Scholarly record
STRESS AND IMMUNITY OF NODULE BACTERIA SINORHIZOBIUM MELILOTI: LOCALIZATION, POLYMORPHISM AND PHYLOGENY OF GENETIC DETERMINANTS
Abstract
Sinorhizobium meliloti are agriculturally valuable species of soil bacteria that form nitrogen-fixing symbiosis with alfalfa plants. Global climate changes lead to an increase of agricultural areas subjected to salinity. Current knowledge about about high-salt stress impact on soil saprophitic root nodulated microsymbionts of legumes is weakly studied and rhizobia gene pool responsible for salt tolerance are fragment and far from clear. An increase of bacteria nonspecific resistance (immune status) to unfavorable stress factors can occur through the induction of defense mechanisms like restrictionmodification systems and CRISPR/cas systems which are aimed to protect bacteria cells from bacteriophages widespread in soil microbiome. The aim of this research was to evaluate the role of the megaplasmid pSymA in the formation of ecological genome of S. meliloti, which is related to stress tolerance and to determine the location of elements of adaptive immune systems protecting root nodule bacteria against external foreign DNA. The analysis was done on 11 genes, products of which involved in response to ion stress and synthesis of osmoprotectors. It was found that 6 out of 11 genes were found in the genomes of all analyzed S. meliloti strains, while it was not a case for other 5 genes. It was found that, unlike chromosome, megaplasmid I of S. meliloti accumulated copies of 4 from 5 genes, except kdpA gene, which is represented by a single copy and localized on megaplasmid I in all so far studied strains. It was predicted that closest phylogenetic relatives of genes whose products are involved in response to ion stress as well in synthesis of osmoprotectors are homologous genes of closely related S. medicae species. The exception was for betI2, for which the closest phylogenetic relative was homologous gene of Klebsiella pneumonia, and another exception is kdpA gene introduced onto megaplasmid-I from actinobacteria. Regarding elements of immune systems it was revealed that nonsymbiotic plasmids of S. meliloti harbored incomplete elements of RMS-I, -II, and - III systems, while the 4 complete RMS-IV systems were detected on a single plasmid. It was found out that corresponding methylases had similarities with similar enzymes detected in nitrogen-fixing strains of Agrobacterium tumefaciens, Mezorhizobium sp., Bradyrhizobium sp. CRISPR sequences were not detected on megaplasmid-I, while they were on chromosome, megaplasmid-II and on cryptic plasmids. So, it was concluded that megaplasmid-I of S. meliloti are enriched in copies of genes related to osmotic stress tolerance, but it role in immune status of rhizobia is requested further elucidation.
Publication Impact Profile
Publication details
References11
Angiuoli S.V., Gussman A., Klimke W., Cochrane G., Field D., Garrity G., Kodira C.D., Kyrpides N., Madupu R., Markowitz,V., Tatusova T., Thomson N., White O. Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation, OMICS, USA, vol. 12, pp 137-141, 2008; DOI: 10.1089/omi.2008.0017
Seemann T. Prokka: rapid prokaryotic genome annotation, Bioinformatics, England, vol. 30/issue 14, pp 2068-2069, 2014; DOI: 10.1093/bioinformatics/btu153
Rozas J., Ferrer-Mata A., Sanchez-DelBarrio J.C., Guirao-Rico S., Librado P., Ramos-Onsins S.E., Sanchez-Gracia A. DnaSP 6: DNA sequence polymorphism analysis of large datasets, Molecular Biology and Evolution, England, vol.34/issue 12, pp 3299-3302, 2017; DOI: 10.1093/molbev/msx248
Korber, B. HIV signature and sequence variation analysis. Computational analysis of HIV molecular sequences, Allen G. Rodrigo and Gerald H. Learn, eds. Dordrecht, Netherlands: Kluwer Academic Publishers, 2000, Chapter 4, pp 555-572;
Pourcel C., Touchon M., Villeriot N., Vernadet J.-P., Couvin D., Toffano-Nioche C., Vergnaud G. CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers, Nucleic Acids Research, England, vol. 48/issue D1, pp D535� D544;
Edgar R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, England, vol. 32/number 5, pp 1792- 1797, 2004; DOI: 10.1093/nar/gkh340
Talavera G., Castresana J., Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments, Systematic Biology, England, vol. 56, pp 564-577, 2007; DOI: 10.1080/10635150701472164
Nguyen L.-T., Schmidt H.A., von Haeseler A., Minh B.Q., IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies, Molecular Biology and Evolution, USA, vol. 32/issue 1, pp 268-274, 2015; DOI: 10.1093/molbev/msu300
Huson D.H., Scornavacca C., Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks, Systematic Biology, England, vol. 61/issue 6, pp 1061-1067, 2012; DOI: 10.1093/sysbio/sys062
Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods, Journal of Molecular Evolution, Germany, vol. 39/issue 3, pp 306-314, 1994; DOI: 10.1007/bf00160154
Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences, Proceedings of the National Academy of Sciences of the USA, USA, vol. 78/number 1, pp 454-458, 1981; DOI: 10.1073/pnas.78.1.454
View or Download full articleAccess options
SWS access login
Login as SWS Scientific CommitteeLogin as SWS Scientific PartnerLogin as SWS AuthorAuthors and approved SWS contributors will read and export their own linked papers after identity matching by SWS profile, email and SGEM GlobalID.
For librarian assistance: [email protected]
Purchase Instant Access
- Article can be downloaded after successful payment.
- Article may be used according to SWS library access terms.
- Article cannot be redistributed.