TY - JOUR

T1 - Reconstruction and computer analysis of the structural and functional organization of the gene network regulating cholesterol biosynthesis in humans and the evolutionary characteristics of the genes involved in the network

AU - Mikhailova, A. d.

AU - Lashin, S. a.

AU - Ivanisenko, V. a.

AU - Demenkov, P. s.

AU - Игнатьева, Елена Васильевна

N1 - Mikhailova A.D., Lashin S.A., Ivanisenko V.A., Demenkov P.S., Ignatieva E.V. Reconstruction and computer analysis of the structural and functional organization of the gene network regulating cholesterol biosynthesis in humans and the evolutionary characteristics of the genes involved in the network. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2024;28(8):864-873. doi 10.18699/vjgb-24-94 The work was supported by the publicly funded project № FWNR-2022-0020 of the Federal Research Center ICG SB RAS.

PY - 2024

Y1 - 2024

N2 - Cholesterol is an essential structural component of cell membranes and a precursor of vitamin D, as well as steroid hormones. Humans and other animal species can absorb cholesterol from food. Cholesterol is also synthesized de novo in the cells of many tissues. We have previously reconstructed the gene network regulating intracellular cholesterol levels, which included regulatory circuits involving transcription factors from the SREBP (Sterol Regulatory Element-Binding Proteins) subfamily. The activity of SREBP transcription factors is regulated inversely depending on the intracellular cholesterol level. This mechanism is implemented with the participation of proteins SCAP, INSIG1, INSIG2, MBTPS1/S1P and MBTPS2/S2P. This group of proteins, together with the SREBP factors, is designated as “cholesterol sensor”. An elevated cholesterol level is a risk factor for the development of cardiovascular diseases and may also be observed in obesity, diabetes and other pathological conditions. Systematization of information about the molecular mechanisms controlling the activity of SREBP factors and cholesterol biosynthesis in the form of a gene network and building new knowledge about the gene network as a single object is extremely important for understanding the molecular mechanisms underlying the predisposition to diseases. With a computer tool, ANDSystem, we have built a gene network regulating cholesterol biosynthesis. The gene network included data on: (1) the complete set of enzymes involved in cholesterol biosynthesis; (2) proteins that function as part of the “cholesterol sensor”; (3) proteins that regulate the activity of the “cholesterol sensor”; (4) genes encoding proteins of these groups; (5) genes whose transcription is regulated by SREBP factors (SREBP target genes). The gene network was analyzed and feedback loops that control the activity of SREBP factors were identified. These feedback loops involved the PPARG, NR0B2/SHP1, LPIN1, and AR genes and the proteins they encode. Analysis of the phylostratigraphic age of the genes showed that the ancestral forms of most human genes encoding the enzymes of cholesterol biosynthesis and the proteins of the “cholesterol sensor” may have arisen at early evolutionary stages (Cellular organisms (the root of the phylostratigraphic tree) and the stages of Eukaryota and Metazoa divergence). However, the mechanism of gene transcription regulation in response to changes in cholesterol levels may only have formed at later evolutionary stages, since the phylostratigraphic age of the genes encoding the transcription factors SREBP1 and SREBP2 corresponds to the stage of Vertebrata divergence.

AB - Cholesterol is an essential structural component of cell membranes and a precursor of vitamin D, as well as steroid hormones. Humans and other animal species can absorb cholesterol from food. Cholesterol is also synthesized de novo in the cells of many tissues. We have previously reconstructed the gene network regulating intracellular cholesterol levels, which included regulatory circuits involving transcription factors from the SREBP (Sterol Regulatory Element-Binding Proteins) subfamily. The activity of SREBP transcription factors is regulated inversely depending on the intracellular cholesterol level. This mechanism is implemented with the participation of proteins SCAP, INSIG1, INSIG2, MBTPS1/S1P and MBTPS2/S2P. This group of proteins, together with the SREBP factors, is designated as “cholesterol sensor”. An elevated cholesterol level is a risk factor for the development of cardiovascular diseases and may also be observed in obesity, diabetes and other pathological conditions. Systematization of information about the molecular mechanisms controlling the activity of SREBP factors and cholesterol biosynthesis in the form of a gene network and building new knowledge about the gene network as a single object is extremely important for understanding the molecular mechanisms underlying the predisposition to diseases. With a computer tool, ANDSystem, we have built a gene network regulating cholesterol biosynthesis. The gene network included data on: (1) the complete set of enzymes involved in cholesterol biosynthesis; (2) proteins that function as part of the “cholesterol sensor”; (3) proteins that regulate the activity of the “cholesterol sensor”; (4) genes encoding proteins of these groups; (5) genes whose transcription is regulated by SREBP factors (SREBP target genes). The gene network was analyzed and feedback loops that control the activity of SREBP factors were identified. These feedback loops involved the PPARG, NR0B2/SHP1, LPIN1, and AR genes and the proteins they encode. Analysis of the phylostratigraphic age of the genes showed that the ancestral forms of most human genes encoding the enzymes of cholesterol biosynthesis and the proteins of the “cholesterol sensor” may have arisen at early evolutionary stages (Cellular organisms (the root of the phylostratigraphic tree) and the stages of Eukaryota and Metazoa divergence). However, the mechanism of gene transcription regulation in response to changes in cholesterol levels may only have formed at later evolutionary stages, since the phylostratigraphic age of the genes encoding the transcription factors SREBP1 and SREBP2 corresponds to the stage of Vertebrata divergence.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85217266743&origin=inward&txGid=3ef2b405f325c7202435974d6e083ecd

U2 - 10.18699/vjgb-24-94

DO - 10.18699/vjgb-24-94

M3 - Article

C2 - 39944801

VL - 28

SP - 864

EP - 873

JO - Вавиловский журнал генетики и селекции

JF - Вавиловский журнал генетики и селекции

SN - 2500-0462

IS - 8

ER -