bluuebunny/crossref_metadata_2025_split huggingface dataset:
The headful packaging nuclease of bacteriophage T4
Authors: Alam Tanfis I. , Draper Bonnie , Kondabagil Kiran , Rentas Francisco J. , Ghosh‐Kumar Manjira , Sun Siyang , Rossmann Michael G. , Rao Venigalla B. 
Published: July 2008

SummaryMost tailed bacteriophages and herpes viruses replicate genome as a concatemer which is cut by a ‘headful’ nuclease upon completion of genome packaging. Here, the catalytic centre of phage T4 headful nuclease, present in the C‐terminal domain of ‘large terminase’ gp17, has been defined by mutational, biochemical and structural analyses. The crystal structure shows that this nuclease has an RNase‐H fold, suggesting that it cuts DNA by a two‐metal ion mechanism. The active centre has a Mg ion co‐ordinated by three acidic residues, D401, E458 and D542. Mutations at any of these residues resulted in loss of nuclease activity, but the mutants can package linear DNA. The gp17's nuclease activity is modulated by the ‘small terminase’, gp16, by the N‐terminal ATPase domain of gp17, and by the assembled packaging motor. These results lead to hypotheses concerning how phage headful nucleases cut the viral genomes before and after, but not during, DNA packaging.
Pheromone‐regulated target genes respond differentially to MAPK phosphorylation of transcription factor Prf1
Authors: Zarnack Kathi , Eichhorn Heiko , Kahmann Regine , Feldbrügge Michael 
Published: July 2008

SummaryPheromone signalling during mating is essential for pathogenicity of Ustilago maydis. The activity of the key transcription factor Prf1 is controlled at the transcriptional level and post‐translationally by mitogen‐activated protein kinase (MAPK) and protein kinase A (PKA) phosphorylation. However, the precise contribution of these regulatory mechanisms to the transcriptional output is unknown. Here, we genetically dissected the three levels of Prf1 regulation. We performed transcriptional profiling of respective mutants to identify and classify targets. This approach revealed that transcriptional regulation of prf1 had only minor influence on target gene expression stressing the importance of post‐translational control. PKA regulation of Prf1 was sufficient to control expression of nine pheromone‐responsive genes including the major transcription factor regulating pathogenicity. MAPK regulation was necessary for the pheromone response of a set of 57 genes. In 35 cases, pheromone responsiveness was completely lost, while in the remaining 22 cases regulation was alleviated. This indicated a novel level of complexity in MAPK signalling suggesting that target genes respond differentially to MAPK phosphorylation of the respective transcription factors.
Complement factor H allotype 402H is associated with increased C3b opsonization and phagocytosis of Streptococcus pyogenes
Authors: Haapasalo Karita , Jarva Hanna , Siljander Tuula , Tewodros Wezenet , Vuopio‐Varkila Jaana , Jokiranta T. Sakari 
Published: July 2008

SummaryThe main virulence factor of group A streptococcus (GAS), M protein, binds plasma complement regulators factor H (FH) and FH‐like protein 1 (FHL‐1) leading to decreased opsonization. The M protein binding site on FH is within domain 7 in which also the age‐related macular degeneration (AMD)‐associated polymorphism Y402H is located. We studied if FH allotypes 402H and 402Y have different binding affinities to GAS. Plasma‐derived FH allotype 402H and its recombinant fragment FH5‐7(402H) showed decreased binding to several GAS strains. Growth of GAS in human blood taken from FH(402H) homozygous individuals was decreased when compared with blood taken from FH(402Y) homozygous individuals. The effect of the allotype 402H can be explained by combining the previous M protein mutagenesis data and the recently published crystal structure of FH6‐8. In conclusion the data indicate that the AMD‐associated allotype 402H leads to diminished binding of FH to GAS and increased opsonophagocytosis of the bacteria in blood. These results suggest that the homozygous presence of the allele 402H could be associated with decreased risk for severe GAS infections offering an explanation for the high frequency of the allele despite its association with visual impairment.
Identification and characterization of two trypanosome TFIIS proteins exhibiting particular domain architectures and differential nuclear localizations
Authors: Uzureau Pierrick , Daniels Jan‐Peter , Walgraffe David , Wickstead Bill , Pays Etienne , Gull Keith , Vanhamme Luc 
Published: July 2008

SummaryNuclear transcription of Trypanosoma brucei displays unusual features. Most protein‐coding genes are organized in large directional gene clusters, which are transcribed polycistronically by RNA polymerase II (pol II) with subsequent processing to generate mature mRNA. Here, we describe the identification and characterization of two trypanosome homologues of transcription elongation factor TFIIS (TbTFIIS1 and TbTFIIS2‐1). TFIIS has been shown to aid transcription elongation by relieving arrested pol II. Our phylogenetic analysis demonstrated the existence of four independent TFIIS expansions across eukaryotes. While TbTFIIS1 contains only the canonical domains II and III, the N‐terminus of TbTFIIS2‐1 contains a PWWP domain and a domain I. TbTFIIS1 and TbTFIIS2‐1 are expressed in procyclic and bloodstream form cells and localize to the nucleus in similar, but distinct, punctate patterns throughout the cell cycle. Neither TFIIS protein was enriched in the major pol II sites of spliced‐leader RNA transcription. Single RNA interference (RNAi)‐mediated knock‐down and knockout showed that neither protein is essential. Double knock‐down, however, impaired growth. Repetitive failure to generate a double knockout of TbTFIIS1 and TbTFIIS2‐1 strongly suggests synthetical lethality and thus an essential function shared by the two proteins in trypanosome growth.
The ylo‐1 gene encodes an aldehyde dehydrogenase responsible for the last reaction in the Neurospora carotenoid pathway
Authors: Estrada Alejandro F. , Youssar Loubna , Scherzinger Daniel , Al‐Babili Salim , Avalos Javier 
Published: July 2008

SummaryThe accumulation of the apocarotenoid neurosporaxanthin and its carotene precursors explains the orange pigmentation of the Neurospora surface cultures. Neurosporaxanthin biosynthesis requires the activity of the albino gene products (AL‐1, AL‐2 and AL‐3), which yield the precursor torulene. Recently, we identified the carotenoid oxygenase CAO‐2, which cleaves torulene to produce the aldehyde β‐apo‐4′‐carotenal. This revealed a last missing step in Neurospora carotenogenesis, namely the oxidation of the CAO‐2 product to the corresponding acid neurosporaxanthin. The mutant ylo‐1, which exhibits a yellow colour, lacks neurosporaxanthin and accumulates several carotenes, but its biochemical basis is unknown. Based on available genetic data, we identified ylo‐1 in the Neurospora genome, which encodes an enzyme representing a novel subfamily of aldehyde dehydrogenases, and demonstrated that it is responsible for the yellow phenotype, by sequencing and complementation of mutant alleles. In contrast to the precedent structural genes in the carotenoid pathway, light does not induce the synthesis of ylo‐1 mRNA. In vitro incubation of purified YLO‐1 protein with β‐apo‐4′‐carotenal produced neurosporaxanthin through the oxidation of the terminal aldehyde into a carboxyl group. We conclude that YLO‐1 completes the set of enzymes needed for the synthesis of this major Neurospora pigment.
A versatile partner of eukaryotic protein complexes that is involved in multiple biological processes: Kti11/Dph3
Authors: Bär Christian , Zabel René , Liu Shihui , Stark Michael J. R. , Schaffrath Raffael 
Published: July 2008

SummaryThe Kluyveromyces lactis killer toxin zymocin insensitive 11 (KTI11) gene from Saccharomyces cerevisiae is allelic with the diphthamide synthesis 3 (DPH3) locus. Here, we present evidence that the KTI11 gene product is a versatile partner of proteins and operates in multiple biological processes. Notably, Kti11 immune precipitates contain Elp2 and Elp5, two subunits of the Elongator complex which is involved in transcription, tRNA modification and zymocin toxicity. KTI11 deletion phenocopies Elongator‐minus cells and causes antisuppression of nonsense and missense suppressor tRNAs (SUP4, SOE1), zymocin resistance and protection against the tRNase attack of zymocin. In addition and unlike Elongator mutants, kti11 mutants resist diphtheria toxin (DT), protect against ADP‐ribosylation of eukaryotic translation elongation factor 2 (eEF2) by DT and induce resistance against sordarin, an eEF2 poisoning antifungal. The latter phenotype applies to all diphthamide mutants (dph1‐dph5) tested and Kti11/Dph3 physically interacts with diphthamide synthesis factors Dph1 and Dph2, presumably as part of a trimeric complex. Moreover, we present a separation of function mutation in KTI11, kti11‐1, which dissociates zymocin resistance from DT sensitivity. It encodes a C‐terminal Kti11 truncation that almost entirely abolishes Elongator interaction without affecting association with Kti13, another Kti11 partner protein.
Mating type influences chromosome loss and replicative senescence in telomerase‐deficient budding yeast by Dnl4‐dependent telomere fusion
Authors: Meyer Damon H. , Bailis Adam M. 
Published: July 2008

SummayAs we age, the majority of our cells gradually lose the capacity to divide because of replicative senescence that results from the inability to replicate the ends of chromosomes. The timing of senescence is dependent on the length of telomeric DNA, which elicits a checkpoint signal when critically short. Critically short telomeres also become vulnerable to deleterious rearrangements, end‐degradation and telomere–telomere fusions. Here we report a novel role of non‐homologous end‐joining (NHEJ), a pathway of double‐strand break repair in influencing both the kinetics of replicative senescence and the rate of chromosome loss in telomerase‐deficient Saccharomyces cerevisiae. In telomerase‐deficient cells, the absence of NHEJ delays replicative senescence, decreases loss of viability during senescence, and suppresses senescence‐associated chromosome loss and telomere–telomere fusion. Differences in mating‐type gene expression in haploid and diploid cells affect NHEJ function, resulting in distinct kinetics of replicative senescence. These results suggest that the differences in the kinetics of replicative senescence in haploid and diploid telomerase‐deficient yeast are determined by changes in NHEJ‐dependent telomere fusion, perhaps through the initiation of the breakage‐fusion‐bridge cycle.
Biosynthesis of mycobacterial arabinogalactan: identification of a novel α(1→3) arabinofuranosyltransferase
Authors: Birch Helen L. , Alderwick Luke J. , Bhatt Apoorva , Rittmann Doris , Krumbach Karin , Singh Albel , Bai Yu , Lowary Todd L. , Eggeling Lothar , Besra Gurdyal S. 
Published: July 2008

SummaryThe cell wall mycolyl‐arabinogalactan–peptidoglycan complex is essential in mycobacterial species, such as Mycobacterium tuberculosis and is the target of several antitubercular drugs. For instance, ethambutol targets arabinogalactan biosynthesis through inhibition of the arabinofuranosyltransferases Mt‐EmbA and Mt‐EmbB. A bioinformatics approach identified putative integral membrane proteins, MSMEG2785 in Mycobacterium smegmatis, Rv2673 in Mycobacterium tuberculosis and NCgl1822 in Corynebacterium glutamicum, with 10 predicted transmembrane domains and a glycosyltransferase motif (DDX), features that are common to the GT‐C superfamily of glycosyltransferases. Deletion of M. smegmatis MSMEG2785 resulted in altered growth and glycosyl linkage analysis revealed the absence of AG α(1→3)‐linked arabinofuranosyl (Araf) residues. Complementation of the M. smegmatis deletion mutant was fully restored to a wild‐type phenotype by MSMEG2785 and Rv2673, and as a result, we have now termed this previously uncharacterized open reading frame, arabinofuranosyltransferase C (aftC). Enzyme assays using the sugar donor β‐d‐arabinofuranosyl‐1‐monophosphoryl‐decaprenol (DPA) and a newly synthesized linear α(1→5)‐linked Ara5 neoglycolipid acceptor together with chemical identification of products formed, clearly identified AftC as a branching α(1→3) arabinofuranosyltransferase. This newly discovered glycosyltransferase sheds further light on the complexities of Mycobacterium cell wall biosynthesis, such as in M. tuberculosis and related species and represents a potential new drug target.
High resolution infrared spectra of NGC 6440 and NGC 6441: two massive bulge globular clusters
Authors: Origlia L. , Valenti E. , Rich R. M. 
Published: July 2008

Abstract
Using the NIRSPEC spectrograph at Keck II, we have obtained infrared echelle spectra covering the 1.5–1.8 μm range for giant stars in the massive bulge globular clusters NGC 6440 and NGC 6441. We report the first high-dispersion abundance for NGC 6440, [Fe/H]=−0.56 ± 0.02 and we find [Fe/H]=−0.50 ± 0.02 for the blue Horizontal Branch cluster NGC 6441. We measure an average α-enhancement of ≈+0.3 dex in both clusters, consistent with previous measurements of other metal rich bulge clusters, and favouring the scenario of a rapid-bulge formation and chemical enrichment. We also measure very low 12C/13C isotopic ratios (≈5 ± 1), suggesting that extra-mixing mechanisms are at work during evolution along the Red Giant Branch also in the high-metallicity regime. We also measure Al abundances, finding average [Al/Fe]= 0.45 ± 0.02 and [Al/Fe]= 0.52 ± 0.02 in NGC 6440 and 6441, respectively, and some Mg–Al anticorrelation in NGC 6441. We also measure radial velocities vr=−76 ± 3 and vr=+14 ± 3 km s−1 and velocity dispersions σ= 9 ± 2 and σ= 10 ± 2 km s−1 in NGC 6440 and 6441, respectively.
The shortest period field contact binary
Authors: Rucinski Slavek M. , Pribulla Theodor 
Published: July 2008

Abstract
Photometric and spectroscopic results for the contact binary GSC 01387–00475 (ASAS 083128+1953.1) are presented. The existence of this binary with the orbital period of P= 0.2178 d strengthens the argument that the cut-off of the period distribution for contact binaries – until now defined by CC Comae – is very sharp. The only case of a still shorter period is known in a globular cluster where more compact contact configurations are in fact expected. While the spectroscopic orbit of GSC 01387–00475 is well defined, the low orbital inclination of the binary and the presence of a spectroscopic companion contributing about 1/3 of the total light conspire to reduce the photometric variability to ≃0.09 mag. The photometric data are currently inadequate to identify the source of the small amplitude (0.02–0.03 mag) intrinsic variability of the system.
Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana
Authors: Petricka Jalean Joyanne , Clay Nicole Kho , Nelson Timothy Mark 
Published: July 2008

SummaryLeaf veins form a closed network that transports essential photosynthates, water and signaling molecules to the developing plant. The formation of the patterns of these networks during leaf ontogeny is an active subject of modeling and computer simulation. To investigate the vein patterning process, we performed screens for defects in juvenile leaf vein patterning in Arabidopsis thaliana lines subjected to mutagenesis via diepoxybutane, activation tagging or the Dissociation/Activator transposon. We identified over 40 vein pattern defective lines, providing a phenotypic resource for the testing of vein patterning models. In addition, we report the chromosomal linkage for 13 of these, eight of which were successfully cloned. We further describe the phenotypes of five of these mutants, which we call the defectively organized tributaries (dot) mutants, and their corresponding molecular identities. The diversity of the individual genes affected in this collection of pattern mutants suggests that vein pattern is highly sensitive to perturbations in many cellular processes. Despite this diversity of causes, the resulting pattern defects fall into a limited number of classes, including parallel, spurred, misaligned, open, midvein gap and irregularly spaced. These classes may represent sensitivities to cellular processes associated with the DOT genes. The ontogeny of common defective patterns should be accommodated into any robust model for the ontogeny and evolution of pattern.
Systematic analysis of protein subcellular localization and interaction using high‐throughput transient transformation of Arabidopsis seedlings
Authors: Marion Jessica , Bach Lien , Bellec Yannick , Meyer Christian , Gissot Lionel , Faure Jean‐Denis 
Published: July 2008

SummaryThe functional genomics approach requires systematic analysis of protein subcellular distribution and interaction networks, preferably by optimizing experimental simplicity and physiological significance. Here, we present an efficient in planta transient transformation system that allows single or multiple expression of constructs containing various fluorescent protein tags in Arabidopsis cotyledons. The optimized protocol is based on vacuum infiltration of agrobacteria directly into young Arabidopsis seedlings. We demonstrate that Arabidopsis epidermal cells show a subcellular distribution of reference markers similar to that in tobacco epidermal cells, and can be used for co‐localization or bi‐molecular fluorescent complementation studies. We then used this new system to investigate the subcellular distribution of enzymes involved in sphingolipid metabolism. In contrast to transformation systems using tobacco epidermal cells or cultured Arabidopsis cells, our system provides the opportunity to take advantage of the extensive collections of mutant and transgenic lines available in Arabidopsis. The fact that this assay uses conventional binary vectors and a conventional Agrobacterium strain, and is compatible with a large variety of fluorescent tags, makes it a versatile tool for construct screening and characterization before stable transformation. Transient expression in Arabidopsis seedlings is thus a fast and simple method that requires minimum handling and potentially allows medium‐ to high‐throughput analyses of fusion proteins harboring fluorescent tags in a whole‐plant cellular context.
AtMYB12 regulates caffeoyl quinic acid and flavonol synthesis in tomato: expression in fruit results in very high levels of both types of polyphenol
Authors: Luo Jie , Butelli Eugenio , Hill Lionel , Parr Adrian , Niggeweg Ricarda , Bailey Paul , Weisshaar Bernd , Martin Cathie 
Published: July 2008

SummaryPlant polyphenolics exhibit a broad spectrum of health‐promoting effects when consumed as part of the diet, and there is considerable interest in enhancing the levels of these bioactive molecules in plants used as foods. AtMYB12 was originally identified as a flavonol‐specific transcriptional activator in Arabidopsis thaliana, and this has been confirmed by ectopic expression in tobacco. AtMYB12 is able to induce the expression of additional target genes in tobacco, leading to the accumulation of very high levels of flavonols. When expressed in a tissue‐specific manner in tomato, AtMYB12 activates the caffeoyl quinic acid biosynthetic pathway, in addition to the flavonol biosynthetic pathway, an activity which probably mirrors that of the orthologous MYB12‐like protein in tomato. As a result of its broad specificity for transcriptional activation in tomato, AtMYB12 can be used to produce fruit with extremely high levels of multiple polyphenolic anti‐oxidants. Our data indicate that transcription factors may have different specificities for target genes in different plants, which is of significance when designing strategies to improve metabolite accumulation and the anti‐oxidant capacity of foods.
Proteolytic processing of a precursor protein for a growth‐promoting peptide by a subtilisin serine protease in Arabidopsis
Authors: Srivastava Renu , Liu Jian‐Xiang , Howell Stephen H. 
Published: July 2008

SummaryPhytosulfokines (PSKs) are secreted, sulfated peptide hormones derived from larger prepropeptide precursors. Proteolytic processing of one of the precursors, AtPSK4, was demonstrated by cleavage of a preproAtPSK4–myc transgene product to AtPSK4–myc. Cleavage of proAtPSK4 was induced by placing root explants in tissue culture. The processing of proAtPSK4 was dependent on AtSBT1.1, a subtilisin‐like serine protease, encoded by one of 56 subtilase genes in Arabidopsis. The gene encoding AtSBT1.1 was up‐regulated following the transfer of root explants to tissue culture, suggesting that activation of the proteolytic machinery that cleaves proAtPSK4 is dependent on AtSBT1.1 expression. We also demonstrated that a fluorogenic peptide representing the putative subtilase recognition site in proAtPSK4 is cleaved in vitro by affinity‐purified AtSBT1.1. An alanine scan through the recognition site peptide indicated that AtSBT1.1 is fairly specific for the AtPSK4 precursor. Thus, this peptide growth factor, which promotes callus formation in culture, is proteolytically cleaved from its precursor by a specific plant subtilase encoded by a gene that is up‐regulated during the process of transfering root explants to tissue culture.
Overexpression of the lemon basil α‐zingiberene synthase gene increases both mono‐ and sesquiterpene contents in tomato fruit
Authors: Davidovich‐Rikanati Rachel , Lewinsohn Efraim , Bar Einat , Iijima Yoko , Pichersky Eran , Sitrit Yaron 
Published: July 2008

Summaryα‐Zingiberene synthase (ZIS), a sesquiterpene synthase gene that was isolated from lemon basil (Ocimum basilicum L.), encodes an enzyme that catalyzes the formation of α‐zingiberene, and other sesquiterpenes, from farnesyl diphosphate. Transgenic tomato fruits overexpressing ZIS under the control of the fruit ripening‐specific tomato polygalacturonase promoter (PG) accumulated high levels of α‐zingiberene (224–1000 ng g−1 fresh weight) and other sesquiterpenes, such as α‐bergamotene, 7‐epi‐sesquithujene, β‐bisabolene and β‐curcumene, whereas no sesquiterpenes were detected in non‐transformed control fruits. The ZIS‐transgenic fruits also produced monoterpenes, such as α‐thujene, α‐pinene, β‐phellandrene and γ‐terpinene (1–22 ng g−1 fresh weight), which were either not detected or were found only in minute concentrations in control fruits. Recombinant ZIS overexpressed in Escherichia coli catalyzed the formation of these monoterpenes from geranyl diphosphate. As the ZIS protein apparently lacks a transit peptide, and is localized in the cytosol, the production of monoterpenes in the transgenic tomatoes suggests that a pool of geranyl diphosphate is available in the cytosol. The phenotype of the ZIS‐transgenic tomatoes was the same as that for wild‐type tomatoes, with regard to plant vigor and shape, but transgenic plants exhibited a small decrease in lycopene content. This study thus showed that the synthesis of both mono‐ and sesquiterpenes can be enhanced by the ectopic expression of a single transgene in tomato fruit, and it further demonstrated the interconnection between the pools of terpenoid precursors in the plastids and the cytosol.