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Special Feature: Recent advances in the nitrogen-fixing symbiosis between Frankia and actinorhizal plants

Niche adaptation of Frankia do not drastically influence their metabolic profiling

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Pages 100-105 | Received 02 Jul 2021, Accepted 04 Jan 2022, Published online: 26 Jan 2022

References

  • Abdellatif G, Swanson E, Amir K, Imen N, Karima H, Faten GG, and Tisa LS. 2017. Permanent draft genome sequences of three Frankia sp. strains that are atypical, noninfective, ineffective isolates. Microbiol Res Announce. 5(15):pp.e00174-17.
  • Akashi H, Gojobori T. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. PNAS. 99(6):3695–3700. doi:10.1073/pnas.062526999.
  • Beale D, Kouremenos K, Palombo E. 2016. Microbial metabolomics. Switzerland: Springer International Publishing.
  • Bernardi G, Bernardi G. 1986. Compositional constraints and genome evolution. J Mol. Evol 24(1–2):1–11. doi:10.1007/BF02099946.
  • Carthew RW. 2020. Gene Regulation and Cellular Metabolism: an Essential Partnership. Trends in Genetics. doi:10.1016/j.tig.2020.09.018
  • Gtari M, Ghodhbane-Gtari F, Nouioui I, Ktari A, Hezbri K, Mimouni W, Boudabous A. 2015. Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains. Sci Rep. 5(1):1–8. doi:10.1038/srep13112.
  • Johnson CH, Ivanisevic J, Benton HP, Siuzdak G. 2015. Bioinformatics: the next frontier of metabolomics. Analyt Chem. 87(1):147–156. doi:10.1021/ac5040693.
  • Kanehisa M. 2002. January The KEGG database. Bock, Gregory, and Goode, Jamie A. eds. Novartis Foundation Symposium. 91–100. Chichester; New York: John Wiley. 1999.
  • Kryazhimskiy S, Plotkin JB. 2008. The population genetics of dN/dS. PLoS Genet. 4(12):e1000304. doi:10.1371/journal.pgen.1000304.
  • Ktari A, Nouioui I, Furnholm T, Swanson E, Ghodhbane-Gtari F, Tisa LS, Gtari M. 2017. Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence of canonical nod genes, which are highly homologous to those detected in Candidatus Frankia Dg1 genome. Stand. In Genomic Sciences. 12(1):1–10.
  • Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, et al. 2012. IMG: the integrated microbial genomes database and comparative analysis system. NAR. 40(D1):D115–D122. doi:10.1093/nar/gkr1044.
  • Meister A. 2012. Biochemistry of the amino acids. New York: Elsevier.
  • Merrick BA, London RE, Bushel PR, Grissom SF, and Paules RS. 2011. Platforms for biomarker analysis using high-throughput approaches in genomics, transcriptomics, proteomics, metabolomics, and bioinformatics. Vol. 163, USA: IARC scientific publications. p. 121–142.
  • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. NAR. 35(suppl_2):W182–W185. doi:10.1093/nar/gkm321.
  • Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Benson DR. 2007. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res. 17(1):7–15. doi:10.1101/gr.5798407.
  • Nouioui I, Gtari M, Göker M, Ghodhbane-Gtari F, Tisa LS, Fernandez MP, … Klenk HP. 2016. Draft genome sequence of Frankia strain G2, a nitrogen-fixing actinobacterium isolated from Casuarina equisetifolia and able to nodulate actinorhizal plants of the order Rhamnales. Genome A. 4(3):e00437–16. doi:10.1128/genomeA.00437-16.
  • Nouioui I, Gueddou A, Ghodhbane-Gtari F, Rhode M, Gtari M, Klenk HP. 2017. Frankia asymbiotica sp. nov., a non-infective actinobacterium isolated from Morella californica root nodule. IJSEM. 67(12):4897–4901. doi:10.1099/ijsem.0.002153.
  • Oshone R, Hurst IV, Abebe-Akele SG, Simpson F, Morris S, Thomas, W. K K, Tisa LS. 2016. Permanent draft genome sequences for two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina. Genome A. 4(1):e01588–15. doi:10.1128/genomeA.01588-15.
  • Peden J. 1997. CodonW. University of Nottingham, England: Trinity College.
  • Pérez-Pantoja D, González B, and Pieper DH. 2010. Aerobic degradation of aromatic hydrocarbons. Berlin, Heidelberg: In Handbook of hydrocarbon and lipid microbiology.
  • Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chertkov O, Berry AM, Bruce DC, Detter C, Tapia R. 2011. Genome sequence of “Candidatus Frankia datiscae” Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot Datisca glomerata. J of Bacteriology. 193(24):24. doi:10.1128/JB.06208-11.
  • Putri SP, Nakayama Y, Matsuda F, Uchikata T, Kobayashi S, Matsubara A, Fukusaki E. 2013. Current metabolomics: practical applications. J. Of Biosc and Bioengi. 115(6):579–589. doi:10.1016/j.jbiosc.2012.12.007.
  • Reaves ML, Rabinowitz JD. 2011. Metabolomics in systems microbiology. Curr Opp in Biotechnol. 22(1):17–25. doi:10.1016/j.copbio.2010.10.001.
  • Sabi R, Volvovitch Daniel R, Tuller T. 2017. stAIcalc: tRNA adaptation index calculator based on species-specific weights. Bioinformatics. 33(4):589–591. doi:10.1093/bioinformatics/btw647.
  • Saha MS, Pal S, Sarkar I, Roy A, Mohapatra PKD, Sen A. 2019. Comparative genomics of Mycobacterium reveals evolutionary trends of M. Avium Complex. Genomics. 111(3):426–435.
  • Sarkar I, Tisa LS, Gtari M, Sen A. 2018. Biosynthetic energy cost of potentially highly expressed proteins varies with niche in selected actinobacteria. Journal of Basic Microbiology. 58(2):154–161. doi:10.1002/jobm.201700350.
  • Shulaev V. 2006. Metabolomics technology and bioinformatics. Brief Bioinform. 7(2):128–139. doi:10.1093/bib/bbl012.
  • Snel B. 2000. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res 28(18):3442–3444. doi:10.1093/nar/28.18.3442.
  • Sun Y, Wen J, Chen R. 2019. Variable protein homeostasis in housekeeping and non-housekeeping pathways under mycotoxins stress. Sci. Rep. 9(1):1–13. doi:10.1038/s41598-018-37186-2.
  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 4(1):1–14. doi:10.1186/1471-2105-4-41.
  • Teale FWJ, Weber G. 1957. Ultraviolet fluorescence of the aromatic amino acids. Biochemical Journal. 65(3):476. doi:10.1042/bj0650476.
  • Thomas GH. 2001. Metabolomics breaks the silence. TIM. 9(4):158.
  • Tisa LS, Beauchemin N, Gtari M, Sen A, Wall LG. 2013. What stories can the Frankia genomes start to tell us? J. Biosci 38(4):719–726. doi:10.1007/s12038-013-9364-1.
  • Wall LG, Beauchemin N, Cantor MN, Chaia E, Chen A, Detter JC, Tisa LS. 2013. Draft genome sequence of Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis. Genome Announc 1(4):e00503–13. doi:10.1128/genomeA.00503-13.
  • Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. 2020. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 181(2):281–292. doi:10.1016/j.cell.2020.02.058.
  • Xia X. 2001. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered 92(4):371–373. doi:10.1093/jhered/92.4.371.
  • Xu YJ, Wang C, Ho WE, Ong CN. 2014. Recent developments and applications of metabolomics in microbiological investigations. Trends Analyt Chem. 56:37–48. doi:10.1016/j.trac.2013.12.009.
  • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586–1591. doi:10.1093/molbev/msm088.
  • Zhang A, Sun H, Wang P, Han Y, Wang X. 2012. Modern analytical techniques in metabolomics analysis. Analyst. 137(2):293–300. doi:10.1039/C1AN15605E.

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