start-ver=1.4
cd-journal=joma
no-vol=
cd-vols=
no-issue=
article-no=
start-page=117
end-page=33
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200818
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical for providing force and structure in many processes, including membrane remodeling. In general, Asgard genomes encode two classes of actin-regulating proteins from sequence analysis, profilins and gelsolins. Asgard profilins were demonstrated to regulate actin filament nucleation. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryotic-like actin depolymerization cycle, and indicate complex actin cytoskeleton regulation in Asgard organisms. Thor gelsolins have homologs in other Asgard archaea and comprise one or two copies of the prototypical gelsolin domain. This appears to be a record of an initial preeukaryotic gene duplication event, since eukaryotic gelsolins are generally comprise three to six domains. X-ray structures of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin or cofilin with actin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for a calcium-controlled Asgard actin cytoskeleton, indicating that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled actin filaments are responsible for shaping filopodia and microvilli. By correlation, we hypothesize that the formation of the protrusions observed from Lokiarchaeota cell bodies may involve the gelsolin-regulated actin structures.
en-copyright=
kn-copyright=

en-aut-name=Ak?lCaner
en-aut-sei=Ak?l
en-aut-mei=Caner
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=TranLinh T.
en-aut-sei=Tran
en-aut-mei=Linh T.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=Orhant-PriouxMagali
en-aut-sei=Orhant-Prioux
en-aut-mei=Magali
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=BaskaranYohendran
en-aut-sei=Baskaran
en-aut-mei=Yohendran
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=ManserEdward
en-aut-sei=Manser
en-aut-mei=Edward
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=BlanchoinLaurent
en-aut-sei=Blanchoin
en-aut-mei=Laurent
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=RobinsonRobert C.
en-aut-sei=Robinson
en-aut-mei=Robert C.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

affil-num=1
en-affil=Institute of Molecular and Cell Biology, Agency for Science, Technology and Research
kn-affil=

affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=3
en-affil=CytomorphoLab, Interdisciplinary Research Institute of Grenoble
kn-affil=

affil-num=4
en-affil=aInstitute of Molecular and Cell Biology, Agency for Science, Technology and Research
kn-affil=

affil-num=5
en-affil=aInstitute of Molecular and Cell Biology, Agency for Science, Technology and Research
kn-affil=

affil-num=6
en-affil=CytomorphoLab, Interdisciplinary Research Institute of Grenoble
kn-affil=

affil-num=7
en-affil=cResearch Institute for Interdisciplinary Science, Okayama University
kn-affil=
en-keyword=actin
kn-keyword=actin
en-keyword=gelsolin
kn-keyword=gelsolin
en-keyword=Asgard archaea
kn-keyword=Asgard archaea
en-keyword=eukaryogenesis
kn-keyword=eukaryogenesis
en-keyword=X-ray crystallography
kn-keyword=X-ray crystallography
END

start-ver=1.4
cd-journal=joma
no-vol=112
cd-vols=
no-issue=27
article-no=
start-page=8221
end-page=8226
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150707
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Solid-liquid critical behavior of water in nanopores
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Nanoconfined liquid water can transform into low-dimensional ices whose crystalline structures are dissimilar to any bulk ices and whose melting point may significantly rise with reducing the pore size, as revealed by computer simulation and confirmed by experiment. One of the intriguing, and as yet unresolved, questions concerns the observation that the liquid water may transform into a low-dimensional ice either via a first-order phase change or without any discontinuity in thermodynamic and dynamic properties, which suggests the existence of solid?liquid critical points in this class of
nanoconfined systems. Here we explore the phase behavior of a model of water in carbon nanotubes in the temperature?pressure?diameter space by molecular dynamics simulation and provide unambiguous evidence to support solid?liquid critical phenomena of nanoconfined water. Solid?liquid first-order phase boundaries are
determined by tracing spontaneous phase separation at various temperatures. All of the boundaries eventually cease to exist at the critical points and there appear loci of response function maxima, or the Widom lines, extending to the supercritical region. The finite-size scaling analysis of the density distribution supports the
presence of both first-order and continuous phase changes between solid and liquid. At around the Widom line, there are microscopic domains of two phases, and continuous solid?liquid phase changes
occur in such a way that the domains of one phase grow and those of the other evanesce as the thermodynamic state departs from the Widom line.
en-copyright=
kn-copyright=

en-aut-name=MochizukiKenji
en-aut-sei=Mochizuki
en-aut-mei=Kenji
kn-aut-name=望月建爾
kn-aut-sei=望月
kn-aut-mei=建爾
aut-affil-num=1
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=甲賀研一郎
kn-aut-sei=甲賀
kn-aut-mei=研一郎
aut-affil-num=2
ORCID=

affil-num=1
en-affil=
kn-affil=岡山大学大学院自然科学研究科

affil-num=2
en-affil=
kn-affil=岡山大学大学院自然科学研究科
en-keyword=water
kn-keyword=water
en-keyword=solid?liquid critical point
kn-keyword=solid?liquid critical point
en-keyword=carbon nanotube
kn-keyword=carbon nanotube
en-keyword=ice
kn-keyword=ice
en-keyword=Widom line
kn-keyword=Widom line
END

start-ver=1.4
cd-journal=joma
no-vol=112
cd-vols=
no-issue=39
article-no=
start-page=E5401
end-page=E5410
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150929
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Wheat varieties with a winter growth habit require long exposures to low temperatures (vernalization) to accelerate flowering. Natural variation in four vernalization genes regulating this requirement has favored wheat adaptation to different environments. The first three genes (VRN1?VRN3) have been cloned and characterized before. Here we show that the fourth gene, VRN-D4, originated by the insertion of a ?290-kb region from chromosome arm 5AL into the proximal region of chromosome arm 5DS. The inserted 5AL region includes a copy of VRN-A1 that carries distinctive mutations in its coding and regulatory regions. Three lines of evidence confirmed that this gene is VRN-D4: it cosegregated with VRN-D4 in a high-density mapping population; it was expressed earlier than other VRN1 genes in the absence of vernalization; and induced mutations in this gene resulted in delayed flowering. VRN-D4 was found in most accessions of the ancient subspecies Triticum aestivum ssp. sphaerococcum from South Asia. This subspecies showed a significant reduction of genetic diversity and increased genetic differentiation in the centromeric region of chromosome 5D, suggesting that VRN-D4 likely contributed to local adaptation and was favored by positive selection. Three adjacent SNPs in a regulatory region of the VRN-D4 first intron disrupt the binding of GLYCINE-RICH RNA-BINDING PROTEIN 2 (TaGRP2), a known repressor of VRN1 expression. The same SNPs were identified in VRN-A1 alleles previously associated with reduced vernalization requirement. These alleles can be used to modulate vernalization requirements and to develop wheat varieties better adapted to different or changing environments.
en-copyright=
kn-copyright=

en-aut-name=KippesNestor
en-aut-sei=Kippes
en-aut-mei=Nestor
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=DebernardiJuan M.
en-aut-sei=Debernardi
en-aut-mei=Juan M.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=Vasquez-GrossHans A.
en-aut-sei=Vasquez-Gross
en-aut-mei=Hans A.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=AkpinarBala A.
en-aut-sei=Akpinar
en-aut-mei=Bala A.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=BudakHikment
en-aut-sei=Budak
en-aut-mei=Hikment
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=KatoKenji
en-aut-sei=Kato
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=ChaoShiaoman
en-aut-sei=Chao
en-aut-mei=Shiaoman
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=AkhunovEduard
en-aut-sei=Akhunov
en-aut-mei=Eduard
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=DubcovskyJorge
en-aut-sei=Dubcovsky
en-aut-mei=Jorge
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

affil-num=1
en-affil=
kn-affil=Department of Plant Sciences, University of California

affil-num=2
en-affil=
kn-affil=Department of Plant Sciences, University of California

affil-num=3
en-affil=
kn-affil=Department of Plant Sciences, University of California

affil-num=4
en-affil=
kn-affil=Faculty of Engineering and Natural Sciences, Sabanci University

affil-num=5
en-affil=
kn-affil=Faculty of Engineering and Natural Sciences, Sabanci University

affil-num=6
en-affil=
kn-affil=Graduate School of Environmental and Life Science, Okayama University

affil-num=7
en-affil=
kn-affil=Biosciences Research Lab, US Department of Agriculture?Agricultural Research Service

affil-num=8
en-affil=
kn-affil=Department of Plant Pathology, Kansas State University

affil-num=9
en-affil=
kn-affil=Department of Plant Sciences, University of California
en-keyword=wheat
kn-keyword=wheat
en-keyword=flowering
kn-keyword=flowering
en-keyword=vernalization
kn-keyword=vernalization
en-keyword=VRN1
kn-keyword=VRN1
en-keyword=Triticum aestivum ssp. sphaerococcum
kn-keyword=Triticum aestivum ssp. sphaerococcum
END

start-ver=1.4
cd-journal=joma
no-vol=121
cd-vols=
no-issue=25
article-no=
start-page=e2318150121
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20240612
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Replication of single viruses across the kingdoms, Fungi, Plantae, and Animalia
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=It is extremely rare that a single virus crosses host barriers across multiple kingdoms. Based on phylogenetic and paleovirological analyses, it has previously been hypothesized that single members of the family Partitiviridae could cross multiple kingdoms. Partitiviridae accommodates members characterized by their simple bisegmented double-stranded RNA genome; asymptomatic infections of host organisms; the absence of an extracellular route for entry in nature; and collectively broad host range. Herein, we show the replicability of single fungal partitiviruses in three kingdoms of host organisms: Fungi, Plantae, and Animalia. Betapartitiviruses of the phytopathogenic fungusRosellinia necatrix could replicate in protoplasts of the carrot (Daucus carota), Nicotiana benthamiana and Nicotiana tabacum, in some cases reaching a level detectable by agarose gel electrophoresis. Moreover, betapartitiviruses showed more robust replication than the tested alphapartitiviruses. One of the fungal betapartitiviruses, RnPV18, could persistently and stably infect carrot plants regenerated from virion-transfected protoplasts. Both alpha- and betapartitiviruses, although with different host preference, could replicate in two insect cell lines derived from the fall armyworm Spodoptera frugiperda and the fruit fly Drosophila melanogaster. Our results indicate the replicability of single partitiviruses in members of three kingdoms and provide insights into virus adaptation, host jumping, and evolution.
en-copyright=
kn-copyright=

en-aut-name=TelengechPaul
en-aut-sei=Telengech
en-aut-mei=Paul
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=HyodoKiwamu
en-aut-sei=Hyodo
en-aut-mei=Kiwamu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=IchikawaHiroaki
en-aut-sei=Ichikawa
en-aut-mei=Hiroaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KuwataRyusei
en-aut-sei=Kuwata
en-aut-mei=Ryusei
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=KondoHideki
en-aut-sei=Kondo
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=SuzukiNobuhiro
en-aut-sei=Suzuki
en-aut-mei=Nobuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

affil-num=1
en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University
kn-affil=

affil-num=2
en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University
kn-affil=

affil-num=3
en-affil=Institute of Agrobiological Sciences, National Agriculture and Food Research Organization
kn-affil=

affil-num=4
en-affil=Faculty of Veterinary Medicine, Okayama University of Science
kn-affil=

affil-num=5
en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University
kn-affil=

affil-num=6
en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University
kn-affil=
en-keyword=cross- kingdom infection
kn-keyword=cross- kingdom infection
en-keyword=partitivirus
kn-keyword=partitivirus
en-keyword=fungal virus
kn-keyword=fungal virus
en-keyword=Plantae
kn-keyword=Plantae
en-keyword=Animalia
kn-keyword=Animalia
END

start-ver=1.4
cd-journal=joma
no-vol=121
cd-vols=
no-issue=25
article-no=
start-page=e2322765121
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20240612
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Argonaute-independent, Dicer-dependent antiviral defense against RNA viruses
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Antiviral RNA interference (RNAi) is conserved from yeasts to mammals. Dicer recognizes and cleaves virus-derived double-stranded RNA (dsRNA) and/or structured single-stranded RNA (ssRNA) into small-interfering RNAs, which guide effector Argonaute to homologous viral RNAs for digestion and inhibit virus replication. Thus, Argonaute is believed to be essential for antiviral RNAi. Here, we show Argonaute-independent, Dicer-dependent antiviral defense against dsRNA viruses using Cryphonectria parasitica (chestnut blight fungus), which is a model filamentous ascomycetous fungus and hosts a variety of viruses. The fungus has two dicer-like genes (dcl1 and dcl2) and four argonaute-like genes (agl1 to agl4). We prepared a suite of single to quadruple agl knockout mutants with or without dcl disruption. We tested these mutants for antiviral activities against diverse dsRNA viruses and ssRNA viruses. Although both DCL2 and AGL2 worked as antiviral players against some RNA viruses, DCL2 without argonaute was sufficient to block the replication of other RNA viruses. Overall, these results indicate the existence of a Dicer-alone defense and different degrees of susceptibility to it among RNA viruses. We discuss what determines the great difference in susceptibility to the Dicer-only defense.
en-copyright=
kn-copyright=

en-aut-name=SatoYukiyo
en-aut-sei=Sato
en-aut-mei=Yukiyo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KondoHideki
en-aut-sei=Kondo
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=SuzukiNobuhiro
en-aut-sei=Suzuki
en-aut-mei=Nobuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil=Institute of Plant Science and Resources, Okayama University
kn-affil=

affil-num=2
en-affil=Institute of Plant Science and Resources, Okayama University
kn-affil=

affil-num=3
en-affil=Institute of Plant Science and Resources, Okayama University
kn-affil=
en-keyword=RNAi
kn-keyword=RNAi
en-keyword=Argonaute
kn-keyword=Argonaute
en-keyword=Dicer
kn-keyword=Dicer
en-keyword=fungal virus
kn-keyword=fungal virus
en-keyword=chestnut blight
kn-keyword=chestnut blight
END