Proteomics in Non-model Organisms: A New Analytical Frontier

Proteogenomics in Nephrology: A New Frontier in Nephrological Research

Proteogenomics represents a transformative intersection in nephrology, uniting genomics, transcriptomics, and proteomics to unravel the molecular intricacies of kidney diseases. This review encapsulates the methodological essence of proteogenomics and its profound implications in chronic kidney disease (CKD) research. We explore the proteogenomic pipeline, highlighting the integrated analysis of genomic, transcriptomic, and proteomic data and its pivotal role in enhancing our understanding of kidney pathologies. Through case studies, we showcase the application of proteogenomics in clear cell renal cell carcinoma (ccRCC) and Autosomal Recessive Polycystic Kidney Disease (ARPKD), emphasizing its potential in personalized treatment strategies and biomarker discovery. The review also addresses the challenges in proteogenomic analysis, including data integration complexities and bioinformatics limitations, and proposes solutions for advancing the field. Ultimately, this review underscores the prospective future of proteogenomics in nephrology, particularly in advancing personalized medicine and providing novel therapeutic insights.

Beyond the model organism-Mechanistic analysis of protein post-translational modifications is ready for all challengers

A historic challenge for shotgun proteomics has been the requirement for high quality, simple, and nonredundant curated protein sequences in small .fasta text files. Due to the intrinsic informatic challenges and time required to assemble these files, proteomics has struggled to expand beyond the confines of a few model organisms. When considering post-translational modifications that may or may not be present on a specific peptide sequence, these factors inevitably compound. A study on how mangos continue to ripen on the shelf may not be the first thing you'd think of as proof of a scientific discipline shedding historic limitations. However, Bautiste-Valle et al., may be just that. These authors present a quantitative comparison of both peptide and glycopeptide alterations through the complexity of the fruit ripening process and in this we see the present state of a field that no longer needs to wait on genomics to obtain deep mechanistic insights.

Protein constraints in genome-scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes

Genome-scale metabolic models provide a valuable resource to study metabolism and cell physiology. These models are employed with approaches from the constraint-based modeling framework to predict metabolic and physiological phenotypes. The prediction performance of genome-scale metabolic models can be improved by including protein constraints. The resulting protein-constrained models consider data on turnover numbers (kcat ) and facilitate the integration of protein abundances. In this systematic review, we present and discuss the current state-of-the-art regarding the estimation of kinetic parameters used in protein-constrained models. We also highlight how data-driven and constraint-based approaches can aid the estimation of turnover numbers and their usage in improving predictions of cellular phenotypes. Finally, we identify standing challenges in protein-constrained metabolic models and provide a perspective regarding future approaches to improve the predictive performance.

Urinary proteomics reveals biological processes related to acute kidney injury in Bothrops atrox envenomings

Acute kidney injury (AKI) is a critical systemic complication caused by Bothrops envenoming, a neglected health problem in the Brazilian Amazon. Understanding the underlying mechanisms leading to AKI is crucial for effectively mitigating the burden of this complication. This study aimed to characterize the urinary protein profile of Bothrops atrox snakebite victims who developed AKI. We analyzed three groups of samples collected on admission: healthy subjects (controls, n = 10), snakebite victims who developed AKI (AKI, n = 10), and those who did not evolve to AKI (No-AKI, n = 10). Using liquid-chromatography tandem mass spectrometry, we identified and quantified (label-free) 1190 proteins. A panel of 65 proteins was identified exclusively in the urine of snakebite victims, with 32 exclusives to the AKI condition. Proteins more abundant or exclusive in AKI's urine were associated with acute phase response, endopeptidase inhibition, complement cascade, and inflammation. Notable proteins include serotransferrin, SERPINA-1, alpha-1B-glycoprotein, and NHL repeat-containing protein 3. Furthermore, evaluating previously reported biomarkers candidates for AKI and renal injury, we found retinol-binding protein, beta-2-microglobulin, cystatin-C, and hepcidin to be significant in cases of AKI induced by Bothrops envenoming. This work sheds light on physiological disturbances caused by Bothrops envenoming, highlighting potential biological processes contributing to AKI. Such insights may aid in better understanding and managing this life-threatening complication.

Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species

New approach methodologies (NAM), including omics and in vitro approaches, are contributing to the implementation of 3R (reduction, refinement and replacement) strategies in regulatory science and risk assessment. In this study, we present an integrative transcriptomics and proteomics analysis workflow for the validation and revision of complex fish genomes and demonstrate how proteogenomics expression matrices can be used to support multi-level omics data integration in non-model species in vivo and in vitro. Using Atlantic salmon as an example, we constructed proteogenomic databases from publicly available transcriptomic data and in-house generated RNA-Seq and LC-MS/MS data. Our analysis identified ∼80,000 peptides, providing direct evidence of translation for over 40,000 RefSeq structures. The data also highlighted 183 co-located peptide groups that supported a single transcript each, and in each case, either corrected a previous annotation, supported Ensembl annotations not present in RefSeq, or identified novel previously unannotated genes. Proteogenomics data-derived expression matrices revealed distinct profiles for the different tissue types analyzed. Focusing on proteins involved in defense against xenobiotics, we detected distinct expression patterns across different salmon tissues and observed homology in the expression of chemical defense proteins between in vivo and in vitro liver systems. Our study demonstrates the potential of proteogenomic analyses in extending our understanding of complex fish genomes and provides an advanced bioinformatic toolkit to support the further development of NAMs and their application in regulatory science and (eco)toxicological studies of non-model species.

Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection

Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB, Artibeus jamaicensis) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Upon infection with SARS-CoV-2, increased viral RNA and subgenomic RNA was detected, but no infectious virus was released, indicating that JFB organoids support only limited viral replication but not viral reproduction. SARS-CoV-2 replication was associated with significantly increased gene expression of type I interferons and inflammatory cytokines. Interestingly, SARS-CoV-2 also caused enhanced formation and growth of JFB organoids. Proteomics revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells mount successful antiviral interferon responses and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.

Diversifying the concept of model organisms in the age of -omics

In today's post-genomic era, it is crucial to rethink the concept of model organisms. While a few historically well-established organisms, e.g. laboratory rodents, have enabled significant scientific breakthroughs, there is now a pressing need for broader inclusion. Indeed, new organisms and models, from complex microbial communities to holobionts, are essential to fully grasp the complexity of biological principles across the breadth of biodiversity. By fostering collaboration between biology, advanced molecular science and omics communities, we can collectively adopt new models, unraveling their molecular functioning, and uncovering fundamental mechanisms. This concerted effort will undoubtedly enhance human health, environmental quality, and biodiversity conservation.

Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin (Tursiops truncatus)

The last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, the continued development of genome quality metrics is imperative. Using the 2016 Atlantic bottlenose dolphin NCBI RefSeq annotation and mass spectrometry-based proteomic analysis of six tissues, we confirmed 10,402 proteins from 4711 protein groups, constituting nearly one-third of the possible predicted proteins. Since the identification of larger proteins with more identified peptides implies reduced database fragmentation and improved gene annotation accuracy, we propose the metric NP10, which attempts to capture this quality improvement. The NP10 metric is calculated by first stratifying proteomic results by identifying the top decile (or 10th 10-quantile) of identified proteins based on the number of peptides per protein and then returns the median molecular weight of the resulting proteins. When using the 2016 versus 2012 Tursiops truncatus genome annotation to search this proteomic data set, there was a 21% improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which showed a 33% improvement in NP10. These results demonstrate that proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets across species to facilitate the evaluation of new de novo and existing genome.

Rapid adaptation to a novel pathogen through disease tolerance in a wild songbird

Animal hosts can adapt to emerging infectious disease through both disease resistance, which decreases pathogen numbers, and disease tolerance, which limits damage during infection without limiting pathogen replication. Both resistance and tolerance mechanisms can drive pathogen transmission dynamics. However, it is not well understood how quickly host tolerance evolves in response to novel pathogens or what physiological mechanisms underlie this defense. Using natural populations of house finches (Haemorhous mexicanus) across the temporal invasion gradient of a recently emerged bacterial pathogen (Mycoplasma gallisepticum), we find rapid evolution of tolerance (<25 years). In particular, populations with a longer history of MG endemism have less pathology but similar pathogen loads compared with populations with a shorter history of MG endemism. Further, gene expression data reveal that more-targeted immune responses early in infection are associated with tolerance. These results suggest an important role for tolerance in host adaptation to emerging infectious diseases, a phenomenon with broad implications for pathogen spread and evolution.

Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives

The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.

Immobility-associated thromboprotection is conserved across mammalian species from bear to human

Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a major cause of morbidity and mortality. Short-term immobility-related conditions are a major risk factor for the development of VTE. Paradoxically, long-term immobilized free-ranging hibernating brown bears and paralyzed spinal cord injury (SCI) patients are protected from VTE. We aimed to identify mechanisms of immobility-associated VTE protection in a cross-species approach. Mass spectrometry-based proteomics revealed an antithrombotic signature in platelets of hibernating brown bears with heat shock protein 47 (HSP47) as the most substantially reduced protein. HSP47 down-regulation or ablation attenuated immune cell activation and neutrophil extracellular trap formation, contributing to thromboprotection in bears, SCI patients, and mice. This cross-species conserved platelet signature may give rise to antithrombotic therapeutics and prognostic markers beyond immobility-associated VTE.

Characterization and bioactivity of extracellular vesicles isolated from pomegranate

In the current study, extracellular vesicles from pomegranate juice (PgEVs) were isolated for the first time using size exclusion chromatography (SEC). This method permitted us to obtain highly enriched EV samples without most of the non-EV co-isolated proteins. The characterization of PgEVs through nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM) allowed the determination of vesicles' concentration/volume, size, and morphology. It was confirmed from the analytical data that PgEVs contain a homogeneous population of vesicles, with a dimension and structure comparable to plant-derived EVs. Proteomic analyses by LC-MS/MS led to the characterization of 131 proteins, and several of them were related commonly to the biogenesis and transport of EVs, and/or proposed as EV markers. PgEVs exerted anti-inflammatory, antioxidant and wound-healing effects when added to the in vitro cultures of monocytic (THP-1) and intestinal (Caco-2) cell lines, respectively.

Sequencing and assembling bear genomes: the bare necessities

Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.

Label-Free Quantification (LFQ) of Fecal Proteins for Potential Pregnancy Detection in Polar Bears

Reliable pregnancy diagnostics would be beneficial for monitoring polar bear (Ursus maritimus) populations both in situ and ex situ, but currently there is no method of non-invasive pregnancy detection in this species. Recent reports in several carnivore species described the identification of fecal proteins that may serve as pregnancy biomarkers; however, repeatability has been limited. The objective of the current analysis was to utilize an unbiased, antibody-free, label-free method for the identification and quantification of fecal proteins to determine if differences associated with pregnancy are detectable in polar bears. Protein was extracted from fecal samples (n = 48) obtained from parturient (n = 6) and non-parturient (n = 6) profiles each at four timepoints: pre-breeding season, embryonic diapause, early placental pregnancy, and mid-placental pregnancy. Protein was prepared and analyzed on the Thermo Orbitrap Eclipse nanoLC-MS/MS system. A total of 312 proteins was identified and quantified; however, coefficients of variation (CV) were high for both abundance ratio variability (384.8 ± 61.0% SEM) and within group variability (86.8 ± 1.5%). Results of this study suggest that the inconsistencies in specific protein concentrations revealed previously by antibody-based assays may not be due to that methodology’s limitations, but rather, are reflective of true variation that exists among samples.

Snake Venomics: Fundamentals, Recent Updates, and a Look to the Next Decade

Venomic research, powered by techniques adapted from proteomics, transcriptomics, and genomics, seeks to unravel the diversity and complexity of venom through which knowledge can be applied in the treatment of envenoming, biodiscovery, and conservation. Snake venom proteomics is most extensively studied, but the methods varied widely, creating a massive amount of information which complicates data comparison and interpretation. Advancement in mass spectrometry technology, accompanied by growing databases and sophisticated bioinformatic tools, has overcome earlier limitations of protein identification. The progress, however, remains challenged by limited accessibility to samples, non-standardized quantitative methods, and biased interpretation of -omic data. Next-generation sequencing (NGS) technologies enable high-throughput venom-gland transcriptomics and genomics, complementing venom proteomics by providing deeper insights into the structural diversity, differential expression, regulation and functional interaction of the toxin genes. Venomic tissue sampling is, however, difficult due to strict regulations on wildlife use and transfer of biological materials in some countries. Limited resources for techniques and funding are among other pertinent issues that impede the progress of venomics, particularly in less developed regions and for neglected species. Genuine collaboration between international researchers, due recognition of regional experts by global organizations (e.g., WHO), and improved distribution of research support, should be embraced.

Communication Lower-Bounds for Distributed-Memory Computations for Mass Spectrometry based Omics Data

Mass spectrometry (MS) based omics data analysis require significant time and resources. To date, few parallel algorithms have been proposed for deducing peptides from mass spectrometry-based data. However, these parallel algorithms were designed, and developed when the amount of data that needed to be processed was smaller in scale. In this paper, we prove that the communication bound that is reached by the existing parallel algorithms is Ω ( m n + 2 r q p ) , where m and n are the dimensions of the theoretical database matrix, q and r are dimensions of spectra, and p is the number of processors. We further prove that communication-optimal strategy with fast-memory M = m n + 2 q r p can achieve Ω ( 2 m n q p ) but is not achieved by any existing parallel proteomics algorithms till date. To validate our claim, we performed a meta-analysis of published parallel algorithms, and their performance results. We show that sub-optimal speedups with increasing number of processors is a direct consequence of not achieving the communication lower-bounds. We further validate our claim by performing experiments which demonstrate the communication bounds that are proved in this paper. Consequently, we assert that next-generation of provable, and demonstrated superior parallel algorithms are urgently needed for MS based large systems-biology studies especially for meta-proteomics, proteogenomic, microbiome, and proteomics for non-model organisms. Our hope is that this paper will excite the parallel computing community to further investigate parallel algorithms for highly influential MS based omics problems.

Deep Time Paleoproteomics: Looking Forward

The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.

A comprehensive review on microbial production of 1,2-propanediol: micro-organisms, metabolic pathways, and metabolic engineering

1,2-Propanediol is an important building block as a component used in the manufacture of unsaturated polyester resin, antifreeze, biofuel, nonionic detergent, etc. Commercial production of 1,2-propanediol through microbial biosynthesis is limited by low efficiency, and chemical production of 1,2-propanediol requires petrochemically derived routes involving wasteful power consumption and high pollution emissions. With the development of various strategies based on metabolic engineering, a series of obstacles are expected to be overcome. This review provides an extensive overview of the progress in the microbial production of 1,2-propanediol, particularly the different micro-organisms used for 1,2-propanediol biosynthesis and microbial production pathways. In addition, outstanding challenges associated with microbial biosynthesis and feasible metabolic engineering strategies, as well as perspectives on the future microbial production of 1,2-propanediol, are discussed.

Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics

Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a “gem” at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.

Host gene expression in wildlife disease: making sense of species-level responses

Emerging infectious diseases are significant threats to wildlife conservation, yet the impacts of pathogen exposure and infection can vary widely among host species. As such, conservation biologists and disease ecologists have increasingly aimed to understand species-specific host susceptibility using molecular methods. In particular, comparative gene expression assays have been used to contrast the transcriptomic responses of disease-resistant and disease-susceptible hosts to pathogen exposure. This work usually assumes that the gene expression responses of disease-resistant species will reveal the activation of molecular pathways contributing to host defence. However, results often show that disease-resistant hosts undergo little gene expression change following pathogen challenge. Here, we discuss the mechanistic implications of these "null" findings and offer methodological suggestions for future molecular studies of wildlife disease. First, we highlight that muted transcriptomic responses with minimal immune system recruitment may indeed be protective for nonsusceptible hosts if they limit immunopathology and promote pathogen tolerance in systems where susceptible hosts suffer from genetic dysregulation. Second, we argue that overly narrow investigation of responses to pathogen exposure may overlook important, constitutively active molecular pathways that underlie species-specific defences. Finally, we outline alternative study designs and approaches that complement interspecific transcriptomic comparisons, including intraspecific gene expression studies and genomic methods to detect signatures of selection. Collectively, these insights will help ecologists extract maximal information from conservation-relevant transcriptomic data sets, leading to a deeper understanding of host defences and, ultimately, the implementation of successful conservation interventions.

Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security

Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Mutual enlightenment: A toolbox of concepts and methods for integrating evolutionary and clinical toxinology via snake venomics and the contextual stance

Snakebite envenoming is a neglected tropical disease that may claim over 100,000 human lives annually worldwide. Snakebite occurs as the result of an interaction between a human and a snake that elicits either a defensive response from the snake or, more rarely, a feeding response as the result of mistaken identity. Snakebite envenoming is therefore a biological and, more specifically, an ecological problem. Snake venom itself is often described as a "cocktail", as it is a heterogenous mixture of molecules including the toxins (which are typically proteinaceous) responsible for the pathophysiological consequences of envenoming. The primary function of venom in snake ecology is pre-subjugation, with defensive deployment of the secretion typically considered a secondary function. The particular composition of any given venom cocktail is shaped by evolutionary forces that include phylogenetic constraints associated with the snake's lineage and adaptive responses to the snake's ecological context, including the taxa it preys upon and by which it is predated upon. In the present article, we describe how conceptual frameworks from ecology and evolutionary biology can enter into a mutually enlightening relationship with clinical toxinology by enabling the consideration of snakebite envenoming from an "ecological stance". We detail the insights that may emerge from such a perspective and highlight the ways in which the high-fidelity descriptive knowledge emerging from applications of -omics era technologies - "venomics" and "antivenomics" - can combine with evolutionary explanations to deliver a detailed understanding of this multifactorial health crisis.

Prospects of Using High-Throughput Proteomics to Underpin the Discovery of Animal Host-Nematode Interactions

Parasitic nematodes impose a significant public health burden, and cause major economic losses to agriculture worldwide. Due to the widespread of anthelmintic resistance and lack of effective vaccines for most nematode species, there is an urgent need to discover novel therapeutic and vaccine targets, informed through an understanding of host-parasite interactions. Proteomics, underpinned by genomics, enables the global characterisation proteins expressed in a particular cell type, tissue and organism, and provides a key to insights at the host-parasite interface using advanced high-throughput mass spectrometry-based proteomic technologies. Here, we (i) review current mass-spectrometry-based proteomic methods, with an emphasis on a high-throughput 'bottom-up' approach; (ii) summarise recent progress in the proteomics of parasitic nematodes of animals, with a focus on molecules inferred to be involved in host-parasite interactions; and (iii) discuss future research directions that could enhance our knowledge and understanding of the molecular interplay between nematodes and host animals, in order to work toward new, improved methods for the treatment, diagnosis and control of nematodiases.

Characterization and differentiation of quinoa seed proteomes by label-free mass spectrometry-based shotgun proteomics

Quinoa seed proteins are of prime importance in human nutrition and in plant breeding for cultivar identification and improvement. In this study, proteins from seeds of black, red, white quinoa from Peru and white quinoa from Bolivia (also known as royal) were extracted, digested and analyzed by nano-liquid chromatography coupled to Orbitrap tandem mass spectrometry (LC-MS/MS). The raw mass spectra data were processed for identification and label-free quantification (LFQ) using MaxQuant/Andromeda against a specific quinoa database from The National Center for Biotechnology Information (NCBI). In total, 1,211 quinoa proteins (85 were uncharacterized) were identified. Inspection and visualization using Venn diagrams, heat maps and Gene Ontology (GO) graphs revealed proteome similarities and differences between the four varieties. The presented data provides the most comprehensive experimental quinoa seed proteome map existing to date in the literature, as a starting point for more specific characterization and nutritional studies of quinoa and quinoa-containing foodstuff.

Affinity Purification-Mass Spectrometry Identifies a Novel Interaction between a Polerovirus and a Conserved Innate Immunity Aphid Protein that Regulates Transmission Efficiency

The vast majority of plant viruses are transmitted by insect vectors, with many crucial aspects of the transmission process being mediated by key protein-protein interactions. Still, very few vector proteins interacting with viruses have been identified and functionally characterized. Potato leafroll virus (PLRV) is transmitted most efficiently by Myzus persicae, the green peach aphid, in a circulative, non-propagative manner. Using affinity purification coupled to high-resolution mass spectrometry (AP-MS), we identified 11 proteins from M. persicaedisplaying a high probability of interaction with PLRV and an additional 23 vector proteins with medium confidence interaction scores. Three of these aphid proteins were confirmed to directly interact with the structural proteins of PLRV and other luteovirid species via yeast two-hybrid. Immunolocalization of one of these direct PLRV-interacting proteins, an orthologue of the human innate immunity protein complement component 1 Q subcomponent-binding protein (C1QBP), shows that MpC1QBP partially co-localizes with PLRV in cytoplasmic puncta and along the periphery of aphid gut epithelial cells. Artificial diet delivery to aphids of a chemical inhibitor of C1QBP leads to increased PLRV acquisition by aphids and subsequently increased titer in inoculated plants, supporting a role for C1QBP in the acquisition and transmission efficiency of PLRV by M. persicae. This study presents the first use of AP-MS for the in vivo isolation of a functionally relevant insect vector-virus protein complex. MS data are available from ProteomeXchange.org using the project identifier PXD022167.

Deconvoluting complex protein interaction networks through reductionist strategies in peptide biochemistry: Modern approaches and research questions

Following the decoding of the first human genome, researchers have vastly improved their understanding of cell biology and its regulation. As a result, it has become clear that it is not merely genetic information, but the aberrant changes in the functionality and connectivity of its encoded proteins that drive cell response to periods of stress and external cues. Therefore, proper utilization of refined methods that help to describe protein signalling or regulatory networks (i.e., functional connectivity), can help us understand how change in the signalling landscape effects the cell. However, given the vast complexity in 'how and when' proteins communicate or interact with each other, it is extremely difficult to define, characterize, and understand these interaction networks in a tangible manner. Herein lies the challenge of tackling the functional proteome; its regulation is encoded in multiple layers of interaction, chemical modification and cell compartmentalization. To address and refine simple research questions, modern reductionist strategies in protein biochemistry have successfully used peptide-based experiments; their summation helping to simplify the overall complexity of these protein interaction networks. In this way, peptides are powerful tools used in fundamental research that can be readily applied to comparative biochemical research. Understanding and defining how proteins interact is one of the key aspects towards understanding how the proteome functions. To date, reductionist peptide-based research has helped to address a wide range of proteome-related research questions, including the prediction of enzymes substrates, identification of posttranslational modifications, and the annotation of protein interaction partners. Peptide arrays have been used to identify the binding specificity of reader domains, which are able to recognise the posttranslational modifications; forming dynamic protein interactions that are dependent on modification state. Finally, representing one of the fastest growing classes of inhibitor molecules, peptides are now begin explored as "disruptors" of protein-protein interactions or enzyme activity. Collectively, this review will discuss the use of peptides, peptide arrays, peptide-oriented computational biochemistry as modern reductionist strategies in deconvoluting the functional proteome.

Surveying the Vampire Bat (Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens

Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet the ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome these limitations by using data-independent acquisition-based shotgun proteomics to survey the serum proteome of 17 vampire bats (Desmodus rotundus) from Belize. Using just 2 μL of sample and relatively short separations of undepleted serum digests, we identified 361 proteins across 5 orders of magnitude. Levels of immunological proteins in vampire bat serum were then compared to human plasma via published databases. Of particular interest were antiviral and antibacterial components, circulating 20S proteasome complex and proteins involved in redox activity. Lastly, we used known virus proteomes to putatively identify Rh186 from Macacine herpesvirus 3 and ORF1a from Middle East respiratory syndrome-related coronavirus, indicating that mass spectrometry-based techniques show promise for pathogen detection. Overall, these results can be used to design targeted mass-spectrometry assays to quantify immunological markers and detect pathogens. More broadly, our findings also highlight the application of proteomics in advancing wildlife immunology and pathogen surveillance.

Proteomics and plant biology: contributions to date and a look towards the next decade

INTRODUCTION

This review presents the view of the author, that is opinionable and even speculative, on the field of proteomics, its application to plant biology knowledge, and translation to biotechnology. Written in a more academic than scientific style, it is based on past original and review articles by the author´s group, and those published by leading scientists in the last two years.

AREAS COVERED

Starting with a general definition and references to historical milestones, it covers sections devoted to the different platforms employed, the plant biology discourse in the protein language, challenges and future prospects, ending with the author opinion.

EXPERT OPINION

In 25 years, five proteomics platform generations have appeared. We are now moving from proteomics to Systems Biology. While feasible with model organisms, proteomics of orphan species remains challenging. Proteomics, even in its simplest approach, sheds light on plant biological processes, central dogma, and molecular bases of phenotypes of interest, and it can be translated to areas such as food traceability and allergen detection. Proteomics should be validated and optimized to each experimental system, objectives, and hypothesis. It has limitations, artifacts, and biases. We should not blindly accept proteomics data and just create a list of proteins, networks, and avoid speculative biological interpretations. From the hundred to thousand proteins identified and quantified, it is important to obtain a focus and validate some of them, otherwise it is merely. We are starting to have the protein pieces, so let, from now, build the proteomics and biological puzzle.

Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments

Cloud-hosted environments offer known benefits when computational needs outstrip affordable local workstations, enabling high-performance computation without a physical cluster. What has been less apparent, especially to novice users, is the transformative potential for cloud-hosted environments to bridge the digital divide that exists between poorly funded and well-resourced laboratories, and to empower modern research groups with remote personnel and trainees. Using cloud-based proteomic bioinformatic pipelines is not predicated on analyzing thousands of files, but instead can be used to improve accessibility during remote work, extreme weather, or working with under-resourced remote trainees. The general benefits of cloud-hosted environments also allow for scalability and encourage reproducibility. Since one possible hurdle to adoption is awareness, this paper is written with the nonexpert in mind. The benefits and possibilities of using a cloud-hosted environment are emphasized by describing how to setup an example workflow to analyze a previously published label-free data-dependent acquisition mass spectrometry data set of mammalian urine. Cost and time of analysis are compared using different computational tiers, and important practical considerations are described. Overall, cloud-hosted environments offer the potential to solve large computational problems, but more importantly can enable and accelerate research in smaller research groups with inadequate infrastructure and suboptimal local computational resources.

Bioactive Molecular Discovery Using Deer Antlers as a Model of Mammalian Regeneration

The ability to activate and regulate stem cells during wound healing and tissue regeneration is a promising field that is resulting in innovative approaches in the field of regenerative medicine. The regenerative capacity of invertebrates has been well documented; however, in mammals, stem cells that drive organ regeneration are rare. Deer antlers are the only known mammalian structure that can annually regenerate to produce a tissue containing dermis, blood vessels, nerves, cartilage, and bone. The neural crest derived stem cells that drive this process result in antlers growing at up to 2 cm/day. Deer antlers thus provide superior attributes compared to lower-order animal models, when investigating the regulation of stem cell-based regeneration. Antler stem cells can therefore be used as a model to investigate the bioactive molecules, biological processes, and pathways involved in the maintenance of a stem cell niche, and their activation and differentiation during organ formation. This review examines stem cell-based regeneration with a focus on deer antlers, a neural crest stem cell-based mammalian regenerative structure. It then discusses the omics technical platforms highlighting the proteomics approaches used for investigating the molecular mechanisms underlying stem cell regulation in antler tissues.

Transglutaminase-2, RNA-binding proteins and mitochondrial proteins selectively traffic to MDCK cell-derived microvesicles following H-Ras-induced epithelial-mesenchymal transition

Epithelial-mesenchymal transition (EMT) describes an evolutionary conserved morphogenic process defined by loss of epithelial characteristics and acquisition of mesenchymal phenotype, and altered patterns of intercellular communication, leading to functional changes in cell migration and invasion. In this regard, we have previously reported that oncogenic H-Ras induced EMT in Madin-Darby Canine Kidney (MDCK) cells (21D1 cells) trigger changes in the protein distribution pattern in cells, exosomes, and soluble protein factors (secretome) which modulate the tumor microenvironment. Here, we report that shed microvesicles (also termed microparticles/ectosomes) secreted from MDCK cells following oncogenic H-Ras-induced EMT (21D1-sMVs) are biochemically distinct from exosomes and parental MDCK-sMVs. The protein spectra of RNA-binding proteins and mitochondrial proteins in 21D1-sMVs differ profoundly compared to those of exosomes, likewise proteins associated with suppression of anoikis. We show that 21D1-sMVs promote cell migration, confer anchorage-independent growth, and induce EMT in parental MDCK cells. An unexpected and novel finding was the selective sorting of tissue transglutaminase-2 (TGM2) into 21D1-sMVs; there was no evidence of TGM2 in MDCK-sMVs. Prior treatment of 21D1-sMVs with neutralizing anti-TGM2 or anti-FN1 antibodies attenuates the invasive capability of fibroblasts. These finding suggest that microvesicle-associated TGM2 may play an important contributory role in the EMT process and warrants further investigation.