Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation
Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from Pseudomonas sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate O-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.
KeywordsBiodegradation Degradation pathway Humic substances Low temperature Soil bacteria
This work was supported by the grants, Functional genomic studies on microbial degradation/conversion pathways of polar soil humic substances (PE13300), The Antarctic organisms: cold-adaptation mechanisms and its application (PE16070), and Modeling responses of terrestrial organisms to environmental changes on King George Island (PE17090), funded by the Korea Polar Research Institute.
- Dari K, Béchet M, Blondeau R (1995) Isolation of soil Streptomyces strains capable of degrading humic acids and analysis of their peroxidase activity. FEMS Microbiol Ecol 16(2):115–122. https://doi.org/10.1111/j.1574-6941.1995.tb00275.x CrossRefGoogle Scholar
- Esham EC, Ye W, Moran MA (2000) Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment. FEMS Microbiol Ecol 34(2):103–111. https://doi.org/10.1111/j.1574-6941.2000.tb00759.x CrossRefPubMedGoogle Scholar
- Lin L, Cheng Y, Pu Y, Sun S, Li X, Jin M, Pierson EA, Gross DC, Dale BE, Dai SY, Ragauskas AJ, Yuan JS (2016) Systems biology-guided biodesign of consolidated lignin conversion. Green Chem 18:5536–5547. https://doi.org/10.1039/C6GC01131D
- Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC (2010) CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. Glycobiology 20(12):1574–1584. https://doi.org/10.1093/glycob/cwq106 CrossRefPubMedGoogle Scholar
- Sainsbury PD, Hardiman EM, Ahmad M, Otani H, Seghezzi N, Eltis LD, Bugg TD (2013) Breaking down lignin to high-value chemicals: the conversion of lignocellulose to vanillin in a gene deletion mutant of Rhodococcusjostii RHA1. ACS Chem Biol 8(10):2151–2156. https://doi.org/10.1021/cb400505a CrossRefPubMedGoogle Scholar
- Stevenson FJ (1994) Humus chemistry: genesis, composition, reactions, 2nd edn. John Wiley & Sons, New YorkGoogle Scholar
- Sul WJ, Park J, Quensen JF 3rd, Rodrigues JL, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM (2009) DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75(17):5501–5506. https://doi.org/10.1128/AEM.00121-09 CrossRefPubMedPubMedCentralGoogle Scholar
- Yang JW, Zheng DJ, Cui BD, Yang M, Chen YZ (2016) RNA-seq transcriptome analysis of a Pseudomonas strain with diversified catalytic properties growth under different culture medium. Microbiology 5:626–636Google Scholar