bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silencing the vacuolar invertase gene GhVIN1 blocks cotton fiber initiation from the ovule epidermis, probably by suppressing a cohort of regulatory genes via sugar signaling
Authors: Wang Lu , Cook Akiko , Patrick John W. , Chen Xiao‐Ya , Ruan Yong‐Ling 
Published: March 2014

SummaryCotton fibers, the most important source of cellulose for the global textile industry, are single‐celled trichomes derived from the ovule epidermis at or just prior to anthesis. Despite progress in understanding cotton fiber elongation and cell‐wall biosynthesis, knowledge regarding the molecular basis of fiber cell initiation, the first step of fiber development determining the fiber yield potential, remains elusive. Here, we provide evidence that expression of a vacuolar invertase (VIN) is an early event that is essential for cotton fiber initiation. RNAi‐mediated suppression of GhVIN1, a major VIN gene that is highly expressed in wild‐type fiber initials, resulted in significant reduction of VIN activity and consequently a fiberless seed phenotype in a dosage dependent manner. The absence of a negative effect on seed development in these fiberless seeds indicates that the phenotype is unlikely to be due to lack of carbon nutrient. Gene expression analyses coupled with in vitro ovule culture experiments revealed that GhVIN1‐derived hexose signaling may play an indispensable role in cotton fiber initiation, probably by regulating the transcription of several MYB transcription factors and auxin signaling components that were previously identified as required for fiber initiation. Together, the data represent a significant advance in understanding the mechanisms of cotton fiber initiation, and provide the first indication that VIN‐mediated hexose signaling may act as an early event modulating the expression of regulatory genes and hence cell differentiation from the ovule epidermis.
RNA‐Seq transcriptome analysis to identify genes involved in metabolism‐based diclofop resistance in Lolium rigidum
Authors: Gaines Todd A. , Lorentz Lothar , Figge Andrea , Herrmann Johannes , Maiwald Frank , Ott Mark‐Christoph , Han Heping , Busi Roberto , Yu Qin , Powles Stephen B. , Beffa Roland 
Published: March 2014

SummaryWeed control failures due to herbicide resistance are an increasing and worldwide problem that significantly affect crop yields. Metabolism‐based herbicide resistance (referred to as metabolic resistance) in weeds is not well characterized at the genetic level. An RNA‐Seq transcriptome analysis was used to find candidate genes that conferred metabolic resistance to the herbicide diclofop in a diclofop‐resistant population (R) of the major global weed Lolium rigidum. A reference cDNA transcriptome (19 623 contigs) was assembled and assigned putative annotations. Global gene expression was measured using Illumina reads from untreated control, adjuvant‐only control, and diclofop treatment of R and susceptible (S). Contigs that showed constitutive expression differences between untreated R and untreated S were selected for further validation analysis, including 11 contigs putatively annotated as cytochrome P450 (CytP450), glutathione transferase (GST), or glucosyltransferase (GT), and 17 additional contigs with annotations related to metabolism or signal transduction. In a forward genetics validation experiment, nine contigs had constitutive up‐regulation in R individuals from a segregating F2 population, including three CytP450, one nitronate monooxygenase (NMO), three GST, and one GT. Principal component analysis using these nine contigs differentiated F2‐R from F2‐S individuals. In a physiological validation experiment in which 2,4‐D pre‐treatment induced diclofop protection in S individuals due to increased metabolism, seven of the nine genetically validated contigs were induced significantly. Four contigs (two CytP450, NMO, and GT) were consistently highly expressed in nine field‐evolved metabolic resistant L. rigidum populations. These four contigs were strongly associated with the resistance phenotype and are major candidates for contributing to metabolic diclofop resistance.
Arabidopsis guard cell integrity involves the epigenetic stabilization of the FLP and FAMA transcription factor genes
Authors: Lee EunKyoung , Lucas Jessica Regan , Goodrich Justin , Sack Fred David 
Published: March 2014

SummaryArabidopsis guard cell (GC) fate is conferred via a transient pulse of expression of FAMA that encodes a bHLH transcription factor. Stomata often function for years, suggesting that the FAMA expression window stabilizes long‐term GC identity or that additional factors operate. Transgenic lines harboring a copy of a FAMA transgene were found to induce the fate resetting of mature GCs to that of lineage‐specific stem cells causing new stomata to arise within shells of the old, a Stoma‐in‐Stoma (SIS) phenotype. These lines disrupt the normal trimethylation on lysine 27 of histone3 (H3K27me3) on stomatal stem cell genes, a phenotype rescued by constitutive expression of the Polycomb Group (PcG) gene CURLY LEAF. Thus the stability of stomatal fate is enforced by a PcG‐mediated reduction in the transcriptional accessibility of stem cell genes and by the endogenous FAMA gene itself. Moreover, a transgenic FOUR LIPS gene, which encodes a MYB protein that is not required for GC fate, also induces a SIS phenotype and disrupts H3K27 trimethylation. Thus FLP might indirectly enforce GC fate as well.
The rice FISH BONE gene encodes a tryptophan aminotransferase, which affects pleiotropic auxin‐related processes
Authors: Yoshikawa Takanori , Ito Momoyo , Sumikura Tsuyoshi , Nakayama Akira , Nishimura Takeshi , Kitano Hidemi , Yamaguchi Isomaro , Koshiba Tomokazu , Hibara Ken‐Ichiro , Nagato Yasuo , Itoh Jun‐Ichi 
Published: March 2014

SummaryAuxin is a fundamental plant hormone and its localization within organs plays pivotal roles in plant growth and development. Analysis of many Arabidopsis mutants that were defective in auxin biosynthesis revealed that the indole‐3‐pyruvic acid (IPA) pathway, catalyzed by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) families, is the major biosynthetic pathway of indole‐3‐acetic acid (IAA). In contrast, little information is known about the molecular mechanisms of auxin biosynthesis in rice. In this study, we identified a auxin‐related rice mutant, fish bone (fib). FIB encodes an orthologue of TAA genes and loss of FIB function resulted in pleiotropic abnormal phenotypes, such as small leaves with large lamina joint angles, abnormal vascular development, small panicles, abnormal organ identity and defects in root development, together with a reduction in internal IAA levels. Moreover, we found that auxin sensitivity and polar transport activity were altered in the fib mutant. From these results, we suggest that FIB plays a pivotal role in IAA biosynthesis in rice and that auxin biosynthesis, transport and sensitivity are closely interrelated.
Draft Genome Comparison of Representatives of the Three Dominant Genotype Groups of Dairy Bacillus licheniformis Strains
Authors: Dhakal Rajat , Seale R. Brent , Deeth Hilton C. , Craven Heather , Turner Mark S. 
Published: March 2014

ABSTRACT

The spore-forming bacterium
Bacillus licheniformis
is a common contaminant of milk and milk products. Strains of this species isolated from dairy products can be differentiated into three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA (RAPD) analysis; however, little is known about the genomic differences between these groups and the identity of the fragments that make up their RAPD profiles. In this work we obtained high-quality draft genomes of representative strains from each of the three RAPD groups (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to
B. licheniformis
ATCC 14580 and
Bacillus subtilis
168. Whole-genome comparison and multilocus sequence typing revealed that strain G-1 contains significant sequence variability and belongs to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding for a type I restriction modification system, urease production, and bacitracin synthesis, as well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In agreement with this, all isolates of group G, but no group F isolates, were found to possess urease activity and antimicrobial activity against
Micrococcus
. Identification of RAPD band sequences revealed that differences in the RAPD profiles were due to differences in gene lengths, 3′ ends of predicted primer binding sites, or gene presence or absence. This work provides a greater understanding of the phylogenetic and phenotypic differences observed within the
B. licheniformis
species.
Sinorhizobium meliloti Chemoreceptor McpU Mediates Chemotaxis toward Host Plant Exudates through Direct Proline Sensing
Authors: Webb Benjamin A. , Hildreth Sherry , Helm Richard F. , Scharf Birgit E. 
Published: March 2014

ABSTRACT

Bacterial chemotaxis is an important attribute that aids in establishing symbiosis between rhizobia and their legume hosts. Plant roots and seeds exude a spectrum of molecules into the soil to attract their bacterial symbionts. The alfalfa symbiont
Sinorhizobium meliloti
possesses eight chemoreceptors to sense its environment and mediate chemotaxis toward its host. The methyl accepting chemotaxis protein McpU is one of the more abundant
S. meliloti
chemoreceptors and an important sensor for the potent attractant proline. We established a dominant role of McpU in sensing molecules exuded by alfalfa seeds. Mass spectrometry analysis determined that a single germinating seed exudes 3.72 nmol of proline, producing a millimolar concentration near the seed surface which can be detected by the chemosensory system of
S. meliloti
. Complementation analysis of the
mcpU
deletion strain verified McpU as the key proline sensor. A structure-based homology search identified tandem Cache (
ca
lcium channels and
che
motaxis receptors) domains in the periplasmic region of McpU. Conserved residues Asp-155 and Asp-182 of the N-terminal Cache domain were determined to be important for proline sensing by evaluating mutant strains in capillary and swim plate assays. Differential scanning fluorimetry revealed interaction of the isolated periplasmic region of McpU (McpU
40-284
) with proline and the importance of Asp-182 in this interaction. Using isothermal titration calorimetry, we determined that proline binds with a

K
d

(dissociation constant) of 104 μM to McpU
40-284
, while binding was abolished when Asp-182 was substituted by Glu. Our results show that McpU is mediating chemotaxis toward host plants by direct proline sensing.
Uptake of Dissolved Organic Carbon by Gammaproteobacterial Subgroups in Coastal Waters of the West Antarctic Peninsula
Authors: Nikrad Mrinalini P. , Cottrell Matthew T. , Kirchman David L. 
Published: March 2014

ABSTRACT

Heterotrophic bacteria are well known to be key players in the turnover of dissolved organic material (DOM) in the oceans, but the relationship between DOM uptake and bacterial clades is still not well understood. Here we explore the turnover and single-cell use of glucose, an amino acid mixture,
N
-acetylglucosamine (NAG), and protein by gammaproteobacterial clades in coastal waters of the West Antarctic Peninsula in summer and fall. More than 60% of the cells within two closely related gammaproteobacterial clades, Ant4D3 and Arctic96B-16, were active in using the amino acid mixture, protein, and NAG. In contrast, an average of only 7% of all SAR86 cells used amino acids and protein even in summer when DOM use was high. In addition to DOM uptake within a group, we explored the contribution of the three gammaproteobacterial groups to total community uptake of a compound. SAR86 contributed 5- to 10-fold less than the other gammaproteobacterial subgroups to the uptake of all compounds. We found that the overall contribution of the Ant4D3 clade to DOM uptake was highest, whereas the SAR86 clade contributed the least to DOM turnover in West Antarctic Peninsula waters. Our results suggest that the low growth activity of a bacterial clade leads to low abundance, fewer active cells and a low contribution to the turnover of DOM components.
Distribution of Burkholderia pseudomallei in Northern Australia, a Land of Diversity
Authors: McRobb Evan , Kaestli Mirjam , Price Erin P. , Sarovich Derek S. , Mayo Mark , Warner Jeffrey , Spratt Brian G. , Currie Bart J. 
Published: March 2014

ABSTRACT

Burkholderia pseudomallei
is a Gram-negative soil bacillus that is the etiological agent of melioidosis and a biothreat agent. Little is known about the biogeography of this bacterium in Australia, despite its hyperendemicity in the northern region of this continent. The population structure of 953 Australian
B. pseudomallei
strains representing 779 and 174 isolates of clinical and environmental origins, respectively, was analyzed using multilocus sequence typing (MLST). Bayesian population structure and network SplitsTree analyses were performed on concatenated MLST loci, and sequence type (ST) diversity and evenness were examined using Simpson's and Pielou's indices and a multivariate dissimilarity matrix. Bayesian analysis found two
B. pseudomallei
populations in Australia that were geographically distinct; isolates from the Northern Territory were grouped mainly into the first population, whereas the majority of isolates from Queensland were grouped in a second population. Differences in ST evenness were observed between sampling areas, confirming that
B. pseudomallei
is widespread and established across northern Australia, with a large number of fragmented habitats. ST analysis showed that
B. pseudomallei
populations diversified as the sampling area increased. This observation was in contrast to smaller sampling areas where a few STs predominated, suggesting that
B. pseudomallei
populations are ecologically established and not frequently dispersed. Interestingly, there was no identifiable ST bias between clinical and environmental isolates, suggesting the potential for all culturable
B. pseudomallei
isolates to cause disease. Our findings have important implications for understanding the ecology of
B. pseudomallei
in Australia and for potential source attribution of this bacterium in the event of unexpected cases of melioidosis.
Chromosomal Insertions in the Lactobacillus casei
upp
Gene That Are Useful for Vaccine Expression
Authors: Song Bai-fen , Ju Long-zhu , Li Yi-jing , Tang Li-jie 
Published: March 2014

ABSTRACT

To develop a stable and marker-free
Lactobacillus
strain useful for the expression of vaccines, we developed a temperature-sensitive suicide plasmid with expression cassettes containing an HCE promoter, a PgsA anchor, the alpha-toxin gene, and an
rrnB
T1T2 terminator (PPαT) that uses a 5-fluorouracil (5-FU) counterselectable marker for
Lactobacillus casei
. Three strains containing the correct PPαT expression cassettes were produced via the selective pressure of 5-FU screening. We confirmed that the
upp
gene was deleted and that the PPαT expression cassettes were inserted into the
upp
site of
L. casei
ATCC 393 by genomic PCR amplification and sequencing. 5-FU resistance in recombinant bacteria could be stably inherited for as long as 40 generations following insertion. However, bacteria containing the integrated DNA grew more slowly than wild-type
L. casei
. An indirect enzyme-linked immunosorbent assay (ELISA) analysis demonstrated that the alpha-toxin gene was expressed. Also, we visualized expression of the protein on the surface of
L. casei
cells using laser confocal microscopy. These results taken together demonstrate that these recombinant bacteria should provide a safe tool for effective vaccine production.
Reconstruction of an Acetogenic 2,3-Butanediol Pathway Involving a Novel NADPH-Dependent Primary-Secondary Alcohol Dehydrogenase
Authors: Köpke Michael , Gerth Monica L. , Maddock Danielle J. , Mueller Alexander P. , Liew FungMin , Simpson Séan D. , Patrick Wayne M. 
Published: March 2014

ABSTRACT

Acetogenic bacteria use CO and/or CO
2
plus H
2
as their sole carbon and energy sources. Fermentation processes with these organisms hold promise for producing chemicals and biofuels from abundant waste gas feedstocks while simultaneously reducing industrial greenhouse gas emissions. The acetogen
Clostridium autoethanogenum
is known to synthesize the pyruvate-derived metabolites lactate and 2,3-butanediol during gas fermentation. Industrially, 2,3-butanediol is valuable for chemical production. Here we identify and characterize the
C. autoethanogenum
enzymes for lactate and 2,3-butanediol biosynthesis. The putative
C. autoethanogenum
lactate dehydrogenase was active when expressed in
Escherichia coli
. The 2,3-butanediol pathway was reconstituted in
E. coli
by cloning and expressing the candidate genes for acetolactate synthase, acetolactate decarboxylase, and 2,3-butanediol dehydrogenase. Under anaerobic conditions, the resulting
E. coli
strain produced 1.1 ± 0.2 mM 2
R
,3
R
-butanediol (23 μM h
−1
optical density unit
−1
), which is comparable to the level produced by
C. autoethanogenum
during growth on CO-containing waste gases. In addition to the 2,3-butanediol dehydrogenase, we identified a strictly NADPH-dependent primary-secondary alcohol dehydrogenase (CaADH) that could reduce acetoin to 2,3-butanediol. Detailed kinetic analysis revealed that CaADH accepts a range of 2-, 3-, and 4-carbon substrates, including the nonphysiological ketones acetone and butanone. The high activity of CaADH toward acetone led us to predict, and confirm experimentally, that
C. autoethanogenum
can act as a whole-cell biocatalyst for converting exogenous acetone to isopropanol. Together, our results functionally validate the 2,3-butanediol pathway from
C. autoethanogenum
, identify CaADH as a target for further engineering, and demonstrate the potential of
C. autoethanogenum
as a platform for sustainable chemical production.
Salivary Microbiota and Metabolome Associated with Celiac Disease
Authors: Francavilla Ruggiero , Ercolini Danilo , Piccolo Maria , Vannini Lucia , Siragusa Sonya , De Filippis Francesca , De Pasquale Ilaria , Di Cagno Raffaella , Di Toma Michele , Gozzi Giorgia , Serrazanetti Diana I. , De Angelis Maria , Gobbetti Marco 
Published: March 2014

ABSTRACT

This study aimed to investigate the salivary microbiota and metabolome of 13 children with celiac disease (CD) under a gluten-free diet (treated celiac disease [T-CD]). The same number of healthy children (HC) was used as controls. The salivary microbiota was analyzed by an integrated approach using culture-dependent and -independent methods. Metabolome analysis was carried out by gas chromatography-mass spectrometry–solid-phase microextraction. Compared to HC, the number of some cultivable bacterial groups (e.g., total anaerobes) significantly (
P
< 0.05) differed in the saliva samples of the T-CD children. As shown by community-level catabolic profiles, the highest Shannon's diversity and substrate richness were found in HC. Pyrosequencing data showed the highest richness estimator and diversity index values for HC. Levels of
Lachnospiraceae
,
Gemellaceae
, and
Streptococcus sanguinis
were highest for the T-CD children.
Streptococcus thermophilus
levels were markedly decreased in T-CD children. The saliva of T-CD children showed the largest amount of
Bacteroidetes
(e.g.,
Porphyromonas
sp.,
Porphyromonas endodontalis
, and
Prevotella nanceiensis
), together with the smallest amount of
Actinobacteria
. T-CD children were also characterized by decreased levels of some
Actinomyces
species,
Atopobium
species, and
Corynebacterium durum
.
Rothia mucilaginosa
was the only
Actinobacteria
species found at the highest level in T-CD children. As shown by multivariate statistical analyses, the levels of organic volatile compounds markedly differentiated T-CD children. Some compounds (e.g., ethyl-acetate, nonanal, and 2-hexanone) were found to be associated with T-CD children. Correlations (false discovery rate [FDR], <0.05) were found between the relative abundances of bacteria and some volatile organic compounds (VOCs). The findings of this study indicated that CD is associated with oral dysbiosis that could affect the oral metabolome.
Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway
Authors: Campillo Tony , Renoud Sébastien , Kerzaon Isabelle , Vial Ludovic , Baude Jessica , Gaillard Vincent , Bellvert Floriant , Chamignon Cécile , Comte Gilles , Nesme Xavier , Lavire Céline , Hommais Florence 
Published: March 2014

ABSTRACT

The soil- and rhizosphere-inhabiting bacterium
Agrobacterium fabrum
(genomospecies G8 of the
Agrobacterium tumefaciens
species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl–CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl–CoA, vanillic acid, and protocatechuic acid. The genes
atu1416
,
atu1417
, and
atu1420
have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes
atu1415
and
atu1421
have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)–CoA β-keto-thiolase, respectively. We thus demonstrated that the
A. fabrum
hydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transform
p
-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.
Anoxic Androgen Degradation by the Denitrifying Bacterium Sterolibacterium denitrificans via the 2,3-seco Pathway
Authors: Wang Po-Hsiang , Yu Chang-Ping , Lee Tzong-Huei , Lin Ching-Wen , Ismail Wael , Wey Shiaw-Pyng , Kuo An-Ti , Chiang Yin-Ru 
Published: March 2014

ABSTRACT

The biodegradation of steroids is a crucial biochemical process mediated exclusively by bacteria. So far, information concerning the anoxic catabolic pathways of androgens is largely unknown, which has prevented many environmental investigations. In this work, we show that
Sterolibacterium denitrificans
DSMZ 13999 can anaerobically mineralize testosterone and some C
19
androgens. By using a
13
C-metabolomics approach and monitoring the sequential appearance of the intermediates, we demonstrated that
S. denitrificans
uses the 2,3-
seco
pathway to degrade testosterone under anoxic conditions. Furthermore, based on the identification of a C
17
intermediate, we propose that the A-ring cleavage may be followed by the removal of a C
2
side chain at C-5 of 17-hydroxy-1-oxo-2,3-
seco
-androstan-3-oic acid (the A-ring cleavage product) via retro-aldol reaction. The androgenic activities of the bacterial culture and the identified intermediates were assessed using the
lacZ
-based yeast androgen assay. The androgenic activity in the testosterone-grown
S. denitrificans
culture decreased significantly over time, indicating its ability to eliminate androgens. The A-ring cleavage intermediate (≤500 μM) did not exhibit androgenic activity, whereas the sterane-containing intermediates did. So far, only two androgen-degrading anaerobes (
Sterolibacterium denitrificans
DSMZ 13999 [a betaproteobacterium] and
Steroidobacter denitrificans
DSMZ 18526 [a gammaproteobacterium]) have been isolated and characterized, and both of them use the 2,3-
seco
pathway to anaerobically degrade androgens. The key intermediate 2,3-
seco
-androstan-3-oic acid can be used as a signature intermediate for culture-independent environmental investigations of anaerobic degradation of C
19
androgens.