Cloning and characterization of the genes coding for two porins in the unicellular cyanobacterium Synechococcus PCC 6301

Biochim Biophys Acta. 1998 Jul 30;1399(1):31-9. doi: 10.1016/s0167-4781(98)00090-6.


The genes somB and somA (Synechococcus outer membrane), lying in tandem organization in the genome of Synechococcus PCC 6301, encode two porins in the outer membrane of this unicellular cyanobacterium. Northern blot and primer extension experiments revealed that somA and somB are not comprising an operon, as each gene encodes a transcript of 1.7 kb length and has a distinct transcriptional start site. The deduced SomA and SomB protein sequences include typical N-terminal signal peptides and reveal 60% homology (50% identical residues) to each other as well as significant homology to six protein sequences deduced from open reading frames sequenced in the genome of the unicellular cyanobacterium Synechocystis PCC 6803. Furthermore, SomA possesses an overall identity of 97% to the functionally not yet characterized outer-membrane protein SomA from the closely related cyanobacterial strain Synechococcus PCC 7942. Analyses performed on the sequences suggest that SomA and SomB form 14- or 16-stranded porin-like beta-barrels. Moreover, all sequences share an N-terminal motif with significant homology to 'S-layer homology' domains, which might form a periplasmic extension. SomA and SomB therefore may, in addition to their porin function, act as linkers connecting the outer membrane with the peptidoglycan layer.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins*
  • Base Sequence
  • Chromosome Mapping
  • Cloning, Molecular
  • Cyanobacteria / genetics*
  • Gene Expression
  • Membrane Glycoproteins*
  • Molecular Sequence Data
  • Periplasm / metabolism
  • Porins / biosynthesis
  • Porins / genetics*
  • Sequence Alignment
  • Sequence Homology


  • Bacterial Proteins
  • Membrane Glycoproteins
  • Porins
  • S-layer proteins

Associated data

  • GENBANK/U70256