bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Engineering of Algae for Enhanced Biofuel Production
Authors: Radakovits Randor , Jinkerson Robert E. , Darzins Al , Posewitz Matthew C. 
Published: February 2010

ABSTRACTThere are currently intensive global research efforts aimed at increasing and modifying the accumulation of lipids, alcohols, hydrocarbons, polysaccharides, and other energy storage compounds in photosynthetic organisms, yeast, and bacteria through genetic engineering. Many improvements have been realized, including increased lipid and carbohydrate production, improved H2yields, and the diversion of central metabolic intermediates into fungible biofuels. Photosynthetic microorganisms are attracting considerable interest within these efforts due to their relatively high photosynthetic conversion efficiencies, diverse metabolic capabilities, superior growth rates, and ability to store or secrete energy-rich hydrocarbons. Relative to cyanobacteria, eukaryotic microalgae possess several unique metabolic attributes of relevance to biofuel production, including the accumulation of significant quantities of triacylglycerol; the synthesis of storage starch (amylopectin and amylose), which is similar to that found in higher plants; and the ability to efficiently couple photosynthetic electron transport to H2production. Although the application of genetic engineering to improve energy production phenotypes in eukaryotic microalgae is in its infancy, significant advances in the development of genetic manipulation tools have recently been achieved with microalgal model systems and are being used to manipulate central carbon metabolism in these organisms. It is likely that many of these advances can be extended to industrially relevant organisms. This review is focused on potential avenues of genetic engineering that may be undertaken in order to improve microalgae as a biofuel platform for the production of biohydrogen, starch-derived alcohols, diesel fuel surrogates, and/or alkanes.
Genetic Modification of theSalmonellaMembrane Physical State Alters the Pattern of Heat Shock Response
Authors: Porta Amalia , Török Zsolt , Horvath Ibolya , Franceschelli Silvia , Vígh László , Maresca Bruno 
Published: February 2010

ABSTRACTIt is now recognized that membranes are not simple physical barriers but represent a complex and dynamic environment that affects membrane protein structures and their functions. Recent data emphasize the role of membranes in sensing temperature changes, and it has been shown that the physical state of the plasma membrane influences the expression of a variety of genes such as heat shock genes. It has been widely shown that minor alterations in lipid membranes are critically involved in the conversion of signals from the environment to the transcriptional activation of heat shock genes. Previously, we have proposed that the composition, molecular arrangement, and physical state of lipid membranes and their organization have crucial roles in cellular responses during stress caused by physical and chemical factors as well as in pathological states. Here, we show that transformation ofSalmonella entericaserovar Typhimurium LT2 (SalmonellaTyphimurium) with a heterologous Δ12-desaturase (or with itstrans-membrane regions) causes major changes in the pathogen's membrane dynamic. In addition, this pathogen is strongly impaired in the synthesis of major stress proteins (heat shock proteins) under heat shock. These data support the hypothesis that the perception of temperature inSalmonellais strictly controlled by membrane order and by a specific membrane lipid/protein ratio that ultimately causes transcriptional activation of heat shock genes. These results represent a previously unrecognized mode of sensing temperature variation used by this pathogen at the onset of infection.
Changes in Membrane Fluid State and Heat Shock Response Cause Attenuation of Virulence
Authors: Porta Amalia , Eletto Annamaria , Török Zsolt , Franceschelli Silvia , Glatz Attila , Vígh László , Maresca Bruno 
Published: February 2010

ABSTRACT

So far attenuation of pathogens has been mainly obtained by chemical or heat treatment of microbial pathogens. Recently, live attenuated strains have been produced by genetic modification. We have previously demonstrated that in several prokaryotes as well as in yeasts and mammalian cells the heat shock response is controlled by the membrane physical state (MPS). We have also shown that in
Salmonella enterica
serovar Typhimurium LT2 (
Salmonella
Typhimurium) overexpression of a Δ
12
-desaturase gene alters the MPS, inducing a sharp impairment of transcription of major heat shock genes and failure of the pathogen to grow inside macrophage (MΦ) (A. Porta et al., J. Bacteriol. 192:1988-1998, 2010). Here, we show that overexpression of a homologous Δ
9
-desaturase sequence in the highly virulent G217B strain of the human fungal pathogen
Histoplasma capsulatum
causes loss of its ability to survive and persist within murine MΦ along with the impairment of the heat shock response. When the attenuated strain of
H. capsulatum
was injected in a mouse model of infection, it did not cause disease. Further, treated mice were protected when challenged with the virulent fungal parental strain. Attenuation of virulence in MΦ of two evolutionarily distant pathogens was obtained by genetic modification of the MPS, suggesting that this is a new method that may be used to produce attenuation or loss of virulence in both other intracellular prokaryotic and eukaryotic pathogens. This new procedure to generate attenuated forms of pathogens may be used eventually to produce a novel class of vaccines based on the genetic manipulation of a pathogen's membrane fluid state and stress response.
Global Regulation of Food Supply by
P
seudomonas p
utida
DOT-T1E
Authors: Daniels Craig , Godoy Patricia , Duque Estrella , Molina-Henares M. Antonia , de la Torre Jesús , del Arco José María , Herrera Carmen , Segura Ana , Guazzaroni M. Eugenia , Ferrer Manuel , Ramos Juan Luis 
Published: February 2010

ABSTRACT

Pseudomonas putida
DOT-T1E was used as a model to develop a “phenomics” platform to investigate the ability of
P. putida
to grow using different carbon, nitrogen, and sulfur sources and in the presence of stress molecules. Results for growth of wild-type DOT-T1E on 90 different carbon sources revealed the existence of a number of previously uncharted catabolic pathways for compounds such as salicylate, quinate, phenylethanol, gallate, and hexanoate, among others. Subsequent screening on the subset of compounds on which wild-type DOT-TIE could grow with four knockout strains in the global regulatory genes Δ
crc
, Δ
crp
, Δ
cyoB
, and Δ
ptsN
allowed analysis of the global response to nutrient supply and stress. The data revealed that most global regulator mutants could grow in a wide variety of substrates, indicating that metabolic fluxes are physiologically balanced. It was found that the Crc mutant did not differ much from the wild-type regarding the use of carbon sources. However, certain pathways are under the preferential control of one global regulator, i.e., metabolism of succinate and
d
-fructose is influenced by CyoB, and
l
-
arginine is influenced by PtsN. Other pathways can be influenced by more than one global regulator; i.e.,
l
-valine catabolism can be influenced by CyoB and Crp (cyclic AMP receptor protein) while phenylethylamine is affected by Crp, CyoB, and PtsN. These results emphasize the cross talk required in order to ensure proper growth and survival. With respect to N sources, DOT-T1E can use a wide variety of inorganic and organic nitrogen sources. As with the carbon sources, more than one global regulator affected growth with some nitrogen sources; for instance, growth with nucleotides, dipeptides,
d
-amino acids, and ethanolamine is influenced by Crp, CyoB, and PtsN. A surprising finding was that the Crp mutant was unable to flourish on ammonium. Results for assayed sulfur sources revealed that CyoB controls multiple points in methionine/cysteine catabolism while PtsN and Crc are needed for
N
-acetyl-
l
-cysteamine utilization. Growth of global regulator mutants was also influenced by stressors of different types (antibiotics, oxidative agents, and metals). Overall and in combination with results for growth in the presence of various stressors, these phenomics assays provide multifaceted insights into the complex decision-making process involved in nutrient supply, optimization, and survival.
Role of the DinB Homologs Rv1537 and Rv3056 in
Mycobacterium tuberculosis
Authors: Kana Bavesh D. , Abrahams Garth L. , Sung Nackmoon , Warner Digby F. , Gordhan Bhavna G. , Machowski Edith E. , Tsenova Liana , Sacchettini James C. , Stoker Neil G. , Kaplan Gilla , Mizrahi Valerie 
Published: February 2010

ABSTRACT

The environment encountered by
Mycobacterium tuberculosis
during infection is genotoxic. Most bacteria tolerate DNA damage by engaging specialized DNA polymerases that catalyze translesion synthesis (TLS) across sites of damage.
M. tuberculosis
possesses two putative members of the DinB class of Y-family DNA polymerases, DinB1 (Rv1537) and DinB2 (Rv3056); however, their role in damage tolerance, mutagenesis, and survival is unknown. Here, both
dinB1
and
dinB2
are shown to be expressed
in vitro
in a growth phase-dependent manner, with
dinB2
levels 12- to 40-fold higher than those of
dinB1
. Yeast two-hybrid analyses revealed that DinB1, but not DinB2, interacts with the β-clamp, consistent with its canonical C-terminal β-binding motif. However, knockout of
dinB1
,
dinB2
, or both had no effect on the susceptibility of
M. tuberculosis
to compounds that form
N
2
-dG adducts and alkylating agents. Similarly, deletion of these genes individually or in combination did not affect the rate of spontaneous mutation to rifampin resistance or the spectrum of resistance-conferring
rpoB
mutations and had no impact on growth or survival in human or mouse macrophages or in mice. Moreover, neither gene conferred a mutator phenotype when expressed ectopically in
Mycobacterium smegmatis
. The lack of the effect of altering the complements or expression levels of
dinB1
and/or
dinB2
under conditions predicted to be phenotypically revealing suggests that the DinB homologs from
M. tuberculosis
do not behave like their counterparts from other organisms.
Effects of SequentialCampylobacter jejuni81-176 Lipooligosaccharide Core Truncations on Biofilm Formation, Stress Survival, and Pathogenesis
Authors: Naito Mizue , Frirdich Emilisa , Fields Joshua A. , Pryjma Mark , Li Jianjun , Cameron Andrew , Gilbert Michel , Thompson Stuart A. , Gaynor Erin C. 
Published: February 2010

ABSTRACTCampylobacter jejuniis a highly prevalent human pathogen for which pathogenic and stress survival strategies remain relatively poorly understood. We previously found that aC. jejunistrain 81-176 mutant defective for key virulence and stress survival attributes was also hyper-biofilm and hyperreactive to the UV fluorescent dye calcofluor white (CFW). We hypothesized that screening for CFW hyperreactive mutants would identify additional genes required forC. jejunipathogenesis properties. Surprisingly, two such mutants harbored lesions in lipooligosaccharide (LOS) genes (waaFandlgtF), indicating a complete loss of the LOS outer core region. We utilized this as an opportunity to explore the role of each LOS core-specific moiety in the pathogenesis and stress survival of this strain and thus also constructed ΔgalTand ΔcstIImutants with more minor LOS truncations. Interestingly, we found that mutants lacking the LOS outer core (ΔwaaFand ΔlgtFbut not ΔgalTor ΔcstIImutants) exhibited enhanced biofilm formation. The presence of the complete outer core was also necessary for resistance to complement-mediated killing. In contrast, any LOS truncation, even that of the terminal sialic acid (ΔcstII), resulted in diminished resistance to polymyxin B. The cathelicidin LL-37 was found to be active againstC. jejuni, with the LOS mutants exhibiting modest but tiled alterations in LL-37 sensitivity. The ΔwaaFmutant but not the other LOS mutant strains also exhibited a defect in intraepithelial cell survival, an aspect ofC. jejunipathogenesis that has only recently begun to be clarified. Finally, using a mouse competition model, we now provide the first direct evidence for the importance of theC. jejuniLOS in host colonization. Collectively, this study has uncovered novel roles for theC. jejuniLOS, highlights the dynamic nature of theC. jejunicell envelope, and provides insight into the contribution of specific LOS core moieties to stress survival and pathogenesis.
Increased Expression of the Type IV Secretion System in Piliated
Neisseria gonorrhoeae
Variants
Authors: Salgado-Pabón Wilmara , Du Ying , Hackett Kathleen T. , Lyons Katelynn M. , Arvidson Cindy Grove , Dillard Joseph P. 
Published: February 2010

ABSTRACT

Neisseria gonorrhoeae
produces a type IV secretion system that secretes chromosomal DNA. The secreted DNA is active in the transformation of other gonococci in the population and may act to transfer antibiotic resistance genes and variant alleles for surface antigens, as well as other genes. We observed that gonococcal variants that produced type IV pili secreted more DNA than variants that were nonpiliated, suggesting that the process may be regulated. Using microarray analysis, we found that a piliated strain showed increased expression of the gene for the putative type IV secretion coupling protein TraD, whereas a nonpiliated variant showed increased expression of genes for transcriptional and translational machinery, consistent with its higher growth rate compared to that of the piliated strain. These results suggested that type IV secretion might be controlled by either
traD
expression or growth rate. A mutant with a deletion in
traD
was found to be deficient in DNA secretion. Further mutation and complementation analysis indicated that
traD
is transcriptionally and translationally coupled to
traI
, which encodes the type IV secretion relaxase. We were able to increase DNA secretion in a nonpiliated strain by inserting a gene cassette with a strong promoter to drive the expression of the putative operon containing
traI
and
traD
. Together, these data suggest a model in which the type IV secretion system apparatus is made constitutively, while its activity is controlled through regulation of
traD
and
traI
.
Myxococcus xanthus
Viability Depends on GroEL Supplied by Either of Two Genes, but the Paralogs Have Different Functions during Heat Shock, Predation, and Development
Authors: Li Jian , Wang Yan , Zhang Cui-ying , Zhang Wen-yan , Jiang De-ming , Wu Zhi-hong , Liu Hong , Li Yue-zhong 
Published: February 2010

ABSTRACT

Myxococcus xanthus
DK1622 contains two paralogous
groEL
gene loci that possess both different sequences and different organizations within the genome. Deletion of either one of these two genes alone does not affect cell viability. However, deletion of both
groEL
genes results in cell death unless a complemented
groEL1
or
groEL2
gene is present. The
groEL1
gene was determined to be essential for cell survival under heat shock conditions; a strain with mutant
groEL2
caused cells to be more sensitive than the wild-type strain to higher temperatures. Mutants with a single deletion of either
groEL1
(
MXAN_4895
) or
groEL2
(
MXAN_4467
) had a growth curve similar to that of the wild-type strain DK1622 in medium containing hydrolyzed proteins as the substrate. However, when cells were cultured on medium containing either
Escherichia coli
cells or casein as the substrate, deletion of
groEL2
, but not
groEL1
, led to a deficiency in cell predation and macromolecular feeding. Furthermore,
groEL1
was found to play an indispensable role in the development and sporulation of cells, but deletion of
groEL2
had no visible effects. Our results suggest that, although alternatively required for cell viability, the products of the two
groEL
genes have divergent functions in the multicellular social life cycle of
M. xanthus
DK1622.
Analyses of the Regulatory Mechanism and Physiological Roles of
Pseudomonas aeruginosa
OhrR, a Transcription Regulator and a Sensor of Organic Hydroperoxides
Authors: Atichartpongkul Sopapan , Fuangthong Mayuree , Vattanaviboon Paiboon , Mongkolsuk Skorn 
Published: February 2010

ABSTRACT

ohrR
encodes an organic hydroperoxide sensor and a transcriptional repressor that regulates organic hydroperoxide-inducible expression of a thiol peroxidase gene,
ohr
, and itself. OhrR binds directly to the operators and represses transcription of these genes. Exposure to an organic hydroperoxide leads to oxidation of OhrR and to subsequent structural changes that result in the loss of the repressor's ability to bind to the operators that allow expression of the target genes. Differential induction of
ohrR
and
ohr
by
tert
-butyl hydroperoxide suggests that factors such as the repressor's dissociation constants for different operators and the chemical nature of the inducer contribute to OhrR-dependent organic hydroperoxide-inducible gene expression.
ohrR
and
ohr
mutants show increased and decreased resistance to organic hydroproxides, respectively, compared to a parental strain. Moreover, the
ohrR
mutant had a reduced-virulence phenotype in the
Pseudomonas aeruginosa
-
Caenorhabditis elegans
pathogenicity model.
Genome Sequence ofStreptococcus gallolyticus: Insights into Its Adaptation to the Bovine Rumen and Its Ability To Cause Endocarditis
Authors: Rusniok Christophe , Couvé Elisabeth , Da Cunha Violette , El Gana Rachida , Zidane Nora , Bouchier Christiane , Poyart Claire , Leclercq Roland , Trieu-Cuot Patrick , Glaser Philippe 
Published: February 2010

ABSTRACTStreptococcus gallolyticus(formerly known asStreptococcus bovisbiotype I) is an increasing cause of endocarditis among streptococci and frequently associated with colon cancer.S. gallolyticusis part of the rumen flora but also a cause of disease in ruminants as well as in birds. Here we report the complete nucleotide sequence of strain UCN34, responsible for endocarditis in a patient also suffering from colon cancer. Analysis of the 2,239 proteins encoded by its 2,350-kb-long genome revealed unique features among streptococci, probably related to its adaptation to the rumen environment and its capacity to cause endocarditis.S. gallolyticushas the capacity to use a broad range of carbohydrates of plant origin, in particular to degrade polysaccharides derived from the plant cell wall. Its genome encodes a large repertoire of transporters and catalytic activities, like tannase, phenolic compounds decarboxylase, and bile salt hydrolase, that should contribute to the detoxification of the gut environment. Furthermore,S. gallolyticussynthesizes all 20 amino acids and more vitamins than any other sequencedStreptococcusspecies. Many of the genes encoding these specific functions were likely acquired by lateral gene transfer from other bacterial species present in the rumen. The surface properties of strain UCN34 may also contribute to its virulence. A polysaccharide capsule might be implicated in resistance to innate immunity defenses, and glucan mucopolysaccharides, three types of pili, and collagen binding proteins may play a role in adhesion to tissues in the course of endocarditis.
TheN-Acetylmuramic Acid 6-Phosphate Etherase Gene Promotes Growth and Cell Differentiation of Cyanobacteria under Light-Limiting Conditions
Authors: Jiang Haibo , Kong Renqiu , Xu Xudong 
Published: February 2010

ABSTRACTInactivation ofsll0861inSynechocystissp. strain PCC 6803 or the homologous genealr2432inAnabaenasp. strain PCC 7120 had no effect on the growth of these organisms at a light intensity of 30 μmol photons m−2s−1but reduced their growth at a light intensity of 5 or 10 μmol photons m−2s−1. InAnabaena, inactivation of the gene also significantly reduced the rate of heterocyst differentiation under low-light conditions. The predicted products ofsll0861andalr2432and homologs of these genes showed similarity toN-acetylmuramic acid 6-phosphate etherase (MurQ), an enzyme involved in peptidoglycan recycling, inEscherichia coli. E. coli murQand the cyanobacterial homologs could functionally substitute for each other. We hypothesize thatmurQin cyanobacteria promotes low-light adaptation through reutilization of peptidoglycan degradation products.
Characterization of a Mannose Utilization System in
Bacillus subtilis
Authors: Sun Tianqi , Altenbuchner Josef 
Published: February 2010

ABSTRACT

The mannose operon of
Bacillus subtilis
consists of three genes,
manP
,
manA
, and
yjdF
, which are responsible for the transport and utilization of mannose. Upstream and in the same orientation as the mannose operon a regulatory gene,
manR
, codes for a transcription activator of the mannose operon, as shown in this study. Both mannose operon transcription and
manR
transcription are inducible by mannose. The presence of mannose resulted in a 4- to 7-fold increase in expression of
lacZ
from the
manP
promoter (

P
manP

) and in a 3-fold increase in expression of
lacZ
from the
manR
promoter (

P
manR

). The transcription start sites of
manPA-yjdF
and
manR
were determined to be a single A residue and a single G residue, respectively, preceded by −10 and −35 boxes resembling a vegetative σ
A
promoter structure. Through deletion analysis the target sequences of ManR upstream of

P
manP

and

P
manR

were identified between bp −80 and −35 with respect to the transcriptional start site of both promoters. Deletion of
manP
(mannose transporter) resulted in constitutive expression from both the

P
manP

and

P
manR

promoters, indicating that the phosphotransferase system (PTS) component EII
Man
has a negative effect on regulation of the mannose operon and
manR
. Moreover, both

P
manP

and

P
manR

are subject to carbon catabolite repression (CCR). By constructing protein sequence alignments a DNA binding motif at the N-terminal end, two PTS regulation domains (PRDs), and an EIIA- and EIIB-like domain were identified in the ManR sequence, indicating that ManR is a PRD-containing transcription activator. Like findings for other PRD regulators, the phosphoenolpyruvate (PEP)-dependent phosphorylation by the histidine protein HPr via His15 plays an essential role in transcriptional activation of

P
manP

and

P
manR

. Phosphorylation of Ser46 of HPr or of the homologous Crh protein by HPr kinase and formation of a repressor complex with CcpA are parts of the
B. subtilis
CCR system. Only in the double mutant with an HPr Ser46Ala mutation and a
crh
knockout mutation was CCR strongly reduced. In contrast,

P
manR

and

P
manP

were not inducible in a
ccpA
deletion mutant.
Gregory of Elvira, Lactantius, and the Reception of the De ira Dei
Authors: Cain Andrew 
Published: February 2010

AbstractGregory of Elvira’s indebtedness to the Latin patristic tradition has been copiously documented. However, until now no scholar has been able to prove that he worked from Lactantius. This article adduces two clear reminiscences of Lactantius in Gregory’s homilies, one of which is the only extended quotation from the De ira Dei to surface in all of Latin patristic literature.
Christianity as Philosophy: Problems and Perspectives of an Ancient Intellectual Project
Authors: Löhr Winrich 
Published: February 2010

AbstractThe article explores the profile, context and consequences of Christianity’s self definition as a philosophy in the ancient world. It proposes a distinction between, on the one hand, the practice of teaching philosophy in small Christian schools, and, on the other hand, an intellectual discourse that proclaimed Christianity as the true and superior philosophy. It is argued that Christianity’s self definition as a philosophy should not be viewed as merely an accommodation to an intellectual fashion. It is shown how Christianity could be understood and practised as a philosophy in the ancient sense of the word. However, as a philosophical practice Christianity underwent a transformation in the 4th century which prevented the emergence of a late antique Christian scholasticism and gave rise to new combinations of Christianity and non-Christian philosophy.