bluuebunny/crossref_metadata_2025_split huggingface dataset:
15,000 Unique Zebrafish EST Clusters and Their Future Use in Microarray for Profiling Gene Expression Patterns During Embryogenesis
Authors: Lo Jane , Lee Sorcheng , Xu Min , Liu Feng , Ruan Hua , Eun Alvin , He Yawen , Ma Weiping , Wang Weefuen , Wen Zilong , Peng Jinrong 
Published: March 2003

A total of 15,590 unique zebrafish EST clusters from two cDNA libraries have been identified. Most significantly, only 22% (3437) of the 15,590 unique clusters matched 2805 (of 15,200) clusters in theDanio rerio UniGene database, indicating that our EST set is complementary to the existing ESTs in the public database and will be invaluable in assisting the annotation of genes based on the upcoming zebrafish genome sequence. Blast search showed that 7824 of our unique clusters matched 6710 known or predicted proteins in the nonredundant database. A cDNA microarray representing ∼3100 unique zebrafish cDNA clusters has been generated and used to profile the gene expression patterns across six different embryonic stages (cleavage, blastula, gastrula, segmentation, pharyngula, and hatching). Analysis of expression data using K-means clustering revealed that genes coding for muscle-specific proteins displayed similar expression patterns, confirming that the coordinate gene expression is important for myogenesis. Our results demonstrate that the combination of microarray technology with the zebrafish model system can provide useful information on how genes are coordinated in a genetic network to control zebrafish embryogenesis and can help to identify novel genes that are important for organogenesis.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to EMBL under accession nos.AL901610–AL928536.]
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Authors: Liu Ge , Program NISC Comparative Sequencing , Zhao Shaying , Bailey Jeffrey A. , Sahinalp S. Cenk , Alkan Can , Tuzun Eray , Green Eric D. , Eichler Evan E. 
Published: March 2003

We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Using a human genomic reference, optimal global alignments were constructed from large (>50-kb) genomic sequence clones. These alignments were examined for the pattern, frequency, and nature of mutational events. Whereas rates of single-nucleotide substitution remain relatively constant (1–2 × 10−9 substitutions/site/year), rates of retrotransposition vary radically among different primate lineages. These differences have lead to a 15%–20% expansion of human genome size over the last 50 million years of primate evolution, 90% of it due to new retroposon insertions. Orthologous comparisons with the chimpanzee suggest that the human genome continues to significantly expand due to shifts in retrotransposition activity. Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively.[Supplemental material is available online at www.genome.org.]
Laser-Capture Microdissection, a Tool for the Global Analysis of Gene Expression in Specific Plant Cell Types: Identification of Genes Expressed Differentially in Epidermal Cells or Vascular Tissues of Maize[W]
Authors: Nakazono Mikio , Qiu Fang , Borsuk Lisa A. , Schnable Patrick S. 
Published: March 2003

AbstractLaser-capture microdissection (LCM) allows for the one-step procurement of large homogeneous populations of cells from tissue sections. In mammals, LCM has been used to conduct cDNA microarray and proteomics studies on specific cell types. However, LCM has not been applied to plant cells, most likely because plant cell walls make it difficult to separate target cells from surrounding cells and because ice crystals can form in the air spaces between cells when preparing frozen sections. By fixing tissues, using a cryoprotectant before freezing, and using an adhesive-coated slide system, it was possible to capture large numbers (&gt;10,000) of epidermal cells and vascular tissues (vascular bundles and bundle sheath cells) from ethanol:acetic acid–fixed coleoptiles of maize. RNA extracted from these cells was amplified with T7 RNA polymerase and used to hybridize a microarray containing ∼8800 maize cDNAs. Approximately 250 of these were expressed preferentially in epidermal cells or vascular tissues. These results demonstrate that the combination of LCM and microarrays makes it feasible to conduct high-resolution global gene expression analyses of plants. This approach has the potential to enhance our understanding of diverse plant cell type–specific biological processes.
Disease Resistance and Abiotic Stress Tolerance in Rice Are Inversely Modulated by an Abscisic Acid–Inducible Mitogen-Activated Protein Kinase[W]
Authors: Xiong Lizhong , Yang Yinong 
Published: March 2003

Abstract
Mitogen-activated protein kinase (MAPK) cascades play an important role in mediating stress responses in eukaryotic organisms. However, little is known about the role of MAPKs in modulating the interaction of defense pathways activated by biotic and abiotic factors. In this study, we have isolated and functionally characterized a stress-responsive MAPK gene (OsMAPK5) from rice. OsMAPK5 is a single-copy gene but can generate at least two differentially spliced transcripts. The OsMAPK5 gene, its protein, and kinase activity were inducible by abscisic acid as well as various biotic (pathogen infection) and abiotic (wounding, drought, salt, and cold) stresses. To determine its biological function, we generated and analyzed transgenic rice plants with overexpression (using the 35S promoter of Cauliflower mosaic virus) or suppression (using double-stranded RNA interference [dsRNAi]) of OsMAPK5. Interestingly, suppression of OsMAPK5 expression and its kinase activity resulted in the constitutive expression of pathogenesis-related (PR) genes such as PR1 and PR10 in the dsRNAi transgenic plants and significantly enhanced resistance to fungal (Magnaporthe grisea) and bacterial (Burkholderia glumae) pathogens. However, these same dsRNAi lines had significant reductions in drought, salt, and cold tolerance. By contrast, overexpression lines exhibited increased OsMAPK5 kinase activity and increased tolerance to drought, salt, and cold stresses. These results strongly suggest that OsMAPK5 can positively regulate drought, salt, and cold tolerance and negatively modulate PR gene expression and broad-spectrum disease resistance.
Uptake of
N
,
N
′-Diacetylchitobiose [(GlcNAc)
2
] via the Phosphotransferase System Is Essential for Chitinase Production by
Serratia marcescens
2170
Authors: Uchiyama Taku , Kaneko Ryousuke , Yamaguchi Junko , Inoue Akane , Yanagida Takahiro , Nikaidou Naoki , Regue Miguel , Watanabe Takeshi 
Published: March 2003

ABSTRACT

The
chiR
gene of
Serratia marcescens
2170, encoding a LysR-type transcriptional activator, was identified previously as an essential factor for expression of chitinases and a chitin-binding protein, CBP21. To identify other genes that are essential for chitinase production, transposon mutagenesis with mini-Tn
5
Km1 was carried out, and 25 mutants that were unable to produce chitinases and CBP21 were obtained. Analysis of the mutated gene of one of the mutants, N22, revealed the presence of a
pts
operon in this bacterium, and a mutation was found in
ptsI
in the operon. In addition to its inability to produce chitinase, N22 did not grow well on
N
-acetyl-
d
-glucosamine (GlcNAc), (GlcNAc)
2
, and some other carbon sources, most of which were phosphotransferase system (PTS) sugars. Thus, the inability to produce chitinase was assumed to be caused by the defect in uptake of (GlcNAc)
2
via the PTS, considering that (GlcNAc)
2
is the minimal substrate for chitinase induction and the major product of chitin hydrolysis by chitinases of this bacterium. To confirm this assumption, the
chb
operon, encoding the (GlcNAc)
2
-specific enzyme II permease, was cloned by reference to its
Escherichia coli
counterpart, and the
Serratia chb
operon was shown to comprise
chbB
,
chbC
,
bglA
,
chbR
, and
chbG
. Disruption of
chbC
drastically reduced production of chitinases and CBP21 and impaired growth on colloidal chitin. These results indicate that uptake of (GlcNAc)
2
is mediated by the PTS and that the (GlcNAc)
2
-specific enzyme II permease constitutes its major pathway. Since (GlcNAc)
2
uptake is essential for induction of chitinases and CBP21 production, (GlcNAc)
2
appears to be the key molecule in recognition and utilization of chitin by
S. marcescens
.
The Activator of GntII Genes for Gluconate Metabolism, GntH, Exerts Negative Control of GntR-Regulated GntI Genes in
Escherichia coli
Authors: Tsunedomi Ryouichi , Izu Hanae , Kawai Takuya , Matsushita Kazunobu , Ferenci Thomas , Yamada Mamoru 
Published: March 2003

ABSTRACT

Gluconate is one of the preferred carbon sources of
Escherichia coli
, and two sets of
gnt
genes (encoding the GntI and GntII systems) are involved in its transport and metabolism. GntR represses the GntI genes
gntKU
and
gntT
, whereas GntH was previously suggested to be an activator for the GntII genes
gntV
and
idnDO-gntWH.
The helix-turn-helix residues of the two regulators GntR and GntH exhibit extensive homologies. The similarity between the two regulators prompted analysis of the cross-regulation of the GntI genes by GntH. Repression of
gntKU
and
gntT
by GntH, as well as GntR, was indeed observed using transcriptional fusions and RNA analysis. High GntH expression, from cloned
gntH
or induced through 5-ketogluconate, was required to observe repression of GntI genes. Two GntR-binding elements were identified in the promoter-operator region of
gntKU
and were also shown to be the target sites of GntH by mutational analysis. However, the GntI genes were not induced by gluconate in the presence of enhanced amounts of GntH, whereas repression by GntR was relieved by gluconate. The repression of GntI genes by GntH is thus unusual in that it is not relieved by the availability of substrate. These results led us to propose that GntH activates GntII and represses the GntI genes in the presence of metabolites derived from gluconate, allowing the organism to switch from the GntI to the GntII system. This cross-regulation may explain the progressive changes in
gnt
gene expression along with phases of cell growth in the presence of gluconate.
Purification and In Vitro Characterization of the
Serratia marcescens
NucC Protein, a Zinc-Binding Transcription Factor Homologous to P2 Ogr
Authors: McAlister Victor , Zou Chao , Winslow Robert H. , Christie Gail E. 
Published: March 2003

ABSTRACT

NucC is structurally and functionally homologous to a family of prokaryotic zinc finger transcription factors required for late gene expression in P2- and P4-related bacteriophages. Characterization of these proteins in vitro has been hampered by their relative insolubility and tendency to aggregate. We report here the successful purification of soluble, active, wild-type NucC protein. Purified NucC exhibits site-specific binding to a conserved DNA sequence that is located upstream of NucC-dependent
Serratia marcescens
promoters and the late promoters of P2-related phages. This sequence is sufficient for binding of NucC in vitro. NucC binding to the
S. marcescens
nuclease promoter P

nucA

and to the sequence upstream of the P2 late promoter P

F

is accompanied by DNA bending. NucC protects about 25 nucleotides of the P

F

upstream region from DNase I digestion, and RNA polymerase protects the promoter region only in the presence of NucC. Template DNA, RNA polymerase holoenzyme, and purified NucC are the only macromolecular components required for transcription from P

F

in vitro.
Analysis of Genome Plasticity in Pathogenic and Commensal
Escherichia coli
Isolates by Use of DNA Arrays
Authors: Dobrindt Ulrich , Agerer Franziska , Michaelis Kai , Janka Andreas , Buchrieser Carmen , Samuelson Martin , Svanborg Catharina , Gottschalk Gerhard , Karch Helge , Hacker Jörg 
Published: March 2003

ABSTRACT

Genomes of prokaryotes differ significantly in size and DNA composition.
Escherichia coli
is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic
E. coli
strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal
E. coli
isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic
E. coli
K-12 strain MG1655 was investigated in 26
E. coli
isolates, including various extraintestinal and intestinal pathogenic
E. coli
isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of
E. coli
was determined using a DNA “pathoarray” developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different
E. coli
strains. Up to 10% of the
E. coli
K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic
E. coli
are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal
E. coli
isolates. Based on these results, the conserved
E. coli
core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among
E. coli
strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.
ARhizobium leguminosarumAcpXL Mutant Produces Lipopolysaccharide Lacking 27-Hydroxyoctacosanoic Acid
Authors: Vedam Vinata , Kannenberg Elmar L. , Haynes Janine G. , Sherrier D. Janine , Datta Anup , Carlson Russell W. 
Published: March 2003

ABSTRACTThe structure of the lipid A fromRhizobium etliandRhizobium leguminosarumlipopolysaccharides (LPSs) lacks phosphate and contains a galacturonosyl residue at its 4′ position, an acylated 2-aminogluconate in place of the proximal glucosamine, and a very long chain ω-1 hydroxy fatty acid, 27-hydroxyoctacosanoic acid (27OHC28:0). The 27OHC28:0 moiety is common in lipid A's among members of theRhizobiaceaeand also among a number of the facultative intracellular pathogens that form chronic infections, e.g.,Brucella abortus,Bartonella henselae, andLegionella pneumophila. In this paper, a mutant ofR. leguminosarumwas created by placing a kanamycin resistance cassette withinacpXL, the gene which encodes the acyl carrier protein for 27OHC28:0. The result was an LPS containing a tetraacylated lipid A lacking 27OHC28:0. A small amount of the mutant lipid A may contain an added palmitic acid residue. The mutant is sensitive to changes in osmolarity and an increase in acidity, growth conditions that likely occur in the nodule microenvironment. In spite of the probably hostile microenvironment of the nodule, theacpXLmutant is still able to form nitrogen-fixing root nodules even though the appearance and development of nodules are delayed. Therefore, it is possible that theacpXLmutant has a host-inducible mechanism which enables it to adapt to these physiological changes.
Comprehensive Studies of Drug Resistance Mediated by Overexpression of Response Regulators of Two-Component Signal Transduction Systems in
Escherichia coli
Authors: Hirakawa Hidetada , Nishino Kunihiko , Hirata Takahiro , Yamaguchi Akihito 
Published: March 2003

ABSTRACT

In
Escherichia coli
, there are 32 open reading frames (ORFs) that are assumed to be response regulator genes of two-component signal transduction systems on the basis of sequence similarities. We cloned all of these 32 ORFs into a multicopy expression vector and investigated whether or not they confer drug resistance via control of drug resistance determinants. Fifteen of these ORFs, i.e.,
baeR
,
citB
,
cpxR
,
evgA
,
fimZ
,
kdpE
,
narL
,
narP
,
ompR
,
rcsB
,
rstA
,
torR
,
yedW
,
yehT
, and
dcuR
, conferred increased single- or multidrug resistance. Two-thirds of them conferred deoxycholate resistance. Five of them, i.e.,
evgA
,
baeR
,
ompR, cpxR
, and
rcsB
, modulated the expression of several drug exporter genes. The drug resistance mediated by
evgA
,
baeR
, and
cpxR
could be assigned to drug exporters by using drug exporter gene knockout strains.
Interactions between the Outer Membrane Ferric Citrate Transporter FecA and TonB: Studies of the FecA TonB Box
Authors: Ogierman Monica , Braun Volkmar 
Published: March 2003

ABSTRACTBoth induction of transcription of the ferric citrate transport genes and transport of ferric citrate by theEscherichia coliouter membrane receptor FecA require energy derived from the proton motive force (PMF) of the inner membrane. The energy is transduced to FecA by the inner membrane complex, TonB, ExbB, and ExbD. Region 160 of TonB and the conserved TonB box of other TonB-dependent receptors are implicated as sites of interaction. In the present study, the postulated TonB box (D80A81L82T83V84) of FecA was deleted in frame, with a subsequent loss of both FecA functions. DALTV of FecA could be functionally replaced with the core TonB boxes of FhuA (DTITV) and FepA (DTIVV). Each residue of the TonB box of FecA was sequentially replaced with cysteine residues, and only the D80C replacement showed a loss (reduction) of both FecA functions. A physical interaction between TonB and FecA was demonstrated using both in vivo site-specific disulfide bond cross-linking and nonspecific formaldehyde (FA) cross-linking. Pairwise combinations of FecA (DALTV)/Cys substitutions were cross-linked via disulfide bond formation with TonBQ160C, TonBQ162C, and TonBY163C. Unexpectedly, this cross-linking was not enhanced by substrate (ferric citrate). In contrast, the TonB-FecA interaction was enhanced by ferric citrate in the FA-cross-linking assay. Energy derived from the PMF was not required for the TonB-FecA interaction in either the disulfide- or FA-cross-linking assay. TonB/CysExbB/ExbD(D25N) was still able to cross-link with the FecA (DALTV)/Cys derivatives in atonB tolQbackground, even though ExbD25N renders the TonB/ExbBD complex nonfunctional (V. Braun, S. Gaisser, C. Herrmann, K. Kampfenkel, H. Killmann, and I. Traub, J. Bacteriol.178:2836-2845, 1996). TonB cross-linked to FecA via FA was not inhibited by either carbonylcyanide-m-chlorophenylhydrazone or 1 mM 2,4-dinitrophenol, which dissipate the electrochemical potential of the cytoplasmic membrane and disrupt both FecA functions. The studies shown here demonstrate the significance of the TonB box for FecA functions and are consistent with the view that it is the structure and not the sequence of the TonB box that is important for activity. Demonstrated here for the first time is the physical interaction of TonB and FecA, which is enhanced by ferric citrate.
Identification of Catabolite Repression as a Physiological Regulator of Biofilm Formation byBacillus subtilisby Use of DNA Microarrays
Authors: Stanley Nicola R. , Britton Robert A. , Grossman Alan D. , Lazazzera Beth A. 
Published: March 2003

ABSTRACTBiofilms are structured communities of cells that are encased in a self-produced polymeric matrix and are adherent to a surface. Many biofilms have a significant impact in medical and industrial settings. The model gram-positive bacteriumBacillus subtilishas recently been shown to form biofilms. To gain insight into the genes involved in biofilm formation by this bacterium, we used DNA microarrays representing >99% of the annotatedB. subtilisopen reading frames to follow the temporal changes in gene expression that occurred as cells transitioned from a planktonic to a biofilm state. We identified 519 genes that were differentially expressed at one or more time points as cells transitioned to a biofilm. Approximately 6% of the genes ofB. subtiliswere differentially expressed at a time when 98% of the cells in the population were in a biofilm. These genes were involved in motility, phage-related functions, and metabolism. By comparing the genes differentially expressed during biofilm formation with those identified in other genomewide transcriptional-profiling studies, we were able to identify several transcription factors whose activities appeared to be altered during the transition from a planktonic state to a biofilm. Two of these transcription factors were Spo0A and sigma-H, which had previously been shown to affect biofilm formation byB. subtilis. A third signal that appeared to be affecting gene expression during biofilm formation was glucose depletion. Through quantitative biofilm assays and confocal scanning laser microscopy, we observed that glucose inhibited biofilm formation through the catabolite control protein CcpA.
Global Characterization of Disulfide Stress inBacillus subtilis
Authors: Leichert Lars Ingo Ole , Scharf Christian , Hecker Michael 
Published: March 2003

ABSTRACTWe used DNA macroarray and proteome analysis to analyze the regulatory networks inBacillus subtilisthat are affected by disulfide stress. To induce disulfide stress, we used the specific thiol oxidant diamide. After addition of 1 mM diamide to an exponentially growing culture, cell growth stopped until the medium was cleared of diamide. Global analysis of the mRNA expression pattern during growth arrest revealed 350 genes that were induced by disulfide stress by greater than threefold. Strongly induced genes included known oxidative stress genes that are under the control of the global repressor PerR and heat shock genes controlled by the global repressor CtsR. Other genes that were strongly induced encode putative regulators of gene expression and proteins protecting against toxic elements and heavy metals. Many genes were substantially repressed by disulfide stress, among them most of the genes belonging to the negative stringent response. Two-dimensional gels of radioactively labeled protein extracts allowed us to visualize and quantitate the massive changes in the protein expression pattern that occurred in response to disulfide stress. The observed dramatic alteration in the protein pattern reflected the changes found in the transcriptome experiments. The response to disulfide stress seems to be a complex combination of different regulatory networks, indicating that redox-sensing cysteines play a key role in different signaling pathways sensing oxidative stress, heat stress, toxic element stress, and growth inhibition.