The effect of chemical structure on the hydrolysis of tetrapeptides along a river-to-ocean transect: AVFA and SWGA

Liu, Zhanfei; Kobiela, Megan E.; McKee, Georgina A.; Tang, Tiantian; Lee, Cindy; Mulholland, Margaret R.; Hatcher, Patrick G.

doi:10.1016/j.marchem.2010.01.005

Cited by 23 publications

(26 citation statements)

References 65 publications

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“…Christian & Karl 1995, Sinsabaugh et al 2009). The results presented here, combined with peptidase studies using fluorogenic substrates in coastal, temperate environments (Obayashi & Suzuki 2005, 2008a,b, Bong et al 2009, Obayashi et al 2010) and studies using a suite of oligopeptides (Pantoja & Lee 1999, Liu et al 2010, demonstrate that pelagic communities can express distinct patterns of extracellular peptidases, and that leucyl aminopeptidase contri butes a variable amount to total peptidolytic potential. The range in aminopeptidase:endopeptidase activity ratios -i.e.…”

supporting

confidence: 54%

“…Leucyl aminopeptidase, however, represents only a small fraction of the total diversity of peptidases, which include 6 major families, each of which has a different active site and mechanism (Dixon & Webb 1979). Several studies have used fluorescently labeled peptides and chromatographic separation of hydrolysis products to demonstrate that the position of specific residues can influence peptide hydrolysis rates (Pantoja et al 1997, Pantoja & Lee 1999, Liu et al 2010. Only a handful of studies, all from temperate coastal environments, have used methylcoumarin (MCA)-type fluorogenic substrate analogs to report activities of peptidases other than leucyl aminopeptidase (Obayashi & Suzuki 2005, 2008a,b, Bong et al 2009, Obayashi et al 2010; these studies demonstrated considerable differences in hydrolysis rates for different classes of peptidases.…”

Section: Introductionmentioning

confidence: 99%

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Extracellular peptidase and carbohydrate hydrolase activities in an Arctic fjord (Smeerenburgfjord, Svalbard)

Steen¹,

Arnosti²

2013

Aquat. Microb. Ecol.

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Measurements of the spectrum of extracellular enzymes present in an environment can indicate the nature of organic substrates available to microorganisms. We report the activities in an Arctic fjord (Smeerenburgfjord, Svalbard) of the extracellular carbohydrate hydrolases α-galactosidase, β-glucosidase, and chitobiase, and the extracellular peptidases leucyl aminopeptidase, trypsin, and chymotrypsin. Among the carbohydrate hydrolases, β-glucosidase had the highest potential activity. Although extracellular leucyl aminopeptidase is frequently assayed in marine systems, activities of other peptidases have only rarely been reported. Peptidase activities were higher than carbohydrate hydrolase activities by approximately 2 orders of magnitude. Activities of leucyl aminopeptidase (an exopeptidase which cleaves terminal residues from a protein) were higher than trypsin and chymotrypsin (both endopeptidases which cleave interior bonds). In contrast to previous measurements from coastal, temperate environments, potential activity of leucyl aminopeptidase in Smeerenburg was higher than that of the endopeptidases trypsin and of chymotrypsin. These results suggest that leucyl aminopeptidase may not always be a reliable proxy for the total peptidolytic potential of microbial communities.

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supporting

confidence: 54%

Section: Introductionmentioning

confidence: 99%

Extracellular peptidase and carbohydrate hydrolase activities in an Arctic fjord (Smeerenburgfjord, Svalbard)

Steen¹,

Arnosti²

2013

Aquat. Microb. Ecol.

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“…In addition to the use of inorganic sources, various phytoplankton species can use dissolved organic nitrogen directly to meet their N needs and heterotrophic uptake of dissolved organic carbon has been observed in a number of dinoflagellates (Lewitus and Caron, 1991) and chrysophytes (Wheeler et al, 1977, Kristiansen, 1990. Bacterioplankton (Liu et al, 2010;Tappin et al, 2012) and phytoplankton (Mulholland and Lee, 2009) can directly utilize oligopeptides by both external hydrolysis and direct assimilation depending on molecular size. Ptacnik et al (2008) and Goebel et al (2014) found positive BEF relationships in the phytoplankton.…”

Section: Exchange Of Limiting Nutrientsmentioning

confidence: 99%

Marine biodiversity and ecosystem function relationships: The potential for practical monitoring applications

Strong

Andonegi

Bizsel³

et al. 2015

Estuarine, Coastal and Shelf Science

128

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There is an increasing demand for environmental assessments of the marine environment to include ecosystem function. However, existing schemes are predominantly based on taxonomic (i.e. structural) measures of biodiversity. Biodiversity and Ecosystem Function (BEF) relationships are suggested to provide a mechanism for converting taxonomic information into surrogates of ecosystem function. This review assesses the evidence for marine BEF relationships and their potential to be used in practical monitoring applications (i.e. operationalized).Five key requirements were identified for the practical application of BEF relationships: 1) a complete understanding of strength, direction and prevalence of marine BEF relationships, 2) an understanding of which biological components are influential within specific BEF relationships, 3) the biodiversity of the selected biological components can be measured easily, 4) detail which ecological mechanisms are the most important for generating marine BEF relationships, e.g. identity effects or complementarity, and 5) establish what proportion of the overall functional variance is explained by biodiversity, and hence BEF relationships.Many positive and some negative BEF relationships were found within the literature, although many reproduced poorly the natural species richness, trophic structures or multiple functions of real ecosystems. Null relationships were also reported. The consistency of the positive and negative relationships was often low that compromised the ability to generalize BEF relationships and confident application of BEF within marine monitoring. Equally, some biological components and functions have received little or no investigation.Expert judgement was used to attribute biological components using spatial extent, presence and functional rate criteria. This approach highlighted the main contributing biological components to the ecosystem functions, and that many of the particularly influential components were found to have received the least amount of research attention.The need for biodiversity to be measureable (requirement 3) is possible for most biological components although difficult within the functionally important microbes. 3Identity effects underpinned most marine BEF relationships (requirement 4). As such, processes that translated structural biodiversity measures into functional diversity were found to generate better BEF relationships.The analysis of the contribution made by biodiversity, over abiotic influences, to the total expression of a particular ecosystem function was rarely measured or considered (requirement 5). Hence it is not possible to determine the overall importance of BEF relationships within the total ecosystem functioning observed. In the few studies where abiotic factors had been considered, it was clear that these modified BEF relationships and have their own direct influence on functional rate.Based on the five requirements, the information required for immediate 'operationalization' of BEF relationships within marin...

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“…Concentrations of AVFA and its hydrolyzed peptide fragments (AVF, VFA, FA, VF) were analyzed using high performance liquid chromatography (HPLC, Shimadzu Prominence) equipped with a photodiode array (PDA) detector following the established protocol 16,41 . In brief, peptides were eluted on a C 18 column (Phenomenex Luna, 5 μm 250 × 4.6 mm) through a gradient program at a flow rate of 1 mL/min.…”

Section: Methodsmentioning

confidence: 99%

“…AVFA is a fragment of ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) that is ubiquitously involved in photosynthesis, and has been applied in our previous peptide decomposition studies 16,25 . These four bacterial strains were chosen because their growth has been often observed in substrate addition incubations in coastal waters [41][42][43][44][45] 100 fold change of relative abundance from amplicon sequencing, Table 1). We aim to obtain direct correlations between individual bacterial strains and their peptide decomposition rates and pathways, which can offer key insights into peptide decomposition in natural seawater.…”

mentioning

confidence: 99%

Distinct capabilities of different Gammaproteobacterial strains on utilizing small peptides in seawater

Liu

2020

Sci Rep

Self Cite

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Proteins and peptides account for 20-75% of marine biota biomass, of which a major fraction is metabolized by bacteria, thus deciphering interactions between bacteria and peptides is important in understanding marine carbon and nitrogen cycling. To better understand capabilities of different bacterial strains on peptide decomposition, four Gammaproteobacteria (Pseudoalteromonas atlantica, Alteromonas sp., Marinobacterium jannaschii, Amphritea japonica) were incubated in autoclaved seawater amended with tetrapeptide alanine-valine-phenylalanine-alanine (AVFA), a fragment of RuBisCO. While AVFA was decomposed greatly by Pseudoalteromonas atlantica and Alteromonas sp, it remained nearly intact in the Marinobacterium jannaschii and Amphritea japonica incubations. Pseudoalteromonas and Alteromonas decomposed AVFA mainly through extracellular hydrolysis pathway, releasing 71-85% of the AVFA as hydrolysis products to the surrounding seawater. Overall, this study showed that Gammaproteobacterial strains differ greatly in their capabilities of metabolizing peptides physiologically, providing insights into interactions of bacteria and labile organic matter in marine environments.The microbial loop plays a significant role in shaping the temporal and spatial distributions and pathways of bioelements such as C, N, P, and Fe in seawater 1 . The microbial loop converts organic matter from dissolved to particulate phase through the buildup of microbial biomass that is further passed to higher trophic levels via grazing, thus the interaction between bacteria and dissolved organic matter (DOM) is one of the major factors determining carbon flux in the ocean 2 . Labile organic matter, such as proteins and peptides in either dissolved or particulate phases, turns over rapidly in seawater, supporting a major fraction of bacterial growth 3,4 . To be available for bacteria, proteins and peptides need to be first cleaved into small peptides (ca. <600 Da) outside cell membrane by extracellular hydrolysis 5 . Therefore, it is important to study decomposition efficiency and pathways of small peptides in order to understand C and N cycling rates and factors controlling the bacteria-DOM interactions in seawater 6-8 .Knowing "who is doing what" is a fundamental question in the field of microbial ecology, and identifying biogeochemical function of different bacteria is key to understanding their ecological niche in the environment and their contribution to biological processes. Previously, differentiating the capability of different bacteria on labile DOM decomposition is mainly based on examining the change of bacterial community structures. Copiotrophic bacteria often dominate bacterial community after labile DOM is introduced to seawater incubations 9-15 . For example, Alphaproteobacteria (including Roseobacter), Gammaproteobacteria (including Alteromonas), Flavobacteria/ Sphingobacteria, Bacteroidetes, and Verrucomicrobia can outcompete other bacterial taxa and dominate bacterial community structure in incubations after specific labile co...

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The effect of chemical structure on the hydrolysis of tetrapeptides along a river-to-ocean transect: AVFA and SWGA

Cited by 23 publications

References 65 publications

Extracellular peptidase and carbohydrate hydrolase activities in an Arctic fjord (Smeerenburgfjord, Svalbard)

Extracellular peptidase and carbohydrate hydrolase activities in an Arctic fjord (Smeerenburgfjord, Svalbard)

Marine biodiversity and ecosystem function relationships: The potential for practical monitoring applications

Distinct capabilities of different Gammaproteobacterial strains on utilizing small peptides in seawater

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