bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii, an Evergreen Tree Indigenous to the Southern Subtropical Region of China
Authors: Yao Yao , Wang Rui , Lu Jun Kun , Sui Xin Hua , Wang En Tao , Chen Wen Xin 
Published: August 2014

ABSTRACT

The nodulation of
Erythrophleum fordii
has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus
Bradyrhizobium
. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes
recA
and
glnII
classified the isolates into four groups: the
Bradyrhizobium elkanii
and
Bradyrhizobium pachyrhizi
groups, comprising the dominant symbionts,
Bradyrhizobium yuanmingense
, and an unclassified group comprising the minor symbionts. The
nodC
and
nifH
phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of
Bradyrhizobium
species associated with
E. fordii
, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize
E. fordii
rhizobia.
Engineering of Bacillus subtilis Strains To Allow Rapid Characterization of Heterologous Diguanylate Cyclases and Phosphodiesterases
Authors: Gao Xiaohui , Dong Xiao , Subramanian Sundharraman , Matthews Paige M. , Cooper Caleb A. , Kearns Daniel B. , Dann Charles E. 
Published: August 2014

ABSTRACT

Microbial processes, including biofilm formation, motility, and virulence, are often regulated by changes in the available concentration of cyclic dimeric guanosine monophosphate (c-di-GMP). Generally, high c-di-GMP concentrations are correlated with decreased motility and increased biofilm formation and low c-di-GMP concentrations are correlated with an increase in motility and activation of virulence pathways. The study of c-di-GMP is complicated, however, by the fact that organisms often encode dozens of redundant enzymes that synthesize and hydrolyze c-di-GMP, diguanylate cyclases (DGCs), and c-di-GMP phosphodiesterases (PDEs); thus, determining the contribution of any one particular enzyme is challenging. In an effort to develop a facile system to study c-di-GMP metabolic enzymes, we have engineered a suite of
Bacillus subtilis
strains to assess the effect of individual heterologously expressed proteins on c-di-GMP levels. As a proof of principle, we characterized all 37 known genes encoding predicted DGCs and PDEs in
Clostridium difficile
using parallel readouts of swarming motility and fluorescence from green fluorescent protein (GFP) expressed under the control of a c-di-GMP-controlled riboswitch. We found that 27 of the 37 putative
C. difficile
630 c-di-GMP metabolic enzymes had either active cyclase or phosphodiesterase activity, with agreement between our motility phenotypes and fluorescence-based c-di-GMP reporter. Finally, we show that there appears to be a threshold level of c-di-GMP needed to inhibit motility in
Bacillus subtilis
.
Genomic Insights into the Evolutionary Origin of Xanthomonas axonopodis pv. citri and Its Ecological Relatives
Authors: Midha Samriti , Patil Prabhu B. 
Published: August 2014

ABSTRACT

Xanthomonas axonopodis
pv. citri (Xac) is the causal agent of citrus bacterial canker (CBC) and is a serious problem worldwide. Like CBC, several important diseases in other fruits, such as mango, pomegranate, and grape, are also caused by
Xanthomonas
pathovars that display remarkable specificity toward their hosts. While citrus and mango diseases were documented more than 100 years ago, the pomegranate and grape diseases have been known only since the 1950s and 1970s, respectively. Interestingly, diseases caused by all these pathovars were noted first in India. Our genome-based phylogenetic studies suggest that these diverse pathogens belong to a single species and these pathovars may be just a group of rapidly evolving strains. Furthermore, the recently reported pathovars, such as those infecting grape and pomegranate, form independent clonal lineages, while the citrus and mango pathovars that have been known for a long time form one clonal lineage. Such an understanding of their phylogenomic relationship has further allowed us to understand major and unique variations in the lineages that give rise to these pathovars. Whole-genome sequencing studies including ecological relatives from their putative country of origin has allowed us to understand the evolutionary history of Xac and other pathovars that infect fruits.
Functional and Phylogenetic Divergence of Fungal Adenylate-Forming Reductases
Authors: Kalb Daniel , Lackner Gerald , Hoffmeister Dirk 
Published: August 2014

ABSTRACT

A key step in fungal
l
-lysine biosynthesis is catalyzed by adenylate-forming
l
-α-aminoadipic acid reductases, organized in domains for adenylation, thiolation, and the reduction step. However, the genomes of numerous ascomycetes and basidiomycetes contain an unexpectedly large number of additional genes encoding similar but functionally distinct enzymes. Here, we describe the functional
in vitro
characterization of four reductases which were heterologously produced in
Escherichia coli
. The
Ceriporiopsis subvermispora
serine reductase Nps1 features a terminal ferredoxin-NADP
+
reductase (FNR) domain and thus belongs to a hitherto undescribed class of fungal multidomain enzymes. The second major class is characterized by the canonical terminal short-chain dehydrogenase/reductase domain and represented by
Ceriporiopsis subvermispora
Nps3 as the first biochemically characterized
l
-α-aminoadipic acid reductase of basidiomycete origin.
Aspergillus flavus
l
-tyrosine reductases LnaA and LnbA are members of a distinct phylogenetic clade. Phylogenetic analysis supports the view that fungal adenylate-forming reductases are more diverse than previously recognized and belong to four distinct classes.
Chemolithotrophic Primary Production in a Subglacial Ecosystem
Authors: Boyd Eric S. , Hamilton Trinity L. , Havig Jeff R. , Skidmore Mark L. , Shock Everett L. 
Published: August 2014

ABSTRACT

Glacial comminution of bedrock generates fresh mineral surfaces capable of sustaining chemotrophic microbial communities under the dark conditions that pervade subglacial habitats. Geochemical and isotopic evidence suggests that pyrite oxidation is a dominant weathering process generating protons that drive mineral dissolution in many subglacial systems. Here, we provide evidence correlating pyrite oxidation with chemosynthetic primary productivity and carbonate dissolution in subglacial sediments sampled from Robertson Glacier (RG), Alberta, Canada. Quantification and sequencing of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) transcripts suggest that populations closely affiliated with
Sideroxydans lithotrophicus
, an iron sulfide-oxidizing autotrophic bacterium, are abundant constituents of microbial communities at RG. Microcosm experiments indicate sulfate production during biological assimilation of radiolabeled bicarbonate. Geochemical analyses of subglacial meltwater indicate that increases in sulfate levels are associated with increased calcite and dolomite dissolution. Collectively, these data suggest a role for biological pyrite oxidation in driving primary productivity and mineral dissolution in a subglacial environment and provide the first rate estimate for bicarbonate assimilation in these ecosystems. Evidence for lithotrophic primary production in this contemporary subglacial environment provides a plausible mechanism to explain how subglacial communities could be sustained in near-isolation from the atmosphere during glacial-interglacial cycles.
Improvement of 2,3-Butanediol Yield in Klebsiella pneumoniae by Deletion of the Pyruvate Formate-Lyase Gene
Authors: Jung Moo-Young , Mazumdar Suman , Shin Sang Heum , Yang Kap-Seok , Lee Jinwon , Oh Min-Kyu 
Published: August 2014

ABSTRACT

Klebsiella pneumoniae
is considered a good host strain for the production of 2,3-butanediol, which is a promising platform chemical with various industrial applications. In this study, three genes, including those encoding glucosyltransferase (
wabG
), lactate dehydrogenase (
ldhA
), and pyruvate formate-lyase (
pflB
), were disrupted in
K. pneumoniae
to reduce both its pathogenic characteristics and the production of several by-products. In flask cultivation with minimal medium, the yield of 2,3-butanediol from rationally engineered
K. pneumoniae
(Δ
wabG
Δ
ldhA
Δ
pflB
) reached 0.461 g/g glucose, which was 92.2% of the theoretical maximum, with a significant reduction in by-product formation. However, the growth rate of the
pflB
mutant was slightly reduced compared to that of its parental strain. Comparison with similar mutants of
Escherichia coli
suggested that the growth defect of
pflB
-deficient
K. pneumoniae
was caused by redox imbalance rather than reduced level of intracellular acetyl coenzyme A (acetyl-CoA). From an analysis of the transcriptome, it was confirmed that the removal of
pflB
from
K. pneumoniae
significantly repressed the expression of genes involved in the formate hydrogen lyase (FHL) system.
The Gene Cluster for
para
-Nitrophenol Catabolism Is Responsible for 2-Chloro-4-Nitrophenol Degradation in Burkholderia sp. Strain SJ98
Authors: Min Jun , Zhang Jun-Jie , Zhou Ning-Yi 
Published: August 2014

ABSTRACT

Burkholderia
sp. strain SJ98 (DSM 23195) utilizes 2-chloro-4-nitrophenol (2C4NP) or
para
-nitrophenol (PNP) as a sole source of carbon and energy. Here, by genetic and biochemical analyses, a 2C4NP catabolic pathway different from those of all other 2C4NP utilizers was identified with chloro-1,4-benzoquinone (CBQ) as an intermediate. Reverse transcription-PCR analysis showed that all of the
pnp
genes in the
pnpABA1CDEF
cluster were located in a single operon, which is significantly different from the genetic organization of all other previously reported PNP degradation gene clusters, in which the structural genes were located in three different operons. All of the Pnp proteins were purified to homogeneity as His-tagged proteins. PnpA, a PNP 4-monooxygenase, was found to be able to catalyze the monooxygenation of 2C4NP to CBQ. PnpB, a 1,4-benzoquinone reductase, has the ability to catalyze the reduction of CBQ to chlorohydroquinone. Moreover, PnpB is also able to enhance PnpA activity
in vitro
in the conversion of 2C4NP to CBQ. Genetic analyses indicated that
pnpA
plays an essential role in the degradation of both 2C4NP and PNP by gene knockout and complementation. In addition to being responsible for the lower pathway of PNP catabolism, PnpCD, PnpE, and PnpF were also found to be likely involved in that of 2C4NP catabolism. These results indicated that the catabolism of 2C4NP and that of PNP share the same gene cluster in strain SJ98. These findings fill a gap in our understanding of the microbial degradation of 2C4NP at the molecular and biochemical levels.
Microbial Ecology Dynamics Reveal a Succession in the Core Microbiota Involved in the Ripening of Pasta Filata Caciocavallo Pugliese Cheese
Authors: De Pasquale Ilaria , Di Cagno Raffaella , Buchin Solange , De Angelis Maria , Gobbetti Marco 
Published: August 2014

ABSTRACT

Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated by
Firmicutes
(53%),
Proteobacteria
(39%),
Bacteroidetes
(7.8%),
Actinobacteria
(0.06%), and
Fusobacteria
(0.03%), with heterogeneity at the genus level. The primary starter
Streptococcus thermophilus
dominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance of
Streptococcus
sp. and especially
St. thermophilus
decreased, while that of
Lactobacillus casei
,
Lactobacillus
sp., and especially
Lactobacillus paracasei
increased consistently. Despite the lower relative abundance compared to
St. thermophilus
, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which seemed to be the main factor responsible for cheese ripening.
ApnI, a Transmembrane Protein Responsible for Subtilomycin Immunity, Unveils a Novel Model for Lantibiotic Immunity
Authors: Deng Yun , Li Cong-Zhi , Zhu Yi-Guang , Wang Peng-Xia , Qi Qing-Dong , Fu Jing-Jing , Peng Dong-Hai , Ruan Li-Fang , Sun Ming 
Published: August 2014

ABSTRACT

Subtilomycin was detected from the plant endophytic strain
Bacillus subtilis
BSn5 and was first reported from
B. subtilis
strain MMA7. In this study, a gene cluster that has been proposed to be related to subtilomycin biosynthesis was isolated from the BSn5 genome and was experimentally validated by gene inactivation and heterologous expression. Comparison of the subtilomycin gene cluster with other verified related lantibiotic gene clusters revealed a particular organization of the genes
apnI
and
apnT
downstream of
apnAPBC
, which may be involved in subtilomycin immunity. Through analysis of expression of the
apnI
and/or
apnT
genes in the subtilomycin-sensitive strain CU1065 and inactivation of
apnI
and
apnT
in the producer strain BSn5, we showed that the single gene
apnI
, encoding a putative transmembrane protein, was responsible for subtilomycin immunity. To our knowledge, evidence for lantibiotic immunity that is solely dependent on a transmembrane protein is quite rare. Further bioinformatic analysis revealed the abundant presence of ApnI-like proteins that may be responsible for lantibiotic immunity in
Bacillus
and
Paenibacillus
. We cloned the
paeI
gene, encoding one such ApnI-like protein, into CU1065 and showed that it confers resistance to paenibacillin. However, no cross-resistance was detected between ApnI and PaeI, even though subtilomycin and paenibacillin share similar structures, suggesting that the protection provided by ApnI/ApnI-like proteins involves a specific-sequence recognition mechanism. Peptide release/binding assays indicated that the recombinant
B. subtilis
expressing
apnI
interacted with subtilomycin. Thus, ApnI represents a novel model for lantibiotic immunity that appears to be common.
Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium
Authors: Milani Christian , Lugli Gabriele Andrea , Duranti Sabrina , Turroni Francesca , Bottacini Francesca , Mangifesta Marta , Sanchez Borja , Viappiani Alice , Mancabelli Leonardo , Taminiau Bernard , Delcenserie Véronique , Barrangou Rodolphe , Margolles Abelardo , van Sinderen Douwe , Ventura Marco 
Published: August 2014

ABSTRACT

Bifidobacteria represent one of the dominant microbial groups that are present in the gut of various animals, being particularly prevalent during the suckling stage of life of humans and other mammals. However, the overall genome structure of this group of microorganisms remains largely unexplored. Here, we sequenced the genomes of 42 representative (sub)species across the
Bifidobacterium
genus and used this information to explore the overall genetic picture of this bacterial group. Furthermore, the genomic data described here were used to reconstruct the evolutionary development of the
Bifidobacterium
genus. This reconstruction suggests that its evolution was substantially influenced by genetic adaptations to obtain access to glycans, thereby representing a common and potent evolutionary force in shaping bifidobacterial genomes.
Identification of Hypoxia-Inducible Target Genes of Aspergillus fumigatus by Transcriptome Analysis Reveals Cellular Respiration as an Important Contributor to Hypoxic Survival
Authors: Kroll Kristin , Pähtz Vera , Hillmann Falk , Vaknin Yakir , Schmidt-Heck Wolfgang , Roth Martin , Jacobsen Ilse D. , Osherov Nir , Brakhage Axel A. , Kniemeyer Olaf 
Published: August 2014

ABSTRACT

Aspergillus fumigatus
is an opportunistic, airborne pathogen that causes invasive aspergillosis in immunocompromised patients. During the infection process,
A. fumigatus
is challenged by hypoxic microenvironments occurring in inflammatory, necrotic tissue. To gain further insights into the adaptation mechanism,
A. fumigatus
was cultivated in an oxygen-controlled chemostat under hypoxic and normoxic conditions. Transcriptome analysis revealed a significant increase in transcripts associated with cell wall polysaccharide metabolism, amino acid and metal ion transport, nitrogen metabolism, and glycolysis. A concomitant reduction in transcript levels was observed with cellular trafficking and G-protein-coupled signaling. To learn more about the functional roles of hypoxia-induced transcripts, we deleted
A. fumigatus
genes putatively involved in reactive nitrogen species detoxification (
fhpA
), NAD
+
regeneration (
frdA
and
osmA
), nitrogen metabolism (
niaD
and
niiA
), and respiration (
rcfB
). We show that the nitric oxygen (NO)-detoxifying flavohemoprotein gene
fhpA
is strongly induced by hypoxia independent of the nitrogen source but is dispensable for hypoxic survival. By deleting the nitrate reductase gene
niaD
, the nitrite reductase gene
niiA
, and the two fumarate reductase genes
frdA
and
osmA
, we found that alternative electron acceptors, such as nitrate and fumarate, do not have a significant impact on growth of
A. fumigatus
during hypoxia, but functional mitochondrial respiratory chain complexes are essential under these conditions. Inhibition studies indicated that primarily complexes III and IV play a crucial role in the hypoxic growth of
A. fumigatus
.
Ascorbic Acid Inhibition of Candida albicans Hsp90-Mediated Morphogenesis Occurs via the Transcriptional Regulator Upc2
Authors: Van Hauwenhuyse Frédérique , Fiori Alessandro , Van Dijck Patrick 
Published: August 2014

ABSTRACT

Morphogenetic transitions of the opportunistic fungal pathogen
Candida albicans
are influenced by temperature changes, with induction of filamentation upon a shift from 30 to 37°C. Hsp90 was identified as a major repressor of an elongated cell morphology at low temperatures, as treatment with specific inhibitors of Hsp90 results in elongated growth forms at 30°C. Elongated growth resulting from a compromised Hsp90 is considered neither hyphal nor pseudohyphal growth. It has been reported that ascorbic acid (vitamin C) interferes with the yeast-to-hypha transition in
C. albicans
. In the present study, we show that ascorbic acid also antagonizes the morphogenetic change caused by hampered Hsp90 function. Further analysis revealed that Upc2, a transcriptional regulator of genes involved in ergosterol biosynthesis, and Erg11, the target of azole antifungals, whose expression is in turn regulated by Upc2, are required for this antagonism. Ergosterol levels correlate with elongated growth and are reduced in cells treated with the Hsp90 inhibitor geldanamycin (GdA) and restored by cotreatment with ascorbic acid. In addition, we show that Upc2 appears to be required for ascorbic acid-mediated inhibition of the antifungal activity of fluconazole. These results identify Upc2 as a major regulator of ascorbic acid-induced effects in
C. albicans
and suggest an association between ergosterol content and elongated growth upon Hsp90 compromise.
A Ric8/Synembryn Homolog Promotes Gpa1 and Gpa2 Activation To Respectively Regulate Cyclic AMP and Pheromone Signaling in Cryptococcus neoformans
Authors: Gong Jinjun , Grodsky Jacob D. , Zhang Zhengguang , Wang Ping 
Published: August 2014

ABSTRACT

The G protein α subunits Gpa1, Gpa2, and Gpa3 mediate signal transduction and are important in the growth and virulence of
Cryptococcus neoformans
. To understand how Gpa1 functions without a conventional Gβ subunit, we characterized a resistance to inhibitors of cholinesterase 8 (Ric8) homolog from
C. neoformans
, which shares amino acid sequence homology with other Ric8 proteins that exhibit guanine nucleotide exchange factor (GEF) activity toward Gα. We found that the
ric8
mutant was reduced in capsule size and melanin formation, which could be suppressed by cyclic AMP (cAMP) supplementation or by introducing the activated
GPA1

Q284L

allele. Consistent with the fact that Ric8 participates in cAMP signaling to regulate virulence, the
ric8
mutant was attenuated in virulence toward mice. Interestingly, disruption of
RIC8
also resulted in opposing effects on pheromone signaling, as the
ric8
mutant showed reduced mating but an enhanced ability to induce the pheromone response in the mating partner. To identify Ric8 functional mechanisms, we examined the interactions between Ric8 and the three Gα proteins. Ric8 interacted with Gpa1 and Gpa2, but not Gpa3. The presence of Gpa1
Q284L
negatively affected its interaction with Ric8, whereas the activated Gpa2
Q203L
allele abolished the interaction. Collectively, these findings suggest that Ric8 functions as a GEF to facilitate the activation of Gpa1-cAMP signaling and to promote Gpa2, affecting mating efficiency. Our study highlights the distinct and conserved characteristics associated with G protein signaling and contributes to our overall understanding of how G protein α subunits function with or without a canonical Gβ partner in
C. neoformans
.
LIA4
Encodes a Chromoshadow Domain Protein Required for Genomewide DNA Rearrangements in Tetrahymena thermophila
Authors: Horrell Scott A. , Chalker Douglas L. 
Published: August 2014

ABSTRACT

Extensive DNA elimination occurs as part of macronuclear differentiation during
Tetrahymena
sexual reproduction. The identification of sequences to excise is guided by a specialized RNA interference (RNAi) machinery that targets the methylation of histone H3 lysine 9 (K9) and K27 on chromatin associated with these internal eliminated sequences (IESs). This modified chromatin is reorganized into heterochromatic subnuclear foci, which is a hallmark of their subsequent elimination. Here, we demonstrate that Lia4, a chromoshadow domain-containing protein, is an essential component in this DNA elimination pathway.
LIA4
knockout (
ΔLIA4
) lines fail to excise IESs from their developing somatic genome and arrest at a late stage of conjugation. Lia4 acts after RNAi-guided heterochromatin formation, as both H3K9 and H3K27 methylation are established. Nevertheless, without
LIA4
, these cells fail to form the heterochromatic foci associated with DNA rearrangement, and Lia4 accumulates in the foci, indicating that Lia4 plays a key role in their structure. These data indicate a critical role for Lia4 in organizing the nucleus during
Tetrahymena
macronuclear differentiation.