Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

Abstract

Background: Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored.

Results: We provide here insight into PTMs in a hydrothermal vent microbial community through integration of metagenomics and metaproteomics. In total, 2919 unique proteins and 1306 unique PTMs were identified, whereas the latter included acetylation, deamination, hydroxylation, methylation, nitrosylation, oxidation, and phosphorylation. These modifications were unevenly distributed among microbial taxonomic and functional categories. A connection between modification types and particular functions was demonstrated. Interestingly, PTMs differed among the orthologous proteins derived from different bacterial groups. Furthermore, proteomic mapping to the draft genome of a Nitrospirae bacterium revealed novel modifications for proteins that participate in energy metabolism, signal transduction, and inorganic ion transport.

Conclusions: Our results suggest that PTMs are enriched in specific functions, which would be important for microbial adaptation to extreme conditions of the hydrothermal vent. PTMs in deep-sea are highly diverse and divergent, and much broader investigations are needed to obtain a better understanding of their functional roles.

Keywords: Hydrothermal vent; Metaproteomics; Nitrospirae; Post-translational modification.

Fig. 1

Taxonomic and functional structures of the metagenome, metaproteome, and PTMs. One metagenomic and two metaproteomic samples were included in the analysis. a Taxonomic classification at the class level based on conserved single-copy proteins. b Functional classification according to the COG categories

Fig. 2

The 40 proteins with the most abundant PTMs. The proteins were annotated according to the KEGG database. The results derived from the two metaproteomes are shown, which were designated as PTM1 and PTM2, respectively

Fig. 3

Correlation between PTM types and functional categories. a Percentages of the seven different PTM types. b Distribution of the seven PTM types among the COG categories. Ac acetylation, De deamination, Hy hydroxylation, Me methylation, Ni nitrosylation, Ox oxidation, Ph phosphorylation

Fig. 4

The metabolic capacities and pathways with enriched PTMs of Nitrospirae bacterium sp. nov. This bacterium possesses multiple pathways for energy metabolism, signal transduction, and inorganic ion transport, which contain several proteins with PTMs (highlighted in red)