TY  - CONF
AU  - Banović Đeri, Bojana
AU  - Nešić, Sofija
AU  - Pantelić, Ana
AU  - Samardžić, Jelena
AU  - Nikolić, Dragana
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2030
AB  - Bacterial small RNAs (sRNAs) represent a highly diverse RNA class ranging from 8 to 200
nucleotides in length, originating from the bacterial chromosome, plasmids or phages.
After syntheses sRNAs can remain inside the bacterial cell, be secreted or packed into
outer membrane vesicles (OMV), enabling various intra- and inter-kingdom interactions.
Different sRNAs biotypes display differences in structure, mechanism of action and level
of regulation (i.e. transcription, translation, mRNA stability, etc.), but could be broadly
grouped in: trans-acting sRNAs (bind to target mRNAs) and cis-encoded sRNAs (or
antisense RNA that may interact not only with mRNAs, but also with proteins and DNA).
Even though the advancement of high-throughput sequencing technology led to a burst
of knowledge on small RNAs complexity and diversity, there are still specific challenges
related to sRNA-seq data analysis that need to be resolved. Two main challenges,
associated to short length of many bacterial sRNA biotypes, are: (i) to discriminate
between functional sRNAs synthesized by bacterial cell and degradation fragments
produced by sample preparation and (ii) to detect functional sRNAs displaying sequence
variation. While loss of very small sized sRNAs could easily be overcome by cutting-off
only the specific adapter sequences that were used in sRNA library preparation, providing
a proper mapping still remains a strenuous task.
The aim of this study was to test five different mapping tools that are widely used in NGS
data analysis (bbmap, bowtie2, bwa, minimap2 and segemehl) for their performances in
mapping of bacterial OMV sRNA-seq data to bacterial reference genome. For this test
publicly available NCBI sRNA-seq dataset from OMVs of Aliivibrio fischeri (PRJNA629425)
was used, as it contained sRNAs of different length and biotype and because A.fischeri
reference genome and annotation were available (PRJNA12986). We evaluated five
mappers using alignment and assignment rates as well as computational time. Alignment
rate was calculated as the ratio of aligned and input reads, while the assignment rate
was calculated as the ratio of assigned and aligned reads. Finally, totals of detected
sRNAs biotypes were compared between different mappers. The statistical analysis was
performed in R (version 4.3.0) and performance metrics are discussed.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles
EP  - 85
SP  - 85
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2030
ER  - 

@conference{
author = "Banović Đeri, Bojana and Nešić, Sofija and Pantelić, Ana and Samardžić, Jelena and Nikolić, Dragana",
year = "2023",
abstract = "Bacterial small RNAs (sRNAs) represent a highly diverse RNA class ranging from 8 to 200
nucleotides in length, originating from the bacterial chromosome, plasmids or phages.
After syntheses sRNAs can remain inside the bacterial cell, be secreted or packed into
outer membrane vesicles (OMV), enabling various intra- and inter-kingdom interactions.
Different sRNAs biotypes display differences in structure, mechanism of action and level
of regulation (i.e. transcription, translation, mRNA stability, etc.), but could be broadly
grouped in: trans-acting sRNAs (bind to target mRNAs) and cis-encoded sRNAs (or
antisense RNA that may interact not only with mRNAs, but also with proteins and DNA).
Even though the advancement of high-throughput sequencing technology led to a burst
of knowledge on small RNAs complexity and diversity, there are still specific challenges
related to sRNA-seq data analysis that need to be resolved. Two main challenges,
associated to short length of many bacterial sRNA biotypes, are: (i) to discriminate
between functional sRNAs synthesized by bacterial cell and degradation fragments
produced by sample preparation and (ii) to detect functional sRNAs displaying sequence
variation. While loss of very small sized sRNAs could easily be overcome by cutting-off
only the specific adapter sequences that were used in sRNA library preparation, providing
a proper mapping still remains a strenuous task.
The aim of this study was to test five different mapping tools that are widely used in NGS
data analysis (bbmap, bowtie2, bwa, minimap2 and segemehl) for their performances in
mapping of bacterial OMV sRNA-seq data to bacterial reference genome. For this test
publicly available NCBI sRNA-seq dataset from OMVs of Aliivibrio fischeri (PRJNA629425)
was used, as it contained sRNAs of different length and biotype and because A.fischeri
reference genome and annotation were available (PRJNA12986). We evaluated five
mappers using alignment and assignment rates as well as computational time. Alignment
rate was calculated as the ratio of aligned and input reads, while the assignment rate
was calculated as the ratio of assigned and aligned reads. Finally, totals of detected
sRNAs biotypes were compared between different mappers. The statistical analysis was
performed in R (version 4.3.0) and performance metrics are discussed.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles",
pages = "85-85",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2030"
}

Banović Đeri, B., Nešić, S., Pantelić, A., Samardžić, J.,& Nikolić, D.. (2023). Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2030

Banović Đeri B, Nešić S, Pantelić A, Samardžić J, Nikolić D. Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles. in 4th Belgrade Bioinformatics Conference. 2023;4:85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2030 .

Banović Đeri, Bojana, Nešić, Sofija, Pantelić, Ana, Samardžić, Jelena, Nikolić, Dragana, "Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles" in 4th Belgrade Bioinformatics Conference, 4 (2023):85-85,
https://hdl.handle.net/21.15107/rcub_imagine_2030 .

TY  - GEN
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2269
AB  - The role of extracellular small RNA (sRNA) in interkingdom communication between
microorganisms and their eukaryotic hosts has been revealed recently. Extracellular vesicles
(EVs) are a significant delivery route of sRNAs, thus regulating gene expression in the recipient
cell. Such interactions have been shown between fungi and plants as well as bacteria and
animals but, little is known about sRNA-mediated host responses between bacteria and plants
or fungi.
This project aims to study the role of sRNAs in the outer membrane vesicles (OMVs) of the
plant growth promoting bacteria (PGPB) (of genera Paraburkholderia, Pseudomonas and
Enterobacter) in the naturally occurring communication with plant (Arabidopsis thaliana) and
phytopathogenic fungi (Botrytis cinerea). Further, we will explore the ability of engineered
OMV-sRNAs to manipulate fungal genes, as a means to suppress fungal diseases of plants.
To monitor the delivery of the OMV cargo into plant and fungi, OMVs and sRNAs will be
fluorescently labeled and OMVs’ interaction with recipient cells, and RNA delivery, will be
monitored by confocal microscopy. sRNA from OMVs and cells of bacteria, grown separately or
in the interaction with the plant or fungus, will be sequenced and compared to define the
criteria for the selection of sRNAs to be packed into OMVs. To identify sRNAs delivered by
OMVs to recipient cells, sRNA-Seq and bioinformatics analysis of plant and fungal cells upon
exposure to bacteria will be performed. The ability of OMV-sRNAs to modulate the expression
of predicted target genes in the host cells will be tested both for endogenous bacterial and
engineered sRNAs, designed to target recipient’s gene(s).
The main expected results: the visualization of OMV cargo delivery to recipient cells; revealing
the selection criteria for sRNA packaging into OMVs; and evidence of OMV-sRNAs mediated
regulation of host genes will be novel, ground-breaking discoveries, impacting many research
fields , from agriculture to medicine. The project will pave the way for using engineered OMVs-
sRNAs to modulate plant/fungal physiology, encouraging further studies of the application of
this process in biocontrol against phytopathogenic fungi, with a potential to its extrapolation to
animal and human fungal pathogens.
T2  - Science Fund of the Republic of Serbia, Program IDEAS
T1  - Exploring Bacterial OMV (Outer Membrane Vesicles)-sRNAs Mediated Interkingdom Communication with Plants and Fungi (ExplOMV)
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2269
ER  - 

@misc{
year = "2021",
abstract = "The role of extracellular small RNA (sRNA) in interkingdom communication between
microorganisms and their eukaryotic hosts has been revealed recently. Extracellular vesicles
(EVs) are a significant delivery route of sRNAs, thus regulating gene expression in the recipient
cell. Such interactions have been shown between fungi and plants as well as bacteria and
animals but, little is known about sRNA-mediated host responses between bacteria and plants
or fungi.
This project aims to study the role of sRNAs in the outer membrane vesicles (OMVs) of the
plant growth promoting bacteria (PGPB) (of genera Paraburkholderia, Pseudomonas and
Enterobacter) in the naturally occurring communication with plant (Arabidopsis thaliana) and
phytopathogenic fungi (Botrytis cinerea). Further, we will explore the ability of engineered
OMV-sRNAs to manipulate fungal genes, as a means to suppress fungal diseases of plants.
To monitor the delivery of the OMV cargo into plant and fungi, OMVs and sRNAs will be
fluorescently labeled and OMVs’ interaction with recipient cells, and RNA delivery, will be
monitored by confocal microscopy. sRNA from OMVs and cells of bacteria, grown separately or
in the interaction with the plant or fungus, will be sequenced and compared to define the
criteria for the selection of sRNAs to be packed into OMVs. To identify sRNAs delivered by
OMVs to recipient cells, sRNA-Seq and bioinformatics analysis of plant and fungal cells upon
exposure to bacteria will be performed. The ability of OMV-sRNAs to modulate the expression
of predicted target genes in the host cells will be tested both for endogenous bacterial and
engineered sRNAs, designed to target recipient’s gene(s).
The main expected results: the visualization of OMV cargo delivery to recipient cells; revealing
the selection criteria for sRNA packaging into OMVs; and evidence of OMV-sRNAs mediated
regulation of host genes will be novel, ground-breaking discoveries, impacting many research
fields , from agriculture to medicine. The project will pave the way for using engineered OMVs-
sRNAs to modulate plant/fungal physiology, encouraging further studies of the application of
this process in biocontrol against phytopathogenic fungi, with a potential to its extrapolation to
animal and human fungal pathogens.",
journal = "Science Fund of the Republic of Serbia, Program IDEAS",
title = "Exploring Bacterial OMV (Outer Membrane Vesicles)-sRNAs Mediated Interkingdom Communication with Plants and Fungi (ExplOMV)",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2269"
}

(2021). Exploring Bacterial OMV (Outer Membrane Vesicles)-sRNAs Mediated Interkingdom Communication with Plants and Fungi (ExplOMV). in Science Fund of the Republic of Serbia, Program IDEAS.
https://hdl.handle.net/21.15107/rcub_imagine_2269

Exploring Bacterial OMV (Outer Membrane Vesicles)-sRNAs Mediated Interkingdom Communication with Plants and Fungi (ExplOMV). in Science Fund of the Republic of Serbia, Program IDEAS. 2021;.
https://hdl.handle.net/21.15107/rcub_imagine_2269 .

"Exploring Bacterial OMV (Outer Membrane Vesicles)-sRNAs Mediated Interkingdom Communication with Plants and Fungi (ExplOMV)" in Science Fund of the Republic of Serbia, Program IDEAS (2021),
https://hdl.handle.net/21.15107/rcub_imagine_2269 .