Cfrench:hemtoppage

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Mainly because we are interested in magnetotactic bacteria, and our sequence searches show that magnetotactic bacteria contain far more different bacteriohemerythrins than any other type of bacteria for which genome data are available. Most species with bacteriohemerythrins have only one or two; a few have five or six, a couple as many as ten. The two species of ''Magnetospirillum'' which have been sequenced appear to contain around thirty different bacteriohemerythrin genes each, and ''Magnetococcus'' at least seventeen. Surely they must be playing some important role in the magnetotactic lifestyle. Some of them, such as those with MCP domains, are probably involved in finding the zone with the low oxygen concentration required for good growth and magnetosome formation; others may be involved in oxygen storage or magnetite synthesis.
Mainly because we are interested in magnetotactic bacteria, and our sequence searches show that magnetotactic bacteria contain far more different bacteriohemerythrins than any other type of bacteria for which genome data are available. Most species with bacteriohemerythrins have only one or two; a few have five or six, a couple as many as ten. The two species of ''Magnetospirillum'' which have been sequenced appear to contain around thirty different bacteriohemerythrin genes each, and ''Magnetococcus'' at least seventeen. Surely they must be playing some important role in the magnetotactic lifestyle. Some of them, such as those with MCP domains, are probably involved in finding the zone with the low oxygen concentration required for good growth and magnetosome formation; others may be involved in oxygen storage or magnetite synthesis.
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===Genera of bacteria and archaea with hemerythrin-like genes===
 
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{|
 
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|-
 
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!Genus!!family!!order!!class/phylum!!number of hemerythrins
 
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|-
 
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|Acidobacteria sp.||Acidobacteriaeae||Acidobacteriales||Acidobacteria||4
 
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|-
 
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|''Acidovorax''||Comamonadaceae||Burkholderiales||Betaproteobacteria||1,3
 
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|-
 
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|''Aeromonas''||Aeromonadaceae||Aeromonadales||Gammaproteobacteria||2
 
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|-
 
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|''Alcanivorax''||Alcanivoraceae||Oceanospirillales||Gammaproteobacteria||1
 
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|-
 
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|''Alkalilimnicola''||Ectothiorhodospiraceae||Chromatiales||Gammaproteobacteria||2
 
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|-
 
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|''Anaeromyxobacter''||Myxococcaceae||Myxococcales||Deltaproteobacteria||8
 
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|-
 
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|''Aquifex''||Aquificaceae||Aquificales||Aquificae||1
 
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|-
 
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|''Azotobacter''||Pseudomonadaceae||Pseudomonadales||Gammaproteobacteria||1
 
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|-
 
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|''Bdellovibrio''||Bdellovibrionaceae||Bdellovibrionales||Deltaproteobacteria||1
 
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|-
 
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|''Bordetella''||Alcaligenaceae||Burkholderiales||Betaproteobacteria||1
 
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|-
 
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|''Burkholderia''||Burkholderiaceae||Burkholderiales||Betaproteobacteria||23 strains 1 each, 1 strain has 3
 
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|-
 
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|''Campylobacter''||Campylobacteraceae||Campylobacterales||Epsilonproteobacteria||7, 2, 6, 3, 5, 5, 5, 5, 3, 2, 2, 5
 
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|-
 
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|''Caldocellulosiruptor''||Syntrophomonadaceae||Clostridiales||Clostridia, Firmicutes||1
 
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|-
 
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|''Clostridium''||Clostridicaeae||Clostridiales||Clostridia, Firmicutes||1, 6, 5, 1, 2
 
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|-
 
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|''Colwellia''||Colwelliaceae||Alteromonadales||Gammaproteobacteria||7
 
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|-
 
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|''Comamonas''||Comamonadaceae||Burkholderiales||Betaproteobacteria||4
 
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|-
 
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|''Dechloromonas''||Rhodocyclaceae||Rhodocyclales||Betaproteobacteria||10
 
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|-
 
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|''Desulfitobacterium''||Peptococcaceae||Clostridiales||Clostridia, Firmicutes||2, 2
 
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|''Desulfotalea''||Desulfobulbaceae||Desulfobacterales||Deltaproteobacteria||3
 
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|-
 
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|''Desulfovibrio''||Desulfovibrionaceae||Desulfovibrionales||Deltaproteobacteria||3, 4, 4
 
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|''Desulfuromonas''||Desulfuromonadaceae||Desulfuromonadales||Deltaproteobacteria||10
 
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|''Leuwenhoekiella''||Flavobacteriaceae||Flavobacteriales||Flavobacteria, Bacteroidetes||1
 
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|''Geobacter''||Geobacteraceae||Desulfuromonadales||Deltaproteobacteria||2, 2, 2, 5
 
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|''Haloarcula''||Halobacteriaceae||Halobacteriales||Halobacteria, Euryarchaeota||1
 
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|''Halorhodospira''||Ectothiorhodospiraceae||Chromatiales||Gammaproteobacteria||1
 
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|''Helicobacter''||Helicobacteraceae||Campylobacterales||Epsilonproteobacteria||2
 
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|''Hydrogenobacter''||Aquificaceae||Aquificales||Aquificae||1
 
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|''Idiomarina''||Idiomarinaceae||Alteromonadales||Gammaproteobacteria||1, 1
 
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|''Janthinobacterium''||Oxalobacteraceae||Burkholderiales||Betaproteobacteria||1 or 2
 
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|''Kuenenia''|| ||Planctomycetales||Planctomycetes||2
 
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|''Magnetococcus''|| || ||Proteobacteria||14 to 19
 
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|''Magnetospirillum''||Rhodospirillaceae||Rhodospirillales||Alphaproteobacteria||approx 29, 29
 
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|''Mariprofundus''|| || ||Proteobacteria||1
 
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|''Mesorhizobium''||Phyllobacteriaceae||Rhizobiales||Alphaproteobacteria||1
 
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|''Methanocaldococcus''||Methanocaldococcaceae||Methanococcales||Methanococci, Euryarchaeota||1
 
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|''Methanospirillum''||Methanospirillaceae||Methanomicrobiales||Methanomicrobia, Euryarchaeota||2
 
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|''Methylococcus''||Methylococcaceae||Methylococcales||Gammaproteobacteria||1
 
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|MLMS1|| || ||Deltaprotebacteria||5?
 
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|''Oceanospirillum''|| ||Oceanospirillales||Gammaproteobacteria||3
 
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|''Pelobacter''||Pelobacteraceae||Desulfuromonadales||Deltaproteobacteria||3, 1
 
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|''Polaromonas''||Comamonadaceae||Burkholderiales||Betaproteobacteria||3
 
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|''Pseudomonas''||Pseudomonadaceae||Pseudomonadales||Gammaproteobacteria||8 strains, 1 each
 
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|-
 
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|''Ralstonia''||Burkholderiaceae||Burkholderiaceae||Betaproteobacteria||2, 2, 1
 
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|''Reinekea''|| || ||Gammaproteobacteria||2
 
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|''Rhodoferax''||Comamonadaceae||Burkholderiales||Betaproteobacteria||2,2
 
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|''Rhodopseudomonas''||Bradyrhizobiaceae||Rhizobiales||Alphaproteobacteria||1, 1, 1
 
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|''Rhodospirillum''||Rhodospirillaceae||Rhodospirillales||Alphaproteobacteria||6
 
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|''Shewanella''||Shewanellaceae||Alteromonadales||Gammaproteobacteria||11 strains, 1 each
 
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|''Solibacter''||Solibacteraceae||Solibacterales||Solibacteres, Acidobacteria||3
 
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|''Symbiobacterium''|| || ||Actinobacteria||1
 
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|''Syntrophomonas''||Syntrophomonadaceae||Clostridiales||Clostridia, Firmicutes||1
 
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|''Thermoanaerobacter''||Thermoanaerobacteriaceae||Thermoanaerobacteriales||Clostridia, Firmicutes||1
 
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|''Thermosynechococcus''|| ||Chroococcales||Cyanobacteria||2
 
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|''Thiomicrospira''||Helicobacteraceae||Campylobacterales||Epsilonproteobacteria||1
 
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|''Verminephrobacter''||Comamonadaceae||Burkholderiales||Betaproteobacteria||1
 
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|''Vibrio''||Vibrionaceae||Vibrionales||Gammaproteobacteria||8 strains, 1 each
 
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|''Wolinella''||Helicobacteraceae||Campylobacterales||Epsilonproteobacteria||1
 
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|''Xanthomonas''||Xanthomonadaceae||Xanthomonadales||Gammaproteobacteria||1, 1, 1, 1
 
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|}
 
[[Cfrench:hemlist1|List of prokaryote genera with putative bacteriohemerythrins]]
[[Cfrench:hemlist1|List of prokaryote genera with putative bacteriohemerythrins]]
[[Cfrench:labtoppage|French lab main page]]
[[Cfrench:labtoppage|French lab main page]]

Revision as of 12:28, 30 November 2006

Contents

Hemerythrins

What are hemerythrins?

Hemerythrins are oxygen binding proteins found in certain invertebrates: sipunculid worms (peanut worms), brachiopods (lamp shells) and some annelid worms. One has also been found in an amoeba. They serve the same function as hemoglobin and myoglobin in vertebrates, but do not contain a heme prosthetic group; instead they contain non-heme iron. Each hemerythin subunit contains two iron atoms bound to a characteristic set of ligands - five histidines, one aspartate and one glutamate.

  • Stenkamp, R.E. 1994. Dioxygen and hemerythin. Chemical Reviews 94, 715-726.
  • Wilkins, R.G. 1992. Binuclear iron centres in proteins. Chemical Society Reviews ?, 171-178.
  • Vanin, S., Negrisolo, E., Bailly, X., Bubacco, L., Beltramini, M., and Salvato, B. 2006. Molecular evolution and phylogeny of sipunculan hemerythrins. Journal of Molecular Evolution 62. 32-41.

What are bacteriohemerythrins?

Recently, proteins with similar sequence to hemerythrins have been found in some bacteria. Two of these, from Methylococcus capsulatus and Desulfovibrio vulgaris, have been expressed in Escherichia coli, purified, and shown to possess iron atoms and to bind oxygen in the same way as animal hemerythrins. Searches of genomic sequence databases have shown that hemerythrin-like proteins (for which we propose the name 'bacteriohemerythrins') are present in many genera of bacteria. Some are simple single-domain hemerythrins like those of animals; in other cases the hemerythrin domain is fused to another domain, most commonly a signal transduction domain such as a methyl-accepting chemotaxis receptor (MCP), a GGDEF domain, or a histidine kinase domain. In these cases the hemerythrin presumably functions as an oxygen-sensing domain.

  • Xiong, J., Kurtz, D.M., Ai, J., and Sanders-Loehr, J. 2000. A hemerythrin-like domain in a bacterial chemotaxis protein. Biochemistry 39, 5117-5125.
  • Kao, W.-C., Chen, Y.-R., Yi, E.C., Lee, H., Tian, Q., Wu, K.-M., Tsai, S.-F., Yu, S.S.-F., Chen, Y.-J., Aebersold, R., and Chan, S.I. 2004. Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath). Journal of Biological Chemistry 279, 51554-51560.
  • Karlsen, O.A., Ramsevik, L., Bruseth, L.J., Larsen, O., Brenner, A., Berven, F.S., Jensen, H.B., and Lillehaug, J.R. 2005. Characterization of a prokaryotic hemerythrin from the methanotrophic bacterium Methylococcus capsulatus (Bath). FEBS Journal 272, 2428-2440.
  • Isaza, C.E., Silaghi-Dumitrescu, R., Iyer, R.B., Kurtz, D.M., and Chan, M.K. 2006. Structural Basis for O2 sensing by the hemerythrin-like domain of a bacterial chemotaxis protein: substrate tunnel and fluxional N-terminus. Biochemistry 45, 9023-9031.

Why are we interested in hemerythrins?

Mainly because we are interested in magnetotactic bacteria, and our sequence searches show that magnetotactic bacteria contain far more different bacteriohemerythrins than any other type of bacteria for which genome data are available. Most species with bacteriohemerythrins have only one or two; a few have five or six, a couple as many as ten. The two species of Magnetospirillum which have been sequenced appear to contain around thirty different bacteriohemerythrin genes each, and Magnetococcus at least seventeen. Surely they must be playing some important role in the magnetotactic lifestyle. Some of them, such as those with MCP domains, are probably involved in finding the zone with the low oxygen concentration required for good growth and magnetosome formation; others may be involved in oxygen storage or magnetite synthesis.

List of prokaryote genera with putative bacteriohemerythrins

French lab main page

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