Determinants of CRISPR array non-canonical adaptation mechanism
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Метаподаци
Приказ свих података о документуАпстракт
CRISPR-cas systems are incredibly diverse and currently are classified in six major types
and over 30 subtypes. Apart from their role in adaptive immunity it has been shown that
some of the CRISPR-cas subtypes are also involved in host gene regulation and even in
collateral damage leading to bacteriostatic or lethal outcomes for the host. CRISPR array
spacers direct and influence canonical and non-canonical functions of the CRISPR-cas
system together with subtype Cas proteins. Better understanding of spacer adaptation
mechanisms is crucial for uncovering intricacies of evolutionary arms race between
prokaryotes and phages.
Here we present large-scale analysis of CRISPR array spacers originating from 31845
complete bacterial genomes. All bacterial and 16388 viral genomes were retrieved using
NCBI datasets API. CRISPRidentify and CRISPRcasIdentifier tools were used for CRISPR
array, Cas genes detection and subtyping. Viral genomes were mapped to their hosts
using the latest v...ersion of the Virus-Host DB. Mapping was performed on the genus level
of the hosts phylogenetic tree. Gumbel extreme value distribution was used to determine
statistical significance of each spacer Smith-Waterman alignment score.
Differences in melting energy and GC content between identified spacers, origin bacterial
genomes and infecting bacteriophages were explored for different CRISPR-cas subtypes
and for different bacterial genera. Spacers from the extremes of the GC content distribution
were aligned to the origin bacterial and infecting phage genomes in order to determine
their origin.
GC content of the spacers was lesser than the GC content of the source bacterial genome
but greater than infecting viral genome. This observation aligns with the hypothesis that
the majority of CRISPR spacers were adapted from the bacteriophage genomes and serve
canonical function. Alignments of the spacers from GC rich distribution tail have shown
their preferential targeting of host genomes which further supports the hypothesis that
GC rich spacers originated from the bacterial genome and have non-canonical function.
Кључне речи:
CRISPR-cas / melting energy / extreme value distributionИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 88-88Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Tumbas, Marko AU - Đorđević, Marko PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2033 AB - CRISPR-cas systems are incredibly diverse and currently are classified in six major types and over 30 subtypes. Apart from their role in adaptive immunity it has been shown that some of the CRISPR-cas subtypes are also involved in host gene regulation and even in collateral damage leading to bacteriostatic or lethal outcomes for the host. CRISPR array spacers direct and influence canonical and non-canonical functions of the CRISPR-cas system together with subtype Cas proteins. Better understanding of spacer adaptation mechanisms is crucial for uncovering intricacies of evolutionary arms race between prokaryotes and phages. Here we present large-scale analysis of CRISPR array spacers originating from 31845 complete bacterial genomes. All bacterial and 16388 viral genomes were retrieved using NCBI datasets API. CRISPRidentify and CRISPRcasIdentifier tools were used for CRISPR array, Cas genes detection and subtyping. Viral genomes were mapped to their hosts using the latest version of the Virus-Host DB. Mapping was performed on the genus level of the hosts phylogenetic tree. Gumbel extreme value distribution was used to determine statistical significance of each spacer Smith-Waterman alignment score. Differences in melting energy and GC content between identified spacers, origin bacterial genomes and infecting bacteriophages were explored for different CRISPR-cas subtypes and for different bacterial genera. Spacers from the extremes of the GC content distribution were aligned to the origin bacterial and infecting phage genomes in order to determine their origin. GC content of the spacers was lesser than the GC content of the source bacterial genome but greater than infecting viral genome. This observation aligns with the hypothesis that the majority of CRISPR spacers were adapted from the bacteriophage genomes and serve canonical function. Alignments of the spacers from GC rich distribution tail have shown their preferential targeting of host genomes which further supports the hypothesis that GC rich spacers originated from the bacterial genome and have non-canonical function. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Determinants of CRISPR array non-canonical adaptation mechanism EP - 88 SP - 88 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_2033 ER -
@conference{ author = "Tumbas, Marko and Đorđević, Marko", year = "2023", abstract = "CRISPR-cas systems are incredibly diverse and currently are classified in six major types and over 30 subtypes. Apart from their role in adaptive immunity it has been shown that some of the CRISPR-cas subtypes are also involved in host gene regulation and even in collateral damage leading to bacteriostatic or lethal outcomes for the host. CRISPR array spacers direct and influence canonical and non-canonical functions of the CRISPR-cas system together with subtype Cas proteins. Better understanding of spacer adaptation mechanisms is crucial for uncovering intricacies of evolutionary arms race between prokaryotes and phages. Here we present large-scale analysis of CRISPR array spacers originating from 31845 complete bacterial genomes. All bacterial and 16388 viral genomes were retrieved using NCBI datasets API. CRISPRidentify and CRISPRcasIdentifier tools were used for CRISPR array, Cas genes detection and subtyping. Viral genomes were mapped to their hosts using the latest version of the Virus-Host DB. Mapping was performed on the genus level of the hosts phylogenetic tree. Gumbel extreme value distribution was used to determine statistical significance of each spacer Smith-Waterman alignment score. Differences in melting energy and GC content between identified spacers, origin bacterial genomes and infecting bacteriophages were explored for different CRISPR-cas subtypes and for different bacterial genera. Spacers from the extremes of the GC content distribution were aligned to the origin bacterial and infecting phage genomes in order to determine their origin. GC content of the spacers was lesser than the GC content of the source bacterial genome but greater than infecting viral genome. This observation aligns with the hypothesis that the majority of CRISPR spacers were adapted from the bacteriophage genomes and serve canonical function. Alignments of the spacers from GC rich distribution tail have shown their preferential targeting of host genomes which further supports the hypothesis that GC rich spacers originated from the bacterial genome and have non-canonical function.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Determinants of CRISPR array non-canonical adaptation mechanism", pages = "88-88", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_2033" }
Tumbas, M.,& Đorđević, M.. (2023). Determinants of CRISPR array non-canonical adaptation mechanism. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 88-88. https://hdl.handle.net/21.15107/rcub_imagine_2033
Tumbas M, Đorđević M. Determinants of CRISPR array non-canonical adaptation mechanism. in 4th Belgrade Bioinformatics Conference. 2023;4:88-88. https://hdl.handle.net/21.15107/rcub_imagine_2033 .
Tumbas, Marko, Đorđević, Marko, "Determinants of CRISPR array non-canonical adaptation mechanism" in 4th Belgrade Bioinformatics Conference, 4 (2023):88-88, https://hdl.handle.net/21.15107/rcub_imagine_2033 .