ABSTRACT
The aim of this study was to compare the proteomics pattern of the kidneys from Cyld knockout mice with that from normal mouse kidneys and establish a preliminary understanding of the role of Cyld in the kidney. Proteins from the kidneys of knockout Cyld mice and wild-type mice were extracted, isobaric tags for relative and absolute quantitation (iTRAQ) was performed, and the proteomics patterns of the two groups were compared. The genotypes of the mice were verified by polymerase chain reaction. A total of 1748 proteins with a local false discovery rate of ≤5% were identified, among which 1437 proteins were reliably recognized and quantified. The expression of two dysregulated proteins was confirmed by Western blotting. Gene ontology and pathway analyses indicated that the proteins identified were involved in biological processes, cell components, and molecular functions, and participated in different pathways. Some of the proteins identified were relevant to renal function or kidney diseases. The difference between the proteomics profiles of kidneys from Cyld knockout mice and wild-type mice was prominent, which correlates to kidney dysfunction and the development of renal diseases.
Subject(s)
Cysteine Endopeptidases/genetics , Kidney/metabolism , Proteomics , Animals , Deubiquitinating Enzyme CYLD , Gene Expression Regulation , Kidney/pathology , Mice , Mice, Knockout , Protein Biosynthesis/geneticsABSTRACT
PIF-like elements are the first-described members of a recently discovered and widespread superfamily of DNA transposons, named PIF/Harbinger. Complete and partial PIF-like elements have been isolated from hundreds of plant species. Previously, we identified 139 partial PIF-like transposases in the Bambusoideae, of which three were from the bamboo species Phyllostachys pubescens. Here we report identification and isolation of the first full-length PIF-like element (PpPIF-1) from P. pubescens; identification was made by chromosome walking, based on a modified magnetic enrichment procedure that allows efficient cloning of flanking sequences up to 3 kb in length. PpPIF-1 is 5953 bp in length, with 20-bp imperfect inverted terminal repeats and 3-bp target site duplications. This element contains two open reading frames, one encoding a putative transposase, including the complete DDE-domain typical of PIF/Harbinger elements from plants, and the other encoding a DNA-binding protein. There are seven termination codons and two frameshift mutations in the open reading frames, probably due to vertical inactivation.
Subject(s)
Bambusa/genetics , Genes, Plant , Amino Acid Sequence , Base Sequence , Chromosome Walking , DNA Primers , Frameshift Mutation , Molecular Sequence Data , Open Reading Frames , Phylogeny , Sequence Homology, Amino Acid , Transposases/chemistry , Transposases/geneticsABSTRACT
Phyllostachys pubescens is a woody bamboo with the highest ecological, economic, and cultural values of all bamboos in Asia. There is more genomic data available for P. pubescens than for any other bamboo species, including 2.12-Mb genome survey sequences (GSS) and 11.4-Mb full-length cDNA sequences (FL-cDNAs) currently deposited in GenBank. Analysis of these sequences revealed that transposable elements (TEs) are abundant, diverse and polyphyletic in the P. pubescens genome, of which Ty3-gypsy and Ty1-copia are the two most abundant families. Phylogenic analysis showed that both elements probably arose before the Bambusoideae separated from the other Poaceae subfamilies. We found evidence that the distribution of some intragenic TEs correlated with transcript profiles, of which Mutator elements preferred to insert in the transcripts of transcription factors. Additionally, we found that the abundance of SSRs in TEs (4.56%) was significantly higher than in GSS (0.098%) and in FL-cDNAs (2.60%) in P. pubescens genome, and TA/AT and CT/AG repeats were found to be intimately associated with En/Spm and Mutator elements, respectively. Our data provide a glimpse of the structure and evolution of P. pubescens genome, although large-scale sequencing of the genome would be required to fully understand the architecture of the P. pubescens genome.
Subject(s)
Bambusa/genetics , DNA, Complementary/genetics , Genome, Plant , Genomics/methods , Microsatellite Repeats , Systems Biology/methods , DNA Transposable Elements , Databases, Genetic , Evolution, Molecular , Phylogeny , Sequence Analysis, DNA , Transcription Factors/geneticsABSTRACT
In floating rice, stem elongation begins much earlier than in non-floating rice, which is the major survival mechanism for flooding. Inheritance of this early elongation ability was studied using diallel and quantitative trait locus (QTL) analyses. The diallel analysis was undertaken using a set of 6x6 half-diallel crosses involving four floating ("Goai", "Habiganj Aman VIII", "Badal 106", and Oryza rufipogon strain W120) and two non-floating ("Latisail" and "Patnai 23") parents. The additive gene effects were higher than the dominant effects. The dominant alleles were concentrated in the cultivated floating parents (("Goai", "Habiganj Aman VIII", "Badal 106"), whereas the recessive alleles were in the wild floating parent (W120). A QTL analysis using a "Patnai 23" x "Goai" F(2) population detected two putative QTLs. Of these QTLs, the one on chromosome 12 behaved as a partially dominant major gene that explained more than half of the total genetic variation.
