Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

Background: The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. Results: The DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life. In-depth investigations suggest that some archaeal and bacterial DUF71 proteins participate in B12 salvage. Conclusions: This detailed analysis of the DUF71 family members provides an example of the power of integrated data-miming for solving important “missing genes” or “missing function” cases and illustrates the danger of functional annotation of protein families by homology alone. Reviewers’ names: This article was reviewed by Arcady Mushegian, Michael Galperin and L. Aravind

The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma

The TINCR (Terminal differentiation-Induced Non-Coding RNA) gene is selectively expressed in epithelium tissues and is involved in the control of human epidermal differentiation and wound healing. Despite its initial report as a long non-coding RNA, the TINCR locus codes for a highly conserved ubiquitin-like microprotein associated with keratinocyte differentiation. Here we report the identification of TINCR as a tumor suppressor in squamous cell carcinoma (SCC). TINCR is upregulated by UV-induced DNA damage in a TP53-dependent manner in human keratinocytes. Decreased TINCR protein expression is prevalently found in skin and head and neck squamous cell tumors and TINCR expression suppresses the growth of SCC cells in vitro and in vivo. Consistently, Tincr knockout mice show accelerated tumor development following UVB skin carcinogenesis and increased penetrance of invasive SCCs. Finally, genetic analyses identify loss-of-function mutations and deletions encompassing the TINCR gene in SCC clinical samples supporting a tumor suppressor role in human cancer. Altogether, these results demonstrate a role for TINCR as protein coding tumor suppressor gene recurrently lost in squamous cell carcinomas.This work was supported by NIH grants P30 CA013696 (Confocal and Specialized Microscopy Shared Resource, Proteomics Shared Resource, Molecular Pathology Shared Resource, Genomics Shared Resource, Herbert Irving Comprehensive Cancer Center), R01 GM102491 (A.S.), K01 CA249038 (T.F.M.), P30 AR069632 (epiCURE SCIM and SIND Core Facilities) and R35 CA210065 (A.A.F.); Dr. Frederick Paulsen Chair/Ferring Pharmaceuticals (A.S.); Plan Nacional de I + D + I/ISCIII grants PI16/00280 and PI19/00560 (J.M.G.-P.), and PI18/01527 (M.F.F. and A.F.F.); CIBERONC grant CB16/12/00390 (J.P.R.), and the FEDER Funding Program from the European Union. Crystallization screening at the National Crystallization Center at HWI was supported through NIH grant R24GM141256. This work used the NE-CAT 24-ID-E beamline (GM124165) and an Eiger detector (OD021527) at the APS (DE-AC02-06CH11357). LMP was supported by a Leukemia and Lymphoma Society Career Development fellowship (grant #5461-18). J.A.B. was the Candy and William Raveis Fellow of the Damon Runyon-Sohn Foundation Pediatric Cancer Fellowship Award (grant no. DRSG-31-19) and supported by the National Cancer Institute of the National Institutes of Health (award no. K99CA267168). R.G.-D. is a recipient of a Severo Ochoa predoctoral fellowship from the Principado de Asturias (grant # BP19-063).Peer reviewe

The Evaluation of Whole-Body Vibration Level in Hand-Held Pneumatic Tools (Rock Drill) by “Pneurop Cagi Test Code” Method

The evaluation of whole-body vibration in hand - held pneumatic tools (Rock drills) used in the Lashotor stone mines in Isfahan by the method PNEUROP CAGI (compressed air and gas institute) TEST CODE. This shows the methods for the use of construction equipment in stone mines under work circumstances. This method is designed to evaluate noise and vibration propagated by the hand – held pneumatic tools. Rock Drills are categorized as the major sources of noise and vibration by the Federal noise control Act of 1972. The paper demonstrates vibration values in three directions X, Y, Z and the three vital indices for workers while working with equipment, compared to standard graphs, produced by “Rock Drill” used in the above specified test method. This paper focuses on measurement and prediction of whole -body vibration indices in a rock drill used in stone mines using a B &amp; K vibration meter type 2512. In order to evaluate them we had to record the whole-body acceleration on the ground where the operator was standing and processing his work. The indices include reduced comfort (RC), fatigue decreased proficiency (FDP), and exposure level (EL) for a frequency response of 1–80 Hz shown Table I. As can be seen in table I, there are high values of rms acceleration in the Z and XY axes for exposure level and fatigue decreased proficiency, respectively. All values are based in a 5-hour exposure time. Although we found high levels of vibration in different axes, the most important index in comparison with its recommended limits can be exposure level, because it is a better index weighted for human vibration in workplaces. The reduced comfort index is not recommended for occupational and industrial use. </jats:p

The Crystal Structure of the Influenza Matrix Protein M1 at Neutral pH: M1–M1 Protein Interfaces Can Rotate in the Oligomeric Structures of M1

AbstractThe influenza matrix protein (M1) forms a protein layer under the viral membrane and is essential for viral stability and integrity. M1 mediates the encapsidation of the viral RNPs into the viral membrane by its membrane and RNP-binding activities. In order to understand the roles of M1–M1 protein interactions in forming the M1 layer, X-ray crystallographic studies of a M1 fragment (1–162) were carried out at neutral pH and compared with an acidic pH structure. At neutral pH the asymmetric unit was a stacked dimer of M1. A long molecular ribbon of neutral stacked dimers was formed by translation as dictated by the P1 space group. The elongated ribbon had a positively charged stripe on one side of the ribbon. A similar M1–M1 stacking interface was also found in the acidic asymmetric unit. However, within the acidic stacked dimer the molecules were not straight, but rotated in relation to each other by slightly changing the M1–M1 stacking interface. The acidic structure possessed an additional M1–M1 twofold interface. Protein docking confirmed that the M1–M1 stacking and M1–M1 twofold interfaces could be used to form a double ribbon of M1 molecules. By iterative repetition of the rotated relationship among the M1 molecules, a helix of M1 was generated. These studies suggest that M1 has the ability to form straight or bent elongated ribbons and helices. These oligomers are consistent with previous electron microscopic studies of M1, which demonstrated that isolated M1 formed elongated and flexible ribbons when isolated from what appeared to be a helical shell of M1 in the influenza virus

Wybutosine biosynthesis: Structural and mechanistic overview

International audienceOver the last 10 years, significant progress has been made in understanding the genetics, enzymology and structural components of the wybutosine (yW) biosynthetic pathway. These studies have played a key role in expanding our understanding of yW biosynthesis and have revealed unexpected evolutionary ties, which are presently being unraveled. The enzymes catalyzing the 5 steps of this pathway, from genetically encoded guanosine to wybutosine base, provide an ensemble of amazing reaction mechanisms that are to be discussed in this review article

Analysis of the effect of hydraulic steering wheel system on decrease in the vibration transmitted to driver’s hand-arm

Background: Vibration of body especially that of hand-arm is a key factor in developing inconvenience in drivers, which decreases efficiency, triggers fatigue and disturbance in physiological activities, and finally predisposes drivers to occupational diseases and traffic accidents. This study examines the effect of hydraulic steering wheel system on controlling and attenuation of the vibrations transmitted to driver’s hand-arm. Methods: This cross-sectional study was carried out according to convenience sampling on two perfectly homogeneous automobile groups (15 with hydraulic steering wheel and 15 without hydraulic steering wheel). Steering wheel vibration measurement was carried out in three vibration axes and three specified positions of automobile movement (in the same atmospheric and physical conditions) using Bruel & Kjaer-2231 Vibrometer. The data were analyzed by SPSS 11.5 using t-test and two-way ANOVA. Results: The results indicated that the superior effective acceleration axis in the two groups. of automobiles and in three measurement positions is axis Y. Comparing the results with the 4-hour standard showed that in all positions the effective acceleration (in rms) is less than the permitted exposure limits and care limits (p<0.05). Also, compared to the standard 8- and 16-hour values, some of the positions were higher than the permitted and care limits (p<0.05) and some had no significance difference from the standards (p≥0.05). Two-way ANOVA showed that the type of steering wheel system, speed, and gear (measurement positions), independently, simultaneously, and jointly, are effective on the vibration transmitted to the drivers’ arm (p<0.05). Conclusion: In contrast to the whole body vibration where axis Z has been reported as axis with superior effective acceleration, in the vibrations derived from steering wheel the axis with superior effective acceleration is axis Y and the hydraulic steering wheel can significantly decrease the vibration transmission to the drivers’ hand and arm. On the other hand, the decrease in hours spent for working with the automobiles without hydraulic steering wheel can be considered as a very useful managerial tool

S-Adenosylmethionine-dependent radical-based modification of biological macromolecules.

International audienceProteins and RNA molecules enjoy a variety of chemically complex post-translational and post-transcriptional modifications. The chemistry at work in these reactions, which was considered to be exclusively ionic in nature has recently been shown to depend on radical mechanisms in some cases. The overwhelming majority of these radical-based reactions are catalyzed by 'Radical-SAM' enzymes. This review article highlights mechanistic and structural aspects of this class of reactions and indicates important research directions to be addressed

<i>Methyl Esterase 1</i> (<i>StMES1</i>) Is Required for Systemic Acquired Resistance in Potato

Whether salicylic acid (SA) plays a role in systemic acquired resistance (SAR) signaling in potato is currently unclear because potato, unlike tobacco and Arabidopsis, contains highly elevated levels of endogenous SA. Recent studies have indicated that the SA derivative methyl salicylate (MeSA) serves as a long-distance phloem-mobile SAR signal in tobacco and Arabidopsis. Once in the distal, uninfected tissue of these plant species, MeSA must be converted into biologically active SA by the esterase activity of SA-binding protein 2 (SABP2) in tobacco or members of the AtMES family in Arabidopsis. In this study, we have identified the potato ortholog of tobacco SABP2 (StMES1) and shown that the recombinant protein converts MeSA to SA; this MeSA esterase activity is feedback inhibited by SA or its synthetic analog, 2, 2, 2, 2′-tetra-fluoroacetophenone (tetraFA). Potato plants (cv. Désirée) in which StMES1 activity was suppressed, due to either tetraFA treatment or silencing of StMES1 expression, were compromised for arachidonic acid (AA)-induced SAR development against Phytophthora infestans. Presumably due to the inability of these plants to convert MeSA to SA, the SAR-defective phenotype correlated with elevated levels of MeSA and reduced expression of pathogenesis-related (PR) genes in the untreated distal tissue. Together, these results strongly suggest that SAR signaling in potato requires StMES1, its corresponding MeSA esterase activity, and MeSA. Furthermore, the similarities between SAR signaling in potato, tobacco, and Arabidopsis suggest that at least certain SAR signaling components are conserved among plants, regardless of endogenous SA levels. </jats:p