The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes

Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called “native conditions” (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein−ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.     

Do we live in a largely top-down regulated world?

Based on a review of mostly recent literature for a public lecture, the question is discussed whether we live in a largely “top-down” regulated world rather than one formed “bottom-up” by the resources for plant and animal growth. Of course, the top-down mechanism is predicated by bottom-up production, especially by the plants. Examples for the effects of grazing and predation for the land and the open sea, but including coral reefs, are discussed. The answer to the question posed by the title is affirmative. Ecosystems altered by man and urgent needs for marine conservation are briefly treated.     

Microbial Food Webs in an Artificially Divided Acidic Bog Lake

The microbial loop of a naturally acidic bog lake, Große Fuchskuhle (Northeastern Germany), that had been artificially divided into 4 basins, was investigated. In the northeast (NE) and southwest (SW) basins, which differ strongly in chemistry and primary production, we conducted intensive studies of the main carbon fluxes through microbial food webs. In the less acidic, NE basin, much higher phytoplankton as well as bacterial biomass and production were found in parallel with negligible numbers of larger zooplankters. Weakly top-down controlled populations of protists were characterized by an exceptionally low numerical proportion of heterotrophic nanoflagellates (HNF) to ciliates (-1.5-3.5). The ciliate community was dominated by a scuticociliate, Cyclidium sp. (>95% of total ciliates), with an estimated grazing rate equal to 46–80% of heterotrophic bacterial production. In contrast, in the more humic, SW basin, both phyto- and bacterioplankton dynamics seemed to be top-down controlled by abundant populations of small fine-filter feeding cladocerans, Ceriodaphnia quadrangula and Diaphanosoma brachyurum. Consequently, ciliates disappeared from the food web structure of the SW basin, HNF dropped to negligible numbers and bacteria showed very uniform morphology, dominated by small cocci or short rods. Our investigations have shown that the division of the lake into separate compartments can lead to very different microbial food web structures with extreme species compositions.     

Phytoplankton associations in a small hypertrophic fishpond in East Hungary during a change from bottom-up to top-down control

Phytoplankton species composition and abundance of a shallow hypertrophic fishpond (Mézeshegyi-tó, East Hungary) was studied for the period 1992–1995. The pond showed a pronounced algal periodicity. High-diversity phytoplankton assemblages occurred in spring and autumn. During the winter period, low diversity values were related either to stable community states, when K-strategist species dominated the plankton, or to a large bloom of r-strategist species. In summer, the stable environment led to low-diversity, high-biomass phytoplankton assemblages, dominated by Cylindrospermopsis raciborskii. At this time, the growth conditions for Cylindrospermopsiswere akin to those prevailing in a continuous fermentor. The overwhelming dominance of this species lasted for more than four months, during which time, the phytoplankton resembled that of one in the tropics. In August, 1993, an unsuccessful chemical treatment for reducing the algal bloom succeeded in killing the pond's entire population of fish. The large fish-stock comprised the planktivorous silver carp. Although the summer of 1994 was one of the warmest summers of this century, the expected Cylindrospermopsis bloom failed to develop probably because of a higher grazing pressure by large zooplankton. In spite of the fact that the temporal and spatial pattern of the phytoplankton is influenced principally by bottom-up effects, changes in cascading trophic interactions may also considerably influence the species composition and biomass.     

Diversity, function and stability in parasitoid communities

The parasitoid assemblages associated with grass-feeding chalcid wasps in Great Britain were used to examine the relationships between diversity (species richness), community function (total parasitism rate) and stability (variability in parasitism rate over time). Species-rich communities did not generate higher parasitism rates than species-poor communities, nor was temporal variation of parasitism rates related to parasitoid community richness. The mechanisms underlying hypotheses linking species richness and community function and stability are discussed in the light of these results. Because all parasitoid species represent a single functional group, a lack of complementarity in the ways they use their resources may explain why diversity is not linked to function or community stability. A second likely reason is that these parasitoid communities are under bottom-up control, thus exerting little or no influence on total system function and variability. This is likely to be common in parasitoid communities.     

Preference-performance linkage in a herbivorous lady beetle: consequences of variability of natural enemies

We investigated the relationship between oviposition preference and offspring performance in a herbivorous lady beetle Epilachna pustulosa on two co-occurring plant species, thistle Cirsium kamtschaticum and blue cohosh Caulophyllum robustum, in 1994 and 1995. The relative importance of bottom-up effects by host plants and top-down effects by natural enemies on offspring performance were determined using field and laboratory experiments. In both years, egg density on blue cohosh was significantly higher than on thistle. A laboratory experiment demonstrated that larval survival from hatching to adult emergence was significantly higher, and developmental period shorter when larvae were reared on blue cohosh compared to thistle. The positive preference-performance linkage varied between years in the field. Top-down effects had a different impact on larval survival on the two host plant species. Arthropod predators, a lady beetle Harmonia axyridis and an earwig Forficula mikado, considerably depressed immature survival on thistle, while they were negligible on blue cohosh. Although the lack of effective predation increased larval survival on blue cohosh, it led to defoliation due to increased larval feeding late in the season. Because of severe intraspecific competition, old larvae had significantly lower survival on blue cohosh than on thistle. In 1994, as larval survival decreased due to defoliation on blue cohosh, the overall survival rate was significantly higher on thistle than on blue cohosh. This survival pattern was opposite to that found in the laboratory experiment. In contrast, in 1995, the increase in predatory lady beetles on thistle caused greater larval mortality. Thus, the overall survival was significantly lower on thistle than on blue cohosh, although severe intraspecific competition occurred on blue cohosh as it had in 1994. Consequently, the offspring performance on the two host plants is largely determined by the relative importance of arthropod predation determining larval survival on thistle and host plant defoliation reducing late larval survival on blue cohosh. These results indicate the important role of spatial and temporal variability of natural enemies on the preference-performance linkage of herbivorous insects. Received: 19 August 1998 / Accepted: 11 January 1999     

Trophic structure of nine Czech reservoirs regularly stocked with piscivorous fish

For nearly 20 years, most Czech reservoirs supplying drinking water have been under statutory protection which permitted reservoir managers to manipulate fish stocks in order to maintain a sustainable water quality. The most common biomanipulative measure adopted was stocking with piscivorous fish (mostly 5 cm fry) using an annual stocking level of approx. 25 000 fish per reservoir. Nine reservoirs were studied for signs of top-down food web effects, as predicted by the trophic cascade hypothesis based on levels of total phosphorus (TP), chlorophyll a (Chl a), zooplankton biomass (ZB) and zooplankton community structure. In all nine reservoirs, only small Daphnia species were recorded, such as D. galeata and D. cucullata. The proportion of large-bodied daphnids retained on a 0.71 mm sieve was less than 10% of the total crustacean biomass in all reservoirs. The relationship of Chl a level – TP, and of ZB – Chl a, was positive under enhanced piscivory and did not differ statistically from the relationships in other reservoirs with natural fish stocks. This implies that bottom-up forces remained stronger than top-down ones in the studied reservoirs, despite the stocking of piscivorous fish. The failure of this attempt at biomanipulation may be due to an insufficient stocking rate of predatory fish and/or inadequate data on the resident planktivorous fish levels.     

Application of Mass Spectrometry in Proteomics

Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.     

Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization

Introduction: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is increasingly utilized as a rapid technique to identify microorganisms including pathogenic bacteria. However, little attention has been paid to the significant proteomic information encoded in the MS peaks that collectively constitute the MS ‘fingerprint’. This review/perspective is intended to explore this topic in greater detail in the hopes that it may spur interest and further research in this area.

Areas covered: This paper examines the recent literature on utilizing MALDI-TOF for bacterial identification. Critical works highlighting protein biomarker identification of bacteria, arguments for and against protein biomarker identification, proteomic approaches to biomarker identification, emergence of MALDI-TOF-TOF platforms and their use for top-down proteomic identification of bacterial proteins, protein denaturation and its effect on protein ion fragmentation, collision cross-sections and energy deposition during desorption/ionization are also explored.

Expert commentary: MALDI-TOF and TOF-TOF mass spectrometry platforms will continue to provide chemical analyses that are rapid, cost-effective and high throughput. These instruments have proven their utility in the taxonomic identification of pathogenic bacteria at the genus and species level and are poised to more fully characterize these microorganisms to the benefit of clinical microbiology, food safety and other fields.