An Efficient, Amine-Specific, and Cost-Effective Method for TMT 6/11-plex Labeling Improves the Proteome Coverage, Quantitative Accuracy and Precision.

Tandem mass tags (TMT) are widely used in proteomics to simultaneously quantify multiple samples in a single experiment. The tags can be easily added to the primary amines of peptides/proteins through chemical reactions. In addition to amines, TMT reagents also partially react with the hydroxyl groups of serine, threonine, and tyrosine residues under alkaline conditions, which significantly compromises the analytical sensitivity and precision. Under alkaline conditions, reducing the TMT molar excess can partially mitigate overlabeling of histidine-free peptides, but has a limited effect on peptides containing histidine and hydroxyl groups. Here, we present a method under acidic conditions to suppress overlabeling while efficiently labeling amines, using only one-fifth of the TMT amount recommended by the manufacturer. In a deep-scale analysis of a yeast/human two-proteome sample, we systematically evaluated our method against the manufacturer's method and a previously reported TMT-reduced method. Our method reduced overlabeled peptides by 9-fold and 6-fold, respectively, resulting in the substantial enhancement in peptide/protein identification rates. More importantly, the quantitative accuracy and precision were improved as overlabeling was reduced, endowing our method with greater statistical power to detect 42% and 12% more statistically significant yeast proteins compared to the standard and TMT-reduced methods, respectively. Mass spectrometric data have been deposited in the ProteomeXchange Consortium via the iProX partner repository with the data set identifier PXD047052.

Overcoming the detrimental O-acylation in TMTpro labeling improves the proteome depth and quantification precision.

BACKGROUND: With the advent of proline-based reporter isobaric Tandem Mass Tag (TMTpro) reagents, the sample multiplexing capacity of tandem mass tags (TMTs) has been expanded, and up to 18 samples can be quantified in a multiplexed manner. Like classic TMT reagents, TMTpro reagents contain a tertiary amine group, which markedly enhances their reactivity toward hydroxyl groups and results in O-acylation of serine, threonine and tyrosine residues. This overlabeling significantly compromises proteome analysis in terms of depth and precision. In particular, the reactivity of hydroxyl-containing residues can be dramatically enhanced when coexisting with a histidine in the same peptides, leading to a severe systematic bias against the analysis of these peptides. Although some protocols using a reduced molar excess of TMT under alkaline conditions can alleviate overlabeling of histidine-free peptides to some extent, they have a limited effect on histidyl- and hydroxyl-containing peptides. RESULTS: Here, we report a novel TMTpro labeling method that overcomes detrimental overlabeling while providing high labeling efficiency of amines. Additionally, our method is cost-effective, as it requires only half the amount of TMTpro reagents recommended by the reagent manufacturer. In a deep-scale analysis of a yeast/human two-proteome model sample, we compared our method with a typical alkaline labeling method using a reduced molar excess of TMTpro. Even at a depth of over 10,000 proteins, our method detected 23.7% more unique peptides and 8.7% more protein groups compared to the alkaline labeling method. Moreover, our method significantly improved the quantitative precision due to the reduced variability in labeling and increased protein sequence coverage. This substantially enhanced the statistical power of our method for detecting differentially abundant proteins, providing an average of 13% more yeast proteins that reached statistical significance. SIGNIFCANCE: We presented a novel TMTpro labeling method that overcomes the detrimental O-acylation and thus significantly improves the depth and quantitative precision for proteome analysis.

Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA.

Pyruvate carboxylase (PC) catalyzes the two-step carboxylation of pyruvate to produce oxaloacetate, playing a key role in the maintenance of metabolic homeostasis in cells. Given its involvement in multiple diseases, PC has been regarded as a potential therapeutic target for obesity, diabetes, and cancer. Albeit acetyl-CoA has been recognized as the allosteric regulator of PC for over 60 years, the underlying mechanism of how acetyl-CoA induces PC activation remains enigmatic. Herein, by using time-resolved cryo-electron microscopy, we have captured the snapshots of PC transitional states during its catalytic cycle. These structures and the biochemical studies reveal that acetyl-CoA stabilizes PC in a catalytically competent conformation, which triggers a cascade of events, including ATP hydrolysis and the long-distance communication between the two reactive centers. These findings provide an integrated picture for PC catalysis and unveil the unique allosteric mechanism of acetyl-CoA in an essential biochemical reaction in all kingdoms of life.

Engineering Leifsonia Alcohol Dehydrogenase for Thermostability and Catalytic Efficiency by Enhancing Subunit Interactions.

Leifsonia alcohol dehydrogenase (LnADH) is a promising biocatalyst for the synthesis of chiral alcohols. However, limitations of wild-type LnADH observed for practical application include low activity and poor stability. In this work, protein engineering was employed to improve its thermostability and catalytic efficiency by altering the subunit interfaces. Residues T100 and S148 were identified to be significant for thermostability and activity, and the melting temperature (ΔTm ) and catalytic efficiency of the mutant T100R/S148I toward ketone substrates was improved by 18.7 °C and 1.8-5.5-fold. Solving the crystal structures of the wild-type enzyme and T100R/S148L revealed beneficial effects of mutations on stability and catalytic activity. The most robust mutant T100R/S148I is promising for industrial applications and can produce 200 g liter-1 day-1 chiral alcohols at 50 °C by only a 1 : 500 ratio of enzyme to substrate.

Taxonomy of the order Bunyavirales: update 2019.

In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV).

The trimeric Hef-associated nuclease HAN is a 3'→5' exonuclease and is probably involved in DNA repair.

Nucleases play important roles in nucleic acid metabolism. Some archaea encode a conserved protein known as Hef-associated nuclease (HAN). In addition to its C-terminal DHH nuclease domain, HAN also has three N-terminal domains, including a DnaJ-Zinc-finger, ribosomal protein S1-like, and oligonucleotide/oligosaccharide-binding fold. To further understand HAN's function, we biochemically characterized the enzymatic properties of HAN from Pyrococcus furiosus (PfuHAN), solved the crystal structure of its DHH nuclease domain, and examined its role in DNA repair. Our results show that PfuHAN is a Mn2+-dependent 3'-exonuclease specific to ssDNA and ssRNA with no activity on blunt and 3'-recessive double-stranded DNA. Domain truncation confirmed that the intrinsic nuclease activity is dependent on the C-terminal DHH nuclease domain. The crystal structure of the DHH nuclease domain adopts a trimeric topology, with each subunit adopting a classical DHH phosphoesterase fold. Yeast two hybrid assay confirmed that the DHH domain interacts with the IDR peptide of Hef nuclease. Knockout of the han gene or its C-terminal DHH nuclease domain in Haloferax volcanii resulted in increased sensitivity to the DNA damage reagent MMS. Our results imply that HAN nuclease might be involved in repairing stalled replication forks in archaea.

A novel tick-borne phlebovirus, closely related to severe fever with thrombocytopenia syndrome virus and Heartland virus, is a potential pathogen.

Tick-borne viral diseases have attracted much attention in recent years because of their increasing incidence and threat to human health. Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV) and Heartland virus (HRTV) were recently identified as tick-borne phleboviruses (TBPVs) in Asia and the United States, respectively, and are associated with severe human diseases with similar clinical manifestations. In this study, we report the first identification and isolation of a novel TBPV named Guertu virus (GTV) from Dermacentor nuttalli ticks in Xinjiang Province, China, where TBPVs had not been previously discovered. Genome sequence and phylogenetic analyses showed that GTV is closely related to SFTSV and HRTV and was classified as a member of the genus Phlebovirus, family Phenuiviridae, order Bunyavirales. In vitro and in vivo investigations of the properties of GTV demonstrated that it was able to infect animal and human cell lines and can suppress type I interferon signaling, similar to SFTSV, that GTV nucleoprotein (NP) can rescue SFTSV replication by replacing SFTSV NP, and that GTV infection can cause pathological lesions in mice. Moreover, a serological survey identified antibodies against GTV from serum samples of individuals living in Guertu County, three of which contained neutralizing antibodies, suggesting that GTV can infect humans. Our findings suggested that this virus is a potential pathogen that poses a threat to animals and humans. Further studies and surveillance of GTV are recommended to be carried out in Xinjiang Province as well as in other locations.

Prevalence and Phylogenetic Analysis of Crimean-Congo Hemorrhagic Fever Virus in Ticks from Different Ecosystems in Xinjiang, China.

The Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the genus Orthonairovirus and family Nairoviridae, is transmitted by ticks and causes severe hemorrhagic disease in humans. To study the epidemiology of CCHFV in different ecosystems in Xinjiang, China, a total of 58,932 ticks were collected from Tarim Basin, Junggar Basin, Tianshan Mountain, and Altai Mountain from 2014 to 2017. Hyalomma asiaticum asiaticum was the dominant tick species in Tarim and Junggar basins, whereas Dermacentor nuttalli and Hyalomma detritum were found in Tianshan Mountain and Altai Mountain, respectively. Reverse transcription-polymerase chain reaction of the CCHFV small (S) genome segment was used for the molecular detection. The CCHFV-positive percentage was 5.26%, 6.85%, 1.94%, and 5.56% in Tarim Basin, Junggar Basin, Tianshan Mountain, and Altai Mountain, respectively. Sequences of the S segment were used for phylogenetic analysis and the results showed that the newly identified CCHFV strains belonged to two clades. Our study confirms that H. asiaticum asiaticum is the major vector of CCHFV in desert habitats which is consistent with previous studies, and also suggests that H. detritum and D. nuttalli are emerging vectors for CCHFV in Xinjiang. Moreover, this study reports the presence of CCHFV in the mountain habitat of Xinjiang for the first time, suggesting that future surveillance of CCHFV should also include mountainous areas.

Uncovering the formation and selection of benzylmalonyl-CoA from the biosynthesis of splenocin and enterocin reveals a versatile way to introduce amino acids into polyketide carbon scaffolds.

Selective modification of carbon scaffolds via biosynthetic engineering is important for polyketide structural diversification. Yet, this scope is currently restricted to simple aliphatic groups due to (1) limited variety of CoA-linked extender units, which lack aromatic structures and chemical reactivity, and (2) narrow acyltransferase (AT) specificity, which is limited to aliphatic CoA-linked extender units. In this report, we uncovered and characterized the first aromatic CoA-linked extender unit benzylmalonyl-CoA from the biosynthetic pathways of splenocin and enterocin in Streptomyces sp. CNQ431. Its synthesis employs a deamination/reductive carboxylation strategy to convert phenylalanine into benzylmalonyl-CoA, providing a link between amino acid and CoA-linked extender unit synthesis. By characterization of its selection, we further validated that AT domains of splenocin, and antimycin polyketide synthases are able to select this extender unit to introduce the phenyl group into their dilactone scaffolds. The biosynthetic machinery involved in the formation of this extender unit is highly versatile and can be potentially tailored for tyrosine, histidine and aspartic acid. The disclosed aromatic extender unit, amino acid-oriented synthetic pathway, and aromatic-selective AT domains provides a systematic breakthrough toward current knowledge of polyketide extender unit formation and selection, and also opens a route for further engineering of polyketide carbon scaffolds using amino acids.

Heat acclimation decreased oxidative DNA damage resulting from exposure to high heat in an occupational setting.

Heat acclimation is a physiologically and biochemically adapted process when species transition from one environmental temperature to one of the increased temperature. There is very limited epidemiological evidence on the heat-related impacts during exposure to extremely high heat in an occupational environment. This study sought to identify a potential biomarker of heat acclimation and the burden of heat on the body. The aim of this study was to elucidate oxidative DNA damage and heat acclimation through a self-comparison study design in navy boiler tenders, subjects exposed to extremely high heat in an occupational setting. Fifty-eight male soldiers who work in a boiler room were recruited for this study. The subjects were initially assessed with a health examination and body composition assessment before sailing. In order to compare the within-subject differences before and after heat exposure, the index-related heat exposure was collected before and after a routine 5-h work shift and 7-day sailing. Urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG), a useful marker of oxidative DNA damage was the measurement by liquid chromatography/tandem mass spectrometry. The median of the change in urinary 8-OHdG was 0.78 µg/g creatinine, as the urinary 8-OHdG after sailing was significantly higher than before sailing (p < 0.01). The urinary 8-OHdG was significantly decreased in heat-acclimated boiler tenders. Oxidative DNA damage was significantly decreased in heat-acclimated subjects. Urinary 8-OHdG can be used as a biomarker to assess the effect of heat stress as a result of occupational exposure to extremely high heat conditions.

[Strategies for discussing death with child cancer sufferers].

Since a curriculum concerning life and death was established and palliative care began to be promoted, people have gradually awakened to the needs of dying patients. Because of the nature of oriental culture, however, ultimate decisions concerning someone with a terminal disease have traditionally been made by family, so dying patients, especially children with cancer, have usually not been told of their true condition. The purpose of this article was to gain an understanding of the necessity of talking about death with child cancer patients and how to communicate with these children. The results show that helping the family to talk about death and decision making concerning treatment can help them to adapt to the grieving period when the children pass away. The tactics that nurses can use for communication with dying children include: to acknowledge the decision maker in the family, adopt the concept of death appropriate to a person of the child's age, discuss the prognosis for the development of the disease, and opt to use the medium of communication. The findings of this article may serve as a source of reference for nurses caring for dying children, and cause greater attention to be paid to these issues.

Urinary 1-hydroxypyrene level relative to vehicle exhaust exposure mediated by metabolic enzyme polymorphisms.

Polycyclic aromatic hydrocarbons (PAH) are common air pollutants generated from incomplete combustion. The inhalation of exhaust fumes in urban areas has been suggested to be an additional contributing factor. This study investigated the influence of urban traffic exposure, personal lifestyle factors and metabolic enzyme polymorphisms on the urinary 1-hydroxypyrene (1-OHP) level, approximating exposure to PAH. With consents, 95 male taxi drivers exposed to vehicle exhaust in traffic and 75 male office employees received health interviews and provided urine samples. The results showed taxi drivers had higher urinary 1-OHP than the office employees (mean +/- standard deviation were 0.17 +/- 0.10 vs. 0.10 +/- 0.07 mol/mol creatinine, p<0.001). The average urinary 1-OHP level increased from 0.07 micromol/mol creatinine for non-smoking office employees to 0.17 micromol/mol creatinine for those who smoked more than 20 cigarettes daily. The values for taxi drivers with similar smoking statuses were 0.12 and 0.25 micromol/mol creatinine, respectively. Among non-smokers, taxi drivers still had higher 1-OHP level than office employees (0.12 +/- 0.05 vs. 0.07 +/- 0.03 micromol/mol creatinine). The subjects with the m1/m2 or m2/m2 genotype of CYP1A1 MspI or GSTM1 deficiency had significantly higher urinary 1-OHP levels than those with other CYP1A1 MspI and GSTM1 genotypes. Multivariate logistic regression analysis showed that taxi drivers (adjusted odds ratio (OR)=5.1, 95% confidence interval (CI)=1.1-13.6), smokers (OR=5.5, 95% CI=1.6-18.4) and subjects with the m1/m2 or m2/m2 genotype of CYP1A1 MspI (OR=9.7, 95% CI=2.7-35.0) had elevated urinary 1-OHP (greater than the overall median value, 0.11 micromol/mol creatinine). The results of this study suggest smoking contributes to the elevated urinary 1-OHP levels in taxi drivers in addition to taxi driving, and the excess level contributed from traffic exhaust and smoke was regulated by the CYP1A1 MspI genotype. Traffic exhaust exposure, smoking and CYP1A1 MspI genotype contributed to the variation in levels of urinary 1-OHP excretion.

Arsenic species contents at aquaculture farm and in farmed mouthbreeder (Oreochromis mossambicus) in blackfoot disease hyperendemic areas.

A study was conducted to measure the arsenic species in farmed mouthbreeder (Oreochromis mossambicus) and culture ponds in water in blackfoot disease (BFD) hyperendemic areas in Taiwan. The relationships between arsenic species of aquaculture ponds and farmed fish were also explored. Biota samples were extracted with methanol/water (1/1, v/v) using a Soxhlet extraction apparatus. The concentrations of arsenite As (III), arsenate As (V), monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA) of extracts were measured by high-performance liquid chromatography (HPLC) linked to a hydride generator and atomic absorption spectrometry (HG-AAS). Moreover, arsenobetaine (AB) was analyzed by HPLC linked to ultra violet (UV) and HG-AAS. Concentrations of arsenic species were determined in 68 mouthbreeder (O. mossambicus) samples and 21 culture ponds from Putai and Yichu Townships of Chiayi County and Hsuehchia and Peimen Townships of Tainan County. The mean arsenic levels of culture ponds in Putai, Yichu, Hsuehchia, and Peimen were 75.8, 15.1, 14.4, and 221.0 microg/l, respectively. The water of culture ponds was dominated by As (V). The inorganic arsenic percentage of fish (7.4%) was higher than that reported by other seafood surveys. Except for the MMA and As (III) levels, As (V), DMA, AB, and total arsenic levels in fish significantly increased with inorganic and total arsenic concentrations of the pond water. Inorganic arsenic species are more toxic than methyl arsenic species. Therefore the effect of inorganic arsenic species might result in a greater number of adverse health effects to the general public. It is of importance to evaluate the inorganic arsenic levels of farmed seafood in arsenic-contaminated areas.