Cloning, Escherichia coli expression, purification, characterization, and enzyme assay of the ribosomal protein S4 from wheat seedlings (Triticum vulgare)

Transcriptome of Pterospermum kingtungense provides implications on the mechanism underlying its rapid vegetative growth and limestone adaption

Pterospermum kingtungense C.Y.Wu ex Hsue is a typical tree species living in the relatively adverse limestone habitat. Due to its excellent wood quality and big size, it is an important timber resource which caused its endangered. We firstly provide the data resources by reporting an annotated transcriptome assembly. 203 million unique Illumina RNA-seq reads were produced with totally 50,333 transcripts, among which 48,778 transcripts were annotated. By a global comparison of homology between P. kingtungense and cacao, we identified 9,507 single copy orthologues and 990 P. kingtungense specific genes. GO enrichment analyses indicate that P. kingtungense specific genes are enriched in defense response, implying potential adaptation to limestone environment. As to cell compartment, the genes are enriched in thylakoid component. Consistently, KEGG enrichment indicates that genes are enriched in photosynthesis. In addition, we identified two genes under positive selection in P. kingtungense species. These results suggest that P. kingtungense have strong photosynthetic capacity, which related to vegetation growth. Our work provides the genomic resources of a limestone specific tree with economic importance to local society and suggests possible mechanism on its characteristics on the limestone adaption and excellent wood properties, which will be important for its conservation and sustainable utilization.

Identification of photoperiod-regulated gene in soybean and functional analysis in Nicotiana benthamiana

Soybean (Glycine max) is a short-day crop and the photoperiod is a crucial factor regulating its flowering time. To investigate the molecular mechanism controlling the flowering time by photoperiod in soybean, cDNA-amplified fragment length polymorphism (cDNA-AFLP) was used to identify photoperiod-regulated genes in leaves of soybean growing under short-day length, neutral photoperiod and long-day length. A total of 36 transcript-derived fragments (TDFs) were identified to be regulated by photoperiod. Among them, 26 TDFs were homologues of genes with known function. These genes are involved in secondary metabolism, cellular metabolism, cell wall components metabolism, ion transport and hormone signalling. Silencing of the homologue genes in Nicotiana benthamiana for 14 TDFs was conducted by virus-induced gene silencing. The flowering time was delayed by silencing of the genes encoding rhodanese and 40S ribosomal protein S4 (RPS4). The results indicated that rhodanese and RPS4 probably play important roles in regulating flowering time.

Arrested cell proliferation through cysteine protease activity of eukaryotic ribosomal protein S4

S4 is an integral protein of the smaller subunit of cytosolic ribosome. In prokaryotes, it regulates the synthesis of ribosomal proteins by feedback inhibition of the α-operon gene expression, and it facilitates ribosomal RNA synthesis by direct binding to RNA polymerase. However, functional roles of S4 in eukaryotes are poorly understood, although its deficiency in humans is thought to produce Turner syndrome. We report here that wheat S4 is a cysteine protease capable of abrogating total protein synthesis in an actively translating cell-free system of rabbit reticulocytes. The translation-blocked medium, imaged by atomic force microscopy, scanning electron microscopy, and transmission electron microscopy, shows dispersed polysomes, and the disbanded polyribosome elements aggregate to form larger bodies. We also show that human embryonic kidney cells transfected with recombinant wheat S4 are unable to grow and proliferate. The mutant S4 protein, where the putative active site residue Cys 41 is replaced by a phenylalanine, can neither suppress protein synthesis nor arrest cell proliferation, suggesting that the observed phenomenon arises from the cysteine protease attribute of S4. The results also inspire many questions concerning in vivo significance of extraribosomal roles of eukaryotic S4 performed through its protease activity.

Cysteine protease attribute of eukaryotic ribosomal protein S4

BACKGROUND

Ribosomal proteins often carry out extraribosomal functions. The protein S4 from the smaller subunit of Escherichia coli, for instance, regulates self synthesis and acts as a transcription factor. In humans, S4 might be involved in Turner syndrome. Recent studies also associate many ribosomal proteins with malignancy, and cell death and survival. The list of extraribosomal functions of ribosomal proteins thus continues to grow.

METHODS

Enzymatic action of recombinant wheat S4 on fluorogenic peptide substrates Ac-XEXD↓-AFC (N-acetyl-residue-Glu-residue-Asp-7-amino-4-trifluoromethylcoumarin) and Z-FR↓-AMC (N-CBZ-Phe-Arg-aminomethylcoumarin) as well as proteins has been examined under a variety of solution conditions.

RESULTS

Eukaryotic ribosomal protein S4 is an endoprotease exhibiting all characteristics of cysteine proteases. The K(m) value for the cleavage of Z-FR↓-AMC by a cysteine mutant (C41F) is about 70-fold higher relative to that for the wild-type protein under identical conditions, implying that S4 is indeed a cysteine protease. Interestingly, activity responses of the S4 protein and caspases toward environmental parameters, including pH, temperature, ionic strength, and Mg(2+) and Zn(2+) concentrations, are quite similar. Respective kinetic constants for their cleavage action on Ac-LEHD↓-AFC are also similar. However, S4 cannot be a caspase, because unlike the latter it also hydrolyzes the cathepsin substrate Z-FR↓-AMC.

GENERAL SIGNIFICANCE

The eukaryotic S4 is a generic cysteine protease capable of hydrolyzing a broad spectrum of synthetic substrates and proteins. The enzyme attribute of eukaryotic ribosomal protein S4 is a new phenomenon. Its possible involvement in cell growth and proliferations are presented in the light of known extraribosomal roles of ribosomal proteins.