bluuebunny/crossref_metadata_2025 huggingface dataset:
A natural variant of the cysteine protease virulence factor of group A
Streptococcus
with an arginine-glycine-aspartic acid (RGD) motif preferentially binds human integrins α
v
β
3
and α
IIb
β
3
Authors: Stockbauer Kathryn E. , Magoun Loranne , Liu Mengyao , Burns Eugene H. , Gubba Siddeswar , Renish Sarah , Pan Xi , Bodary Sarah C. , Baker Elizabeth , Coburn Jenifer , Leong John M. , Musser James M.
Published: July 2002

The human pathogenic bacterium group A
Streptococcus
produces an extracellular cysteine protease [streptococcal pyrogenic exotoxin B (SpeB)] that is a critical virulence factor for invasive disease episodes. Sequence analysis of the
speB
gene from 200 group A
Streptococcus
isolates collected worldwide identified three main mature SpeB (mSpeB) variants. One of these variants (mSpeB2) contains an Arg-Gly-Asp (RGD) sequence, a tripeptide motif that is commonly recognized by integrin receptors. mSpeB2 is made by all isolates of the unusually virulent serotype M1 and several other geographically widespread clones that frequently cause invasive infections. Only the mSpeB2 variant bound to transfected cells expressing integrin α
v
β
3
(also known as the vitronectin receptor) or α
IIb
β
3
(platelet glycoprotein IIb-IIIa), and binding was blocked by a mAb that recognizes the streptococcal protease RGD motif region. In addition, mSpeB2 bound purified platelet integrin α
IIb
β
3
. Defined β
3
mutants that are altered for fibrinogen binding were defective for SpeB binding. Synthetic peptides with the mSpeB2 RGD motif, but not the RSD sequence present in other mSpeB variants, blocked binding of mSpeB2 to transfected cells expressing α
v
β
3
and caused detachment of cultured human umbilical vein endothelial cells. The results (
i
) identify a Gram-positive virulence factor that directly binds integrins, (
ii
) identify naturally occurring variants of a documented Gram-positive virulence factor with biomedically relevant differences in their interactions with host cells, and (
iii
) add to the theme that subtle natural variation in microbial virulence factor structure alters the character of host-pathogen interactions.
poc1
: An
Arabidopsis
mutant perturbed in phytochrome signaling because of a T DNA insertion in the promoter of
PIF3
, a gene encoding a phytochrome-interacting bHLH protein
Authors: Halliday Karen J. , Hudson Matthew , Ni Min , Qin Minmin , Quail Peter H.
Published: July 2002

The phytochrome family of informational photoreceptors has a central role in regulating light-responsive gene expression, but the mechanism of intracellular signal transduction has remained elusive. In a genetic screen for T DNA-tagged
Arabidopsis
mutants affected in early signaling intermediates, we identified
poc1
(
p
h
o
to
c
urrent 1), which exhibits enhanced responsiveness to red light. This phenotype is absent in a
phyB
(
phy
tochrome
B
) null mutant background, indicating that the
poc1
mutation enhances phyB signal transduction. The T DNA insertion in
poc1
was found to be located in the promoter region of
PIF3
, a gene encoding a basic helix–loop–helix protein. The mutant phenotype seems to result from insertion-induced overexpression of this gene in red-light-grown seedlings, consistent with PIF3 functioning as a positively acting signaling intermediate. These findings, combined with data from a separate yeast two-hybrid screen that identified PIF3 as a phytochrome-interacting factor necessary for normal signaling, provide evidence that phytochrome signal transduction may include a direct pathway to photoresponsive nuclear genes via physical interaction of the photoreceptor molecules with the potential transcriptional regulator PIF3.
Accurate quantitation of protein expression and site-specific phosphorylation
Authors: Oda Y. , Huang K. , Cross F. R. , Cowburn D. , Chait B. T.
Published: July 2002

A mass spectrometry-based method is described for simultaneous identification and quantitation of individual proteins and for determining changes in the levels of modifications at specific sites on individual proteins. Accurate quantitation is achieved through the use of whole-cell stable isotope labeling. This approach was applied to the detection of abundance differences of proteins present in wild-type versus mutant cell populations and to the identification of
in vivo
phosphorylation sites in the PAK-related yeast Ste20 protein kinase that depend specifically on the G1 cyclin Cln2. The present method is general and affords a quantitative description of cellular differences at the level of protein expression and modification, thus providing information that is critical to the understanding of complex biological phenomena.
Colinearity and its exceptions in orthologous
adh
regions of maize and sorghum
Authors: Tikhonov Alexander P. , SanMiguel Phillip J. , Nakajima Yuko , Gorenstein Nina M. , Bennetzen Jeffrey L. , Avramova Zoya
Published: July 2002

Orthologous
adh
regions of the sorghum and maize genomes were sequenced and analyzed. Nine known or candidate genes, including
adh1
, were found in a 225-kilobase (kb) maize sequence. In a 78-kb space of sorghum, the nine homologues of the maize genes were identified in a colinear order, plus five additional genes. The major fraction of DNA in maize, occupying 166 kb (74%), is represented by 22 long terminal repeat (LTR) retrotransposons. About 6% of the sequence belongs to 33 miniature inverted-repeat transposable elements (MITEs), remnants of DNA transposons, 4 simple sequence repeats, and low-copy-number DNAs of unknown origin. In contrast, no LTR retroelements were detected in the orthologous sorghum region. The unconserved sorghum DNA is composed of 20 putative MITEs, transposon-like elements, 5 simple sequence repeats, and low-copy-number DNAs of unknown origin. No MITEs were discovered in the 166 kb of DNA occupied by the maize LTR retrotransposons. In both species, MITEs were found in the space between genes and inside introns, indicating specific insertion and/or retention for these elements. Two adjacent sorghum genes, including one gene missing in maize, had colinear homologues on
Arabidopsis
chromosome IV, suggesting two rearrangements in the sorghum and three in the maize genome in comparison to a four-gene region of
Arabidopsis
. Hence, multiple small rearrangements may be present even in largely colinear genomic regions. These studies revealed a much higher degree of diversity at a microstructural level than predicted by genetic mapping studies for closely related grass species, as well as for comparisons of monocots and dicots.
Intracellular Ca
2+
oscillations drive spontaneous contractions in cardiomyocytes during early development
Authors: Viatchenko-Karpinski S. , Fleischmann B. K. , Liu Q. , Sauer H. , Gryshchenko O. , Ji G. J. , Hescheler J.
Published: July 2002

Activity of cardiac pacemaker cells is caused by a balanced interplay of ion channels. However, it is not known how the rhythmic beating is initiated during early stages of cardiomyogenesis, when the expression of ion channels is still incomplete. Based on the observation that early-stage embryonic stem cell-derived cardiomyocytes continuously contracted in high extracellular K
+
solution, here we provide experimental evidence that the spontaneous activity of these cells is not generated by transmembrane ion currents, but by intracellular [Ca
2+
]
i
oscillations. This early activity was clearly independent of voltage dependent L-type Ca
2+
channels and the interplay between these and ryanodine sensitive Ca
2+
stores. We also show that intracellular Ca
2+
oscillations evoke small membrane depolarizations and that these can trigger L-type Ca
2+
channel driven action potentials.
Stromal cell-derived factor 1 (SDF-1) and antenatal human B cell lymphopoiesis: Expression of SDF-1 by mesothelial cells and biliary ductal plate epithelial cells
Authors: Coulomb-L’Herminé Aurore , Amara Ali , Schiff Claudine , Durand-Gasselin Ingrid , Foussat Arnaud , Delaunay Thierry , Chaouat Gérard , Capron Frédérique , Ledee Nathalie , Galanaud Pierre , Arenzana-Seisdedos Fernando , Emilie Dominique
Published: July 2002

The chemokine stromal cell-derived factor 1 (SDF-1) stimulates the growth of pre-B cellsin vitro, and mice with a disrupted SDF-1 gene have abnormal fetal liver B cell lymphopoiesis. The origin of SDF-1 production has not been determined yet. Using an anti-SDF-1 mAb, we performed immunohistochemical studies in four human embryos and five fetuses to define which cells express the SDF-1 protein at sites of antenatal B cell lymphopoiesis. All mesothelial cells contained SDF-1 at all stages of development, including in the intraembryonic splanchnopleuric mesoderm early into gestation. In fetal lungs and kidneys, SDF-1 was expressed by epithelial cells, and a few B lymphoid precursors, expressing V pre-B chains, were also detected. In the fetal liver, in addition to mesothelial cells, biliary epithelial cells were the only cells to contain SDF-1. Pre-B cells expressing V chains were abundant and exclusively located around the edge of portal spaces, in close contact with biliary ductal plate epithelial cells. They did not colocalize with biliary collecting ducts. Biliary ductal plate epithelial cells and liver B cell lymphopoiesis display a parallel development and disappearance during fetal life. These results indicate that early B cell lymphopoiesis in the splanchnopleura may be triggered by mesothelial cells producing SDF-1. Later into gestation, biliary ductal plate epithelial cells may support B cell lymphopoiesis, thus playing a role similar to that of epithelial cells in the avian bursa of Fabricius, and of thymic epithelial cells for T cell lymphopoiesis.
Novelty acquisition is associated with induction of hippocampal long-term depression
Authors: Manahan-Vaughan Denise , Braunewell Karl-Heinz
Published: July 2002

Homosynaptic long-term depression (LTD) consists of a persistent nonpathological decrease in synaptic transmission, which is induced by low-frequency stimulation.
In vivo
, low-frequency stimulation (1 Hz, 900 pulses) induces LTD in Wistar but not Hooded Lister rats. In this study, we investigated the influence of behavioral learning and behavioral state on the expression of LTD in both rat strains. Recordings were taken from freely moving animals that had undergone chronic implantation of a recording electrode in the hippocampal CA1 region and a bipolar stimulating electrode in the ipsilateral Schaffer collateral–commissural pathway. Exposure of the rat strains to stress induced a significant elevation in serum corticosterone levels but did not facilitate LTD expression. However, LFS given during exploration of a novel environment resulted in LTD expression in Hooded Lister, and LTD enhancement in Wistar, rats. Reexposure to the same environment did not result in new expression of LTD. Behavioral comparison between the first and second environmental exposure confirmed that the animals had habituated to the novel environment. These observations strongly implicate an association between novelty acquisition and LTD.
Functional genomics
Authors: Fields Stanley , Kohara Yuji , Lockhart David J.
Published: July 2002

Complete genome sequences are providing a framework to allow
the investigation of biological processes by the use of comprehensive
approaches. Genome analysis also is having a dramatic impact on
medicine through its identification of genes and mutations involved in
disease and the elucidation of entire microbial gene sets. Studies of
the sequences of model organisms, such as that of the nematode worm
Caenorhabditis elegans
,
are
providing extraordinary insights into development and differentiation
that aid the study of these processes in humans. The field of
functional genomics seeks to devise and apply technologies that take
advantage of the growing body of sequence information to analyze the
full complement of genes and proteins encoded by an organism.
Chitin synthase III: Synthetic lethal mutants and “stress related” chitin synthesis that bypasses the
CSD3/CHS6
localization pathway
Authors: Osmond Barbara C. , Specht Charles A. , Robbins Phillips W.
Published: July 2002

We screened
Saccharomyces
strains for mutants that are synthetically lethal with deletion of the major chitin synthase gene
CHS3
. In addition to finding, not surprisingly, that mutations in major cell wall-related genes such as
FKS1
(glucan synthase) and mutations in any of the Golgi glycosylation complex genes (
MNN9
family) are lethal in combination with
chs3
Δ, we found that a mutation in Srv2p, a bifunctional regulatory gene, is notably lethal in the
chs3
deletion. In extending studies of
fks1
-chitin synthase 3 interactions, we made the surprising discovery that deletion of
CSD3/CHS6
, a gene normally required for Chs3p delivery and activity
in vivo
, was not lethal with
fks1
and, in fact, that lack of Csd3p/Chs6p did not decrease the high level of stress-related chitin made in the
fks1
mutant. This finding suggests that “stress response” chitin synthesis proceeds through an alternate Chs3p targeting pathway.
Oncogenic homeodomain transcription factor E2A-Pbx1 activates a novel WNT gene in pre-B acute lymphoblastoid leukemia
Authors: McWhirter John R. , Neuteboom Saskia T. C. , Wancewicz Edward V. , Monia Brett P. , Downing James R. , Murre Cornelis
Published: July 2002

A large fraction of pediatric pre-B acute lymphoblastoid leukemias (ALL) consistently contain a t(1;19) chromosomal translocation. The t(1;19) translocation results in the production of a chimeric transcription factor containing the N-terminal transactivation domain of E2A fused to the C-terminal DNA-binding homeodomain of Pbx1. Here, we show that the E2A-Pbx1 fusion protein activates the expression of a novel WNT gene, WNT-16. WNT-16 normally is expressed in peripheral lymphoid organs such as spleen, appendix, and lymph nodes, but not in bone marrow. In contrast, high levels of WNT-16 transcripts are present in bone marrow and cell lines derived from pre-B ALL patients carrying the E2A-Pbx1 hybrid gene. Inhibition of E2A-Pbx1 expression leads to a significant decrease in WNT-16 mRNA levels, suggesting that WNT-16 is a downstream target of E2A-Pbx1. Three putative WNT receptors, FZ-2, FZ-3, and FZ-5, are expressed in cells of the B lineage, including pre-B ALL cells aberrantly expressing WNT-16. We propose that a WNT-16-mediated autocrine growth mechanism contributes to the development of t(1;19) pre-B ALL.
The solution structure of the Zα domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA
Authors: Schade Markus , Turner Christopher J. , Kühne Ronald , Schmieder Peter , Lowenhaupt Ky , Herbert Alan , Rich Alexander , Oschkinat Hartmut
Published: July 2002

Double-stranded RNA deaminase I (ADAR1) contains the Z-DNA binding domain Zα. Here we report the solution structure of free Zα and map the interaction surface with Z-DNA, confirming roles previously assigned to residues by mutagenesis. Comparison with the crystal structure of the (Zα)
2
/Z-DNA complex shows that most Z-DNA contacting residues in free Zα are prepositioned to bind Z-DNA, thus minimizing the entropic cost of binding. Comparison with homologous (α+β)helix–turn–helix/B-DNA complexes suggests that binding of Zα to B-DNA is disfavored by steric hindrance, but does not eliminate the possibility that related domains may bind to both B- and Z-DNA.
BAC-VAC, a novel generation of (DNA) vaccines: A bacterial artificial chromosome (BAC) containing a replication-competent, packaging-defective virus genome induces protective immunity against herpes simplex virus 1
Authors: Suter Mark , Lew Andrew M. , Grob Philipp , Adema Gosse J. , Ackermann Mathias , Shortman Ken , Fraefel Cornel
Published: July 2002

This study aimed to exploit bacterial artificial chromosomes (BAC) as large antigen-capacity DNA vaccines (BAC-VAC) against complex pathogens, such as herpes simplex virus 1 (HSV-1). The 152-kbp HSV-1 genome recently has been cloned as an F-plasmid-based BAC inEscherichia coli(fHSV), which can efficiently produce infectious virus progeny upon transfection into mammalian cells. A safe modification of fHSV, fHSVΔpac, does not give rise to progeny virus because the signals necessary to package DNA into virions have been excluded. However, in mammalian cells fHSVΔpac DNA can still replicate, express the HSV-1 genes, cause cytotoxic effects, and produce virus-like particles. Because these functions mimic the lytic cycle of the HSV-1 infection, fHSVΔpac was expected to stimulate the immune system as efficiently as a modified live virus vaccine. To test this hypothesis, mice were immunized with fHSVΔpac DNA applied intradermally by gold-particle bombardment, and the immune responses were compared with those induced by infection with disabled infectious single cycle HSV-1. Immunization with either fHSVΔpac or disabled infectious single cycle HSV-1 induced the priming of HSV-1-specific cytotoxic T cells and the production of virus-specific antibodies and conferred protection against intracerebral injection of wild-type HSV-1 at a dose of 200 LD50. Protection probably was cell-mediated, as transfer of serum from immunized mice did not protect naive animals. We conclude that BAC-VACsper se, or in combination with genetic elements that support replicative amplification of the DNA in the cell nucleus, represent a useful new generation of DNA-based vaccination strategies for many viral and nonviral antigens.
Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region
Authors: Shiina Takashi , Tamiya Gen , Oka Akira , Takishima Nobusada , Yamagata Tetsushi , Kikkawa Eri , Iwata Kyoko , Tomizawa Maiko , Okuaki Noriko , Kuwano Yuko , Watanabe Koji , Fukuzumi Yasuhito , Itakura Shoko , Sugawara Chiyo , Ono Ayako , Yamazaki Masaaki , Tashiro Hiroyuki , Ando Asako , Ikemura Toshimichi , Soeda Eiichi , Kimura Minoru , Bahram Seiamak , Inoko Hidetoshi
Published: July 2002

The intensely studied MHC has become the paradigm for understanding the architectural evolution of vertebrate multigene families. The 4-Mb human MHC (also known as the HLA complex) encodes genes critically involved in the immune response, graft rejection, and disease susceptibility. Here we report the continuous 1,796,938-bp genomic sequence of the HLA class I region, linking genes betweenMICBandHLA-F. A total of 127 genes or potentially coding sequences were recognized within the analyzed sequence, establishing a high gene density of one per every 14.1 kb. The identification of 758 microsatellite provides tools for high-resolution mapping of HLA class I-associated disease genes. Most importantly, we establish that the repeated duplication and subsequent diversification of a minimal building block,MIC-HCGIX-3.8–1-P5-HCGIV-HLA class I-HCGII, engendered the present-day MHC. That the currently nonessentialHLA-FandMICEgenes have acted as progenitors to today’s immune-competentHLA-ABCandMICA/Bgenes provides experimental evidence for evolution by “birth and death,” which has general relevance to our understanding of the evolutionary forces driving vertebrate multigene families.
A test of alternative models of diversification in tropical rainforests: Ecological gradients vs. rainforest refugia
Authors: Schneider Christopher J. , Smith Thomas B. , Larison Brenda , Moritz Craig
Published: July 2002

Comparison of mitochondrial and morphological divergence in eight populations of a widespread leaf-litter skink is used to determine the relative importance of geographic isolation and natural selection in generating phenotypic diversity in the Wet Tropics Rainforest region of Australia. The populations occur in two geographically isolated regions, and within each region, in two different habitats (closed rainforest and tall open forest) that span a well characterized ecological gradient. Morphological differences among ancient geographic isolates (separated for several million years, judging by their mitochondrial DNA sequence divergence) were slight, but morphological and life history differences among habitats were large and occurred despite moderate to high levels of mitochondrial gene flow. A field experiment identified avian predation as one potential agent of natural selection. These results indicate that natural selection operating across ecological gradients can be more important than geographic isolation in similar habitats in generating phenotypic diversity. In addition, our results indicate that selection is sufficiently strong to overcome the homogenizing effects of gene flow, a necessary first step toward speciation in continuously distributed populations. Because ecological gradients may be a source of evolutionary novelty, and perhaps new species, their conservation warrants greater attention. This is particularly true in tropical regions, where most reserves do not include ecological gradients and transitional habitats.
Social status regulates growth rate: Consequences for life-history strategies
Authors: Hofmann Hans A. , Benson Mark E. , Fernald Russell D.
Published: July 2002

The life-history strategies of organisms are sculpted over evolutionary time by the relative prospects of present and future reproductive success. As a consequence, animals of many species show flexible behavioral responses to environmental and social change. Here we show that disruption of the habitat of a colony of African cichlid fish,Haplochromis burtoni(Günther) caused males to switch social status more frequently than animals kept in a stable environment.H. burtonimales can be either reproductively active, guarding a territory, or reproductively inactive (nonterritorial). Although on average 25–50% of the males are territorial in both the stable and unstable environments, during the 20-week study, nearly two-thirds of the animals became territorial for at least 1 week. Moreover, many fish changed social status several times. Surprisingly, the induced changes in social status caused changes in somatic growth. Nonterritorial males and animals ascending in social rank showed an increased growth rate whereas territorial males and animals descending in social rank slowed their growth rate or even shrank. Similar behavioral and physiological changes are caused by social change in animals kept in stable environmental conditions, although at a lower rate. This suggests that differential growth, in interaction with environmental conditions, is a central mechanism underlying the changes in social status. Such reversible phenotypic plasticity in a crucial life-history trait may have evolved to enable animals to shift resources from reproduction to growth or vice versa, depending on present and future reproductive prospects.
Dissociation of HIV-1 from follicular dendritic cells during HAART: Mathematical analysis
Authors: Hlavacek William S. , Wofsy Carla , Perelson Alan S.
Published: July 2002

Follicular dendritic cells (FDC) provide a reservoir for HIV type 1 (HIV-1) that may reignite infection if highly active antiretroviral therapy (HAART) is withdrawn before virus on FDC is cleared. To estimate the treatment time required to eliminate HIV-1 on FDC, we develop deterministic and stochastic models for the reversible binding of HIV-1 to FDC via ligand–receptor interactions and examine the consequences of reducing the virus available for binding to FDC. Analysis of these models shows that the rate at which HIV-1 dissociates from FDC during HAART is biphasic, with an initial period of rapid decay followed by a period of slower exponential decay. The speed of the slower second stage of dissociation and the treatment time required to eradicate the FDC reservoir of HIV-1 are insensitive to the number of virions bound and their degree of attachment to FDC before treatment. In contrast, the expected time required for dissociation of an individual virion from FDC varies sensitively with the number of ligands attached to the virion that are available to interact with receptors on FDC. Although most virions may dissociate from FDC on the time scale of days to weeks, virions coupled to a higher-than-average number of ligands may persist on FDC for years. This result suggests that HAART may not be able to clear all HIV-1 trapped on FDC and that, even if clearance is possible, years of treatment will be required.
Female choice increases offspring fitness in an arctiid moth (
Utetheisa ornatrix
)
Authors: Iyengar Vikram K. , Eisner Thomas
Published: July 2002

In
Utetheisa ornatrix
(Lepidoptera, Arctiidae), the
female mates preferentially with larger males. Having a larger father
results in the eggs being more richly endowed with defensive
pyrrolizidine alkaloid (which the female receives from the male with
the sperm package, in quantity proportional to the male's body mass,
and passes on to the eggs); having a larger father also results in the
sons and daughters themselves being larger (body mass is heritable in
Utetheisa
). We provide evidence herein that these
consequences enhance the fitness of the offspring. Eggs sired by larger
males are less vulnerable to predation (presumably because of their
higher alkaloid content), whereas sons and daughters, by virtue of
being larger, are, respectively, more successful in courtship and more
fecund. The female
Utetheisa
, therefore, by being
choosy, reaps both direct phenotypic and indirect genetic benefits.
Neurotransplantation of magnetically labeled oligodendrocyte progenitors: Magnetic resonance tracking of cell migration and myelination
Authors: Bulte J. W. M. , Zhang S.-C. , van Gelderen P. , Herynek V. , Jordan E. K. , Duncan I. D. , Frank J. A.
Published: July 2002

Demyelination is a common pathological finding in human neurological diseases and frequently persists as a result of failure of endogenous repair. Transplanted oligodendrocytes and their precursor cells can (re)myelinate axons, raising the possibility of therapeutic intervention. The migratory capacity of transplanted cells is of key importance in determining the extent of (re)myelination and can, at present, be evaluated only by using invasive and irreversible procedures. We have exploited the transferrin receptor as an efficient intracellular delivery device for magnetic nanoparticles, and transplanted tagged oligodendrocyte progenitor cells into the spinal cord of myelin-deficient rats. Cell migration could be easily detected by using three-dimensional magnetic resonance microscopy, with a close correlation between the areas of contrast enhancement and the achieved extent of myelination. The present results demonstrate that magnetic resonance tracking of transplanted oligodendrocyte progenitors is feasible; this technique has the potential to be easily extended to other neurotransplantation studies involving different precursor cell types.
RNA editing in
Arabidopsis
mitochondria effects 441 C to U changes in ORFs
Authors: Giegé Philippe , Brennicke Axel
Published: July 2002

On the basis of the sequence of the mitochondrial genome in the flowering plant
Arabidopsis thaliana,
RNA editing events were systematically investigated in the respective RNA population. A total of 456 C to U, but no U to C, conversions were identified exclusively in mRNAs, 441 in ORFs, 8 in introns, and 7 in leader and trailer sequences. No RNA editing was seen in any of the rRNAs or in several tRNAs investigated for potential mismatch corrections. RNA editing affects individual coding regions with frequencies varying between 0 and 18.9% of the codons. The predominance of RNA editing events in the first two codon positions is not related to translational decoding, because it is not correlated with codon usage. As a general effect, RNA editing increases the hydrophobicity of the coded mitochondrial proteins. Concerning the selection of RNA editing sites, little significant nucleotide preference is observed in their vicinity in comparison to unedited C residues. This sequence bias is,
per se
, not sufficient to specify individual C nucleotides in the total RNA population in
Arabidopsis
mitochondria.
The
Arabidopsis
cullin AtCUL1 is modified by the ubiquitin-related protein RUB1
Authors: del Pozo J. C. , Estelle M.
Published: July 2002

The ubiquitin-like protein RUB1 is conjugated to target proteins by a mechanism similar to that of ubiquitin conjugation. Genetic studies in
Arabidopsis thaliana
have implicated the RUB-conjugation pathway in auxin response. The first step in the pathway is RUB activation by a bipartite enzyme composed of the AXR1 and ECR1 proteins. Ubiquitin activation is an ATP-dependent process that involves the formation of an AMP-ubiquitin intermediate. Here we show that RUB activation by AXR1-ECR1 also involves formation of an AMP-RUB intermediate and that this reaction is catalyzed by the ECR1 subunit alone. In addition, we identified an Arabidopsis protein called RCE1 that is a likely RUB-conjugating enzyme. RCE1 works together with AXR1-ECR1 to promote formation of a stable RUB conjugate with the Arabidopsis cullin AtCUL1
in vitro
. Using a tagged version of RUB1, we show that this modification occurs
in vivo
. Because AtCUL1 is a component of the ubiquitin protein ligase SCF
TIR1
, a complex that also functions in auxin response, we propose that RUB modification of AtCUL1 is important for auxin response.
Defective collagen crosslinking in bone, but not in ligament or cartilage, in Bruck syndrome: Indications for a bone-specific telopeptide lysyl hydroxylase on chromosome 17
Authors: Bank Ruud A. , Robins Simon P. , Wijmenga Cisca , Breslau-Siderius Liesbeth J. , Bardoel Alfons F. J. , Van der Sluijs Hans A. , Pruijs Hans E. H. , TeKoppele Johan M.
Published: July 2002

Bruck syndrome is characterized by the presence of osteoporosis, joint contractures, fragile bones, and short stature. We report that lysine residues within the telopeptides of collagen type I in bone are underhydroxylated, leading to aberrant crosslinking, but that the lysine residues in the triple helix are normally modified. In contrast to bone, cartilage and ligament show unaltered telopeptide hydroxylation as evidenced by normal patterns of crosslinking. The results provide compelling evidence that collagen crosslinking is regulated primarily by tissue-specific enzymes that hydroxylate only telopeptide lysine residues and not those destined for the helical portion of the molecule. This new family of enzymes appears to provide the primary regulation for controlling the different pathways of collagen crosslinking and explains why crosslink patterns are tissue specific and not related to a genetic collagen type. A genome screen identified only a single region on chromosome 17p12 where all affected sibs shared a cluster of haplotypes identical by descent; this might be the
BS
(Bruck syndrome) locus and consequently the region where bone telopeptidyl lysyl hydroxylase is located. Further knowledge of this enzyme has important implications for conditions where aberrant expression of telopeptide lysyl hydroxylase occurs, such as fibrosis and scar formation.
The minimal gene set member
msrA
, encoding peptide methionine sulfoxide reductase, is a virulence determinant of the plant pathogen
Erwinia chrysanthemi
Authors: Hassouni Mohammed El , Chambost Jean Pierre , Expert Dominique , Van Gijsegem Frederique , Barras Frederic
Published: July 2002

Peptide methionine sulfoxide reductase (MsrA), which repairs oxidized proteins, is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [Mushegian, A. R. & Koonin, E. V., (1996)
Proc. Natl. Acad. Sci. USA
93, 10268–10273]. In this work, we report that MsrA is required for full virulence of the plant pathogen
Erwinia chrysanthemi
. The following differences were observed between the wild-type and a MsrA
−
mutant: (
i
) the MsrA
−
mutant was more sensitive to oxidative stress; (
ii
) the MsrA
−
mutant was less motile on solid surface; (
iii
) the MsrA
−
mutant exhibited reduced virulence on chicory leaves; and (
iv
) no systemic invasion was observed when the MsrA
−
mutant was inoculated into whole
Saintpaulia ionantha
plants. These results suggest that plants respond to virulent pathogens by producing active oxygen species, and that enzymes repairing oxidative damage allow virulent pathogens to survive the host environment, thereby supporting the theory that active oxygen species play a key role in plant defense.
Cloning and characterization of a cell surface receptor for xenotropic and polytropic murine leukemia viruses
Authors: Tailor Chetankumar S. , Nouri Ali , Lee Chun G. , Kozak Christine , Kabat David
Published: July 2002

Xenotropic and polytropic murine leukemia viruses (X-MLVs and P-MLVs) cross-interfere to various extents in non-mouse species and in wild Asian mice, suggesting that they might use a common receptor for infection. Consistent with this hypothesis, the susceptibility of some wild mice to X-MLVs has been mapped to the P-MLV receptor locus at the distal end of mouse chromosome 1. In this study, we report the isolation and characterization of a cDNA for the human X-MLV cell surface receptor (X-receptor) by using a human T lymphocyte cDNA library in a retroviral vector. The predicted X-receptor contains 696 amino acids with multiple hydrophobic potential membrane-spanning sequences and with weak homologies to the yeast proteins SYG1, of unknown function, and PHO81, which has been implicated in a system that regulates transport of inorganic phosphate. Expression of the X-receptor in Chinese hamster ovary cells, which are substantially resistant to P-MLVs and to X-MLVs, made them susceptible to both of these virus groups. The mouse homologue of the X-receptor was mapped by hybridization to the distal end of chromosome 1 at the same position as the P-MLV receptor gene
Rmc1
. These results strongly support the hypothesis that a common gene encodes the receptors for X-MLVs and P-MLVs, with the human X-receptor preferentially mediating X-MLV infections and the homologous protein of inbred mice mediating only P-MLV infections. We propose that X-MLVs and P-MLVs comprise a single family of retroviruses that have coevolved in response to diversification in X-receptor genes of the host.
Molecular model of muscle contraction
Authors: Duke T. A. J.
Published: July 2002

A quantitative stochastic model of the mechanochemical cycle of myosin, the protein that drives muscle contraction, is proposed. It is based on three premises: (
i
) the myosin head incorporates a lever arm, whose equilibrium position adjusts as each of the products of ATP hydrolysis dissociates from the nucleotide pocket; (
ii
) the chemical reaction rates are modified according to the work done in moving the arm; and (
iii
) the compliance of myosin’s elastic element is designed to permit many molecules to work together efficiently. The model has a minimal number of parameters and provides an explanation, at the molecular level, of many of the mechanical and thermodynamic properties of steadily shortening muscle. In particular, the inflexion in the force–velocity curve at a force approaching the isometric load is reproduced. Moreover, the model indicates that when large numbers of myosin molecules act collectively, their chemical cycles can be synchronized, and that this leads to stepwise motion of the thin filament. The oscillatory transient response of muscle to abrupt changes of load is interpreted in this light.
Ontogeny of T cell tolerance to peripherally expressed antigens
Authors: Morgan David J. , Kurts Christian , Kreuwel Huub T. C. , Holst Karen L. , Heath William R. , Sherman Linda A.
Published: July 2002

Transgenic expression of the influenza virus hemagglutinin (HA) in the pancreatic islet β cells of InsHA mice leads to peripheral tolerance of HA-specific T cells. To examine the onset of tolerance, InsHA mice were immunized with influenza virus A/PR/8 at different ages, and the presence of nontolerant T cells was determined by the induction of autoimmune diabetes. The data revealed a neonatal period wherein T cells were not tolerant and influenza virus infection led to HA-specific β cell destruction and autoimmune diabetes. The ability to induce autoimmunity gradually waned, such that adult mice were profoundly tolerant to viral HA and were protected from diabetes. Because cross-presentation of islet antigens by professional antigen-presenting cells had been reported to induce peripheral tolerance, the temporal relationship between tolerance induction and activation of HA-specific T cells in the lymph nodes draining the pancreas was examined. In tolerant adult mice, but not in 1-week-old neonates, activation and proliferation of HA-specific CD8+T cells occurred in the pancreatic lymph nodes. Thus, lack of tolerance in the perinatal period correlated with lack of activation of antigen-specific CD8+T cells. This work provides evidence for the developmental regulation of peripheral tolerance induction.
Two heads of myosin are better than one for generating force and motion
Authors: Tyska M. J. , Dupuis D. E. , Guilford W. H. , Patlak J. B. , Waller G. S. , Trybus K. M. , Warshaw D. M. , Lowey S.
Published: July 2002

Several classes of the myosin superfamily are distinguished by their “double-headed” structure, where each head is a molecular motor capable of hydrolyzing ATP and interacting with actin to generate force and motion. The functional significance of this dimeric structure, however, has eluded investigators since its discovery in the late 1960s. Using an optical-trap transducer, we have measured the unitary displacement and force produced by double-headed and single-headed smooth- and skeletal-muscle myosins. Single-headed myosin produces approximately half the displacement and force (≈6 nm; 0.7 pN) of double-headed myosin (≈10 nm; 1.4 pN) during a unitary interaction with actin. These data suggest that muscle myosins require both heads to generate maximal force and motion.
Identification by UV resonance Raman spectroscopy of an imino tautomer of 5-hydroxy-2′-deoxycytidine, a powerful base analog transition mutagen with a much higher unfavored tautomer frequency than that of the natural residue 2′-deoxycytidine
Authors: Suen Wu , Spiro Thomas G. , Sowers Lawrence C. , Fresco Jacques R.
Published: July 2002

UV resonance Raman spectroscopy was used to detect and estimate the frequency of the unfavored imino tautomer of the transition mutagen 5-hydroxy-2′-deoxycytidine (HO
5
dCyt) in its anionic form. In DNA, this 2′-deoxycytidine analog arises from the oxidation of 2′-deoxycytidine and induces C → T transitions with 10
2
greater frequency than such spontaneous transitions. An imino tautomer marker carbonyl band (≈1650 cm
−1
) is enhanced at ≈65°C against an otherwise stable spectrum of bands associated with the favored amino tautomer. This band is similarly present in the UV resonance Raman spectra of the imino cytidine analogs
N
3
-methylcytidine at high pH and
N
4
-methoxy-2′-deoxycytidine at pH 7 and displays features attributable to the imino form of C residues and their derivatives. The fact that the imino tautomer of HO
5
dCyt occurs at a frequency consistent with its high mutagenic enhancement lends strong support to the hypothesis that unfavored base tautomers play important roles in the mispair intermediates of replication leading to substitution mutations.
Long-term kinetics of T cell production in HIV-infected subjects treated with highly active antiretroviral therapy
Authors: Fleury S. , Rizzardi G. P. , Chapuis A. , Tambussi G. , Knabenhans C. , Simeoni E. , Meuwly J.-Y. , Corpataux J.-M. , Lazzarin A. , Miedema F. , Pantaleo G.
Published: July 2002

The long-term kinetics of T cell production following highly active antiretroviral therapy (HAART) were investigated in blood and lymph node in a group of HIV-infected subjects at early stage of established infection and prospectively studied for 72 wk. Before HAART, CD4 and CD8 T cell turnover was increased. However, the total number of proliferating CD4+T lymphocytes, i.e., CD4+Ki67+T lymphocytes, was not significantly different in HIV-infected (n= 73) and HIV-negative (n= 15) subjects, whereas proliferating CD8+Ki67+T lymphocytes were significantly higher in HIV-infected subjects. After HAART, the total body number of proliferating CD4+Ki67+T lymphocytes increased over time and was associated with an increase of both naive and memory CD4+T cells. The maximal increase (2-fold) was observed at week 36, whereas at week 72 the number of proliferating CD4+T cells dropped to baseline levels, i.e., before HAART. The kinetics of the fraction of proliferating CD4 and CD8 T cells were significantly correlated with the changes in the total body number of these T cell subsets. These results demonstrate a direct relationship betweenex vivomeasures of T cell production and quantitative changes in total body T lymphocyte populations. This study provides advances in the delineation of the kinetics of T cell production in HIV infection in the presence and/or in the absence of HAART.
Estrogen receptor specificity in the regulation of skeletal growth and maturation in male mice
Authors: Vidal Olle , Lindberg Marie K. , Hollberg Karin , Baylink David J. , Andersson Göran , Lubahn Dennis B. , Mohan Subburaman , Gustafsson Jan-Åke , Ohlsson Claes
Published: July 2002

Androgens may regulate the male skeleton directly through a stimulation of androgen receptors or indirectly through aromatization of androgens into estrogen and, thereafter, through stimulation of estrogen receptors (ERs). The relative importance of ER subtypes in the regulation of the male skeleton was studied in ERα-knockout (ERKO), ERβ-knockout (BERKO), and double ERα/β-knockout (DERKO) mice. ERKO and DERKO, but not BERKO, demonstrated decreased longitudinal as well as radial skeletal growth associated with decreased serum levels of insulin-like growth factor I. Therefore, ERα, but not ERβ, mediates important effects of estrogen in the skeleton of male mice during growth and maturation.
Expression of a nonmyristylated variant of the catalytic subunit of protein kinase A during male germ-cell development
Authors: Desseyn Jean-Luc , Burton Kimberly A. , McKnight G. Stanley
Published: July 2002

The catalytic subunits of protein kinase A are transcribed in all mouse tissues from two distinct genes that code for the Cα and Cβ isoforms. Alternative promoters exist for the Cβ gene that are used in a tissue-specific fashion and give rise to variants that differ in their amino-terminal sequences. We have characterized an alternative promoter that is present in the first intron of the Cα gene and is transcriptionally active in male germ cells. Transcription from this promoter is coincident with the appearance of pachytene spermatocytes and leads to a Cα protein (Cα2) that contains a distinctive 7 amino acid amino-terminus differing from the 14 amino acid amino-terminus of Cα1. The Cα2 protein does not contain the myristylation signal present on Cα1 and migrates at a lower molecular weight on SDS/PAGE gels. By Western blotting, we estimate that most or all of the Cα protein present in mature sperm is Cα2. The amino-terminal sequence of Cα2 is similar to that of ovine sperm C as previously reported [San Agustin, J. T., Leszyk, J. D., Nuwaysir, L. M. & Witman, G. B. (1998)
J. Biol. Chem
. 273, 24874–24883], and we show by cDNA cloning that human sperm also express a highly related Cα2 homolog. The Cα2 subunit forms holoenzymes with either RIIα or RIα, and both activate at the same concentration of cyclic nucleotide. Because protein kinase A is thought to play a pivotal role in sperm motility and capacitation, the distinctive biochemical properties of the unmyristylated Cα2 may be essential for fertility in the male.
Long-range order in the src SH3 folding transition state
Authors: Grantcharova Viara P. , Riddle David S. , Baker David
Published: July 2002

One of the outstanding questions in protein folding concerns the degree of heterogeneity in the folding transition state ensemble: does a protein fold via a large multitude of diverse “pathways,” or are the elements of native structure assembled in a well defined order? Herein, we build on previous point mutagenesis studies of the src SH3 by directly investigating the association of structural elements and the loss of backbone conformational entropy during folding. Double-mutant analysis of polar residues in the distal β-hairpin and the diverging turn indicates that the hydrogen bond network between these elements is largely formed in the folding transition state. A 10-glycine insertion in the n-src loop (which connects the distal hairpin and the diverging turn) and a disulfide crosslink at the base of the distal β-hairpin exclusively affect the folding rate, showing that these structural elements are nearly as ordered in the folding transition state as in the native state. In contrast, crosslinking the base of the RT loop or the N and C termini dramatically slows down the unfolding rate, suggesting that dissociation of the termini and opening of the RT loop precede the rate-limiting step in unfolding. Taken together, these results suggest that essentially all conformations in the folding transition state ensemble have the central three-stranded β-sheet formed, indicating that, for the src homology 3 domain, there is a discrete order to structure assembly during folding.
Isolation and characterization of BEN, a member of the TFII-I family of DNA-binding proteins containing distinct helix–loop–helix domains
Authors: Bayarsaihan Dashzeveg , Ruddle Frank H.
Published: July 2002

The transcriptional regulation of the Hoxc8 gene is controlled during early mouse embryogenesis by an enhanceosome-like control region, termed the early enhancer (EE), located 3 kb upstream from the Hoxc8 translation start site. The EE is involved in establishing the posterior expression pattern of Hoxc8 at embryonic day (E) 8.5–9.0. Genetic and biochemical data have shown that nuclear factors interact with this region in a sequence-specific manner. We have used a yeast one-hybrid screen in a search for transcription factors that bind to EE motifs and have isolated a novel murine DNA-binding protein, termed BEN (binding factor for early enhancer). The ORF of BEN encodes a protein of 1072 amino acids and contains six helix–loop–helix domains, a hydrophobic leucine zipper-like motif, and a serine-rich repeat. The murine BEN gene is structurally similar to the human gene TFII-I in that both genes encode unique 95-amino acid long helix–loop/span–helix domains. The BEN gene produces several major transcripts (3.6, 4.4, and 5.9 kb) present in most adult tissues and shows discrete spatial and temporal domains of expression in areas of epithelial-mesenchymal interaction during mouse embryogenesis from E9.5 to E12.5. Several BEN-encoded polypeptides of different sizes ranging from 165 to 40 kDa were identified by Western blot analysis using BEN-specific polyclonal Abs. We propose, on the bases of sequence homology, that BEN is the mouse ortholog of the recently described human gene, WBSCR11, known also as GTF2IRD1, GTF3, Cream1, and MusTRD1. This gene is deleted hemizygously in individuals with Williams Syndrome, an autosomal dominant genetic condition characterized by complex physical, cognitive, and behavioral traits resulting from a perturbed developmental process.