Studies of protein and genome structure in the single-stranded RNA bacteriophages

Elektroniskā versija nesatur pielikumusVairāki vienpavediena RNS bakteriofāgu dzīves cikla aspekti vēl arvien ir maz izprasti, it sevišķi no strukturālā skatpunkta. Darba gaitā tika noskaidrota bakteriofāga Qβ minorā apvalka proteīna A1 trīsdimensionālā struktūra, kas atklāja neredzētu proteīnu folda veidu un citas interesantas iezīmes. Tika noteikta kristālstruktūra arī Qβ apvalka proteīna kompleksam ar RNS matadatas veida struktūru replikāzes gēna sākumā, kuru apvalka proteīns specifiski saista. Šī struktūra parādīja veidu, kā apvalka proteīns atpazīst RNS, izmantojot galvenokārt tās pamatķēdes konformāciju, nevis daudzas sekvences specifiskas mijiedarbības. Papildus ieskats fāgu genomu un tajos esošo RNS sekundāro struktūru evolūcijā tika gūts, nosekvenējot genomu RNS bakteriofāgam M, kā arī analizējot bakteriofāga φCb5 genoma sekvenci. Atslēgas vārdi: RNS bakteriofāgs; proteīnu struktūra; proteīnu – RNS mijiedarbība; RNS sekundārā struktūraSeveral aspects of the life cycle of the single-stranded RNA bacteriophages are still poorly understood, particularly from the structural viewpoint. During this work, the three-dimensional structure of the minor coat protein A1 from bacteriophage Qβ was determined, which revealed a new protein fold and other intriguing features. A crystal structure was also solved of the Qβ coat protein in complex with an RNA hairpin at the beginning of the replicase gene, which the coat protein specifically binds to. The structure showed how the coat protein recognizes RNA based primarily on its backbone conformation instead of many sequence-specific interactions. Further insight into the evolution of phage genomes and RNA secondary structures in them was gained by sequencing the genome of RNA phage M and by analyzing the genome sequence of phage φCb5. Keywords: RNA bacteriophage; protein structure; protein – RNA interaction; RNA secondary structur

Guidance for creating individual and batch latinized binomial virus species names

The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages

The Mystical Practice of Sufism and its Parallels in the Tradition of Hesychasm

Mūsdienās, kad pasaules globalizācijas laikmetā islāma un kristietības pasaules pārklājas vai saduras vairāk, kā jebkad iepriekš pasaules vēsturē, šis darbs pievēršas šo divu reliģiju aspektam, kam ir plašākais potenciāls tās tuvināt. Patiesi, gan hesihasms, gan sūfisms aicina uz mieru, mīlestību un sevis izkopšanu, taču jautājums, vai to starpā nav saskatāmas arī sīkāka rakstura paralēles un vai šīs prakses var pastāvēt līdzās. Darba gaitā pētīti abi mistiskie novirzieni no vēsturiskā, doktrinālā, kā arī praktiskā aspekta, paralēli meklējot līdzības starp tiem. Rezultātā iegūti secinājumi un atrastas paralēles vairākos aspektos, kas ļauj izvērtēt darba hipotēzi, proti, ka sūfismu un hesihasmu saista paralēles gan domās un doktrīnā, gan arī praksē un rituālos, kā rezultātā šie pacifistiskie misticisma novirzieni nav savstarpēji izslēdzoši.With the modern globalized world having forced the religions of Islam and Christianity to overlap and collide more than ever, the present study addresses a certain aspect of both that has the potential of bringing them closer. Indeed, both Sufism and Hesychasm uphold peace, love and self-improvement; however the question arises, whether more subtle parallels can be found between them and is there the potential for coexistence. Both mystical paths are addressed from the historical, doctrinal as well as the practical aspect indicating the parallels found among them. As a result several conclusions have arisen which help evaluate the hypothesis of the study – Sufism and Hesychasm is interlinked by parallels in thought and doctrine, as well as practice and rituals as a result of which these pacifistic mystic paths are not mutually exclusive

Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data

Abstract Background Protein shells assembled from viral coat proteins are an attractive platform for development of new vaccines and other tools such as targeted bioimaging and drug delivery agents. Virus-like particles (VLPs) derived from the single-stranded RNA (ssRNA) bacteriophage coat proteins (CPs) have been important and successful contenders in the area due to their simplicity and robustness. However, only a few different VLP types are available that put certain limitations on continued developments and expanded adaptation of ssRNA phage VLP technology. Metagenomic studies have been a rich source for discovering novel viral sequences, and in recent years have unraveled numerous ssRNA phage genomes significantly different from those known before. Here, we describe the use of ssRNA CP sequences found in metagenomic data to experimentally produce and characterize novel VLPs. Results Approximately 150 ssRNA phage CP sequences were sourced from metagenomic sequence data and grouped into 14 different clusters based on CP sequence similarity analysis. 110 CP-encoding sequences were obtained by gene synthesis and expressed in bacteria which in 80 cases resulted in VLP assembly. Production and purification of the VLPs was straightforward and compatible with established protocols, with the only exception that a considerable proportion of the CPs had to be produced at a lower temperature to ensure VLP assembly. The VLP morphology was similar to that of the previously studied phages, although a few deviations such as elongated or smaller particles were noted in certain cases. In addition, stabilizing inter-subunit disulfide bonds were detected in six VLPs and several possible candidate RNA structures in the phage genomes were identified that might bind to the coat protein and ensure specific RNA packaging. Conclusions Compared to the few types of ssRNA phage VLPs that were used before, several dozens of new particles representing ten distinct similarity groups are now available with a notable potential for biotechnological applications. It is believed that the novel VLPs described in this paper will provide the groundwork for future development of new vaccines and other applications based on ssRNA bacteriophage VLPs

Guidance for creating individual and batch latinized binomial virus species names

International audienceThe International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

International audienceThis article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae , Siphoviridae , and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved