Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11.

In mammals, one of the most pronounced consequences of viral infection is the induction of type I interferons, cytokines with potent antiviral activity. Schlafen (Slfn) genes are a subset of interferon-stimulated early response genes (ISGs) that are also induced directly by pathogens via the interferon regulatory factor 3 (IRF3) pathway. However, many ISGs are of unknown or incompletely understood function. Here we show that human SLFN11 potently and specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1). Our study revealed that SLFN11 has no effect on the early steps of the retroviral infection cycle, including reverse transcription, integration and transcription. Rather, SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner. We further find that SLFN11 binds transfer RNA, and counteracts changes in the tRNA pool elicited by the presence of HIV. Our studies identified a novel antiviral mechanism within the innate immune response, in which SLFN11 selectively inhibits viral protein synthesis in HIV-infected cells by means of codon-bias discrimination.

Evidence for late resolution of the aux codon box in evolution.

Recognition strategies for tRNA aminoacylation are ancient and highly conserved, having been selected very early in the evolution of the genetic code. In most cases, the trinucleotide anticodons of tRNA are important identity determinants for aminoacylation by cognate aminoacyl-tRNA synthetases. However, a degree of ambiguity exists in the recognition of certain tRNA(Ile) isoacceptors that are initially transcribed with the methionine-specifying CAU anticodon. In most organisms, the C34 wobble position in these tRNA(Ile) precursors is rapidly modified to lysidine to prevent recognition by methionyl-tRNA synthetase (MRS) and production of a chimeric Met-tRNA(Ile) that would compromise translational fidelity. In certain bacteria, however, lysidine modification is not required for MRS rejection, indicating that this recognition strategy is not universally conserved and may be relatively recent. To explore the actual distribution of lysidine-dependent tRNA(Ile) rejection by MRS, we have investigated the ability of bacterial MRSs from different clades to differentiate cognate tRNACAU(Met) from near-cognate tRNACAU(Ile). Discrimination abilities vary greatly and appear unrelated to phylogenetic or structural features of the enzymes or sequence determinants of the tRNA. Our data indicate that tRNA(Ile) identity elements were established late and independently in different bacterial groups. We propose that the observed variation in MRS discrimination ability reflects differences in the evolution of genetic code machineries of emerging bacterial clades.

Misacylation of specific nonmethionyl tRNAs by a bacterial methionyl-tRNA synthetase.

Aminoacyl-tRNA synthetases perform a critical step in translation by aminoacylating tRNAs with their cognate amino acids. Although high fidelity of aminoacyl-tRNA synthetases is often thought to be essential for cell biology, recent studies indicate that cells tolerate and may even benefit from tRNA misacylation under certain conditions. For example, mammalian cells selectively induce mismethionylation of nonmethionyl tRNAs, and this type of misacylation contributes to a cell's response to oxidative stress. However, the enzyme responsible for tRNA mismethionylation and the mechanism by which specific tRNAs are mismethionylated have not been elucidated. Here we show by tRNA microarrays and filter retention that the methionyl-tRNA synthetase enzyme from Escherichia coli (EcMRS) is sufficient to mismethionylate two tRNA species, and , indicating that tRNA mismethionylation is also present in the bacterial domain of life. We demonstrate that the anticodon nucleotides of these misacylated tRNAs play a critical role in conferring mismethionylation identity. We also show that a certain low level of mismethionylation is maintained for these tRNAs, suggesting that mismethionylation levels may have evolved to confer benefits to the cell while still preserving sufficient translational fidelity to ensure cell viability. EcMRS mutants show distinct effects on mismethionylation, indicating that many regions in this synthetase enzyme influence mismethionylation. Our results show that tRNA mismethionylation can be carried out by a single protein enzyme, mismethionylation also requires identity elements in the tRNA, and EcMRS has a defined structure-function relationship for tRNA mismethionylation.

Summer climbing incidents occurring on Fujisan's north face from 1989 to 2008.

OBJECTIVE: Few studies exist on climbing-related incidents at Fujisan, although it is Japan's highest peak at 3776 m, and attracts dense crowds of summer climbers. A retrospective review was thus conducted to analyze the types of incidents and the demographics of climbers involved. METHODS: Police reports of summer climbing incidents occurring along the Yoshida trail on Fujisan's north face from 1989 to 2008 were reviewed. Variables assessed included climber age, sex, experience, gear, altitude of incident, and whether the incident occurred during ascent or descent, as well as the cause and severity of any associated injury. RESULTS: A total of 155 incident reports were assessed, including 28 deaths mostly attributable to cardiac events occurring among male climbers during ascent. The majority of nonfatal incidents occurred during descent and most involved tripping. More than half of all incidents were reported at the 8th step (approximately 3000 m). The frequent appearance of male climbers without experience or adequate footwear reflects Fujisan's summer demographics, yet the injury rate appears higher among older climbers more than 50 years of age. There were also 28 noninjury incidents attributed to acute mountain sickness or fatigue. CONCLUSIONS: This retrospective review describes the demographics of summer climbing incidents on Fujisan's north face. Additionally, limitations to the current method of incident reporting were identified. More comprehensive recordkeeping would increase understanding of injuries and illness, which could improve resource allocation and reduce the risk of fatalities from out-of-hospital cardiac events.

Building eco-surplus culture among urban residents as a novel strategy to improve finance for conservation in protected areas.

The rapidly declining biosphere integrity, representing one of the core planetary boundaries, is alarming. In particular, the global numbers of mammals, birds, fishes, and plants declined by 68% from 1970 to 2016. One of the most widely accepted measures to halt the rate of biodiversity loss is to maintain and expand protected areas that are effectively managed. However, doing so requires substantial finance derived from nature-based tourism, specifically visitors from urban areas. Using the Bayesian Mindsponge Framework (BMF) for conducting analysis on 535 Vietnamese urban residents, the current study examined how their biodiversity loss perceptions can affect their willingness to pay for the entrance fee and conservation in protected areas. We found that perceived environmental degradation, loss of economic growth, loss of nature-based recreation opportunities, and loss of knowledge as consequences of biodiversity loss indirectly affect the willingness to pay through the mediation of the attitude towards conservation. Notably, perceived knowledge loss also has a direct positive influence on the willingness to pay for the entrance fee and conservation. In contrast, perceived loss of health is negatively associated with the attitude towards conservation. Based on these findings, we suggest that building an eco-surplus culture among urban residents by stimulating their subjective cost-benefit judgments towards biodiversity loss can be a promising way to generate more finance from nature-based tourism for conservation in protected areas and ease the domestic government's and international organizations' funding allocation problems. Eco-surplus culture is a set of pro-environmental attitudes, values, beliefs, and behaviors shared by a group of people to reduce negative anthropogenic impacts on the environment and conserve and restore nature.

Prevalence of acute mountain sickness on Mount Fuji: A pilot study.

BACKGROUND: Few studies have investigated climbing-related acute mountain sickness (AMS) on Mt Fuji. Although several studies of AMS have been conducted elsewhere, Mt Fuji is unique because there are many mountain lodges between the fifth station (a common starting point for climbers at an altitude of 2305 m) and the summit (3776 m), and many climbers commonly sleep overnight at mountain lodges during their ascents. This study surveyed the prevalence of AMS among climbers on Mt Fuji to determine which factors, if any, were related to the risk of developing AMS. METHODS: This study collected data from 345 participants who climbed Mt Fuji in August 2013, including information regarding age, sex, climbing experience and whether the climber stayed at a mountain lodge (n = 239). AMS was surveyed using the Lake Louise Score (LLS) questionnaire. The item on perceived sleep quality was excluded for those who did not stay at a mountain lodge (n = 106). RESULTS: The overall prevalence of AMS was 29.5% (≥ 3 LLS with headache). According to a univariate analysis, AMS was not associated with sex (male vs female), age group (20-29, 30-39, 40-49 or >50 years) or stay at a mountain lodge (single day vs overnight stay). Conversely, prior experience climbing Mt Fuji (no prior attempts vs one or more prior attempts) was related to the risk of AMS. In addition, there was a significant deviation in the number of participants reporting poor sleep, and total sleep time was significantly shorter in participants with AMS. CONCLUSIONS: These preliminary findings suggest that no single factor can explain the risk for developing AMS while climbing Mt Fuji. In addition, impaired perceived sleep quality was associated with the severity of AMS in climbers who stayed overnight at a mountain lodge.

An operational RNA code for faithful assignment of AUG triplets to methionine.

The assignment of AUG codons to methionine remains a central question of the evolution of the genetic code. We have unveiled a strategy for the discrimination among tRNAs containing CAU (AUG-decoding) anticodons. Mycoplasma penetrans methionyl-tRNA synthetase can directly differentiate between tRNA(Ile)(CAU) and tRNA(Met)(CAU) transcripts (a recognition normally achieved through the modification of anticodon bases). This discrimination mechanism is based only on interactions with the acceptor stems of tRNA(Ile)(CAU) and tRNA(Met)(CAU). Thus, in certain species, the fidelity of translation of methionine codons requires a discrimination mechanism that is independent of the information contained in the anticodon.

Trypanosoma seryl-tRNA synthetase is a metazoan-like enzyme with high affinity for tRNASec.

Trypanosomatids are important human pathogens that form a basal branch of eukaryotes. Their evolutionary history is still unclear as are many aspects of their molecular biology. Here we characterize essential components required for the incorporation of serine and selenocysteine into the proteome of Trypanosoma. First, the biological function of a putative Trypanosoma seryl-tRNA synthetase was characterized in vivo. Secondly, the molecular recognition by Trypanosoma seryl-tRNA synthetase of its cognate tRNAs was dissected in vitro. The cellular distribution of tRNA(Sec) was studied, and the catalytic constants of its aminoacylation were determined. These were found to be markedly different from those reported in other organisms, indicating that this reaction is particularly efficient in trypanosomatids. Our functional data were analyzed in the context of a new phylogenetic analysis of eukaryotic seryl-tRNA synthetases that includes Trypanosoma and Leishmania sequences. Our results show that trypanosomatid seryl-tRNA synthetases are functionally and evolutionarily more closely related to their metazoan homologous enzymes than to other eukaryotic enzymes. This conclusion is supported by sequence synapomorphies that clearly connect metazoan and trypanosomatid seryl-tRNA synthetases.