1.Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans.
Meyer B1, Wurm JP2, Sharma S3, Immer C2, Pogoryelov D4, Kötter P1, Lafontaine DL3, Wöhnert J5, Entian KD6. Nucleic Acids Res. 2016 Apr 15. pii: gkw244. [Epub ahead of print]
The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA. While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive. Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells. In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation. The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode. This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate. Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes.
2.Genome-wide identification and expression analysis of the metacaspase gene family in Hevea brasiliensis.
Liu H1, Deng Z2, Chen J3, Wang S4, Hao L5, Li D6. Plant Physiol Biochem. 2016 Apr 7;105:90-101. doi: 10.1016/j.plaphy.2016.04.011. [Epub ahead of print]
Metacaspases, a family of cysteine proteases, have been suggested to play important roles in programmed cell death (PCD) during plant development and stress responses. To date, no systematic characterization of this gene family has been reported in rubber tree (Hevea brasiliensis). In the present study, nine metacaspase genes, designated as HbMC1 to HbMC9, were identified from whole-genome sequence of rubber tree. Multiple sequence alignment and phylogenetic analyses suggested that these genes were divided into two types: type I (HbMC1-HBMC7) and type II (HbMC8 and HbMC9). Gene structure analysis demonstrated that type I and type II HbMCs separately contained four and two introns, indicating the conserved exon-intron organization of HbMCs. Quantitative real-time PCR analysis revealed that HbMCs showed distinct expression patterns in different tissues, suggesting the functional diversity of HbMCs in various tissues during development. Most of the HbMCs were regulated by drought, cold, and salt stress, implying their possible functions in regulating abiotic stress-induced cell death.
3.Development of a microfluidic paper-based analytical device for the determination of salivary aldehydes.
Ramdzan AN1, Almeida MI1, McCullough MJ2, Kolev SD3. Anal Chim Acta. 2016 May 5;919:47-54. doi: 10.1016/j.aca.2016.03.030. Epub 2016 Mar 19.
A low cost, disposable and easy to use microfluidic paper-based analytical device (μPAD) was developed for simple and non-invasive determination of total aldehydes in saliva with a potential to be used in epidemiological studies to assess oral cancer risk. The μPAD is based on the colour reaction between aldehydes (e.g. acetaldehyde, formaldehyde), 3-methyl-2-benzothiazolinone hydrazone (MBTH) and iron(III) to form an intense blue coloured formazan dye. The newly developed μPAD has a 3D design with two overlapping paper layers. The first layer comprises 15 circular detection zones (8 mm in diameter), each impregnated with 8 μL of MBTH, while the second layer contains 15 reagent zones (4 mm in diameter). Two μL of iron(III) chloride are added to each one of the second layer zones after the addition of sample to the detection zones in the first layer. All hydrophilic zones of the μPAD are defined by wax printing using a commercial wax printer.
4.Cold-dependent alternative splicing of a Jumonji C domain-containing gene MtJMJC5 in Medicago truncatula.
Shen Y1, Wu X1, Liu D2, Song S3, Liu D2, Wang H4. Biochem Biophys Res Commun. 2016 Apr 13. pii: S0006-291X(16)30564-2. doi: 10.1016/j.bbrc.2016.04.062. [Epub ahead of print]
Histone methylation is an epigenetic modification mechanism that regulates gene expression in eukaryotic cells. Jumonji C domain-containing demethylases are involved in removal of methyl groups at lysine or arginine residues. The JmjC domain-only member, JMJ30/JMJD5 of Arabidopsis, is a component of the plant circadian clock. Although some plant circadian clock genes undergo alternative splicing in response to external cues, there is no evidence that JMJ30/JMJD5 is regulated by alternative splicing. In this study, the expression of an Arabidopsis JMJ30/JMJD5 ortholog in Medicago truncatula, MtJMJC5, in response to circadian clock and abiotic stresses were characterized. The results showed that MtJMJC5 oscillates with a circadian rhythm, and undergoes cold specifically induced alternative splicing. The cold-induced alternative splicing could be reversed after ambient temperature returning to the normal. Sequencing results revealed four alternative splicing RNA isoforms including a full-length authentic protein encoding variant, and three premature termination condon-containing variants due to alternative 3' splice sites at the first and second intron.