System, trends and perspectives of proteomics in dicot plants Part I: Technologies in proteome establishment

The first 3 years of the 21st century have seen the impact of plant proteomics on functional genomics that has enhanced our understanding, not only on the plant genome(s), but also more importantly, on the functional aspect of proteins. This is mainly due to availability of the complete genome sequence of the Arabidopsis thaliana-a dicotyledoneous (dicot) model plant-and technological advancements in proteomics. Proteomic analyses of a variety of dicot plants, including both Arabidopsis and the model legume species, barrel medic (Medicago truncatula), have greatly helped in an efficient separation, identification and cataloguing of a large number of proteins, and thereby defining their proteomes. Therefore, we have composed an inclusive review on dicot plant materials, as of February 2004, that provides system, trends and perspectives of proteomics in growth and development and the environment. The review is summarized and discussed as three individual, but interlinked, entities: Part I, technologies in proteome establishment (this review), Part II, proteomes of the complex developmental stages [G.K. Agrawal, M. Yonekura, Y. Iwahashi, H. Iwahashi, R. Rakwal, J. Chromatogr. B (2004)], and Part III, unraveling the proteomes influenced by the environment, and at the levels of function and genetic relationships [G.K. Agrawal, M. Yonekura, Y. Iwahashi, H. Iwahashi, R. Rakwal, J. Chromatogr. B (2004)]. This review deals with the diverse proteomic technologies being used in proteome development of different dicot plants.     

LRRK2 at the interface of autophagosomes,endosomes and lysosomes

Over the past 20 years, substantial progress has been made in identifying the underlying genetics of Parkinson’s disease (PD). Of the known genes, LRRK2 is a major genetic contributor to PD. However, the exact function of LRRK2 remains to be elucidated. In this review, we discuss how familial forms of PD have led us to hypothesize that alterations in endomembrane trafficking play a role in the pathobiology of PD. We will discuss the major observations that have been made to elucidate the role of LRRK2 in particular, including LRRK2 animal models and high-throughput proteomics approaches. Taken together, these studies strongly support a role of LRRK2 in vesicular dynamics. We also propose that targeting these pathways may not only be beneficial for developing therapeutics for LRRK2-driven PD, but also for other familial and sporadic cases.     

Contribution of genomics and proteomics in understanding the role of modifying factors in Parkinson's disease

Parkinson's disease (PD) is a complex neurological disorder, characterized by selective degeneration of nigrostriatal dopaminergic neurons. It is a multi-factorial disease, contributed by a combination of age, genetic and environmental factors. Etiology of sporadic PD and mechanism underlying selective loss of dopaminergic neurons has not yet been clearly understood. Recent developments in genomics and proteomics have revolutionized the research on PD at genetic level. Differential gene expression patterns (DNA biochip technology), age-dependent complex genetic patterns (SNP genotyping), and protein expression profiles (proteomics) of PD patients have started providing the specific and rigorous molecular explanation and role of modifying factors in PD. Genomics and proteomics are further expected to help in developing biomarkers for diagnosis of early onset PD and also to develop valuable and potential therapeutic strategies for its treatment. In this review, we have discussed the progress made by genomics and proteomics, in understanding the role of modifying factors in PD.     

A molecular perspective: biology of the emerging pathogen Batrachochytrium dendrobatidis

Ten years after the first discovery of the chytrid pathogen Batrachochytrium dendrobatidis (Bd), the catastrophic effect of Bd on wild amphibian populations is indisputable. However, a number of persistent questions remain about Bd's origin and mechanisms of pathogenicity. Here we discuss the promise of genetic and genomic tools for answering these previously intractable questions about the biology and evolutionary history of Bd. Full genomes of 2 Bd strains have recently been sequenced, and Bd research on this species using population genetics, phylogenetics, proteomics, comparative genomics and functional genomics is already underway. We review some of the insights gleaned from the first studies using these genome-scale approaches focusing particularly on Bd's genomic architecture, patterns of global genetic variation, virulence factors and genetic interactions with hosts. Avenues of future research promise to be particularly fruitful and highlight the need for integrative studies that unite genetic, ecological and spatial data in both Bd and its amphibian hosts.     

Nonconventional yeasts: their genetics and biotechnological applications

To date, more than 500 species of yeasts have been described. Most of the genetic and biochemical studies have, however, been carried out with Saccharomyces cerevisiae. Although a considerable amount of knowledge has been accumulated on fundamental processes and biotechnological applications of this industrially important yeast, the large variety of other yeast genera and species may offer various advantages for experimental study as well as for product formation in biotechnology. The genetic investigation of these so-called unconventional yeasts is poorly developed and information about corresponding data is dispersed. It is the aim of this review to summarize and discuss the main results of genetic studies and biotechnological applications of unconventional yeasts and to serve as a guide for scientists who wish to enter this field or are interested in only some aspects of these yeasts.     

Acquisition of virulence-associated factors by the enteric pathogens Escherichia coli and Salmonella enterica

In this review we summarize recent genomic studies that shed light on the mechanism through which pathogenic Escherichia coli and Salmonella enterica have evolved. We show how acquisition of DNA at specific sites on the chromosome has contributed to increased genetic variation and virulence of these two genera of the Enterobacteriaceae.     

Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology

There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.     

A proteomics strategy for the analysis of bacterial biodegradation pathways

Bacterial biodegradation (bioremediation) is the use of microorganisms to break down organic materials into simpler compounds; it plays a pivotal role in the clean-up of hazardous wastes in the environment. Following the completion of genome sequencing in bacteria capable of biodegradation, functional genomic studies have played a major role in obtaining information on bacterial biodegradation pathways. Novel proteomics technologies have recently been developed to make it possible to analyze global protein expression. Proteomics can also provide important information on the life cycle, regulation, and post-translational modification of proteins induced under specific conditions. Proteomics technologies have been applied to the comprehensive study of bacterial biodegradation. In this paper, we introduce the proteomics technologies applicable to bacterial biodegradation studies, review the results of the proteomics analysis of representative biodegrading bacteria, and discuss the potential use of proteomics technologies in future biodegradation studies.     

CNS proteomes in alcohol and drug abuse and dependence

Drugs of abuse, including alcohol, can induce dependency formation and/or brain damage in brain regions important for cognition. ‘High-throughput’ approaches, such as cDNA microarray and proteomics, allow the analysis of global expression profiles of genes and proteins. These technologies have recently been applied to human brain tissue from patients with psychiatric illnesses, including substance abuse/dependence and appropriate animal models to help understand the causes and secondary effects of these complex disorders. Although these types of studies have been limited in number and by proteomics techniques that are still in their infancy, several interesting hypotheses have been proposed. Focusing on CNS proteomics, we aim to review and update current knowledge in this rapidly advancing area.     

CNS proteomes in alcohol and drug abuse and dependence

Drugs of abuse, including alcohol, can induce dependency formation and/or brain damage in brain regions important for cognition. 'High-throughput' approaches, such as cDNA microarray and proteomics, allow the analysis of global expression profiles of genes and proteins. These technologies have recently been applied to human brain tissue from patients with psychiatric illnesses, including substance abuse/dependence and appropriate animal models to help understand the causes and secondary effects of these complex disorders. Although these types of studies have been limited in number and by proteomics techniques that are still in their infancy, several interesting hypotheses have been proposed. Focusing on CNS proteomics, we aim to review and update current knowledge in this rapidly advancing area.     

Proteomics of organelles and large cellular structures

The mass-spectrometry-based identification of proteins has created opportunities for the study of organelles, transport intermediates and large subcellular structures. Traditional cell-biology techniques are used to enrich these structures for proteomics analyses, and such analyses provide insights into the biology and functions of these structures. Here, we review the state-of-the-art proteomics techniques for the analysis of subcellular structures and discuss the biological insights that have been derived from such studies.     

Advances in shotgun proteomics and the analysis of membrane proteomes

The emergence of shotgun proteomics has facilitated the numerous biological discoveries made by proteomic studies. However, comprehensive proteomic analysis remains challenging and shotgun proteomics is a continually changing field. This review details the recent developments in shotgun proteomics and describes emerging technologies that will influence shotgun proteomics going forward. In addition, proteomic studies of integral membrane proteins remain challenging due to the hydrophobic nature in integral membrane proteins and their general low abundance levels. However, there have been many strategies developed for enriching, isolating and separating membrane proteins for proteomic analysis that have moved this field forward. In summary, while shotgun proteomics is a widely used and mature technology, the continued pace of improvements in mass spectrometry and proteomic technology and methods indicate that future studies will have an even greater impact on biological discovery.     

Description of a new species of Parasesarma (Crustacea; Decapoda; Brachyura; Sesarmidae) from the Persian Gulf, based on morphological and genetic characteristics

The genera Parasesarma and Perisesarma are common inhabitants of mangroves and estuaries of the Indo-West Pacific. These, overall similar, genera of sesarmid crabs can be told apart by the presence or absence of an anterolateral tooth, but recent and ongoing studies show that they are not reciprocally monophyletic. In recent years, detailed morphological studies have revealed a surprising number of undescribed new species within these genera. In the present paper, we describe a new species of the genus Parasesarma from the relatively poorly studied Persian Gulf. So far, these specimens had been referred to as Parasesarma plicatum (Latreille, 1803), but morphological and genetic characteristics clearly allow separation of the two species. Consequently, the species from the Persian Gulf is here described as new and morphological and mitochondrial genetic characters are provided that allow recognition of the species.     

Contribution of proteomics of Leishmania spp. to the understanding of differentiation, drug resistance mechanisms, vaccine and drug development

Leishmania spp., protozoan parasites with a digenetic life cycle, cause a spectrum of diseases in humans. Recently several Leishmania spp. have been sequenced which significantly boosted the number and quality of proteomic studies conducted. Here a historic review will summarize work of the pre-genomic era and then focus on studies after genome information became available. Firstly works comparing the different life cycle stages, in order to identify stage specific proteins, will be discussed. Identifying post-translational modifications by proteomics especially phosphorylation events will be discussed. Further the contribution of proteomics to the understanding of the molecular mechanism of drug resistance and the investigation of immunogenic proteins for the identification of vaccine candidates will be summarized. Approaches of how potentially secreted proteins were identified are discussed. So far 30-35% of the total predicted proteome of Leishmania spp. have been identified. This comprises mainly the abundant proteins, therefore the last section will look into technological approaches on how this coverage may be increased and what the gel-free and gel-based proteomics have to offer will be compared.     

Proteomic analysis of polyketide and nonribosomal peptide biosynthesis

Polyketides and non-ribosomal peptides are in a class of natural products important both as drug sources and as dangerous toxins and virulence factors. While studies over the last two decades have provided substantial characterization of the modular synthases that produce these compounds at the genetic level, their understanding at the protein level is much less understood. New proteomic platforms called an orthogonal active site identification system (OASIS) and proteomic interrogation of secondary metabolism (PrISM) have been developed to identify and quantify natural product synthase enzymes. Reviewed here, these tools offer the means to discover and analyze modular synthetic pathways that are limited by genetic techniques, opening the tools of contemporary proteomics to natural product sciences.     

One-step sample concentration, purification, and albumin depletion method for urinary proteomics

Workflows in urinary proteomics studies are often complex and require many steps to enrich, purify, deplete, and separate the complex mixture. Many of these methods are laborious, are time-consuming, and have the potential for error. Although individual steps of these methods have been previously studied, their downstream compatibilities with fractionation technologies such as off-gel electrophoresis have not been investigated. We developed a one-step sample preparation workflow that simultaneously (i) concentrates proteins, (ii) purifies by removing salts and other low molecular weight compounds, and (iii) depletes (albumin) from urine samples. This simple and robust workflow can be multiplexed and is compatible with a diverse range of downstream multidimensional separation technologies. Additionally, because of its high reproducibility and flexibility in processing samples with different volumes and concentrations, it has the potential to be used for standardization of urinary proteomics studies, as well as for studying other body fluids of similar complexity.     

A synopsis of the endemic plant genera of Borneo

The large, tropical island of Borneo has some of the world's richest habitats for plant life, but faces increasing pressures from anthropogenic activities that threaten its biodiversity. With a good portion of the Bornean flora not critically studied, a comprehensive documentation of the numerous endemic taxa expected for the island is not yet complete. It is not known what the relative significance of endemic genera is compared to Bornean centres of endemism documented or predicted through modelling, and if they can inform current conservation plans. As a first step, we here present a synopsis of the endemic genera of Borneo, based on a comprehensive study of literature, herbarium specimens and distributional data, and an investigation of whether the genera have been included in molecular phylogenetic studies that confirm their monophyly. Such a review is timely since many generic delimitations have been shaped by molecular evidence used to test morphology-based taxonomy, while botanical collection and revisionary efforts continue. Our findings suggest that 65 vascular plant genera from 25 families may be considered endemic to Borneo. More than two-thirds (48) of these genera have had at least one species included in molecular phylogenetic studies, but of these, only 39 have been sufficiently sampled to be considered monophyletic with high confidence, or they are monotypic. Slightly over half (38) of the endemic genera are herbaceous. A majority of the genera have fruits or seeds specialised for dispersal by abiotic vectors, or unspecialised seeds. Almost two-thirds (42) of the endemic genera are monotypic, and some of these could represent relict lineages. We expect the current list of endemic genera to be relatively stable and aligned with recent taxonomic concepts, and that it serves to illuminate an interesting aspect of Borneo's unique assemblage of endemic species.