DOCSLIB.ORG

Discovery of Recombinases Enables Genome Mining of Cryptic

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Discovery of Recombinases Enables Genome Mining of Cryptic Discovery of recombinases enables genome mining PNAS PLUS of cryptic biosynthetic gene clusters in Burkholderiales species Xue Wanga,1, Haibo Zhoua,1, Hanna Chena,b,1, Xiaoshu Jinga, Wentao Zhenga, Ruijuan Lia, Tao Suna, Jiaqi Liua, Jun Fua, Liujie Huoa, Yue-zhong Lia, Yuemao Shena, Xiaoming Dingc, Rolf Müllerd, Xiaoying Biana,2, and Youming Zhanga,2 aShandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, 266237 Qingdao, China; bHunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, People’s Republic of China; cCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, 200433 Shanghai, China; and dDepartment of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved March 28, 2018 (received for review December 1, 2017) Bacterial genomes encode numerous cryptic biosynthetic gene RecE/RecT from Rac prophage, encoded in the E. coli chromosome clusters (BGCs) that represent a largely untapped source of drugs (10–13). Full-length RecE and RecT mediate linear−linear ho- or pesticides. Mining of the cryptic products is limited by the mologous recombination (LLHR), which can be used to directly unavailability of streamlined genetic tools in native producers. clone large DNA regions from genomic DNA into E. coli ex- Precise genome engineering using bacteriophage recombinases is pression vectors (14), while Redα and Redβ promote homolo- particularly useful for genome mining. However, recombinases gous recombination between linear and circular DNA molecule are usually host-specific. The genome-guided discovery of novel [linear plus circular homologous recombination (LCHR)]. In recombinases and their transient expression could boost cryptic addition, Redαβ recombineering is particularly relevant to bacterial BGC mining. Herein, we reported a genetic system employing Red genome engineering for genome mining, because the linear targeting recombinases from Burkholderiales strain DSM 7029 for efficient DNA carrying short homology regions (conveniently generated by genome engineering in several Burkholderiales species that currently PCR) is sufficient for gene modification, and dedicated targeting lack effective genetic tools. Using specialized recombinases-assisted plasmids are not required, unlike in single- or double-crossover in situ insertion of functional promoters, we successfully mined five mutagenesis (15). The Redαβ system from E. coli has been directly cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, applied to several closely related Gram-negative bacteria for genome two of which were silent. Two classes of lipopeptides, glidopeptins engineering, e.g., Salmonella enterica (16), Klebsiella pneumo- and rhizomides, were identified through extensive spectroscopic niae (17), Agrobacterium tumefaciens (18), Pantoea ananatis characterization. This recombinase expression strategy offers utility (19), and naturally transformable Burkholderia species (20, 21). within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities. Significance recombinases | genome mining | Burkholderiales | lipopeptide | natural product Natural products biosynthesized by cryptic gene clusters rep- resent a largely untapped source for drug discovery. However, mining of these products by promoter engineering is restricted acteria represent an important source of medicines and by the lack of streamlined genetic tools, especially in nonmodel pesticides (1, 2). Current genome sequencing projects have B biosynthetic gene cluster (BGC)-rich bacteria. Here, we describe revealed a large number of biosynthetic gene clusters (BGCs), the discovery of a pair of bacteriophage recombinases and but their natural products have not yet been identified (3–5). The application of recombinase-assisted promoter engineering to enzymes encoded by these unexploited biosynthetic genes may rapidly identify and activate several cryptic biosynthetic gene synthesize metabolites that could serve as a reservoir of novel clusters in two Burkholderiales strains that currently lack ef- scaffolds for drug screening (6). Two major genome mining fective genetic tools. Construction of an efficient genome en- strategies, featuring homologous and heterologous expression, gineering platform in a natural product producer expedites were employed to mine cryptic BGCs (7). Homologous expres- mining of cryptic BGCs in their native backgrounds, and host sion in the native producers ensures proper substrates, precur- melioration for yield or structure optimization. This strategy MICROBIOLOGY sors, cofactors, and accessory factors for biosynthesis, which enables potentially scalable discovery of novel metabolites could maximize generation of cryptic BGC biosynthesis prod- with intriguing bioactivities from many other bacteria. ucts. However, this strategy requires efficient genetic manipu- lation tools in the producers to meet the demand of high- Author contributions: X.B. and Y.Z. designed research; X.W., H.Z., H.C., X.J., W.Z., T.S., and throughput genome mining in the postgenomic era. Recently, J.L. performed research; R.L. and J.F. contributed new reagents/analytic tools; X.W., H.Z., H.C., L.H., Y.-z.L., Y.S., X.D., R.M., X.B., and Y.Z. analyzed data; and X.W., H.Z., H.C., X.B., yeast homologous recombination and CRISPR-Cas9 strategies and Y.Z. wrote the paper. were harnessed to activate silent BGCs by promoter engineering The authors declare no conflict of interest. CHEMISTRY in metagenomic DNA and natural product proficient strepto- This article is a PNAS Direct Submission. mycetes, respectively (8, 9). However, in other natural product This open access article is distributed under Creative Commons Attribution-NonCommercial- producers, such as bacilli, Burkholderiales, myxobacteria, and NoDerivatives License 4.0 (CC BY-NC-ND). cyanobacteria, scalable and efficient genome manipulation is still 1X.W., H.Z., and H.C. contributed equally to this work. a frustrating challenge. 2To whom correspondence may be addressed. Email: [email protected] or Red/ET recombineering is an in vivo homologous recombination- [email protected]. based genetic engineering method employed primarily in Escherichia This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. coli by using short homology arms (∼50 bp) based on the expression of 1073/pnas.1720941115/-/DCSupplemental. either Redα/Redβ from the Red operon of λ phage or the analogous Published online April 16, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1720941115 PNAS | vol. 115 | no. 18 | E4255–E4263 Downloaded by guest on October 2, 2021 However, it is not functional in other Burkholderiales strains (20, recombinases were also applied to other Burkholderiales strains 21). In more distant species, host-specific Redαβ or RecET ho- that currently lack effective genetic tools and native Redαβ homo- molog systems are mandatory (22–29). logs, which resulted in the successful identification of two cryptic The order Burkholderiales belongs to β-Proteobacteria and NRPS BGCs. Two of five identified BGCs were silent (i.e., products includes several pathogenic bacteria and several environmental not detectable by liquid chromatography-mass spectrometry (LC- species. A number of Burkholderiales genomes contain plentiful MS) analysis in their native hosts under the given conditions). In putative natural product BGCs (4, 5, 30, 31). The proportion of addition, two classes of lipopeptides, glidopeptins and rhizomides, polyketide synthases (PKSs) and nonribosomal peptide synthe- were identified from DSM 7029 and Paraburkholderia rhizoxinica tases (NRPSs) in Burkholderia genomes is second only to that of HKI 454 (36), respectively. actinobacteria and is higher than that of bacilli, cyanobacteria, and myxobacteria (32). Burkholderia species also exhibit great Results biosynthetic potential for production of siderophores and lip- Host-Specific Phage-Derived Recombinase Pairs in Burkholderiales. It opeptides (31). Thus, Burkholderiales species have emerged as a had been shown that the Redαβ or RecET recombinases from new source of natural products with a plethora of BGCs still E. coli could not be applied to nonnaturally transformable Bur- cryptic or silent (31–34). To access these BGCs, it is urgent to kholderia strains (21). This study also confirmed that Redαβ was invent Burkholderiales specific homologous expression systems, not functional in the Burkholderiales strain DSM 7029 (Fig. 2). particularly, novel Red/ET recombinases from Burkholderiales BlastP analysis using the amino acid sequences from E. coli Redαβ strains for efficient genome engineering. or RecET as queries revealed 7 Redαβ-like and 10 RecET-like This study invented a workflow for the discovery of novel recombinase pairs in ∼1,000 Burkholderiales strains (most of which recombinases and the associated transient expression system to belong to Burkholderia and Paraburkholderia genera) (SI Appendix, facilitate in situ promoter insertion for cryptic BGC mining (Fig.
Load more

Recommended publications
  • Multilayered Horizontal Operon Transfers from Bacteria Reconstruct a Thiamine Salvage Pathway in Yeasts
    Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts Carla Gonçalvesa and Paula Gonçalvesa,1 aApplied Molecular Biosciences Unit-UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved September 22, 2019 (received for review June 14, 2019) Horizontal acquisition of bacterial genes is presently recognized as nisms presumed to have facilitated a transition from bacterial an important contribution to the adaptation and evolution of operon transcription to eukaryotic-style gene expression were eukaryotic genomes. However, the mechanisms underlying ex- proposed, such as gene fusion giving rise to multifunctional pro- pression and consequent selection and fixation of the prokaryotic teins (6, 23, 24), increase in intergenic distances between genes to genes in the new eukaryotic setting are largely unknown. Here we generate room for eukaryotic promoters, and independent tran- show that genes composing the pathway for the synthesis of the scription producing mRNAs with poly(A) tails have been dem- essential vitamin B1 (thiamine) were lost in an ancestor of a yeast onstrated (22). In the best documented study, which concerns a lineage, the Wickerhamiella/Starmerella (W/S) clade, known to bacterial siderophore biosynthesis operon acquired by yeasts be- harbor an unusually large number of genes of alien origin. The longing to the Wickerhamiella/Starmerella (W/S) clade, the bacte- thiamine pathway was subsequently reassembled, at least twice, rial genes acquired as an operon were shown to be functional (22). by multiple HGT events from different bacterial donors involving Thiamine, commonly known as vitamin B1, is essential for all both single genes and entire operons.
    [Show full text]
  • The Burkholderia Genus: Between Mutualism and Pathogenicity
    The Burkholderia genus: between mutualism and pathogenicity El género Burkholderia: entre el mutualismo y la patogenicidad David Espinosa-Victoria*, Laboratorio Interacción Molecular Planta-Microorganismo, 1Programa de Edafo- logía Colegio de Postgraduados, Carretera México-Texcoco Km 36.5, Montecillo Estado de México, México, 56230; Lucía López-Reyes, Moisés Graciano Carcaño-Montiel, Laboratorio Microbiología de Suelos, Bene- mérita Universidad Autónoma de Puebla, Avenida San Claudio s/n, Ciudad Universitaria, La Hacienda, Puebla, Puebla, 72592; 1María Serret-López. *Autor para correspondencia: [email protected] Recibido: 28 de Abril, 2020. Aceptado: 04 de Junio, 2020. Espinosa-Victoria D, López-Reyes L, Carcaño-Montiel Abstract. Burkholderia is an ambivalent genus MG and Serret-López M. 2020. The Burkholderia ge- because some of its species establish symbiotic- nus: between mutualism and pathogenicity. Mexican Jo- mutualistic relationships with plants, and urnal of Phytopathology 38(3): 337-359. symbiotic-pathogenic relationships with plants, DOI: 10.18781/R.MEX.FIT.2004-5 animals, and humans. Since the phytopathogenic bacterium B. cepacia was reported as a nosocomial Primera publicación DOI: 17 de Junio, 2020. opportunist, associated with cystic fibrosis, the First DOI publication: June 17, 2020. concern about possible infections in humans arose. The objective of this contribution was to make an analysis of Burkholderia’s functional versatility Resumen. Burkholderia es un género ambivalen- and its effect on human health. Burkholderia te debido a que algunas de sus especies establecen harbored about 100 species and the B. cepacia relaciones simbiótico-mutualistas con las plantas, y complex (BCC) consisting of 22 species. At the simbiótico-patogénicas con plantas, animales y hu- beginning, the existence of two lineages within manos.
    [Show full text]
  • Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
    The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified;
    [Show full text]
  • Burkholderia Cenocepacia Integrates Cis-2-Dodecenoic Acid and Cyclic Dimeric Guanosine Monophosphate Signals to Control Virulence
    Burkholderia cenocepacia integrates cis-2-dodecenoic acid and cyclic dimeric guanosine monophosphate signals to control virulence Chunxi Yanga,b,c,d,1, Chaoyu Cuia,b,c,1, Qiumian Yea,b, Jinhong Kane, Shuna Fua,b, Shihao Songa,b, Yutong Huanga,b, Fei Hec, Lian-Hui Zhanga,c, Yantao Jiaf, Yong-Gui Gaod, Caroline S. Harwoodb,g,2, and Yinyue Denga,b,c,2 aState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; bGuangdong Innovative Research Team of Sociomicrobiology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; cIntegrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; dSchool of Biological Sciences, Nanyang Technological University, Singapore 637551; eCenter for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; fState Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and gDepartment of Microbiology, University of Washington, Seattle, WA 98195 Contributed by Caroline S. Harwood, October 30, 2017 (sent for review June 1, 2017; reviewed by Maxwell J. Dow and Tim Tolker-Nielsen) Quorum sensing (QS) signals are used by bacteria to regulate N-octanoyl homoserine lactone (C8-HSL). The two QS systems biological functions in response to cell population densities. Cyclic have both distinct and overlapping effects on gene expression diguanosine monophosphate (c-di-GMP) regulates cell functions in (16, 17). response to diverse environmental chemical and physical signals One of the ways in which QS systems can act is by controlling that bacteria perceive. In Burkholderia cenocepacia, the QS signal levels of intracellular cyclic diguanosine monophosphate (c-di-GMP) receptor RpfR degrades intracellular c-di-GMP when it senses the in bacteria (18–21).
    [Show full text]
  • Microbial Community Response to Heavy and Light Crude Oil in the Great Lakes
    Microbial Community Response to Heavy and Light Crude Oil in the Great Lakes Stephen Techtmann 10/24/19 Microbial Sensors Techtmann Lab @ MTU Investigating the applications of environmental microbial communities Hydraulic Fracturing Related Antibiotic Resistance Oil Bioremediation Techtmann Lab @ MTU Overview • Background on oil biodegradation • Microbial response to light and heavy crude oil in the Great Lakes • Machine learning for prediction of contamination in the Great Lakes. Oil Spills Deepwater Horizon Enbridge Line 6B Deepwater Horizon Oil Spill • 4,1000,000 bbl of oil released • Light Sweet Crude oil released • April 20, 2010 • 1101.7 miles of shoreline oiled Atlas and Hazen 2011 Enbridge Line 6B Spill – Marshall MI • 20,082 bbl of oil released • Diluted Bitumen • July 26, 2010 • 70 miles of shoreline oiled https://www.mlive.com/news/kalamazoo/2010/07/state_of_emergency_declared_as.html Oil Transmissions Pipelines in the Great Lakes Region Line 5: • 645 miles from Superior WI to Sarnia Ontario • 540,000 barrels per day • Light crude and natural gas liquids (NGLs) Crude oil Oil types and API Gravity Microbes and Biotechnology (Bioremediation) Low cost input Microbe High value output Decreased Cost Contaminant Increased Efficiency Carbon dioxide or non- toxic daughter products Carbon dioxide Microbial Biomass Petroleum Microbe Daughter Products Water Microbial Ecology and Biotechnology Low cost input Microbe High value output Decreased Cost/Increased Efficiency Complex input Input A Microbe Microbe Output A Input B Microbe Output
    [Show full text]
  • Burkholderia Cenocepacia Intracellular Activation of the Pyrin
    Activation of the Pyrin Inflammasome by Intracellular Burkholderia cenocepacia Mikhail A. Gavrilin, Dalia H. A. Abdelaziz, Mahmoud Mostafa, Basant A. Abdulrahman, Jaykumar Grandhi, This information is current as Anwari Akhter, Arwa Abu Khweek, Daniel F. Aubert, of September 29, 2021. Miguel A. Valvano, Mark D. Wewers and Amal O. Amer J Immunol 2012; 188:3469-3477; Prepublished online 24 February 2012; doi: 10.4049/jimmunol.1102272 Downloaded from http://www.jimmunol.org/content/188/7/3469 Supplementary http://www.jimmunol.org/content/suppl/2012/02/24/jimmunol.110227 Material 2.DC1 http://www.jimmunol.org/ References This article cites 71 articles, 17 of which you can access for free at: http://www.jimmunol.org/content/188/7/3469.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 29, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2012 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Activation of the Pyrin Inflammasome by Intracellular Burkholderia cenocepacia Mikhail A.
    [Show full text]
  • Genomic Plasticity of the Causative Agent of Melioidosis, Burkholderia Pseudomallei
    Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei Matthew T. G. Holdena, Richard W. Titballb,c, Sharon J. Peacockd,e, Ana M. Cerden˜ o-Ta´ rragaa, Timothy Atkinsb, Lisa C. Crossmana, Tyrone Pittf, Carol Churchera, Karen Mungalla, Stephen D. Bentleya, Mohammed Sebaihiaa, Nicholas R. Thomsona, Nathalie Basona, Ifor R. Beachamg, Karen Brooksa, Katherine A. Brownh, Nat F. Browng, Greg L. Challisi, Inna Cherevacha, Tracy Chillingwortha, Ann Cronina, Ben Crossetth, Paul Davisa, David DeShazerj, Theresa Feltwella, Audrey Frasera, Zahra Hancea, Heidi Hausera, Simon Holroyda, Kay Jagelsa, Karen E. Keithh, Mark Maddisona, Sharon Moulea, Claire Pricea, Michael A. Quaila, Ester Rabbinowitscha, Kim Rutherforda, Mandy Sandersa, Mark Simmondsa, Sirirurg Songsivilaik, Kim Stevensa, Sarinna Tumapae, Monkgol Vesaratchaveste, Sally Whiteheada, Corin Yeatsa, Bart G. Barrella, Petra C. F. Oystonb, and Julian Parkhilla,l aWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; bDefence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom; cDepartment of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom; dNuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, United Kingdom; eFaculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; fLaboratory of Hospital Infection, Division of Nosocomial Infection Prevention and Control, Central Public Health Laboratory, London NW9 5HT, United Kingdom; gSchool of Health Science, Griffith University, Gold Coast, Queensland 9726, Australia; hDepartment of Biological Sciences, Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College, London SW7 2AZ, United Kingdom; iDepartment of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom; jU.S.
    [Show full text]
  • Rational Construction of Genome-Reduced Burkholderiales Chassis Facilitates Efficient Heterologous Production of Natural Products from Proteobacteria
    ARTICLE https://doi.org/10.1038/s41467-021-24645-0 OPEN Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria Jiaqi Liu1, Haibo Zhou1, Zhiyu Yang1, Xue Wang1, Hanna Chen1, Lin Zhong1, Wentao Zheng1, Weijing Niu1, Sen Wang2, Xiangmei Ren2, Guannan Zhong1, Yan Wang3, Xiaoming Ding4, Rolf Müller 5, Youming Zhang1 & ✉ Xiaoying Bian 1 1234567890():,; Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for het- erologous BGC expression, but its cells undergo early autolysis, hindering further applica- tions. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chit- inimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression. 1 Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China. 2 Core Facilities for Life and Environmental Sciences, Shandong University, Qingdao, Shandong, China. 3 College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
    [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]
  • Lifestyle Preferences Drive the Structure and Diversity of Bacterial and Archaeal Communities in a Small Riverine Reservoir
    www.nature.com/scientificreports OPEN Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir Carles Borrego1,2, Sergi Sabater1,3* & Lorenzo Proia1,4 Spatial heterogeneity along river networks is interrupted by dams, afecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil diferences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Diferences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir. Spatial heterogeneity of river networks results from the sequence of lotic segments—which promote the transport and quick transformation of materials—and lentic segments such as large pools and wetlands—which mostly contribute to the process and storage of organic matter 1,2.
    [Show full text]
  • Characterization of the Burkholderia Cenocepacia J2315 Surface-Exposed Immunoproteome
    Article Characterization of the Burkholderia cenocepacia J2315 Surface-Exposed Immunoproteome 1, 1, 1, Sílvia A. Sousa * , António M.M. Seixas y , Manoj Mandal y, Manuel J. Rodríguez-Ortega 2 and Jorge H. Leitão 1,* 1 iBB–Institute for Bioengineering and Biosciences, 1049-001 Lisbon, Portugal; [email protected] (A.M.M.S.); [email protected] (M.M.) 2 Departament of Biochemistry and Molecular Biology, Córdoba University, 14071 Córdoba, Spain; [email protected] * Correspondence: [email protected] (S.A.S.); [email protected] (J.H.L.); Tel.: +351-2184-19986 (S.A.S.); +351-2184-17688 (J.H.L.) Both authors contributed equally to the work. y Received: 31 July 2020; Accepted: 3 September 2020; Published: 6 September 2020 Abstract: Infections by the Burkholderia cepacia complex (Bcc) remain seriously life threatening to cystic fibrosis (CF) patients, and no effective eradication is available. A vaccine to protect patients against Bcc infections is a highly attractive therapeutic option, but none is available. A strategy combining the bioinformatics identification of putative surface-exposed proteins with an experimental approach encompassing the “shaving” of surface-exposed proteins with trypsin followed by peptide identification by liquid chromatography and mass spectrometry is here reported. The methodology allowed the bioinformatics identification of 263 potentially surface-exposed proteins, 16 of them also experimentally identified by the “shaving” approach. Of the proteins identified, 143 have a high probability of containing B-cell epitopes that are surface-exposed. The immunogenicity of three of these proteins was demonstrated using serum samples from Bcc-infected CF patients and Western blotting, validating the usefulness of this methodology in identifying potentially immunogenic surface-exposed proteins that might be used for the development of Bcc-protective vaccines.
    [Show full text]
  • The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia Sp
    fmicb-11-00581 April 19, 2020 Time: 8:50 # 1 ORIGINAL RESEARCH published: 21 April 2020 doi: 10.3389/fmicb.2020.00581 The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato Johannes B. Herpell1, Florian Schindler1, Mersad Bejtovic´ 1, Lena Fragner1,2, Bocar Diallo1, Anke Bellaire3, Susanne Kublik4, Bärbel U. Foesel4, Silvia Gschwendtner4, Melina Kerou5, Michael Schloter4 and Wolfram Weckwerth1,2* 1 Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria, 2 Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria, 3 Division of Structural and Functional Botany, Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria, 4 Research Unit Edited by: for Comparative Microbiome Analysis, German Research Center for Environmental Health, Helmholtz Zentrum München, 5 Michele Perazzolli, Neuherberg, Germany, Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Trento, Italy University of Vienna, Vienna, Austria Reviewed by: Stéphane Compant, The genus Paraburkholderia includes a variety of species with promising features for Austrian Institute of Technology (AIT), sustainable biotechnological solutions in agriculture through increasing crop productivity. Austria Lionel Moulin, Here, we present a novel Paraburkholderia isolate, a permanent and predominant Institut de Recherche Pour le member of the Dioscoreae bulbifera (yam family, Dioscoreaceae)
    [Show full text]