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BMC Genomics Biomed Central
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central BMC Genomics BioMed Central Research article Open Access A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement Adriana Ravagnani†, Christopher L Finan† and Michael Young* Address: Institute of Biological Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3DD, UK Email: Adriana Ravagnani - [email protected]; Christopher L Finan - [email protected]; Michael Young* - [email protected] * Corresponding author †Equal contributors Published: 17 March 2005 Received: 21 September 2004 Accepted: 17 March 2005 BMC Genomics 2005, 6:39 doi:10.1186/1471-2164-6-39 This article is available from: http://www.biomedcentral.com/1471-2164/6/39 © 2005 Ravagnani et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine resuscitation-promoting factor (Rpf) is the founder member of a family of proteins found throughout and confined to the actinobacteria (high G + C Gram-positive bacteria). The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria) and obtain information about how they may control bacterial growth and resuscitation. Results: In silico analysis of the accessory domains of the Rpf proteins permitted their classification into several subfamilies. -
Enzymes from Deep-Sea Microorganisms - Takami, Hideto
EXTREMOPHILES – Vol. III - Enzymes from Deep-Sea Microorganisms - Takami, Hideto ENZYMES FROM DEEP-SEA MICROORGANISMS Takami, Hideto Microbial Genome Research Group, Japan Marine Science and Technology Center, 2- 15 Natsushima, Yokosuka, 237-0061 Japan Keywords: Mariana Trench, Challenger Deep, Deep-sea environments, Microbial flora, Bacteria, Actinomycetes, Yeast, Fungi, Extremophiles, Halophiles, 16S rDNA, Phylogenetic tree, Psychrophiles, Thermophiles, Alkaliphiles, Amylase, α- maltotetraohydrase (G4-amylase), Protease, Pseudomonas strain MS300, Hydrostatic pressure, Shinkai 2000, Shinkai 6500, Kaiko Contents 1. Introduction 2. Collection of Deep-sea Mud 3. Isolation of Microorganisms from Deep-sea Mud 3.1. Bacteria From The Mariana Trench 3.2. Bacteria From Other Deep-Sea Sites Located Off Southern Japan 4. 16S rDNA Sequences of Deep-sea Isolates 5. Exploring Unique Enzyme Producers Among Deep-sea Isolates 5.1. Screening for Amylase Producers 5.2. Purification of Amylase Produced By Pseudomonas Strain MS300 5.3. Enzyme Profiles Acknowledgments Glossary Bibliography Biographical Sketch Summary In an attempt to characterize the microbial flora on the deep-sea floor, we isolated thousands of microbes from samples collected at various deep-sea (1 050–10 897 m) sites located in the Mariana Trench and off southern Japan. Various types of bacteria, such as alkaliphiles, thermophiles, psychrophiles, and halophiles were recovered on agar platesUNESCO at atmospheric pressure at a –frequency EOLSS of 0.8 x 102–2.3 x 104/g of dry sea mud. No acidophiles were recovered. Similarly, non extremophilic bacteria were recovered at a frequency of 8.1 x 102–2.3 x 105. These deep-sea isolates were widely distributed and detectedSAMPLE at each deep-sea site , andCHAPTERS the frequency of isolation of microbes from the deep-sea mud was not directly influenced by the depth of the sampling site. -
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment. -
Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas Sp
microorganisms Article Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1 Dong Liang 1,† , Changyixin Xiao 1,† , Fuping Song 2, Haitao Li 1 , Rongmei Liu 1,* and Jiguo Gao 1,* 1 College of Life Science, Northeast Agricultural University, Harbin 150038, China; [email protected] (D.L.); [email protected] (C.X.); [email protected] (H.L.) 2 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] * Correspondence: [email protected] (R.L.); [email protected] (J.G.); Tel.: +86-133-5999-0992 (J.G.) † These authors contributed equally to this work. Abstract: The genus Pseudomonas is widely recognized for its potential for environmental reme- diation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmen- tal stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrad- ing various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency Citation: Liang, D.; Xiao, C.; Song, F.; liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger Li, H.; Liu, R.; Gao, J. -
Patterns of Horizontal Gene Transfer Into the Geobacillus Clade
Imperial College London London Institute of Medical Sciences Patterns of Horizontal Gene Transfer into the Geobacillus Clade Alexander Dmitriyevich Esin September 2018 Submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy of Imperial College London For my grandmother, Marina. Without you I would have never been on this path. Your unwavering strength, love, and fierce intellect inspired me from childhood and your memory will always be with me. 2 Declaration I declare that the work presented in this submission has been undertaken by me, including all analyses performed. To the best of my knowledge it contains no material previously published or presented by others, nor material which has been accepted for any other degree of any university or other institute of higher learning, except where due acknowledgement is made in the text. 3 The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work. 4 Abstract Horizontal gene transfer (HGT) is the major driver behind rapid bacterial adaptation to a host of diverse environments and conditions. Successful HGT is dependent on overcoming a number of barriers on transfer to a new host, one of which is adhering to the adaptive architecture of the recipient genome. -
Isolation and Diversity of Sediment Bacteria in The
bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Isolation and Diversity of Sediment Bacteria in the 2 Hypersaline Aiding Lake, China 3 4 Tong-Wei Guan, Yi-Jin Lin, Meng-Ying Ou, Ke-Bao Chen 5 6 7 Institute of Microbiology, Xihua University, Chengdu 610039, P. R. China. 8 9 Author for correspondence: 10 Tong-Wei Guan 11 Tel/Fax: +86 028 87720552 12 E-mail: [email protected] 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 29 Abstract A total of 343 bacteria from sediment samples of Aiding Lake, China, were isolated using 30 nine different media with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria recovered 31 from the different media significantly varied, indicating the need to optimize the isolation conditions. 32 The results showed an unexpected level of bacterial diversity, with four phyla (Firmicutes, 33 Actinobacteria, Proteobacteria, and Rhodothermaeota), fourteen orders (Actinopolysporales, 34 Alteromonadales, Bacillales, Balneolales, Chromatiales, Glycomycetales, Jiangellales, Micrococcales, 35 Micromonosporales, Oceanospirillales, Pseudonocardiales, Rhizobiales, Streptomycetales, and 36 Streptosporangiales), including 17 families, 41 genera, and 71 species. -
Nicotinamidase from Oceanobacillus Iheyensis HTE831
Biochemical and Mutational Analysis of a Novel Nicotinamidase from Oceanobacillus iheyensis HTE831 Guiomar Sa´nchez-Carro´ n1, Marı´a Inmaculada Garcı´a-Garcı´a1,2, Rube´n Zapata-Pe´rez1, Hideto Takami3, Francisco Garcı´a-Carmona1,2,A´ lvaro Sa´nchez-Ferrer1,2* 1 Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence ‘‘Campus Mare Nostrum’’, University of Murcia, Campus Espinardo, Murcia, Spain, 2 Murcia Biomedical Research Institute (IMIB), Murcia, Spain, 3 Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan Abstract Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia, an important reaction in the NAD+ salvage pathway. This paper reports a new nicotinamidase from the deep-sea extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831 (OiNIC). The enzyme was active towards nicotinamide and several analogues, including the 21 21 prodrug pyrazinamide. The enzyme was more nicotinamidase (kcat/Km = 43.5 mM s ) than pyrazinamidase (kcat/ 21 21 Km = 3.2 mM s ). Mutational analysis was carried out on seven critical amino acids, confirming for the first time the importance of Cys133 and Phe68 residues for increasing pyrazinamidase activity 2.9- and 2.5-fold, respectively. In addition, the change in the fourth residue involved in the ion metal binding (Glu65) was detrimental to pyrazinamidase activity, decreasing it 6-fold. This residue was also involved in a new distinct structural motif DAHXXXDXXHPE described in this paper for Firmicutes nicotinamidases. Phylogenetic analysis revealed that OiNIC is the first nicotinamidase described for the order Bacillales. -
Reorganising the Order Bacillales Through Phylogenomics
Systematic and Applied Microbiology 42 (2019) 178–189 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Reorganising the order Bacillales through phylogenomics a,∗ b c Pieter De Maayer , Habibu Aliyu , Don A. Cowan a School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, South Africa b Technical Biology, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Germany c Centre for Microbial Ecology and Genomics, University of Pretoria, South Africa a r t i c l e i n f o a b s t r a c t Article history: Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant Received 7 August 2018 on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, Received in revised form these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in 21 September 2018 the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. Accepted 18 October 2018 However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome- Keywords: based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A Bacillales Lactobacillales suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of Bacillaceae eight families (and six family incertae sedis taxa) within the order Bacillales. -
The Life-Cycle of Operons
The Life-Cycle of Operons Morgan N. Price1,2, Adam P. Arkin1,2,3,4, Eric J. Alm1,2¤* 1 Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 2 Virtual Institute for Microbial Stress and Survival, University of California San Francisco, San Francisco, California, United States of America, 3 Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America, 4 Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America Operons are a major feature of all prokaryotic genomes, but how and why operon structures vary is not well understood. To elucidate the life-cycle of operons, we compared gene order between Escherichia coli K12 and its relatives and identified the recently formed and destroyed operons in E. coli. This allowed us to determine how operons form, how they become closely spaced, and how they die. Our findings suggest that operon evolution may be driven by selection on gene expression patterns. First, both operon creation and operon destruction lead to large changes in gene expression patterns. For example, the removal of lysA and ruvA from ancestral operons that contained essential genes allowed their expression to respond to lysine levels and DNA damage, respectively. Second, some operons have undergone accelerated evolution, with multiple new genes being added during a brief period. Third, although genes within operons are usually closely spaced because of a neutral bias toward deletion and because of selection against large overlaps, genes in highly expressed operons tend to be widely spaced because of regulatory fine-tuning by intervening sequences. -
Phylogenetic Identification of Marine Bacteria Isolated from Deep-Sea
da Silva et al. SpringerPlus 2013, 2:127 http://www.springerplus.com/content/2/1/127 a SpringerOpen Journal RESEARCH Open Access Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern South Atlantic Ocean Marcus Adonai Castro da Silva1*, Angélica Cavalett1, Ananda Spinner1, Daniele Cristina Rosa1, Regina Beltrame Jasper1, Maria Carolina Quecine3, Maria Letícia Bonatelli3, Aline Pizzirani-Kleiner3, Gertrudes Corção2 and André Oliveira de Souza Lima1 Abstract The deep-sea environments of the South Atlantic Ocean are less studied in comparison to the North Atlantic and Pacific Oceans. With the aim of identifying the deep-sea bacteria in this less known ocean, 70 strains were isolated from eight sediment samples (depth range between 1905 to 5560 m) collected in the eastern part of the South Atlantic, from the equatorial region to the Cape Abyssal Plain, using three different culture media. The strains were classified into three phylogenetic groups, Gammaproteobacteria, Firmicutes and Actinobacteria, by the analysis of 16s rRNA gene sequences. Gammaproteobacteria and Firmicutes were the most frequently identified groups, with Halomonas the most frequent genus among the strains. Microorganisms belonging to Firmicutes were the only ones observed in all samples. Sixteen of the 41 identified operational taxonomic units probably represent new species. The presence of potentially new species reinforces the need for new studies in the deep-sea environments of the South Atlantic. Keywords: Deep-sea sediments, South Atlantic Ocean, Phylogenetic identification, Cultivable bacteria, Halomonas Background despite the great diversity that these environments may Deep-sea environments are the largest continuous ecosys- harbor (Smith et al. -
Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus Jeddahense Sp
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/301533830 Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov Article in Omics: a journal of integrative biology · April 2016 Impact Factor: 2.36 · DOI: 10.1089/omi.2016.0004 READS 45 12 authors, including: Fehmeeda Imran Olivier Croce King Abdulaziz University French National Centre for Scientific Research 34 PUBLICATIONS 135 CITATIONS 62 PUBLICATIONS 190 CITATIONS SEE PROFILE SEE PROFILE Asif Jiman-Fatani Catherine Robert King Abdulaziz University Aix-Marseille Université 34 PUBLICATIONS 75 CITATIONS 273 PUBLICATIONS 21,597 CITATIONS SEE PROFILE SEE PROFILE All in-text references underlined in blue are linked to publications on ResearchGate, Available from: Jean-Christophe Lagier letting you access and read them immediately. Retrieved on: 02 May 2016 OMICS A Journal of Integrative Biology Volume 20, Number 4, 2016 ª Mary Ann Liebert, Inc. DOI: 10.1089/omi.2016.0004 Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov. Saber Khelaifia,1* Jean-Christophe Lagier,1* Fehmida Bibi,2* Esam Ibraheem Azhar,2,3 Olivier Croce,1 Roshan Padmanabhan,1 Asif Ahmad Jiman-Fatani,4 Muhammad Yasir,2 Catherine Robert,1 Claudia Andrieu,1 Pierre-Edouard Fournier,1 and Didier Raoult1,2 Abstract Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono- genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T,(= CSUR P1091 = DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. -
Metagenomics and Metatranscriptomics of Lake Erie Ice
METAGENOMICS AND METATRANSCRIPTOMICS OF LAKE ERIE ICE Opeoluwa F. Iwaloye A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2021 Committee: Scott Rogers, Advisor Paul Morris Vipaporn Phuntumart © 2021 Opeoluwa Iwaloye All Rights Reserved iii ABSTRACT Scott Rogers, Lake Erie is one of the five Laurentian Great Lakes, that includes three basins. The central basin is the largest, with a mean volume of 305 km2, covering an area of 16,138 km2. The ice used for this research was collected from the central basin in the winter of 2010. DNA and RNA were extracted from this ice. cDNA was synthesized from the extracted RNA, followed by the ligation of EcoRI (NotI) adapters onto the ends of the nucleic acids. These were subjected to fractionation, and the resulting nucleic acids were amplified by PCR with EcoRI (NotI) primers. The resulting amplified nucleic acids were subject to PCR amplification using 454 primers, and then were sequenced. The sequences were analyzed using BLAST, and taxonomic affiliations were determined. Information about the taxonomic affiliations, important metabolic capabilities, habitat, and special functions were compiled. With a watershed of 78,000 km2, Lake Erie is used for agricultural, forest, recreational, transportation, and industrial purposes. Among the five great lakes, it has the largest input from human activities, has a long history of eutrophication, and serves as a water source for millions of people. These anthropogenic activities have significant influences on the biological community. Multiple studies have found diverse microbial communities in Lake Erie water and sediments, including large numbers of species from the Verrucomicrobia, Proteobacteria, Bacteroidetes, and Cyanobacteria, as well as a diverse set of eukaryotic taxa.