Chromosome evolution with naked eye: palindromic context of the life origin

Mycobacterium Lrp/AsnC family transcriptional factor modulates the arginase pathway as both a sensor and a transcriptional repressor

L-Arginine is the precursor of nitric oxide (NO), a host immune effector against intracellular pathogens including Mycobacterium tuberculosis (M. tb). Pathogens including M. tb have evolved various strategies targeting arginine to block the production of NO for better survival and proliferation. However, L-arginine metabolism and regulation in Mycobacterium are poorly understood. Here, we report the identification of M. smegmatis MSMEG_1415 (homolog of M. tb Rv2324) as an arginine-responsive transcriptional factor regulating the arginase pathway. In the absence of L-arginine, MSMEG_1415 acts as a repressor to inhibit the transcription of the roc (for arginine, ornithine catabolism) gene cluster, thereby switching off the arginase pathway. Treatment with L-arginine relieves the transcriptional inhibition of MSMEG_1415 on the roc gene cluster to activate the arginase pathway. Moreover, the L-arginine-MSMEG_1415 complex activates the transcription of the roc gene cluster by recognizing and binding a 15-bp palindrome motif, thereby preventing the excess accumulation of L-arginine in M. smegmatis. Physiologically, MSMEG_1415 confers mycobacteria resistance to starvation and fluoroquinolones exposure, suggestive of its important role in M. smegmatis persistence. The results uncover a unique regulatory mechanism of arginine metabolism in mycobacteria and identify M. tb Rv2324 as an attractive candidate target for the design of drugs against tuberculosis.

Mapping Biomolecular Sequences: Graphical Representations - their Origins, Applications and Future Prospects

The exponential growth in the depositories of biological sequence data have generated an urgent need to store, retrieve and analyse the data efficiently and effectively for which the standard practice of using alignment procedures are not adequate due to high demand on computing resources and time. Graphical representation of sequences has become one of the most popular alignment-free strategies to analyse the biological sequences where each basic unit of the sequences - the bases adenine, cytosine, guanine and thymine for DNA/RNA, and the 20 amino acids for proteins - are plotted on a multi-dimensional grid. The resulting curve in 2D and 3D space and the implied graph in higher dimensions provide a perception of the underlying information of the sequences through visual inspection; numerical analyses, in geometrical or matrix terms, of the plots provide a measure of comparison between sequences and thus enable study of sequence hierarchies. The new approach has also enabled studies of comparisons of DNA sequences over many thousands of bases and provided new insights into the structure of the base compositions of DNA sequences In this article we review in brief the origins and applications of graphical representations and highlight the future perspectives in this field.

Alignment-Free Analyses of Nucleic Acid Sequences Using Graphical Representation (with Special Reference to Pandemic Bird Flu and Swine Flu)

The exponential growth in database of bio-molecular sequences have spawned many approaches towards storage, retrieval, classification and analyses requirements. Alignment-free techniques such as graphical representations and numerical characterisation (GRANCH) methods have enabled some detailed analyses of large sequences and found a number of different applications in the eukaryotic and prokaryotic domain. In particular, recalling the history of pandemic influenza in brief, we have followed the progress of viral infections such as bird flu of 1997 onwards and determined that the virus can spread conserved over space and time, that influenza virus can undergo fairly conspicuous recombination-like events in segmented genes, that certain segments of the neuraminidase and hemagglutinin surface proteins remain conserved and can be targeted for peptide vaccines. We recount in some detail a few of the representative GRANCH techniques to provide a glimpse of how these methods are used in formulating quantitative sequence descriptors to analyse DNA, RNA and protein sequences to derive meaningful results. Finally, we survey the surveillance techniques with a special reference to how the GRANCH techniques can be used for the purpose and recount the forecasts made of possible metamorphosis of pandemic bird flu to pandemic human infecting agents.

Descriptors of 2D-dynamic graphs as a classification tool of DNA sequences

A new tool of the classification of DNA sequences is introduced. The method is based on 2D-dynamic graphs and their descriptors. Using the descriptors created by centers of masses, moments of inertia, angles between the x axis and the principal axis of inertia of the 2D-dynamic graphs one can obtain classification diagrams in which similar sequences are clustered in separated areas.

Analysis of compensatory substitution and gene evolution on the MAGEA/CSAG-palindrome of the primate X chromosomes

The human X chromosome contains a large number of inverted repeat DNA palindromes. Although arbitrary substitutions destroyed the inverted repeat structure of MAGEA/CSAG-palindrome during the evolutionary process of the primates, most of the substitutions are compensatory. Using maximum parsimony, it is demonstrated that the compensatory substitutions are prone to occur between bases with similar structures on the human, chimpanzee and orangutan MAGEA/CSAG-palindromes. Furthermore, it is found that MAGEA/CSAG genes also exist in orangutan and rhesus monkey palindromes by homologous searching. This suggests that the MAGEA/CSAG-palindrome might predate the divergence of human and other primate lineages. Comparative sequence analysis of the arms and genes on the primate MAGEA/CSAG-palindromes provides possible evidence of subsequently arm to arm gene conversion. These compensatory substitutions on the MAGEA/CSAG-palindrome of the primate X chromosomes play an important role in maintaining their structural symmetry during the process of formation.

Intermittency as a universal characteristic of the complete chromosome DNA sequences of eukaryotes: from protozoa to human genomes

Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. Using the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent in these sequences, such as segmental duplications, tandem repeats, and other complex sequence structures. It is shown that the recently discovered gene number balance on the strands is not of a random nature, and certain subsystems of a complete chromosome DNA sequence exhibit the properties of deterministic chaos.

Graphical representation and mathematical characterization of protein sequences and applications to viral proteins

Graphical representation and numerical characterization (GRANCH) of nucleotide and protein sequences is a new field that is showing a lot of promise in analysis of such sequences. While formulation and applications of GRANCH techniques for DNA/RNA sequences started just over a decade ago, analyses of protein sequences by these techniques are of more recent origin. The emphasis is still on developing the underlying technique, but significant results have been achieved in using these methods for protein phylogeny, mass spectral data of proteins and protein serum profiles in parasites, toxicoproteomics, determination of different indices for use in QSAR studies, among others. We briefly mention these in this chapter, with some details on protein phylogeny and viral diseases. In particular, we cover a systematic method developed in GRANCH to determine conserved surface exposed peptide segments in selected viral proteins that can be used for drug and vaccine targeting. The new GRANCH techniques and applications for DNAs and proteins are covered briefly to provide an overview to this nascent field.

Computational analysis and determination of a highly conserved surface exposed segment in H5N1 avian flu and H1N1 swine flu neuraminidase

Background

Catalytic activity of influenza neuraminidase (NA) facilitates elution of progeny virions from infected cells and prevents their self-aggregation mediated by the catalytic site located in the body region. Research on the active site of the molecule has led to development of effective inhibitors like oseltamivir, zanamivir etc, but the high rate of mutation and interspecies reassortment in viral sequences and the recent reports of oseltamivir resistant strains underlines the importance of determining additional target sites for developing future antiviral compounds. In a recent computational study of 173 H5N1 NA gene sequences we had identified a 50-base highly conserved region in 3'-terminal end of the NA gene.

Results

We extend the graphical and numerical analyses to a larger number of H5N1 NA sequences (514) and H1N1 swine flu sequences (425) accessed from GenBank. We use a 2D graphical representation model for the gene sequences and a Graphical Sliding Window Method (GSWM) for protein sequences scanning the sequences as a block of 16 amino acids at a time. Using a protein sequence descriptor defined in our model, the protein sliding scan method allowed us to compare the different strains for block level variability, which showed significant statistical correlation to average solvent accessibility of the residue blocks; single amino acid position variability results in no correlation, indicating the impact of stretch variability in chemical environment. Close to the C-terminal end the GSWM showed less descriptor-variability with increased average solvent accessibility (ASA) that is also supported by conserved predicted secondary structure of 3' terminal RNA and visual evidence from 3D crystallographic structure.

Conclusion

The identified terminal segment, strongly conserved in both RNA and protein sequences, is especially significant as it is surface exposed and structural chemistry reveals the probable role of this stretch in tetrameric stabilization. It could also participate in other biological processes associated with conserved surface residues. A RNA double hairpin secondary structure found in this segment in a majority of the H5N1 strains also supports this observation. In this paper we propose this conserved region as a probable site for designing inhibitors for broad-spectrum pandemic control of flu viruses with similar NA structure.

Empirical relationship between intra-purine and intra-pyrimidine differences in conserved gene sequences

DNA sequences seen in the normal character-based representation appear to have a formidable mixing of the four nucleotides without any apparent order. Nucleotide frequencies and distributions in the sequences have been studied extensively, since the simple rule given by Chargaff almost a century ago that equates the total number of purines to the pyrimidines in a duplex DNA sequence. While it is difficult to trace any relationship between the bases from studies in the character representation of a DNA sequence, graphical representations may provide a clue. These novel representations of DNA sequences have been useful in providing an overview of base distribution and composition of the sequences and providing insights into many hidden structures. We report here our observation based on a graphical representation that the intra-purine and intra-pyrimidine differences in sequences of conserved genes generally follow a quadratic distribution relationship and show that this may have arisen from mutations in the sequences over evolutionary time scales. From this hitherto undescribed relationship for the gene sequences considered in this report we hypothesize that such relationships may be characteristic of these sequences and therefore could become a barrier to large scale sequence alterations that override such characteristics, perhaps through some monitoring process inbuilt in the DNA sequences. Such relationship also raises the possibility of intron sequences playing an important role in maintaining the characteristics and could be indicative of possible intron-late phenomena.

Hidden chromosome symmetry: in silico transformation reveals symmetry in 2D DNA walk trajectories of 671 chromosomes

Maps of 2D DNA walk of 671 examined chromosomes show composition complexity change from symmetrical half-turn in bacteria to pseudo-random trajectories in archaea, fungi and humans. In silico transformation of gene order and strand position returns most of the analyzed chromosomes to a symmetrical bacterial-like state with one transition point. The transformed chromosomal sequences also reveal remarkable segmental compositional symmetry between regions from different strands located equidistantly from the transition point. Despite extensive chromosome rearrangement the relation of gene numbers on opposite strands for chromosomes of different taxa varies in narrow limits around unity with Pearson coefficient r = 0.98. Similar relation is observed for total genes' length (r = 0.86) and cumulative GC (r = 0.95) and AT (r = 0.97) skews. This is also true for human coding sequences (CDS), which comprise only several percent of the entire chromosome length. We found that frequency distributions of the length of gene clusters, continuously located on the same strand, have close values for both strands. Eukaryotic gene distribution is believed to be non-random. Contribution of different subsystems to the noted symmetries and distributions, and evolutionary aspects of symmetry are discussed.

Genome Projector: zoomable genome map with multiple views

BACKGROUND

Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional nature of biological information, software interfaces for database browsing should provide an intuitive interface that allows for rapid migration across different views and scales. The Zoomable User Interface (ZUI) and tabbed browsing have proven successful for this purpose in other areas, especially to navigate the vast information in the World Wide Web.

RESULTS

This paper presents Genome Projector, a Web-based gateway for genomics information with a zoomable user interface using Google Maps API, equipped with four seamlessly accessible and searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. The Web application for 320 bacterial genomes is available at http://www.g-language.org/GenomeProjector/. All data and software including the source code, documentations, and development API are freely available under the GNU General Public License. Zoomable maps can be easily created from any image file using the development API, and an online data mapping service for Genome Projector is also available at our Web site.

CONCLUSION

Genome Projector is an intuitive Web application for browsing genomics information, implemented with a zoomable user interface and tabbed browsing utilising Google Maps API and Asynchronous JavaScript and XML (AJAX) technology.