Breakthroughs and Views On the origin of genomic adaptation at high temperature for prokaryotic organisms Surajit Basak, Tapash Chandra Ghosh * Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India Received 6 February 2005 Available online 11 March 2005 Abstract For a long time, the central issue of evolutionary genomics was to find out the adaptive strategy of nucleic acid molecules of various microorganisms having different optimal growth temperatures (T opt ). Long-standing controversies exist regarding the cor- relations between genomic G + C content and T opt , and this debate has not been yet settled. We address this problem by considering the fact that adaptation to growth at high temperature requires a coordinated set of evolutionary changes affecting: (i) nucleic acid thermostability and (ii) stability of codon–anticodon interactions. In the present study, we analyzed 16 prokaryotic genomes having intermediate G + C content and widely varying optimal growth temperatures. Results show that elevated growth temperature imposes selective constraints not only on nucleic acid level but also affects the stability of codon–anticodon interaction. We observed a decrease in the frequency of SSC and SSG codons with the increase in T opt to avoid the formation of side-by-side GC base pairs in the codon–anticodon interaction, thereby making it impossible for a genome to increase GC composition uniformly through the whole coding sequence. Thus, we suggest that any attempt to obtain a generalized relation between genomic GC composition and optimal growth temperature would hardly evolve any satisfactory result. Ó 2005 Elsevier Inc. All rights reserved. Keywords: Prokaryotes; Thermophiles; G + C contents; Codon–anticodon; Optimal growth temperature Evolutionary biology has long been attempted to find the adaptive mechanism of nucleic acids molecules under high growth temperatures. Considerable varia- tion in the guanine (G) and cytosine (C) content exists among the microorganisms. The causes of variation in the base compositions have remained the core issue be- tween selectionists and neutralists [1–4]. Thermal adap- tation hypothesis proposed by Bernardi gives a link between GC content and temperature if there exists considerable variation of guanine (G) and cytosine (C) content between species [4,5]. G:C pairs are ther- mally more stable than A:T pairs, G:C pairs being connected by three hydrogen bonds and A:T pairs by two [6]. However, some authors have failed to make any correlation between GC composition (or GC3) and temperature [7,8]. Recently, Musto et al. [9] claimed that positive correlation between genomic GC content and optimal growth temperature exists in most of the bacterial families they studied; but some anomalies have already been pointed out [10,11] regarding the flawless- ness of the data set considered by Musto et al. in their analysis. At the transcriptome level, interestingly, Galtier and Lobry [7] demonstrated that there is a significant corre- lation between G + C content of structural RNAs (such as ribosomal and transfer RNAs) and growth tempera- ture. Lobry and Chessel [12] observed a preference to- wards C- and G-ending codons for duet amino acids in thermophiles. However, they did not provide any 0006-291X/$ - see front matter Ó 2005 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2005.02.134 * Corresponding author. Fax: +91 33 2334 3886. E-mail address: tapash@boseinst.ernet.in (T.C. Ghosh). www.elsevier.com/locate/ybbrc Biochemical and Biophysical Research Communications 330 (2005) 629–632 BBRC