Boletín de la Sociedad Geológica Mexicana ISSN: 1405-3322 [email protected] Sociedad Geológica Mexicana, A.C. México Vázquez, Héctor G.; Becerra, Arturo DNA structure and architecture in the chromosome and plasmid of hyperthermophilic organisms, a theoretical approach Boletín de la Sociedad Geológica Mexicana, vol. 68, núm. 1, 2016, pp. 1-8 Sociedad Geológica Mexicana, A.C. Distrito Federal, México Available in: http://www.redalyc.org/articulo.oa?id=94344822016 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative DNA structure in hypertermophiles 1 Boletín de la Sociedad Geológica Mexicana Volumen 68, núm. 1, 2016, p. ###-### D GEOL DA Ó E G I I C C O A S 1904 M 2004 . C EX . ICANA A C i e n A ñ o s DNA structure and architecture in the chromosome and plasmid of hyperthermophilic organisms, a theoretical approach Héctor G. Vázquez1, Arturo Becerra1,* 1 Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Delegación Coyoacán, 04510 México, D.F., México. * [email protected] Abstract Hyperthermophilic organisms have been recognized as an important element in the origin and early evolution of life on Earth, but also as a model for exobiological studies. Analyzing their molecular dynamics can help us understand this important lifestyle. In this study, using bioinformatic tools, the DNA composition in chromosomes and plasmids of hyperthemophilic organism were compared, and their structure, probable amino acid bias and DNA flexibility were analyzed. In some chromosomes and plasmids shows differen- tial features of DNA flexibility and skews in mutation rate, which suggests that only some molecular elements show high values of variability, contrary to the proposal of the flexible genome theory. Keywords: chromosome, plasmids, Quintana values, DNA twisting, codon usage, hyperthermophiles. Resumen Los organismos hipertermofílicos han sido reconocidos tanto como un elemento importante en el origen y la evolución temprana de la vida en la Tierra, como un modelo en estudios de exobiología. Analizar sus dinámicas moleculares nos puede ayudar a entender este importante estilo de vida. En este estudio, usando scripts y software, se comparó la composición del DNA en los cromosomas y plásmidos de organismos hipertermófilos, y se analizó su estructura, su probable sesgo en el uso de aminoácidos y la flexibilidad del DNA. En algunos cromosomas y plásmidos se presentaron características diferenciales de flexibilidad del DNA y sesgos en su tasa de mutación, lo cual sugiere que sólo algunos elementos moleculares muestran altos niveles de variabilidad, contrariamente a lo propuesto en la teoría de genoma flexible. Palabras clave: cromosoma, plásmidos, valores de Quintana, torsión de DNA, uso de codones, hipertermófilos. 1. Introduction limits of parameters such as temperature, pH and salinity, and can have biochemical dependencies on different Studies on extremophilic microorganisms have been organic and inorganic compounds like sulfur, nitrogen, a breakthrough for the fields of biochemistry (Xu and methane or even ferrous oxides (respectively) (Stetter Glansdorff, 2002; Conners et al., 2006), biotechnology et al., 1990). The respiration reactions of these organisms (Vieille and Zeikus, 2001; Guiral et al., 2012) and early increase our awareness of what we might find outside our evolution, broadening our understanding of the limits of planet (Trent, 2000). It is necessary to integrate a clear life (Nisbet and Sleep, 2001; Allers and Mevarech, 2005). approach to the study of these organisms to recognize new Extremophiles are organisms that surpass the mesophilic trends and molecular signatures in different environments. 2 Vázquez & Becerra One of the extremophilic lifestyles that has been heavily to different phylogenetic groups. studied due to its impact in early evolution (Islas et al., Since codon usage have a differential appearance in 2003) and its biochemical diversification is the group the coding sequences, there are different ways to measure of hyperthermophilic prokaryotes from the Archaea the structure and topology of the genome. One approach and Bacteria domains (Stetter, 2006). A large number consists of recognizing dinucleotide interaction in the of studies involving hyperthermophilic prokaryotes are entire DNA sequence and correlating it with the DNA based on their multiple strategies for survival and their twist profile. As noted by Quintanaet al. (1992), the DNA stability in high-temperature environments (Stetter et al., crystallography profiles correlate the DNA twist with the 1990). There is no single molecule or metabolic pathway space and configuration among dimers. The High twist unique for this lifestyle (Atomi et al., 2004), and finding a profile (H value) indicates the incidence of sequence of pattern or common properties in all the described species dinucleotides GC or GA, and elevated values of DNA remains elusive (Trent, 2000; Allers and Mevarech, 2005). twist and space among nucleotide dimers. In contrast, the However, it is possible to associate some molecular Low twist profile (L value) is present where the sequence traits with nucleotide and amino acid levels, beyond any has a high frequency of CC, CT, TT, AA, AG and GG phylogenetic groups with hyperthermophilic character. dimers. These configurations present the values of twist and In this regard, Groussin and Gouy (2011) recognize two separation between the dimers. The Variable twist profile main characteristic processes in the hyperthermophilic (V value) is a combination of both configurations and is lifestyle: a) the molecular evolutionary rate is skewed correlated with the incidence of pyrimidine and purine by the optimal growth temperature and tRNA-coding dimers, a conformation that is strongly susceptible to the genes, and b) it is possible to correlate the optimal growth influence of the environment. temperature with multiple components of coding and non- This paper focuses primarily on the comparative coding sequences. Also, Klipcan et al. (2006) correlated genomics, with special emphasis on the evolution of the the optimal growth temperature with the proportion and extremophilic genomes. For the codon usage analysis, type of aminoacyl-tRNA synthases (aatRNAs). Agarwal we review Jaenicke et al. (1991), which implied that a and Grover (2008) recognize a purine bias that modifies decrease in non-charged amino acids allows discrimination the amino acid frequency and codon usage. Therefore, between extremophile and mesophile proteomes. Also, it has not yet been possible to recognize common genes Zeldovich et al. (2007) correlate the increase in the use of for all the hyperthermophilic genomes, but it is feasible seven amino acids (IVYWREL) with a raise in the optimal to discover biases and proportions in amino acids and growth temperature. Using both approaches—analysis in nucleotides that could define a differential composition in DNA twist profile and codon usage—we tried to identify a this lifestyle. As it has been proposed (Cordero and Polz, shared trait among the chromosomes and plasmids of some 2014), the hyperthermophilic genome can be studied in two hyperthermophilic organisms. If found, we might recognize main sections: 1) the core genome that is composed of all common characteristics for the hyperthermophilic lifestyle. the housekeeping genes involved in basic metabolism, and 2) the flexible genome, which is shaped by genes related to habitat-specific properties, as well as interaction between 2. Methods viruses and predators. These genes have a variable presence in the entire genome, and are involved in horizontal gene In order to classify and recognize the optimal temperature transfer events, gene loss and high rates of gene turnovers. interval for the proposed archaeal and bacterial species, we With these pangenomic studies, it is possible to infer use the National Center for Biotechnology and Information that the bacterial chromosomes are composed of genes from (NCBI) database (www.ncbi.nlm.nih.gov). These data are the core and flexible genomes, but the extrachromosomal compiled in Table 1. A total of eight hyperthermophilic materials, like the plasmids, are composed mainly of genes species with complete chromosome and plasmid sequences related with the flexible genome. were obtained from the ftp site of NCBI. The eight species By studying the plasmid genome, it is possible to include three Crenarchaeota (Sulfolobus islandicus L.D.8.5, recognize the arrangement of the structure of the DNA Sulfolobus islandicus Y.N.15.51, and Thermofilum pendens and the variance of codon usage in the same organism. Hrk5), four Euryarchaeota (Archaeoglobus profundus DSM Berg and Kurland (2002) and Cordero and Polz (2014) 5631, Methanococcus maripaludis C5, Pyrococcus abyssi proposed that the study of the flexible genome allows the and Thermococcus barophilus MP), and one species from identification of global or individual genes that can be used Bacteria (Aquifex aeolicus VF5). A mesophilic organism as the reflection of the prokaryotic community sharing the (Escherichia coli O157 H7) was used as a negative control same environmental conditions. Also, according to Cooper organism. We chose this strain because of their mesophilic et al. (2010), secondary bioinformational elements (like lifestyle