1
|
Kerfahi D, Dong K, Tripathi B, Adams JM. Global comparison shows that soil bacterial communities in extreme pH soils are more structured by deterministic processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173662. [PMID: 38830413 DOI: 10.1016/j.scitotenv.2024.173662] [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: 12/12/2023] [Revised: 05/12/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
A major aim of microbial ecology is the search for basic 'rules' that dominate variation in microbial communities. An earlier comparison of several soil successional series showed that pH explained variation in the relative importance of stochastic versus deterministic processes in bacterial communities. In neutral pH soils, bacterial communities were more strongly influenced by stochastic processes than in low or high pH soils. Here, we took a broad level approach to attempt a more definitive answer of whether soil pH dominates bacterial community structuring using the global database of 237 samples. The beta-NTI showed that at both a global and continental scale, samples with low pH were dominated by deterministic processes, while in samples at around neutral pH, stochastic processes dominated. At high pH, stochasticity dominated on the global scale, but on several continents, the beta-NTI showed determinism predominating. Overall, it appears that bacterial community structuring is strongly and predictably affected by pH, with the most consistent difference observed between determinism at low pH and stochasticity at neutral pH. There is a need for hypothesis testing to explain why this trend exists. It is possible that at low pH, there is a greater selection for consortia to exploit resources, which leads to more predictable, deterministic combinations of species co-occurring. Additionally, the high energy demands for homeostasis and the constraints from the lack of available nutrient resources may impose greater niche-based competition, resulting in more deterministic community structuring at low pH.
Collapse
Affiliation(s)
- Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu 42601, Republic of Korea
| | - Ke Dong
- Department of Life Science, Kyonggi University, Suwon-si 16227, Republic of Korea
| | - Binu Tripathi
- Division of Plant and Soil Sciences, West Virginia University, United States of America.
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing 210008, China.
| |
Collapse
|
2
|
Gavriil A, Giannenas I, Skandamis PN. A current insight into Salmonella's inducible acid resistance. Crit Rev Food Sci Nutr 2024:1-21. [PMID: 39014992 DOI: 10.1080/10408398.2024.2373387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Salmonella is a diverse and ubiquitous group of bacteria and a major zoonotic pathogen implicated in several foodborne disease outbreaks worldwide. With more than 2500 distinct serotypes, this pathogen has evolved to survive in a wide spectrum of environments and across multiple hosts. The primary and most common source of transmission is through contaminated food or water. Although the main sources have been primarily linked to animal-related food products, outbreaks due to the consumption of contaminated plant-related food products have increased in the last few years. The perceived ability of Salmonella to trigger defensive mechanisms following pre-exposure to sublethal acid conditions, namely acid adaptation, has renewed a decade-long attention. The impact of acid adaptation on the subsequent resistance against lethal factors of the same or multiple stresses has been underscored by multiple studies. Α plethora of studies have been published, aiming to outline the factors that- alone or in combination- can impact this phenomenon and to unravel the complex networking mechanisms underlying its induction. This review aims to provide a current and updated insight into the factors and mechanisms that rule this phenomenon.
Collapse
Affiliation(s)
- Alkmini Gavriil
- Department of Natural Resources Management and Agricultural Engineering, Agricultural University of Athens, Athens, Greece
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Ilias Giannenas
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis N Skandamis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| |
Collapse
|
3
|
Rizo J, Encarnación-Guevara S. Bacterial protein acetylation: mechanisms, functions, and methods for study. Front Cell Infect Microbiol 2024; 14:1408947. [PMID: 39027134 PMCID: PMC11254643 DOI: 10.3389/fcimb.2024.1408947] [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: 03/29/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Lysine acetylation is an evolutionarily conserved protein modification that changes protein functions and plays an essential role in many cellular processes, such as central metabolism, transcriptional regulation, chemotaxis, and pathogen virulence. It can alter DNA binding, enzymatic activity, protein-protein interactions, protein stability, or protein localization. In prokaryotes, lysine acetylation occurs non-enzymatically and by the action of lysine acetyltransferases (KAT). In enzymatic acetylation, KAT transfers the acetyl group from acetyl-CoA (AcCoA) to the lysine side chain. In contrast, acetyl phosphate (AcP) is the acetyl donor of chemical acetylation. Regardless of the acetylation type, the removal of acetyl groups from acetyl lysines occurs only enzymatically by lysine deacetylases (KDAC). KATs are grouped into three main superfamilies based on their catalytic domain sequences and biochemical characteristics of catalysis. Specifically, members of the GNAT are found in eukaryotes and prokaryotes and have a core structural domain architecture. These enzymes can acetylate small molecules, metabolites, peptides, and proteins. This review presents current knowledge of acetylation mechanisms and functional implications in bacterial metabolism, pathogenicity, stress response, translation, and the emerging topic of protein acetylation in the gut microbiome. Additionally, the methods used to elucidate the biological significance of acetylation in bacteria, such as relative quantification and stoichiometry quantification, and the genetic code expansion tool (CGE), are reviewed.
Collapse
Affiliation(s)
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
4
|
Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. Annu Rev Biophys 2024; 53:487-510. [PMID: 38382113 DOI: 10.1146/annurev-biophys-030822-032215] [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: 02/23/2024]
Abstract
Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.
Collapse
Affiliation(s)
- Wei-Chang Lo
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | | | - Teuta Pilizota
- School of Biological Sciences, Centre for Engineering Biology, University of Edinburgh, Edinburgh, United Kingdom;
| |
Collapse
|
5
|
Steuber J, Fritz G. The Na +-translocating NADH:quinone oxidoreductase (Na +-NQR): Physiological role, structure and function of a redox-driven, molecular machine. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149485. [PMID: 38955304 DOI: 10.1016/j.bbabio.2024.149485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
Many bacterial processes are powered by the sodium motive force (smf) and in case of pathogens, the smf contributes to virulence. Vibrio cholerae, the causative agent of Cholera disease, possesses a Na+-translocating NADH:quinone oxidoreductase (NQR), a six-subunit membrane protein assembly. The 3D structure of NQR revealed the arrangement of the six subunits NqrABCDEF, the position of all redox cofactors (four flavins, two [2Fe-2S] centers) and the binding sites for the substrates NADH (in NqrF) and ubiquinone (in NqrB). Upon oxidation of NADH, electrons are shuttled twice across the membrane, starting with cytoplasmic FADNqrF and electron transfer to the [2Fe2S] clusterNqrF and from there to an intra-membranous [2Fe-2S] clusterNqrDE, periplasmic FMNNqrC, FMNNqrB and from there to riboflavinNqrB. This riboflavin is located at the cytoplasmic entry site of the sodium channel in NqrB, and it donates electrons to ubiquinone-8 positioned at the cytoplasmic side of NqrB. Targeting the substrate binding sites of NQR is a promising strategy to identify new inhibitors against many bacterial pathogens. Detailed structural information on the binding mode of natural inhibitors and small molecules in the active sites of NQR is now available, paving the way for the development of new antibiotics. The NQR shows different conformations as revealed in recent cryo-EM and crystallographic studies combined with spectroscopic analyses. These conformations represent distinct steps in the catalytic cycle. Considering the structural and functional data available, we propose a mechanism of Na+-NQR based on conformational coupling of electron transfer and Na+ translocation reaction steps.
Collapse
Affiliation(s)
- Julia Steuber
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany.
| | - Günter Fritz
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany.
| |
Collapse
|
6
|
Bhakta K, Roy M, Samanta S, Ghosh A. Functional diversity in archaeal Hsp60: a molecular mosaic of Group I and Group II chaperonin. FEBS J 2024. [PMID: 38923213 DOI: 10.1111/febs.17213] [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: 02/19/2024] [Revised: 05/23/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
External stress disrupts the balance of protein homeostasis, necessitating the involvement of heat shock proteins (Hsps) in restoring equilibrium and ensuring cellular survival. The thermoacidophilic crenarchaeon Sulfolobus acidocaldarius, lacks the conventional Hsp100, Hsp90, and Hsp70, relying solely on a single ATP-dependent Group II chaperonin, Hsp60, comprising three distinct subunits (α, β, and γ) to refold unfolded substrates and maintain protein homeostasis. Hsp60 forms three different complexes, namely Hsp60αβγ, Hsp60αβ, and Hsp60β, at temperatures of 60 °C, 75 °C, and 90 °C, respectively. This study delves into the intricacies of Hsp60 complexes in S. acidocaldarius, uncovering their ability to form oligomeric structures in the presence of ATP. The recognition of substrates by Hsp60 involves hydrophobic interactions, and the subsequent refolding process occurs in an ATP-dependent manner through charge-driven interactions. Furthermore, the Hsp60β homo-oligomeric complex can protect the archaeal and eukaryotic membrane from stress-induced damage. Hsp60 demonstrates nested cooperativity in ATP hydrolysis activity, where MWC-type cooperativity is nested within KNF-type cooperativity. Remarkably, during ATP hydrolysis, Hsp60β, and Hsp60αβ complexes exhibit a mosaic behavior, aligning with characteristics observed in both Group I and Group II chaperonins, adding a layer of complexity to their functionality.
Collapse
Affiliation(s)
- Koustav Bhakta
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Mousam Roy
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Shirsha Samanta
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Abhrajyoti Ghosh
- Department of Biological Sciences, Bose Institute, Kolkata, India
| |
Collapse
|
7
|
Jasinska W, Dindo M, Cordoba SMC, Serohijos AWR, Laurino P, Brotman Y, Bershtein S. Non-consecutive enzyme interactions within TCA cycle supramolecular assembly regulate carbon-nitrogen metabolism. Nat Commun 2024; 15:5285. [PMID: 38902266 PMCID: PMC11189929 DOI: 10.1038/s41467-024-49646-7] [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: 11/29/2023] [Accepted: 06/14/2024] [Indexed: 06/22/2024] Open
Abstract
Enzymes of the central metabolism tend to assemble into transient supramolecular complexes. However, the functional significance of the interactions, particularly between enzymes catalyzing non-consecutive reactions, remains unclear. Here, by co-localizing two non-consecutive enzymes of the TCA cycle from Bacillus subtilis, malate dehydrogenase (MDH) and isocitrate dehydrogenase (ICD), in phase separated droplets we show that MDH-ICD interaction leads to enzyme agglomeration with a concomitant enhancement of ICD catalytic rate and an apparent sequestration of its reaction product, 2-oxoglutarate. Theory demonstrates that MDH-mediated clustering of ICD molecules explains the observed phenomena. In vivo analyses reveal that MDH overexpression leads to accumulation of 2-oxoglutarate and reduction of fluxes flowing through both the catabolic and anabolic branches of the carbon-nitrogen intersection occupied by 2-oxoglutarate, resulting in impeded ammonium assimilation and reduced biomass production. Our findings suggest that the MDH-ICD interaction is an important coordinator of carbon-nitrogen metabolism.
Collapse
Affiliation(s)
- Weronika Jasinska
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mirco Dindo
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Medicine and Surgery, Section of Physiology and Biochemistry, University of Perugia, Perugia, Italy
| | - Sandra M C Cordoba
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Adrian W R Serohijos
- Departement de Biochimie, Universite de Montreal, Quebec, Canada
- Centre Robert-Cedergren en Bio-informatique et Genomique, Universite de Montreal, Quebec, Canada
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Institute for Protein Research, Osaka University, Suita, Japan.
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| |
Collapse
|
8
|
Besteman MS, Doloman A, Sousa DZ. Transcriptomic evidence for an energetically advantageous relationship between Syntrophomonas wolfei and Methanothrix soehngenii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13276. [PMID: 38733087 PMCID: PMC11087674 DOI: 10.1111/1758-2229.13276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Syntrophic interactions are key in anaerobic food chains, facilitating the conversion of complex organic matter into methane. A typical example involves acetogenic bacteria converting fatty acids (e.g., butyrate and propionate), a process thermodynamically reliant on H2 consumption by microorganisms such as methanogens. While most studies focus on H2-interspecies transfer between these groups, knowledge on acetate cross-feeding in anaerobic systems is lacking. This study investigated butyrate oxidation by co-cultures of Syntrophomonas wolfei and Methanospirillum hungatei, both with and without the addition of the acetate scavenger Methanothrix soehngenii. Growth and gene expression patterns of S. wolfei and M. hungatei were followed in the two conditions. Although butyrate consumption rates remained constant, genes in the butyrate degradation pathway of S. wolfei were less expressed in the presence of M. soehngenii, including genes involved in reverse electron transport. Higher expression of a type IV-pili operon in S. wolfei hints to the potential for direct interspecies electron transfer between S. wolfei and M. soehngenii and an energetically advantageous relationship between the two microorganisms. Overall, the presence of the acetate scavenger M. soehngenii positively influenced the energy metabolism of S. wolfei and highlighted the relevance of including acetate scavengers when investigating syntrophic fatty acid degradation.
Collapse
Affiliation(s)
- Maaike S. Besteman
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Anna Doloman
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
- Centre for Living TechnologiesEWUU AllianceUtrechtThe Netherlands
| |
Collapse
|
9
|
Li J, Li Y, Koide A, Kuang H, Torres VJ, Koide S, Wang DN, Traaseth NJ. Proton-coupled transport mechanism of the efflux pump NorA. Nat Commun 2024; 15:4494. [PMID: 38802368 PMCID: PMC11130294 DOI: 10.1038/s41467-024-48759-3] [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: 11/10/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Efflux pump antiporters confer drug resistance to bacteria by coupling proton import with the expulsion of antibiotics from the cytoplasm. Despite efforts there remains a lack of understanding as to how acid/base chemistry drives drug efflux. Here, we uncover the proton-coupling mechanism of the Staphylococcus aureus efflux pump NorA by elucidating structures in various protonation states of two essential acidic residues using cryo-EM. Protonation of Glu222 and Asp307 within the C-terminal domain stabilized the inward-occluded conformation by forming hydrogen bonds between the acidic residues and a single helix within the N-terminal domain responsible for occluding the substrate binding pocket. Remarkably, deprotonation of both Glu222 and Asp307 is needed to release interdomain tethering interactions, leading to opening of the pocket for antibiotic entry. Hence, the two acidic residues serve as a "belt and suspenders" protection mechanism to prevent simultaneous binding of protons and drug that enforce NorA coupling stoichiometry and confer antibiotic resistance.
Collapse
Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, New York, NY, USA
| | - Yan Li
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Huihui Kuang
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
| | | |
Collapse
|
10
|
Versluis DM, Schoemaker R, Looijesteijn E, Geurts JM, Merks RM. 2'-Fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations. iScience 2024; 27:109085. [PMID: 38380251 PMCID: PMC10877688 DOI: 10.1016/j.isci.2024.109085] [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: 04/25/2023] [Revised: 11/16/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
A reduced capacity for butyrate production by the early infant gut microbiota is associated with negative health effects, such as inflammation and the development of allergies. Here, we develop new hypotheses on the effect of the prebiotic galacto-oligosaccharides (GOS) or 2'-fucosyllactose (2'-FL) on butyrate production by the infant gut microbiota using a multiscale, spatiotemporal mathematical model of the infant gut. The model simulates a community of cross-feeding gut bacteria in metabolic detail. It represents the community as a grid of bacterial populations that exchange metabolites, using 20 different subspecies-specific metabolic networks taken from the AGORA database. The simulations predict that both GOS and 2'-FL promote the growth of Bifidobacterium, whereas butyrate producing bacteria are only consistently abundant in the presence of propane-1,2-diol, a product of 2'-FL metabolism. In absence of prebiotics or in presence of only GOS, however, Bacteroides vulgatus and Cutibacterium acnes outcompete butyrate producers by consuming intermediate metabolites.
Collapse
Affiliation(s)
- David M. Versluis
- Leiden University, Institute of Biology, 2300 RA Leiden, the Netherlands
| | | | | | | | - Roeland M.H. Merks
- Leiden University, Institute of Biology, 2300 RA Leiden, the Netherlands
- Leiden University, Mathematical Institute, 2300 RA Leiden, the Netherlands
| |
Collapse
|
11
|
Ullrich SR, Fuchs H, Ashworth-Güth C. Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level. Front Microbiol 2024; 15:1357152. [PMID: 38384274 PMCID: PMC10879576 DOI: 10.3389/fmicb.2024.1357152] [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: 12/17/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
The tendency of the periplasmic redox proteins in acidophiles to have more positive redox potentials (Em) than their homologous counterparts in neutrophiles suggests an adaptation to acidic pH at protein level, since thermodynamics of electron transfer processes are also affected by acidic pH. Since this conclusion is mainly based on the electrochemical characterization of redox proteins from extreme acidophiles of the genus Acidithiobacillus, we aimed to characterize three recombinant redox proteins of the more moderate acidophile Ferrovum sp. PN-J47-F6. We applied protein film voltammetry and linear sweep voltammetry coupled to UV/Vis spectroscopy to characterize the redox behavior of HiPIP-41, CytC-18, and CytC-78, respectively. The Em-values of HiPIP-41 (571 ± 16 mV), CytC-18 (276 ± 8 mV, 416 ± 2 mV), and CytC-78 (308 ± 7 mV, 399 ± 7 mV) were indeed more positive than those of homologous redox proteins in neutrophiles. Moreover, our findings suggest that the adaptation of redox proteins with respect to their Em occurs more gradually in response to the pH, since there are also differences between moderate and more extreme acidophiles. In order to address structure function correlations in these redox proteins with respect to structural features affecting the Em, we conducted a comparative structural analysis of the Ferrovum-derived redox proteins and homologs of Acidithiobacillus spp. and neutrophilic proteobacteria. Hydrophobic contacts in the redox cofactor binding pockets resulting in a low solvent accessibility appear to be the major factor contributing to the more positive Em-values in acidophile-derived redox proteins. While additional cysteines in HiPIPs of acidophiles might increase the effective shielding of the [4Fe-4S]-cofactor, the tight shielding of the heme centers in acidophile-derived cytochromes is achieved by a drastic increase in hydrophobic contacts (A.f. Cyc41), and by a larger fraction of aromatic residues in the binding pockets (CytC-18, CytC-78).
Collapse
Affiliation(s)
- Sophie R. Ullrich
- Environmental Microbiology Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
- Biohydrometallurgy Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Helena Fuchs
- Biohydrometallurgy Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Charlotte Ashworth-Güth
- Salt and Mineral Chemistry Group, Institute for Inorganic Chemistry, TU Bergakademie Freiberg, Freiberg, Germany
| |
Collapse
|
12
|
Egas RA, Sahonero-Canavesi DX, Bale NJ, Koenen M, Yildiz Ç, Villanueva L, Sousa DZ, Sánchez-Andrea I. Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans. Environ Microbiol 2024; 26:e16565. [PMID: 38356112 DOI: 10.1111/1462-2920.16565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024]
Abstract
Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.
Collapse
Affiliation(s)
- Reinier A Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Çağlar Yildiz
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Environmental Sciences and Sustainability Department, Science & Technology School, IE University, Segovia, Spain
| |
Collapse
|
13
|
Fujikawa T, Sasamoto T, Zhao F, Yamagishi A, Akanuma S. Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat. Sci Rep 2024; 14:398. [PMID: 38172176 PMCID: PMC10764835 DOI: 10.1038/s41598-023-50828-4] [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: 05/22/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.
Collapse
Affiliation(s)
- Takayuki Fujikawa
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Takahiro Sasamoto
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Fangzheng Zhao
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan.
| |
Collapse
|
14
|
Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K. Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress. mSystems 2023; 8:e0103723. [PMID: 37909716 PMCID: PMC10746267 DOI: 10.1128/msystems.01037-23] [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] [Received: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.
Collapse
Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| |
Collapse
|
15
|
Thangaraj S, Kim HR, Heo JM, Son S, Ryu J, Park JW, Kim JH, Kim SY, Jung HK, Kim IN. Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean. MARINE POLLUTION BULLETIN 2023; 196:115569. [PMID: 37922593 DOI: 10.1016/j.marpolbul.2023.115569] [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: 04/10/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023]
Abstract
Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.
Collapse
Affiliation(s)
- Satheeswaran Thangaraj
- Department of Marine Science, Incheon National University, Incheon, South Korea; Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel; Interuniversity Institute for Marine Sciences, Eilat, Israel; Department of Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Hyo-Ryeon Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jang-Mu Heo
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Seunghyun Son
- Cooperative Institute for Satellite Earth System Studies (CISESS) / Earth System Science Interdisciplinary Center (ESSIC), University of Maryland, USA
| | - Jongseong Ryu
- Department of Marine Biotechnology, Anyang University, Incheon, South Korea
| | - Jong-Woo Park
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan, South Korea
| | - Ju-Hyoung Kim
- Department of Aquaculture and Aquatic Science, Kunsan National University, Gunsan, South Korea
| | - Seo-Young Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Hae-Kun Jung
- Environment and Fisheries Resources Research Division, East Sea Fisheries Institute, National Institute of Fisheries Science, Gangneung, South Korea
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea.
| |
Collapse
|
16
|
Alwraikat A, Jaradat A, Marji SM, Bayan MF, Alomari E, Naser AY, Alyami MH. Development of a Novel, Ecologically Friendly Generation of pH-Responsive Alginate Nanosensors: Synthesis, Calibration, and Characterisation. SENSORS (BASEL, SWITZERLAND) 2023; 23:8453. [PMID: 37896546 PMCID: PMC10610811 DOI: 10.3390/s23208453] [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: 08/22/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Measurement of the intracellular pH is particularly crucial for the detection of numerous diseases, such as carcinomas, that are characterised by a low intracellular pH. Therefore, pH-responsive nanosensors have been developed by many researchers due to their ability to non-invasively detect minor changes in the pH of many biological systems without causing significant biological damage. However, the existing pH-sensitive nanosensors, such as the polyacrylamide, silica, and quantum dots-based nanosensors, require large quantities of organic solvents that could cause detrimental damage to the ecosystem. As a result, this research is aimed at developing a new generation of pH-responsive nanosensors comprising alginate natural polymers and pH-sensitive fluorophores using an organic, solvent-free, and ecologically friendly method. Herein, we successfully synthesised different models of pH-responsive alginate nanoparticles by varying the method of fluorophore conjugation. The synthesised pH nanosensors demonstrated a low MHD with a relatively acceptable PDI when using the lowest concentration of the cross-linker Ca+2 (1.25 mM). All the pH nanosensors showed negative zeta potential values, attributed to the free carboxylate groups surrounding the nanoparticles' surfaces, which support the colloidal stability of the nanosensors. The synthesised models of pH nanosensors displayed a high pH-responsiveness with various correlations between the pH measurements and the nanosensors' fluorescence signal. In summation, pH-responsive alginate nanosensors produced using organic, solvent-free, green technology could be harnessed as potential diagnostics for the intracellular and extracellular pH measurements of various biological systems.
Collapse
Affiliation(s)
- Abdalaziz Alwraikat
- Department of Applied Pharmaceutical Sciences and Clinical Pharmacy, Faculty of Pharmacy, Isra University, P.O. Box 33, Amman 11622, Jordan; (A.A.); (A.J.); (E.A.); (A.Y.N.)
| | - Abdolelah Jaradat
- Department of Applied Pharmaceutical Sciences and Clinical Pharmacy, Faculty of Pharmacy, Isra University, P.O. Box 33, Amman 11622, Jordan; (A.A.); (A.J.); (E.A.); (A.Y.N.)
| | - Saeed M. Marji
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan; (S.M.M.); (M.F.B.)
| | - Mohammad F. Bayan
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan; (S.M.M.); (M.F.B.)
| | - Esra’a Alomari
- Department of Applied Pharmaceutical Sciences and Clinical Pharmacy, Faculty of Pharmacy, Isra University, P.O. Box 33, Amman 11622, Jordan; (A.A.); (A.J.); (E.A.); (A.Y.N.)
| | - Abdallah Y. Naser
- Department of Applied Pharmaceutical Sciences and Clinical Pharmacy, Faculty of Pharmacy, Isra University, P.O. Box 33, Amman 11622, Jordan; (A.A.); (A.J.); (E.A.); (A.Y.N.)
| | - Mohammad H. Alyami
- Department of Pharmaceutics, College of Pharmacy, Najran University, Najran 66462, Saudi Arabia
| |
Collapse
|
17
|
Rebelo A, Almeida A, Peixe L, Antunes P, Novais C. Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2023; 12:1474. [PMID: 37760770 PMCID: PMC10525130 DOI: 10.3390/antibiotics12091474] [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: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.
Collapse
Affiliation(s)
- Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| |
Collapse
|
18
|
Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol 2023; 14:1219779. [PMID: 37649629 PMCID: PMC10465181 DOI: 10.3389/fmicb.2023.1219779] [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: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.
Collapse
Affiliation(s)
- Beverly K. Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Kiel University, Kiel, Germany
| | - Öykü Z. Mete
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Erin M. Eggleston
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
| |
Collapse
|
19
|
Ni G, Leung PM, Daebeler A, Guo J, Hu S, Cook P, Nicol GW, Daims H, Greening C. Nitrification in acidic and alkaline environments. Essays Biochem 2023; 67:753-768. [PMID: 37449414 PMCID: PMC10427799 DOI: 10.1042/ebc20220194] [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: 03/31/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.
Collapse
Affiliation(s)
- Gaofeng Ni
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Anne Daebeler
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Perran Cook
- School of Chemistry, Monash University, Melbourne, Victoria, Australia
| | - Graeme W Nicol
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134 Ecully, France
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Securing Antarctica's Environmental Future, Monash University, Melbourne, Victoria, Australia
- Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
20
|
Benyamin MS, Perisin MP, Hellman CA, Schwalm ND, Jahnke JP, Sund CJ. Modeling control and transduction of electrochemical gradients in acid-stressed bacteria. iScience 2023; 26:107140. [PMID: 37404371 PMCID: PMC10316662 DOI: 10.1016/j.isci.2023.107140] [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: 09/15/2022] [Revised: 03/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Transmembrane electrochemical gradients drive solute uptake and constitute a substantial fraction of the cellular energy pool in bacteria. These gradients act not only as "homeostatic contributors," but also play a dynamic and keystone role in several bacterial functions, including sensing, stress response, and metabolism. At the system level, multiple gradients interact with ion transporters and bacterial behavior in a complex, rapid, and emergent manner; consequently, experiments alone cannot untangle their interdependencies. Electrochemical gradient modeling provides a general framework to understand these interactions and their underlying mechanisms. We quantify the generation, maintenance, and interactions of electrical, proton, and potassium potential gradients under lactic acid-stress and lactic acid fermentation. Further, we elucidate a gradient-mediated mechanism for intracellular pH sensing and stress response. We demonstrate that this gradient model can yield insights on the energetic limitations of membrane transport, and can predict bacterial behavior across changing environments.
Collapse
Affiliation(s)
- Marcus S. Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Matthew P. Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Caleb A. Hellman
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Nathan D. Schwalm
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Justin P. Jahnke
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Christian J. Sund
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| |
Collapse
|
21
|
Fathinejad F, Ghafouri H, Barzegari E, Sarikhan S, Alizadeh A, Howard N. Gene cloning and characterization of a novel recombinant 40-kDa heat shock protein from Mesobacillus persicus B48. World J Microbiol Biotechnol 2023; 39:248. [PMID: 37436487 DOI: 10.1007/s11274-023-03693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
The present study reports the recognition and characterization of the gene encoding the co-chaperone DnaJ in the halophilic strain Mesobacillus persicus B48. The new extracted gene was sequenced and cloned in E. coli, followed by protein purification using a C-terminal His-tag. The stability and function of the recombinant DnaJ protein under salt and pH stress conditions were evaluated. SDS-PAGE revealed a band on nearly 40-kDa region. The homology model structure of new DnaJ demonstrated 56% similarity to the same protein from Streptococcus pneumonia. Fluorescence spectra indicated several hydrophobic residues located on the protein surface, which is consistent with the misfolded polypeptide recognition function of DnaJ. Spectroscopic results showed 56% higher carbonic anhydrase activity in the presence of the recombinant DnaJ homolog compared to its absence. In addition, salt resistance experiments showed that the survival of recombinant E. coli+DnaJ was 2.1 times more than control cells in 0.5 M NaCl. Furthermore, the number of recombinant E. coli BL21+DnaJ colonies was 7.7 times that of the control colonies in pH 8.5. Based on the results, DnaJ from the M. persicus can potentially be employed for improving the functional features of enzymes and other proteins in various applications.
Collapse
Affiliation(s)
- Fatemeh Fathinejad
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Hossein Ghafouri
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran.
- Department of Marine Sciences, The Caspian Sea Basin Research Center, University of Guilan, Rasht, Iran.
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajjad Sarikhan
- Molecular Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Arghavan Alizadeh
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Newton Howard
- Nuffield Department of Surgical Science, University of Oxford, Oxford, UK
| |
Collapse
|
22
|
Yu F, Luo W, Xie W, Li Y, Liu Y, Ye X, Peng T, Wang H, Huang T, Hu Z. The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms. CHEMOSPHERE 2023; 325:138412. [PMID: 36925001 DOI: 10.1016/j.chemosphere.2023.138412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.
Collapse
Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Yongjin Liu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China.
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong Province, China.
| |
Collapse
|
23
|
Jurdzinski KT, Mehrshad M, Delgado LF, Deng Z, Bertilsson S, Andersson AF. Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity. SCIENCE ADVANCES 2023; 9:eadg2059. [PMID: 37235649 PMCID: PMC10219603 DOI: 10.1126/sciadv.adg2059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.
Collapse
Affiliation(s)
- Krzysztof T. Jurdzinski
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luis Fernando Delgado
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ziling Deng
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| |
Collapse
|
24
|
Wang Y, Wang Y, Zhang Q, Fan H, Wang X, Wang J, Zhou Y, Chen Z, Sun F, Cui X. Saline-Alkali Soil Property Improved by the Synergistic Effects of Priestia aryabhattai JL-5, Staphylococcus pseudoxylosus XW-4, Leymus chinensis and Soil Microbiota. Int J Mol Sci 2023; 24:ijms24097737. [PMID: 37175442 PMCID: PMC10178608 DOI: 10.3390/ijms24097737] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Two saline-alkali-tolerant bacterial strains, Priestia aryabhattai JL-5 and Staphylococcus pseudoxylosus XW-4, were isolated, with high capabilities of hydrolyzing phosphate and producing cellulase, respectively. The molecular mechanisms regulating the saline-alkali tolerance in the strain JL-5 were further investigated using transcriptome analysis. The contents of lactic acid and proline and the enzymatic activity of glutamine synthetase in the strain JL-5 were significantly increased. The properties of saline-alkali soils were significantly improved by the enhanced growth of the indicator plant Leymus chinensis under the combined applications of the strains JL-5 and XW-4 mixed with corn straw. The contents of catalase, peroxidase, superoxide dismutase and proline of L. chinensis were significantly increased, and the content of malondialdehyde was significantly decreased in the combined treatment of both bacterial strains. The contents of available nitrogen, phosphorus and potassium and organic matters in the soil treated with both strains were significantly increased, as well as the diversity and abundance of the soil microbiota. Our study evidently demonstrated the synergistic effects of the strains JL-5 and XW-4, indicator plants and the local microbiota in terms of improving the saline-alkali soil properties, providing strong experimental evidence to support the commercial development of the combined application of both strains to improve the properties of saline-alkali soils.
Collapse
Affiliation(s)
- Yujue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Yan Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Qian Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Hangzhe Fan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Xinyu Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Jianan Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Ying Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Zhanyu Chen
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Fengjie Sun
- Department of Biological Sciences, School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Xiyan Cui
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| |
Collapse
|
25
|
Jia YL, Li J, Nong FT, Yan CX, Ma W, Zhu XF, Zhang LH, Sun XM. Application of Adaptive Laboratory Evolution in Lipid and Terpenoid Production in Yeast and Microalgae. ACS Synth Biol 2023; 12:1396-1407. [PMID: 37084707 DOI: 10.1021/acssynbio.3c00179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Due to the complexity of metabolic and regulatory networks in microorganisms, it is difficult to obtain robust phenotypes through artificial rational design and genetic perturbation. Adaptive laboratory evolution (ALE) engineering plays an important role in the construction of stable microbial cell factories by simulating the natural evolution process and rapidly obtaining strains with stable traits through screening. This review summarizes the application of ALE technology in microbial breeding, describes the commonly used methods for ALE, and highlights the important applications of ALE technology in the production of lipids and terpenoids in yeast and microalgae. Overall, ALE technology provides a powerful tool for the construction of microbial cell factories, and it has been widely used in improving the level of target product synthesis, expanding the range of substrate utilization, and enhancing the tolerance of chassis cells. In addition, in order to improve the production of target compounds, ALE also employs environmental or nutritional stress strategies corresponding to the characteristics of different terpenoids, lipids, and strains.
Collapse
Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Jin Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Fang-Tong Nong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Chun-Xiao Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Wang Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiao-Feng Zhu
- College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Li-Hui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|
26
|
Li D, Ren Z, Zhou Y, Jiang L, Zheng M, Liu G. Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations. Appl Environ Microbiol 2023; 89:e0004723. [PMID: 36912626 PMCID: PMC10056971 DOI: 10.1128/aem.00047-23] [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] [Received: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.
Collapse
Affiliation(s)
- Deyong Li
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhichang Ren
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yangqi Zhou
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Lugao Jiang
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guoqiang Liu
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| |
Collapse
|
27
|
Dopson M, González-Rosales C, Holmes DS, Mykytczuk N. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies. Front Microbiol 2023; 14:1149903. [PMID: 37007468 PMCID: PMC10050440 DOI: 10.3389/fmicb.2023.1149903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
Collapse
Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- *Correspondence: Mark Dopson
| | - Carolina González-Rosales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Nadia Mykytczuk
- Goodman School of Mines, Laurentian University, Sudbury, ON, Canada
| |
Collapse
|
28
|
Xu J, Guo L, Zhao N, Meng X, Zhang J, Wang T, Wei X, Fan M. Response mechanisms to acid stress of acid-resistant bacteria and biotechnological applications in the food industry. Crit Rev Biotechnol 2023; 43:258-274. [PMID: 35114869 DOI: 10.1080/07388551.2021.2025335] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Acid-resistant bacteria are more and more widely used in industrial production due to their unique acid-resistant properties. In order to survive in various acidic environments, acid-resistant bacteria have developed diverse protective mechanisms such as sensing acid stress and signal transduction, maintaining intracellular pH homeostasis by controlling the flow of H+, protecting and repairing biological macromolecules, metabolic modification, and cross-protection. Acid-resistant bacteria have broad biotechnological application prospects in the food field. The production of fermented foods with high acidity and acidophilic enzymes are the main applications of this kind of bacteria in the food industry. Their acid resistance modules can also be used to construct acid-resistant recombinant engineering strains for special purposes. However, they can also cause negative effects on foods, such as spoilage and toxicity. Herein, the aim of this paper is to summarize the research progress of molecular mechanisms against acid stress of acid-resistant bacteria. Moreover, their effects on the food industry were also discussed. It is useful to lay a foundation for broadening our understanding of the physiological metabolism of acid-resistant bacteria and better serving the food industry.
Collapse
Affiliation(s)
- Junnan Xu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Li Guo
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Ning Zhao
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Xuemei Meng
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Jie Zhang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Tieru Wang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| |
Collapse
|
29
|
Razia S, Hadibarata T, Lau SY. Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions. Bioprocess Biosyst Eng 2023; 46:341-358. [PMID: 36602611 DOI: 10.1007/s00449-022-02844-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023]
Abstract
Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.
Collapse
Affiliation(s)
- Sultana Razia
- Environmental Engineering Program, Faculty of Engineering and Science, Curtin University, Miri, Malaysia
| | - Tony Hadibarata
- Environmental Engineering Program, Faculty of Engineering and Science, Curtin University, Miri, Malaysia.
| | - Sie Yon Lau
- Department of Chemical and Energy Engineering, Faculty of Engineering and Science, Curtin University, Miri, Malaysia
| |
Collapse
|
30
|
Borah ST, Das B, Biswas P, Mallick AI, Gupta P. Aqua-friendly organometallic Ir-Pt complexes: pH-responsive AIPE-guided imaging of bacterial cells. Dalton Trans 2023; 52:2282-2292. [PMID: 36723088 DOI: 10.1039/d2dt03390a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In this work, the aggregation-induced photoluminescence emission (AIPE) of three water-soluble heterobimetallic Ir-Pt complexes was reported with insight into their photophysical and electrochemical properties and imaging of bacterial cells. An alkyne appended Schiff's base L, bridges bis-cyclometalated iridium(III) and platinum(II) terpyridine centre. The Schiff's base (N-N fragment) serves as the ancillary ligand to the iridium(III) centre, while the alkynyl end is coordinated to platinum(II). The pH and ionic strength influence the aggregation kinetics of the alkynylplatinum(II) fragment, leading to metal-metal and π-π interactions with the emergence of a triplet metal-metal-to-ligand charge transfer (3MMLCT) emission. The excellent reversibility and photostability of aggregation-induced emission (AIE) of these aqua-friendly complexes were tested for their ability to sense and selectively image E. coli cells at various pH values.
Collapse
Affiliation(s)
- Sakira Tabassum Borah
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Bishnu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Prakash Biswas
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Amirul I Mallick
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Parna Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| |
Collapse
|
31
|
Xu Q, Zhang S, Ren J, Li K, Li J, Guo Y. Uptake of Selenite by Rahnella aquatilis HX2 Involves the Aquaporin AqpZ and Na +/H + Antiporter NhaA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2371-2379. [PMID: 36734488 DOI: 10.1021/acs.est.2c07028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbial transformation of selenite [Se(IV)] to elemental selenium nanoparticles (SeNPs) is known to be an important process for removing toxic soluble selenium (Se) oxyanions and recovery of Se from the environment as valuable nanoparticles. However, the mechanism of selenite uptake by microorganisms, the first step through which Se exerts its cellular function, remains not well studied. In this study, the effects of selenite concentration, time, pH, metabolic inhibitors, and anionic analogues on selenite uptake in Rahnella aquatilis HX2 were investigated. Selenite uptake by R. aquatilis HX2 was concentration- and time-dependent, and its transport activity was significantly dependent on pH. In addition, selenite uptake in R. aquatilis HX2 was significantly inhibited by the aquaporin inhibitor AgNO3 and sulfite (SO32-), and partially inhibited by carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and 2,4-dinitrophenol (2,4-DNP) treatments. Three mutants with in-frame deletions of aqpZ, glpF, and nhaA genes were constructed. The transport assay showed that the water channel protein AqpZ, and not GlpF, was a key channel of selenite uptake by R. aquatilis HX2, and sulfite and selenite had a common uptake pathway. In addition, the Na+/H+ antiporter NhaA is also involved in selenite uptake in R. aquatilis HX2.
Collapse
Affiliation(s)
- Qiaolin Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Sasa Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Jing Ren
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Kui Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Jing Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| |
Collapse
|
32
|
Yao X, Wang J, Hu B. How methanotrophs respond to pH: A review of ecophysiology. Front Microbiol 2023; 13:1034164. [PMID: 36687570 PMCID: PMC9853399 DOI: 10.3389/fmicb.2022.1034164] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.
Collapse
Affiliation(s)
- Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China,*Correspondence: Baolan Hu ✉
| |
Collapse
|
33
|
Van Riet S, Tadesse W, Mortier J, Schlegel S, Simoens K, Bernaerts K, Dal Co A, Aertsen A. Heterogeneity and Evolutionary Tunability of Escherichia coli Resistance against Extreme Acid Stress. Microbiol Spectr 2022; 10:e0375722. [PMID: 36453903 PMCID: PMC9769608 DOI: 10.1128/spectrum.03757-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 12/05/2022] Open
Abstract
Since acidic environments often serve as an important line of defense against bacterial pathogens, it is important to fully understand how the latter manage to mount and evolve acid resistance mechanisms. Escherichia coli, a species harboring many pathovars, is typically equipped with the acid fitness island (AFI), a genomic region encoding the GadE master regulator together with several GadE-controlled functions to counter acid stress. This study reveals that gadE and consequently AFI functions are heterogeneously expressed even in the absence of any prior acid stress, thereby preemptively creating acid-resistant subpopulations within a clonal E. coli population. Directed evolution efforts selecting for modulated gadE expression confirm that a gain-of-function mutation in the EvgS sensor kinase can constitutively upregulate gadE expression and concomitant acid resistance. However, we reveal that such upregulation of EvgS also causes cross-resistance to heat stress because of SafA-mediated cross-activation of the PhoPQ regulon. Surprisingly, loss of function of the serC gene (encoding phosphoserine/phosphohydroxythreonine aminotransferase) can also significantly upregulate gadE expression, acid resistance, and heat cross-resistance, although via a currently cryptic mechanism. As such, our data reveal a noisy expression of gadE in E. coli that is functional for the survival of sudden acid stress and that can readily be genetically tuned. IMPORTANCE Acidic environments constitute one of the most important stresses for enteric bacteria and can be encountered in both natural (e.g., host gastrointestinal tract) and manmade (e.g., food processing) environments. The enteric species Escherichia coli harbors many pathovars and is well known for its ability to cope with acid stress. In this study, we uncover that E. coli's acid fitness island (AFI), a genomic region that encodes important functions to deal with acid stress, is by default expressed in a heterogeneous manner. In fact, using microfluidics-based single-cell approaches, we further demonstrate that this heterogeneity preemptively creates a clonal subpopulation that is much better equipped to survive a sudden acid shock. In addition, we reveal that environments with recurring acid stress can readily select for mutants displaying a higher fraction of AFI-expressing cells. These new insights are important to properly understand and anticipate the survival characteristics of E. coli.
Collapse
Affiliation(s)
- Stefanie Van Riet
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
| | - Wubishet Tadesse
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
| | - Julien Mortier
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
| | - Susan Schlegel
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Kenneth Simoens
- Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | | | - Alma Dal Co
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Abram Aertsen
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
| |
Collapse
|
34
|
Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
Collapse
Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| |
Collapse
|
35
|
Neira G, Vergara E, Holmes DS. Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments. Front Microbiol 2022; 13:900531. [PMID: 36212841 PMCID: PMC9543262 DOI: 10.3389/fmicb.2022.900531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2–3) and moderately thermophilic conditions (50–60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including “first line of defense” mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the “second line of defense” where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.
Collapse
Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes
| |
Collapse
|
36
|
Comparison of Various Antimicrobial Agents for Thermoplastic Polymeric Retainers. Polymers (Basel) 2022; 14:polym14183753. [PMID: 36145897 PMCID: PMC9502766 DOI: 10.3390/polym14183753] [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: 07/20/2022] [Revised: 08/21/2022] [Accepted: 09/02/2022] [Indexed: 11/26/2022] Open
Abstract
The thermoplastic retainers indicated a rising incidence of cariogenic bacteria such as Streptococcus mutans. A report suggested the case of a patient with severe gingival inflammation and dental caries as a result of inadequate appliance cleaning. This study aims to compare the various antimicrobial agents for thermoplastic polymeric retainers. A minimum bactericidal concentration (MBC) of acetic acid was determined. Streptococcus mutans biofilm was formed on punched 4-mm copolyester (Essix ACE®) and polyurethane (Vivera®) retainers after they were submerged in 0.12% chlorhexidine (CHX group), acetic acid (AA group), Polident Denture Cleanser® (PD group), and Polident Pro Guard & Retainer® (PR group). A crystal violet (CV) test was performed. The biofilm imaging was assessed by confocal laser scanning microscopy (CLSM). The results showed that all chemical disinfectants exhibited statistically significant differences (p < 0.05) compared to the positive control. This novel finding elucidated that 0.625% acetic acid is effective for antimicrobial in both copolyester and polyurethane retainers. However, only the CHX, PD, and PR groups could reduce biofilm mass. In addition, the CV assay cannot provide information about the actual number of living and dead bacteria. Furthermore, the LIVE/DEAD BacLight assay was able to show the bacterial viability.
Collapse
|
37
|
Lange A, Sawosz E, Daniluk K, Wierzbicki M, Małolepszy A, Gołębiewski M, Jaworski S. Bacterial Surface Disturbances Affecting Cell Function during Exposure to Three-Compound Nanocomposites Based on Graphene Materials. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3058. [PMID: 36080095 PMCID: PMC9459733 DOI: 10.3390/nano12173058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Combating pathogenic microorganisms in an era of ever-increasing drug resistance is crucial. The aim of the study was to evaluate the antibacterial mechanism of three-compound nanocomposites that were based on graphene materials. To determine the nanomaterials' physicochemical properties, an analysis of the mean hydrodynamic diameter and zeta potential, transmission electron microscope (TEM) visualization and an FT-IR analysis were performed. The nanocomposites' activity toward bacteria species was defined by viability, colony forming units, conductivity and surface charge, cell wall integrity, ATP concentration, and intracellular pH. To ensure the safe usage of nanocomposites, the presence of cytokines was also analyzed. Both the graphene and graphene oxide (GO) nanocomposites exhibited a high antibacterial effect toward all bacteria species (Enterobacter cloacae, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus), as well as exceeded values obtained from exposure to single nanoparticles. Nanocomposites caused the biggest membrane damage, along with ATP depletion. Nanocomposites that were based on GO resulted in lower toxicity to the cell line. In view of the many aspects that must be considered when investigating such complex structures as are three-component nanocomposites, studies of their mechanism of action are crucial to their potential antibacterial use.
Collapse
Affiliation(s)
- Agata Lange
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland
| | - Ewa Sawosz
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland
| | - Karolina Daniluk
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland
| | - Mateusz Wierzbicki
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland
| | - Artur Małolepszy
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, 00-654 Warsaw, Poland
| | - Marcin Gołębiewski
- Department of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences, 02-786 Warsaw, Poland
| | - Sławomir Jaworski
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland
| |
Collapse
|
38
|
Naranjo D. A scenario for the origin of life: Volume regulation by bacteriorhodopsin required extremely voltage sensitive Na‐channels and very selective K‐channels. Bioessays 2022; 44:e2100210. [DOI: 10.1002/bies.202100210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/25/2022]
Affiliation(s)
- David Naranjo
- Instituto de Neurociencia, Facultad de Ciencias Universidad de Valparaíso Playa Ancha Valparaíso Chile
| |
Collapse
|
39
|
Prokaryotic Na+/H+ Exchangers—Transport Mechanism and Essential Residues. Int J Mol Sci 2022; 23:ijms23169156. [PMID: 36012428 PMCID: PMC9408914 DOI: 10.3390/ijms23169156] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
Na+/H+ exchangers are essential for Na+ and pH homeostasis in all organisms. Human Na+/H+ exchangers are of high medical interest, and insights into their structure and function are aided by the investigation of prokaryotic homologues. Most prokaryotic Na+/H+ exchangers belong to either the Cation/Proton Antiporter (CPA) superfamily, the Ion Transport (IT) superfamily, or the Na+-translocating Mrp transporter superfamily. Several structures have been solved so far for CPA and Mrp members, but none for the IT members. NhaA from E. coli has served as the prototype of Na+/H+ exchangers due to the high amount of structural and functional data available. Recent structures from other CPA exchangers, together with diverse functional information, have allowed elucidation of some common working principles shared by Na+/H+ exchangers from different families, such as the type of residues involved in the substrate binding and even a simple mechanism sufficient to explain the pH regulation in the CPA and IT superfamilies. Here, we review several aspects of prokaryotic Na+/H+ exchanger structure and function, discussing the similarities and differences between different transporters, with a focus on the CPA and IT exchangers. We also discuss the proposed transport mechanisms for Na+/H+ exchangers that explain their highly pH-regulated activity profile.
Collapse
|
40
|
Roy Chowdhury A, Sah S, Varshney U, Chakravortty D. Salmonella Typhimurium outer membrane protein A (OmpA) renders protection from nitrosative stress of macrophages by maintaining the stability of bacterial outer membrane. PLoS Pathog 2022; 18:e1010708. [PMID: 35969640 PMCID: PMC9410544 DOI: 10.1371/journal.ppat.1010708] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 08/25/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Bacterial porins are highly conserved outer membrane proteins used in the selective transport of charged molecules across the membrane. In addition to their significant contributions to the pathogenesis of Gram-negative bacteria, their role(s) in salmonellosis remains elusive. In this study, we investigated the role of outer membrane protein A (OmpA), one of the major outer membrane porins of Salmonella, in the pathogenesis of Salmonella Typhimurium (STM). Our study revealed that OmpA plays an important role in the intracellular virulence of Salmonella. An ompA deficient strain of Salmonella (STM ΔompA) showed compromised proliferation in macrophages. We found that the SPI-2 encoded virulence factors such as sifA and ssaV are downregulated in STM ΔompA. The poor colocalization of STM ΔompA with LAMP-1 showed that disruption of SCV facilitated its release into the cytosol of macrophages, where it was assaulted by reactive nitrogen intermediates (RNI). The enhanced recruitment of nitrotyrosine on the cytosolic population of STM ΔompAΔsifA and ΔompAΔssaV compared to STM ΔsifA and ΔssaV showed an additional role of OmpA in protecting the bacteria from host nitrosative stress. Further, we showed that the generation of greater redox burst could be responsible for enhanced sensitivity of STM ΔompA to the nitrosative stress. The expression of several other outer membrane porins such as ompC, ompD, and ompF was upregulated in STM ΔompA. We found that in the absence of ompA, the enhanced expression of ompF increased the outer membrane porosity of Salmonella and made it susceptible to in vitro and in vivo nitrosative stress. Our study illustrates a novel mechanism for the strategic utilization of OmpA by Salmonella to protect itself from the nitrosative stress of macrophages. Salmonella Typhimurium majorly uses SPI-1 and SPI-2 encoded T3SS and virulence factors for thriving in the host macrophages. But the role of non-SPI genes in Salmonella pathogenesis remains unknown. This article illustrates a novel mechanism of how a non-SPI virulent protein, OmpA, helps Salmonella Typhimurium to survive in murine macrophages. Our data revealed that Salmonella lacking OmpA (STM ΔompA) is deficient in producing SPI-2 effector proteins and has a severe defect in maintaining the stability of its outer membrane. It is released into the cytosol of macrophages during infection after disrupting the SCV membrane. STM ΔompA was severely challenged with reactive nitrogen intermediates in the cytosol, which reduced their proliferation in macrophages. We further showed that the deletion of OmpA increased the expression of other larger porins (ompC, ompD, and ompF) on the surface of Salmonella. It was observed that the enhanced expression of OmpF in STM ΔompA increased the outer membrane permeability and made the bacteria more susceptible to in vitro and in vivo nitrosative stress. Altogether our study proposes new insights into the role of Salmonella OmpA as an essential virulence factor.
Collapse
Affiliation(s)
- Atish Roy Chowdhury
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail:
| |
Collapse
|
41
|
Shen J, Luo Y, Tao Q, White PJ, Sun G, Li M, Luo J, He Y, Li B, Li Q, Xu Q, Cai Y, Li H, Wang C. The exacerbation of soil acidification correlates with structural and functional succession of the soil microbiome upon agricultural intensification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154524. [PMID: 35288138 DOI: 10.1016/j.scitotenv.2022.154524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Agricultural intensification driven by land-use changes has caused continuous and cumulative soil acidification (SA) throughout the global agroecosystem. Microorganisms mediate acid-generating reactions; however, the microbial mechanisms responsible for exacerbating SA feedback remain largely unknown. To determine the microbial community composition and putative function associated with SA, we conducted a metagenomic analysis of soils across a chronosequence that has elapsed since the conversion of rice-wheat (RW) to rice-vegetable (RV) rotations. Compared to RW rotations, soil pH decreased by 0.50 and 1.56 units (p < 0.05) in response to 10-year and 20-year RV rotations, respectively. Additionally, acid saturation ratios were increased by 7.3% and 36.2% (p < 0.05), respectively. The loss of microbial beta-diversity was a key element that contributed to the exacerbation of SA in the RV. Notably, the 20-year RV-enriched microbial taxa were more hydrogen (H+)-, aluminium (Al3+)-, and nitrate nitrogen (NO3--N) -dependent and contained more genera exhibiting dehydrogenation functions than did RW-enriched taxa. "M00115, M00151, M00417, and M00004" and "M00531 and M00135" that are the "proton-pumping" and "proton-consuming" gene modules, respectively, were linked to the massive recruitment of acid-dependent biomarkers in 20-year RV soils, particularly Rhodanobacter, Gemmatirosa, Sphingomonas, and Streptomyces. Collectively, soils in long-term RV rotations were highly acidified and acid-sensitive, as the enrichment of microbial dehydrogenation genes allowing for soil buffering capacity is more vulnerable to H+ loading and consequently promotes the colonization of more acid-tolerant and acidogenic microbes, and ultimately provide new clues for researchers to elucidate the interaction between SA and the soil microbiome.
Collapse
Affiliation(s)
- Jie Shen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Youlin Luo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Geng Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Meng Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Jipeng Luo
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuting He
- Chengdu Popularization of Agricultural Technique Station, Chengdu 610041, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiquan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Xu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Cai
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanxiu Li
- Fruit and Vegetable Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| |
Collapse
|
42
|
Qian L, Ouyang H, Gordils-Valentin L, Hong J, Jayaraman A, Zhu X. Identification of Gut Bacterial Enzymes for Keto-Reductive Metabolism of Xenobiotics. ACS Chem Biol 2022; 17:1665-1671. [PMID: 35687750 DOI: 10.1021/acschembio.2c00312] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human gastrointestinal microbiota are known for the keto-reductive metabolism of small-molecule pharmaceuticals; however, the responsible enzymes remain poorly understood. Through in vitro biochemical assays, we report the identification of enzymes encoded in the genome of Clostridium bolteae that can reduce the ketone groups of nabumetone, hydrocortisone, and tacrolimus. The homologues to a newly identified enzyme (i.e., DesE) are potentially widely distributed in the gut microbiome. The selected enzymes display different levels of activities against additional chemicals such as two dietary compounds (i.e., raspberry ketone and zingerone), chemotherapeutic drug doxorubicin, and its aglycone metabolite doxorubicinone. Thus, our results expand the repertoire of enzymes that can reduce the ketone groups in small molecules and could serve as the basis for future personalized medicine approaches.
Collapse
Affiliation(s)
- Liangyu Qian
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Huanrong Ouyang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Lois Gordils-Valentin
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.,Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua Hong
- Department of Biology, Texas A&M University, College Station, Texas 77843, United States
| | - Arul Jayaraman
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.,Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Xuejun Zhu
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.,Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
43
|
Nayak T, Basak S, Deb A, Dhal PK. A systematic review on groundwater radon distribution with human health consequences and probable mitigation strategy. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2022; 247:106852. [PMID: 35305305 DOI: 10.1016/j.jenvrad.2022.106852] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Groundwater radon contamination is a serious global concern for its eco-toxicological effects. The major health hazard occurs due to toxic indoor air inhalation and consumption of contaminated drinking water supplied from different distribution systems, especially groundwater. There are fragmented reports on the measurement of radon contamination and their health consequences with physical radon removal strategies as well as characterization of inhabitant microbial communities. As it concerned with human health, collective information is much essential on their groundwater distribution, their physicochemical properties and possible mitigation strategies, not done so far. In such prospect, this review summarizes the physicochemical properties of radon, their sources, global as well as Indian groundwater radon contamination scenario, health effects and inhabitant microbes along with their survival strategies. It also summarizes the physical radon removal techniques and especially emphasizes the microbes based bioremediation process as well as a combination of both as a future effective radon remediation process.
Collapse
Affiliation(s)
- Tilak Nayak
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India
| | - Sohom Basak
- Department of Biotechnology, Bengal Institute of Technology, Kolkata, 700091, India
| | - Argha Deb
- School of Studies in Environmental Radiation and Archaeological Sciences & Department of Physics, Jadavpur University, Kolkata, 700032, India
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
| |
Collapse
|
44
|
Kiatwarawut K, Rokaya D, Sirisoontorn I. Antimicrobial Activity of Various Disinfectants to Clean Thermoplastic Polymeric Appliances in Orthodontics. Polymers (Basel) 2022; 14:polym14112256. [PMID: 35683929 PMCID: PMC9183154 DOI: 10.3390/polym14112256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
There is a lack of research evidence on the risk–benefits of the various disinfectants in cleaning products and cleansing regimens. This systematic review compared the antimicrobial activity of various chemical disinfectants to disinfect the thermoplastic polymeric appliances in orthodontics. The study was carried out using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Cochrane Handbook of Systematic Reviews of Interventions. An electronic search was conducted on Pubmed, Google Scholar, Scopus, ScienceDirect, and Springer. Two authors independently investigated the risk of bias in duplication. A total of 225 articles were collected. After removing duplicates, 221 articles remained, and after filtering their titles and abstracts, 11 articles met eligibility qualifications remained. Finally, nine articles that met the criteria were selected. It showed that both over-the-counter orthodontic appliance cleaners and applied-chemical disinfectants were effective against bacteria. The duration and frequency of usage guidelines cannot be concluded.
Collapse
|
45
|
Ade C, Marcelino TF, Dulchavsky M, Wu K, Bardwell JCA, Städler B. Microreactor equipped with naturally acid-resistant histidine ammonia lyase from an extremophile. MATERIALS ADVANCES 2022; 3:3649-3662. [PMID: 36238657 PMCID: PMC9555226 DOI: 10.1039/d2ma00051b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Extremophile enzymes are useful in biotechnology and biomedicine due to their abilities to withstand harsh environments. The abilities of histidine ammonia lyases from different extremophiles to preserve their catalytic activities after exposure to acid were assessed. Thermoplasma acidophilum histidine ammonia lyase was identified as an enzyme with a promising catalytic profile following acid treatment. The fusion of this enzyme with the maltose-binding protein or co-incubation with the chaperone HdeA further helped Thermoplasma acidophilum histidine ammonia lyase to withstand acid treatments down to pH 2.8. The assembly of a microreactor by encapsulation of MBP-Thermoplasma acidophilum histidine ammonia lyase into a photocrosslinked poly(vinyl alcohol) hydrogel allowed the enzyme to recover over 50% of its enzymatic activity following exposure to simulated gastric and intestinal fluids. Our results show that using engineered proteins obtained from extremophiles in combination with polymer-based encapsulation can advance the oral formulations of biologicals.
Collapse
Affiliation(s)
- Carina Ade
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Thaís F Marcelino
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, China
| | - Mark Dulchavsky
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kevin Wu
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| |
Collapse
|
46
|
Visualizing the pH in Escherichia coli Colonies via the Sensor Protein mCherryEA Allows High-Throughput Screening of Mutant Libraries. mSystems 2022; 7:e0021922. [PMID: 35430898 PMCID: PMC9238402 DOI: 10.1128/msystems.00219-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cytoplasmic pH in bacteria is tightly regulated by diverse active mechanisms and interconnected regulatory processes. Many processes and regulators underlying pH homeostasis have been identified via phenotypic screening of strain libraries for nongrowth at low or high pH values. Direct screens with respect to changes of the internal pH in mutant strain collections are limited by laborious methods, which include fluorescent dyes and radioactive probes. Genetically encoded biosensors equip single organisms or strain libraries with an internal sensor molecule during the generation of the strain. Here, we used the pH-sensitive mCherry variant mCherryEA as a ratiometric pH biosensor. We visualized the internal pH of Escherichia coli colonies on agar plates by the use of a GelDoc imaging system. Combining this imaging technology with robot-assisted colony picking and spotting allowed us to screen and select mutants with altered internal pH values from a small transposon mutagenesis-derived E. coli library. Identification of the transposon (Tn) insertion sites in strains with altered internal pH levels revealed that the transposon was inserted into trkH (encoding a transmembrane protein of the potassium uptake system) or rssB (encoding the adaptor protein RssB, which mediates the proteolytic degradation of the general stress response regulator RpoS), two genes known to be associated with pH homeostasis and pH stress adaptation. This successful screening approach demonstrates that the pH sensor-based analysis of arrayed colonies on agar plates is a sensitive approach for the rapid identification of genes involved in pH homeostasis or pH stress adaptation in E. coli. IMPORTANCE Phenotypic screening of strain libraries on agar plates has become a versatile tool to understand gene functions and to optimize biotechnological platform organisms. Screening is supported by genetically encoded biosensors that allow to easily measure intracellular processes. For this purpose, transcription factor-based biosensors have emerged as the sensor type of choice. Here, the target stimulus initiates the activation of a response gene (e.g., a fluorescent protein), followed by transcription, translation, and maturation. Due to this mechanistic principle, biosensor readouts are delayed and cannot report the actual intracellular state of the cell in real time. To capture rapid intracellular processes adequately, fluorescent reporter proteins are extensively applied. However, these sensor types have not previously been used for phenotypic screenings. To take advantage of their properties, we established here an imaging method that allows application of a rapid ratiometric sensor protein for assessing the internal pH of colonies in a high-throughput manner.
Collapse
|
47
|
Boase K, González C, Vergara E, Neira G, Holmes D, Watkin E. Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus. Front Microbiol 2022; 13:848410. [PMID: 35516430 PMCID: PMC9062700 DOI: 10.3389/fmicb.2022.848410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Acidihalobacter is a genus of acidophilic, gram-negative bacteria known for its ability to oxidize pyrite minerals in the presence of elevated chloride ions, a capability rare in other iron-sulfur oxidizing acidophiles. Previous research involving Acidihalobacter spp. has focused on their applicability in saline biomining operations and their genetic arsenal that allows them to cope with chloride, metal and oxidative stress. However, an understanding of the molecular adaptations that enable Acidihalobacter spp. to thrive under both acid and chloride stress is needed to provide a more comprehensive understanding of how this genus can thrive in such extreme biomining conditions. Currently, four genomes of the Acidihalobacter genus have been sequenced: Acidihalobacter prosperus DSM 5130T, Acidihalobacter yilgarnensis DSM 105917T, Acidihalobacter aeolianus DSM 14174T, and Acidihalobacter ferrooxydans DSM 14175T. Phylogenetic analysis shows that the Acidihalobacter genus roots to the Chromatiales class consisting of mostly halophilic microorganisms. In this study, we aim to advance our knowledge of the genetic repertoire of the Acidihalobacter genus that has enabled it to cope with acidic stress. We provide evidence of gene gain events that are hypothesized to help the Acidihalobacter genus cope with acid stress. Potential acid tolerance mechanisms that were found in the Acidihalobacter genomes include multiple potassium transporters, chloride/proton antiporters, glutamate decarboxylase system, arginine decarboxylase system, urease system, slp genes, squalene synthesis, and hopanoid synthesis. Some of these genes are hypothesized to have entered the Acidihalobacter via vertical decent from an inferred non-acidophilic ancestor, however, horizontal gene transfer (HGT) from other acidophilic lineages is probably responsible for the introduction of many acid resistance genes.
Collapse
Affiliation(s)
- Katelyn Boase
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - David Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes,
| | - Elizabeth Watkin
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Elizabeth Watkin,
| |
Collapse
|
48
|
Liu Q, Yang M, Meng X, Han X, Nazare M, Xu Y, Hu HY, Zhang Q. Donor manipulation for constructing a pH sensing thermally activated delayed fluorescent probe to detect alkaliphiles. Talanta 2022; 246:123493. [PMID: 35489098 DOI: 10.1016/j.talanta.2022.123493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022]
Abstract
pH homeostasis is essential for alkaliphiles, given their widespread use in biotechnological applications. However, quantitative monitoring of alkaline pH in alkaliphiles remains challenging. Here, we synthesized for the first time, a thermally activated delayed fluorescent (TADF) pH probe: NI-D-OH. Our probe exhibits a good linear relationship between fluorescence intensity and pH in the neutral to alkaline range (pH 7.0-8.6), as well as long-lived TADF emission. We further show that NI-D-OH can be used to monitor intracellular pH in living organisms, and evaluate the effect of Na+ on the pH homeostasis, demonstrating the potential for alkaline pH monitoring and time-resolved fluorescence imaging.
Collapse
Affiliation(s)
- Qian Liu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Miao Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China; School of Pharmaceutical Engineering and Key Laboratory of Structure-Based Drug Design & Discovery (Ministry of Education), Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xiangchuan Meng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xiaowan Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Marc Nazare
- Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin, 13125, Berlin, Germany
| | - Youjun Xu
- School of Pharmaceutical Engineering and Key Laboratory of Structure-Based Drug Design & Discovery (Ministry of Education), Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Qingyang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| |
Collapse
|
49
|
Division of labor and collective functionality in Escherichia coli under acid stress. Commun Biol 2022; 5:327. [PMID: 35393532 PMCID: PMC8989999 DOI: 10.1038/s42003-022-03281-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
The acid stress response is an important factor influencing the transmission of intestinal microbes such as the enterobacterium Escherichia coli. E. coli activates three inducible acid resistance systems - the glutamate decarboxylase, arginine decarboxylase, and lysine decarboxylase systems to counteract acid stress. Each system relies on the activity of a proton-consuming reaction catalyzed by a specific amino acid decarboxylase and a corresponding antiporter. Activation of these three systems is tightly regulated by a sophisticated interplay of membrane-integrated and soluble regulators. Using a fluorescent triple reporter strain, we quantitatively illuminated the cellular individuality during activation of each of the three acid resistance (AR) systems under consecutively increasing acid stress. Our studies highlight the advantages of E. coli in possessing three AR systems that enable division of labor in the population, which ensures survival over a wide range of low pH values.
Collapse
|
50
|
Rivera-Lugo R, Deng D, Anaya-Sanchez A, Tejedor-Sanz S, Tang E, Reyes Ruiz VM, Smith HB, Titov DV, Sauer JD, Skaar EP, Ajo-Franklin CM, Portnoy DA, Light SH. Listeria monocytogenes requires cellular respiration for NAD + regeneration and pathogenesis. eLife 2022; 11:75424. [PMID: 35380108 PMCID: PMC9094743 DOI: 10.7554/elife.75424] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
Cellular respiration is essential for multiple bacterial pathogens and a validated antibiotic target. In addition to driving oxidative phosphorylation, bacterial respiration has a variety of ancillary functions that obscure its contribution to pathogenesis. We find here that the intracellular pathogen Listeria monocytogenes encodes two respiratory pathways which are partially functionally redundant and indispensable for pathogenesis. Loss of respiration decreased NAD+ regeneration, but this could be specifically reversed by heterologous expression of a water-forming NADH oxidase (NOX). NOX expression fully rescued intracellular growth defects and increased L. monocytogenes loads >1000-fold in a mouse infection model. Consistent with NAD+ regeneration maintaining L. monocytogenes viability and enabling immune evasion, a respiration-deficient strain exhibited elevated bacteriolysis within the host cytosol and NOX expression rescued this phenotype. These studies show that NAD+ regeneration represents a major role of L. monocytogenes respiration and highlight the nuanced relationship between bacterial metabolism, physiology, and pathogenesis. Cellular respiration is one of the main ways organisms make energy. It works by linking the oxidation of an electron donor (like sugar) to the reduction of an electron acceptor (like oxygen). Electrons pass between the two molecules along what is known as an ‘electron transport chain’. This process generates a force that powers the production of adenosine triphosphate (ATP), a molecule that cells use to store energy. Respiration is a common way for cells to replenish their energy stores, but it is not the only way. A simpler process that does not require a separate electron acceptor or an electron transport chain is called fermentation. Many bacteria have the capacity to perform both respiration and fermentation and do so in a context-dependent manner. Research has shown that respiration can contribute to bacterial diseases, like tuberculosis and listeriosis (a disease caused by the foodborne pathogen Listeria monocytogenes). Indeed, some antibiotics even target bacterial respiration. Despite being often discussed in the context of generating ATP, respiration is also important for many other cellular processes, including maintaining the balance of reduced and oxidized nicotinamide adenine dinucleotide (NAD) cofactors. Because of these multiple functions, the exact role respiration plays in disease is unknown. To find out more, Rivera-Lugo, Deng et al. developed strains of the bacterial pathogen Listeria monocytogenes that lacked some of the genes used in respiration. The resulting bacteria were still able to produce energy, but they became much worse at infecting mammalian cells. The use of a genetic tool that restored the balance of reduced and oxidized NAD cofactors revived the ability of respiration-deficient L. monocytogenes to infect mammalian cells, indicating that this balance is what the bacterium requires to infect. Research into respiration tends to focus on its role in generating ATP. But these results show that for some bacteria, this might not be the most important part of the process. Understanding the other roles of respiration could change the way that researchers develop antibacterial drugs in the future. This in turn could help with the growing problem of antibiotic resistance.
Collapse
Affiliation(s)
- Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - David Deng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Andrea Anaya-Sanchez
- Graduate Group in Microbiology, University of California, Berkeley, Berkeley, United States
| | | | - Eugene Tang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Valeria M Reyes Ruiz
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Hans B Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States
| | - Denis V Titov
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - John Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | | | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Samuel H Light
- Department of Microbiology, University of Chicago, Chicago, United States
| |
Collapse
|