201
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Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiol Mol Biol Rev 2024; 88:e0018123. [PMID: 38856222 DOI: 10.1128/mmbr.00181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
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Affiliation(s)
- Alexander J Foster
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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202
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Cissé OH, Ma L, Kovacs JA. Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii. Microbiol Mol Biol Rev 2024; 88:e0020222. [PMID: 38587383 DOI: 10.1128/mmbr.00202-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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203
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Uesaka K, Banba M, Chiba S, Fujita Y. Restoration of the Functional nif Gene Cluster by Complex Recombination Events during Heterocyst Development in the Nitrogen-Fixing Cyanobacterium Calothrix sp. NIES-4101. PLANT & CELL PHYSIOLOGY 2024; 65:1050-1064. [PMID: 38305573 PMCID: PMC11249958 DOI: 10.1093/pcp/pcae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/03/2024]
Abstract
In the genome of the heterocystous cyanobacterium Calothrix sp. NIES-4101 (NIES-4101), the four genes essential for nitrogen fixation (nifB, nifH, nifD and nifK) are highly fragmented into 13 parts in a 350-kb chromosomal region, and four of these parts are encoded in the reverse strand. Such a complex fragmentation feature makes it difficult to restore the intact nifBHDK genes by the excision mechanism found in the nifD gene of the Anabaena sp. PCC 7120 heterocyst. To examine the nitrogen-fixing ability of NIES-4101, we confirmed that NIES-4101 grew well on a combined nitrogen-free medium and showed high nitrogenase activity, which strongly suggested that the complete nifBHDK genes are restored by a complex recombination process in heterocysts. Next, we resequenced the genome prepared from cells grown under nitrogen-fixing conditions. Two contigs covering the complete nifHDK and nifB genes were found by de novo assembly of the sequencing reads. In addition, the DNA fragments covering the nifBHDK operon were successfully amplified by PCR. We propose that the process of nifBHDK restoration occurs as follows. First, the nifD-nifK genes are restored by four excision events. Then, the complete nifH and nifB genes are restored by two excision events followed by two successive inversion events between the inverted repeat sequences and one excision event, forming the functional nif gene cluster, nifB-fdxN-nifS-nifU-nifH-nifD-nifK. All genes coding recombinases responsible for these nine recombination events are located close to the terminal repeat sequences. The restoration of the nifBHDK genes in NIES-4101 is the most complex genome reorganization reported in heterocystous cyanobacteria.
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Affiliation(s)
- Kazuma Uesaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Mari Banba
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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204
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Sepúlveda VE, Goldman WE, Matute DR. Genotypic diversity, virulence, and molecular genetic tools in Histoplasma. Microbiol Mol Biol Rev 2024; 88:e0007623. [PMID: 38819148 DOI: 10.1128/mmbr.00076-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Abstract
SUMMARYHistoplasmosis is arguably the most common fungal respiratory infection worldwide, with hundreds of thousands of new infections occurring annually in the United States alone. The infection can progress in the lung or disseminate to visceral organs and can be difficult to treat with antifungal drugs. Histoplasma, the causative agent of the disease, is a pathogenic fungus that causes life-threatening lung infections and is globally distributed. The fungus has the ability to germinate from conidia into either hyphal (mold) or yeast form, depending on the environmental temperature. This transition also regulates virulence. Histoplasma and histoplasmosis have been classified as being of emergent importance, and in 2022, the World Health Organization included Histoplasma as 1 of the 19 most concerning human fungal pathogens. In this review, we synthesize the current understanding of the ecological niche, evolutionary history, and virulence strategies of Histoplasma. We also describe general patterns of the symptomatology and epidemiology of histoplasmosis. We underscore areas where research is sorely needed and highlight research avenues that have been productive.
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Affiliation(s)
- Victoria E Sepúlveda
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William E Goldman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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205
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Beaussart A, Paiva TO, Geiger CJ, Baker AE, O'Toole GA, Dufrêne YF. Atomic force microscopy analysis of Pel polysaccharide- and type IV pili-mediated adhesion of Pseudomonas aeruginosa PA14 to an abiotic surface. NANOSCALE 2024; 16:12134-12141. [PMID: 38832761 DOI: 10.1039/d4nr01415d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Type IV pili (TFP) contribute to the ability of microbes such as Pseudomonas aeruginosa to engage with and move across surfaces. We reported previously that P. aeruginosa TFP generate retractive forces of ∼30 pN and provided indirect evidence that TFP-mediated surface attachment was enhanced in the presence of the Pel polysaccharide. Here, we use different mutants defective in flagellar, Pel production or TFP production - alone or in combination - to decipher the relative contribution of these biofilm-promoting factors for P. aeruginosa adhesion. By means of atomic force microscopy (AFM), we show that mutating the flagellum (ΔflgK mutant) results in an increase in Pel polysaccharide production, but this increase in Pel does not result in an increase in surface adhesive properties compared to those previously described for the WT strain. By blocking Pel production in the ΔflgK mutant (ΔflgKΔpel), we directly show that TFP play a major role in the adhesion of the bacteria to hydrophobic AFM tips, but that the adhesion force is only slightly impaired by the absence of Pel. Inversely, performing single-cell force spectroscopy measurements with the mutant lacking TFP (ΔflgKΔpilA) reveals that the Pel can modulate the attachment of the bacteria to a hydrophobic substrate in a time-dependent manner. Finally, little adhesion was detected for the ΔflgKΔpilAΔpelA triple mutant, suggesting that both TFP and Pel polysaccharide make a substantial contribution to bacteria-substratum interaction events. Altogether, our data allow us to decipher the relative contribution of Pel and TFP in the early attachment by P. aeruginosa.
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Affiliation(s)
- Audrey Beaussart
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, L7.07.07, B-1348 Louvain-la-Neuve, Belgium.
| | - Telmo O Paiva
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, L7.07.07, B-1348 Louvain-la-Neuve, Belgium.
| | - Christopher J Geiger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, USA.
| | - Amy E Baker
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, USA.
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, USA.
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, L7.07.07, B-1348 Louvain-la-Neuve, Belgium.
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206
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Chernyshov SV, Masulis IS, Mikoulinskaia GV. From DNA to lytic proteins: transcription and translation of the bacteriophage T5 holin/endolysin operon. World J Microbiol Biotechnol 2024; 40:256. [PMID: 38926173 DOI: 10.1007/s11274-024-04063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
The analysis of transcriptional activity of the bacteriophage T5 hol/endo operon conducted in the paper revealed a strong constitutive promoter recognized by E. coli RNA polymerase and a transcription initiation point of the operon. It was also shown that the only translational start codon for holin was a non-canonical TTG. Translation initiation regions (TIRs) of both genes of the operon (hol and endo) were further analyzed using chimeric constructs, in which parts of the hol/endo regulatory regions were fused with the gene of a reporter protein (EGFP). It was found that TIR of hol was 20 times less effective than that of endo. As it turned out, the level of EGFP production was influenced by the composition of the constructs and the type of the hol start codon. Apparently, the translational suppression of holin's accumulation and posttranslational activation of endolysin by Ca2+ are the main factors ensuring the proper timing of the host cell lysis by bacteriophage T5. The approach based on the use of chimeric constructs proposed in the paper can be recommended for studying other native or artificial operons of any complexity: analyzing the impacts of separate DNA regions, as well as their coupled effect, on the processes of transcription and translation of recombinant protein(s).
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Affiliation(s)
- Sergei V Chernyshov
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS, Prospekt Nauki, 6, Pushchino, Moscow region, Pushchino, Moscow region, 142290, Russia
| | - Irina S Masulis
- Institute of Cell Biophysics RAS PBC RAS, Institutskaya ul., 3, Pushchino, Pushchino, Moscow region, 142290, Russia
| | - Galina V Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS, Prospekt Nauki, 6, Pushchino, Moscow region, Pushchino, Moscow region, 142290, Russia.
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207
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Atay G, Holyavkin C, Can H, Arslan M, Topaloğlu A, Trotta M, Çakar ZP. Evolutionary engineering and molecular characterization of cobalt-resistant Rhodobacter sphaeroides. Front Microbiol 2024; 15:1412294. [PMID: 38993486 PMCID: PMC11236759 DOI: 10.3389/fmicb.2024.1412294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
With its versatile metabolism including aerobic and anaerobic respiration, photosynthesis, photo-fermentation and nitrogen fixation, Rhodobacter sphaeroides can adapt to diverse environmental and nutritional conditions, including the presence of various stressors such as heavy metals. Thus, it is an important microorganism to study the molecular mechanisms of bacterial stress response and resistance, and to be used as a microbial cell factory for biotechnological applications or bioremediation. In this study, a highly cobalt-resistant and genetically stable R. sphaeroides strain was obtained by evolutionary engineering, also known as adaptive laboratory evolution (ALE), a powerful strategy to improve and characterize genetically complex, desired microbial phenotypes, such as stress resistance. For this purpose, successive batch selection was performed in the presence of gradually increased cobalt stress levels between 0.1-15 mM CoCl2 for 64 passages and without any mutagenesis of the initial population prior to selection. The mutant individuals were randomly chosen from the last population and analyzed in detail. Among these, a highly cobalt-resistant and genetically stable evolved strain called G7 showed significant cross-resistance against various stressors such as iron, magnesium, nickel, aluminum, and NaCl. Growth profiles and flame atomic absorption spectrometry analysis results revealed that in the presence of 4 mM CoCl2 that significantly inhibited growth of the reference strain, the growth of the evolved strain was unaffected, and higher levels of cobalt ions were associated with G7 cells than the reference strain. This may imply that cobalt ions accumulated in or on G7 cells, indicating the potential of G7 for cobalt bioremediation. Whole genome sequencing of the evolved strain identified 23 single nucleotide polymorphisms in various genes that are associated with transcriptional regulators, NifB family-FeMo cofactor biosynthesis, putative virulence factors, TRAP-T family transporter, sodium/proton antiporter, and also in genes with unknown functions, which may have a potential role in the cobalt resistance of R. sphaeroides.
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Affiliation(s)
- Güneş Atay
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Can Holyavkin
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Hanay Can
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Mevlüt Arslan
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Massimo Trotta
- IPCF-CNR Istituto per I processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
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208
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Cruz-Navarrete FA, Griffin WC, Chan YC, Martin MI, Alejo JL, Brady RA, Natchiar SK, Knudson IJ, Altman RB, Schepartz A, Miller SJ, Blanchard SC. β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism. ACS CENTRAL SCIENCE 2024; 10:1262-1275. [PMID: 38947208 PMCID: PMC11212133 DOI: 10.1021/acscentsci.4c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024]
Abstract
Templated synthesis of proteins containing non-natural amino acids (nnAAs) promises to expand the chemical space available to biological therapeutics and materials, but existing technologies are still limiting. Addressing these limitations requires a deeper understanding of the mechanism of protein synthesis and how it is perturbed by nnAAs. Here we examine the impact of nnAAs on the formation and ribosome utilization of the central elongation substrate: the ternary complex of native, aminoacylated tRNA, thermally unstable elongation factor, and GTP. By performing ensemble and single-molecule fluorescence resonance energy transfer measurements, we reveal that both the (R)- and (S)-β2 isomers of phenylalanine (Phe) disrupt ternary complex formation to levels below in vitro detection limits, while (R)- and (S)-β3-Phe reduce ternary complex stability by 1 order of magnitude. Consistent with these findings, (R)- and (S)-β2-Phe-charged tRNAs were not utilized by the ribosome, while (R)- and (S)-β3-Phe stereoisomers were utilized inefficiently. (R)-β3-Phe but not (S)-β3-Phe also exhibited order of magnitude defects in the rate of translocation after mRNA decoding. We conclude from these findings that non-natural amino acids can negatively impact the translation mechanism on multiple fronts and that the bottlenecks for improvement must include the consideration of the efficiency and stability of ternary complex formation.
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Affiliation(s)
- F. Aaron Cruz-Navarrete
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Wezley C. Griffin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Yuk-Cheung Chan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Maxwell I. Martin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Jose L. Alejo
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Ryan A. Brady
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - S. Kundhavai Natchiar
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Isaac J. Knudson
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Roger B. Altman
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Alanna Schepartz
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Molecular
and Cell Biology, University of California,
Berkeley, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
- Innovation
Investigator, ARC Institute, Palo Alto, California 94304, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Scott C. Blanchard
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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209
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Billini M, Hoffmann T, Kühn J, Bremer E, Thanbichler M. The cytoplasmic phosphate level has a central regulatory role in the phosphate starvation response of Caulobacter crescentus. Commun Biol 2024; 7:772. [PMID: 38926609 PMCID: PMC11208175 DOI: 10.1038/s42003-024-06469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
In bacteria, the availability of environmental inorganic phosphate is typically sensed by the conserved PhoR-PhoB two-component signal transduction pathway, which uses the flux through the PstSCAB phosphate transporter as a readout of the extracellular phosphate level to control phosphate-responsive genes. While the sensing of environmental phosphate is well-investigated, the regulatory effects of cytoplasmic phosphate are unclear. Here, we disentangle the physiological and transcriptional responses of Caulobacter crescentus to changes in the environmental and cytoplasmic phosphate levels by uncoupling phosphate uptake from the activity of the PstSCAB system, using an additional, heterologously produced phosphate transporter. This approach reveals a two-pronged response of C. crescentus to phosphate limitation, in which PhoR-PhoB signaling mostly facilitates the utilization of alternative phosphate sources, whereas the cytoplasmic phosphate level controls the morphological and physiological adaptation of cells to growth under global phosphate limitation. These findings open the door to a comprehensive understanding of phosphate signaling in bacteria.
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Affiliation(s)
- Maria Billini
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Tamara Hoffmann
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Juliane Kühn
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Erhard Bremer
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043, Marburg, Germany.
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Center for Synthetic Microbiology, 35043, Marburg, Germany.
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210
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Cao X, Zhang Y, Ding Y, Wan Y. Identification of RNA structures and their roles in RNA functions. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00748-6. [PMID: 38926530 DOI: 10.1038/s41580-024-00748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The development of high-throughput RNA structure profiling methods in the past decade has greatly facilitated our ability to map and characterize different aspects of RNA structures transcriptome-wide in cell populations, single cells and single molecules. The resulting high-resolution data have provided insights into the static and dynamic nature of RNA structures, revealing their complexity as they perform their respective functions in the cell. In this Review, we discuss recent technical advances in the determination of RNA structures, and the roles of RNA structures in RNA biogenesis and functions, including in transcription, processing, translation, degradation, localization and RNA structure-dependent condensates. We also discuss the current understanding of how RNA structures could guide drug design for treating genetic diseases and battling pathogenic viruses, and highlight existing challenges and future directions in RNA structure research.
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Affiliation(s)
- Xinang Cao
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Yueying Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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211
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Zeng Y, Lockhart AC, Jin RU. The preclinical discovery and development of zolbetuximab for the treatment of gastric cancer. Expert Opin Drug Discov 2024:1-14. [PMID: 38919123 DOI: 10.1080/17460441.2024.2370332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Gastric cancer remains a formidable challenge in oncology with high mortality rates and few advancements in treatment. Claudin-18.2 (CLDN18.2) is a tight junction protein primarily expressed in the stomach and is frequently overexpressed in certain subsets of gastric cancers. Targeting CLDN18.2 with monoclonal antibodies, such as zolbetuximab (IMAB362), has shown promising efficacy results in combination with chemotherapy. AREAS COVERED The molecular cell biology of CLDN18.2 is discussed along with studies demonstrating the utility of CLDN18.2 expression as a biomarker and therapeutic target. Important clinical studies are reviewed, including Phase III trials, SPOTLIGHT and GLOW, which demonstrate the efficacy of zolbetuximab in combination with chemotherapy in patients with CLDN18.2-positive advanced gastric cancer. EXPERT OPINION CLDN18.2 is involved in gastric differentiation through maintenance of epithelial barrier function and coordination of signaling pathways, and its expression in gastric cancers reflects a 'gastric differentiation' program. Targeting Claudin-18.2 represents the first gastric cancer specific 'targeted' treatment. Further studies are needed to determine its role within current gastric cancer treatment sequencing, including HER2-targeted therapies and immunotherapies. Management strategies will also be needed to better mitigate zolbetuximab-related treatment side effects, including gastrointestinal (GI) toxicities.
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Affiliation(s)
- Yongji Zeng
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, USA
| | - A Craig Lockhart
- Division of Hematology/Oncology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Ramon U Jin
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, Houston, USA
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212
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Xu W, Yu F, Addison O, Zhang B, Guan F, Zhang R, Hou B, Sand W. Microbial corrosion of metallic biomaterials in the oral environment. Acta Biomater 2024:S1742-7061(24)00346-5. [PMID: 38942189 DOI: 10.1016/j.actbio.2024.06.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/29/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024]
Abstract
A wide variety of microorganisms have been closely linked to metal corrosion in the form of adherent surface biofilms. Biofilms allow the development and maintenance of locally corrosive environments and/or permit direct corrosion including pitting corrosion. The presence of numerous genetically distinct microorganisms in the oral environment poses a threat to the integrity and durability of the surface of metallic prostheses and implants used in routine dentistry. However, the association between oral microorganisms and specific corrosion mechanisms is not clear. It is of practical importance to understand how microbial corrosion occurs and the associated risks to metallic materials in the oral environment. This knowledge is also important for researchers and clinicians who are increasingly concerned about the biological activity of the released corrosion products. Accordingly, the main goal was to comprehensively review the current literature regarding oral microbiologically influenced corrosion (MIC) including characteristics of biofilms and of the oral environment, MIC mechanisms, corrosion behavior in the presence of oral microorganisms and potentially mitigating technologies. Findings included that oral MIC has been ascribed mostly to aggressive metabolites secreted during microbial metabolism (metabolite-mediated MIC). However, from a thermodynamic point of view, extracellular electron transfer mechanisms (EET-MIC) through pili or electron transfer compounds cannot be ruled out. Various MIC mitigating methods have been demonstrated to be effective in short term, but long term evaluations are necessary before clinical applications can be considered. Currently most in-vitro studies fail to simulate the complexity of intraoral physiological conditions which may either reduce or exacerbate corrosion risk, which must be addressed in future studies. STATEMENT OF SIGNIFICANCE: A thorough analysis on literature regarding oral MIC (microbiologically influenced corrosion) of biomedical metallic materials has been carried out, including characteristics of oral environment, MIC mechanisms, corrosion behaviors in the presence of typical oral microorganisms and potential mitigating methods (materials design and surface design). There is currently a lack of mechanistic understanding of oral MIC which is very important not only to corrosion researchers but also to dentists and clinicians. This paper discusses the significance of biofilms from a biocorrosion perspective and summarizes several aspects of MIC mechanisms which could be caused by oral microorganisms. Oral MIC has been closely associated with not only the materials research but also the dental/clinical research fields in this work.
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Affiliation(s)
- Weichen Xu
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China.
| | - Fei Yu
- School of Basic Medicine, Qingdao Medical College, Qingdao University, 308 Ningxia Road, Qingdao 266021, China.
| | - Owen Addison
- Centre for Oral Clinical Translational Science, Faculty of Dentistry Oral and Craniofacial Sciences, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Binbin Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Fang Guan
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Ruiyong Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Baorong Hou
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Wolfgang Sand
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Biofilm Centre, University of Duisburg-Essen, 45141 Essen, Germany
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213
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Bak DW, Weerapana E. Proteomic strategies to interrogate the Fe-S proteome. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119791. [PMID: 38925478 DOI: 10.1016/j.bbamcr.2024.119791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Iron‑sulfur (Fe-S) clusters, inorganic cofactors composed of iron and sulfide, participate in numerous essential redox, non-redox, structural, and regulatory biological processes within the cell. Though structurally and functionally diverse, the list of all proteins in an organism capable of binding one or more Fe-S clusters is referred to as its Fe-S proteome. Importantly, the Fe-S proteome is highly dynamic, with continuous cluster synthesis and delivery by complex Fe-S cluster biogenesis pathways. This cluster delivery is balanced out by processes that can result in loss of Fe-S cluster binding, such as redox state changes, iron availability, and oxygen sensitivity. Despite continued expansion of the Fe-S protein catalogue, it remains a challenge to reliably identify novel Fe-S proteins. As such, high-throughput techniques that can report on native Fe-S cluster binding are required to both identify new Fe-S proteins, as well as characterize the in vivo dynamics of Fe-S cluster binding. Due to the recent rapid growth in mass spectrometry, proteomics, and chemical biology, there has been a host of techniques developed that are applicable to the study of native Fe-S proteins. This review will detail both the current understanding of the Fe-S proteome and Fe-S cluster biology as well as describing state-of-the-art proteomic strategies for the study of Fe-S clusters within the context of a native proteome.
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Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
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214
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Suari Y, Topaz T, Bassa O, Gilboa M, Sedaka H, Sade T, Chefetz B, Yahel G. Nutrient concentration, loads and retention in a semiarid micro-estuary: The relative contribution of baseflow and flood events. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172805. [PMID: 38692314 DOI: 10.1016/j.scitotenv.2024.172805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
Estuaries are a significant source of nutrients to the marine environment. The magnitude of this source is a function of nutrients load reaching the estuary and removal (attenuation) within estuaries. Most estuarine research is conducted in large estuaries, which do not reflect the processes in small estuaries in urban and semi-arid regions where flood water is a substantial portion of the annual discharge and the estuarine baseflow is often low and dominated by wastewater. To improve the understanding of nutrient attenuation and load into the Mediterranean, we conducted high-resolution nutrient sampling in the eutrophic Alexander micro-estuary as a test case. We sampled once per month during baseflows (years 2014-2019) and hourly during floods (years 2016-2018). The concentrations of inorganic nutrients (phosphorous (P) and nitrogen (N)) were extremely high during baseflows. Dissolved ammonium and particulate P were the only nutrients that were in the estuary (by 55 % and 30 %, respectively). Floods were rare, occurring ~4 % of the time, but contributed 62 % of the annual water discharge of the Alexander micro-estuary (14.7 ± 3.8 106 m3 y-1). The concentration of all dissolved nutrients decreased during floods but was higher than expected (DIN 584 ± 50 μmol L-1, phosphate 21 ± 2 μmol L-1), accounting for 42 % and 55 % of the overall annual DIN (123.5 ± 44.9-ton yr-1) and P (6.7 ± 1.9 ton yr-1) loads to sea, respectively. The N:P ratios were 16 and 34 during baseflow and flood events, respectively. Previously, nutrient loads were calculated by multiplying baseflow-measured concentrations by the total water volume of baseflow and floods. Our calculations, based on high-resolution sampling, revealed lower annual loads of P and N to the sea that were 56 % and 89 % of previous estimates, which is a considerable difference in an oligotrophic system such as the eastern Mediterranean.
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Affiliation(s)
- Y Suari
- Ruppin Academic Center, School of Marine Sciences, Israel.
| | - T Topaz
- Ruppin Academic Center, School of Marine Sciences, Israel
| | - O Bassa
- Ruppin Academic Center, School of Marine Sciences, Israel; Department of Soil and Water Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - M Gilboa
- Ruppin Academic Center, School of Marine Sciences, Israel
| | - H Sedaka
- Ruppin Academic Center, School of Marine Sciences, Israel
| | - T Sade
- Ruppin Academic Center, School of Marine Sciences, Israel
| | - B Chefetz
- Ruppin Academic Center, School of Marine Sciences, Israel; Department of Soil and Water Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - G Yahel
- Ruppin Academic Center, School of Marine Sciences, Israel
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215
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Sun M, Gao J, Tang H, Wu T, Ma Q, Zhang S, Zuo Y, Li Q. Increasing CRISPR/Cas9-mediated gene editing efficiency in T7 phage by reducing the escape rate based on insight into the survival mechanism. Acta Biochim Biophys Sin (Shanghai) 2024; 56:937-944. [PMID: 38761011 DOI: 10.3724/abbs.2024030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024] Open
Abstract
Bacteriophages have been used across various fields, and the utilization of CRISPR/Cas-based genome editing technology can accelerate the research and applications of bacteriophages. However, some bacteriophages can escape from the cleavage of Cas protein, such as Cas9, and decrease the efficiency of genome editing. This study focuses on the bacteriophage T7, which is widely utilized but whose mechanism of evading the cleavage of CRISPR/Cas9 has not been elucidated. First, we test the escape rates of T7 phage at different cleavage sites, ranging from 10 -2 to 10 -5. The sequencing results show that DNA point mutations and microhomology-mediated end joining (MMEJ) at the target sites are the main causes. Next, we indicate the existence of the hotspot DNA region of MMEJ and successfully reduce MMEJ events by designing targeted sites that bypass the hotspot DNA region. Moreover, we also knock out the ATP-dependent DNA ligase 1. 3 gene, which may be involved in the MMEJ event, and the frequency of MMEJ at 4. 3 is reduced from 83% to 18%. Finally, the genome editing efficiency in T7 Δ 1. 3 increases from 20% to 100%. This study reveals the mechanism of T7 phage evasion from the cleavage of CRISPR/Cas9 and demonstrates that the special design of editing sites or the deletion of key gene 1. 3 can reduce MMEJ events and enhance gene editing efficiency. These findings will contribute to advancing CRISPR/Cas-based tools for efficient genome editing in phages and provide a theoretical foundation for the broader application of phages.
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Affiliation(s)
- Mingjun Sun
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Jie Gao
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Hongjie Tang
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Ting Wu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Qinqin Ma
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Suyi Zhang
- Luzhou Laojiao Co, Ltd, Luzhou 646000, China
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, China
| | - Yong Zuo
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
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216
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Xiong R, He X, Gao N, Li Q, Qiu Z, Hou Y, Shen W. Soil pH amendment alters the abundance, diversity, and composition of microbial communities in two contrasting agricultural soils. Microbiol Spectr 2024:e0416523. [PMID: 38916324 DOI: 10.1128/spectrum.04165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/30/2024] [Indexed: 06/26/2024] Open
Abstract
Soil microorganisms are the most active participants in terrestrial ecosystems, and have key roles in biogeochemical cycles and ecosystem functions. Despite the extensive research on soil pH as a key predictor of microbial community and composition, a limitation of these studies lies in determining whether bacterial and/or fungal communities are directly or indirectly influenced by pH. We conducted a controlled laboratory experiment to investigate the effects of soil pH amendment (+/- 1-2 units) with six levels on soil microbial communities in two contrasting Chinese agricultural soils (pH 8.43 in Dezhou, located in the North China Plain, Shandong vs pH 6.17 in Wuxi, located in the Taihu Lake region, Jiangsu, east China). Results showed that the fungal diversity and composition were related to soil pH, but the effects were much lower than the effects of soil pH on bacterial community in two soils. The diversity and composition of bacterial communities were more closely associated with soil pH in Wuxi soils compared to Dezhou soils. The alpha diversity of bacterial communities peaked near in situ pH levels in both soils, displaying a quadratic fitting pattern. Redundancy analysis and variation partition analysis indicated that soil pH affected bacterial community and composition by directly imposing a physiological constraint on soil bacteria and indirectly altering soil characteristics (e.g., nutrient availability). The study also examined complete curves of taxa relative abundances at the phylum and family levels in response to soil pH, with most relationships conforming to a quadratic fitting pattern, indicating soil pH is a reliable predictor. Furthermore, soil pH amendment affected the transformation of nitrogen and the abundances of functional genes involved in the nitrogen cycle, and methane production and consumption. Overall, results from this study would enhance our comprehension of how soil microorganisms in contrasting farmlands will respond to soil pH changes, and would contribute to more effective soil management and conservation strategies. IMPORTANCE This study delves into the impact of soil pH on microbial communities, investigating whether pH directly or indirectly influences bacterial and fungal communities. The research involved two contrasting soils subjected to a 1-2 pH unit amendment. Results indicate bacterial community composition was shaped by soil pH through physiological constraints and nutrient limitations. We found that most taxa relative abundances at the phylum and family levels responded to pH with a quadratic fitting pattern, indicating that soil pH is a reliable predictor. Additionally, soil pH was found to significantly influence the predicted abundance of functional genes involved in the nitrogen cycle as well as in methane production and consumption processes. These insights can contribute to develop more effective soil management and conservation strategies.
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Affiliation(s)
- Ruonan Xiong
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xinhua He
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
- Department of Land, Air and Water Resources, University of California at Davis, Davis, California, USA
| | - Nan Gao
- National Engineering Research Center for Biotechnology, School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Qing Li
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Zijian Qiu
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Yixin Hou
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Weishou Shen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
- Institute of Soil Health and Climate-Smart Agriculture, Nanjing University of Information Science and Technology, Nanjing, China
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217
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Ferrando J, Miñana-Galbis D, Picart P. The Construction of an Environmentally Friendly Super-Secreting Strain of Bacillus subtilis through Systematic Modulation of Its Secretory Pathway Using the CRISPR-Cas9 System. Int J Mol Sci 2024; 25:6957. [PMID: 39000067 PMCID: PMC11240994 DOI: 10.3390/ijms25136957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Achieving commercially significant yields of recombinant proteins in Bacillus subtilis requires the optimization of its protein production pathway, including transcription, translation, folding, and secretion. Therefore, in this study, our aim was to maximize the secretion of a reporter α-amylase by overcoming potential bottlenecks within the secretion process one by one, using a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system. The strength of single and tandem promoters was evaluated by measuring the relative α-amylase activity of AmyQ integrated into the B. subtilis chromosome. Once a suitable promoter was selected, the expression levels of amyQ were upregulated through the iterative integration of up to six gene copies, thus boosting the α-amylase activity 20.9-fold in comparison with the strain harboring a single amyQ gene copy. Next, α-amylase secretion was further improved to a 26.4-fold increase through the overexpression of the extracellular chaperone PrsA and the signal peptide peptidase SppA. When the final expression strain was cultivated in a 3 L fermentor for 90 h, the AmyQ production was enhanced 57.9-fold. The proposed strategy allows for the development of robust marker-free plasmid-less super-secreting B. subtilis strains with industrial relevance.
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Affiliation(s)
| | | | - Pere Picart
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; (J.F.); (D.M.-G.)
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218
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Contini L, Paul A, Mazzei L, Ciurli S, Roncarati D, Braga D, Grepioni F. Is bismuth(III) able to inhibit the activity of urease? Puzzling results in the quest for soluble urease complexes for agrochemical and medicinal applications. Dalton Trans 2024; 53:10553-10562. [PMID: 38847020 DOI: 10.1039/d4dt00778f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Bismuth(III) complexes have been reported to act as inhibitors of the enzyme urease, ubiquitously present in soils and implicated in the pathogenesis of several microorganisms. The general insolubility of Bi(III) complexes in water at neutral pH, however, is an obstacle to their utilization. In our quest to improve the solubility of Bi(III) complexes, we selected a compound reported to inhibit urease, namely [Bi(HEDTA)]·2H2O, and co-crystallized it with (i) racemic DL-histidine to obtain the conglomerate [Bi2(HEDTA)2(μ-D-His)2]·6H2O + [Bi2(HEDTA)2(μ-L-His)2]·6H2O, (ii) enantiopure L-histidine to yield [Bi2(HEDTA)2(μ-L-His)2]·6H2O, and (iii) cytosine to obtain [Bi(HEDTA)]·Cyt·2H2O. All compounds, synthesised by mechanochemical methods and by slurry, were characterized in the solid state by calorimetric (DSC and TGA) and spectroscopic (IR) methods, and their structures were determined using powder X-ray diffraction (PXRD) data. All compounds show an appreciable solubility in water, with values ranging from 6.8 mg mL-1 for the starting compound [Bi(HEDTA)]·2H2O to 36 mg mL-1 for [Bi2(HEDTA)2(μ-L-His)2]·6H2O. The three synthesized compounds as well as [Bi(HEDTA)]·2H2O were then tested for inhibition activity against urease. Surprisingly, no enzymatic inhibition was observed during in vitro assays using Canavalia ensiformis urease and in vivo assays using cultures of Helicobacter pylori, raising questions on the efficacy of Bi(III) compounds to counteract the negative effects of urease activity in the agro-environment and in human health.
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Affiliation(s)
- Laura Contini
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Arundhati Paul
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Dario Braga
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Fabrizia Grepioni
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
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219
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Jeyasri R, Muthuramalingam P, Priya A, Alexpandi R, Shanmugam NRS, Nivetha S, Shin H, Pandian SK, Ravi AV, Ramesh M. Comprehensive in vitro and in vivo evaluation of therapeutic potential of Bacopa-derived asiatic acid against a human oral pathogen Streptococcus mutans. Front Microbiol 2024; 15:1404012. [PMID: 38983632 PMCID: PMC11231090 DOI: 10.3389/fmicb.2024.1404012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/20/2024] [Indexed: 07/11/2024] Open
Abstract
Dental caries is a common human oral disease worldwide, caused by an acid-producing bacteria Streptococcus mutans. The use of synthetic drugs and antibiotics to prevent dental caries has been increasing, but this can lead to severe side effects. To solve this issue, developing and developed countries have resorted to herbal medicines as an alternative to synthetic drugs for the treatment and prevention of dental caries. Therefore, there is an urgent need for plant-derived products to treat such diseases. Bacopa monnieri, a well-documented medicinal plant, contains 52 phytocompounds, including the pentacyclic triterpenoid metabolite known as asiatic acid (ASTA). Hence, this study aimed to demonstrate, for the first time, the antibacterial activity of phytocompound ASTA against S. mutans. The findings revealed that ASTA significantly inhibited the growth of S. mutans and the production of virulence factors such as acidurity, acidogenicity, and eDNA synthesis. Molecular docking analysis evaluated the potential activity of ASTA against S. mutans virulence genes, including VicR and GtfC. Furthermore, toxicity assessment of ASTA in human buccal epithelial cells was performed, and no morphological changes were observed. An in vivo analysis using Danio rerio (zebrafish) confirmed that the ASTA treatment significantly increased the survival rates of infected fish by hindering the intestinal colonization of S. mutans. Furthermore, the disease protection potential of ASTA against the pathognomonic symptom of S. mutans infection was proven by the histopathological examination of the gills, gut, and kidney. Overall, these findings suggest that ASTA may be a promising therapeutic and alternative drug for the treatment and prevention of oral infection imposed by S. mutans.
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Affiliation(s)
- Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
- Division of Horticultural Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Arumugam Priya
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
- Department of Medicine, Division of Gastroenterology and Hepatology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Rajaiah Alexpandi
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
- School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, China
| | - N. R. Siva Shanmugam
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska - Lincoln, Lincoln, NE, United States
| | - Saminathan Nivetha
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Hyunsuk Shin
- Division of Horticultural Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | | | - Arumugam Veera Ravi
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
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220
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D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
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Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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221
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Stewart DI, Vasconcelos EJR, Burke IT, Baker A. Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172507. [PMID: 38657818 DOI: 10.1016/j.scitotenv.2024.172507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024]
Abstract
Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.
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Affiliation(s)
- Douglas I Stewart
- School of Civil Engineering, University of Leeds, Leeds LS2 9JT, UK.
| | | | - Ian T Burke
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK.
| | - Alison Baker
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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222
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Melo-Silva CR, Sigal LJ. Innate and adaptive immune responses that control lymph-borne viruses in the draining lymph node. Cell Mol Immunol 2024:10.1038/s41423-024-01188-0. [PMID: 38918577 DOI: 10.1038/s41423-024-01188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
The interstitial fluids in tissues are constantly drained into the lymph nodes (LNs) as lymph through afferent lymphatic vessels and from LNs into the blood through efferent lymphatics. LNs are strategically positioned and have the appropriate cellular composition to serve as sites of adaptive immune initiation against invading pathogens. However, for lymph-borne viruses, which disseminate from the entry site to other tissues through the lymphatic system, immune cells in the draining LN (dLN) also play critical roles in curbing systemic viral dissemination during primary and secondary infections. Lymph-borne viruses in tissues can be transported to dLNs as free virions in the lymph or within infected cells. Regardless of the entry mechanism, infected myeloid antigen-presenting cells, including various subtypes of dendritic cells, inflammatory monocytes, and macrophages, play a critical role in initiating the innate immune response within the dLN. This innate immune response involves cellular crosstalk between infected and bystander innate immune cells that ultimately produce type I interferons (IFN-Is) and other cytokines and recruit inflammatory monocytes and natural killer (NK) cells. IFN-I and NK cell cytotoxicity can restrict systemic viral spread during primary infections and prevent serious disease. Additionally, the memory CD8+ T-cells that reside or rapidly migrate to the dLN can contribute to disease prevention during secondary viral infections. This review explores the intricate innate immune responses orchestrated within dLNs that contain primary viral infections and the role of memory CD8+ T-cells following secondary infection or CD8+ T-cell vaccination.
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Affiliation(s)
- Carolina R Melo-Silva
- Department of Microbiology and Immunology, Thomas Jefferson University, Bluemle Life Sciences Building Room 709, 233 South 10th Street, Philadelphia, PA, 19107, USA.
| | - Luis J Sigal
- Department of Microbiology and Immunology, Thomas Jefferson University, Bluemle Life Sciences Building Room 709, 233 South 10th Street, Philadelphia, PA, 19107, USA.
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223
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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224
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Pereira AP, Antunes P, Peixe L, Freitas AR, Novais C. Current insights into the effects of cationic biocides exposure on Enterococcus spp. Front Microbiol 2024; 15:1392018. [PMID: 39006755 PMCID: PMC11242571 DOI: 10.3389/fmicb.2024.1392018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024] Open
Abstract
Cationic biocides (CBs), such as quaternary ammonium compounds and biguanides, are critical for controlling the spread of bacterial pathogens like Enterococcus spp., a leading cause of multidrug-resistant healthcare-associated infections. The widespread use of CBs in recent decades has prompted concerns about the potential emergence of Enterococcus spp. populations exhibiting resistance to both biocides and antibiotics. Such concerns arise from their frequent exposure to subinhibitory concentrations of CBs in clinical, food chain and diverse environmental settings. This comprehensive narrative review aimed to explore the complexity of the Enterococcus' response to CBs and of their possible evolution toward resistance. To that end, CBs' activity against diverse Enterococcus spp. collections, the prevalence and roles of genes associated with decreased susceptibility to CBs, and the potential for co- and cross-resistance between CBs and antibiotics are reviewed. Significant methodological and knowledge gaps are identified, highlighting areas that future studies should address to enhance our comprehension of the impact of exposure to CBs on Enterococcus spp. populations' epidemiology. This knowledge is essential for developing effective One Health strategies that ensure the continued efficacy of these critical agents in safeguarding Public Health.
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Affiliation(s)
- Ana P Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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225
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Li B, Hussain W, Jiang ZL, Wang JY, Hussain S, Yasoob TB, Zhai YK, Ji XY, Dang YL. Nuclear proteins and diabetic retinopathy: a review. Biomed Eng Online 2024; 23:62. [PMID: 38918766 PMCID: PMC11197269 DOI: 10.1186/s12938-024-01258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/23/2024] [Indexed: 06/27/2024] Open
Abstract
Diabetic retinopathy (DR) is an eye disease that causes blindness and vision loss in diabetic. Risk factors for DR include high blood glucose levels and some environmental factors. The pathogenesis is based on inflammation caused by interferon and other nuclear proteins. This review article provides an overview of DR and discusses the role of nuclear proteins in the pathogenesis of the disease. Some core proteins such as MAPK, transcription co-factors, transcription co-activators, and others are part of this review. In addition, some current advanced treatment resulting from the role of nuclear proteins will be analyzes, including epigenetic modifications, the use of methylation, acetylation, and histone modifications. Stem cell technology and the use of nanobiotechnology are proposed as promising approaches for a more effective treatment of DR.
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Affiliation(s)
- Bin Li
- Department of Ophthalmology, The First Affiliated Hospital, Henan University, Kaifeng, 475004, Henan, China
| | - Wahab Hussain
- School of Stomatology, Henan University, Kaifeng, 475000, China
- Kaifeng Municipal Key Laboratory for Infection and Biosafety, Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medicine Science, Henan University, Kaifeng, 475000, China
| | - Zhi-Liang Jiang
- School of Clinical Medicine, Henan University, Kaifeng, 475004, Henan, China
| | - Jia-Yi Wang
- San-Quan College, XinXiang Medical University, No. 688 Xiangyang Road, Hongmen Town, Hongqi District, Xinxiang City, Henan, 453003, China
| | - Sarfraz Hussain
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Talat Bilal Yasoob
- Department of Animal Sciences, Ghazi University, Dera Ghazi Khan, 32200, Pakistan
| | - Yuan-Kun Zhai
- School of Stomatology, Henan University, Kaifeng, 475000, China.
- Kaifeng Key Laboratory of Periodontal Tissue Engineering, Kaifeng, 475000, China.
| | - Xin-Ying Ji
- Kaifeng Municipal Key Laboratory for Infection and Biosafety, Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medicine Science, Henan University, Kaifeng, 475000, China.
- Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Mazhai, Erqi District, Zhengzhou, 450064, Henan, China.
| | - Ya-Long Dang
- Department of Ophthalmology, Sanmenxia Central Hospital, Henan University of Science and Technology, Sanmenxia, Henan, China.
- Department of Ophthalmology, Sanmenxia Eye Hospital, Sanmenxia, Henan, China.
- Department of Ophthalmology, Henan University of Science and Technology School of Medicine, Luoyang, Henan, China.
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226
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Rossi MN, Fiorucci C, Mariottini P, Cervelli M. Unveiling the hidden players: noncoding RNAs orchestrating polyamine metabolism in disease. Cell Biosci 2024; 14:84. [PMID: 38918813 PMCID: PMC11202255 DOI: 10.1186/s13578-024-01235-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/19/2024] [Indexed: 06/27/2024] Open
Abstract
Polyamines (PA) are polycations with pleiotropic functions in cellular physiology and pathology. In particular, PA have been involved in the regulation of cell homeostasis and proliferation participating in the control of fundamental processes like DNA transcription, RNA translation, protein hypusination, autophagy and modulation of ion channels. Indeed, their dysregulation has been associated to inflammation, oxidative stress, neurodegeneration and cancer progression. Accordingly, PA intracellular levels, derived from the balance between uptake, biosynthesis, and catabolism, need to be tightly regulated. Among the mechanisms that fine-tune PA metabolic enzymes, emerging findings highlight the importance of noncoding RNAs (ncRNAs). Among the ncRNAs, microRNA, long noncoding RNA and circRNA are the most studied as regulators of gene expression and mRNA metabolism and their alteration have been frequently reported in pathological conditions, such as cancer progression and brain diseases. In this review, we will discuss the role of ncRNAs in the regulation of PA genes, with a particular emphasis on the changes of this modulation observed in health disorders.
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Affiliation(s)
| | | | - Paolo Mariottini
- Department of Sciences, University of Roma Tre, 00146, Rome, Italy
| | - Manuela Cervelli
- Department of Sciences, University of Roma Tre, 00146, Rome, Italy.
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227
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García-Contreras R, de la Mora J, Mora-Montes HM, Martínez-Álvarez JA, Vicente-Gómez M, Padilla-Vaca F, Vargas-Maya NI, Franco B. The inorganic pyrophosphatases of microorganisms: a structural and functional review. PeerJ 2024; 12:e17496. [PMID: 38938619 PMCID: PMC11210485 DOI: 10.7717/peerj.17496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/09/2024] [Indexed: 06/29/2024] Open
Abstract
Pyrophosphatases (PPases) are enzymes that catalyze the hydrolysis of pyrophosphate (PPi), a byproduct of the synthesis and degradation of diverse biomolecules. The accumulation of PPi in the cell can result in cell death. Although the substrate is the same, there are variations in the catalysis and features of these enzymes. Two enzyme forms have been identified in bacteria: cytoplasmic or soluble pyrophosphatases and membrane-bound pyrophosphatases, which play major roles in cell bioenergetics. In eukaryotic cells, cytoplasmic enzymes are the predominant form of PPases (c-PPases), while membrane enzymes (m-PPases) are found only in protists and plants. The study of bacterial cytoplasmic and membrane-bound pyrophosphatases has slowed in recent years. These enzymes are central to cell metabolism and physiology since phospholipid and nucleic acid synthesis release important amounts of PPi that must be removed to allow biosynthesis to continue. In this review, two aims were pursued: first, to provide insight into the structural features of PPases known to date and that are well characterized, and to provide examples of enzymes with novel features. Second, the scientific community should continue studying these enzymes because they have many biotechnological applications. Additionally, in this review, we provide evidence that there are m-PPases present in fungi; to date, no examples have been characterized. Therefore, the diversity of PPase enzymes is still a fruitful field of research. Additionally, we focused on the roles of H+/Na+ pumps and m-PPases in cell bioenergetics. Finally, we provide some examples of the applications of these enzymes in molecular biology and biotechnology, especially in plants. This review is valuable for professionals in the biochemistry field of protein structure-function relationships and experts in other fields, such as chemistry, nanotechnology, and plant sciences.
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Affiliation(s)
- Rodolfo García-Contreras
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Héctor Manuel Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - José A. Martínez-Álvarez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Marcos Vicente-Gómez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Naurú Idalia Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
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228
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Yan X, Liu D, de Smit SM, Komin V, Buisman CJN, Ter Heijne A. Oxygen-to-ammonium-nitrogen ratio as an indicator for oxygen supply management in microoxic bioanodic ammonium oxidation. WATER RESEARCH 2024; 261:121993. [PMID: 38968732 DOI: 10.1016/j.watres.2024.121993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/16/2024] [Accepted: 06/22/2024] [Indexed: 07/07/2024]
Abstract
Microbial electrolysis cells (MECs) have been proven effective for oxidizing ammonium (NH4+), where the anode acts as an electron acceptor, reducing the energy input by substituting oxygen (O2). However, O2 has been proved to be essential for achieving high removal rates MECs. Thus, precise control of oxygen supply is crucial for optimizing treatment performance and minimizing energy consumption. Unlike previous studies focusing on dissolved oxygen (DO) levels, this study introduces the O2/NH4+-N ratio as a novel control parameter for balancing oxidation rates and the selectivity of NH4+ oxidation towards dinitrogen gas (N2) under limited oxygen condition. Our results demonstrated that the O2/NH4+-N ratio is a more relevant oxygen supply indicator compared to DO level. Oxygen served as a more favorable electron acceptor than the electrode, increasing NH4+ oxidation rates but also resulting in more oxidized products such as nitrate (NO3-). Additionally, nitrous oxide (N2O) and N2 production were higher with the electrode as the electron acceptor compared to oxygen alone. An O2/NH4+-N ratio of 0.5 was found to be optimal, achieving a balance between product selectivity for N2 (51.4 % ± 4.5 %) and oxidation rates (344.6 ± 14.7 mg-N/L*d), with the columbic efficiency of 30.7 % ± 2.0 %. Microbial community analysis revealed that nitrifiers and denitrifiers were the primary bacteria involved, with oxygen promoting the growth of nitrite-oxidizing bacteria, thus facilitating complete NH4+ oxidation to NO3-. Our study provides new insights and guidelines on the appropriate oxygen dosage, offering strategies into optimizing operational conditions for NH4+ removal using MECs.
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Affiliation(s)
- Xiaofang Yan
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Dandan Liu
- Paqell B.V., Reactorweg 301, 3542 CE Utrecht, the Netherlands
| | - Sanne M de Smit
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Vera Komin
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Cees J N Buisman
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Annemiek Ter Heijne
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands.
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229
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Hachimi O, Falender R, Davis G, Wafula RV, Sutton M, Bancroft J, Cieslak P, Kelly C, Kaya D, Radniecki T. Evaluation of molecular-based methods for the detection and quantification of Cryptosporidium spp. in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174219. [PMID: 38917908 DOI: 10.1016/j.scitotenv.2024.174219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Cryptosporidium poses significant public health risks as a cause of waterborne disease worldwide. Clinical surveillance of cryptosporidiosis is largely underreported due to the asymptomatic and mildly symptomatic infections, clinical misdiagnoses, and barriers to access testing. Wastewater surveillance overcomes these limitations and could serve as an effective tool for identifying cryptosporidiosis at the population level. Despite its potential, the lack of standardized wastewater surveillance methods for Cryptosporidium spp. challenges implementation design and the comparability between studies. Thus, this study compared and contrasted Cryptosporidium wastewater surveillance methods for concentrating wastewater oocysts, extracting oocyst DNA, and detecting Cryptosporidium genetic markers. The evaluated concentration methods included electronegative membrane filtration, Envirocheck HV capsule filtration, centrifugation, and Nanotrap Microbiome Particles, with and without additional immunomagnetic separation purification (except for the Nanotrap Microbiome Particles). Oocyst DNA extraction by either the DNeasy Powersoil Pro kit and the QIAamp DNA Mini kit were evaluated and the impact of bead beating and freeze-thaw pretreatments on DNA recoveries was assessed. Genetic detection via qPCR assays targeting either the Cryptosporidium 18S rRNA gene or the Cryptosporidium oocyst wall protein gene were tested. Oocyst recovery percentages were highest for centrifugation (39-77 %), followed by the Nanotrap Microbiome Particles (24 %), electronegative filtration with a PBST elution (22 %), and Envirocheck HV capsule filtration (13 %). Immunomagnetic separation purification was found to be unsuitable due to interference from the wastewater matrix. Bead-beating pretreatment enhanced DNA recoveries from both the DNeasy Powersoil Pro kit (314 gc/μL DNA) and the QIAamp DNA Mini kit (238 gc/μL DNA). In contrast, freeze-thaw pretreatment reduced DNA recoveries to under 92 gc/μL DNA, likely through DNA degradation. Finally, while both qPCR assays were specific to Cryptosporidium spp., the 18S rRNA assay had a 5-fold lower detection limit and could detect a wider range of Cryptosporidium spp. than the Cryptosporidium oocyst wall protein assay.
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Affiliation(s)
- Oumaima Hachimi
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Rebecca Falender
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - Gabriel Davis
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Rispa Vranka Wafula
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Melissa Sutton
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - June Bancroft
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - Paul Cieslak
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - Christine Kelly
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Devrim Kaya
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Tyler Radniecki
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA.
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230
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Schlosserová K, Daniel O, Labská K, Jakubů V, Stárková T, Bílý J, Dresler J, Lang C, Fruth A, Flieger A, Žemličková H, Bielaszewska M, Havlíčková M. Enteroaggregative Escherichia coli: Frequent, yet underdiagnosed pathotype among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic. Int J Med Microbiol 2024; 316:151628. [PMID: 38936338 DOI: 10.1016/j.ijmm.2024.151628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/27/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) strains including those of serogroup O111 are important causes of diarrhea in children. In the Czech Republic, no information is available on the etiological role of EAEC in pediatric diarrhea due to the lack of their targeted surveillance. To fill this gap, we determined the proportion of EAEC among E. coli O111 isolates from children with gastrointestinal disorders ≤ 2 years of age submitted to the National Reference Laboratory for E. coli and Shigella during 2013-2022. EAEC accounted for 177 of 384 (46.1 %) E. coli O111 isolates, being the second most frequent E. coli O111 pathotype. Most of them (75.7 %) were typical EAEC that carried aggR, usually with aaiC and aatA marker genes; the remaining 24.3 % were atypical EAEC that lacked aggR but carried aaiC and/or aatA. Whole genome sequencing of 11 typical and two atypical EAEC O111 strains demonstrated differences in serotypes, sequence types (ST), virulence gene profiles, and the core genomes between these two groups. Typical EAEC O111:H21/ST40 strains resembled by their virulence profiles including the presence of the aggregative adherence fimbriae V (AAF/V)-encoding cluster to such strains from other countries and clustered with them in the core genome multilocus sequence typing (cgMLST). Atypical EAEC O111:H12/ST10 strains lacked virulence genes of typical EAEC and differed from them in cgMLST. All tested EAEC O111 strains displayed stacked-brick aggregative adherence to human intestinal epithelial cells. The AAF/V-encoding cluster was located on a plasmid of 95,749 bp or 93,286 bp (pAAO111) which also carried aggR, aap, aar, sepA, and aat cluster. EAEC O111 strains were resistant to antibiotics, in particular to aminopenicillins and cephalosporins; 88.3 % produced AmpC β-lactamase, and 4.1 % extended spectrum β-lactamase. We conclude that EAEC are frequent among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic. To reliably assess the etiological role of EAEC in pediatric diarrhea, a serotype-independent, PCR-based pathotype surveillance system needs to be implemented in the future.
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Affiliation(s)
- Klára Schlosserová
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 2nd Faculty of Medicine, Charles University, Prague, V Úvalu 84, Prague 150 06, Czech Republic
| | - Ondřej Daniel
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 2nd Faculty of Medicine, Charles University, Prague, V Úvalu 84, Prague 150 06, Czech Republic
| | - Klára Labská
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
| | - Vladislav Jakubů
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 3rd Faculty of Medicine, Charles University, Prague, Ruská 87, Prague 100 00, Czech Republic
| | - Tereza Stárková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
| | - Jan Bílý
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
| | - Jiří Dresler
- Central Military Medical Institute, Military University Hospital, U Vojenské nemocnice 1200, Prague 160 01, Czech Republic
| | - Christina Lang
- Division of Enteropathogenic Bacteria and Legionella and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Burgstrasse 37, Wernigerode 38855, Germany
| | - Angelika Fruth
- Division of Enteropathogenic Bacteria and Legionella and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Burgstrasse 37, Wernigerode 38855, Germany
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Burgstrasse 37, Wernigerode 38855, Germany
| | - Helena Žemličková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 3rd Faculty of Medicine, Charles University, Prague, Ruská 87, Prague 100 00, Czech Republic
| | - Martina Bielaszewska
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 2nd Faculty of Medicine, Charles University, Prague, V Úvalu 84, Prague 150 06, Czech Republic.
| | - Monika Havlíčková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
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231
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Nayak R, Duan M, Ling B, Jin Z, Malounda D, Shapiro MG. Harmonic imaging for nonlinear detection of acoustic biomolecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599141. [PMID: 38948831 PMCID: PMC11212972 DOI: 10.1101/2024.06.18.599141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Gas vesicles (GVs) based on acoustic reporter genes have emerged as potent contrast agents for cellular and molecular ultrasound imaging. These air-filled, genetically encoded protein nanostructures can be expressed in a variety of cell types in vivo to visualize cell location and activity or injected systemically to label and monitor tissue function. Distinguishing GVs from tissue signal deep inside intact organisms requires imaging approaches such as amplitude modulation (AM) or collapse-based pulse sequences, however they have limitations in sensitivity or require irreversible collapse of the GVs that restricts its scope for imaging dynamic cellular processes. To address these limitations, this study explores the utility of harmonic imaging to enhance the sensitivity of non-destructive imaging of GVs and cellular processes. Traditional fundamental-frequency imaging utilizing cross-wave AM (xAM) sequences has been deemed optimal for GV imaging. Contrary to this, we hypothesize that harmonic imaging, integrated with xAM could significantly elevate GV detection sensitivity. To verify our hypothesis, we conducted imaging on tissue-mimicking phantoms embedded with purified GVs, mammalian cells genetically modified to express GVs, and live mice after systemic GV infusion. Our findings reveal that harmonic xAM (HxAM) imaging markedly surpasses traditional xAM in isolating GVs' nonlinear acoustic signature, showcasing significant enhancements in signal-to-background and contrast-to-background ratios across all tested samples. Further investigation into the backscattered spectra elucidates the efficacy of harmonic imaging in conjunction with xAM. HxAM imaging enables the detection of lower concentrations of GVs and cells with ultrasound and extends the imaging depth in vivo by up to 20% and imaging performance metrics by up to 10dB. These advancements bolster the capabilities of ultrasound for molecular and cellular imaging, underscoring the potential of using harmonic signals to amplify GV detection.
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232
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Perez-Gil J, Behrendorff J, Douw A, Vickers CE. The methylerythritol phosphate pathway as an oxidative stress sense and response system. Nat Commun 2024; 15:5303. [PMID: 38906898 PMCID: PMC11192765 DOI: 10.1038/s41467-024-49483-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/05/2024] [Indexed: 06/23/2024] Open
Abstract
The methylerythritol phosphate (MEP) pathway is responsible for biosynthesis of the precursors of isoprenoid compounds in eubacteria and plastids. It is a metabolic alternative to the well-known mevalonate pathway for isoprenoid production found in archaea and eukaryotes. Recently, a role for the MEP pathway in oxidative stress detection, signalling, and response has been identified. This role is executed in part through the unusual cyclic intermediate, methylerythritol cyclodiphosphate (MEcDP). We postulate that this response is triggered through the oxygen sensitivity of the MEP pathway's terminal iron-sulfur (Fe-S) cluster enzymes. MEcDP is the substrate of IspG, the first Fe-S cluster enzyme in the pathway; it accumulates under oxidative stress conditions and acts as a signalling molecule. It may also act as an antioxidant. Furthermore, evidence is emerging for a broader and highly nuanced role of the MEP pathway in oxidative stress responses, implemented through a complex system of differential regulation and sensitivity at numerous nodes in the pathway. Here, we explore the evidence for such a role (including the contribution of the Fe-S cluster enzymes and different pathway metabolites, especially MEcDP), the evolutionary implications, and the many questions remaining about the behaviour of the MEP pathway in the presence of oxidative stress.
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Affiliation(s)
- Jordi Perez-Gil
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - James Behrendorff
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Andrew Douw
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
- BioBuilt Solutions, Corinda, QLD, 4075, Australia.
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233
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Schorn S, Graf JS, Littmann S, Hach PF, Lavik G, Speth DR, Schubert CJ, Kuypers MMM, Milucka J. Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility. Nat Commun 2024; 15:5293. [PMID: 38906896 PMCID: PMC11192741 DOI: 10.1038/s41467-024-49602-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d-1. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.
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Affiliation(s)
- Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Carsten J Schubert
- Department of Surface Waters, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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234
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Khanduja S, Bloom SM, Raman V, Deshpande CP, Hall CL, Forbes NS. Intracellular delivery of oncolytic viruses with engineered Salmonella causes viral replication and cell death. iScience 2024; 27:109813. [PMID: 38799578 PMCID: PMC11126981 DOI: 10.1016/j.isci.2024.109813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/12/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
As therapies, oncolytic viruses regress tumors and have the potential to induce antitumor immune responses that clear hard-to-treat and late-stage cancers. Despite this promise, clearance from the blood prevents treatment of internal solid tumors. To address this issue, we developed virus-delivering Salmonella (VDS) to carry oncolytic viruses into cancer cells. The VDS strain contains the PsseJ-lysE delivery circuit and has deletions in four homologous recombination genes (ΔrecB, ΔsbcB, ΔsbcCD, and ΔrecF) to preserve essential hairpins in the viral genome required for replication and infectivity. VDS delivered the genome for minute virus of mice (MVMp) to multiple cancers, including breast, pancreatic, and osteosarcoma. Viral delivery produced functional viral particles that are cytotoxic and infective to neighboring cells. The release of mature virions initiated new rounds of infection and amplified the infection. Using Salmonella for delivery will circumvent the limitations of oncolytic viruses and will provide a new therapy for many cancers.
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Affiliation(s)
- Shradha Khanduja
- Department of Chemical Engineering, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Shoshana M.K. Bloom
- Department of Chemical Engineering, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Vishnu Raman
- Department of Chemical Engineering, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Chinmay P. Deshpande
- Department of Chemical Engineering, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Christopher L. Hall
- Department of Chemical Engineering, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Neil S. Forbes
- Department of Chemical Engineering, University of Massachusetts, Amherst, Amherst, MA, USA
- Molecular and Cell Biology Program, University of Massachusetts, Amherst, Amherst, MA, USA
- Institute for Applied Life Science, University of Massachusetts, Amherst, Amherst, MA, USA
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235
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Song X, Zhao Y, Ren Y, Liu R, Zhang M, Zhang Z, Meng Q, Zhu T, Yin J, Yu Z. Development of a Quorum Sensing-Mediated Bacterial Autolytic System in Escherichia coli for Automatic Release of Intracellular Products. ACS Synth Biol 2024; 13:1956-1962. [PMID: 38860508 DOI: 10.1021/acssynbio.4c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Escherichia coli, one of the most efficient expression hosts for recombinant proteins, is widely used in chemical, medical, food, and other industries. De novo engineering of gene regulation circuits and cell density-controlled E. coli cell lysis are promising directions for the release of intracellular bioproducts. Here, we developed an E. coli autolytic system, named the quorum sensing-mediated bacterial autolytic (QS-BA) system, by incorporating an acyl-homoserine lactone (AHL)-based YasI/YasR-type quorum sensing circuit from Pseudoalteromonas into E. coli cells. The results showed that the E. coli QS-BA system can release the intracellular bioproducts into the cell culture medium in terms of E. coli cell density, which offers an environmentally-friendly, economical, efficient, and flexible E. coli lysis platform for production of recombinant proteins. The QS-BA system has the potential to serve as an integrated system for the large-scale production of target products in E. coli for medical and industrial applications.
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Affiliation(s)
- Xiaofei Song
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yifan Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yixuan Ren
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Ruoyu Liu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Mengting Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Zhikai Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Qiu Meng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Tingheng Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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Yang F, Ma Q, Zhang X, Shang Y, Ngando FJ, Ren L, Cai J. The gut bacterial composition across life stages of Sarcophaga peregrina (Diptera: Sarcophagidae) and the effects of amikacin on their development. JOURNAL OF MEDICAL ENTOMOLOGY 2024:tjae071. [PMID: 38902886 DOI: 10.1093/jme/tjae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024]
Abstract
Insects and microorganisms, ubiquitous organisms in the natural world, have developed intricate relationships throughout their evolutionary histories. However, most studies have concentrated on specific time points or life stages, but some limited studies have investigated the dynamics of microbial diversity within insects across life stages. Here, 16S rDNA sequencing technology was used to investigate the gut bacterial community across the life stages of Sarcophaga peregrina (Robineau-Desvoidy) (Diptera: Sarcophagidae). The results revealed that the gut bacterial diversity of S. peregrina varied with life stage and showed similarity in the nearby life stages. Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in S. peregrina. Genera such as Providencia, Ignatzschineria, and Myroides are implicated in potentially pivotal roles during the developmental processes of this flesh fly. Furthermore, the effects of amikacin on the growth and development of S. peregrina were not statistically significant. However, we did observe significant changes at the protein level, which suggests a close association between protein-level alterations and growth and development. Additionally, we speculate that S. peregrina regulates its nutritional status during nonfeeding stages to meet the demands of eclosion. This study represents the first comprehensive examination of the intestinal bacterial composition across various life stages of S. peregrina. Our findings deepen our understanding of the gut microbiota in this flesh fly and lay the groundwork for further exploration into the intricate interactions between microorganisms and insects.
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Affiliation(s)
- Fengqin Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan, Changsha, China
| | - Qiongshan Ma
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan, Changsha, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan, Changsha, China
| | - Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan, Changsha, China
| | - Fernand Jocelin Ngando
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan, Changsha, China
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan, Changsha, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan, Changsha, China
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237
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Liu J, Wang J, Zhang Z, Bai Q, Pan X, Chen R, Yao H, Yu Y, Ma J. Streptococcus suis Deploys Multiple ATP-Dependent Proteases for Heat Stress Adaptation. J Basic Microbiol 2024:e2400030. [PMID: 39031597 DOI: 10.1002/jobm.202400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/24/2024] [Accepted: 05/19/2024] [Indexed: 07/22/2024]
Abstract
Streptococcus suis is an important zoonotic pathogen, causing cytokine storms of Streptococcal toxic shock-like syndrome amongst humans after a wound infection into the bloodstream. To overcome the challenges of fever and leukocyte recruitment, invasive S. suis must deploy multiple stress responses forming a network and utilize proteases to degrade short-lived regulatory and misfolded proteins induced by adverse stresses, thereby adapting and evading host immune responses. In this study, we found that S. suis encodes multiple ATP-dependent proteases, including single-chain FtsH and double-subunit Clp protease complexes ClpAP, ClpBP, ClpCP, and ClpXP, which were activated as the fever of infected mice in vivo. The expression of genes ftsH, clpA/B/C, and clpP, but not clpX, were significantly upregulated in S. suis in response to heat stress, while were not changed notably under the treatments with several other stresses, including oxidative, acidic, and cold stimulation. FtsH and ClpP were required for S. suis survival within host blood under heat stress in vitro and in vivo. Deletion of ftsH or clpP attenuated the tolerance of S. suis to heat, oxidative and acidic stresses, and significantly impaired the bacterial survival within macrophages. Further analysis identified that repressor CtsR directly binds and controls the clpA/B/C and clpP operons and is relieved by heat stress. In summary, the deployments of multiple ATP-dependent proteases form a flexible heat stress response network that appears to allow S. suis to fine-tune the degradation or refolding of the misfolded proteins to maintain cellular homeostasis and optimal survival during infection.
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Affiliation(s)
- Jianan Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Jianzhong Wang
- Suzhou Xiangcheng Fisheries Technology Promotion Center, Suzhou Animal Disease Prevention and Control Center, Suzhou, China
| | - Zhen Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Qiankun Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Xinming Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Rong Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Yong Yu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Jiale Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
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238
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Halim MA, Bieser JMH, Thomas SC. Large, sustained soil CO 2 efflux but rapid recovery of CH 4 oxidation in post-harvest and post-fire stands in a mixedwood boreal forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172666. [PMID: 38653415 DOI: 10.1016/j.scitotenv.2024.172666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
The net effect of forest disturbances, such as fires and harvesting, on soil greenhouse gas fluxes is determined by their impacts on both biological and physical factors, as well as the temporal dynamics of these effects post-disturbance. Although harvesting and fire may have distinct effects on soil carbon (C) dynamics, the temporal patterns in soil CO2 and CH4 fluxes and the potential differences between types of disturbances, remain poorly characterized in boreal forests. In this study, we measured soil CO2 and CH4 fluxes using a off-axis integrated cavity output spectroscopy system in snow-free seasons over two years in post-harvest and post-fire chronosequence sites within a mixedwood boreal forest in northwestern Ontario, Canada. Soil CO2 efflux showed a post-disturbance peak, with differing dynamics depending on the disturbance type: post-harvest stands exhibited a nearly tenfold increase (from ∼1 to ∼11 μmol CO2.m-2.s-1) from 1 to 9-10 years post-disturbance, followed by a steep decline; post-fire stands showed a more gradual increase, peaking at ∼6-7.2 μmol CO2.m-2.s-1 after ∼12-15 years. The youngest post-harvest stands were net sources of CH4,whereas post-fire stands were never net CH4 sources. In both disturbance types, the strength of the CH4 sink increased with stand age, approaching ∼2.4 nmol.m-2.s-1 by 15 years post-disturbance. Volumetric water content, bulk density, litter depth, and pH were significant predictors of CO2 fluxes; for CH4 fluxes, litter depth, pH, and the interaction of VWC and soil temperature were significant predictors in both disturbance types, with EC also showing a relationship in post-harvest stands. Our findings indicate that while soil CH4 oxidation rapidly recovers following disturbance, both post-harvest and post-fire stands show a multi-decade release of soil CO2 that is too large to be offset by C gains over this period.
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Affiliation(s)
- Md Abdul Halim
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks Street, M5S 3B3 Toronto, Canada; Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Jillian M H Bieser
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks Street, M5S 3B3 Toronto, Canada
| | - Sean C Thomas
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks Street, M5S 3B3 Toronto, Canada
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239
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Husaini AM, Sohail M. Agrochemical-free genetically modified and genome-edited crops: Towards achieving the United Nations sustainable development goals and a 'greener' green revolution. J Biotechnol 2024; 389:68-77. [PMID: 38663518 DOI: 10.1016/j.jbiotec.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/28/2024]
Abstract
Sustainable farming on ever-shrinking agricultural land and declining water resources for the growing human population is one of the greatest environmental and food security challenges of the 21st century. Conventional, age-old organic farming practices alone, and foods based on costly cellular agriculture, do not have the potential to be upscaled to meet the food supply challenges for feeding large populations. Additionally, agricultural practices relying on chemical inputs have a well-documented detrimental impact on human health and the environment. As the available farming methods have reached their productivity limits, new approaches to agriculture, combining friendly, age-old farming practices with modern technologies that exclude chemical interventions, are necessary to address the food production challenges. Growing genetically modified (GM) crops without chemical inputs can allow agricultural intensification with reduced adverse health and environmental impacts. Additionally, integrating high-value pleiotropic genes in their genetic improvement coupled with the use of modern agricultural technologies, like robotics and artificial intelligence (AI), will further improve productivity. Such 'organic-GM' crops will offer consumers healthy, agrochemical-free GM produce. We believe these agricultural practices will lead to the beginning of a potentially new chemical-free GM agricultural revolution in the era of Agriculture 4.0 and help meet the targets of the United Nations Sustainable Development Goals (SDGs). Furthermore, given the advancement in the genome editing (GE) toolbox, we ought to develop a new category of 'trait-reversible GM crops' to avert the fears of those who believe in ecological damage by GM crops. Thus, in this article, we advocate farming with no or minimal chemical use by combining chemical-free organic farming with the existing biofortified and multiple stress tolerant GM crops, while focusing on the development of novel 'biofertilizer-responsive GE crops' and 'trait-reversible GE crops' for the future.
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Affiliation(s)
- Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir, India.
| | - Muhammad Sohail
- Wolfson College, Lintodn Road, University of Oxford, Oxford, United Kingdom
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240
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Campbell M, Barton IS, Roop RM, Chien P. Comparison of CcrM-dependent methylation in Caulobacter crescentus and Brucella abortus by nanopore sequencing. J Bacteriol 2024; 206:e0008324. [PMID: 38722176 DOI: 10.1128/jb.00083-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 05/21/2024] Open
Abstract
Bacteria rely on DNA methylation for restriction-modification systems and epigenetic control of gene expression. Here, we use direct detection of methylated bases by nanopore sequencing to monitor global DNA methylation in Alphaproteobacteria, where use of this technique has not yet been reported. One representative of this order, Caulobacter crescentus, relies on DNA methylation to control cell cycle progression, but it is unclear whether other members of this order, such as Brucella abortus, depend on the same systems. We addressed these questions by first measuring CcrM-dependent DNA methylation in Caulobacter and showing excellent correlation between nanopore-based detection and previously published results. We then directly measure the impact of Lon-mediated CcrM degradation on the epigenome, verifying that loss of Lon results in pervasive methylation. We also show that the AlkB demethylase has no global impact on DNA methylation during normal growth. Next, we report on the global DNA methylation in B. abortus for the first time and find that CcrM-dependent methylation is reliant on Lon but impacts the two chromosomes differently. Finally, we explore the impact of the MucR transcription factor, known to compete with CcrM methylation, on the Brucella methylome and share the results with a publicly available visualization package. Our work demonstrates the utility of nanopore-based sequencing for epigenome measurements in Alphaproteobacteria and reveals new features of CcrM-dependent methylation in a zoonotic pathogen.IMPORTANCEDNA methylation plays an important role in bacteria, maintaining genome integrity and regulating gene expression. We used nanopore sequencing to directly measure methylated bases in Caulobacter crescentus and Brucella abortus. In Caulobacter, we showed that stabilization of the CcrM methyltransferase upon loss of the Lon protease results in prolific methylation and discovered that the putative methylase AlkB is unlikely to have a global physiological effect. We measured genome-wide methylation in Brucella for the first time, revealing a similar role for CcrM in cell-cycle methylation but a more complex regulation by the Lon protease than in Caulobacter. Finally, we show how the virulence factor MucR impacts DNA methylation patterns in Brucella.
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Affiliation(s)
- Maxwell Campbell
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Ian Scott Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, South Carolina, USA
| | - R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, South Carolina, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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González-López A, Larsson DSD, Koripella RK, Cain BN, Chavez MG, Hergenrother PJ, Sanyal S, Selmer M. Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane. Sci Rep 2024; 14:14253. [PMID: 38902339 PMCID: PMC11190147 DOI: 10.1038/s41598-024-64868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024] Open
Abstract
The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 Å resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 Å resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target.
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Affiliation(s)
- Adrián González-López
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Daniel S D Larsson
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Ravi Kiran Koripella
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, USA
| | - Brett N Cain
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin Garcia Chavez
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden.
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242
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Balák J, Drábová L, Ilko V, Maršík D, Jarošová Kolouchová I. Preliminary Investigation of Fruit Mash Inoculation with Pure Yeast Cultures: A Case of Volatile Profile of Industrial-Scale Plum Distillates. Foods 2024; 13:1955. [PMID: 38928895 PMCID: PMC11202686 DOI: 10.3390/foods13121955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
This study investigates the effect of pure yeast culture fermentation versus spontaneous fermentation on the volatile compound profile of industrially produced plum brandy. Using traditional distillation methods, the evolution of key volatile compounds is monitored at seven different moments during the distillation process. By integrating advanced analytical techniques such as GC-MS and sensory evaluation, significant differences in the composition of the distillates are highlighted, particularly in terms of ethyl esters and higher alcohols which are key to the sensory properties of the final product. Distillates produced with the addition of pure cultures gave higher concentrations of esters than those obtained by wild fermentation. The results of our industrial research show that the most critical step is to limit the storage of the input raw material, thereby reducing the subsequent risk of producing higher concentrations of 1-propanol. Furthermore, our results indicate that the heart of the distillate can only be removed up to an ethanol content of approximately 450 g/L and that the removal of additional ethanol results in only a 10% increase in the total volume of the distillate, which in turn results in an increase in boiler heating costs of approximately 30%.
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Affiliation(s)
- Josef Balák
- Department of Biotechnology, University of Chemistry and Technology, 6 Technická 5, 166 28 Prague, Czech Republic; (J.B.); (D.M.)
| | - Lucie Drábová
- Department of of Food Analysis and Nutrition, University of Chemistry and Technology, 6 Technická 5, 166 28 Prague, Czech Republic; (L.D.); (V.I.)
| | - Vojtěch Ilko
- Department of of Food Analysis and Nutrition, University of Chemistry and Technology, 6 Technická 5, 166 28 Prague, Czech Republic; (L.D.); (V.I.)
| | - Dominik Maršík
- Department of Biotechnology, University of Chemistry and Technology, 6 Technická 5, 166 28 Prague, Czech Republic; (J.B.); (D.M.)
| | - Irena Jarošová Kolouchová
- Department of Biotechnology, University of Chemistry and Technology, 6 Technická 5, 166 28 Prague, Czech Republic; (J.B.); (D.M.)
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243
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Gillieatt BF, Coleman NV. Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. FEMS Microbiol Rev 2024; 48:fuae017. [PMID: 38897736 PMCID: PMC11253441 DOI: 10.1093/femsre/fuae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/09/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024] Open
Abstract
The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.
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Affiliation(s)
- Brodie F Gillieatt
- School of Life and Environmental Sciences, The University of Sydney, F22 - LEES Building, NSW 2006, Australia
| | - Nicholas V Coleman
- School of Natural Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, 6 Wally’s Walk, Macquarie Park, NSW 2109, Australia
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244
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Yeter-Alat H, Belgareh-Touzé N, Le Saux A, Huvelle E, Mokdadi M, Banroques J, Tanner NK. The RNA Helicase Ded1 from Yeast Is Associated with the Signal Recognition Particle and Is Regulated by SRP21. Molecules 2024; 29:2944. [PMID: 38931009 PMCID: PMC11206880 DOI: 10.3390/molecules29122944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The DEAD-box RNA helicase Ded1 is an essential yeast protein involved in translation initiation that belongs to the DDX3 subfamily. The purified Ded1 protein is an ATP-dependent RNA-binding protein and an RNA-dependent ATPase, but it was previously found to lack substrate specificity and enzymatic regulation. Here we demonstrate through yeast genetics, yeast extract pull-down experiments, in situ localization, and in vitro biochemical approaches that Ded1 is associated with, and regulated by, the signal recognition particle (SRP), which is a universally conserved ribonucleoprotein complex required for the co-translational translocation of polypeptides into the endoplasmic reticulum lumen and membrane. Ded1 is physically associated with SRP components in vivo and in vitro. Ded1 is genetically linked with SRP proteins. Finally, the enzymatic activity of Ded1 is inhibited by SRP21 in the presence of SCR1 RNA. We propose a model where Ded1 actively participates in the translocation of proteins during translation. Our results provide a new understanding of the role of Ded1 during translation.
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Affiliation(s)
- Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Naïma Belgareh-Touzé
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226 CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France;
| | - Agnès Le Saux
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology, LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis 1002, Tunisia
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, Tunis 1080, Tunisia
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
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245
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Kim YM, Son JY, Ahn DK. Botulinum toxin type A is a potential therapeutic drug for chronic orofacial pain. J Oral Biosci 2024:S1349-0079(24)00141-5. [PMID: 38908515 DOI: 10.1016/j.job.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND Botulinum toxin type A (BTX-A), produced by the gram-positive anaerobic bacterium Clostridium botulinum, acts by cleaving synaptosome-associated protein-25 (SNAP-25), an essential component of the presynaptic neuronal membrane that is necessary for fusion with the membrane proteins of neurotransmitter-containing vesicles. Recent studies have highlighted the efficacy of BTX-A in treating chronic pain conditions, including lower back pain, chronic neck pain, neuropathic pain, and trigeminal neuralgia, particularly when patients are unresponsive to traditional painkillers. This review focuses on the analgesic effects of BTX-A in various chronic pain conditions, with a particular emphasis on the orofacial region. HIGHLIGHT This review focuses on the mechanisms by which BTX-A induces analgesia in patients with inflammatory and temporomandibular joint pain. This review also highlights the fact that BTX-A can effectively manage neuropathic pain and trigeminal neuralgia, which are difficult-to-treat chronic pain conditions. Herein, we present a comprehensive assessment of the central analgesic effects of BTX-A and a discussion of its various applications in clinical dental practice. CONCLUSION BTX-A is an approved treatment option for various chronic pain conditions. Although there is evidence of axonal transport of BTX-A from peripheral to central endings in motor neurons, the precise mechanism underlying its pain-modulating effects remains unclear. This review discusses the evidence supporting the effectiveness of BTX-A in controlling chronic pain conditions in the orofacial region. BTX-A is a promising therapeutic agent for treating pain conditions that do not respond to conventional analgesics.
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Affiliation(s)
- Yu Mi Kim
- Department of Oral Physiology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Jo Young Son
- Department of Oral Physiology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Dong Kuk Ahn
- Department of Oral Physiology, School of Dentistry, Kyungpook National University, Daegu, Korea.
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246
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Sharma D, Chetri PB, Ranga V, Sen S, Sarmah BK, Barooah M. Genomic analysis of acid tolerance genes and deciphering the function of ydaG gene in mitigating acid tolerance in Priestia megaterium. Front Microbiol 2024; 15:1414777. [PMID: 38966390 PMCID: PMC11222612 DOI: 10.3389/fmicb.2024.1414777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P. megaterium, shedding light on potential applications in agriculture and industry.
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Affiliation(s)
- Darshana Sharma
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Purna Bahadur Chetri
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Vipin Ranga
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Subhajit Sen
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Bidyut Kumar Sarmah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Madhumita Barooah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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247
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Khairunnisa Z, Tuygunov N, Cahyanto A, Aznita WH, Purwasena IA, Noor NSM, Azami NH, Zakaria MN. Potential of microbial-derived biosurfactants for oral applications-a systematic review. BMC Oral Health 2024; 24:707. [PMID: 38898470 PMCID: PMC11186162 DOI: 10.1186/s12903-024-04479-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Biosurfactants are amphiphilic compounds produced by various microorganisms. Current research evaluates diverse types of biosurfactants against a range of oral pathogens. OBJECTIVES This systematic review aims to explore the potential of microbial-derived biosurfactants for oral applications. METHODOLOGY A systematic literature search was performed utilizing PubMed-MEDLINE, Scopus, and Web of Science databases with designated keywords. The results were registered in the PROSPERO database and conducted following the PRISMA checklist. Criteria for eligibility, guided by the PICOS framework, were established for both inclusion and exclusion criteria. The QUIN tool was used to assess the bias risk for in vitro dentistry studies. RESULTS Among the initial 357 findings, ten studies were selected for further analysis. The outcomes of this systematic review reveal that both crude and purified forms of biosurfactants exhibit antimicrobial and antibiofilm properties against various oral pathogens. Noteworthy applications of biosurfactants in oral products include mouthwash, toothpaste, and implant coating. CONCLUSION Biosurfactants have garnered considerable interest and demonstrated their potential for application in oral health. This is attributed to their surface-active properties, antiadhesive activity, biodegradability, and antimicrobial effectiveness against a variety of oral microorganisms, including bacteria and fungi.
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Affiliation(s)
- Z Khairunnisa
- Department of Restorative Dentistry, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
- Department of Oral Biology, Faculty of Dentistry, University of Jenderal Achmad Yani, Cimahi, 40525, Indonesia
| | - N Tuygunov
- Department of Restorative Dentistry, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - A Cahyanto
- Department of Restorative Dentistry, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - W H Aznita
- Department of Oral & Craniofacial Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - I A Purwasena
- Department of Microbiology, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - N S M Noor
- Department of Restorative Dentistry, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - N H Azami
- Department of Restorative Dentistry, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - M N Zakaria
- Department of Restorative Dentistry, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
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Higueras C, Sainz Á, García-Sancho M, Rodríguez-Franco F, Rey AI. Faecal Short-Chain, Long-Chain, and Branched-Chain Fatty Acids as Markers of Different Chronic Inflammatory Enteropathies in Dogs. Animals (Basel) 2024; 14:1825. [PMID: 38929444 PMCID: PMC11201139 DOI: 10.3390/ani14121825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/28/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Chronic inflammatory enteropathies (CIEs) are classified based on treatment trials, and new methods are being sought for earlier differentiation and characterization. Giardia infection (GIA) is one of the first differential diagnoses and may be present in CIE-affected dogs. The aim of this study was to evaluate the faecal characteristics and faecal fatty acid profile (short, medium, long, and branched-chain fatty acids) in dogs with food-responsive enteropathy (FRE), immunosuppressant-responsive enteropathy (IRE), and dogs infected with Giardia compared to healthy control (HC) animals as a potential non-invasive indicator of intestinal health that helps in the differentiation of CIEs. The C16:1n-7 percentage (p = 0.0001) and C16:1n-7/C16:0 ratio (p = 0.0001) served to differentiate between HC, FRE, and IRE. IRE dogs presented lower levels of short-chain fatty acids (∑SCFAs) (p = 0.0008) and acetic acid (C2) (p = 0.0007) compared to the other three groups and lower propionic acid (C3) (p = 0.0022) compared to HCs. IRE and GIA presented higher faecal fat content (p = 0.0080) and ratio of iso/anteiso branched-chain fatty acids (BCFAs) compared to HC and FRE. Correlations between some fatty acids and desaturation indices with the canine inflammatory bowel disease activity index and faecal characteristics were observed, suggesting that these compounds could play an important role in the pathogenesis of these diseases.
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Affiliation(s)
- Cristina Higueras
- Department of Animal Production, Animal Nutrition, College of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Ángel Sainz
- Department of Animal Medicine and Surgery, College of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain; (Á.S.)
| | - Mercedes García-Sancho
- Department of Animal Medicine and Surgery, College of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain; (Á.S.)
| | - Fernando Rodríguez-Franco
- Department of Animal Medicine and Surgery, College of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain; (Á.S.)
| | - Ana I. Rey
- Department of Animal Production, Animal Nutrition, College of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
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Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024; 15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
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Affiliation(s)
- Emanuel Lange
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Lena Kranert
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jacob Krüger
- Engineering of Software-Intensive Systems, Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dirk Benndorf
- Applied Biosciences and Bioprocess Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Robert Heyer
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional Omics Data Analysis, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Jeong S, Singh H, Jung JH, Jung KW, Ryu S, Lim S. Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains. Front Microbiol 2024; 15:1410024. [PMID: 38962131 PMCID: PMC11219805 DOI: 10.3389/fmicb.2024.1410024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024] Open
Abstract
The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/β hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.
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Affiliation(s)
- Soyoung Jeong
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, India
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Kwang-Woo Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sangyong Lim
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, Republic of Korea
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