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Peng D, Jackson D, Palicha B, Kernfeld E, Laughner N, Shoemaker A, Celniker SE, Loganathan R, Cahan P, Andrew DJ. Organogenetic transcriptomes of the Drosophila embryo at single cell resolution. Development 2024; 151:dev202097. [PMID: 38174902 PMCID: PMC10820837 DOI: 10.1242/dev.202097] [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: 06/16/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
To gain insight into the transcription programs activated during the formation of Drosophila larval structures, we carried out single cell RNA sequencing during two periods of Drosophila embryogenesis: stages 10-12, when most organs are first specified and initiate morphological and physiological specialization; and stages 13-16, when organs achieve their final mature architectures and begin to function. Our data confirm previous findings with regards to functional specialization of some organs - the salivary gland and trachea - and clarify the embryonic functions of another - the plasmatocytes. We also identify two early developmental trajectories in germ cells and uncover a potential role for proteolysis during germline stem cell specialization. We identify the likely cell type of origin for key components of the Drosophila matrisome and several commonly used Drosophila embryonic cell culture lines. Finally, we compare our findings with other recent related studies and with other modalities for identifying tissue-specific gene expression patterns. These data provide a useful community resource for identifying many new players in tissue-specific morphogenesis and functional specialization of developing organs.
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Affiliation(s)
- Da Peng
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dorian Jackson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bianca Palicha
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Kernfeld
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathaniel Laughner
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ashleigh Shoemaker
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rajprasad Loganathan
- Department of Biological Sciences, Wichita State University, Wichita, KS 67260, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Deborah J. Andrew
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Loganathan R, Levings DC, Kim JH, Wells MB, Chiu H, Wu Y, Slattery M, Andrew DJ. Ribbon boosts ribosomal protein gene expression to coordinate organ form and function. J Cell Biol 2022; 221:213030. [PMID: 35195669 PMCID: PMC9237840 DOI: 10.1083/jcb.202110073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/19/2021] [Accepted: 01/24/2022] [Indexed: 11/22/2022] Open
Abstract
Cell growth is well defined for late (postembryonic) stages of development, but evidence for early (embryonic) cell growth during postmitotic morphogenesis is limited. Here, we report early cell growth as a key characteristic of tubulogenesis in the Drosophila embryonic salivary gland (SG) and trachea. A BTB/POZ domain nuclear factor, Ribbon (Rib), mediates this early cell growth. Rib binds the transcription start site of nearly every SG-expressed ribosomal protein gene (RPG) and is required for full expression of all RPGs tested. Rib binding to RPG promoters in vitro is weak and not sequence specific, suggesting that specificity is achieved through cofactor interactions. Accordingly, we demonstrate Rib’s ability to physically interact with each of the three known regulators of RPG transcription. Surprisingly, Rib-dependent early cell growth in another tubular organ, the embryonic trachea, is not mediated by direct RPG transcription. These findings support a model of early cell growth customized by transcriptional regulatory networks to coordinate organ form and function.
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Affiliation(s)
| | - Daniel C Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN
| | - Ji Hoon Kim
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Michael B Wells
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Hannah Chiu
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Yifan Wu
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN
| | - Deborah J Andrew
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
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4
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Acquistapace IM, Zi Etek MA, Li AWH, Salmon M, Kühn I, Bedford MR, Brearley CA, Hemmings AM. Snapshots during the catalytic cycle of a histidine acid phytase reveal an induced-fit structural mechanism. J Biol Chem 2020; 295:17724-17737. [PMID: 33454010 PMCID: PMC7762957 DOI: 10.1074/jbc.ra120.015925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/10/2020] [Indexed: 11/16/2022] Open
Abstract
Highly engineered phytases, which sequentially hydrolyze the hexakisphosphate ester of inositol known as phytic acid, are routinely added to the feeds of monogastric animals to improve phosphate bioavailability. New phytases are sought as starting points to further optimize the rate and extent of dephosphorylation of phytate in the animal digestive tract. Multiple inositol polyphosphate phosphatases (MINPPs) are clade 2 histidine phosphatases (HP2P) able to carry out the stepwise hydrolysis of phytate. MINPPs are not restricted by a strong positional specificity making them attractive targets for development as feed enzymes. Here, we describe the characterization of a MINPP from the Gram-positive bacterium Bifidobacterium longum (BlMINPP). BlMINPP has a typical HP2P-fold but, unusually, possesses a large α-domain polypeptide insertion relative to other MINPPs. This insertion, termed the U-loop, spans the active site and contributes to substrate specificity pockets underpopulated in other HP2Ps. Mutagenesis of U-loop residues reveals its contribution to enzyme kinetics and thermostability. Moreover, four crystal structures of the protein along the catalytic cycle capture, for the first time in an HP2P, a large ligand-driven α-domain motion essential to allow substrate access to the active site. This motion recruits residues both downstream of a molecular hinge and on the U-loop to participate in specificity subsites, and mutagenesis identified a mobile lysine residue as a key determinant of positional specificity of the enzyme. Taken together, these data provide important new insights to the factors determining stability, substrate recognition, and the structural mechanism of hydrolysis in this industrially important group of enzymes.
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Affiliation(s)
| | - Monika A Zi Etek
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Arthur W H Li
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Melissa Salmon
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | | | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Andrew M Hemmings
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom; School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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5
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Ucuncu E, Rajamani K, Wilson MSC, Medina-Cano D, Altin N, David P, Barcia G, Lefort N, Banal C, Vasilache-Dangles MT, Pitelet G, Lorino E, Rabasse N, Bieth E, Zaki MS, Topcu M, Sonmez FM, Musaev D, Stanley V, Bole-Feysot C, Nitschké P, Munnich A, Bahi-Buisson N, Fossoud C, Giuliano F, Colleaux L, Burglen L, Gleeson JG, Boddaert N, Saiardi A, Cantagrel V. MINPP1 prevents intracellular accumulation of the chelator inositol hexakisphosphate and is mutated in Pontocerebellar Hypoplasia. Nat Commun 2020; 11:6087. [PMID: 33257696 PMCID: PMC7705663 DOI: 10.1038/s41467-020-19919-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Inositol polyphosphates are vital metabolic and secondary messengers, involved in diverse cellular functions. Therefore, tight regulation of inositol polyphosphate metabolism is essential for proper cell physiology. Here, we describe an early-onset neurodegenerative syndrome caused by loss-of-function mutations in the multiple inositol-polyphosphate phosphatase 1 gene (MINPP1). Patients are found to have a distinct type of Pontocerebellar Hypoplasia with typical basal ganglia involvement on neuroimaging. We find that patient-derived and genome edited MINPP1−/− induced stem cells exhibit an inefficient neuronal differentiation combined with an increased cell death. MINPP1 deficiency results in an intracellular imbalance of the inositol polyphosphate metabolism. This metabolic defect is characterized by an accumulation of highly phosphorylated inositols, mostly inositol hexakisphosphate (IP6), detected in HEK293 cells, fibroblasts, iPSCs and differentiating neurons lacking MINPP1. In mutant cells, higher IP6 level is expected to be associated with an increased chelation of intracellular cations, such as iron or calcium, resulting in decreased levels of available ions. These data suggest the involvement of IP6-mediated chelation on Pontocerebellar Hypoplasia disease pathology and thereby highlight the critical role of MINPP1 in the regulation of human brain development and homeostasis. Tight regulation of inositol polyphosphate metabolism is essential for proper cell physiology. Here, the authors describe an early-onset neurodegenerative syndrome caused by loss-of-function mutations in the MINPP1 gene, characterised by intracellular imbalance of inositol polyphosphate metabolism.
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Affiliation(s)
- Ekin Ucuncu
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Karthyayani Rajamani
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Miranda S C Wilson
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BT, London, UK
| | - Daniel Medina-Cano
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Nami Altin
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Pierre David
- Transgenesis Platform, Laboratoire d'Expérimentation Animale et Transgenèse (LEAT), Imagine Institute, Structure Fédérative de Recherche Necker INSERM US24/CNRS UMS3633, 75015, Paris, France
| | - Giulia Barcia
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.,Département de Génétique Médicale, AP-HP, Hôpital Necker-Enfants Malades, F-75015, Paris, France
| | - Nathalie Lefort
- Université de Paris, iPSC Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Céline Banal
- Université de Paris, iPSC Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | | | - Gaële Pitelet
- Service de Neuropédiatrie, CHU Nice, 06200, Nice, France
| | - Elsa Lorino
- ESEAN, 44200 Nantes, Service de maladies chroniques de l'enfant, CHU Nantes, 44093, Nantes, France
| | - Nathalie Rabasse
- Service de pédiatrie, hôpital d'Antibes-Juan-les-Pins, 06600, Antibes-Juan-les-Pins, France
| | - Eric Bieth
- Service de Génétique Médicale, CHU Toulouse, 31059, Toulouse, France
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Meral Topcu
- Department of Child Neurology, Faculty of Medicine, Hacettepe University, Ankara, 06100, Turkey
| | - Fatma Mujgan Sonmez
- Guven Hospital, Child Neurology Department, Ankara, Turkey.,Department of Child Neurology, Faculty of Medicine, Karadeniz Technical University, Trabzon, 61080, Turkey
| | - Damir Musaev
- Laboratory for Pediatric Brain Diseases, Rady Children's Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Diseases, Rady Children's Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christine Bole-Feysot
- Université de Paris, Genomics Platform, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Patrick Nitschké
- Université de Paris, Bioinformatics Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Arnold Munnich
- Université de Paris, Translational Genetics Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Nadia Bahi-Buisson
- Université de Paris, Genetics and Development of the Cerebral Cortex Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Catherine Fossoud
- Centre de Référence des Troubles des Apprentissages, Hôpitaux Pédiatriques de Nice CHU-Lenval, 06200, Nice, France
| | - Fabienne Giuliano
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nice, 06202, Nice, France
| | - Laurence Colleaux
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Lydie Burglen
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.,Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Département de Génétique, AP-HP, Sorbonne Université, Hôpital Trousseau, 75012, Paris, France
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Diseases, Rady Children's Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nathalie Boddaert
- Département de radiologie pédiatrique, INSERM UMR 1163 and INSERM U1000, AP-HP, Hôpital Necker-Enfants Malades, F-75015, Paris, France
| | - Adolfo Saiardi
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BT, London, UK.
| | - Vincent Cantagrel
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.
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