1
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Malard F, Dias K, Baudy M, Thore S, Vialet B, Barthélémy P, Fribourg S, Karginov FV, Campagne S. Molecular Basis for the Calcium-Dependent Activation of the Ribonuclease EndoU. RESEARCH SQUARE 2024:rs.3.rs-4654759. [PMID: 39070628 PMCID: PMC11275989 DOI: 10.21203/rs.3.rs-4654759/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Ribonucleases (RNases) are ubiquitous enzymes that process or degrade RNA, essential for cellular functions and immune responses. The EndoU-like superfamily includes endoribonucleases conserved across bacteria, eukaryotes, and certain viruses, with an ancient evolutionary link to the ribonuclease A-like superfamily. Both bacterial EndoU and animal RNase A share a similar fold and function independently of cofactors. In contrast, the eukaryotic EndoU catalytic domain requires divalent metal ions for catalysis, possibly due to an N-terminal extension near the catalytic core. In this study, we used biophysical and computational techniques along with in vitro assays to investigate the calcium-dependent activation of human EndoU. We determined the crystal structure of EndoU bound to calcium and found that calcium binding remote from the catalytic triad triggers water-mediated intramolecular signaling and structural changes, activating the enzyme through allostery. Calcium-binding involves residues from both the catalytic core and the N-terminal extension, indicating that the N-terminal extension interacts with the catalytic core to modulate activity in response to calcium. Our findings suggest that similar mechanisms may be present across all eukaryotic EndoUs, highlighting a unique evolutionary adaptation that connects endoribonuclease activity to cellular signaling in eukaryotes.
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Affiliation(s)
- Florian Malard
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
| | - Kristen Dias
- Department of Molecular, Cell and Systems Biology, Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Margaux Baudy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
| | - Stéphane Thore
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Brune Vialet
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Fedor V Karginov
- Department of Molecular, Cell and Systems Biology, Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Sébastien Campagne
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
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2
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Hespanhol JT, Karman L, Sanchez-Limache DE, Bayer-Santos E. Intercepting biological messages: Antibacterial molecules targeting nucleic acids during interbacterial conflicts. Genet Mol Biol 2023; 46:e20220266. [PMID: 36880694 PMCID: PMC9990079 DOI: 10.1590/1678-4685-gmb-2022-0266] [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: 09/21/2022] [Accepted: 12/25/2022] [Indexed: 03/08/2023] Open
Abstract
Bacteria live in polymicrobial communities and constantly compete for resources. These organisms have evolved an array of antibacterial weapons to inhibit the growth or kill competitors. The arsenal comprises antibiotics, bacteriocins, and contact-dependent effectors that are either secreted in the medium or directly translocated into target cells. During bacterial antagonistic encounters, several cellular components important for life become a weak spot prone to an attack. Nucleic acids and the machinery responsible for their synthesis are well conserved across the tree of life. These molecules are part of the information flow in the central dogma of molecular biology and mediate long- and short-term storage for genetic information. The aim of this review is to summarize the diversity of antibacterial molecules that target nucleic acids during antagonistic interbacterial encounters and discuss their potential to promote the emergence antibiotic resistance.
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Affiliation(s)
- Julia Takuno Hespanhol
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Lior Karman
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | | | - Ethel Bayer-Santos
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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3
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Bartelli NL, Passanisi VJ, Michalska K, Song K, Nhan DQ, Zhou H, Cuthbert BJ, Stols LM, Eschenfeldt WH, Wilson NG, Basra JS, Cortes R, Noorsher Z, Gabraiel Y, Poonen-Honig I, Seacord EC, Goulding CW, Low DA, Joachimiak A, Dahlquist FW, Hayes CS. Proteolytic processing induces a conformational switch required for antibacterial toxin delivery. Nat Commun 2022; 13:5078. [PMID: 36038560 PMCID: PMC9424206 DOI: 10.1038/s41467-022-32795-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 08/12/2022] [Indexed: 02/08/2023] Open
Abstract
Many Gram-negative bacteria use CdiA effector proteins to inhibit the growth of neighboring competitors. CdiA transfers its toxic CdiA-CT region into the periplasm of target cells, where it is released through proteolytic cleavage. The N-terminal cytoplasm-entry domain of the CdiA-CT then mediates translocation across the inner membrane to deliver the C-terminal toxin domain into the cytosol. Here, we show that proteolysis not only liberates the CdiA-CT for delivery, but is also required to activate the entry domain for membrane translocation. Translocation function depends on precise cleavage after a conserved VENN peptide sequence, and the processed ∆VENN entry domain exhibits distinct biophysical and thermodynamic properties. By contrast, imprecisely processed CdiA-CT fragments do not undergo this transition and fail to translocate to the cytoplasm. These findings suggest that CdiA-CT processing induces a critical structural switch that converts the entry domain into a membrane-translocation competent conformation.
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Affiliation(s)
- Nicholas L Bartelli
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Victor J Passanisi
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Karolina Michalska
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Kiho Song
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Dinh Q Nhan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Bonnie J Cuthbert
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | - Lucy M Stols
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
| | - William H Eschenfeldt
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
| | - Nicholas G Wilson
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Jesse S Basra
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Ricardo Cortes
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Zainab Noorsher
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Youssef Gabraiel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Isaac Poonen-Honig
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Elizabeth C Seacord
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Celia W Goulding
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
- Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - David A Low
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Christopher S Hayes
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA.
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.
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4
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Tian Y, Zeng F, Raybarman A, Fatma S, Carruthers A, Li Q, Huang RH. Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB. Proc Natl Acad Sci U S A 2022; 119:e2202464119. [PMID: 35858322 PMCID: PMC9304027 DOI: 10.1073/pnas.2202464119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/10/2022] [Indexed: 01/14/2023] Open
Abstract
RtcB is involved in transfer RNA (tRNA) splicing in archaeal and eukaryotic organisms. However, most RtcBs are found in bacteria, whose tRNAs have no introns. Because tRNAs are the substrates of archaeal and eukaryotic RtcB, it is assumed that bacterial RtcBs are for repair of damaged tRNAs. Here, we show that a subset of bacterial RtcB, denoted RtcB2 herein, specifically repair ribosomal damage in the decoding center. To access the damage site for repair, however, the damaged 70S ribosome needs to be dismantled first, and this is accomplished by bacterial PrfH. Peptide-release assays revealed that PrfH is only active with the damaged 70S ribosome but not with the intact one. A 2.55-Å cryo-electron microscopy structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into PrfH discriminating between the damaged and the intact ribosomes via specific recognition of the cleaved 3'-terminal nucleotide. RNA repair assays demonstrated that RtcB2 efficiently repairs the damaged 30S ribosomal subunit but not the damaged tRNAs. Cell-based assays showed that the RtcB2-PrfH pair reverse the damage inflicted by ribosome-specific ribotoxins in vivo. Thus, our combined biochemical, structural, and cell-based studies have uncovered a bacterial defense system specifically evolved to reverse the lethal ribosomal damage in the decoding center for cell survival.
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Affiliation(s)
- Yannan Tian
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fuxing Zeng
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, People’s Republic of China
| | - Adrika Raybarman
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Shirin Fatma
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Amy Carruthers
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Qingrong Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, People’s Republic of China
| | - Raven H. Huang
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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5
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Verhoeve VI, Fauntleroy TD, Risteen RG, Driscoll TP, Gillespie JJ. Cryptic Genes for Interbacterial Antagonism Distinguish Rickettsia Species Infecting Blacklegged Ticks From Other Rickettsia Pathogens. Front Cell Infect Microbiol 2022; 12:880813. [PMID: 35592653 PMCID: PMC9111745 DOI: 10.3389/fcimb.2022.880813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/04/2022] [Indexed: 01/28/2023] Open
Abstract
Background The genus Rickettsia (Alphaproteobacteria: Rickettsiales) encompasses numerous obligate intracellular species with predominantly ciliate and arthropod hosts. Notable species are pathogens transmitted to mammals by blood-feeding arthropods. Mammalian pathogenicity evolved from basal, non-pathogenic host-associations; however, some non-pathogens are closely related to pathogens. One such species, Rickettsia buchneri, is prevalent in the blacklegged tick, Ixodes scapularis. While I. scapularis transmits several pathogens to humans, it does not transmit Rickettsia pathogens. We hypothesize that R. buchneri established a mutualism with I. scapularis, blocking tick superinfection with Rickettsia pathogens. Methods To improve estimates for assessing R. buchneri infection frequency in blacklegged tick populations, we used comparative genomics to identify an R. buchneri gene (REIS_1424) not present in other Rickettsia species present throughout the I. scapularis geographic range. Bioinformatic and phylogenomics approaches were employed to propose a function for the hypothetical protein (263 aa) encoded by REIS_1424. Results REIS_1424 has few analogs in other Rickettsiales genomes and greatest similarity to non-Proteobacteria proteins. This cohort of proteins varies greatly in size and domain composition, possessing characteristics of Recombination hotspot (Rhs) and contact dependent growth inhibition (CDI) toxins, with similarity limited to proximal C-termini (~145 aa). This domain was named CDI-like/Rhs-like C-terminal toxin (CRCT). As such proteins are often found as toxin-antidote (TA) modules, we interrogated REIS_1423 (151 aa) as a putative antidote. Indeed, REIS_1423 is similar to proteins encoded upstream of CRCT domain-containing proteins. Accordingly, we named these proteins CDI-like/Rhs-like C-terminal toxin antidotes (CRCA). R. buchneri expressed both REIS_1423 and REIS_1424 in tick cell culture, and PCR assays showed specificity for R. buchneri over other rickettsiae and utility for positive detection in three tick populations. Finally, phylogenomics analyses uncovered divergent CRCT/CRCA modules in varying states of conservation; however, only R. buchneri and related Tamurae/Ixodes Group rickettsiae carry complete TA modules. Conclusion We hypothesize that Rickettsia CRCT/CRCA modules circulate in the Rickettsia mobile gene pool, arming rickettsiae for battle over arthropod colonization. While its functional significance remains to be tested, R. buchneri CRCT/CRCA serves as a marker to positively identify infection and begin deciphering the role this endosymbiont plays in the biology of the blacklegged tick.
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Affiliation(s)
- Victoria I. Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Tyesha D. Fauntleroy
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Riley G. Risteen
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Timothy P. Driscoll
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- *Correspondence: Joseph J. Gillespie,
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6
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Cuthbert BJ, Hayes CS, Goulding CW. Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. Front Mol Biosci 2022; 9:866854. [PMID: 35558562 PMCID: PMC9086364 DOI: 10.3389/fmolb.2022.866854] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/25/2022] Open
Abstract
Bacteria live in complex communities and environments, competing for space and nutrients. Within their niche habitats, bacteria have developed various inter-bacterial mechanisms to compete and communicate. One such mechanism is contact-dependent growth inhibition (CDI). CDI is found in many Gram-negative bacteria, including several pathogens. These CDI+ bacteria encode a CdiB/CdiA two-partner secretion system that delivers inhibitory toxins into neighboring cells upon contact. Toxin translocation results in the growth inhibition of closely related strains and provides a competitive advantage to the CDI+ bacteria. CdiB, an outer-membrane protein, secretes CdiA onto the surface of the CDI+ bacteria. When CdiA interacts with specific target-cell receptors, CdiA delivers its C-terminal toxin region (CdiA-CT) into the target-cell. CdiA-CT toxin proteins display a diverse range of toxic functions, such as DNase, RNase, or pore-forming toxin activity. CDI+ bacteria also encode an immunity protein, CdiI, that specifically binds and neutralizes its cognate CdiA-CT, protecting the CDI+ bacteria from auto-inhibition. In Gram-negative bacteria, toxin/immunity (CdiA-CT/CdiI) pairs have highly variable sequences and functions, with over 130 predicted divergent toxin/immunity complex families. In this review, we will discuss biochemical and structural advances made in the characterization of CDI. This review will focus on the diverse array of CDI toxin/immunity complex structures together with their distinct toxin functions. Additionally, we will discuss the most recent studies on target-cell recognition and toxin entry, along with the discovery of a new member of the CDI loci. Finally, we will offer insights into how these diverse toxin/immunity complexes could be harnessed to fight human diseases.
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Affiliation(s)
- Bonnie J. Cuthbert
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Christopher S. Hayes
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Celia W. Goulding
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
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7
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Li H, Tan Y, Zhang D. Genomic discovery and structural dissection of a novel type of polymorphic toxin system in gram-positive bacteria. Comput Struct Biotechnol J 2022; 20:4517-4531. [PMID: 36051883 PMCID: PMC9424270 DOI: 10.1016/j.csbj.2022.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022] Open
Abstract
Bacteria have developed several molecular conflict systems to facilitate kin recognition and non-kin competition to gain advantages in the acquisition of growth niches and of limited resources. One such example is a large class of so-called polymorphic toxin systems (PTSs), which comprise a variety of the toxin proteins secreted via T2SS, T5SS, T6SS, T7SS and many others. These systems are highly divergent in terms of sequence/structure, domain architecture, toxin-immunity association, and organization of the toxin loci, which makes it difficult to identify and characterize novel systems using traditional experimental and bioinformatic strategies. In recent years, we have been developing and utilizing unique genome-mining strategies and pipelines, based on the organizational principles of both domain architectures and genomic loci of PTSs, for an effective and comprehensive discovery of novel PTSs, dissection of their components, and prediction of their structures and functions. In this study, we present our systematic discovery of a new type of PTS (S8-PTS) in several gram-positive bacteria. We show that the S8-PTS contains three components: a peptidase of the S8 family (subtilases), a polymorphic toxin, and an immunity protein. We delineated the typical organization of these polymorphic toxins, in which a N-terminal signal peptide is followed by a potential receptor binding domain, BetaH, and one of 16 toxin domains. We classified each toxin domain by the distinct superfamily to which it belongs, identifying nine BECR ribonucleases, one Restriction Endonuclease, one HNH nuclease, two novel toxin domains homologous to the VOC enzymes, one toxin domain with the Frataxin-like fold, and several other unique toxin families such as Ntox33 and HicA. Accordingly, we identified 20 immunity families and classified them into different classes of folds. Further, we show that the S8-PTS-associated peptidases are analogous to many other processing peptidases found in T5SS, T7SS, T9SS, and many proprotein-processing peptidases, indicating that they function to release the toxin domains during secretion. The S8-PTSs are mostly found in animal and plant-associated bacteria, including many pathogens. We propose S8-PTSs will facilitate the competition of these bacteria with other microbes or contribute to the pathogen-host interactions.
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Affiliation(s)
- Huan Li
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA
- Program of Bioinformatics and Computational Biology, College of Arts & Sciences, Saint Louis University, MO 63103, USA
- Corresponding author at: Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA.
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8
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Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt W(S, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia‐Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021; 89:1647-1672. [PMID: 34561912 PMCID: PMC8616854 DOI: 10.1002/prot.26247] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022]
Abstract
The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.
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Affiliation(s)
- Leila T. Alexander
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | | | - Athanassios Adamopoulos
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Markus Alahuhta
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Ann M. Arvin
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Yannick J. Bomble
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | - Valerio Chiarini
- Program in Structural Biology and BiophysicsInstitute of Biotechnology, University of HelsinkiHelsinkiFinland
| | - Naga babu Chinnam
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
| | - Wah Chiu
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
- BioengineeringStanford University School of MedicineStanfordCaliforniaUSA
- Division of Cryo‐EM and Bioimaging SSRLSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Rhys Grinter
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Gagan D. Gupta
- Radiation Biology & Health Sciences DivisionBhabha Atomic Research CentreMumbaiIndia
| | - Marcus D. Hartmann
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental BiologyUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
- Biomolecular Science and Engineering ProgramUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Tatjana Heidebrecht
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of the National Research Council of Italy (CNR)RomeItaly
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Romain Linares
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | | | - Vladimir V. Lunin
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Andrei N. Lupas
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Cihan Makbul
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John Moult
- Department of Cell Biology and Molecular GeneticsInstitute for Bioscience and Biotechnology Research, University of MarylandRockvilleMarylandUSA
| | - Prasun K. Mukherjee
- Nuclear Agriculture & Biotechnology DivisionBhabha Atomic Research CentreMumbaiIndia
| | - William (Sam) Nutt
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Stefan L. Oliver
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
| | - Anastassis Perrakis
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lucy Stols
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John A. Tainer
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
- Department of Cancer BiologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College LondonLondonUK
- Centre for Structural Systems Biology, Leibniz‐Institut für Experimentelle VirologieHamburgGermany
| | - Susan E. Tsutakawa
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | | | - Torsten Schwede
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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9
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Lipidation of Class IV CdiA Effector Proteins Promotes Target Cell Recognition during Contact-Dependent Growth Inhibition. mBio 2021; 12:e0253021. [PMID: 34634941 PMCID: PMC8510554 DOI: 10.1128/mbio.02530-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Contact-dependent growth inhibition (CDI) systems enable the direct transfer of protein toxins between competing Gram-negative bacteria. CDI+ strains produce cell surface CdiA effector proteins that bind specific receptors on neighboring bacteria to initiate toxin delivery. Three classes of CdiA effectors that recognize different outer membrane protein receptors have been characterized in Escherichia coli to date. Here, we describe a fourth effector class that uses the lipopolysaccharide (LPS) core as a receptor to identify target bacteria. Selection for CDI-resistant target cells yielded waaF and waaP “deep-rough” mutants, which are unable to synthesize the full LPS core. The CDI resistance phenotypes of other waa mutants suggest that phosphorylated inner-core heptose residues form a critical CdiA recognition epitope. Class IV cdi loci also encode putative lysyl acyltransferases (CdiC) that are homologous to enzymes that lipidate repeats-in-toxin (RTX) cytolysins. We found that catalytically active CdiC is required for full target cell killing activity, and we provide evidence that the acyltransferase appends 3-hydroxydecanoate to a specific Lys residue within the CdiA receptor-binding domain. We propose that the lipid moiety inserts into the hydrophobic leaflet of lipid A to anchor CdiA interactions with the core oligosaccharide. Thus, LPS-binding CDI systems appear to have co-opted an RTX toxin-activating acyltransferase to increase the affinity of CdiA effectors for the target cell outer membrane.
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10
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Jia F, Chi C, Han M. Regulation of Nucleotide Metabolism and Germline Proliferation in Response to Nucleotide Imbalance and Genotoxic Stresses by EndoU Nuclease. Cell Rep 2021; 30:1848-1861.e5. [PMID: 32049015 PMCID: PMC7050212 DOI: 10.1016/j.celrep.2020.01.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/06/2019] [Accepted: 01/15/2020] [Indexed: 12/23/2022] Open
Abstract
Nucleotide deprivation and imbalance present detrimental conditions for animals and are thus expected to trigger cellular responses that direct protective changes in metabolic, developmental, and behavioral programs, albeit such mechanisms are vastly underexplored. Following our previous finding that Caenorhabditis elegans shut down germ cell proliferation in response to pyrimidine deprivation, we find in this study that endonuclease ENDU-2 regulates nucleotide metabolism and germ cell proliferation in response to nucleotide imbalance and other genotoxic stress, and that it affects mitotic chromosomal segregation in the intestine and lifespan. ENDU-2 expression is induced by nucleotide imbalance and genotoxic stress, and ENDU-2 exerts its function in the intestine, mostly by inhibiting the phosphorylation of CTPS-1 through repressing the PKA pathway and histone deacetylase HDA-1. Human EndoU also affects the response to genotoxic drugs. Our work reveals an unknown role of ENDU-2 in regulating nucleotide metabolism and animals' response to genotoxic stress, which may link EndoU function to cancer treatment.
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Affiliation(s)
- Fan Jia
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Colorado at Boulder, Boulder, CO 80309-0347, USA.
| | - Congwu Chi
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Colorado at Boulder, Boulder, CO 80309-0347, USA
| | - Min Han
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Colorado at Boulder, Boulder, CO 80309-0347, USA
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11
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Kim Y, Wower J, Maltseva N, Chang C, Jedrzejczak R, Wilamowski M, Kang S, Nicolaescu V, Randall G, Michalska K, Joachimiak A. Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. Commun Biol 2021; 4:193. [PMID: 33564093 PMCID: PMC7873276 DOI: 10.1038/s42003-021-01735-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site. Our findings provide new insights for the development of uracil scaffold-based drugs. Youngchang Kim, Jacek Wower, and colleagues explore the sequence specificity, metal ion dependence and catalytic mechanism of the Nsp15 endoribonuclease NendoU from SARS-CoV-2. The authors also solve five new crystal structures of the enzyme in complex with 5’UMP, 3’UMP, 5’cGpU, uridine 2′,3′-vanadate (transition state analog) and Tipiracil (uracil mimic), and demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Jacek Wower
- Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Changsoo Chang
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Mateusz Wilamowski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA
| | - Soowon Kang
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA. .,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA.
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12
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Genetic Evidence for SecY Translocon-Mediated Import of Two Contact-Dependent Growth Inhibition (CDI) Toxins. mBio 2021; 12:mBio.03367-20. [PMID: 33531386 PMCID: PMC7858069 DOI: 10.1128/mbio.03367-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Many bacterial species interact via direct cell-to-cell contact using CDI systems, which provide a mechanism to inject toxins that inhibit bacterial growth into one another. Here, we find that two CDI toxins, one that depolarizes membranes and another that degrades RNA, exploit the universally conserved SecY translocon machinery used to export proteins for target cell entry. The C-terminal (CT) toxin domains of contact-dependent growth inhibition (CDI) CdiA proteins target Gram-negative bacteria and must breach both the outer and inner membranes of target cells to exert growth inhibitory activity. Here, we examine two CdiA-CT toxins that exploit the bacterial general protein secretion machinery after delivery into the periplasm. A Ser281Phe amino acid substitution in transmembrane segment 7 of SecY, the universally conserved channel-forming subunit of the Sec translocon, decreases the cytotoxicity of the membrane depolarizing orphan10 toxin from enterohemorrhagic Escherichia coli EC869. Target cells expressing secYS281F and lacking either PpiD or YfgM, two SecY auxiliary factors, are fully protected from CDI-mediated inhibition either by CdiA-CTo10EC869 or by CdiA-CTGN05224, the latter being an EndoU RNase CdiA toxin from Klebsiella aerogenes GN05224 that has a related cytoplasm entry domain. RNase activity of CdiA-CTGN05224 was reduced in secYS281F target cells and absent in secYS281F ΔppiD or secYS281F ΔyfgM target cells during competition co-cultures. Importantly, an allele-specific mutation in secY (secYG313W) renders ΔppiD or ΔyfgM target cells specifically resistant to CdiA-CTGN05224 but not to CdiA-CTo10EC869, further suggesting a direct interaction between SecY and the CDI toxins. Our results provide genetic evidence of a unique confluence between the primary cellular export route for unfolded polypeptides and the import pathways of two CDI toxins.
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13
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Chatterjee A, Willett JLE, Dunny GM, Duerkop BA. Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria. PLoS Genet 2021; 17:e1009204. [PMID: 33411815 PMCID: PMC7790226 DOI: 10.1371/journal.pgen.1009204] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (phages) are being considered as alternative therapeutics for the treatment of multidrug resistant bacterial infections. Considering phages have narrow host-ranges, it is generally accepted that therapeutic phages will have a marginal impact on non-target bacteria. We have discovered that lytic phage infection induces transcription of type VIIb secretion system (T7SS) genes in the pathobiont Enterococcus faecalis. Membrane damage during phage infection induces T7SS gene expression resulting in cell contact dependent antagonism of different Gram positive bystander bacteria. Deletion of essB, a T7SS structural component, abrogates phage-mediated killing of bystanders. A predicted immunity gene confers protection against T7SS mediated inhibition, and disruption of its upstream LXG toxin gene rescues growth of E. faecalis and Staphylococcus aureus bystanders. Phage induction of T7SS gene expression and bystander inhibition requires IreK, a serine/threonine kinase, and OG1RF_11099, a predicted GntR-family transcription factor. Additionally, sub-lethal doses of membrane targeting and DNA damaging antibiotics activated T7SS expression independent of phage infection, triggering T7SS antibacterial activity against bystander bacteria. Our findings highlight how phage infection and antibiotic exposure of a target bacterium can affect non-target bystander bacteria and implies that therapies beyond antibiotics, such as phage therapy, could impose collateral damage to polymicrobial communities. Renewed interest in phages as alternative therapeutics to combat multi-drug resistant bacterial infections, highlights the importance of understanding the consequences of phage-bacteria interactions in the context of microbial communities. Although it is well established that phages are highly specific for their host bacterium, there is no clear consensus on whether or not phage infection (and thus phage therapy) would impose collateral damage to non-target bacteria in polymicrobial communities. Here we provide direct evidence of how phage infection of a clinically relevant pathogen triggers an intrinsic type VII secretion system (T7SS) antibacterial response that consequently restricts the growth of neighboring bacterial cells that are not susceptible to phage infection. Phage induction of T7SS activity is a stress response and in addition to phages, T7SS antagonism can be induced using sub-inhibitory concentrations of antibiotics that facilitate membrane or DNA damage. Together these data show that a bacterial pathogen responds to diverse stressors to induce T7SS activity which manifests through the antagonism of neighboring non-kin bystander bacterial cells.
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Affiliation(s)
- Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Julia L. E. Willett
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
- * E-mail:
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14
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Lin HH, Filloux A, Lai EM. Role of Recipient Susceptibility Factors During Contact-Dependent Interbacterial Competition. Front Microbiol 2020; 11:603652. [PMID: 33281802 PMCID: PMC7690452 DOI: 10.3389/fmicb.2020.603652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Bacteria evolved multiple strategies to survive and develop optimal fitness in their ecological niche. They deployed protein secretion systems for robust and efficient delivery of antibacterial toxins into their target cells, therefore inhibiting their growth or killing them. To maximize antagonism, recipient factors on target cells can be recognized or hijacked to enhance the entry or toxicity of these toxins. To date, knowledge regarding recipient susceptibility (RS) factors and their mode of action is mostly originating from studies on the type Vb secretion system that is also known as the contact-dependent inhibition (CDI) system. Yet, recent studies on the type VI secretion system (T6SS), and the CDI by glycine-zipper protein (Cdz) system, also reported the emerging roles of RS factors in interbacterial competition. Here, we review these RS factors and their mechanistic impact in increasing susceptibility of recipient cells in response to CDI, T6SS, and Cdz. Past and future strategies for identifying novel RS factors are also discussed, which will help in understanding the interplay between attacker and prey upon secretion system-dependent competition. Understanding these mechanisms would also provide insights for developing novel antibacterial strategies to antagonize aggressive bacteria-killing pathogens.
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Affiliation(s)
- Hsiao-Han Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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15
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Ruhe ZC, Low DA, Hayes CS. Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery. Annu Rev Microbiol 2020; 74:497-520. [PMID: 32680451 DOI: 10.1146/annurev-micro-020518-115638] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
All bacteria must compete for growth niches and other limited environmental resources. These existential battles are waged at several levels, but one common strategy entails the transfer of growth-inhibitory protein toxins between competing cells. These antibacterial effectors are invariably encoded with immunity proteins that protect cells from intoxication by neighboring siblings. Several effector classes have been described, each designed to breach the cell envelope of target bacteria. Although effector architectures and export pathways tend to be clade specific, phylogenetically distant species often deploy closely related toxin domains. Thus, diverse competition systems are linked through a common reservoir of toxin-immunity pairs that is shared via horizontal gene transfer. These toxin-immunity protein pairs are extraordinarily diverse in sequence, and this polymorphism underpins an important mechanism of self/nonself discrimination in bacteria. This review focuses on the structures, functions, and delivery mechanisms of polymorphic toxin effectors that mediate bacterial competition.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
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16
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Kim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M, Godzik A, Michalska K, Joachimiak A. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci 2020; 29:1596-1605. [PMID: 32304108 PMCID: PMC7264519 DOI: 10.1002/pro.3873] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is rapidly spreading around the world. There is no existing vaccine or proven drug to prevent infections and stop virus proliferation. Although this virus is similar to human and animal SARS-CoVs and Middle East Respiratory Syndrome coronavirus (MERS-CoVs), the detailed information about SARS-CoV-2 proteins structures and functions is urgently needed to rapidly develop effective vaccines, antibodies, and antivirals. We applied high-throughput protein production and structure determination pipeline at the Center for Structural Genomics of Infectious Diseases to produce SARS-CoV-2 proteins and structures. Here we report two high-resolution crystal structures of endoribonuclease Nsp15/NendoU. We compare these structures with previously reported homologs from SARS and MERS coronaviruses.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Natalia I Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Michael Endres
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Adam Godzik
- Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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17
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Convergent Evolution of the Barnase/EndoU/Colicin/RelE (BECR) Fold in Antibacterial tRNase Toxins. Structure 2019; 27:1660-1674.e5. [PMID: 31515004 DOI: 10.1016/j.str.2019.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/03/2019] [Accepted: 08/20/2019] [Indexed: 11/20/2022]
Abstract
Contact-dependent growth inhibition (CDI) is a form of interbacterial competition mediated by CdiB-CdiA two-partner secretion systems. CdiA effector proteins carry polymorphic C-terminal toxin domains (CdiA-CT), which are neutralized by specific CdiI immunity proteins to prevent self-inhibition. Here, we present the crystal structures of CdiA-CT⋅CdiI complexes from Klebsiella pneumoniae 342 and Escherichia coli 3006. The toxins adopt related folds that resemble the ribonuclease domain of colicin D, and both are isoacceptor-specific tRNases that cleave the acceptor stem of deacylated tRNAGAUIle. Although the toxins are similar in structure and substrate specificity, CdiA-CTKp342 activity requires translation factors EF-Tu and EF-Ts, whereas CdiA-CTEC3006 is intrinsically active. Furthermore, the corresponding immunity proteins are unrelated in sequence and structure. CdiIKp342 forms a dimeric β sandwich, whereas CdiIEC3006 is an α-solenoid monomer. Given that toxin-immunity genes co-evolve as linked pairs, these observations suggest that the similarities in toxin structure and activity reflect functional convergence.
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18
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Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 2019; 87:1037-1057. [PMID: 31442339 PMCID: PMC6851490 DOI: 10.1002/prot.25805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
Abstract
The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.
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Affiliation(s)
- Rosalba Lepore
- BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Harshul A Veraszto
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Joshua C Bufton
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Alex N Bullock
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Cody Caba
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Hongnan Cao
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ambroise Desfosses
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, Zurich, Switzerland
| | | | - Celia W Goulding
- Department of Molecular Biology and Biochemistry; Pharmaceutical Sciences, University of California Irvine, Irvine, California
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Karolina Michalska
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne
| | - Ignacio Mir-Sanchis
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - A K Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, Rockville, Maryland, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Daniel M Pinkas
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, UK
| | - Jonathan D Walton
- Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - Torsten Schwede
- Biozentrum University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland
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19
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Bartelli NL, Sun S, Gucinski GC, Zhou H, Song K, Hayes CS, Dahlquist FW. The Cytoplasm-Entry Domain of Antibacterial CdiA Is a Dynamic α-Helical Bundle with Disulfide-Dependent Structural Features. J Mol Biol 2019; 431:3203-3216. [PMID: 31181288 PMCID: PMC6727969 DOI: 10.1016/j.jmb.2019.05.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/01/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
Many Gram-negative bacterial species use contact-dependent growth inhibition (CDI) systems to compete with neighboring cells. CDI+ strains express cell-surface CdiA effector proteins, which carry a toxic C-terminal region (CdiA-CT) that is cleaved from the effector upon transfer into the periplasm of target bacteria. The released CdiA-CT consists of two domains. The C-terminal domain is typically a nuclease that inhibits cell growth, and the N-terminal "cytoplasm-entry" domain mediates toxin translocation into the target-cell cytosol. Here, we use NMR and circular dichroism spectroscopic approaches to probe the structure, stability, and dynamics of the cytoplasm-entry domain from Escherichia coli STEC_MHI813. Chemical shift analysis reveals that the CdiA-CTMHI813 entry domain is composed of a C-terminal helical bundle and a dynamic N-terminal region containing two disulfide linkages. Disruption of the disulfides by mutagenesis or chemical reduction destabilizes secondary structure over the N-terminus, but has no effect on the C-terminal helices. Although critical for N-terminal structure, the disulfides have only modest effects on global thermodynamic stability, and the entry domain exhibits characteristics of a molten globule. We find that the disulfides form in vivo as the entry domain dwells in the periplasm of inhibitor cells prior to target-cell recognition. CdiA-CTMHI813 variants lacking either disulfide still kill target bacteria, but disruption of both bonds abrogates growth inhibition activity. We propose that the entry domain's dynamic structural features are critical for function. In its molten globule-like state, the domain resists degradation after delivery, yet remains pliable enough to unfold for membrane translocation.
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Affiliation(s)
- Nicholas L Bartelli
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Sheng Sun
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Grant C Gucinski
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States
| | - Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Kiho Song
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States; Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States.
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States; Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States; Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States.
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20
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Ruhe ZC, Subramanian P, Song K, Nguyen JY, Stevens TA, Low DA, Jensen GJ, Hayes CS. Programmed Secretion Arrest and Receptor-Triggered Toxin Export during Antibacterial Contact-Dependent Growth Inhibition. Cell 2019; 175:921-933.e14. [PMID: 30388452 DOI: 10.1016/j.cell.2018.10.033] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/31/2018] [Accepted: 09/05/2018] [Indexed: 12/21/2022]
Abstract
Contact-dependent growth inhibition (CDI) entails receptor-mediated delivery of CdiA-derived toxins into Gram-negative target bacteria. Using electron cryotomography, we show that each CdiA effector protein forms a filament extending ∼33 nm from the cell surface. Remarkably, the extracellular filament represents only the N-terminal half of the effector. A programmed secretion arrest sequesters the C-terminal half of CdiA, including the toxin domain, in the periplasm prior to target-cell recognition. Upon binding receptor, CdiA secretion resumes, and the periplasmic FHA-2 domain is transferred to the target-cell outer membrane. The C-terminal toxin region of CdiA then penetrates into the target-cell periplasm, where it is cleaved for subsequent translocation into the cytoplasm. Our findings suggest that the FHA-2 domain assembles into a transmembrane conduit for toxin transport into the periplasm of target bacteria. We propose that receptor-triggered secretion ensures that FHA-2 export is closely coordinated with integration into the target-cell outer membrane. VIDEO ABSTRACT.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Poorna Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kiho Song
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Josephine Y Nguyen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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21
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Diversity of Contact-Dependent Growth Inhibition Systems of Pseudomonas aeruginosa. J Bacteriol 2019; 201:JB.00776-18. [PMID: 31036723 DOI: 10.1128/jb.00776-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) systems are used in bacterial competition to hinder the growth of neighboring microbes. These systems utilize a two-partner secretion mechanism to display the CdiA exoprotein at the bacterial cell surface. CdiA forms a long filamentous stalk that facilitates binding to a target cell and delivery of a C-terminal toxin (CT) domain. This CT domain is processed and delivered into the cytoplasm of a target cell upon contact. CDI systems also encode a cognate immunity protein (CdiI) that protects siblings and resistant targeted cells from intoxication by high-affinity binding to the CT. CdiA CT domains vary among strains within a species, and many alleles encode enzymatic functions that target nucleic acids. This variation is thought to help drive diversity and adaptation within a species. CdiA diversity is well studied in Escherichia coli and several other bacteria, but little is known about the extent of this diversity in Pseudomonas aeruginosa. The purpose of this review is to highlight the variability that exists in CDI systems of P. aeruginosa. We show that this diversity is apparent even among strains isolated from a single geographical region, suggesting that CDI systems play an important role in the ecology of P. aeruginosa.
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