The utility of proteases in proteomics,from sequence profiling to structure and function analysis

In mass spectrometry (MS)-based bottom-up proteomics, protease digestion plays an essential role in profiling both proteome sequences and post-translational modifications (PTMs). Trypsin is the gold standard in digesting intact proteins into small-size peptides, which are more suitable for high-performance liquid chromatography (HPLC) separation and tandem MS (MS/MS) characterization. However, protein sequences lacking Lys and Arg cannot be cleaved by trypsin and may be missed in conventional proteomic analysis. Proteases with cleavage sites complementary to trypsin are widely applied in proteomic analysis to greatly improve the coverage of proteome sequences and PTM sites. In this review, we survey the common and newly emerging proteases used in proteomics analysis mainly in the last 5 years, focusing on their unique cleavage features and specific proteomics applications such as missing protein characterization, new PTM discovery, and de novo sequencing. In addition, we summarize the applications of proteases in structural proteomics and protein function analysis in recent years. Finally, we discuss the future development directions of new proteases and applications in proteomics.     

Early butyrate induced acetylation of histone H4 is proteoform specific and linked to methylation state

Histone posttranslational modifications (PTMs) help regulate DNA templated processes; however, relatively little work has unbiasedly explored the single-molecule combinations of histone PTMs, their dynamics on short timescales, or how these preexisting histone PTMs modulate further histone modifying enzyme activity. We use quantitative top down proteomics to unbiasedly measure histone H4 proteoforms (single-molecule combinations of PTMs) upon butyrate treatment. Our results show that histone proteoforms change in cells within 10 minutes of application of sodium butyrate. Cells recover from treatment within 30 minutes after removal of butyrate. Surprisingly, K20me2 containing proteoforms are the near-exclusive substrate of histone acetyltransferases upon butyrate treatment. Single-molecule hierarchies of progressive PTMs mostly dictate the addition and removal of histone PTMs (K16ac > K12ac ≥ K8ac > K5ac, and the reverse on recovery). This reveals the underlying single-molecule mechanism that explains the previously reported but indistinct and unexplained patterns of H4 acetylation. Thus, preexisting histone PTMs strongly modulate histone modifying enzyme activity and this suggests that proteoform constrained reaction pathways are crucial mechanisms that enable the long-term stability of the cellular epigenetic state.     

A peptidoform based proteomic strategy for studying functions of post-translational modifications

Protein post-translational modifications (PTMs) generate an enormous, but as yet undetermined, expansion of the produced proteoforms. In this Viewpoint, we firstly reviewed the concepts of proteoform and peptidoform. We show that many of the current PTM biological investigation and annotation studies largely follow a PTM site-specific rather than proteoform-specific approach. We further illustrate a potentially useful matching strategy in which a particular “modified peptidoform” is matched to the corresponding “unmodified peptidoform” as a reference for the quantitative analysis between samples and conditions. We suggest this strategy has the potential to provide more directly relevant information to learn the PTM site-specific biological functions. Accordingly, we advocate for the wider use of the nomenclature “peptidoform” in future bottom-up proteomic studies.     

中国在翻译后修饰的生物信息学研究领域的进展与前瞻

翻译后修饰在调控蛋白质构象变化、活性以及功能方面具有重要作用,并参与了几乎所有细胞通路和过程。蛋白质翻译后修饰的鉴定是阐明细胞内分子机理的基础。相对于劳动密集的、耗费时间的实验工作,利用各种生物信息学方法开展翻译后修饰预测,能够提供准确、简便和快速的研究方案,并产生有价值的信息为进一步实验研究提供参考。文章主要综述了中国生物信息学者在翻译后修饰生物信息学领域所取得的研究进展,包括修饰底物与位点预测的计算方法学设计与完善、在线或本地化工具的设计与维护、修饰相关数据库及数据资源的构建及基于修饰蛋白质组学数据的生物信息学分析。通过比较国内外的同类研究,发现优势和不足,并对未来的研究作出前瞻。     

A review: limnological management and biomanipulation in the London reservoirs

Low algal biomasses and high water transparencies are a feature of the storage reservoirs that supply most of London's treated water. This is a result of knowledgeable limnological management and biomanipulation and despite the eutrophic nature of the River Thames with its high nutrients (7 gN m⁻³; 1 gP m⁻³) and particulate organic carbon (2 gC m⁻³). Built-in possibilities of jetting input water are managed to prevent stratification, to ensure isothermy, to mix chemicals and plankton vertically and horizontally and to manipulate the mixed-depth of the algal populations such that their potential for biomass growth is reduced by light-energy limitation. Spring algal growth is delayed and the spring peak is reduced and curtailed by the grazing impact of considerable biomasses of large-bodied daphnid populations (Daphnia magna, pulicaria & hyalina) whose development is also supported by the continuous input of high riverine algal crops. The existence of a large-bodied daphnid zooplankton in the reservoirs is associated with low levels of fish predation since the late 1960s. Variations in the intensity and nature of this vertebrate predation during the subsequent twenty years (1968–88) are illustrated by the changes that have occurred in the relationship between the phytoplankton and zooplankton biomasses of the April-May-June quarter of the year. This example of the London reservoirs serves to illustrate biomanipulation in deep water bodies by bottom-up as well as top-down effects.     

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.     

A unified treatment of top-down and bottom-up control of reproduction in populations

Generalizations describing how top‐down and bottom‐up processes jointly influence the production of offspring (recruitment) and the number of reproducing adults are lacking. This is a deficiency because (1) it is widely recognized that both top‐down and bottom‐up processes are common in ecosystems; and (2) the relationship between the number of individuals recruiting and number of reproductively active individuals present in that population is of fundamental importance in all branches of ecology. Here we derive a model to consider the joint effects of top‐down and bottom‐up forcing in any ecosystem. In general, during the lifetime of a cohort, bottom‐up effects are likely to limit recruitment over longer periods of time than top‐down effects. Top‐down effects are likely to be most important early in the life history when potential recruits are small in size, and such effects will be more recognizable in small cohorts comprised of slowly growing individuals.     

Enzymology and significance of protein histidine methylation

Cells synthesize proteins using 20 standard amino acids and expand their biochemical repertoire through intricate enzyme-mediated post-translational modifications (PTMs). PTMs can either be static and represent protein editing events or be dynamically regulated as a part of a cellular response to specific stimuli. Protein histidine methylation (Hme) was an elusive PTM for over 5 decades and has only recently attracted considerable attention through discoveries concerning its enzymology, extent, and function. Here, we review the status of the Hme field and discuss the implications of Hme in physiological and cellular processes. We also review the experimental toolbox for analysis of Hme and discuss the strengths and weaknesses of different experimental approaches. The findings discussed in this review demonstrate that Hme is widespread across cells and tissues and functionally regulates key cellular processes such as cytoskeletal dynamics and protein translation. Collectively, the findings discussed here showcase Hme as a regulator of key cellular functions and highlight the regulation of this modification as an emerging field of biological research.     

Reverse-Phase Protein Array: Technology,Application, Data Processing,and Integration

Reverse-phase protein array (RPPA) is a high-throughput antibody-based targeted proteomics platform that can quantify hundreds of proteins in thousands of samples derived from tissue or cell lysates, serum, plasma, or other body fluids. Protein samples are robotically arrayed as microspots on nitrocellulose-coated glass slides. Each slide is probed with a specific antibody that can detect levels of total protein expression or post-translational modifications, such as phosphorylation as a measure of protein activity. Here we describe workflow protocols and software tools that we have developed and optimized for RPPA in a core facility setting that includes sample preparation, microarray mapping and printing of protein samples, antibody labeling, slide scanning, image analysis, data normalization and quality control, data reporting, statistical analysis, and management of data. Our RPPA platform currently analyzes ∼240 validated antibodies that primarily detect proteins in signaling pathways and cellular processes that are important in cancer biology. This is a robust technology that has proven to be of value for both validation and discovery proteomic research and integration with other omics data sets.     

The relative importance of resources and natural enemies in determining herbivore abundance: thistles, tephritids and parasitoids

1. The relative importance of host-plant resources and natural enemies in influencing the abundance of insect herbivores was investigated in potted plant and natural population experiments, using tephritid (Diptera: Tephritidae) flies, their host plant, creeping thistle Cirsium arvense, and their Hymenoptera parasitoids. 2. Experimental manipulation of host-plant quality (i.e. levels of host-plant nutrients) and resource availability (i.e. the number of buds) increased tephritid abundance. There was no evidence that the seed-feeding tephritid fly Xyphosia miliaria preferentially oviposited on fertilized C. arvense. 3. At low thistle densities, X. miliaria showed a constant rate of resource exploitation. At higher thistle densities, a threshold was detected, above which additional buds were not attacked. 4. Parasitism attack was variable across host (tephritid) densities but levels of parasitism were consistently higher on the fertilized thistles. 5. Experimental manipulation of host-plant quality and resource availability (quantity) not only directly affects the tephritid population but also, indirectly, leads to high rates of parasitism. Both chemical and physical characteristics of host plants affect the performance of natural enemies. 6. Both top-down and bottom-up forces act to influence tephritid abundance, with bottom-up influences appearing to be the most important.     

Natural enemies act faster than endophytic fungi in population control of cereal aphids

1. Fast-growing populations of phytophagous insects can be limited by the presence of natural enemies and by alkaloids that are produced by symbiotic associations of many temperate grass species with endophytic fungi. It is unclear if and how acquired plant defences derived from endophytic fungi interact with natural enemies to affect phytophagous insect populations. 2. To assess the relative importance of endophytic fungi compared to that of natural enemies on the population dynamics of phytophagous insects, we carried out a fully factorial field experiment, in which the presence of natural enemies and the presence of endophytic fungi were manipulated simultaneously. Target colonies of aphids were monitored for 8 weeks starting from their natural appearance in the field to the end of the aphid season. 3. We show that on Lolium perenne increased natural enemy densities reduced the individual numbers of two common cereal aphids, Rhopalosiphum padi and Metopolophium festucae. 4. The presence of the endophytic fungi Neotyphodium lolii reduced the number of M. festucae but did not affect the number of R. padi. The reduction in R. padi numbers by predators and parasitoids was not influenced by the presence of endophytes. For adult M. festucae, however, the negative effects of natural enemies were significant only in the absence of endophytes. 5. Over the duration of the experiment, the effect of natural enemies on aphid colony growth was much stronger than the effect of the endophytic fungi N. lolii, presumably because predator and parasitoid action on aphid colonies is much faster than any effects of endophytes. 6. Our results demonstrate that with simultaneous action of acquired endosymbionts and natural enemies, both factors can control aphid colony growth but they generally act independently of each other.     

Identification of SUMO Targets by a Novel Proteomic Approach in Plants

Post-translational modifications (PTMs) chemically and physically alter the properties of proteins, including their folding, subcellular localization, stability, activity, and consequently their function. In spite of their relevance, studies on PTMs in plants are still limited. Small Ubiquitin-like Modifier (SUMO) modification regulates several biological processes by affecting protein-protein interactions, or changing the subcellular localizations of the target proteins. Here, we describe a novel proteomic approach to identify SUMO targets that combines 2-D liquid chromatography, immunodetection, and mass spectrometry (MS) analyses. We have applied this approach to identify nuclear SUMO targets in response to heat shock. Using a bacterial SUMOylation system, we validated that some of the targets identified here are, in fact, labeled with SUMO1. Interestingly, we found that GIGANTEA (GI), a photoperiodic-pathway protein, is modified with SUMO in response to heat shock both in vitro and in vivo.     

Crayfish in lakes and streams: individual and population responses to predation, productivity and substratum availability

1. In a correlative study, we investigated the relative importance of fish predation, refuge availability and resource supply in determining the abundance and size distributions of the introduced and omnivorous signal crayfish (Pacifastacus leniusculus) in lakes and streams. Moreover, the biomass and food selection of predatory fish was estimated in each habitat type and stable isotopes of carbon and nitrogen were measured in perch (Perca fluviatilis), the dominant predator in the lakes, and in its potential food sources (crayfish, juvenile roach and isopods). 2. In lakes, crayfish were the most frequent prey in large perch (46%), followed by other macroinvertebrates (26%, including the isopod Asellus aquaticus) and small fish (25%). Crayfish and fish dominated the gut contents of large perch with respect to biomass. Nitrogen signatures showed that perch were one trophic level above crayfish (approx. 3.4‰) and a two‐source mixing model using nitrogen isotope values indicated that crayfish (81%) contributed significantly more to perch isotope values than did juvenile roach (19%). A positive correlation was found between the abundance of crayfish and the biomass of large perch. Crayfish abundance in lakes was also positively correlated with the proportion of cobbles in the littoral zone. Lake productivity (chlorophyll a) was positively correlated with crayfish size, but not with crayfish abundance. 3. In streams, brown trout (Salmo trutta) were the most abundant predatory fish. Gut contents of large trout in a forested stream showed that terrestrial insects were the most frequently found prey (60%), followed by small crayfish (27%) and isopods (27%). In contrast to lakes, the relative abundance of crayfish was negatively correlated with the total biomass of predatory fish and with total biomass of trout. However, abundance of crayfish at sites with a low biomass of predatory fish varied considerably and was related to substratum grain size, with fewer crayfish being caught when the substratum was sandy or dominated by large boulders. The mean size of crayfish was greater at stream sites with a high standing stock of periphyton, but neither predator biomass nor substratum grain size was correlated with crayfish size. 4. Our results suggest that bottom‐up processes influence crayfish size in lakes and streams independent of predator biomass and substratum availability. However, bottom‐up processes do not influence crayfish abundance. Instead, substratum availability (lakes) and interactions between predation and substratum grain size (streams) need to be considered in order to predict crayfish abundance.     

ABRF-PRG04: differentiation of protein isoforms.

Accurate protein identification sometimes requires careful discrimination between closely related protein isoforms that may differ by as little as a single amino acid substitution or post-translational modification. The ABRF Proteomics Research Group sent a mixture of three picomoles each of three closely related proteins to laboratories who requested it in the form of intact proteins, and participating laboratories were asked to identify the proteins and report their results. The primary goal of the ABRF-PRG04 Study was to give participating laboratories a chance to evaluate their capabilities and practices with regards to sample fractionation (1D- or 2D-PAGE, HPLC, or none), protein digestion methods (in-solution, in-gel, enzyme choice), and approaches to protein identification (instrumentation, use of software, and/or manual techniques to facilitate interpretation), as well as determination of amino acid or post-translational modifications. Of the 42 laboratories that responded, 8 (19%) correctly identified all three isoforms and N-terminal acetylation of each, 16 (38%) labs correctly identified two isoforms, 9 (21%) correctly identified two isoforms but also made at least one incorrect identification, and 9 (21%) made no correct protein identifications. All but one lab used mass spectrometry, and data submitted enabled a comparison of strategies and methods used.     

The fluctuating world of a tundra predator guild: bottom‐up constraints overrule top‐down species interactions in winter

Global warming is predicted to change ecosystem functioning and structure in Arctic ecosystems by strengthening top‐down species interactions, i.e. predation pressure on small herbivores and interference between predators. Yet, previous research is biased towards the summer season. Due to greater abiotic constraints, Arctic ecosystem characteristics might be more pronounced in winter. Here we test the hypothesis that top‐down species interactions prevail over bottom‐up effects in Scandinavian mountain tundra (Northern Sweden) where effects of climate warming have been observed and top‐down interactions are expected to strengthen. But we test this ‘a priori’ hypothesis in winter and throughout the 3–4 yr rodent cycle, which imposes additional pulsed resource constraints. We used snowtracking data recorded in 12 winters (2004–2015) to analyse the spatial patterns of a tundra predator guild (arctic fox Vulpes lagopus, red fox Vulpes vulpes, wolverine Gulo gulo) and small prey (ptarmigan, Lagopus spp). The a priori top‐down hypothesis was then tested through structural equation modelling, for each phase of the rodent cycle. There was weak support for this hypothesis, with top‐down effects only discerned on arctic fox (weakly, by wolverine) and ptarmigan (by arctic fox) at intermediate and high rodent availability respectively. Overall, bottom‐up constraints appeared more influential on the winter community structure. Cold specialist predators (arctic fox and wolverine) showed variable landscape associations, while the boreal predator (red fox) appeared strongly dependent on productive habitats and ptarmigan abundance. Thus, we suggest that the unpredictability of food resources determines the winter ecology of the cold specialist predators, while the boreal predator relies on resource‐rich habitats. The constraints imposed by winters and temporary resource lows should therefore counteract productivity‐driven ecosystem change and have a stabilising effect on community structure. Hence, the interplay between summer and winter conditions should determine the rate of Arctic ecosystem change in the context of global warming.     

Nonenzymatic biotinylation of a biotin carboxyl carrier protein: unusual reactivity of the physiological target lysine

Enzyme-catalyzed addition of biotin to proteins is highly specific. In any single organism one or a small number of proteins are biotinylated and only a single lysine on each of these proteins is modified. A detailed understanding of the structural basis for the selective biotinylation process has not yet been elucidated. Recently certain mutants of the Escherichia coli biotin protein ligase have been shown to mediate "promiscuous" biotinylation of proteins. It was suggested that the reaction involved diffusion of a reactive activated biotin intermediate, biotinoyl-5'-AMP, with nonspecific proteins. In this work the reactivity of this chemically synthesized intermediate toward the natural target of enzymatic biotinylation, the biotin carboxyl carrier protein, was investigated. The results indicate that the intermediate does, indeed, react with target protein, albeit at a significantly slower rate than the enzyme-catalyzed process. Surprisingly, analysis of the products of nonenzymatic biotinylation indicates that of five lysine residues in the protein only the physiological target side chain is modified. These results indicate that either the environment of this lysine residue or its intrinsic properties render it highly reactive to nonenzymatic biotinylation mediated by biotinoyl-5'-AMP. This reactivity may be important for its selective biotinylation in vivo.     

Plankton dynamics in a tropical floodplain lake: fish, nutrients, and the relative importance of bottom-up and top-down control

1. Two enclosure experiments were carried out in Laguna Bufeos, a neotropical várzea lake located in the floodplain of River Ichilo (Bolivia). The experiments aimed (i) to assess the relative importance of bottom‐up and top‐down control on the plankton community, (ii) to assess the relative impact of direct and indirect effects of planktivorous fish on the zooplankton, and (iii) to attempt to identify the mechanisms responsible for these effects. 2. During the first experiment, bottom‐up control seemed to dominate the planktonic food web. Compared with fishless enclosures, oxygen concentrations, chlorophyll a levels and the population densities of all cladoceran zooplankton taxa increased in enclosures with fish. Birth rates of Moina minuta, the dominant taxon, were substantially higher in the presence than in the absence of fish, whereas death rates did not differ between treatments. These results are the first to suggest that the positive effects of fish on crustacean zooplankton via effects on nutrient cycling and the enhancement of primary production can compensate for losses because of fish‐related mortality. 3. During the second experiment, the direction of control appeared to vary between trophic levels: the phytoplankton appeared to be bottom‐up controlled whereas the zooplankton was mainly top‐down controlled. Chlorophyll a concentrations were enhanced by both fish and nutrient additions. The majority of the zooplankton taxa were reduced by the presence of fish. Birth rates of most cladoceran taxa did not differ between treatments, whereas death rates were higher in the enclosures with fish than in the fishless enclosures. Bosminopsis deitersi reached higher densities in the presence of fish, probably because of a release from predation by Chaoborus. 4. We convincingly showed strong deviations from trophic cascade‐based expectations, supporting the idea that trophic cascades may be weak in tropical lakes.