ライフサイエンスコーパス: eubacterial

1 equencing of the variable V3-4 region of the eubacterial 16 S rDNA gene on the Illumina MiSeq platfor

2 cus, which lies near the deepest root of the eubacterial 16 S rRNA-based phylogenetic tree, CCA addit

3 c sites in the Escherichia coli and in other eubacterial 16 S rRNAs.

4 extracted, the variable V3-V4 region of the eubacterial 16S ribosomal RNA gene was amplified, and sa

5 rs specific for the conserved regions of the eubacterial 16S rRNA gene was designed for use with the

6 orescent in situ hybridization (FISH) with a eubacterial 16S rRNA probe.

7 the implementation of a PCR for detection of eubacterial 16S rRNA with the TaqMan system will continu

8 dtii, composed of the coding sequence of the eubacterial aadA gene (conferring spectinomycin resistan

9 a Chlamydomonas reinhardtii, expression of a eubacterial aadA gene, conferring spectinomycin resistan

10 s contain more genes of archaebacterial than eubacterial affinity.

11 g and cleavage studies, which establish this eubacterial Ago as a bona fide guide DNA strand-mediated

12 oxins of higher organisms than to most other eubacterial AhpC proteins.

13 ing components of eubacterial Mo-independent eubacterial alternative nitrogenases and other methanoge

14 1 with clear homology to vnfG, a hallmark of eubacterial alternative nitrogenases.

15 itochondria and hydrogenosomes have a common eubacterial ancestor and imply that the earliest-branchi

16 Genes of archaebacterial and eubacterial ancestry tend to perform different functions

17 uorescence in situ hybridization (FISH) with eubacterial and "H. heilmannii"-specific probes was empl

18 oteins were compared to the N termini of 810 eubacterial and 175 archaeal proteins, which are rarely

19 found to occur in 2.0% of archaean, 4.2% of eubacterial and 33.0% of eukaryotic proteins.

20 By comparing the eubacterial and archaeal 5' nucleases, we show that the

21 g 89 complete microbial chromosomes from the eubacterial and archaeal domains.

22 ferentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms.

23 ling case for the divergent evolution of the eubacterial and archaeal TGTs.

24 s that the gating motif is conserved between eubacterial and archaebacterial SecY and eukaryotic Sec6

25 Dps, a ferritin-like protein found in many eubacterial and archaebacterial species, appears to prot

26 tiple sequence alignment of lambdaPP with 28 eubacterial and archeal phosphoesterases identified acti

27 ms have been most thoroughly explored in the eubacterial and eukaryotic branches of life.

28 hows low sequence identity (16-20%) with its eubacterial and eukaryotic counterparts.

29 ships among members of this gene family from eubacterial and eukaryotic genomes.

30 A polymerase are highly conserved throughout eubacterial and eukaryotic kingdoms.

31 , with the inner core structure of PGIs from eubacterial and eukaryotic sources, confirms this enzyme

32 cribed aquaporin water channels from diverse eubacterial and eukaryotic species but not from the thir

33 rresponding to conserved regions between the eubacterial and first halobacterial phototaxis transduce

34 hat is absent from the gamma subunits of the eubacterial and mitochondrial enzymes.

35 odest numbers, and thus far, only in certain eubacterial and organellar genomes.

36 hat the C1xA72 base pair mismatch, unique to eubacterial and organellar initiator tRNAs, may also be

37 , despite their evolutionary distance, these eubacterial and vertebrate rhodopsins start to isomerize

38 orted monophyletic clusters with eukaryotic, eubacterial, and archaeal hosts.

39 urified yeast Sir2p and homologous Archaeal, eubacterial, and human proteins, and depends completely

40 t of the predicted structure for the related eubacterial apocarotenal oxygenase.

41 lications with respect to the three putative eubacterial, archaeal, and eukaryote domains of life and

42 nserved catalytic domains that are common to eubacterial, archaeal, and eukaryotic nuclear-encoded RN

43 s, from bacteria, appeared in 1995 and other eubacterial, archaebacterial and eukaryotic genomes were

44 variety of cellular Activities) are found in eubacterial, archaebacterial, and eukaryotic species and

45 acterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chi

46 Unlike other eubacterial arginases, B. anthracis arginase displays un

47 tides thought to represent homologues of the eubacterial B/B' subunits, and a fifth with unclear homo

48 polypeptides representing homologues of the eubacterial beta/beta' subunits, and a fifth that is lik

49 ass II HMG-CoA reductase, the first class II eubacterial biosynthetic enzyme isolated.

50 PYP) is a member of the xanthopsin family of eubacterial blue-light photoreceptors.

51 The eubacterial CADs are found in metalloproteases, while CA

52 We also find that the eubacterial CCA-, CC-, and A-adding enzymes, as well as

53 No other eubacterial cell division gene homologs were found adjac

54 Many type I signal peptidases from eubacterial cells appear to contain a serine/lysine cata

55 dent escape of the first archaebacterial and eubacterial cells from their hydrothermal hatchery, with

56 bly an adaptation to the anaerobic nature of eubacterial cells with poor tolerance for oxygen.

57 a recent addition to the known complement of eubacterial chaperones.

58 nal-transducing protein (HtrI) homologous to eubacterial chemotaxis receptors.

59 s exist in the Archaeon H. salinarium: (i) a eubacterial chemotaxis transducer type with two hydropho

60 deduced protein sequence of HtrII predicts a eubacterial chemotaxis transducer type with two hydropho

61 proposed that the Clostridia are the oldest Eubacterial class and the ubiquity of TFP in this class

62 e for the first time the inducible nature of eubacterial CoM biosynthesis.

63 ss sequences not present in the archaeal and eubacterial counterparts and that the additional sequenc

64 f NpSRII and NpHtrII and fusion hybrids with eubacterial cytoplasmic domains and analyze their functi

65 amino termini of secreted proteins from the eubacterial cytosol based on cycles of reversible bindin

66 t is the first description of a thermophilic eubacterial DAHP synthase.

67 sms associated with intestinal diseases from Eubacteriales, Desulfovibrionales and Methanobacteriales

68 ay algorithm consists of initial broad-range eubacterial detection, followed by Gram typing and speci

69 se family that emerged prior to the archaeal-eubacterial divergence.

70 , all wounds contained significantly greater eubacterial diversity than contralateral skin (P < 0.05)

71 le chronic wounds generally harbored greater eubacterial diversity than healthy skin, the isolation o

72 although no significant difference in total eubacterial diversity was detected between wounds from w

73 ycobacterium smegmatis protein homologous to eubacterial DivIVA-like proteins, including M. tuberculo

74 ty and specificity for 16S PCR for detecting eubacterial DNA compared with those of standard culture

75 uggest a novel substrate binding mode of the eubacterial DNA polymerase enzymes, called a 5' nuclease

76 Many eubacterial DNA polymerases are bifunctional molecules h

77 the first sensory rhodopsin observed in the eubacterial domain, a green light-activated photorecepto

78 them with their homologs in the archaeal and eubacterial domains.

79 ddition, protein L28, which is unique to the eubacterial E site, overlaps the site occupied by 13-deo

80 s between eukaryotic eIF-2gamma proteins and eubacterial EF-Tu proteins, we previously proposed a maj

81 powerhouses of our cells, are remnants of a eubacterial endosymbiont.

82 uences were carried into eukaryotes by early eubacterial endosymbionts about 2 billion years ago, onl

83 Some highly conserved eubacterial enzymes appear not to be encoded by U. ureal

84 s, we show that the polymerase domain of the eubacterial enzymes is critical for the activity of the

85 etylases share nine motifs with archaeal and eubacterial enzymes, including acetoin utilization prote

86 aspartyl residues in the human, archael, and eubacterial enzymes.

87 archaeal Sulfolobus shibatae class I and the eubacterial Escherichia coli class II CCA-adding enzymes

88 The eubacterial, eukaryotic, and archaeal CCA-adding enzymes

89 polymerases tested were inhibited, while no eubacterial, eukaryotic, or bacteriophage enzymes showed

90 The eubacterial flagellum is a complex structure with an elo

91 FtsZ and that it is biochemically similar to eubacterial FtsZs.

92 nd an S-loop with characteristic features of eubacterial GAPDH.

93 es in secondary structure when compared with eubacterial GAPDHs, with an overall increase in the numb

94 is likely to play a broad role in modulating eubacterial gene expression.

95 imilarities to RecJ have been found in every eubacterial genome sequenced to date, with the exception

96 ar attention to the 22 complete archaeal and eubacterial genome sequences.

97 of an ATP-dependent DNA ligase encoded by a eubacterial genome.

98 sts and mitochondria have retained relics of eubacterial genomes and a protein-synthesizing machinery

99 ) are highly expressed essential proteins in eubacterial genomes and in eukaryotic organelles.

100 Many eubacterial genomes including those of Salmonella typhim

101 se encoding RecJ can be found in most of the eubacterial genomes sequenced to date.

102 than was previously reported from studies of eubacterial genomes, including that of the aphid endosym

103 -expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capabl

104 of the parF gene are widely disseminated on eubacterial genomes, suggesting that ParF-mediated parti

105 oded by the mitochondrial genome and by many eubacterial genomes.

106 he morphologically and biochemically complex eubacterial genus Streptomyces.

107 rimers derived from conserved regions of the eubacterial groESL heat shock operon were used to amplif

108 MarathonRT is encoded within a eubacterial group II intron, and it has been shown to ef

109 lances of these same enzymes among the major eubacterial groups suggest that the cyanobacteria and Gr

110 d protein of 39 kDa is divergent relative to eubacterial homologs, with 32% identity to Escherichia c

111 ific for glucose and glucosamine, as are its eubacterial homologs.

112 and a small insertion, as compared to their eubacterial homologs.

113 hus profoundly different between CCT and its eubacterial homologue GroEL, consistent with their diffe

114 ryotic ribosomal proteins that do not have a eubacterial homologue.

115 host-derived properties, lost much of their eubacterial identity, and were transformed into extraord

116 ion domain of IF2(mt) mimics the function of eubacterial IF1, by blocking the ribosomal aminoacyl-tRN

117 itochondrial ribosomal proteins appear to be eubacterial in origin but to have evolved additional fun

118 n the ribosome that would be occupied by the eubacterial initiation factor IF1, which is absent in mi

119 tent inhibitor of Escherichia coli and other eubacterial isoleucyl-tRNA synthetases, but not of eukar

120 uence to eukaryote cytoplasmic than to other eubacterial isoleucyl-tRNA synthetases.

121 elial protein has implications that span the eubacterial kingdom.

122 ng protein has broad implications across the eubacterial kingdom.

123 he high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them

124 Ribosomal protein L27 is a component of the eubacterial large ribosomal subunit that has been shown

125 a polypeptide of just 148 amino acids with a eubacterial-like acidic C-terminus.

126 The eubacterial-like RNA polymerase of plastids is composed

127 Eubacterial Lon proteases contain an N-terminal domain,

128 A 16-aa insertion loop present in eubacterial methionyl-tRNA formyltransferases (MTF) is c

129 C-terminal domain has high homology with the eubacterial methyl-accepting chemotaxis protein.

130 equences and much diminished matching to all eubacterial, mitochondrial, and chloroplast sequences.

131 ationships with genes encoding components of eubacterial Mo-independent eubacterial alternative nitro

132 uirements one hundred-fold lower than common eubacterial model systems.

133 rchaebacterial DNA that remained attached to eubacterial motility structures and became the microtubu

134 oli outer membrane protein A, a beta-barrel, eubacterial MP, (ii) Halobacterium salinarum bacteriorho

135 of Cell, clarify the end of translation on a eubacterial mRNA.

136 16 amino acid insertion loop, present in all eubacterial MTF's (residues 34-49 in the E. coli enzyme)

137 We demonstrate that eubacterial MTSs interact directly with lipid bilayers a

138 EmrE belongs to a family of eubacterial multidrug transporters that confer resistanc

139 lutamine, is the physiological substrate for eubacterial NAD synthetases and that low activity comple

140 and the BRCT domain that are present in all eubacterial NAD(+) ligases.

141 Evolutionary analysis indicates that eubacterial NADP-dependent isocitrate dehydrogenases (EC

142 Sequence conservation among eubacterial NATs is restricted to structural residues of

143 LeuT, a thermostable eubacterial NSS homolog, has been exploited as a model p

144 d slower for the non-hydrogen-bonded Val 38 (eubacterial numbering).

145 bly more similar to eukaryotic ones than are eubacterial ones.

146 no in vivo characterization of a simplified eubacterial or archaebacterial proteasome has been repor

147 ir origins to horizontal gene transfer (from eubacterial or Dictostelium genomes) or to more conventi

148 seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ri

149 The eubacterial organism is either a proteobacterium, or a m

150 lmonis and Acholeplasma laidlawii, which are eubacterial organisms lacking a cell wall.

151 POR, ADHE, and FD cloned from eukaryotic and eubacterial organisms.

152 The rRNA gene exhibited typical eubacterial organization (16S-tRNAs-23S-5S).

153 , phylogenetic analysis demonstrates a clear eubacterial origin of this gene and strongly suggests it

154 ondria have retained many hallmarks of their eubacterial origin.

155 ion suggests that L30, which has no apparent eubacterial ortholog, is responsible for establishing th

156 d, they are either outliers or mixed in with eubacterial orthologs.

157 ynthetic gene clusters as observed for other eubacterial PAL genes.

158 his data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomyce

159 pyranose (BacAc(2)) is found in a variety of eubacterial pathogens.

160 estrated by SmpB and tmRNA, is the principal eubacterial pathway for resolving stalled translation co

161 otein motifs found in the active site of all eubacterial peptide deformylases, and N-terminal extensi

162 rity exists between the protozoan enzyme and eubacterial phosphatidylinositol-phospholipases C.

163 Photoactive yellow protein (PYP) is a eubacterial photoreceptor and a structural prototype of

164 ation of photoactive yellow protein (PYP), a eubacterial photosensor.

165 These results indicate that eubacterial photosensory perception is mediated by light

166 l protein biosynthesis is used in nearly all eubacterial phyla, but the specific RNA structures that

167 ch these RNA structures are conserved across eubacterial phyla, we created multiple sequence alignmen

168 , occurs in organisms belonging to only five eubacterial phyla: Cyanobacteria, Proteobacteria, Chloro

169 gs to the Gram-positive bacteria (one of ten eubacterial "phyla")--more precisely to the so-called lo

170 that spirochetes are an ancient and distinct eubacterial phylum.

171 ecA facilitates protein transport across the eubacterial plasma membrane by its association with carg

172 to promote protein translocation across the eubacterial plasma membrane.

173 on to drive protein translocation across the eubacterial plasma membrane.

174 and A-adding enzymes, as well as the related eubacterial poly(A) polymerases, each fall into phylogen

175 m-typing probes correctly identified 100% of eubacterial positive samples as to gram-positive or gram

176 ctly identified the etiologic agent in 16/20 eubacterial positive samples.

177 Myxobacteria are single-celled, but social, eubacterial predators.

178 nella felis was amplified by using universal eubacterial primers and was subsequently cloned and sequ

179 Broad-range eubacterial primers selected from the 16S rRNA gene were

180 The PCR product generated with the eubacterial primers was transferred to a charged nylon m

181 The 16S rDNA V3 region was amplified with eubacterial primers, and the amplification products deri

182 encing of the 16S rRNA gene with broad-range eubacterial primers.

183 RNA polymerase binding in several classes of eubacterial promoters, but the sequences themselves are

184 this promoter are, in fact, prototypical of eubacterial promoters.

185 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with

186 A ATPase motor is a central component of the eubacterial protein translocation machinery.

187 localize to mitochondria and are related to eubacterial proteins that facilitate essential steps in

188 identify closely related LOV domains in two eubacterial proteins that suggests the light-induced con

189 Some highly conserved eubacterial proteins, such as GroEL and GroES, are notab

190 ino acid-sequence properties of human versus eubacterial proteins, which likely reflect differences i

191 atory characterized eukaryotic (hamster) and eubacterial (Pseudomonas mevalonii) 3-hydroxy-3-methylgl

192 e parabasalid clade was a robust part of the eubacterial radiation of GAPDH and showed no relationshi

193 e sequences reveal extended alignments among eubacterial RecA and separately among eukaryotic/archaeb

194 d51 and the closely related archeal RadA and eubacterial RecA proteins place the ATPase site at the p

195 insights into the workings of these complex eubacterial regulatory systems.

196 NA polymerase beta, thereby proving that the eubacterial replicating polymerase, but not the eukaryot

197 d the DnaG primase unwinds duplex DNA at the eubacterial replication fork and synthesizes the Okazaki

198 the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that

199 none biosynthesis, and complexes I-IV of the eubacterial respiratory chain that functions in the halo

200 One of the distinctive features of eubacterial retinal-based proton pumps, proteorhodopsins

201 ts with the first structurally characterized eubacterial retinylidene photoreceptor Anabaena sensory

202 We present the structure of a eubacterial rhodopsin, which differs from those of previ

203 Eubacterial ribosomal large-subunit methyltransferase H

204 central domain of MrpL36p that is similar to eubacterial ribosomal large-subunit protein L31 is suffi

205 bosomal components are clearly homologous to eubacterial ribosomal proteins, but others appear unique

206 mplex with initiator fMet-tRNA(iMet) and the eubacterial ribosome.

207 ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian

208 mycin S, and telithromycin bound explain why eubacterial ribosomes containing the mutation A2058G are

209 ntibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepa

210 universal factors, alone and in complex with eubacterial ribosomes, point to the structural homology

211 Ribosomal protein L9 is a component of all eubacterial ribosomes, yet deletion strains display only

212 a protein homologous to the L14 proteins of eubacterial ribosomes.

213 3-deoxytedanolide, precluding its binding to eubacterial ribosomes.

214 rchaeal and eukaryotic ribosomes, but not of eubacterial ribosomes.

215 lying the differences between eukaryotic and eubacterial ribosomes.

216 ore RNA and a higher number of proteins than eubacterial ribosomes.

217 The sigma subunit of eubacterial RNA polymerase is essential for initiation o

218 The sigma subunit of eubacterial RNA polymerase is required throughout initia

219 the extra-cytoplasmic function subfamily of eubacterial RNA polymerase sigma factors.

220 Eubacterial RNA polymerase uses the sigma (sigma) subuni

221 NAs, 25 species of tRNA, three subunits of a eubacterial RNA polymerase, 17 ribosomal proteins, and a

222 or rifampin, an inhibitor of organellar and eubacterial RNA polymerase, both showed disappearance of

223 localization of bacteria-like structures and eubacterial-RNA within 14(th) weeks fetal gut lumen.

224 isms of transcription and those of canonical eubacterial RNAPs and the related non-canonical nvRNAP o

225 rease in the number of protein subunits over eubacterial RNase P is consistent with an increase in fu

226 s corresponding to a conserved region of the eubacterial rRNA genes.

227 of interaction of YS11, the yeast homolog of eubacterial S17, with 18 S rRNA was obtained by assessin

228 Here, we outline how the universal eubacterial second messenger cyclic di-GMP impacts the p

229 A homologue of eubacterial SecY called cpSecY is localized to the thyla

230 ater differences between archaebacterial and eubacterial sequences indicate these two groups may have

231 ly related to fungal proteases than to other eubacterial sequences.

232 cyanobacterial and high-G + C, Gram-positive eubacterial sequences.

233 of evolutionary conservation across 63 RecA eubacterial sequences.

234 nd other members of the heat shock family of eubacterial sigma factors.

235 activating transcription by the alternative eubacterial sigmaN (sigma54) RNA polymerase holoenzyme.

236 Amino acids critical to the eubacterial signal peptidases and Sec11p are, however, p

237 The eubacterial SOS system is a paradigm of cellular DNA dam

238 In the chloroplasts of plants and in several eubacterial species ALA is formed in a two-step process

239 family with representatives in several other eubacterial species and to the prediction that the membe

240 omolecular synthesis operon present in other eubacterial species but is part of an operon with a dgt

241 A rapid assay for eubacterial species identification is described using hi

242 mechanics of cell septation in conventional eubacterial species is believed to be mediated by cell-w

243 The eubacterial species Streptomyces coelicolor proceeds thr

244 Genes from 10 of 14 eubacterial species studied and one eukaryote, the yeast

245 allows for highly sensitive detection of any eubacterial species with simultaneous species identifica

246 of the dnaK and groE operons in at least 27 eubacterial species.

247 rse prokaryotes, including many Archaeal and Eubacterial species.

248 disease cannot be a spiroplasma or any other eubacterial species.

249 ancient rooting, with clear members found in eubacterial species.

250 bosomal peptide synthesis, and to screen for eubacterial-specific drugs.

251 Thus eubacterial SSBs are homotetrameric whilst the eucaryal

252 rse range of eukaryote, archaebacterial, and eubacterial taxa has revealed that the evolutionary orig

253 The X-ray crystal structure of a eubacterial TGT bound to preQ1 suggested that aspartate

254 complex with preQ(1) (the substrate for the eubacterial TGT).

255 ent with the idea that the Cys145 evolved in eubacterial TGTs to recognize preQ(1) but not queuine, w

256 alent attachment of electrophilic ligands in eubacterial TGTs.

257 are highly conserved in a novel subfamily of eubacterial topoisomerases found largely in Actinobacter

258 RNA polymerases I, II and III than it is to eubacterial transcription systems.

259 y to the signaling and methylation domain of eubacterial transducer Tsr.

260 Eubacterial transducers are transmembrane, methyl-accept

261 representing the highest homology region of eubacterial transducers.

262 In eubacterial translation, lack of a stop codon on the mRN

263 ccessfully recover organisms from across the eubacterial tree of life.

264 show that the absA locus encodes a putative eubacterial two-component sensor kinase-response regulat

265 the RNAP assembly may be a unique feature of eubacterial-type enzymes.

266 oma brucei are composed of 9S and 12S rRNAs, eubacterial-type ribosomal proteins, polypeptides lackin

267 hloroplast-encoded RNA polymerase (PEP) is a eubacterial-type RNA polymerase that is presumed to asse

268 s transcribed from a sigma70 promoter by the eubacterial-type RNA polymerase.

269 properties characteristic of known essential eubacterial UMP kinases.

270 itive eubacterium and the other resembling a eubacterial V nitrogenase gene cluster, suggests horizon

271 d for sirtuin enzymes derived from archaeal, eubacterial, yeast, metazoan, and mammalian species, sug

272 ctionally homologous to the P2 Ogr family of eubacterial zinc finger transcription factors required f