Wide-Range High-Resolution Transmission Electron Microscopy Reveals Morphological and Distributional Changes of Endomembrane Compartments during Log to Stationary Transition of Growth Phase in Tobacco BY-2 Cells

Toyooka, Kiminori; Sato, Mayuko; Kutsuna, Natsumaro; Higaki, Takumi; Sawaki, Fumie; Wakazaki, Mayumi; Goto, Yumi; Hasezawa, Seiichiro; Nagata, Noriko; Matsuoka, Ken

doi:10.1093/pcp/pcu084

Cited by 27 publications

(20 citation statements)

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“…Cells were prefixed with 2.5% (w/v) glutaraldehyde for 2 h. The specimens were frozen in a high-pressure freezing apparatus (EM-PACT2, Leica) 50 . The frozen samples were substituted with 2% OsO 4 in acetone for 3–4 days at - 80°C, and the samples were warmed gradually to room temperature, rinsed with acetone embedded in epoxy resin (TAAB) Thin sections (70 nm) were cut with a ultramicrotome (EM-UC7, Leica).…”

Section: Methodsmentioning

confidence: 99%

Isolation of an archaeon at the prokaryote-eukaryote interface

Imachi

Nobu

Nakahara

et al. 2019

Preprint

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34The origin of eukaryotes remains enigmatic. Current data suggests that eukaryotes may 35 have risen from an archaeal lineage known as "Asgard archaea". Despite the eukaryote-36 like genomic features found in these archaea, the evolutionary transition from archaea to 37 eukaryotes remains unclear due to the lack of cultured representatives and corresponding 38 physiological insight. Here we report the decade-long isolation of a Lokiarchaeota-related 39Asgard archaeon from deep marine sediment. The archaeon, "Candidatus 40Prometheoarchaeum syntrophicum strain MK-D1", is an anaerobic, extremely slow-41 growing, small cocci (~550 nm), that degrades amino acids through syntrophy. Although 42 eukaryote-like intracellular complexities have been proposed for Asgard archaea, the 43 isolate has no visible organella-like structure. Ca. P. syntrophicum instead displays 44 morphological complexity -unique long, and often, branching protrusions. Based on 45 cultivation and genomics, we propose an "Entangle-Engulf-Enslave (E 3 ) model" for 46 eukaryogenesis through archaea-alphaproteobacteria symbiosis mediated by the physical 47 complexities and metabolic dependency of the hosting archaeon. 48 49 How did the first eukaryotic cell emerge? So far, among various competing evolutionary 50 models, the most widely accepted are the symbiogenetic models in which an archaeal 51 host cell and an alphaproteobacterial endosymbiont merged to become the first eukaryotic 52 cell 1-4 . Recent metagenomic discovery of Lokiarchaeota (and the Asgard archaea 53 superphylum) led to the theory that eukaryotes originated from an archaeon closely 54 related to Asgard archaea 5,6 . The Asgard archaea genomes encode a repertory of proteins 55 hitherto only found in Eukarya (eukaryotic signature proteins -ESPs), including those 56 involved in membrane trafficking, vesicle formation/transportation, ubiquitin and 57 cytoskeleton formation 6 . Subsequent metagenomic studies have suggested that Asgard 58 archaea have a wide variety of physiological properties, including hydrogen-dependent 59 anaerobic autotrophy 7 , peptide or short-chain hydrocarbon-dependent organotrophy 8-11 60 and rhodopsin-based phototrophy 12,13 . A recent study suggests that an ancient Asgard 61 archaea degraded organic substances and syntrophically handed off reducing equivalents 62 (e.g., hydrogen and electrons) to a bacterial partner, and further proposes a symbiogenetic 63 model for the origin of eukaryotes based on this interaction 14 . However, at present, no 64 single representative of the Asgard archaea has been cultivated and, thus, the physiology 65 and cell biology of this clade remains unclear. In an effort to close this knowledge gap, 66 3 we successfully isolated the first Asgard archaeon and here report the physiological 67 characteristics, potentially key insights into the evolution of eukaryotes. 68 69 Isolation of an Asgard archaeon 70Setting out to isolate uncultivated deep marine sediment microorganisms, we engineered 71 and operated a methane-fed continuous-fl...

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Section: Methodsmentioning

confidence: 99%

Isolation of an archaeon at the prokaryote-eukaryote interface

Imachi

Nobu

Nakahara

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…Cells were prefixed with 2.5% (w/v) glutaraldehyde for 2 h. The specimens were frozen in a high-pressure freezing apparatus (EM-PACT2, Leica) 59 . The frozen samples were substituted with 2% OsO 4 in acetone for 3-4 days at −80 °C, and the samples were warmed gradually to room temperature, rinsed with acetone embedded in epoxy resin (TAAB).…”

Section: Ultrathin Sectioning and Temmentioning

confidence: 99%

Isolation of an archaeon at the prokaryote–eukaryote interface

Imachi

Nobu

Nakahara

et al. 2020

Nature

534

493

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Setting out to isolate uncultivated deep marine sediment microorganisms, we engineered and operated a methane-fed continuous-flow bioreactor system for more than 2,000 days to enrich such organisms from anaerobic marine methane-seep sediments 15 (Supplementary Note 1). We successfully enriched many phylogenetically diverse yetto-be cultured microorganisms, including Asgard archaea members (Loki-, Heimdall-and Odinarchaeota) 15. For further enrichment and isolation, samples of the bioreactor community were inoculated in glass tubes with simple substrates and basal medium. After approximately one year, we found faint cell turbidity in a culture containing casamino acids supplemented with four bacteria-suppressing antibiotics (Supplementary Note 2) that was incubated at 20 °C. Clone librarybased small subunit (SSU) rRNA gene analysis revealed a simple community that contained Halodesulfovibrio and a small population of Lokiarchaeota (Extended Data Table 1). In pursuit of this archaeon, which we designated strain MK-D1, we repeated subcultures when MK-D1 reached maximum cell densities as measured by quantitative PCR (qPCR). This approach gradually enriched the archaeon, which has an extremely slow growth rate and low cell yield (Fig. 1a). The culture consistently had a 30-60-day lag phase and required more

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“…In this study, we demonstrate the onset of SCW production is accompanied by significant proliferation in the number of Golgi stacks. Increase in the abundance of Golgi stacks also occurs during the onset of mucilage production in Arabidopsis seed epidermal cells (Young et al, 2008) and during mitosis (Garcia-Herdugo et al, 1988;Seguí-Simarro and Staehelin, 2006;Toyooka et al, 2014). The prevailing model for Golgi biogenesis in plants proposes Golgi stacks increase in diameter before cisternal fission, creating two new stacks with the same number of cisterna as the 'parent' Golgi (Ito et al, 2014).…”

Section: Multitasking Of the Golgi Apparatus During Scw Synthesismentioning

confidence: 99%

“…The Golgi apparatus is a central component of the endomembrane system involved in protein processing and trafficking in addition to synthesis of cell wall polysaccharides like xylan. During primary cell wall (PCW) production, increased demand for Golgi products is met, in part, by a proliferation in the number of Golgi stacks making up the Golgi apparatus (Garcia-Herdugo et al, 1988;Seguí-Simarro and Staehelin, 2006;Young et al, 2008;Toyooka et al, 2014). Whether the onset of xylan synthesis during SCW development results in similar increases in Golgi number is unknown.…”

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confidence: 99%

“…In the context of xylan biosynthesis, cisternal maturation implies xylan moves through the Golgi with the maturation of the cisternae, whereas the xylan biosynthetic enzymes are actively recycled to previous cisternae to maintain their position in the Golgi. Because all reports of xylan biosynthetic proteins demonstrate strict Golgi localization, these proteins must also be sequestered from the xylan product no later than the trans most cisternae, where this final flattened cisterna matures into TGN/secretory vesicle clusters (Kang et al, 2011;Toyooka et al, 2014), although the mechanism by which this occurs has not been resolved. In addition to the cis-trans polarity of Golgi stacks, each cisterna also varies in structure and composition between the flat center of the cisternae and their swollen outer margins with associated vesicles and fenestrations (Mogelsvang et al, 2003;Mogelsvang et al, 2004;Koga and Ushiki, 2006;Kang and Staehelin, 2008;Kang et al, 2011;Donohoe et al, 2013).…”

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confidence: 99%

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Organization of Xylan Production in the Golgi During Secondary Cell Wall Biosynthesis

et al. 2019

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Secondary cell wall (SCW) production during xylem development requires massive up-regulation of hemicellulose (e.g. glucuronoxylan) biosynthesis in the Golgi. Although mutant studies have revealed much of the xylan biosynthetic machinery, the precise arrangement of these proteins and their products in the Golgi apparatus is largely unknown. We used a fluorescently tagged xylan backbone biosynthetic protein (IRREGULAR XYLEM9; IRX9) as a marker of xylan production in the Golgi of developing protoxylem tracheary elements in Arabidopsis (Arabidopsis thaliana). Both live-cell confocal and transmission electron microscopy (TEM) revealed SCW deposition is accompanied by a significant proliferation of Golgi stacks. Furthermore, although Golgi stacks were randomly distributed, the organization of the cytoplasm ensured their close proximity to developing SCWs. Quantitative immuno-TEM revealed IRX9 is present in a specific subdomain of the Golgi stack and was most abundant in the ring of the inner margins of medial cisternae where fenestrations are abundant. Conversely, the xylan product accumulated in swollen trans cisternal margins and the Trans-Golgi network (TGN). The irx9 mutant lacked this expansion for both the cisternal margins and the TGN, whereas Golgi stack proliferation was unaffected. Golgi in irx9 also displayed dramatic changes in their structure, with increases in cisternal fenestration and tubulation. Our data support a new model where xylan biosynthesis and packaging into secretory vesicles are localized in distinct structural and functional domains of the Golgi. Rather than polysaccharide biosynthesis occurring in the center of the cisternae, IRX9 and the xylan product are arranged in successive concentric rings in Golgi cisternae. 1 This work was supported by the Gouvernement of Canada j Natural Sciences and Engineering Research Council of Canada (Conseil de recherches en sciences naturelles et en génie du Canada) (discovery grants to S.D.M. and A.L.S.); Canada postgraduate scholarships (to M.J.M.); and the Faculty of Graduate Studies, University of British Columbia (four-year fellowship to M.J.M.

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Wide-Range High-Resolution Transmission Electron Microscopy Reveals Morphological and Distributional Changes of Endomembrane Compartments during Log to Stationary Transition of Growth Phase in Tobacco BY-2 Cells

Cited by 27 publications

References 48 publications

Isolation of an archaeon at the prokaryote-eukaryote interface

Isolation of an archaeon at the prokaryote-eukaryote interface

Isolation of an archaeon at the prokaryote–eukaryote interface

Organization of Xylan Production in the Golgi During Secondary Cell Wall Biosynthesis

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