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Title: ANALYSIS OF CRISPR CASSETTE ELEMENTS IN NATIVE ISOLATES OF SINORHIZOBIUM MELILOTI ISOLATED IN THE CENTRAL ASIAN ORIGIN OF PLANT DIVERSITY
ANALYSIS OF CRISPR CASSETTE ELEMENTS IN NATIVE ISOLATES OF SINORHIZOBIUM MELILOTI ISOLATED IN THE CENTRAL ASIAN ORIGIN OF PLANT DIVERSITY

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Elizaveta Pernak; Mariia Vladimirova; Viktoria Muntyan; Alexey Afonin; Marina Roumiantseva
10.5593/sgem2023/6.1/s25.13
10.5593/sgem2023/6.1
1314-2704
978-619-7603-61-3
English
23
6.1
•    Prof. DSc. Oleksandr Trofymchuk, UKRAINE 
•    Prof. Dr. hab. oec. Baiba Rivza, LATVIA
Advances in Biotechnology
CRISPR-Cas adaptive immunity systems of prokaryotes have been identified in 42% of bacteria and 85% of archaea [1] and are actively used in genetic engineering. However, in nitrogen-fixing nodule bacteria required for agriculture, these systems are very poorly characterized. Therefore, in this study, we evaluated the diversity of CRISPR-Cas systems in the genomes of 39 isolates of alfalfa nodule bacteria Sinorhizobium meliloti recovered from soil samples from Kazakhstan and Turkmenistan, which belong to the Central Asian origion of plants diversity.
The diversity of detected CRISPR elements was assessed by changes in the size of the PCR amplified DNA fragments. As a result, the presence of 7 species-specific CRISPR loci (CR1- CR7) was shown for each of 39 isolates, of which three (CR4, CR5 and CR6) were selected for further analysis. It was shown that structural changes in the analyzed CRISPR loci sequences were significantly 2-fold more frequent in strains from Turkmenistan than in strains from Kazakhstan (?2=4.07, P<0.05).
The most frequent changes in the size of the amplified sequences were detected at the CR6 locus (frequency 0.39), and 7.5-fold less frequent at the CR4 locus. Analysis of the nucleotide sequences of the loci for which changes in the size of amplified fragments were detected showed that at the CR4 locus one spacer was replaced with another; at the CR6 locus a deletion of the spacer and one direct repeat were involved. No changes were detected in the sequences of the CR-5 locus.
The results suggest that strains in which changes in cassette compositions have occurred may have significant differences in resistance to lytic phages. The possibility of directionally modulating the spacers sequence in the CRISPR loci of nodule bacteria used in bioproducts may undoubtedly be of interest for agrobiotechnology.
[1] Makarova KS, et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2020 Feb; 18 (2):67-83.
[2] Rao Y., Yang X., Pan C., Wang C., Wang K. (2022). Advance of clustered regularly interspaced short palindromic repeats-Cas9 system and its application in crop improvement. Front. Plant Sci. 13, 839001.
[3] Kuluev B.R., BaimievA.Kh.,Chemeris D.A., Matniyazov R.T., Gerashchenkov G.A. The use of CRISPR loci is not for editing genomes. Biomics 9(3), 271-283.
[4] Makarova K.S., Koonin E.V., Annotation and Classification of CRISPR-Cas Systems, Methods in molecular biology, United States, vol. 1311, pp 47-75, 2015.
[5] BaimievAn.Kh., Kuluev B.R., Vershinina Z.R., Knyazev A.V., Chemeris D.A., Rozhnova N.A., Gerashchenkov G.A., Mikhailova E.V., Baimiev Al.Kh., Chemeris A.V. CRISPR/Cas genome editing (plants) and society // Biomika. 2017. V.9. pp.183- 202.
[6] Rafael Pinilla-Redondo and others, CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids, Nucleic Acids Research, Volume 50, Issue 8, 6 May 2022, Pages 4315–4328.
[7] Pourcel C., Touchon M., Villeriot N. et al., 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.
[8] Roumiantseva M.L., Muntyan V.S., Cherkasova M.E. et al., Genomic islands in Sinorhizobium meliloti Rm1021, nitrogen-fixing symbiont of alfalfa, Russian journal of genetics, Russia, vol. 54/issue 7, pp759-769, 2018.
[9] Saramago M., Robledo M., Matos R.G. et al. Sinorhizobium meliloti RNase III: Catalytic Features and Impact on Symbiosis. Frontiers in genetics, Switzerland, vol. 9, 2018.
[10] Saramago M., Barria C., Dos Santos R.F., et al., The role of RNases in the regulation of small RNAs, Current opinion in microbiology, England, vol.18, pp 105- 115, 2014.
[11] Maniatis T., Fritsch E., Sambrook J. Methods of genetic engineering. Molecular cloning / A.A. Baeva and K.G. Scriabin. - M.: Mir, 1984. - 479 p.
[12] "CRISPR-Cas++" [Electronic resource]. – Access mode: https://crisprcas.i2bc.paris-saclay.fr/ (Date of access: 05/26/2023).
[13] Primer3Plus [Electronic resource]. – Access mode: https://www.primer3plus.com/ (Date of access: 05/25/2023).
[14] Rumyantseva M.L. Biological diversity of nodule bacteria in ecosystems and agrocenoses. Theoretical foundations and methods / Rumyantseva M.L., Simarov B.V., Onischuk O.P., Belova V.S., Chizhevskaya E.P., Andronov E.E., Kurchak O.N., Muntyan A. N., Rumyantseva T.B., Zatovskaya T.V. - St. Petersburg: VNIISKhM, 2011. - 104 p.
[15] Monarch® set. [Electronic resource]. – Access mode: https://www.skygen.com/katalog/reagenty_i_rashodnye_materialy/new_england_biolab s/vydelenie_i_ochistka_nk/vydelenie_i_ochistka_dnk/nabor_monarch_dlya_vydeleniya _dnk_iz_agaroznogo_gelya/ (Date of access: 05/25/2023).
[16] Sanger F., Air G.M., Barrell B.G. et al. Nucleotide sequence of bacteriophage fX174 DNA. // Nature, 1977. – V.265. – pp. 687-695.
[17] Central Collective Use Centerof the ARRIM. [Electronic resource]. – Access mode: https://arriam.ru/ckp/ (Date of access: 06/07/2023).
[18] Vector NTI [Electronic resource]. – Access mode: https://www.thermofisher.com/ru/ru/home/life-science/cloning/vector-nti-software.html (Date of access: 05/25/2023).
[19] viruSite [Electronic resource]. – Access mode: http://virusite.org/index.php (Date of access: 05/24/2023).
[20] Roumiantseva, M.L.; Vladimirova, M.E.; Saksaganskaia, A.S.; Muntyan, V.S.; Kozlova, A.P.; Afonin, A.M.; Baturina, O.A.; Simarov, B.V. Ensifer meliloti L6-AK89, an Effective Inoculant of Medicago lupulina Varieties: Phenotypic and Deep-Genome Screening. Agronomy 2022, 12, 766. https://doi.org/10.3390/agronomy12040766
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https://doi.org/10.5593/sgem2023/6.1/s25.13
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Proceedings of 23rd International Multidisciplinary Scientific GeoConference SGEM 2023
23rd International Multidisciplinary Scientific GeoConference SGEM 2023, 03 - 09 July, 2023
Proceedings Paper
STEF92 Technology
International Multidisciplinary Scientific GeoConference SGEM
SWS Scholarly Society; Acad Sci Czech Republ; Latvian Acad Sci; Polish Acad Sci; Serbian Acad Sci and Arts; Natl Acad Sci Ukraine; Natl Acad Sci Armenia; Sci Council Japan; European Acad Sci, Arts and Letters; Acad Fine Arts Zagreb Croatia; Croatian Acad Sci and Arts; Acad Sci Moldova; Montenegrin Acad Sci and Arts; Georgian Acad Sci; Acad Fine Arts and Design Bratislava; Turkish Acad Sci.
113-120
03 - 09 July, 2023
website
9225
spacers, CRISPR cassette, Sinorhizobium meliloti, populations, origin of plant diversity