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9Section 8
COMPUTER BIOLOGY, MEDICINE AND BIOTECHNOLOGY
Molecular evolution of proteins, containing phospholipase A2 domain in flatworms
M. E. Lachynova1,2, D. A. Afonnikov1
1Institute of Cytology and Genetics SB RAS
2Novosibirsk State University
Email: m.bocharnikova@g.nsu.ru
DOI 10.24412/cl-35065-2021-1-02-36
Phospholipases are a group of enzymes (a class of hydrolases) that catalyze the hydrolysis of phospholip-
ids. Depending on the position of the hydrolyzed bond in the phospholipid, there are 4 main classes of phos-
pholipases: A, B, C, and D. In this work we will consider phospholipases A2, which cleave SN-2 acyl chain [1].
Phospholipases A2 are known for being snake venom toxins. These proteins are also widely represented in
mammals and perform a number of important basic functions at the cellur level and the whole organism [2].
Disruption of human phospholipase A2 functions is often associated with cancer [2].
The parasitic worms pose a threat to the health of Siberian population (high incidence of opisthorchiasis in
Western Siberia). The disease may cause complications (cholelithiasis or cancer) [3]. In this regard, phospho-
lipases are of interest for study because they can participate in the process of "parasite-host" interactions. The
aim of this work is to study the peculiarities of the structure, functions and evolution of proteins containing
phospholipase A2 domain in flatworms. A bioinformatic approach for detecting phospholipase A2 family pro-
teins in flatworms has been proposed. In flatworms, classes of phospholipases A2 of 11 families were identi-
fied for the first time.
References
1. Knorre D.G., Myzina S. D. Biological Chemistry. M.: High School, 1998.
2. Dennis E. A. et al. Phospholipase A2 enzymes: physical structure, biological function, disease implication, chemical
inhibition, and therapeutic intervention // Chemical reviews. 2011. Vol. 111. No. 10. P. 6130-6185.
3. Report G. On the State of Sanitary and Epidemiological Welfare of the Population in the Russian Federation in
2014: State Report. M.: Rospotrebnadzor, 2015. Vol. 206.
In silico design of new ethylene sensors in plants based on genome-wide analysis of EIN3 transcription
factor binding sites
V. A. Dolgikh1, V. G. Levitsky1,2, D. Y. Oshchepkov1, E. V. Zemlyanskaya1,2
1Institute of Cytology and Genetics SB RAS
2Novosibirsk State University
Email: ezemlyanskaya@bionet.nsc.ru
DOI 10.24412/cl-35065-2021-1-02-37
ETHYLENE INSENSITIVE 3 (EIN3) transcription factor is the master regulator of gene expression in response
to plant hormone ethylene. It binds a short nucleotide sequence referred to as EBS to induce transcription.
Arabidopsis thaliana reporter EBS:GUS driven by the classical variant of the EIN3 binding site is widely used as
a sensor for detection of ethylene signaling. However, very little is known about the role of structural variants
of EBS in EIN3 functioning. Here we accomplish a systematic bioinformatics analysis of EIN3 bound sequences
in Arabidopsis genome.
We used publicly available ChIP-seq data on EIN3 binding, RNA-seq data on ethylene-induced trans-
criptomes in Arabidopsis seedlings [1] and DAP-seq data [2]. We used Homer [3] for de novo motif search in
the peaks, and MCOT [4] for enrichment analysis of EBS repeats. Associations of EBS configurations with peaks
and genes features were estimated with Fisher�s exact test. We discovered a previously unknown EBS architec-
ture that is enriched in EIN3 bound sequences to a much greater extent than a single EBS motif. This new con-
figuration is a tail-to-tail inverted repeat of EBS-like sequences with 1 bp overlap referred to as 2EBS(-1). We
also demonstrated that the inverted repeat of the coreEBS with the overlap of the motifs but not with a spacer
is enriched in the Arabidopsis genome. We further showed that of all EBS configurations under study only
2EBS(-1) was significantly associated with transcriptional response of EIN3 targets to ethylene treatment.
Moreover, it tended to cause a more pronounced transcriptional response than other EBS configurations.
Based on these findings we consider that 2EBS(-1) is a preferred EIN3 binding site in A. thailana genome. We
applied these findings to design a new genetic sensor for highly sensitive detection of ethylene signaling. Tak-
en together, this work provides new insight on the molecular mechanisms utilized for regulation of transcrip-
tional response to ethylene in plants and offers a workflow for the inference of the cis-regulatory code.
This work was supported by the Russian Science Foundation (grant no. 20-14-00140).
References
1. Chang K.N. et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in
Arabidopsis // Elife. 2013. V. 2, P. e00675.
2. O'Malley R.C. et al. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape // Cell. 2016. V. 165,
N. 5, P. 1280-1292.
3. Heinz S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements
required for macrophage and b cell identities // Mol. Cell. 2010. V. 38, N. 4, P. 576-589.
4. Levitsky V. et al. A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with
MCOT package // Nucleic Acids Res. 2019. V. 47, N. 21, P. e139.
Changes in transcriptome profiles during enzymatic degradation of cell walls in fig (Ficus carica L.) leaves
A. V. Doroshkov1,2, U. S. Zubairova1,2, O. V. Kryvenko3, O. M. Kuleshova3, I. V. Mitrofanova4
1Institute of Cytology and Genetics SB RAS
2Novosibirsk State University
3A.O. Kovalevsky Institute of Biology of the Southern Seas, Sevastopol
4Nikita Botanical Gardens - National Scientific Center, Yalta
Email: ad@bionet.nsc.ru
DOI 10.24412/cl-35065-2021-1-02-38
Isolated protoplasts provide an opportunity to study a wide variety of cellular processes. As usual, the iso-
lation of protoplasts from plant tissues occurs due to the cell wall enzymatic degradation. While this process,
the pattern of gene expression changes from that characteristic to a mature cell towards undifferentiated
cells. In this work, we analyzed the leaves of a typical variety, �Sabrucia Rosea�, obtained from microshoots
grown in vitro were incubated in an enzymatic mixture. Several successive steps in the protoplast isolation
protocol served as sampling points. For control, RNA was obtained from the original tissue. For all mRNA
isoforms, expression levels were normalized relative to expression levels at the point corresponding to the
transcriptome of untouched leaves. Based on the principal component analysis and k-means clustering, we
identified groups with similar behavior. Among them, several mRNA isoforms showed significant changes in
the expression level throughout the experiment. These data could be used to search for genes that act as
