Size Distribution and Amino Acid Chemistry of Base-extractable Proteins from Washington Coast Sediments

Abstract

Proteinaceous components from four Washington coast margin sediments were extracted with base, fractionated into one of four size classes (<3 kDa, 3-10 kDa, 10-100 kDa, >100 kDa), and analyzed for their amino acid contents. Base-extracted material accounts for $30% of the total hydrolyzable amino acids (THAA) and each size fraction has a unique composition, regardless of where the sediment was collected (shelf or upper slope). The <3 kDa size fraction ($10% of baseextractable THAA) is relatively enriched in glycine ($30 mol%), lysine ($5 mol%), and nonprotein amino acids ($5 mol%). Glycine and non-protein amino acids are common degradation products, and lysine is very surface active. We suggest that the <3 kDa size fraction, therefore, represents a diagenetic mixture of fragments produced during the degradation of larger proteins. The 3-10 and 10-100 kDa size fractions ($10% and 42% of base-extractable THAA, respectively) have similar amino acid distributions dominated by aspartic acid ($ 30 mol%). Enrichments in Asp is likely due to both preservation of Asp-rich proteins and the production of Asp during degradation. The >100 kDa size fraction ($38% of base-extractable THAA) is not dominated by any particular amino acid and can not be modeled by mixing the amino acid compositions of the other size fractions. We propose that the larger size fractions (10-100 kDa and >100 kDa) represent intact, or near intact, proteins. Estimates of isoelectric points and relative hydrophobicity suggest the base-extractable proteins are primarily acidic and have globular structures. Statistical comparisons to several known proteins indicates that the base-extractable component is most similar to planktonic cytoplasmic proteins.

The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation

“…An additional complication expected from in situ environmental samples, such as sediments, is the presence of a vast array of proteins from numerous diverse organisms. The high number of contaminating, nonpeptide spectra collected at later time points in the degradation experiment (Table 1) suggests that additional isolation steps will be needed for many environmental matrices (Nunn et al 2006). To date, all discovery-based proteomic methods rely first on tandem mass spectrometry to provide a survey of the peptide ions present in a sample, and second on the ability of the resulting tandem mass spectra to be correlated with a peptide sequence and protein identification.…”

“…Particulate samples at time 0 provided the greatest amount of protein and allowed for additional MS analyses using gas-phase fractionation (GPF). Gasphase fractionation is a technique that enhances protein identifications by performing repeat analyses of the sample across several narrow, but overlapping, mass to charge (m/z) ranges (e.g., 500-600), rather than one wide m/z range (e.g., 350-2000) (Nunn et al 2006).…”

“…While analyses of whole cells and cellular fractions are well established for the identification of protein mixtures, there are several difficulties inherent in the detection and identification of proteins from oceanic particulate material (Pantoja et al 1997;Nguyen and Harvey 2001;Nunn and Keil 2006). Natural organic matter is a composite of multiple organisms and is subject to numerous chemical processes, which yield a concentrated mixture of dilute peptide components.…”

Geochemical Characteristics of Amino Acids in Sediments of Lake Taihu, A Large, Shallow, Eutrophic Freshwater Lake of China

“…The spatial distributions of THAA concentrations in sediments of Taihu were less variable than those previously reported from sediments in other aquatic environments (Ingalls et al 2004;Lomstein et al 2006Lomstein et al , 2009Nunn and Keil 2005). Surface sediment THAA concentrations (0-3 cm) ranged from 6.84 to 38.24 lmol g -1 , with a mean of 16.92 ± 8.24 lmol g -1 (Table 1).…”

Marine proteomics

“…Previously, the majority of oceanic protein analyses involved complete hydrolysis of all peptide linkages, breaking proteins into the original amino acid monomers: complex mixtures of proteins and peptides were chemically hydrolyzed (150°C, 6 N HCl, 1 h) to amino acids for interpretation (e.g. Cowie & Hedges 1992, Keil & Kirchman 1993, McCarthy et al 1997, Nunn & Keil 2005. As a result, any information that might have been gained pertaining to the sequence, structure, function or source of the protein was lost.…”