Comparative genomics of Prauserella sp. Am3, an actinobacterium isolated from root nodules of Alnus nepalensis in India

Abstract

A novel actinomycete strain, assigned as Am3, was isolated from the root nodules of Alnus nepalensis at Mirik hills, India. Analysis of the 16s rRNA gene sequence placed this new strain within the genus Prauserella. The genome was sequenced by Illumina sequencing and resulting 5.33-Mbp high quality draft genome sequenced with a G + C content of 70.0 % and 4828 candidate protein-encoding genes. Phylogenetically, Prauserella clusters very close to Amycolatopsis and was previously placed under the genus Amycolatopsis. Our main focus was to reveal the genomic similarities and dissimilarities of the newly sequenced Prauserella sp. Am3 with the type strain, Prauserella rugosa DSM 43194 T, and to determine its relationship with Amycolatopsis, which is happened to be the closest genus of Prauserella. Taking an in silico approach, bioinformatic analysis revealed that the core genome of Amycolatopsis and Prauserella contained 1589 genes. The two Prauserella genomes shared approximately 4224 genes, and 237 and 245 unique genes were found in the P. rugosa and Prauserella sp. Am3 genomes, respectively. Analysis of various phylogenetic trees including a 16s rRNA gene tree, MLSA protein-based tree and concatenated core-genome-based tree, placed both Prauserella genomes together with Amycolatopsis halophila YIM 93233 as its closest neighbor. Blast Matrix analysis of the predicted proteomes revealed about 86 % homology between the two Prauserella genomes. Analysis of the strand variation property revealed the absence of replication-transcriptional selection. Overall, a high degree of similarity was found between the two Prauserella genomes and a high percentage of similarity occurred among the Prauserella genomes and Amycolatopsis halophila.

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References

  1. Armengol ,L, Pujana MA, Cheung J, Scherer SW, Estivill X (2003) Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum Mol Genet 12:2201–2208

    CAS  Article  PubMed  Google Scholar 

  2. Bajwa BS (2004) Molecular characterization of Frankia and Alder-Frankia symbiosis in Eastern India. Ph. D Thesis, NBU, Siliguri

  3. Benson DR, Silvester WB (1993) Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol Rev 57:293

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T (2013) antiSMASH 2.0–a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41:W204–W212. doi:10.1093/nar/gkt449

    Article  PubMed  PubMed Central  Google Scholar 

  5. Bose D, Sen A (2006) Isolation and heavy metal resistance pattern of Frankia from Casuarina equisetifolia nodules. Indian J Med Microbiol 46:9

    CAS  Google Scholar 

  6. Carro L et al. (2013) Micromonospora is a normal occupant of actinorhizal nodules. J Biosci 38:685–693

    Article  PubMed  Google Scholar 

  7. Chen X, Zhang J (2013) Why are genes encoded on the lagging strand of the bacterial genome? GBE 5:2436–2439

    PubMed  PubMed Central  Google Scholar 

  8. Das S, Paul S, Dutta C (2006) Evolutionary constraints on codon and amino acid usage in two strains of human pathogenic actinobacteria Tropheryma whipplei. J Mol Evol 62:645–658

    CAS  Article  PubMed  Google Scholar 

  9. De Mendoza A, Suga H, Ruiz-Trillo I (2010) Evolution of the MAGUK protein gene family in premetazoan lineages. BMC Evol Biol 10:93

    Article  PubMed  PubMed Central  Google Scholar 

  10. Di Marco A, Spalla C (1957) La produzione di cobalamine da fermentazione con una nuova specie di Nocardia: Nocardia rugosa. Giorn Microbiol 4:24–30

    Google Scholar 

  11. Ghodhbane-Gtari F, Tisa LS (2014) Ecology and physiology of non-frankia actinobacteria from actinorhizal plants. In: Plasticity in plant-growth-promoting and phytopathogenic bacteria. Springer, New York, p 27–42

  12. Ghodhbane-Gtari F, Essoussi I, Chattaoui M, et al. (2010) Isolation and characterization of non-Frankia actinobacteria from root nodules of Alnus glutinosa, Casuarina glauca and Elaeagnus angustofolia. Symbiosis 50:51–57

    CAS  Article  Google Scholar 

  13. Gnerre S et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PNAS 108:1513–1518

    CAS  Article  PubMed  Google Scholar 

  14. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224

    CAS  Article  PubMed  Google Scholar 

  15. Hibbs DE, Cromack K Jr. (1990) Actinorhizal plants in Pacific Northwest forests. In: Schwintzer CR, Tjepkema JD (eds) The biology of frankia and actinorhizal plants. Academic Press, San Diego, p 343–363

  16. Hoagland DR, Arnon DI (1950) The water-culture method for growing plants without soil. Calif Agr Expt Sta Circ 347(2):32

    Google Scholar 

  17. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi:10.1186/1471-2105-11-119

    Article  PubMed  PubMed Central  Google Scholar 

  18. Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299–314

    Google Scholar 

  19. Kim SB, Goodfellow M (1999) Reclassification of Amycolatopsis rugosa lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. Int J Syst Evol Microbiol 49:507–512

    Google Scholar 

  20. Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    CAS  Article  PubMed  Google Scholar 

  21. Kuhn K et al. (2004) A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 14:2347–2356

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. Lalonde M, Calvert HE (1979) Production of Frankia hyphae and spores as an infective inoculant for Alnus species. Symbiotic Nitrogen Fixation in the Management of Temperate Forests 95:110

    Google Scholar 

  23. Lechevalier MP, Prauser H, Labeda DP, Ruan JS (1986) Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Evol Microbiol 36:29–37

    Google Scholar 

  24. Li K-B (2003) ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19:1585–1586

    Article  PubMed  Google Scholar 

  25. Li W-J, Xu P, Tang S-K, Xu L-H, Kroppenstedt RM, Stackebrandt E, Jiang C-L (2003) Prauserella halophila sp. nov. and Prauserella alba sp. nov., moderately halophilic actinomycetes from saline soil. Int J Syst Evol Microbiol 53:1545–1549

    CAS  Article  PubMed  Google Scholar 

  26. Li Y, Tang S-K, Chen Y-G, Wu J-Y, Zhi X-Y, Zhang Y-Q, Li W-J (2009) Prauserella salsuginis sp. nov., Prauserella flava sp. nov., Prauserella aidingensis sp. nov. and Prauserella sediminis sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 59:2923–2928

    CAS  Article  PubMed  Google Scholar 

  27. Liu N, Wang H, Liu M, Gu Q, Zheng W, Huang Y (2009) Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis. Int J Syst Evol Microbiol 59:254–258

    CAS  Article  PubMed  Google Scholar 

  28. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. Maldonado LA, Quintana ET (2015) Unexpected properties of Micromonosporae from marine origin. Adv Microbiol 5:452–456

    Article  Google Scholar 

  30. Markowitz VM et al. (2006) The integrated microbial genomes(IMG) system. Nucleic Acids Res 34:D344–D348. doi:10.1093/Nar/Gkj024

    CAS  Article  PubMed  Google Scholar 

  31. Markowitz VM et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122

    CAS  Article  PubMed  Google Scholar 

  32. Mavromatis K, Ivanova NN, Chen IMA, Szeto E, Markowitz VM, Kyrpides NC (2009) The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 1:63

    Article  PubMed  PubMed Central  Google Scholar 

  33. Medema MH et al. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346. doi:10.1093/Nar/Gkr466

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Meier-Kolthoff JP, Auch AF, Klenk H-P, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60

    Article  PubMed  PubMed Central  Google Scholar 

  35. Normand P, Fernandez MP (2008) Evolution and diversity of Frankia. In: Prokaryotic symbionts in plants. Springer Berlin Heidelberg, pp 103–125

  36. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7:455–457

    CAS  Article  PubMed  Google Scholar 

  37. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196. doi:10.1093/nar/gkm864

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. Roy A, Mukhopadhyay S, Sarkar I, Sen A (2015) Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium.World J Microbiol Biotechnol 31(6):959–981. doi:10.1007/s11274-015-1850-1

  39. Schafer J, Martin K, Kamfer P (2010) Prauserella muralis sp. nov., from the indoor environment. Int J Syst Evol Microbiol 60:287–290

    Article  PubMed  Google Scholar 

  40. Sen et al. (2014) The phylogeny of 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 64:3821–3832

    Article  PubMed  Google Scholar 

  41. Siguier P, Parochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32–D36

    CAS  Article  PubMed  Google Scholar 

  42. Solanki P, Kothari V (2011) Halophilic actinomycetes: salt-loving filaments. Int J Life Sci Technol 4:7–13

    Google Scholar 

  43. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690

    CAS  Article  PubMed  Google Scholar 

  44. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539

    CAS  Article  PubMed  Google Scholar 

  45. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    CAS  Article  PubMed  Google Scholar 

  46. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  47. Thomas TD (2008) The role of activated charcoal in plant tissue culture. Biotechnol Adv 26:618–631

    CAS  Article  PubMed  Google Scholar 

  48. Touchon M, Rocha EPC (2007) Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 24:969–981

    CAS  Article  PubMed  Google Scholar 

  49. Trujillo ME, Kroppenstedt RM, Schumann P, Carro L, Martanez-Molina E (2006) Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia. Int J Syst Evol Microbiol 56:2381–2385

    CAS  Article  PubMed  Google Scholar 

  50. Valdes M, Parez N-O, Estrada-de Los Santos P, Caballero-Mellado J, Pe-Cabriales JJ, Normand P, Hirsch AM (2005) Non-frankia actinomycetes isolated from surface-sterilized roots of Casuarina equisetifolia fix nitrogen. Appl Environ Microbiol 71:460–466

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  51. Vesth T, Lagesen K, Ãn A, Ussery D (2013) CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One 8:e60120

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. Wall LG (2000) The actinorhizal symbiosis. J Plant Growth Regul 19:167–182

    CAS  PubMed  Google Scholar 

  53. Wang J et al. (2010) Prauserella marina sp. nov., isolated from ocean sediment of the South China Sea. Int J Syst Evol Microbiol 60:985–989

    CAS  Article  PubMed  Google Scholar 

  54. Wheeler CT, Miller IM (1990) Current and potential uses of actinorhizal plants in Europe. The Biology of Frankia and Actinorhizal Plants 365:389

    Google Scholar 

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Acknowledgments

This work was supported by the USDA National Institute of Food and Agriculture Hatch 022821 (LST), and Department of Biotechnology, Govt. of West Bengal, India through grant no. 206/Bt (Estd.)/RD-22/2014 (AS). Authors acknowledge Department of Biotechnology, Govt. of India for the creation of Bioinformatics Facility at North Bengal University. IS acknowledges the receipt of BSR, UGC fellowship. Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number 2643. Sequencing was performed on an Illumina HiSeq2500 purchased with an NSF MRI Grant: DBI-1229361to WKThomas.

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Correspondence to Arnab Sen.

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

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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 USDA National Institute of Food and Agriculture Hatch 022821.

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The authors declare that they have no conflict of interest.

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Bose, D., Sarkar, I., Labar, R. et al. Comparative genomics of Prauserella sp. Am3, an actinobacterium isolated from root nodules of Alnus nepalensis in India. Symbiosis 70, 49–58 (2016). https://doi.org/10.1007/s13199-016-0401-3

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Keywords

  • Sequencing
  • MLSA
  • ANI score
  • Genome plasticity
  • Pan-core plot