1
|
van der Horst D, Kurmasheva N, Marqvorsen MHS, Assil S, Rahimic AHF, Kollmann CF, Silva da Costa L, Wu Q, Zhao J, Cesari E, Iversen MB, Ren F, Jensen TI, Narita R, Schack VR, Zhang BC, Bak RO, Sette C, Fenton RA, Mikkelsen JG, Paludan SR, Olagnier D. SAM68 directs STING signaling to apoptosis in macrophages. Commun Biol 2024; 7:283. [PMID: 38454028 PMCID: PMC10920828 DOI: 10.1038/s42003-024-05969-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
DNA is a danger signal sensed by cGAS to engage signaling through STING to activate innate immune functions. The best-studied downstream responses to STING activation include expression of type I interferon and inflammatory genes, but STING also activates other pathways, including apoptosis. Here, we report that STING-dependent induction of apoptosis in macrophages occurs through the intrinsic mitochondrial pathway and is mediated via IRF3 but acts independently of gene transcription. By intersecting four mass spectrometry datasets, we identify SAM68 as crucial for the induction of apoptosis downstream of STING activation. SAM68 is essential for the full activation of apoptosis. Still, it is not required for STING-mediated activation of IFN expression or activation of NF-κB. Mechanistic studies reveal that protein trafficking is required and involves SAM68 recruitment to STING upon activation, with the two proteins associating at the Golgi or a post-Golgi compartment. Collectively, our work identifies SAM68 as a STING-interacting protein enabling induction of apoptosis through this DNA-activated innate immune pathway.
Collapse
Affiliation(s)
- Demi van der Horst
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Naziia Kurmasheva
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Mikkel H S Marqvorsen
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Sonia Assil
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Anna H F Rahimic
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Christoph F Kollmann
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Leandro Silva da Costa
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Qi Wu
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Jian Zhao
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Eleonora Cesari
- GSTEP-Organoids Core Facility, IRCCS Fondazione Policlinico Agostino Gemelli, 00168, Rome, Italy
| | - Marie B Iversen
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Fanghui Ren
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Trine I Jensen
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Ryo Narita
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Vivien R Schack
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Bao-Cun Zhang
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Claudio Sette
- GSTEP-Organoids Core Facility, IRCCS Fondazione Policlinico Agostino Gemelli, 00168, Rome, Italy
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, 00168, Rome, Italy
| | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Jacob G Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark.
| | - David Olagnier
- Department of Biomedicine, Aarhus University, Høegh Guldbergsgade 10, 8000, Aarhus C, Denmark.
| |
Collapse
|
2
|
Liu X, McPherson JN, Andersen CE, Jørgensen MSB, Larsen RW, Yutronkie NJ, Wilhelm F, Rogalev A, Giménez-Marqués M, Mínguez Espallargas G, Göb CR, Pedersen KS. A zero-valent palladium cluster-organic framework. Nat Commun 2024; 15:1177. [PMID: 38331922 PMCID: PMC10853280 DOI: 10.1038/s41467-024-45363-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Acquiring spatial control of nanoscopic metal clusters is central to their function as efficient multi-electron catalysts. However, dispersing metal clusters on surfaces or in porous hosts is accompanied by an intrinsic heterogeneity that hampers detailed understanding of the chemical structure and its relation to reactivities. Tethering pre-assembled molecular metal clusters into polymeric, crystalline 2D or 3D networks constitutes an unproven approach to realizing ordered arrays of chemically well-defined metal clusters. Herein, we report the facile synthesis of a {Pd3} cluster-based organometallic framework from a molecular triangulo-Pd3(CNXyl)6 (Xyl = xylyl; Pd3) cluster under chemically mild conditions. The formally zero-valent Pd3 cluster readily engages in a complete ligand exchange when exposed to a similar, ditopic isocyanide ligand, resulting in polymerization into a 2D coordination network (Pd3-MOF). The structure of Pd3-MOF could be unambiguously determined by continuous rotation 3D electron diffraction (3D-ED) experiments to a resolution of ~1.0 Å (>99% completeness), showcasing the applicability of 3D-ED to nanocrystalline, organometallic polymers. Pd3-MOF displays Pd03 cluster nodes, which possess significant thermal and aerobic stability, and activity towards hydrogenation catalysis. Importantly, the realization of Pd3-MOF paves the way for the exploitation of metal clusters as building blocks for rigidly interlocked metal nanoparticles at the molecular limit.
Collapse
Affiliation(s)
- Xiyue Liu
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - James N McPherson
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark.
| | - Carl Emil Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - Mike S B Jørgensen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - René Wugt Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - Nathan J Yutronkie
- European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble Cedex 9, France
| | - Fabrice Wilhelm
- European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble Cedex 9, France
| | - Andrei Rogalev
- European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble Cedex 9, France
| | - Mónica Giménez-Marqués
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, Paterna, 46980, Valencia, Spain
| | | | - Christian R Göb
- Rigaku Europe SE, Hugenottenallee 167, 63263, Neu-Isenburg, Germany
| | - Kasper S Pedersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark.
| |
Collapse
|
3
|
Swalethorp R, Landry MR, Semmens BX, Ohman MD, Aluwihare L, Chargualaf D, Thompson AR. Anchovy boom and bust linked to trophic shifts in larval diet. Nat Commun 2023; 14:7412. [PMID: 38052790 DOI: 10.1038/s41467-023-42966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/27/2023] [Indexed: 12/07/2023] Open
Abstract
Although massive biomass fluctuations of coastal-pelagic fishes are an iconic example of the impacts of climate variability on marine ecosystems, the mechanisms governing these dynamics are often elusive. We construct a 45-year record of nitrogen stable isotopes measured in larvae of Northern Anchovy (Engraulis mordax) in the California Current Ecosystem to assess patterns in food chain length. Larval trophic efficiency associated with a shortened food chain increased larval survival and produced boom periods of high adult biomass. In contrast, when larval food chain length increased, and energy transfer efficiency decreased, the population crashed. We propose the Trophic Efficiency in Early Life (TEEL) hypothesis, which states that larval fishes must consume prey that confer sufficient energy for survival, to help explain natural boom-bust dynamics of coastal pelagic fishes. Our findings illustrate a potential for trophic indicators to generally inform larval survival and adult population dynamics of coastal-pelagic fishes.
Collapse
Affiliation(s)
- Rasmus Swalethorp
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, CA, USA.
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, CA, USA.
- National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark, Kgs., Lyngby, Denmark.
| | - Michael R Landry
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, CA, USA
| | - Brice X Semmens
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, CA, USA
| | - Mark D Ohman
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, CA, USA
| | - Lihini Aluwihare
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, CA, USA
| | - Dereka Chargualaf
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, CA, USA
| | - Andrew R Thompson
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, CA, USA
| |
Collapse
|
4
|
Frank M, Fechete LI, Tedeschi F, Nadzieja M, Nørgaard MMM, Montiel J, Andersen KR, Schierup MH, Reid D, Andersen SU. Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus. Nat Commun 2023; 14:7171. [PMID: 37935666 PMCID: PMC10630511 DOI: 10.1038/s41467-023-42911-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.
Collapse
Affiliation(s)
- Manuel Frank
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Lavinia Ioana Fechete
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Francesca Tedeschi
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | | | - Jesus Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
- Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
| | - Kasper Røjkjær Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Australia.
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.
| |
Collapse
|
5
|
Fontana P, Buch-Larsen SC, Suyari O, Smith R, Suskiewicz MJ, Schützenhofer K, Ariza A, Rack JGM, Nielsen ML, Ahel I. Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling. Nat Commun 2023; 14:3200. [PMID: 37268618 PMCID: PMC10238386 DOI: 10.1038/s41467-023-38793-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
In the mammalian DNA damage response, ADP-ribosylation signalling is of crucial importance to mark sites of DNA damage as well as recruit and regulate repairs factors. Specifically, the PARP1:HPF1 complex recognises damaged DNA and catalyses the formation of serine-linked ADP-ribosylation marks (mono-Ser-ADPr), which are extended into ADP-ribose polymers (poly-Ser-ADPr) by PARP1 alone. Poly-Ser-ADPr is reversed by PARG, while the terminal mono-Ser-ADPr is removed by ARH3. Despite its significance and apparent evolutionary conservation, little is known about ADP-ribosylation signalling in non-mammalian Animalia. The presence of HPF1, but absence of ARH3, in some insect genomes, including Drosophila species, raises questions regarding the existence and reversal of serine-ADP-ribosylation in these species. Here we show by quantitative proteomics that Ser-ADPr is the major form of ADP-ribosylation in the DNA damage response of Drosophila melanogaster and is dependent on the dParp1:dHpf1 complex. Moreover, our structural and biochemical investigations uncover the mechanism of mono-Ser-ADPr removal by Drosophila Parg. Collectively, our data reveal PARP:HPF1-mediated Ser-ADPr as a defining feature of the DDR in Animalia. The striking conservation within this kingdom suggests that organisms that carry only a core set of ADP-ribosyl metabolising enzymes, such as Drosophila, are valuable model organisms to study the physiological role of Ser-ADPr signalling.
Collapse
Affiliation(s)
- Pietro Fontana
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Sara C Buch-Larsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Marcin J Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071, Orléans, France
| | - Kira Schützenhofer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Michael L Nielsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| |
Collapse
|
6
|
Shuoker B, Pichler MJ, Jin C, Sakanaka H, Wu H, Gascueña AM, Liu J, Nielsen TS, Holgersson J, Nordberg Karlsson E, Juge N, Meier S, Morth JP, Karlsson NG, Abou Hachem M. Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria. Nat Commun 2023; 14:1833. [PMID: 37005422 PMCID: PMC10067855 DOI: 10.1038/s41467-023-37533-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/21/2023] [Indexed: 04/04/2023] Open
Abstract
The mucolytic human gut microbiota specialist Akkermansia muciniphila is proposed to boost mucin-secretion by the host, thereby being a key player in mucus turnover. Mucin glycan utilization requires the removal of protective caps, notably fucose and sialic acid, but the enzymatic details of this process remain largely unknown. Here, we describe the specificities of ten A. muciniphila glycoside hydrolases, which collectively remove all known sialyl and fucosyl mucin caps including those on double-sulfated epitopes. Structural analyses revealed an unprecedented fucosidase modular arrangement and explained the sialyl T-antigen specificity of a sialidase of a previously unknown family. Cell-attached sialidases and fucosidases displayed mucin-binding and their inhibition abolished growth of A. muciniphila on mucin. Remarkably, neither the sialic acid nor fucose contributed to A. muciniphila growth, but instead promoted butyrate production by co-cultured Clostridia. This study brings unprecedented mechanistic insight into the initiation of mucin O-glycan degradation by A. muciniphila and nutrient sharing between mucus-associated bacteria.
Collapse
Affiliation(s)
- Bashar Shuoker
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
- Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Michael J Pichler
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Chunsheng Jin
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hiroka Sakanaka
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Haiyang Wu
- Quadram Institute Bioscience, Norwich, UK
| | | | - Jining Liu
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tine Sofie Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Jan Holgersson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark.
| | - Niclas G Karlsson
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark.
| |
Collapse
|
7
|
Abildgaard AB, Nielsen SV, Bernstein I, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Lynch syndrome, molecular mechanisms and variant classification. Br J Cancer 2023; 128:726-734. [PMID: 36434153 PMCID: PMC9978028 DOI: 10.1038/s41416-022-02059-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Patients with the heritable cancer disease, Lynch syndrome, carry germline variants in the MLH1, MSH2, MSH6 and PMS2 genes, encoding the central components of the DNA mismatch repair system. Loss-of-function variants disrupt the DNA mismatch repair system and give rise to a detrimental increase in the cellular mutational burden and cancer development. The treatment prospects for Lynch syndrome rely heavily on early diagnosis; however, accurate diagnosis is inextricably linked to correct clinical interpretation of individual variants. Protein variant classification traditionally relies on cumulative information from occurrence in patients, as well as experimental testing of the individual variants. The complexity of variant classification is due to (1) that variants of unknown significance are rare in the population and phenotypic information on the specific variants is missing, and (2) that individual variant testing is challenging, costly and slow. Here, we summarise recent developments in high-throughput technologies and computational prediction tools for the assessment of variants of unknown significance in Lynch syndrome. These approaches may vastly increase the number of interpretable variants and could also provide important mechanistic insights into the disease. These insights may in turn pave the road towards developing personalised treatment approaches for Lynch syndrome.
Collapse
Affiliation(s)
- Amanda B Abildgaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Inge Bernstein
- Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Institute of Clinical Medicine, Aalborg University Hospital, Aalborg University, Aalborg, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
8
|
Hallstrøm S, Raina JB, Ostrowski M, Parks DH, Tyson GW, Hugenholtz P, Stocker R, Seymour JR, Riemann L. Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N 2 fixation in the pelagic ocean. ISME J 2022; 16:2525-2534. [PMID: 35915168 PMCID: PMC9561647 DOI: 10.1038/s41396-022-01299-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 06/05/2023]
Abstract
Heterotrophic bacterial diazotrophs (HBDs) are ubiquitous in the pelagic ocean, where they have been predicted to carry out the anaerobic process of nitrogen fixation within low-oxygen microenvironments associated with marine pelagic particles. However, the mechanisms enabling particle colonization by HBDs are unknown. We hypothesized that HBDs use chemotaxis to locate and colonize suitable microenvironments, and showed that a cultivated marine HBD is chemotactic toward amino acids and phytoplankton-derived DOM. Using an in situ chemotaxis assay, we also discovered that diverse HBDs at a coastal site are motile and chemotactic toward DOM from various phytoplankton taxa and, indeed, that the proportion of diazotrophs was up to seven times higher among the motile fraction of the bacterial community compared to the bulk seawater community. Finally, three of four HBD isolates and 16 of 17 HBD metagenome assembled genomes, recovered from major ocean basins and locations along the Australian coast, each encoded >85% of proteins affiliated with the bacterial chemotaxis pathway. These results document the widespread capacity for chemotaxis in diverse and globally relevant marine HBDs. We suggest that HBDs could use chemotaxis to seek out and colonize low-oxygen microenvironments suitable for nitrogen fixation, such as those formed on marine particles. Chemotaxis in HBDs could therefore affect marine nitrogen and carbon biogeochemistry by facilitating nitrogen fixation within otherwise oxic waters, while also altering particle degradation and the efficiency of the biological pump.
Collapse
Affiliation(s)
- Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
| |
Collapse
|
9
|
Naundrup A, Bohman B, Kwadha CA, Jensen AB, Becher PG, De Fine Licht HH. Pathogenic fungus uses volatiles to entice male flies into fatal matings with infected female cadavers. ISME J 2022; 16:2388-2397. [PMID: 35831484 PMCID: PMC9477817 DOI: 10.1038/s41396-022-01284-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/17/2022]
Abstract
To ensure dispersal, many parasites and pathogens behaviourally manipulate infected hosts. Other pathogens and certain insect-pollinated flowers use sexual mimicry and release deceptive mating signals. However, it is unusual for pathogens to rely on both behavioural host manipulation and sexual mimicry. Here, we show that the host-specific and behaviourally manipulating pathogenic fungus, Entomophthora muscae, generates a chemical blend of volatile sesquiterpenes and alters the profile of natural host cuticular hydrocarbons in infected female housefly (Musca domestica) cadavers. Healthy male houseflies respond to the fungal compounds and are enticed into mating with female cadavers. This is advantageous for the fungus as close proximity between host individuals leads to an increased probability of infection. The fungus exploits the willingness of male flies to mate and benefits from altering the behaviour of uninfected male host flies. The altered cuticular hydrocarbons and emitted volatiles thus underlie the evolution of an extended phenotypic trait.
Collapse
Affiliation(s)
- Andreas Naundrup
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, København, Denmark.
| | - Björn Bohman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Charles A Kwadha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Annette B Jensen
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, København, Denmark
| | - Paul G Becher
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Henrik H De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, København, Denmark.
| |
Collapse
|
10
|
Benavides M, Bonnet S, Le Moigne FAC, Armin G, Inomura K, Hallstrøm S, Riemann L, Berman-Frank I, Poletti E, Garel M, Grosso O, Leblanc K, Guigue C, Tedetti M, Dupouy C. Sinking Trichodesmium fixes nitrogen in the dark ocean. ISME J 2022; 16:2398-2405. [PMID: 35835942 PMCID: PMC9478103 DOI: 10.1038/s41396-022-01289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 01/04/2023]
Abstract
The photosynthetic cyanobacterium Trichodesmium is widely distributed in the surface low latitude ocean where it contributes significantly to N2 fixation and primary productivity. Previous studies found nifH genes and intact Trichodesmium colonies in the sunlight-deprived meso- and bathypelagic layers of the ocean (200-4000 m depth). Yet, the ability of Trichodesmium to fix N2 in the dark ocean has not been explored. We performed 15N2 incubations in sediment traps at 170, 270 and 1000 m at two locations in the South Pacific. Sinking Trichodesmium colonies fixed N2 at similar rates than previously observed in the surface ocean (36-214 fmol N cell-1 d-1). This activity accounted for 40 ± 28% of the bulk N2 fixation rates measured in the traps, indicating that other diazotrophs were also active in the mesopelagic zone. Accordingly, cDNA nifH amplicon sequencing revealed that while Trichodesmium accounted for most of the expressed nifH genes in the traps, other diazotrophs such as Chlorobium and Deltaproteobacteria were also active. Laboratory experiments simulating mesopelagic conditions confirmed that increasing hydrostatic pressure and decreasing temperature reduced but did not completely inhibit N2 fixation in Trichodesmium. Finally, using a cell metabolism model we predict that Trichodesmium uses photosynthesis-derived stored carbon to sustain N2 fixation while sinking into the mesopelagic. We conclude that sinking Trichodesmium provides ammonium, dissolved organic matter and biomass to mesopelagic prokaryotes.
Collapse
Affiliation(s)
- Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
- Turing Center for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | - Sophie Bonnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Frédéric A C Le Moigne
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
- LEMAR, Laboratoire des Sciences de l'Environnement Marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280, Plouzané, Technopôle Brest-Iroise, France
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt, Carmel, Haifa, Israel
| | - Emilie Poletti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Garel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Olivier Grosso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Karine Leblanc
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Catherine Guigue
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Tedetti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Cécile Dupouy
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| |
Collapse
|
11
|
Horwitz R, Norin T, Watson SA, Pistevos JCA, Beldade R, Hacquart S, Gattuso JP, Rodolfo-Metalpa R, Vidal-Dupiol J, Killen SS, Mills SC. Near-future ocean warming and acidification alter foraging behaviour, locomotion, and metabolic rate in a keystone marine mollusc. Sci Rep 2020; 10:5461. [PMID: 32214174 PMCID: PMC7096400 DOI: 10.1038/s41598-020-62304-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 02/26/2020] [Indexed: 11/23/2022] Open
Abstract
Environmentally-induced changes in fitness are mediated by direct effects on physiology and behaviour, which are tightly linked. We investigated how predicted ocean warming (OW) and acidification (OA) affect key ecological behaviours (locomotion speed and foraging success) and metabolic rate of a keystone marine mollusc, the sea hare Stylocheilus striatus, a specialist grazer of the toxic cyanobacterium Lyngbya majuscula. We acclimated sea hares to OW and/or OA across three developmental stages (metamorphic, juvenile, and adult) or as adults only, and compare these to sea hares maintained under current-day conditions. Generally, locomotion speed and time to locate food were reduced ~1.5- to 2-fold when the stressors (OW or OA) were experienced in isolation, but reduced ~3-fold when combined. Decision-making was also severely altered, with correct foraging choice nearly 40% lower under combined stressors. Metabolic rate appeared to acclimate to the stressors in isolation, but was significantly elevated under combined stressors. Overall, sea hares that developed under OW and/or OA exhibited a less severe impact, indicating beneficial phenotypic plasticity. Reduced foraging success coupled with increased metabolic demands may impact fitness in this species and highlight potentially large ecological consequences under unabated OW and OA, namely in regulating toxic cyanobacteria blooms on coral reefs.
Collapse
Affiliation(s)
- Rael Horwitz
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Moorea, French Polynesia.
- Laboratoire d'Excellence "CORAIL", Nouméa, Nouvelle-Calédonie, France.
| | - Tommy Norin
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, Glasgow, G12 8QQ, United Kingdom
- Technical University of Denmark, DTU Aqua: National Institute of Aquatic Resources, 2800 Kgs, Lyngby, Denmark
| | - Sue-Ann Watson
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Jennifer C A Pistevos
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Moorea, French Polynesia
- Laboratoire d'Excellence "CORAIL", Nouméa, Nouvelle-Calédonie, France
| | - Ricardo Beldade
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Moorea, French Polynesia
- Pontificia Universidad Católica de Chile, Departamento de Ecología, Facultad de Ciencias Biológicas, Santiago, Chile
| | - Simon Hacquart
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Moorea, French Polynesia
| | - Jean-Pierre Gattuso
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, 181 chemin du Lazaret, F-06230, Villefranche-sur-mer, France
- Institute for Sustainable Development and International Relations, Sciences Po, 27 rue Saint Guillaume, F-75007, Paris, France
| | - Riccardo Rodolfo-Metalpa
- Laboratoire d'Excellence "CORAIL", Nouméa, Nouvelle-Calédonie, France
- ENTROPIE IRD - Université de La Réunion - CNRS, Nouméa, 98848, Nouvelle-Calédonie, France
| | - Jeremie Vidal-Dupiol
- Laboratoire d'Excellence "CORAIL", Nouméa, Nouvelle-Calédonie, France
- IFREMER, UMR 241 EIO, BP 7004, 98719, Taravao, Tahiti, French Polynesia
- IHPE, Université Montpellier, CNRS, IFREMER, Université Perpignan Via Domitia, F-34095, Montpellier, France
| | - Shaun S Killen
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, Glasgow, G12 8QQ, United Kingdom
| | - Suzanne C Mills
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Moorea, French Polynesia
- Laboratoire d'Excellence "CORAIL", Nouméa, Nouvelle-Calédonie, France
| |
Collapse
|
12
|
Brandt M, Hiernaux P, Rasmussen K, Tucker CJ, Wigneron JP, Diouf AA, Herrmann SM, Zhang W, Kergoat L, Mbow C, Abel C, Auda Y, Fensholt R. Changes in rainfall distribution promote woody foliage production in the Sahel. Commun Biol 2019; 2:133. [PMID: 31044158 PMCID: PMC6478729 DOI: 10.1038/s42003-019-0383-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/13/2019] [Indexed: 11/09/2022] Open
Abstract
Dryland ecosystems comprise a balance between woody and herbaceous vegetation. Climate change impacts rainfall timing, which may alter the respective contributions of woody and herbaceous plants on the total vegetation production. Here, we apply 30 years of field-measured woody foliage and herbaceous mass from Senegal and document a faster increase in woody foliage mass (+17 kg ha-1 yr-1) as compared to herbaceous mass (+3 kg ha-1 yr-1). Annual rainfall trends were partitioned into core wet-season rains (+0.7 mm yr-1), supporting a weak but periodic (5-year cycles) increase in herbaceous mass, and early/late rains (+2.1 mm yr-1), explaining the strongly increased woody foliage mass. Satellite observations confirm these findings for the majority of the Sahel, with total herbaceous/woody foliage mass increases by 6%/20%. We conclude that the rainfall recovery in the Sahel does not benefit herbaceous vegetation to the same extent as woody vegetation, presumably favoured by increased early/late rains.
Collapse
Affiliation(s)
- Martin Brandt
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Pierre Hiernaux
- Pastoralisme Conseil, 30 chemin de Jouanal, 82160 Caylus, France
| | - Kjeld Rasmussen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Compton J. Tucker
- NASA Goddard Space Flight Center, Mail Code 610.9, Greenbelt, MD 20771 USA
| | | | | | - Stefanie M. Herrmann
- Agricultural and Biosystems Engineering, The University of Arizona, 1177 E. 4th Street, Tucson, AZ 85721 USA
| | - Wenmin Zhang
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Laurent Kergoat
- Geosciences Environnement Toulouse (GET), Observatoire Midi-Pyrénées, UMR 5563 (CNRS/UPS/IRD/CNES), 14 Avenue Edouard Belin, 31400 Toulouse, France
| | - Cheikh Mbow
- START International Inc., 2000 Florida Ave NW, Washington, DC 20009 USA
| | - Christin Abel
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Yves Auda
- Geosciences Environnement Toulouse (GET), Observatoire Midi-Pyrénées, UMR 5563 (CNRS/UPS/IRD/CNES), 14 Avenue Edouard Belin, 31400 Toulouse, France
| | - Rasmus Fensholt
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| |
Collapse
|