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Sharkey LKR, Guerillot R, Walsh CJ, Turner AM, Lee JYH, Neville SL, Klatt S, Baines SL, Pidot SJ, Rossello FJ, Seemann T, McWilliam HEG, Cho E, Carter GP, Howden BP, McDevitt CA, Hachani A, Stinear TP, Monk IR. The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus. mBio 2023; 14:e0226223. [PMID: 37850732 PMCID: PMC10746227 DOI: 10.1128/mbio.02262-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
Among the 16 two-component systems in the opportunistic human pathogen Staphylococcus aureus, only WalKR is essential. Like the orthologous systems in other Bacillota, S. aureus WalKR controls autolysins involved in peptidoglycan remodeling and is therefore intimately involved in cell division. However, despite the importance of WalKR in S. aureus, the basis for its essentiality is not understood and the regulon is poorly defined. Here, we defined a consensus WalR DNA-binding motif and the direct WalKR regulon by using functional genomics, including chromatin immunoprecipitation sequencing, with a panel of isogenic walKR mutants that had a spectrum of altered activities. Consistent with prior findings, the direct regulon includes multiple autolysin genes. However, this work also revealed that WalR directly regulates at least five essential genes involved in lipoteichoic acid synthesis (ltaS): translation (rplK), DNA compaction (hup), initiation of DNA replication (dnaA, hup) and purine nucleotide metabolism (prs). Thus, WalKR in S. aureus serves as a polyfunctional regulator that contributes to fundamental control over critical cell processes by coordinately linking cell wall homeostasis with purine biosynthesis, protein biosynthesis, and DNA replication. Our findings further address the essentiality of this locus and highlight the importance of WalKR as a bona fide target for novel anti-staphylococcal therapeutics. IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.
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Affiliation(s)
- Liam K. R. Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Calum J. Walsh
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Adrianna M. Turner
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Y. H. Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando J. Rossello
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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Kulkarni A, Ewen-Campen B, Terao K, Matsumoto Y, Li Y, Watanabe T, Kao JA, Parhad SS, Ylla G, Mizunami M, Extavour CG. oskar acts with the transcription factor Creb to regulate long-term memory in crickets. Proc Natl Acad Sci U S A 2023; 120:e2218506120. [PMID: 37192168 PMCID: PMC10214185 DOI: 10.1073/pnas.2218506120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/28/2023] [Indexed: 05/18/2023] Open
Abstract
Novel genes have the potential to drive the evolution of new biological mechanisms, or to integrate into preexisting regulatory circuits and contribute to the regulation of older, conserved biological functions. One such gene, the novel insect-specific gene oskar, was first identified based on its role in establishing the Drosophila melanogaster germ line. We previously showed that this gene likely arose through an unusual domain transfer event involving bacterial endosymbionts and played a somatic role before evolving its well-known germ line function. Here, we provide empirical support for this hypothesis in the form of evidence for a neural role for oskar. We show that oskar is expressed in the adult neural stem cells of a hemimetabolous insect, the cricket Gryllus bimaculatus. In these stem cells, called neuroblasts, oskar is required together with the ancient animal transcription factor Creb to regulate long-term (but not short-term) olfactory memory. We provide evidence that oskar positively regulates Creb, which plays a conserved role in long-term memory across animals, and that oskar in turn may be a direct target of Creb. Together with previous reports of a role for oskar in nervous system development and function in crickets and flies, our results are consistent with the hypothesis that oskar's original somatic role may have been in the insect nervous system. Moreover, its colocalization and functional cooperation with the conserved pluripotency gene piwi in the nervous system may have facilitated oskar's later co-option to the germ line in holometabolous insects.
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Affiliation(s)
- Arpita Kulkarni
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Ben Ewen-Campen
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Kanta Terao
- Graduate School of Life Science, Hokkaido University, Sapporo060-0810, Japan
| | | | - Yaolong Li
- Graduate School of Life Science, Hokkaido University, Sapporo060-0810, Japan
| | - Takayuki Watanabe
- Faculty of Science, Hokkaido University, Sapporo060-0810, Japan
- Research Center for Integrative Evolutionary Science, School of Advanced Sciences, Sokendai-Hayama, Kanagawa240-0193, Japan
| | - Jonchee A. Kao
- Department of Molecular and Cellular Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Swapnil S. Parhad
- University of Massachusetts Chan Medical School, Program in Molecular Medicine, Worcester, MA01655
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Makoto Mizunami
- Faculty of Science, Hokkaido University, Sapporo060-0810, Japan
| | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
- HHMI, Chevy Chase, MD20815
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Nachmias D, Melnikov N, Zorea A, Sharon M, Yemini R, De-Picchoto Y, Tsirkas I, Aharoni A, Frohn B, Schwille P, Zarivach R, Mizrahi I, Elia N. Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery. THE ISME JOURNAL 2023; 17:117-129. [PMID: 36221007 PMCID: PMC9751279 DOI: 10.1038/s41396-022-01328-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
The archaeal Asgard superphylum currently stands as the most promising prokaryotic candidate, from which eukaryotic cells emerged. This unique superphylum encodes for eukaryotic signature proteins (ESP) that could shed light on the origin of eukaryotes, but the properties and function of these proteins is largely unresolved. Here, we set to understand the function of an Asgard archaeal protein family, namely the ESCRT machinery, that is conserved across all domains of life and executes basic cellular eukaryotic functions, including membrane constriction during cell division. We find that ESCRT proteins encoded in Loki archaea, express in mammalian and yeast cells, and that the Loki ESCRT-III protein, CHMP4-7, resides in the eukaryotic nucleus in both organisms. Moreover, Loki ESCRT-III proteins associated with chromatin, recruited their AAA-ATPase VPS4 counterpart to organize in discrete foci in the mammalian nucleus, and directly bind DNA. The human ESCRT-III protein, CHMP1B, exhibited similar nuclear properties and recruited both human and Asgard VPS4s to nuclear foci, indicating interspecies interactions. Mutation analysis revealed a role for the N terminal region of ESCRT-III in mediating these phenotypes in both human and Asgard ESCRTs. These findings suggest that ESCRT proteins hold chromatin binding properties that were highly preserved through the billion years of evolution separating Asgard archaea and humans. The conserved chromatin binding properties of the ESCRT membrane remodeling machinery, reported here, may have important implications for the origin of eukaryogenesis.
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Affiliation(s)
- Dikla Nachmias
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Nataly Melnikov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Alvah Zorea
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Maya Sharon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Reut Yemini
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Yasmin De-Picchoto
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Ioannis Tsirkas
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Bela Frohn
- Department of Cellular and Molecular Biophysics, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Natalie Elia
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
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Cozzolino F, Iacobucci I, Monaco V, Monti M. Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era. J Proteome Res 2021; 20:3018-3030. [PMID: 33961438 PMCID: PMC8280749 DOI: 10.1021/acs.jproteome.1c00074] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
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The fields of application
of functional proteomics are not limited
to the study of protein–protein interactions; they also extend
to those involving protein complexes that bind DNA or RNA. These interactions
affect fundamental processes such as replication, transcription, and
repair in the case of DNA, as well as transport, translation, splicing,
and silencing in the case of RNA. Analytical or preparative experimental
approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins
by exploiting the advantage of the affinity shown by these proteins
toward a specific oligonucleotide sequence. The present review proposes
an overview of the approaches most commonly employed in proteomics
applications for the identification of nucleic acid-binding proteins,
such as affinity purification (AP) protocols, EMSA, chromatin purification
methods, and CRISPR-based chromatin affinity purification, which are
generally associated with mass spectrometry methodologies for the
unbiased protein identification.
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Affiliation(s)
- Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.,Interuniversity Consortium National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro, 305-00136 Rome, Italy
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
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Gel-Based Analysis of Protein-Nucleic Acid Interactions. Methods Mol Biol 2021; 2263:321-339. [PMID: 33877605 PMCID: PMC7614308 DOI: 10.1007/978-1-0716-1197-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Electrophoretic mobility shift assays (EMSAs) are among the most frequently used and straightforward experiments for studying protein-nucleic acid interactions. EMSAs rely on the principle that protein-nucleic acid complexes have reduced electrophoretic mobility in a native gel matrix compared to free nucleic acid due to their larger size and reduced negative charge. Therefore, bands for the protein-nucleic acid complexes are shifted in a gel and can be distinguished from free nucleic acids. EMSAs remain a popular technique since they do not require specialist equipment and the complexes formed are easily visualized. Furthermore, the technique can be adapted to enable various aspects of protein-nucleic acid interactions to be investigated, including sequence specificity, estimated binding affinity, and binding stoichiometry.
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Genetic variability of the U5 and downstream sequence of major HIV-1 subtypes and circulating recombinant forms. Sci Rep 2020; 10:13214. [PMID: 32764600 PMCID: PMC7411029 DOI: 10.1038/s41598-020-70083-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 07/03/2020] [Indexed: 11/08/2022] Open
Abstract
The critical role of the regulatory elements at the 5′ end of the HIV-1 genome in controlling the life cycle of HIV-1 indicates that this region significantly influences virus fitness and its biological properties. In this study, we performed a detailed characterization of strain-specific variability of sequences from the U5 to upstream of the gag gene start codon of diverse HIV-1 strains by using next-generation sequencing (NGS) techniques. Overall, we found that this region of the HIV-1 genome displayed a low degree of intra-strain variability. On the other hand, inter-strain variability was found to be as high as that reported for gag and env genes (13–17%). We observed strain-specific single point and clustered mutations in the U5, PBS, and gag leader sequences (GLS), generating potential strain-specific transcription factor binding sites (TFBS). Using an infrared gel shift assay, we demonstrated the presence of potential TFBS such as E-box in CRF22_01A, and Stat 6 in subtypes A and G, as well as in their related CRFs. The strain-specific variation found in the sequence corresponding at the RNA level to functional domains of the 5ʹ UTR, could also potentially impact the secondary/tertiary structural rearrangement of this region. Thus, the variability observed in this 5′ end of the genomic region of divergent HIV-1 strains strongly suggests that functions of this region might be affected in a strain-specific manner. Our findings provide new insights into DNA–protein interactions that regulate HIV-1 replication and the influence of strain characterization on the biology of HIV-1 infection.
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Abstract
The use of RNA electrophoretic mobility shift assays (REMSAs) for analysis of RNA-protein interactions have been limited to lengthy assay time and qualitative assessment. To vastly improve assay efficiency, feasibility and quality of data procured from REMSAs, we combine here some of the best-known labeling and electrophoretic techniques. Nucleic acid fragments are end-labeled with fluorescent tags, as opposed to the radioactive or biotin tags. The fluorescent probes may be detected directly from the electrophoresis gel, eliminating the need for cumbersome membrane transfer and immunoblotting. Modifying the REMSA protocol to include low-molarity, lithium borate conductive media and near-infrared-labeled probes allows for a reduction assay time, quantitative comparison between experimental conditions and crisp band resolution (i.e., optimized results).
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