Metallomics: An integrated biometal science

Analytical Methodologies for Agrometallomics: A Critical Review

Agrometallomics, as an independent interdiscipline, is first defined and described in this review. Metallic elements widely exist in agricultural plants, animals and edible fungi, seed, fertilizer, pesticide, feedstuff, as well as the agricultural environment and ecology, and even functional and pathogenic microorganisms. So, the agrometallome plays a vital role in molecular and organismic mechanisms like environmetallomics, metabolomics, proteomics, lipidomics, glycomics, immunomics, genomics, etc. To further reveal the inner and mutual mechanism of the agrometallome, comprehensive and systematic methodologies for the analysis of beneficial and toxic metals are indispensable to investigate elemental existence, concentration, distribution, speciation, and forms in agricultural lives and media. Based on agrometallomics, this review summarizes and discusses the advanced technical progress and future perspectives of metallic analytical approaches, which are categorized into ultrasensitive and high-throughput analysis, elemental speciation and state analysis, and spatial- and microanalysis. Furthermore, the progress of agrometallomic innovativeness greatly depends on the innovative development of modern metallic analysis approaches including, but not limited to, high sensitivity, elemental coverage, and anti-interference; high-resolution isotopic analysis; solid sampling and nondestructive analysis; metal chemical species and metal forms, associated molecular clusters, and macromolecular complexes analysis; and metal-related particles or metal within the microsize and even single cell or subcellular analysis.

Comparative nanometallomics as a new tool for nanosafety evaluation

Nanosafety evaluation is paramount since it is necessary not only for human health protection and environmental integrity but also as a cornerstone for industrial and regulatory bodies. The current nanometallomics did not cover non-metallic nanomaterials, which is an important part of nanomaterials. In this critical review, the concept of nanometallomics was expanded to incorporate all nanomaterials. The impacts on metal(loid) and metallo-biomolecular homeostasis by nanomaterials will be focused upon in nanometallomics study. Besides, the impacts on elemental and biomolecular homeostasis by metallo-nanomaterials are also considered as the research subjects of nanometallomics. Based on the new concept of nanometallomics, comparative nanometallomics was proposed as a new tool for nanosafety evaluation, which is high throughput and will be precise considering the nature of machine learning techniques. The perspectives of nanometallomics like metallo-wide association study and non-target nanometallomics were put forward.

Di-2-picolylamine triggers caspase-independent apoptosis by inducing oxidative stress in human liver hepatocellular carcinoma cells

Di-2-picolylamine (DPA) is an organic compound that has been shown to possess antioxidant properties when conjugated to form a metal complex. The basis of this study was to determine the effects of DPA on the proliferation and apoptosis of human hepatocellular carcinoma cells and elucidate the possible mechanisms. The methylthiazol tetrazolium assay served to measure cell viability and generated an IC₅₀ of 1591 µM. Luminometry was used to investigate caspase activity and ATP concentration. It was observed that the decreased cell viability was associated with reduced ATP levels. Despite increased Bax and caspase 9 activity, cell death was caspase independent as indicated by the reduction in caspase 3/7 activity. This was associated with the downregulation poly(ADP-ribose) polymerase cleavage (Western blotting). However, the Hoescht assay depicted nuclear condensation and apoptotic body formation with elevated DPA levels suggesting DNA damage in HepG2 cells. DNA damage assessed by the comet assay confirmed an increased comet tail formation. The presence of oxidative stress was investigated by quantifying reactive species (malondialdehyde and nitrates concentration) and Western blotting to confirm the expression of antioxidant proteins. The DPA increased lipid peroxidation (RNS), a marker of oxidative stress, consequently causing cell death. The accompanying upregulation of stress-associated proteins superoxide dismutase (SOD2), nuclear factor (erythroid-derived 2)-like 2 (Nrf2), and Hsp70 verifies oxidative stress.

Advanced Nuclear and Related Techniques for Metallomics and Nanometallomics

Metallomics, focusing on the global and systematic understanding of the metal uptake, trafficking, role, and excretion in biological systems, has attracted more and more attention. Metal-related nanomaterials, including metallic and metal-containing nanomaterials, have unique properties compared to their macroscale counterparts and therefore require special attention. The absorption, distribution, metabolism, excretion (ADME) behavior of metal-related nanomaterials in the biological systems is influenced by their physicochemical properties, the exposure route, and the microenvironment of the deposition site. Nanomaterials not only may interact directly or indirectly with genes, proteins, and other molecules to bring genotoxicity, immunotoxicity, DNA damage, and cytotoxicity but may also stimulate the immune responses, circumvent tumor resistance, and inhibit tumor metastasis. Because of their advantages of absolute quantification, high sensitivity, excellent accuracy and precision, low matrix effects, and nondestructiveness, nuclear and related analytical techniques have been playing important roles in the study of metallomics and nanometallomics. In this chapter, we present a comprehensive overview of nuclear and related analytical techniques applied to the quantification of metallome and nanometallome, the biodistribution, bioaccumulation, and transformation of metallome and nanometallome in vivo, and the structural analysis. Besides, metallomics and nanometallomics need to cooperate with other -omics, like genomics, proteomics, and metabolomics, to obtain the knowledge of underlying mechanisms and therefore to improve the application performance and to reduce the potential risk of metallome and nanometallome.

The evolution of environmental metalloproteomics over the last 15 years through bibliometric techniques

Metalloproteomic studies in environmental scenarios are of significant value in elucidating metal uptake, trafficking, accumulation and metabolism linked to biomolecules in biological systems. The advent of this field occurred in the early 2000s, and it has since become an interesting and growing area of interdisciplinary research, although the number of publications in Environmental Metalloprotemics is still very low compared to other metallomic areas. In this context, the evolution of Environmental Metalloprotemics in the last decades was evaluated herein through the use of bibliometric techniques, identifying variables that may aid researchers in this area to form collaborative networks with established scientists in this regard, such as main authors, published articles, institutions, countries and established collaborations involved in academic research on this subject. Results indicate a growing trend of publications over time, reflecting the interest of the scientific community in Environmental Metalloprotemics, but also demonstrated that the research interactions in this field are still country- and organization-specific. Higher amounts of publications are observed from the late 2000's onwards, related to the increasing technological advances in the area, such as the development of techniques combining atomic spectroscopy and biochemical or proteomic techniques. The retrieved publications also indicate that the recent advances in genomic, proteomic and metallomic areas have allowed for extended applications of Environmental Metalloprotemics in non-model organisms. The results reported herein indicate that Environmental Metalloprotemics seems to now be reaching a more mature stage, in which analytical techniques are now well established and can be routinely applied in environmental scenarios, benefitting researchers and allowing for further insights into this fascinating field.

Investigation of thermostable metalloproteins in Perna perna mussels from differentially contaminated areas in Southeastern Brazil by bioanalytical techniques

Metallomic studies regarding environmental contamination by metals are of value in elucidating metal uptake, trafficking, accumulation and metabolism in biological systems. Many proven bioindicator species, such as bivalves, have not yet, however, been well-characterized regarding their metalloprotein expression in response to environmental contaminants. In this context, the aim of the present study was to investigate metalloprotein expressions in the thermostable protein fraction of muscle tissue and digestive glands from mussels (Perna perna) from three differentially metal-contaminated sites in Southeastern Brazil in comparison with a reference site. The thermostable protein fractions were analyzed by SDS-PAGE and SEC-HPLC-ICP-MS. Metal content was also determined in both the crude and the purified extracts. Several inter-organ differences were observed, which is to be expected, while inter-site differences regarding thermostable protein content were also verified, indicating accumulation of these elements in muscle tissue and digestive glands and disruption of homeostasis of essential elements, with detoxification attempts by metal-bound proteins, since all metalloproteins present in both matrices eluted bound to at least one non-essential metal. These results are also noteworthy with regard to the adopted reference site, that also seems to be contaminated by toxic metals.

Bacterial phosphoproteomic analysis reveals the correlation between protein phosphorylation and bacterial pathogenicity

Increasing evidence shows that protein phosphorylation on serine, threonine and tyrosine residues is a major regulatory post-translational modification in the bacteria. This review focuses on the implications of bacterial phosphoproteome in bacterial pathogenicity and highlights recent development of methods in phosphoproteomics and the connectivity of the phosphorylation networks. Recent technical developments in the high accuracy mass spectrometry have dramatically transformed proteomics and made it possible the characterization of a few exhaustive site-specific bacterial phosphoproteomes. The high abundance of tyrosine phosphorylations in a few bacterial phosphoproteomes suggests their roles in the pathogenicity, especially in the case of pathogen–host interactions; the high abundance of multi-phosphorylation sites in bacterial phosphoprotein is a compensation of the relatively small phosphorylation size and an indicator of the delicate regulation of protein functions.