One-dimensional and two-dimensional polyacrylamide gel electrophoresis: a tool for protein characterisation in aquatic samples

Dissolved organic nitrogen (DON) represents the least understood part of the nitrogen cycle. Due to recent methodological developments, proteins now represent a potentially characterisable fraction of DON at the macromolecular level. We have applied polyacrylamide gel electrophoresis to characterise proteins in samples from a range of aquatic environments in the Everglades National Park, Florida, USA. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed that each sample has a complex and characteristic protein distribution. Some proteins appeared to be common to more than one site, and these might derive from dominant higher plant vegetation. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) provided better resolution; however, strong background hindered interpretation. Our results suggest that the two techniques can be used in parallel as a tool for protein characterisation: SDS-PAGE to provide a sample-specific fingerprint and 2D-PAGE to focus on the characterisation of individual protein molecules.

Molecular characterization of proteinaceous material in the Florida coastal Everglades

Dissolved organic nitrogen (DON) is the least known component of the nitrogen cycle, in part as a result of the lack of adequate analytical methods for its molecular characterization. In this study proteinaceous material in DON, collected at six geomorphologically different sites in the Florida coastal Everglades, was characterized by amino acid analysis and protein gel electrophoresis. The amino acid composition of the samples suggests that the canal DON was more degraded and subject to higher microbial inputs than the mangrove marshwater and marine end-member stations. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) results supported this observation as distinctly different protein profiles were obtained for the canal waters compared to samples collected at other stations. These preliminary results highlight the potential of combining amino acid and intact protein analysis to fingerprint the sources of DON in different aquatic environments, and show SDS-PAGE as a potentially useful method to characterize DON.