Abstract
The TTA codon, one of the six available codons for the amino acid leucine, is the rarest codon among the high GC genomes of Actinobacteria including Frankia. This codon has been implicated in various regulatory mechanisms involving secondary metabolism and morphological development. TTA-mediated gene regulation is well documented in Streptomyces coelicolor, but that role has not been investigated in other Actinobacteria including Frankia. Among the various Actinomycetes with a GC content of more than 70%, Frankia genomes had the highest percentages of TTA-containing genes ranging from 5.2 to 10.68% of the genome. In contrast, TTA-bearing genes comprised 1.7, 3.4 and 4.1% of the Streptomyces coelicolor, S. avermitilis and Nocardia farcinia genomes, respectively. We analyzed their functional role, evolutionary significance, horizontal acquisition and the codon-anticodon interaction. The TTA-bearing genes were found to be well represented in metabolic genes involved in amino acid transport and secondary metabolism. A reciprocal Blast search reveal that many of the TTA-bearing genes have orthologs in the other Frankia genomes, and some of these orthologous genes also have a TTA codon in them. The gene expression level of TTA-containing genes was estimated by the use of the codon adaption index (CAI), and the CAI values were found to have a positive correlation with the GC3 (GC content at the 3rd codon position). A full-atomic 3D model of the leucine tRNA recognizing the TTA (UUA) codon was generated and utilized for in silico docking to determine binding affinity in codon-anticodon interaction. We found a proficient codon-anticodon interaction for this codon which is perhaps why so many genes hold on to this rare codon without compromising their translational efficiency.
This is a preview of subscription content, log in via an institution to check access.
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
An CS, Willis JH, Riggsby WS, Mullin BC (1983) Deoxyribonucleic acid base composition of 12 Frankia isolates. Can J Bot 61:2859–2862
Baker D, Newcomb W, Torrey JG (1980) Characterization of an ineffective actinorhizal microsymbiont, Frankia sp. EuI1 (Actinomycetales). Can J Microbiol 26:1072–1089
Benson DR, Silvester WB (1993) Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol Rev 57:293–319
Bickhart D, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009) Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia. BMC Genomics 10:468
Chandra G, Chater KF (2008) Evolutionary flux of potentially bldA-dependent Streptomyces genes containing the rare leucine codon TTA. Anton van Leewen 94:111–126
Chater KF (2006) Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics. Philos Trans R Soc Lond B Biol Sci 361:761–768
Davis IW, Leaver-Fay A, Chen VB, Block JN et al (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375–W383
dos Reis M, Savva R, Wernisch L (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 32:5036–5044
Grosjean H, Fiers W (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18:199–209
Han K, Nepal C (2007) PRI-modeler: extracting RNA structural elements from PDB files of protein–RNA complexes. FEBS Lett 581:1881–1890
Havgaard JH, Torarinsson E, Gorodkin J (2007) Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLOS Comput Biol 3:1896–1908
Hu T, Banzhaf W (2008) Nonsynonymous to synonymous substitution ratio ka/ks: measurement for rate of evolution in evolutionary computation. PPSN X. LNCS 5199:448–457
Hurst L (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet 18:486–489
Jonikas MA, Radmer RJ, Altman RB (2009) Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics 25:3259–3266
Lawrence JG, Ochman H (1997) Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383–397
Leskiw BK, Bibb MJ, Chater KF (1991) The use of a rare codon specifically during development? Mol Microbiol 5:2861–2867
Li W, Wu J, Tao W, Zhao C, Wang Y, He X, Chandra G et al (2007) A genetic and bioinformatic analysis of Streptomyces coelicolor genes containing TTA codons, possible targets for regulation by a developmentally significant tRNA. FEMS Microbiol Lett 266:20–28
Lindahl E, Hess B, Vander Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–307
Lodwig EM, Hosie AH, Bourdès A, Findlay K, Allaway D et al (2003) Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature 422:722–726
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
Markowitz VM, Ivanova N, Palaniappan K, Szeto E et al (2006) An experimental metagenome data management and analysis system. Bioinformatics 22:e359–e367
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639–1662
Normand P, Lapierre P, Tisa LS, Gogarten JP et al (2007) Genome characteristics of facultative symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 7:7–15
Peden J (1999) Analysis of codon usage. PhD thesis, The University of Nottingham, UK
Puigbò P, Bravo IG, Garcia-Vallve S (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct 3:38
Sen A, Sur S, Bothra AK, Benson DR, Normand P, Tisa LS (2008) The implication of life style of codon usage patterns and predicted highly expressed genes for three Frankia genomes. Anton van Leewen 93:335–346
Sharp PM, Li WH (1987) The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295
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
Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, Sinderen DV (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71:495–548
Zhang Z, Li J, Zhao XQ, Whang J, Wang GK, Yu J (2006) KaKs_calculator: calculating Ka and Ks through model selection and model averaging. Genomic Proteomic Bioinform 4:259–263
Acknowledgments
The authors are grateful to the Department of Biotechnology, Government of India, for providing financial help in setting up Bioinformatics Centre, in the Department of Botany, University of North Bengal. A Sen acknowledges the receipt of Department of Biotechnology, Overseas Associateship. ST would like to thanks University Grant Commission for providing the UGC-BSR Research Fellowship.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by Erko Stackebrandt.
Electronic supplementary material
Below is the link to the electronic supplementary material.
203_2011_731_MOESM2_ESM.xls
Supplemental Table 2: List of TTA- containing genes with their proposed function in different Frankia genomes. Supplementary material 2 (XLS 1121 kb)
203_2011_731_MOESM3_ESM.xls
Supplemental Table 3: List of Potentially highly expressed genes with TTA codon in different Frankia genomes. Supplementary material 3 (XLS 40 kb)
Rights and permissions
About this article
Cite this article
Sen, A., Thakur, S., Bothra, A.K. et al. Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes. Arch Microbiol 194, 35–45 (2012). https://doi.org/10.1007/s00203-011-0731-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00203-011-0731-8