Structure of the Avian Mitochondrial Cytochrome bc 1 Complex

There are now four structures of vertebrate mitochondrial bc ₁ complexes available in theprotein databases and structures from yeast and bacterial sources are expected soon. Thisreview summarizes the new information with emphasis on the avian cytochrome bc ₁ complex(PDB entries 1BCC and 3BCC). The Rieske iron–sulfur protein is mobile and this has beenproposed to be important for catalysis. The binding sites for quinone have been located basedon structures containing inhibitors and, in the case of the quinone reduction site Qi, thequinone itself.     

Olfactomedin-1 Has a V-shaped Disulfide-linked Tetrameric Structure

Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system development. It binds a number of secreted proteins and cell surface-bound receptors to induce cell signaling processes. Using a combined approach of x-ray crystallography, solution scattering, analytical ultracentrifugation, and electron microscopy we determined that full-length Olfm1 forms disulfide-linked tetramers with a distinctive V-shaped architecture. The base of the “V” is formed by two disulfide-linked dimeric N-terminal domains. Each of the two V legs consists of a parallel dimeric disulfide-linked coiled coil with a C-terminal β-propeller dimer at the tips. This agrees with our crystal structure of a C-terminal coiled-coil segment and β-propeller combination (Olfm1^coil-Olf) that reveals a disulfide-linked dimeric arrangement with the β-propeller top faces in an outward exposed orientation. Similar to its family member myocilin, Olfm1 is stabilized by calcium. The dimer-of-dimers architecture suggests a role for Olfm1 in clustering receptors to regulate signaling and sheds light on the conformation of several other olfactomedin domain family members.     

Retroviral Splicing Suppressor Requires Three Nonconsensus Uridines in a 5′ Splice Site-Like Sequence

Rous sarcoma virus RNA contains a negative regulator of splicing (NRS) element that aids in maintenance of unspliced RNA. The NRS binds U1 snRNA at a sequence that deviates from the 5' splice site consensus by substitution of U's for A's at three positions: -2, +3, and +4. All three of these U's are important for NRS-mediated splicing suppression. Substitution of a single nonconsensus C or G at any of these sites diminished NRS activity, whereas substitution of a single A generated a preferred 5' splice site within the NRS.     

Structure of Nucleophosmin DNA-binding Domain and Analysis of Its Complex with a G-quadruplex Sequence from the c-MYC Promoter

Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a key role in several cellular functions, including ribosome maturation and export, centrosome duplication, and response to stress stimuli. More than 50 mutations at the terminal exon of the NPM1 gene have been identified so far in acute myeloid leukemia; the mutated proteins are aberrantly and stably localized in the cytoplasm due to high destabilization of the NPM1 C-terminal domain and the appearance of a new nuclear export signal. We have shown previously that the 70-residue NPM1 C-terminal domain (NPM1-C70) is able to bind with high affinity a specific region at the c-MYC gene promoter characterized by parallel G-quadruplex structure. Here we present the solution structure of the NPM1-C70 domain and NMR analysis of its interaction with a c-MYC-derived G-quadruplex. These data were used to calculate an experimentally restrained molecular docking model for the complex. The NPM1-C70 terminal three-helix bundle binds the G-quadruplex DNA at the interface between helices H1 and H2 through electrostatic interactions with the G-quadruplex phosphate backbone. Furthermore, we show that the 17-residue lysine-rich sequence at the N terminus of the three-helix bundle is disordered and, although necessary, does not participate directly in the contact surface in the complex.     

Dance Choreography Is Coordinated with Song Repertoire in a Complex Avian Display

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Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities

The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5’-TCCRAC-3’; R = purine) and provides a molecular basis for changing specificity at four of the six base pairs of the recognition sequence (5’-TCCRAC-3’). Surprisingly, the enzyme is resilient to specificity changes at the first position of the recognition sequence (5’-TCCRAC-3’). Collectively, the structure provides a basis for engineering further derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable to alterations than others.     

Avian Community Structure Along a Mountain Big Sagebrush Successional Gradient

Abstract: We compared vegetative structure and bird communities among 4 successional states in central Oregon representing a continuum from 1) postburn grassland, 2) mountain big sagebrush—Idaho fescue (Artemisia tridentatA—Festuca idahoensis) shrub—steppe, 3) sagebrush—steppe—juniper (Juniperus occidentalis), to 4) old-growth western juniper. Species richness, evenness, and diversity of bird communities were highest in old-growth and mid-successional juniper (22.9 species/transect and 23.6 species/transect, respectively) but lowest in the grasslands (17.6 species/transect). Bird species diversity was positively correlated with physiognomic cover diversity (r = 0.74, P = 0.001). Density of breeding birds was greatest in old-growth juniper (6.6 birds/ha) and lowest in postburn grasslands (3.6 birds/ha) but similar in shrub—steppe and sagebrush—steppe—juniper (6.0 birds/ha and 5.5 birds/ha, respectively). Old-growth juniper had the highest total densities of both tree and cavity nesters. Mountain chickadees (Parus gambeli), Cassin's finches (Carpodacus cassinii), chipping sparrows (Spizella passerina), brown-headed cowbirds (Molothrus ater), mountain bluebirds (Sialia currucoides), dark-eyed juncos (Junco hyemalis), Empidonax flycatchers, ash-throated flycatchers (Myiarchus cinerascens), and northern flickers (Colaptes auratus) were more abundant in cover types dominated by junipers. Vesper sparrows (Pooecetes gramineus), western meadowlarks (Sturnella neglecta), green-tailed towhees (Pipilo chlorurus), and horned larks (Eremophila alpestris) were associated with grassland communities. Brewer's sparrows (Spizella breweri), sage sparrows (Amphispiza belli), sage thrashers (Oreoscoptes montanus), and horned larks (Eremophila alpestris) were most abundant in sagebrush cover types. Management strategies should restore or maintain the desired proportions of the different successional states to maintain populations of grassland and sagebrush birds while providing habitat for tree and cavity nesting species.     

RNA Sequence Features Are at the Core of Influenza A Virus Genome Packaging

The influenza A virus (IAV), a respiratory pathogen for humans, poses serious medical and economic challenges to global healthcare systems. The IAV genome, consisting of eight single-stranded viral RNA segments, is incorporated into virions by a complex process known as genome packaging. Specific RNA sequences within the viral RNA segments serve as signals that are necessary for genome packaging. Although efficient packaging is a prerequisite for viral infectivity, many of the mechanistic details about this process are still missing. In this review, we discuss the recent advances toward the understanding of IAV genome packaging and focus on the RNA features that play a role in this process.     

果树—平菇复合生态结构

农业生态结构调控与建造,是提高农业生态系统功能的关键。针对我国人多耕地少的特点,如何建造一些资源利用率高、稳定性强、经济效益可观的新结构,是我国农业发展的重要课题。为此我们进行了一些新模式建造试验,有的已取得了理想的效果。现介绍华北地     

A Ribosome-Binding, 3' Translational Enhancer Has a T-Shaped Structure and Engages in a Long-Distance RNA-RNA Interaction

Many plant RNA viruses contain elements in their 3' untranslated regions (3' UTRs) that enhance translation. The PTE (Panicum mosaic virus-like translational enhancer) of Pea enation mosaic virus (PEMV) binds to eukaryotic initiation factor 4E (eIF4E), but how this affects translation from the 5' end is unknown. We have discovered a three-way branched element just upstream of the PEMV PTE that engages in a long-distance kissing-loop interaction with a coding sequence hairpin that is critical for the translation of a reporter construct and the accumulation of the viral genome in vivo. Loss of the long-distance interaction was more detrimental than elimination of the adjacent PTE, indicating that the RNA-RNA interaction supports additional translation functions besides relocating the PTE to the 5' end. The branched element is predicted by molecular modeling and molecular dynamics to form a T-shaped structure (TSS) similar to the ribosome-binding TSS of Turnip crinkle virus (TCV). The PEMV element binds to plant 80S ribosomes with a K(d) (dissociation constant) of 0.52 μM and to 60S subunits with a K(d) of 0.30 μM. Unlike the TCV TSS, the PEMV element also binds 40S subunits (K(d), 0.36 μM). Mutations in the element that suppressed translation reduced either ribosome binding or the RNA-RNA interaction, suggesting that ribosome binding is important for function. This novel, multifunctional element is designated a kl-TSS (kissing-loop T-shaped structure) to distinguish it from the TCV TSS. The kl-TSS has sequence and structural features conserved with the upper portion of most PTE-type elements, which, with the exception of the PEMV PTE, can engage in similar long-distance RNA-RNA interactions.     

Complete Genome Sequence of a J Subgroup Avian Leukosis Virus Isolated from Local Commercial Broilers

Subgroup J avian leukosis virus (ALV-J) isolate GDKP1202 was isolated from a 50-day-old local yellow commercial broiler in the Guangdong province of China in 2012. Here we report the complete genomic sequence of the GDKP1202 isolate, which caused high mortality, serious growth suppression, thymic atrophy, and liver enlargement in commercial broilers. A novel potential binding site (5′-GGCACCTCC-3′) for c-myb was identified in the GDKP1202 genome. These findings will provide additional insights into the molecular characteristics in the genomes and pathogenicity of ALV-J.     

An MΨ-Containing Heterologous RNA, but Not env mRNA, Is Efficiently Packaged into Avian Retroviral Particles

Retroviruses preferentially package full-length genomic RNA over spliced viral messages. For most retroviruses, this preference is likely due to the absence of all or part of the packaging signal on subgenomic RNAs. In avian leukosis-sarcoma virus, however, we have shown that the minimal packaging signal, MPsi, is located upstream of the 5' splice site and therefore is present on both genomic and spliced RNAs. We now show that an MPsi-containing heterologous RNA is packaged only 2.6-fold less efficiently than genomic Rous sarcoma virus RNA. Thus, few additional packaging sequences and/or structures exist outside of MPsi. In contrast, we found that env mRNA is not efficiently packaged. These results indicate that either MPsi is not functional on this RNA or the RNA is somehow segregated from the packaging machinery. Finally, deletion of sequences from the 3' end of MPsi was found to reduce the packaging efficiency of heterologous RNAs.     

鸡传染性支气管炎病毒变异株的分离及其S1基因序列分析

本实验对山东省泰安地区某蛋鸡场产蛋下降鸡群发生的临床症状疑似鸡传染性支气管炎病例,无菌采集气管、肺脏、肾脏等组织,接种SPF鸡胚,经病毒形态观察、血凝特性试验、动物回归试验等证实,我们鉴定到一株鸡传染性支气管炎病毒(IBV);病毒中和试验表明,该病毒为一株变异毒株,使用国外针对IBV793/B血清型发表的血清型特异性引物经RTPCR方法获得了该毒株的免疫原基因S1基因,初步确定该传染性支气管炎病毒变异毒株为793/B血清型。     

鸡传染性支气管炎病毒变异株的分离及其S1基因序列分析

本实验对山东省泰安地区某蛋鸡场产蛋下降鸡群发生的临床症状疑似鸡传染性支气管炎病例,无菌采集气管、肺脏、肾脏等组织,接种SPF鸡胚,经病毒形态观察、血凝特性试验、动物回归试验等证实,我们鉴定到一株鸡传染性支气管炎病毒(IBV);病毒中和试验表明,该病毒为一株变异毒株,使用国外针对IBV 793/B血清型发表的血清型特异性引物经RT-PCR方法获得了该毒株的免疫原基因S1基因,初步确定该传染性支气管炎病毒变异毒株为793/B血清型.     

Genome Sequence of a Novel Reassortant H3N2 Avian Influenza Virus in Southern China

The distribution and prevalence of H3 subtype influenza viruses in avian and mammalian hosts constitutes a potential threat to both human and avian health. We report a complete genome sequence of a novel reassortant H3N2 avian influenza virus. Phylogenetic analysis showed that HA and NA showed the highest sequence homologies with those of A/white-backed munia/Hong Kong/4519/2009 (H3N2). However, the internal genes had the highest sequence homologies with those of H6 and H7 subtypes. The data provide further evidence of the existence of a natural reassortant H3N2 strain in southern China.