Structure of monoubiquitinated PCNA

Ubiquitination of proliferating cell nuclear antigen (PCNA) to ub-PCNA is essential for DNA replication across bulky template lesions caused by UV radiation and alkylating agents, as ub-PCNA orchestrates the recruitment and switching of translesion synthesis (TLS) polymerases with replication polymerases. This allows replication to proceed, leaving the DNA to be repaired subsequently. Defects in a TLS polymerase, Pol η, lead to a form of Xeroderma pigmentosum, a disease characterized by severe skin sensitivity to sunlight damage and an increased incidence of skin cancer. Structurally, however, information on how ub-PCNA orchestrates the switching of these two classes of polymerases is lacking. We have solved the structure of ub-PCNA and demonstrate that the ubiquitin molecules in ub-PCNA are radially extended away from the PCNA without structural contact aside from the isopeptide bond linkage. This unique orientation provides an open platform for the recruitment of TLS polymerases through ubiquitin-interacting domains. However, the ubiquitin moieties, to the side of the equatorial PCNA plane, can place spatial constraints on the conformational flexibility of proteins bound to ub-PCNA. We show that ub-PCNA is impaired in its ability to support the coordinated actions of Fen1 and Pol δ in assays mimicking Okazaki fragment processing. This provides evidence for the novel concept that ub-PCNA may modulate additional DNA transactions other than TLS polymerase recruitment and switching.     

Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins

In crude extract-based cell-free protein synthesis (CFPS), DNA templates are transcribed and translated into functional proteins. Although linear expression templates (LETs) are less laborious and expensive to generate, plasmid templates are often desired over polymerase chain reaction-generated LETs due to increased stability and protection against exonucleases present in the extract of the reaction. Here we demonstrate that addition of a double stranded DNA-binding protein to the CFPS reaction, termed single-chain Cro protein (scCro), achieves terminal protection of LETs. This CroP-LET (scCro-based protection of LET) method effectively increases superfolder green fluorescent protein (sfGFP) expression levels from LETs in Escherichia coli CFPS reactions by sixfold. Our yields are comparable to other strategies that provide chemical and enzymatic DNA stabilization in E. coli CFPS. Notably, we also report that the CroP-LET method successfully enhanced yields in CFPS platforms derived from nonmodel organisms. Our results show that CroP-LET increased sfGFP yields by 18-fold in the Vibrio natriegens CFPS platform. With the fast-expanding applications of CFPS platforms, this method provides a practical and generalizable solution to protect linear expression DNA templates.     

Genus Bembidion Latreille (Coleoptera: Carabidae) in New Zealand: A revision

The cosmopolitan genus Bembidion is represented in New Zealand by 20 species, of which 19 are endemic; B. brullei appears to be a recent introduction. On phenetic characters the species fall into 7 subgenera, as follows: Zeplataphus n.subg.—maorinum Bates, dehiscens Broun, charile Bates, granuliferum n.sp., townsendi n.sp., tairuense Bates; Zeactedium Netolitzky—orbiferum Bates, musae Broun; Zeperyphodes n.subg.—callipeplum Bates; Zeperyphus n.subg.—actuarium Broun; Zemetal‐lina n.subg.—chalceipes Bates, solitarium n.sp., anchonoderum Bates, tekapoense Broun, wanakense n.sp., urewerense n.sp., hokitikense Bates, parviceps Bates; Ananotaphus Netolitzky—rotundicolle Bates; Notaphus Stephens—brullei Gemminger & Harold. The North Island population of maorinum is distinct from the typical South Island form in having reduced microscrulpture on the elytra, and is here separated as levatum n.ssp. An apparent geographic isolate of anchonoderum, represented by 2 females from Stewart Island, is provisionally recognised as stewartense n.ssp. The polymorphic complex within subg. Ananotaphus is here regarded as a single species, of which the North Island population is sufficiently distinct to warrant subspecific status as eustictum Bates; however, intergrades occur in the north‐west of the South Island. The following names fall into synonymy: latiusculum Broun (= maorinum); diaphanum Broun (= musae); nesophilum Broun (= callipeplum)’, tinctellum Broun (= chalceipes);antipodum Broun (= anchonoderum)’, tantillum Broun and probably attenuatum Broun (=hokitikense)’, clevedonense Broun and waikatoense Broun (= rotundicolle, ssp. eustictum)’, gameani Jeannel (= brullei). The relationships and aspects of the biology and ecology of the New Zealand Bembidion fauna are discussed.     

Defining the Epigenetic Mechanism of Asymmetric Cell Division of Schizosaccharomyces japonicus Yeast

A key question in developmental biology addresses the mechanism of asymmetric cell division. Asymmetry is crucial for generating cellular diversity required for development in multicellular organisms. As one of the potential mechanisms, chromosomally borne epigenetic difference between sister cells that changes mating/cell type has been demonstrated only in the Schizosaccharomyces pombe fission yeast. For technical reasons, it is nearly impossible to determine the existence of such a mechanism operating during embryonic development of multicellular organisms. Our work addresses whether such an epigenetic mechanism causes asymmetric cell division in the recently sequenced fission yeast, S. japonicus (with 36% GC content), which is highly diverged from the well-studied S. pombe species (with 44% GC content). We find that the genomic location and DNA sequences of the mating-type loci of S. japonicus differ vastly from those of the S. pombe species. Remarkably however, similar to S. pombe, the S. japonicus cells switch cell/mating type after undergoing two consecutive cycles of asymmetric cell divisions: only one among four “granddaughter” cells switches. The DNA-strand–specific epigenetic imprint at the mating-type locus1 initiates the recombination event, which is required for cellular differentiation. Therefore the S. pombe and S. japonicus mating systems provide the first two examples in which the intrinsic chirality of double helical structure of DNA forms the primary determinant of asymmetric cell division. Our results show that this unique strand-specific imprinting/segregation epigenetic mechanism for asymmetric cell division is evolutionary conserved. Motivated by these findings, we speculate that DNA-strand–specific epigenetic mechanisms might have evolved to dictate asymmetric cell division in diploid, higher eukaryotes as well.     

A polymetamorphic protein

Arc repressor is a homodimeric protein with a ribbon‐helix–helix fold. A single polar‐to‐hydrophobic substitution (N11L) at a solvent‐exposed position leads to population of an alternate dimeric fold in which 3₁₀ helices replace a β‐sheet. Here we find that the variant Q9V/N11L/R13V (S‐VLV), with two additional polar‐to‐hydrophobic surface mutations in the same β‐sheet, forms a highly stable, reversibly folded octamer with approximately half the?α‐helical content of wild‐type Arc. At low protein concentration and low ionic strength, S‐VLV also populates both dimeric topologies previously observed for N11L, as judged by NMR chemical shift comparisons. Thus, accumulation of simple hydrophobic mutations in Arc progressively reduces fold specificity, leading first to a sequence with two folds and then to a manifold bridge sequence with at least three different topologies. Residues 9–14 of S‐VLV form a highly hydrophobic stretch that is predicted to be amyloidogenic, but we do not observe aggregates of higher order than octamer. Increases in sequence hydrophobicity can promote amyloid aggregation but also exert broader and more complex effects on fold specificity. Altered native folds, changes in fold coupled to oligomerization, toxic pre‐amyloid oligomers, and amyloid fibrils may represent a near continuum of accessible alternatives in protein structure space.     

计算机视觉在线虫进食行为自动分析中的应用

秀丽隐杆线虫被广泛地用作研究基因与行为关系的绝佳模式生物.线虫的咽部神经元回路控制着复杂的进食行为.为了研究进食行为的分子机制,有必要对线虫进食行为表型分析鉴定.然而,目前为止,几乎所有的线虫进食行为表型鉴定都是通过人眼来判断.因为其泵入食物的肌肉运动频率高,该行为的分析是很困难而且效率低下的.为解决这个问题,我们设计了基于计算机视觉技术的自动化成像系统来高通量分析线虫进食行为表型.此成像系统对进食表型的检测准确率达到98%以上,并使得连续可靠地分析其表型细微变化成为可能.同时,在保证高准确率的前提下单位时间内分析数据的效率比人工分析提高了3倍.     

Fish reduce anuran abundance and decrease herpetofaunal species richness in wetlands

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Active‐Site Imprinting: Preparation of Fe–N–C Catalysts from Zinc Ion–Templated Ionothermal Nitrogen‐Doped Carbons

Atomically dispersed Fe–N–C catalysts are considered the most promising precious‐metal‐free alternative to state‐of‐the‐art Pt‐based oxygen reduction electrocatalysts for proton‐exchange membrane fuel cells. The exceptional progress in the field of research in the last ≈30 years is currently limited by the moderate active site density that can be obtained. Behind this stands the dilemma of metastability of the desired FeN₄ sites at the high temperatures that are believed to be a requirement for their formation. It is herein shown that Zn²⁺ ions can be utilized in the novel concept of active‐site imprinting based on a pyrolytic template ion reaction throughout the formation of nitrogen‐doped carbons. As obtained atomically dispersed Zn–N–Cs comprising ZnN₄ sites as well as metal‐free N₄ sites can be utilized for the coordination of Fe²⁺ and Fe³⁺ ions to form atomically dispersed Fe–N–C with Fe loadings as high as 3.12 wt%. The Fe–N–Cs are active electocatalysts for the oxygen reduction reaction in acidic media with an onset potential of E₀ = 0.85 V versus RHE in 0.1 m HClO₄. Identical location atomic resolution transmission electron microscopy imaging, as well as in situ electrochemical flow cell coupled to inductively coupled plasma mass spectrometry measurements, is employed to directly prove the concept of the active‐site imprinting approach.