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Jiang H, Milanov M, Jüngert G, Angebauer L, Flender C, Smudde E, Gather F, Vogel T, Jessen HJ, Koch HG. Control of a chemical chaperone by a universally conserved ATPase. iScience 2024; 27:110215. [PMID: 38993675 PMCID: PMC11237923 DOI: 10.1016/j.isci.2024.110215] [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: 12/19/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The universally conserved YchF/Ola1 ATPases regulate stress response pathways in prokaryotes and eukaryotes. Deletion of YchF/Ola1 leads to increased resistance against environmental stressors, such as reactive oxygen species, while their upregulation is associated with tumorigenesis in humans. The current study shows that in E. coli, the absence of YchF stimulates the synthesis of the alternative sigma factor RpoS by a transcription-independent mechanism. Elevated levels of RpoS then enhance the transcription of major stress-responsive genes. In addition, the deletion of ychF increases the levels of polyphosphate kinase, which in turn boosts the production of the evolutionary conserved and ancient chemical chaperone polyphosphate. This potentially provides a unifying concept for the increased stress resistance in bacteria and eukaryotes upon YchF/Ola1 deletion. Intriguingly, the simultaneous deletion of ychF and the polyphosphate-degrading enzyme exopolyphosphatase causes synthetic lethality in E. coli, demonstrating that polyphosphate production needs to be fine-tuned to prevent toxicity.
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Affiliation(s)
- Hong Jiang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriela Jüngert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Clara Flender
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Eva Smudde
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Fabian Gather
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute for Organic Chemistry, Faculty of Chemistry and Pharmacy, University Freiburg 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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2
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Quaiyum S, Yuan Y, Sun G, Ratnayake RMMN, Hutinet G, Dedon PC, Minnick MF, de Crécy-Lagard V. Queuosine Salvage in Bartonella henselae Houston 1: A Unique Evolutionary Path. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.570228. [PMID: 38106016 PMCID: PMC10723273 DOI: 10.1101/2023.12.05.570228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Queuosine (Q) stands out as the sole tRNA modification that can be synthesized via salvage pathways. Comparative genomic analyses identified specific bacteria that showed a discrepancy between the projected Q salvage route and the predicted substrate specificities of the two identified salvage proteins: 1) the distinctive enzyme tRNA guanine-34 transglycosylase (bacterial TGT, or bTGT), responsible for inserting precursor bases into target tRNAs; and 2) Queuosine Precursor Transporter (QPTR), a transporter protein that imports Q precursors. Organisms like the facultative intracellular pathogen Bartonella henselae, which possess only bTGT and QPTR but lack predicted enzymes for converting preQ1 to Q, would be expected to salvage the queuine (q) base, mirroring the scenario for the obligate intracellular pathogen Chlamydia trachomatis. However, sequence analyses indicate that the substrate-specificity residues of their bTGTs resemble those of enzymes inserting preQ1 rather than q. Intriguingly, mass spectrometry analyses of tRNA modification profiles in B. henselae reveal trace amounts of preQ1, previously not observed in a natural context. Complementation analysis demonstrates that B. henselae bTGT and QPTR not only utilize preQ1, akin to their Escherichia coli counterparts, but can also process q when provided at elevated concentrations. The experimental and phylogenomic analyses suggest that the Q pathway in B. henselae could represent an evolutionary transition among intracellular pathogens-from ancestors that synthesized Q de novo to a state prioritizing the salvage of q. Another possibility that will require further investigations is that the insertion of preQ1 has fitness advantages when B. henselae is growing outside a mammalian host.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael F. Minnick
- Division of Biological Sciences, University of Montana, Missoula, Montana, MT 59812
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
- Genetic Institute, University of Florida, FL 32611
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3
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Quaiyum S, Sun J, Marchand V, Sun G, Reed CJ, Motorin Y, Dedon PC, Minnick MF, de Crécy-Lagard V. Mapping the tRNA modification landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse. Front Microbiol 2024; 15:1369018. [PMID: 38544857 PMCID: PMC10965804 DOI: 10.3389/fmicb.2024.1369018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens-Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana. Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. Bartonella quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Virginie Marchand
- Université de Lorraine, UAR2008/US40 IBSLor, EpiRNA-Seq Core Facility and UMR7365 IMoPA, CNRS-Inserm, Biopôle UL, Nancy, France
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Yuri Motorin
- Université de Lorraine, UAR2008/US40 IBSLor, EpiRNA-Seq Core Facility and UMR7365 IMoPA, CNRS-Inserm, Biopôle UL, Nancy, France
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Michael F. Minnick
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
- Genetic Institute, University of Florida, Gainesville, FL, United States
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4
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Ding D, Fang Z, Kim SC, O’Flaherty DK, Jia X, Stone TB, Zhou L, Szostak JW. Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying. J Am Chem Soc 2024; 146:3861-3871. [PMID: 38293747 PMCID: PMC10870715 DOI: 10.1021/jacs.3c11158] [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: 10/09/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
2-Thiouridine (s2U) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing s2U:s2U compared to those with U:U pairs. Notably, the C═O···H-N hydrogen bond in the U:U pair is replaced with a C═S···H-N hydrogen bond in the s2U:s2U base pair. The thermodynamic stability of the s2U:s2U base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that s2U:s2U base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:s2U base pair outcompetes the slightly weaker s2U:s2U base pair. In addition, even if an s2U is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with s2U. Our findings suggest that s2U may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.
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Affiliation(s)
- Dian Ding
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Ziyuan Fang
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Seohyun Chris Kim
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Derek K. O’Flaherty
- Department
of Chemistry, College of Engineering and Physical Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Xiwen Jia
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Talbot B. Stone
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lijun Zhou
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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5
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Kompatscher M, Bartosik K, Erharter K, Plangger R, Juen F, Kreutz C, Micura R, Westhof E, Erlacher M. Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons. Nucleic Acids Res 2024; 52:1374-1386. [PMID: 38050960 PMCID: PMC10853795 DOI: 10.1093/nar/gkad1136] [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: 09/13/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.
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Affiliation(s)
- Maria Kompatscher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kevin Erharter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Raphael Plangger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Fabian Sebastian Juen
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Matthias D Erlacher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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Viering B, Balogh H, Cox CF, Kirpekar OK, Akers AL, Federico VA, Valenzano GZ, Stempel R, Pickett HL, Lundin PM, Blackledge MS, Miller HB. Loratadine Combats Methicillin-Resistant Staphylococcus aureus by Modulating Virulence, Antibiotic Resistance, and Biofilm Genes. ACS Infect Dis 2024; 10:232-250. [PMID: 38153409 PMCID: PMC10788911 DOI: 10.1021/acsinfecdis.3c00616] [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: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has evolved to become resistant to multiple classes of antibiotics. New antibiotics are costly to develop and deploy, and they have a limited effective lifespan. Antibiotic adjuvants are molecules that potentiate existing antibiotics through nontoxic mechanisms. We previously reported that loratadine, the active ingredient in Claritin, potentiates multiple cell-wall active antibiotics in vitro and disrupts biofilm formation through a hypothesized inhibition of the master regulatory kinase Stk1. Loratadine and oxacillin combined repressed the expression of key antibiotic resistance genes in the bla and mec operons. We hypothesized that additional genes involved in antibiotic resistance, biofilm formation, and other cellular pathways would be modulated when looking transcriptome-wide. To test this, we used RNA-seq to quantify transcript levels and found significant effects in gene expression, including genes controlling virulence, antibiotic resistance, metabolism, transcription (core RNA polymerase subunits and sigma factors), and translation (a plethora of genes encoding ribosomal proteins and elongation factor Tu). We further demonstrated the impacts of these transcriptional effects by investigating loratadine treatment on intracellular ATP levels, persister formation, and biofilm formation and morphology. Loratadine minimized biofilm formation in vitro and enhanced the survival of infected Caenorhabditis elegans. These pleiotropic effects and their demonstrated outcomes on MRSA virulence and survival phenotypes position loratadine as an attractive anti-infective against MRSA.
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Affiliation(s)
- Brianna
L. Viering
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Halie Balogh
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Chloe F. Cox
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Owee K. Kirpekar
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - A. Luke Akers
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Victoria A. Federico
- Department
of Biology, High Point University, High Point, North Carolina 27268, United States
| | - Gabriel Z. Valenzano
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Robin Stempel
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Hannah L. Pickett
- Department
of Biology, High Point University, High Point, North Carolina 27268, United States
| | - Pamela M. Lundin
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Meghan S. Blackledge
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Heather B. Miller
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
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7
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Quaiyum S, Sun J, Marchand V, Sun G, Reed CJ, Motorin Y, Dedon PC, Minnick MF, de Crécy-Lagard V. Mapping the tRNA Modification Landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574729. [PMID: 38260440 PMCID: PMC10802484 DOI: 10.1101/2024.01.08.574729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens- Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana . Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. B. quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
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8
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Hao H, Zhang X, Chen S, Lan S, Li Z, Liu S, Yan X, Gao P, Chu Y. Comparative untargeted and targeted metabonomics reveal discriminations in metabolite profiles between Mycoplasma capricolum subsp. capripneumoniae and Mycoplasma capricolum subsp. capricolum. Front Microbiol 2023; 14:1294055. [PMID: 38143857 PMCID: PMC10740972 DOI: 10.3389/fmicb.2023.1294055] [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: 09/14/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Background Mycoplasmas are among the smallest prokaryotic microbes that can grow and proliferate on non-living media. They have reduced genomes, which may be associated with a concomitant reduction in their metabolic capacity. Mycoplasma capricolum subsp. capripneumoniae (Mccp) and Mycoplasma capricolum subsp. capricolum (Mcc), both belong to the Mycoplasma mycoides cluster, are significant important pathogenic Mycoplasma species in veterinary research field. They share high degree of genome homology but Mcc grows markedly faster and has higher growth titer than Mccp. Methods This study investigated the metabolites of these two pathogenic bacteria from the middle and late stages of the logarithmic growth phase through liquid chromatography-mass spectrometry-based metabolomics and targeted energy metabolomics. The multivariate analysis was conducted to identify significant differences between the two important Mycoplasma species. Results A total of 173 metabolites were identified. Of them, 33 and 34 metabolites involved in purine and pyrimidine, pyruvate metabolism, and amino acid synthesis were found to significantly differ in the middle and late stages, respectively. The abundance of fructose 1,6-bisphosphate, ADP, and pyruvate was higher in Mcc than in Mccp during the whole logarithmic period. Lactate was upregulated in slow-growing Mccp. The pH buffering agent N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid] added to media effectively prevented pH reduction and increase bacterial viability and protein biomass. The multivariate analysis revealed that the two Mycoplasma species significantly differed in glucose metabolism, growth factor transport and metabolism, cholesterol utilization, and environmental regulation. Conclusion The study data are beneficial for understanding the metabolomic characteristics of these two crucial Mycoplasma species and shedding more light on mycoplasma metabolism, and serve as a resource for the pathogenesis and development of related vaccines.
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Affiliation(s)
- Huafang Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Xiaoliang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Shengli Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Shimei Lan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Zhangcheng Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Shuang Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Xinmin Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Pengcheng Gao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Yuefeng Chu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
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9
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Weber M, Sogues A, Yus E, Burgos R, Gallo C, Martínez S, Lluch‐Senar M, Serrano L. Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium. Mol Syst Biol 2023; 19:e11301. [PMID: 37642167 PMCID: PMC10568206 DOI: 10.15252/msb.202211301] [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: 08/16/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.
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Affiliation(s)
- Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Adrià Sogues
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Eva Yus
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martínez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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10
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Breaker RR, Harris KA, Lyon SE, Wencker FDR, Fernando CM. Evidence that OLE RNA is a component of a major stress-responsive ribonucleoprotein particle in extremophilic bacteria. Mol Microbiol 2023; 120:324-340. [PMID: 37469248 DOI: 10.1111/mmi.15129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/30/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
OLE RNA is a ~600-nucleotide noncoding RNA present in many Gram-positive bacteria that thrive mostly in extreme environments, including elevated temperature, salt, and pH conditions. The precise biochemical functions of this highly conserved RNA remain unknown, but it forms a ribonucleoprotein (RNP) complex that localizes to cell membranes. Genetic disruption of the RNA or its essential protein partners causes reduced cell growth under various stress conditions. These phenotypes include sensitivity to short-chain alcohols, cold intolerance, reduced growth on sub-optimal carbon sources, and intolerance of even modest concentrations of Mg2+ . Thus, many bacterial species appear to employ OLE RNA as a component of an intricate RNP apparatus to monitor fundamental cellular processes and make physiological and metabolic adaptations. Herein we hypothesize that the OLE RNP complex is functionally equivalent to the eukaryotic TOR complexes, which integrate signals from various diverse pathways to coordinate processes central to cell growth, replication, and survival.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Kimberly A Harris
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Seth E Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Freya D R Wencker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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11
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Zheng R, Wang C, Cai R, Shan Y, Sun C. Mechanisms of nucleic acid degradation and high hydrostatic pressure tolerance of a novel deep-sea wall-less bacterium. mBio 2023; 14:e0095823. [PMID: 37551978 PMCID: PMC10470597 DOI: 10.1128/mbio.00958-23] [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: 04/16/2023] [Accepted: 06/26/2023] [Indexed: 08/09/2023] Open
Abstract
Wall-less bacteria are broadly distributed in diverse habitats. They evolved from a common ancestor within the Firmicutes phylum through reductive evolution. Here, we report the cultivation, characterization, and polyphasic taxonomic analysis of the novel free-living wall-less bacterium, Hujiaoplasma nucleasis zrk29. We demonstrated that strain zrk29 had a strong ability to degrade DNA and RNA both under laboratory conditions and in the deep sea. We found that nucleic acids induced strain zrk29 to release chronic bacteriophages which supported strain zrk29 and other marine bacteria to metabolize nucleic acids without lysing host cells. We also showed that strain zrk29 tolerated high hydrostatic pressure via two pathways: (i) by transporting cations into its cells to increase intracellular osmotic pressure and (ii) by adjusting the unsaturated fatty acid chain content in its cell membrane phospholipids to increase cell membrane fluidity. This study extends our understanding of free-living wall-less bacteria and provides a useful model to explore the unique adaptation mechanisms of deep-sea microbes. IMPORTANCE The unique physiology and survival strategies of the Tenericutes bacterium-a typical wall-less bacterium-have fascinated scientists and the public, especially in extreme deep-sea environments where there is high hydrostatic pressure (HHP) and limited availability of nutrients. Here, we have isolated a novel free-living Tenericutes strain from deep-sea sediment and have found that it metabolizes nucleic acids with the support of chronic bacteriophages. This Tenericutes strain tolerates HHP stress by increasing intracellular osmotic pressure and the unsaturated fatty acid chain content of phospholipids in its cell membrane. Our results provide insights into the unique physiology of deep-sea free-living Tenericutes bacteria and highlight the significant role that chronic bacteriophages play in assisting wall-less bacteria to adapt to harsh conditions.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yeqi Shan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
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12
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Alings F, Scharmann K, Eggers C, Böttcher B, Sokołowski M, Shvetsova E, Sharma P, Roth J, Rashiti L, Glatt S, Brunke S, Leidel SA. Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA. Nucleic Acids Res 2023; 51:8133-8149. [PMID: 37462076 PMCID: PMC10450187 DOI: 10.1093/nar/gkad564] [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: 08/25/2022] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 08/26/2023] Open
Abstract
Fungal pathogens threaten ecosystems and human health. Understanding the molecular basis of their virulence is key to develop new treatment strategies. Here, we characterize NCS2*, a point mutation identified in a clinical baker's yeast isolate. Ncs2 is essential for 2-thiolation of tRNA and the NCS2* mutation leads to increased thiolation at body temperature. NCS2* yeast exhibits enhanced fitness when grown at elevated temperatures or when exposed to oxidative stress, inhibition of nutrient signalling, and cell-wall stress. Importantly, Ncs2* alters the interaction and stability of the thiolase complex likely mediated by nucleotide binding. The absence of 2-thiolation abrogates the in vivo virulence of pathogenic baker's yeast in infected mice. Finally, hypomodification triggers changes in colony morphology and hyphae formation in the common commensal pathogen Candida albicans resulting in decreased virulence in a human cell culture model. These findings demonstrate that 2-thiolation of tRNA acts as a key mediator of fungal virulence and reveal new mechanistic insights into the function of the highly conserved tRNA-thiolase complex.
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Affiliation(s)
- Fiona Alings
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Karin Scharmann
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Cristian Eggers
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Böttcher
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Mikołaj Sokołowski
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ekaterina Shvetsova
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Joël Roth
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Leon Rashiti
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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13
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Xue C, Zhang Y, Li H, Liu Z, Gao W, Liu M, Wang H, Liu P, Zhao J. The genome of Candidatus phytoplasma ziziphi provides insights into their biological characteristics. BMC PLANT BIOLOGY 2023; 23:251. [PMID: 37173622 PMCID: PMC10176825 DOI: 10.1186/s12870-023-04243-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023]
Abstract
Phytoplasmas are obligate cell wall-less prokaryotic bacteria that primarily multiply in plant phloem tissue. Jujube witches' broom (JWB) associated with phytoplasma is a destructive disease of jujube (Ziziphus jujuba Mill.). Here we report the complete 'Candidatus Phytoplasma ziziphi' chromosome of strain Hebei-2018, which is a circular genome of 764,108-base pairs with 735 predicted CDS. Notably, extra 19,825 bp (from 621,995 to 641,819 bp) compared to the previously reported one complements the genes involved in glycolysis, such as pdhA, pdhB, pdhC, pdhD, ackA, pduL and LDH. The synonymous codon usage bias (CUB) patterns by using comparative genomics analysis among the 9 phytoplasmas were similar for most codons. The ENc-GC3s analysis among the 9 phytoplasmas showed a greater effect under the selection on the CUBs of phytoplasmas genes than mutation and other factors. The genome exhibited a strongly reduced ability in metabolic synthesis, while the genes encoding transporter systems were well developed. The genes involved in sec-dependent protein translocation system were also identified.The expressions of nine FtsHs encoding membrane associated ATP-dependent Zn proteases and Mn-SodA with redox capacity in the Ca. P. ziziphi was positively correlated with the phytoplasma concentration. Taken together, the genome will not only expand the number of phytoplasma species and provide some new information about Ca. P. ziziphi, but also contribute to exploring its pathogenic mechanism.
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Affiliation(s)
- Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Hongtai Li
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China
| | - Weilin Gao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Ping Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China.
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China.
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China.
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14
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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15
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Matsuike D, Tahara YO, Nonaka T, Wu HN, Hamaguchi T, Kudo H, Hayashi Y, Arai M, Miyata M. Structure and Function of Gli123 Involved in Mycoplasma mobile Gliding. J Bacteriol 2023; 205:e0034022. [PMID: 36749051 PMCID: PMC10029712 DOI: 10.1128/jb.00340-22] [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] [Indexed: 02/08/2023] Open
Abstract
Mycoplasma mobile is a fish pathogen that glides on solid surfaces by means of its own gliding machinery composed of internal and surface structures. In the present study, we focused on the function and structure of Gli123, a surface protein that is essential for the localization of other surface proteins. The amino acid sequence of Gli123, which is 1,128 amino acids long, contains lipoprotein-specific repeats. We isolated the native Gli123 protein from M. mobile cells and a recombinant protein, rGli123, from Escherichia coli. The isolated rGli123 complemented a nonbinding and nongliding mutant of M. mobile that lacked Gli123. Circular dichroism and rotary-shadowing electron microscopy (EM) showed that rGli123 has a structure that is not significantly different from that of the native protein. Rotary-shadowing EM suggested that Gli123 adopts two distinct globular and rod-like structures, depending on the ionic strength of the solution. Negative-staining EM coupled with single-particle analysis revealed that Gli123 forms a globular structure featuring a small protrusion with dimensions of approximately 15.7, 14.7, and 14.1 nm for the "height," major axis and minor axis, respectively. Small-angle X-ray scattering analyses indicated a rod-like structure composed of several tandem globular domains with total dimensions of approximately 34 nm in length and 6 nm in width. Both molecular structures were suggested to be dimers, based on the predicted molecular size and structure. Gli123 may have evolved by multiplication of repeating lipoprotein units and acquired a role for Gli521 and Gli349 assembly. IMPORTANCE Mycoplasmas are pathogenic bacteria that are widespread in animals. They are characterized by small cell and genome sizes but are equipped with unique abilities for infection, such as surface variation and gliding. Here, we focused on a surface-localizing protein named Gli123 that is essential for Mycoplasma mobile gliding. This study suggested that Gli123 undergoes drastic conformational changes between its rod-like and globular structures. These changes may be caused by a repetitive structure common in the surface proteins that is responsible for the modulation of the cell surface structure and related to the assembly process for the surface gliding machinery. An evolutionary process for surface proteins essential for this mycoplasma gliding was also suggested in the present study.
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Affiliation(s)
- Daiki Matsuike
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Yuhei O Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
- OCU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Takahiro Nonaka
- Graduate School of Science, Osaka City University, Osaka, Japan
| | - Heng Ning Wu
- Graduate School of Science, Osaka City University, Osaka, Japan
| | - Tasuku Hamaguchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, Japan
| | - Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Nada, Kobe, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan
- Environmental Science Center, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
- OCU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
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16
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Raval PK, Ngan WY, Gallie J, Agashe D. The layered costs and benefits of translational redundancy. eLife 2023; 12:81005. [PMID: 36862572 PMCID: PMC9981150 DOI: 10.7554/elife.81005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/25/2023] [Indexed: 03/03/2023] Open
Abstract
The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species' evolutionary history with feasts and famines.
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Affiliation(s)
- Parth K Raval
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
| | - Wing Yui Ngan
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Jenna Gallie
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Deepa Agashe
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
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17
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Kasai T, Miyata M. Motility Assays of Mycoplasma mobile Under Light Microscopy. Methods Mol Biol 2023; 2646:321-325. [PMID: 36842126 DOI: 10.1007/978-1-0716-3060-0_26] [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: 02/27/2023]
Abstract
Mycoplasma mobile forms a membrane protrusion at a pole as an organelle. M. mobile cells bind to solid surfaces and glide in the direction of the protrusion. In gliding motility, M. mobile cells catch, pull and release sialylated oligosaccharides on host cells. The observation of Mycoplasma species under light microscopy is useful for the analysis of adhesion ability and the motility mechanism.
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Affiliation(s)
- Taishi Kasai
- College of Science, Department of Life Science, Rikkyo University, Tokyo, Japan.
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Japan.,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan.,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
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18
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Toyonaga T, Miyata M. Purification and Structural Analysis of the Gliding Motility Machinery in Mycoplasma mobile. Methods Mol Biol 2023; 2646:311-319. [PMID: 36842125 DOI: 10.1007/978-1-0716-3060-0_25] [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: 02/27/2023]
Abstract
Isolating functional units from large insoluble protein complexes are a complex but valuable approach for quantitative and structural analysis. Mycoplasma mobile, a gliding bacterium, contains a large insoluble protein complex called gliding machinery. The machinery contains several chain structures formed by motors that are evolutionarily related to the F1-ATPase. Recently, we developed a method to purify functional motors and their chain structures using Triton X-100 and a high salt concentration buffer and resolved their structures using electron microscopy. In this chapter, we describe the processes of purification and structural analysis of functional motors for the gliding of M. mobile using negative-staining electron microscopy.
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Affiliation(s)
- Takuma Toyonaga
- Graduate School of Science, Osaka City University, Osaka, Japan. .,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan. .,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan.
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Japan.,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan.,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
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19
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Kiyama H, Kakizawa S, Sasajima Y, Tahara YO, Miyata M. Reconstitution of a minimal motility system based on Spiroplasma swimming by two bacterial actins in a synthetic minimal bacterium. SCIENCE ADVANCES 2022; 8:eabo7490. [PMID: 36449609 PMCID: PMC9710875 DOI: 10.1126/sciadv.abo7490] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 10/14/2022] [Indexed: 05/24/2023]
Abstract
Motility is one of the most important features of life, but its evolutionary origin remains unknown. In this study, we focused on Spiroplasma, commensal, or parasitic bacteria. They swim by switching the helicity of a ribbon-like cytoskeleton that comprises six proteins, each of which evolved from a nucleosidase and bacterial actin called MreB. We expressed these proteins in a synthetic, nonmotile minimal bacterium, JCVI-syn3B, whose reduced genome was computer-designed and chemically synthesized. The synthetic bacterium exhibited swimming motility with features characteristic of Spiroplasma swimming. Moreover, combinations of Spiroplasma MreB4-MreB5 and MreB1-MreB5 produced a helical cell shape and swimming. These results suggest that the swimming originated from the differentiation and coupling of bacterial actins, and we obtained a minimal system for motility of the synthetic bacterium.
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Affiliation(s)
- Hana Kiyama
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shigeyuki Kakizawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Sasajima
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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20
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Sasajima Y, Kato T, Miyata T, Kawamoto A, Namba K, Miyata M. Isolation and structure of the fibril protein, a major component of the internal ribbon for Spiroplasma swimming. Front Microbiol 2022; 13:1004601. [PMID: 36274716 PMCID: PMC9582952 DOI: 10.3389/fmicb.2022.1004601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Abstract
Spiroplasma, which are known pathogens and commensals of arthropods and plants, are helical-shaped bacteria that lack a peptidoglycan layer. Spiroplasma swim by alternating between left- and right-handed helicity. Of note, this system is not related to flagellar motility, which is widespread in bacteria. A helical ribbon running along the inner side of the helical cell should be responsible for cell helicity and comprises the bacterial actin homolog, MreB, and a protein specific to Spiroplasma, fibril. Here, we isolated the ribbon and its major component, fibril filament, for electron microscopy (EM) analysis. Single-particle analysis of the fibril filaments using the negative-staining EM revealed a three-dimensional chain structure composed of rings with a size of 11 nm wide and 6 nm long, connected by a backbone cylinder with an 8.7 nm interval with a twist along the filament axis. This structure was verified through EM tomography of quick-freeze deep-etch replica sample, with a focus on its handedness. The handedness and pitch of the helix for the isolated ribbon and fibril filament agreed with those of the cell in the resting state. Structures corresponding to the alternative state were not identified. These results suggest that the helical cell structure is supported by fibril filaments; however, the helical switch is caused by the force generated by the MreB proteins. The isolation and structural outline of the fibril filaments provide crucial information for an in-depth clarification of the unique swimming mechanism of Spiroplasma.
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Affiliation(s)
- Yuya Sasajima
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan,RIKEN Center for Biosystems Dynamics Research and Spring-8 Center, Suita, Osaka, Japan,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Osaka, Japan,*Correspondence: Makoto Miyata,
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21
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Bommisetti P, Young A, Bandarian V. Elucidation of the substrate of tRNA-modifying enzymes MnmEG leads to in vitro reconstitution of an evolutionarily conserved uridine hypermodification. J Biol Chem 2022; 298:102548. [PMID: 36181794 PMCID: PMC9626948 DOI: 10.1016/j.jbc.2022.102548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG collectively install a carboxymethylaminomethyl (cmnm) group at the fifth position of wobble uridines of several tRNA species. While the reaction catalyzed by MnmEG is one of the central steps in the biosynthesis of the methylaminomethyl (mnm) posttranscriptional tRNA modification, details of the reaction remain elusive. Glycine is known to be the source of the carboxy methylamino moiety of cmnm, and a tetrahydrofolate (THF) analog is thought to supply the one carbon that is appended to the fifth position of U. However, the nature of the folate analog remains unknown. This article reports the in vitro biochemical reconstitution of the MnmEG reaction. Using isotopically labeled methyl and methylene THF analogs, we demonstrate that methylene THF is the true substrate. We also show that reduced FAD is required for the reaction and that DTT can replace the NADH in its role as a reductant. We discuss the implications of these methylene-THF and reductant requirements on the mechanism of this key tRNA modification catalyzed by MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony Young
- Soliome Inc, 479 Jessie Street, San Francisco, CA 94103, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States.
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22
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Genome Editing of Veterinary Relevant Mycoplasmas Using a CRISPR-Cas Base Editor System. Appl Environ Microbiol 2022; 88:e0099622. [PMID: 36000854 PMCID: PMC9469718 DOI: 10.1128/aem.00996-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasmas are minimal bacteria that infect humans, wildlife, and most economically relevant livestock species. Mycoplasma infections cause a large range of chronic inflammatory diseases, eventually leading to death in some animals. Due to the lack of efficient recombination and genome engineering tools for most species, the production of mutant strains for the identification of virulence factors and the development of improved vaccine strains is limited. Here, we demonstrate the adaptation of an efficient Cas9-Base Editor system to introduce targeted mutations into three major pathogenic species that span the phylogenetic diversity of these bacteria: the avian pathogen Mycoplasma gallisepticum and the two most important bovine mycoplasmas, Mycoplasma bovis and Mycoplasma mycoides subsp. mycoides. As a proof of concept, we successfully used an inducible SpdCas9-pmcDA1 cytosine deaminase system to disrupt several major virulence factors in these pathogens. Various induction times and inducer concentrations were evaluated to optimize editing efficiency. The optimized system was powerful enough to disrupt 54 of 55 insertion sequence transposases in a single experiment. Whole-genome sequencing of the edited strains showed that off-target mutations were limited, suggesting that most variations detected in the edited genomes are Cas9-independent. This effective, rapid, and easy-to-use genetic tool opens a new avenue for the study of these important animal pathogens and likely the entire class Mollicutes. IMPORTANCE Mycoplasmas are minimal pathogenic bacteria that infect a wide range of hosts, including humans, livestock, and wild animals. Major pathogenic species cause acute to chronic infections involving still poorly characterized virulence factors. The lack of precise genome editing tools has hampered functional studies of many species, leaving multiple questions about the molecular basis of their pathogenicity unanswered. Here, we demonstrate the adaptation of a CRISPR-derived base editor for three major pathogenic species: Mycoplasma gallisepticum, Mycoplasma bovis, and Mycoplasma mycoides subsp. mycoides. Several virulence factors were successfully targeted, and we were able to edit up to 54 target sites in a single step. The availability of this efficient and easy-to-use genetic tool will greatly facilitate functional studies of these economically important bacteria.
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23
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Tsurumaki M, Saito M, Tomita M, Kanai A. Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis. RNA (NEW YORK, N.Y.) 2022; 28:1041-1057. [PMID: 35688647 PMCID: PMC9297842 DOI: 10.1261/rna.079103.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/06/2022] [Indexed: 06/01/2023]
Abstract
The candidate phyla radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and they often lack ribosomal proteins uL1, bL9, and/or uL30, which are basically ubiquitous in non-CPR bacteria. Here, we comprehensively analyzed the genomic information on CPR bacteria and identified their unique properties. The distribution of protein lengths in CPR bacteria peaks at around 100-150 amino acids, whereas the position of the peak varies in the range of 100-300 amino acids in free-living non-CPR bacteria, and at around 100-200 amino acids in most symbiotic non-CPR bacteria. These results show that the proteins of CPR bacteria are smaller, on average, than those of free-living non-CPR bacteria, like those of symbiotic non-CPR bacteria. We found that ribosomal proteins bL28, uL29, bL32, and bL33 have been lost in CPR bacteria in a taxonomic lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins of CPR differ, in part, from those of non-CPR bacteria, with missing regions or specifically added regions. We also found that several regions in the 16S, 23S, and 5S rRNAs of CPR bacteria are lacking, which presumably caused the total predicted lengths of the three rRNAs of CPR bacteria to be smaller than those of non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than those in free-living non-CPR bacteria, with simplified surface structures.
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Affiliation(s)
- Megumi Tsurumaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Motofumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
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24
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Evsyutina DV, Semashko TA, Galyamina MA, Kovalchuk SI, Ziganshin RH, Ladygina VG, Fisunov GY, Pobeguts OV. Molecular Basis of the Slow Growth of Mycoplasma hominis on Different Energy Sources. Front Cell Infect Microbiol 2022; 12:918557. [PMID: 35873139 PMCID: PMC9301678 DOI: 10.3389/fcimb.2022.918557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/15/2022] [Indexed: 12/05/2022] Open
Abstract
Mycoplasma hominis is an opportunistic urogenital pathogen in vertebrates. It is a non-glycolytic species that produces energy via arginine degradation. Among genital mycoplasmas, M. hominis is the most commonly reported to play a role in systemic infections and can persist in the host for a long time. However, it is unclear how M. hominis proceeds under arginine limitation. The recent metabolic reconstruction of M. hominis has demonstrated its ability to catabolize deoxyribose phosphate to produce ATP. In this study, we cultivated M. hominis on two different energy sources (arginine and thymidine) and demonstrated the differences in growth rate, antibiotic sensitivity, and biofilm formation. Using label-free quantitative proteomics, we compared the proteome of M. hominis under these conditions. A total of 466 proteins were identified from M. hominis, representing approximately 85% of the predicted proteome, while the levels of 94 proteins changed significantly. As expected, we observed changes in the levels of metabolic enzymes. The energy source strongly affects the synthesis of enzymes related to RNA modifications and ribosome assembly. The translocation of lipoproteins and other membrane-associated proteins was also impaired. Our study, the first global characterization of the proteomic switching of M. hominis in arginine-deficiency media, illustrates energy source-dependent control of pathogenicity factors and can help to determine the mechanisms underlying the interaction between the growth rate and fitness of genome-reduced bacteria.
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Affiliation(s)
- Daria V. Evsyutina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
- *Correspondence: Daria V. Evsyutina,
| | - Tatiana A. Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
| | - Maria A. Galyamina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10, Moscow, Russia
| | - Valentina G. Ladygina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
| | - Gleb Y. Fisunov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
| | - Olga V. Pobeguts
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
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25
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Imaging Minimal Bacteria at the Nanoscale: a Reliable and Versatile Process to Perform Single-Molecule Localization Microscopy in Mycoplasmas. Microbiol Spectr 2022; 10:e0064522. [PMID: 35638916 PMCID: PMC9241803 DOI: 10.1128/spectrum.00645-22] [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] [Indexed: 11/24/2022] Open
Abstract
Mycoplasmas are the smallest free-living organisms. These bacteria are important models for both fundamental and synthetic biology, owing to their highly reduced genomes. They are also relevant in the medical and veterinary fields, as they are pathogenic to both humans and most livestock species. Mycoplasma cells have minute sizes, often in the 300- to 800-nm range. As these dimensions are close to the diffraction limit of visible light, fluorescence imaging in mycoplasmas is often poorly informative. Recently developed superresolution imaging techniques can break this diffraction limit, improving the imaging resolution by an order of magnitude and offering a new nanoscale vision of the organization of these bacteria. These techniques have, however, not been applied to mycoplasmas before. Here, we describe an efficient and reliable protocol to perform single-molecule localization microscopy (SMLM) imaging in mycoplasmas. We provide a polyvalent transposon-based system to express the photoconvertible fluorescent protein mEos3.2, enabling photo-activated localization microscopy (PALM) in most Mycoplasma species. We also describe the application of direct stochastic optical reconstruction microscopy (dSTORM). We showcase the potential of these techniques by studying the subcellular localization of two proteins of interest. Our work highlights the benefits of state-of-the-art microscopy techniques for mycoplasmology and provides an incentive to further the development of SMLM strategies to study these organisms in the future. IMPORTANCE Mycoplasmas are important models in biology, as well as highly problematic pathogens in the medical and veterinary fields. The very small sizes of these bacteria, well below a micron, limits the usefulness of traditional fluorescence imaging methods, as their resolution limit is similar to the dimensions of the cells. Here, to bypass this issue, we established a set of state-of-the-art superresolution microscopy techniques in a wide range of Mycoplasma species. We describe two strategies: PALM, based on the expression of a specific photoconvertible fluorescent protein, and dSTORM, based on fluorophore-coupled antibody labeling. With these methods, we successfully performed single-molecule imaging of proteins of interest at the surface of the cells and in the cytoplasm, at lateral resolutions well below 50 nm. Our work paves the way toward a better understanding of mycoplasma biology through imaging of subcellular structures at the nanometer scale.
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26
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Talenton V, Baby V, Gourgues G, Mouden C, Claverol S, Vashee S, Blanchard A, Labroussaa F, Jores J, Arfi Y, Sirand-Pugnet P, Lartigue C. Genome Engineering of the Fast-Growing Mycoplasma feriruminatoris toward a Live Vaccine Chassis. ACS Synth Biol 2022; 11:1919-1930. [PMID: 35511588 PMCID: PMC9128628 DOI: 10.1021/acssynbio.2c00062] [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] [Indexed: 12/12/2022]
Abstract
Development of a new generation of vaccines is a key challenge for the control of infectious diseases affecting both humans and animals. Synthetic biology methods offer new ways to engineer bacterial chassis that can be used as vectors to present heterologous antigens and train the immune system against pathogens. Here, we describe the construction of a bacterial chassis based on the fast-growing Mycoplasma feriruminatoris, and the first steps toward its application as a live vaccine against contagious caprine pleuropneumonia (CCPP). To do so, the M. feriruminatoris genome was cloned in yeast, modified by iterative cycles of Cas9-mediated deletion of loci encoding virulence factors, and transplanted back in Mycoplasma capricolum subsp. capricolum recipient cells to produce the designed M. feriruminatoris chassis. Deleted genes encoded the glycerol transport and metabolism systems GtsABCD and GlpOKF and the Mycoplasma Ig binding protein-Mycoplasma Ig protease (MIB-MIP) immunoglobulin cleavage system. Phenotypic assays of the M. feriruminatoris chassis confirmed the corresponding loss of H2O2 production and IgG cleavage activities, while growth remained unaltered. The resulting mycoplasma chassis was further evaluated as a platform for the expression of heterologous surface proteins. A genome locus encoding an inactivated MIB-MIP system from the CCPP-causative agent Mycoplasma capricolum subsp. capripneumoniae was grafted in replacement of its homolog at the original locus in the chassis genome. Both heterologous proteins were detected in the resulting strain using proteomics, confirming their expression. This study demonstrates that advanced genome engineering methods are henceforth available for the fast-growing M. feriruminatoris, facilitating the development of novel vaccines, in particular against major mycoplasma diseases.
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Affiliation(s)
- Vincent Talenton
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | - Vincent Baby
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
- Département de Biologie, Université de Sherbrooke, J1K 2R1 Sherbrooke, Québec, Canada
| | - Geraldine Gourgues
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | | | - Stephane Claverol
- Plateforme Proteome, University of Bordeaux, F-33076 Bordeaux, France
| | - Sanjay Vashee
- J. Craig Venter Institute, Rockville, Maryland 20850, United States
| | - Alain Blanchard
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | - Fabien Labroussaa
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Yonathan Arfi
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | | | - Carole Lartigue
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
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27
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Garzón MJ, Reyes-Prieto M, Gil R. The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes. Front Microbiol 2022; 13:858983. [PMID: 35479634 PMCID: PMC9035817 DOI: 10.3389/fmicb.2022.858983] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
The current theoretical proposals of minimal genomes have not attempted to outline the essential machinery for proper translation in cells. Here, we present a proposal of a minimal translation machinery based on (1) a comparative analysis of bacterial genomes of insects’ endosymbionts using a machine learning classification algorithm, (2) the empiric genomic information obtained from Mycoplasma mycoides JCVI-syn3.0 the first minimal bacterial genome obtained by design and synthesis, and (3) a detailed functional analysis of the candidate genes based on essentiality according to the DEG database (Escherichia coli and Bacillus subtilis) and the literature. This proposed minimal translational machinery is composed by 142 genes which must be present in any synthetic prokaryotic cell designed for biotechnological purposes, 76.8% of which are shared with JCVI-syn3.0. Eight additional genes were manually included in the proposal for a proper and efficient translation.
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Affiliation(s)
| | - Mariana Reyes-Prieto
- Institute for Integrative Systems Biology, Universitat de València–Consejo Superior de Investigaciones Científicas, Paterna, Spain
- Sequencing and Bioinformatics Service, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community, Valencia, Spain
| | - Rosario Gil
- Departament de Genètica, Universitat de València, Burjassot, Spain
- Institute for Integrative Systems Biology, Universitat de València–Consejo Superior de Investigaciones Científicas, Paterna, Spain
- *Correspondence: Rosario Gil,
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28
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Jüttner M, Ferreira-Cerca S. Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis. Mol Biol Evol 2022; 39:6547259. [PMID: 35275997 PMCID: PMC8997704 DOI: 10.1093/molbev/msac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.
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Affiliation(s)
- Michael Jüttner
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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29
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Han NC, Kavoor A, Ibba M. Characterizing the amino acid activation center of the naturally editing-deficient aminoacyl-tRNA synthetase PheRS in Mycoplasma mobile. FEBS Lett 2022; 596:947-957. [PMID: 35038769 DOI: 10.1002/1873-3468.14287] [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: 07/05/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 11/09/2022]
Abstract
To ensure correct amino acids are incorporated during protein synthesis, aminoacyl-tRNA synthetases (aaRSs) employ proofreading mechanisms collectively referred to as editing. Although editing is important for viability, editing-deficient aaRSs have been identified in host-dependent organisms. In Mycoplasma mobile, editing-deficient PheRS and LeuRS have been identified. We characterized the amino acid activation site of MmPheRS and identified a previously unknown hyperaccurate mutation, L287F. Additionally, we report that m-Tyr, an oxidation byproduct of Phe which is toxic to editing-deficient cells, is poorly discriminated by MmPheRS activation and is not subjected to editing. Furthermore, expressing MmPheRS and the hyperaccurate variants renders Escherichia coli susceptible to m-Tyr stress, indicating that active site discrimination is insufficient in tolerating excess m-Tyr.
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Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA
| | - Arundhati Kavoor
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA.,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA.,Schmid College of Science and Technology, Chapman university, Orange, CA, 92866, USA
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30
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Ho AT, Hurst LD. Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage. Mol Biol Evol 2022; 39:msab326. [PMID: 34751397 PMCID: PMC8789281 DOI: 10.1093/molbev/msab326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3'untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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31
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Jüttner M, Ferreira-Cerca S. A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life. Methods Mol Biol 2022; 2533:3-22. [PMID: 35796979 PMCID: PMC9761495 DOI: 10.1007/978-1-0716-2501-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Ribosomes are universally conserved ribonucleoprotein complexes involved in the decoding of the genetic information contained in messenger RNAs into proteins. Accordingly, ribosome biogenesis is a fundamental cellular process required for functional ribosome homeostasis and to preserve satisfactory gene expression capability.Although the ribosome is universally conserved, its biogenesis shows an intriguing degree of variability across the tree of life . These differences also raise yet unresolved questions. Among them are (a) what are, if existing, the remaining ancestral common principles of ribosome biogenesis ; (b) what are the molecular impacts of the evolution history and how did they contribute to (re)shape the ribosome biogenesis pathway across the tree of life ; (c) what is the extent of functional divergence and/or convergence (functional mimicry), and in the latter case (if existing) what is the molecular basis; (d) considering the universal ribosome conservation, what is the capability of functional plasticity and cellular adaptation of the ribosome biogenesis pathway?In this review, we provide a brief overview of ribosome biogenesis across the tree of life and try to illustrate some potential and/or emerging answers to these unresolved questions.
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Affiliation(s)
- Michael Jüttner
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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Ferreira-Cerca S. The dark side of the ribosome life cycle. RNA Biol 2022; 19:1045-1049. [PMID: 36082947 PMCID: PMC9467602 DOI: 10.1080/15476286.2022.2121421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Thanks to genetics, biochemistry, and structural biology many features of the ribosome´s life cycles in models of bacteria, eukaryotes, and some organelles have been revealed to near-atomic details. Collectively, these studies have provided a very detailed understanding of what are now well-established prototypes for ribosome biogenesis and function as viewed from a 'classical' model organisms perspective. However, very important challenges remain ahead to explore the functional and structural diversity of both ribosome biogenesis and function across the biological diversity on earth. Particularly, the 'third domain of life', the archaea, and also many non-model bacterial and eukaryotic organisms have been comparatively neglected. Importantly, characterizing these additional biological systems will not only offer a yet untapped window to enlighten the evolution of ribosome biogenesis and function but will also help to unravel fundamental principles of molecular adaptation of these central cellular processes.
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Affiliation(s)
- Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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The Role of the Universally Conserved ATPase YchF/Ola1 in Translation Regulation during Cellular Stress. Microorganisms 2021; 10:microorganisms10010014. [PMID: 35056463 PMCID: PMC8779481 DOI: 10.3390/microorganisms10010014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
The ability to respond to metabolic or environmental changes is an essential feature in all cells and involves both transcriptional and translational regulators that adjust the metabolic activity to fluctuating conditions. While transcriptional regulation has been studied in detail, the important role of the ribosome as an additional player in regulating gene expression is only beginning to emerge. Ribosome-interacting proteins are central to this translational regulation and include universally conserved ribosome interacting proteins, such as the ATPase YchF (Ola1 in eukaryotes). In both eukaryotes and bacteria, the cellular concentrations of YchF/Ola1 determine the ability to cope with different stress conditions and are linked to several pathologies in humans. The available data indicate that YchF/Ola1 regulates the stress response via controlling non-canonical translation initiation and via protein degradation. Although the molecular mechanisms appear to be different between bacteria and eukaryotes, increased non-canonical translation initiation is a common consequence of YchF/Ola1 regulated translational control in E. coli and H. sapiens. In this review, we summarize recent insights into the role of the universally conserved ATPase YchF/Ola1 in adapting translation to unfavourable conditions.
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Sasajima Y, Miyata M. Prospects for the Mechanism of Spiroplasma Swimming. Front Microbiol 2021; 12:706426. [PMID: 34512583 PMCID: PMC8432965 DOI: 10.3389/fmicb.2021.706426] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/12/2021] [Indexed: 11/18/2022] Open
Abstract
Spiroplasma are helical bacteria that lack a peptidoglycan layer. They are widespread globally as parasites of arthropods and plants. Their infectious processes and survival are most likely supported by their unique swimming system, which is unrelated to well-known bacterial motility systems such as flagella and pili. Spiroplasma swims by switching the left- and right-handed helical cell body alternately from the cell front. The kinks generated by the helicity shift travel down along the cell axis and rotate the cell body posterior to the kink position like a screw, pushing the water backward and propelling the cell body forward. An internal structure called the "ribbon" has been focused to elucidate the mechanisms for the cell helicity formation and swimming. The ribbon is composed of Spiroplasma-specific fibril protein and a bacterial actin, MreB. Here, we propose a model for helicity-switching swimming focusing on the ribbon, in which MreBs generate a force like a bimetallic strip based on ATP energy and switch the handedness of helical fibril filaments. Cooperative changes of these filaments cause helicity to shift down the cell axis. Interestingly, unlike other motility systems, the fibril protein and Spiroplasma MreBs can be traced back to their ancestors. The fibril protein has evolved from methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase, which is essential for growth, and MreBs, which function as a scaffold for peptidoglycan synthesis in walled bacteria.
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Affiliation(s)
- Yuya Sasajima
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
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Londei P, Ferreira-Cerca S. Ribosome Biogenesis in Archaea. Front Microbiol 2021; 12:686977. [PMID: 34367089 PMCID: PMC8339473 DOI: 10.3389/fmicb.2021.686977] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/14/2021] [Indexed: 12/02/2022] Open
Abstract
Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.
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Affiliation(s)
- Paola Londei
- Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
| | - Sébastien Ferreira-Cerca
- Biochemistry III - Regensburg Center for Biochemistry, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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Abstract
Mycoplasma mobile, a fish pathogen, exhibits gliding motility using ATP hydrolysis on solid surfaces, including animal cells. The gliding machinery can be divided into surface and internal structures. The internal structure of the motor is composed of 28 so-called “chains” that are each composed of 17 repeating protein units called “particles.” These proteins include homologs of the catalytic α and β subunits of F1-ATPase. In this study, we isolated the particles and determined their structures using negative-staining electron microscopy and high-speed atomic force microscopy. The isolated particles were composed of five proteins, MMOB1660 (α-subunit homolog), -1670 (β-subunit homolog), -1630, -1620, and -4530, and showed ATP hydrolyzing activity. The two-dimensional (2D) structure, with dimensions of 35 and 26 nm, showed a dimer of hexameric ring approximately 12 nm in diameter, resembling F1-ATPase catalytic (αβ)3. We isolated the F1-like ATPase unit, which is composed of MMOB1660, -1670, and -1630. Furthermore, we isolated the chain and analyzed the three-dimensional (3D) structure, showing that dimers of mushroom-like structures resembling F1-ATPase were connected and aligned along the dimer axis at 31-nm intervals. An atomic model of F1-ATPase catalytic (αβ)3 from Bacillus PS3 was successfully fitted to each hexameric ring of the mushroom-like structure. These results suggest that the motor for M. mobile gliding shares an evolutionary origin with F1-ATPase. Based on the obtained structure, we propose possible force transmission processes in the gliding mechanism.
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Valach M, Gonzalez Alcazar JA, Sarrasin M, Lang BF, Gray MW, Burger G. An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome. Mol Biol Evol 2021; 38:788-804. [PMID: 32886790 PMCID: PMC7947838 DOI: 10.1093/molbev/msaa223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling. Since most experimental information on mitoribosome makeup comes from eukaryotes having derived mitochondrial genomes and mt-rRNAs, we tested this assumption by investigating the mitochondrial translation machinery of jakobids, a lineage of unicellular protists with the most bacteria-like mitochondrial genomes. We report here proteomics analyses of the Andalucia godoyi small mitoribosomal subunit and in silico transcriptomic and comparative genome analyses of four additional jakobids. Jakobids have mt-rRNA structures that minimally differ from their bacterial counterparts. Yet, with at least 31 small subunit and 44 large subunit mtRPs, the mitoriboproteome of Andalucia is essentially as complex as that in animals or fungi. Furthermore, the relatively high conservation of jakobid sequences has helped to clarify the identity of several mtRPs, previously considered to be lineage-specific, as divergent homologs of conserved M-mtRPs, notably mS22 and mL61. The coexistence of bacteria-like mt-rRNAs and a complex mitoriboproteome refutes the view that M-mtRPs were ancestrally recruited to stabilize deviations of mt-rRNA structural elements. We postulate instead that the numerous M-mtRPs acquired in the last eukaryotic common ancestor allowed mt-rRNAs to pursue a broad range of evolutionary trajectories across lineages: from dramatic reduction to acquisition of novel elements to structural conservatism.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - José Angel Gonzalez Alcazar
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Matt Sarrasin
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - B Franz Lang
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gertraud Burger
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
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Nikolaeva DD, Gelfand MS, Garushyants SK. Simplification of Ribosomes in Bacteria with Tiny Genomes. Mol Biol Evol 2021; 38:58-66. [PMID: 32681797 PMCID: PMC7782861 DOI: 10.1093/molbev/msaa184] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
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Affiliation(s)
- Daria D Nikolaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
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Lucas BA, Himes BA, Xue L, Grant T, Mahamid J, Grigorieff N. Locating macromolecular assemblies in cells by 2D template matching with cisTEM. eLife 2021; 10:e68946. [PMID: 34114559 PMCID: PMC8219381 DOI: 10.7554/elife.68946] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022] Open
Abstract
For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software cisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated Mycoplasma pneumoniae cells with high precision and sensitivity, demonstrating that this is a versatile tool for in situ visual proteomics and in situ structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.
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Affiliation(s)
- Bronwyn A Lucas
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Benjamin A Himes
- Howard Hughes Medical Institute, RNA Therapeutics Institute, The University of Massachusetts Medical SchoolWorcesterUnited States
| | - Liang Xue
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Timothy Grant
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Nikolaus Grigorieff
- Howard Hughes Medical Institute, RNA Therapeutics Institute, The University of Massachusetts Medical SchoolWorcesterUnited States
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Yi X, He S, Wang S, Zhao H, Wu M, Liu S, Sun X. Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1. Arch Anim Breed 2021; 64:147-155. [PMID: 34084913 PMCID: PMC8162237 DOI: 10.5194/aab-64-147-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/26/2021] [Indexed: 02/07/2023] Open
Abstract
The tRNA modification gene in eukaryotes is relatively
conservative. As an important modification gene, the TRDMT1 gene plays an
important role in maintaining tRNA structural maintenance and reducing
mistranslation of protein translation by methylation of specific tRNA
subpopulations. Mouse and zebrafish TRDMT1 knockout experiments indicate that it
may mediate growth and development through tRNA modification. However, there
are no systematic reports on the function of tRNA-modified genes in
livestock. In this study, Qinchuan cattle DNA pool sequencing technology
was used. A G>C mutation in the -1223 bp position upstream of
the TRDMT1 translation initiator codon was found. At this locus, the dual-luciferase assay indicated that different genotypes cause differences in
transcriptional activity (P<0.05). Our experiment detected a natural
genetic variation of a tRNA modification gene TRDMT1, which may provide potential
natural molecular materials for the study of tRNA modification.
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Affiliation(s)
- Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Shuai He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Shirong Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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Zhou J, Lénon M, Ravanat JL, Touati N, Velours C, Podskoczyj K, Leszczynska G, Fontecave M, Barras F, Golinelli-Pimpaneau B. Iron-sulfur biology invades tRNA modification: the case of U34 sulfuration. Nucleic Acids Res 2021; 49:3997-4007. [PMID: 33744947 PMCID: PMC8053098 DOI: 10.1093/nar/gkab138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Sulfuration of uridine 34 in the anticodon of tRNAs is conserved in the three domains of life, guaranteeing fidelity of protein translation. In eubacteria, it is catalyzed by MnmA-type enzymes, which were previously concluded not to depend on an iron-sulfur [Fe-S] cluster. However, we report here spectroscopic and iron/sulfur analysis, as well as in vitro catalytic assays and site-directed mutagenesis studies unambiguously showing that MnmA from Escherichia coli can bind a [4Fe-4S] cluster, which is essential for sulfuration of U34-tRNA. We propose that the cluster serves to bind and activate hydrosulfide for nucleophilic attack on the adenylated nucleoside. Intriguingly, we found that E. coli cells retain s2U34 biosynthesis in the ΔiscUA ΔsufABCDSE strain, lacking functional ISC and SUF [Fe-S] cluster assembly machineries, thus suggesting an original and yet undescribed way of maturation of MnmA. Moreover, we report genetic analysis showing the importance of MnmA for sustaining oxidative stress.
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Affiliation(s)
- Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Marine Lénon
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, UMR CNRS 2001, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, F-38000 Grenoble, France
| | - Nadia Touati
- IR CNRS Renard, Chimie-ParisTech, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Frédéric Barras
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, UMR CNRS 2001, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
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Abstract
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.
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Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax TEF, Albers SV, Oeffinger M, Ferreira-Cerca S. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucleic Acids Res 2021; 49:1662-1687. [PMID: 33434266 PMCID: PMC7897474 DOI: 10.1093/nar/gkaa1268] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.
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Affiliation(s)
- Robert Knüppel
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Michael Kern
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Felix Grünberger
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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44
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Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution. Genes (Basel) 2021; 12:genes12020140. [PMID: 33499018 PMCID: PMC7912444 DOI: 10.3390/genes12020140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical L-shaped architecture. Paradoxically, despite the high conservation of modified nucleotides in the T-loop, enzymes catalyzing their formation depend mostly on the considered organism, attesting for an independent but convergent evolution of the post-transcriptional modification processes. The driving force behind this is the preservation of a native conformation of the tRNA elbow that underlies the various interactions of tRNA molecules with different cellular components.
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Nikolaeva DD, Gelfand MS, Garushyants SK. Simplification of Ribosomes in Bacteria with Tiny Genomes. Mol Biol Evol 2021. [PMID: 32681797 DOI: 10.1101/755876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
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Affiliation(s)
- Daria D Nikolaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
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O'Reilly FJ, Xue L, Graziadei A, Sinn L, Lenz S, Tegunov D, Blötz C, Singh N, Hagen WJH, Cramer P, Stülke J, Mahamid J, Rappsilber J. In-cell architecture of an actively transcribing-translating expressome. Science 2020; 369:554-557. [PMID: 32732422 DOI: 10.1126/science.abb3758] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae We combined whole-cell cross-linking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at subnanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA at the interface between a NusG-bound elongating RNAP and the ribosome and propose that it can mediate transcription-translation coupling. Translation inhibition dissociated the expressome, whereas transcription inhibition stalled and rearranged it. Thus, the active expressome architecture requires both translation and transcription elongation within the cell.
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Affiliation(s)
- Francis J O'Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Liang Xue
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Ludwig Sinn
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Swantje Lenz
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Dimitry Tegunov
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Cedric Blötz
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Neil Singh
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany. .,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
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Rose S, Auxilien S, Havelund JF, Kirpekar F, Huber H, Grosjean H, Douthwaite S. The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications. Nucleic Acids Res 2020; 48:6906-6918. [PMID: 32459340 PMCID: PMC7337903 DOI: 10.1093/nar/gkaa411] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/19/2020] [Accepted: 05/06/2020] [Indexed: 01/31/2023] Open
Abstract
The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis grow physically coupled under identical hyperthermic conditions. We report here two fundamentally different routes by which these archaea modify the key conserved nucleotide U54 within their tRNA T-loops. In N. equitans, this nucleotide is methylated by the S-adenosylmethionine-dependent enzyme NEQ053 to form m5U54, and a recombinant version of this enzyme maintains specificity for U54 in Escherichia coli. In N. equitans, m5U54 is subsequently thiolated to form m5s2U54. In contrast, I. hospitalis isomerizes U54 to pseudouridine prior to methylating its N1-position and thiolating the O4-position of the nucleobase to form the previously uncharacterized nucleotide m1s4Ψ. The methyl and thiol groups in m1s4Ψ and m5s2U are presented within the T-loop in a spatially identical manner that stabilizes the 3′-endo-anti conformation of nucleotide-54, facilitating stacking onto adjacent nucleotides and reverse-Hoogsteen pairing with nucleotide m1A58. Thus, two distinct structurally-equivalent solutions have evolved independently and convergently to maintain the tertiary fold of tRNAs under extreme hyperthermic conditions.
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Affiliation(s)
- Simon Rose
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Sylvie Auxilien
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jesper F Havelund
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Finn Kirpekar
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Harald Huber
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Henri Grosjean
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stephen Douthwaite
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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de Crécy-Lagard V, Jaroch M. Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. Trends Microbiol 2020; 29:41-53. [PMID: 32718697 DOI: 10.1016/j.tim.2020.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Modified nucleotides in tRNA are critical components of the translation apparatus, but their importance in the process of translational regulation had until recently been greatly overlooked. Two breakthroughs have recently allowed a fuller understanding of the importance of tRNA modifications in bacterial physiology. One is the identification of the full set of tRNA modification genes in model organisms such as Escherichia coli K12. The second is the improvement of available analytical tools to monitor tRNA modification patterns. The role of tRNA modifications varies greatly with the specific modification within a given tRNA and with the organism studied. The absence of these modifications or reductions can lead to cell death or pleiotropic phenotypes or may have no apparent visible effect. By linking translation through their decoding functions to metabolism through their biosynthetic pathways, tRNA modifications are emerging as important components of the bacterial regulatory toolbox.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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50
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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