Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

Abstract

Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

Comparative Genomics Reveals Genetic Diversity and Metabolic Potentials of the Genus Qipengyuania and Suggests Fifteen Novel Species

“…Strains Q. algicida KEMB 9005-328 T and 6D47A T possessed the most and second-most genes encoding CAZymes, with 35 and 32, which were almost three times as many as strain Q. sediminis CGMCC 1.12928 T , which possessed the fewest genes, with 12. Contrary to the genera Arthrobacter ( 37 ) and Bacillus ( 38 ), the low number of genes encoding CAZymes may mirror the weak ability of the genus Qipengyuania to utilize different carbohydrates as carbon and energy sources, which was confirmed by the carbohydrate utilization tests described below.…”

Complete Genome Sequencing of Polar Arthrobacter sp. PAMC25284, Copper Tolerance Potential Unraveled with Genomic Analysis

“…Even though multi-copper oxidase domain-containing genes were found in both Gram-positive and Gram-negative bacteria, another strain of Arthrobacter sp. PAMC25564 isolated from cryoconite [ 43 ] did not have any multi-copper oxidase domain-containing genes. Therefore, this study suggested that even if microorganisms are isolated from the same polar region, their functional genes differ depending on their habitat.…”

Complete genome of Nakamurella sp. PAMC28650: genomic insights into its environmental adaptation and biotechnological potential

“…Not much research has been conducted that particularly focuses on the survival of organisms in zero and subzero temperature in relation to carbohydrate metabolism. However, carbohydrate’s metabolisms, such as starch, glycogen, and trehalose metabolisms, are known as sources of energy for cold-tolerant microorganisms (Han et al 2021 ). Another recently published paper also highlighted the importance of cellulose and hemicellulose metabolism for survival in harsh environment (Shen et al 2021 ).…”

“…CAZymes, on the other hand, might also play a significant role in the survival of the microorganisms in freezing temperature. Polysaccharides, such as glycogen, trehalose, and maltodextrin, are major carbohydrates present in cold-adapted microorganisms, and bacteria with their complete metabolic pathways indicate the ability to conserve energy and its utilization (Han et al 2021 ). Psychrophilic microorganisms are also affected by high UV radiation, oxidative stress, and desiccation (Lauritano and Rizzo 2020 ).…”