Saritas-Yildirim B et al. (2015), Genome-Wide Identification and Expression of Xe...

XB-ART-51230

PLoS One 2015 Sep 01;109:e0136929. doi: 10.1371/journal.pone.0136929.

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Genome-Wide Identification and Expression of Xenopus F-Box Family of Proteins.

Saritas-Yildirim B , Pliner HA , Ochoa A , Silva EM .

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Protein degradation via the multistep ubiquitin/26S proteasome pathway is a rapid way to alter the protein profile and drive cell processes and developmental changes. Many key regulators of embryonic development are targeted for degradation by E3 ubiquitin ligases. The most studied family of E3 ubiquitin ligases is the SCF ubiquitin ligases, which use F-box adaptor proteins to recognize and recruit target proteins. Here, we used a bioinformatics screen and phylogenetic analysis to identify and annotate the family of F-box proteins in the Xenopus tropicalis genome. To shed light on the function of the F-box proteins, we analyzed expression of F-box genes during early stages of Xenopus development. Many F-box genes are broadly expressed with expression domains localized to diverse tissues including brain, spinal cord, eye, neural crest derivatives, somites, kidneys, and heart. All together, our genome-wide identification and expression profiling of the Xenopus F-box family of proteins provide a foundation for future research aimed to identify the precise role of F-box dependent E3 ubiquitin ligases and their targets in the regulatory circuits of development.

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Species referenced: Xenopus tropicalis
Genes referenced: btrc ccnf eloa fbxl14 fbxl15 fbxl19 fbxl22 fbxl3 fbxo11 fbxo28 fbxo3 fbxo33 fbxo43 fbxo46 fbxo7 fbxo8 fbxo9 fbxw2 fbxw7 fbxw9 gnat1 kdm2b odc1 tnf XB5721468 XB5727064 XB5799768 XB5964270

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References [+] :

Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997, Pubmed

	Fig 1. Identification and annotation of X. tropicalis F-box family of proteins. Full-length protein sequences of F-box proteins categorized into subgroups were used to construct maximum likelihood phylogenies; A. F-box proteins with WD40 repeats (Fbxw), B. F-box proteins with leucine rich repeats (Fbxl), and C. F-box proteins with other domains (Fbxo). A Xenopus F-box protein (red) is considered homologous if it clusters with mammalian proteins. Green shaded branch shows Xenopus specific Fbxw7-like genes. Xenopus Fbxl sequences in green lack an identifiable LRR domain but are found to be highly associated with Fbxl proteins (see S1 Fig). Bootstrap values higher than 50 are shown. Arrowheads show X. tropicalis specific F-box proteins. doi:10.1371/journal.pone.0136929.g001
	Fig 2. Domain structures of the Xenopus F-box proteins. Domains identified by Pfam include F-box motif (F, green), WD40 repeat (WD, gray), leucine-rich repeat (L, orange), F-box-associated domain (FBA), between-ring domain (IBR), Kelch repeat, zf-CXXC zing finger domain (zf-C or zf), Cyclin N and Cyclin C domains, SMI1 KNR4, microtubule interacting and trafficking domain (MIT), zinc finger in N-recognin (Zf-UBR), SPla and the RYanodine Receptor (SPRY), TNF-receptor associated factor (TRAF), Elongin A (E), FIST C domain, Transglutaminase-like superfamily (Transglut), Hemimethylated DNA-binding protein YccV like (YccV), UvrD Helicase (H). doi:10.1371/journal.pone.0136929.g002
	Fig 3. Phylogenetic analysis of five novel X. tropicalis-specific Fbxw proteins and Fbxw7 isoforms shows that the novel Xenopus proteins are similar to Fbxw7. Fbxw7-like genes show moderate similarity to Fbxw7, are in a distinct location in the genome, and expressed in X. tropicalis (NCBI EST and Unigene databases). doi:10.1371/journal.pone.0136929.g003
	Fig 4. Temporal expression of F-box genes during X. laevis development. RT-PCR analysis of F-box gene during early embryonic development. ODC was used for loading control.–RT was performed for each gene but a representative for ODC was shown. Expression panels are grouped by shared temporal expression: genes expressed at all 4 stages are in the left column; in 3 zygotic stages in the top middle; in neurula and tailbud in the bottom middle and in a random pattern in the right column. The asterisks indicate the genes whose spatial expressions are shown in Fig 5. N.e. represents genes that are not expressed doi:10.1371/journal.pone.0136929.g004
	Fig 5. Spatial expression of F-box genes during X. laevis development using in situ hybridizations. Embryos positions: egg and blastula embryos, lateral view with animal side up; gastrula embryos, lateral view with dorsal up and vegetal to the right; neurula embryos dorso-lateral view with anterior to the right; tailbud embryos, lateral view with anterior to the right. Black arrowheads indicate neural tissue, blue—neural crest, green—pre or somitic mesoderm and red–heart. doi:10.1371/journal.pone.0136929.g005
	S2 Fig. Spatial expression of F-box genes with diffused expression during X. laevis development using in situ hybridizations. Embryos positions: egg and blastula embryos, lateral view with animal side up; gastrula embryos, lateral view with dorsal up and vegetal to the right; neurula embryos dorso-lateral view with anterior to the right; tailbud embryos, lateral view with anterior to the right. doi:10.1371/journal.pone.0136929.s002
	kdm2b (lysine (K)-specific demethylase 2B) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 26, lateral view, anterior left, dorsal up.
	fbxl19 (F-box and leucine-rich repeat protein 19) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 10, lateral view, animal up.
	fbxl19 (F-box and leucine-rich repeat protein 19) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 26, lateral view, anterior left, dorsal up.
	fbxl14 (F-box and leucine-rich repeat protein 14) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 20, dorsal view, anterior left.
	fbxl14 (F-box and leucine-rich repeat protein 14) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 26, lateral view, anterior left, dorsal up.
	fbxl15 (F-box and leucine-rich repeat protein 15) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 10, lateral view, animal up.
	fbxl15 (F-box and leucine-rich repeat protein 15) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxl22 (F-box and leucine-rich repeat protein 22) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 20, dorsal view, anterior left.
	fbxl22 (F-box and leucine-rich repeat protein 22) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	ccnf (cyclin F) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxo9 (F-box protein 9) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxw7 (F-box and WD repeat domain containing 7) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	btrc (beta-transducin repeat containing E3 ubiquitin ) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxo7 (F-box protein 7) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxl3 (F-box and leucine-rich repeat protein 3) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 20, dorsal view, anterior left up.
	fbxo3 ( F-box protein 3 ) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxo8 ( F-box protein 8) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 8, lateral view, animal up.
	fbxo11 (F-box protein 11) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxo28 (F-box protein 28) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 26, lateral view, anterior left, dorsal up.
	fbxo33 ( F-box protein 33 ) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 8, lateral view, animal up.
	fbxo46 (F-box protein 46) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 30, lateral view, anterior left, dorsal up.
	fbxw2 (F-box and WD repeat domain containing 2) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 26, lateral view, anterior left, dorsal up.