bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Genomic Approach to Suberin Biosynthesis and Cork Differentiation
Authors: Soler Marçal , Serra Olga , Molinas Marisa , Huguet Gemma , Fluch Silvia , Figueras Mercè 
Published: March 2007

Abstract
Cork (phellem) is a multilayered dead tissue protecting plant mature stems and roots and plant healing tissues from water loss and injuries. Cork cells are made impervious by the deposition of suberin onto cell walls. Although suberin deposition and cork formation are essential for survival of land plants, molecular studies have rarely been conducted on this tissue. Here, we address this question by combining suppression subtractive hybridization together with cDNA microarrays, using as a model the external bark of the cork tree (Quercus suber), from which bottle cork is obtained. A suppression subtractive hybridization library from cork tree bark was prepared containing 236 independent sequences; 69% showed significant homology to database sequences and they corresponded to 135 unique genes. Out of these genes, 43.5% were classified as the main pathways needed for cork biosynthesis. Furthermore, 19% could be related to regulatory functions. To identify genes more specifically required for suberin biosynthesis, cork expressed sequence tags were printed on a microarray and subsequently used to compare cork (phellem) to a non-suberin-producing tissue such as wood (xylem). Based on the results, a list of candidate genes relevant for cork was obtained. This list includes genes for the synthesis, transport, and polymerization of suberin monomers such as components of the fatty acid elongase complexes, ATP-binding cassette transporters, and acyltransferases, among others. Moreover, a number of regulatory genes induced in cork have been identified, including MYB, No-Apical-Meristem, and WRKY transcription factors with putative functions in meristem identity and cork differentiation.
E2F RegulatesFASCIATA1, a Chromatin Assembly Gene Whose Loss Switches on the Endocycle and Activates Gene Expression by Changing the Epigenetic Status
Authors: Ramirez-Parra Elena , Gutierrez Crisanto 
Published: March 2007

AbstractMaintenance of genome integrity depends on histone chaperone-mediated chromatin reorganization. DNA replication-associated nucleosome deposition relies on chromatin assembly factor-1 (CAF-1). Depletion of CAF-1 in human cells leads to cell death, whereas in Arabidopsis (Arabidopsis thaliana), where it is involved in heterochromatin compaction and homologous recombination, plants are viable. The mechanism that makes the lack of CAF-1 activity compatible with development is not known. Here, we show that the FASCIATA1 (FAS1) gene, which encodes the CAF-1 large subunit, is a target of E2F transcription factors. Mutational studies demonstrate that one of the two E2F binding sites in its promoter has an activator role, whereas the other has a repressor function. Loss of FAS1 results in reduced type A cyclin-dependent kinase activity, inhibits mitotic progression, and promotes a precocious and systemic switch to the endocycle program. Selective up-regulation of the expression of a subset of genes, including those involved in activation of the G2 DNA damage checkpoint, also occurs upon FAS1 loss. This activation is not the result of a global change in chromatin structure, but depends on selective epigenetic changes in histone acetylation and methylation within a small region in their promoters. This suggests that correct chromatin assembly during the S-phase is required to prevent unscheduled changes in the epigenetic marks of target genes. Interestingly, activation of the endocycle switch as well as introduction of activating histone marks in the same set of G2 checkpoint genes are detected upon treatment of wild-type plants with DNA-damaging treatments. Our results are consistent with a model in which defects in chromatin assembly during the S-phase and DNA damage signaling share part of a pathway, which ultimately leads to mitotic arrest and triggers the endocycle program. Together, this might be a bypass mechanism that makes development compatible with cell division arrest induced by DNA damage stress.
AWUSCHEL-LIKE HOMEOBOXGene Represses aYABBYGene Expression Required for Rice Leaf Development
Authors: Dai Mingqiu , Hu Yongfeng , Zhao Yu , Liu Huifang , Zhou Dao-Xiu 
Published: March 2007

AbstractYABBY and WUSCHEL-LIKE HOMEOBOX (WOX) genes have been shown to play important roles in lateral organ formation and meristem function. Here, we report the characterization of functional relationship between rice (Oryza sativa) YAB3 and WOX3 in rice leaf development. Rice YAB3 is closely related to maize (Zea mays) ZmYAB14 and Arabidopsis (Arabidopsis thaliana) FILAMENTOUS FLOWER (FIL), whereas rice WOX3 is highly conserved with maize narrow sheath1 (NS1) and NS2 and Arabidopsis PRESSED FLOWER (PRS). In situ hybridization experiments revealed that the expression of both genes was excluded from the shoot apical meristem, but the transcripts were detected in leaf primordia, young leaves, and reproductive organs without any polar distribution. The function of the two genes was studied by both overexpression and RNA interference (RNAi) in transgenic rice. YAB3 RNAi induced twisted and knotted leaves lacking specialized structures such as ligule and auricles, while no phenotypic change was observed in YAB3 overexpression plants, suggesting that rice YAB3 may be required for leaf cell growth and differentiation. Overexpression of WOX3 repressed YAB3 and showed a YAB3 RNAi phenotype. The expression of class I KNOTTED-LIKE HOMEOBOX (KNOX) genes was ectopically induced in leaves of YAB3 RNAi or WOX3 overexpression plants. Data from inducible WOX3 expression and DNA-protein interaction assays suggested that WOX3 acted as a transcriptional repressor of YAB3. These data reveal a regulatory network involving YAB3, WOX3, and KNOX genes required for rice leaf development.
Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing
Authors: Weber Andreas P.M. , Weber Katrin L. , Carr Kevin , Wilkerson Curtis , Ohlrogge John B. 
Published: March 2007

AbstractMassively parallel sequencing of DNA by pyrosequencing technology offers much higher throughput and lower cost than conventional Sanger sequencing. Although extensively used already for sequencing of genomes, relatively few applications of massively parallel pyrosequencing to transcriptome analysis have been reported. To test the ability of this technology to provide unbiased representation of transcripts, we analyzed mRNA from Arabidopsis (Arabidopsis thaliana) seedlings. Two sequencing runs yielded 541,852 expressed sequence tags (ESTs) after quality control. Mapping of the ESTs to the Arabidopsis genome and to The Arabidopsis Information Resource 7.0 cDNA models indicated: (1) massively parallel pyrosequencing detected transcription of 17,449 gene loci providing very deep coverage of the transcriptome. Performing a second sequencing run only increased the number of genes identified by 10%, but increased the overall sequence coverage by 50%. (2) Mapping of the ESTs to their predicted full-length transcripts indicated that all regions of the transcript were well represented regardless of transcript length or expression level. Furthermore, short, medium, and long transcripts were equally represented. (3) Over 16,000 of the ESTs that mapped to the genome were not represented in the existing dbEST database. In some cases, the ESTs provide the first experimental evidence for transcripts derived from predicted genes, and, for at least 60 locations in the genome, pyrosequencing identified likely protein-coding sequences that are not now annotated as genes. Together, the results indicate massively parallel pyrosequencing provides novel information helpful to improve the annotation of the Arabidopsis genome. Furthermore, the unbiased representation of transcripts will be particularly useful for gene discovery and gene expression analysis of nonmodel plants with less complete genomic information.
The Thylakoid Lumen Protease Deg1 Is Involved in the Repair of Photosystem II from Photoinhibition in Arabidopsis
Authors: Kapri-Pardes Einat , Naveh Leah , Adam Zach 
Published: March 2007

Abstract
Deg1 is a Ser protease peripherally attached to the lumenal side of the thylakoid membrane. Its physiological function is unknown, but its localization makes it a suitable candidate for participation in photoinhibition repair by degradation of the photosystem II reaction center protein D1. We transformed Arabidopsis thaliana with an RNA interference construct and obtained plants with reduced levels of Deg1. These plants were smaller than wild-type plants, flowered earlier, were more sensitive to photoinhibition, and accumulated more of the D1 protein, probably in an inactive form. Two C-terminal degradation products of the D1 protein, of 16 and 5.2 kD, accumulated at lower levels compared with the wild type. Moreover, addition of recombinant Deg1 to inside-out thylakoid membranes isolated from the mutant could induce the formation of the 5.2-kD D1 C-terminal fragment, whereas the unrelated proteases trypsin and thermolysin could not. Immunoblot analysis revealed that mutants containing less Deg1 also contain less FtsH protease, and FtsH mutants contain less Deg1. These results suggest that Deg1 cooperates with the stroma-exposed proteases FtsH and Deg2 in degrading D1 protein during repair from photoinhibition by cleaving lumen-exposed regions of the protein. In addition, they suggest that accumulation of Deg1 and FtsH proteases may be coordinated.
A Core Subunit of the RNA-Processing/Degrading Exosome Specifically Influences Cuticular Wax Biosynthesis inArabidopsis
Authors: Hooker Tanya S. , Lam Patricia , Zheng Huanquan , Kunst Ljerka 
Published: March 2007

AbstractThe cuticle is an extracellular matrix composed of cutin polyester and waxes that covers aerial organs of land plants and protects them from environmental stresses. The Arabidopsis thaliana cer7 mutant exhibits reduced cuticular wax accumulation and contains considerably lower transcript levels of ECERIFERUM3/WAX2/YORE-YORE (CER3/WAX2/YRE), a key wax biosynthetic gene. We show here that CER7 protein is a putative 3′-5′ exoribonuclease homologous to yeast Ribonuclease PH45 (RRP45p), a core subunit of the RNA processing and degrading exosome that controls the expression of CER3/WAX2/YRE. We propose that CER7 acts by degrading a specific mRNA species encoding a negative regulator of CER3/WAX2/YRE transcription. A second RRP45p homolog found in Arabidopsis, designated At RRP45a, is partially functionally redundant with CER7, and complete loss of RRP45 function in Arabidopsis is lethal. To our knowledge, CER7 is currently the only example of a core exosomal subunit specifically influencing a cellular process.
Effect of the Mycorrhizosphere on the Genotypic and Metabolic Diversity of the Bacterial Communities Involved in Mineral Weathering in a Forest Soil
Authors: Uroz S. , Calvaruso C. , Turpault M. P. , Pierrat J. C. , Mustin C. , Frey-Klett P. 
Published: March 2007

ABSTRACT

To date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. However, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. In this study, we characterized a collection of 61 bacterial strains isolated from
Scleroderma citrinum
mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. The ability of bacteria to weather biotite was assessed with a new microplate bioassay that measures the pH and the quantity of iron released from this mineral. We showed that weathering bacteria occurred more frequently in the vicinity of
S. citrinum
than in the bulk soil. Moreover, the weathering efficacy of the mycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera
Burkholderia
,
Collimonas
,
Pseudomonas
, and
Sphingomonas
, and their carbon metabolism was characterized by the BIOLOG method. The most efficient isolates belonged to the genera
Burkholderia
and
Collimonas
. Multivariate analysis resulted in identification of three metabolic groups, one of which contained mainly bacterial isolates associated with
S. citrinum
and exhibiting high mineral-weathering potential. Therefore, our results support the hypothesis that by its carbon metabolism this fungus selects in the bulk soil reservoir a bacterial community with high weathering potential, and they also address the question of functional complementation between mycorrhizal fungi and bacteria in the ectomycorrhizal complex for the promotion of tree nutrition.
Characterization of
Fusarium oxysporum
β-1,6-Galactanase, an Enzyme That Hydrolyzes Larch Wood Arabinogalactan
Authors: Sakamoto Tatsuji , Taniguchi Yuya , Suzuki Shiho , Ihara Hideshi , Kawasaki Haruhiko 
Published: March 2007

ABSTRACT

A type II arabinogalactan-degrading enzyme (FoGal1) was purified from
Fusarium oxysporum
12S, and the corresponding cDNA was isolated. FoGal1 had high similarity to enzymes of glycoside hydrolase family 5. Treatment of larch wood arabinogalactan with the recombinant enzyme indicated that FoGal1 is a β-1,6-galactanase that preferentially debranches β-1,6-galactobiose from the substrate.
VanA-Type Enterococci from Humans, Animals, and Food: Species Distribution, Population Structure, Tn
1546
Typing and Location, and Virulence Determinants
Authors: Biavasco F. , Foglia G. , Paoletti C. , Zandri G. , Magi G. , Guaglianone E. , Sundsfjord A. , Pruzzo C. , Donelli G. , Facinelli B. 
Published: March 2007

ABSTRACT

VanA-type human (
n
= 69), animal (
n
= 49), and food (
n
= 36) glycopeptide-resistant enterococci (GRE) from different geographic areas were investigated to study their possible reservoirs and transmission routes. Pulsed-field gel electrophoresis (PFGE) revealed two small genetically related clusters, M39 (
n
= 4) and M49 (
n
= 13), representing
Enterococcus faecium
isolates from animal and human feces and from clinical and fecal human samples. Multilocus sequence typing showed that both belonged to the epidemic lineage of CC17.
purK
allele analysis of 28 selected isolates revealed that type 1 was prevalent in human strains (8/11) and types 6 and 3 (14/15) were prevalent in poultry (animals and meat). One hundred and five of the 154 VanA GRE isolates, encompassing different species, origins, and PFGE types, were examined for Tn
1546
type and location (plasmid or chromosome) and the incidence of virulence determinants. Hybridization of S1- and I-CeuI-digested total DNA revealed a plasmid location in 98% of the isolates. Human intestinal and animal
E. faecium
isolates bore large (>150 kb)
vanA
plasmids. Results of PCR-restriction fragment length polymorphism and sequencing showed the presence of prototype Tn
1546
in 80% of strains and the G-to-T mutation at position 8234 in three human intestinal and two pork
E. faecium
isolates. There were no significant associations (
P
> 0.5) between Tn
1546
type and GRE source or enterococcal species. Virulence determinants were detected in all reservoirs but were significantly more frequent (
P
< 0.02) among clinical strains. Multiple determinants were found in clinical and meat
Enterococcus faecalis
isolates. The presence of indistinguishable
vanA
elements (mostly plasmid borne) and virulence determinants in different species and PFGE-diverse populations in the presence of host-specific
purK
housekeeping genes suggested that all GRE might be potential reservoirs of resistance determinants and virulence traits transferable to human-adapted clusters.
The
dasABC
Gene Cluster, Adjacent to
dasR
, Encodes a Novel ABC Transporter for the Uptake of
N
,
N
′-Diacetylchitobiose in
Streptomyces coelicolor
A3(2)
Authors: Saito Akihiro , Shinya Tomonori , Miyamoto Katsushiro , Yokoyama Tomofumi , Kaku Hanae , Minami Eiichi , Shibuya Naoto , Tsujibo Hiroshi , Nagata Yoshiho , Ando Akikazu , Fujii Takeshi , Miyashita Kiyotaka 
Published: March 2007

ABSTRACT

N
,
N
′-Diacetylchitobiose [(GlcNAc)
2
] induces the transcription of chitinase (
chi
) genes in
Streptomyces coelicolor
A3(2). Physiological studies showed that (GlcNAc)
2
addition triggered
chi
expression and increased the rate of (GlcNAc)
2
concentration decline in culture supernatants of mycelia already cultivated with (GlcNAc)
2
, suggesting that (GlcNAc)
2
induced the synthesis of its own uptake system. Four open reading frames (SCO0531, SCO0914, SCO2946, and SCO5232) encoding putative sugar-binding proteins of ABC transporters were found in the genome by probing the 12-bp repeat sequence required for regulation of
chi
transcription. SCO5232, named
dasA
, showed transcriptional induction by (GlcNAc)
2
and
N
,
N
′,
N
‴-triacetylchitotriose [(GlcNAc)
3
]. Surface plasmon resonance analysis showed that recombinant DasA protein exhibited the highest affinity for (GlcNAc)
2
(equilibrium dissociation constant [

K
D

] = 3.22 × 10
−8
). In the
dasA
-null mutant, the rate of decline of the (GlcNAc)
2
concentration in the culture supernatant was about 25% of that in strain M145. The in vitro and in vivo data clearly demonstrated that
dasA
is involved in (GlcNAc)
2
uptake. Upstream and downstream of
dasA
, the transcriptional regulator gene (
dasR
) and two putative integral membrane protein genes (
dasBC
) are located in the opposite and same orientations, respectively. The expression of
dasR
and
dasB
, which seemed independent of
dasA
transcription, was also induced by (GlcNAc)
2
and (GlcNAc)
3
.
Adherence of Enterohemorrhagic
Escherichia coli
O157, O26, and O111 Strains to Bovine Intestinal Explants Ex Vivo
Authors: Girard Francis , Dziva Francis , van Diemen Pauline , Phillips Alan D. , Stevens Mark P. , Frankel Gad 
Published: March 2007

ABSTRACT

We used bovine intestinal organ culture to study infection by enterohemorrhagic
Escherichia coli
serogroups O157, O26, and O111. We show colonization and attaching and effacing lesion formation on explants derived from the ileum, colon, and rectum. Intimin and Tir were detected at the sites of adherent bacteria; Tir was essential for colonization.
Second Acyl Homoserine Lactone Production System in the Extreme AcidophileAcidithiobacillus ferrooxidans
Authors: Rivas Mariella , Seeger Michael , Jedlicki Eugenia , Holmes David S. 
Published: March 2007

ABSTRACTThe acidophilic proteobacteriumAcidithiobacillus ferrooxidansis involved in the industrial biorecovery of copper. It is found in acidic environments in biofilms and is important in the biogeochemical cycling of metals and nutrients. Its genome contains a cluster of four genes,glyQ,glysS,gph, andact, that are predicted to encode the α and β subunits of glycine tRNA synthetase, a phosphatase, and an acyltransferase, respectively (GenBank accession no. DQ149607).act, cloned and expressed inEscherichia coli, produces acyl homoserine lactones (AHLs) principally of chain length C14according to gas chromatography and mass spectrometry measurements. The AHLs have biological activity as shown by in vivo studies using the reporter strainSinorhizobium melilotiRm41 SinI−. Reverse transcription-PCR (RT-PCR) experiments indicate that the four genes are expressed as a single transcript, demonstrating that they constitute an operon. According to semiquantitative RT-PCR results,actis expressed more highly whenA. ferrooxidansis grown in medium containing iron than when it is grown in medium containing sulfur. Since AHLs are important intercellular signaling molecules used by many bacteria to monitor their population density in quorum-sensing control of gene expression, this result suggests thatA. ferrooxidanshas two quorum-sensing systems, one based on Act, as described herein, and the other based on a Lux-like quorum-sensing system, reported previously. The latter system was shown to be upregulated inA. ferrooxidansgrown in sulfur medium, suggesting that the two quorum-sensing systems respond to different environmental signals that may be related to their abilities to colonize and use different solid sulfur- and iron-containing minerals.
Microbial Reductive Dechlorination of Aroclor 1260 in Baltimore Harbor Sediment Microcosms Is Catalyzed by Three Phylotypes within the Phylum
Chloroflexi
Authors: Fagervold Sonja K. , May Harold D. , Sowers Kevin R. 
Published: March 2007

ABSTRACT

The specific dechlorination pathways for Aroclor 1260 were determined in Baltimore Harbor sediment microcosms developed with the 11 most predominant congeners from this commercial mixture and their resulting dechlorination intermediates. Most of the polychlorinated biphenyl (PCB) congeners were dechlorinated in the
meta
position, and the major products were tetrachlorobiphenyls with unflanked chlorines. Using PCR primers specific for the 16S rRNA genes of known PCB-dehalogenating bacteria, we detected three phylotypes within the microbial community that had the capability to dechlorinate PCB congeners present in Aroclor 1260 and identified their selective activities. Phylotype DEH10, which has a high level of sequence identity to
Dehalococcoides
spp., removed the double-flanked chlorine in 234-substituted congeners and exhibited a preference for
para
-flanked
meta
-chlorines when no double-flanked chlorines were available. Phylotype SF1 had similarity to the
o
-17/DF-1 group of PCB-dechlorinating bacteria. Phylotype SF1 dechlorinated all of the 2345-substituted congeners, mostly in the double-flanked
meta
position and 2356-, 236-, and 235-substituted congeners in the
ortho
-flanked
meta
position, with a few exceptions. A phylotype with 100% sequence identity to PCB-dechlorinating bacterium
o
-17 was responsible for an
ortho
and a double-flanked
meta
dechlorination reaction. Most of the dechlorination pathways supported the growth of all three phylotypes based on competitive PCR enumeration assays, which indicates that PCB-impacted environments have the potential to sustain populations of these PCB-dechlorinating microorganisms. The results demonstrate that the variation in dechlorination patterns of congener mixtures typically observed at different PCB impacted sites can potentially be mediated by the synergistic activities of relatively few dechlorinating species.
Adopting Selected Hydrogen Bonding and Ionic Interactions fromAspergillus fumigatusPhytase Structure Improves the Thermostability ofAspergillus nigerPhyA Phytase
Authors: Zhang Wanming , Mullaney Edward J. , Lei Xin Gen 
Published: March 2007

ABSTRACTAlthough it has been widely used as a feed supplement to reduce manure phosphorus pollution of swine and poultry,Aspergillus nigerPhyA phytase is unable to withstand heat inactivation during feed pelleting. Crystal structure comparisons with its close homolog, the thermostableAspergillus fumigatusphytase (Afp), suggest associations of thermostability with several key residues (E35, S42, R168, and R248) that form a hydrogen bond network in the E35-to-S42 region and ionic interactions between R168 and D161 and between R248 and D244. In this study, loss-of-function mutations (E35A, R168A, and R248A) were introduced singularly or in combination into seven mutants of Afp. All seven mutants displayed decreases in thermostability, with the highest loss (25% [P< 0.05]) in the triple mutant (E35A R168A R248A). Subsequently, a set of corresponding substitutions were introduced into nine mutants of PhyA to strengthen the hydrogen bonding and ionic interactions. While four mutants showed improved thermostability, the best response came from the quadruple mutant (A58E P65S Q191R T271R), which retained 20% greater (P< 0.05) activity after being heated at 80°C for 10 min and had a 7°C higher melting temperature than that of wild-type PhyA. This study demonstrates the functional importance of the hydrogen bond network and ionic interaction in supporting the high thermostability of Afp and the feasibility of adopting these structural units to improve the thermostability of a homologous PhyA phytase.