bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering Filamentous Fungi for Conversion of
d
-Galacturonic Acid to
l
-Galactonic Acid
Authors: Kuivanen Joosu , Mojzita Dominik , Wang Yanming , Hilditch Satu , Penttilä Merja , Richard Peter , Wiebe Marilyn G. 
Published: October 2012

ABSTRACT

d
-Galacturonic acid, the main monomer of pectin, is an attractive substrate for bioconversions, since pectin-rich biomass is abundantly available and pectin is easily hydrolyzed.
l
-Galactonic acid is an intermediate in the eukaryotic pathway for
d
-galacturonic acid catabolism, but extracellular accumulation of
l
-galactonic acid has not been reported. By deleting the gene encoding
l
-galactonic acid dehydratase (
lgd1
or
gaaB
) in two filamentous fungi, strains were obtained that converted
d
-galacturonic acid to
l
-galactonic acid. Both
Trichoderma reesei
Δ
lgd1
and
Aspergillus niger
Δ
gaaB
strains produced
l
-galactonate at yields of 0.6 to 0.9 g per g of substrate consumed. Although
T. reesei
Δ
lgd1
could produce
l
-galactonate at pH 5.5, a lower pH was necessary for
A. niger
Δ
gaaB
. Provision of a cosubstrate improved the production rate and titer in both strains. Intracellular accumulation of
l
-galactonate (40 to 70 mg g biomass
−1
) suggested that export may be limiting. Deletion of the
l
-galactonate dehydratase from
A. niger
was found to delay induction of
d
-galacturonate reductase and overexpression of the reductase improved initial production rates. Deletion of the
l
-galactonate dehydratase from
A. niger
also delayed or prevented induction of the putative
d
-galacturonate transporter An14g04280. In addition,
A. niger
Δ
gaaB
produced
l
-galactonate from polygalacturonate as efficiently as from the monomer.
Functional Analysis of the Lactobacillus casei BL23 Sortases
Authors: Muñoz-Provencio Diego , Rodríguez-Díaz Jesús , Collado María Carmen , Langella Philippe , Bermúdez-Humarán Luis G. , Monedero Vicente 
Published: October 2012

ABSTRACT

Sortases are a class of enzymes that anchor surface proteins to the cell wall of Gram-positive bacteria.
Lactobacillus casei
BL23 harbors four sortase genes, two belonging to class A (
srtA1
and
srtA2
) and two belonging to class C (
srtC1
and
srtC2
). Class C sortases were clustered with genes encoding their putative substrates that were homologous to the SpaEFG and SpaCBA proteins that encode mucus adhesive pili in
Lactobacillus rhamnosus
GG. Twenty-three genes encoding putative sortase substrates were identified in the
L. casei
BL23 genome with unknown (35%), enzymatic (30%), or adhesion-related (35%) functions. Strains disrupted in
srtA1
,
srtA2
,
srtC1
, and
srtC2
and an
srtA1 srtA2
double mutant were constructed. The transcription of all four sortase encoding genes was detected, but only the mutation of
srtA1
resulted in a decrease in bacterial surface hydrophobicity. The β-
N
-acetyl-glucosaminidase and cell wall proteinase activities of whole cells diminished in the
srtA1
mutant and, to a greater extent, in the
srtA1 srtA2
double mutant. Cell wall anchoring of the staphylococcal NucA reporter protein fused to a cell wall sorting sequence was also affected in the
srtA
mutants, and the percentages of adhesion to Caco-2 and HT-29 intestinal epithelial cells were reduced for the
srtA1 srtA2
strain. Mutations in
srtC1
or
srtC2
result in an undetectable phenotype. Together, these results suggest that SrtA1 is the housekeeping sortase in
L. casei
BL23 and SrtA2 would carry out redundant or complementary functions that become evident when SrtA1 activity is absent.
3′ Untranslated Region-Dependent Degradation of the
aceA
mRNA, Encoding the Glyoxylate Cycle Enzyme Isocitrate Lyase, by RNase E/G in Corynebacterium glutamicum
Authors: Maeda Tomoya , Wachi Masaaki 
Published: October 2012

ABSTRACT

We previously reported that the
Corynebacterium glutamicum
RNase E/G encoded by the
rneG
gene (NCgl2281) is required for the 5′ maturation of 5S rRNA. In the search for the intracellular target RNAs of RNase E/G other than the 5S rRNA precursor, we detected that the amount of isocitrate lyase, an enzyme of the glyoxylate cycle, increased in
rneG
knockout mutant cells grown on sodium acetate as the sole carbon source. Rifampin chase experiments showed that the half-life of the
aceA
mRNA was about 4 times longer in the
rneG
knockout mutant than in the wild type. Quantitative real-time PCR analysis also confirmed that the level of
aceA
mRNA was approximately 3-fold higher in the
rneG
knockout mutant strain than in the wild type. Such differences were not observed in other mRNAs encoding enzymes involved in acetate metabolism. Analysis by 3′ rapid amplification of cDNA ends suggested that RNase E/G cleaves the
aceA
mRNA at a single-stranded AU-rich region in the 3′ untranslated region (3′-UTR). The
lacZ
fusion assay showed that the 3′-UTR rendered
lacZ
mRNA RNase E/G dependent. These findings indicate that RNase E/G is a novel regulator of the glyoxylate cycle in
C. glutamicum
.
Population Genetic Structure of 4,12:a:− Salmonella enterica Strains from Harbor Porpoises
Authors: Haase Jana K. , Brown Derek J. , Weill François-Xavier , Mather Henry , Foster Geoffrey , Brisse Sylvain , Wain John , Achtman Mark 
Published: October 2012

ABSTRACT

According to pulsed-field gel electrophoresis (PFGE) typing, 4,12:a:−
Salmonella enterica
isolates from harbor porpoises are highly diverse. However, porpoise isolates belong to only two multilocus sequence types within the eBurst group 18 (eBG18) genetic cluster, which also includes
S. enterica
serovars Bispebjerg and Abortusequi. Isolates of other, serologically similar serovars belong to unrelated eBGs. These assignments to eBGs were supported by eBG-specific sequences of the flagellar gene
fliC
.
Glucosylation and Other Biotransformations of T-2 Toxin by Yeasts of the Trichomonascus Clade
Authors: McCormick Susan P. , Price Neil P. J. , Kurtzman Cletus P. 
Published: October 2012

ABSTRACT

Trichothecenes are sesquiterpenoid toxins produced by
Fusarium
species. Since these mycotoxins are very stable, there is interest in microbial transformations that can remove toxins from contaminated grain or cereal products. Twenty-three yeast species assigned to the
Trichomonascus
clade (Saccharomycotina, Ascomycota), including four
Trichomonascus
species and 19 anamorphic species presently classified in
Blastobotrys
, were tested for their ability to convert the trichothecene T-2 toxin to less-toxic products. These species gave three types of biotransformations: acetylation to 3-acetyl T-2 toxin, glycosylation to T-2 toxin 3-glucoside, and removal of the isovaleryl group to form neosolaniol. Some species gave more than one type of biotransformation. Three
Blastobotrys
species converted T-2 toxin into T-2 toxin 3-glucoside, a compound that has been identified as a masked mycotoxin in
Fusarium
-infected grain. This is the first report of a microbial whole-cell method for producing trichothecene glycosides, and the potential large-scale availability of T-2 toxin 3-glucoside will facilitate toxicity testing and development of methods for detection of this compound in agricultural and other products.
Staphylococcus aureus CC398 Clade Associated with Human-to-Human Transmission
Authors: McCarthy Alex J. , van Wamel Willem , Vandendriessche Stien , Larsen Jesper , Denis Olivier , Garcia-Graells Cristina , Uhlemann Ann-Catrin , Lowy Franklin D. , Skov Robert , Lindsay Jodi A. 
Published: October 2012

ABSTRACT

Staphylococcus aureus
clonal complex 398 (CC398) isolates colonize livestock and can spread to human contacts. Genetic analysis of isolates epidemiologically associated with human-to-human, but not livestock, transmission in multiple countries and continents identified a common clade that was negative for
tet
(M) and positive for bacteriophage ϕ3. Another group of human-to-human-transmitted isolates belonged to the common livestock-associated clade but had acquired a unique ϕ7 bacteriophage.
Biosynthesis and Functions of a Melanoid Pigment Produced by Species of the Sporothrix Complex in the Presence of
l
-Tyrosine
Authors: Almeida-Paes Rodrigo , Frases Susana , Araújo Glauber de Sousa , de Oliveira Manoel Marques Evangelista , Gerfen Gary J. , Nosanchuk Joshua D. , Zancopé-Oliveira Rosely Maria 
Published: October 2012

ABSTRACT

Sporothrix schenckii
is the etiological agent of sporotrichosis, the main subcutaneous mycosis in Latin America. Melanin is an important virulence factor of
S. schenckii
, which produces dihydroxynaphthalene melanin (DHN-melanin) in conidia and yeast cells. Additionally,
l
-dihydroxyphenylalanine (
l
-DOPA) can be used to enhance melanin production on these structures as well as on hyphae. Some fungi are able to synthesize another type of melanoid pigment, called pyomelanin, as a result of tyrosine catabolism. Since there is no information about tyrosine catabolism in
Sporothrix
spp., we cultured 73 strains, including representatives of newly described
Sporothrix
species of medical interest, such as
S. brasiliensis
,
S. schenckii
, and
S. globosa
, in minimal medium with tyrosine. All strains but one were able to produce a melanoid pigment with a negative charge in this culture medium after 9 days of incubation. An
S. schenckii
DHN-melanin mutant strain also produced pigment in the presence of tyrosine. Further analysis showed that pigment production occurs in both the filamentous and yeast phases, and pigment accumulates in supernatants during stationary-phase growth. Notably, sulcotrione inhibits pigment production. Melanin ghosts of wild-type and DHN mutant strains obtained when the fungus was cultured with tyrosine were similar to melanin ghosts yielded in the absence of the precursor, indicating that this melanin does not polymerize on the fungal cell wall. However, pyomelanin-producing fungal cells were more resistant to nitrogen-derived oxidants and to UV light. In conclusion, at least three species of the
Sporothrix
complex are able to produce pyomelanin in the presence of tyrosine, and this pigment might be involved in virulence.
Genetic Diversity among Clostridium botulinum Strains Harboring
bont/A2
and
bont/A3
Genes
Authors: Lúquez Carolina , Raphael Brian H. , Joseph Lavin A. , Meno Sarah R. , Fernández Rafael A. , Maslanka Susan E. 
Published: October 2012

ABSTRACT

Clostridium botulinum
type A strains are known to be genetically diverse and widespread throughout the world. Genetic diversity studies have focused mainly on strains harboring one type A botulinum toxin gene,
bont/A1
, although all reported
bont/A
gene variants have been associated with botulism cases. Our study provides insight into the genetic diversity of
C. botulinum
type A strains, which contain
bont/A2
(
n
= 42) and
bont/A3
(
n
= 4) genes, isolated from diverse samples and geographic origins. Genetic diversity was assessed by using
bont
nucleotide sequencing, content analysis of the
bont
gene clusters, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Sequences of
bont
genes obtained in this study showed 99.9 to 100% identity with other
bont/A2
or
bont/A3
gene sequences available in public databases. The neurotoxin gene clusters of the subtype A2 and A3 strains analyzed in this study were similar in gene content.
C. botulinum
strains harboring
bont/A2
and
bont/A3
genes were divided into six and two MLST profiles, respectively. Four groups of strains shared a similarity of at least 95% by PFGE; the largest group included 21 out of 46 strains. The strains analyzed in this study showed relatively limited genetic diversity using either MLST or PFGE.
Some Like It Hot: Evolution and Ecology of Novel Endosymbionts in Bat Flies of Cave-Roosting Bats (Hippoboscoidea, Nycterophiliinae)
Authors: Morse Solon F. , Dick Carl W. , Patterson Bruce D. , Dittmar Katharina 
Published: October 2012

ABSTRACTWe investigated previously unknown associations between bacterial endosymbionts and bat flies of the subfamily Nycterophiliinae (Diptera, Streblidae). Molecular analyses revealed a novel clade ofGammaproteobacteriainNycterophiliabat flies. This clade was not closely related toArsenophonus-like microbes found in its sister genusPhalconomusand other bat flies. High population infection rates inNycterophiliaacross a wide geographic area, the presence of the symbionts in pupae, the general codivergence between hosts and symbionts, and high AT composition bias in symbiont genes together suggest that this host-symbiont association is obligate in nature and ancient in origin. SomeNycterophiliasamples (14.8%) also containedWolbachiasupergroup F (Alphaproteobacteria), suggesting a facultative symbiosis. Likelihood-based ancestral character mapping revealed that, initially, obligate symbionts exhibited association with host-specificNycterophiliabat flies that use a broad temperature range of cave environments for pupal development. As this mutualism evolved, the temperature range of bat flies narrowed to an exclusive use of hot caves, which was followed by a secondary broadening of the bat flies' host associations. These results suggest that the symbiosis has influenced the environmental tolerance of parasite life history stages. Furthermore, the contingent change to an expanded host range ofNycterophiliabat flies upon narrowing the ecological niche of their developmental stages suggests that altered environmental tolerance across life history stages may be a crucial factor in shaping parasite-host relationships.
Lipase and Protease Double-Deletion Mutant of Pseudomonas fluorescens Suitable for Extracellular Protein Production
Authors: Son Myunghan , Moon Yuseok , Oh Mi Jin , Han Sang Bin , Park Ki Hyun , Kim Jung-Gon , Ahn Jung Hoon 
Published: October 2012

ABSTRACT

Pseudomonas fluorescens
, a widespread Gram-negative bacterium, is an ideal protein manufacturing factory (PMF) because of its safety, robust growth, and high protein production.
P. fluorescens
possesses a type I secretion system (T1SS), which mediates secretion of a thermostable lipase (TliA) and a protease (PrtA) through its ATP-binding cassette (ABC) transporter. Recombinant proteins in
P. fluorescens
are attached to the C-terminal signal region of TliA for transport as fusion proteins to the extracellular medium. However, intrinsic TliA from the
P. fluorescens
genome interferes with detection of the recombinant protein and the secreted recombinant protein is hydrolyzed, due to intrinsic PrtA, resulting in decreased efficiency of the PMF. In this research, the lipase and protease genes of
P. fluorescens
SIK W1 were deleted using the targeted gene knockout method. Deletion mutant
P. fluorescens
Δ
tliA
Δ
prtA
secreted fusion proteins without TliA or protein degradation. Using wild-type
P. fluorescens
as an expression host, degradation of the recombinant protein varied depending on the type of culture media and aeration; however, degradation did not occur with the
P. fluorescens
Δ
tliA
Δ
prtA
double mutant irrespective of growth conditions. By homologous expression of
tliA
and the ABC transporter in a plasmid, TliA secreted from
P. fluorescens
Δ
prtA
and
P. fluorescens
Δ
tliA
Δ
prtA
cells was found to be intact, whereas that secreted from the wild-type
P. fluorescens
and
P. fluorescens
Δ
tliA
cells was found to be hydrolyzed. Our results demonstrate that the
P. fluorescens
Δ
tliA
Δ
prtA
deletion mutant is a promising T1SS-mediated PMF that enhances production and detection of recombinant proteins in extracellular media.
Characterization of Two Virulent Phages of Lactobacillus plantarum
Authors: Briggiler Marcó Mariángeles , Garneau Josiane E. , Tremblay Denise , Quiberoni Andrea , Moineau Sylvain 
Published: October 2012

ABSTRACT

We characterized two
Lactobacillus plantarum
virulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eight
L. plantarum
strains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least two
L. plantarum
strains, LMG9211 and WCSF1. The linear double-stranded DNA genome of the
pac
-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that of
Pediococcus damnosus
phage clP1 and 77% identity with that of
L. plantarum
phage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of the
cos
-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those of
Bacillus
and
Lactobacillus
strains as well as phages. Some phage B2 genes were similar to ORFs from
L. plantarum
phage LP65 of the
Myoviridae
family. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.
Distribution of the SELMA Translocon in Secondary Plastids of Red Algal Origin and Predicted Uncoupling of Ubiquitin-Dependent Translocation from Degradation
Authors: Stork Simone , Moog Daniel , Przyborski Jude M. , Wilhelmi Ilka , Zauner Stefan , Maier Uwe G. 
Published: October 2012

ABSTRACT

Protein import into complex plastids of red algal origin is a multistep process including translocons of different evolutionary origins. The
s
ymbiont-derived
E
RAD-
l
ike
ma
chinery (SELMA), shown to be of red algal origin, is proposed to be the transport system for preprotein import across the periplastidal membrane of heterokontophytes, haptophytes, cryptophytes, and apicomplexans. In contrast to the canonical endoplasmic reticulum-associated degradation (ERAD) system, SELMA translocation is suggested to be uncoupled from proteasomal degradation. We investigated the distribution of known and newly identified SELMA components in organisms with complex plastids of red algal origin by intensive data mining, thereby defining a set of core components present in all examined organisms. These include putative pore-forming components, a ubiquitylation machinery, as well as a Cdc48 complex. Furthermore, the set of known 20S proteasomal components in the periplastidal compartment (PPC) of diatoms was expanded. These newly identified putative SELMA components, as well as proteasomal subunits, were
in vivo
localized as PPC proteins in the diatom
Phaeodactylum tricornutum
. The presented data allow us to speculate about the specific features of SELMA translocation in contrast to the canonical ERAD system, especially the uncoupling of translocation from degradation.
Iron-Inducible Nuclear Translocation of a Myb3 Transcription Factor in the Protozoan Parasite Trichomonas vaginalis
Authors: Hsu Hong-Ming , Lee Yu , Indra Dharmu , Wei Shu-Yi , Liu Hsing-Wei , Chang Lung-Chun , Chen Chinpan , Ong Shiou-Jeng , Tai Jung-Hsiang 
Published: October 2012

ABSTRACT

In
Trichomonas vaginalis
, a novel nuclear localization signal spanning the folded R2R3 DNA-binding domain of a Myb2 protein was previously identified. To study whether a similar signal is used for nuclear translocation by other Myb proteins, nuclear translocation of Myb3 was examined in this report. When overexpressed, hemagglutinin-tagged Myb3 was localized to nuclei of transfected cells, with a cellular distribution similar to that of endogenous Myb3. Fusion to a bacterial tetracycline repressor, R2R3, of Myb3 that spans amino acids (aa) 48 to 156 was insufficient for nuclear translocation of the fusion protein, unless its C terminus was extended to aa 167. The conserved isoleucine in helix 2 of R2R3, which is important for Myb2's structural integrity in maintaining DNA-binding activity and nuclear translocation, was also vital for the former activity of Myb3, but less crucial for the latter. Sequential nuclear influx and efflux of Myb3, which require further extension of the nuclear localization signal to aa 180, were immediately induced after iron repletion. Sequence elements that regulate nuclear translocation with cytoplasmic retention, nuclear influx, and nuclear efflux were identified within the C-terminal tail. These results suggest that the R2R3 DNA-binding domain also serves as a common module for the nuclear translocation of both Myb2 and Myb3, but there are intrinsic differences between the two nuclear localization signals.
Deletion of the Fungal Gene
soft
Disrupts Mutualistic Symbiosis between the Grass Endophyte Epichloë festucae and the Host Plant
Authors: Charlton Nikki D. , Shoji Jun-Ya , Ghimire Sita R. , Nakashima Jin , Craven Kelly D. 
Published: October 2012

ABSTRACT

Hyphal anastomosis, or vegetative hyphal fusion, establishes the interconnection of individual hyphal strands into an integrated network of a fungal mycelium. In contrast to recent advances in the understanding of the molecular basis for hyphal anastomosis, knowledge of the physiological role of hyphal anastomosis in the natural habitats of filamentous fungi is still very limited. To investigate the role of hyphal anastomosis in fungal endophyte-plant interactions, we generated mutant strains lacking the
Epichloë festucae soft
(
so
) gene, an ortholog of the hyphal anastomosis gene
so
in the endophytic fungus
E. festucae
. The
E. festucae
Δ
so
mutant strains grew similarly to the wild-type strain in culture but with reduced aerial hyphae and completely lacked hyphal anastomosis. The most striking phenotype of the
E. festucae
Δ
so
mutant strain was that it failed to establish a mutualistic symbiosis with the tall fescue plant host (
Lolium arundinaceum
); instead, it killed the host plant within 2 months after the initial infection. Microscopic examination revealed that the death of the tall fescue plant host was associated with the distortion and disorganization of plant cells. This study suggests that hyphal anastomosis may have an important role in the establishment/maintenance of fungal endophyte-host plant mutualistic symbiosis.
Roles of Hsl1p and Hsl7p in Swe1p Degradation: beyond Septin Tethering
Authors: King Kindra , Jin Michelle , Lew Daniel 
Published: October 2012

ABSTRACT

The morphogenesis checkpoint in
Saccharomyces cerevisiae
couples bud formation to the cell division cycle by delaying nuclear division until cells have successfully constructed a bud. The cell cycle delay is due to the mitosis-inhibitory kinase Swe1p, which phosphorylates the cyclin-dependent kinase Cdc28p. In unperturbed cells, Swe1p is degraded via a mechanism thought to involve its tethering to a cortical scaffold of septin proteins at the mother-bud neck. In cells that experience stresses that delay bud formation, Swe1p is stabilized, accumulates, and promotes a G
2
delay. The tethering of Swe1p to the neck requires two regulators, called Hsl1p and Hsl7p. Hsl1p interacts with septins, and Hsl7p interacts with Swe1p; tethering occurs when Hsl1p interacts with Hsl7p. Here we created a version of Swe1p that is artificially tethered to the neck by fusion to a septin so that Swe1p no longer requires Hsl1p or Hsl7p for its localization to the neck. We show that the interaction between Hsl1p and Hsl7p, required for normal Swe1p degradation, is no longer needed for septin-Swe1p degradation, supporting the idea that the Hsl1p-Hsl7p interaction serves mainly to tether Swe1p to the neck. However, both Hsl1p and Hsl7p are still required for Swe1p degradation, implying that these proteins play additional roles beyond localizing Swe1p to the neck.