bluuebunny/crossref_metadata_2025_split huggingface dataset:
Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types
Authors: Santamaría Rosa Isela , Bustos Patricia , Sepúlveda-Robles Omar , Lozano Luis , Rodríguez César , Fernández José Luis , Juárez Soledad , Kameyama Luis , Guarneros Gabriel , Dávila Guillermo , González Víctor 
Published: November 2013

ABSTRACT

In this work, we isolated and characterized 14 bacteriophages that infect
Rhizobium etli
. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48
R. etli
strains. We obtained the complete genome sequence of nine phages. Four phages were resistant to several restriction enzymes and
in vivo
cloning, probably due to nucleotide modifications. The genome size of the sequenced phages varied from 43 kb to 115 kb, with a median size of ∼45 to 50 kb. A large proportion of open reading frames of these phage genomes (65 to 70%) consisted of hypothetical and orphan genes. The remainder encoded proteins needed for phage morphogenesis and DNA synthesis and processing, among other functions, and a minor percentage represented genes of bacterial origin. We classified these phages into four genomic types on the basis of their genomic similarity, gene content, and host range. Since there are no reports of similar sequences, we propose that these bacteriophages correspond to novel species.
Genomic Investigation of Lysogen Formation and Host Lysis Systems of the Salmonella Temperate Bacteriophage SPN9CC
Authors: Shin Hakdong , Lee Ju-Hoon , Yoon Hyunjin , Kang Dong-Hyun , Ryu Sangryeol 
Published: November 2013

ABSTRACT

To understand phage infection and host cell lysis mechanisms in pathogenic
Salmonella
, a novel
Salmonella enterica
serovar Typhimurium-targeting bacteriophage, SPN9CC, belonging to the
Podoviridae
family was isolated and characterized. The phage infects
S
. Typhimurium via the O antigen of lipopolysaccharide (LPS) and forms clear plaques with cloudy centers due to lysogen formation. Phylogenetic analysis of phage major capsid proteins revealed that this phage is a member of the lysogen-forming P22-like phage group. However, comparative genomic analysis of SPN9CC with P22-like phages indicated that their lysogeny control regions and host cell lysis gene clusters show very low levels of identity, suggesting that lysogen formation and host cell lysis mechanisms may be diverse among phages in this group. Analysis of the expression of SPN9CC host cell lysis genes encoding holin, endolysin, and Rz/Rz1-like proteins individually or in combinations in
S
. Typhimurium and
Escherichia coli
hosts revealed that collaboration of these lysis proteins is important for the lysis of both hosts and that holin is a key protein. To further investigate the role of the lysogeny control region in phage SPN9CC, a Δ
cI
mutant (SPN9CCM) of phage SPN9CC was constructed. The mutant does not produce a cloudy center in the plaques, suggesting that this mutant phage is virulent and no longer temperate. Subsequent comparative one-step growth analysis and challenge assays revealed that SPN9CCM has shorter eclipse/latency periods and a larger burst size, as well as higher host cell lysis activity, than SPN9CC. The present work indicates the possibility of engineering temperate phages as promising biocontrol agents similar to virulent phages.
Signature Protein of the PVC Superphylum
Authors: Lagkouvardos Ilias , Jehl Marc-André , Rattei Thomas , Horn Matthias 
Published: November 2013

ABSTRACT

The phyla
Planctomycetes
,
Verrucomicrobia
,
Chlamydiae
,
Lentisphaerae
, and “
Candidatus
Omnitrophica (OP3)” comprise bacteria that share an ancestor but show highly diverse biological and ecological features. Together, they constitute the PVC superphylum. Using large-scale comparative genome sequence analysis, we identified a protein uniquely shared among all of the known members of the PVC superphylum. We provide evidence that this signature protein is expressed by representative members of the PVC superphylum. Its predicted structure, physicochemical characteristics, and overexpression in
Escherichia coli
and gel retardation assays with purified signature protein suggest a housekeeping function with unspecific DNA/RNA binding activity. Phylogenetic analysis demonstrated that the signature protein is a suitable phylogenetic marker for members of the PVC superphylum, and the screening of published metagenome data indicated the existence of additional PVC members. This study provides further evidence of a common evolutionary history of the PVC superphylum and presents a unique case in which a single protein serves as an evolutionary link among otherwise highly diverse members of major bacterial groups.
The Combined Effects of Bacterial Symbionts and Aging on Life History Traits in the Pea Aphid, Acyrthosiphon pisum
Authors: Laughton Alice M. , Fan Maretta H. , Gerardo Nicole M. 
Published: November 2013

ABSTRACT

While many endosymbionts have beneficial effects on hosts under specific ecological conditions, there can also be associated costs. In order to maximize their own fitness, hosts must facilitate symbiont persistence while preventing symbiont exploitation of resources, which may require tight regulation of symbiont populations. As a host ages, the ability to invest in such mechanisms may lessen or be traded off with demands of other life history traits, such as survival and reproduction. Using the pea aphid,
Acyrthosiphon pisum
, we measured survival, lifetime fecundity, and immune cell counts (hemocytes, a measure of immune capacity) in the presence of facultative secondary symbionts. Additionally, we quantified the densities of the obligate primary bacterial symbiont,
Buchnera aphidicola
, and secondary symbionts across the host's lifetime. We found life history costs to harboring some secondary symbiont species. Secondary symbiont populations were found to increase with host age, while
Buchnera
populations exhibited a more complicated pattern. Immune cell counts peaked at the midreproductive stage before declining in the oldest aphids. The combined effects of immunosenescence and symbiont population growth may have important consequences for symbiont transmission and maintenance within a host population.
High-Sensitivity Monoclonal Antibodies Specific for Homoserine Lactones Protect Mice from Lethal Pseudomonas aeruginosa Infections
Authors: Palliyil Soumya , Downham Christina , Broadbent Ian , Charlton Keith , Porter Andrew J. 
Published: November 2013

ABSTRACT

A number of bacteria, including pathogens like
Pseudomonas aeruginosa
, utilize homoserine lactones (HSLs) as quorum sensing (QS) signaling compounds and engage in cell-to-cell communication to coordinate their behavior. Blocking this bacterial communication may be an attractive strategy for infection control as QS takes a central role in
P. aeruginosa
biology. In this study, immunomodulation of HSL molecules by monoclonal antibodies (MAbs) was used as a novel approach to prevent
P. aeruginosa
infections and as tools to detect HSLs in bodily fluids as a possible first clue to an undiagnosed Gram-negative infection. Using sheep immunization and recombinant antibody technology, a panel of sheep-mouse chimeric MAbs were generated which recognized HSL compounds with high sensitivity (nanomolar range) and cross-reactivity. These MAbs retained their nanomolar sensitivity in complex matrices and were able to recognize HSLs in
P. aeruginosa
cultures grown in the presence of urine. In a nematode slow-killing assay, HSL MAbs significantly increased the survival of worms fed on the antibiotic-resistant strain PA058. The therapeutic benefit of these MAbs was further studied using a mouse model of
Pseudomonas
infection in which groups of mice treated with HSL-2 and HSL-4 MAbs survived, 7 days after pathogen challenge, in significantly greater numbers (83 and 67%, respectively) compared with the control groups. This body of work has provided early proof-of-concept data to demonstrate the potential of HSL-specific, monoclonal antibodies as theranostic clinical leads suitable for the diagnosis, prevention, and treatment of life-threatening bacterial infections.
Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by
carB
-Based Oligonucleotide Microarray
Authors: Shin Hwa Hui , Hwang Byeong Hee , Seo Jeong Hyun , Cha Hyung Joon 
Published: November 2013

ABSTRACT

It is important to rapidly and selectively detect and analyze pathogenic
Salmonella enterica
subsp.
enterica
in contaminated food to reduce the morbidity and mortality of
Salmonella
infection and to guarantee food safety. In the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the
carB
gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficiently detect and discriminate three
S. enterica
subsp.
enterica
serotypes: Choleraesuis, Enteritidis, and Typhimurium. Using the developed microarray system, three serotype targets were successfully analyzed in a range as low as 1.6 to 3.1 nM and were specifically discriminated from each other without nonspecific signals. In addition, the constructed microarray did not have cross-reactivity with other common pathogenic bacteria and even enabled the clear discrimination of the target
Salmonella
serotype from a bacterial mixture. Therefore, these results demonstrated that our novel
carB
-based oligonucleotide microarray can be used as an effective and specific detection system for
S. enterica
subsp.
enterica
serotypes.
Higher Water Temperature and Incubation under Aerobic and Microaerobic Conditions Increase the Recovery and Diversity of Arcobacter spp. from Shellfish
Authors: Levican Arturo , Collado Luis , Yustes Clara , Aguilar Carme , Figueras Maria José 
Published: November 2013

ABSTRACT

Some
Arcobacter
species are considered emerging food-borne and waterborne pathogens, and shellfish have been suggested as one of their reservoirs. However, only a few studies have investigated the presence of
Arcobacter
in this kind of food. This study assesses the prevalence and diversity of
Arcobacter
spp. in shellfish by multiplex PCR (m-PCR) and culturing methods (under different atmospheric conditions) and evaluates the possible influence of environmental parameters (temperature, salinity, and harvesting bay).
Arcobacter
was detected by m-PCR and/or culturing in 61 (29.9%) of 204 shellfish samples. Of the positive samples by culturing, 41.1% were obtained under only aerobic incubation conditions, while 23.2% were obtained under only microaerobic conditions. Of 476 investigated isolates, 118 belonged to different enterobacterial repetitive intergenic consensus (ERIC)-PCR genotypes (strains) and to 11 different species. This study shows the highest diversity of
Arcobacter
species ever observed in samples from any origin. The most prevalent species was
Arcobacter butzleri
(60.2%), followed by
Arcobacter molluscorum
(21.2%). The prevalence of
Arcobacter
was significantly higher during the summer than in other seasons, being associated with an increase in water temperature. Results confirm that shellfish are a reservoir for a remarkable diversity of
Arcobacter
spp.
Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary
Authors: Zheng Yanling , Hou Lijun , Newell Silvia , Liu Min , Zhou Junliang , Zhao Hui , You Lili , Cheng Xunliang 
Published: November 2013

ABSTRACT

Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (
amoA
) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of
amoA
genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB
amoA
genes was greater than that of AOA
amoA
genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal
amoA
gene abundance and not with bacterial
amoA
gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments.
The CLO3403/CLO3404 Two-Component System of Clostridium botulinum E1 Beluga Is Important for Cold Shock Response and Growth at Low Temperatures
Authors: Mascher Gerald , Derman Yağmur , Kirk David G. , Palonen Eveliina , Lindström Miia , Korkeala Hannu 
Published: November 2013

ABSTRACT

In order to survive a temperature downshift, bacteria have to sense the changing environment and adjust their metabolism and structure. Two-component signal transduction systems (TCSs) play a central role in sensing and responding to many different environmental stimuli. Although the nonproteolytic (group II)
Clostridium botulinum
represents a major hazard in chilled foods, the cold adaption mechanisms of group II
C. botulinum
organisms are not known. Here, we show that the CLO3403/CLO3404 TCS of
C. botulinum
E1 Beluga is involved in the cold shock response and growth at 12°C. Cold shock induced the expression of the genes encoding the histidine kinase (
clo3403
) and the response regulator (
clo3404
) by more than 100-fold after 5 h relative to their expression in a nonshocked culture at the corresponding time point. The involvement of CLO3403/CLO3404 in growth at low temperature was demonstrated by impaired growth of the insertional
clo3403
and
clo3404
knockout mutants at 12°C compared to the growth of the wild-type culture. Additionally, the inactivation of
clo3403
had a negative effect on motility. The growth efficiency at 12°C of the TCS mutants and the motility of the kinase mutants were restored by introducing a plasmid harboring the operon of the CLO3403/CLO3404 TCS. The results suggest that the CLO3403/CLO3404 TCS is important for the cold tolerance of
C. botulinum
E1 Beluga.
Genetic and Functional Investigation of Zn2Cys6Transcription Factors RSE2 and RSE3 in Podospora anserina
Authors: Bovier Elodie , Sellem Carole H. , Humbert Adeline , Sainsard-Chanet Annie 
Published: November 2013

ABSTRACTInPodospora anserina, the two zinc cluster proteins RSE2 and RSE3 are essential for the expression of the gene encoding the alternative oxidase (aox) when the mitochondrial electron transport chain is impaired. In parallel, they activated the expression of gluconeogenic genes encoding phosphoenolpyruvate carboxykinase (pck) and fructose-1,6-biphosphatase (fbp). Orthologues of these transcription factors are present in a wide range of filamentous fungi, and no other role than the regulation of these three genes has been evidenced so far. In order to better understand the function and the organization of RSE2 and RSE3, we conducted a saturated genetic screen based on the constitutive expression of theaoxgene. We identified 10 independent mutations in 9 positions inrse2and 11 mutations in 5 positions inrse3. Deletions were generated at some of these positions and the effects analyzed. This analysis suggests the presence of central regulatory domains and a C-terminal activation domain in both proteins. Microarray analysis revealed 598 genes that were differentially expressed in the strains containing gain- or loss-of-function mutations inrse2orrse3. It showed that in addition toaox,fbp, andpck, RSE2 and RSE3 regulate the expression of genes encoding the alternative NADH dehydrogenase, a Zn2Cys6transcription factor, a flavohemoglobin, and various hydrolases. As a complement to expression data, a metabolome profiling approach revealed that both anrse2gain-of-function mutation and growth on antimycin result in similar metabolic alterations in amino acids, fatty acids, and α-ketoglutarate pools.
C-Terminal Truncations of the Saccharomyces cerevisiae PMA1 H
+
-ATPase Have Major Impacts on Protein Conformation, Trafficking, Quality Control, and Function
Authors: Mason A. Brett , Allen Kenneth E. , Slayman Carolyn W. 
Published: November 2013

ABSTRACT

The C-terminal tail of yeast plasma membrane (PM) H
+
-ATPase extends approximately 38 amino acids beyond the final membrane-spanning segment (TM10) of the protein and is known to be required for successful trafficking, stability, and regulation of enzyme activity. To carry out a detailed functional survey of the entire length of the tail, we generated 15 stepwise truncation mutants. Eleven of them, lacking up to 30 amino acids from the extreme terminus, were able to support cell growth, even though there were detectable changes in plasma membrane expression, protein stability, and ATPase activity. Three functionally distinct regions of the C terminus could be defined. (i) Truncations upstream of Lys
889
, removing more than 30 amino acid residues, yielded no viable mutants, and conditional expression of such constructs supported the conclusion that the stretch from Ala
881
(at the end of TM10) to Gly
888
is required for stable folding and PM targeting. (ii) The stretch between Lys
889
and Lys
916
, a region known to be subject to kinase-mediated posttranslational modification, was shown here to be ubiquitinated in carbon-starved cells as part of cellular quality control and to be essential for normal ATPase folding and stability, as well as for autoinhibition of ATPase activity during glucose starvation. (iii) Finally, removal of even one or two residues (Glu
917
and Thr
918
) from the extreme C terminus led to visibly reduced expression of the ATPase at the plasma membrane. Thus, the C terminus is much more than a simple appendage and profoundly influences the structure, biogenesis, and function of the yeast H
+
-ATPase.
Global Expression Analysis of the Yeast Lachancea (Saccharomyces) kluyveri Reveals New
URC
Genes Involved in Pyrimidine Catabolism
Authors: Andersson Rasmussen Anna , Kandasamy Dineshkumar , Beck Halfdan , Crosby Seth D. , Björnberg Olof , Schnackerz Klaus D. , Piškur Jure 
Published: November 2013

ABSTRACT

Pyrimidines are important nucleic acid precursors which are constantly synthesized, degraded, and rebuilt in the cell. Four degradation pathways, two of which are found in eukaryotes, have been described. One of them, the
URC
pathway, has been initially discovered in our laboratory in the yeast
Lachancea kluyveri
. Here, we present the global changes in gene expression in
L. kluyveri
in response to different nitrogen sources, including uracil, uridine, dihydrouracil, and ammonia. The expression pattern of the known
URC
genes,
URC1-6
, helped to identify nine putative novel
URC
genes with a similar expression pattern. The microarray analysis provided evidence that both the
URC
and
PYD
genes are under nitrogen catabolite repression in
L. kluyveri
and are induced by uracil or dihydrouracil, respectively. We determined the function of
URC8
, which was found to catalyze the reduction of malonate semialdehyde to 3-hydroxypropionate, the final degradation product of the pathway. The other eight genes studied were all putative permeases. Our analysis of double deletion strains showed that the
L. kluyveri
Fui1p protein transported uridine, just like its homolog in
Saccharomyces cerevisiae
, but we demonstrated that is was not the only uridine transporter in
L. kluyveri
. We also showed that the
L. kluyveri
homologs of
DUR3
and
FUR4
do not have the same function that they have in
S. cerevisiae
, where they transport urea and uracil, respectively. In
L. kluyveri
, both of these deletion strains grew normally on uracil and urea.
WetA Is Required for Conidiogenesis and Conidium Maturation in the Ascomycete Fungus Fusarium graminearum
Authors: Son Hokyoung , Kim Myung-Gu , Min Kyunghun , Lim Jae Yun , Choi Gyung Ja , Kim Jin-Cheol , Chae Suhn-Kee , Lee Yin-Won 
Published: November 2013

ABSTRACT

Fusarium graminearum
, a prominent fungal pathogen that infects major cereal crops, primarily utilizes asexual spores to spread disease. To understand the molecular mechanisms underlying conidiogenesis in
F. graminearum
, we functionally characterized the
F. graminearum
ortholog of
Aspergillus nidulans
wetA
, which has been shown to be involved in conidiogenesis and conidium maturation. Deletion of
F. graminearum
wetA
did not alter mycelial growth, sexual development, or virulence, but the
wetA
deletion mutants produced longer conidia with fewer septa, and the conidia were sensitive to acute stresses, such as oxidative stress and heat stress. Furthermore, the survival rate of aged conidia from the
F. graminearum
wetA
deletion mutants was reduced. The
wetA
deletion resulted in vigorous generation of single-celled conidia through autophagy-dependent microcycle conidiation, indicating that WetA functions to maintain conidial dormancy by suppressing microcycle conidiation in
F. graminearum
. Transcriptome analyses demonstrated that most of the putative conidiation-related genes are expressed constitutively and that only a few genes are specifically involved in
F. graminearum
conidiogenesis. The conserved and distinct roles identified for WetA in
F. graminearum
provide new insights into the genetics of conidiation in filamentous fungi.
The NIMA Kinase Is Required To Execute Stage-Specific Mitotic Functions after Initiation of Mitosis
Authors: Govindaraghavan Meera , Lad Alisha A. , Osmani Stephen A. 
Published: November 2013

ABSTRACT

The G
2
-M transition in
Aspergillus nidulans
requires the NIMA kinase, the founding member of the Nek kinase family. Inactivation of NIMA results in a late G
2
arrest, while overexpression of NIMA is sufficient to promote mitotic events independently of cell cycle phase. Endogenously tagged NIMA-GFP has dynamic mitotic localizations appearing first at the spindle pole body and then at nuclear pore complexes before transitioning to within nuclei and the mitotic spindle and back at the spindle pole bodies at mitotic exit, suggesting that it functions sequentially at these locations. Since NIMA is indispensable for mitotic entry, it has been difficult to determine the requirement of NIMA for subaspects of mitosis. We show here that when NIMA is partially inactivated, although mitosis can be initiated, a proportion of cells fail to successfully generate two daughter nuclei. We further define the mitotic defects to show that normal NIMA function is required for the formation of a bipolar spindle, nuclear pore complex disassembly, completion of chromatin segregation, and the normal structural rearrangements of the nuclear envelope required to generate two nuclei from one. In the remaining population of cells that enter mitosis with inadequate NIMA, two daughter nuclei are generated in a manner dependent on the spindle assembly checkpoint, indicating highly penetrant defects in mitotic progression without sufficient NIMA activity. This study shows that NIMA is required not only for mitotic entry but also sequentially for successful completion of stage-specific mitotic events.