vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-22-98vavilov-3583Research ArticleКОМПЬЮТЕРНАЯ ГЕНОМИКАCOMPUTATIONAL GENOMICSСравнительный генетический анализ О-антигенов бактерий семейства Oxalobacteraceae: уникальность или тривиальность?Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae familyhttps://orcid.org/0000-0001-7969-8015АфонниковаС. Д.AfonnikovaS. D.

Новосибирск

Novosibirsk

svetaafonnikova@gmail.comhttps://orcid.org/0000-0001-6981-7316КомиссаровА. С.KomissarovA. S.

Санкт-Петербург

St. Petersburg

https://orcid.org/0000-0002-9415-577XКучурП. Д.KuchurP. D.

Санкт-Петербург

St. Petersburg

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityRussian FederationНациональный исследовательский университет ИТМО, Институт SCAMTРоссияITMO University, SCAMT InstituteRussian Federation202205012023268810818Copyright © Афонникова С.Д., Комиссаров А.С., Кучур П.Д., 20232023Афонникова С.Д., Комиссаров А.С., Кучур П.Д.Afonnikova S.D., Komissarov A.S., Kuchur P.D.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3583

Многие растения и животные способны устанавливать симбиотические взаимоотношения с микроорганизмами, в том числе с бактериями. Специфика этих взаимодействий может приводить к разным последствиям для организма-хозяина. Взаимоотношения могут быть нейтральными, негативными либо выгодными для одной или обеих сторон. Примечательно, что взаимоотношения бактерия-хозяин не являются статичными: они могут изменяться в течение жизни организмов и в ходе их эволюции. Одной из структур, определяющих направление изменчивости, является О-антиген. В зависимости от особенностей его компонентов бактерия может избегать иммунного ответа со стороны организма-хозяина, становясь патогеном, либо устанавливать с хозяином мутуалистические отношения. О-антиген – это ключевой компонент наружной мембраны грамотрицательных бактерий. Этот компонент обеспечивает взаимодействие между бактериями и иммунной системой хозяина или фагами. Вариабельность структуры О-антигенов тесно связана с изменчивостью генов, кодирующих компоненты его синтеза. Гены и пути синтеза О-антигенов наиболее детально изучены у бактерий из семейства Enterobacteriaceae. С учетом высокого генетического и молекулярного разнообразия этой структуры даже между штаммами эти результаты могут не отражать все разнообразие О-антигенов, представленное у немодельных видов. В настоящей работе проведен сравнительный анализ генов, участвующих в синтезе О-антигена, для бактерий из семейства Oxalobacteraceae. В отличиe от существующих исследований, преимущественно основанных на методе ПЦР, в нашей работе использован биоинформатический подход, а сравнение проведено не на уровне одиночных генов, а на уровне кластеров. Мы обнаружили, что в случае Oxalobacteraceae генетическая организация О-антигена представлена несколькими кластерами, находящимися на значительном удалении друг от друга в геноме бактерий. Наибольшее сходство кластеров наблюдалось внутри отдельных родов бактерий, что объясняется высокой изменчивостью О-антигенов. В работе описано сходство генов О-антигенов, присущее семейству в целом, а также рассмотрены отдельные уникальные случаи изменчивости их генетической структуры у отдельных бактерий.

Many plants and animals have symbiotic relationships with microorganisms, including bacteria. The interactions between bacteria and their hosts result in different outcomes for the host organism. The outcome can be neutral, harmful or have beneficial effects for participants. Remarkably, these relationships are not static, as they change throughout an organism’s lifetime and on an evolutionary scale. One of the structures responsible for relationships in bacteria is O-antigen. Depending on the characteristics of its components, the bacteria can avoid the host’s immune response or establish a mutualistic relationship with it. O-antigen is a key component in Gram-negative bacteria’s outer membrane. This component facilitates interaction between the bacteria and host immune system or phages. The variability of the physical structure is caused by the genomic variability of genes encoding O-antigen synthesis components. The genes and pathways of O-polysaccharide (OPS) synthesis were intensively investigated mostly for Enterobacteriaceae species. Considering high genetic and molecular diversity of this structure even between strains, these findings may not have caught the entire variety possibly presented in non-model species. The current study presents a comparative analysis of genes associated with O-antigen synthesis in bacteria of the Oxalobacteraceae family. In contrast to existing studies based on PCR methods, we use a bioinformatics approach and compare O- anti gens at the level of clusters rather than individual genes. We found that the O-antigen genes of these bacteria are represented by several clusters located at a distance from each other. The greatest similarity of the clusters is observed within individual bacterial genera, which is explained by the high variability of O-antigens. The study describes similarities of OPS genes inherent to the family as a whole and also considers individual unique cases of O-antigen genetic variability inherent to individual bacteria.

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The authors declare that there are no conflicts of interest present.