利用序列保守模体和局部构象信息预测转录因子结合位点

转录因子结合位点的计算预测是研究基因转录调控的重要环节,但常用的位置特异得分矩阵方法预测特异性偏低.通过深入分析结合位点的生物特征,提出了一种综合利用序列保守模体和局部构象信息的结合位点预测方法,以极大相关得分矩阵作为保守模体的描述模型,并根据二苷参数模型计算位点序列的局部构象,将两类信息得分组合为多维特征向量,在二次判别分析的框架下进行训练和滑动预测.预测过程中还引入了位置信息量以优化似然得分和过滤备选结果.针对大肠杆菌CRP和Fis结合位点数据的留一法测试结果表明,描述模型的改进和多种信息的融合能有效地改善预测方法的性能,大幅度提高特异性.     

Mixed linear model association mapping for low chloride accumulation rate in oriental-type tobacco (Nicotiana tabaccum L.) germplasm

Chloride is an essential micronutrient in tobacco (Nicotiana tabaccum L.) cultivation. However, large amounts of it have many adverse effects on burning quality of tobacco leaves. The objective of this study was to evaluate the genetic variability among 70 oriental-type tobacco genotypes and determine the genomic regions associated with chloride accumulation rate using mixed linear model (MLM) procedure. A total number of 66 alleles were detected by 26 simple sequence repeat (SSR) loci with an average of 2.53 alleles per locus. A model-based Bayesian approach subdivided 70 tobacco genotypes into the three subgroups. Almost 5.85% of the 325 marker pairs showed a significant level of linkage disequilibrium (P ≤ 0.01). Using MLM procedure, 1 SSR locus (pt30027) from linkage group 13 was identified to be associated with the gene(s) controlling low chloride accumulation in oriental tobacco genotypes. Identified markers could be of great interest in marker-assisted selection in tobacco breeding programs.     

Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha‐helical ubiquitin interacting motif

Ubiquitin interacting motifs (UIMs) are short α‐helices found in a number of eukaryotic proteins. UIMs interact weakly but specifically with ubiquitin conjugated to other proteins, and in so doing, mediate specific cellular signals. Here we used phage display to generate ubiquitin variants (UbVs) targeting the N‐terminal UIM of the yeast Vps27 protein. Selections yielded UbV.v27.1, which recognized the cognate UIM with high specificity relative to other yeast UIMs and bound with an affinity more than two orders of magnitude higher than that of ubiquitin. Structural and mutational studies of the UbV.v27.1‐UIM complex revealed the molecular details for the enhanced affinity and specificity of UbV.v27.1, and underscored the importance of changes at the binding interface as well as at positions that do not contact the UIM. Our study highlights the power of the phage display approach for selecting UbVs with unprecedented affinity and high selectivity for particular α‐helical UIM domains within proteomes, and it establishes a general approach for the development of inhibitors targeting interactions of this type.     

Engineering Strontium Binding Affinity in an EF-hand Motif: A Quantum Chemical and Molecular Dynamics Study

Abstract

Proteins with the ability to specifically bind strontium would potentially be of great use in the field of nuclear waste management. Unfortunately, no such peptides or proteins are known—indeed, it is uncertain whether they exist under natural conditions due to low environmental concentrations of strontium. To investigate the possibility of devising such molecules, one of us (CV), in a previous experimental study [J. Biol. Inorg. Chem. 8, 33440 (2003)], proposed starting from an EF-hand motif of the protein calmodulin and mutating some residues to change the motif's specificity for calcium into one for strontium. In this paper, which represents a theoretical complement to the experimental work, we analyzed small-molecule crystallographic structures and performed quantum chemical calculations to identify possible mutations. We then constructed seven mutant sequences of the EF-hand motif and analyzed their dynamical and binding behaviors using molecular dynamics simulations and free-energy calculations (using the MM/PBSA method). As a result of these analyzes we were able to isolate some characteristics that could lead to mutant peptides with enhanced strontium affinity.     

Multiple Modes of Protein–Protein Interactions Promote RNP Granule Assembly

Eukaryotic cells are known to contain a wide variety of RNA–protein assemblies, collectively referred to as RNP granules. RNP granules form from a combination of RNA–RNA, protein–RNA, and protein–protein interactions. In addition, RNP granules are enriched in proteins with intrinsically disordered regions (IDRs), which are frequently appended to a well-folded domain of the same protein. This structural organization of RNP granule components allows for a diverse set of protein–protein interactions including traditional structured interactions between well-folded domains, interactions of short linear motifs in IDRs with the surface of well-folded domains, interactions of short motifs within IDRs that weakly interact with related motifs, and weak interactions involving at most transient ordering of IDRs and folded domains with other components. In addition, both well-folded domains and IDRs in granule components frequently interact with RNA and thereby can contribute to RNP granule assembly. We discuss the contribution of these interactions to liquid–liquid phase separation and the possible role of phase separation in the assembly of RNP granules. We expect that these principles also apply to other non-membrane bound organelles and large assemblies in the cell.     

Biotransformation of linear alkylbenzene sulfonate (LAS) by Phanerochaete chrysosporium: oxidation of alkyl side-chain

The white rot fungus Phanerochaete chrysosporium, which generally mineralizes substituted aromatics to CO₂, transformed linear alkylbenzene sulfonate (LAS) surfactants mainly at their alkyl side chain. Degradation of LAS was evidenced by a zone of clearing on LAS-containing agar plates and colorimetric analysis of liquid cultures. Disappearance of LAS was virtually complete within 10 days in low nitrogen (2.4 mM N), high nitrogen (24 mM N) and malt extract (ME) liquid media. After 5 days of incubation in ME medium, transformation of LAS was complete at concentrations4 mg l^-1, but decreased at higher concentrations. The LAS degradation was not dependent on lignin peroxidases (LiPs) and manganese-dependent peroxidases (MnPs). Mineralization of¹⁴C-ring-LAS to ¹⁴CO₂ by P. chrysosporium was <1% regardless of the culture conditions used. Thin layer chromatography and mass spectral analyses indicated that P. chrysosporium transformed LAS to sulfophenyl carboxylates (SPCs) through oxidative shortening of the alkyl side-chains. While LAS disappearance in the cultures was not dependent on LiPs and MnPs, transformation of the parent LAS moieties to SPCs was more extensive in low N medium that favors expression of these enzymes. The SPCs produced in LN cultures were shorter in chain-length than those produced in ME cultures. Also there was a notable shift in the relative abundance of odd and even chain length metabolites compared to the starting LAS particularly in the low N cultures suggesting the possible involvement of processes other than or in addition to-oxidation in the chain-shortening process.     

Calcyon, a mammalian specific NEEP21 family member, interacts with adaptor protein complex 3 (AP-3) and regulates targeting of AP-3 cargoes

Calcyon is a neural enriched, single transmembrane protein that interacts with clathrin light chain and stimulates clathrin assembly and clathrin‐mediated endocytosis. A similar property is shared by the heterotetrameric adaptor protein (AP) complexes AP‐1, AP‐2, and AP‐3 which recruit cargoes for insertion into clathrin coated transport vesicles. Here we report that AP medium (μ) subunits interact with a YXXØ‐type tyrosine motif located at residues 133–136 in the cytoplasmic domain of calcyon. Site specific mutagenesis of the critical tyrosine and bulky hydrophobic residues tyrosine 133 and methionine 136 preferentially abrogated binding of the ubiquitous and neuronal isoforms of μ3, and also impacted μ1 and μ2 binding to a lesser degree. The relevance of these interactions was explored in vivo using mice harboring null alleles of calcyon. As seen in the mutagenesis studies, calcyon deletion in mice preferentially altered the subcellular distribution of AP‐3 suggesting that calcyon could regulate membrane‐bound pools of AP‐3 and AP‐3 function. To test this hypothesis, we focused on the hilar region of hippocampus, where levels of calcyon, AP‐3, and AP‐3 cargoes are abundant. We analyzed brain cryosections from control and calcyon null mice for zinc transporter 3 (ZnT3), and phosphatidylinositol‐4‐kinase type II alpha (PI4KIIα), two well‐defined AP‐3 cargoes. Confocal microscopy indicated that ZnT3 and PI4KIIα are significantly reduced in the hippocampal mossy fibers of calcyon knock‐out brain, a phenotype previously described in AP‐3 deficiencies. Altogether, our data suggest that calcyon directly interacts with μ3A and μ3B, and regulates the subcellular distribution of AP‐3 and the targeting of AP‐3 cargoes.     

Geographic range determinants of two commercially important marine molluscs

Aim We modelled the spatial abundance patterns of two abalone species (Haliotis rubra Donovan 1808 and H. laevigata Leach 1814) inhabiting inshore rocky reefs to better understand the importance of current sea surface temperature (SST) (among other predictors) and, ultimately, the effect of future climate change, on marine molluscs. Location Southern Australia. Methods We used an ensemble species distribution modelling approach that combined likelihood‐based generalized linear models and boosted regression trees. For each modelling technique, a two‐step procedure was used to predict: (1) the current probability of presence, followed by (2) current abundance conditional on presence. The resulting models were validated using an independent, spatially explicit dataset of abalone abundance patterns in Victoria. Results For both species, the presence of reef was the main driver of abalone occurrence, while SST was the main driver of spatial abundance patterns. Predictive maps at c. 1‐km resolution showed maximal abundance on shallow coastal reefs characterized by mild winter SSTs for both species. Main conclusions Sea surface temperature was a major driver of abundance patterns for both abalone species, and the resulting ensemble models were used to build fine‐resolution predictive range maps (c. 1 km) that incorporate measures of habitat suitability and quality in support of resource management. By integrating this output with structured spatial population models, a more robust understanding of the potential impacts of threatening human processes such as climate change can be established.