bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exceptional Production of both Prodigiosin and Cycloprodigiosin as Major Metabolic Constituents by a Novel Marine Bacterium, Zooshikella rubidus S1-1
Authors: Lee Jong Suk , Kim Yong-Sook , Park Sooyeon , Kim Jihoon , Kang So-Jung , Lee Mi-Hwa , Ryu Sangryeol , Choi Jong Myoung , Oh Tae-Kwang , Yoon Jung-Hoon 
Published: June 2011

ABSTRACT

A Gram-negative, red-pigment-producing marine bacterial strain, designated S1-1, was isolated from the tidal flat sediment of the Yellow Sea, Korea. On the basis of phenotypic, phylogenetic, and genetic data, strain S1-1 (KCTC 11448BP) represented a new species of the genus
Zooshikella
. Thus, we propose the name
Zooshikella rubidus
sp. nov. Liquid chromatography and mass spectrometry of the red pigments produced by strain S1-1 revealed that the major metabolic compounds were prodigiosin and cycloprodigiosin. In addition, this organism produced six minor prodigiosin analogues, including two new structures that were previously unknown. To our knowledge, this is the first description of a microorganism that simultaneously produces prodigiosin and cycloprodigiosin as two major metabolites. Both prodigiosin and cycloprodigiosin showed antimicrobial activity against several microbial species. These bacteria were approximately 1.5-fold more sensitive to cycloprodigiosin than to prodigiosin. The metabolites also showed anticancer activity against human melanoma cells, which showed significantly more sensitivity to prodigiosin than to cycloprodigiosin. The secondary metabolite profiles of strain S1-1 and two reference bacterial strains were compared by liquid chromatography-mass spectrometry. Multivariate statistical analyses based on secondary metabolite profiles by liquid chromatography-mass spectrometry indicated that the metabolite profile of strain S1-1 could clearly be distinguished from those of two phylogenetically related, prodigiosin-producing bacterial strains.
Decay of Bacterial Pathogens, Fecal Indicators, and Real-Time Quantitative PCR Genetic Markers in Manure-Amended Soils
Authors: Rogers Shane W. , Donnelly Matthew , Peed Lindsay , Kelty Catherine A. , Mondal Sumona , Zhong Zirong , Shanks Orin C. 
Published: June 2011

ABSTRACT

This study examined persistence and decay of bacterial pathogens, fecal indicator bacteria (FIB), and emerging real-time quantitative PCR (qPCR) genetic markers for rapid detection of fecal pollution in manure-amended agricultural soils. Known concentrations of transformed green fluorescent protein-expressing
Escherichia coli
O157:H7/pZs and red fluorescent protein-expressing
Salmonella enterica
serovar Typhimurium/pDs were added to laboratory-scale manure-amended soil microcosms with moisture contents of 60% or 80% field capacity and incubated at temperatures of −20°C, 10°C, or 25°C for 120 days. A two-stage first-order decay model was used to determine stage 1 and stage 2 first-order decay rate coefficients and transition times for each organism and qPCR genetic marker in each treatment. Genetic markers for FIB (
Enterococcus
spp.,
E. coli
, and
Bacteroidales
) exhibited decay rate coefficients similar to that of
E. coli
O157:H7/pZs but not of
S. enterica
serovar Typhimurium/pDs and persisted at detectable levels longer than both pathogens. Concentrations of these two bacterial pathogens, their counterpart qPCR genetic markers (
stx1
and
ttrRSBCA
, respectively), and FIB genetic markers were also correlated (
r
= 0.528 to 0.745). This suggests that these qPCR genetic markers may be reliable conservative surrogates for monitoring fecal pollution from manure-amended land. Host-associated qPCR genetic markers for microbial source tracking decayed rapidly to nondetectable concentrations, long before FIB,
Salmonella enterica
serovar Typhimurium/pDs, and
E. coli
O157:H7/pZs. Although good indicators of point source or recent nonpoint source fecal contamination events, these host-associated qPCR genetic markers may not be reliable indicators of nonpoint source fecal contamination events that occur weeks following manure application on land.
Temporal and Spatial Variability in Culturable Pathogenic Vibrio spp. in Lake Pontchartrain, Louisiana, following Hurricanes Katrina and Rita
Authors: Nigro Olivia D. , Hou Aixin , Vithanage Gayatri , Fujioka Roger S. , Steward Grieg F. 
Published: June 2011

ABSTRACTWe investigated the abundance, distribution, and virulence gene content ofVibrio cholerae,V. parahaemolyticus, andV. vulnificusin the waters of southern Lake Pontchartrain in Louisiana on four occasions from October 2005 to September 2006, using selective cultivation and molecular assays. The three targeted pathogenic vibrios were generally below the detection level in January 2006, when the water was cold (13°C), and most abundant in September 2006, when the lake water was warmest (30°C). The maximum values for these species were higher than reported previously for the lake by severalfold to orders of magnitude. The only variable consistently correlated with total vibrio abundance within a single sampling was distance from shore (P= 0.000). Multiple linear regression of the entire data set revealed that distance from shore, temperature, and turbidity together explained 82.1% of the variability in total vibrio CFU. The log-transformed mean abundance ofV. vulnificusCFU in the lake was significantly correlated with temperature (P= 0.014), but not salinity (P= 0.625). Virulence-associated genes ofV. cholerae(ctx) andV. parahaemolyticus(trhandtdh) were not detected in any isolates of these species (n= 128 andn= 20, respectively). In contrast, 16S rRNA typing ofV. vulnificus(n= 298) revealed the presence of both environmental (type A) and clinical (type B) strains. The percentage of the B-typeV. vulnificuswas significantly higher in the lake in October 2005 (35.8% of the total) than at other sampling times (P≤ 0.004), consistent with the view that these strains represent distinct ecotypes.
Synthesis and Characterization of Chimeric Proteins Based on Cellulase and Xylanase from an Insect Gut Bacterium
Authors: Adlakha Nidhi , Rajagopal Raman , Kumar Saravanan , Reddy Vanga Siva , Yazdani Syed Shams 
Published: June 2011

ABSTRACT

Insects living on wood and plants harbor a large variety of bacterial flora in their guts for degrading biomass. We isolated a
Paenibacillus
strain, designated ICGEB2008, from the gut of a cotton bollworm on the basis of its ability to secrete a variety of plant-hydrolyzing enzymes. In this study, we cloned, expressed, and characterized two enzymes, β-1,4-endoglucanase (Endo5A) and β-1,4-endoxylanase (Xyl11D), from the ICGEB2008 strain and synthesized recombinant bifunctional enzymes based on Endo5A and Xyl11D. The gene encoding Endo5A was obtained from the genome of the ICGEB2008 strain by shotgun cloning. The gene encoding Xyl11D was obtained using primers for conserved xylanase sequences, which were identified by aligning xylanase sequences in other species of
Paenibacillus
. Endo5A and Xyl11D were overexpressed in
Escherichia coli
, and their optimal activities were characterized. Both Endo5A and Xyl11D exhibited maximum specific activity at 50°C and pH 6 to 7. To take advantage of this feature, we constructed four bifunctional chimeric models of Endo5A and Xyl11D by fusing the encoding genes either end to end or through a glycine-serine (GS) linker. We predicted three-dimensional structures of the four models using the I-TASSER server and analyzed their secondary structures using circular dichroism (CD) spectroscopy. The chimeric model Endo5A-GS-Xyl11D, in which a linker separated the two enzymes, yielded the highest C-score on the I-TASSER server, exhibited secondary structure properties closest to the native enzymes, and demonstrated 1.6-fold and 2.3-fold higher enzyme activity than Endo5A and Xyl11D, respectively. This bifunctional enzyme could be effective for hydrolyzing plant biomass owing to its broad substrate range.
Investigating Antibacterial Effects of Garlic (Allium sativum) Concentrate and Garlic-Derived Organosulfur Compounds on Campylobacter jejuni by Using Fourier Transform Infrared Spectroscopy, Raman Spectroscopy, and Electron Microscopy
Authors: Lu Xiaonan , Rasco Barbara A. , Jabal Jamie M. F. , Aston D. Eric , Lin Mengshi , Konkel Michael E. 
Published: June 2011

ABSTRACT

Fourier transform infrared (FT-IR) spectroscopy and Raman spectroscopy were used to study the cell injury and inactivation of
Campylobacter jejuni
from exposure to antioxidants from garlic.
C. jejuni
was treated with various concentrations of garlic concentrate and garlic-derived organosulfur compounds in growth media and saline at 4, 22, and 35°C. The antimicrobial activities of the diallyl sulfides increased with the number of sulfur atoms (diallyl sulfide < diallyl disulfide < diallyl trisulfide). FT-IR spectroscopy confirmed that organosulfur compounds are responsible for the substantial antimicrobial activity of garlic, much greater than those of garlic phenolic compounds, as indicated by changes in the spectral features of proteins, lipids, and polysaccharides in the bacterial cell membranes. Confocal Raman microscopy (532-nm-gold-particle substrate) and Raman mapping of a single bacterium confirmed the intracellular uptake of sulfur and phenolic components. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed to verify cell damage. Principal-component analysis (PCA), discriminant function analysis (DFA), and soft independent modeling of class analogs (SIMCA) were performed, and results were cross validated to differentiate bacteria based upon the degree of cell injury. Partial least-squares regression (PLSR) was employed to quantify and predict actual numbers of healthy and injured bacterial cells remaining following treatment. PLSR-based loading plots were investigated to further verify the changes in the cell membrane of
C. jejuni
treated with organosulfur compounds. We demonstrated that bacterial injury and inactivation could be accurately investigated by complementary infrared and Raman spectroscopies using a chemical-based, “whole-organism fingerprint” with the aid of chemometrics and electron microscopy.
Temporal Variability of Coastal Planctomycetes Clades at Kabeltonne Station, North Sea
Authors: Pizzetti Ilaria , Fuchs Bernhard M. , Gerdts Gunnar , Wichels Antje , Wiltshire Karen H. , Amann Rudolf 
Published: June 2011

ABSTRACT

Members of the bacterial phylum
Planctomycetes
are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of
Planctomycetes
in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence
in situ
hybridization (CARD-FISH). Generally
Planctomycetes
are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that
Planctomycetes
abundance was correlated to the
Centrales
diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ∼90% of the
Planctomycetes
reside in the >3-μm size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named
Planctomyces
-related group A, uncultured
Planctomycetes
group B, and
Pirellula
-related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured
Planctomycetes
group B was most abundant in autumn samples, while
Planctomyces
-related group A was present in high numbers only during late autumn and winter. The levels of
Pirellula
-related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the
Planctomycetes
is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates.
Differential Proteomic Analysis of Rickettsia prowazekii Propagated in Diverse Host Backgrounds
Authors: Tucker Aimee M. , Driskell Lonnie O. , Pannell Lewis K. , Wood David O. 
Published: June 2011

ABSTRACT

The obligate intracellular growth of
Rickettsia prowazekii
places severe restrictions on the analysis of rickettsial gene expression. With a small genome, predicted to code for 835 proteins, identifying which proteins are differentially expressed in rickettsiae that are isolated from different hosts or that vary in virulence is critical to an understanding of rickettsial pathogenicity. We employed a liquid chromatography (LC)-linear trap quadrupole (LTQ)-Orbitrap mass spectrometer for simultaneous acquisition of quantitative mass spectrometry (MS)-only data and tandem mass spectrometry (MS-MS) sequence data. With the use of a combination of commercially available algorithms and in-house software, quantitative MS-only data and comprehensive peptide coverage generated from MS-MS were integrated, resulting in the assignment of peptide identities with intensity values, allowing for the differential comparison of complex protein samples. With the use of these protocols, it was possible to directly compare protein abundance and analyze changes in the total proteome profile of
R. prowazekii
grown in different host backgrounds. Total protein extracted from rickettsiae grown in murine, tick, and insect cell lines or hen egg yolk sacs was analyzed. Here, we report the fold changes, including an upregulation of shock-related proteins, in rickettsiae cultivated in tissue culture compared to the level for rickettsiae harvested from hen yolk sacs. The ability to directly compare, in a complex sample, differential rickettsial protein expression provides a snapshot of host-specific proteomic profiles that will help to identify proteins important in intracellular growth and virulence.
A Pmk1-Interacting Gene Is Involved in Appressorium Differentiation and Plant Infection in
Magnaporthe oryzae
Authors: Zhang Haifeng , Xue Chaoyang , Kong Lingan , Li Guotian , Xu Jin-Rong 
Published: June 2011

ABSTRACT

In the rice blast fungus
Magnaporthe oryzae
, the
PMK1
mitogen-activated protein (MAP) kinase gene regulates appressorium formation and infectious growth. Its homologs in many other fungi also play critical roles in fungal development and pathogenicity. However, the targets of this important MAP kinase and its interacting genes are not well characterized. In this study, we constructed two yeast two-hybrid libraries of
M. oryzae
and screened for Pmk1-interacting proteins. Among the nine Pmk1-interacting clones (PICs) identified, two of them,
PIC1
and
PIC5
, were selected for further characterization. Pic1 has one putative nuclear localization signal and one putative MAP kinase phosphorylation site. Pic5 contains one transmembrane domain and two functionally unknown CTNS (cystinosin/ERS1p repeat) motifs. The interaction of Pmk1 with Pic1 or Pic5 was confirmed by coimmunoprecipitation assays. Targeted gene deletion of
PIC1
had no apparent effects on vegetative growth and pathogenicity but resulted in a significant reduction in conidiation and abnormal germ tube differentiation on onion epidermal cells. Deletion of
PIC5
led to a reduction in conidiation and hyphal growth. Autolysis of aerial hyphae became visible in cultures older than 4 days. The
pic5
mutant was defective in germ tube growth and appressorium differentiation. It was reduced in appressorial penetration and virulence on the plant. Both
PIC1
and
PIC5
are conserved in filamentous ascomycetes, but none of their orthologs have been functionally characterized. Our data indicate that
PIC5
is a novel virulence factor involved in appressorium differentiation and pathogenesis in
M. oryzae
.
Clustering of Nuclei in Multinucleated Hyphae Is Prevented by Dynein-Driven Bidirectional Nuclear Movements and Microtubule Growth Control in Ashbya gossypii
Authors: Grava Sandrine , Keller Miyako , Voegeli Sylvia , Seger Shanon , Lang Claudia , Philippsen Peter 
Published: June 2011

ABSTRACT

During filamentous fungus development, multinucleated hyphae employ a system for long-range nuclear migration to maintain an equal nuclear density. A decade ago the microtubule motor dynein was shown to play a central role in this process. Previous studies with
Ashbya gossypii
revealed extensive bidirectional movements and bypassings of nuclei, an autonomous cytoplasmic microtubule (cMT) cytoskeleton emanating from each nucleus, and pulling of nuclei by sliding of cMTs along the cortex. Here, we show that dynein is the sole motor for bidirectional movements and bypassing because these movements are concomitantly decreased in mutants carrying truncations of the dynein heavy-chain
DYN1
promoter. The dynactin component Jnm1, the accessory proteins Dyn2 and Ndl1, and the potential dynein cortical anchor Num1 are also involved in the dynamic distribution of nuclei. In their absence, nuclei aggregate to different degrees, whereby the mutants with dense nuclear clusters grow extremely long cMTs. As in budding yeast, we found that dynein is delivered to cMT plus ends, and its activity or processivity is probably controlled by dynactin and Num1. Together with its role in powering nuclear movements, we propose that dynein also plays (directly or indirectly) a role in the control of cMT length. Those combined dynein actions prevent nuclear clustering in
A. gossypii
and thus reveal a novel cellular role for dynein.
Rab11 Function in Trypanosoma brucei: Identification of Conserved and Novel Interaction Partners
Authors: Gabernet-Castello Carme , DuBois Kelly N. , Nimmo Camus , Field Mark C. 
Published: June 2011

ABSTRACT

The Ras-like GTPase Rab11 is implicated in multiple aspects of intracellular transport, including maintenance of plasma membrane composition and cytokinesis. In metazoans, these functions are mediated in part via coiled-coil Rab11-interacting proteins (FIPs) acting as Rab11 effectors. Additional interaction between Rab11 and the exocyst subunit Sec15 connects Rab11 with exocytosis. We find that FIPs are metazoan specific, suggesting that other factors mediate Rab11 functions in nonmetazoans. We examined Rab11 interactions in
Trypanosoma brucei
, where endocytosis is well studied and the role of Rab11 in recycling well documented. TbSec15 and TbRab11 interact, demonstrating evolutionary conservation. By yeast two-hybrid screening, we identified additional Rab11 interaction partners. Tb927.5.1640 (designated RBP74) interacted with both Rab11 and Rab5. RBP74 shares a coiled-coil architecture with metazoan FIPs but is unrelated by sequence and appears to play a role in coordinating endocytosis and recycling. A second coiled-coil protein, Tb09.211.4830 (TbAZI1), orthologous to AZI1 in
Homo sapiens
, interacts exclusively with Rab11. AZI1 is restricted to taxa with motile cilia/flagella. These data suggest that Rab11 functions are mediated by evolutionarily conserved (i.e., AZI1 and Sec15) and potentially lineage-specific (RBP74) interactions essential for the integration of the endomembrane system.
Multiple Roles of Ypd1 Phosphotransfer Protein in Viability, Stress Response, and Virulence Factor Regulation in Cryptococcus neoformans
Authors: Lee Jang-Won , Ko Young-Joon , Kim Seo-Young , Bahn Yong-Sun 
Published: June 2011

ABSTRACT

Ypd1 is a key phosphorelay protein that controls eukaryotic two-component systems, but its function in
Cryptococcus neoformans
is not known. Here, we report that Ypd1 is required for the viability of
C. neoformans
via the Hog1 mitogen-activated protein kinase (MAPK) pathway but plays multiple cellular roles in both a Hog1-dependent and -independent manner.
Helicobacter pyloriPossesses Four Coiled-Coil-Rich Proteins That Form Extended Filamentous Structures and Control Cell Shape and Motility
Authors: Specht Mara , Schätzle Sarah , Graumann Peter L. , Waidner Barbara 
Published: June 2011

ABSTRACTWe identified two additional genes ofHelicobacter pyloriencoding Ccrp proteins. All four Ccrps have different multimerization and filamentation properties and different types of smallest subunits and do not copurify, suggesting a system of individual Ccrp filaments. Despite the presence of morphologically unaltered flagella, allccrpmutants displayed significantly reduced motility.
Identification of Amino Acid Residues Critical for Catalysis of Holliday Junction Resolution by Mycoplasma genitalium RecU
Authors: Sluijter Marcel , Aslam Mohammad , Hartwig Nico G. , van Rossum Annemarie M. C. , Vink Cornelis 
Published: June 2011

ABSTRACT

The RecU protein from
Mycoplasma genitalium
, RecU

Mge

, is a 19.4-kDa Holliday junction (HJ) resolvase that binds in a nonspecific fashion to HJ substrates and, in the presence of Mn
2+
, cleaves these substrates at a specific sequence (5′-G/TC↓C/TTA/GG-3′). To identify amino acid residues that are crucial for HJ binding and/or cleavage, we generated a series of 16 deletion mutants (9 N- and 7 C-terminal deletion mutants) and 31 point mutants of RecU

Mge

. The point mutations were introduced at amino acid positions that are highly conserved among bacterial RecU-like sequences. All mutants were purified and tested for the ability to bind to, and cleave, HJ substrates. We found the five N-terminal and three C-terminal amino acid residues of RecU

Mge

to be dispensable for its catalytic activities. Among the 31 point mutants, 7 mutants were found to be inactive in both HJ binding and cleavage. Interestingly, in 12 other mutants, these two activities were uncoupled; while these proteins displayed HJ-binding characteristics similar to those of wild-type RecU

Mge

, they were unable to cleave HJ substrates. Thus, 12 amino acid residues were identified (E11, K31, D57, Y58, Y66, D68, E70, K72, T74, K76, Q88, and L92) that may play either a direct or indirect role in the catalysis of HJ resolution.
Multiplicity of 3-Ketosteroid-9α-Hydroxylase Enzymes in Rhodococcus rhodochrous DSM43269 for Specific Degradation of Different Classes of Steroids
Authors: Petrusma Mirjan , Hessels Gerda , Dijkhuizen Lubbert , van der Geize Robert 
Published: June 2011

ABSTRACT

The well-known large catabolic potential of rhodococci is greatly facilitated by an impressive gene multiplicity. This study reports on the multiplicity of
kshA
, encoding the oxygenase component of 3-ketosteroid 9α-hydroxylase, a key enzyme in steroid catabolism. Five
kshA
homologues (
kshA1
to
kshA5
) were previously identified in
Rhodococcus rhodochrous
DSM43269. These KshA
DSM43269
homologues are distributed over several phylogenetic groups. The involvement of these KshA homologues in the catabolism of different classes of steroids, i.e., sterols, pregnanes, androstenes, and bile acids, was investigated. Enzyme activity assays showed that all KSH enzymes with KshA
DSM43269
homologues are C-9 α-hydroxylases acting on a wide range of 3-ketosteroids, but not on 3-hydroxysteroids. KshA5 appeared to be the most versatile enzyme, with the broadest substrate range but without a clear substrate preference. In contrast, KshA1 was found to be dedicated to cholic acid catabolism. Transcriptional analysis and functional complementation studies revealed that
kshA5
supported growth on any of the different classes of steroids tested, consistent with its broad expression induction pattern. The presence of multiple
kshA
genes in the
R. rhodochrous
DSM43269 genome, each displaying unique steroid induction patterns and substrate ranges, appears to facilitate a dynamic and fine-tuned steroid catabolism, with C-9 α-hydroxylation occurring at different levels during microbial steroid degradation.