1
|
Neale DB, Zimin AV, Zaman S, Scott AD, Shrestha B, Workman RE, Puiu D, Allen BJ, Moore ZJ, Sekhwal MK, De La Torre AR, McGuire PE, Burns E, Timp W, Wegrzyn JL, Salzberg SL. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3 (BETHESDA, MD.) 2022; 12:6460957. [PMID: 35100403 PMCID: PMC8728005 DOI: 10.1093/g3journal/jkab380] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.
Collapse
Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Alison D Scott
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Bikash Shrestha
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Rachael E Workman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Zane J Moore
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Emily Burns
- Save the Redwoods League, San Francisco, CA 94104, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| |
Collapse
|
2
|
Ibl V. ESCRTing in cereals: still a long way to go. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1144-1152. [PMID: 31327097 DOI: 10.1007/s11427-019-9572-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/28/2019] [Indexed: 01/28/2023]
Abstract
The multivesicular body (MVB) sorting pathway provides a mechanism for the delivery of cargo destined for degradation to the vacuole or lysosome. The endosomal sorting complex required for transport (ESCRT) is essential for the MVB sorting pathway by driving the cargo sorting to its destination. Many efforts in plant research have identified the ESCRT machinery and functionally characterised the first plant ESCRT proteins. However, most studies have been performed in the model plant Arabidopsis thaliana that is genetically and physiologically different to crops. Cereal crops are important for animal feed and human nutrition and have further been utilized as promising candidates for recombinant protein production. In this review, I summarize the role of plant ESCRT components in cereals that are involved in efficient adaptation to environmental stress and grain development. A special focus is on barley (Hordeum vulgare L.) ESCRT proteins, where recent studies show their quantitative mapping during grain development, e.g. associating HvSNF7.1 with protein trafficking to protein bodies (PBs) in starchy endosperm. Thus, it is indispensable to identify the molecular key-players within the endomembrane system including ESCRT proteins to optimize and possibly enhance tolerance to environmental stress, grain yield and recombinant protein production in cereal grains.
Collapse
Affiliation(s)
- Verena Ibl
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090, Vienna, Austria.
| |
Collapse
|
3
|
Horner DS, Pasini ME, Beltrame M, Mastrodonato V, Morelli E, Vaccari T. ESCRT genes and regulation of developmental signaling. Semin Cell Dev Biol 2017; 74:29-39. [PMID: 28847745 DOI: 10.1016/j.semcdb.2017.08.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/06/2017] [Accepted: 08/18/2017] [Indexed: 11/30/2022]
Abstract
ESCRT (Endosomal Sorting Complex Required for Transport) proteins have been shown to control an increasing number of membrane-associated processes. Some of these, and prominently regulation of receptor trafficking, profoundly shape signal transduction. Evidence in fungi, plants and multiple animal models support the emerging concept that ESCRTs are main actors in coordination of signaling with the changes in cells and tissues occurring during development and homeostasis. Consistent with their pleiotropic function, ESCRTs are regulated in multiple ways to tailor signaling to developmental and homeostatic needs. ESCRT activity is crucial to correct execution of developmental programs, especially at key transitions, allowing eukaryotes to thrive and preventing appearance of congenital defects.
Collapse
Affiliation(s)
- David S Horner
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Maria E Pasini
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Monica Beltrame
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Valeria Mastrodonato
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Elena Morelli
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Thomas Vaccari
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy.
| |
Collapse
|
4
|
Hilscher J, Kapusi E, Stoger E, Ibl V. Cell layer-specific distribution of transiently expressed barley ESCRT-III component HvVPS60 in developing barley endosperm. PROTOPLASMA 2016; 253:137-53. [PMID: 25796522 PMCID: PMC4712231 DOI: 10.1007/s00709-015-0798-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/09/2015] [Indexed: 05/29/2023]
Abstract
The significance of the endosomal sorting complexes required for transport (ESCRT)-III in cereal endosperm has been shown by the identification of the recessive mutant supernumerary aleurone layer1 (SAL1) in maize. ESCRT-III is indispensable in the final membrane fission step during biogenesis of multivesicular bodies (MVBs), responsible for protein sorting to vacuoles and to the cell surface. Here, we annotated barley ESCRT-III members in the (model) crop Hordeum vulgare and show that all identified members are expressed in developing barley endosperm. We used fluorescently tagged core ESCRT-III members HvSNF7a/CHMP4 and HvVPS24/CHMP3 and the associated ESCRT-III component HvVPS60a/CHMP5 for transient localization studies in barley endosperm. In vivo confocal microscopic analyses show that the localization of recombinantly expressed HvSNF7a, HvVPS24 and HvVPS60a differs within barley endosperm. Whereas HvSNF7a induces large agglomerations, HvVPS24 shows mainly cytosolic localization in aleurone and subaleurone. In contrast, HvVPS60a localizes strongly at the plasma membrane in aleurone. In subaleurone, HvVPS60a was found to a lesser extent at the plasma membrane and at vacuolar membranes. These results indicate that the steady-state association of ESCRT-III may be influenced by cell layer-specific protein deposition or trafficking and remodelling of the endomembrane system in endosperm. We show that sorting of an artificially mono-ubiquitinated Arabidopsis plasma membrane protein is inhibited by HvVPS60a in aleurone. The involvement of HvVPS60a in different cell layer-specific trafficking pathways, reflected by localization of HvVPS60a at the plasma membrane in aleurone and at the PSV membrane in subaleurone, is discussed.
Collapse
Affiliation(s)
- Julia Hilscher
- Department of Applied Genetics and Cell Biology, Division of Molecular Cell Biology and Glycobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Eszter Kapusi
- Department of Applied Genetics and Cell Biology, Division of Molecular Cell Biology and Glycobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, Division of Molecular Cell Biology and Glycobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Verena Ibl
- Department of Applied Genetics and Cell Biology, Division of Molecular Cell Biology and Glycobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| |
Collapse
|
5
|
Bhutta MS, McInerny CJ, Gould GW. ESCRT function in cytokinesis: location, dynamics and regulation by mitotic kinases. Int J Mol Sci 2014; 15:21723-39. [PMID: 25429432 PMCID: PMC4284674 DOI: 10.3390/ijms151221723] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 11/17/2014] [Accepted: 11/17/2014] [Indexed: 01/22/2023] Open
Abstract
Mammalian cytokinesis proceeds by constriction of an actomyosin ring and furrow ingression, resulting in the formation of the midbody bridge connecting two daughter cells. At the centre of the midbody resides the Flemming body, a dense proteinaceous ring surrounding the interlocking ends of anti-parallel microtubule arrays. Abscission, the terminal step of cytokinesis, occurs near the Flemming body. A series of broad processes govern abscission: the initiation and stabilisation of the abscission zone, followed by microtubule severing and membrane scission-The latter mediated by the endosomal sorting complex required for transport (ESCRT) proteins. A key goal of cell and developmental biologists is to develop a clear understanding of the mechanisms that underpin abscission, and how the spatiotemporal coordination of these events with previous stages in cell division is accomplished. This article will focus on the function and dynamics of the ESCRT proteins in abscission and will review recent work, which has begun to explore how these complex protein assemblies are regulated by the cell cycle machinery.
Collapse
Affiliation(s)
- Musab S Bhutta
- Henry Wellcome Laboratory of Cell Biology, Davidson Building, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Christopher J McInerny
- Henry Wellcome Laboratory of Cell Biology, Davidson Building, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Gwyn W Gould
- Henry Wellcome Laboratory of Cell Biology, Davidson Building, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| |
Collapse
|
7
|
Spallek T, Beck M, Ben Khaled S, Salomon S, Bourdais G, Schellmann S, Robatzek S. ESCRT-I mediates FLS2 endosomal sorting and plant immunity. PLoS Genet 2013; 9:e1004035. [PMID: 24385929 PMCID: PMC3873229 DOI: 10.1371/journal.pgen.1004035] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 11/01/2013] [Indexed: 11/19/2022] Open
Abstract
The plant immune receptor FLAGELLIN SENSING 2 (FLS2) is present at the plasma membrane and is internalized following activation of its ligand flagellin (flg22). We show that ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT (ESCRT)-I subunits play roles in FLS2 endocytosis in Arabidopsis. VPS37-1 co-localizes with FLS2 at endosomes and immunoprecipitates with the receptor upon flg22 elicitation. Vps37-1 mutants are reduced in flg22-induced FLS2 endosomes but not in endosomes labeled by Rab5 GTPases suggesting a defect in FLS2 trafficking rather than formation of endosomes. FLS2 localizes to the lumen of multivesicular bodies, but this is altered in vps37-1 mutants indicating compromised endosomal sorting of FLS2 by ESCRT-I loss-of-function. VPS37-1 and VPS28-2 are critical for immunity against bacterial infection through a role in stomatal closure. Our findings identify that VPS37-1, and likewise VPS28-2, regulate late FLS2 endosomal sorting and reveals that ESCRT-I is critical for flg22-activated stomatal defenses involved in plant immunity. Plants deploy plasma membrane immune receptors to survey their environment for potential threats. One of these receptors, FLAGELIN SENSING 2 (FLS2) recognizes bacterial flagellin (flg22) and thereby triggers a multitude of defense responses, enhancing immunity against infectious pathogens. Regulation of the subcellular localization of FLS2 is therefore an important aspect in plant disease resistance. FLS2 is known to shuttle between the plasma membrane and endosomal compartments but enters the late endosomal trafficking pathway upon ligand-dependent activation. A key question is the regulation of activated FLS2 in late endosomal trafficking. Here, we show that FLS2 is internalized into the lumen of multivesicular bodies and discovered by genetic inhibition that this step is regulated by components of the ENDOSOMAL SORTING COMPLEXES REQUIRED FOR TRANSPORT-I (ESCRT-I). Furthermore, we reveal that these ESCRT-I components play crucial roles in plant immunity impacting the flg22-triggered closure of stomata, prominent entry points of pathogenic bacteria, which occurred downstream of the known flg22 responses. These findings highlight the roles of endosomal trafficking in regulating FLS2 subcellular localization and plant immunity.
Collapse
Affiliation(s)
- Thomas Spallek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Martina Beck
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sara Ben Khaled
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Susanne Salomon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Gildas Bourdais
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | | | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail:
| |
Collapse
|