Laboratory of bioinformatics approaches in combinatorial chemistry and biology

Department of functioning of living systems

Head: Pavel Baranov, Ph.D.

bioinformatics, genomics, sequence analysis, ribosome profiling, mass spectrometry, protein structure prediction, micropeptides, proteoforms

The laboratory was founded in 2019. The laboratory develops software for the analysis and processing of high-throughput genomics data (RNA-seq, ribosome profiling, mass spectrometry, etc) for the detection of novel protein-coding regions and functional characterization of their products. For these purposes, the laboratory also uses molecular evolution approaches and protein structure modeling.

 

The laboratory closely collaborates with LAPTI laboratory in Cork, Ireland

- Studying the mechanisms of gene expression regulation and protein synthesis control.

- Identification, and characterization of translated regions in genomes and transcriptomes, including coding for proteins and proteoforms.

- Characterization of the natural genetic decoding diversity.

- Software development for the analysis of biological data.

- Development of computational methods for the identification of biologically active molecules using the screening of combinatorial peptide libraries.

- Modeling of protein structures and their interactions with peptides.

Discovery and characterization of POLGARF, a product of non-AUG initiated ORF overlapping with CDS of  POLG encoding mitochondrial DNA polymerase  (Loughran et al doi: 10.1101/2020.03.06.980391).

All publications (show selected)

Loading...

Pavel Baranov

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. , office.

bimcocheb@gmail.com

Liquid drop of DNA libraries reveals total genome information

In collaboration with Laboratory of biocatalysis,  Laboratory of hormonal regulation proteins,  Laboratory of proteolytic enzyme chemistry

Researchers from the Laboratory of biocatalysis, Laboratory of proteolytic enzyme chemistry, Laboratory of bioinformatics approaches in combinatorial chemistry and biology, Laboratory of hormonal regulation proteins IBCh RAS together with their Russian and foreign colleagues showed that amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.

Publications

  1. Terekhov SS, Eliseev IE, Ovchinnikova LA, Kabilov MR, Prjibelski AD, Tupikin AE, Smirnov IV, Belogurov AA, Severinov KV, Lomakin YA, Altman S, Gabibov AG (2020). Liquid drop of DNA libraries reveals total genome information. Proc Natl Acad Sci U S A 117 (44), 27300–27306

Deciphering Ribosomes’ Actions in Living Cells

Researchers from the Laboratory of Bioinformatics Approaches in Combinatorial Chemistry and Biology IBCH RAS, in collaboration with Irish colleagues, recently published a review in WIRES RNA that compiles the computational approaches, software tools, and data resources that have been developed over the last ten years for ribosome profiling data processing and analysis.

Publications

  1. Kiniry SJ, Michel AM, Baranov PV (2019). Computational methods for ribosome profiling data analysis. Wiley Interdiscip Rev RNA 11 (3), e1577

Discovery of the novel protein encoded in mammalian mitochondrial DNA polymerase gene POL

Mitochondrial DNA polymeraseis essential for mitochondrial DNA replication. It consists of two subunits. POLG gene, which codes for catalytic subunit of polymerase, is notorious for more than 200 mutations linked to devastating inherited diseases. It is proposed that POLG mutations lead to progressive accumulation of mitochondrial DNA mutations and, subsequently, to organism disfunction and death. Andreev and colleagues discovered an efficient CUG start-codon in 5’-leader of POLG mRNA which initiates translation of a long alternative reading frame overlapping with POLG ORF. The new open reading frame is rather long (260 triplets in humans) and is conserved in placental mammals. The new protein was named POLGARF (POLG Alternative Reading Frame). POLGARF accumulates in nucleoli, but upon certain mitogenic stimuli is cleaved and secreted outside of cells. It has been proposed that POLGARF evolved approximately 100-200 mln years ago by MIR transposon insertion into POLG gene, which allows alternative reading frame translation and evolution of POLGARF protein coding function.

Publications

  1. Loughran G, Zhdanov AV, Mikhaylova MS, Rozov FN, Datskevich PN, Kovalchuk SI, Serebryakova MV, Kiniry SJ, Michel AM, OConnor PBF, Papkovsky DB, Atkins JF, Baranov PV, Shatsky IN, Andreev DE (2020). Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF. Proc Natl Acad Sci U S A 117 (40), 24936–24946

Start codon context and occurrence of AUG codons in the beginning of protein coding open reading frames co-evolve

Researchers from IBCh RAS together with their international collаborators discovered an evolutionary link between efficiency of start codons and the probability of AUG codon occurrence in the 5'-end parts of protein-coding sequences. When start codons are inefficient the next AUG codon is more likely to be found in the same reading frame. At the same time in case of highly efficient start codons, the next AUG codon is more likely to be found in alternative frames. They also have shown that weak initiation at the first starts is associated with the synthesis of shortened proteoforms as a result of initiation at the second starts.

Publications

  1. Benitez-Cantos MS, Yordanova MM, OConnor PBF, Zhdanov AV, Kovalchuk SI, Papkovsky DB, Andreev DE, Baranov PV (2020). Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context. Genome Res 30 (7), 974–984

Liquid drop of DNA libraries reveals total genome information

In collaboration with Laboratory of hormonal regulation proteins,  Laboratory of proteolytic enzyme chemistry,  Laboratory of biocatalysis

IBCh RAS together with their Russian and foreign colleagues showed that amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.

Publications

  1. Terekhov SS, Eliseev IE, Ovchinnikova LA, Kabilov MR, Prjibelski AD, Tupikin AE, Smirnov IV, Belogurov AA, Severinov KV, Lomakin YA, Altman S, Gabibov AG (2020). Liquid drop of DNA libraries reveals total genome information. Proc Natl Acad Sci U S A 117 (44), 27300–27306

Selective Eradication of Staphylococcus aureus by the Designer Genetically Programmed Yeast Biocontrol Agent

In collaboration with Laboratory of biocatalysis,  Laboratory of proteolytic enzyme chemistry

Staphylococcus aureus is a common human pathogen that is particularly often associated with antibiotic resistance. The eradication of this ubiquitous infectious agent from its ecological niches and contaminated surfaces is especially complicated by excessive biofilm formation and persisting cells, which evade the antibacterial activity of conventional antibiotics. Here, we present an alternative view of the problem of specific S. aureus eradication. The constitutive heterologous production of highly specific bacteriolytic protease lysostaphin in yeast Pichia pastoris provides an e_cient biocontrol agent, specifically killing S. aureus in coculture. A yeast-based anti-S. aureus probiotic was efficient in a high range of temperatures and target-to-effector ratios, indicating its robustness and versatility in eliminating S. aureus cells. The efficient eradication of S. aureus by live lysostaphin-producing P.pastoris was achieved at high scales, providing a simple, biocompatible, and cost-effective strategy for S. aureus lysis in bioproduction and surface decontamination. Future biomedical applications based on designer yeast biocontrol agents require evaluation in in vivo models. However, we believe that this strategy is very promising since it provides highly safe, effcient and selective genetically programmed probiotics and targeted biocontrol agents.