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Bhoobalan-Chitty Y, Xu S, Martinez-Alvarez L, Karamycheva S, Makarova KS, Koonin EV, Peng X. Regulatory sequence-based discovery of anti-defense genes in archaeal viruses. Nat Commun 2024; 15:3699. [PMID: 38698035 PMCID: PMC11065993 DOI: 10.1038/s41467-024-48074-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024] Open
Abstract
In silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait. However, the low number and limited spread of the characterized archaeal Acrs and Aca hinders our ability to identify Acrs using guilt-by-association. Here, based on the observation that the few characterized archaeal Acrs and Aca are transcribed immediately post viral infection, we hypothesize that these genes, and many other unidentified anti-defense genes (ADG), are under the control of conserved regulatory sequences including a strong promoter, which can be used to predict anti-defense genes in archaeal viruses. Using this consensus sequence based method, we identify 354 potential ADGs in 57 archaeal viruses and 6 metagenome-assembled genomes. Experimental validation identified a CRISPR subtype I-A inhibitor and the first virally encoded inhibitor of an archaeal toxin-antitoxin based immune system. We also identify regulatory proteins potentially akin to Acas that can facilitate further identification of ADGs combined with the guilt-by-association approach. These results demonstrate the potential of regulatory sequence analysis for extensive identification of ADGs in viruses of archaea and bacteria.
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Affiliation(s)
| | - Shuanshuan Xu
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | | | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
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2
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Saito M, Xu P, Faure G, Maguire S, Kannan S, Altae-Tran H, Vo S, Desimone A, Macrae RK, Zhang F. Fanzor is a eukaryotic programmable RNA-guided endonuclease. Nature 2023; 620:660-668. [PMID: 37380027 PMCID: PMC10432273 DOI: 10.1038/s41586-023-06356-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
RNA-guided systems, which use complementarity between a guide RNA and target nucleic acid sequences for recognition of genetic elements, have a central role in biological processes in both prokaryotes and eukaryotes. For example, the prokaryotic CRISPR-Cas systems provide adaptive immunity for bacteria and archaea against foreign genetic elements. Cas effectors such as Cas9 and Cas12 perform guide-RNA-dependent DNA cleavage1. Although a few eukaryotic RNA-guided systems have been studied, including RNA interference2 and ribosomal RNA modification3, it remains unclear whether eukaryotes have RNA-guided endonucleases. Recently, a new class of prokaryotic RNA-guided systems (termed OMEGA) was reported4,5. The OMEGA effector TnpB is the putative ancestor of Cas12 and has RNA-guided endonuclease activity4,6. TnpB may also be the ancestor of the eukaryotic transposon-encoded Fanzor (Fz) proteins4,7, raising the possibility that eukaryotes are also equipped with CRISPR-Cas or OMEGA-like programmable RNA-guided endonucleases. Here we report the biochemical characterization of Fz, showing that it is an RNA-guided DNA endonuclease. We also show that Fz can be reprogrammed for human genome engineering applications. Finally, we resolve the structure of Spizellomyces punctatus Fz at 2.7 Å using cryogenic electron microscopy, showing the conservation of core regions among Fz, TnpB and Cas12, despite diverse cognate RNA structures. Our results show that Fz is a eukaryotic OMEGA system, demonstrating that RNA-guided endonucleases are present in all three domains of life.
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Affiliation(s)
- Makoto Saito
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Peiyu Xu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Samantha Maguire
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Soumya Kannan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Han Altae-Tran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Sam Vo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - AnAn Desimone
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Rhiannon K Macrae
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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3
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Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 2022; 377:eabm4096. [PMID: 35951700 PMCID: PMC10028730 DOI: 10.1126/science.abm4096] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
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Affiliation(s)
- Linyi Alex Gao
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA
- Correspondence: (F.Z.) or (L.A.G.)
| | - Max E. Wilkinson
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan Strecker
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (F.Z.) or (L.A.G.)
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Abstract
The principal biological function of bacterial and archaeal CRISPR systems is RNA-guided adaptive immunity against viruses and other mobile genetic elements (MGEs). These systems show remarkable evolutionary plasticity and functional versatility at multiple levels, including both the defense mechanisms that lead to direct, specific elimination of the target DNA or RNA and those that cause programmed cell death (PCD) or induction of dormancy. This flexibility is also evident in the recruitment of CRISPR systems for nondefense functions. Defective CRISPR systems or individual CRISPR components have been recruited by transposons for RNA-guided transposition, by plasmids for interplasmid competition, and by viruses for antidefense and interviral conflicts. Additionally, multiple highly derived CRISPR variants of yet unknown functions have been discovered. A major route of innovation in CRISPR evolution is the repurposing of diverged repeat variants encoded outside CRISPR arrays for various structural and regulatory functions. The evolutionary plasticity and functional versatility of CRISPR systems are striking manifestations of the ubiquitous interplay between defense and “normal” cellular functions. The CRISPR systems show remarkable functional versatility beyond their principal function as an adaptive immune mechanism. This Essay discusses how derived CRISPR systems have been recruited by transposons on multiple occasions and mediate RNA-guided transposition; derived CRISPR RNAs are frequently recruited for regulatory functions.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Zhang Y, Marchisio MA. Type II anti-CRISPR proteins as a new tool for synthetic biology. RNA Biol 2021; 18:1085-1098. [PMID: 32991234 PMCID: PMC8244766 DOI: 10.1080/15476286.2020.1827803] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/03/2020] [Accepted: 09/20/2020] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) system represents, in prokaryotes, an adaptive and inheritable immune response against invading DNA. The discovery of anti-CRISPR proteins (Acrs), which are inhibitors of CRISPR-Cas, mainly encoded by phages and prophages, showed a co-evolution history between prokaryotes and phages. In the past decade, the CRISPR-Cas systems together with the corresponding Acrs have been turned into a genetic-engineering tool. Among the six types of CRISPR-Cas characterized so far, type II CRISPR-Cas system is the most popular in biotechnology. Here, we discuss about the discovery, the reported inhibitory mechanisms, and the applications in both gene editing and gene transcriptional regulation of type II Acrs. Moreover, we provide insights into future potential research and feasible applications.
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Affiliation(s)
- Yadan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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6
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) together with their accompanying cas (CRISPR-associated) genes are found frequently in bacteria and archaea, serving to defend against invading foreign DNA, such as viral genomes. CRISPR-Cas systems provide a uniquely powerful defense because they can adapt to newly encountered genomes. The adaptive ability of these systems has been exploited, leading to their development as highly effective tools for genome editing. The widespread use of CRISPR-Cas systems has driven a need for methods to control their activity. This review focuses on anti-CRISPRs (Acrs), proteins produced by viruses and other mobile genetic elements that can potently inhibit CRISPR-Cas systems. Discovered in 2013, there are now 54 distinct families of these proteins described, and the functional mechanisms of more than a dozen have been characterized in molecular detail. The investigation of Acrs is leading to a variety of practical applications and is providing exciting new insight into the biology of CRISPR-Cas systems.
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Affiliation(s)
- Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Wang-Ting Lu
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Sabrina Y Stanley
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Jingrui Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Marios Mejdani
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Chantel N Trost
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Brian T Hicks
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Jooyoung Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; ,
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; ,
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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7
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Sereme Y, Mezouar S, Grine G, Mege JL, Drancourt M, Corbeau P, Vitte J. Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases. Clin Rev Allergy Immunol 2020; 57:456-466. [PMID: 31522353 DOI: 10.1007/s12016-019-08766-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.
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Affiliation(s)
- Youssouf Sereme
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Soraya Mezouar
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Ghiles Grine
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Jean Louis Mege
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Pierre Corbeau
- Institute of Human Genetics, UMR9002, CNRS-Montpellier University, Montpellier, France
- Montpellier University, Montpellier, France
- Immunology Department, University Hospital, Nîmes, France
| | - Joana Vitte
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France.
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France.
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France.
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8
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Behler J, Hess WR. Approaches to study CRISPR RNA biogenesis and the key players involved. Methods 2020; 172:12-26. [PMID: 31325492 DOI: 10.1016/j.ymeth.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/29/2019] [Accepted: 07/15/2019] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins provide an inheritable and adaptive immune system against phages and foreign genetic elements in many bacteria and archaea. The three stages of CRISPR-Cas immunity comprise adaptation, CRISPR RNA (crRNA) biogenesis and interference. The maturation of the pre-crRNA into mature crRNAs, short guide RNAs that target invading nucleic acids, is crucial for the functionality of CRISPR-Cas defense systems. Mature crRNAs assemble with Cas proteins into the ribonucleoprotein (RNP) effector complex and guide the Cas nucleases to the cognate foreign DNA or RNA target. Experimental approaches to characterize these crRNAs, the specific steps toward their maturation and the involved factors, include RNA-seq analyses, enzyme assays, methods such as cryo-electron microscopy, the crystallization of proteins, or UV-induced protein-RNA crosslinking coupled to mass spectrometry analysis. Complex and multiple interactions exist between CRISPR-cas-encoded specific riboendonucleases such as Cas6, Cas5d and Csf5, endonucleases with dual functions in maturation and interference such as the enzymes of the Cas12 and Cas13 families, and nucleases belonging to the cell's degradosome such as RNase E, PNPase and RNase J, both in the maturation as well as in interference. The results of these studies have yielded a picture of unprecedented diversity of sequences, enzymes and biochemical mechanisms.
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Affiliation(s)
- Juliane Behler
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
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9
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Liu Q, Zhang H, Huang X. Anti-CRISPR proteins targeting the CRISPR-Cas system enrich the toolkit for genetic engineering. FEBS J 2020; 287:626-644. [PMID: 31730297 DOI: 10.1111/febs.15139] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/08/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas adaptive immune defense systems, which are widely distributed in bacteria and Archaea, can provide sequence-specific protection against foreign DNA or RNA in some cases. However, the evolution of defense systems in bacterial hosts did not lead to the elimination of phages, and some phages carry anti-CRISPR genes that encode products that bind to the components mediating the defense mechanism and thus antagonize CRISPR-Cas immune systems of bacteria. Given the extensive application of CRISPR-Cas9 technologies in gene editing, in this review, we focus on the anti-CRISPR proteins (Acrs) that inhibit CRISPR-Cas systems for gene editing. We describe the discovery of Acrs in immune systems involving type I, II, and V CRISPR-Cas immunity, discuss the potential function of Acrs in inactivating type II and V CRISPR-Cas systems for gene editing and gene modulation, and provide an outlook on the development of important biotechnology tools for genetic engineering using Acrs.
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Affiliation(s)
- Qiong Liu
- Department of Medical Microbiology, School of Medicine, Nanchang University, China
| | - Hongxia Zhang
- Department of Medical Microbiology, School of Medicine, Nanchang University, China
| | - Xiaotian Huang
- Department of Medical Microbiology, School of Medicine, Nanchang University, China
- Key Laboratory of Tumor Pathogenesis and Molecular Pathology, School of Medicine, Nanchang University, China
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10
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Abstract
Many powerful molecular biology tools have their origin in nature. From restriction enzymes to CRISPR-Cas9, microbes utilize a diverse array of systems to get ahead evolutionarily. We are exploring this natural diversity through bioinformatics, biochemical, and molecular work to better understand the fundamental ways in which microbes and other living organisms sense and respond to their environment and as possible to develop these natural systems as molecular tools and to improve human health. Building on our demonstration that Cas9 can be repurposed for precision genome editing in mammalian cells, we look for novel CRISPR-Cas systems that are different and may have other useful properties. This led to the discovery of several new CRISPR systems, including the CRISPR-Cas13 family that target RNA, rather than DNA. We have developed a toolbox for RNA modulation based on Cas13, including methods for precision base editing, adding to our robust toolbox for DNA based on Cas9 and Cas12. We are expanding our biodiscovery efforts to search for new microbial proteins that may be adapted for applications beyond genome and transcriptome modulation, capitalizing on the growing volume of microbial genomic sequences. We are particularly interested in identifying new therapeutic modalities and vehicles for delivering them into patients. We hope that additional robust tools and delivery options will further accelerate research into human disease and open up new therapeutic possibilities.
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Affiliation(s)
- Feng Zhang
- Broad Institute of MIT and Harvard, McGovern Institute for Brain Research at MIT, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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11
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Chakraborty S. Inconclusive studies on possible CRISPR-Cas off-targets should moderate expectations about enzymes that have evolved to be non-specific. J Biosci 2018; 43:225-228. [PMID: 29872009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Sandeep Chakraborty
- R-44/1, Celia Engineers, T. T. C Industrial Area, Rabale, Navi Mumbai 400701, India,
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12
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Abstract
Prokaryotic organisms survive under constant pressure of viruses. CRISPR-Cas system provides its prokaryotic host with an adaptive immune defense against viruses that have been previously encountered. It consists of two components: Cas-proteins that cleave the foreign DNA and CRISPR array that suits as a virus recognition key. CRISPR array consists of a series of spacers, short pieces of DNA that originate from and match the corresponding parts of viral DNA called protospacers. Here we estimate the number of spacers in a CRISPR array of a prokaryotic cell which maximizes its protection against a viral attack. The optimality follows from a competition between two trends: too few distinct spacers make host vulnerable to an attack by a virus with mutated corresponding protospacers, while an excessive variety of spacers dilutes the number of the CRISPR complexes armed with the most recent and thus most useful spacers. We first evaluate the optimal number of spacers in a simple scenario of an infection by a single viral species and later consider a more general case of multiple viral species. We find that depending on such parameters as the concentration of CRISPR-Cas interference complexes and its preference to arm with more recently acquired spacers, the rate of viral mutation, and the number of viral species, the predicted optimal number of spacers lies within a range that agrees with experimentally-observed values. CRISPR-Cas systems provide adaptive immunity defense in bacteria and archaea against viruses. They function by accumulating in prokaryotic genome an array of spacers, or fragments of virus DNA from previous attacks. By matching spacers to corresponding parts of viral DNA called protospacers, a CRISPR-Cas system identifies and destroys intruder DNA. Here we theoretically estimate the number of spacers that maximizes prokaryotic host cell survival. This optimum emerges from a competition between two trends: More spacers allow a prokaryotic cell to hedge against mutations in viral protospacers. However, the older spacers loose efficiency as corresponding protospacers mutate. For a limited pool of CRISPR-Cas molecular machines, keeping too many spacers leaves fewer of such machines armed with more efficient young (most recently acquired) spacers. We have shown that a higher efficiency of CRISPR-Cas system allows a prokaryotic cell to utilize more spacers, increasing the optimal number of spacers. On contrary, a higher viral mutation rate makes older spacers useless and favors shorter arrays. A higher diversity in viral species reduces the efficiency of CRISPR-Cas but does not necessary lead to longer arrays. Our study provides a new viewpoint at a variety of the observed array spacer number and could be used as a base for evolutionary models of host-phage coexistence.
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Affiliation(s)
- Alexander Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- * E-mail: (II); (AM)
| | - Konstantin Severinov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Iaroslav Ispolatov
- Department of Physics, University of Santiago de Chile, Santiago, Chile
- * E-mail: (II); (AM)
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13
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Abstract
The elucidation of the CRISPR (clustered, regularly interspaced, short palindromic repeats) adaptive immune system endogenous to most microbial life has culminated in progress in a diversity of scientific disciplines. The concurrently promising and eccentric nature of its theoretically plausible applications has wrought enthusiasm in the research community globally, potentiating advancements in human and animal health, ecological stability, and economic wellbeing, that would hitherto be considered the unattainable fancies of a futurist. It may be supposed that the tomes of science fiction are the true books of prophecy. Here, we narrate the scientific dialogue regarding CRISPR/Cas biotechnologies, from the happenstantial initial observation of the locus to the litany of intriguing contemporary endeavors. We discuss the mechanistic underpinnings in detail, and the corpulent body of literature on CRISPR-based biotech is digested into a germane and informative review. CRISPR applications such as microbiome engineering in order to enhance the human immune system beyond the fortitude of the wild type, bacterial genome editing in industrial and medical aspects, conquering antibiotic resistance, the development of novel antimicrobial techniques, the harvesting of solventogenic microbes, the development of antifungal therapies, and investigation of the genetic properties of fungi, are here represented, and the authors posit unconventional, and at times gainfully tangential, thoughts and concepts in order to encourage a reflective disposition towards this sophisticated device of nature: a panacea in progress, such that the most impassive and technical writing still carries the ring of poetry.
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Affiliation(s)
- Michael Carroll
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiaohui Zhou
- Department of Pathobiology and Veterinary Science, the University of Connecticut, 61 N. Eagleville Rd, Storrs, CT, 06269-3089, United States; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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14
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Abstract
Adaptive immunity had been long thought of as an exclusive feature of animals. However, the discovery of the CRISPR-Cas defense system, present in almost half of prokaryotic genomes, proves otherwise. Because of the everlasting parasite-host arms race, CRISPR-Cas has rapidly evolved through horizontal transfer of complete loci or individual modules, resulting in extreme structural and functional diversity. CRISPR-Cas systems are divided into two distinct classes that each consist of three types and multiple subtypes. We discuss recent advances in CRISPR-Cas research that reveal elaborate molecular mechanisms and provide for a plausible scenario of CRISPR-Cas evolution. We also briefly describe the latest developments of a wide range of CRISPR-based applications.
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Affiliation(s)
- Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Bernd Zetsche
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands.
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15
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Abstract
Bacteria and archaea have evolved sophisticated adaptive immune systems that reply on CRISPR loci and a diverse cassette of Cas genes that are classified into three main types and at least eleven subtypes. All CRISPR-Cas immune systems operate through three main stages: acquisition, biogenesis, and interference. This SnapShot summarizes our current knowledge of these fascinating immune systems.
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Affiliation(s)
- Joshua Carter
- Montana State University, Department of Microbiology and Immunology, Bozeman, MT 59715, USA
| | - Blake Wiedenheft
- Montana State University, Department of Microbiology and Immunology, Bozeman, MT 59715, USA
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16
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying Cas proteins constitute the adaptive CRISPR-Cas immune system in bacteria and archaea. This DNA-encoded, RNA-mediated defense system provides sequence-specific recognition, targeting and degradation of exogenous nucleic acid. Though the primary established role of CRISPR-Cas systems is in bona fide adaptive antiviral defense in bacteria, a growing body of evidence indicates that it also plays critical functional roles beyond immunity, such as endogenous transcriptional control. Furthermore, benefits inherent to maintaining genome homeostasis also come at the cost of reduced uptake of beneficial DNA, and preventing strategic adaptation to the environment. This opens new avenues for the investigation of CRISPR-Cas systems and their functional characterization beyond adaptive immunity.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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17
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Blanco Y, Rivas LA, García-Moyano A, Aguirre J, Cruz-Gil P, Palacín A, van Heerden E, Parro V. Deciphering the prokaryotic community and metabolisms in South African deep-mine biofilms through antibody microarrays and graph theory. PLoS One 2014; 9:e114180. [PMID: 25531640 PMCID: PMC4273990 DOI: 10.1371/journal.pone.0114180] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/05/2014] [Indexed: 11/18/2022] Open
Abstract
In the South African deep mines, a variety of biofilms growing in mine corridor walls as water seeps from intersections or from fractures represents excellent proxies for deep-subsurface environments. However, they may be greatly affected by the oxygen inputs through the galleries of mining activities. As a consequence, the interaction between the anaerobic water coming out from the walls with the oxygen inputs creates new conditions that support rich microbial communities. The inherent difficulties for sampling these delicate habitats, together with transport and storage conditions may alter the community features and composition. Therefore, the development of in situ monitoring methods would be desirable for quick evaluation of the microbial community. In this work, we report the usefulness of an antibody-microarray (EMChip66) immunoassay for a quick check of the microbial diversity of biofilms located at 1.3 km below surface within the Beatrix deep gold mine (South Africa). In addition, a deconvolution method, previously described and used for environmental monitoring, based on graph theory and applied on antibody cross-reactivity was used to interpret the immunoassay results. The results were corroborated and further expanded by 16S rRNA gene sequencing analysis. Both culture-independent techniques coincided in detecting features related to aerobic sulfur-oxidizers, aerobic chemoorganotrophic Alphaproteobacteria and metanotrophic Gammaproteobacteria. 16S rRNA gene sequencing detected phylotypes related to nitrate-reducers and anaerobic sulfur-oxidizers, whereas the EMChip66 detected immunological features from methanogens and sulfate-reducers. The results reveal a diverse microbial community with syntrophic metabolisms both anaerobic (fermentation, methanogenesis, sulphate and nitrate reduction) and aerobic (methanotrophy, sulphur oxidation). The presence of oxygen-scavenging microbes might indicate that the system is modified by the artificial oxygen inputs from the mine galleries.
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Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Luis A. Rivas
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Antonio García-Moyano
- TIA/UFS Metagenomics Platform, Department of Biotechnology, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
| | - Jacobo Aguirre
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Patricia Cruz-Gil
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Arantxa Palacín
- Centro de Biotecnología y Genómica de Plantas, Campus de Montegancedo, Autopista M40, km 38, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Esta van Heerden
- TIA/UFS Metagenomics Platform, Department of Biotechnology, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
- * E-mail:
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18
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Krupovic M, Makarova KS, Forterre P, Prangishvili D, Koonin EV. Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity. BMC Biol 2014; 12:36. [PMID: 24884953 PMCID: PMC4046053 DOI: 10.1186/1741-7007-12-36] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 05/13/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Diverse transposable elements are abundant in genomes of cellular organisms from all three domains of life. Although transposons are often regarded as junk DNA, a growing body of evidence indicates that they are behind some of the major evolutionary innovations. With the growth in the number and diversity of sequenced genomes, previously unnoticed mobile elements continue to be discovered. RESULTS We describe a new superfamily of archaeal and bacterial mobile elements which we denote casposons because they encode Cas1 endonuclease, a key enzyme of the CRISPR-Cas adaptive immunity systems of archaea and bacteria. The casposons share several features with self-synthesizing eukaryotic DNA transposons of the Polinton/Maverick class, including terminal inverted repeats and genes for B family DNA polymerases. However, unlike any other known mobile elements, the casposons are predicted to rely on Cas1 for integration and excision, via a mechanism similar to the integration of new spacers into CRISPR loci. We identify three distinct families of casposons that differ in their gene repertoires and evolutionary provenance of the DNA polymerases. Deep branching of the casposon-encoded endonuclease in the Cas1 phylogeny suggests that casposons played a pivotal role in the emergence of CRISPR-Cas immunity. CONCLUSIONS The casposons are a novel superfamily of mobile elements, the first family of putative self-synthesizing transposons discovered in prokaryotes. The likely contribution of capsosons to the evolution of CRISPR-Cas parallels the involvement of the RAG1 transposase in vertebrate immunoglobulin gene rearrangement, suggesting that recruitment of endonucleases from mobile elements as ready-made tools for genome manipulation is a general route of evolution of adaptive immunity.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Docteur Roux, 75015 Paris, France
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Patrick Forterre
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Docteur Roux, 75015 Paris, France
| | - David Prangishvili
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Docteur Roux, 75015 Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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19
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Abstract
Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack. This arsenal has been expanded by the recent discovery of the versatile CRISPR-Cas system, which has two novel features. First, the host can specifically incorporate short sequences from invading genetic elements (virus or plasmid) into a region of its genome that is distinguished by clustered regularly interspaced short palindromic repeats (CRISPRs). Second, when these sequences are transcribed and precisely processed into small RNAs, they guide a multifunctional protein complex (Cas proteins) to recognize and cleave incoming foreign genetic material. This adaptive immunity system, which uses a library of small noncoding RNAs as a potent weapon against fast-evolving viruses, is also used as a regulatory system by the host. Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed.
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MESH Headings
- Adaptive Immunity
- Archaea/chemistry
- Archaea/genetics
- Archaea/immunology
- Archaea/virology
- Bacteria/chemistry
- Bacteria/genetics
- Bacteria/immunology
- Bacteria/virology
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/immunology
- Bacteriophages/genetics
- Bacteriophages/immunology
- CRISPR-Associated Proteins
- Computational Biology
- Endodeoxyribonucleases/chemistry
- Endodeoxyribonucleases/genetics
- Escherichia coli Proteins
- Evolution, Molecular
- Gene Expression Regulation, Archaeal
- Gene Expression Regulation, Bacterial
- Genetic Loci
- Plasmids/immunology
- RNA Interference
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/immunology
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/immunology
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/immunology
- Transcription, Genetic
- Virus Diseases/genetics
- Virus Diseases/immunology
- Virus Diseases/virology
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Affiliation(s)
- Devaki Bhaya
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA.
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20
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Hook SE, Wright ADG, McBride BW. Methanogens: methane producers of the rumen and mitigation strategies. Archaea 2010; 2010:945785. [PMID: 21253540 PMCID: PMC3021854 DOI: 10.1155/2010/945785] [Citation(s) in RCA: 252] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Revised: 11/03/2010] [Accepted: 12/07/2010] [Indexed: 01/01/2023]
Abstract
Methanogens are the only known microorganisms capable of methane production, making them of interest when investigating methane abatement strategies. A number of experiments have been conducted to study the methanogen population in the rumen of cattle and sheep, as well as the relationship that methanogens have with other microorganisms. The rumen methanogen species differ depending on diet and geographical location of the host, as does methanogenesis, which can be reduced by modifying dietary composition, or by supplementation of monensin, lipids, organic acids, or plant compounds within the diet. Other methane abatement strategies that have been investigated are defaunation and vaccines. These mitigation methods target the methanogen population of the rumen directly or indirectly, resulting in varying degrees of efficacy. This paper describes the methanogens identified in the rumens of cattle and sheep, as well as a number of methane mitigation strategies that have been effective in vivo.
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Affiliation(s)
- Sarah E Hook
- Department of Animal & Poultry Science, University of Guelph, ON, Canada.
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21
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Wright ADG, Kennedy P, O'Neill CJ, Toovey AF, Popovski S, Rea SM, Pimm CL, Klein L. Reducing methane emissions in sheep by immunization against rumen methanogens. Vaccine 2005; 22:3976-85. [PMID: 15364447 DOI: 10.1016/j.vaccine.2004.03.053] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 03/05/2004] [Accepted: 03/31/2004] [Indexed: 11/19/2022]
Abstract
This work was conducted to determine if methane emissions from sheep immunized with an anti-methanogen vaccine were significantly lower than methane emissions from non-immunized sheep, to test the effectiveness of two different vaccine formulations (VF) on methane abatement, and to compare methane emissions measured using a closed-circuit respiration chamber and the sulphur-hexafluoride (SF6) tracer technique. Thirty mature wether sheep were randomly allocated to three treatment groups (n = 10). One group received an immunization of adjuvant only on days 0 and 153 (control), a second group received an immunization with a 3-methanogen mix on days 0 and 153 (VF3 + 3), and a third group received an immunization of a 7-methanogen mix on day 0 followed by a 3-methanogen mix on day 153 (VF7 + 3). Four weeks post-secondary immunization, there was a significant 7.7% reduction in methane production per kg dry matter intake in the VF7 + 3 group compared to the controls (P = 0.051). However, methane emissions from sheep immunized with VF7 + 3 were not significantly different when compared to the sheep in the control group (P = 0.883). The average IgG and IgA antibody titres in both plasma and saliva of the VF3 + 3 immunized sheep were four to nine times higher than those immunized with VF7 + 3 (P< 0.001) at both 3 and 6 weeks post-secondary immunization. Data also revealed that SF6 methane estimates were consistently higher than the respiration chamber estimates and that there was no significant correlation between the SF6 methane estimates and the respiration chamber methane estimates (R2 = 0.11).
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Affiliation(s)
- A D G Wright
- CSIRO Livestock Industries, Centre for Environment and Life Sciences, Private Bag 5, Wembley, Western Australia, Perth 6913, Australia.
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22
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Gurnani K, Kennedy J, Sad S, Sprott GD, Krishnan L. Phosphatidylserine Receptor-Mediated Recognition of Archaeosome Adjuvant Promotes Endocytosis and MHC Class I Cross-Presentation of the Entrapped Antigen by Phagosome-to-Cytosol Transport and Classical Processing. J Immunol 2004; 173:566-78. [PMID: 15210818 DOI: 10.4049/jimmunol.173.1.566] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Archaeal isopranoid glycerolipid vesicles (archaeosomes) serve as strong adjuvants for cell-mediated responses to entrapped Ag. We analyzed the processing pathway of OVA entrapped in archaeosomes composed of Methanobrevibacter smithii lipids, high in archaetidylserine (OVA-archaeosomes). In vitro, OVA-archaeosomes stimulated spleen cells from OVA-TCR-transgenic mice, D011.10 (CD4(+) cells expressing OVA(323-339) TCR) or OT1 (>90% CD8(+) OVA(257-264) cells), indicating both MHC class I and II presentations. In vivo, when naive (Thy1.2(+)) CFSE-labeled OT1 cells were transferred into OVA-archaeosome-immunized Thy 1.1(+) recipient mice, there was profound accumulation and cycling of donor-specific cells, and differentiation of H-2K(b)Ova(257-264) CD8(+) T cells into CD44(high)CD62L(low) effectors. Both macrophages and dendritic cells (DCs) efficiently cross-presented OVA-archaeosomes on MHC class I. Blocking phagocytosis by phosphatidylserine-specific receptor agonists strongly inhibited MHC class I presentation of OVA-archaeosomes, whereas blocking mannose receptors or FcRs lacked effect, indicating specific recognition of the archaetidylserine head group of M. smithii lipids by APCs. In addition, inhibitors of endosomal acidification blocked MHC class I processing of OVA-archaeosomes, whereas endosomal protease inhibitors lacked effect, suggesting acidification-dependent phagosome-to-cytosol diversion. Proteasomal inhibitors blocked OVA-archaeosome MHC class I presentation, confirming cytosolic processing. Both in vitro and in vivo, OVA-archaeosome MHC class I presentation required TAP. Ag-free archaeosomes also activated DC costimulation and cytokine production, without overt inflammation. Phosphatidylserine-specific receptor-mediated endocytosis is a mechanism of apoptotic cell clearance and DCs cross-present Ags sampled from apoptotic cells. Our results reveal the novel ability of archaeosomes to exploit this mechanism for cytosolic MHC class I Ag processing, and provide an effective particulate vaccination strategy.
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Affiliation(s)
- Komal Gurnani
- Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
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23
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Sprott GD, Sad S, Fleming LP, Dicaire CJ, Patel GB, Krishnan L. Archaeosomes varying in lipid composition differ in receptor-mediated endocytosis and differentially adjuvant immune responses to entrapped antigen. Archaea 2003; 1:151-64. [PMID: 15803661 PMCID: PMC2685569 DOI: 10.1155/2003/569283] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2002] [Accepted: 12/10/2002] [Indexed: 11/18/2022]
Abstract
Archaeosomes prepared from total polar lipids extracted from six archaeal species with divergent lipid compositions had the capacity to deliver antigen for presentation via both MHC class I and class II pathways. Lipid extracts from Halobacterium halobium and from Halococcus morrhuae strains 14039 and 16008 contained archaetidylglycerol methylphosphate and sulfated glycolipids rich in mannose residues, and lacked archaetidylserine, whereas the opposite was found in Methanobrevibacter smithii, Methanosarcina mazei and Methanococcus jannaschii. Annexin V labeling revealed a surface orientation of phosphoserine head groups in M. smithii, M. mazei and M. jannaschii archaeosomes. Uptake of rhodamine-labeled M. smithii or M. jannaschii archaeosomes by murine peritoneal macrophages was inhibited by unlabeled liposomes containing phosphatidylserine, by the sulfhydryl inhibitor N-ethylmaleimide, and by ATP depletion using azide plus fluoride, but not by H. halobium archaeosomes. In contrast, N-ethylmaleimide failed to inhibit uptake of the four other rhodamine-labeled archaeosome types, and azide plus fluoride did not inhibit uptake of H. halobium or H. morrhuae archaeosomes. These results suggest endocytosis of archaeosomes rich in surface-exposed phosphoserine head groups via a phosphatidylserine receptor, and energy-independent surface adsorption of certain other archaeosome composition classes. Lipid composition affected not only the endocytic mechanism, but also served to differentially modulate the activation of dendritic cells. The induction of IL-12 secretion from dendritic cells exposed to H. morrhuae 14039 archaeosomes was striking compared with cells exposed to archaeosomes from 16008. Thus, archaeosome types uniquely modulate antigen delivery and dendritic cell activation.
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Affiliation(s)
- G Dennis Sprott
- Institute for Biological Sciences, National Research Council, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6.
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24
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Krishnan L, Sad S, Patel GB, Sprott GD. Archaeosomes induce long-term CD8+ cytotoxic T cell response to entrapped soluble protein by the exogenous cytosolic pathway, in the absence of CD4+ T cell help. J Immunol 2000; 165:5177-85. [PMID: 11046050 DOI: 10.4049/jimmunol.165.9.5177] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The unique ether glycerolipids of Archaea can be formulated into vesicles (archaeosomes) with strong adjuvant activity for MHC class II presentation. Herein, we assess the ability of archaeosomes to facilitate MHC class I presentation of entrapped protein Ag. Immunization of mice with OVA entrapped in archaeosomes resulted in a potent Ag-specific CD8(+) T cell response, as measured by IFN-gamma production and cytolytic activity toward the immunodominant CTL epitope OVA(257-264). In contrast, administration of OVA with aluminum hydroxide or entrapped in conventional ester-phospholipid liposomes failed to evoke significant CTL response. The archaeosome-mediated CD8(+) T cell response was primarily perforin dependent because CTL activity was undetectable in perforin-deficient mice. Interestingly, a long-term CTL response was generated with a low Ag dose even in CD4(+) T cell deficient mice, indicating that the archaeosomes could mediate a potent T helper cell-independent CD8(+) T cell response. Macrophages incubated in vitro with OVA archaeosomes strongly stimulated cytokine production by OVA-specific CD8(+) T cells, indicating that archaeosomes efficiently delivered entrapped protein for MHC class I presentation. This processing of Ag was Brefeldin A sensitive, suggesting that the peptides were transported through the endoplasmic reticulum and presented by the cytosolic MHC class I pathway. Finally, archaeosomes induced a potent memory CTL response to OVA even 154 days after immunization. This correlated to strong Ag-specific up-regulation of CD44 on splenic CD8(+) T cells. Thus, delivery of proteins in self-adjuvanting archaeosomes represents a novel strategy for targeting exogenous Ags to the MHC class I pathway for induction of CTL response.
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Affiliation(s)
- L Krishnan
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada.
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25
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Krishnan L, Dicaire CJ, Patel GB, Sprott GD. Archaeosome vaccine adjuvants induce strong humoral, cell-mediated, and memory responses: comparison to conventional liposomes and alum. Infect Immun 2000; 68:54-63. [PMID: 10603368 PMCID: PMC97101 DOI: 10.1128/iai.68.1.54-63.2000] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/1999] [Accepted: 10/19/1999] [Indexed: 11/20/2022] Open
Abstract
Ether glycerolipids extracted from various archaeobacteria were formulated into liposomes (archaeosomes) possessing strong adjuvant properties. Mice of varying genetic backgrounds, immunized by different parenteral routes with bovine serum albumin (BSA) entrapped in archaeosomes ( approximately 200-nm vesicles), demonstrated markedly enhanced serum anti-BSA antibody titers. These titers were often comparable to those achieved with Freund's adjuvant and considerably more than those with alum or conventional liposomes (phosphatidylcholine-phosphatidylglycerol-cholesterol, 1. 8:0.2:1.5 molar ratio). Furthermore, antigen-specific immunoglobulin G1 (IgG1), IgG2a, and IgG2b isotype antibodies were all induced. Association of BSA with the lipid vesicles was required for induction of a strong response, and >80% of the protein was internalized within most archaeosome types, suggesting efficient release of antigen in vivo. Encapsulation of ovalbumin and hen egg lysozyme within archaeosomes showed similar immune responses. Antigen-archaeosome immunizations also induced a strong cell-mediated immune response: antigen-dependent proliferation and substantial production of cytokines gamma interferon (Th1) and interleukin-4 (IL-4) (Th2) by spleen cells in vitro. In contrast, conventional liposomes induced little cell-mediated immunity, whereas alum stimulated only an IL-4 response. In contrast to alum and Freund's adjuvant, archaeosomes composed of Thermoplasma acidophilum lipids evoked a dramatic memory antibody response to the encapsulated protein (at approximately 300 days) after only two initial immunizations (days 0 and 14). This correlated with increased antigen-specific cell cycling of CD4(+) T cells: increase in synthetic (S) and mitotic (G(2)/M) and decrease in resting (G(1)) phases. Thus, archaeosomes may be potent vaccine carriers capable of facilitating strong primary and memory humoral, and cell-mediated immune responses to the entrapped antigen.
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Affiliation(s)
- L Krishnan
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A 0R6.
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26
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Baensch M, Frank R, Khl J. Conservation of the amino-terminal epitope of elongation factor Tu in eubacteria and Archaea. Microbiology (Reading) 1998; 144 ( Pt 8):2241-2246. [PMID: 9720046 DOI: 10.1099/00221287-144-8-2241] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An epitope of elongation factor Tu (EF-Tu), which is found in organisms in both the bacterial and archaeal domains, was recently defined by mAb 900. To localize the conserved epitope within the EF-Tu molecule and to determine its sequence, SPOTScan analysis of synthetic peptides, Western blot analysis of purified EF-Tu domains and site-directed mutagenesis studies were used. Analysis of mAb 900 binding to overlapping 15-mer peptides encompassing the complete sequence of EF-Tu of Escherichia coli was inconclusive, suggesting three distinct regions may be epitopes. Western blot analysis of EF-Tu domains 1-3 of Thermus thermophilus suggested that the epitope was located at the N terminus. This was confirmed by site-directed mutagenesis of EF-Tu domain 1 of Mycoplasma hominis. By C-terminal truncation of the N-terminal 15-mer peptide the epitope was mapped to EF-Tu residues 1-6. Replacement of each of the residues in the epitope peptide demonstrated that only positions 5 and 6 were indispensable for antibody binding. These data provide evidence that the highly conserved epitope recognized by mAb 900 in the bacterial and archaeal domains is located at the very end of the N terminus of the EF-Tu molecule.
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Affiliation(s)
- Melanie Baensch
- Institute of Medical Microbiology, Medical School Hannover30623 HannoverGermany
| | - Ronald Frank
- AG Molecular Recognition, GBF (Gesellschaft fr Biotechnologische Forschung)BraunschweigGermany
| | - Jrg Khl
- Institute of Medical Microbiology, Medical School Hannover30623 HannoverGermany
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27
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Abstract
The humoral immune response mounted in BALB/c mice against bovine serum albumin or cholera toxin B subunit was compared when the antigens were associated with liposomes composed of either archaeal ether lipids or conventional lipids. Antibody titres in sera from mice immunised intraperitoneally were elevated to an extent comparable to those achieved with Freund's adjuvant by encapsulating bovine serum albumin in archaeal lipid vesicles (archaeosomes) of about 200 nm diameter. Comparison among six archaeosome and three conventional liposome compositions established that archaeosomes were generally much superior in potentiating an immune response. Further, only two immunisations, at the most, were needed to achieve close to the maximum antibody titre, as shown with archaeosomes composed of the polar lipids from Methanobrevibacter smithii, an inhabitant of the human colon. A similar positive response to presenting the more immunogenic cholera B subunit protein to the immune system of mice was shown for M. smithii archaeosomes. Encapsulation of the antigen in the archaeosome was necessary to achieve the full humoral response. This represents the first study to our knowledge where archaeosomes have been evaluated in vivo as possible antigen carriers.
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Affiliation(s)
- G D Sprott
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ont., Canada.
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28
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Abstract
A monoclonal antibody (MAb), MAb 900, which detects a 43-kDa protein present on Escherichia coli was found. Subsequently, more than 90 organisms, belonging to either the bacterial, archaeal, or eucaryal domain, were tested for reactivity to this MAb. Of the bacterial and archaeal domains, almost all species proved to be positive, whereas all organisms from the eucaryal domain gave negative results. The 43-kDa protein was purified by affinity chromatography and subsequently analyzed by microsequencing methods. Two peptide sequences which showed a high degree of homology (> 99%) to the prokaryotic elongation factor Tu (EF-Tu) were obtained. Western blot (immunoblot) analysis using both purified EF-Tu and EF-Tu domains confirmed that the unknown protein was EF-Tu. The panbacterial distribution of EF-Tu, which is present in large amounts in every prokaryotic cell, renders this protein a good candidate for a diagnostic approach. In consequence, we have used the anti-EF-Tu MAb 900 to design both a dot blot assay and an enzyme-linked immunosorbent assay. From either blood culture, urine, or gall-bladder fluid, bacterial contamination could be detected. The sensitivity of these tests is currently 10(4) bacteria per ml.
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Affiliation(s)
- S Weber
- Institut für Medizinische Mikrobiologie, Medizinische Hochschule Hannover, Germany
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29
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Abstract
Liposomes made of 1,2-di(3RS,7R,11R-phytanyl)-sn-glycero-3-phosphocholine (DPhyPC), which was synthesized as one of the model lipids existing in archaebacterial halophiles, showed excellent stability. Because of this high stability, DPhyPC liposomes could be constituted high ratios (50%) of N-[4-(p-maleimidophenyl) butyryl] dipalmitoyl phosphatidylethanolamine (MPB-DPPE), and consequently could bind large amounts of antigen (alpha-chymotrypsinogen A) on the liposome surface in comparison with those made of ordinary lipids, such as dipalmitoylphosphatidylcholine (DPPC). Though the characteristics of the DPhyPC liposomal membranes in lysis by the classical complement pathway were similar to those of DPPC liposomes, a high sensitivity and a low detection limit in the liposome immune lysis assay (LILA) of antibodies were attained by binding large amounts of the antigen. Further, by coupling sufficient amounts of antigen, almost all the DPhyPC liposome surface was covered with the antigen, and such liposomes showed higher resistance against non-specific lysis caused by complement activity in serum samples, which may be effective in reducing positive-false errors in LILA.
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Affiliation(s)
- K Tomioka
- Engineering Research Laboratories, Research Institute, Kaneka Corporation, Hyogo, Japan
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30
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Alam M, Hazelbauer GL. Structural features of methyl-accepting taxis proteins conserved between archaebacteria and eubacteria revealed by antigenic cross-reaction. J Bacteriol 1991; 173:5837-42. [PMID: 1909323 PMCID: PMC208317 DOI: 10.1128/jb.173.18.5837-5842.1991] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A number of eubacterial species contain methyl-accepting taxis proteins that are antigenically and thus structurally related to the well-characterized methyl-accepting chemotaxis proteins of Escherichia coli. Recent studies of the archaebacterium Halobacterium halobium have characterized methyl-accepting taxis proteins that in some ways resemble and in other ways differ from the analogous eubacterial proteins. We used immunoblotting with antisera raised to E. coli transducers to probe shared structural features of methyl-accepting proteins from archaebacteria and eubacteria and found substantial antigenic relationships. This implies that the genes for the contemporary methyl-accepting proteins are related through an ancestral gene that existed before the divergence of arachaebacteria and eubacteria. Analysis by immunoblot of mutants of H. halobium defective in taxis revealed that some strains were deficient in covalent modification of methyl-accepting proteins although the proteins themselves were present, while other strains appeared to be missing specific methyl-accepting proteins.
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Affiliation(s)
- M Alam
- Department of Biochemistry/Biophysics, Washington State University, Pullman 99164-4660
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31
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Krishnan G, Altekar W. An unusual class I (Schiff base) fructose-1,6-bisphosphate aldolase from the halophilic archaebacterium Haloarcula vallismortis. Eur J Biochem 1991; 195:343-50. [PMID: 1900049 DOI: 10.1111/j.1432-1033.1991.tb15712.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An electrophoretically homogeneous class I (Schiff base) alsolase has been isolated for the first time from the archaebacterial halophile Haloarcula (Halobacterium) vallismortis. The aldolase was characterized with respect to its molecular mass, amino acid composition, salt dependency, immunological cross-reactivity and kinetic properties. The subunit mass of aldolase is 27 kDa, which is much smaller than other class I aldolases. By the gel filtration method, the molecular mass of the halobacterial enzyme was estimated as 280 +/- 10 kDa, suggesting a decameric nature. In contrast to many halobacterial proteins, the H. vallismortis aldolase, though a halophilic enzyme, did not show an excess of acidic residues. Unlike the eukaryotic aldolases, the activity of the halobacterial enzyme was not affected by carboxypeptidase digestion. The general catalytic features of the enzyme were similar to its counterparts from other sources. No antigenic similarity could be detected between the H. vallismortis aldolase and class I aldolase from eubacteria and eukaryotes or class II halobacterial aldolases.
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Affiliation(s)
- G Krishnan
- Biochemistry Division, Bhabha Atomic Research Centre, Bombay, India
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32
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Konishi J, Denda K, Oshima T, Wakagi T, Uchida E, Ohsumi Y, Anraku Y, Matsumoto T, Wakabayashi T, Mukohata Y. Archaebacterial ATPases: relationship to other ion-translocating ATPase families examined in terms of immunological cross-reactivity. J Biochem 1990; 108:554-9. [PMID: 1963431 DOI: 10.1093/oxfordjournals.jbchem.a123241] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Immunological cross-reactivity among three types of H(+)-ATPases, that is, three archaebacterial ATPases, the F1-ATPase from thermophilic bacterium PS3 (TF1) and the vacuolar membrane ATPase from Saccharomyces cerevisiae, was examined by means of immunoblot analyses. The three archaebacterial ATPases were very similar in immunological cross-reactivity, suggesting that they belong to the same family of ATPases. Cross-reaction was also observed between the ATPase from Sulfolobus acidocaldarius, one of the three archaebacteria, and TF1. S. cerevisiae vacuolar ATPase reacted with the antibodies prepared against each of the three archaebacterial ATPases, but did not react with the antibody against TF1. Electron microscopic examination revealed that the oligomeric structure of Sulfolobus ATPase was very similar to that of F1-ATPase. These results, taken together, suggest that the archaebacterial ATPases share close structural similarities with the vacuolar ATPases, and, to a lesser degree, with the F0F1-ATPases.
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Affiliation(s)
- J Konishi
- Department of Life Science, Tokyo Institute of Technology, Kanagawa
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33
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Cammarano P, Tiboni O, Sanangelantoni AM. Phylogenetic conservation of antigenic determinants in archaebacterial elongation factors (Tu proteins). Can J Microbiol 1989; 35:2-10. [PMID: 2470483 DOI: 10.1139/m89-002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
By using affinity chromatography methods, we have purified elongation factor Tu (EF-Tu) proteins from a host of archaebacteria covering all known divisions in the archaebacterial tree except halophiles, and from such distantly related eubacteria as Thermotoga maritima and Escherichia coli. Polyclonal antibodies were raised against the Tu proteins of Sulfolobus solfataricus, Thermoproteus tenax, Thermococcus celer, Pyrococcus wosei, Archaeoglobus fulgidus, Methanococcus thermolitotrophicus, Thermoplasma acidophilum, and Thermotoga and used to probe the immunochemical relatedness of elongation factors both within and across kingdom boundaries. A selection of the results, presented here, indicates that (i) every archaebacterial EF-Tu is closer (immunochemically) to every other archaebacterial EF-Tu than to the functionally analogous proteins of eubacteria and eukaryotes, with only one possible exception concerning the recognition of eukaryotic (EF-1 alpha) factors by Thermococcus EF-Tu antibodies, and (ii) within the archaebacteria there appears to be a correlation between EF-Tu immunochemical similarities and the phylogenetic relatedness of the organisms inferred from other (sequence) criteria. On the whole, immunochemical similarity data argue against the proposal that the archaebacterial taxon should be split and redistributed between two superkingdoms.
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Affiliation(s)
- P Cammarano
- Dipartimento di Biopatologia Umana, Università di Roma I, Italy
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34
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Abstract
RNA polymerase purified from vegetative cells of the cyanobacterium Anabaena sp. strain PCC 7120 contains a dissociable sigma factor and a core of five subunits: the beta', beta, and two alpha subunits characteristic of all eubacteria and an additional 66,000-molecular-weight polypeptide called gamma. Fifteen of fifteen strains of unicellular and filamentous cyanobacteria tested contained a serologically related gamma protein. Antiserum to gamma reacted with Escherichia coli beta' and the A subunit of RNA polymerase of the archaebacterium Sulfolobus acidocaldarius. Thus the evolution of the RNA polymerase beta' subunit has followed different paths in three groups of procaryotes: cyanobacteria, other eubacteria, and archaebacteria.
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Affiliation(s)
- G J Schneider
- Department of Biochemistry and Molecular Biology, Illinois 60637
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35
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Abstract
The antigenic fingerprints of eight halophilic archaebacteria representing the groups recently outlined by molecular and chemical analyses were determined with calibrated antibody probes. Comparison with the antigenic fingerprints of methanogens encompassing all described families and most genera demonstrated that these two archaebacterial groups are themselves antigenically coherent but immunologically distinct.
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36
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Abstract
The antigenic map of 17 methanogenic bacteria representing the entire range of available species was determined by multiple assay with antibody probes. Four major clusters of antigenically related strains coincide with the females proposed on the basis of 16S ribosomal RNA analysis. Immunological mapping uncovered relationships not yet shown by other methods and allowed identification and classification of two new bacterial isolates.
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