From the Cover: Accessory factors promote AlfA-dependent plasmid segregation by regulating filament nucleation,disassembly, and bundling

In bacteria, some plasmids are partitioned to daughter cells by assembly of actin-like proteins (ALPs). The best understood ALP, ParM, has a core set of biochemical properties that contributes to its function, including dynamic instability, spontaneous nucleation, and bidirectional elongation. AlfA, an ALP that pushes plasmids apart in Bacillus, relies on a different set of underlying properties to segregate DNA. AlfA elongates unidirectionally and is not dynamically unstable; its assembly and disassembly are regulated by a cofactor, AlfB. Free AlfB breaks up AlfA bundles and promotes filament turnover. However, when AlfB is bound to the centromeric DNA sequence, parN, it forms a segrosome complex that nucleates and stabilizes AlfA filaments. When reconstituted in vitro, this system creates polarized, motile comet tails that associate by antiparallel filament bundling to form bipolar, DNA-segregating spindles.The first filament-forming actin-like protein (ALP) was identified in bacteria in 2001 (1), and subsequent work identified more than 30 additional classes of ALPs in eubacteria and archaea (2). These proteins are involved in a variety of cellular processes, including assembly of the cell wall (1, 3–5), positioning of organelles (6), anchoring of cytokinesis machinery (7), and segregation of DNA (8). Most DNA-segregating ALPs participate in type II plasmid partitioning systems, which consist of three components: (i) a centromeric DNA sequence; (ii) a DNA-binding protein that interacts with the centromeric sequence to form a segrosome complex; and (iii) a polymer-forming ALP, whose self-assembly moves the segrosome through the cytoplasm (SI Appendix, Fig. S1). In the best understood type II segregation system, bidirectional polymerization of the ALP, ParM, pushes pairs of plasmids to opposite poles of rod-shaped cells. Extensive studies, both in vivo and in vitro, have produced detailed models of ParM-mediated DNA segregation (9, 10), but it is unclear to what extent these models can be generalized to describe other ALP-dependent DNA segregation systems.To better understand the diversity of molecular mechanisms underlying plasmid segregation, we studied a type II plasmid partitioning system encoded by the alf operon from the Bacillus subtilis plasmid pLS32 (11). The alf operon was first identified based on its ability to maintain plasmids through the process of sporulation, presumably by actively pushing a plasmid into the forespore at one end of the cell. In addition, the alf operon confers approximately eightfold greater stability to plasmids in rapidly dividing cells. The alf operon itself contains a centromeric sequence, parN, with three short, repeated sequences, and it encodes both an ALP, AlfA, and a DNA-binding protein, AlfB. The AlfA protein shares 15% sequence identity with ParM (2), whereas AlfB shares only 8% identity with ParR and has no significant BLAST hits (expect value < 1). In addition to sequence differences, AlfA and ParM also differ biochemically. ParM filaments are dynamically unstable and do not form bundles in the absence of molecular crowding agents. AlfA, in contrast, displays no evidence of dynamic instability and forms stable filaments that self-assemble into mixed-polarity bundles, even in high salt concentrations (12, 13). The dynamic instability of ParM filaments is thought to play an important role in plasmid segregation, in part by providing the energy required to move the plasmids in a directed fashion. Energy must be expended to disassemble unneeded filaments and raise the concentration of monomers above the critical concentration required to elongate cargo-attached filaments. Otherwise, monomer and polymer reach a stable, steady-state ratio, and directed motion ceases. In eukaryotic cells, several proteins, including the actin-binding proteins cofilin and profilin, collaborate to maintain a high concentration of monomeric actin, orders of magnitude higher than the critical concentration for polymerization. In bacteria, the dynamic instability of unattached ParM filaments maintains the concentration of monomeric ParM approximately fourfold above the critical concentration of filaments attached to segrosomes (9, 14). If assembly of AlfA filaments drives plasmid movement, then how, in the absence of dynamic instability, is the concentration of monomeric AlfA maintained at a level sufficient to drive the growth of segrosome-attached filaments? To understand how AlfA filaments assemble and move DNA, we followed AlfA-dependent plasmid segregation in vivo and reconstituted the process in vitro using purified components. Like the par system, the alf system relies on assembly of actin-like polymers to push plasmids, but the two systems use different sets of underlying molecular mechanisms to favor the assembly of cargo-attached filaments over free filaments. AlfB binds to parN DNA, creating a segrosome complex that nucleates AlfA filaments and remains attached to their growing ends. Remarkably, however, the AlfB protein by itself also debundles and destabilizes AlfA filaments and maintains a high concentration of monomeric AlfA sufficient to drive plasmid movement. Once formed, AlfA filaments elongate in a polarized manner, from only one end, and binding of the segrosome complex increases filament stability, even in the presence of high concentrations of free AlfB. Together, these properties produce treadmilling AlfA “comet tails” that move DNA similar to the way polarized actin comet tails move cargo in eukaryotic cytoplasm. In sporulating cells, these monopolar comet tails would be sufficient to push plasmids into the forespore so that they would survive sporulation. In actively growing cells, antiparallel association of these comet tails can also segregate plasmids to opposite poles and decrease the rate of plasmid loss.     

Spatial organization of a replicating bacterial chromosome

Emerging evidence indicates that the global organization of the bacterial chromosome is defined by its physical map. This architectural understanding has been gained mainly by observing the localization and dynamics of specific chromosomal loci. However, the spatial and temporal organization of the entire mass of newly synthesized DNA remains elusive. To visualize replicated DNA within living cells, we developed an experimental system in the bacterium Bacillus subtilis whereby fluorescently labeled nucleotides are incorporated into the chromosome as it is being replicated. Here, we present the first visualization of replication morphologies exhibited by the bacterial chromosome. At the start of replication, newly synthesized DNA is translocated via a helical structure from midcell toward the poles, where it accumulates. Next, additionally synthesized DNA forms a second, visually distinct helix that interweaves with the original one. In the final stage of replication, the space between the two helices is filled up with the very last synthesized DNA. This striking geometry provides insight into the three-dimensional conformation of the replicating chromosome.     

From the Cover: PNAS Plus: Pan-neuronal imaging in roaming Caenorhabditis elegans

We present an imaging system for pan-neuronal recording in crawling Caenorhabditis elegans. A spinning disk confocal microscope, modified for automated tracking of the C. elegans head ganglia, simultaneously records the activity and position of ∼80 neurons that coexpress cytoplasmic calcium indicator GCaMP6s and nuclear localized red fluorescent protein at 10 volumes per second. We developed a behavioral analysis algorithm that maps the movements of the head ganglia to the animal’s posture and locomotion. Image registration and analysis software automatically assigns an index to each nucleus and calculates the corresponding calcium signal. Neurons with highly stereotyped positions can be associated with unique indexes and subsequently identified using an atlas of the worm nervous system. To test our system, we analyzed the brainwide activity patterns of moving worms subjected to thermosensory inputs. We demonstrate that our setup is able to uncover representations of sensory input and motor output of individual neurons from brainwide dynamics. Our imaging setup and analysis pipeline should facilitate mapping circuits for sensory to motor transformation in transparent behaving animals such as C. elegans and Drosophila larva.Understanding how brain dynamics creates behaviors requires quantifying the flow and transformation of sensory information to motor output in behaving animals. Optical imaging using genetically encoded calcium or voltage fluorescent probes offers a minimally invasive method to record neural activity in intact animals. The nematode Caenorhabditis elegans is particularly ideal for optical neurophysiology owing to its small size, optical transparency, compact nervous system, and ease of genetic manipulation. Imaging systems for tracking the activity of small numbers of neurons have been effective in determining their role during nematode locomotion and navigational behaviors like chemotaxis, thermotaxis, and the escape response (1–6). Recordings from large numbers of interconnected neurons are required to understand how neuronal ensembles carry out the systematic transformations of sensory input into motor patterns that build behavioral decisions.Several methods for fast 3D imaging of neural activity in a fixed imaging volume have been developed for different model organisms (7–14). High-speed light sheet microscopy, light field microscopy, multifocus microscopy, and two-photon structured illumination microscopy have proved effective for rapidly recording large numbers of neurons in immobilized, intact, transparent animals like larval zebrafish and nematodes (15–19). However, these methods are problematic when attempting to track many neurons within the bending and moving body of a behaving animal. Panneuronal recording in moving animals poses higher demands on spatial and temporal resolution. Furthermore, extracting neuronal signals from recordings in a behaving animal requires an effective analysis pipeline to segment image volumes into the activity patterns of discrete and identifiable neurons.Here, we use high-speed spinning disk confocal microscopy—modified for automated tracking using real-time image analysis and motion control software—to volumetrically image the head ganglia of behaving C. elegans adults at single-cell resolution. Our setup can simultaneously track ∼80 neurons with 0.45 × 0.45 × 2-μm resolution at 10 Hz. Activity was reported by the ultrasensitive calcium indicator GCaMP6s expressed throughout the cytosol under the control of the pan-neuronal rgef-1 promoter (a gift from D. Pilgrim, University of Alberta, Edmonton, Alberta, Canada) (20). To facilitate segmentation into individual identifiable neurons, nuclei were tracked using calcium-insensitive, nuclear-bound red fluorescent protein (RFP), TagRFP, under the control of another pan-neuronal rab-3 promoter (a gift from O. Hobert, Columbia University, New York) (21). We developed an image analysis pipeline that converts the gross movements of the head into the time-varying position and posture of the crawling worm, and converts fluorescence measurements into near simultaneous activity patterns of all imaged neurons.A similar approach to brainwide imaging in moving C. elegans using the same transgenic strain has recently been reported (22). Although both setups use customized spinning disk confocal microscopes, the strategies for tracking the moving neurons and analyzing behavioral and neural activity patterns are different. Nguyen et al. (22) use a low power objective to track the posture of the animal and a high power objective to locate and image the nerve ring. The advantage of our single objective setup is that it affords the flexibility, for example, to deliver thermosensory inputs using an opaque temperature controlled stage below the animal. The advantage of low-magnification imaging is that it provides a direct measurement of animal posture, which we must infer. These new technologies for pan-neuronal imaging in roaming animals now enables correlating brainwide dynamics to sensory inputs and motor outputs in transparent behaving animals like C. elegans and Drosophila larvae.     

From the Cover: PNAS Plus: Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans

The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals is needed to provide new insights into how populations of neurons generate animal behavior. We present an instrument capable of recording intracellular calcium transients from the majority of neurons in the head of a freely behaving Caenorhabditis elegans with cellular resolution while simultaneously recording the animal’s position, posture, and locomotion. This instrument provides whole-brain imaging with cellular resolution in an unrestrained and behaving animal. We use spinning-disk confocal microscopy to capture 3D volumetric fluorescent images of neurons expressing the calcium indicator GCaMP6s at 6 head-volumes/s. A suite of three cameras monitor neuronal fluorescence and the animal’s position and orientation. Custom software tracks the 3D position of the animal’s head in real time and two feedback loops adjust a motorized stage and objective to keep the animal’s head within the field of view as the animal roams freely. We observe calcium transients from up to 77 neurons for over 4 min and correlate this activity with the animal’s behavior. We characterize noise in the system due to animal motion and show that, across worms, multiple neurons show significant correlations with modes of behavior corresponding to forward, backward, and turning locomotion.How do patterns of neural activity generate an animal’s behavior? To answer this question, it is important to develop new methods for recording from large populations of neurons in animals as they move and behave freely. The collective activity of many individual neurons appears to be critical for generating behaviors including arm reach in primates (1), song production in zebrafinch (2), the choice between swimming or crawling in leech (3), and decision-making in mice during navigation (4). New methods for recording from larger populations of neurons in unrestrained animals are needed to better understand neural coding of these behaviors and neural control of behavior more generally.Calcium imaging has emerged as a promising technique for recording dynamics from populations of neurons. Calcium-sensitive proteins are used to visualize changes in intracellular calcium levels in neurons in vivo which serve as a proxy for neural activity (5). To resolve the often weak fluorescent signal of an individual neuron in a dense forest of other labeled cells requires a high magnification objective with a large numerical aperture that, consequently, can image only a small field of view. Calcium imaging has traditionally been performed on animals that are stationary from anesthetization or immobilization to avoid imaging artifacts induced by animal motion. As a result, calcium imaging studies have historically focused on small brain regions in immobile animals that exhibit little or no behavior (6).No previous neurophysiological study has attained whole-brain imaging with cellular resolution in a freely behaving unrestrained animal. Previous whole-brain cellular resolution calcium imaging studies of populations of neurons that involve behavior investigate either fictive locomotion (3, 7), or behaviors that can be performed in restrained animals, such as eye movements (8) or navigation of a virtual environment (9). One exception has been the development of fluorescence endoscopy, which allows recording from rodents during unrestrained behavior, although imaging is restricted to even smaller subbrain regions (10).Investigating neural activity in small transparent organisms allows one to move beyond studying subbrain regions to record dynamics from entire brains with cellular resolution. Whole-brain imaging was performed first in larval zebrafish using two-photon microscopy (7). More recently, whole-brain imaging was performed in Caenorhabditis elegans using two-photon (11) and light-field microscopy (12). Animals in these studies were immobilized, anesthetized, or both and thus exhibited no gross behavior.C. elegans’ compact nervous system of only 302 neurons and small size of only 1 mm make it ideally suited for the development of new whole-brain imaging techniques for studying behavior. There is a long and rich history of studying and quantifying the behavior of freely moving C. elegans dating back to the mid-1970s (13, 14). Many of these works involved quantifying animal body posture as the worm moved, for example as in ref. 15. To facilitate higher-throughput recordings of behavior, a number of tracking microscopes (16–18) or multiworm imagers were developed (19, 20) along with sophisticated behavioral analysis software and analytical tools (21, 22). Motivated in part to understand these behaviors, calcium imaging systems were also developed that could probe neural activity in at first partially immobilized (23) and then freely moving animals, beginning with ref. 24 and and then developing rapidly (17, 18, 25–29). One limitation of these freely moving calcium imaging systems is that they are limited to imaging only a very small subset of neurons and lack the ability to distinguish neurons that lie atop one another in the axial direction of the microscope. Despite this limitation, these studies, combined with laser-ablation experiments, have identified a number of neurons that correlate or affect changes in particular behaviors including the AVB neuron pair and VB-type motor neurons for forward locomotion; the AVA, AIB, and AVE neuron pairs and VA-type motor neurons for backward locomotion; and the RIV, RIB, and SMD neurons and the DD-type motor neurons for turning behaviors (17, 18, 25, 26, 28, 30, 31). To move beyond these largely single-cell studies, we sought to record simultaneously from the entire brain of C. elegans with cellular resolution and record its behavior as it moved about unrestrained.     

From the Cover: PNAS Plus: Prehistoric genomes reveal the genetic foundation and cost of horse domestication

The domestication of the horse ∼5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski’s horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the “cost of domestication” hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.The domestication of the horse had a far-reaching impact on the sociopolitical and economic trajectories of human societies (1). It not only provided meat and milk (2) but also enabled the development of continent-sized nomadic empires, by transforming warfare and allowing for the rapid spread of goods and information over long distances. However, despite the characterization of the genome of modern horses (3), an understanding of the genetic processes underlying horse domestication is still lacking. In other organisms, such an understanding is usually achieved by comparing the genomes of domesticated species and their wild relatives (4–6), but this approach is not directly applicable to horses. Recent genome-wide analyses have shown that Przewalski’s horse, the last truly wild horse population remaining today, is not the direct ancestor of domesticated horses (7, 8). Instead, it likely represents a sister population that separated from the ancestral population of domesticated horses some 38–72 kya (9). This date significantly predates not only the widely accepted date for the beginning of horse domestication, ca. 5.5 kya (2), but also the earliest potential evidence for horse domestication, ca. 7.5 kya (10). In addition, the current Przewalski’s horse population descends from a captive stock consisting of only 13 founder individuals (7). This severe demographic bottleneck, together with inbreeding resulting from unequal contributions from different captive lineages, likely caused a substantial loss of the diversity once present in Przewalski’s horses. As a result, no modern horse population can fully represent the genetic diversity ancestral to the modern, domesticated gene pool (11–13).Ancient DNA allows tracking of past population histories through time, accessing the gene pools of wild animals predating domestication and exploring genetic variation that has been lost in extant populations. Recovery of ancient DNA, coupled with low-throughput gene candidate analyses, has previously been used to investigate changes in the genetic diversity of horses over time. This approach revealed coat color variation as one early result of domestication, by showing that the selection of multiple alleles driving diverse coloration patterns was already ongoing in the Early Bronze Age (14). It has also revealed a loss of Y-chromosomal haplotypes on both the Przewalski’s and domestic horse lineages (12).Using next-generation sequencing, the complete genome sequence of ancient individuals can now be deciphered (15), with qualities rivaling the qualities of modern genomes (16–18). We characterized complete genome sequences of two ancient horse specimens predating the earliest evidence of horse domestication to reveal the population context in which horse domestication took place. We compared the genomic information of these specimens with genomic information of six domestic horses, representing five breeds, and one Przewalski’s horse (9), ranging from a 7.4- to 32.7-fold average depth of coverage. We also included the domestic donkey as an outgroup, which represents a sister lineage of modern horses and shares a most common recent ancestor with horses 4.0–4.5 Mya ago (9). This comparison enabled us to reconstruct the relationships between wild and domesticated horses, and to explore the genetic mechanisms underlying the behavioral, physiological, and other biological changes that accompanied horse domestication.     

From the Cover: PNAS Plus: Single-molecule visualization of RecQ helicase reveals DNA melting,nucleation, and assembly are required for processive DNA unwinding

DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40–60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.DNA helicases are ubiquitous enzymes involved in many aspects of DNA metabolism, including DNA replication, repair, and recombination. These enzymes work by coupling the hydrolysis of nucleoside triphosphates (NTPs) to unwinding of double-stranded DNA (dsDNA) to produce single-stranded DNA (ssDNA) (1). This activity allows the cell’s machinery to access the information stored within the bases of the double helix. RecQ helicase from Escherichia coli is the founding member of the RecQ family of helicases (2). These enzymes belong to the superfamily 2 (SF2) group of helicases, yet share greater sequence homology with their own family members, and they play important roles in the maintenance of genomic integrity by DNA recombination and repair (1, 3). Mutations in the human RecQ-like helicases, Bloom (BLM), Werner (WRN), and RecQ4 proteins, lead to Bloom’s, Werner’s, and Rothmund–Thomson syndromes, respectively. These genetic disorders are characterized by genomic instability and an increased incidence of cancers (4).E. coli RecQ is a 3′ → 5′ helicase that functions in DNA-break repair by homologous recombination (2, 5, 6). RecQ and RecJ, a 5′ → 3′ exonuclease, process ssDNA gaps or dsDNA breaks into ssDNA for recombinational repair by RecA (7–10). In addition, RecQ ensures recombination fidelity in vivo by removing inappropriately paired joint molecules to prevent illegitimate recombination and also by disrupting joint molecule intermediates to facilitate repair by synthesis-dependent strand annealing, preventing chromosomal crossing over (7, 9, 11, 12). RecQ also functions with topoisomerase III (Topo III), a type I topoisomerase, to catenate and decatenate DNA molecules and to separate converged replication forks (13, 14). RecQ and Topo III provide an alternative to the RuvABC pathway for disengaging double Holliday junctions and do so without producing chromosomal crossovers (15).In vitro, RecQ can unwind a multitude of DNA substrates and does not require a ssDNA tail, or even a dsDNA end, to initiate unwinding; consequently, it is distinctive in being able to unwind covalently closed circular plasmid DNA (16, 17). The winged-helix domain of RecQ is important for the recognition of this broad array of DNA substrates (18). This domain binds to dsDNA yet it adopts a flexible conformation that allows it to adapt to many DNA structures. A curious feature of RecQ is that maximal unwinding requires nearly stoichiometric amounts of protein relative to the DNA (one protein per ∼10 bp), which can be partially mitigated (one protein per ∼30 bp) by including the ssDNA binding protein, SSB (5, 6, 16, 19). This behavior is compatible with the low processivity of ssDNA translocation (∼30–100 nucleotides) by RecQ (20–22) and other RecQ members (23). Paradoxically, at limiting concentrations, most RecQ helicases nonetheless efficiently unwind several kilobases of dsDNA in the course of their normal functions (9, 16, 24–26), suggesting a dynamic unwinding process. Although RecQ can unwind DNA as a monomer, it also shows a functional cooperativity when unwinding DNA with an ssDNA tail (27–29). Thus, multiple monomers can bind to ssDNA to unwind long dsDNA regions.Fluorescence techniques coupled with single-molecule microscopy have emerged as a powerful method for studying the unwinding mechanism of helicases (30–35). These assays measure individual enzymes directly or indirectly through their actions on individual DNA molecules, thus alleviating many of the drawbacks of ensemble experiments. In particular, total internal reflection fluorescence (TIRF) microscopy permits the detection of individual fluorophores with high sensitivity in the presence of a high background (30). To visualize the activity of DNA binding proteins and helicases, TIRF microscopy can be coupled with microfluidic techniques to facilitate visualization of molecules and exchange of solution components (36–39).Ensemble assays have elucidated many features of DNA unwinding by the RecQ helicase family, but the need to average over a heterogeneous and unsynchronized population of enzymes has precluded a thorough understanding of this diverse and universally important helicase family. To permit a more insightful analysis, we directly visualized unwinding of individual molecules of DNA by RecQ helicase. Unwinding was monitored using fluorescent SSB to visualize generation of ssDNA. On single DNA molecules, we could see tracks of the fluorescent SSB binding to ssDNA produced by the helicase activity of RecQ. We show that RecQ initiates DNA unwinding via melting of duplex DNA at internal sites. Once initiated, DNA unwinding propagates either uni- or bidirectionally via the cooperative action of multiple RecQ molecules at the junction of ssDNA with dsDNA. Collectively, these observations define a stable oligomeric complex of subunits involved in processive helicase action, which is concordant with both biochemical and biological function of RecQ helicases and other helicases.     

Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein

We show that translation initiation factor EF-Tu plays a second important role in cell shape maintenance in the bacterium Bacillus subtilis. EF-Tu localizes in a helical pattern underneath the cell membrane and colocalizes with MreB, an actin-like cytoskeletal element setting up rod cell shape. The localization of MreB and of EF-Tu is interdependent, but in contrast to the dynamic MreB filaments, EF-Tu structures are more static and may serve as tracks for MreB filaments. In agreement with this idea, EF-Tu and MreB interact in vivo and in vitro. Lowering of the EF-Tu levels had a minor effect on translation but a strong effect on cell shape and on the localization of MreB, and blocking of the function of EF-Tu in translation did not interfere with the localization of MreB, showing that, directly or indirectly, EF-Tu affects the cytoskeletal MreB structure and thus serves two important functions in a bacterium.     

From the Cover: PNAS Plus: Phosphoinositide 5- and 3-phosphatase activities of a voltage-sensing phosphatase in living cells show identical voltage dependence

Voltage-sensing phosphatases (VSPs) are homologs of phosphatase and tensin homolog (PTEN), a phosphatidylinositol 3,4-bisphosphate [PI(3,4)P₂] and phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P₃] 3-phosphatase. However, VSPs have a wider range of substrates, cleaving 3-phosphate from PI(3,4)P₂ and probably PI(3,4,5)P₃ as well as 5-phosphate from phosphatidylinositol 4,5-bisphosphate [PI(4,5)P₂] and PI(3,4,5)P₃ in response to membrane depolarization. Recent proposals say these reactions have differing voltage dependence. Using Förster resonance energy transfer probes specific for different PIs in living cells with zebrafish VSP, we quantitate both voltage-dependent 5- and 3-phosphatase subreactions against endogenous substrates. These activities become apparent with different voltage thresholds, voltage sensitivities, and catalytic rates. As an analytical tool, we refine a kinetic model that includes the endogenous pools of phosphoinositides, endogenous phosphatase and kinase reactions connecting them, and four exogenous voltage-dependent 5- and 3-phosphatase subreactions of VSP. We show that apparent voltage threshold differences for seeing effects of the 5- and 3-phosphatase activities in cells are not due to different intrinsic voltage dependence of these reactions. Rather, the reactions have a common voltage dependence, and apparent differences arise only because each VSP subreaction has a different absolute catalytic rate that begins to surpass the respective endogenous enzyme activities at different voltages. For zebrafish VSP, our modeling revealed that 3-phosphatase activity against PI(3,4,5)P₃ is 55-fold slower than 5-phosphatase activity against PI(4,5)P₂; thus, PI(4,5)P₂ generated more slowly from dephosphorylating PI(3,4,5)P₃ might never accumulate. When 5-phosphatase activity was counteracted by coexpression of a phosphatidylinositol 4-phosphate 5-kinase, there was accumulation of PI(4,5)P₂ in parallel to PI(3,4,5)P₃ dephosphorylation, emphasizing that VSPs can cleave the 3-phosphate of PI(3,4,5)P₃.This paper concerns the substrate specificity and voltage dependence of a unique voltage-sensitive phosphoinositide (PI) phosphatase in intact live cells. Bioelectricity, caused by ion channels and differences in ion concentrations between the inside and outside of a cell, regulates essential biological activities like generation, propagation, and processing of neuronal signals; muscle contraction; and secretion of hormones. Voltage-gated ion channels were the first protein family identified that possessed bioelectric voltage-sensing domains (VSDs) and participated in these signaling activities. Recently, a quite unanticipated voltage-sensing enzyme with a VSD was cloned from the sea squirt Ciona intestinalis (1). Biochemical and electrophysiological examination revealed a voltage-dependent phosphatase activity toward polyphospho-PIs that was given the name C. intestinalis voltage-sensing phosphatase (Ci-VSP). Since then, homologs have been discovered in other vertebrates, for example, Danio rerio (zebrafish; Dr-VSP), African frog (Xi-VSP and Xt-VSP), chicken (Gg-VSP), and salamander (Hn-VSP and Cp-VSP) (2–5). In addition, two mammalian homologs have been discovered in human Hs-transmembrane phosphatase with tensin homology (TPTE) and mouse (Mm-VSP) tissues (6, 7). Although knowledge about the physiological function of these two proteins is still lacking, a recent study showed that mouse VSP seems to be localized to intracellular membranes of neuronal cells, suggesting a different role for mammalian VSPs than for plasma membrane-localized Ci-VSP or Dr-VSP (7). As in voltage-gated ion channels, the VSD of VSPs consists of four transmembrane segments, S1–S4, with the charged voltage-sensing S4 segment being moved by the intense electric fields across the plasma membrane upon depolarization (8). However, VSPs are monomeric and have a cytosolic catalytic domain instead of the pore-forming domain (S5–S6) of ion channels. This enzyme domain is homologous to tumor suppressor phosphatase and tensin homolog (PTEN), a phosphoinositide 3-phosphatase that dephosphorylates both phosphatidylinositol 3,4-bisphosphate [PI(3,4)P₂] and phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P₃] (1). Three distinctive regions of PTEN, an N-terminal phospholipid-binding motif that anchors the protein at the plasma membrane, a phosphatase domain that has the enzymatic site, and a C-terminal lipid-interacting C2 domain (9, 10), are well conserved in sequence and structure in the VSPs (11–14).Propagation of the depolarization-induced conformational changes of the VSD to the cytosolic catalytic domain activates the unique voltage-activated phosphoinositide phosphatase activity (12, 14, 15). Unlike its analog PTEN, which has only 3-phosphatase activity (9, 16), Ci-VSP was seen initially to cleave the 5-phosphate from phosphatidylinositol 4,5-bisphosphate [PI(4,5)P₂] and PI(3,4,5)P₃ in response to membrane depolarization, generating phosphatidylinositol 4-phosphate [PI(4)P] and PI(3,4)P₂, respectively (1, 17–19). Subsequently, VSPs were reported to cleave 3-phosphate from PI(3,4)P₂, generating PI(4)P upon larger depolarization (20), and, very recently, Ci-VSP was indicated to cleave 3-phosphate from PI(3,4,5)P₃, generating PI(4,5)P₂ (21, 22). Because different substrate reactions are best seen at different voltages, several authors have suggested that changing electric fields can drive VSPs successively through several catalytically active states that favor one set of substrates or reactions over another (20–22). The active site of VSPs is well conserved among species (12) and shows only a single amino acid difference from the active site of PTEN (1). When this residue in Ci-VSP was mutated to the corresponding amino acid of the PTEN active site, the mutated Ci-VSP still showed both 5- and 3-phosphatase activities toward polyphosphoinositides (14). Therefore, the observed substrate specificity and the voltage-dependent dual phosphatase activity of VSPs might be determined by the environment surrounding the active site rather than only by the active site itself (14). When the entire enzymatic domain of Ci-VSP was replaced by PTEN, the resulting chimera, called VSPTEN, had the enzymatic properties of a voltage-dependent pure 3-phosphatase (23).VSPs are found in remarkably diverse tissues, including the testis and brain of mice (7, 24, 25); testis, brain, and stomach of humans (6); testis and neuronal complex of the ascidian (1); and testis, ovary, kidney, and liver of the African frog (26). Surprisingly, the physiological functions of this widespread enzyme remain a puzzle. Recent work suggests that VSPs might have roles in egg fertilization (26) and in neuronal signaling in the brain (7). To understand its physiological enzymology more completely, we screened Dr-VSP–induced phosphoinositide changes in living cells by engineered Förster resonance energy transfer (FRET) probes that specifically report the cellular dynamics of PI(4)P, PI(3,4)P₂, PI(4,5)P₂, and PI(3,4,5)P₃. Our results show that when exogenous expression of PI(4)P 5-kinase type Iγ (PIPKIγ) was used selectively to counteract the 5-phosphatase activity of Dr-VSP, PI(4,5)P₂ accumulated, revealing an intrinsic 3-phosphatase activity of VSP toward PI(3,4,5)P₃. The voltage dependence and substrate specificity of 3- and 5-phosphatase subreactions of Dr-VSP were then extracted quantitatively by a comprehensive kinetic systems analysis. Together, our data demonstrate that Dr-VSP possesses both 3- and 5-phosphatase activities toward PI(3,4,5)P₃, with the same voltage dependence but with quite different absolute catalytic rates. These results should help clarify the roles of VSPs in fertilization, neural computations, and other signaling events that involve voltage changes.     

From the Cover: Osmotrophy in modular Ediacara organisms

The Ediacara biota include macroscopic, morphologically complex soft-bodied organisms that appear globally in the late Ediacaran Period (575–542 Ma). The physiology, feeding strategies, and functional morphology of the modular Ediacara organisms (rangeomorphs and erniettomorphs) remain debated but are critical for understanding their ecology and phylogeny. Their modular construction triggered numerous hypotheses concerning their likely feeding strategies, ranging from micro-to-macrophagus feeding to photoautotrophy to osmotrophy. Macrophagus feeding in rangeomorphs and erniettomorphs is inconsistent with their lack of oral openings, and photoautotrophy in rangeomorphs is contradicted by their habitats below the photic zone. Here, we combine theoretical models and empirical data to evaluate the feasibility of osmotrophy, which requires high surface area to volume (SA/V) ratios, as a primary feeding strategy of rangeomorphs and erniettomorphs. Although exclusively osmotrophic feeding in modern ecosystems is restricted to microscopic bacteria, this study suggests that (i) fractal branching of rangeomorph modules resulted in SA/V ratios comparable to those observed in modern osmotrophic bacteria, and (ii) rangeomorphs, and particularly erniettomorphs, could have achieved osmotrophic SA/V ratios similar to bacteria, provided their bodies included metabolically inert material. Thus, specific morphological adaptations observed in rangeomorphs and erniettomorphs may have represented strategies for overcoming physiological constraints that typically make osmotrophy prohibitive for macroscopic life forms. These results support the viability of osmotrophic feeding in rangeomorphs and erniettomorphs, help explain their taphonomic peculiarities, and point to the possible importance of earliest macroorganisms for cycling dissolved organic carbon that may have been present in abundance during Ediacaran times.     

From the Cover: Cytoplasmic streaming in plant cells emerges naturally by microfilament self-organization

Many cells exhibit large-scale active circulation of their entire fluid contents, a process termed cytoplasmic streaming. This phenomenon is particularly prevalent in plant cells, often presenting strikingly regimented flow patterns. The driving mechanism in such cells is known: myosin-coated organelles entrain cytoplasm as they process along actin filament bundles fixed at the periphery. Still unknown, however, is the developmental process that constructs the well-ordered actin configurations required for coherent cell-scale flow. Previous experimental works on streaming regeneration in cells of Characean algae, whose longitudinal flow is perhaps the most regimented of all, hint at an autonomous process of microfilament self-organization driving the formation of streaming patterns during morphogenesis. Working from first principles, we propose a robust model of streaming emergence that combines motor dynamics with both microscopic and macroscopic hydrodynamics to explain how several independent processes, each ineffectual on its own, can reinforce to ultimately develop the patterns of streaming observed in the Characeae and other streaming species.     

From the Cover: PNAS Plus: Chloride transport-driven alveolar fluid secretion is a major contributor to cardiogenic lung edema

Alveolar fluid clearance driven by active epithelial Na⁺ and secondary Cl⁻ absorption counteracts edema formation in the intact lung. Recently, we showed that impairment of alveolar fluid clearance because of inhibition of epithelial Na⁺ channels (ENaCs) promotes cardiogenic lung edema. Concomitantly, we observed a reversal of alveolar fluid clearance, suggesting that reversed transepithelial ion transport may promote lung edema by driving active alveolar fluid secretion. We, therefore, hypothesized that alveolar ion and fluid secretion may constitute a pathomechanism in lung edema and aimed to identify underlying molecular pathways. In isolated perfused lungs, alveolar fluid clearance and secretion were determined by a double-indicator dilution technique. Transepithelial Cl⁻ secretion and alveolar Cl⁻ influx were quantified by radionuclide tracing and alveolar Cl⁻ imaging, respectively. Elevated hydrostatic pressure induced ouabain-sensitive alveolar fluid secretion that coincided with transepithelial Cl⁻ secretion and alveolar Cl⁻ influx. Inhibition of either cystic fibrosis transmembrane conductance regulator (CFTR) or Na⁺-K⁺-Cl⁻ cotransporters (NKCC) blocked alveolar fluid secretion, and lungs of CFTR^−/− mice were protected from hydrostatic edema. Inhibition of ENaC by amiloride reproduced alveolar fluid and Cl⁻ secretion that were again CFTR-, NKCC-, and Na⁺-K⁺-ATPase–dependent. Our findings show a reversal of transepithelial Cl⁻ and fluid flux from absorptive to secretory mode at hydrostatic stress. Alveolar Cl⁻ and fluid secretion are triggered by ENaC inhibition and mediated by NKCC and CFTR. Our results characterize an innovative mechanism of cardiogenic edema formation and identify NKCC1 as a unique therapeutic target in cardiogenic lung edema.Traditionally, the formation of cardiogenic pulmonary edema has been attributed to passive fluid filtration across an intact alveolocapillary barrier along an increased hydrostatic pressure gradient. However, recent studies show that cardiogenic edema is critically regulated by active signaling processes. Activation of mechanosensitive endothelial ion channels increases lung vascular permeability (1), whereas alveolar epithelial cells lose their physiological ability to clear the distal airspaces from excess fluid by their capacity to actively transport ions across the epithelial barrier (2–4).In the intact lung, the predominant force driving alveolar fluid clearance is an active transepithelial Na⁺ transport from the alveolar into the interstitial space. A major portion of the apical Na⁺ entry is mediated by the amiloride-inhibitable epithelial Na⁺ channel (ENaC), with basolateral Na⁺ extrusion through the Na⁺-K⁺-ATPase (5). Cl⁻ and water are considered to follow paracellularly for electroneutrality and osmotic balance. In cardiogenic lung edema, the physiological protection against alveolar flooding provided by an intact alveolar fluid clearance is largely attenuated (3, 4). Previously, we have outlined the signaling events at the alveolocapillary barrier that underlie this inhibition of alveolar fluid clearance by showing that hydrostatic stress increases endothelial NO production in lung capillaries (6), which in turn, blocks alveolar Na⁺ and liquid absorption by a cGMP-dependent inhibition of epithelial ENaC (2).Unexpectedly, however, we observed that increased hydrostatic pressure not only blocks alveolar fluid clearance but reverses transepithelial fluid transport, resulting in effective alveolar fluid secretion that accounts for up to 70% of the total alveolar fluid influx at elevated hydrostatic pressure (2). This effect is not explicable by impaired alveolar fluid clearance and/or passive fluid leakage, and thus, it points to a previously unrecognized and potentially therapeutically exploitable pathomechanism in cardiogenic lung edema, namely alveolar fluid secretion driven by active transepithelial ion transport.Here, we aimed to analyze alveolar fluid secretion and its underlying cellular mechanisms in cardiogenic lung edema. We considered the Cl⁻ channel cystic fibrosis transmembrane conductance regulator (CFTR) as a putative key ion channel in this scenario, because it permits bidirectional permeation of anions under physiologically relevant conditions (7). Hence, the direction of Cl⁻ flux by CFTR may reverse depending on actual electrochemical gradients, thus turning an absorptive into a secretory epithelium or vice versa. This notion is supported by reports describing CFTR as both an absorptive and secretory channel in the regulation of alveolar fluid homeostasis (8, 9). By a combination of indicator dilution, imaging, and radioactive tracer techniques for the measurement of alveolar ion and fluid fluxes in the isolated lung, we show a critical role for CFTR-mediated Cl⁻ secretion in cardiogenic lung edema and identify the Na⁺-K⁺-2Cl⁻ cotransporter 1 (NKCC1) as a therapeutic target in this pathology.     

From the Cover: A Trojan horse mechanism of bacterial pathogenesis against nematodes

Understanding the mechanisms of host–pathogen interaction can provide crucial information for successfully manipulating their relationships. Because of its genetic background and practical advantages over vertebrate model systems, the nematode Caenorhabditis elegans model has become an attractive host for studying microbial pathogenesis. Here we report a “Trojan horse” mechanism of bacterial pathogenesis against nematodes. We show that the bacterium Bacillus nematocida B16 lures nematodes by emitting potent volatile organic compounds that are much more attractive to worms than those from ordinary dietary bacteria. Seventeen B. nematocida-attractant volatile organic compounds are identified, and seven are individually confirmed to lure nematodes. Once the bacteria enter the intestine of nematodes, they secrete two proteases with broad substrate ranges but preferentially target essential intestinal proteins, leading to nematode death. This Trojan horse pattern of bacterium–nematode interaction enriches our understanding of microbial pathogenesis.     

From the Cover: Stem cells are units of natural selection for tissue formation,for germline development,and in cancer development

It is obvious that natural selection operates at the level of individuals and collections of individuals. Nearly two decades ago we showed that in multi-individual colonies of protochordate colonial tunicates sharing a blood circulation, there exists an exchange of somatic stem cells and germline stem cells, resulting in somatic chimeras and stem cell competitions for gonadal niches. Stem cells are unlike other cells in the body in that they alone self-renew, so that they form clones that are perpetuated for the life of the organism. Stem cell competitions have allowed the emergence of competitive somatic and germline stem cell clones. Highly successful germline stem cells usually outcompete less successful competitors both in the gonads of the genotype partner from which they arise and in the gonads of the natural parabiotic partners. Therefore, natural selection also operates at the level of germline stem cell clones. In the colonial tunicate Botryllus schlosseri the formation of natural parabionts is prevented by a single-locus highly polymorphic histocompatibility gene called Botryllus histocompatibility factor. This limits germline stem cell predation to kin, as the locus has hundreds of alleles. We show that in mice germline stem cells compete for gonad niches, and in mice and humans, blood-forming stem cells also compete for bone marrow niches. We show that the clonal progression from blood-forming stem cells to acute leukemias by successive genetic and epigenetic events in blood stem cells also involves competition and selection between clones and propose that this is a general theme in cancer.     

Disclosure of the mycobacterial outer membrane: cryo-electron tomography and vitreous sections reveal the lipid bilayer structure

The cell walls of mycobacteria form an exceptional permeability barrier, and they are essential for virulence. They contain extractable lipids and long-chain mycolic acids that are covalently linked to peptidoglycan via an arabinogalactan network. The lipids were thought to form an asymmetrical bilayer of considerable thickness, but this could never be proven directly by microscopy or other means. Cryo-electron tomography of unperturbed or detergent-treated cells of Mycobacterium smegmatis embedded in vitreous ice now reveals the native organization of the cell envelope and its delineation into several distinct layers. The 3D data and the investigation of ultrathin frozen-hydrated cryosections of M. smegmatis, Myobacterium bovis bacillus Calmette-Guérin, and Corynebacterium glutamicum identified the outermost layer as a morphologically symmetrical lipid bilayer. The structure of the mycobacterial outer membrane necessitates considerable revision of the current view of its architecture. Conceivable models are proposed and discussed. These results are crucial for the investigation and understanding of transport processes across the mycobacterial cell wall, and they are of particular medical relevance in the case of pathogenic mycobacteria.     

From the Cover: Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain

Phylogenetic analysis of Plasmodium parasites has indicated that their modern-day distribution is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia. A major outstanding question is the phylogenetic affinity of the malaria causing parasites Plasmodium vivax and falciparum in historic southern Europe—where it was endemic until the mid-20th century, after which it was eradicated across the region. Resolving the identity of these parasites will be critical for answering several hypotheses on the malaria dispersal. Recently, a set of slides with blood stains of malaria-affected people from the Ebro Delta (Spain), dated between 1942 and 1944, have been found in a local medical collection. We extracted DNA from three slides, two of them stained with Giemsa (on which Plasmodium parasites could still be seen under the microscope) and another one consisting of dried blood spots. We generated the data using Illumina sequencing after using several strategies aimed at increasing the Plasmodium DNA yield: depletion of the human genomic (g)DNA content through hybridization with human gDNA baits, and capture-enrichment using gDNA derived from P. falciparum. Plasmodium mitochondrial genome sequences were subsequently reconstructed from the resulting data. Phylogenetic analysis of the eradicated European P. vivax mtDNA genome indicates that the European isolate is closely related to the most common present-day American haplotype and likely entered the American continent post-Columbian contact. Furthermore, the European P. falciparum mtDNA indicates a link with current Indian strains that is in agreement with historical accounts.The genus Plasmodium contains two of the most significant human pathogenic organisms. One, Plasmodium vivax, is the most widely distributed human malaria parasite outside of Africa, with a range that extends well into temperate zones (1), whereas the other, Plasmodium falciparum, is the predominant malaria parasite of humans in subsaharan Africa and the one that causes >90% malarial deaths (2).Although an increasing number of studies have attempted to investigate the present-day distribution of Plasmodium parasites using DNA sourced from modern isolates of the pathogens, their origin and dispersal around the planet remain controversial. For example, the current global distribution of P. vivax includes Asia, the Middle East, South and Central America, and parts of Africa (3) and has likely resulted from complex dispersals involving intercontinental human population movements (4, 5). Although an African origin is likely (6), the current strains from this continent show little genetic polymorphism compared with the rest of the world (4), a fact that has been related to the emergence of Duffy-negative blood types—resistant to P. vivax—in human populations from this continent (7). Alternatively, it has been suggested that modern African parasites, at least in the Horn of Africa and Madagascar, could have been reintroduced via the import of East Asian/Indian P. vivax to the coastal areas of East Africa by early sea-going traders and that this could explain their lack of diversity (4). Intriguingly, the diversity of the American strains is comparable to those found in Oceania and Asia (8), raising questions regarding the origin of these strains. Some of the American strains are thought to have been brought there from Europe by Spanish sailors and colonists in the last few centuries (4, 9). An alternative possibility would imply a pre-Columbian entrance through the Bering Straits during the initial peopling of the Americas, although this seems unlikely due to the climatic conditions of this passage (9) and the long Beringian standstill that likely lasted up to several thousands of years (10). However, the existence of divergent mitochondrial lineages in the Americas seems to rule out the possibility of a single, recent introduction of P. vivax from Europe into this continent (8). At the nuclear level, the American isolates show geographic differentiation but also a common clustering regarding the Old World populations (5).With regard to the evolutionary history of P. falciparum, genetic analyses of Laveriana parasite species found in African chimpanzees and gorillas, considered to be precursors of the human parasites, prove an African origin (11), but the time by which the parasite dispersed out of Africa remains controversial. Although some suggest that the pathogen followed the original Homo sapiens dispersals around 60,000 y ago (12), others support a recent expansion within the last 5,000–10,000 y associated to the advent of agriculture (2). The recent analysis of 44 Indian field isolates showed, however, a higher than expected diversity and suggested that the Indian strains are also part of the ancestral distribution range of P. falciparum (13). Historical accounts seem to indicate that malaria spread from India into the Mediterranean at the time of Classical Greece; therefore, the now extinct European P. falciparum could be genetically related to some of these Indian parasites.The current controversies on the recent evolutionary history of P. vivax and P. falciparum partly relate to the lack of genetic evidence from the European parasite that was eradicated more than half century ago. In Spain, malaria had remained endemic until the early 20th century, in particular in Andalucia, Extremadura, and Ebro delta regions; it was declared oficially eradicated in 1964 (14). P. vivax and P. falciparum have been transmitted in southern Spain by two former malaria vectors: Anopheles atroparvus and Anopheles labranchiae. Both were present in the country but whereas An. atroparvus is still widely spread, An. labranchiae has not been found since the middle of the last century (15). An. atroparvus from different geographic origins are infected in laboratory with different world strains of P. vivax, whereas it is very difficult to do the same in the case of P. falciparum (16). Thus, the lack of genetic evidence of the former Plasmodium European parasites also hampers our understanding of their biology.To clarify the phylogenetic position of the extinct European Plasmodium strains, we report here the retrieval of the European P. vivax and P. falciparum genetic data from the analysis of three recently discovered old slides with blood drops from malaria-infected people living at the Ebro Delta in Spain in the first half of the 20th century that corresponds to local epidemics (Fig. 1).Open in a separate windowFig. 1.(A) Two of the Giemsa-stained slides analyzed in this study, labeled CM and CA (inferior stain). (B) Visualization of some Plasmodium parasites (arrows) in the CM slide under the microscope (400×).