Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation

I. Sarkar Philippe Normand 1 L. S. Tisa M. Gtari A. Bothra A. Sen
1 LEM - Laboratoire d'Ecologie Microbienne - UMR 5557
Abstract : 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.
Keywords : Domain-domain interaction signal transduction Structure-based phylogeny developmental biology ecology evolutionary biology Microbiology Plant Sciences Biological network Co-domain
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Submitted on : Tuesday, February 4, 2020 - 11:32:37 AM
Last modification on : Thursday, February 20, 2020 - 7:21:11 PM

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I. Sarkar, Philippe Normand, L. S. Tisa, M. Gtari, A. Bothra, et al.. Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis, Springer Verlag, 2016, 70 (1-3), pp.69-78. ⟨10.1007/s13199-016-0413-z⟩. ⟨hal-02466002⟩

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