Towards practical applications in quantum computational biology.

Fascinating progress in understanding our world at the smallest scales moves us to the border of a new technological revolution governed by quantum physics. By taking advantage of quantum phenomena, quantum computing devices allow a speedup in solving diverse tasks. In this Perspective, we discuss the potential impact of quantum computing on computational biology. Bearing in mind the limitations of existing quantum computing devices, we attempt to indicate promising directions for further research in the emerging area of quantum computational biology.

Regulation and evolution of malonate and propionate catabolism in proteobacteria.

Bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. In various bacteria, transcription of these genes is controlled by the GntR family transcription factors (TFs) MatR/MdcY and/or the LysR family transcription factor MdcR. Propionate is metabolized via the methylcitrate pathway, comprising enzymes encoded by the prp and acn genes. PrpR, the Fis family sigma 54-dependent transcription factor, is known to be a transcriptional activator of the prp genes. Here, we report a detailed comparative genomic analysis of malonate and propionate metabolism and its regulation in proteobacteria. We characterize genomic loci and gene regulation and identify binding motifs for four new TFs and also new regulon members, in particular, tripartite ATP-independent periplasmic (TRAP) transporters. We describe restructuring of the genomic loci and regulatory interactions during the evolution of proteobacteria.

Complete genome and proteome of Acholeplasma laidlawii.

We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.

A case of disseminated histoplasmosis following autologous stem cell transplantation for Hodgkin's lymphoma: an initial misdiagnosis with a false-positive serum galactomannan assay.

Systemic histoplasmosis is uncommonly reported in patients who have undergone bone marrow or solid organ transplantation. Diagnosis of systemic histoplasmosis in recipients of transplants may be hampered by lack of consideration of this infection in the differential diagnosis and may be confounded by conflicting information from other testing performed to evaluate for opportunistic infections in this population. We report successful treatment of a case of disseminated histoplasmosis in a patient with Hodgkin's lymphoma who had undergone autologous stem cell transplantation. The diagnosis was delayed by the finding of a positive serum galactomannan assay.

Use of the flux model of amino acid metabolism of Escherichia coli.

A program implementing a flux model of Escherichia coli metabolism was used to analyze the effects of the addition of amino acids (tryptophan, tyrosine, phenylalanine, leucine, isoleucine, valine, histidine, lysine, threonine, cysteine, methionine, arginine, proline) to minimal medium or media lacking nitrogen, carbon, or both. The overall response of the metabolic system to the addition of various amino acids to the minimal medium is similar. Glycolysis and the synthesis of pyruvate with its subsequent degradation to acetate via acetyl-CoA become more efficient, whereas the fluxes through the pentose phosphate pathway and the TCA cycle decrease. If amino acids are used as the sole source of carbon, nitrogen, or both, the changes in the flux distribution are determined mainly by the carbon limitation. The phosphoenolpyruvate to glucose-6-phosphate flux increases; the flux through the pentose phosphate path is directed towards ribulose-5-phosphate. Other changes are determined by the compounds that are the primary products of catabolism of the added amino acid.

Comparative genomics of regulation of heavy metal resistance in Eubacteria.

BACKGROUND: Heavy metal resistance (HMR) in Eubacteria is regulated by a variety of systems including transcription factors from the MerR family (COG0789). The HMR systems are characterized by the complex signal structure (strong palindrome within a 19 or 20 bp promoter spacer), and usually consist of transporter and regulator genes. Some HMR regulons also include detoxification systems. The number of sequenced bacterial genomes is constantly increasing and even though HMR resistance regulons of the COG0789 type usually consist of few genes per genome, the computational analysis may contribute to the understanding of the cellular systems of metal detoxification. RESULTS: We studied the mercury (MerR), copper (CueR and HmrR), cadmium (CadR), lead (PbrR), and zinc (ZntR) resistance systems and demonstrated that combining protein sequence analysis and analysis of DNA regulatory signals it was possible to distinguish metal-dependent members of COG0789, assign specificity towards particular metals to uncharacterized loci, and find new genes involved in the metal resistance, in particular, multicopper oxidase and copper chaperones, candidate cytochromes from the copper regulon, new cadmium transporters and, possibly, glutathione-S-transferases. CONCLUSION: Our data indicate that the specificity of the COG0789 systems can be determined combining phylogenetic analysis and identification of DNA regulatory sites. Taking into account signal structure, we can adequately identify genes that are activated using the DNA bending-unbending mechanism. In the case of regulon members that do not reside in single loci, analysis of potential regulatory sites could be crucial for the correct annotation and prediction of the specificity.

Alternative splicing and protein function.

BACKGROUND: Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data. RESULTS: We have developed a method that generates possible mRNA isoforms for human genes contained in the EDAS database, taking into account the effects of nonsense-mediated decay and translation initiation rules, and a procedure for offsetting the effects of uneven EST coverage. Then we computed the number of mRNA isoforms for genes from different functional categories. Genes encoding ribosomal proteins and genes in the category "Small GTPase-mediated signal transduction" tend to have fewer isoforms than the average, whereas the genes in the category "DNA replication and chromosome cycle" have more isoforms than the average. Genes encoding proteins involved in protein-protein interactions tend to be alternatively spliced more often than genes encoding non-interacting proteins, although there is no significant difference in the number of isoforms of alternatively spliced genes. CONCLUSION: Filtering for functional isoforms satisfying biological constraints and accounting for uneven EST coverage allowed us to describe differences in alternative splicing of genes from different functional categories. The observations seem to be consistent with expectations based on current biological knowledge: less isoforms for ribosomal and signal transduction proteins, and more alternative splicing of interacting and cell cycle proteins.

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.

MOTIVATION: Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured DNA motifs that are inverted or direct repeats or spaced motif pairs. However, these motifs are often difficult to identify owing to their high divergence. The motif structure included explicitly into the motif recognition algorithm improves recognition efficiency for highly divergent motifs as well as estimation of motif geometric parameters. RESULT: We present a modification of the Gibbs sampling motif extraction algorithm, SeSiMCMC (Sequence Similarities by Markov Chain Monte Carlo), which finds structured motifs of these types, as well as non-structured motifs, in a set of unaligned DNA sequences. It employs improved estimators of motif and spacer lengths. The probability that a sequence does not contain any motif is accounted for in a rigorous Bayesian manner. We have applied the algorithm to a set of upstream regions of genes from two Escherichia coli regulons involved in respiration. We have demonstrated that accounting for a symmetric motif structure allows the algorithm to identify weak motifs more accurately. In the examples studied, ArcA binding sites were demonstrated to have the structure of a direct spaced repeat, whereas NarP binding sites exhibited the palindromic structure. AVAILABILITY: The WWW interface of the program, its FreeBSD (4.0) and Windows 32 console executables are available at http://bioinform.genetika.ru/SeSiMCMC

Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.

Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.

Heat shock (sigma32 and HrcA/CIRCE) regulons in beta-, gamma- and epsilon-proteobacteria.

During heat shock, the main strategy of an organism is defense from denatured proteins. This is performed by chaperones that refold and proteases that cut abnormal proteins. In studying the sigma(32) and HrcA regulons in beta- and gamma-proteobacteria, we have found some new potential participants in the heat shock response and proposed the protein disulfide isomerase function for one of them. We describe the connection between the two regulons through cross-regulation of the HrcA repressor and sigma(32) in some beta-proteobacteria. Finally, we predict the binding signal for HrcA in epsilon-proteobacteria.

Finding weak motifs in DNA sequences.

Recognition of regulatory sites in unaligned DNA sequences is an old and well-studied problem in computational molecular biology. Recently, large-scale expression studies and comparative genomics brought this problem into a spotlight by generating a large number of samples with unknown regulatory signals. Here we develop algorithms for recognition of signals in corrupted samples (where only a fraction of sequences contain sites) with biased nucleotide composition. We further benchmark these and other algorithms on several bacterial and archaeal sites in a setting specifically designed to imitate the situations arising in comparative genomics studies.

Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.

In Bacillus subtilis, utilisation of xylose, arabinose and ribose is controlled by the transcriptional factors XylR, AraR and RbsR, respectively. Here we apply the comparative approach to the analysis of these regulons in the Bacillus/Clostridium group. Evolutionary variability of operon structures is demonstrated and operator sites for the main transcription factors are predicted. The consensus sequences for the XylR and RbsR binding sites vary in different subgroups of genomes. The functional coupling of gene clusters and the conservation of regulatory sites allow for detection of non-orthologous gene displacement of ribulose kinase in Enterococcus faecium and Clostridium acetobutylicum. Moreover, candidate catabolite responsive elements found upstream of most pentose-utilising genes suggest CcpA-mediated catabolite repression.

Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria.

The comparative approach to the recognition of transcription regulatory sites is based on the assumption that as long as a regulator is conserved in several genomes, one can expect that sets of co-regulated genes (regulons) and regulatory sites for the regulator in these genomes are conserved as well. We used this approach to analyze the ribose (RbsR), arabinose (AraC), and xylose (XylR) regulons of gamma Proteobacteria for which (almost) completely sequenced genomes were available. Candidate binding sites for RbsR and AraC were detected. The improved XylR site consensus was proposed. Potential new members of the xylose regulons were found in the Escherichia coli, Salmonella typhi, and Klebsiella pneumoniae genomes. The function of these new xylose-regulated operons is likely to be the utilization of oligosaccharides containing xylose. Finally, candidate cAMP receptor-protein sites were identified in the regulatory regions of the majority of RbsR-, AraC-, and XylR-regulated operons.

Gene recognition in eukaryotic DNA by comparison of genomic sequences.

MOTIVATION: Sequencing of complete eukaryotic genomes and large syntenic fragments of genomes makes it possible to apply genomic comparison for gene recognition. RESULTS: This paper describes a spliced alignment algorithm that aligns candidate exon chains of two homologous genomic sequence fragments from different species. The algorithm is implemented in Pro-Gen software. Unlike other algorithms, Pro-Gen does not assume conservation of the exon-intron structure. Amino acid sequences obtained by the formal translation of candidate exons are aligned instead of nucleotide sequences, which allows for distant comparisons. The algorithm was tested on a sample of human-mammal (mouse), human-vertebrate (Xenopus ) and human-invertebrate (Drosophila ) gene pairs. Surprisingly, the best results, 97-98% correlation between the actual and predicted genes, were obtained for more distant comparisons, whereas the correlation on the human-mouse sample was only 93%. The latter value increases to 95% if conservation of the exon-intron structure is assumed. This is caused by a large amount of sequence conservation in non-coding regions of the human and mouse genes probably due to regulatory elements. AVAILABILITY: Pro-Gen v. 3.0 is available to academic researchers free of charge at http://www.anchorgen.com/pro_gen/pro_gen.html.

Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria.

Computational comparative techniques were applied to analysis of the aromatic amino acid regulons in gamma-proteobacteria. This resulted in characterization of the TrpR and TyrR regulons in the genomes of Yersinia pestis, Haemophilus influenzae, Vibrio cholerae and other bacteria and identification of new members of the PhhR regulon in the genome of Pseudomonas aeruginosa. Candidate attenuators were constructed for all studied genomes, including the trpBA operon of the very distantly related bacterium Chlamidia trachomatis. The pheA attenuator of Y. pestis is an integration site for the insertion element IS-200. It was shown that the triplication of the DAHP-synthase genes occurred prior to the divergence of families Enterobacteriaceae, Vibrionaceae and Alteromonadaceae. The candidate allosteric control site of the DAHP-syntheases was identified. This site is deteriorated in AroH of Buchnera sp. APS. The known DAHP-synthase of Bordetella pertussis is likely to be feedback-inhibited by phenylalanine, and the DAHP-synthase of Corynebacterium glutamicum could be inhibited by tyrosine. Overall, the most extensive regulation was observed in Escherichia coli, whereas the regulation in other genomes seems to be less developed. At the extreme, the tryptophan production in the aphid endosymbiont Buchnera sp. APS is free from transcriptional, attenuation, and allosteric control.