Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation
- 168 Downloads
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.
KeywordsSignal 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
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.
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.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Alloisio N et al. (2010) The Frankia alni symbiotic transcriptome. Mol Plant Microbe In 23.5: 593-607Google Scholar
- Eswar N, Eramian D, Webb B, Shen M-Y, Sali A (2008) Protein structure modeling with MODELLER. In: Structural proteomics, vol 426. Springer, p 145–159Google Scholar
- Fijalkowska IJ, Jonczyk P, Tkaczyk MM, Bialoskorska M, Schaaper RM (1998) Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc Natl Acad Sci USA 95(17): PMC21454Google Scholar
- Hefti MH, Franaoijs KJ, De Vries SC, Dixon R, Vervoort J (2004) The PAS fold European. J Biochem 271:1198–1208Google Scholar
- Rickman L, Saldanha JW, Hunt DM, Hoar DN, Colston MJ, Millar JB, Buxton RS (2004) A two-component signal transduction system with a PAS domain-containing sensor is required for virulence of Mycobacterium tuberculosis in mice. Biochem Biophys Res Commun 314:259–267CrossRefPubMedPubMedCentralGoogle Scholar
- Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P (2014) Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol 64:3821–3832CrossRefPubMedGoogle Scholar
- Sievers et al. (2011) Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol Sys Biol 7(1)Google Scholar
- Tice H et al (2010) Complete genome sequence of Nakamurella multipartita type strain (Y-104) Stand. Gsenomic Sci 2:168–175Google Scholar