View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Plymouth Electronic Archive and Research Library Standards in Genomic Sciences Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria --Manuscript Draft-- Manuscript Number: SIGS-D-16-00109R3 Full Title: Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria Article Type: Short genome report Funding Information: U.S. Department of Energy Dr Nikos C Kyrpides (DE-AC02-05CH11231) Royal Society Dr Rich Boden (RG120444) Abstract: Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur- oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur- oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the Proteobacteria that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans. Corresponding Author: Rich Boden, Ph.D B.Sc University of Plymouth Plymouth, Devon UNITED KINGDOM Corresponding Author Secondary Information: Corresponding Author's Institution: University of Plymouth Corresponding Author's Secondary Institution: First Author: Lee P Hutt First Author Secondary Information: Order of Authors: Lee P Hutt Marcel Huntemann Alicia Clum Manoj Pillay Krishnaveni Palaniappan Neha Varghese Natalia Mikhailova Dimitrios Stamatis Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Tatiparthi Reddy Chris Daum Nicole Shapiro Natalia Ivanova Nikos C Kyrpides Tanja Woyke Rich Boden, Ph.D B.Sc Order of Authors Secondary Information: Response to Reviewers: In response to request to add 2 percentages to one of the tables (which could have been added in proof tbh), they are done. Hopefully this is now final. Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Manuscript Click here to download Manuscript R4.docx Click here to view linked References 1 2 3 4 5 6 7 8 9 10 11 1 12 Permanent draft genome of Thiobacillus thioparus 13 14 T 15 2 DSM 505 , an obligately chemolithoautotrophic 16 17 18 3 member of the Betaproteobacteria 19 20 21 22 4 Lee P. Hutt1,2, Marcel Huntemann3, Alicia Clum3, Manoj Pillay3, Krishnaveni 23 24 5 Palaniappan3, Neha Varghese3, Natalia Mikhailova3, Dimitrios Stamatis3, 25 26 3 3 3 3 27 6 Tatiparthi Reddy , Chris Daum , Nicole Shapiro , Natalia Ivanova , Nikos 28 3 3 1,2 29 7 Kyrpides , Tanja Woyke , Rich Boden * 30 31 8 32 33 9 [1] School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, 34 35 10 UK. 36 37 11 [2] Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK. 38 39 40 12 [3] DOE Joint Genome Institute, Walnut Creek, CA 94598, USA. 41 42 13 * Corresponding author ([email protected]) 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 1 2 3 4 5 6 7 8 9 10 11 14 Abstract 12 13 15 Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur-oxidising 14 15 16 Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is 16 17 Culture CT (=DSM 505T = ATCC 8158T) isolated by Starkey in 1934 from agricultural soil at Rutgers 17 18 18 University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the 19 20 19 oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix 21 22 20 carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 23 21 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 24 25 22 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin- 26 27 23 Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith’s 28 24 biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. 29 30 25 cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox 31 32 26 operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but 33 27 lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other 34 35 28 members of the ‘Proteobacteria’ that can use trithionate as an energy source. In spite of apparently not 36 37 29 growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of 38 30 denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. 39 40 31 denitrificans. 41 42 32 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 1 2 3 4 5 6 7 8 9 10 11 33 Keywords: 12 13 34 Thiobacillus thioparus, Betaproteobacteria, sulfur oxidation, 14 15 35 chemolithoautotroph, carboxysome, denitrification 16 17 18 19 36 Abbreviations 20 21 37 ATCC – American Type Culture Collection 22 23 24 38 BLAST – Basic Linear Alignment Search Tool 25 26 39 CIP – Collection de L’institut Pasteur 27 28 29 40 COG – Clusters of Orthologous Groups 30 31 32 41 DSMZ - Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH 33 34 42 GEBA – Genomic Encyclopedia of Bacteria and Archaea. 35 36 37 43 IMG – Integrated Microbial Genomes database. 38 39 40 44 JCM – Japan Collection of Microorganisms 41 42 45 JGI – Joint Genome Institute 43 44 45 46 KMG – 1,000 Microbial Genomes project 46 47 47 NBRC – NITE Biological Resource Center 48 49 50 48 NCBI – National Center for Biotechnology Information 51 52 53 49 RuBisCO - ribulose-1,5-bisphosphate carboxylase/oxygenase 54 55 56 57 58 59 60 61 62 63 64 65 1 2 3 4 5 6 7 8 9 10 11 50 Introduction 12 13 51 In 1902, Thiobacillus thioparus was one of the first two obligately chemolithoautrophic sulfur-oxidizing 14 15 52 Bacteria to be isolated, (along with what is now Halothiobacillus neapolitanus), and was named in 1904 16 53 [1, 2]. The original isolates were lost, but Thiobacillus thioparus is now the type species of the genus (a 17 18 54 member of the Betaproteobacteria) and the type strain is an isolate from Starkey (1934) (= Culture CT = 19 20 55 DSM 505T = ATCC 8158T = CIP 104484T = JCM 3859T = NBRC 103402T) [3, 4]. Originally, the 21 22 56 characteristic of utilizing inorganic sulfur compounds as an energy source was thought to be a taxonomic 23 57 trait unique to Thiobacillus and at its height the genus contained in at least 32 different ‘species’ [4]. With 24 25 58 phylogenetic methods however, many of these strains have since been reassigned to different, often new 26 T 27 59 genera with T. thioparus DSM 505 being one of four species with validly published names left in the 28 60 genus. Compared to other inorganic sulfur-oxidisers, surprisingly little research has been conducted on T. 29 30 61 thioparus DSM 505T in terms of physiology and biochemistry or genetics, possibly due to the low growth 31 32 62 yields of this species when compared to T. denitrificans and T. aquaesulis [5, 6] making it more 33 63 challenging to study. It may, however, give extended and contrasted insights into autotrophic sulfur- 34 35 64 oxidation in the Bacteria. It was selected for genome sequencing as part of the Department of Energy 36 37 65 DOE-CSP 2012 initiative – as type species of a genus. 38 39 40 66 Organism Information 41 42 67 Classification and features 43 44 68 Thiobacillus thioparus DSM 505T was isolated from sandy loam soil from the New Jersey Agricultural 45 46 69 Experimental Station planted with unspecified vegetable crops using 20mM thiosulfate as sole energy 47 48 70 source in basal medium at pH 8.5 by Starkey (1934) [3] and is currently one of four species with validly 49 71 published names within the genus. It forms small white colonies of 1-3 mm diameter after 2-3 days that 50 51 72 turn pink or brown with age and which become coated with yellow-ish elementary sulfur.