Elsevier

Organic Geochemistry

Volume 47, June 2012, Pages 9-21
Organic Geochemistry

Analysis of natural diatom communities reveals novel insights into the diversity of long chain polyamine (LCPA) structures involved in silica precipitation

https://doi.org/10.1016/j.orggeochem.2012.02.010Get rights and content

Abstract

The intricately nanopatterned siliceous frustules of diatoms are formed under the control of template organic molecules, some of which are tightly incorporated into the frustule during formation. Long chain polyamines (LCPAs) attract dissolved silicic acid species, enhance silica precipitation and play a role in frustule nanopattern formation. LCPAs thus play a central biogeochemical role, linking the cycling of organic matter with the cycling of silicic acid in the photic zone of the upper ocean. Their distribution and molecular diversity in the environment are as yet unknown. We used high performance liquid chromatography electrospray ionization–mass spectrometry (HPLC–ESI–MSn) to investigate the distribution and molecular diversity of aliphatic LCPAs extracted from the frustules of diatoms in mixed marine plankton communities collected within the euphotic zone of the northeastern Pacific coast, Bering Sea, and Puget Sound estuary. An astonishing variety of over 100 natural LCPAS with complex distribution patterns was found in each sample. Structural variation included degree of methylation, overall chain length, presence of secondary amine functionalities, incorporation of quaternary ammonium and occurrence of sulfonated derivatives. Putrescine-based LCPAs with various degrees of methylation and N-methyl propylamine repeat units were ubiquitous. Although some LCPA species overlapped between samples, there were regional differences in composition and structural characteristics. The structural variety of LCPAs employed by diatoms to produce their nanopatterned silicified exoskeleton could inform biomimetic studies of silica precipitation.

Highlights

► First report of long chain polyamines (LCPAs) in frustules of natural mixed marine diatom populations. ► Astonishing variety of >100 natural LCPAs with complex distribution found in each plankton tow sample. ► Clear regional differences in molecular composition and structural characteristics. ► Sulfated LCPAs are produced by diatoms.

Introduction

Unicellular photoautotrophic eukaryotes called diatoms secrete ornate and mesoporous cell walls, called frustules, made up of amorphous hydrated glass (SiO2nH2O). Each species produces unique cell wall morphology by precipitating silicic acid via a precisely directed biochemical machinery. The molecular mechanisms of silicic acid precipitation and morphogenesis of a species-specific solid, highly organized and nanopatterned frustule are thought to be controlled by an organic template composed of proteins and aliphatic long chain polyamines (LCPAs; Kröger and Poulsen, 2007). A few of these compounds, apparently involved in biosilicification of diatom frustules, have been characterized in pure lab cultures and consist of (i) silaffins (highly zwitterionic and highly modified phosphoproteins that play a direct role in silica polymerization), (ii) silacidins (highly acidic phosphopeptides), (iii) cingulins (protein components of a ring shaped organic matrix associated with the girdle band silica) and (iv) LCPAs which induce and control the shape of silica precipitation and the morphology of the frustules (Kröger et al., 2000, Poulsen and Kröger, 2004, Sumper et al., 2005, Sumper and Lehmann, 2006, Wenzl et al., 2008, Bridoux and Ingalls, 2010, Bridoux et al., 2011, Scheffel et al., 2011). The complex pool of LCPAs produced by diatoms appears to be synthesized in a species-specific manner, suggesting an important function in structure formation of the silica cell wall. LCPAs seem to be actively involved in the morphogenesis of the nanopatterned frustules (Pohnert, 2002, Foo et al., 2004, Sumper, 2004, Sumper and Kröger, 2004, Sumper and Brunner, 2006), via electrostatic attraction of silicic acid species and by catalyzing the polycondensation of silicic acid in water (Mizutani et al., 1998). Upon precipitation, LCPAs seem to be tightly bound and embedded within the opal, as they are only solubilized by dissolution of the silica. The LCPA composition of Chaetoceros debilis, Chaetoceros didynum, Coscinodiscus asteromphalus, Coscinodiscus granii, Coscinodiscus wailesii, Cylindrotheca fusiformis, Eucampia zodiacus, Navicula, Stephanopyxis turris and Thalassiosira pseudonana revealed that they occur mainly as N-methylated derivatives of oligo-propyleneimine chains attached to a putrescine, ornithine, propylamine, spermine, spermidine and 1,3-diaminopropane building block (Kröger et al., 2000, Sumper et al., 2005, Sumper and Lehmann, 2006). Each species was found to contain LCPAs exhibiting characteristic chain length, variation in the degree of N-methylation and position of secondary and tertiary amine functionalities, as well as incorporation of site-specific quaternary ammonium groups.

The biosynthetic pathways, leading to the production and methylation of these unusual aliphatic long chain polyamines are unknown but are thought to be derived from the existing spermidine/spermine route, where ornithine is the primary precursor. This view has been strengthened by the fact that specific inhibition of ornithine decarboxylase in T. pseudonana significantly altered the morphology of the silicified frustule (Frigeri et al., 2005). Recent analysis of the genomes of T. pseudonana, Phaeodactylum tricornutum and Fragilariopsis cylindrus revealed that these diatoms encode a set of molecular machines that use the enzymes S-adenosylmethionine decarboxylase and aminopropyltransferase for LCPA biosynthesis and methylation, via iterative addition of aminopropyl groups. The process may be derived from bacterial polyamine biosynthetic enzyme fusions, chromatin protein modification and binding domains (Michaels, 2011). While the LCPA composition of ten diatom species is known, it is not known how representative these structures are among a wider range of diatom species.

We recently developed a high performance liquid chromatography–electrospray ionization–mass spectrometry (HPLC–ESI–MS) method that employs an ion pairing agent, offering rapid analysis of underivatized aliphatic polyamines, while also providing structural information (Bridoux et al., 2011). Application of the method demonstrated the occurrence of LCPAs in sedimentary diatom frustules throughout the Holocene and the Last Glacial Maximum (Bridoux and Ingalls, 2010).

Here, we report the widespread occurrence of frustule-bound aliphatic long chain polyamines in mixed marine diatom communities from the northeastern Pacific coast, Bering Sea and Puget Sound estuary. Our goal was to gain insight into the diversity of LCPAs and evaluate whether differences exist among geographical locations. By studying mixed natural diatom communities from different environments, we hoped to capture the full array of LCPAs synthesized by diatoms.

Section snippets

Plankton tows

Water column plankton material was collected from the Northeast Pacific coast, on May 25th 2010 aboard the R.V. Wecoma. Net tow samples (25 μm mesh) were taken from Station GH6 (47.0°N, 124.1°W). Horizontal tows were conducted at 1 knot for 10 min at the chlorophyll maximum determined from the CTD cast. Plankton trapped in the cod end was poured into centrifuge tubes and kept on ice. In the laboratory, the tubes being centrifuged (2800g) and the water discarded. The resulting pellet was frozen at

Results and discussion

The diatom-rich plankton tow samples were first cleaned of any surface-bound, exogenous organic matter (OM), including the OM coating the frustules (frustuline, chitin, mucilage and potential exogenous OM). Intracellular components and membranes were then removed using a boiling solution of 2% SDS/100 mM EDTA (Kröger et al., 2000). SEM images taken from the solvent and SDS–EDTA cleaned plankton tow samples revealed cleaned diatom skeletons with clearly visible striaes, a sign of proper diatom

Conclusions

This is the first report of long chain polyamines extracted from the frustules of mixed marine diatom populations. Frustules collected from the surface waters of the northeast Pacific Ocean, Bering Sea and Puget Sound revealed an extremely complex mixture of natural LCPAs, with >100 individual polyamine species in each sample. LCPAs differed by starter group (putrescine, propylamine), degree of methylation, N-methyl propylamine chain length, presence of secondary amines, as well as the

Acknowledgements

We thank L. Truxal for assistance in the laboratory, R. Horner for assistance with diatom identification, R. Sambrotto (Lamont-Doherty Earth Observatory) for providing the Bering Sea plankton tow sample and two anonymous reviewers for constructive comments. The work was supported by Grants from the NSF OCE0525829 (AEI) and by the Gary C. Comer Science and Education Foundation. The SEM work was conducted at the shared experimental facilities of Genetically Engineered Materials Science and

References (36)

  • L.G. Frigeri et al.

    Identification of proteins from a cell wall fraction of the diatom Thalassiosira pseudonana

    Molecular and Cellular Proteomics

    (2005)
  • N. Kröger et al.

    Species-specific polyamines from diatoms control silica morphology

    Proceedings of the National Academy of Sciences USA

    (2000)
  • N. Kröger et al.

    Biochemistry and molecular genetics of silica biomineralization in diatoms

  • U.K. Laemmli

    Cleavage of structural proteins during the assembly of the head of bacteriophage T4

    Nature

    (1970)
  • K. Lutz et al.

    Biomimetic silica formation: Analysis of the phosphate-induced self-assembly of polyamines

    Physical Chemistry Chemical Physics

    (2005)
  • V. Martin-Jézéquel et al.

    Silicon metabolism in diatoms: implications for growth

    Journal of Phycology

    (2000)
  • S. Matsunaga et al.

    Long chain polyamines (LCPAs) from marine sponge: possible implication in spicule formation

    Chemistry and BioChemistry

    (2007)
  • McLafferty, F.W., Turecek, F., 1993. Interpretation of Mass Spectra, fourth ed., ISBN: 0935702253; Library: QC454.M22...
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