Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation
Functional domains are semi-autonomous parts of proteins. The Per-Arnt-Sim (PAS) domain functions as signal-sensor in two-component systems of several bacteria. This domain exhibits large sequence diversity and is linked to other co-domains to modulate their function. In the present study, we analyzed the PAS domains found in the proteomes of several actinobacteria representing a variety of niches. PAS-domain containing proteins were identified with the HMMER program and characterized via an in silico approach. In general, the PAS proteins were found to be in the COG T (signal transduction) category implying their role was indeed in signal transduction. Most of the PAS proteins were found to be structurally conserved and moderately expressed. However, they showed a strong bias towards the lagging strand which may be a result of their involvement in adaptive evolution. A structure based phylogenetic analysis showed that PAS domains with similar interacting co-domains grouped together in a cluster irrespective of the bacterial genus from which they were identified. Thus, we may say that the association of PAS with its co-domains is based upon the PAS domain structure and not on the sequence.
Digital Object Identifier (DOI)
Sarkar, I., P. Normand, L.S. Tisa, A. Bothra, and A. Sen. 2016. Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis 70:69-78 (DOI 10.1007/s13199-016-0413-z)
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