MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs

Piwi-interacting RNAs (piRNAs) comprise a broad class of small noncoding RNAs that function as an endogenous defense system against transposable elements. Here we show that the putative DExD-box helicase MOV10-like-1 (MOV10L1) is essential for silencing retrotransposons in the mouse male germline. Mov10l1 is specifically expressed in germ cells with increasing expression from gonocytes/type A spermatogonia to pachytene spermatocytes. Primary spermatocytes of Mov10l1^−/− mice show activation of LTR and LINE-1 retrotransposons, followed by cell death, causing male infertility and a complete block of spermatogenesis at early prophase of meiosis I. Despite the early expression of Mov10l1, germline stem cell maintenance appears unaffected in Mov10l1^−/− mice. MOV10L1 interacts with the Piwi proteins MILI and MIWI. MOV10L1 also interacts with heat shock 70-kDa protein 2 (HSPA2), a testis-enriched chaperone expressed in pachytene spermatocytes and also essential for male fertility. These studies reveal a crucial role of MOV10L1 in male fertility and piRNA-directed retrotransposon silencing in male germ cells and suggest that MOV10L1 functions as a key component of a safeguard mechanism for the genetic information in male germ cells of mammals.     

Transfer RNA is an essential component of the ubiquitin- and ATP-dependent proteolytic system.

Protein degradation via the nonlysosomal ATP-dependent pathway in rabbit reticulocytes involves a number of components. In the initial event, ubiquitin, an abundant 76-residue polypeptide, becomes covalently linked to the protein substrate in an ATP-requiring reaction. Once marked in this way, the conjugated protein is proteolyzed in a reaction that also requires ATP. Ubiquitin-marking appears to be important to the progression of cells from one stage to another of the cell cycle; it may also be involved in gene activation. Here we show that tRNA is another essential component of the system. Ribonucleases strongly inhibit the ubiquitin- and ATP-dependent degradation of 125I-labeled bovine serum albumin in the reticulocyte system in vitro. RNAs extracted from fractions of the reticulocyte extract or from mouse cells restore proteolytic activity. When the RNA is fractionated by gel electrophoresis, only the tRNA fraction is active in restoring proteolysis. Furthermore, pure mouse tRNAHis, isolated by immunoprecipitation with patient autoimmune sera, restores the proteolytic activity. The possibility that the level of uncharged tRNA in mammalian cells regulates the ubiquitin- and ATP-dependent proteolytic system is discussed.     

Reduction of toxic RNAs in myotonic dystrophies type 1 and type 2 by the RNA helicase p68/DDX5

Myotonic dystrophies type 1 (DM1) and type 2 (DM2) are neuromuscular diseases, caused by accumulation of CUG and CCUG RNAs in toxic aggregates. Here we report that the increased stability of the mutant RNAs in both types of DM is caused by deficiency of RNA helicase p68. We have identified p68 by studying CCUG-binding proteins associated with degradation of the mutant CCUG repeats. Protein levels of p68 are reduced in DM1 and DM2 biopsied skeletal muscle. Delivery of p68 in DM1/2 cells causes degradation of the mutant RNAs, whereas delivery of p68 in skeletal muscle of DM1 mouse model reduces skeletal muscle myopathy and atrophy. Our study shows that correction of p68 may reduce toxicity of the mutant RNAs in DM1 and in DM2.Myotonic dystrophy type 1 (DM1) is a neuromuscular disease characterized by myotonia, distal muscle weakness, heart conduction defects, and, in the congenital form, a delay in myogenesis and severe cognitive abnormalities (1). DM1 is caused by expanded CTG repeats within the 3′ untranslated region of the DMPK gene (2). Myotonic dystrophy type 2 (DM2) is a late-onset disease that is caused by expanded CCTG repeats in intron 1 of the ZNF9/CNBP gene (3). Development of therapeutic approaches for DM1 or DM2 is an urgent need. Numerous data suggest that DM1 and DM2 are caused by RNA gain-of-function mechanisms (4–6). Initial studies showed that mutant RNAs mainly affect two RNA-binding proteins, CUG-binding protein 1 (CUGBP1) and muscleblind-like protein 1 (MBNL1) (7–9). CUG repeats elevate protein levels of CUGBP1 by increasing its stability (5). In addition, CUG repeats change signal transduction pathways, such as the glycogen synthase kinase 3β (GSK3β)–cyclin D3 pathway, regulating CUGBP1 activity (5, 10). CUG and CCUG repeats form double-stranded hairpin structures and sequester MBNL1 (9, 11, 12). Several other RNA-binding proteins, such as Staufen1 and two members of the DEAD-box RNA helicases family, DDX5/p68 and DDX6, are also involved in DM1 (13–15).We showed that the mutant CUG and CCUG RNAs are very stable (16), suggesting that the activity of RNA-binding proteins regulating RNA decay is reduced in DM1 and in DM2. In this study, we tested this hypothesis by isolation and analysis of several CCUG-binding proteins. We found that the levels of one of these proteins, p68, are reduced in DM1 and DM2 biopsied muscle and that correction of p68 leads to degradation of the mutant CUG and CCUG RNAs, disintegration of RNA foci, and reduction of DM muscle pathology.     

Structure and assembly of the essential RNA ring component of a viral DNA packaging motor

Prohead RNA (pRNA) is an essential component in the assembly and operation of the powerful bacteriophage ϕ29 DNA packaging motor. The pRNA forms a multimeric ring via intermolecular base-pairing interactions between protomers that serves to guide the assembly of the ring ATPase that drives DNA packaging. Here we report the quaternary structure of this rare multimeric RNA at 3.5 Å resolution, crystallized as tetrameric rings. Strong quaternary interactions and the inherent flexibility helped rationalize how free pRNA is able to adopt multiple oligomerization states in solution. These characteristics also allowed excellent fitting of the crystallographic pRNA protomers into previous prohead/pRNA cryo-EM reconstructions, supporting the presence of a pentameric, but not hexameric, pRNA ring in the context of the DNA packaging motor. The pentameric pRNA ring anchors itself directly to the phage prohead by interacting specifically with the fivefold symmetric capsid structures that surround the head-tail connector portal. From these contacts, five RNA superhelices project from the pRNA ring, where they serve as scaffolds for binding and assembly of the ring ATPase, and possibly mediate communication between motor components. Construction of structure-based designer pRNAs with little sequence similarity to the wild-type pRNA were shown to fully support the packaging of ϕ29 DNA.     

PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit

Two forms of a plant-specific RNA polymerase (Pol), PolIV(PolIVa) and PolV(PolIVb), currently defined by their respective largest subunits [NRPD1(NRPD1a) and NRPE1(NRPD1b)], have been implicated in the production and activity of 24-nt small RNAs (sRNAs) in RNA-directed DNA methylation (RdDM). Prevailing models support the view that PolIV(PolIVa) plays an upstream role in RdDM by producing the 24-nt sRNAs, whereas PolV(PolIVb) would act downstream at a structural rather than an enzymatic level to reinforce sRNA production by PolIV(PolIVa) and mediate DNA methylation. However, the composition and mechanism of action of PolIV(PolIVa)/PolV(PolIVb) remain unclear. In this work, we have identified a plant-specific PolV(PolIVb) subunit, NRPE5a, homologous to NRPB5a, a common subunit shared by PolI-III and shown here to be present in PolIV(PolIVa). Our results confirm the combinatorial diversity of PolIV(PolIVa)/PolV(PolIVb) subunit composition and indicate that these plant-specific Pols are eukaryotic-type polymerases. Moreover, we show that nrpe5a-1 mutation differentially impacts sRNAs accumulation at various PolIV(PolIVa)/PolV(PolIVb)-dependent loci, indicating a target-specific requirement for NRPE5a in the process of PolV(PolIVb)-dependent gene silencing. We then describe that the triad aspartate motif present in the catalytic center of PolV(PolIVb) is required for recapitulation of all activities associated with this Pol complex in RdDM, suggesting that RNA polymerization is important for PolV(PolIVb) to perform its regulatory functions.     

RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth

How cells achieve their final sizes is a pervasive biological question. One strategy to increase cell size is for the cell to amplify its chromosomal DNA content through endoreduplication cycles. Although endoreduplication is widespread in eukaryotes, we know very little about its molecular mechanisms. Successful progression of the endoreduplication cycle in Arabidopsis requires a plant homologue of archaeal DNA topoisomerase (topo) VI. To further understand how DNA is endoreduplicated and how this process is regulated, we isolated a dwarf Arabidopsis mutant, hyp7 (hypocotyl 7), in which various large cell types that in the wild type normally endoreduplicate multiple times complete only the first two rounds of endoreduplication and stall at 8C. HYP7 encodes the RHL1 (ROOT HAIRLESS 1) protein, and sequence analysis reveals that RHL1 has similarity to the C-terminal domain of mammalian DNA topo IIalpha, another type II topo that shares little sequence homology with topo VI. RHL1 shows DNA binding activity in vitro, and we present both genetic and in vivo evidence that RHL1 forms a multiprotein complex with plant topo VI. We propose that RHL1 plays an essential role in the topo VI complex to modulate its function and that the two distantly related topos, topo II and topo VI, have evolved a common domain that extends their function. Our data suggest that plant topo II and topo VI play distinct but overlapping roles during the mitotic cell cycle and endoreduplication cycle.     

Antisense strategy shows that Mcl-1 rather than Bcl-2 or Bcl-x(L) is an essential survival protein of human myeloma cells

Multiple myeloma (MM) is a plasma cell malignancy that occurs mainly in bone marrow. As MM cells proliferate slowly, it would seem essential to find means of preventing their growth and accumulation inside bone marrow. The present study used an antisense strategy to elucidate the respective roles of Bcl-2, Bcl-x(L), and Mcl-1 proteins in myeloma cell survival. Each antisense oligonucleotide (ASO; Bcl-2, Bcl-x(L), or Mcl-1 ASO) introduced into human myeloma cell lines by electroporation induced a marked reduction in the level of the corresponding protein. Mcl-1 ASO triggers an important decrease of viability in all myeloma cell lines tested and in 2 primary myeloma cells, whereas neither Bcl-2 nor Bcl-x(L) ASO affected the viability of myeloma cells. The decrease of cell viability induced by Mcl-1 ASO treatment was associated with an induction of apoptosis that occurred through the disruption of mitochondrial membrane potential Delta Psi m and the activation of executioner caspase-3. Furthermore, we have shown that interleukin 6 cannot prevent the Mcl-1 ASO-induced apoptosis. Finally, although Bcl-2 ASO treatment alone has no effect, it can sensitize myeloma cell lines to dexamethasone (Dex), whereas Bcl-x(L) ASO in combination with Dex still had no effect. As MM remains an incurable disease despite intensive chemotherapy, these results suggest that Mcl-1 antisense strategy rather than Bcl-2 antisense strategy could be of considerable importance in the treatment of MM.     

From the Cover: Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements

Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.

Eusociality is defined by a reproductive division of labor where some individuals forego independent breeding to cooperatively rear others’ young (1). Recent advances in molecular biology have enabled researchers to begin to uncover the genomic underpinnings of eusociality by identifying associated genetic variants and pathways (2–4) and highlighting the importance of recombination (5), gene regulation (6), novel genes (7), genetic accommodation (8), epigenetics (9, 10), and developmental plasticity (11–13) in the transition toward social complexity. Yet, more recently there has been a shift toward also considering the phenotypic (14, 15), demographic (16–18), and genomic consequences (17, 19) of living in complex social groups. Indeed, cooperative group living, or sociality, has been hypothesized to influence the architecture of the genome, including its size and structure, since changes in demography resulting from increased reproductive skew and a reproductive division of labor (20) will impact effective population sizes, recombination rates, and the strength of purifying selection (17, 19).The genome is dynamic, changing in both size and structure over evolutionary time (21–23). Genome size, the total amount of DNA contained within a haploid chromosome set, is a basic property of every genome that can vary considerably among species, even closely related ones (24). Because eukaryotic genomes often have large and varying quantities of noncoding and repetitive DNA (25), genome size in eukaryotes is generally unrelated to organismal complexity (26) and is instead associated with the abundance of repetitive regions like transposable elements (TEs) (27). Several studies in insects have suggested a relationship between eusociality and genome architecture, including both genome size and structure. For example, ants, which are all eusocial, tend to have smaller genomes than other insects (28). Similarly, across 131 Hymenoptera, eusocial and parasitoid species have smaller genomes than solitary and nonparasitoid species, with the eusocial honey bees Apis mellifera and Apis cerana having some of the smallest genomes among all Hymenoptera (29). Yet, the relationship between eusociality and genome size is quite different in termites, where despite the fact that eusocial species also have smaller genomes than their noneusocial relatives (30), the genome size of the socially more complex Macrotermes natalensi is twice that of the socially less complex Zootermopsis nevadensis (31). This difference between Hymenoptera and termites in the relationship between social organization and genome size extends to genome structure, where social complexity is associated with a reduced abundance and diversity of TEs in Hymenoptera (32), but an increased abundance of TEs in termites (31). Some of these TEs have been hypothesized to play a causal role in gene family expansion that is associated with the transition to eusociality in termites (33), as they have in other forms of adaptive evolution (34–37). Ultimately, these contrasting patterns in different eusocial insect lineages suggest that the relationship between social organization and genome architecture may be a complex and fluid one that we do not yet fully understand.Untangling the linkages between social organization and genome architecture requires a group of organisms that shows interspecific variation in both of these traits. Species of sponge-dwelling snapping shrimps in the genus Synalpheus not only exhibit great social diversity, they also show some of the most extreme interspecific variation in genome size of any animal group studied. Social organization in Synalpheus ranges from pair-living to communal breeding (multiple mating pairs in the same sponge) to eusociality (one or a few queens and a larger number of nonsterile workers of both sexes) (14, 38–40). Although Synalpheus shrimps in the West Atlantic gambarelloides group represent a relatively young lineage that radiated between ∼5 and 7 Mya (41), eusociality has evolved at least four times within this group (40), and eusocial and communal breeding species both evolved independently from pair-living ancestors (42). Furthermore, the genus Synalpheus shows a more than fivefold difference in genome size across species (43), ranging from roughly 4 Gb to more than 20 Gb, and their genomes—particularly those of eusocial species—harbor many repetitive elements (44, 45).Here, we examine the dynamic relationship between eusociality and genome architecture—both genome size and structure—across 33 Synalpheus species using phylogenetically informed analyses. First, we determine whether eusocial shrimp species have smaller or larger genomes than noneusocial species (pair-living and communal breeding combined). Next, we use double-digest restriction site-associated DNA sequencing (ddRAD-seq) to extract the abundance of repetitive elements (the proportions of TEs and microsatellite repeats) from the genomes of each species to explore the relationships among social organization, genome structure, and genome size. This reduced-representation approach has been shown to accurately estimate the relative proportions of TEs in the genomes of nonmodel species by comparing this method to whole-genome assemblies and simulated ddRAD-seq markers across arthropods (46). We then use phylogenetic path analysis and ancestral state reconstruction to examine the relative importance of alternative causal relationships linking these traits. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, potentially through changes in demography resulting from a reproductive division of labor (20), or whether an initial accumulation of repetitive elements (i.e., TEs) leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution (33). Ultimately, exploring the relationship between eusociality and genome architecture will not only help elucidate the genomic consequences of living in complex societies, it will also improve our understanding of the interacting relationship between genome evolution and social evolution.     

反义及小干扰RNA对大鼠肝星状细胞金属蛋白酶组织抑制因子-1表达的抑制作用

目的观察以腺相关病毒（AAV）为载体，含有针对大鼠金属蛋白酶组织抑制因子（TIMP）-1的反义RNA及小干扰RNA（siRNA）的重组AAV（rAAV／ANTI-TIMP—1／neo及rAAV／siRNA—TIMP—1／neo）感染大鼠肝星状细胞系HSC—T6后，TIMP—1表达的受抑制情况。方法经聚合酶链反应（PCR）扩增及酶切后连接，将针对TIMP—1的反义RNA片段及甄RNA片段分别构建于AAV载体中并测序鉴定，将其包装成重组病毒后感染大鼠肝星状细胞系HSC—T6，同时设空白对照组。经G418以400ug／m1的浓度筛选30d后，分别应用荧光定量PCR技术及Westernblot检测重组病毒感染组及空白对照组HSC-T6 TIMP-1的基因转录及蛋白质表达水平。结果经PCR、酶切及序列测定证实，两种重组AAV载体质粒（pd16-95／ANTI—TIMP-1／neo和pd16—95／siRNA-TIMP-1／neo）克隆成功。将重组质粒包装成病毒感染HSC—T6细胞30d后，通过荧光定量PCR技术及Westernblot分析显示，重组病毒rAAV／siRNA-TIMP-1／neo组与对照组细胞相比，HSC—T6中的TIMP-1基因的转录被抑制（P〈0．01），且表达水平与对照组相比约下降60％。而rAAV／ANTI—TIMP—1／neo组及空载体组与对照组相比TIMP—1基因的转录及表达水平差异无统计学意义（P〉0．05）。结论通过AAV载体技术重组病毒rAAV／siRNA-TIMP—1／neo可有效地抑制TIMP-1基因的表达，而针对TIMP—1基因全长的重组病毒rAAV／ANTI—TIMP—1／neo对体外培养的HSC—T6细胞TIMP—1基因的转录与表达无明显抑制作用。     

The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae

The modified nucleoside 1-methyladenosine (m(1)A) is found at position 58 in the TPsiC loop of many eukaryotic tRNAs. The absence of m(1)A from all tRNAs in Saccharomyces cerevisiae mutants lacking Gcd10p elicits severe defects in processing and stability of initiator methionine tRNA (tRNA(i)(Met)). Gcd10p is found in a complex with Gcd14p, which contains conserved motifs for binding S-adenosylmethionine (AdoMet). These facts, plus our demonstration that gcd14Delta cells lacked m(1)A, strongly suggested that Gcd10p/Gcd14p complex is the yeast tRNA(m(1)A)methyltransferase [(m(1)A)MTase]. Supporting this prediction, affinity-purified Gcd10p/Gcd14p complexes used AdoMet as a methyl donor to synthesize m(1)A in either total tRNA or purified tRNA(i)(Met) lacking only this modification. Kinetic analysis of the purified complex revealed K(M) values for AdoMet or tRNA(i)(Met) of 5.0 microM and 2.5 nM, respectively. Mutations in the predicted AdoMet-binding domain destroyed GCD14 function in vivo and (m(1)A)MTase activity in vitro. Purified Flag-tagged Gcd14p alone had no enzymatic activity and was severely impaired for tRNA-binding compared with the wild-type complex, suggesting that Gcd10p is required for tight binding of the tRNA substrate. Our results provide a demonstration of a two-component tRNA MTase and suggest that binding of AdoMet and tRNA substrates depends on different subunits of the complex.     

Cloning of serum RNA associated with hepatitis C infection suggesting heterogeneity of the agent(s) responsible for the infection

Fifty-six lambda gt11-random-primed-cDNA recombinants of which translation products react with antibodies in the serum drawn from patients with hepatitis C (blood-borne non-A, non-B hepatitis) were cloned from serum pooled from donors presumably infected with hepatitis C. The specificity of these clones for hepaitits C infection was determined using 3 test panels. Of these 29 clones were determined to be specific for Japanese hepatitis C infection. However one of the 29 clones was positive for 1 out of 5 normals in an American test panel while 12 clones were positive for the American panel as well. The remaining 28 clones reacted well with serum from transfusion associated chronic hepatitis C comparing to the sporadic cases in the Japanese panel. When they were tested with normal donors, another clone reacted with a distinct donor group with which the other clones did not react. These results may suggest the presence of heterogeneity in Japanese hepatitis C.