Newly Identified Motifs within PAS Domains of Filamentous Cyanobacteria

Many cyanobacterial genome projects have been finished or are ongoing. Now, complete genome sequence of Anabaena sp. PCC 7120 (Anabaena)[1] and draft genome sequence of Nostoc punctiforme (Nostoc)[3] are available. Phylogenetically, these species are closely related. These species have extremely abundant signal-transduction proteins, especially PAS domain-containing proteins (PAScontaining proteins)[5]. PAS domain is known to be multi-functional domain superfamily with highly conserved 3D structure [6]. We formerly detected 142 and 180 PAS domains in 60 and 84 PAScontaining proteins from Anabaena and Nostoc, respectively. Clutering analysis showed that they were classified into 64 distinct subclasses and 36 “orphans”. On the other hand, we detected 35 pairs of PAS-containing proteins that are orthologous to each other between the two species. PAS domains in these orthologous poteins were classified into two groups: orthologous and non-orthologous ones. We interpreted the non-orthologous PAS domains in the orthologous proteins as generated by domain shuffling after branching of the two related species. Finally, 60 pairs of the orthologous PAS domains were highlighted as candidates for functionality [4]. Here, we extended our trial to unravel the complex PAS superfamily by finding novel motifs, which may interact each other in the 3-dimensional configuration.