Summary: The genes for adenosine-5′-phosphosulfate (APS) reductase, aprBA, and sirohaem sulfite reductase, dsrAB, from the sulfur-oxidizing phototrophic bacterium Chromatium vinosum strain D (DSMZ 180T) were cloned and sequenced. Statistically significant sequence similarities and similar physicochemical properties suggest that the aprBA and dsrAB gene products from Chr. vinosum are true homologues of their counterparts from the sulfate-reducing chemotrophic archaeon Archaeoglobus fulgidus and the sulfate-reducing chemotrophic bacterium Desulfovibrio vulgaris. Evidence for the proposed duplication of a common ancestor of the dsrAB genes is provided. Phylogenetic analyses revealed a greater evolutionary distance between the enzymes from Chr. vinosum and D. vulgaris than between those from A. fulgidus and D. vulgaris. The data reported in this study are most consistent with the concept of common ancestral protogenotic genes both for dissimilatory sirohaem sulfite reductases and for APS reductases. The aprA gene was demonstrated to be a suitable DNA probe for the identification of apr genes from organisms of different phylogenetic positions. PCR primers and conditions for the amplification of apr homologous regions are described.
BaldenspergerJ.,
GarciaJ.-L.1975; Reduction of oxidized inorganic nitrogen compounds by a new strain of Thiobacillus denitrificans
. Arch Microbiol 103:31–36
Benachenhou-LahfaN.,
ForterreP.,
LabedanB.1993; Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. J Mol Biol 36:335–346
ChouQ.,
RussellM.,
BirchD. E.,
RaymondJ.,
BlochW.1992; Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplification. Nucleic Acids Res 20:1717–1723
CraneB. R.,
SiegelL. M.,
GetzoffE. D.1995; Sulfite reductase structure at 1.6 Å: evolution and catalysis for reduction of inorganic anions. Science 270:59–67
DahlC.1996; Insertional gene inactivation in a phototrophic sulphur bacterium:APS-reductase-deficient mutants of Chromatium vinosum
. Microbiology1423363–3372
DahlC.,
KochH. G.,
KeukenO.,
TrüperH. G.1990; Purification and characterization of ATP sulfurylase from the extremely thermophilic archaebacterial sulfate reducer, Archaeoglobus fulgidus
. FEMS Microbiol Lett 67:27–32
DahlC.,
KredichN. M.,
DeutzmannR.,
TrüperH. G.1993; Dissimilatory sulphite reductase from Archaeoglobus fulgidus: physico-chemical properties of the enzyme and cloning, sequencing and analysis of the reductase genes. J Gen Microbiol 139:1817–1828
FauqueG.,
LeGallJ.,
BartonL.1991; Sulfate-reducing and sulfur-reducing bacteria. In Variations in Autotrophic Life pp. 271–337 Edited by
ShivelyJ. M.,
BartonL.
New York: Academic Press;
FelsensteinJ.1993; phylip (Phylogeny Inference Package) version 3.5c. ftp.bio.indiana.edu/molbio/evolve.
FischerU.1989; Enzymatic steps and dissimilatory sulfur metabolism by whole cells of anoxyphotobacteria. In Biogenic Sulfur in the Environment pp. 262–279 Edited by
SaltzmanE. S.,
CooperW. J.
Washington, DC: American Chemical Society;
GeourjonC.,
DeleageG.1995; sopma: significant improvements in protein secondary structure prediction by prediction from multiple alignments. Comput Appl Biosci11681–684
GogartenJ. P.1994; Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages. J Mol Biol 39:541–543
HippW. M.1996The Red Book Bulletin. Current Protocols in Molecular Biology suppl. 3, units 2 9.2–2.10. Edited by
AusubelF. A.
,
BrentR.
,
KingstonR. E.
,
MooreD. D.
,
SeidmanJ. G.
,
J. A.Smith
,
StruhlK.
.
New York: John Wiley;
ImhoffJ. F.1992; The family Ectothiorhodospiraceae. In The Prokaryotes 2nd edn, pp. 3222–3229 Edited by
BalowsA.,
TrüperH. G.,
DworkinM.,
HarderW.,
SchleiferK.-H.
New York: Springer;
ImhoffJ. F.,
TrüperH. G.1992; The genus Rhodospirillum and related genera. In The Prokaryotes 2nd edn, pp. 2141–2155 Edited by
BalowsA.,
TrüperH. G.,
DworkinM.,
HarderW.,
SchleiferK.-H.
New York: Springer;
IwabeN.,
KumaK.-I.,
HasegawaM.,
OsawaS.,
MiyataT.1989; Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86:9355–9359
IwasakiT.,
WakagiT.,
IsogaiY.,
TanakaK.,
lizukaT.,
OshimaT.1994; Functional and evolutionary implications of a [3Fe–4S] cluster of the dicluster-type ferredoxin from the thermoacidophilic archaeon, Sulfolobus sp. strain 7. J Biol Chem 269:29444–29450
Karkhoff-SchweizerR. R.,
HuberD. P. W.,
VoordouwG.1995; Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl Environ Microbiol 61:290–296
KumarS.1996; phyltest : a program for testing phylogenetic hypothesis, version 2.0. imeg@psuvm.psu.edu.
LampreiaJ.,
MouraI.,
TeixeiraM.,
PeckH. D.,
Jr, LeGallJ.,
HuynhB. H.,
MouraJ. J. G.1990; The active centers of adenylylsulfate reductase from Desulfovibrio gigas
. Eur J Biochem 188:653–664
MehtaP. K.,
HeringaJ.,
ArgosP.1995; A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70 %. Protein Sci 4:2517–2525
MolitorM.1966; Molekularbiologische und physikochemische Charakterisierung der dissimilatorischen Sulfitreduktasen aus Pyrobaculum islandicum und Desulfovibrio simplex. PhD thesis University of Bonn;
NakamuraK.,
YamakiM.,
SaradaM.,
NakayamaS.,
VibatC. R. T.,
GennisR. B.,
NakayashikiT.,
InokuchiH.,
KojimaS.,
KitaK.1996; Two hydrophobic subunits are essential for the heme b ligation and functional assembly of complex II (succinate-ubiquinone oxidoreductase) from Escherichia coli
. J Biol Chem 271:521–527
OdomJ. M.,
JessieK.,
KnodelE.,
EmptageM.1991; Immunological cross-reactivities of adenosine-5ʹ-phosphosulfate reductases from sulfate-reducing and sulfide-oxidizing bacteria. Appl Environ Microbiol 57:727–733
OstrowskiJ.,
WuJ.-Y.,
RuegerD. C.,
MillerB. E.,
Siegel, LM.,
KredichN. M.1989; Characterization of the cysJIH regions of Salmonella typhimurium and Escherichia coli B. J Biol Chem 264:15726–15737
PfennigN.,
TrüperH. G.1992; The family Chromatiaceae. In The Prokaryotes 2nd edn, pp. 3200–3221 Edited by
BalowsA.,
TrüperH. G.,
DworkinM.,
HarderW.,
SchleiferK.-H.
New York: Springer;
RobinsonK. M.,
LemireB. D.1996; Covalent attachment of FAD to the yeast succinate dehydrogenase flavoprotein requires import into mitochondria, presequence removal, and folding. J Biol Chem 271:4055–4060
SchedelM.,
TrüperH. G.1979; Purification of Thiobacillus denitrificans siroheme sulfite reductase and investigation of some molecular and catalytic properties. Biochim Biophys Acta 568:454–467
SchedelM.,
VanselowM.,
TrüperH. G.1979; Siroheme sulfite reductase isolated from Chromatium vinosum. Purification and investigation of some of its molecular and catalytic properties. Arch Microbiol 121:29–36
SchidlowskiM.1986; Evolution of the early sulphur cycle. In Proceedings of the International Meeting on Geochemistry of the Earth Surface and Processes of Mineral Formation, Granada, Spain pp. 29–49 Edited by
Rodriguez-ClementeR.,
TardyY.
Madrid: Consejo Superior de Investigaciones Cientificas;
SchrӧderI.,
GunsalusR. P.,
AckrellB. A. C.,
CochranB.,
CecchiniG.1991; Identification of active site residues of Escherichia coli fumarate reductase by site-directed mutagenesis. J Biol Chem 266:13572–13579
SkyringG. W.,
DonnellyT. H.1982; Precambrian sulfur isotopes and a possible role for sulfite in the evolution of biological sulfate reduction. Precambrian Res 17:41–61
SpeichN.,
DahlC.,
HeisigP.,
KleinA.,
LottspeichF.,
StetterK. O.,
TrüperH. G.1994; Adenylylsulphate reductase from the sulphate-reducing archaeon Archaeoglobus fulgidus: cloning and characterization of the genes and comparison of the enzyme with other iron-sulphur flavoproteins. Microbiology 140:1273–1284
ThauerR. K.1989; Energy metabolism of sulfate-reducing bacteria. In Autotrophic Bacteria pp. 397–413 Edited by
SchlegelH. G.,
BowienB.
Madison, WI: Science Tech Publishers;
TrüperH. G.,
FischerU.1982; Anaerobic oxidation of sulfur compounds as electron donors for bacterial photosynthesis. Philos Trans R Soc Lond B Biol Sci 298:529–542
VerhagenM. F. J.,
M., KooterI. M.,
WolbertR. B. G.,
HagenW. R.1994; On the iron-sulfur cluster of adenosine phosphosulfate reductase from Desulfovibrio vulgaris (Hildenborough). Eur J Biochem 221:831–837
WestM. W.,
HechtM. H.1995; Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Protein Sci 4:2032–2039
WierengaR. K.,
TerpstraP.,
HoIW. G. J.1986; Prediction of the occurrence of the ADP-binding beta-alpha-beta-fold in proteins, using an amino acid sequence fingerprint. J Mol Biol 187:101–107