Polarity in action: asymmetric protein localization in bacteria

Spatial control of bacterial division-site placement

The site of cell division in bacterial cells is placed with high fidelity at a designated position, usually the midpoint of the cell. In normal cell division in Escherichia coli this is accomplished by the action of the Min proteins, which maintain a high concentration of a septation inhibitor near the ends of the cell, and a low concentration at midcell. This leaves the midcell site as the only available location for formation of the division septum. In other species, such as Bacillus subtilis, this general paradigm is maintained, although some of the proteins differ and the mechanisms used to localize the proteins vary. A second mechanism of negative regulation, the nucleoid-occlusion system, prevents septa forming over nucleoids. This system functions in Gram-negative and Gram-positive bacteria, and is especially important in cells that lack the Min system or in cells in which nucleoid replication or segregation are defective. Here, we review the latest findings on these two systems.

Molecules into cells: specifying spatial architecture

A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth.

Clustering requires modified methyl-accepting sites in low-abundance but not high-abundance chemoreceptors of Escherichia coli

Chemotaxis signalling complexes of Escherichia coli, composed of chemoreceptors, CheA and CheW, form clusters located predominantly at cell poles. As the only kind of receptor in a cell, high-abundance receptors are polar and clustered whereas low-abundance chemoreceptors are polar but largely unclustered. We found that clustering was a function of the cytoplasmic, carboxyl-terminal domain and that effective clustering was conferred on low-abundance receptors by addition of the approximately 20-residue sequence from the carboxyl terminus of either high-abundance receptor. These sequences are different but share a carboxyl-terminal pentapeptide that enhances adaptational covalent modification and allows a physiological balance between modified and unmodified methyl-accepting sites, implying that receptor modification might influence clustering. Thus we investigated directly effects of modification state on chemoreceptor clustering. As the sole receptor type in a cell, low-abundance receptors were clustered only if modified, but high-abundance receptors were clustered independent of extent of modification. This difference could mean that the two receptor types are fundamentally different or that they are poised at different positions in the same conformational equilibrium. Notably, no receptor perturbation we tested altered a predominant location at cell poles, emphasizing a distinction between determinants of clustering and polar localization.

Assembly of motor proteins, PomA and PomB, in the Na+-driven stator of the flagellar motor

PomA and PomB are transmembrane proteins that form the stator complex in the sodium-driven flagellar motor of Vibrio alginolyticus and are believed to surround the rotor part of the flagellar motor. We constructed and observed green fluorescent protein (GFP) fusions of the stator proteins PomA and PomB in living cells to clarify how stator proteins are assembled and installed into the flagellar motor. We were able to demonstrate that GFP-PomA and GFP-PomB localized to a cell pole dependent on the presence of the polar flagellum. Localization of the GFP-fused stator proteins required their partner subunit, PomA or PomB, and the C-terminal domain of PomB, which has a peptidoglycan-binding motif. Each of the GFP-fused stator proteins was co-isolated with its partner subunit from detergent-solubilized membrane. From these lines of evidence, we have demonstrated that the stator proteins are incorporated into the flagellar motor as a PomA/PomB complex and are fixed to the cell wall via the C-terminal domain of PomB.

Conserved glycine residues in the cytoplasmic domain of the aspartate receptor play essential roles in kinase coupling and on-off switching

The aspartate receptor of the bacterial chemotaxis pathway serves as a scaffold for the formation of a multiprotein signaling complex containing the receptor and the cytoplasmic pathway components. Within this complex, the receptor regulates the autophosphorylation activity of histidine kinase CheA, thereby controlling the signals sent to the flagellar motor and the receptor adaptation system. The receptor cytoplasmic domain, which controls the on-off switching of CheA, possesses 14 glycine residues that are highly conserved in related receptors. In principle, these conserved glycines could be required for static turns, bends, or close packing in the cytoplasmic domain, or they could be required for conformational dynamics during receptor on-off switching. To determine which glycines are essential and to probe their functional roles, we have substituted each conserved glycine with both alanine and cysteine, and then measured the effects on receptor function in vivo and in vitro. The results reveal a subset of six glycines which are required for receptor function during cellular chemotaxis. Two of these essential glycines (G388 and G391) are located at a hairpin turn at the distal end of the folded cytoplasmic domain, where they are required for the tertiary fold of the signaling subdomain and for CheA kinase activation. Three other essential glycines (G338, G339, and G437) are located at the border between the adaptation and signaling subdomains, where they play key roles in CheA kinase activation and on-off switching. These three glycines form a ring around the four-helix bundle that comprises the receptor cytoplasmic domain, yielding a novel architectural feature termed a bundle hinge. The final essential glycine (G455) is located in the adaptation subdomain where it is required for on-off switching. Overall, the findings confirm that six of the 14 conserved cytoplasmic glycines are essential for receptor function because they enable helix turns and bends required for native receptor structure, and in some cases for switching between the on and off signaling states. An initial working model proposes that the novel bundle hinge enables the four-helix bundle to bend, perhaps during the assembly of the receptor trimer of dimers or during on-off switching. More generally, the findings predict that certain human disease states, including specific cancers, could be triggered by lock-on mutations at essential glycine positions that control the on-off switching of receptors and signaling proteins.

Roseicyclus mahoneyensis gen. nov., sp. nov., an aerobic phototrophic bacterium isolated from a meromictic lake

Eight strains of Gram-negative bacteria able to form ring-like cells were isolated from Mahoney Lake, a meromictic lake in south-central British Columbia, Canada. All strains were pink–purple and contained bacteriochlorophyll a incorporated into the light-harvesting 1 and 2 and reaction-centre pigment–protein complexes. Growth did not occur anaerobically under illuminated conditions; these strains were obligately aerobic, prompting their designation as members of the aerobic phototrophic bacteria. Physiological characterization revealed that these isolates share a similar tolerance to high levels of salinity and pH, as would be expected of bacteria from a highly saline lake; however, the strains exhibited marked differences in their ability to utilize organic substrates for aerobic heterotrophic growth. 16S rRNA sequence analysis showed that the strains are closely related to members of the non-phototrophic genera Octadecabacter (92·0–92·9 %) and Ketogulonicigenium (92·2–92·6 %), as well as to aerobic phototrophs of the genera Roseivivax (92·2–92·9 %) and Roseovarius (91·7–92·4 %) within the ‘Alphaproteobacteria’. The DNA G+C content was 66·2 mol%. The unusual light-harvesting complex 2, the distinct morphological features and physiological traits of these strains as well as the phylogenetic data support the proposal of the novel genus and species Roseicyclus mahoneyensis gen. nov., sp. nov., with ML6T (=DSM 16097T=VKM B-2346T) as the type strain.

Adaptation mechanism of the aspartate receptor: electrostatics of the adaptation subdomain play a key role in modulating kinase activity

The aspartate receptor of the Escherichia coli and Salmonella typhimurium chemotaxis pathway generates a transmembrane signal that regulates the activity of the cytoplasmic kinase CheA. Previous studies have identified a region of the cytoplasmic domain that is critical to receptor adaptation and kinase regulation. This region, termed the adaptation subdomain, contains a high density of acidic residues, including specific glutamate residues that serve as receptor adaptation sites. However, the mechanism of signal propagation through this region remains poorly understood. This study uses site-directed mutagenesis to neutralize each acidic residue within the subdomain to probe the hypothesis that electrostatics in this region play a significant role in the mechanism of kinase activation and modulation. Each point mutant was tested for its ability to regulate chemotaxis in vivo and kinase activity in vitro. Four point mutants (D273N, E281Q, D288N, and E477Q) were found to superactivate the kinase relative to the wild-type receptor, and all four of these kinase-activating substitutions are located along the same intersubunit interface as the adaptation sites. These activating substitutions retained the wild-type ability of the attractant-occupied receptor to inhibit kinase activity. When combined in a quadruple mutant (D273N/E281Q/D288N/E477Q), the four charge-neutralizing substitutions locked the receptor in a kinase-superactivating state that could not be fully inactivated by the attractant. Similar lock-on character was observed for a charge reversal substitution, D273R. Together, these results implicate the electrostatic interactions at the intersubunit interface as a major player in signal transduction and kinase regulation. The negative charge in this region destabilizes the local structure in a way that enhances conformational dynamics, as detected by disulfide trapping, and this effect is reversed by charge neutralization of the adaptation sites. Finally, two substitutions (E308Q and E463Q) preserved normal kinase activation in vitro but blocked cellular chemotaxis in vivo, suggesting that these sites lie within the docking site of an adaptation enzyme, CheR or CheB. Overall, this study highlights the importance of electrostatics in signal transduction and regulation of kinase activity by the cytoplasmic domain of the aspartate receptor.

A polymerization-depolymerization model that accurately generates the self-sustained oscillatory system involved in bacterial division site placement

Determination of the proper site for division in Escherichia coli and other bacteria involves a unique spatial oscillatory system in which membrane-associated structures composed of the MinC, MinD and MinE proteins oscillate rapidly between the two cell poles. In vitro evidence indicates that this involves ordered cycles of assembly and disassembly of MinD polymers. We propose a mathematical model to explain this behavior. Unlike previous attempts, the present approach is based on the expected behavior of polymerization-depolymerization systems and incorporates current knowledge of the biochemical properties of MinD and MinE. Simulations based on the model reproduce all of the known topological and temporal characteristics of the in vivo oscillatory system.

Phosphatidylethanolamine domains and localization of phospholipid synthases in Bacillus subtilis membranes

Application of the cardiolipin (CL)-specific fluorescent dye 10-N-nonyl-acridine orange has recently revealed CL-rich domains in the septal regions and at the poles of the Bacillus subtilis membrane (F. Kawai, M. Shoda, R. Harashima, Y. Sadaie, H. Hara, and K. Matsumoto, J. Bacteriol. 186:1475-1483, 2004). This finding prompted us to examine the localization of another phospholipid, phosphatidylethanolamine (PE), with the cyclic peptide probe, Ro09-0198 (Ro), that binds specifically to PE. Treatment with biotinylated Ro followed by tetramethyl rhodamine-conjugated streptavidin revealed that PE is localized in the septal membranes of vegetative cells and in the membranes of the polar septum and the engulfment membranes of sporulating cells. When the mutant cells of the strains SDB01 (psd1::neo) and SDB02 (pssA10::spc), which both lack PE, were examined under the same conditions, no fluorescence was observed. The localization of the fluorescence thus evidently reflected the localization of PE-rich domains in the septal membranes. Similar PE-rich domains were observed in the septal regions of the cells of many Bacillus species. In Escherichia coli cells, however, no PE-rich domains were found. Green fluorescent protein fusions to the enzymes that catalyze the committed steps in PE synthesis, phosphatidylserine synthase, and in CL synthesis, CL synthase and phosphatidylglycerophosphate synthase, were localized mainly in the septal membranes in B. subtilis cells. The majority of the lipid synthases were also localized in the septal membranes; this includes 1-acyl-glycerol-3-phosphate acyltransferase, CDP-diacylglycerol synthase, phosphatidylserine decarboxylase, diacylglycerol kinase, glucolipid synthase, and lysylphosphatidylglycerol synthase. These results suggest that phospholipids are produced mostly in the septal membranes and that CL and PE are kept from diffusing out to lateral ones.

Helical disposition of proteins and lipopolysaccharide in the outer membrane of Escherichia coli

In bacteria, several physiological processes once thought to be the products of uniformly dispersed reactions are now known to be highly asymmetric, with some exhibiting interesting geometric localizations. In particular, the cell envelope of Escherichia coli displays a form of subcellular differentiation in which peptidoglycan and outer membrane proteins at the cell poles remain stable for generations while material in the lateral walls is diluted by growth and turnover. To determine if material in the side walls was organized in any way, we labeled outer membrane proteins with succinimidyl ester-linked fluorescent dyes and then grew the stained cells in the absence of dye. Labeled proteins were not evenly dispersed in the envelope but instead appeared as helical ribbons that wrapped around the outside of the cell. By staining the O8 surface antigen of E. coli 2443 with a fluorescent derivative of concanavalin A, we observed a similar helical organization for the lipopolysaccharide (LPS) component of the outer membrane. Fluorescence recovery after photobleaching indicated that some of the outer membrane proteins remained freely diffusible in the side walls and could also diffuse into polar domains. On the other hand, the LPS O antigen was virtually immobile. Thus, the outer membrane of E. coli has a defined in vivo organization in which a subfraction of proteins and LPS are embedded in stable domains at the poles and along one or more helical ribbons that span the length of this gram-negative rod.

Recent advances on the development of bacterial poles

In rod-shaped bacteria, a surprisingly large number of proteins are localized to the cell poles. Polar positioning of proteins is crucial to many fundamental cellular processes. Formation of the pole occurs at the time of a prior cell division event and involves coordination of the cell division machinery with septal placement of newly-synthesized peptidoglycan. Development of polar peptidoglycan and outer membrane depends on the formation of the cytokinetic FtsZ ring at midcell. By contrast, positioning of at least two polar proteins depends on signals independent of both the assembly of the FtsZ ring and the synthesis of septal and polar peptidoglycan. We propose a model for distinct but interrelated developmental pathways for polar cell envelope synthesis and positional information recognized by polar proteins.

Aging and death in an organism that reproduces by morphologically symmetric division

In macroscopic organisms, aging is often obvious; in single-celled organisms, where there is the greatest potential to identify the molecular mechanisms involved, identifying and quantifying aging is harder. The primary results in this area have come from organisms that share the traits of a visibly asymmetric division and an identifiable juvenile phase. As reproductive aging must require a differential distribution of aged and young components between parent and offspring, it has been postulated that organisms without these traits do not age, thus exhibiting functional immortality. Through automated time-lapse microscopy, we followed repeated cycles of reproduction by individual cells of the model organism Escherichia coli, which reproduces without a juvenile phase and with an apparently symmetric division. We show that the cell that inherits the old pole exhibits a diminished growth rate, decreased offspring production, and an increased incidence of death. We conclude that the two supposedly identical cells produced during cell division are functionally asymmetric; the old pole cell should be considered an aging parent repeatedly producing rejuvenated offspring. These results suggest that no life strategy is immune to the effects of aging, and therefore immortality may be either too costly or mechanistically impossible in natural organisms.

Detailed time lapse photography reveals that organisms that divide symmetrically, such as the bacterium E. coli, can indeed age and consequently that no organism is immune to mortality

Recent trends on the molecular biology of pneumococcal capsules, lytic enzymes, and bacteriophage

Streptococcus pneumoniae has re-emerged as a major cause of morbidity and mortality throughout the world and its continuous increase in antimicrobial resistance is rapidly becoming a leading cause of concern for public health. This review is focussed on the analysis of recent insights on the study of capsular polysaccharide biosynthesis, and cell wall (murein) hydrolases, two fundamental pneumococcal virulence factors. Besides, we have also re-evaluated the molecular biology of the pneumococcal phage, their possible role in pathogenicity and in the shaping of natural populations of S. pneumoniae. Precise knowledge of the topics reviewed here should facilitate the rationale to move towards the design of alternative ways to combat pneumococcal disease.

Zipper-like interaction between proteins in adjacent daughter cells mediates protein localization

Protein localization is crucial for cellular morphogenesis and intracellular signal transduction cascades. Here we describe an interaction between two membrane proteins expressed in different cells of the Bacillus subtilis sporangium, the mother cell protein SpoIIIAH and the forespore protein SpoIIQ. We used affinity chromatography, coimmunoprecipitation, and the yeast two-hybrid system to demonstrate that the extracellular domains of these proteins interact, tethering SpoIIIAH to the sporulation septum, and directing its assembly with SpoIIQ into helical arcs and foci around the forespore. We also demonstrate that this interaction can direct proteins made in the same cell to active division sites, as when SpoIIQ is made in the mother cell, it localizes to nascent septa in a SpoIIIAH-dependent manner. Both SpoIIIAH and SpoIIQ are necessary for activation of the second forespore-specific transcription factor (sigma(G)) after engulfment, and we propose that the SpoIIIAH-SpoIIQ complex contributes to a morphological checkpoint coupling sigma(G) activation to engulfment. In keeping with this hypothesis, SpoIIIAH localization depends on the first step of engulfment, septal thinning. The SpoIIQ-SpoIIIAH complex reaches from the mother cell cytoplasm to the forespore cytoplasm and is ideally positioned to govern the activity of engulfment-dependent transcription factors.

The Aer protein of Escherichia coli forms a homodimer independent of the signaling domain and flavin adenine dinucleotide binding

In vivo cross-linking between native cysteines in the Aer receptor of Escherichia coli showed dimer formation at the membrane anchor and in the putative HAMP domain. Dimers also formed in mutants that did not bind flavin adenine dinucleotide and in truncated peptides without a signaling domain and part of the HAMP domain.

Branching sites and morphological abnormalities behave as ectopic poles in shape-defective Escherichia coli

Certain mutants in Escherichia coli lacking multiple penicillin-binding proteins (PBPs) produce misshapen cells containing kinks, bends and branches. These deformed regions exhibit two structural characteristics of normal cell poles: the peptidoglycan is inert to dilution by new synthesis or turnover, and a similarly stable patch of outer membrane caps the sites. To test the premise that these aberrant sites represent biochemically functional but misplaced cell poles, we assessed the intracellular distribution of proteins that localize specifically to bacterial poles. Green fluorescent protein (GFP) hybrids containing polar localization sequences from the Shigella flexneri IcsA protein or from the Vibrio cholerae EpsM protein formed foci at the poles of wild-type E. coli and at the poles and morphological abnormalities in PBP mutants. In addition, secreted wild-type IcsA localized to the outer membrane overlying these aberrant domains. We conclude that the morphologically deformed sites in these mutants represent fully functional poles or pole fragments. The results suggest that prokaryotic morphology is driven, at least in part, by the controlled placement of polar material, and that one or more of the low-molecular-weight PBPs participate in this process. Such mutants may help to unravel how particular proteins are targeted to bacterial poles, thereby creating important biochemical and functional asymmetries.

Three-dimensional electron microscopic imaging of membrane invaginations in Escherichia coli overproducing the chemotaxis receptor Tsr

Electron tomography is a powerful method for determining the three-dimensional structures of large macromolecular assemblies, such as cells, organelles, and multiprotein complexes, when crystallographic averaging methods are not applicable. Here we used electron tomographic imaging to determine the molecular architecture of Escherichia coli cells engineered to overproduce the bacterial chemotaxis receptor Tsr. Tomograms constructed from fixed, cryosectioned cells revealed that overproduction of Tsr led to formation of an extended internal membrane network composed of stacks and extended tubular structures. We present an interpretation of the tomogram in terms of the packing arrangement of Tsr using constraints derived from previous X-ray and electron-crystallographic studies of receptor clusters. Our results imply that the interaction between the cytoplasmic ends of Tsr is likely to stabilize the presence of the membrane networks in cells overproducing Tsr. We propose that membrane invaginations that are potentially capable of supporting axial interactions between receptor clusters in apposing membranes could also be present in wild-type E. coli and that such receptor aggregates could play an important role in signal transduction during bacterial chemotaxis.

Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB

Advanced techniques for observing protein localization in live bacteria show that the distributions are dynamic. For technical reasons, most such techniques have not been applied to outer membrane proteins in Gram-negative bacteria. We have developed two novel live-cell imaging techniques to observe the surface distribution of LamB, an abundant integral outer membrane protein in Escherichia coli responsible for maltose uptake and for attachment of bacteriophage lambda. Using fluorescently labelled bacteriophage lambda tails, we quantitatively described the spatial distribution and dynamic movement of LamB in the outer membrane. LamB accumulated in spiral patterns. The distribution depended on cell length and changed rapidly. The majority of the protein diffused along spirals extending across the cell body. Tracking single particles, we found that there are two populations of LamB--one shows very restricted diffusion and the other shows greater mobility. The presence of two populations recalls the partitioning of eukaryotic membrane proteins between 'mobile' and 'immobile' populations. In this study, we have demonstrated that LamB moves along the bacterial surface and that these movements are restricted by an underlying dynamic spiral pattern.

Targeting of the chemotaxis methylesterase/deamidase CheB to the polar receptor-kinase cluster in an Escherichia coli cell

Chemotactic adaptation to persisting stimulation involves reversible methylation of the chemoreceptors that form complexes with the histidine kinase CheA at a cell pole. The methyltransferase CheR targets to the C-terminal NWETF sequence of the chemoreceptor. In contrast, localization of the methylesterase CheB is largely unknown, although regulation of its activity via phosphorylation is central to adaptation. In this study, green fluorescent protein was fused to full-length CheB or its various parts: the N-terminal regulatory domain (N), the C-terminal catalytic domain (C) and the linker (L). The full-length and NL fusions and, to a lesser extent, the LC fusion localized to a pole. Deletion of the P2 domain from CheA abolished polar localization of the full-length and NL fusions, but did not affect that of the LC fusion. Pull-down assays demonstrated that the NL fragment, but not the LC fragment, binds to the P2 fragment of CheA. These results indicate that binding of the NL domain to the P2 domain targets CheB to the polar signalling complex. The LC fusion, like the chemoreceptor, partially localized in the absence of CheA, suggesting that the LC domain may interact with its substrate sites, either as part of the protein or as a proteolytic fragment.

Side chains at the membrane-water interface modulate the signaling state of a transmembrane receptor

Previous model studies of peptides and proteins have shown that protein-lipid interactions, primarily involving amino acid side chains near the membrane-water interface, modulate the position of transmembrane helices in bilayers. The present study examines whether such interfacial side chains stabilize the signaling states of a transmembrane signaling helix in a representative receptor, the aspartate receptor of bacterial chemotaxis. To examine the functional roles of signaling helix side chains at the periplasmic and cytoplasmic membrane-water interfaces, arginine and cysteine substitutions were scanned through these two interfacial regions. The chemical reactivities of the cysteine residues were first measured to determine the positions at which the helix crosses the membrane-water interface in both the periplasmic and cytoplasmic compartments. Subsequently, two antisymmetric in vitro activity measurements were carried out to determine the effect of each interfacial arginine or cysteine substitution on receptor signaling. Substitutions that stabilize the receptor on-state cause upregulation of receptor-coupled kinase activity and inhibition of methylation at receptor adaptation sites, while substitutions that stabilize the off-state have the opposite effects on these two activities. Notably, four substitutions at aromatic tryptophan and phenylalanine positions buried in the membrane near the membrane-water interface were found to stabilize the native on- or off-signaling state. The striking ability of these substitutions to drive the receptor toward a specific signaling state indicates that interfacial side chains are highly optimized to correctly position the native signaling helix in the membrane and to allow normal switching between the on- and off-signaling states. The analogous substitutions in model transmembrane helices are known to drive small piston-type displacements of the helix normal to the membrane. Thus, the simplest molecular interpretation of the present findings is that the signal-stabilizing substitutions drive piston displacements of the signaling helix, providing further support for the piston model for transmembrane signaling in bacterial chemoreceptors. More generally, the findings indicate that the interfacial phenylalanine, tryptophan, and arginine side chains widespread in the transmembrane alpha-helices of receptors, channels, and transporters can play important roles in modulating transitions between signaling and conformational states.

Restricted Mobility of Cell Surface Proteins in the Polar Regions of Escherichia coli

The polar regions of the Escherichia coli murein sacculus are metabolically inert and stable in time. Because the sacculus and the outer membrane are tightly associated, we investigated whether polar inert murein could restrict the mobility of other cell envelope elements. Cells were covalently labeled with a fluorescent reagent, chased in dye-free medium, and observed by microscopy. Fluorescent material was more efficiently retained at the cell poles than at any other location. The boundary between high and low fluorescence intensity areas was rather sharp. Labeled material consisted mostly of cell envelope proteins, among them the free and murein-bound forms of Braun's lipoprotein. Our results indicate that the mobility of at least some cell envelope proteins is restrained at regions in correspondence with underlying areas of inert murein.

Spatial and temporal control of differentiation and cell cycle progression in Caulobacter crescentus

The dimorphic and intrinsically asymmetric bacterium Caulobacter crescentus has become an important model organism to study the bacterial cell cycle, cell polarity, and polar differentiation. A multifaceted regulatory network orchestrates the precise coordination between the development of polar organelles and the cell cycle. One master response regulator, CtrA, directly controls the initiation of chromosome replication as well as several aspects of polar morphogenesis and cell division. CtrA activity is temporally and spatially regulated by multiple partially redundant control mechanisms, such as transcription, phosphorylation, and targeted proteolysis. A multicomponent signal transduction network upstream CtrA, containing histidine kinases CckA, PleC, DivJ, and DivL and the essential response regulator DivK, contributes to the control of CtrA activity in response to cell cycle and developmental cues. An intriguing feature of this signaling network is the dynamic cell cycle-dependent polar localization of its components, which is believed to have a novel regulatory function.

Polar-biased localization of the cold stress-induced RNA helicase, CrhC, in the Cyanobacterium Anabaena sp. strain PCC 7120

Shift of the filamentous cyanobacterium, Anabaena sp. strain PCC 7120, from 30 degrees C to 20 degrees C induces expression of a cold shock response gene encoding the RNA helicase CrhC. Subcellular localization using cellular fractionation and membrane purification indicated that CrhC is localized to the plasma membrane with no evidence of a soluble-cytoplasmic form. Treatment of spheroplasts with trypsin and membrane fractions with various denaturing agents identified CrhC as an integral membrane protein associated with the cytoplasmic face of the plasma membrane. Immunoelectron microscopy confirmed the plasma membrane association of CrhC. Interestingly, a higher specific labelling was observed at the cell poles on the septa between adjacent cells within cell filaments. On a per cell area basis, CrhC localization to the cell pole was 3.5- and >1000-fold higher than to the lateral portion of the plasma membrane or cytoplasm respectively. In addition, CrhC also localizes to new cell poles forming within a dividing cell. Polar-biased localization of the CrhC RNA helicase implies a role in RNA metabolism that is plasma membrane associated and preferentially occurs at the cell poles during cyanobacterial response to cold stress.

A Bacterial Cell-Cycle Regulatory Network Operating in Time and Space

Transcriptional regulatory circuits provide only a fraction of the signaling pathways and regulatory mechanisms that control the bacterial cell cycle. The CtrA regulatory network, important in control of the Caulobacter cell cycle, illustrates the critical role of nontranscriptional pathways and temporally and spatially localized regulatory proteins. The system architecture of Caulobacter cell-cycle control involves top-down control of modular functions by a small number of master regulatory proteins with cross-module signaling coordinating the overall process. Modeling the cell cycle probably requires a top-down modeling approach and a hybrid control system modeling paradigm to treat its combined discrete and continuous characteristics.

Genetics of motility and chemotaxis of a fascinating group of bacteria: the spirochetes

Spirochetes are a medically important and ecologically significant group of motile bacteria with a distinct morphology. Outermost is a membrane sheath, and within this sheath is the protoplasmic cell cylinder and subterminally attached periplasmic flagella. Here we address specific and unique aspects of their motility and chemotaxis. For spirochetes, translational motility requires asymmetrical rotation of the two internally located flagellar bundles. Consequently, they have swimming modalities that are more complex than the well-studied paradigms. In addition, coordinated flagellar rotation likely involves an efficient and novel signaling mechanism. This signal would be transmitted over the length of the cell, which in some cases is over 100-fold greater than the cell diameter. Finally, many spirochetes, including Treponema, Borrelia, and Leptospira, are highly invasive pathogens. Motility is likely to play a major role in the disease process. This review summarizes the progress in the genetics of motility and chemotaxis of spirochetes, and points to new directions for future experimentation.

Mapping out regions on the surface of the aspartate receptor that are essential for kinase activation

The aspartate receptor of bacterial chemotaxis is representative of a large family of taxis receptors widespread in prokaryotes. The homodimeric receptor associates with cytoplasmic components to form a receptor-kinase signaling complex. Within this complex the receptor is known to directly contact the histidine kinase CheA, the coupling protein CheW, and other receptor dimers. However, the locations and extents of the contact regions on the receptor surface remain ambiguous. The present study applies the protein-interactions-by-cysteine-modification (PICM) method to map out surfaces on the aspartate receptor that are essential for kinase stimulation in the assembled receptor-kinase complex. The approach utilizes 52 engineered cysteine positions scattered over the surface of the receptor periplasmic and cytoplasmic domains. When the bulky, anionic probe 5-fluorescein-maleimide is coupled to these positions, large effects on receptor-mediated kinase stimulation are observed at eight cytoplasmic locations. By contrast, no large effects are observed for probe attachment at exposed positions in the periplasmic domain. The results indicate that essential receptor surface regions are located near the hairpin turn at the distal end of the cytoplasmic domain and in the cytoplasmic adaptation site region. These surface regions include the docking sites for CheA, CheW, and other receptor dimers, as well as surfaces that transmit information from the receptor adaptation sites to the kinase. Smaller effects observed in the cytoplasmic linker or HAMP region suggest this region may also play a role in kinase regulation. A comparison of the activity perturbations caused by a dianionic, bulky probe (5-fluorescein-maleimide), a zwitterionic, bulky probe (5-tetramethyl-rhodamine-maleimide), and a nonionic, smaller probe (N-ethyl-maleimide) reveals the roles of probe size and charge in generating the observed effects on kinase activity. Overall, the results indicate that interactions between the periplasmic domains of different receptor dimers are not required for kinase activation in the signaling complex. By contrast, the observed spatial distribution of protein contact surfaces on the cytoplasmic domain is consistent with both (i) distinct docking sites for cytoplasmic proteins and (ii) interactions between the cytoplasmic domains of different dimers to form a trimer-of-dimers.

Quantitative analysis of aspartate receptor signaling complex reveals that the homogeneous two-state model is inadequate: development of a heterogeneous two-state model

The two-state model of receptor activation, in which a receptor population exists in equilibrium between a single on-state and a single off-state, has long been considered a viable model for the signaling behavior of bacterial chemoreceptors. Here, we show that this simple, homogeneous two-state model is adequate for a pure receptor population with just one adaptation state, but fails to account quantitatively for the observed linear relationship between the apparent attractant affinity (K(1/2)) and kinase activity (V(obs)(apo)) as the adaptation state is varied. Further analysis reveals that the available data are instead consistent with a heterogeneous two-state model in which covalent modification of receptor adaptation sites changes the microscopic properties of the on-state or off-state. In such a system, each receptor molecule retains a single on-state and off-state, but covalent adaptation generates a heterogeneous population of receptors exhibiting a range of different on-states or off-states with different microscopic parameters and conformations. It follows that covalent adaptation transforms the receptor from a simple, two-state toggle switch into a variable switch. In order to identify the microscopic parameters most sensitive to covalent adaptation, six modified, two-state models were examined in which covalent adaptation alters a different microscopic parameter. The analysis suggests that covalent adaptation primarily alters the ligand-binding affinity of the receptor off-state (K(D1)). By contrast, models in which covalent adaptation alters the ligand-binding affinity of the receptor on-state, the maximal kinase stimulation of the on-state or off-state, cooperative interactions between receptors, or the assembly of the receptor-kinase signaling complex are inconsistent with the available evidence. Overall, the findings support a heterogeneous two-state model in which modification of the receptor adaptation sites generates a population of receptors with heterogeneous off-states differing in their attractant affinities. In the process of testing the effects of covalent adaptation on the assembly of the receptor-kinase signaling complex, a new method for estimating the stoichiometric ratio of receptor and CheA in the ternary signaling complex was devised. This method suggests that the ratio of receptor dimers to CheA dimers in the assembled complex is 6:1 or less.

Recognizing and interpreting the fossils of early eukaryotes

Using molecular sequence data, biologists can generate hypotheses of protistan phylogeny and divergence times. Fossils, however, provide our only direct constraints on the timing and environmental context of early eukaryotic diversification. For this reason, recognition of eukaryotic fossils in Proterozoic rocks is key to the integration of geological and comparative biological perspectives on protistan evolution. Microfossils preserved in shales of the ca. 1500 Ma Roper Group, northern Australia, display characters that ally them to the Eucarya, but, at present, attribution to any particular protistan clade is uncertain. Continuing research on wall ultrastructure and microchemistry promises new insights into the nature and systematic relationships of early eukaryotic fossils.

Transient genetic asymmetry and cell fate in a bacterium

Certain species of Gram-positive bacteria can initiate a developmental program that results in the formation of two daughter cells with different fates. One cell develops into a spore and the other cell undergoes programmed lysis, with each process being mediated by a cascade of cell-type-specific transcription factors. An early and critical step in this developmental pathway is the formation of a division septum near one pole, creating two compartments of different sizes. But how is this morphological asymmetry translated into the transcriptional asymmetry of the two compartments? Recent results suggest that the chromosomal position of the genes encoding several key components of the transcriptional regulatory network has an important role in this process.

Subunit organization in a soluble complex of tar, CheW, and CheA by electron microscopy

The Salmonella and Escherichia coli aspartate receptor, Tar, is representative of a large class of membrane receptors that generate chemotaxis responses by regulating the activity of an associated histidine protein kinase, CheA. Tar is composed of an NH(2)-terminal periplasmic ligand-binding domain linked through a transmembrane sequence to a COOH-terminal coiled-coil signaling domain in the cytoplasm. The isolated cytoplasmic domain of Tar fused to a leucine zipper sequence forms a soluble complex with CheA and the Src homology 3-like kinase activator, CheW. Activity of the CheA kinase in the soluble complex is essentially the same as in fully active complexes with the intact receptor in the membrane. The soluble complex is composed of approximately 28 receptor cytoplasmic domain chains, 6 CheW chains, and 4 CheA chains. It has a molecular weight of 1,400,000 (Liu, I., Levit, M., Lurz, R., Surette, M.G., and Stock, J.B. (1997) EMBO J. 16, 7231-7240). Electron microscopy reveals an elongated barrel-like structure with a largely hollow center. Immunoelectron microscopy has provided a general picture of the subunit and domain organization of the complex. CheA and CheW appear to be in the middle of the complex with the leucine zippers of the receptor construct at the ends. These findings show that the receptor signaling complex forms higher ordered structures with defined geometric architectures. Coupled with atomic models of the subunits, our results provide insights into the functional architecture by which the receptor regulates CheA kinase activity during bacterial chemotaxis.

Dynamic and clustering model of bacterial chemotaxis receptors: structural basis for signaling and high sensitivity

Bacterial chemotaxis receptors can detect a small concentration gradient of attractants and repellents in the environment over a wide range of background concentration. The clustering of these receptors to form patches observed in vivo and in vitro has been suspected as a reason for the high sensitivity, and such wide dynamic range is thought to be due to the resetting of the receptor sensitivity threshold by methylation/demethylation of the receptors. However, the mechanisms by which such high sensitivity is achieved and how the methylation/demethylation resets the sensitivity are not well understood. A molecular modeling of an intact bacterial chemotaxis receptor based on the crystal structures of a cytoplasmic domain and a periplasmic domain suggests an interesting clustering of three dimeric receptors and a two-dimensional, close-packed lattice formation of the clusters, where each receptor dimer contacts two other receptor dimers at the cytoplasmic domain and two yet different receptor dimers at the periplasmic domain. This interconnection of the receptors to form a patch of receptor clusters suggests a structural basis for the high sensitivity of the bacterial chemotaxis receptors. Furthermore, we present crystallographic data suggesting that, in contrast to most molecular signaling by conformational changes and/or oligomerization of the signaling molecules, the changes in dynamic property of the receptors on ligand binding or methylation may be the language of the signaling by the chemotaxis receptors. Taken together, the changes of the dynamic property of one receptor propagating mechanically to many others in the receptor patch provides a plausible, simple mechanism for the high sensitivity and the dynamic range of the receptors.

Purification and polar localization of pneumococcal LytB, a putative endo-beta-N-acetylglucosaminidase: the chain-dispersing murein hydrolase

The DNA region encoding the mature form of a pneumococcal murein hydrolase (LytB) was cloned and expressed in Escherichia coli. LytB was purified by affinity chromatography, and its activity was suggested to be the first identified endo-beta-N-acetylglucosaminidase of Streptococcus pneumoniae. LytB can remove a maximum of only 25% of the radioactivity from [(3)H]choline-labeled pneumococcal cell walls in in vitro assays. Inactivation of the lytB gene of wild-type strain R6 (R6B mutant) led to the formation of long chains but did not affect either total cell wall hydrolytic activity at the stationary phase of growth or development of genetic competence. Longer chains were formed when the lytB mutation was introduced into the M31 strain (M31B mutant), which harbors a complete deletion of lytA, which codes for the major autolysin. Furthermore, the use of this mutant revealed that LytB is the first nonautolytic murein hydrolase of pneumococcus. Purified LytB added to pneumococcal cultures of R6B or M31B was capable of dispersing, in a dose-dependent manner, the long chains characteristic of these mutants into diplococci or short chains, the typical morphology of R6 and M31 strains, respectively. In vitro acetylation of purified pneumococcal cell walls did not affect the activity of LytB, whereas that of the LytA amidase was drastically reduced. On the other hand, the use of a translational fusion between the gene (gfp) coding for the green fluorescent protein (GFP) and lytB supports the notion that LytB accumulates in the cell poles of either the wild-type R6, lytB mutants, or ethanolamine-containing cells (EA cells). The GFP-LytB fusion protein was also able to unchain the lytB mutants but not the EA cells. In contrast, translational fusion protein GFP-LytA preferentially bound to the equatorial regions of choline-containing cells but did not affect their average chain length. These observations suggest the existence of specific receptors for LytB that are positioned at the polar region on the pneumococcal surface, allowing localized peptidoglycan hydrolysis and separation of the daughter cells.

Asymmetrical flagellar rotation in Borrelia burgdorferi nonchemotactic mutants

The Lyme disease spirochete Borrelia burgdorferi has bundles of periplasmic flagella subpolarly located at each cell end. These bundles rotate in opposite directions during translational motility. When not translating, they rotate in the same direction, and the cells flex. Here, we present evidence that asymmetrical rotation of the bundles during translation does not depend upon the chemotaxis signal transduction system. The histidine kinase CheA is known to be an essential component in the signaling pathway for bacterial chemotaxis. Mutants of cheA in flagellated bacteria continually rotate their flagella in one direction. B. burgdorferi has two copies of cheA designated cheA1 and cheA2. Both genes were found to be expressed in growing cells. We reasoned that if chemotaxis were essential for asymmetrical rotation of the flagellar bundles, and if the flagellar motors at both cell ends were identical, inactivation of the two cheA genes should result in cells that constantly flex. To test this hypothesis, the signaling pathway was completely blocked by constructing the double mutant cheA1kan cheA2ermC. This double mutant was deficient in chemotaxis. Rather than flexing, it failed to reverse, and it continually translated only in one direction. Video microscopy of mutant cells indicated that both bundles actively rotated. The results indicate that asymmetrical rotation of the flagellar bundles of spirochetes does not depend upon the chemotaxis system but rather upon differences between the two flagellar bundles. We propose that certain factors within the spirochete localize at the flagellar motors at one end of the cell to effect this asymmetry.

Polar location and functional domains of the Agrobacterium tumefaciens DNA transfer protein VirD4

Agrobacterium tumefaciens VirD4 is essential for DNA transfer to plants. VirD4 presumably functions as a coupling factor that facilitates communication between a substrate and the transport pore. To serve as a coupling protein, VirD4 may be required to localize near the transport apparatus. In a previous study, we observed that several constituents of the transport apparatus localize to the cell membranes. In this study, we demonstrate that VirD4 has a unique cellular location. In immunofluorescence microscopy, cells probed with anti-VirD4 antibodies had foci of fluorescence primarily at the cell poles, indicating that VirD4 localizes to the cell pole. Polar location of VirD4 was not dependent on T-DNA processing, the formation of the transport apparatus and the presence of other Vir proteins. VirD4 is an integral membrane protein with one periplasmic domain. The large cytoplasmic region contains a nucleotide-binding domain. To investigate the role of these domains in DNA transfer, we introduced mutations in virD4 and studied the effect of a mutation on substrate transfer. A deletion of most of the periplasmic domain as well as the alterations of glycine 151 to serine and lysine 152 to alanine led to the complete loss of DNA transfer, indicating that both domains are essential for substrate transfer. Subcellular localization of the mutant proteins indicated that both the periplasmic and the nucleotide-binding domains are required for polar localization of VirD4. The periplasmic domain mutant VirD4Delta36-61 was distributed throughout the cell membrane, whereas the nucleotide binding site mutant VirD4G151S localized to sites other than the cell poles. Polar location of VirD4 suggests a role for the cell pole in DNA transfer.

Evidence that both ligand binding and covalent adaptation drive a two-state equilibrium in the aspartate receptor signaling complex

The transmembrane aspartate receptor of bacterial chemotaxis regulates an associated kinase protein in response to both attractant binding to the receptor periplasmic domain and covalent modification of four adaptation sites on the receptor cytoplasmic domain. The existence of at least 16 covalent modification states raises the question of how many stable signaling conformations exist. In the simplest case, the receptor could have just two stable conformations ("on" and "off") yielding the two-state behavior of a toggle-switch. Alternatively, covalent modification could incrementally shift the receptor between many more than two stable conformations, thereby allowing the receptor to function as a rheostatic switch. An important distinction between these models is that the observed functional parameters of a toggle-switch receptor could strongly covary as covalent modification shifts the equilibrium between the on- and off-states, due to population-weighted averaging of the intrinsic on- and off-state parameters. By contrast, covalent modification of a rheostatic receptor would create new conformational states with completely independent parameters. To resolve the toggle-switch and rheostat models, the present study has generated all 16 homogeneous covalent modification states of the receptor adaptation sites, and has compared their effects on the attractant affinity and kinase activity of the reconstituted receptor-kinase signaling complex. This approach reveals that receptor covalent modification modulates both attractant affinity and kinase activity up to 100-fold, respectively. The regulatory effects of individual adaptation sites are not perfectly additive, indicating synergistic interactions between sites. The three adaptation sites at positions 295, 302, and 309 are more important than the site at position 491 in regulating attractant affinity and kinase activity, thereby explaining the previously observed dominance of the former three sites in in vivo studies. The most notable finding is that covalent modification of the adaptation sites alters the receptor attractant affinity and the receptor-regulated kinase activity in a highly correlated fashion, strongly supporting the toggle-switch model. Similarly, certain mutations that drive the receptor into the kinase activating state are found to have correlated effects on attractant affinity. Together these results provide strong evidence that chemotaxis receptors possess just two stable signaling conformations and that the equilibrium between these pure on- and off-states is modulated by both attractant binding and covalent adaptation. It follows that the attractant and adaptation signals drive the same conformational change between the two settings of a toggle. An approach that quantifies the fractional occupancy of the on- and off-states is illustrated.

Directed polar secretion of protease from single cells of Vibrio cholerae via the type II secretion pathway

Bacteria have long been thought of as little more than sacks of homogeneously distributed enzymes. However, recent cytological studies indicate that bacteria are compartmentalized with proteins involved in processes such as cell division, motility, chemotaxis, and development located at distinct sites. We have used the green fluorescent protein as a reporter to determine the cellular distribution of the extracellular protein secretion (eps)-encoded type II secretion complex responsible for extracellular secretion of cholera toxin and hemagglutinin/protease in Vibrio cholerae. Real-time monitoring of green fluorescent protein fused to EpsM in living cells indicated that, like the single polar flagellum, the Eps complex is located at the old pole after cell division. Eps-dependent protease secretion was also visualized in single cells by fluorescence microscopy by using intramolecularly quenched casein. This analysis demonstrated that active protease secretion is focused at the poles and colocalizes with the site of the polar Eps apparatus. These results suggest that the type II secretion complex is responsible for directed delivery of virulence factors during cholera pathogenesis.

Cellular location and temperature-dependent assembly of IncHI1 plasmid R27-encoded TrhC-associated conjugative transfer protein complexes

Conjugal transfer of IncHI plasmid DNA between Gram-negative bacteria is temperature sensitive, as mating is optimal between 22 degrees C and 30 degrees C but is inhibited at 37 degrees C. R27, isolated from Salmonella enterica serovar Typhi, is an IncHI1 plasmid of 180 kbp that has been sequenced completely. The gene encoding green fluorescent protein (GFP) was inserted into R27 in frame with trhC. TrhC is a mating pair formation (Mpf) protein that is essential for plasmid transfer and H-pilus production. Fluorescence microscopy allowed visualization of the TrhC-GFP fusion protein, and Escherichia coli cells were examined for the subcellular localization and temperature-dependent production of TrhC-GFP. At 27 degrees C, TrhC-GFP was found at the periphery of cells as discrete foci, indicating an association of TrhC within protein complexes in the bacterial cell membrane, whereas at 37 degrees C, little fluorescence was detected. These foci probably represent the intracellular position of protein complexes involved in conjugative transfer, as the formation of foci was dependent upon the presence of other Mpf proteins. During temperature shift experiments from 37 degrees C to 27 degrees C, a long lag period was required for generation of GFP foci. Conversely, during short shifts from 27 degrees C to 37 degrees C, the GFP foci remained stable. These results suggest that the expression of transfer genes in the Tra2 region of R27 is temperature dependent. Subcellular localization of TrhC was verified by cellular fractionation. Expression patterns of TrhC-GFP were confirmed with immunoblot analysis and reverse transcriptase-polymerase chain reaction (RT-PCR). These results allow us to propose mechanisms to explain the temperature-sensitive transfer of R27.