TonB-dependent transporters and their occurrence in cyanobacteria

BMC Biol. 2009 Oct 12;7:68. doi: 10.1186/1741-7007-7-68.

Abstract

Background: Different iron transport systems evolved in Gram-negative bacteria during evolution. Most of the transport systems depend on outer membrane localized TonB-dependent transporters (TBDTs), a periplasma-facing TonB protein and a plasma membrane localized machinery (ExbBD). So far, iron chelators (siderophores), oligosaccharides and polypeptides have been identified as substrates of TBDTs. For iron transport, three uptake systems are defined: the lactoferrin/transferrin binding proteins, the porphyrin-dependent transporters and the siderophore-dependent transporters. However, for cyanobacteria almost nothing is known about possible TonB-dependent uptake systems for iron or other substrates.

Results: We have screened all publicly available eubacterial genomes for sequences representing (putative) TBDTs. Based on sequence similarity, we identified 195 clusters, where elements of one cluster may possibly recognize similar substrates. For Anabaena sp. PCC 7120 we identified 22 genes as putative TBDTs covering almost all known TBDT subclasses. This is a high number of TBDTs compared to other cyanobacteria. The expression of the 22 putative TBDTs individually depends on the presence of iron, copper or nitrogen.

Conclusion: We exemplified on TBDTs the power of CLANS-based classification, which demonstrates its importance for future application in systems biology. In addition, the tentative substrate assignment based on characterized proteins will stimulate the research of TBDTs in different species. For cyanobacteria, the atypical dependence of TBDT gene expression on different nutrition points to a yet unknown regulatory mechanism. In addition, we were able to clarify a hypothesis of the absence of TonB in cyanobacteria by the identification of according sequences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anabaena / genetics
  • Anabaena / metabolism
  • Bacterial Outer Membrane Proteins / genetics
  • Bacterial Outer Membrane Proteins / metabolism
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Biological Transport, Active / genetics
  • Cluster Analysis
  • Copper / metabolism
  • Culture Media / chemistry
  • Cyanobacteria / genetics*
  • Cyanobacteria / metabolism
  • Databases, Nucleic Acid
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial*
  • Ion Transport / genetics*
  • Iron / metabolism
  • Ligands
  • Markov Chains
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism*
  • Membrane Transport Proteins / classification
  • Membrane Transport Proteins / genetics*
  • Membrane Transport Proteins / metabolism
  • Nitrogen / metabolism
  • Operon / genetics
  • Phylogeny
  • Sequence Homology, Nucleic Acid
  • Software
  • Systems Biology / methods

Substances

  • Bacterial Outer Membrane Proteins
  • Bacterial Proteins
  • Culture Media
  • Ligands
  • Membrane Proteins
  • Membrane Transport Proteins
  • tonB protein, Bacteria
  • Copper
  • Iron
  • Nitrogen