Ecological proteomics: is the field ripe for integrating proteomics into evolutionary ecology research?

A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring

Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.

Toxic Habits: An Analysis of General Trends and Biases in Snake Venom Research

Biases in snake venom research have been partially identified but seldomly quantified. Using the Google Scholar web search engine, we collected a total of 267 articles published between 1964 and 2021, and reviewed them to assess the main trends in this field of study. We developed a 4-category classification of the harmful potential of each of the 298 snake species retrieved from the analysed publications, and tested whether taxonomy, realm of origin, and/or assigned hazard category could affect how often each of them appeared in the articles considered. Overall, viperids were significantly more represented than any other snake taxon retrieved. The Neotropics were the most represented biogeographic realm for number of studied species, whereas information about the country of origin of the analysed specimens was often incomplete. The vast majority of the publications focused on snake venom characterisation, whereas more ecology-related topics were rarely considered. Hazard category and biogeographic realm of origin of each species had a significant effect on the number of articles dedicated to it, suggesting that a snake's harmful potential and place of origin influence its popularity in venom studies. Our analysis showed an overall positive trend in the number of snake venom studies published yearly, but also underlined severe neglect of snake families of supposedly minor medical relevance (e.g., Atractaspididae), underrepresentation of some of the areas most impacted by snakebite (i.e., Indomalayan and Afrotropic realms), and limited interest in the ecological and functional context of snake venom.

Widespread alterations upon exposure to the estrogenic endocrine disruptor ethinyl estradiol in the liver proteome of the marine male fish Cyprinodon variegatus

Quantitative proteomic changes in the liver of adult males of Sheepshead minnow (Cyprinodon variegatus) upon exposure to ethinyl estradiol (EE2) were assessed to provide an advanced understanding of the metabolic pathways affected by estrogenic endocrine disruption in marine fish, and to identify potential novel molecular biomarkers for the environmental exposure to estrogens. From a total of 3188 identified protein groups (hereafter proteins), 463 showed a statistically significant difference in their abundance between EE2 treatment and solvent control samples. The most affected biological processes upon EE2 exposure were related to ribosomal biogenesis, protein synthesis and transport of nascent proteins to endoplasmic reticulum, and nuclear mRNA catabolism. Within the group of upregulated proteins, a subset of 14 proteins, involved in egg production (Vitellogenin, Zona Pellucida), peptidase activity (Cathepsine E, peptidase S1, Serine/threonine-protein kinase PRP4 homolog, Isoaspartyl peptidase and Whey acidic protein), and nucleic acid binding (Poly [ADP-ribose] polymerase 14) were significantly upregulated with fold-change values higher than 3. In contrast, Collagen alpha-2, involved in the process of response to steroid hormones, among others, was significantly downregulated (fold change = 0.2). This pattern of alterations in the liver proteome of adult males of C. variegatus can be used to identify promising novel biomarkers for the characterization of exposure of marine fish to estrogens. The Whey acidic protein-like showed the highest upregulation in EE2-exposed individuals (21-fold over controls), suggesting the utility of abundance levels of this protein in male liver as a novel biomarker of xenoestrogen exposure.

The bisphenol A metabolite MBP causes proteome alterations in male Cyprinodon variegatus fish characteristic of estrogenic endocrine disruption

The toxicological status of bisphenol A (BPA) is under strong debate. Whereas in vitro it is an agonist of the estrogen receptor with a potency ca. 10⁵-fold lower than the natural female hormone estradiol, in vivo exposure causes only mild effects at concentration thresholds environmentally not relevant and inconsistent among species. By using a proteomic approach, shotgun liver proteome analysis, we show that 7-d exposure to 10 μg/L of the BPA metabolite, 4-methyl-2,4-bis(4-hydroxyphenyl)pent-1-ene (MBP), and not the same exposure to the parental molecule BPA, alters the liver proteome of male Cyprinodon variegatus fish. Different physiological and environmental conditions leading to biotransformation of BPA to MBP may partly explain the conflicting results so far reported for in vivo BPA exposures. The pattern of alteration induced by MBP is similar to that caused by estradiol, and indicative of estrogenic endocrine disruption. MBP enhanced ribosomal activity, protein synthesis and transport, with upregulation of 91% of the ribosome-related proteins, and 12 proteins whose expression is regulated by estrogen-responsive elements, including vitellogenin and zona pellucida. Whey acidic protein (WAP) was the protein most affected by MBP exposure (FC = 68). This result points at WAP as novel biomarker for xenoestrogens.

Vitellogenin gene expression in marine mussels exposed to ethinylestradiol: No induction at the transcriptional level

Vitellogenin (Vtg), a large multidomain protein precursor of egg-yolk proteins, is used as an endocrine disruption biomarker in fish, and in the last decades, its use has been extended to invertebrates like mollusks. However, it remains unclear whether invertebrate endocrine system produces Vtg in response to estrogens, like it occurs in oviparous vertebrates. In a previous study, no evidence of induction of Vtg expression at protein level was found in gonads of the marine mussel Mytilus galloprovincialis after exposure to the estrogenic chemical 17α-ethinylestradiol (EE2). In the present follow-up study, it was investigated whether there is any effect of EE2 on Vtg abundance at transcriptional level in M. galloprovincialis gonads. To this aim, RT-qPCR analysis targeting three different domains of Vtg transcript was performed on gonads of mussels that were exposed either 4 or 24 days to 100 ng/L EE2. In addition, several reference genes were analysed and a selection of these for potential use in further RT-qPCR analyses on mussel male and female gonads is provided. Results showed higher expression in females than in males for the three analysed Vtg domains, and no evidence of Vtg mRNA induction due to EE2 either in females or males. The present results, together with those obtained from previous analysis at protein level, support that Vtg is not an adequate biomarker for xenoestrogenicity in marine mussels. Additionally, nucleotide sequences of Vtg transcripts of three closely-related species from Mytilus edulis complex (M. galloprovincialis, M. edulis and M. trossulus) are provided and compared with Vtg sequences from other mollusk species to assess the level of conservation and evolutionary relationships among species.

A Primer and Guidelines for Shotgun Proteomic Analysis in Non-model Organisms

During the last decade, we have witnessed outstanding advances in proteomics led mostly by great technological improvements in mass spectrometry field allowing high-throughput production of high-quality data used for massive protein identification and quantification. From a practical viewpoint, these advances have been mainly exploited in research projects involving model organisms with abundant genomic and proteomic information available in public databases. However, there is a growing number of organisms of high interest in different disciplines, such as ecological, biotechnological, and evolutionary research, yet poorly represented in these databases. Important advances in massive parallel sequencing technology and easy accessibility of this technology to many research laboratories have made nowadays possible to produce customized genomic and proteomic databases of any organism. Along this line, the use of proteogenomic approaches by combining in the same analysis the data obtained from different omic levels has emerged as a very useful and powerful strategy to run shotgun proteomic experiments specially focused on non-model organisms. In this chapter, we provide detailed procedures to undertake shotgun quantitative proteomic experiments following either a label-free or an isobaric labeling approach in non-model organisms, emphasizing also a few key aspects related to experimental design and data analysis.

No evidence that vitellogenin protein expression is induced in marine mussels after exposure to an estrogenic chemical

A wide variety of endocrine disrupting chemicals reach the marine environment and can cause harmful effects in different marine organisms. Vitellogenin (Vtg), the egg-yolk precursor, is a commonly used endocrine disruption biomarker in fish and more recently in marine invertebrates under the assumption of high expected similarities in the endocrine system of vertebrates and invertebrates. However, this assumption has been recently questioned. The results from previous studies focused on bivalve molluscs showed that Vtg induction could be misleading because of the use of either non-robust or indirect techniques to measure Vtg. In this study, mussels (Mytilus galloprovincialis) were exposed to either 10 or 100 ng/L of the synthetic hormone 17α-ethinylestradiol (EE2) at different exposure times (4 and 24 days) and under different feeding regimes (representing different energy balances), and Vtg levels in both male and female mussel gonads were quantified by label free shotgun LC-MS/MS proteomic analysis. Vtg protein was not detected in male gonads. In female gonads, Vtg levels were not significantly affected by EE2 at any exposure time or EE2 concentration tested, whereas a significant correlation was found between the degree of maturation of the gonad and Vtg levels in females. Results obtained in the present study critically question the use of Vtg as a biomarker of endocrine disruption in marine mussels, and show that the degree of maturation of the gonad can be an important confounding factor in the attempts to evaluate estrogenic effects through Vtg measurement in mussel gonads.

Proteomic profiling of ascidians as a tool for biomonitoring marine environments

Applying a proteomic approach for biomonitoring marine environments offers a useful tool for identifying organisms' stress responses, with benthic filter-feeders being ideal candidates for this practice. Here, we investigated the proteomic profile of two solitary ascidians (Chordata, Ascidiacea): Microcosmus exasperatus, collected from five sites along the Mediterranean coast of Israel; and Polycarpa mytiligera collected from four sites along the Red Sea coast. 193 and 13 proteins in M. exasperatus and P. mytiligera, respectively, demonstrated a significant differential expression. Significant differences were found between the proteomes from the northern and the southern sites along both the Mediterranean and the Red Sea coasts. Some of the significant proteins had previously been shown to be affected by environmental stressors, and thus have the potential to be further developed as biomarkers. Obtaining a proteomic profile of field-collected ascidians provides a useful tool for the early-detection of a stress response in ascidians worldwide.

RNA-seq coupled to proteomic analysis reveals high sperm proteome variation between two closely related marine mussel species

Speciation mechanisms in marine organisms have attracted great interest because of the apparent lack of substantial barriers to genetic exchange in marine ecosystems. Marine mussels of the Mytilus edulis species complex provide a good model to study mechanisms underlying species formation. They hybridise extensively at many localities and both pre- and postzygotic isolating mechanisms may be operating. Mussels have external fertilisation and sperm cells should show specific adaptations for survival and successful fertilisation. Sperm thus represent key targets in investigations of the molecular mechanisms underlying reproductive isolation. We undertook a deep transcriptome sequencing (RNA-seq) of mature male gonads and a 2DE/MS-based proteome analysis of sperm from Mytilus edulis and M. galloprovincialis raised in a common environment. We provide evidence of extensive expression differences between the two mussel species, and general agreement between the transcriptomic and proteomic results in the direction of expression differences between species. Differential expression is marked for mitochondrial genes and for those involved in spermatogenesis, sperm motility, sperm-egg interactions, the acrosome reaction, sperm capacitation, ATP reserves and ROS production. Proteins and their corresponding genes might thus be good targets in further genomic analysis of reproductive barriers between these closely related species. SIGNIFICANCE: Model systems for the study of fertilization include marine invertebrates with external fertilisation, such as abalones, sea urchins and mussels, because of the ease with which large quantities of gametes released into seawater can be collected after induced spawning. Unlike abalones and sea urchins, hybridisation has been reported between mussels of different Mytilus spp., which thus makes them very appealing for the study of reproductive isolation at both pre- and postzygotic levels. There is a lack of empirical proteomic studies on sperm samples comparing different Mytilus species, which could help to advance this study. A comparative analysis of sperm proteomes across different taxa may provide important insights into the fundamental molecular processes and mechanisms involved in reproductive isolation. It might also contribute to a better understanding of sperm function and of the adaptive evolution of sperm proteins in different taxa. There is now growing evidence from genomics studies that multiple protein complexes and many individual proteins might have important functions in sperm biology and the fertilisation process. From an applied perspective, the identification of sperm-specific proteins could also contribute to the improved understanding of fertility problems and as targets for fertility control.

Absolute venomics: Absolute quantification of intact venom proteins through elemental mass spectrometry

We report the application of a hybrid element and molecular MS configuration for the parallel absolute quantification of μHPLC-separated intact sulfur-containing venom proteins, via ICP triple quadrupole MS and ³²S/³⁴S isotope dilution analysis, and identification by ESI-QToF-MS of the toxins of the medically important African black-necked spitting cobra, Naja nigricollis (Tanzania); New Guinea small-eyed snake, Micropechis ikaheka; and Papuan black snake, Pseudechis papuanus. The main advantage of this approach is that only one generic sulfur-containing standard is required to quantify each and all intact Cys- and/or Met-containing toxins of the venom proteome. The results of absolute quantification are in reasonably good agreement with previously reported relative quantification of the most abundant protein families. However, both datasets depart in the quantification of the minor ones, showing a tendency for this set of proteins to be underestimated in standard peptide-centric venomics approaches. The molecular identity, specific toxic activity, and concentration in the venom, are the pillars on which the toxicovenomics-aimed discovery of the most medically-relevant venom toxins, e.g. those that need to be neutralized by an effective therapeutic antivenom, should be based. The pioneering venom proteome-wide absolute quantification shown in this paper represents thus a significant advance towards this goal. The potential of ICP triple quadrupole MS in proteomics in general, and venomics in particular, is critically discussed.

BIOLOGICAL SIGNIFICANCE

Animal venoms provide excellent model systems for investigating interactions between predators and prey, and the molecular mechanisms that contribute to adaptive protein evolution. On the other hand, numerous cases of snake bites occur yearly by encounters of humans and snakes in their shared natural environment. Snakebite envenoming is a serious global public health issue that affects the most impoverished and geopolitically disadvantaged rural communities in many tropical and subtropical countries. Unveiling the temporal and spatial patterns of venom variability is of fundamental importance to understand the molecular basis of envenoming, a prerequisite for developing therapeutic strategies against snakebite envenoming. Research on venoms has been continuously enhanced by advances in technology. The combined application of next-generation transcriptomic and venomic workflows has demonstrated unparalleled capabilities for venom characterization in unprecedented detail. However, mass spectrometry is not inherently quantitative, and this analytical limitation has sparked the development of methods to determine absolute abundance of proteins in biological samples. Here we show the potential of a hybrid element and molecular MS configuration for the parallel ESI-QToF-MS and ICP-QQQ detection and absolute quantification of intact sulfur-containing venom proteins via ³²S/³⁴S isotope dilution analysis. This configuration has been applied to quantify the toxins of the medically important African snake Naja nigricollis (Tanzania), and the Papuan species Micropechis ikaheka and Pseudechis papuanus.

Protein-species quantitative venomics: looking through a crystal ball

In this paper we discuss recent significant developments in the field of venom research, specifically the emergence of top-down proteomic applications that allow achieving compositional resolution at the level of the protein species present in the venom, and the absolute quantification of the venom proteins (the term “protein species” is used here to refer to all the different molecular forms in which a protein can be found. Please consult the special issue of Jornal of Proteomics “Towards deciphering proteomes via the proteoform, protein speciation, moonlighting and protein code concepts” published in 2016, vol. 134, pages 1-202). Challenges remain to be solved in order to achieve a compact and automated platform with which to routinely carry out comprehensive quantitative analysis of all toxins present in a venom. This short essay reflects the authors’ view of the immediate future in this direction for the proteomic analysis of venoms, particularly of snakes.

Strategies in 'snake venomics' aiming at an integrative view of compositional, functional, and immunological characteristics of venoms

This work offers a general overview on the evolving strategies for the proteomic analysis of snake venoms, and discusses how these may be combined through diverse experimental approaches with the goal of achieving a more comprehensive knowledge on the compositional, toxic, and immunological characteristics of venoms. Some recent developments in this field are summarized, highlighting how strategies have evolved from the mere cataloguing of venom components (proteomics/venomics), to a broader exploration of their immunological (antivenomics) and functional (toxicovenomics) characteristics. Altogether, the combination of these complementary strategies is helping to build a wider, more integrative view of the life-threatening protein cocktails produced by venomous snakes, responsible for thousands of deaths every year.

Venomics: integrative venom proteomics and beyond*

Venoms are integrated phenotypes that evolved independently in, and are used for predatory and defensive purposes by, a wide phylogenetic range of organisms. The same principles that contribute to the evolutionary success of venoms, contribute to making the study of venoms of great interest in such diverse fields as evolutionary ecology and biotechnology. Evolution is profoundly contingent, and nature also reinvents itself continuosly. Changes in a complex phenotypic trait, such as venom, reflect the influences of prior evolutionary history, chance events, and selection. Reconstructing the natural history of venoms, particularly those of snakes, which will be dealt with in more detail in this review, requires the integration of different levels of knowledge into a meaningful and comprehensive evolutionary framework for separating stochastic changes from adaptive evolution. The application of omics technologies and other disciplines have contributed to a qualitative and quantitative advance in the road map towards this goal. In this review we will make a foray into the world of animal venoms, discuss synergies and complementarities of the different approaches used in their study, and identify current bottlenecks that prevent inferring the evolutionary mechanisms and ecological constraints that molded snake venoms to their present-day variability landscape.

Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.

Venomic Analysis of the Poorly Studied Desert Coral Snake, Micrurus tschudii tschudii, Supports the 3FTx/PLA₂ Dichotomy across Micrurus Venoms

The venom proteome of the poorly studied desert coral snake Micrurus tschudii tschudii was unveiled using a venomic approach, which identified ≥38 proteins belonging to only four snake venom protein families. The three-finger toxins (3FTxs) constitute, both in number of isoforms (~30) and total abundance (93.6% of the venom proteome), the major protein family of the desert coral snake venom. Phospholipases A₂ (PLA₂s; seven isoforms, 4.1% of the venom proteome), 1–3 Kunitz-type proteins (1.6%), and 1–2 l-amino acid oxidases (LAO, 0.7%) complete the toxin arsenal of M. t. tschudii. Our results add to the growing evidence that the occurrence of two divergent venom phenotypes, i.e., 3FTx- and PLA₂-predominant venom proteomes, may constitute a general trend across the cladogenesis of Micrurus. The occurrence of a similar pattern of venom phenotypic variability among true sea snake (Hydrophiinae) venoms suggests that the 3FTx/PLA₂ dichotomy may be widely distributed among Elapidae venoms.