The Spt-Ada-Gcn5 Acetyltransferase (SAGA) Complex in Aspergillus nidulans

A mutation screen in Aspergillus nidulans uncovered mutations in the acdX gene that led to altered repression by acetate, but not by glucose. AcdX of A. nidulans is highly conserved with Spt8p of Saccharomyces cerevisiae, and since Spt8p is a component of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, the SAGA complex may have a role in acetate repression in A. nidulans. We used a bioinformatic approach to identify genes encoding most members of the SAGA complex in A. nidulans, and a proteomic analysis to confirm that most protein components identified indeed exist as a complex in A. nidulans. No apparent compositional differences were detected in mycelia cultured in acetate compared to glucose medium. The methods used revealed apparent differences between Yeast and A. nidulans in the deubiquitination (DUB) module of the complex, which in S. cerevisiae consists of Sgf11p, Sus1p, and Ubp8p. Although a convincing homologue of S. cerevisiae Ubp8p was identified in the A. nidulans genome, there were no apparent homologues for Sus1p and Sgf11p. In addition, when the SAGA complex was purified from A. nidulans, members of the DUB module were not co-purified with the complex, indicating that functional homologues of Sus1p and Sgf11p were not part of the complex. Thus, deubiquitination of H2B-Ub in stress conditions is likely to be regulated differently in A. nidulans compared to S. cerevisiae.     

Snf1p-dependent Spt-Ada-Gcn5-acetyltransferase (SAGA) recruitment and chromatin remodeling activities on the HXT2 and HXT4 promoters

We previously showed that the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex is recruited to the activated HXT2 and HXT4 genes and plays a role in the association of TBP-associated factors. Using the HXT2 and HXT4 genes, we now present evidence for a functional link between Snf1p-dependent activation, recruitment of the SAGA complex, histone H3 removal, and H3 acetylation. Recruitment of the SAGA complex is dependent on the release of Ssn6p-Tup1p repression by Snf1p. In addition, we found that the Gcn5p subunit of the SAGA complex preferentially acetylates histone H3K18 on the HXT2 and HXT4 promoters and that Gcn5p activity is required for removal of histone H3 from the HXT4 promoter TATA region. In contrast, histone H3 removal from the HXT2 promoter does not require Gcn5p. In conclusion, although similar protein complexes are involved, induction of HXT2 and HXT4 displays important mechanistic differences.     

Genome Wide Identification,Phylogeny and Expression of Zinc Transporter Genes in Common Carp

Background

Zinc is an essential trace element in organisms, which serves as a cofactor for hundreds of enzymes that are involved in many pivotal biological processes including growth, development, reproduction and immunity. Therefore, the homeostasis of zinc in the cell is fundamental. The zinc transporter gene family is a large gene family that encodes proteins which regulate the movement of zinc across cellular and intracellular membranes. However, studies on teleost zinc transporters are mainly limited to model species.

Methodology/Principal Findings

We identified a set of 37 zinc transporters in common carp genome, including 17 from SLC30 family (ZnT), and 20 from SLC39 family (ZIP). Phylogenetic and syntenic analysis revealed that most of the zinc transporters are highly conserved, though recent gene duplication and gene losses do exist. Through examining the copy number of zinc transporter genes across several vertebrate genomes, thirteen zinc transporters in common carp are found to have undergone the gene duplications, including SLC30A1, SLC30A2, SLC30A5, SLC30A7, SLC30A9, SLC30A10, SLC39A1, SLC39A3, SLC39A4, SLC39A5, SLC39A6, SLC39A7 and SLC39A9. The expression patterns of all zinc transporters were established in various tissues, including blood, brain, gill, heart, intestine, liver, muscle, skin, spleen and kidney, and showed that most of the zinc transporters were ubiquitously expressed, indicating the critical role of zinc transporters in common carp.

Conclusions

To some extent, examination of gene families with detailed phylogenetic or orthology analysis could verify the authenticity and accuracy of assembly and annotation of the recently published common carp whole genome sequences. The gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp zinc transporters provides an important genomic resource for future biochemical, toxicological and physiological studies of zinc in teleost.     

Medicinal Plants in the Atlantic Forest (Brazil): Knowledge, Use, and Conservation

This study focuses on knowledge of medicinal plants among the Caiçaras (rural inhabitants of the Atlantic Forest coast, Brazil). In particular, we examine the use of medicinal plants according to sex and age to reveal general patterns of Caiçara knowledge and use of plant resources. Data collected through 449 interviews at 12 Caiçara communities (Rio de Janeiro and São Paulo coastal sites) include citations of 249 plants and identification of 227 species. We show the importance of introduced as opposed to native plants and of key individuals for the conservation of the Caiçaras-Atlantic Forest.     

葡萄NIP基因家族的鉴定与表达分析

类根瘤菌26膜内在蛋白(nodulin 26 like intrinsic proteins,NIPs)是水通道蛋白的亚类,在植物营养获取和胁迫应答过程中发挥着重要作用。该研究利用多种生物信息学软件,对葡萄NIP家族基因进行分析,并采用RT PCR方法克隆得到4个NIP家族基因,利用qRT PCR方法分析非生物胁迫下NIP基因的表达特征。结果显示：(1)在葡萄基因组中,共鉴定到8个NIP基因,分布于葡萄4条染色体上,主要定位在质膜中;结构上含有6个跨膜结构域和两个典型的保守结构域NPA;氨基酸序列中存在很多个可能的磷酸化位点。(2)进化分析表明葡萄和拟南芥NIP基因具有较高的同源性,基因结构包含外显子数4~6个,保守基序种类和数量相似;基因启动子上游2 kb包含多种应答逆境和激素的顺式调控元件,其数量差异可能与基因本身功能相关。(3)NIP家族基因在不同组织中表达水平差异较大,多数成员在叶中表达水平较高,在茎中较低;成功克隆得到4个葡萄VvNIP基因,其长度分别为789 bp、606 bp、897 bp、789 bp,分别编码262、201、298、293个氨基酸。(4)qRT PCR结果显示,不同胁迫处理下NIP基因在葡萄叶片中的表达水平不同：低温处理下葡萄NIP基因大多呈显著下调表达;盐胁迫下,除VvNIP2 1、VvNIP4 2外其余家族基因均呈下调表达;干旱胁迫下VvNIP4 2显著上调。研究表明,VvNIP基因对多种胁迫均有响应,为葡萄逆境胁迫机制研究提供了参考。     

Brachiocephalic Muscular Arrangements in Cavioid Rodents (Caviomorpha): a Functional,Anatomical, and Evolutionary Study

Journal of Mammalian Evolution - In cursorial mammals, reduction or loss of the clavicle is usually associated with the constitution of the m. brachiocephalicus, a continuous muscle that extends...     

无序蛋白质的判定及其结构、功能和进化特征

固有无序蛋白质(intrinsically disordered proteins,IDPs)是天然条件下自身不能折叠为明确唯一的空间结构,却具有生物学功能的一类新发现的蛋白质.这类蛋白质的发现是对传统的"结构-功能"关系认识模式的挑战.本文首先总结了无序蛋白质的实验鉴定手段、预测方法、数据库;并介绍了无序蛋白质结构(包括一级结构、二级结构、结构域无序性及变构效应)和功能特征;然后重点总结了无序蛋白质在进化角度研究的进展,包括无序区域产生的进化机制、进化速率,蛋白无序性的进化在蛋白质功能进化及生物学复杂性增加等方面的重要作用;最后展望了无序蛋白质在医药方面的应用前景.本文对于深入认识无序蛋白质的形成机制、结构和功能特征及其潜在的临床应用前景具有重要意义.     

Genomic Resources for Gene Discovery,Functional Genome Annotation,and Evolutionary Studies of Maize and Its Close Relatives

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.     

Population Structure in the Roundtail Chub (Gila robusta Complex) of the Gila River Basin as Determined by Microsatellites: Evolutionary and Conservation Implications

Ten microsatellite loci were characterized for 34 locations from roundtail chub (Gila robusta complex) to better resolve patterns of genetic variation among local populations in the lower Colorado River basin. This group has had a complex taxonomic history and previous molecular analyses failed to identify species diagnostic molecular markers. Our results supported previous molecular studies based on allozymes and DNA sequences, which found that most genetic variance was explained by differences among local populations. Samples from most localities were so divergent species-level diagnostic markers were not found. Some geographic samples were discordant with current taxonomy due to admixture or misidentification; therefore, additional morphological studies are necessary. Differences in spatial genetic structure were consistent with differences in connectivity of stream habitats, with the typically mainstem species, G. robusta, exhibiting greater genetic connectedness within the Gila River drainage. No species exhibited strong isolation by distance over the entire stream network, but the two species typically found in headwaters, G. nigra and G. intermedia, exhibited greater than expected genetic similarity between geographically proximate populations, and usually clustered with individuals from the same geographic location and/or sub-basin. These results highlight the significance of microevolutionary processes and importance of maintaining local populations to maximize evolutionary potential for this complex. Augmentation stocking as a conservation management strategy should only occur under extreme circumstances, and potential source populations should be geographically proximate stocks of the same species, especially for the headwater forms.