, Volume 70, Issue 1–3, pp 69–78 | Cite as

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

  • Indrani Sarkar
  • Philippe Normand
  • Louis S. Tisa
  • Maher Gtari
  • Asim Bothra
  • Arnab SenEmail author


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.


Signal transduction Co-domain Structure-based phylogeny Domain-domain interaction Biological network 


PAS proteins

PAS domain containing proteins

PAS genes

Gene sequence of PAS domain containing proteins


Effective number of codons


Correspondence analysis


Codon adaptation index



This work is partially supported by Department of Biotechnology, Govt. of West Bengal, India through grant no. 206/Bt (Estd.)/RD-22/2014. IS acknowledges the receipt of BSR, UGC fellowship. AS is grateful to the DBT, for providing CREST Award and help in setting up Bioinformatics Centre, in the Department of Botany, University of North Bengal. LST is supported in part by a Hatch NH585.

Authors’ contribution

AS conceived the idea. IS, PN, AS designed the experiments. IS, LT, MG and AB performed data analysis. IS, AS, LT, MG and PN drafted the manuscript. All authors prepared the final manuscript and approved the final version.

Compliance with ethical standards


This work is also partially supported by Department of Biotechnology, Govt. of West Bengal, India through grant no. 206/Bt(Estd.)/RD-22/2014. LST is supported in part by a Hatch NH585.

Conflict of interest

All of the authors of this study declare that he/she has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Indrani Sarkar
    • 1
  • Philippe Normand
    • 2
  • Louis S. Tisa
    • 3
  • Maher Gtari
    • 4
  • Asim Bothra
    • 5
  • Arnab Sen
    • 1
    Email author
  1. 1.NBU Bioinformatics Facility, Department of BotanyUniversity of North BengalSiliguriIndia
  2. 2.Université de Lyon; Université Lyon 1; CNRS, Ecologie Microbienne UMR5557; INRA, UMR1418, CedexVilleurbanneFrance
  3. 3.Department of Molecular, Cellular & Biomedical Sciences, University of New HampshireDurhamUSA
  4. 4.Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT)TunisTunisia
  5. 5.Bioinformatics Chemoinformatics Laboratory, Department of Chemistry, Raiganj University CollegeRaiganjIndia

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