DOCSLIB.ORG

The Genetics of Metal Uptake in Caulobacter

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Genetics of Metal Uptake in Caulobacter Clemson University TigerPrints All Dissertations Dissertations 12-2010 THE GENETICS OF METAL UPTAKE IN CAULOBACTER CRESCENTUS: CHARACTERIZATION OF REGULATORS AND IDENTIFICATION OF RECEPTORS Leah Howell Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Genetics and Genomics Commons Recommended Citation Howell, Leah, "THE GENETICS OF METAL UPTAKE IN CAULOBACTER CRESCENTUS: CHARACTERIZATION OF REGULATORS AND IDENTIFICATION OF RECEPTORS" (2010). All Dissertations. 622. https://tigerprints.clemson.edu/all_dissertations/622 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. THE GENETICS OF METAL UPTAKE IN CAULOBACTER CRESCENTUS: CHARACTERIZATION OF REGULATORS AND IDENTIFICATION OF RECEPTORS A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Genetics by Leah Williamson Howell December 2010 Accepted by: Dr. Harry Kurtz Jr., Committee Chair Dr. Julia Frugoli Dr. Amy Lawton-Rauh Dr. Kerry Smith ABSTRACT Caulobacter crescentus is an oligotrophic, Gram negative bacterium with a dimorphic lifecycle. It is a model system for cell cycle regulation and cellular development. Since C. crescentus resides primarily in freshwater, this microorganism can also serve as a model system for nutrient uptake by oligotrophic freshwater species. This study focused on TonB-dependent receptors and metal-dependent regulators in C. crescentus. To maintain appropriate levels of iron within the cell, bacteria have evolved mechanisms to control iron uptake, storage, and use. In microbes, there are two protein families possessing members that accomplish this: Fur and Rrf2. In the C. crescentus genome, there are two putative members from each family. I conducted a phylogenetic analysis to better understand the role of these four proteins. The Fur family proteins were most closely related to regulatory proteins that sense manganese (Mur-like) and zinc (Zur-like). In the Rrf2 family, one protein shared homology with IscR, which regulates Fe-S synthesis and utilization pathways, while the other protein apparently represents a new member of Rrf2 family of regulatory proteins. I found that this protein is produced in response to metal limitation. Future work on this complex topic will focus on determining which metal or metals each of these regulatory proteins responds to, as well as determining the binding sites. ii TonB-dependent receptors are responsible for transporting ferric- siderophore complexes into the periplasm of the cell. I was able to reduce the potential number of TonB-dependent receptors that might possess iron regulation to nine. However, results from another laboratory likely expand that number to thirteen. I found that C. crescentus is capable of utilizing at least five siderophores. Deletion analysis of three receptors, CC0028, CC1666, and CC3336, did not allow for linking a specific complex to a receptor. However, I found that CC0028 and CC3336 transcripts were up regulated 2.5 and 2.0 fold respectively in iron limited conditions. Interestingly, CC3336 is apparently regulated by both iron and carbon starvation. With one possible exception, this is the only TonB-dependent receptor seen to be regulated by two different stressors, one of which has been shown to utilize a sRNA. iii DEDICATION My loving husband, Jonathan Howell, has been by my side in good times and bad throughout my graduate school career. I could never have done this without him, and I want to dedicate this dissertation to him. I also want to dedicate this to my parents, Charlie and Gina Williamson, who have always loved me, encouraged me, and believed in me. Without them, I would never have been confident enough to take my education this far. iv ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Harry Kurtz, who has been a truly great mentor. He has always believed in me and practiced extreme patience. He was always there to answer questions, and his guidance throughout this project was crucial. I would like to thank my committee members, Dr. Julia Frugoli, Dr. Kerry Smith, and Dr. Amy Lawton-Rauh. Their suggestions and guidance were very helpful to me and always insightful. I would like to acknowledge Amy Lawton-Rauh and Brad Rauh for their valuable assistance on the phylogeny work in this dissertation. I would also like to thank the present and past members of the Kurtz lab who were often very helpful and supportive. Finally, I would like to express gratitude to my family and friends for all of their love and support during my graduate school career. I am truly lucky to have such wonderful people in my life. v TABLE OF CONTENTS Page TITLE PAGE .......................................................................................................i ABSTRACT........................................................................................................ ii DEDICATION.................................................................................................... iv ACKNOWLEDGMENTS ....................................................................................v LIST OF TABLES.............................................................................................viii LIST OF FIGURES ........................................................................................... ix CHAPTER I. LITERATURE REVIEW .....................................................................1 Introduction...................................................................................1 The biological significance of iron.................................................2 Iron toxicity ...................................................................................5 Other important metals.................................................................7 Metal-dependent regulation..........................................................8 Iron uptake .................................................................................15 Environmental iron levels ...........................................................19 Purpose of research ...................................................................23 II. METAL-DEPENDENT REGULATORS IN C. CRESCENTUS .........35 Introduction.................................................................................35 Methods......................................................................................40 Results .......................................................................................45 Discussion ..................................................................................56 III. TONB-DEPENDENT IRON UPTAKE IN C. CRESCENTUS............65 Introduction.................................................................................65 Methods......................................................................................69 Results .......................................................................................90 Discussion ................................................................................106 vi Table of Contents (Continued) Page IV.SUMMARY AND FUTURE DIRECTIONS .................................................114 Introduction...............................................................................114 Metal-dependent regulators......................................................115 Iron-regulated TonB-dependent receptors................................120 Conclusion................................................................................125 vii LIST OF TABLES Table Page 1.1 Several proteins that require iron to function properly .......................4 2.1 Fur family pairwise comparison .......................................................46 2.2 Rrf2 family pairwise comparison ......................................................50 3.1 Primers used to construct and test for deletions ..............................72 3.2 Primer pairs used for RT-PCR and for RNA slot blots for each ORF ...................................................................................78 3.3 Slot blots to confirm the iron regulation of TonB-dependent receptors ..................................................................................100 3.4 Summary of findings from three experiments ................................101 viii LIST OF FIGURES Figure Page 1.1 The action of Fur at the Fur box of target genes..............................10 1.2 Model of TonB-dependent transport of iron .....................................17 1.3 Representation of the amount of iron available in the North Atlantic and North Pacific in colloidal iron and free iron forms ..........................................................................................20 1.4 Concentration of free iron in metal polluted, eutrophic, and mesotrophic freshwater sources.................................................22 2.1 The action of Fur at the Fur box of target genes..............................36 2.2 Bayesian Fur family phylogeny ........................................................47 2.3 Maximum Likelihood Fur family phylogeny ......................................48 2.4 Bayesian Rrf2 family phylogeny.......................................................51 2.5 Maximum Likelihood Rrf2 family phylogeny.....................................52
Load more

Recommended publications
  • Accepted Manuscript
    Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane Item Type Article Authors Jeong, Sanghyun; Cho, Kyungjin; Jeong, Dawoon; Lee, Seockheon; Leiknes, TorOve; Vigneswaran, Saravanamuthu; Bae, Hyokwan Citation Jeong S, Cho K, Jeong D, Lee S, Leiknes T, et al. (2017) Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane. Water Research. Available: http://dx.doi.org/10.1016/ j.watres.2017.07.064. Eprint version Post-print DOI 10.1016/j.watres.2017.07.064 Publisher Elsevier BV Journal Water Research Rights NOTICE: this is the author’s version of a work that was accepted for publication in Water Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Water Research, [, , (2017-07-25)] DOI: 10.1016/j.watres.2017.07.064 . © 2017. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ Download date 03/10/2021 04:43:40 Link to Item http://hdl.handle.net/10754/625270 Accepted Manuscript Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane Sanghyun Jeong, Kyungjin Cho, Dawoon Jeong, Seockheon Lee, TorOve Leiknes, Saravanamuthu Vigneswaran, Hyokwan Bae PII: S0043-1354(17)30637-1 DOI: 10.1016/j.watres.2017.07.064 Reference: WR 13107 To appear in: Water Research Received Date: 19 January 2017 Revised Date: 11 May 2017 Accepted Date: 24 July 2017 Please cite this article as: Jeong, S., Cho, K., Jeong, D., Lee, S., Leiknes, T., Vigneswaran, S., Bae, H., Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane, Water Research (2017), doi: 10.1016/j.watres.2017.07.064.
    [Show full text]
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Succession and Persistence of Microbial Communities and Antimicrobial Resistance Genes Associated with International Space Stati
    Singh et al. Microbiome (2018) 6:204 https://doi.org/10.1186/s40168-018-0585-2 RESEARCH Open Access Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces Nitin Kumar Singh1, Jason M. Wood1, Fathi Karouia2,3 and Kasthuri Venkateswaran1* Abstract Background: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms. Results: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii,andAspergillus lentulus.EventhoughRhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3.
    [Show full text]
  • 1 Supplementary Information Ugly Ducklings – the Dark Side of Plastic
    Supplementary Information Ugly ducklings – The dark side of plastic materials in contact with potable water Lisa Neu1,2, Carola Bänziger1, Caitlin R. Proctor1,2, Ya Zhang3, Wen-Tso Liu3, Frederik Hammes1,* 1 Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland 2 Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland 3 Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, USA Table of contents Table S1 Exemplary online blog entries on biofouling in bath toys Figure S1 Images of all examined bath toys Figure S2 Additional images of bath toy biofilms by OCT Figure S3 Additional images on biofilm composition by SEM Figure S4 Number of bacteria and proportion of intact cells in bath toy biofilms Table S2 Classification of shared OTUs between bath toys Table S3 Shared and ‘core’ communities in bath toys from single households Table S4 Richness and diversity Figure S5 Classification of abundant OTUs in real bath toy biofilms Table S5 Comparison of most abundant OTUs in control bath toy biofilms Figure S6 Fungal community composition in bath toy biofilms Table S6 Conventional plating results for indicator bacteria and groups Table S7 Bioavailability of migrating carbon from control bath toys’ material Water chemistry Method and results (Table S8) Table S9 Settings for Amplification PCR and Index PCR reactions 1 Table S1: Exemplary online blog entries on biofouling inside bath toys Issue - What is the slime? Link Rub-a-dub-dub, https://www.babble.com/baby/whats-in-the-tub/ what’s in the tub? What’s the black stuff http://blogs.babycenter.com/momstories/whats-the-black- in your squeeze toys? stuff-in-your-squeeze-toys/ Friday Find: NBC’s http://www.bebravekeepgoing.com/2010/03/friday-find-nbcs- Today Show segment: today-show-segment-do.html Do bath toys carry germs? Yuck.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Microbial Production and Consumption of Hydrocarbons in the Global Ocean
    ARTICLES https://doi.org/10.1038/s41564-020-00859-8 Microbial production and consumption of hydrocarbons in the global ocean Connor R. Love1,4, Eleanor C. Arrington1,4, Kelsey M. Gosselin1, Christopher M. Reddy2, Benjamin A. S. Van Mooy 2, Robert K. Nelson2 and David L. Valentine 3 ✉ Seeps, spills and other oil pollution introduce hydrocarbons into the ocean. Marine cyanobacteria also produce hydrocarbons from fatty acids, but little is known about the size and turnover of this cyanobacterial hydrocarbon cycle. We report that cyano- bacteria in an oligotrophic gyre mainly produce n-pentadecane and that microbial hydrocarbon production exhibits stratifica- tion and diel cycling in the sunlit surface ocean. Using chemical and isotopic tracing we find that pentadecane production mainly occurs in the lower euphotic zone. Using a multifaceted approach, we estimate that the global flux of cyanobacteria-produced pentadecane exceeds total oil input in the ocean by 100- to 500-fold. We show that rapid pentadecane consumption sustains a population of pentadecane-degrading bacteria, and possibly archaea. Our findings characterize a microbial hydrocarbon cycle in the open ocean that dwarfs oil input. We hypothesize that cyanobacterial hydrocarbon production selectively primes the ocean’s microbiome with long-chain alkanes whereas degradation of other petroleum hydrocarbons is controlled by factors including proximity to petroleum seepage. ydrocarbons are released into the ocean via natural oil seeps total, we quantified alkane concentration in 441 particulate samples and industrial spills associated with extraction, transpor- (≥0.2 μm), mainly in triplicate (Methods, Supplementary Table 4 and 1 Htation and consumption of oil, totalling ~1.3 Tg per year .
    [Show full text]
  • Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment
    antibiotics Article Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment Alicia Sorgen 1, James Johnson 2, Kevin Lambirth 2, Sandra M. Clinton 3 , Molly Redmond 1 , Anthony Fodor 2 and Cynthia Gibas 2,* 1 Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (A.S.); [email protected] (M.R.) 2 Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (J.J.); [email protected] (K.L.); [email protected] (A.F.) 3 Department of Geography & Earth Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-704-687-8378 Abstract: Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify Citation: Sorgen, A.; Johnson, J.; phenotypically resistant cultivable portions of these bacterial communities and characterized the Lambirth, K.; Clinton,
    [Show full text]
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
    [Show full text]
  • Bacterial Avidins Are a Widely Distributed Protein Family in Actinobacteria, Proteobacteria and Bacteroidetes Olli H
    Laitinen et al. BMC Ecol Evo (2021) 21:53 BMC Ecology and Evolution https://doi.org/10.1186/s12862-021-01784-y RESEARCH ARTICLE Open Access Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes Olli H. Laitinen1†, Tanja P. Kuusela1†, Sampo Kukkurainen1†, Anssi Nurminen1, Aki Sinkkonen2 and Vesa P. Hytönen1,3* Abstract Background: Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classifed potential avidins according to taxonomy and the ecological niches utilized by host bacteria. Results: Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal patho- gens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fx nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fxing bacteria. Conclusions: Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological signifcance of biotin-binding capacity.
    [Show full text]
  • Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
    Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively).
    [Show full text]
  • Contact-Dependent Killing by Caulobacter Crescentus Via Cell Surface-Associated, Glycine Zipper Proteins Leonor Garcı´A-Bayona1,2,3, Monica S Guo1, Michael T Laub1,2*
    RESEARCH ARTICLE Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins Leonor Garcı´a-Bayona1,2,3, Monica S Guo1, Michael T Laub1,2* 1Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; 2Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States; 3Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, United States Abstract Most bacteria are in fierce competition with other species for limited nutrients. Some bacteria can kill nearby cells by secreting bacteriocins, a diverse group of proteinaceous antimicrobials. However, bacteriocins are typically freely diffusible, and so of little value to planktonic cells in aqueous environments. Here, we identify an atypical two-protein bacteriocin in the a-proteobacterium Caulobacter crescentus that is retained on the surface of producer cells where it mediates cell contact-dependent killing. The bacteriocin-like proteins CdzC and CdzD harbor glycine-zipper motifs, often found in amyloids, and CdzC forms large, insoluble aggregates on the surface of producer cells. These aggregates can drive contact-dependent killing of other organisms, or Caulobacter cells not producing the CdzI immunity protein. The Cdz system uses a type I secretion system and is unrelated to previously described contact-dependent inhibition systems. However, Cdz-like systems are found in many bacteria, suggesting that this form of contact-dependent inhibition is common. DOI: 10.7554/eLife.24869.001 *For correspondence: laub@mit. Introduction edu To survive within complex microbial communities such as those found in the guts of animals or in Competing interest: See soil, bacteria have evolved, and now rely on, a sophisticated array of strategies that allow them to page 22 compete for a limited set of resources.
    [Show full text]
  • Caulobacter Crescentus
    Biochemistry of the key spatial regulators MipZ and PopZ in Caulobacter crescentus Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg vorgelegt von Yacine Refes aus Algier, Algerien Marburg, im November 2017 Vom Fachbereich Biologie der Philipps-Universität Marburg (Hochschulkennziffer: 1180) als Dissertation angenommen am: 22.01.2018 Erstgutachter: Prof. Dr. Martin Thanbichler Zweitgutachter: Prof. Dr. Torsten Waldminghaus Tag der mündlichen Prüfung am: 26.01.2018 Die Untersuchungen zur vorliegenden Arbeit wurden von November 2013 bis Juni 2017 am Max-Planck-Institut für terrestrische Mikrobiologie und an der Philipps Universität Marburg unter der Leitung von Prof. Dr. Martin Thanbichler durchgeführt. Publications Refes Y, He B, Corrales-Guerrero L, Steinchen W, Bange G, and Thanbichler M. Determinants of DNA binding by the bacterial cell division regulator MipZ. In preparation Corrales-Guerrero L, Refes Y, He B, Ramm B, Muecksch J, Steinchen W, Heimerl T, Knopp J, Bange G, Schwille P, and Thanbichler M. Regulation of cell division protein FtsZ by MipZ in Caulobacter crescentus. In preparation ...dans les champs de l'observation le hasard ne favorise que les esprits préparés - Louis Pasteur Abstract Bacteria are known to tightly control the spatial distribution of certain proteins by positioning them to distinct regions of the cell, particularly the cell poles. These regions represent important organizing platforms for several processes essential for bacterial survival and reproduction. The proteins localized at the cell poles are recruited to these positions by interaction with other polar proteins or protein complexes. The α-proteobacterium Caulobacter crescentus possesses a self- organizing polymeric polar matrix constituted of the scaffolding protein PopZ.
    [Show full text]