. However, their subcellular distribution in particular areas of the cytoplasm, periplasm, or within the membrane has never been investigated. We used chromosomal replacement to generate P.aeruginosa strains producing fluorescent fusions with PvdA, one of the initial enzymes in the biosynthetic pathway of PVDI in the cytoplasm, and PvdQ, involved in the maturation of PVDI in the periplasm. Cellular fractionation indicated that a substantial amount of PvdA-YFP was located in the membrane fraction. Epifluorescence microscopy imaging showed that PvdA-YFP was mainly clustered at the old cell pole of bacteria, indicating a polar segregation of the protein. Epifluorescence and TIRF imaging on cells expressing labelled PvdQ showed that this enzyme was uniformly distributed in the periplasm, in contrast with PvdA-YFP. The description of the intracellular distribution of these enzymes contributes to the understanding of the PVDI biosynthetic pathway.

Decoding Caulobacter development

Caulobacter crescentus uses a multi-layered system of oscillating regulators to program different developmental fates into each daughter cell at division. This is achieved by superimposing gene expression, subcellular localization, phosphorylation, and regulated proteolysis to form a complex regulatory network that integrates chromosome replication, segregation, polar differentiation, and cytokinesis. In this review, we outline the current state of research in the field of Caulobacter development, emphasizing new findings that elaborate how the developmental program is modulated by factors such as the environment or the metabolic state of the cell.

From water and ions to crowded biomacromolecules: in vivo structuring of a prokaryotic cell

The interactions and processes which structure prokaryotic cytoplasm (water, ions, metabolites, and biomacromolecules) and ensure the fidelity of the cell cycle are reviewed from a physicochemical perspective. Recent spectroscopic and biological evidence shows that water has no active structuring role in the cytoplasm, an unnecessary notion still entertained in the literature; water acts only as a normal solvent and biochemical reactant. Subcellular structuring arises from localizations and interactions of biomacromolecules and from the growth and modifications of their surfaces by catalytic reactions. Biomacromolecular crowding is a fundamental physicochemical characteristic of cells in vivo. Though some biochemical and physiological effects of crowding (excluded volume effect) have been documented, crowding assays with polyglycols, dextrans, etc., do not properly mimic the compositional variety of biomacromolecules in vivo. In vitro crowding assays are now being designed with proteins, which better reflect biomacromolecular environments in vivo, allowing for hydrophobic bonding and screened electrostatic interactions. I elaborate further the concept of complex vectorial biochemistry, where crowded biomacromolecules structure the cytosol into electrolyte pathways and nanopools that electrochemically "wire" the cell. Noncovalent attractions between biomacromolecules transiently supercrowd biomacromolecules into vectorial, semiconducting multiplexes with a high (35 to 95%)-volume fraction of biomacromolecules; consequently, reservoirs of less crowded cytosol appear in order to maintain the experimental average crowding of ∼25% volume fraction. This nonuniform crowding model allows for fast diffusion of biomacromolecules in the uncrowded cytosolic reservoirs, while the supercrowded vectorial multiplexes conserve the remarkable repeatability of the cell cycle by preventing confusing cross talk of concurrent biochemical reactions.

New insights into eyespot placement and assembly in Chlamydomonas

Aspects of cellular architecture, such as cytoskeletal asymmetry cues, play critical roles in directing the placement of organelles and establishing the sites of their formation. In the model green alga Chlamydomonas, the photosensory eyespot occupies a defined position in relation to the flagella and microtubule cytoskeleton. Investigations into the cellular mechanisms of eyespot placement and assembly have aided our understanding of the interplay between cytoskeletal and plastid components of the cell. The eyespot, which must be assembled anew after each cell division, is a multi-layered organelle consisting of stacks of carotenoid-filled pigment granules in the chloroplast and rhodopsin photoreceptors in the plasma membrane. Placement of the eyespot is determined on both the latitudinal and longitudinal axes of the cell by the daughter four-membered (D4) microtubule rootlet. Recent findings have contributed to the hypothesis that the eyespot photoreceptor molecules are directed from the Golgi to the daughter hemisphere of the cell and trafficked along the D4 microtubule rootlet. EYE2, a chloroplast-envelope protein, forms an elliptical patch together with the photoreceptors and establishes the site for assembly of the pigment granule arrays in the chloroplast, connecting the positioning information of the cytoskeleton to assembly of the pigment granule arrays in the chloroplast.

Polarity and the diversity of growth mechanisms in bacteria

Bacterial cell growth is a complex process consisting of two distinct phases: cell elongation and septum formation prior to cell division. Although bacteria have evolved several different mechanisms for cell growth, it is clear that tight spatial and temporal regulation of peptidoglycan synthesis is a common theme. In this review, we discuss bacterial cell growth with a particular emphasis on bacteria that utilize tip extension as a mechanism for cell elongation. We describe polar growth among diverse bacteria and consider the advantages and consequences of this mode of cell elongation.

Poles apart: prokaryotic polar organelles and their spatial regulation

While polar organelles hold the key to understanding the fundamentals of cell polarity and cell biological principles in general, they have served in the past merely for taxonomical purposes. Here, we highlight recent efforts in unraveling the molecular basis of polar organelle positioning in bacterial cells. Specifically, we detail the role of members of the Ras-like GTPase superfamily and coiled-coil-rich scaffolding proteins in modulating bacterial cell polarity and in recruiting effector proteins to polar sites. Such roles are well established for eukaryotic cells, but not for bacterial cells that are generally considered diffusion-limited. Studies on spatial regulation of protein positioning in bacterial cells, though still in their infancy, will undoubtedly experience a surge of interest, as comprehensive localization screens have yielded an extensive list of (polarly) localized proteins, potentially reflecting subcellular sites of functional specialization predicted for organelles.

Form equals function? Bacterial shape and its consequences for pathogenesis

Bacteria exhibit a wide variety of morphologies. This could simply be a consequence of an elaboration of bacterial cellular architecture akin to the famous decorative but not structurally essential Spandrels in the Basilica di San Marco in Venice that are a side-effect of an adaptation, rather than a direct product of natural selection. However, it is more likely that particular morphologies facilitate a specific function in cellular physiology. Two recent publications including one in this issue of Molecular Microbiology and another in Cell provide new insights into the molecular basis for the helical shape of the bacterium Helicobacter pylori and the role of this shape in pathogenesis. They identify a novel endopeptidase that is necessary to generate the helical shape by processing the peptidoglycan and report that catalytically inactive mutants lead to defects in colonization that appear to be independent of an effect on cellular motility. Here, we put these findings in the context of some of what is known about peptidoglycan and cell shape and suggest that the role of this endopeptidase in forming coccoid morphology may be critical for pathogenesis.

Bacterial polarity

Many recent studies have revealed exquisite subcellular localization of proteins, DNA, and other molecules within bacterial cells, giving credence to the concept of prokaryotic anatomy. Common sites for localized components are the poles of rod-shaped cells, which are dynamically modified in composition and function in order to control cellular physiology. An impressively diverse array of mechanisms underlies bacterial polarity, including oscillatory systems, phospho-signaling pathways, the sensing of membrane curvature, and the integration of cell cycle regulators with polar maturation.

Protein localization by recognition of membrane curvature

Bacteria often sort proteins to specific subcellular locations, but many of the chemical beacons that specify those sites and subsequently recruit proteins have not been identified. Recent reports suggest that some bacterial proteins localize to specific subcellular sites by recognizing either convex or concave membrane curvature. Thus, degrees of membrane curvature, dictated by the shape of the cell, can define a geometric cue for the recruitment of curvature-sensing proteins.

Symmetry breaking in biology

Symmetry breaking is essential for cell movement, polarity, and developmental patterning. Amplification of initial asymmetry is key to the conserved mechanisms involved.