title: Streptomyces thermoautotrophicus does not fix nitrogen.
abstract: Streptomyces thermoautotrophicus UBT1 has been described as a moderately thermophilic chemolithoautotroph with a novel nitrogenase enzyme that is oxygen-insensitive. We have cultured the UBT1 strain, and have isolated two new strains (H1 and P1-2) of very similar phenotypic and genetic characters. These strains show minimal growth on ammonium-free media, and fail to incorporate isotopically labeled N2 gas into biomass in multiple independent assays. The sdn genes previously published as the putative nitrogenase of S. thermoautotrophicus have little similarity to anything found in draft genome sequences, published here, for strains H1 and UBT1, but share >99% nucleotide identity with genes from Hydrogenibacillus schlegelii, a draft genome for which is also presented here. H. schlegelii similarly lacks nitrogenase genes and is a non-diazotroph. We propose reclassification of the species containing strains UBT1, H1, and P1-2 as a non-Streptomycete, non-diazotrophic, facultative chemolithoautotroph and conclude that the existence of the previously proposed oxygen-tolerant nitrogenase is extremely unlikely.
authors.affiliation: Harvard Medical School, 200 Longwood Ave, Boston MA 02130.|Wyss Institute, 3 Blackfan Cir, Boston MA 02115.
authors.forename: Drew
authors.initials: D
authors.lastname: MacKellar
authors.affiliation: Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina.|Dept. Life Sciences, Imperial College, London, SW7 2AZ, UK.
authors.forename: Lucas
authors.initials: L
authors.lastname: Lieber
authors.affiliation: Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI USA 48824.
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Norman
authors.affiliation: Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
authors.forename: Anthony
authors.initials: A
authors.lastname: Bolger
authors.affiliation: TheLab Inc, 1340 E. 6th Street Suite 603, Los Angeles, CA USA 90021.
authors.forename: Cory
authors.initials: C
authors.lastname: Tobin
authors.affiliation: Dept. Life Sciences, Imperial College, London, SW7 2AZ, UK.
authors.forename: James W
authors.initials: JW
authors.lastname: Murray
authors.affiliation: Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
authors.forename: Mehtap
authors.initials: M
authors.lastname: Oksaksin
authors.affiliation: Harvard Medical School, 200 Longwood Ave, Boston MA 02130.
authors.forename: Roger L
authors.initials: RL
authors.lastname: Chang
authors.affiliation: Harvard Medical School, 200 Longwood Ave, Boston MA 02130.
authors.forename: Tyler J
authors.initials: TJ
authors.lastname: Ford
authors.affiliation: Wyss Institute, 3 Blackfan Cir, Boston MA 02115.
authors.forename: Peter Q
authors.initials: PQ
authors.lastname: Nguyen
authors.affiliation: Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI USA 48824.
authors.forename: Jimmy
authors.initials: J
authors.lastname: Woodward
authors.affiliation: Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina.
authors.forename: Hugo R
authors.initials: HR
authors.lastname: Permingeat
authors.affiliation: Wyss Institute, 3 Blackfan Cir, Boston MA 02115.
authors.forename: Neel S
authors.initials: NS
authors.lastname: Joshi
authors.affiliation: Harvard Medical School, 200 Longwood Ave, Boston MA 02130.|Wyss Institute, 3 Blackfan Cir, Boston MA 02115.
authors.forename: Pamela A
authors.initials: PA
authors.lastname: Silver
authors.affiliation: Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Usadel
authors.affiliation: Dept. Life Sciences, Imperial College, London, SW7 2AZ, UK.
authors.forename: Alfred W
authors.initials: AW
authors.lastname: Rutherford
authors.affiliation: Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI USA 48824.
authors.forename: Maren L
authors.initials: ML
authors.lastname: Friesen
authors.affiliation: Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Prell
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial; D007553:Isotope Labeling; D009584:Nitrogen / Q000378:metabolism; D009586:Nitrogen Fixation; D009591:Nitrogenase / Q000235:genetics / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D013302:Streptomyces / Q000235:genetics* / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D009591:Nitrogenase; D009584:Nitrogen
references.citation: BMC Genomics. 2012 May 03;13:162
references.pmid: 22554235
references.citation: J Biol Chem. 1997 Oct 17;272(42):26627-33
references.pmid: 9334244
references.citation: J Clin Pathol. 1960 Mar;13:156-9
references.pmid: 13821779
references.citation: Arch Microbiol. 1992;157(3):301-4
references.pmid: 1510563
references.citation: Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):593-598
references.pmid: 15774630
references.citation: Microbiol Mol Biol Rev. 2012 Mar;76(1):66-112
references.pmid: 22390973
references.citation: Chem Commun (Camb). 2013 Dec 4;49(93):10893-907
references.pmid: 24129752
references.citation: Arch Microbiol. 1989;152(4):335-41
references.pmid: 2818128
references.citation: Zentralbl Mikrobiol. 1985;140(7):547-54
references.pmid: 4090765
references.citation: Annu Rev Biochem. 2009;78:701-22
references.pmid: 19489731
references.citation: Syst Biol. 2007 Aug;56(4):564-77
references.pmid: 17654362
references.citation: J Bacteriol. 2004 May;186(9):2629-35
references.pmid: 15090503
references.citation: Appl Environ Microbiol. 1990 Dec;56(12):3727-34
references.pmid: 16348374
references.citation: J Clin Microbiol. 2007 Sep;45(9):2761-4
references.pmid: 17626177
references.citation: Mol Syst Biol. 2011 Oct 11;7:539
references.pmid: 21988835
references.citation: Philos Trans A Math Phys Eng Sci. 2005 Apr 15;363(1829):971-84; discussion 1035-40
references.pmid: 15901546
references.citation: PLoS One. 2012;7(9):e42304
references.pmid: 23028432
references.citation: Appl Environ Microbiol. 1996 Mar;62(3):986-93
references.pmid: 16535283
references.citation: Nat Rev Microbiol. 2007 Feb;5(2):107-18
references.pmid: 17224920
references.citation: Can J Microbiol. 1968 Jan;14(1):25-31
references.pmid: 5644401
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8
references.pmid: 24253303
references.citation: Bioinformatics. 2014 Aug 1;30(15):2114-20
references.pmid: 24695404
references.citation: Annu Rev Microbiol. 1980;34:183-207
references.pmid: 6776883
references.citation: Environ Microbiol. 2013 Nov;15(11):3040-53
references.pmid: 23663433
references.citation: Cold Spring Harb Protoc. 2013 Sep 01;2013(9):820-34
references.pmid: 24003196
references.citation: J Bacteriol. 1986 Apr;166(1):180-6
references.pmid: 3457004
references.citation: Eur J Biochem. 1979 Jul;98(1):275-84
references.pmid: 111934
references.citation: Int J Syst Evol Microbiol. 2013 May;63(Pt 5):1723-1727
references.pmid: 22922537
references.citation: PLoS One. 2014 Oct 17;9(10):e110335
references.pmid: 25329300
references.citation: Nature. 1997 May 22;387(6631):370-6
references.pmid: 9163420
references.citation: Res Microbiol. 2013 Sep;164(7):718-28
references.pmid: 23608518
references.citation: Biochim Biophys Acta. 1973 Jan 18;292(1):256-70
references.pmid: 4705133
references.citation: BMC Bioinformatics. 2013 Feb 21;14:60
references.pmid: 23432962
references.citation: J Bacteriol. 2005 Jan;187(2):405-14
references.pmid: 15629911
references.citation: Mol Biol Evol. 2004 Mar;21(3):541-54
references.pmid: 14694078
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30
references.pmid: 24288371
references.citation: Proc Natl Acad Sci U S A. 1978 Jun;75(6):2699-702
references.pmid: 275837
references.citation: Biochem J. 1988 Jul 1;253(1):287-9
references.pmid: 2844170
references.citation: J Bacteriol. 1992 Nov;174(21):6840-3
references.pmid: 1400234
references.citation: Appl Microbiol. 1971 Mar;21(3):527-33
references.pmid: 4928607
references.citation: Nature. 2005 Sep 15;437(7057):376-80
references.pmid: 16056220
references.citation: Mol Biol Evol. 2013 Dec;30(12):2725-9
references.pmid: 24132122
references.citation: FEMS Microbiol Lett. 2011 Jun;319(1):1-10
references.pmid: 21320158
references.citation: J Bacteriol. 2011 Sep;193(17):4534-6
references.pmid: 21725008
references.citation: J Comput Biol. 2012 May;19(5):455-77
references.pmid: 22506599
references.citation: Annu Rev Microbiol. 1983;37:277-310
references.pmid: 6416144
references.citation: J Biosci Bioeng. 2014 Jan;117(1):28-32
references.pmid: 23849805
references.citation: Science. 2010 Oct 8;330(6001):192-6
references.pmid: 20929768
references.citation: J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
references.pmid: 10890397
references.citation: Trends Biochem Sci. 1994 May;19(5):199-200
references.pmid: 8048161
references.citation: Mol Microbiol. 2006 Feb;59(4):1073-82
references.pmid: 16430685
references.citation: J Gen Microbiol. 1969 Oct;58(2):277-85
references.pmid: 5360480
references.citation: Appl Environ Microbiol. 2008 Apr;74(8):2461-70
references.pmid: 18296538