International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

Tag

methanotrophs

2 RESULTS
Systems computational biology: analysis, mathematical modeling and information technologies symposiumIntegration of transcriptomics data into a genome-scale metabolic model of the methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20ZR

Integration of transcriptomics data into a genome-scale metabolic model of the methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20ZR

No Comment on Integration of transcriptomics data into a genome-scale metabolic model of the methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20ZR

Mikhail Kulyashov1, Ivan S. Evshin2, Nikita V. Ivanisenko3, Semyon K. Kolmykov4, Tamara M. Khlebodarova5, Ilya R. Akberdin6
1BIOSOFT.RU, LLC ; Novosibirsk State University; FRC Institute of Cytology and Genetics SB RAS, m.kulyashov@mail.ru
2BIOSOFT.RU, LLC; Institute of Computational Technologies SB RAS, ivan@developmentontheedge.com
3FRC Institute of Cytology and Genetics SB RAS, n.ivanisenko@gmail.com
4BIOSOFT.RU, LLC; Institute of Computational Technologies SB RAS; FRC Institute of Cytology and Genetics SB RAS, semyonk@developmentontheedge.com
5FRC Institute of Cytology and Genetics SB RAS, tamara@bionet.nsc.ru
6BIOSOFT.RU, LLC; FRC Institute of Cytology and Genetics SB RAS; Novosibirsk State University, akberdinir@gmail.com

Aerobic methane-oxidizing bacteria or methanotrophs have the unique ability to grow on methane as their sole source of carbon and energy. The main metabolic steps of the methane utilization by microorganisms have been identified and well-studied to date. However, a detailed understanding of molecular genetic mechanisms that provide an adaptive response at the level of transcription regulation to various growth conditions, high and low pH, temperature, and salinity is still elusive. To solve the issue we have conducted a detailed theoretical study of the molecular mechanisms of gene expression regulation in the bacterium Methylotuvimicrobium alcaliphilum 20ZR (hereinafter 20ZR) based on the integration of original omics data into genome-scale metabolic model of the 20ZR.

Genomics, transcriptomics, bioinformatics symposiumFunctional annotation of the transcription factors from Methylotuvimicrobium alcaliphilum 20ZR

Functional annotation of the transcription factors from Methylotuvimicrobium alcaliphilum 20ZR

No Comment on Functional annotation of the transcription factors from Methylotuvimicrobium alcaliphilum 20ZR

Semyon K. Kolmykov1, Nikita V. Ivanisenko2, Ivan S. Evshin3, Mikhail Kulyashov4, Tamara M. Khlebodarova5, Ilya R. Akberdin6
1Institute of Computational Technologies SB RAS, kolmykovsk@gmail.com
2FRC Institute of Cytology and Genetics SB RAS, n.ivanisenko@gmail.com
3Institute of Computational Technologies SB RAS, ivan@biosoft.ru
4Institute of Computational Technologies SB RAS, m.kulyashov@mail.ru
5FRC Institute of Cytology and Genetics SB RAS, tamara@bionet.nsc.ru
6FRC Institute of Cytology and Genetics SB RAS, akberdinir@gmail.com

Methane is a promising carbon source for biosynthesis of biotechnologically useful compounds using aerobic methanotrophic bacteria as biocatalysts. Despite more than a century-long history of discovering and studying of methanotrophic microorganisms, knowledge of the molecular mechanisms of gene expression regulation by transcription factors in these bacteria is very limited with only a few isolated cases being published. Therefore, the identification of potential transcription factors for methanotrophic organisms and their target genes is not only a foreground fundamental problem in the research field of methanotrophy, but it is also especially relevant for the active development of biotechnological application of methane-oxidizing microorganisms. In this study a comparative genomics approach together with the structural modeling techniques were applied to reveal the TFs in the 20ZR genome and predict their target regulatory genes.