Abstract
Seed plants express cellulose synthase (CESA) protein isoforms with non-redundant functions, but how the isoforms function differently is unknown. Compared to bacterial cellulose synthases, CESAs have two insertions in the large cytosolic loop: the relatively well-conserved Plant Conserved Region (P-CR) and a Class Specific Region (CSR) that varies between CESAs. Absent any atomic structure of a plant CESA, we used ab initio protein structure prediction and molecular modeling to explore how these plant-specific regions may modulate CESA function. We modeled P-CR and CSR peptides from Arabidopsis thaliana CESAs representing the six clades of seed plant CESAs. As expected, the predicted wild type P-CR structures were similar. Modeling of the mutant P-CR of Atcesa8 R362K (fra6) suggested that changes in local structural stability and surface electrostatics may cause the mutant phenotype. Among CSRs within CESAs required for primary wall cellulose synthesis, the amino sequence and the modeled arrangement of helices was most similar in AtCESA1 and AtCESA3. Genetic complementation of known Arabidopsis mutants showed that the CSRs of AtCESA1 and AtCESA3 can function interchangeably in vivo. Analysis of protein surface electrostatics led to ideas about how the surface charges on CSRs may mediate protein–protein interactions. Refined modeling of the P-CR and CSR regions of GhCESA1 from cotton modified their tertiary structures, spatial relationships to the catalytic domain, and preliminary predictions about CESA oligomer formation. Cumulatively, the results provide structural clues about the function of plant-specific regions of CESA.
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References
Arioli T et al (1998) Molecular analysis of cellulose biosynthesis in Arabidopsis. Science 279:717–720. doi:10.1126/science.279.5351.717
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037–10041. doi:10.1073/pnas.181342398
Berenger F, Shrestha R, Zhou Y, Simoncini D, Zhang KYJ (2012) Durandal: fast exact clustering of protein decoys. J Comput Chem 33:471–474. doi:10.1002/jcc.21988
Bringmann M, Li E, Sampathkumar A, Kocabek T, Hauser MT, Persson S (2012) POM-POM2/cellulose synthase interacting1 is essential for the functional association of cellulose synthase and microtubules in Arabidopsis. Plant Cell 24:163–177. doi:10.1105/tpc.111.093575
Carroll A, Specht CD (2011) Understanding plant cellulose synthases through a comprehensive investigation of the cellulose synthase family sequences. Front Plant Sci 2:5. doi:10.3389/fpls.2011.00005
Carroll A, Mansoori N, Li SD, Lei L, Vernhettes S, Visser RGF, Somerville C, Gu Y, Trindade LM (2012) Complexes with mixed primary and secondary cellulose synthases are functional in Arabidopsis plants. Plant Physiol 160:726–737. doi:10.1104/pp.112.199208
Case DA et al (2010) AMBER 11. University of California, San Fancisco
Chen SL, Ehrhardt DW, Somerville CR (2010) Mutations of cellulose synthase (CESA1) phosphorylation sites modulate anisotropic cell expansion and bidirectional mobility of cellulose synthase. Proc Natl Acad Sci USA 107:17188–17193. doi:10.1073/pnas.1012348107
Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743. doi:10.1046/j.1365-313x.1998.00343.x
Craft JW, Legge GB (2005) An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations. J Biomol NMR 33:15–24. doi:10.1007/s10858-005-1199-0
Das R, Baker D (2008) Macromolecular modeling with Rosetta. Annu Rev Biochem 77:363–382. doi:10.1146/annurev.biochem.77.062906.171838
Desprez T, Juraniec M, Crowell EF, Jouy H, Pochylova Z, Parcy F, Hofte H, Gonneau M, Vernhettes S (2007) Organization of cellulose synthase complexes involved in primary cell wall synthesis in Arabidopsis thaliana. Proc Natl Acad Sci USA 104:15572–15577. doi:10.1073/pnas.0706569104
Dolinsky T, Nielsen J, McCammon J, Baker N (2004) PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32:W665–W667. doi:10.1093/nar/gkh381
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35:W522–W525. doi:10.1093/nar/gkm276
Giddings TH, Brower DL, Staehelin LA (1980) Visualization of particle complexes in the plasma-membrane of Micrasterias denticulata associated with the formation of cellulose fibrils in primary and secondary cell-walls. J Cell Biol 84:327–339. doi:10.1083/jcb.84.2.327
Gu Y, Kaplinsky N, Bringmann M, Cobb A, Carroll A, Sampathkumar A, Baskin TI, Persson S, Somerville CR (2010) Identification of a cellulose synthase-associated protein required for cellulose biosynthesis. Proc Natl Acad Sci USA 107:12866–12871. doi:10.1073/pnas.1007092107
Han J, Kamber M (2006) Data mining: concepts and techniques, 2nd edn. Morgan Kaufmann, San Francisco
Harder T, Borg M, Boomsma W, Røgen P, Hamelryck T (2012) Fast large-scale clustering of protein structures using Gauss integrals. Bioinformatics 28:510–515. doi:10.1093/bioinformatics/btr692
Harris D, DeBolt S (2008) Relative crystallinity of plant biomass: studies on assembly, adaptation and acclimation. PLoS ONE. doi:10.1371/journal.pone.0002897
Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51–59. doi:10.1016/0378-1119(89)90358-2
Jarvis MC (2013) Cellulose biosynthesis: counting the chains. Plant Physiol 163:1485–1486. doi:10.1104/pp.113.231092
Kim HS, Ha SH, Sethaphong L, Koo YM, Yingling YG (2014) The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study. Phys Chem Chem Phys 16:2944–2953. doi:10.1039/c3cp52516c
Kimura S, Laosinchai W, Itoh T, Cui X, Linder RC, Brown RM (1999) Immunogold labeling of rosette terminal cellulose-synthesizing complexes in the vascular vlant Vigna angularis. Plant Cell 11:2075–2085. doi:10.1105/tpc.11.11.2075
Kumar M, Turner S (2015) Plant cellulose synthesis: CESA proteins crossing kingdoms. Phytochemistry 112:91–99. doi:10.1016/j.phytochem.2014.07.009
Lei L et al (2014) The jiaoyao1 mutant is an allele of korrigan that affects the organization of both cellulose microfibrils and microtubules in Arabidopsis. Plant Cell 26:2601–2616. doi:10.1105/tpc.114.126193
Li SD, Lei L, Somerville CR, Gu Y (2012) Cellulose synthase interactive protein 1 (CSI1) links microtubules and cellulose synthase complexes. Proc Natl Acad Sci USA 109:185–190. doi:10.1073/pnas.1118560109
Lindorff-Larsen K, Maragakis P, Piana S, Eastwood M, Dror R, Shaw D (2012) Systematic validation of protein force fields against experimental data. PLoS ONE 7:e32131. doi:10.1371/journal.pone.0032131
Lloyd SP (1982) Least squares quantization in PCM. IEEE Trans Inf Theory 28:128–137. doi:10.1109/TIT.1982.1056489
McFarlane HE, Döring A, Persson S (2014) The cell biology of cellulose synthesis. Annu Rev Plant Biol 65:69–94. doi:10.1146/annurev-arplant-050213-040240
Molloy K, Saleh S, Shehu A (2013) Probabilistic search and energy guidance for biased decoy sampling in ab initio protein structure prediction. IEEE/ACM Trans Comput Biol Bioinf 10:1162–1167. doi:10.1109/TCBB.2013.29
Morgan J, Strumillo J, Zimmer J (2013) Crystallographic snapshot of cellulose synthesis and membrane translocation. Nature 493:181–186. doi:10.1038/nature11744
Morgan JL, McNamara JT, Zimmer J (2014) Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP. Nat Struct Mol Biol 21:489–496. doi:10.1038/nsmb.2803
Mueller SC, Brown RM (1980) Evidence for an intramembrane component associated with a cellulose microfibril-synthesizing complex in higher plants. J Cell Biol 84:315–326. doi:10.1083/jcb.84.2.315
Omadjela O, Narahari A, Strumillo J, Mélida H, Mazur O, Bulone V, Zimmer J (2013) BcsA and BcsB form the catalytically active core of bacterial cellulose synthase sufficient for in vitro cellulose synthesis. Proc Natl Acad Sci USA 110:17856–17861. doi:10.1073/pnas.1314063110
Pear JR, Kawagoe Y, Schreckengost WE, Delmer DP, Stalker DM (1996) Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Proc Natl Acad Sci USA 93:12637–12642. doi:10.1073/pnas.93.22.12637
Pei J, Grishin NV (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17:700–712. doi:10.1093/bioinformatics/17.8.700
Persson S, Paredez A, Carroll A, Palsdottir H, Doblin M, Poindexter P, Khitrov N, Auer M, Somerville CR (2007) Genetic evidence for three unique components in primary cell-wall cellulose synthase complexes in Arabidopsis. Proc Natl Acad Sci USA 104:15566–15571. doi:10.1073/pnas.0706592104
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612. doi:10.1002/jcc.20084
Pierce B, Wiehe K, Hwang H, Kim B, Vreven T, Weng Z (2014) ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers. Bioinformatics 30:1771–1773. doi:10.1093/bioinformatics/btu097
Pysh L, Alexander N, Swatzyna L, Harbert R (2012) Four alleles of AtCESA3 form an allelic series with respect to root phenotype in Arabidopsis thaliana. Physiol Plant 144:369–381. doi:10.1111/j.1399-3054.2012.01575.x
Ramakrishnan C, Dani VS, Ramasarma T (2002) A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins. Protein Eng 15:783–798. doi:10.1093/protein/15.10.783
Rees DC, Johnson E, Lewinson O (2009) ABC transporters: the power to change. Nat Rev Mol Cell Biol 10:218–227. doi:10.1038/nrm2646
Roberts EM, Roberts AW (2009) A cellulose synthase (Cesa) gene from the red alga Porphyra yezoensis (rhodophyta). J Phycol 45:203–212. doi:10.1111/j.1529-8817.2008.00626.x
Scheible WR, Eshed R, Richmond T, Delmer D, Somerville C (2001) Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in Arabidopsis Ixr1 mutants. Proc Natl Acad Sci USA 98:10079–10084. doi:10.1073/pnas.191361598
Sethaphong L, Haigler CH, Kubicki JD, Zimmer J, Bonetta D, DeBolt S, Yingling YG (2013) Tertiary model of a plant cellulose synthase. Proc Natl Acad Sci USA 110:7512–7517. doi:10.1073/pnas.1301027110
Sheinerman FB, Norel R, Honig B (2000) Electrostatic aspects of protein–protein interactions. Curr Opin Struct Biol 10:153–159. doi:10.1016/S0959-440X(00)00065-8
Shortle D, Simons KT, Baker D (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 95:11158–11162. doi:10.1073/pnas.95.19.11158
Slabaugh E, Davis JK, Haigler CH, Yingling YG, Zimmer J (2014a) Cellulose synthases: new insights from crystallography and modeling. Trends Plant Sci 19:99–106. doi:10.1016/j.tplants.2013.09.009
Slabaugh E, Sethaphong L, Xiao C, Amick J, Anderson CT, Haigler CH, Yingling YG (2014b) Computational and genetic evidence that different structural conformations of a non-catalytic region affect the function of plant cellulose synthase. J Exp Bot 65:6645–6653. doi:10.1093/jxb/eru383
Somerville CR (2006) Cellulose synthesis in higher plants. Annu Rev Cell Dev Biol 22:53–78. doi:10.1146/annurev.cellbio.22.022206.160206
Steinbrecher T, Latzer J, Case DA (2012) Revised AMBER parameters for bioorganic phosphates. J Chem Theory Comput 8:4405–4412. doi:10.1021/ct300613v
Taylor SS, Kornev AP (2011) Protein kinases: evolution of dynamic regulatory proteins. Trends Biochem Sci 36:65–77. doi:10.1016/j.tibs.2010.09.006
Thomas LH, Forsyth VT, Šturcová A, Kennedy CJ, May RP, Altaner CM, Apperley DC, Wess TJ, Jarvis MC (2013) Structure of cellulose microfibrils in primary cell walls from collenchyma. Plant Physiol 161:465–476. doi:10.1104/pp.112.206359
Tsekos I (1999) The sites of cellulose synthesis in algae: diversity and evolution of cellulose-synthesizing enzyme complexes. J Phycol 35:635–655. doi:10.1046/j.1529-8817.1999.3540635.x
Vain T et al (2014) The cellulase KORRIGAN is part of the cellulose synthase complex. Plant Physiol 165:1521–1532. doi:10.1104/pp.114.241216
Vergara CE, Carpita NC (2001) β-d-glycan synthases and the CesA gene family: lessons to be learned from the mixed-linkage (1 → 3), (1 → 4)β-d-glucan synthase. Plant Mol Biol 47:145–160. doi:10.1023/A:1010631431620
Wang J, Howles PA, Cork AH, Birch RJ, Williamson RE (2006) Chimeric proteins suggest that the catalytic and/or C-terminal domains give CesA1 and CesA3 access to their specific sites in the cellulose synthase of primary walls. Plant Physiol 142:685–695. doi:10.1104/pp.106.084004
Whittinghofer A, Vetter IR (2011) Structure-function relationships of the G domain, a canonical switch motif. Annu Rev Biochem 80:943–971. doi:10.1146/annurev-biochem-062708-134043
Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–W410. doi:10.1093/nar/gkm290
Williamson RE, Burn JE, Birch R, Baskin TI, Arioli T, Betzner AS, Cork A (2001) Morphology of rsw1, a cellulose-deficient mutant of Arabidopsis thaliana. Protoplasma 215:116–127. doi:10.1007/BF01280308
Woods AS, Ferre S (2005) Amazing stability of the arginine-phosphate electrostatic interaction. J Proteome Res 4:1397–1402. doi:10.1021/pr050077s
Zhong RQ, Morrison WH, Freshour GD, Hahn MG, Ye ZH (2003) Expression of a mutant form of cellulose synthase AtCesA7 causes dominant negative effect on cellulose biosynthesis. Plant Physiol 132:786–795. doi:10.1104/pp.102.019331
Zhou Z (2012) Ensemble methods: foundations and algorithms. Machine learning and pattern recognition. Chapman & Hall/CRC Press, New York
Acknowledgments
The authors thank Carmen Wilson for her assistance in the generation, propagation, and phenotyping of stable Arabidopsis transformants used in this study.
Funding
This work was supported as part of The Center for LignoCellulose Structure and Formation, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Basic Energy Sciences (Award Number DE-SC0001090).
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Sethaphong, L., Davis, J.K., Slabaugh, E. et al. Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis. Cellulose 23, 145–161 (2016). https://doi.org/10.1007/s10570-015-0789-6
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DOI: https://doi.org/10.1007/s10570-015-0789-6