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Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains

  • Arnab Sen
  • Louis S. Tisa
  • Maher Gtari
  • Indrani Sarkar
Original Paper

Abstract

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.

Keywords

Carbohydrate active enzymes Frankia Nodulation Codon usage Amino acid usage Comparative genomics Evolution Phylogeny 

Notes

Authors contribution

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.

Funding

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.

Ethical approval

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

Supplementary material

10482_2018_1173_MOESM1_ESM.tif (931 kb)
ESM1: COG analysis of total genomes for considered Frankia strains. (TIFF 931 kb)
10482_2018_1173_MOESM2_ESM.pdf (621 kb)
ESM2a: Spearman Rank Correlation among codon usage indices of 26 considered Frankia strains. ** marks with green cell color indicates positive correlation at p < 0.001 level. # marks with light blue cell color indicates negative correlation at p < 0.001. Light red cells with NS indicates non-significant correlation among the investigated parameters. The strain numbers are indicated in red color. Black color indicates correlation coefficient 1. ESM2b: Spearman Rank Correlation among codon usage indices of CAZyme genes from 26 considered Frankia strains. ** marks with green cell color indicates positive correlation at p < 0.001 level. # marks with light blue cell color indicates negative correlation at p < 0.001. Light red cells with NS indicates non-significant correlation among the investigated parameters. The strain numbers are indicated in red color. Black color indicates correlation coefficient 1. (PDF 620 kb)
10482_2018_1173_MOESM3_ESM.xlsx (71 kb)
ESM3: Microarray data of Frankia alni ACN14a revealed the high expression level of CAZyme set in every condition (both host association and free living conditions). The microarray data was obtained from NCBI GEO database with accession id GSE18190. (XLSX 71 kb)
10482_2018_1173_MOESM4_ESM.pdf (419 kb)
ESM4b: Spearman Rank Correlation among amino acid usage indices of CAZyme genes from 26 considered Frankia strains. ** marks with green cell color indicates positive correlation at p < 0.001 level. # marks with light blue cell color indicates negative correlation at p < 0.001. Light red cells with NS indicates non-significant correlation among the investigated parameters. The strain numbers are indicated in red color. Black color indicates correlation coefficient 1. ESM 5a: An all against all protein comparison was performed among considered Frankia theoretical proteomes using BLAST to define homologs. A BLAST hit is considered significant if 50% of the alignment consists of identical matches and the length of the alignment is 50% of the longest gene. Internal homology (paralogs) is defined as proteins within a genome matching the same 50–50 requirement as for between- theoretical proteome comparisons. (PDF 418 kb)
10482_2018_1173_MOESM5_ESM.pdf (2.5 mb)
ESM 5b: An all against all protein comparison was performed among CAZyme proteins of considered Frankia using BLAST to define homologs. A BLAST hit is considered significant if 50% of the alignment consists of identical matches and the length of the alignment is 50% of the longest gene. Internal homology (paralogs) is de-fined as proteins within a genome matching the same 50–50 requirement as for between- theoretical proteome comparisons. Self-matches are here ignored. For better resolution we have used only strain names in this figures. (PDF 2538 kb)

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Arnab Sen
    • 1
  • Louis S. Tisa
    • 2
  • Maher Gtari
    • 3
  • Indrani Sarkar
    • 1
  1. 1.NBU Bioinformatics Facility, Department of BotanyUniversity of North BengalSiliguriIndia
  2. 2.Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamUSA
  3. 3.Institut National des Sciences Appliquées et de TechnologieUniversité CarthageTunis CedexTunisia

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