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Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
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Complete Genome Sequence and Comparative Genome Analysis of
Prasansah Shrestha1, Jayram Karmacharya1, So-Ra Han1
1Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Republic of Korea.
International Journal of Microbiology
|June 5, 2023
Summary
This study analyzes the trehalose metabolic pathways in Antarctic Variovorax strains, revealing key genes for survival in extreme environments. Findings highlight trehalose biosynthesis and degradation enzymes
Area of Science:
- Microbiology
- Genomics
- Biochemistry
Background:
- Trehalose is crucial for bacterial survival under osmotic stress and extreme temperatures.
- Antarctic environments pose significant challenges for microbial life.
- The trehalose metabolic pathway in Variovorax strains, particularly Antarctic isolates, remains underexplored.
Purpose of the Study:
- To investigate the trehalose metabolic pathways in Antarctic Variovorax strains (PAMC28711, PAMC28562, PAMC26660).
- To identify genes involved in trehalose biosynthesis and degradation.
- To understand the role of these pathways in adaptation to extreme Antarctic conditions.
Main Methods:
- Genomic data retrieval from NCBI and CAZyme databases.
- Bioinformatic analysis using Prokka, dbCAN2 Meta server, Multiple Sequence Alignment, ANI calculator, and PATRIC database.
- Identification of trehalose biosynthetic (OtsA/OtsB, TS, TreY/TreZ) and degradation (trehalases) genes.
Main Results:
- Variovorax strains PAMC28711 and PAMC28562 possess three trehalose biosynthetic pathways, while PAMC26660 has one.
- Strain PAMC28711 uniquely contains two trehalases (GH37 and GH15) and auxiliary activities (AAs).
- Genomic analysis revealed variations in trehalose pathway components among the Antarctic isolates.
Conclusions:
- The study elucidates the genetic basis of trehalose metabolism in Antarctic Variovorax, contributing to understanding extremophile adaptation.
- Identified trehalose biosynthesis and degradation genes are vital for survival in harsh Antarctic conditions.
- The enzymes involved show potential for biotechnological applications.
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