Preservation of protein in marine systems: Hydrophobic and other noncovalent associations as major stabilizing forces

Nguyen, Reno T.; Harvey, H. Rodger

doi:10.1016/s0016-7037(00)00621-9

Cited by 77 publications

(53 citation statements)

References 49 publications

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“…In comparing our shipboard incubations to field collected material from the same location (Moore et al 2012a), it is striking that the number of identified proteins and ratios of THAA/OC and THAA-N/PN for incubations times of 22, 35, 47, and 53 d were very similar to those seen in deep basin sediments (3490 m), over wintered shelf sediments (101 m), and suspended particles (50 m, 100 m) of the Bering Sea. Although this finding suggests that the rapid protein losses seen in shipboard incubations are realistic, it also supports findings that intact proteins contribute to a fraction of marine sedimentary amino acids (Pantoja & Lee 1999, Nguyen & Harvey 2001, Nunn et al 2010, Moore et al 2012a. The distribution of remaining proteins observed after 22 d also indicates that abundant chloroplast proteins make up the majority of identified preserved proteins.…”

Section: Identifiable Protein Correlates To Organic Matter Degradatiosupporting

confidence: 80%

Protein recycling in Bering Sea algal incubations

Moore

Harvey

Faux

et al. 2014

Mar. Ecol. Prog. Ser.

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Protein present in phytoplankton represents a large fraction of the organic nitrogen and carbon transported from its synthesis in surface waters to marine sediments. Yet relatively little is known about the longevity of identifiable protein in situ, or the potential modifications to proteins that occur during bloom termination, protein recycling and degradation. To address this knowledge gap, diatom-dominated phytoplankton was collected during the Bering Sea spring blooms of 2009 and 2010, and incubated under darkness in separate shipboard degradation ex periments spanning 11 and 53 d, respectively. In each experiment, the protein distribution was monited over time using shotgun proteomics, along with total hydrolyzable amino acids (THAAs), total protein, particulate organic carbon (POC) and nitrogen (PN), and bacterial cell abundance. Identifiable proteins, total protein and THAAs were rapidly lost during the first 5 d of enclosure in darkness in both incubations. Thereafter the loss rate was slower, and it declined further after 22 d. The initial loss of identifiable biosynthetic, glycolysis, metabolism and translation proteins after 12 h may represent shutdown of cellular activity among algal cells. Additional peptides with glycan modifications were identified in early incubation time points, suggesting that such protein modifications could be used as a marker for internal recycling processes and possibly cell death. Protein recycling was not uniform, with a subset of algal proteins including fucoxanthin chlorophyll binding proteins and RuBisCO identified after 53 d of degradation. Non-metric multidimensional scaling was used to compare the incubations with previous environmental results. The results confirmed recent observations that some fraction of algal proteins can survive water column recycling and undergo transport to marine sediments, thus contributing organic nitrogen to the benthos.

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Section: Identifiable Protein Correlates To Organic Matter Degradatiosupporting

confidence: 80%

Protein recycling in Bering Sea algal incubations

Moore

Harvey

Faux

et al. 2014

Mar. Ecol. Prog. Ser.

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“…These identified proteins represent material that may have been preserved after burial [12,[54][55][56][57] or mixed from the surface into deeper sediments by bioturbators [58][59][60]. Thus, it is expected that fewer proteins, with potentially lower sequence coverage, would be identified in the Bering Sea 8-to 10-cm core section than in surface sediments observed by Moore et al [16,29].…”

Section: Resultsmentioning

confidence: 89%

“…Peptides identified in smaller than expected molecular weight ranges could be due to partial hydrolysis [50]. Covalent modifications [13,51,52], hydrophobic interactions [12,13] and sequestration in potential energy fields [53] have been proposed as mechanisms for enhanced protein preservation, which could influence the gel migration of proteins to be in larger than expected molecular weight sections. The denaturing conditions of the SDS-PAGE gels used in this study indicate that charge alteration could also play a role in protein mobility.…”

Section: Resultsmentioning

confidence: 99%

“…Identifying intact proteins and peptides buried in marine sediments would give valuable information towards understanding marine biogeochemical cycles and reconstructing algal/microbial populations [9,10]. The complex matrix effects of sediments [11][12][13], however, have made extracting buried proteins for further analysis a challenge [14][15][16]. New bioseparation methods are needed to successfully extract proteins from deep sediments for subsequent analyses.…”

Section: Introductionmentioning

confidence: 99%

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Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments

et al. 2014

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Abstract:Proteins are the largest defined molecular component of marine organic nitrogen, and hydrolysable amino acids, the building blocks of proteins, are important components of particulate nitrogen in marine sediments. In oceanic systems, the largest contributors are phytoplankton proteins, which have been tracked from newly produced bloom material through the water column to surface sediments in the Bering Sea, but it is not known if proteins buried deeper in sediment systems can be identified with confidence. Electrophoretic gel protein extraction methods followed by proteomic mass spectrometry and database searching were used as the methodology to identify buried phytoplankton proteins in sediments from the 8-10 cm section of a Bering Sea sediment core. More peptides and proteins were identified using an SDS-PAGE tube gel than a standard 1D flat gel or digesting the sediment directly with trypsin. The majority of proteins identified correlated to the marine diatom, Thalassiosira pseudonana, rather than bacterial protein sequences, indicating an algal source not only dominates the input, but also the preserved protein fraction. Abundant RuBisCO and fucoxanthin chlorophyll a/c binding proteins were identified, supporting algal sources of these proteins and reinforcing the proposed mechanisms that might protect proteins for long time periods. Some preserved peptides were identified in OPEN ACCESSChromatography 2014, 1 177 unexpected gel molecular weight ranges, indicating that some structural changes or charge alteration influenced the mobility of these products during electrophoresis isolation. Identifying buried photosystem proteins suggests that algal particulate matter is a significant fraction of the preserved organic carbon and nitrogen pools in marine sediments.

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“…Two main mechanisms are accepted for OM transformation and preservation during diagenesis, catagenesis and metagenesis: degradation/recondensation (Tissot & Welte 1978) and selective preservation (Tegelaar et al 1989) (the discussion on the merits of each one is beyond the purpose of this work; see Largeau & Derenne 1993, Tyson 1995 for a discussion about this subject). Carbohydrates and proteins are regarded as components with low diagenetic preservation potential (although a fraction of these macromolecules can be preserved in sediments, see Nguyen & Harvey 2001, Jensen et al 2005 and references therein). Lipids, on the other hand, are thought to be more resistant.…”

Section: Biogeochemistry: High Lipid Content As Indicative Of Oxygen mentioning

confidence: 99%

Can biogeochemistry aid in the palaeoenvironmental/early diagenesis reconstruction of the &tilde;187 Ma (Pliensbachian) organic-rich hemipelagic series of the Lusitanian Basin (Portugal)?

Silva¹,

Filho²,

Silva³

et al. 2012

Bull. Geosci.

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Data on lipids, carbohydrates and proteins of the most expressive black shale (s.l.) intervals of the Early-Late Pliensbachian (Early Jurassic,~187 Ma) organic-rich hemipelagic series of the Lusitanian Basin (Portugal) were determined using a method that has been successfully applied over the last two decades in the characterization of biomass and very immature sediments. The goal of this paper is to test the applicability of these techniques to the ancient geological record. To our knowledge, this is the first time that this type of biogeochemical data from sedimentary series older than Oligocene is reported and tentatively used for palaeoenvironmental/diagenetic inferences. Carbohydrates and proteins are present in low concentrations, reaching up to 385.13 and 451.13 μg/g rock, respectively. The main variations are observed in the lipid contents, ranging from 197.67 to 8446.36 μg/g rock. The samples with the highest amounts of lipids seem to correlate with low [O 2 ] time intervals determined by independent data, such as organic petrography, micropalaeontology and sedimentology. This was probably related with selective lipid preservation under oxygen and hydrogen sulfide-rich depleted environments. The good overall match between the determined lipid contents and specific depositional/early diagenetical conditions seem to favor the idea that the easy to perform and inexpensive method applied here has the potential to add useful information to the study of ancient organic-rich carbonate sedimentary series.

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Preservation of protein in marine systems: Hydrophobic and other noncovalent associations as major stabilizing forces

Cited by 77 publications

References 49 publications

Protein recycling in Bering Sea algal incubations

Protein recycling in Bering Sea algal incubations

Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments

Can biogeochemistry aid in the palaeoenvironmental/early diagenesis reconstruction of the &tilde;187 Ma (Pliensbachian) organic-rich hemipelagic series of the Lusitanian Basin (Portugal)?

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