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1.  MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus 
The Journal of antibiotics  2013;67(1):99-104.
Most (75%) of the anti-infectives that save countless lives and enormously improve quality of life originate from microbes found in nature. Herein, we described a global visualization of the detectable molecules produced from a single microorganism, which we define as the ‘molecular network’ of that organism, followed by studies to characterize the cellular effects of antibacterial molecules. We demonstrate that Streptomyces roseosporus produces at least four non-ribosomal peptide synthetase-derived molecular families and their gene subnetworks (daptomycin, arylomycin, napsamycin and stenothricin) were identified with different modes of action. A number of previously unreported analogs involving truncation, glycosylation, hydrolysis and biosynthetic intermediates and/or shunt products were also captured and visualized by creation of a map through MS/MS networking. The diversity of antibacterial compounds produced by S. roseosporus highlights the importance of developing new approaches to characterize the molecular capacity of an organism in a more global manner. This allows one to more deeply interrogate the biosynthetic capacities of microorganisms with the goal to streamline the discovery pipeline for biotechnological applications in agriculture and medicine. This is a contribution to a special issue to honor Chris Walsh’s amazing career.
PMCID: PMC3919142  PMID: 24149839
BioMAP; biosynthesis; cyclic peptides; cytological profiling; mass spectrometry; metabolic exchange
2.  Impact of a Transposon Insertion in phzF2 on the Specialized Metabolite Production and Interkingdom Interactions of Pseudomonas aeruginosa 
Journal of Bacteriology  2014;196(9):1683-1693.
In microbiology, gene disruption and subsequent experiments often center on phenotypic changes caused by one class of specialized metabolites (quorum sensors, virulence factors, or natural products), disregarding global downstream metabolic effects. With the recent development of mass spectrometry-based methods and technologies for microbial metabolomics investigations, it is now possible to visualize global production of diverse classes of microbial specialized metabolites simultaneously. Using imaging mass spectrometry (IMS) applied to the analysis of microbiology experiments, we can observe the effects of mutations, knockouts, insertions, and complementation on the interactive metabolome. In this study, a combination of IMS and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to visualize the impact on specialized metabolite production of a transposon insertion into a Pseudomonas aeruginosa phenazine biosynthetic gene, phzF2. The disruption of phenazine biosynthesis led to broad changes in specialized metabolite production, including loss of pyoverdine production. This shift in specialized metabolite production significantly alters the metabolic outcome of an interaction with Aspergillus fumigatus by influencing triacetylfusarinine production.
PMCID: PMC3993319  PMID: 24532776
3.  Bistable Forespore Engulfment in Bacillus subtilis by a Zipper Mechanism in Absence of the Cell Wall 
PLoS Computational Biology  2014;10(10):e1003912.
To survive starvation, the bacterium Bacillus subtilis forms durable spores. The initial step of sporulation is asymmetric cell division, leading to a large mother-cell and a small forespore compartment. After division is completed and the dividing septum is thinned, the mother cell engulfs the forespore in a slow process based on cell-wall degradation and synthesis. However, recently a new cell-wall independent mechanism was shown to significantly contribute, which can even lead to fast engulfment in 60 of the cases when the cell wall is completely removed. In this backup mechanism, strong ligand-receptor binding between mother-cell protein SpoIIIAH and forespore-protein SpoIIQ leads to zipper-like engulfment, but quantitative understanding is missing. In our work, we combined fluorescence image analysis and stochastic Langevin simulations of the fluctuating membrane to investigate the origin of fast bistable engulfment in absence of the cell wall. Our cell morphologies compare favorably with experimental time-lapse microscopy, with engulfment sensitive to the number of SpoIIQ-SpoIIIAH bonds in a threshold-like manner. By systematic exploration of model parameters, we predict regions of osmotic pressure and membrane-surface tension that produce successful engulfment. Indeed, decreasing the medium osmolarity in experiments prevents engulfment in line with our predictions. Forespore engulfment may thus not only be an ideal model system to study decision-making in single cells, but its biophysical principles are likely applicable to engulfment in other cell types, e.g. during phagocytosis in eukaryotes.
Author Summary
When the bacterium B. subtilis runs out of food, it undergoes a fundamental development process by which it forms durable spores. Sporulation is initiated by asymmetric cell division after which the larger mother cell engulfs the smaller forespore, followed by spore maturation and release. This survival strategy is so robust that engulfment even proceeds when cells are deprived of their protective cell wall. Under these severe perturbations, 60 of the mother cells still engulf their forespores in only 10 of the normal engulfment time, while the remaining 40 of mother cells withdraw from engulfment. This all-or-none outcome of engulfment suggests decision-making, which was recently also identified in other types of engulfment, e.g. during phagocytosis when immune cells engulf and destroy pathogens. Here, we developed a biophysical model to explain fast bistable forespore engulfment in absence of the cell wall and energy sources. Our discovered principles may prove very general, thus predicting key ingredients of successful engulfment across all kingdoms of life.
PMCID: PMC4214620  PMID: 25356555
4.  The SpoIIQ landmark protein has different requirements for septal localization and immobilization 
Molecular microbiology  2013;89(6):1053-1068.
Bacillus subtilis sporulation depends on the forespore membrane protein SpoIIQ, which interacts with the mother cell protein SpoIIIAH at the septum to localize other sporulation proteins. It has remained unclear how SpoIIQ localizes. We demonstrate that localization of SpoIIQ is achieved by two pathways: SpoIIIAH and the SpoIID, SpoIIM, SpoIIP engulfment proteins. SpoIIQ shows diffuse localization only in a mutant lacking both pathways. Super-resolution imaging shows that in the absence of SpoIIIAH, SpoIIQ forms fewer, slightly larger foci than in wild type. Surprisingly, photobleaching experiments demonstrate that, although SpoIIQ localizes without SpoIIIAH, it is no longer immobilized, and is therefore able to exchange subunits within a localized pool. SpoIIQ mobility is further increased by the additional absence of the engulfment proteins. However an enzymatically inactive SpoIID protein immobilizes SpoIIQ even in the absence of SpoIIIAH, indicating that complete septal thinning is not required for SpoIIQ localization. This suggests that SpoIIQ interacts with both SpoIIIAH and the engulfment proteins or their peptidoglycan cleavage products. They further demonstrate that apparently normal localization of a protein without a binding partner can mask dramatic alterations in protein mobility. We speculate that SpoIIQ assembles foci along the path defined by engulfment proteins degrading peptidoglycan.
PMCID: PMC3901584  PMID: 23859254
5.  Functional requirements for bacteriophage growth: Gene essentiality and expression in Mycobacteriophage Giles 
Molecular microbiology  2013;88(3):577-589.
Bacteriophages represent a majority of all life forms, and the vast, dynamic population with early origins is reflected in their enormous genetic diversity. A large number of bacteriophage genomes have been sequenced. They are replete with novel genes without known relatives. We know little about their functions, which genes are required for lytic growth, and how they are expressed. Furthermore, the diversity is such that even genes with required functions – such as virion proteins and repressors – cannot always be recognized. Here we describe a functional genomic dissection of mycobacteriophage Giles, in which the virion proteins are identified, genes required for lytic growth are determined, the repressor is identified, and the transcription patterns determined. We find that although all of the predicted phage genes are expressed either in lysogeny or in lytic growth, 45% of the predicted genes are non-essential for lytic growth. We also describe genes required for DNA replication, show that recombination is required for lytic growth, and that Giles encodes a novel repressor. RNAseq analysis reveals abundant expression of a small non-coding RNA in a lysogen and in late lytic growth, although it is non-essential for lytic growth and does not alter lysogeny.
PMCID: PMC3641587  PMID: 23560716
Bacteriophage; Transcription; RNAseq
6.  Peptidoglycan transformations during Bacillus subtilis sporulation 
Molecular microbiology  2013;88(4):673-686.
While vegetative Bacillus subtilis cells and mature spores are both surrounded by a thick layer of peptidoglycan (PG, a polymer of glycan strands cross-linked by peptide bridges), it has remained unclear whether PG surrounds prespores during engulfment. To clarify this issue, we generated a slender ΔponA mutant that enabled high-resolution electron cryotomographic imaging. Three-dimensional reconstructions of whole cells in near-native states revealed a thin PG-like layer extending from the lateral cell wall around the prespore throughout engulfment. Cryotomography of purified sacculi and fluorescent labelling of PG in live cells confirmed that PG surrounds the prespore. The presence of PG throughout engulfment suggests new roles for PG in sporulation, including a new model for how PG synthesis might drive engulfment, and obviates the need to synthesize a PG layer de novo during cortex formation. In addition, it reveals that B. subtilis can synthesize thin, Gram-negative-like PG layers as well as its thick, archetypal Gram-positive cell wall. The continuous transformations from thick to thin and back to thick during sporulation suggest that both forms of PG have the same basic architecture (circumferential). Endopeptidase activity may be the main switch that governs whether a thin or a thick PG layer is assembled.
PMCID: PMC3893088  PMID: 23531131
7.  Radiation-Dependent Limit for the Viability of Bacterial Spores in Halite Fluid Inclusions and on Mars 
Radiation research  2003;159(6):722-729.
Kminek, G., Bada, J. L., Pogliano, K. and Ward, J. F. Radiation-Dependent Limit for the Viability of Bacterial Spores in Halite Fluid Inclusions and on Mars. Radiat. Res. 159, 722–729 (2003).
When claims for the long-term survival of viable organisms are made, either within terrestrial minerals or on Mars, considerations should be made of the limitations imposed by the naturally occurring radiation dose to which they have been exposed. We investigated the effect of ionizing radiation on different bacterial spores by measuring the inactivation constants for B. subtilis and S. marismortui spores in solution as well as for dry spores of B. subtilis and B. thuringiensis. S. marismortui is a halophilic spore that is genetically similar to the recently discovered 2-9-3 bacterium from a halite fluid inclusion, claimed to be 250 million years old (Vreeland et al., Nature 407, 897–900, 2000). B. thuringiensis is a soil bacterium that is genetically similar to the human pathogens B. anthracis and B. cereus (Helgason et al., Appl. Environ. Microbiol. 66, 2627–2630, 2000). To relate the inactivation constant to some realistic environments, we calculated the radiation regimen in a halite fluid inclusion and in the Martian subsurface over time. Our conclusion is that the ionizing dose of radiation in those environments limits the survival of viable bacterial spores over long periods. In the absence of an active repair mechanism in the dormant state, the long-term survival of spores is limited to less than 109 million years in halite fluid inclusions, to 100 to 160 million years in the Martian subsurface below 3 m, and to less than 600,000 years in the uppermost meter of Mars.
PMCID: PMC3919141  PMID: 12751954
8.  Chromosome segregation in Eubacteria 
Current opinion in microbiology  2003;6(6):586-593.
It is now clear that bacterial chromosomes rapidly separate in a manner independent of cell elongation, suggesting the existence of a mitotic apparatus in bacteria. Recent studies of bacterial cells reveal filamentous structures similar to the eukaryotic cytoskeleton, proteins that mediate polar chromosome anchoring during Bacillus subtilis sporulation, and SMC interacting proteins that are involved in chromosome condensation. A picture is thereby developing of how bacterial chromosomes are organized within the cell, how they are separated following duplication, and how these processes are coordinated with the cell cycle.
PMCID: PMC3919143  PMID: 14662354
9.  Microbial metabolic exchange—the chemotype-to-phenotype link 
Nature chemical biology  2011;8(1):10.1038/nchembio.739.
The function of microbial interactions is to enable microorganisms to survive by establishing a homeostasis between microbial neighbors and local environments. A microorganism can respond to environmental stimuli using metabolic exchange—the transfer of molecular factors, including small molecules and proteins. Microbial interactions not only influence the survival of the microbes but also have roles in morphological and developmental processes of the organisms themselves and their neighbors. This, in turn, shapes the entire habitat of these organisms. Here we highlight our current understanding of metabolic exchange as well as the emergence of new technologies that are allowing us to eavesdrop on microbial conversations comprising dozens to hundreds of secreted metabolites that control the behavior, survival and differentiation of members of the community. The goal of the rapidly advancing field studying multifactorial metabolic exchange is to devise a microbial ‘Rosetta stone’ in order to understand the language by which microbial interactions are negotiated and, ultimately, to control the outcome of these conversations.
PMCID: PMC3869239  PMID: 22173357
10.  The Bacillus subtilis cannibalism toxin SDP collapses the proton motive force and induces autolysis 
Molecular microbiology  2012;84(3):10.1111/j.1365-2958.2012.08038.x.
Bacillus subtilis SDP is a peptide toxin that kills cells outside the biofilm to support continued growth. We show that purified SDP acts like endogenously produced SDP; it delays sporulation, and the SdpI immunity protein confers SDP resistance. SDP kills a variety of Gram-positive bacteria in the phylum Firmicutes, as well as E. coli with a compromised outer membrane, suggesting it participates in defense of the B. subtilis biofilm against Gram-positive bacteria as well as cannibalism. Fluorescence microscopy reveals that the effect of SDP on cells differs from that of nisin, nigericin, valinomycin and vancomycin-KCl, but resembles that of CCCP, DNP and azide. Indeed, SDP rapidly collapses the PMF as measured by fluorometry and flow cytometry, which triggers the slower process of autolysis. This secondary consequence of SDP treatment is not required for cell death since the autolysin-defective lytC, lytD, lytE, lytF strain fails to be lysed but is nevertheless killed by SDP. Collapsing the PMF is an ideal mechanism for a toxin involved in cannibalism and biofilm defense, since this would incapacitate neighboring cells by inhibiting motility and secretion of proteins and toxins. It would also induce autolysis in many Gram-positive species, thereby releasing nutrients that promote biofilm growth.
PMCID: PMC3839633  PMID: 22469514
Antimicrobial peptide; mechanism of action; PMF; autolysis; biofilm; microbial interactions
11.  Primer on Agar-Based Microbial Imaging Mass Spectrometry 
Journal of Bacteriology  2012;194(22):6023-6028.
Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry (IMS) applied directly to microbes on agar-based medium captures global information about microbial molecules, allowing for direct correlation of chemotypes to phenotypes. This tool was developed to investigate metabolic exchange factors of intraspecies, interspecies, and polymicrobial interactions. Based on our experience of the thousands of images we have generated in the laboratory, we present five steps of microbial IMS: culturing, matrix application, dehydration of the sample, data acquisition, and data analysis/interpretation. We also address the common challenges encountered during sample preparation, matrix selection and application, and sample adherence to the MALDI target plate. With the practical guidelines described herein, microbial IMS use can be extended to bio-based agricultural, biofuel, diagnostic, and therapeutic discovery applications.
PMCID: PMC3486372  PMID: 22821974
12.  Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry 
Microbiology  2011;157(Pt 9):2485-2492.
Microbial competition exists in the general environment, such as soil or aquatic habitats, upon or within unicellular or multicellular eukaryotic life forms. The molecular actions that govern microbial competition, leading to niche establishment and microbial monopolization, remain undetermined. The emerging technology of imaging mass spectrometry (IMS) enabled the observation that there is directionality in the metabolic output of the organism Bacillus subtilis when co-cultured with Staphylococcus aureus. The directionally released antibiotic alters S. aureus virulence factor production and colonization. Therefore, IMS provides insight into the largely hidden nature of competitive microbial encounters and niche establishment, and provides a paradigm for future antibiotic discovery.
PMCID: PMC3352172  PMID: 21719540
13.  Automated Quantitative Live Cell Fluorescence Microscopy 
Advances in microscopy automation and image analysis have given biologists the tools to attempt large scale systems-level experiments on biological systems using microscope image readout. Fluorescence microscopy has become a standard tool for assaying gene function in RNAi knockdown screens and protein localization studies in eukaryotic systems. Similar high throughput studies can be attempted in prokaryotes, though the difficulties surrounding work at the diffraction limit pose challenges, and targeting essential genes in a high throughput way can be difficult. Here we will discuss efforts to make live-cell fluorescent microscopy based experiments using genetically encoded fluorescent reporters an automated, high throughput, and quantitative endeavor amenable to systems-level experiments in bacteria. We emphasize a quantitative data reduction approach, using simulation to help develop biologically relevant cell measurements that completely characterize the cell image. We give an example of how this type of data can be directly exploited by statistical learning algorithms to discover functional pathways.
The diffraction limit makes high-throughput fluorescence microscopy more challenging in prokaryotes, but approaches such as quantitative data reduction now allow systems-level analysis of bacteria by this technique.
PMCID: PMC2908775  PMID: 20591990
14.  Isolation and Characterization of a Psychropiezophilic Alphaproteobacterium▿† 
Applied and Environmental Microbiology  2011;77(22):8145-8153.
Cultivated psychropiezophilic (low-temperature- and high-pressure-adapted) bacteria are currently restricted to phylogenetically narrow groupings capable of growth under nutrient-replete conditions, limiting current knowledge of the extant functional attributes and evolutionary constraints of diverse microorganisms inhabiting the cold, deep ocean. This study documents the isolation of a deep-sea bacterium following dilution-to-extinction cultivation using a natural seawater medium at high hydrostatic pressure and low temperature. To our knowledge, this isolate, designated PRT1, is the slowest-growing (minimal doubling time, 36 h) and lowest cell density-producing (maximal densities of 5.0 × 106 cells ml−1) piezophile yet obtained. Optimal growth was at 80 MPa, correlating with the depth of capture (8,350 m), and 10°C, with average cell sizes of 1.46 μm in length and 0.59 μm in width. Through detailed growth studies, we provide further evidence for the temperature-pressure dependence of the growth rate for deep-ocean bacteria. PRT1 was phylogenetically placed within the Roseobacter clade, a bacterial lineage known for widespread geographic distribution and assorted lifestyle strategies in the marine environment. Additionally, the gene transfer agent (GTA) g5 capsid protein gene was amplified from PRT1, indicating a potential mechanism for increased genetic diversification through horizontal gene transfer within the hadopelagic environment. This study provides a phylogenetically novel isolate for future investigations of high-pressure adaptation, expands the known physiological traits of cultivated members of the Roseobacter lineage, and demonstrates the feasibility of cultivating novel microbial members from the deep ocean using natural seawater.
PMCID: PMC3208983  PMID: 21948832
15.  Forespore Engulfment Mediated by a Ratchet-Like Mechanism 
Cell  2006;126(5):917-928.
A key step in bacterial endospore formation is engulfment, during which one bacterial cell engulfs another in a phagocytosis-like process that normally requires SpoIID, SpoIIM, and SpoIIP (DMP). We here describe a second mechanism involving the zipper-like interaction between the forespore protein SpoIIQ and its mother cell ligand SpoIIIAH, which are essential for engulfment when DMP activity is reduced or SpoIIB is absent. They are also required for the rapid engulfment observed during the enzymatic removal of peptidoglycan, a process that does not require DMP. These results suggest the existence of two separate engulfment machineries that compensate for one another in intact cells, thereby rendering engulfment robust. Photobleaching analysis demonstrates that SpoIIQ assembles a stationary structure, suggesting that SpoIIQ and SpoIIIAH function as a ratchet that renders forward membrane movement irreversible. We suggest that ratchet-mediated engulfment minimizes the utilization of chemical energy during this dramatic cellular reorganization, which occurs during starvation.
PMCID: PMC3266857  PMID: 16959571
16.  Cellular Architecture Mediates DivIVA Ultrastructure and Regulates Min Activity in Bacillus subtilis 
mBio  2011;2(6):e00257-11.
The assembly of the cell division machinery at midcell is a critical step of cytokinesis. Many rod-shaped bacteria position septa using nucleoid occlusion, which prevents division over the chromosome, and the Min system, which prevents division near the poles. Here we examined the in vivo assembly of the Bacillus subtilis MinCD targeting proteins DivIVA, a peripheral membrane protein that preferentially localizes to negatively curved membranes and resembles eukaryotic tropomyosins, and MinJ, which recruits MinCD to DivIVA. We used structured illumination microscopy to demonstrate that both DivIVA and MinJ localize as double rings that flank the septum and first appear early in septal biosynthesis. The subsequent recruitment of MinCD to these double rings would separate the Min proteins from their target, FtsZ, spatially regulating Min activity and allowing continued cell division. Curvature-based localization would also provide temporal regulation, since DivIVA and the Min proteins would localize to midcell after the onset of division. We use time-lapse microscopy and fluorescence recovery after photobleaching to demonstrate that DivIVA rings are highly stable and are constructed from newly synthesized DivIVA molecules. After cell division, DivIVA rings appear to collapse into patches at the rounded cell poles of separated cells, with little or no incorporation of newly synthesized subunits. Thus, changes in cell architecture mediate both the initial recruitment of DivIVA to sites of cell division and the subsequent collapse of these rings into patches (or rings of smaller diameter), while curvature-based localization of DivIVA spatially and temporally regulates Min activity.
The Min systems of Escherichia coli and Bacillus subtilis both inhibit FtsZ assembly, but one key difference between these two species is that whereas the E. coli Min proteins localize to the poles, the B. subtilis proteins localize to nascent division sites by interaction with DivIVA and MinJ. It is unclear how MinC activity at midcell is regulated to prevent it from interfering with FtsZ engaged in medial cell division. We used superresolution microscopy to demonstrate that DivIVA and MinJ, which localize MinCD, assemble double rings that flank active division sites and septa. This curvature-based localization mechanism holds MinCD away from the FtsZ ring at midcell, and we propose that this spatial organization is the primary mechanism by which MinC activity is regulated to allow division at midcell. Curvature-based localization also conveys temporal regulation, since it ensures that MinC localizes after the onset of division.
PMCID: PMC3225972  PMID: 22108385
17.  Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution 
Pope, Welkin H. | Jacobs-Sera, Deborah | Russell, Daniel A. | Peebles, Craig L. | Al-Atrache, Zein | Alcoser, Turi A. | Alexander, Lisa M. | Alfano, Matthew B. | Alford, Samantha T. | Amy, Nichols E. | Anderson, Marie D. | Anderson, Alexander G. | Ang, Andrew A. S. | Ares, Manuel | Barber, Amanda J. | Barker, Lucia P. | Barrett, Jonathan M. | Barshop, William D. | Bauerle, Cynthia M. | Bayles, Ian M. | Belfield, Katherine L. | Best, Aaron A. | Borjon, Agustin | Bowman, Charles A. | Boyer, Christine A. | Bradley, Kevin W. | Bradley, Victoria A. | Broadway, Lauren N. | Budwal, Keshav | Busby, Kayla N. | Campbell, Ian W. | Campbell, Anne M. | Carey, Alyssa | Caruso, Steven M. | Chew, Rebekah D. | Cockburn, Chelsea L. | Cohen, Lianne B. | Corajod, Jeffrey M. | Cresawn, Steven G. | Davis, Kimberly R. | Deng, Lisa | Denver, Dee R. | Dixon, Breyon R. | Ekram, Sahrish | Elgin, Sarah C. R. | Engelsen, Angela E. | English, Belle E. V. | Erb, Marcella L. | Estrada, Crystal | Filliger, Laura Z. | Findley, Ann M. | Forbes, Lauren | Forsyth, Mark H. | Fox, Tyler M. | Fritz, Melissa J. | Garcia, Roberto | George, Zindzi D. | Georges, Anne E. | Gissendanner, Christopher R. | Goff, Shannon | Goldstein, Rebecca | Gordon, Kobie C. | Green, Russell D. | Guerra, Stephanie L. | Guiney-Olsen, Krysta R. | Guiza, Bridget G. | Haghighat, Leila | Hagopian, Garrett V. | Harmon, Catherine J. | Harmson, Jeremy S. | Hartzog, Grant A. | Harvey, Samuel E. | He, Siping | He, Kevin J. | Healy, Kaitlin E. | Higinbotham, Ellen R. | Hildebrandt, Erin N. | Ho, Jason H. | Hogan, Gina M. | Hohenstein, Victoria G. | Holz, Nathan A. | Huang, Vincent J. | Hufford, Ericka L. | Hynes, Peter M. | Jackson, Arrykka S. | Jansen, Erica C. | Jarvik, Jonathan | Jasinto, Paul G. | Jordan, Tuajuanda C. | Kasza, Tomas | Katelyn, Murray A. | Kelsey, Jessica S. | Kerrigan, Larisa A. | Khaw, Daryl | Kim, Junghee | Knutter, Justin Z. | Ko, Ching-Chung | Larkin, Gail V. | Laroche, Jennifer R. | Latif, Asma | Leuba, Kohana D. | Leuba, Sequoia I. | Lewis, Lynn O. | Loesser-Casey, Kathryn E. | Long, Courtney A. | Lopez, A. Javier | Lowery, Nicholas | Lu, Tina Q. | Mac, Victor | Masters, Isaac R. | McCloud, Jazmyn J. | McDonough, Molly J. | Medenbach, Andrew J. | Menon, Anjali | Miller, Rachel | Morgan, Brandon K. | Ng, Patrick C. | Nguyen, Elvis | Nguyen, Katrina T. | Nguyen, Emilie T. | Nicholson, Kaylee M. | Parnell, Lindsay A. | Peirce, Caitlin E. | Perz, Allison M. | Peterson, Luke J. | Pferdehirt, Rachel E. | Philip, Seegren V. | Pogliano, Kit | Pogliano, Joe | Polley, Tamsen | Puopolo, Erica J. | Rabinowitz, Hannah S. | Resiss, Michael J. | Rhyan, Corwin N. | Robinson, Yetta M. | Rodriguez, Lauren L. | Rose, Andrew C. | Rubin, Jeffrey D. | Ruby, Jessica A. | Saha, Margaret S. | Sandoz, James W. | Savitskaya, Judith | Schipper, Dale J. | Schnitzler, Christine E. | Schott, Amanda R. | Segal, J. Bradley | Shaffer, Christopher D. | Sheldon, Kathryn E. | Shepard, Erica M. | Shepardson, Jonathan W. | Shroff, Madav K. | Simmons, Jessica M. | Simms, Erika F. | Simpson, Brandy M. | Sinclair, Kathryn M. | Sjoholm, Robert L. | Slette, Ingrid J. | Spaulding, Blaire C. | Straub, Clark L. | Stukey, Joseph | Sughrue, Trevor | Tang, Tin-Yun | Tatyana, Lyons M. | Taylor, Stephen B. | Taylor, Barbara J. | Temple, Louise M. | Thompson, Jasper V. | Tokarz, Michael P. | Trapani, Stephanie E. | Troum, Alexander P. | Tsay, Jonathan | Tubbs, Anthony T. | Walton, Jillian M. | Wang, Danielle H. | Wang, Hannah | Warner, John R. | Weisser, Emilie G. | Wendler, Samantha C. | Weston-Hafer, Kathleen A. | Whelan, Hilary M. | Williamson, Kurt E. | Willis, Angelica N. | Wirtshafter, Hannah S. | Wong, Theresa W. | Wu, Phillip | Yang, Yun jeong | Yee, Brandon C. | Zaidins, David A. | Zhang, Bo | Zúniga, Melina Y. | Hendrix, Roger W. | Hatfull, Graham F.
PLoS ONE  2011;6(1):e16329.
Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.
PMCID: PMC3029335  PMID: 21298013
18.  SpoIID-Mediated Peptidoglycan Degradation Is Required throughout Engulfment during Bacillus subtilis Sporulation▿ † 
Journal of Bacteriology  2010;192(12):3174-3186.
SpoIID is a membrane-anchored enzyme that degrades peptidoglycan and is essential for engulfment and sporulation in Bacillus subtilis. SpoIID is targeted to the sporulation septum, where it interacts with two other proteins required for engulfment: SpoIIP and SpoIIM. We changed conserved amino acids in SpoIID to alanine to determine whether there was a correlation between the effect of each substitution on the in vivo and in vitro activities of SpoIID. We identified one amino acid substitution, E88A, that eliminated peptidoglycan degradation activity and one, D210A, that reduced it, as well as two substitutions that destabilized the protein in B. subtilis (R106A and K203A). Using these mutants, we show that the peptidoglycan degradation activity of SpoIID is required for the first step of engulfment (septal thinning), as well as throughout membrane migration, and we show that SpoIID levels are substantially above the minimum required for engulfment. The inactive mutant E88A shows increased septal localization compared to the wild type, suggesting that the degradation cycle of the SpoIID/SpoIIP complex is accompanied by the activity-dependent release of SpoIID from the complex and subsequent rebinding. This mutant is also capable of moving SpoIIP across the sporulation septum, suggesting that SpoIID binding, but not peptidoglycan degradation activity, is needed for relocalization of SpoIIP. Finally, the mutant with reduced activity (D210A) causes uneven engulfment and time-lapse microscopy indicates that the fastest-moving membrane arm has greater concentrations of SpoIIP than the slower-moving arm, demonstrating a correlation between SpoIIP protein levels and the rate of membrane migration.
PMCID: PMC2901704  PMID: 20382772
19.  Cell wall synthesis is necessary for membrane dynamics during sporulation of Bacillus subtilis 
Molecular microbiology  2010;76(4):956-970.
During Bacillus subtilis sporulation, an endocytic-like process called engulfment results in one cell being entirely encased in the cytoplasm of another cell. The driving force underlying this process of membrane movement has remained unclear, although components of the machinery have been characterized. Here we provide evidence that synthesis of peptidoglycan, the rigid, strength bearing extracellular polymer of bacteria, is a key part of the missing force-generating mechanism for engulfment. We observed that sites of peptidoglycan synthesis initially coincide with the engulfing membrane and later with the site of engulfment membrane fission. Furthermore, compounds that block muropeptide synthesis or polymerization prevented membrane migration in cells lacking a component of the engulfment machinery (SpoIIQ), and blocked the membrane fission event at the completion of engulfment in all cells. In addition, these compounds inhibited bulge and vesicle formation that occur in spoIID mutant cells unable to initiate engulfment, as did genetic ablation of a protein that polymerizes muropeptides. This is the first report to our knowledge that peptidoglycan synthesis is necessary for membrane movements in bacterial cells and has implications for the mechanism of force generation during cytokinesis.
PMCID: PMC2893020  PMID: 20444098
20.  Divergent stalling sequences sense and control cellular physiology 
Recent studies have identified several amino acid sequences that interact with the ribosomal interior components and arrest their own elongation. Whereas stalling of the inducible class depends on specific low-molecular weight compounds, that of the intrinsic class is released when the nascent chain is transported across or inserted into the membrane. The stalled ribosome alters messenger RNA secondary structure and thereby contributes to regulation of the cis-located target gene expression at different levels. The stalling sequences are divergent but likely to utilize non-uniform nature of the peptide bond formation reactions and are recruited relatively recently to different biological systems, possibly including those to be identified in forthcoming studies.
PMCID: PMC2885147  PMID: 20117091
Ribosome stalling; Translation regulation; Elongation arrest; Nascent polypeptide; Protein localization; Peptidyl transferase center; Exit tunnel
21.  Dual localization pathways for the engulfment proteins during Bacillus subtilis sporulation 
Molecular microbiology  2007;65(6):1534-1546.
Engulfment in Bacillus subtilis is mediated by two complementary systems, SpoIID, SpoIIM and SpoIIP (DMP), which are essential for engulfment, and the SpoIIQ-SpoIIIAGH (Q-AH) zipper, which provides a secondary engulfment mechanism and recruits other proteins to the septum. We here identify two mechanisms by which DMP localizes to the septum. The first depends on SpoIIB, which is recruited to the septum during division and provides a septal landmark for efficient DMP localization. However, sporangia lacking SpoIIB ultimately localize DMP and complete engulfment, suggesting a second mechanism for DMP localization. This secondary targeting pathway depends on SpoIVFA and SpoIVFB, which are recruited to the septum by the Q-AH zipper. The absence of a detectable localization phenotype in mutants lacking only SpoIVFAB (or Q-AH) suggests that SpoIIB provides the primary DMP localization pathway while SpoIVFAB provides a secondary pathway. In keeping with this hypothesis, the spoIIB spoIVFAB mutant strain has a synergistic engulfment defect at septal thinning (which requires DMP) and is completely defective in DMP localization. Thus, the Q-AH zipper both provides a compensatory mechanism for engulfment when DMP activity is reduced, and indirectly provides a compensatory mechanism for septal localization of DMP when its primary targeting pathway is disrupted.
PMCID: PMC2885130  PMID: 17824930
22.  Cell-specific SpoIIIE assembly and DNA translocation polarity are dictated by chromosome orientation 
Molecular microbiology  2007;66(5):1066-1079.
SpoIIIE and FtsK are related proteins that translocate chromosomes across septa. Previous results suggested that SpoIIIE exports DNA and that translocation polarity is governed by the cell-specific regulation of its assembly, but that FtsK is a reversible motor for which translocation polarity is governed by its DNA substrate. Seeking to reconcile these conclusions, we used cell-specific GFP tagging to demonstrate that SpoIIIE assembles a complex only in the mother cell, from which DNA is exported, but that DNA translocation-defective SpoIIIE proteins assemble in both cells. Altering chromosome architecture by soj-spo0J and racA soj-spo0J mutations allowed wild-type SpoIIIE to assemble in the forespore and export the forespore chromosome. Combining LacI-CFP tagging of oriC with time-lapse microscopy, we demonstrate that the chromosome is exported from the forespore when oriC fails to be trapped in the forespore. Thus, the position of oriC after septation determines which cell will receive the chromosome and which will assemble SpoIIIE.
PMCID: PMC2885133  PMID: 18001347
23.  Evidence that the SpoIIIE DNA translocase participates in membrane fusion during cytokinesis and engulfment 
Molecular microbiology  2006;59(4):1097-1113.
During Bacillus subtilis sporulation, SpoIIIE is required for translocation of the trapped forespore chromosome across the sporulation septum, for compartmentalization of cell-specific gene expression, and for membrane fusion after engulfment. We isolated mutations within the SpoIIIE membrane domain that block localization and function. One mutant protein initially localizes normally and completes DNA translocation, but shows reduced membrane fusion after engulfment. Fluorescence recovery after photobleaching experiments demonstrate that in this mutant the sporulation septum remains open, allowing cytoplasmic contents to diffuse between daughter cells, suggesting that it blocks membrane fusion after cytokinesis as well as after engulfment. We propose that SpoIIIE catalyses these topologically opposite fusion events by assembling or disassembling a proteinaceous fusion pore. Mutants defective in SpoIIIE assembly also demonstrate that the ability of SpoIIIE to provide a diffusion barrier is directly proportional to its ability to assemble a focus at the septal midpoint during DNA translocation. Thus, SpoIIIE mediates compartmentalization by two distinct mechanisms: the SpoIIIE focus first provides a temporary diffusion barrier during DNA translocation, and then mediates the completion of membrane fusion after division to provide a permanent diffusion barrier. SpoIIIE-like proteins might therefore serve to couple the final step in cytokinesis, septal membrane fusion, to the completion of chromosome segregation.
PMCID: PMC2885140  PMID: 16430687
24.  Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis 
In prokaryotes, the transfer of DNA between cellular compartments is essential for the segregation and exchange of genetic material. SpoIIIE and FtsK are AAA+ ATPases responsible for intercompartmental chromosome translocation in bacteria. Despite functional and sequence similarities, these motors were proposed to use drastically different mechanisms: SpoIIIE was suggested to be a unidirectional DNA transporter that exports DNA from the compartment in which it assembles, whereas FtsK was shown to establish translocation directionality by interacting with highly skewed chromosomal sequences. Here we use a combination of single-molecule, bioinformatics and in vivo fluorescence methodologies to study the properties of DNA translocation by SpoIIIE in vitro and in vivo. These data allow us to propose a sequence-directed DNA exporter model that reconciles previously proposed models for SpoIIIE and FtsK, constituting a unified model for directional DNA transport by the SpoIIIE/FtsK family of AAA+ ring ATPases.
PMCID: PMC2885143  PMID: 18391964
25.  Engulfment-regulated proteolysis of SpoIIQ: evidence that dual checkpoints control σK activity 
Molecular microbiology  2005;58(1):102-115.
During Bacillus subtilis sporulation, the engulfment checkpoint is thought to directly regulate late fore-spore transcription but to indirectly regulate late mother cell transcription, via the σG-produced pro-tease SpoIVB. We here demonstrate that SpoIIQ is subject to σG-independent, but engulfment-dependent, proteolysis that depends on SpoIVB. Thus, SpoIVB produced before engulfment supports some SpoIVB-dependent events, suggesting that its activity or access to substrates must be regulated by engulfment. Furthermore, a mutation (bofA) that allows σK to be active without σG does not allow σK activity in engulfment mutants, although the pro-σK processing enzyme (SpoIVFB) is localized to the septum in engulfment mutants, suggesting that engulfment comprises a second checkpoint for σK Finally, we find that SpoIIQ and another protein required for σG activity (SpoIIIAH), which directly interact and assemble helical structures around the forespore, recruit the σK-processing enzyme SpoIVFB to the forespore and these structures. We suggest that these foci serve a synapse-like role, allowing engulfment to simultaneously control both σG and σK, and integrating multiple checkpoints and signalling pathways.
PMCID: PMC2885156  PMID: 16164552

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