URLhttps://www.bco-dmo.org/dataset/640505
Download URLhttps://www.bco-dmo.org/dataset/640505/data/download
Media Typetext/tab-separated-values
CreatedMarch 14, 2016
ModifiedAugust 19, 2016
StatePreliminary and in progress
Brief DescriptionInhibition data for 3 peptidases at Bogue Sound NC and Tennessee River at Knoxville.

Acquisition Description

Inhibition parameters were measured from vo of Arg-AMC, Leu-AMC, and Pro-AMC, as a function of the concentration of various pNA inhibitors, as described in Steen et al (2015) (doi:10.3354/ame01755)

Processing Description

Data processing is described in more detail in the Steen et al. (2015) paper (doi:10.3354/ame01755). Full R code and all raw data is given at http://github.com/adsteen/subspec.

BCO-DMO processing:
- modified parameter names to conform with BCO-DMO naming conventions;
- replaced "NA" with "nd" (no data).

Parameters

amino_acid [unknown]
Details
amino_acid
Amino acid.
association with a community-wide standard parameter is not yet defined
AA_abbrev [unknown]
Details
AA_abbrev
Single-letter amino acid abbreviation.
association with a community-wide standard parameter is not yet defined
delta_Gr [unknown]
Details
delta_Gr
?
association with a community-wide standard parameter is not yet defined
pNA_subs [unknown]
Details
pNA_subs
?
association with a community-wide standard parameter is not yet defined
polarity [unknown]
Details
polarity
Description of polarity.
association with a community-wide standard parameter is not yet defined
hydrophobicity [unknown]
Details
hydrophobicity
Hydrophobicity.
association with a community-wide standard parameter is not yet defined
MW [unknown]
Details
MW
Molecular weight of the amino acid.
association with a community-wide standard parameter is not yet defined
Dauwe_score1 [unknown]
Details
Dauwe_score1
?
association with a community-wide standard parameter is not yet defined
Dauwe_score2 [unknown]
Details
Dauwe_score2
?
association with a community-wide standard parameter is not yet defined
location [unknown]
Details
location
Sampling location.
association with a community-wide standard parameter is not yet defined
substrate [unknown]
Details
substrate
Substrate.
association with a community-wide standard parameter is not yet defined
inhib_slope [unknown]
Details
inhib_slope
Inhibition slope.
association with a community-wide standard parameter is not yet defined
inhib_slope_SE [unknown]
Details
inhib_slope_SE
Standard error of inhibition slope.
association with a community-wide standard parameter is not yet defined
rsq [unknown]
Details
rsq
?
association with a community-wide standard parameter is not yet defined
pval [unknown]
Details
pval
?
association with a community-wide standard parameter is not yet defined
is_homologous [unknown]
Details
is_homologous
?
association with a community-wide standard parameter is not yet defined
rel_Ki [unknown]
Details
rel_Ki
Inhibition binding constant, Ki. Given relative to the homologous pNA substrate, as described in Steen et al. (2015).
association with a community-wide standard parameter is not yet defined
rel_Ki_SE [unknown]
Details
rel_Ki_SE
Standard error of inhibition binding constant, Ki. Given relative to the homologous pNA substrate, as described in Steen et al. (2015).
association with a community-wide standard parameter is not yet defined
low_err [unknown]
Details
low_err
?
association with a community-wide standard parameter is not yet defined
high_err [unknown]
Details
high_err
?
association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Andrew D. SteenUniversity of Tennessee Knoxville (UTK)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleNovel peptidases in subsurface sediments: Activities and substrate specificities
AcronymSEDpep
URLhttps://www.bco-dmo.org/project/636401
CreatedJanuary 25, 2016
ModifiedJanuary 25, 2016
Project Description

Description from C-DEBI:
The goal of this project was to explore the mechanisms of subsurface organoheterotrophy by identifying the range of extracellular peptidases present in sediments of the White Oak River, NC, consistent with C-DEBI Research Theme 1, Activity in the Deep Subseafloor Biosphere: function & rates of global biogeochemical processes. This grant funded two sampling expeditions to the White Oak River as well as extensive laboratory work with a purified peptidase that was supplied by collaborators Andrzej Joachimiak and Karolina Michalska of Argonne National Laboratory and preparatory work on peptidases of the Tennessee River. So far this dataset has led to the submission of two manuscripts, with one more manuscript in preparation. The White Oak River work showed that a wide range of peptidases are present in depths up to 80 cm in the White Oak River, which is deeper than the zone of methanogenesis. Although absolute peptidase activities declined with depth, activities normalized to cell abundance were roughly constant, and activities normalized to organic carbon oxidation rates increased nearly two orders of magnitude relative to the surface, indicating that extracellular peptidases were important to the subsurface ecosystem. Biochemical analysis of a purified peptidase that was expressed by the Argonne group showed it to be a novel aminopeptidase with specificity for N-terminal cysteine, a function not previously observed in peptidses. In summary, in situ and in vitro studies of subsurface peptidases revealed that they are ecologically important and may contain novel properties.

Project Maintainers
NameAffiliationRoleContact
Andrew D. SteenUniversity of Tennessee Knoxville (UTK)Principal Investigator
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