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

Symbiosis volume 70, pages 69–78 (2016)Cite this article

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.

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Abbreviations

PAS proteins:

PAS domain containing proteins

PAS genes:

Gene sequence of PAS domain containing proteins

ENc:

Effective number of codons

COA:

Correspondence analysis

CAI:

Codon adaptation index

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Acknowledgments

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.

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Authors and Affiliations

  1. NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, 734013, India

    Indrani Sarkar & Arnab Sen

  2. Université de Lyon; Université Lyon 1; CNRS, Ecologie Microbienne UMR5557; INRA, UMR1418, Cedex, 69622, Villeurbanne, France

    Philippe Normand

  3. Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH, 03824-2617, USA

    Louis S. Tisa

  4. Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092, Tunis, Tunisia

    Maher Gtari

  5. Bioinformatics Chemoinformatics Laboratory, Department of Chemistry, Raiganj University College, Raiganj, India

    Asim Bothra

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  1. Indrani Sarkar
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  2. Philippe Normand
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Correspondence to Arnab Sen.

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Funding

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.

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Sarkar, I., Normand, P., Tisa, L.S. et al. Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis 70, 69–78 (2016). https://doi.org/10.1007/s13199-016-0413-z

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Keywords

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