Certain adenylated non-coding RNAs, including 5' leader sequences of primary microRNA transcripts, accumulate in mouse cells following depletion of the RNA helicase MTR4

RNA surveillance plays an important role in posttranscriptional regulation. Seminal work in this field has largely focused on yeast as a model system, whereas exploration of RNA surveillance in mammals is only recently begun. The increased transcriptional complexity of mammalian systems provides a wider array of targets for RNA surveillance, and, while many questions remain unanswered, emerging data suggest the nuclear RNA surveillance machinery exhibits increased complexity as well. We have used a small interfering RNA in mouse N2A cells to target the homolog of a yeast protein that functions in RNA surveillance (Mtr4p). We used high-throughput sequencing of polyadenylated RNAs (PA-seq) to quantify the effects of the mMtr4 knockdown (KD) on RNA surveillance. We demonstrate that overall abundance of polyadenylated protein coding mRNAs is not affected, but several targets of RNA surveillance predicted from work in yeast accumulate as adenylated RNAs in the mMtr4KD. microRNAs are an added layer of transcriptional complexity not found in yeast. After Drosha cleavage separates the pre-miRNA from the microRNA's primary transcript, the byproducts of that transcript are generally thought to be degraded. We have identified the 5′ leading segments of pri-miRNAs as novel targets of mMtr4 dependent RNA surveillance.

Effects of bridge construction on songbirds and small mammals at Blennerhassett Island, Ohio River, USA

Construction of man-made objects such as roads and bridges may have impacts on wildlife depending on species or location. We investigated songbirds and small mammals along the Ohio River, WV, USA at a new bridge both before and after construction and at a bridge crossing that was present throughout the study. Comparisons were made at each site over three time periods (1985-1987 [Phase I] and 1998-2000 [Phase II] [pre-construction], 2007-2009 [Phase III] [post-construction]) and at three distances (0, 100, 300 m) from the bridge or proposed bridge location. Overall, 70 songbirds and 10 small mammals were detected during the study. Cliff swallows (Petrochelidon pyrrhonota) and rock pigeons (Columba livia) showed high affinity for bridges (P < 0.05). Combined small mammal abundances increased between Phases I and II (P < 0.05), but did not differ between Phases II and III (P > 0.05). Species richness and diversity for songbirds and small mammals did not differ before and after bridge construction (P > 0.05). We found that most species sampled did not respond to the bridge crossing, and believe that the bridge is not causing any measurable negative density impacts to the species we investigated. The new bridge does provide habitat for exotic rock pigeons that are adjusted to man-made structures for nesting.

The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex

Many steps in nuclear RNA processing, surveillance, and degradation require TRAMP, a complex containing the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for decay or trimming by the nuclear exosome. It has been unclear how polyadenylation by TRAMP differs from polyadenylation by conventional poly(A) polymerase, which produces poly(A) tails that stabilize RNAs. Using reconstituted S. cerevisiae TRAMP, we show that TRAMP inherently suppresses poly(A) addition after only 3-4 adenosines. This poly(A) tail length restriction is controlled by Mtr4p. The helicase detects the number of 3'-terminal adenosines and, over several adenylation steps, elicits precisely tuned adjustments of ATP affinities and rate constants for adenylation and TRAMP dissociation. Our data establish Mtr4p as a critical regulator of polyadenylation by TRAMP and reveal that an RNA helicase can control the activity of another enzyme in a highly complex fashion and in response to features in RNA.

Unexpected accumulation of ncm(5)U and ncm(5)S(2) (U) in a trm9 mutant suggests an additional step in the synthesis of mcm(5)U and mcm(5)S(2)U

BACKGROUND

Transfer RNAs are synthesized as a primary transcript that is processed to produce a mature tRNA. As part of the maturation process, a subset of the nucleosides are modified. Modifications in the anticodon region often modulate the decoding ability of the tRNA. At position 34, the majority of yeast cytosolic tRNA species that have a uridine are modified to 5-carbamoylmethyluridine (ncm(5)U), 5-carbamoylmethyl-2'-O-methyluridine (ncm(5)Um), 5-methoxycarbonylmethyl-uridine (mcm(5)U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U). The formation of mcm(5) and ncm(5) side chains involves a complex pathway, where the last step in formation of mcm(5) is a methyl esterification of cm(5) dependent on the Trm9 and Trm112 proteins.

METHODOLOGY AND PRINCIPAL FINDINGS

Both Trm9 and Trm112 are required for the last step in formation of mcm(5) side chains at wobble uridines. By co-expressing a histidine-tagged Trm9p together with a native Trm112p in E. coli, these two proteins purified as a complex. The presence of Trm112p dramatically improves the methyltransferase activity of Trm9p in vitro. Single tRNA species that normally contain mcm(5)U or mcm(5)s(2)U nucleosides were isolated from trm9Δ or trm112Δ mutants and the presence of modified nucleosides was analyzed by HPLC. In both mutants, mcm(5)U and mcm(5)s(2)U nucleosides are absent in tRNAs and the major intermediates accumulating were ncm(5)U and ncm(5)s(2)U, not the expected cm(5)U and cm(5)s(2)U.

CONCLUSIONS

Trm9p and Trm112p function together at the final step in formation of mcm(5)U in tRNA by using the intermediate cm(5)U as a substrate. In tRNA isolated from trm9Δ and trm112Δ strains, ncm(5)U and ncm(5)s(2)U nucleosides accumulate, questioning the order of nucleoside intermediate formation of the mcm(5) side chain. We propose two alternative explanations for this observation. One is that the intermediate cm(5)U is generated from ncm(5)U by a yet unknown mechanism and the other is that cm(5)U is formed before ncm(5)U and mcm(5)U.

Using two classification schemes to develop vegetation indices of biological integrity for wetlands in West Virginia, USA

Bioassessment methods for wetlands, and other bodies of water, have been developed worldwide to measure and quantify changes in "biological integrity." These assessments are based on a classification system, meant to ensure appropriate comparisons between wetland types. Using a local site-specific disturbance gradient, we built vegetation indices of biological integrity (Veg-IBIs) based on two commonly used wetland classification systems in the USA: One based on vegetative structure and the other based on a wetland's position in a landscape and sources of water. The resulting class-specific Veg-IBIs were comprised of 1-5 metrics that varied in their sensitivity to the disturbance gradient (R2=0.14-0.65). Moreover, the sensitivity to the disturbance gradient increased as metrics from each of the two classification schemes were combined (added). Using this information to monitor natural and created wetlands will help natural resource managers track changes in biological integrity of wetlands in response to anthropogenic disturbance and allows the use of vegetative communities to set ecological performance standards for mitigation banks.

5-ureidobenzofuranone indoles as potent and efficacious inhibitors of PI3 kinase-alpha and mTOR for the treatment of breast cancer

A series of 5-ureidobenzofuran-3-one indoles as potent inhibitors of PI3Kalpha and mTOR has been developed. The best potency in cells was obtained when the urea group was extended to a 4-[2-(dimethylamino)ethyl]methylamino amidophenyl group. A 7-fluoro group on the indole ring also enhanced cellular potency. Compound 18i, incorporating the optimal functional groups, showed high potency in cellular lines and was further studied in vivo. It was able to inhibit the biomarker phosphorylation for 8h when dosed at 25 mg/kg iv. In the MDA-MB-361 breast cancer model, it shrank the tumor size remarkably when dosed at 25 mg/kg iv on days 1, 5, and 9.

Using dual classifications in the development of avian wetland indices of biological integrity for wetlands in West Virginia, USA

Considerable resources are being used to develop and implement bioassessment methods for wetlands to ensure that "biological integrity" is maintained under the United States Clean Water Act. Previous research has demonstrated that avian composition is susceptible to human impairments at multiple spatial scales. Using a site-specific disturbance gradient, we built avian wetland indices of biological integrity (AW-IBI) specific to two wetland classification schemes, one based on vegetative structure and the other based on the wetland's position in the landscape and sources of water. The resulting class-specific AW-IBI was comprised of one to four metrics that varied in their sensitivity to the disturbance gradient. Some of these metrics were specific to only one of the classification schemes, whereas others could discriminate varying levels of disturbance regardless of classification scheme. Overall, all of the derived biological indices specific to the vegetative structure-based classes of wetlands had a significant relation with the disturbance gradient; however, the biological index derived for floodplain wetlands exhibited a more consistent response to a local disturbance gradient. We suspect that the consistency of this response is due to the inherent nature of the connectivity of available habitat in floodplain wetlands.

Effects of highway construction on stream water quality and macroinvertebrate condition in a mid-atlantic highlands watershed, USA

Refining best management practices (BMPs) for future highway construction depends on a comprehensive understanding of environmental impacts from current construction methods. Based on a before-after-control impact (BACI) experimental design, long-term stream monitoring (1997-2006) was conducted at upstream (as control, n = 3) and downstream (as impact, n = 6) sites in the Lost River watershed of the Mid-Atlantic Highlands region, West Virginia. Monitoring data were analyzed to assess impacts of during and after highway construction on 15 water quality parameters and macroinvertebrate condition using the West Virginia stream condition index (WVSCI). Principal components analysis (PCA) identified regional primary water quality variances, and paired t tests and time series analysis detected seven highway construction-impacted water quality parameters which were mainly associated with the second principal component. In particular, impacts on turbidity, total suspended solids, and total iron during construction, impacts on chloride and sulfate during and after construction, and impacts on acidity and nitrate after construction were observed at the downstream sites. The construction had statistically significant impacts on macroinvertebrate index scores (i.e., WVSCI) after construction, but did not change the overall good biological condition. Implementing BMPs that address those construction-impacted water quality parameters can be an effective mitigation strategy for future highway construction in this highlands region.

Nuclear RNA surveillance: no sign of substrates tailing off

The production of cellular RNAs is tightly regulated to ensure gene expression is limited to appropriate times and locations. Elimination of RNA can be rapid and programmed to quickly terminate gene expression, or can be used to purge old, damaged or inappropriately formed RNAs. It is elimination of RNAs through the action of a polyadenylation complex (TRAMP), first described in the yeast Saccharomyces cerevisiae, which is the focus of this review. The discovery of TRAMP and presence of orthologs in most eukaryotes, along with an increasing number of potential TRAMP substrates in the form of new small non-coding RNAs, many of which emanate from areas of genomes once thought transcriptionally silent; promise to make this area of research of great interest for the foreseeable future.

Microhabitat use by white-footed mice Peromyscus leucopus in forested and old-field habitats occupied by Morrow’s honeysuckle Lonicera morrowii

We quantified microhabitat use by white-footed mice Peromyscus leucopus in forest and old-field habitats occupied by Morrow’s honeysuckle Lonicera morrowii, an invasive exotic shrub imported from Japan. Microhabitat characteristics were compared between trails used by mice (n = 124) and randomly selected trails (n = 127) in 4 study plots located at Fort Necessity National Battlefield, Farmington, Pennsylvania, USA. We compared 10 microhabitat variables between used and random trails using non-metric multidimensional scaling (NMDS) and classification and regression tree (CART) analysis. Trails used by mice were statistically different from randomly selected trails in both forested plots (P < 0.008) and old-field plots (P < 0.001). In the forested plots, trails of white-footed mice were more often associated with a greater percent cover (% cover) of coarse woody debris (CWD) than were randomly selected trails. In the old-field plots, mouse trails were commonly characterized by having a lower % cover of exotic herbaceous vegetation, a greater % cover of shrubs, and a greater % cover of Morrow’s honeysuckle than randomly selected trails. Our study indicates that white-footed mice do not move randomly and prefer areas of high structural complexity, thereby showing significant microhabitat preference. The preference of white-footed mice for areas with a relatively high percent cover of Morrow’s honeysuckle could 1) be a factor in the aggressive nature of the exotic honeysuckle shrub’s spread throughout the Battlefield or 2) cause the shrub to spread even faster into adjacent areas not yet occupied by Morrow’s honeysuckle.

Rex1p deficiency leads to accumulation of precursor initiator tRNAMet and polyadenylation of substrate RNAs in Saccharomyces cerevisiae

A synthetic genetic array was used to identify lethal and slow-growth phenotypes produced when a mutation in TRM6, which encodes a tRNA modification enzyme subunit, was combined with the deletion of any non-essential gene in Saccharomyces cerevisiae. We found that deletion of the REX1 gene resulted in a slow-growth phenotype in the trm6-504 strain. Previously, REX1 was shown to be involved in processing the 3′ ends of 5S rRNA and the dimeric tRNA^Arg-tRNA^Asp. In this study, we have discovered a requirement for Rex1p in processing the 3′ end of tRNA_i^Met precursors and show that precursor tRNA_i^Met accumulates in a trm6-504 rex1Δ strain. Loss of Rex1p results in polyadenylation of its substrates, including tRNA_i^Met, suggesting that defects in 3′ end processing can activate the nuclear surveillance pathway. Finally, purified Rex1p displays Mg²⁺-dependent ribonuclease activity in vitro, and the enzyme is inactivated by mutation of two highly conserved amino acids.

Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p

Effective turnover of many incorrectly processed RNAs in yeast, including hypomodified tRNA(iMet), requires the TRAMP complex, which appends a short poly(A) tail to RNA designated for decay. The poly(A) tail stimulates degradation by the exosome. The TRAMP complex contains the poly(A) polymerase Trf4p, the RNA-binding protein Air2p, and the DExH RNA helicase Mtr4p. The role of Mtr4p in RNA degradation processes involving the TRAMP complex has been unclear. Here we show through a genetic analysis that MTR4 is required for degradation but not for polyadenylation of hypomodified tRNA(iMet). A suppressor of the trm6-504 mutation in the tRNA m(1)A58 methyltransferase (Trm6p/Trm61p), which causes a reduced level of tRNA(iMet), was mapped to MTR4. This mtr4-20 mutation changed a single amino acid in the conserved helicase motif VI of Mtr4p. The mutation stabilizes hypomodified tRNA(iMet) in vivo but has no effect on TRAMP complex stability or polyadenylation activity in vivo or in vitro. We further show that purified recombinant Mtr4p displays RNA-dependent ATPase activity and unwinds RNA duplexes with a 3'-to-5' polarity in an ATP-dependent fashion. Unwinding and RNA-stimulated ATPase activities are strongly reduced in the recombinant mutant Mtr4-20p, suggesting that these activities of Mtr4p are critical for degradation of polyadenylated hypomodified tRNA(iMet).

Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding

In Saccharomyces cerevisiae, a two-subunit methyltransferase (Mtase) encoded by the essential genes TRM6 and TRM61 is responsible for the formation of 1-methyladenosine, a modified nucleoside found at position 58 in tRNA that is critical for the stability of tRNA(Met)i The crystal structure of the homotetrameric m1A58 tRNA Mtase from Mycobacterium tuberculosis, TrmI, has been solved and was used as a template to build a model of the yeast m1A58 tRNA Mtase heterotetramer. We altered amino acids in TRM6 and TRM61 that were predicted to be important for the stability of the heteroligomer based on this model. Yeast strains expressing trm6 and trm61 mutants exhibited growth phenotypes indicative of reduced m1A formation. In addition, recombinant mutant enzymes had reduced in vitro Mtase activity. We demonstrate that the mutations introduced do not prevent heteroligomer formation and do not disrupt binding of the cofactor S-adenosyl-L-methionine. Instead, amino acid substitutions in either Trm6p or Trm61p destroy the ability of the yeast m1A58 tRNA Mtase to bind tRNA(Met)i, indicating that each subunit contributes to tRNA binding and suggesting a structural alteration of the substrate-binding pocket occurs when these mutations are present.

The exosome subunit Rrp44 plays a direct role in RNA substrate recognition

The exosome plays key roles in RNA maturation and surveillance, but it is unclear how target RNAs are identified. We report the functional characterization of the yeast exosome component Rrp44, a member of the RNase II family. Recombinant Rrp44 and the purified TRAMP polyadenylation complex each specifically recognized tRNA(i)(Met) lacking a single m(1)A(58) modification, even in the presence of a large excess of total tRNA. This tRNA is otherwise mature and functional in translation in vivo but is presumably subtly misfolded. Complete degradation of the hypomodified tRNA required both Rrp44 and the poly(A) polymerase activity of TRAMP. The intact exosome lacking only the catalytic activity of Rrp44 failed to degrade tRNA(i)(Met), showing this to be a specific Rrp44 substrate. Recognition of hypomodified tRNA(i)(Met) by Rrp44 is genetically separable from its catalytic activity on other substrates, with the mutations mapping to distinct regions of the protein.

Change in nutritional status modulates the abundance of critical pre-initiation intermediate complexes during translation initiation in vivo

In eukaryotic translation initiation, eIF2GTP-Met-tRNA(i)(Met) ternary complex (TC) interacts with eIF3-eIF1-eIF5 complex to form the multifactor complex (MFC), while eIF2GDP associates with eIF2B for guanine nucleotide exchange. Gcn2p phosphorylates eIF2 to inhibit eIF2B. Here we evaluate the abundance of eIFs and their pre-initiation intermediate complexes in gcn2 deletion mutant grown under different conditions. We show that ribosomes are three times as abundant as eIF1, eIF2 and eIF5, while eIF3 is half as abundant as the latter three and hence, the limiting component in MFC formation. By quantitative immunoprecipitation, we estimate that approximately 15% of the cellular eIF2 is found in TC during rapid growth in a complex rich medium. Most of the TC is found in MFC, and important, approximately 40% of the total eIF2 is associated with eIF5 but lacks tRNA(i)(Met). When the gcn2Delta mutant grows less rapidly in a defined complete medium, TC abundance increases threefold without altering the abundance of each individual factor. Interestingly, the TC increase is suppressed by eIF5 overexpression and Gcn2p expression. Thus, eIF2B-catalyzed TC formation appears to be fine-tuned by eIF2 phosphorylation and the novel eIF2/eIF5 complex lacking tRNA(i)(Met).

Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA

1-Methyladenosine modification at position 58 of tRNA is catalyzed by a two-subunit methyltransferase composed of Trm6p and Trm61p in Saccharomyces cerevisiae. Initiator tRNA (tRNAi(Met)) lacking m1A58 (hypomethylated) is rendered unstable through the cooperative function of the poly(A) polymerases, Trf4p/Trf5p, and the nuclear exosome. We provide evidence that a catalytically active Trf4p poly(A) polymerase is required for polyadenylation of hypomethylated tRNAi(Met) in vivo. DNA sequence analysis of tRNAi(Met) cDNAs and Northern hybridizations of poly(A)+ RNA provide evidence that nascent pre-tRNAi(Met) transcripts are targeted for polyadenylation and degradation. We determined that a mutant U6 snRNA and an aberrant form of 5S rRNA are stabilized in the absence of Trf4p, supporting that Trf4p facilitated RNA surveillance is a global process that stretches beyond hypomethylated tRNAi(Met). We conclude that an array of RNA polymerase III transcripts are targeted for Trf4p/ Trf5p-dependent polyadenylation and turnover to eliminate mutant and variant forms of normally stable RNAs.