Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com

Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages

Bacteriophages infecting Mycobacterium smegmatis mc2155 are numerous and, hence, are classified into clusters based on nucleotide sequence similarity. Analyzing phages belonging to clusters/subclusters can help gain deeper insights into their biological features and potential therapeutic applications. In this study, for genomic characterization of B1 subcluster mycobacteriophages, a framework of online tools was developed, which enabled functional annotation of about 55% of the previously deemed hypothetical proteins in B1 phages. We also studied the phenotype, lysogeny status, and antimycobacterial activity of 10 B1 phages against biofilm and an antibiotic-resistant M. smegmatis strain (4XR1). All 10 phages belonged to the Siphoviridae family, appeared temperate based on their spontaneous release from the putative lysogens and showed antibiofilm activity. The highest inhibitory and disruptive effects on biofilm were 64% and 46%, respectively. This systematic characterization using a combination of genomic and experimental tools is a promising approach to furthering our understanding of viral dark matter.

Modeling the vibrational couplings of nucleobases

Vibrational spectroscopy, in particular infrared spectroscopy, has been widely used to probe the three-dimensional structures and conformational dynamics of nucleic acids. As commonly used chromophores, the C=O and C=C stretch modes in the nucleobases exhibit distinct spectral features for different base pairing and stacking configurations. To elucidate the origin of their structural sensitivity, in this work, we develop transition charge coupling (TCC) models that allow one to efficiently calculate the interactions or couplings between the C=O and C=C chromophores based on the geometric arrangements of the nucleobases. To evaluate their performances, we apply the TCC models to DNA and RNA oligonucleotides with a variety of secondary and tertiary structures and demonstrate that the predicted couplings are in quantitative agreement with the reference values. We further elucidate how the interactions between the paired and stacked bases give rise to characteristic IR absorption peaks and show that the TCC models provide more reliable predictions of the coupling constants as compared to the transition dipole coupling scheme. The TCC models, together with our recently developed through-bond coupling constants and vibrational frequency maps, provide an effective theoretical strategy to model the vibrational Hamiltonian, and hence the vibrational spectra of nucleic acids in the base carbonyl stretch region directly from atomistic molecular simulations.

Systematics for types and effects of RNA variations

Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.