1
|
Diene SM, Pontarotti P, Azza S, Armstrong N, Pinault L, Chabrière E, Colson P, Rolain JM, Raoult D. Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms. Cells 2023; 12:1752. [PMID: 37443786 PMCID: PMC10340364 DOI: 10.3390/cells12131752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities.
Collapse
Affiliation(s)
- Seydina M. Diene
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Pierre Pontarotti
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- CNRS SNC5039, 13005 Marseille, France
| | - Saïd Azza
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Nicholas Armstrong
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Lucile Pinault
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Eric Chabrière
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Philippe Colson
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Jean-Marc Rolain
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Didier Raoult
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| |
Collapse
|
2
|
Islas-Morales PF, Cárdenas A, Mosqueira MJ, Jiménez-García LF, Voolstra CR. Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon. Front Microbiol 2023; 14:1075071. [PMID: 36819014 PMCID: PMC9932318 DOI: 10.3389/fmicb.2023.1075071] [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: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023] Open
Abstract
Nucleoli are subcellular compartments where transcription and maturation of pre-ribosomal RNAs occur. While the transcription of ribosomal RNAs is common to all living cells, the presence and ultrastructure of nucleoli has been only documented in eukaryotes. Asgard-Archaea, the closest prokaryotic relatives of eukaryotes, and their near relatives TACK-Archaea have homologs of nucleolar proteins and RNAs in their genome, but the cellular organization of both is largely unexplored. Here we provide ultrastructural and molecular evidence for the presence of putative nucleolus-like subcellular domains in the TACK crenarchaeon Saccharolobus solfataricus (formerly known as Sulfolobus solfataricus). Transmission electron microscopy (TEM) revealed consistent electron-dense fibro-granular compartments, also positive to the specific silver staining for nucleolar organizer regions (AgNOR). TEM also confirmed that ribosomal DNA (rDNA) is spatially distributed in non-random, clustered arrays underlying fine structures, as observed by ultrastructural in situ hybridization (UISH). To further explore these observations, proteomic sequencing of isolated bands from AgNOR-stained protein gels was conducted and compared against a compiled inventory of putative nucleolar homologs from the S. solfataricus P1 genome. Sequenced AgNOR-sensitive peptides encoded homologs of eukaryotic nucleoli proteins, enriched for nucleolus-related functions. Our results provide first evidence that subcellular domains of nucleolar-like nature are not exclusive to eukaryotes. Based on our data, we propose a model for a putative nucleolus in S. solfataricus. Whereas technical limitations and further aspects remain a matter for future functional studies, our data supports the origin of nucleoli within the common ancestor of Eukarya and TACK-Archaea, based on a two-domain tree of life.
Collapse
Affiliation(s)
- Parsifal F. Islas-Morales
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, UNAM, Mexico City, Mexico,UNESCO Chair on Science Diplomacy and Scientific Heritage, Instituto de Biología, UNAM, Mexico City, Mexico,Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,Department of Biology, University of Konstanz, Konstanz, Germany,Department of Biology, American University, Washington, DC, United States
| | - María J. Mosqueira
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,NEOM, Saudi Arabia
| | - Luis Felipe Jiménez-García
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, UNAM, Mexico City, Mexico,Department of Cell Biology, Faculty of Sciences, UNAM, Mexico City, Mexico,*Correspondence: Luis Felipe Jiménez-García, ✉
| | - Christian R. Voolstra
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,Department of Biology, University of Konstanz, Konstanz, Germany,Christian R. Voolstra, ✉
| |
Collapse
|
3
|
Jin T, Yin J. Patterns of virus growth across the diversity of life. Integr Biol (Camb) 2021; 13:44-59. [PMID: 33616184 DOI: 10.1093/intbio/zyab001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
Although viruses in their natural habitats add up to less than 10% of the biomass, they contribute more than 90% of the genome sequences [1]. These viral sequences or 'viromes' encode viruses that populate the Earth's oceans [2, 3] and terrestrial environments [4, 5], where their infections impact life across diverse ecological niches and scales [6, 7], including humans [8-10]. Most viruses have yet to be isolated and cultured [11-13], and surprisingly few efforts have explored what analysis of available data might reveal about their nature. Here, we compiled and analyzed seven decades of one-step growth and other data for viruses from six major families, including their infections of archaeal, bacterial and eukaryotic hosts [14-191]. We found that the use of host cell biomass for virus production was highest for archaea at 10%, followed by bacteria at 1% and eukarya at 0.01%, highlighting the degree to which viruses of archaea and bacteria exploit their host cells. For individual host cells, the yield of virus progeny spanned a relatively narrow range (10-1000 infectious particles per cell) compared with the million-fold difference in size between the smallest and largest cells. Furthermore, healthy and infected host cells were remarkably similar in the time they needed to multiply themselves or their virus progeny. Specifically, the doubling time of healthy cells and the delay time for virus release from infected cells were not only correlated (r = 0.71, p < 10-10, n = 101); they also spanned the same range from tens of minutes to about a week. These results have implications for better understanding the growth, spread and persistence of viruses in complex natural habitats that abound with diverse hosts, including humans and their associated microbes.
Collapse
Affiliation(s)
- Tianyi Jin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| |
Collapse
|
4
|
Paez-Segala MG, Sun MG, Shtengel G, Viswanathan S, Baird MA, Macklin JJ, Patel R, Allen JR, Howe ES, Piszczek G, Hess HF, Davidson MW, Wang Y, Looger LL. Fixation-resistant photoactivatable fluorescent proteins for CLEM. Nat Methods 2015; 12:215-8, 4 p following 218. [PMID: 25581799 PMCID: PMC4344411 DOI: 10.1038/nmeth.3225] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/12/2014] [Indexed: 12/17/2022]
Abstract
Fluorescent proteins facilitate a variety of imaging paradigms in live and fixed samples. However, they lose their fluorescence after heavy fixation, hindering applications such as correlative light and electron microscopy (CLEM). Here we report engineered variants of the photoconvertible Eos fluorescent protein that fluoresce and photoconvert normally in heavily fixed (0.5-1% OsO4), plastic resin-embedded samples, enabling correlative super-resolution fluorescence imaging and high-quality electron microscopy.
Collapse
Affiliation(s)
- Maria G Paez-Segala
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Mei G Sun
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Gleb Shtengel
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Sarada Viswanathan
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Michelle A Baird
- 1] National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA. [2] Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - John J Macklin
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Ronak Patel
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - John R Allen
- 1] National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA. [2] Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Elizabeth S Howe
- 1] National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA. [2] Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | | | - Harald F Hess
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Michael W Davidson
- 1] National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA. [2] Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yalin Wang
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| |
Collapse
|
5
|
Rachel R, Meyer C, Klingl A, Gürster S, Heimerl T, Wasserburger N, Burghardt T, Küper U, Bellack A, Schopf S, Wirth R, Huber H, Wanner G. Analysis of the ultrastructure of archaea by electron microscopy. Methods Cell Biol 2010; 96:47-69. [PMID: 20869518 DOI: 10.1016/s0091-679x(10)96003-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ultrastructural characterization of archaeal cells is done with both types of electron microscopy, transmission electron microscopy, and scanning electron microscopy. Depending on the scientific question, different preparation methods have to be employed and need to be optimized, according to the special cultivation conditions of these-in many cases extreme-microorganisms. Recent results using various electron microscopy techniques show that archaeal cells have a variety of cell appendages, used for motility as well as for establishing cell-cell and cell-surface contacts. Cryo-preparation methods, in particular high-pressure freezing and freeze-substitution, are crucial for obtaining results: (1) showing the cells in ultrathin sections in a good structural preservation, often with unusual shapes and subcellular complexity, and (2) enabling us to perform immunolocalization studies. This is an important tool to make a link between biochemical and ultrastructural studies.
Collapse
Affiliation(s)
- Reinhard Rachel
- Centre for Electron Microscopy, University of Regensburg, D-93053 Regensburg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Müller SA, Aebi U, Engel A. What transmission electron microscopes can visualize now and in the future. J Struct Biol 2008; 163:235-45. [PMID: 18614377 DOI: 10.1016/j.jsb.2008.05.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 05/21/2008] [Indexed: 11/18/2022]
Abstract
Our review concentrates on the progress made in high-resolution transmission electron microscopy (TEM) in the past decade. This includes significant improvements in sample preparation by quick-freezing aimed at preserving the specimen in a close-to-native state in the high vacuum of the microscope. Following advances in cold stage and TEM vacuum technology systems, the observation of native, frozen hydrated specimens has become a widely used approach. It fostered the development of computer guided, fully automated low-dose data acquisition systems allowing matched pairs of images and diffraction patterns to be recorded for electron crystallography, and the collection of entire tilt-series for electron tomography. To achieve optimal information transfer to atomic resolution, field emission electron guns combined with acceleration voltages of 200-300 kV are now routinely used. The outcome of these advances is illustrated by the atomic structure of mammalian aquaporin-O and by the pore-forming bacterial cytotoxin ClyA resolved to 12 A. Further, the Yersinia injectisome needle, a bacterial pseudopilus and the binding of phalloidin to muscle actin filaments were chosen to document the advantage of the high contrast offered by dedicated scanning transmission electron microscopy (STEM) and/or the STEM's ability to measure the mass of protein complexes and directly link this to their shape. Continued progress emerging from leading research laboratories and microscope manufacturers will eventually enable us to determine the proteome of a single cell by electron tomography, and to more routinely solve the atomic structure of membrane proteins by electron crystallography.
Collapse
Affiliation(s)
- Shirley A Müller
- Maurice E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstr. 70, CH-4056 Basel, Switzerland.
| | | | | |
Collapse
|