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1. Introducing the ArsR-Regulated Arsenic Stimulon

   https://doi.org/10.3389/fmicb.2021.630562  

   Rawle, Rachel; Saley, Tara C.; Kang, Yoon-Suk; Wang, Qian; Walk, Seth; Bothner, Brian; McDermott, Timothy R. (March 2021, Frontiers in Microbiology)

   null (Ed.)

   The microbial ars operon encodes the primary bacterial defense response to the environmental toxicant, arsenic. An important component of this operon is the arsR gene, which encodes ArsR, a member of the family of proteins categorized as DNA-binding transcriptional repressors. As currently documented, ArsR regulates its own expression as well as other genes in the same ars operon. This study examined the roles of four ArsR proteins in the well-developed model Gram-negative bacterium Agrobacterium tumefaciens 5A. RNASeq was used to compare and characterize gene expression profiles in ± arsenite-treated cells of the wild-type strain and in four different arsR mutants. We report that ArsR-controlled transcription regulation is truly global, extending well beyond the current ars operon model, and includes both repression as well as apparent activation effects. Many cellular functions are significantly influenced, including arsenic resistance, phosphate acquisition/metabolism, sugar transport, chemotaxis, copper tolerance, iron homeostasis, and many others. While there is evidence of some regulatory overlap, each ArsR exhibits its own regulatory profile. Furthermore, evidence of a regulatory hierarchy was observed; i.e. ArsR1 represses arsR4 , ArsR4 activates arsR2 , and ArsR2 represses arsR3 . Additionally and unexpectedly, aioB (arsenite oxidase small subunit) expression was shown to be under partial positive control by ArsR2 and ArsR4. Summarizing, this study demonstrates the regulatory portfolio of arsenite-activated ArsR proteins and includes essentially all major cellular functions. The broad bandwidth of arsenic effects on microbial metabolism assists in explaining and understanding the full impact of arsenic in natural ecosystems, including the mammalian gut. 

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2. Analysis of Crassostrea Virginica Protein Metal Complexes after Exposure to Toxic Environmental Pollutant Cadmium

   https://doi.org/10.1096/fasebj.2022.36.S1.R2428  

   Wellek, Jacob B; Sherrer, Shanen M (May 2022, The FASEB Journal)

   Cadmium is a metal found in the parts per million of the earth’s crust, and it has been shown to have toxic effects on various plants, animals and humans. Exposure to cadmium occurs mainly through use of tobacco‐based products or industrial pollution. Once ingested, it is observed to take 20 to 30 years for cadmium concentration to reduce in half, which means it is difficult to clear from the body. A protein that is involved in the detoxification of harmful metals in cells is metallothionein. Having a strong binding affinity to divalent metals, metallothioneins allow cells to shuttle cadmium and other toxic metals away from important biological processes. Our current research aims to determine the effects of cadmium on the proteins withinCrassostrea Virginica(oysters) living in the Chesapeake Bay area and how fast these changes occur. After homogenizing oyster samples and testing the amount of total protein, the protein structural differences will be analyzed using circular dichroism spectroscopy and Western blot techniques with metallothionein and other proteins as well. The quantification of cadmium uptake in oysters and final destinations of cadmium within protein complexes of samples will also be examined. Knowing the impacts of this heavy metal on oysters is directly useful for increasing insights into the toxic effects from industrialization on our ecosystem, as well as elucidating the functional aspects of macromolecular complexes containing cadmium. 

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3. Protein-Cadmium Interactions in Crowded Biomolecular Environments Probed by In-cell and Lysate NMR Spectroscopy

   Sachin S. Katti, Tatyana I. (November 2023, bioRxiv)

   One of the mechanisms by which toxic metal ions interfere with cellular functions is ionic mimicry, where they bind to protein sites in lieu of native metals Ca2+ and Zn2+. The influence of crowded intracellular environments on these interactions is not well understood. Here, we demonstrate the application of in-cell and lysate NMR spectroscopy to obtain atomic-level information on how a potent environmental toxin cadmium interacts with its protein targets. The experiments, conducted in intact E. coli cells and their lysates, revealed that Cd2+ can profoundly affect the quinary interactions of its protein partners, and can replace Zn2+ in both labile and non-labile protein structural sites without significant perturbation of the membrane binding function. Surprisingly, in crowded molecular environments Cd2+ can effectively target not only all-sulfur and mixed sulfur/nitrogen but also all-oxygen coordination sites. The sulfur-rich coordination environments show significant promise for bioremedial applications, as demonstrated by the ability of the designed protein scaffold α3DIV to sequester intracellular cadmium. Our data suggests that in-cell NMR spectroscopy is a powerful tool for probing interactions of toxic metal ions with their potential protein targets, and for the assessment of potency of sequestering agents. 

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4. mebipred : identifying metal-binding potential in protein sequence

   https://doi.org/10.1093/bioinformatics/btac358  

   Aptekmann, A. A.; Buongiorno, J.; Giovannelli, D.; Glamoclija, M.; Ferreiro, D. U.; Bromberg, Y.; Cowen, ed., Lenore (May 2022, Bioinformatics)

   Abstract Motivationmetal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. Resultswe developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred’s utility in analyzing microbiome metal requirements. Availability and implementationmebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/. Supplementary informationSupplementary data are available at Bioinformatics online. 

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5. Ribosomal Protein Cluster Organization in Asgard Archaea

   https://doi.org/10.1155/2023/5512414  

   Tirumalai, Madhan R; Sivaraman, Raghavan V; Kutty, Layla A; Song, Eric L; Fox, George E (September 2023, Archaea)

   Spring, Stefan (Ed.)

   It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately. 

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