ライフサイエンスコーパス: archaea

1 197 complete genomes (780 eukaryotes and 417 archaea).

2 logical niche-for example, ammonia-oxidizing archaea.

3 R-Cas systems in populations of bacteria and archaea.

4 ain groups of extant viruses of bacteria and archaea.

5 ation mechanism is prevalent in bacteria and archaea.

6 house gas in methanogenic and methanotrophic archaea.

7 cycle by chemolithoautotrophic bacteria and archaea.

8 hanotrophic and short-chain alkane-oxidizing archaea.

9 much less complicated than in eukaryotes or archaea.

10 chitectural role filled by histones in other archaea.

11 this delay differs widely among bacteria and archaea.

12 transcription apparatus) that is observed in Archaea.

13 receptors are widely present in Bacteria and Archaea.

14 onments by acquiring genes from bacteria and archaea.

15 are found in a diverse range of bacteria and archaea.

16 ights into the metabolic capabilities of the Archaea.

17 (protists and animals) and trace amounts of Archaea.

18 methane oxidation observed in methanotrophic archaea.

19 oxidizing enzyme found previously in several Archaea.

20 the evolution of these traits throughout the Archaea.

21 infect hosts across the domains Bacteria and Archaea.

22 rcating Etfs found in anaerobic bacteria and archaea.

23 s the occurrence of an epigenetic process in archaea.

24 zyme complex with the orthologous enzymes in archaea.

25 s of these domains are not yet understood in Archaea.

26 distinct communities of bacteria, fungi and archaea.

27 ion of methane to methanol by methanotrophic archaea.

28 ism is fully possible for all eukaryotes and archaea.

29 d energy conservation systems of MCR-bearing archaea.

30 pact on DNA replication in hyperthermophilic Archaea.

31 n of the replication forks of eukaryotes and archaea.

32 prehensive investigation of these mesophilic archaea.

33 zed by a pair of proteins (YcaO and TfuA) in Archaea.

34 an analog of methanofuran from methanogenic archaea.

35 e rapidly assimilated by marine bacteria and archaea.

36 s-responsive transcriptional programs in the Archaea.

37 er phyla and in Thermoplasma acidophilum, an Archaea.

38 and affects their spread among bacteria and archaea.

39 ent with a Turing patterning system in these archaea.

40 ctors that affect GDGT cyclization in extant archaea.

41 tous nanomachines widespread in Bacteria and Archaea.

42 Histones are also common in archaea.

43 ns of life, from humans to hyperthermophilic archaea.

44 nt over a million new names for Bacteria and Archaea.

45 appreciated mechanism of genome expansion in archaea.

46 hes are revolutionizing our understanding of Archaea.

47 ated cellular control system in Bacteria and Archaea.

48 tion of S-layer proteins across bacteria and archaea.

49 n-coding RNA and mRNA from hyperthermophilic archaea.

50 synthesized by only a subset of bacteria and archaea.

51 MP (c-di-AMP) is formed by many bacteria and archaea.

52 have been applied to the study of halophilic archaea [1-5], our ability to explore the cell biology o

53 dant adaptive immune systems in bacteria and archaea(1,2).

54 s between the cell biology of eukaryotes and archaea [10-15].

55 ith 59 phyla, but also represented were nine Archaea, 18 Animalia, 14 Chromista, eight Protozoa, two

56 ic microalgae) and prokaryotes (bacteria and archaea), 2 microbial groups that play a major role in t

57 ich facilitates cryo-EM 3D reconstruction of archaea 20S proteasomes at a record high resolution of ~

58 ylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the l

59 The discovery of the Asgard archaea, a proposed archaeal superphylum that includes L

60 mputer simulations to reveal that halophilic archaea achieve chemotaxis with power requirements one h

61 adaptive immune systems protect bacteria and archaea against their invading genetic parasites, includ

62 CRISPR adaptation immunizes bacteria and archaea against viruses.

63 DP-dependent kinases were first described in archaea, although their presence has also been reported

64 t on the abundances of the ammonia-oxidizing archaea amoA gene, ammonia-oxidizing bacteria amoA and n

65 itrifying anaerobic methane oxidation (DAMO) archaea, Anammox bacteria and DAMO bacteria jointly domi

66 We used sequences from 100 archaea and 683 bacteria species as input to train two C

67 genome replication dynamics in prokaryotes, archaea and a wide range of eukaryotes, including yeasts

68 context for the observed caspase activity in Archaea and add new insight to understanding the role of

69 d short palindromic repeats) system protects archaea and bacteria by eliminating nucleic acid invader

70 principal function of CRISPR-Cas systems in archaea and bacteria is defence against mobile genetic e

71 In 720 genomes of archaea and bacteria representing all major phyla, we id

72 rkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were l

73 reates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged wit

74 m is a part of the adaptive immune system in archaea and bacteria to defend against invasive nucleic

75 based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop

76 to molybdenum nitrogenases are also found in archaea and bacteria, but they have a different transiti

77 Type III systems are found in diverse archaea and bacteria, including the human pathogen Mycob

78 ight translational coupling is widespread in archaea and bacteria.

79 from 63,701 genomes across 33 390 species of archaea and bacteria.

80 rgent need for huge numbers of new names for Archaea and Bacteria.

81 cteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene

82 p of modular enzymes widespread in Bacteria, Archaea and Eukarya.

83 s conserved throughout evolution, present in archaea and eukaryotes from yeast to humans, where it lo

84 Kingdom-wide analysis in prokaryotes, archaea and eukaryotes reveals that between 5 and 10% of

85 In archaea and eukaryotes, tRNA intron removal is catalyzed

86 ired for every single transcription event in archaea and eukaryotes.

87 thods to interrogate >3,000 gene families in archaea and eukaryotes.

88 ment, and explored the assembly of bacteria, archaea and fungi in different sediment niches, which we

89 aled that microbial composition of bacteria, archaea and fungi in saline soils was affected by ACC am

90 the most intensively studied members of TACK archaea and have well-established molecular genetics [6-

91 e relationship between eukaryotes and Asgard archaea and identify the Heimdallarchaeota as the curren

92 many Archaea and some Bacteria, of which all Archaea and most Bacteria also encode an RNA-based RNase

93 otective protein coats which form around all archaea and most bacterial cells.

94 Methanogenic Archaea and several potential syntrophic bacterial partn

95 uifex RNase P (HARP) were identified in many Archaea and some Bacteria, of which all Archaea and most

96 refront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protos

97 Although ANME-1 archaea and SRB are present in low relative abundances,

98 s, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation

99 organic molecules between methane-oxidizing archaea and sulfate-reducing bacteria, (2) the delivery

100 ogenetic studies suggest that DSR is rare in archaea and that it originated in Vulcanisaeta, independ

101 e (Tad) pili were horizontally acquired from Archaea and that T2SSs were relatively recently repurpos

102 me, originating before the divergence of the Archaea and the Bacteria.

103 teract with Smc-kleisin rings from bacteria, archaea and the eukaryotic Smc5-6 complex, but not with

104 lone is sufficient to rehydrate methanogenic archaea and to reactivate their metabolism under conditi

105 PINA is conserved in archaea and vital for S. islandicus viability.

106 lies absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression

107 (EVs) is a common feature among eukaryotes, archaea, and bacteria.

108 gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and

109 In bacteria, archaea, and eukaryotes PRF is used to downregulate prot

110 ts into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cr

111 role in natural populations of bacteria and archaea, and experimental demonstrations with a few spec

112 d DNA (dsDNA) viruses infecting bacteria and archaea, and herpesviruses infecting animals and humans,

113 il the presence and accumulation of polyP in Archaea, and little information is available on its func

114 hanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evoluti

115 mily predates the divergence of Bacteria and Archaea, and show how duplications, acquisitions, and lo

116 characterized nucleases present in bacteria, archaea, and some viruses.

117 ms to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect the

118 teria, syntrophic bacteria, and methanogenic archaea, and their interspecies symbioses allow complex

119 us of CARF and SAVED domains in bacteria and archaea, and their sequence- and structure-based classif

120 than molybdenum nitrogenase in bacteria and archaea, and they are less efficient.

121 he two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some

122 hese anaerobic multi-carbon alkane-oxidizing archaea (ANKA) use enzymes homologous to MCR named alkyl

123 Anaerobic methanotrophic archaea (ANME) consume methane in marine sediments, limi

124 n of CH(4) (AOM) by anaerobic methanotrophic archaea (ANME) of ANME-2d, which proposes another plausi

125 out 20 years ago anaerobic methane-oxidizing archaea (ANME) were discovered that use MCR enzymes to a

126 d bacteria (Methylococcales) and AOM-related archaea (ANME-2 and ANME-3) at the MV420 sites.

127 n, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria a

128 Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechan

129 Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying ni

130 te oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizer

131 leaceae), and abundance of ammonia-oxidizing archaea (AOA), nirS, nirK and nosZ, whereas the cleared

132 marily by chemoautotrophic ammonia-oxidizing archaea (AOA), the production of NO(y) is mediated in la

133 t investigations have provided evidence that Archaea are a constant but highly variable component of

134 Archaea are a distinct and deeply rooted lineage that ha

135 The recently discovered DPANN archaea are a potentially deep-branching, monophyletic r

136 Archaea are bona fide prokaryotes but employ a eukaryote

137 at EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including c

138 at the information processing machineries of archaea are far more closely related to those of eukaryo

139 Bacteria and archaea are frequently attacked by viruses and other mob

140 ey contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and cons

141 debate how such studies reveal how important Archaea are in mediating an array of ecological processe

142 Methanogenic archaea are major contributors to the global carbon cycl

143 Methanogenic archaea are major players in the global carbon cycle and

144 We reveal that chromosomes of Sulfolobus archaea are organized into CID-like topological domains

145 Cultured Asgard archaea are typically prokaryotic in both size and inter

146 in antiviral defense systems in bacteria and archaea as well as in eukaryotes.

147 e the adaptive immune system of bacteria and archaea, as a sequence-specific nucleic acid targeting d

148 clease that is commonly present in bacteria, Archaea, as well as in the chloroplasts of higher plants

149 e similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved

150 ogical production of methane by methanogenic archaea, as well as the first step in the anaerobic oxid

151 Globins (Glbs) are widely distributed in archaea, bacteria and eukaryotes.

152 s) are an ubiquitous protein family found in archaea, bacteria and eukaryotes.

153 nomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from

154 P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play importan

155 essential to the physiology of virtually all archaea, bacteria, and eukaryotes.

156 obal predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades us

157 being widely distributed across bacteria and archaea, bactofilins are also present in a few eukaryoti

158 bon toxicity: ammonia-oxidizing bacteria and archaea being 100 and 1000 times more sensitive than typ

159 not only for enhancing our understanding of archaea but also for improving the development of biotec

160 ter is widely distributed among bacteria and archaea, but its mechanism of transport has not been ful

161 known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined

162 s to extremophiles such as hyperthermophilic archaea can also generate high current densities.

163 idation in a previously undescribed class of archaea ('Candidatus Methanoliparia').

164 ly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consump

165 in the metabolism of anaerobic bacteria and archaea, catalyzing the reversible synthesis of acetyl-C

166 ysis of ultratrace Se, Ag, Sb, Pb, and Bi in archaea cells and single conodont samples.

167 Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% of Shivlinga's mic

168 ains of life involving Eukarya, Bacteria and Archaea demonstrate its roles in regulating a variety of

169 nded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 euka

170 ed into proteins expressed in E. coli, using archaea-derived tyrosyl and pyrrolysyl pairs.

171 ributed heavy metal, which some Bacteria and Archaea detoxify by the reduction of ionic Hg (Hg[II]) t

172 In Eukarya and most Archaea, DNA-bound histone proteins represent the most c

173 Many bacteria and archaea do not produce sphingolipids but they are ubiqui

174 versal common ancestor into the Bacteria and Archaea domains.

175 Bacteria and archaea employ CRISPR (clustered, regularly, interspaced

176 Bacteria and archaea employ dedicated signal transduction systems tha

177 The majority of archaea encode CRISPR-Cas systems but only a few CRISPR-

178 For the two archaea examined, most triangular cells divide as predic

179 of these N-glycans has been determined, but archaea exhibit extensive variation in their glycans, me

180 Chemosynthetic bacteria and archaea form the foundation of vent ecosystems by exploi

181 CRISPR-Cas systems protect bacteria and archaea from phages and other mobile genetic elements, w

182 e system that exists to protect bacteria and archaea from viruses and infections with other mobile ge

183 the Factor that terminates transcription in Archaea (FttA).

184 belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent

185 The bacteria, archaea, fungi, and viruses that thrive within these com

186 t are from microbes, predominantly bacteria, archaea, fungi, and viruses.

187 rs had a higher representation of halophilic archaea Halobacteriaceae, phylum Chloroflexi, and classe

188 ion of the division plane in two pleomorphic archaea, Haloferax volcanii and Haloarcula japonica, and

189 to explore the cell biology of thermophilic archaea has been limited by the technical challenges of

190 Methanogenic archaea have been shown to reduce iron from ferric [Fe(I

191 The crystal structures of Glt(Ph) from archaea have been used in computational studies to under

192 Like many organisms, bacteria and archaea have both innate and adaptive immune systems to

193 Bacteria and archaea have evolved sophisticated adaptive immune syste

194 Archaea have evolved to survive in some of the most extr

195 Many bacteria and archaea have the unique ability to heritably alter their

196 crobes, including viruses, phage, fungi, and archaea, have not been characterized, and little is know

197 However, recent work with GDGT-making archaea highlight the roles of other factors, such as pH

198 uch near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Ha

199 In archaea, histones are widespread but not universal: seve

200 Using archaea homologs, we construct asymmetric forms of prote

201 activity system that has both eukaryotic and archaea homologs.

202 increase the known diversity of Bacteria and Archaea; however, while 'omics can be used to infer phys

203 yotes consistently originate from within the archaea in a two-domains tree when due consideration is

204 zing methane-producing microbe of the domain Archaea In contrast to all flavodoxins, FldA is homodime

205 The role of archaea in microbial mats is poorly understood.

206 single-gene diversity surveys to understand Archaea in nature.

207 ent of specific taxa, including methanogenic archaea, in their rhizosphere that differ from those of

208 ANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses sugg

209 Intriguingly, however, many archaea, including members of the genus Sulfolobus do no

210 ect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undisc

211 ch indicated that n-DAMO bacteria and n-DAMO archaea indeed contributed jointly to the methane remova

212 viously showed that liposomes made from pure Archaea-inspired bipolar tetraether lipids exhibit excep

213 Motility in archaea is facilitated by a unique structure termed the

214 dation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous o

215 lation, which is essential in eukaryotes and archaea, is catalysed by the Box C/D RNP complex in an R

216 By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that

217 nammox bacteria, n-DAMO bacteria, and n-DAMO archaea jointly dominated the biofilm, and their respect

218 This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofund

219 Studies on viruses infecting archaea living in the most extreme environments continue

220 Many Archaea maintain the fluidity and permeability of their

221 ), Chytridiomycota (fungi) and Nanoarcheota (archaea) may be considered as radiation-tolerant.

222 om Azotobacter vinelandii with NifB from the archaea Methanocaldococcus infernus or Methanothermobact

223 ker protein 10 gene in the methane-producing archaea Methanosarcina acetivorans Using an array of app

224 ia metabolic activity for three methanogenic archaea: Methanosarcina mazei, M. barkeri and M. soligel

225 a-proteobacteria living within single-celled Archaea more than a billion years ago.

226 In Archaea, motility is mediated by the archaellum, a rotat

227 ent denitrifying anaerobic methane oxidizing archaea (n-damo) oxidize methane and reduce nitrate to n

228 s are widespread in microbes from the domain Archaea, none have been isolated and characterized.

229 microbiome-associated with hyperthermophilic archaea of the order Sulfolobales recovered directly fro

230 Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous mor

231 Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most

232 Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organ

233 obile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the p

234 usively of putative anaerobic methanotrophic archaea of which ANME-1 was the sole archaeal taxon.

235 l lineages of bacteria carry out DSR, but in archaea only Archaeoglobus, which acquired DSR genes fro

236 been shown to benefit their hosts (bacteria, archaea or phages).

237 es in the pioneer bacteria (class level) and archaea (order level) populations under the various cond

238 gether, and away from all other bacteria and archaea, partly due to proteins without recognizable hom

239 s of phenylalanine and tyrosine in bacteria, archaea, plants, and fungi.

240 Marine bacteria and archaea play key roles in global biogeochemistry.

241 Many bacteria and most archaea possess a crystalline protein surface layer (S-l

242 Some bacteria and archaea possess an immune system, based on the CRISPR-Ca

243 al Park to investigate whether deeply-rooted archaea possess and express novel mcrA genes in situ.

244 Surprisingly, many archaea possess spacers that match chromosomal genes of

245 l of certain obligate anaerobic bacteria and archaea possessing the hgcAB gene cluster.

246 response to viral infection of bacteria and archaea, potentiating an immune response by binding and

247 Many bacteria and some archaea produce the second messenger cyclic diadenosine

248 s significantly less common on bacterial and archaea proteins.

249 Thus, archaea provide the means not only to study transcriptio

250 The CRISPR system in bacteria and archaea provides adaptive immunity against mobile geneti

251 ire, with families inherited from the Asgard archaea-related host being duplicated most.

252 ow that membrane lipids of marine planktonic archaea reliably record both the carbon isotope excursio

253 In contrast, the translational landscape in Archaea remains mostly unexplored.

254 aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histo

255 ) genes are found frequently in bacteria and archaea, serving to defend against invading foreign DNA,

256 Because archaea share similar cell division and chemotaxis machi

257 phosphate 1-kinase 1 (ITPK1)-found in Asgard archaea, social amoeba, plants, and animals-phosphorylat

258 ins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a

259 We found that KARI from archaea Sulfolobus solfataricus (Sso-KARI) is unusual in

260 Archaea swim using the archaellum (archaeal flagellum),

261 Archaea-targeted PCR sequencing and metagenomics confirm

262 overy of an archaeal virus, one that infects archaea, tentatively named Thermoproteus spherical pilif

263 Genomic loci in bacteria and archaea, termed clustered regularly interspaced short pa

264 ane cycling (mcrA) is more widespread in the Archaea than previously thought.

265 y two major groups of organisms: a subset of Archaea that appears to be cells simplified to the limit

266 m at deep-sea gas seeps(10-12) suggests that archaea that are able to oxidize ethane through ethyl-Co

267 CRISPR-Cas systems in many bacteria and most archaea that await functional characterization and repur

268 Recently, archaea that have the ability to anaerobically oxidize n

269 widespread second messenger in bacteria and archaea that is involved in the maintenance of osmotic p

270 Methanogens are a diverse group of archaea that play a critical role in the global carbon c

271 Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over t

272 Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-,

273 In methanogenic archaea, the alpha subunit of MCR (McrA) typically conta

274 The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of l

275 TFEalpha-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko).

276 Candidatus Methanoperedens spp. archaea thought to perform anaerobic oxidation of methan

277 The ability of Archaea to adjust membrane composition and packing may b

278 delivery of disulfide from methane-oxidizing archaea to bacteria for disproportionation and (3) direc

279 XPB is conserved from archaea to human.

280 species of metabolically active bacteria and archaea, unveiling a previously unreported habitat for m

281 Most methanogenic archaea use the rudimentary hydrogenotrophic pathway-fro

282 fer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to

283 We assembled genomes of bacteria and archaea using DNA that had previously been characterized

284 enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, pro

285 Archaea utilize features similar to those found in both

286 crobiota is a complex community of bacteria, archaea, viruses, protists and fungi(1,2).

287 ove our understanding of alkane oxidation in archaea, we identified three directions for future resea

288 Archaea were not directly involved in full methane oxida

289 ene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had

290 ethylators while Firmicutes and methanogenic Archaea were typically ~50% less abundant.

291 Rqc2 homologs are also found in bacteria and archaea; whether prokaryotic Rqc2 has an RQC-related fun

292 The discovery of the Asgard archaea, which harbor close phylogenetic ties to the euk

293 he co-presence of n-DAMO bacteria and n-DAMO archaea, while anammox bacteria were detected with a low

294 MAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated viru

295 Delineating the spatial distribution of archaea with mat depth will enable resolution of putativ

296 CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile geneti

297 prompted or facilitated these losses and how archaea without histones organize their chromatin remain

298 The pioneer bacteria and archaea (without filtration) were identified by next-gen

299 In archaea, XPB is associated with a nuclease Bax1.

300 here life primarily consists of bacteria and archaea, yet knowledge of their co-occurring viruses is