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Karampelias C, Băloiu B, Rathkolb B, da Silva-Buttkus P, Bachar-Wikström E, Marschall S, Fuchs H, Gailus-Durner V, Chu L, Hrabě de Angelis M, Andersson O. Examining the liver-pancreas crosstalk reveals a role for the molybdenum cofactor in β-cell regeneration. Life Sci Alliance 2024; 7:e202402771. [PMID: 39159974 PMCID: PMC11333758 DOI: 10.26508/lsa.202402771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/21/2024] Open
Abstract
Regeneration of insulin-producing β-cells is an alternative avenue to manage diabetes, and it is crucial to unravel this process in vivo during physiological responses to the lack of β-cells. Here, we aimed to characterize how hepatocytes can contribute to β-cell regeneration, either directly or indirectly via secreted proteins or metabolites, in a zebrafish model of β-cell loss. Using lineage tracing, we show that hepatocytes do not directly convert into β-cells even under extreme β-cell ablation conditions. A transcriptomic analysis of isolated hepatocytes after β-cell ablation displayed altered lipid- and glucose-related processes. Based on the transcriptomics, we performed a genetic screen that uncovers a potential role of the molybdenum cofactor (Moco) biosynthetic pathway in β-cell regeneration and glucose metabolism in zebrafish. Consistently, molybdenum cofactor synthesis 2 (Mocs2) haploinsufficiency in mice indicated dysregulated glucose metabolism and liver function. Together, our study sheds light on the liver-pancreas crosstalk and suggests that the molybdenum cofactor biosynthesis pathway should be further studied in relation to glucose metabolism and diabetes.
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Affiliation(s)
- Christos Karampelias
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Bianca Băloiu
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Birgit Rathkolb
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Patricia da Silva-Buttkus
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Etty Bachar-Wikström
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Susan Marschall
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helmut Fuchs
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Valerie Gailus-Durner
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lianhe Chu
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Hrabě de Angelis
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Olov Andersson
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
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2
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Gyger J, Torrens G, Cava F, Bernhardt TG, Fumeaux C. A potential space-making role in cell wall biogenesis for SltB1and DacB revealed by a beta-lactamase induction phenotype in Pseudomonas aeruginosa. mBio 2024; 15:e0141924. [PMID: 38920394 PMCID: PMC11253642 DOI: 10.1128/mbio.01419-24] [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: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
Pseudomonas aeruginosa encodes the beta-lactamase AmpC, which promotes resistance to beta-lactam antibiotics. Expression of ampC is induced by anhydro-muropeptides (AMPs) released from the peptidoglycan (PG) cell wall upon beta-lactam treatment. AmpC can also be induced via genetic inactivation of PG biogenesis factors such as the endopeptidase DacB that cleaves PG crosslinks. Mutants in dacB occur in beta-lactam-resistant clinical isolates of P. aeruginosa, but it has remained unclear why DacB inactivation promotes ampC induction. Similarly, the inactivation of lytic transglycosylase (LT) enzymes such as SltB1 that cut PG glycans has also been associated with ampC induction and beta-lactam resistance. Given that LT enzymes are capable of producing AMP products that serve as ampC inducers, this latter observation has been especially difficult to explain. Here, we show that ampC induction in sltB1 or dacB mutants requires another LT enzyme called MltG. In Escherichia coli, MltG has been implicated in the degradation of nascent PG strands produced upon beta-lactam treatment. Accordingly, in P. aeruginosa sltB1 and dacB mutants, we detected the MltG-dependent production of pentapeptide-containing AMP products that are signatures of nascent PG degradation. Our results therefore support a model in which SltB1 and DacB use their PG-cleaving activity to open space in the PG matrix for the insertion of new material. Thus, their inactivation mimics low-level beta-lactam treatment by reducing the efficiency of new PG insertion into the wall, causing the degradation of some nascent PG material by MltG to produce the ampC-inducing signal. IMPORTANCE Inducible beta-lactamases like the ampC system of Pseudomonas aeruginosa are a common determinant of beta-lactam resistance among gram-negative bacteria. The regulation of ampC is elegantly tuned to detect defects in cell wall synthesis caused by beta-lactam drugs. Studies of mutations causing ampC induction in the absence of drug therefore promise to reveal new insights into the process of cell wall biogenesis in addition to aiding our understanding of how resistance to beta-lactam antibiotics arises in the clinic. In this study, the ampC induction phenotype for mutants lacking a glycan-cleaving enzyme or an enzyme that cuts cell wall crosslinks was used to uncover a potential role for these enzymes in making space in the wall matrix for the insertion of new material during cell growth.
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Affiliation(s)
- Joël Gyger
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gabriel Torrens
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Umea, Sweden
- Department of Molecular Biology, Science for Life Laboratory (SciLifeLab), Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Umea, Sweden
- Department of Molecular Biology, Science for Life Laboratory (SciLifeLab), Umeå University, Umeå, Sweden
| | - Thomas G. Bernhardt
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Coralie Fumeaux
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
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3
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Vogler NW, Chen R, Virkler A, Tu VY, Gottfried JA, Geffen MN. Direct piriform-to-auditory cortical projections shape auditory-olfactory integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.602976. [PMID: 39071445 PMCID: PMC11275881 DOI: 10.1101/2024.07.11.602976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
In a real-world environment, the brain must integrate information from multiple sensory modalities, including the auditory and olfactory systems. However, little is known about the neuronal circuits governing how odors influence and modulate sound processing. Here, we investigated the mechanisms underlying auditory-olfactory integration using anatomical, electrophysiological, and optogenetic approaches, focusing on the auditory cortex as a key locus for cross-modal integration. First, retrograde and anterograde viral tracing strategies revealed a direct projection from the piriform cortex to the auditory cortex. Next, using in vivo electrophysiological recordings of neuronal activity in the auditory cortex of awake mice, we found that odor stimuli modulate auditory cortical responses to sound. Finally, we used in vivo optogenetic manipulations during electrophysiology to demonstrate that olfactory modulation in auditory cortex, specifically, odor-driven enhancement of sound responses, depends on direct input from the piriform cortex. Together, our results identify a novel cortical circuit shaping olfactory modulation in the auditory cortex, shedding new light on the neuronal mechanisms underlying auditory-olfactory integration.
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Affiliation(s)
- Nathan W. Vogler
- Department of Otorhinolaryngology, Perelman School of Medicine, University of Pennsylvania
| | - Ruoyi Chen
- Department of Otorhinolaryngology, Perelman School of Medicine, University of Pennsylvania
| | - Alister Virkler
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania
| | - Violet Y. Tu
- Department of Otorhinolaryngology, Perelman School of Medicine, University of Pennsylvania
| | - Jay A. Gottfried
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania
| | - Maria N. Geffen
- Department of Otorhinolaryngology, Perelman School of Medicine, University of Pennsylvania
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4
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Son JE, Park SH, Choi U, Lee CR. Lytic transglycosylase repertoire diversity enables intrinsic antibiotic resistance and daughter cell separation in Escherichia coli under acidic stress. Antimicrob Agents Chemother 2024; 68:e0037224. [PMID: 38884456 PMCID: PMC11232391 DOI: 10.1128/aac.00372-24] [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: 03/07/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Peptidoglycan (PG) is an important architectural element that imparts physical toughness and rigidity to the bacterial envelope. It is also a dynamic structure that undergoes continuous turnover or autolysis. Escherichia coli possesses redundant PG degradation enzymes responsible for PG turnover; however, the advantage afforded by the existence of numerous PG degradation enzymes remains incompletely understood. In this study, we elucidated the physiological roles of MltE and MltC, members of the lytic transglycosylase (LTG) family that catalyze the cleavage of glycosidic bonds between disaccharide subunits within PG strands. MltE and MltC are acidic LTGs that exhibit increased enzymatic activity and protein levels under acidic pH conditions, respectively, and deletion of these two LTGs results in a pronounced growth defect at acidic pH. Furthermore, inactivation of these two LTGs induces increased susceptibility at acidic pH against various antibiotics, particularly vancomycin, which seems to be partially caused by elevated membrane permeability. Intriguingly, inactivation of these LTGs induces a chaining morphology, indicative of daughter cell separation defects, only under acidic pH conditions. Simultaneous deletion of PG amidases, known contributors to daughter cell separation, exacerbates the chaining phenotype at acidic pH. This suggests that the two LTGs may participate in the cleavage of glycan strands between daughter cells under acidic pH conditions. Collectively, our findings highlight the role of LTG repertoire diversity in facilitating bacterial survival and antibiotic resistance under stressful conditions.
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Affiliation(s)
- Ji Eun Son
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Si Hyoung Park
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Umji Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
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5
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Avila‐Cobian LF, De Benedetti S, Hoshino H, Nguyen VT, El‐Araby AM, Sader S, Hu DD, Cole SL, Kim C, Fisher JF, Champion MM, Mobashery S. Lytic transglycosylase Slt of Pseudomonas aeruginosa as a periplasmic hub protein. Protein Sci 2024; 33:e5038. [PMID: 38864725 PMCID: PMC11168074 DOI: 10.1002/pro.5038] [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: 12/01/2023] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 06/13/2024]
Abstract
Peptidoglycan is a major constituent of the bacterial cell wall. Its integrity as a polymeric edifice is critical for bacterial survival and, as such, it is a preeminent target for antibiotics. The peptidoglycan is a dynamic crosslinked polymer that undergoes constant biosynthesis and turnover. The soluble lytic transglycosylase (Slt) of Pseudomonas aeruginosa is a periplasmic enzyme involved in this dynamic turnover. Using amber-codon-suppression methodology in live bacteria, we incorporated a fluorescent chromophore into the structure of Slt. Fluorescent microscopy shows that Slt populates the length of the periplasmic space and concentrates at the sites of septation in daughter cells. This concentration persists after separation of the cells. Amber-codon-suppression methodology was also used to incorporate a photoaffinity amino acid for the capture of partner proteins. Mass-spectrometry-based proteomics identified 12 partners for Slt in vivo. These proteomics experiments were complemented with in vitro pulldown analyses. Twenty additional partners were identified. We cloned the genes and purified to homogeneity 22 identified partners. Biophysical characterization confirmed all as bona fide Slt binders. The identities of the protein partners of Slt span disparate periplasmic protein families, inclusive of several proteins known to be present in the divisome. Notable periplasmic partners (KD < 0.5 μM) include PBPs (PBP1a, KD = 0.07 μM; PBP5 = 0.4 μM); other lytic transglycosylases (SltB2, KD = 0.09 μM; RlpA, KD = 0.4 μM); a type VI secretion system effector (Tse5, KD = 0.3 μM); and a regulatory protease for alginate biosynthesis (AlgO, KD < 0.4 μM). In light of the functional breadth of its interactome, Slt is conceptualized as a hub protein within the periplasm.
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Affiliation(s)
- Luis F. Avila‐Cobian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Stefania De Benedetti
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Hidekazu Hoshino
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Van T. Nguyen
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Amr M. El‐Araby
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Safaa Sader
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Daniel D. Hu
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Sara L. Cole
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Choon Kim
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew M. Champion
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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6
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Meylakh N, Crawford LS, Mills EP, Macefield VG, Vickers ER, Macey PM, Keay KA, Henderson LA. Altered Corticobrainstem Connectivity during Spontaneous Fluctuations in Pain Intensity in Painful Trigeminal Neuropathy. eNeuro 2024; 11:ENEURO.0522-23.2024. [PMID: 38997145 PMCID: PMC11277291 DOI: 10.1523/eneuro.0522-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 07/14/2024] Open
Abstract
Chronic neuropathic pain can result from nervous system injury and can persist in the absence of external stimuli. Although ongoing pain characterizes the disorder, in many individuals, the intensity of this ongoing pain fluctuates dramatically. Previously, it was identified that functional magnetic resonance imaging signal covariations between the midbrain periaqueductal gray (PAG) matter, rostral ventromedial medulla (RVM), and spinal trigeminal nucleus are associated with moment-to-moment fluctuations in pain intensity in individuals with painful trigeminal neuropathy (PTN). Since this brainstem circuit is modulated by higher brain input, we sought to determine which cortical sites might be influencing this brainstem network during spontaneous fluctuations in pain intensity. Over 12 min, we recorded the ongoing pain intensity in 24 PTN participants and classified them as fluctuating (n = 13) or stable (n = 11). Using a PAG seed, we identified connections between the PAG and emotional-affective sites such as the hippocampal and posterior cingulate cortices, the sensory-discriminative posterior insula, and cognitive-affective sites such as the dorsolateral prefrontal (dlPFC) and subgenual anterior cingulate cortices that were altered dependent on spontaneous high and low pain intensity. Additionally, sliding-window functional connectivity analysis revealed that the dlPFC-PAG connection anticorrelated with perceived pain intensity over the entire 12 min period. These findings reveal cortical systems underlying moment-to-moment changes in perceived pain in PTN, which likely cause dysregulation in the brainstem circuits previously identified, and consequently alter the appraisal of pain across time.
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Affiliation(s)
- Noemi Meylakh
- School of Medical Sciences (Neuroscience), Brain and Mind Centre, University of Sydney, Sydney, New South Wales 2050, Australia
| | - Lewis S Crawford
- School of Medical Sciences (Neuroscience), Brain and Mind Centre, University of Sydney, Sydney, New South Wales 2050, Australia
| | - Emily P Mills
- School of Medical Sciences (Neuroscience), Brain and Mind Centre, University of Sydney, Sydney, New South Wales 2050, Australia
| | - Vaughan G Macefield
- Department of Neuroscience, Monash University, Melbourne, Victoria 3800, Australia
| | - E Russell Vickers
- School of Medical Sciences (Neuroscience), Brain and Mind Centre, University of Sydney, Sydney, New South Wales 2050, Australia
| | - Paul M Macey
- UCLA School of Nursing and Brain Research Institute, University of California, Los Angeles, California 90095
| | - Kevin A Keay
- School of Medical Sciences (Neuroscience), Brain and Mind Centre, University of Sydney, Sydney, New South Wales 2050, Australia
| | - Luke A Henderson
- School of Medical Sciences (Neuroscience), Brain and Mind Centre, University of Sydney, Sydney, New South Wales 2050, Australia
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7
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Sladky VC, Strong MA, Tapias-Gomez D, Jewett CE, Drown CG, Scott PM, Holland AJ. The AID2 system offers a potent tool for rapid, reversible, or sustained degradation of essential proteins in live mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597287. [PMID: 38895390 PMCID: PMC11185741 DOI: 10.1101/2024.06.04.597287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Studying essential genes required for dynamic processes in live mice is challenging as genetic perturbations are irreversible and limited by slow protein depletion kinetics. The first-generation auxin-inducible-degron (AID) system is a powerful tool for analyzing inducible protein loss in cultured cells. However, auxin administration is toxic to mice, preventing its long-term use in animals. Here, we use an optimized second-generation AID system to achieve the conditional and reversible loss of the essential centrosomal protein CEP192 in live mice. We show that the auxin derivative 5-Ph-IAA is well tolerated over two weeks and drives near-complete CEP192-mAID degradation in less than one hour in vivo. Prolonged CEP192 loss led to cell division failure and cell death in proliferative tissues. Thus, the second-generation AID system is well suited for rapid and/or sustained protein depletion in live mice, offering a valuable new tool for interrogating protein function in vivo.
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Affiliation(s)
- Valentina C Sladky
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 21205, MD, Baltimore, USA
| | - Margaret A Strong
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 21205, MD, Baltimore, USA
| | - Daniel Tapias-Gomez
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 21205, MD, Baltimore, USA
| | - Cayla E Jewett
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 21205, MD, Baltimore, USA
| | - Chelsea G Drown
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 21205, MD, Baltimore, USA
| | - Phillip M Scott
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 21205, MD, Baltimore, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 21205, MD, Baltimore, USA
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8
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Leuthner TC, Zhang S, Kohrn BF, Stapleton HM, Baugh LR. Structure-specific variation in per- and polyfluoroalkyl substances toxicity among genetically diverse Caenorhabditis elegans strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596269. [PMID: 38854041 PMCID: PMC11160736 DOI: 10.1101/2024.05.29.596269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background There are >14,500 structurally diverse per- and polyfluoroalkyl substances (PFAS). Despite knowledge that these "forever chemicals" are in 99% of humans, mechanisms of toxicity and adverse health effects are incompletely known. Furthermore, the contribution of genetic variation to PFAS susceptibility and health consequences is unknown. Objectives We determined the toxicity of a structurally distinct set of PFAS in twelve genetically diverse strains of the genetic model system Caenorhabditis elegans. Methods Dose-response curves for four perfluoroalkyl carboxylic acids (PFNA, PFOA, PFPeA, and PFBA), two perfluoroalkyl sulfonic acids (PFOS and PFBS), two perfluoroalkyl sulfonamides (PFOSA and PFBSA), two fluoroether carboxylic acids (GenX and PFMOAA), one fluoroether sulfonic acid (PFEESA), and two fluorotelomers (6:2 FCA and 6:2 FTS) were determined in the C. elegans laboratory reference strain, N2, and eleven genetically diverse wild strains. Body length was quantified by image analysis at each dose after 48 hr of developmental exposure of L1 arrest-synchronized larvae to estimate effective concentration values (EC50). Results There was a significant range in toxicity among PFAS: PFOSA > PFBSA ≈ PFOS ≈ PFNA > PFOA > GenX ≈ PFEESA > PFBS ≈ PFPeA ≈ PFBA. Long-chain PFAS had greater toxicity than short-chain, and fluorosulfonamides were more toxic than carboxylic and sulfonic acids. Genetic variation explained variation in susceptibility to PFBSA, PFOS, PFBA, PFOA, GenX, PFEESA, PFPeA, and PFBA. There was significant variation in toxicity among C. elegans strains due to chain length, functional group, and between legacy and emerging PFAS. Conclusion C. elegans respond to legacy and emerging PFAS of diverse structures, and this depends on specific structures and genetic variation. Harnessing the natural genetic diversity of C. elegans and the structural complexity of PFAS is a powerful New Approach Methodology (NAM) to investigate structure-activity relationships and mechanisms of toxicity which may inform regulation of other PFAS to improve human and environmental health.
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Affiliation(s)
- Tess C. Leuthner
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Sharon Zhang
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Heather M. Stapleton
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, North Carolina, USA
- Center for Genomic and Computational Biology, Duke University, North Carolina, USA
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9
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Fonda BD, Kato M, Li Y, Murray DT. Cryo-EM and Solid State NMR Together Provide a More Comprehensive Structural Investigation of Protein Fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596698. [PMID: 38853912 PMCID: PMC11160737 DOI: 10.1101/2024.05.30.596698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Tropomyosin 1 isoform I/C C-terminal domain (Tm1-LC) fibril structure is studied jointly with cryogenic electron microscopy (cryo-EM) and solid state nuclear magnetic resonance (NMR). This study demonstrates the complementary nature of these two structural biology techniques. Chemical shift assignments from solid state NMR are used to determine the secondary structure at the level of individual amino acids, which is faithfully seen in cryo-EM reconstructions. Additionally, solid state NMR demonstrates that the region not observed in the reconstructed cryo-EM density is primarily in a highly mobile random coil conformation rather than adopting multiple rigid conformations. Overall, this study illustrates the benefit of investigations combining cryo-EM and solid state NMR to investigate protein fibril structure.
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Affiliation(s)
- Blake D. Fonda
- Department of Chemistry, University of California, Davis, California, 95616, United States of America
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - Dylan T. Murray
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, 06269, United States of America
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10
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Clayton KK, McGill M, Awwad B, Stecyk KS, Kremer C, Skerleva D, Narayanan DP, Zhu J, Hancock KE, Kujawa SG, Kozin ED, Polley DB. Cortical determinants of loudness perception and auditory hypersensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596691. [PMID: 38853938 PMCID: PMC11160727 DOI: 10.1101/2024.05.30.596691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Parvalbumin-expressing inhibitory neurons (PVNs) stabilize cortical network activity, generate gamma rhythms, and regulate experience-dependent plasticity. Here, we observed that activation or inactivation of PVNs functioned like a volume knob in the mouse auditory cortex (ACtx), turning neural and behavioral classification of sound level up or down over a 20dB range. PVN loudness adjustments were "sticky", such that a single bout of 40Hz PVN stimulation sustainably suppressed ACtx sound responsiveness, potentiated feedforward inhibition, and behaviorally desensitized mice to loudness. Sensory sensitivity is a cardinal feature of autism, aging, and peripheral neuropathy, prompting us to ask whether PVN stimulation can persistently desensitize mice with ACtx hyperactivity, PVN hypofunction, and loudness hypersensitivity triggered by cochlear sensorineural damage. We found that a single 16-minute bout of 40Hz PVN stimulation session restored normal loudness perception for one week, showing that perceptual deficits triggered by irreversible peripheral injuries can be reversed through targeted cortical circuit interventions.
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Affiliation(s)
- Kameron K Clayton
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Matthew McGill
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Bshara Awwad
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Kamryn S Stecyk
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Caroline Kremer
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | | | - Divya P Narayanan
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Jennifer Zhu
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Kenneth E Hancock
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Sharon G Kujawa
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Elliott D Kozin
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
| | - Daniel B Polley
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston MA 02114
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Hagan CE, Snyder AG, Headley M, Oberst A. Apoptotic cells promote circulating tumor cell survival and metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595217. [PMID: 38826267 PMCID: PMC11142129 DOI: 10.1101/2024.05.21.595217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
During tumor progression and especially following cytotoxic therapy, cell death of both tumor and stromal cells is widespread. Despite clinical observations that high levels of apoptotic cells correlate with poorer patient outcomes, the physiological effects of dying cells on tumor progression remain incompletely understood. Here, we report that circulating apoptotic cells robustly enhance tumor cell metastasis to the lungs. Using intravenous metastasis models, we observed that the presence of apoptotic cells, but not cells dying by other mechanisms, supports circulating tumor cell (CTC) survival following arrest in the lung vasculature. Apoptotic cells promote CTC survival by recruiting platelets to the forming metastatic niche. Apoptotic cells externalize the phospholipid phosphatidylserine to the outer leaflet of the plasma membrane, which we found increased the activity of the coagulation initiator Tissue Factor, thereby triggering the formation of platelet clots that protect proximal CTCs. Inhibiting the ability of apoptotic cells to induce coagulation by knocking out Tissue Factor, blocking phosphatidylserine, or administering the anticoagulant heparin abrogated the pro-metastatic effect of apoptotic cells. This work demonstrates a previously unappreciated role for apoptotic cells in facilitating metastasis by establishing CTC-supportive emboli, and suggests points of intervention that may reduce the pro-metastatic effect of apoptotic cells. GRAPHICAL ABSTRACT
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12
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Rossi Sebastiano A, Poles K, Gualtiero S, Romeo M, Galigani M, Bruno V, Fossataro C, Garbarini F. Balancing the Senses: Electrophysiological Responses Reveal the Interplay between Somatosensory and Visual Processing During Body-Related Multisensory Conflict. J Neurosci 2024; 44:e1397232024. [PMID: 38508711 PMCID: PMC11079966 DOI: 10.1523/jneurosci.1397-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 03/22/2024] Open
Abstract
In the study of bodily awareness, the predictive coding theory has revealed that our brain continuously modulates sensory experiences to integrate them into a unitary body representation. Indeed, during multisensory illusions (e.g., the rubber hand illusion, RHI), the synchronous stroking of the participant's concealed hand and a fake visible one creates a visuotactile conflict, generating a prediction error. Within the predictive coding framework, through sensory processing modulation, prediction errors are solved, inducing participants to feel as if touches originated from the fake hand, thus ascribing the fake hand to their own body. Here, we aimed to address sensory processing modulation under multisensory conflict, by disentangling somatosensory and visual stimuli processing that are intrinsically associated during the illusion induction. To this aim, we designed two EEG experiments, in which somatosensory- (SEPs; Experiment 1; N = 18; F = 10) and visual-evoked potentials (VEPs; Experiment 2; N = 18; F = 9) were recorded in human males and females following the RHI. Our results show that, in both experiments, ERP amplitude is significantly modulated in the illusion as compared with both control and baseline conditions, with a modality-dependent diametrical pattern showing decreased SEP amplitude and increased VEP amplitude. Importantly, both somatosensory and visual modulations occur in long-latency time windows previously associated with tactile and visual awareness, thus explaining the illusion of perceiving touch at the sight location. In conclusion, we describe a diametrical modulation of somatosensory and visual processing as the neural mechanism that allows maintaining a stable body representation, by restoring visuotactile congruency under the occurrence of multisensory conflicts.
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Affiliation(s)
| | - Karol Poles
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Stefano Gualtiero
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Marcella Romeo
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
- IMT School for Advanced Studies Lucca, Lucca 55100, Italy
| | - Mattia Galigani
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Valentina Bruno
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Carlotta Fossataro
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Francesca Garbarini
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
- Neuroscience Institute of Turin (NIT), Turin 10124, Italy
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Gizzio J, Thakur A, Haldane A, Post CB, Levy RM. Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584161. [PMID: 38559238 PMCID: PMC10979876 DOI: 10.1101/2024.03.08.584161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches - tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory "folded" conformation, due to intrinsic sequence effects. Here we investigated the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a novel thermodynamic cycle involving many (n=108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation "DFG-out Activation Loop Folded", is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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Hogan AM, Motnenko A, Rahman ASMZ, Cardona ST. Cell envelope structural and functional contributions to antibiotic resistance in Burkholderia cenocepacia. J Bacteriol 2024; 206:e0044123. [PMID: 38501654 PMCID: PMC11025338 DOI: 10.1128/jb.00441-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Antibiotic activity is limited by the physical construction of the Gram-negative cell envelope. Species of the Burkholderia cepacia complex (Bcc) are known as intrinsically multidrug-resistant opportunistic pathogens with low permeability cell envelopes. Here, we re-examined a previously performed chemical-genetic screen of barcoded transposon mutants in B. cenocepacia K56-2, focusing on cell envelope structural and functional processes. We identified structures mechanistically important for resistance to singular and multiple antibiotic classes. For example, susceptibility to novobiocin, avibactam, and the LpxC inhibitor, PF-04753299, was linked to the BpeAB-OprB efflux pump, suggesting these drugs are substrates for this pump in B. cenocepacia. Defects in peptidoglycan precursor synthesis specifically increased susceptibility to cycloserine and revealed a new putative amino acid racemase, while defects in divisome accessory proteins increased susceptibility to multiple β-lactams. Additionally, disruption of the periplasmic disulfide bond formation system caused pleiotropic defects on outer membrane integrity and β-lactamase activity. Our findings highlight the layering of resistance mechanisms in the structure and function of the cell envelope. Consequently, we point out processes that can be targeted for developing antibiotic potentiators.IMPORTANCEThe Gram-negative cell envelope is a double-layered physical barrier that protects cells from extracellular stressors, such as antibiotics. The Burkholderia cell envelope is known to contain additional modifications that reduce permeability. We investigated Burkholderia cell envelope factors contributing to antibiotic resistance from a genome-wide view by re-examining data from a transposon mutant library exposed to an antibiotic panel. We identified susceptible phenotypes for defects in structures and functions in the outer membrane, periplasm, and cytoplasm. Overall, we show that resistance linked to the cell envelope is multifaceted and provides new targets for the development of antibiotic potentiators.
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Affiliation(s)
- Andrew M. Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Silvia T. Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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15
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Reddy NA, Clements RG, Brooks JCW, Bright MG. Simultaneous cortical, subcortical, and brainstem mapping of sensory activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589099. [PMID: 38659741 PMCID: PMC11042175 DOI: 10.1101/2024.04.11.589099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Non-painful tactile sensory stimuli are processed in the cortex, subcortex, and brainstem. Recent functional magnetic resonance imaging (fMRI) studies have highlighted the value of whole-brain, systems-level investigation for examining pain processing. However, whole-brain fMRI studies are uncommon, in part due to challenges with signal to noise when studying the brainstem. Furthermore, the differentiation of small sensory brainstem structures such as the cuneate and gracile nuclei necessitates high resolution imaging. To address this gap in systems-level sensory investigation, we employed a whole-brain, multi-echo fMRI acquisition at 3T with multi-echo independent component analysis (ME-ICA) denoising and brainstem-specific modeling to enable detection of activation across the entire sensory system. In healthy participants, we examined patterns of activity in response to non-painful brushing of the right hand, left hand, and right foot, and found the expected lateralization, with distinct cortical and subcortical responses for upper and lower limb stimulation. At the brainstem level, we were able to differentiate the small, adjacent cuneate and gracile nuclei, corresponding to hand and foot stimulation respectively. Our findings demonstrate that simultaneous cortical, subcortical, and brainstem mapping at 3T could be a key tool to understand the sensory system in both healthy individuals and clinical cohorts with sensory deficits.
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Affiliation(s)
- Neha A. Reddy
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, United States
| | - Rebecca G. Clements
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, United States
| | | | - Molly G. Bright
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, United States
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16
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Singer A, Ramos A, Keating AE. Elaboration of the Homer1 Recognition Landscape Reveals Incomplete Divergence of Paralogous EVH1 Domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576863. [PMID: 38645240 PMCID: PMC11030225 DOI: 10.1101/2024.01.23.576863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Short sequences that mediate interactions with modular binding domains are ubiquitous throughout eukaryotic proteomes. Networks of Short Linear Motifs (SLiMs) and their corresponding binding domains orchestrate many cellular processes, and the low mutational barrier to evolving novel interactions provides a way for biological systems to rapidly sample selectable phenotypes. Mapping SLiM binding specificity and the rules that govern SLiM evolution is fundamental to uncovering the pathways regulated by these networks and developing the tools to manipulate them. We used high-throughput screening of the human proteome to identify sequences that bind to the Enabled/VASP homology 1 (EVH1) domain of the postsynaptic density scaffolding protein Homer1. In doing so, we expanded current understanding of the determinants of Homer EVH1 binding preferences and defined a new motif that can facilitate the discovery of additional Homer-mediated interactions. Interestingly, the Homer1 EVH1 domain preferentially binds to sequences containing an N-terminally overlapping motif that is bound by the paralogous family of Ena/VASP actin polymerases, and many of these sequences can bind to EVH1 domains from both protein families. We provide evidence from orthologous EVH1 domains in pre-metazoan organisms that the overlap in human Ena/VASP and Homer binding preferences corresponds to an incomplete divergence from a common Ena/VASP ancestor. Given this overlap in binding profiles, promiscuous sequences that can be recognized by both families either achieve specificity through extrinsic regulatory strategies or may provide functional benefits via multi-specificity. This may explain why these paralogs incompletely diverged despite the accessibility of further diverged isoforms.
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Affiliation(s)
- Avinoam Singer
- MIT Department of Biology, Cambridge, Massachusetts, USA
| | | | - Amy E. Keating
- MIT Department of Biology, Cambridge, Massachusetts, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
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17
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Carbo CR, Faromiki OG, Nan B. A lytic transglycosylase connects bacterial focal adhesion complexes to the peptidoglycan cell wall. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588103. [PMID: 38617213 PMCID: PMC11014575 DOI: 10.1101/2024.04.04.588103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The Gram-negative bacterium Myxococcus xanthus glides on solid surfaces. Dynamic bacterial focal adhesion complexes (bFACs) convert proton motive force from the inner membrane into mechanical propulsion on the cell surface. It is unclear how the mechanical force transmits across the rigid peptidoglycan (PG) cell wall. Here we show that AgmT, a highly abundant lytic PG transglycosylase homologous to Escherichia coli MltG, couples bFACs to PG. Coprecipitation assay and single-particle microscopy reveal that the gliding motors fail to connect to PG and thus are unable to assemble into bFACs in the absence of an active AgmT. Heterologous expression of E. coli MltG restores the connection between PG and bFACs and thus rescues gliding motility in the M. xanthus cells that lack AgmT. Our results indicate that bFACs anchor to AgmT-modified PG to transmit mechanical force across the PG cell wall.
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Affiliation(s)
- Carlos Ramirez Carbo
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- The Genetics and Genomics Interdisciplinary Program, Texas A&M University, College Station, TX 77843, USA
- C. R. C and O. G. F. contribute equally to this work
| | - Olalekan G. Faromiki
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- C. R. C and O. G. F. contribute equally to this work
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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18
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Razew A, Herail Q, Miyachiro M, Anoyatis-Pelé C, Bougault C, Dessen A, Arthur M, Simorre JP. Monitoring Drug-Protein Interactions in the Bacterial Periplasm by Solution Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2024; 146:9252-9260. [PMID: 38500259 DOI: 10.1021/jacs.4c00604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The rapid spread of antimicrobial resistance across bacterial pathogens poses a serious risk to the efficacy and sustainability of available treatments. This puts pressure on research concerning the development of new drugs. Here, we present an in-cell NMR-based research strategy to monitor the activity of the enzymes located in the periplasmic space delineated by the inner and outer membranes of Gram-negative bacteria. We demonstrate its unprecedented analytical power in monitoring in situ and in real time (i) the hydrolysis of β-lactams by β-lactamases, (ii) the interaction of drugs belonging to the β-lactam family with their essential targets, and (iii) the binding of inhibitors to these enzymes. We show that in-cell NMR provides a powerful analytical tool for investigating new drugs targeting the molecular components of the bacterial periplasm.
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Affiliation(s)
- Alicja Razew
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Quentin Herail
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Mayara Miyachiro
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | | | - Catherine Bougault
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Andrea Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Jean-Pierre Simorre
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
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Gharat V, Peter F, de Quervain DJF, Papassotiropoulos A, Stetak A. Role of GLR-1 in Age-Dependent Short-Term Memory Decline. eNeuro 2024; 11:ENEURO.0420-23.2024. [PMID: 38519128 PMCID: PMC11005081 DOI: 10.1523/eneuro.0420-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/10/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
As the global elderly population grows, age-related cognitive decline is becoming an increasingly significant healthcare issue, often leading to various neuropsychiatric disorders. Among the many molecular players involved in memory, AMPA-type glutamate receptors are known to regulate learning and memory, but how their dynamics change with age and affect memory decline is not well understood. Here, we examined the in vivo properties of the AMPA-type glutamate receptor GLR-1 in the AVA interneuron of the Caenorhabditis elegans nervous system during physiological aging. We found that both total and membrane-bound GLR-1 receptor levels decrease with age in wild-type worms, regardless of their location along the axon. Using fluorescence recovery after photobleaching, we also demonstrated that a reduction in GLR-1 abundance correlates with decreased local, synaptic GLR-1 receptor dynamics. Importantly, we found that reduced GLR-1 levels strongly correlate with the age-related decline in short-term associative memory. Genetic manipulation of GLR-1 stability, by either deleting msi-1 or expressing a ubiquitination-defective GLR-1 (4KR) variant, prevented this age-related reduction in receptor abundance and improved the short-term memory performance in older animals, which reached performance levels similar to those of young animals. Overall, our data indicate that AMPA-type glutamate receptor abundance and dynamics are key factors in maintaining memory function and that changes in these parameters are linked to age-dependent short-term memory decline.
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Affiliation(s)
- Vaibhav Gharat
- Division of Molecular Neuroscience, Department of Biomedicine, University of Basel, Basel 4055, Switzerland
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, Basel 4055, Switzerland
| | - Fabian Peter
- Division of Molecular Neuroscience, Department of Biomedicine, University of Basel, Basel 4055, Switzerland
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, Basel 4055, Switzerland
| | - Dominique J-F de Quervain
- Division of Molecular Neuroscience, Department of Biomedicine, University of Basel, Basel 4055, Switzerland
- Division of Cognitive Neuroscience, Department of Biomedicine, University of Basel, Basel 4055, Switzerland
- University Psychiatric Clinics, University of Basel, Basel 4002, Switzerland
| | - Andreas Papassotiropoulos
- Division of Molecular Neuroscience, Department of Biomedicine, University of Basel, Basel 4055, Switzerland
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, Basel 4055, Switzerland
- University Psychiatric Clinics, University of Basel, Basel 4002, Switzerland
| | - Attila Stetak
- Division of Molecular Neuroscience, Department of Biomedicine, University of Basel, Basel 4055, Switzerland
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, Basel 4055, Switzerland
- University Psychiatric Clinics, University of Basel, Basel 4002, Switzerland
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20
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Alvarado Obando M, Rey-Varela D, Cava F, Dörr T. Genetic interaction mapping reveals functional relationships between peptidoglycan endopeptidases and carboxypeptidases. PLoS Genet 2024; 20:e1011234. [PMID: 38598601 PMCID: PMC11034669 DOI: 10.1371/journal.pgen.1011234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/22/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulators in Vibrio cholerae. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. dacA1 is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in dacA1. A subsequent suppressor screen to restore viability of ΔdacA1 in LB medium identified hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote EP activation. Our data thus reveal a more complex role of DacA1 in maintaining PG homeostasis than previously assumed.
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Affiliation(s)
- Manuela Alvarado Obando
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Diego Rey-Varela
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host-Microbe Interactions and Disease (CIHMID), Ithaca, New York, United States of America
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21
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Birch S, McGee L, Provencher C, DeMio C, Plachetzki D. Phototactic preference and its genetic basis in the planulae of the colonial Hydrozoan Hydractinia symbiolongicarpus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.585045. [PMID: 38617216 PMCID: PMC11014542 DOI: 10.1101/2024.03.28.585045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Background Marine organisms with sessile adults commonly possess motile larval stages that make settlement decisions based on integrating environmental sensory cues. Phototaxis, the movement toward or away from light, is a common behavioral characteristic of aquatic and marine metazoan larvae, and of algae, protists, and fungi. In cnidarians, behavioral genomic investigations of motile planulae larvae have been conducted in anthozoans (corals and sea anemones) and scyphozoans (true jellyfish), but such studies are presently lacking in hydrozoans. Here, we examined the behavioral genomics of phototaxis in planulae of the hydrozoan Hydractinia symbiolongicarpus. Results A behavioral phototaxis study of day 3 planulae indicated preferential phototaxis to green (523 nm) and blue (470 nm) wavelengths of light, but not red (625 nm) wavelengths. A developmental transcriptome study where planula larvae were collected from four developmental time points for RNA-seq revealed that many genes critical to the physiology and development of ciliary photosensory systems are dynamically expressed in planula development and correspond to the expression of phototactic behavior. Microscopical investigations using immunohistochemistry and in situ hybridization demonstrated that several transcripts with predicted function in photoreceptors, including cnidops class opsin, CNG ion channel, and CRX-like transcription factor, localize to ciliated bipolar sensory neurons of the aboral sensory neural plexus, which is associated with the direction of phototaxis and the site of settlement. Conclusions The phototactic preference displayed by planulae is consistent with the shallow sandy marine habitats they experience in nature. Our genomic investigations add further evidence of similarities between cnidops-mediated photoreceptors of hydrozoans and other cnidarians and ciliary photoreceptors as found in the eyes of humans and other bilaterians, suggesting aspects of their shared evolutionary history.
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Affiliation(s)
- Sydney Birch
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
- Department of Biological Sciences; University of North Carolina Charlotte; Charlotte, NC, 28223; USA
| | - Lindy McGee
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
| | - Curtis Provencher
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
| | - Christine DeMio
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
| | - David Plachetzki
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
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22
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Petty GH, Bruno RM. Attentional modulation of secondary somatosensory and visual thalamus of mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586242. [PMID: 38585833 PMCID: PMC10996504 DOI: 10.1101/2024.03.22.586242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Each sensory modality has its own primary and secondary thalamic nuclei. While the primary thalamic nuclei are well understood to relay sensory information from the periphery to the cortex, the role of secondary sensory nuclei is elusive. One hypothesis has been that secondary nuclei may support feature-based attention. If this is true, one would also expect the activity in different nuclei to reflect the degree to which modalities are or are not behaviorally relevant in a task. We trained head-fixed mice to attend to one sensory modality while ignoring a second modality, namely to attend to touch and ignore vision, or vice versa. Arrays were used to record simultaneously from secondary somatosensory thalamus (POm) and secondary visual thalamus (LP). In mice trained to respond to tactile stimuli and ignore visual stimuli, POm was robustly activated by touch and largely unresponsive to visual stimuli. A different pattern was observed when mice were trained to respond to visual stimuli and ignore touch, with POm now more robustly activated during visual trials. This POm activity was not explained by differences in movements (i.e., whisking, licking, pupil dilation) resulting from the two tasks. Post hoc histological reconstruction of array tracks through POm revealed that subregions varied in their degree of plasticity. LP exhibited similar phenomena. We conclude that behavioral training reshapes activity in secondary thalamic nuclei. Secondary nuclei may respond to behaviorally relevant, reward-predicting stimuli regardless of stimulus modality.
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Affiliation(s)
- Gordon H Petty
- Department of Neuroscience, Columbia University, New York, NY 10027 USA
| | - Randy M Bruno
- Department of Neuroscience, Columbia University, New York, NY 10027 USA
- Department of Physiology, Anatomy, & Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
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23
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Paul S, McCourt PM, Le LTM, Ryu J, Czaja W, Bode AM, Contreras-Galindo R, Dong Z. Fyn-mediated phosphorylation of Menin disrupts telomere maintenance in stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.04.560876. [PMID: 37873235 PMCID: PMC10592958 DOI: 10.1101/2023.10.04.560876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Telomeres protect chromosome ends and determine the replication potential of dividing cells. The canonical telomere sequence TTAGGG is synthesized by telomerase holoenzyme, which maintains telomere length in proliferative stem cells. Although the core components of telomerase are well-defined, mechanisms of telomerase regulation are still under investigation. We report a novel role for the Src family kinase Fyn, which disrupts telomere maintenance in stem cells by phosphorylating the scaffold protein Menin. We found that Fyn knockdown prevented telomere erosion in human and mouse stem cells, validating the results with four telomere measurement techniques. We show that Fyn phosphorylates Menin at tyrosine 603 (Y603), which increases Menin's SUMO1 modification, C-terminal stability, and importantly, its association with the telomerase RNA component (TR). Using mass spectrometry, immunoprecipitation, and immunofluorescence experiments we found that SUMO1-Menin decreases TR's association with telomerase subunit Dyskerin, suggesting that Fyn's phosphorylation of Menin induces telomerase subunit mislocalization and may compromise telomerase function at telomeres. Importantly, we find that Fyn inhibition reduces accelerated telomere shortening in human iPSCs harboring mutations for dyskeratosis congenita.
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Affiliation(s)
- Souren Paul
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Preston M. McCourt
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Le Thi My Le
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Joohyun Ryu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Wioletta Czaja
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Genetics, University of Alabama, Birmingham, AL 35294, USA
| | - Ann M. Bode
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Rafael Contreras-Galindo
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Genetics, University of Alabama, Birmingham, AL 35294, USA
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Henan, China 450001
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24
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Kaul M, Meher SK, Nallamotu KC, Reddy M. Glycan strand cleavage by a lytic transglycosylase, MltD contributes to the expansion of peptidoglycan in Escherichia coli. PLoS Genet 2024; 20:e1011161. [PMID: 38422114 DOI: 10.1371/journal.pgen.1011161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 03/12/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Peptidoglycan (PG) is a protective sac-like exoskeleton present in most bacterial cell walls. It is a large, covalently crosslinked mesh-like polymer made up of many glycan strands cross-bridged to each other by short peptide chains. Because PG forms a continuous mesh around the bacterial cytoplasmic membrane, opening the mesh is critical to generate space for the incorporation of new material during its expansion. In Escherichia coli, the 'space-making activity' is known to be achieved by cleavage of crosslinks between the glycan strands by a set of redundant PG endopeptidases whose absence leads to rapid lysis and cell death. Here, we demonstrate a hitherto unknown role of glycan strand cleavage in cell wall expansion in E. coli. We find that overexpression of a membrane-bound lytic transglycosylase, MltD that cuts the glycan polymers of the PG sacculus rescues the cell lysis caused by the absence of essential crosslink-specific endopeptidases, MepS, MepM and MepH. We find that cellular MltD levels are stringently controlled by two independent regulatory pathways; at the step of post-translational stability by a periplasmic adaptor-protease complex, NlpI-Prc, and post-transcriptionally by RpoS, a stationary-phase specific sigma factor. Further detailed genetic and biochemical analysis implicated a role for MltD in cleaving the nascent uncrosslinked glycan strands generated during the expansion of PG. Overall, our results show that the combined activity of PG endopeptidases and lytic transglycosylases is necessary for successful expansion of the cell wall during growth of a bacterium.
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Affiliation(s)
- Moneca Kaul
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suraj Kumar Meher
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Krishna Chaitanya Nallamotu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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25
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Jin B, Gongwer MW, Ohanian L, Holden-Wingate L, Le B, Darmawan A, Nakayama Y, Rueda Mora SA, DeNardo LA. A developmental brain-wide screen identifies retrosplenial cortex as a key player in the emergence of persistent memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574554. [PMID: 38260633 PMCID: PMC10802387 DOI: 10.1101/2024.01.07.574554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Memories formed early in life are short-lived while those formed later persist. Recent work revealed that infant memories are stored in a latent state. But why they fail to be retrieved is poorly understood. Here we investigated brain-wide circuit mechanisms underlying infantile amnesia in mice. We performed a screen that combined activity-dependent neuronal tagging at different postnatal ages, tissue clearing and light sheet microscopy. We observed striking developmental transitions in the organization of fear memory networks and changes in the activity and functional connectivity of the retrosplenial cortex (RSP) that aligned with the emergence of persistent memory. 7 days after learning, chemogenetic reactivation of tagged RSP ensembles enhanced memory in adults but not in infants. But after 33 days, reactivating infant-tagged RSP ensembles recovered forgotten memories. These studies show that RSP ensembles store latent infant memories, reveal the time course of RSP functional maturation, and suggest that immature RSP functional networks contribute to infantile amnesia.
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26
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van der Molen T, Spaeth A, Chini M, Bartram J, Dendukuri A, Zhang Z, Bhaskaran-Nair K, Blauvelt LJ, Petzold LR, Hansma PK, Teodorescu M, Hierlemann A, Hengen KB, Hanganu-Opatz IL, Kosik KS, Sharf T. Protosequences in human cortical organoids model intrinsic states in the developing cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.29.573646. [PMID: 38234832 PMCID: PMC10793448 DOI: 10.1101/2023.12.29.573646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Neuronal firing sequences are thought to be the basic building blocks of neural coding and information broadcasting within the brain. However, when sequences emerge during neurodevelopment remains unknown. We demonstrate that structured firing sequences are present in spontaneous activity of human brain organoids and ex vivo neonatal brain slices from the murine somatosensory cortex. We observed a balance between temporally rigid and flexible firing patterns that are emergent phenomena in human brain organoids and early postnatal murine somatosensory cortex, but not in primary dissociated cortical cultures. Our findings suggest that temporal sequences do not arise in an experience-dependent manner, but are rather constrained by an innate preconfigured architecture established during neurogenesis. These findings highlight the potential for brain organoids to further explore how exogenous inputs can be used to refine neuronal circuits and enable new studies into the genetic mechanisms that govern assembly of functional circuitry during early human brain development.
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Affiliation(s)
- Tjitse van der Molen
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Alex Spaeth
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mattia Chini
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, Hamburg Center of Neuroscience, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Julian Bartram
- Department of Biosystems Science and Engineering, ETH Zürich, Klingelbergstrasse 48, 4056 Basel, Switzerland
| | - Aditya Dendukuri
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Zongren Zhang
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106
| | - Kiran Bhaskaran-Nair
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lon J. Blauvelt
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Linda R. Petzold
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Paul K. Hansma
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106
| | - Mircea Teodorescu
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zürich, Klingelbergstrasse 48, 4056 Basel, Switzerland
| | - Keith B. Hengen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ileana L. Hanganu-Opatz
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, Hamburg Center of Neuroscience, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Kenneth S. Kosik
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Tal Sharf
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Institute for the Biology of Stem Cells, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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27
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Kimura H, Lahouel K, Tomasetti C, Roberts NJ. Functional characterization of all CDKN2A missense variants and comparison to in silico models of pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.28.573507. [PMID: 38234851 PMCID: PMC10793438 DOI: 10.1101/2023.12.28.573507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Interpretation of variants identified during genetic testing is a significant clinical challenge. In this study, we developed a high-throughput CDKN2A functional assay and characterized all possible CDKN2A missense variants. We found that 40% of all missense variants were functionally deleterious. We also used our functional classification to assess the performance of in silico models that predict the effect of variants, including recently reported models based on machine learning. Notably, we found that all in silico models similarly when compared to our functional classifications with accuracies of 54.6 - 70.9%. Furthermore, while we found that functionally deleterious variants were enriched within ankyrin repeats, rarely were all missense variants at a single residue functionally deleterious. Our functional classifications are a resource to aid the interpretation of CDKN2A variants and have important implications for the application of variant interpretation guidelines, particularly the use of in silico models for clinical variant interpretation.
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28
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Suri H, Salgado-Puga K, Wang Y, Allen N, Lane K, Granroth K, Olivei A, Nass N, Rothschild G. A Cortico-Striatal Circuit for Sound-Triggered Prediction of Reward Timing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568134. [PMID: 38045246 PMCID: PMC10690153 DOI: 10.1101/2023.11.21.568134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
A crucial aspect of auditory perception is the ability to use sound cues to predict future events and to time actions accordingly. For example, distinct smartphone notification sounds reflect a call that needs to be answered within a few seconds, or a text that can be read later; the sound of an approaching vehicle signals when it is safe to cross the street. Other animals similarly use sounds to plan, time and execute behaviors such as hunting, evading predation and tending to offspring. However, the neural mechanisms that underlie sound-guided prediction of upcoming salient event timing are not well understood. To address this gap, we employed an appetitive sound-triggered reward time prediction behavior in head-fixed mice. We find that mice trained on this task reliably estimate the time from a sound cue to upcoming reward on the scale of a few seconds, as demonstrated by learning-dependent well-timed increases in reward-predictive licking. Moreover, mice showed a dramatic impairment in their ability to use sound to predict delayed reward when the auditory cortex was inactivated, demonstrating its causal involvement. To identify the neurophysiological signatures of auditory cortical reward-timing prediction, we recorded local field potentials during learning and performance of this behavior and found that the magnitude of auditory cortical responses to the sound prospectively encoded the duration of the anticipated sound-reward time interval. Next, we explored how and where these sound-triggered time interval prediction signals propagate from the auditory cortex to time and initiate consequent action. We targeted the monosynaptic projections from the auditory cortex to the posterior striatum and found that chemogenetic inactivation of these projections impairs animal's ability to predict sound-triggered delayed reward. Simultaneous neural recordings in the auditory cortex and posterior striatum during task performance revealed coordination of neural activity across these regions during the sound cue predicting the time interval to reward. Collectively, our findings identify an auditory cortical-striatal circuit supporting sound-triggered timing-prediction behaviors.
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29
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Johnson AG, Mayer ML, Schaefer SL, McNamara-Bordewick NK, Hummer G, Kranzusch PJ. Structure and assembly of a bacterial gasdermin pore. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537723. [PMID: 37131678 PMCID: PMC10153256 DOI: 10.1101/2023.04.20.537723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis1-33. Studies of human and mouse GSDM pores reveal the functions and architectures of 24-33 protomers assemblies4-9, but the mechanism and evolutionary origin of membrane targeting and GSDM pore formation remain unknown. Here we determine a structure of a bacterial GSDM (bGSDM) pore and define a conserved mechanism of pore assembly. Engineering a panel of bGSDMs for site-specific proteolytic activation, we demonstrate that diverse bGSDMs form distinct pore sizes that range from smaller mammalian-like assemblies to exceptionally large pores containing >50 protomers. We determine a 3.3 Å cryo-EM structure of a Vitiosangium bGSDM in an active slinky-like oligomeric conformation and analyze bGSDM pores in a native lipid environment to create an atomic-level model of a full 52-mer bGSDM pore. Combining our structural analysis with molecular dynamics simulations and cellular assays, our results support a stepwise model of GSDM pore assembly and suggest that a covalently bound palmitoyl can leave a hydrophobic sheath and insert into the membrane before formation of the membrane-spanning β-strand regions. These results reveal the diversity of GSDM pores found in nature and explain the function of an ancient post-translational modification in enabling programmed host cell death.
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Affiliation(s)
- Alex G. Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Megan L. Mayer
- Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan L. Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
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30
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Arora C, Matic M, DiChiaro P, Rosa NDO, Carli F, Clubb L, Fard LAN, Kargas G, Diaferia G, Vukotic R, Licata L, Wu G, Natoli G, Gutkind JS, Raimondi F. The landscape of cancer rewired GPCR signaling axes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532291. [PMID: 37398064 PMCID: PMC10312480 DOI: 10.1101/2023.03.13.532291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We explored the dysregulation of GPCR ligand signaling systems in cancer transcriptomics datasets to uncover new therapeutics opportunities in oncology. We derived an interaction network of receptors with ligands and their biosynthetic enzymes, which revealed that multiple GPCRs are differentially regulated together with their upstream partners across cancer subtypes. We showed that biosynthetic pathway enrichment from enzyme expression recapitulated pathway activity signatures from metabolomics datasets, providing valuable surrogate information for GPCRs responding to organic ligands. We found that several GPCRs signaling components were significantly associated with patient survival in a cancer type-specific fashion. The expression of both receptor-ligand (or enzymes) partners improved patient stratification, suggesting a synergistic role for the activation of GPCR networks in modulating cancer phenotypes. Remarkably, we identified many such axes across several cancer molecular subtypes, including many pairs involving receptor-biosynthetic enzymes for neurotransmitters. We found that GPCRs from these actionable axes, including e.g., muscarinic, adenosine, 5-hydroxytryptamine and chemokine receptors, are the targets of multiple drugs displaying anti-growth effects in large-scale, cancer cell drug screens. We have made the results generated in this study freely available through a webapp (gpcrcanceraxes.bioinfolab.sns.it).
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Affiliation(s)
- Chakit Arora
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Marin Matic
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Pierluigi DiChiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Natalia De Oliveira Rosa
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Francesco Carli
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Lauren Clubb
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lorenzo Amir Nemati Fard
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Giorgos Kargas
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Giuseppe Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Ranka Vukotic
- Azienda Ospedaliero-Universitaria Pisana, Via Roma, 67, 56126 Pisa
| | - Luana Licata
- Department of Biology, University of Rome ‘Tor Vergata’, Rome 00133, Italy
| | - Guanming Wu
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - J. Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Francesco Raimondi
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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31
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Costacurta F, Dodaro A, Bante D, Schöppe H, Sprenger B, Moghadasi SA, Fleischmann J, Pavan M, Bassani D, Menin S, Rauch S, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Ho J, Harris RS, Stefan E, Schneider R, Kaserer T, Moro S, von Laer D, Heilmann E. A comprehensive study of SARS-CoV-2 main protease (M pro) inhibitor-resistant mutants selected in a VSV-based system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558628. [PMID: 37808638 PMCID: PMC10557589 DOI: 10.1101/2023.09.22.558628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Nirmatrelvir was the first protease inhibitor (PI) specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available PIs (nirmatrelvir and ensitrelvir) with cell-based and biochemical assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease-inhibitor-resistance mechanisms and show the relevance of specific mutations in the clinic, thereby informing treatment decisions.
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Affiliation(s)
- Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Bernhard Sprenger
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jakob Fleischmann
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Silvia Menin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, United States
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, United States
| | - Eduard Stefan
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Rainer Schneider
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
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32
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Avila‐Cobian LF, Hoshino H, Horsman ME, Nguyen VT, Qian Y, Feltzer R, Kim C, Hu DD, Champion MM, Fisher JF, Mobashery S. Amber-codon suppression for spatial localization and in vivo photoaffinity capture of the interactome of the Pseudomonas aeruginosa rare lipoprotein A lytic transglycosylase. Protein Sci 2023; 32:e4781. [PMID: 37703013 PMCID: PMC10536563 DOI: 10.1002/pro.4781] [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: 07/27/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
The 11 lytic transglycosylases of Pseudomonas aeruginosa have overlapping activities in the turnover of the cell-wall peptidoglycan. Rare lipoprotein A (RlpA) is distinct among the 11 by its use of only peptidoglycan lacking peptide stems. The spatial localization of RlpA and its interactome within P. aeruginosa are unknown. We employed suppression of introduced amber codons at sites in the rlpA gene for the introduction of the unnatural-amino-acids Νζ -[(2-azidoethoxy)carbonyl]-l-lysine (compound 1) and Nζ -[[[3-(3-methyl-3H-diazirin-3-yl)propyl]amino]carbonyl]-l-lysine (compound 2). In live P. aeruginosa, full-length RlpA incorporating compound 1 into its sequence was fluorescently tagged using strained-promoted alkyne-azide cycloaddition and examined by fluorescence microscopy. RlpA is present at low levels along the sidewall length of the bacterium, and at higher levels at the nascent septa of replicating bacteria. In intact P. aeruginosa, UV photolysis of full-length RlpA having compound 2 within its sequence generated a transient reactive carbene, which engaged in photoaffinity capture of neighboring proteins. Thirteen proteins were identified. Three of these proteins-PBP1a, PBP5, and MreB-are members of the bacterial divisome. The use of the complementary methodologies of non-canonical amino-acid incorporation, photoaffinity proximity analysis, and fluorescent microscopy confirm a dominant septal location for the RlpA enzyme of P. aeruginosa, as a divisome-associated activity. This accomplishment adds to the emerging recognition of the value of these methodologies for identification of the intracellular localization of bacterial proteins.
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Affiliation(s)
- Luis F. Avila‐Cobian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Hidekazu Hoshino
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Mark E. Horsman
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Van T. Nguyen
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Yuanyuan Qian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Rhona Feltzer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Choon Kim
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Daniel D. Hu
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew M. Champion
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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McGinnis MM, Sutter BM, Jahangiri S, Tu BP. Exonuclease Xrn1 regulates TORC1 signaling in response to SAM availability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559955. [PMID: 37808861 PMCID: PMC10557749 DOI: 10.1101/2023.09.28.559955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Autophagy is a conserved process of cellular self-digestion that promotes survival during nutrient stress. In yeast, methionine starvation is sufficient to induce autophagy. One pathway of autophagy induction is governed by the SEACIT complex, which regulates TORC1 activity in response to amino acids through the Rag GTPases Gtr1 and Gtr2. However, the precise mechanism by which SEACIT senses amino acids and regulates TORC1 signaling remains incompletely understood. Here, we identify the conserved 5'-3' RNA exonuclease Xrn1 as a surprising and novel regulator of TORC1 activity in response to methionine starvation. This role of Xrn1 is dependent on its catalytic activity, but not on degradation of any specific class of mRNAs. Instead, Xrn1 modulates the nucleotide-binding state of the Gtr1/2 complex, which is critical for its interaction with and activation of TORC1. This work identifies a critical role for Xrn1 in nutrient sensing and growth control that extends beyond its canonical housekeeping function in RNA degradation and indicates an avenue for RNA metabolism to function in amino acid signaling into TORC1.
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Affiliation(s)
- Madeline M McGinnis
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin M Sutter
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samira Jahangiri
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Elorette C, Fujimoto A, Stoll FM, Fujimoto SH, Fleysher L, Bienkowska N, Russ BE, Rudebeck PH. The neural basis of resting-state fMRI functional connectivity in fronto-limbic circuits revealed by chemogenetic manipulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545778. [PMID: 37745436 PMCID: PMC10515745 DOI: 10.1101/2023.06.21.545778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Measures of fMRI resting-state functional connectivity (rs-FC) are an essential tool for basic and clinical investigations of fronto-limbic circuits. Understanding the relationship between rs-FC and neural activity in these circuits is therefore vital. Here we introduced inhibitory designer receptors exclusively activated by designer drugs (DREADDs) into the macaque amygdala and activated them with a highly selective and potent DREADD agonist, deschloroclozapine. We evaluated the causal effect of activating the DREADD receptors on rs-FC and neural activity within circuits connecting amygdala and frontal cortex. Interestingly, activating the inhibitory DREADD increased rs-FC between amygdala and ventrolateral prefrontal cortex. Neurophysiological recordings revealed that the DREADD-induced increase in fMRI rs-FC was associated with increased local field potential coherency in the alpha band (6.5-14.5Hz) between amygdala and ventrolateral prefrontal cortex. Thus, our multi-disciplinary approach reveals the specific signature of neuronal activity that underlies rs-FC in fronto-limbic circuits.
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Affiliation(s)
- Catherine Elorette
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
| | - Atsushi Fujimoto
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
| | - Frederic M. Stoll
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
| | - Satoka H. Fujimoto
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
| | - Lazar Fleysher
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
| | - Niranjana Bienkowska
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
| | - Brian E. Russ
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY 10962
- Department of Psychiatry, New York University at Langone, One, 8, Park Ave, New York, NY 10016
| | - Peter H. Rudebeck
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029
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Klune CB, Goodpaster CM, Gongwer MW, Gabriel CJ, Chen R, Jones NS, Schwarz LA, DeNardo LA. Developmentally distinct architectures in top-down circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.27.555010. [PMID: 37693480 PMCID: PMC10491090 DOI: 10.1101/2023.08.27.555010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The medial prefrontal cortex (mPFC) plays a key role in learning, mood and decision making, including in how individuals respond to threats 1-6 . mPFC undergoes a uniquely protracted development, with changes in synapse density, cortical thickness, long-range connectivity, and neuronal encoding properties continuing into early adulthood 7-21 . Models suggest that before adulthood, the slow-developing mPFC cannot adequately regulate activity in faster-developing subcortical centers 22,23 . They propose that during development, the enhanced influence of subcortical systems underlies distinctive behavioural strategies of juveniles and adolescents and that increasing mPFC control over subcortical structures eventually allows adult behaviours to emerge. Yet it has remained unclear how a progressive strengthening of top-down control can lead to nonlinear changes in behaviour as individuals mature 24,25 . To address this discrepancy, here we monitored and manipulated activity in the developing brain as animals responded to threats, establishing direct causal links between frontolimbic circuit activity and the behavioural strategies of juvenile, adolescent and adult mice. Rather than a linear strengthening of mPFC synaptic connectivity progressively regulating behaviour, we uncovered multiple developmental switches in the behavioural roles of mPFC circuits targeting the basolateral amygdala (BLA) and nucleus accumbens (NAc). We show these changes are accompanied by axonal pruning coinciding with functional strengthening of synaptic connectivity in the mPFC-BLA and mPFC-NAc pathways, which mature at different rates. Our results reveal how developing mPFC circuits pass through distinct architectures that may make them optimally adapted to the demands of age-specific challenges.
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Gallego-López GM, Guzman EC, Knoll LJ, Skala M. Metabolic changes to host cells with Toxoplasma gondii infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552811. [PMID: 37609172 PMCID: PMC10441426 DOI: 10.1101/2023.08.10.552811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular parasite that infects warm-blooded vertebrates across the world. In humans, seropositivity rates of T. gondii range from 10% to 90%. Despite its prevalence, few studies address how T. gondii infection changes the metabolism of host cells. Here, we investigate how T. gondii manipulates the host cell metabolic environment by monitoring metabolic response over time using non-invasive autofluorescence lifetime imaging of single cells, seahorse metabolic flux analysis, reactive oxygen species (ROS) production, and metabolomics. Autofluorescence lifetime imaging indicates that infected host cells become more oxidized and have an increased proportion of bound NAD(P)H with infection. These findings are consistent with changes in mitochondrial and glycolytic function, decrease of intracellular glucose, fluctuations in lactate and ROS production in infected cells over time. We also examined changes associated with the pre-invasion "kiss and spit" process using autofluorescence lifetime imaging, which similarly showed a more oxidized host cell with an increased proportion of bound NAD(P)H over 48 hours. Glucose metabolic flux analysis indicated that these changes are driven by NADH and NADP+ in T. gondii infection. In sum, metabolic changes in host cells with T. gondii infection were similar during full infection, and kiss and spit. Autofluorescence lifetime imaging can non-invasively monitor metabolic changes in host cells over a microbial infection time-course.
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Affiliation(s)
- Gina M. Gallego-López
- Morgridge Institute for Research, Madison, WI, 53706
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706
| | | | - Laura J. Knoll
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706
| | - Melissa Skala
- Morgridge Institute for Research, Madison, WI, 53706
- Department of Biomedical Engineering, University of Wisconsin- Madison, WI 53706, USA
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Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial Genome Diversity across the Subphylum Saccharomycotina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551029. [PMID: 37577532 PMCID: PMC10418067 DOI: 10.1101/2023.07.28.551029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
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Affiliation(s)
- John F. Wolters
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Abigail L. LaBella
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC, 28223, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Dana A. Opulente
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Biology Department Villanova University, Villanova, PA 19085, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53726, USA
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Obando MA, Dörr T. Novel role for peptidoglycan carboxypeptidases in maintaining the balance between bacterial cell wall synthesis and degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548665. [PMID: 37503280 PMCID: PMC10369974 DOI: 10.1101/2023.07.12.548665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulation factors in Vibrio cholerae. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. dacA1 is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in dacA1. A subsequent suppressor screen to restore viability of ΔdacA1 in LB medium was answered by hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote PG degradation. Our data thus reveal a key role of DacA1 in maintaining the balance between PG synthesis and degradation.
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Affiliation(s)
- Manuela Alvarado Obando
- Department of Microbiology, Cornell University, Ithaca, NY
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, NY
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
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Norris MR, Dunn SS, Aravamuthan BR, McCall JG. Spared nerve injury causes motor phenotypes unrelated to pain in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548155. [PMID: 37461475 PMCID: PMC10350052 DOI: 10.1101/2023.07.07.548155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Most animal models of neuropathic pain use targeted nerve injuries quantified with motor reflexive measures in response to an applied noxious stimulus. These motor reflexive measures can only accurately represent a pain response if motor function in also intact. The commonly used spared nerve injury (SNI) model, however, damages the tibial and common peroneal nerves that should result in motor phenotypes (i.e., an immobile or "flail" foot) not typically captured in sensory assays. To test the extent of these issues, we used DeepLabCut, a deep learning-based markerless pose estimation tool to quantify spontaneous limb position in C57BL/6J mice during tail suspension following either SNI or sham surgery. Using this granular detail, we identified the expected flail foot-like impairment, but we also found SNI mice hold their injured limb closer to the body midline compared to shams. These phenotypes were not present in the Complete Freunds Adjuvant model of inflammatory pain and were not reversed by multiple analgesics with different mechanisms of action, suggesting these SNI-specific phenotypes are not directly related to pain. Together these results suggest SNI causes previously undescribed phenotypes unrelated to altered sensation that are likely underappreciated while interpreting preclinical pain research outcomes.
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Affiliation(s)
- Makenzie R. Norris
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA; Department of Pharmaceutical and Administrative Sciences University of Health Sciences & Pharmacy in St. Louis, St. Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy in St. Louis and Washington University School of Medicine, St. Louis, MO, USA; Washington University Pain Center, Washington University in St. Louis, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha S. Dunn
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA; Department of Pharmaceutical and Administrative Sciences University of Health Sciences & Pharmacy in St. Louis, St. Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy in St. Louis and Washington University School of Medicine, St. Louis, MO, USA; Washington University Pain Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Bhooma R. Aravamuthan
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA; Department of Pharmaceutical and Administrative Sciences University of Health Sciences & Pharmacy in St. Louis, St. Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy in St. Louis and Washington University School of Medicine, St. Louis, MO, USA; Washington University Pain Center, Washington University in St. Louis, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jordan G. McCall
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA; Department of Pharmaceutical and Administrative Sciences University of Health Sciences & Pharmacy in St. Louis, St. Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy in St. Louis and Washington University School of Medicine, St. Louis, MO, USA; Washington University Pain Center, Washington University in St. Louis, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
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Rudibaugh TT, Keung AJ. Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544782. [PMID: 37398046 PMCID: PMC10312668 DOI: 10.1101/2023.06.13.544782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Dopamine signaling in the adult ventral forebrain regulates behavior, stress response, and memory formation and in neurodevelopment regulates neural differentiation and cell migration. Excessive dopamine levels including due to cocaine use both in utero and in adults could lead to long-term adverse consequences. The mechanisms underlying both homeostatic and pathological changes remain unclear, partly due to the diverse cellular responses elicited by dopamine and the reliance on animal models that exhibit species-specific differences in dopamine signaling. To address these limitations, 3-D cerebral organoids have emerged as human-derived models, recapitulating salient features of human cell signaling and neurodevelopment. Organoids have demonstrated responsiveness to external stimuli, including substances of abuse, making them valuable investigative models. In this study we utilize the Xiang-Tanaka ventral forebrain organoid model and characterize their response to acute and chronic dopamine or cocaine exposure. The findings revealed a robust immune response, novel response pathways, and a potential critical role for reactive oxygen species (ROS) in the developing ventral forebrain. These results highlight the potential of cerebral organoids as in vitro human models for studying complex biological processes in the brain.
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Affiliation(s)
- Thomas T. Rudibaugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606
| | - Albert J. Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606
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41
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Tague N, Andreani V, Fan Y, Timp W, Dunlop MJ. Comprehensive screening of a light-inducible split Cre recombinase with domain insertion profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542511. [PMID: 37293111 PMCID: PMC10245967 DOI: 10.1101/2023.05.26.542511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Splitting proteins with light- or chemically-inducible dimers provides a mechanism for post-translational control of protein function. However, current methods for engineering stimulus-responsive split proteins often require significant protein engineering expertise and laborious screening of individual constructs. To address this challenge, we use a pooled library approach that enables rapid generation and screening of nearly all possible split protein constructs in parallel, where results can be read out using sequencing. We perform our method on Cre recombinase with optogenetic dimers as a proof of concept, resulting in comprehensive data on split sites throughout the protein. To improve accuracy in predicting split protein behavior, we develop a Bayesian computational approach to contextualize errors inherent to experimental procedures. Overall, our method provides a streamlined approach for achieving inducible post-translational control of a protein of interest.
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Keller MR, Dörr T. Bacterial metabolism and susceptibility to cell wall-active antibiotics. Adv Microb Physiol 2023; 83:181-219. [PMID: 37507159 PMCID: PMC11024984 DOI: 10.1016/bs.ampbs.2023.04.002] [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] [Indexed: 07/30/2023]
Abstract
Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.
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Affiliation(s)
- Megan Renee Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States; Department of Microbiology, Cornell University, Ithaca, NY, United States; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States.
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Weaver A, Taguchi A, Dörr T. Masters of Misdirection: Peptidoglycan Glycosidases in Bacterial Growth. J Bacteriol 2023; 205:e0042822. [PMID: 36757204 PMCID: PMC10029718 DOI: 10.1128/jb.00428-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The dynamic composition of the peptidoglycan cell wall has been the subject of intense research for decades, yet how bacteria coordinate the synthesis of new peptidoglycan with the turnover and remodeling of existing peptidoglycan remains elusive. Diversity and redundancy within peptidoglycan synthases and peptidoglycan autolysins, enzymes that degrade peptidoglycan, have often made it challenging to assign physiological roles to individual enzymes and determine how those activities are regulated. For these reasons, peptidoglycan glycosidases, which cleave within the glycan strands of peptidoglycan, have proven veritable masters of misdirection over the years. Unlike many of the broadly conserved peptidoglycan synthetic complexes, diverse bacteria can employ unrelated glycosidases to achieve the same physiological outcome. Additionally, although the mechanisms of action for many individual enzymes have been characterized, apparent conserved homologs in other organisms can exhibit an entirely different biochemistry. This flexibility has been recently demonstrated in the context of three functions critical to vegetative growth: (i) release of newly synthesized peptidoglycan strands from their membrane anchors, (ii) processing of peptidoglycan turned over during cell wall expansion, and (iii) removal of peptidoglycan fragments that interfere with daughter cell separation during cell division. Finally, the regulation of glycosidase activity during these cell processes may be a cumulation of many factors, including protein-protein interactions, intrinsic substrate preferences, substrate availability, and subcellular localization. Understanding the true scope of peptidoglycan glycosidase activity will require the exploration of enzymes from diverse organisms with equally diverse growth and division strategies.
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Affiliation(s)
- Anna Weaver
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Atsushi Taguchi
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
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Keller M, Han X, Dörr T. Disrupting Central Carbon Metabolism Increases β-Lactam Antibiotic Susceptibility in Vibrio cholerae. J Bacteriol 2023; 205:e0047622. [PMID: 36840595 PMCID: PMC10029711 DOI: 10.1128/jb.00476-22] [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: 12/21/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
Antibiotic tolerance, the ability of bacteria to sustain viability in the presence of typically bactericidal antibiotics for extended time periods, is an understudied contributor to treatment failure. The Gram-negative pathogen Vibrio cholerae, the causative agent of cholera, becomes highly tolerant to β-lactam antibiotics (penicillin and related compounds) in a process requiring the two-component system VxrAB. VxrAB is induced by exposure to cell wall damaging conditions, which results in the differential regulation of >100 genes. While the effectors of VxrAB are relatively well known, VxrAB environment-sensing and activation mechanisms remain a mystery. Here, we used transposon mutagenesis to screen for mutants that spontaneously upregulate VxrAB signaling. This screen was answered by genes known to be required for proper cell envelope homeostasis, validating the approach. Unexpectedly, we also uncovered a new connection between central carbon metabolism and antibiotic tolerance in Vibrio cholerae. Inactivation of pgi (vc0374, coding for glucose-6-phosphate isomerase) resulted in an intracellular accumulation of glucose-6-phosphate and fructose-6-phosphate, concomitant with a marked cell envelope defect, resulting in VxrAB induction. Deletion of pgi also increased sensitivity to β-lactams and conferred a growth defect on salt-free LB, phenotypes that could be suppressed by deleting sugar uptake systems and by supplementing cell wall precursors in the growth medium. Our data suggest an important connection between central metabolism and cell envelope integrity and highlight a potential new target for developing novel antimicrobial agents. IMPORTANCE Antibiotic tolerance (the ability to survive exposure to antibiotics) is a stepping stone toward antibiotic resistance (the ability to grow in the presence of antibiotics), an increasingly common cause of antibiotic treatment failure. The mechanisms promoting tolerance are poorly understood. Here, we identified central carbon metabolism as a key contributor to antibiotic tolerance and resistance. A strain with a mutation in a sugar utilization pathway accumulates metabolites that likely shut down the synthesis of cell wall precursors, which weakens the cell wall and thus increases susceptibility to cell wall-active drugs. Our results illuminate the connection between central carbon metabolism and cell wall homeostasis in V. cholerae and suggest that interfering with metabolism may be a fruitful future strategy for the development of antibiotic adjuvants.
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Affiliation(s)
- Megan Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
| | - Xiang Han
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
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45
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Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers B, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Multiscale integration of human and single-cell variations reveals unadjuvanted vaccine high responders are naturally adjuvanted. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.20.23287474. [PMID: 37090674 PMCID: PMC10120791 DOI: 10.1101/2023.03.20.23287474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Advances in multimodal single cell analysis can empower high-resolution dissection of human vaccination responses. The resulting data capture multiple layers of biological variations, including molecular and cellular states, vaccine formulations, inter- and intra-subject differences, and responses unfolding over time. Transforming such data into biological insight remains a major challenge. Here we present a systematic framework applied to multimodal single cell data obtained before and after influenza vaccination without adjuvants or pandemic H5N1 vaccination with the AS03 adjuvant. Our approach pinpoints responses shared across or unique to specific cell types and identifies adjuvant specific signatures, including pro-survival transcriptional states in B lymphocytes that emerged one day after vaccination. We also reveal that high antibody responders to the unadjuvanted vaccine have a distinct baseline involving a rewired network of cell type specific transcriptional states. Remarkably, the status of certain innate immune cells in this network in high responders of the unadjuvanted vaccine appear "naturally adjuvanted": they resemble phenotypes induced early in the same cells only by vaccination with AS03. Furthermore, these cell subsets have elevated frequency in the blood at baseline and increased cell-intrinsic phospho-signaling responses after LPS stimulation ex vivo in high compared to low responders. Our findings identify how variation in the status of multiple immune cell types at baseline may drive robust differences in innate and adaptive responses to vaccination and thus open new avenues for vaccine development and immune response engineering in humans.
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Affiliation(s)
- Matthew P. Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Brian Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juan A. Quiel
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Arjun Jain
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Pamela L. Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cell Signaling and Immunity Section, NIAID, NIH, Bethesda, MD, USA
| | - John S. Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
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46
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Liang Y, Zhao Y, Kwan J, Wang Y, Qiao Y. Escherichia coli has robust regulatory mechanisms against elevated peptidoglycan cleavage by lytic transglycosylases. J Biol Chem 2023; 299:104615. [PMID: 36931392 PMCID: PMC10139938 DOI: 10.1016/j.jbc.2023.104615] [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: 12/19/2022] [Revised: 02/25/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Peptidoglycan (PG) is an essential and conserved exoskeletal component in all bacteria that protects cells from lysis. Gram-negative bacteria such as Escherichia coli encode multiple redundant lytic transglycosylases (LTs) that engage in PG cleavage, a potentially lethal activity requiring proper regulation to prevent autolysis. To elucidate the potential effects and cellular regulatory mechanisms of elevated LT activity, we individually cloned the periplasmic domains of two membrane-bound LTs, MltA and MltB under the control of the arabinose-inducible system for overexpression in the periplasmic space in E. coli. Interestingly, upon induction, the culture undergoes an initial period of cell lysis followed by robust growth restoration. The LT-overexpressing E. coli exhibits altered morphology with larger spherical cells, which is in line with the weakening of the PG layer due to aberrant LT activity. On the other hand, the restored cells display a similar rod shape and peptidoglycan profile that is indistinguishable from the uninduced control. Quantitative proteomics analysis of the restored cells identified significant protein enrichment in the regulator of capsule synthesis (Rcs) regulon, a two-component stress response known to be specifically activated by PG damage. We showed that LT-overexpressing E. coli with an inactivated Rcs system partially impairs the growth restoration process, supporting the involvement of the Rcs system in countering aberrant PG cleavage. Furthermore, we demonstrated that the elevated LT activity specifically potentiates β-lactam antibiotics against E. coli with a defective Rcs regulon, suggesting the dual effects of augmented PG cleavage and blocked PG synthesis as a potential antimicrobial strategy.
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Affiliation(s)
- Yaquan Liang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371
| | - Yilin Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371
| | - JericMunChung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371
| | - Yue Wang
- A*STAR Infectious Disease Labs, Singapore 138648
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371.
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47
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Li JY, Glickfeld LL. Input-specific synaptic depression shapes temporal integration in mouse visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526211. [PMID: 36778279 PMCID: PMC9915496 DOI: 10.1101/2023.01.30.526211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Efficient sensory processing requires the nervous system to adjust to ongoing features of the environment. In primary visual cortex (V1), neuronal activity strongly depends on recent stimulus history. Existing models can explain effects of prolonged stimulus presentation, but remain insufficient for explaining effects observed after shorter durations commonly encountered under natural conditions. We investigated the mechanisms driving adaptation in response to brief (100 ms) stimuli in L2/3 V1 neurons by performing in vivo whole-cell recordings to measure membrane potential and synaptic inputs. We find that rapid adaptation is generated by stimulus-specific suppression of excitatory and inhibitory synaptic inputs. Targeted optogenetic experiments reveal that these synaptic effects are due to input-specific short-term depression of transmission between layers 4 and 2/3. Thus, distinct mechanisms are engaged following brief and prolonged stimulus presentation and together enable flexible control of sensory encoding across a wide range of time scales.
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Affiliation(s)
- Jennifer Y Li
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27701, USA
| | - Lindsey L Glickfeld
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27701, USA
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48
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Fanunza E, Cheng AZ, Auerbach AA, Stefanovska B, Moraes SN, Lokensgard JR, Biolatti M, Dell’Oste V, Bierle CJ, Bresnahan WA, Harris RS. Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526383. [PMID: 36778493 PMCID: PMC9915650 DOI: 10.1101/2023.01.30.526383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The APOBEC3 family of DNA cytosine deaminases comprises an important arm of the innate antiviral defense system. The gamma-herpesviruses EBV and KSHV and the alpha-herpesviruses HSV-1 and HSV-2 have evolved an efficient mechanism to avoid APOBEC3 restriction by directly binding to APOBEC3B and facilitating its exclusion from the nuclear compartment. The only viral protein required for APOBEC3B relocalization is the large subunit of the ribonucleotide reductase (RNR). Here, we ask whether this APOBEC3B relocalization mechanism is conserved with the beta-herpesvirus human cytomegalovirus (HCMV). Although HCMV infection causes APOBEC3B relocalization from the nucleus to the cytoplasm in multiple cell types, the viral RNR (UL45) is not required. APOBEC3B relocalization occurs rapidly following infection suggesting involvement of an immediate early or early (IE-E) viral protein. In support of this mechanism, cycloheximide treatment of HCMV-infected cells prevents the expression of viral proteins and simultaneously blocks APOBEC3B relocalization. In comparison, the treatment of infected cells with phosphonoacetic acid, which is a viral DNA synthesis inhibitor affecting late protein expression, still permits A3B relocalization. These results combine to show that the beta-herpesvirus HCMV uses a fundamentally different, RNR-independent molecular mechanism to antagonize APOBEC3B. Importance Human cytomegalovirus (HCMV) infections can range from asymptomatic to severe, particularly in neonates and immunocompromised patients. HCMV has evolved strategies to overcome host-encoded antiviral defenses in order to achieve lytic viral DNA replication and dissemination and, under some conditions, latency and long-term persistence. Here, we show that HCMV infection causes the antiviral factor, APOBEC3B, to relocalize from the nuclear compartment to the cytoplasm. This overall strategy resembles that used by related herpesviruses. However, the HCMV relocalization mechanism utilizes a different viral factor(s) and available evidence suggests the involvement of at least one protein expressed at the early stages of infection. This knowledge is important because a greater understanding of this mechanism could lead to novel antiviral strategies that enable APOBEC3B to naturally restrict HCMV infection.
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Affiliation(s)
- Elisa Fanunza
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ashley A. Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - James R. Lokensgard
- Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, 10126, Italy
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, 10126, Italy
| | - Craig J. Bierle
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wade A. Bresnahan
- Department of Microbiology and Immunology, University of Minnesota, MN 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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49
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Daitch AK, Orsburn BC, Chen Z, Alvarez L, Eberhard CD, Sundararajan K, Zeinert R, Kreitler DF, Jakoncic J, Chien P, Cava F, Gabelli SB, Goley ED. EstG is a novel esterase required for cell envelope integrity in Caulobacter. Curr Biol 2023; 33:228-240.e7. [PMID: 36516849 PMCID: PMC9877181 DOI: 10.1016/j.cub.2022.11.037] [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: 05/13/2022] [Revised: 10/17/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022]
Abstract
Proper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the ⍺-proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell-wall-targeting antibiotics, EstG does not demonstrate biochemical activity toward cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. This molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which are important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.
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Affiliation(s)
- Allison K Daitch
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA
| | - Benjamin C Orsburn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA
| | - Zan Chen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA
| | - Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Colten D Eberhard
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA
| | - Kousik Sundararajan
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA
| | - Rilee Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Bldg 745, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000, USA
| | - Jean Jakoncic
- National Synchrotron Light Source II, Bldg 745, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA.
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50
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Applegate MC, Gutnichenko KS, Mackevicius EL, Aronov D. An entorhinal-like region in food-caching birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522940. [PMID: 36711539 PMCID: PMC9881956 DOI: 10.1101/2023.01.05.522940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The mammalian entorhinal cortex routes inputs from diverse sources into the hippocampus. This information is mixed and expressed in the activity of many specialized entorhinal cell types, which are considered indispensable for hippocampal function. However, functionally similar hippocampi exist even in non-mammals that lack an obvious entorhinal cortex, or generally any layered cortex. To address this dilemma, we mapped extrinsic hippocampal connections in chickadees, whose hippocampi are used for remembering numerous food caches. We found a well-delineated structure in these birds that is topologically similar to the entorhinal cortex and interfaces between the hippocampus and other pallial regions. Recordings of this structure revealed entorhinal-like activity, including border and multi-field grid-like cells. These cells were localized to the subregion predicted by anatomical mapping to match the dorsomedial entorhinal cortex. Our findings uncover an anatomical and physiological equivalence of vastly different brains, suggesting a fundamental nature of entorhinal-like computations for hippocampal function.
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Affiliation(s)
| | | | | | - Dmitriy Aronov
- Zuckerman Mind Brain Behavior Institute, Columbia University,Corresponding author:
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