Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics

Appl Environ Microbiol. 2015 Mar;81(6):2125-36. doi: 10.1128/AEM.03387-14. Epub 2015 Jan 16.

Abstract

The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (≤52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (≤356 U mg(-1)) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atlantic Ocean
  • Carboxylic Ester Hydrolases / genetics
  • Carboxylic Ester Hydrolases / isolation & purification*
  • Carboxylic Ester Hydrolases / metabolism
  • Decapoda / microbiology*
  • Enzyme Activators / metabolism
  • Enzyme Inhibitors / metabolism
  • Enzyme Stability
  • Gills / microbiology*
  • Hydrothermal Vents
  • Metagenome*
  • Metagenomics
  • Microbiota*
  • Molecular Sequence Data
  • Salts / metabolism
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Temperature

Substances

  • Enzyme Activators
  • Enzyme Inhibitors
  • Salts
  • Carboxylic Ester Hydrolases

Associated data

  • GENBANK/KC986402
  • GENBANK/KF831416
  • GENBANK/KF831417
  • PDB/3V46