Browse > Article
http://dx.doi.org/10.4051/ibc.2012.4.1.0001

Members of Ectocarpus siliculosus F-box Family Are Subjected to Differential Selective Forces  

Mahmood, Niaz (Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka)
Moosa, Mahdi Muhammad (Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka)
Matin, S. Abdul (DataSoft Systems Bangladesh Limited)
Khan, Haseena (Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka)
Publication Information
Interdisciplinary Bio Central / v.4, no.1, 2012 , pp. 1.1-1.7 More about this Journal
Abstract
Background: The F-box proteins represent one of the largest families of proteins in eukaryotes. Apart from being a component of the ubiquitin (Ub)/26 S proteasome pathways, their regulatory roles in other cellular and developmental pathways have also been reported. One interesting feature of the genes encoding the proteins of this particular family is their variable selection patterns across different lineages. This resulted in the presence of lineage specific F-box proteins across different species. Findings: In this study, 48 non-redundant F-box proteins in E. siliculosus have been identified by a homology based approach and classified into three classes based on their variable C-terminal domains. A greater number of the F-box proteins have domains similar to the ones identified in other species. On the other hand, when the proteins having unknown or no C-terminal domain (as predicted by InterProScan) were analyzed, it was found that some of them have the polyglutamine repeats. To gain evolutionary insights on the genes encoding the F-box proteins, their selection patterns were analyzed and a strong positive selection was observed which indicated the adaptation potential of the members of this family. Moreover, four lineage specific F-box genes were found in E. siliculosus with no identified homolog in any other species. Conclusions: This study describes a genome wide in silico analysis of the F-box proteins in E. siliculosus which sheds light on their evolutionary patterns. The results presented in this study provide a strong foundation to select candidate sequences for future functional analysis.
Keywords
Ectocarpus siliculosus; heterokont lineage; brown algae; F-box; ubiquitinylation; evolutionary analyses;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Smalle, J., and Vierstra, R.D. (2004). The ubiquitin 26S proteasome proteolytic pathway. Annu Rev Plant Biol 55, 555-590.   DOI   ScienceOn
2 Stone, S.L., and Callis, J. (2007). Ubiquitin ligases mediate growth and development by promoting protein death. Curr Opin Plant Biol 10, 624-632.   DOI   ScienceOn
3 Samach, A., Klenz, J.E., Kohalmi, S.E., Risseeuw, E., Haughn, G.W., and Crosby, W.L. (1999). The UNUSUAL FLORAL ORGANS gene of Arabidopsis thaliana is an F box protein required for normal patterning and growth in the floral meristem. Plant J 20, 433-445.   DOI   ScienceOn
4 Yoon, H.S., Hackett, J.D., Ciniglia, C., Pinto, G., and Bhattacharya, D. (2004). A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol 21, 809-818.   DOI   ScienceOn
5 Lau, S., Jurgens, G., and De Smet, I. (2008). The evolving complexity of the auxin pathway. Plant Cell 20, 1738-1746.   DOI   ScienceOn
6 Baldauf, S.L. (2008). An overview of the phylogeny and diversity of eukaryotes. J Syst Evol 46, 263-273.
7 Simon, D., and Sylvie, R. (2011). Microarray estimation of genomic inter- strain variability in the genus Ectocarpus (Phaeophyceae). BMC Mol Biol 12, 1-12.   DOI
8 Le Bail, A., Billoud, B., Kowalczyk, N., Kowalczyk, M., Gicquel, M., Le Panse, S., Stewart, S., Scornet, D., Cock, J.M., and Ljung, K. (2010). Auxin metabolism and function in the multicellular brown alga Ectocarpus siliculosus. Plant Physiol 153, 128-144.   DOI   ScienceOn
9 Thomas, J.H. (2006). Adaptive evolution in two large families of ubiquitin- ligase adapters in nematodes and plants. Genome Res 16, 1017- 1030.   DOI   ScienceOn
10 Clark, R.M., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T.T., Fu, G., and Hinds, D.A. (2007). Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317, 338-342.   DOI
11 Jin, J., Cardozo, T., Lovering, R.C., Elledge, S.J., Pagano, M., and Harper, J.W. (2004). Systematic analysis and nomenclature of mammalian Fbox proteins. Gene Dev 18, 2573-2580.   DOI   ScienceOn
12 Cenciarelli, C., Chiaur, D., Guardavaccaro, D., Parks, W., Vidal, M., and Pagano, M. (1999). Identification of a family of human F-box proteins. Curr Biol 9, 1177-1179, S1171-S1173.   DOI   ScienceOn
13 Bernhard, G., Yann, G., and Mark, C.J. (2008). HECTAR: A method to predict subcellular targeting in heterokonts. BMC Bioinformatics 9, 393.   DOI
14 Larkin, M., Blackshields, G., Brown, N., Chenna, R., McGettigan, P., Mc- William, H., Valentin, F., Wallace, I., Wilm, A., Lopez, R. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.   DOI   ScienceOn
15 Morgenstern, B., and Atchley, W.R. (1999). Evolution of bHLH transcription factors: modular evolution by domain shuffling? Mol Biol Evol 16, 1654.   DOI   ScienceOn
16 Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and Lopez, R. (2005). InterProScan: protein domains identifier. Nucleic Acids Res 33, W116-120.   DOI   ScienceOn
17 Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
18 Tamura, K., Dudley, J., Nei, M., and Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.   DOI   ScienceOn
19 Zhang, J., Rosenberg, H.F., and Nei, M. (1998). Positive Darwinian selection after gene duplication in primate ribonuclease genes. PNAS 95, 3708-3713.   DOI   ScienceOn
20 Feldman, R., Correll, C.C., Kaplan, K.B., and Deshaies, R.J. (1997). A complex of Cdc4p, Skp1p, and Cdc53p/cullin catalyzes ubiquitination of the phosphorylated CDK inhibitor Sic1p. Cell 91, 221-230.   DOI   ScienceOn
21 Cardozo, T., and Pagano, M. (2004). The SCF ubiquitin ligase: insights into a molecular machine. Nat Rev Mol Cell Biol 5, 739-751.   DOI
22 Schulman, B.A., Carrano, A.C., Jeffrey, P.D., Bowen, Z., Kinnucan, E.R.E., Finnin, M.S., Elledge, S.J., Harper, J.W., Pagano, M., and Pavletich, N.P. (2000). Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex. Nature 408, 381-386.   DOI   ScienceOn
23 Cao, P.R., Kim, H.J., and Lecker, S.H. (2005). Ubiquitin-protein ligases in muscle wasting. The Int J Biochem Cell Biol 37, 2088-2097.   DOI   ScienceOn
24 Bai, C., Sen, P., Hofmann, K., Ma, L., Goebl, M., Harper, J.W., and Elledge, S.J. (1996). SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box. Cell 86, 263-274.   DOI   ScienceOn
25 Clifford, R., Lee, M.H., Nayak, S., Ohmachi, M., Giorgini, F., and Schedl, T. (2000). FOG-2, a novel F-box containing protein, associates with the GLD-1 RNA binding protein and directs male sex determination in the C. elegans hermaphrodite germline. Development 127, 5265-5276.
26 Galan, J.M., Wiederkehr, A., Seol, J.H., Haguenauer-Tsapis, R., Deshaies, R.J., Riezman, H., and Peter, M. (2001). Skp1p and the F-box protein Rcy1p form a non-SCF complex involved in recycling of the SNARE Snc1p in yeast. Mol Cell Biol 21, 3105-3117.   DOI   ScienceOn
27 Smaldone, S., Laub, F., Else, C., Dragomir, C., and Ramirez, F. (2004). Identification of MoKA, a novel F-box protein that modulates Kruppellike transcription factor 7 activity. Mol Cell Biol 24, 1058-1069.   DOI   ScienceOn
28 Levin, J.Z., and Meyerowitz, E.M. (1995). UFO: an Arabidopsis gene involved in both floral meristem and floral organ development. Plant Cell 7, 529-548.   DOI
29 Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., Kapoor, S., Tyagi, A., and Khurana, J. (2007). F-box proteins in rice. Genomewide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143, 1467-1483.   DOI   ScienceOn
30 Winston, J.T., Koepp, D.M., Zhu, C., Elledge, S.J., and Harper, J.W. (1999). A family of mammalian F-box proteins. Curr Biol 9, 1180-1182.   DOI   ScienceOn
31 Bella, J., Hindle, K., McEwan, P., and Lovell, S. (2008). The leucine-rich repeat structure. Cell Mol Life Sci 65, 2307-2333.   DOI   ScienceOn
32 Andrade, M.A., Perez-Iratxeta, C., and Ponting, C.P. (2001). Protein repeats: structures, functions, and evolution. J Struct Biol 134, 117-131.   DOI   ScienceOn
33 Neer, E.J., Schmidt, C.J., Nambudripad, R., and Smith, T.F. (1994). The ancient regulatory-protein family of WD-repeat proteins. Nature 371, 297-300.   DOI   ScienceOn
34 Smith, T.F., Gaitatzes, C., Saxena, K., and Neer, E.J. (1999). The WD repeat: a common architecture for diverse functions. Trends Biochem Sci 24, 181-185.   DOI   ScienceOn
35 Clissold, P.M., and Ponting, C.P. (2001). JmjC: cupin metalloenzymelike domains in jumonji, hairless and phospholipase A2 [beta]. Trends Biochem Sci 26, 7-9.   DOI
36 Tsukada, Y., Fang, J., Erdjument-Bromage, H., Warren, M.E., Borchers, C.H., Tempst, P., and Zhang, Y. (2006). Histone demethylation by a family of JmjC domain-containing proteins. Nature 439, 811-816.   DOI
37 Lu, F., Li, G., Cui, X., Liu, C., Wang, X. J., and Cao, X. (2008). Comparative Analysis of JmjC Domain-containing Proteins Reveals the Potential Histone Demethylases in Arabidopsis and Rice. J Integr Plant Biol 50, 886-896.   DOI   ScienceOn
38 Ponting, C., Schultz, J., and Bork, P. (1997). SPRY domains in ryanodine receptors (Ca2+-release channels). Trends Biochem Sci 22, 193-194.   DOI
39 Bailey, T.L., and Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2, 28-36.
40 Schumann, N., Navarro-Quezada, A., Ullrich, K., Kuhl, C., and Quint, M. (2011). Molecular Evolution and Selection Patterns of Plant F-Box Proteins with C-Terminal Kelch Repeats. Plant Physiol 155, 835-850.   DOI
41 Bailey, T.L., Williams, N., Misleh, C., and Li, W.W. (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34, W369-373.   DOI   ScienceOn
42 Crooks, G.E., Hon, G., Chandonia, J.M., and Brenner, S.E. (2004). WebLogo: a sequence logo generator. Genome Res 14, 1188-1190.   DOI   ScienceOn
43 Imafuku, I., Waragai, M., Takeuchi, S., Kanazawa, I., Kawabata, M., Mouradian, M.M., and Okazawa, H. (1998). Polar amino acid-rich sequences bind to polyglutamine tracts. Biochem Biophys Res Comm 253, 16- 20.   DOI   ScienceOn
44 Tajima, T., Oda, A., Nakagawa, M., Kamada, H., and Mizoguchi, T. (2007). Natural variation of polyglutamine repeats of a circadian clock gene ELF3 in Arabidopsis. Plant Biotechnol 2, 237-240.
45 Saleem, Q., Anand, A., Jain, S., and Brahmachari, S.K. (2001). The polyglutamine motif is highly conserved at the Clock locus in various organisms and is not polymorphic in humans. Hum Genet 109, 136-142.   DOI   ScienceOn
46 Lindqvist, C., Laakkonen, L., and Albert, V. (2007). Polyglutamine variation in a flowering time protein correlates with island age in a Hawaiian plant radiation. BMC Evol Biol 7, 105.   DOI
47 Cavalier-Smith, T. (2003). Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). Phil Trans R Soc B 358, 109.   DOI   ScienceOn