Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains
Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. The CAZymes were found to be potentially highly expressed (PHX) proteins and contained more aromatic amino acids, which increased their biosynthetic energy cost. These energy rich amino acids were present in the active sites of CAZymes aiding in their carbohydrate binding capacity. Phylogenetic and evolutionary analyses showed that, in Frankia strains with the capacity to nodulate host plants, CAZymes were evolving slower than the other PHX genes, whereas similar genes from non-nodulating (or ineffectively nodulating) Frankia strains showed little variation in their evolutionary constraints compared to other PHX genes. Thus, the present study revealed the persistence of a strong purifying selection on CAZymes of Frankia indicating their crucial role.
KeywordsCarbohydrate active enzymes Frankia Nodulation Codon usage Amino acid usage Comparative genomics Evolution Phylogeny
Indrani Sarkar conceived the idea. Arnab Sen and Indrani Sarkar designed the study, performed research. Arnab Sen, Louis S. Tisa, Maher Gtari and Indrani Sarkar analysed data. All the authors wrote the paper and approved.
IS acknowledges UGC-BSR senior research fellowship, Govt, of India. AS is thankful to DBT Govt. of India for Bioinformatics Facility, University of North Bengal. LST was supported by the USDA National Institute of Food and Agriculture Hatch 022821.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by anyof the authors.
- Andrade AC, Fróes A, Lopes FÁC, Thompson FL, Krüger RH, Dinsdale E, Bruce T (2017) Diversity of microbial carbohydrate-active enzymes (CAZymes) associated with freshwater and soil samples from caatinga biome. Microbialecology 74(1):89–105Google Scholar
- Normand P, Benson DR, Berry AM, Tisa LS (2014) The family frankiaceae. In: The prokaryotes. Springer, Berlin, pp 339–356Google Scholar
- Peden J (1997) CodonW. Trinity College, DublinGoogle 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 64:3821–3832CrossRefGoogle Scholar
- Simonet P, Normand P, Hirsch AM, Akkermans AD (1990) The genetics of the Frankia-actinorhizal symbiosis. In: Molecular biology of symbiotic nitrogen fixation, pp 77–109Google Scholar