Steve van Nocker

Steve van Nocker

vannocke@msu.edu
Cellphone: (517) 775-5218

Department of Horticulture

Professor

1066 Bogue St, Room A390-C
East Lansing, MI 48824

Plant developmental genetics

Area of Expertise:

Developmental genetics of plants, traits important for production including flowering, chromatin regulation of gene expression


Plant Developmental Genetics

What are the underlying genetic mechanisms that determine plant form, and how are these controlled? What are the key genes that influence agriculturally important traits such as flowering?  What parallels exist between plant and human development, and can studies in plants shed light on issues such as cancer and stem cell biology?

Current Projects

Transcriptional mechanisms driving development of multicellular organisms. As an organism develops, cells may proliferate to maintain a pool of stem cells, or differentiate to form specialized tissues. We are studying the mechanisms by which states of gene activity are propagated within and across mitotic boundaries, specifically in relation to chromatin-associated proteins and modifications of DNA and histones at specific genetic sites. In Arabidopsis, we identified a class of protein required for maintaining transcriptional activity of a subset of developmental regulatory genes by counteracting the repressive activity of the so-called Polycomb-group proteins.

Identity and function of genes influencing juvenility and flowering in apple. The transition from vegetative growth to flowering is a developmentally regulated process that is crucial for production of most horticultural crops. The molecular-genetic pathways of flowering have been extensively studied only in herbaceous model plants. We are developing the domestic apple, Malus x. domestica, as a reference for understanding the genetic and molecular control of flowering in woody perennials. This includes identifying important genes and processes associated with the switch from juvenile to adult phase, the seasonal timing of flowering, and repression of flowering by fruit and endogenous hormones including gibberellins.

Education

Ph.D., Cell and Molecular Biology, University of Wisconsin

B.S. Genetics, Cornell University

Teaching

HRT860 Scientific Writing: Workshop
This small-group workshop will train graduate students in scientific writing through reading and analysis of representative publications from a variety of general and plant-related journals. Optionally, students writing a paper, thesis or grant proposal may bring copies and distribute these to other students in the group. The writing will be discussed and suggestions for improvement will be made collectively by instructor and class members.

HRT/PLB865 Plant Growth and Development (co-instructed with Dr. Jianping Hu, Plant Biology
This course focuses on the genetic, molecular and biochemical mechanisms influencing development in higher plants, including the patterning, cellular organization, formation of tissues and organs, mechanisms underlying developmental diversity, and biosynthesis, regulation and activity of phytohormones. To be offered next in Fall 2020!

Publications

An apple (Malus domestica) NAC transcription factor enhances drought tolerance in transgenic apple plants.
Jia D, Jiang Q, van Nocker S, Gong X, Ma F.
Plant Physiol Biochem. 2019 Jun;139:504-512. doi: 10.1016/j.plaphy.2019.04.011. Epub 2019 Apr PMID: 31015089

Apple whole genome sequences: recent advances and new prospects.
Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S.
Hortic Res. 2019 Apr 5;6:59. doi: 10.1038/s41438-019-0141-7. eCollection 2019. Review. PMID: 30962944

Overexpression of the RNA binding protein MhYTP1 in transgenic apple enhances drought tolerance and WUE by improving ABA level under drought condition.
Guo T, Wang N, Xue Y, Guan Q, van Nocker S, Liu C, Ma F.
Plant Sci. 2019 Mar;280:397-407. doi: 10.1016/j.plantsci.2018.11.018. Epub 2018 Nov PMID: 30824018

Overexpression of a protein kinase gene MpSnRK2.10 from Malus prunifolia confers tolerance to drought stress in transgenic Arabidopsis thaliana and apple.
Shao Y, Zhang X, van Nocker S, Gong X, Ma F.
Gene. 2019 Apr 15;692:26-34. doi: 10.1016/j.gene.2018.12.070. Epub 2019 Jan PMID: 30641216

Hybrids without hybridization-can it revolutionize horticulture?
van Nocker S.
Hortic Res. 2018 Dec 21;5:76. doi: 10.1038/s41438-018-0113-3. eCollection 2018. PMID: 30588321

Comprehensive genomic analysis of the TYROSINE AMINOTRANSFERASE (TAT) genes in apple (Malus domestica) allows the identification of MdTAT2 conferring tolerance to drought and osmotic stresses in plants.
Wang H, Dong Q, Duan D, Zhao S, Li M, van Nocker S, Ma F, Mao K.
Plant Physiol Biochem. 2018 Dec;133:81-91. doi: 10.1016/j.plaphy.2018.10.033. Epub 2018 Oct PMID: 30391815

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system.
Pratas MI, Aguiar B, Vieira J, Nunes V, Teixeira V, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP.
Sci Rep. 2018 Jan 29;8(1):1717. doi: 10.1038/s41598-018-19820- PMID: 29379047

An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple.
Xie Y, Chen P, Yan Y, Bao C, Li X, Wang L, Shen X, Li H, Liu X, Niu C, Zhu C, Fang N, Shao Y, Zhao T, Yu J, Zhu J, Xu L, van Nocker S, Ma F, Guan Q.
New Phytol. 2018 Apr;218(1):201-218. doi: 10.1111/nph.14952. Epub 2017 Dec PMID: 29266327

Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes.
Li Y, Zhu Y, Yao J, Zhang S, Wang L, Guo C, van Nocker S, Wang X.
Sci Rep. 2017 Oct 3;7(1):12638. doi: 10.1038/s41598-017-12988-y. Erratum in: Sci Rep. 2017 Nov 17;7(1): PMID: 28974771

Expression of the Grape VaSTS19 Gene in Arabidopsis Improves Resistance to Powdery Mildew and Botrytis cinerea but Increases Susceptibility to Pseudomonas syringe pv Tomato DC
Wang Y, Wang D, Wang F, Huang L, Tian X, van Nocker S, Gao H, Wang X.
Int J Mol Sci. 2017 Sep 17;18(9). pii: E2000. doi: 10.3390/ijms PMID: 28926983

Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple.
Xu J, Zhou S, Gong X, Song Y, van Nocker S, Ma F, Guan Q.
Plant Biotechnol J. 2018 Feb;16(2):672-687. doi: 10.1111/pbi.12820. Epub 2017 Sep PMID: 28796917

Identification and expression analysis of the apple (Malus × domestica) basic helix-loop-helix transcription factor family.
Yang J, Gao M, Huang L, Wang Y, van Nocker S, Wan R, Guo C, Wang X, Gao H.
Sci Rep. 2017 Feb 9;7(1):28. doi: 10.1038/s41598-017-00040-y. PMID: 28174429

Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica).
Li X, Kui L, Zhang J, Xie Y, Wang L, Yan Y, Wang N, Xu J, Li C, Wang W, van Nocker S, Dong Y, Ma F, Guan Q.
Gigascience. 2016 Aug 8;5(1):35. doi: 10.1186/s13742-016-0139- PMID: 27503335

In silico analysis of histone H3 gene expression during human brain development.
Ren M, van Nocker S.
Int J Dev Biol. 2016;60(4-6):167-73. doi: 10.1387/ijdb.150334sv. PMID: 27251074

Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus.
Aguiar B, Vieira J, Cunha AE, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP.
PLoS One. 2015 May 19;10(5):e0126138. doi: 10.1371/journal.pone.0126138. eCollection PMID: 25993016

Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops.
van Nocker S, Gardiner SE.
Hortic Res. 2014 May 14;1:14022. doi: 10.1038/hortres.2014.22. eCollection 2014. Review. PMID: 26504538

Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes.
Alkio M, Jonas U, Declercq M, Van Nocker S, Knoche M.
Hortic Res. 2014 Mar 12;1:11. doi: 10.1038/hortres.2014.11. eCollection PMID: 26504533

Diversity in seasonal bloom time and floral development among apple (Malus) species and hybrids.
Gottschalk C, van Nocker S.
J Amer Soc Hort Sci. 2013. 138:367-374

Genetic diversity of red-fleshed apples (Malus).
van Nocker S, Berry G, Najdowski J, Michelutti R, Luffman M, Forsline P, ALsmairat N, Beadry R, Nair MG and Ordidge M.
Euphytica. 2012. 185:281-293.

Genomic and gene-level distribution of histone H3 dimethyl lysine-27 (H3K27me2) in Arabidopsis.
Park S, Oh S, van Nocker S.
PLoS One. 2012;7(12):e52855. doi: 10.1371/journal.pone.0052855. Epub 2012 Dec PMID: 23285203

Identification of putative candidate genes involved in cuticle formation in Prunus avium (sweet cherry) fruit.
Alkio M, Jonas U, Sprink T, van Nocker S, Knoche M.
Ann Bot. 2012 Jul;110(1):101-12. doi: 10.1093/aob/mcs087. Epub 2012 May PMID: 22610921

Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the polymerase associated factor 1 complex in seed dormancy.
Liu Y, Geyer R, van Zanten M, Carles A, Li Y, Hörold A, van Nocker S, Soppe WJ.
PLoS One. 2011;6(7):e22241. doi: 10.1371/journal.pone.0022241. Epub 2011 Jul PMID: 21799800

Potential role of Arabidopsis PHP as an accessory subunit of the PAF1 transcriptional cofactor.
Park S, Ek-Ramos MJ, Oh S, van Nocker S.
Plant Signal Behav. 2011 Aug;6(8):1094-6. doi: 10.4161/psb.6.8.16364. Epub 2011 Aug PMID: 21720211

Analysis of promoter activity of members of the PECTATE LYASE-LIKE (PLL) gene family in cell separation in Arabidopsis.
Sun L, van Nocker S.
BMC Plant Biol. 2010 Jul 22;10:152. doi: 10.1186/1471-2229-10- PMID: 20649977

PLANT HOMOLOGOUS TO PARAFIBROMIN is a component of the PAF1 complex and assists in regulating expression of genes within H3K27ME3-enriched chromatin.
Park S, Oh S, Ek-Ramos J, van Nocker S.
Plant Physiol. 2010 Jun;153(2):821-31. doi: 10.1104/pp.110.155838. Epub 2010 Apr PMID: 20363855

Genetics of flowering in apple.
Mookerjee S and van Nocker S.
In Genomics of fruits and vegetable crops: Apples. 2010. Ed. Aldwinckle HS and Malnoy M. Science Publishers, Enfield NH.

Development of the abscission zone.
van Nocker S.
Stewart Postharvest Reviews. 2009. 5:1-5

Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis.
Oh S, Park S, van Nocker S.
PLoS Genet. 2008 Aug 22;4(8):e1000077. doi: 10.1371/journal.pgen. PMID: 18725930

Cultivars of apple fruits that are not marketed with potential for anthocyanin production.
Mulabagal V, Van Nocker S, Dewitt DL, Nair MG.
J Agric Food Chem. 2007 Oct 3;55(20):8165-9. Epub 2007 Sep PMID: 17822290

Control of flowering time.
van Nocker S, Ek-Ramos J.
In Regulation of transcription in plants. 2007. Grasser KD Ed. Plant Reviews (Blackwell Publishing, Ltd.)

Identification of genes with potential roles in apple fruit development and biochemistry through large-scale statistical analysis of expressed sequence tags.
Park S, Sugimoto N, Larson MD, Beaudry R, van Nocker S.
Plant Physiol. 2006 Jul;141(3):811- PMID: 16825339

A mechanism related to the yeast transcriptional regulator Paf1c is required for expression of the Arabidopsis FLC/MAF MADS box gene family.
Oh S, Zhang H, Ludwig P, van Nocker S.
Plant Cell. 2004 Nov;16(11):2940-53. Epub 2004 Oct PMID: 15472079

The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function.
van Nocker S, Ludwig P.
BMC Genomics. 2003 Dec 12;4(1): PMID: 14672542

CAF-1 and MSI1-related proteins: linking nucleosome assembly with epigenetics.
van Nocker S.
Trends Plant Sci. 2003 Oct;8(10):471-3. Review. No abstract available. PMID: 14557043

Genetic analysis of early flowering mutants in Arabidopsis defines a class of pleiotropic developmental regulator required for expression of the flowering-time switch flowering locus C.
Zhang H, Ransom C, Ludwig P, van Nocker S.
Genetics. 2003 May;164(1):347- PMID: 12750345

Fruit ripening in sour cherry (P. cerasus L.): Changes in expression of genes encoding expansins and other cell-wall-modifying enzymes.
Yoo SD, Gao Z, Cantini C, Loescher WH and van Nocker S.
J Amer Soc Hort Sci 2003. 128, 16-22.

Cloning, expression, and characterization of sorbitol transporters from developing sour cherry fruit and leaf sink tissues.
Gao Z, Maurousset L, Lemoine R, Yoo SD, van Nocker S, Loescher W.
Plant Physiol. 2003 Apr;131(4):1566- PMID: 12692316

The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C.
Zhang H, van Nocker S.
Plant J. 2002 Sep;31(5):663- PMID: 12207655 Free Article

Cold signalling associated with vernalization in Arabidopsis thaliana does not involve CBF1 or abscisic acid.
Liu J, Gilmour SJ, Thomashow MF, Van Nocker S.
Physiol Plant. 2002 Jan;114(1):125- PMID: 11982943

Structure and functional analysis of the 26S proteasome subunits from plants.
Fu H, Girod PA, Doelling JH, van Nocker S, Hochstrasser M, Finley D, Vierstra RD.
Mol Biol Rep. 1999 Apr;26(1-2):137-46. Review. PMID: 10363660

Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb
Fu H, Sadis S, Rubin DM, Glickman M, van Nocker S, Finley D, Vierstra RD.
J Biol Chem. 1998 Jan 23;273(4):1970- PMID: 9442033 Free Article

ATPase and ubiquitin-binding proteins of the yeast proteasome.
Rubin DM, van Nocker S, Glickman M, Coux O, Wefes I, Sadis S, Fu H, Goldberg A, Vierstra R, Finley D.
Mol Biol Rep. 1997 Mar;24(1-2):17- PMID: 9228276

The multiubiquitin-chain-binding protein Mcb1 is a component of the 26S proteasome in Saccharomyces cerevisiae and plays a nonessential, substrate-specific role in protein turnover.
van Nocker S, Sadis S, Rubin DM, Glickman M, Fu H, Coux O, Wefes I, Finley D, Vierstra RD.
Mol Cell Biol. 1996 Nov;16(11):6020- PMID: 8887631

The Arabidopsis thaliana UBC7/13/14 genes encode a family of multiubiquitin chain-forming E2 enzymes.
van Nocker S, Walker JM, Vierstra RD.
J Biol Chem. 1996 May 24;271(21):12150- PMID: 8647807 Free Article

Molecular cloning and expression of a multiubiquitin chain binding subunit of the human 26S protease.
Ferrell K, Deveraux Q, van Nocker S, Rechsteiner M.
FEBS Lett. 1996 Feb 26;381(1-2):143- PMID: 8641424 Free Article

Arabidopsis MBP1 gene encodes a conserved ubiquitin recognition component of the 26S proteasome.
van Nocker S, Deveraux Q, Rechsteiner M, Vierstra RD.
Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):856- PMID: 8570648

Inhibition of ubiquitin-mediated proteolysis by the Arabidopsis 26 S protease subunit S5a.
Deveraux Q, van Nocker S, Mahaffey D, Vierstra R, Rechsteiner M.
J Biol Chem. 1995 Dec 15;270(50):29660- PMID: 8530351 Free Article

Multiubiquitin chains linked through lysine 48 are abundant in vivo and are competent intermediates in the ubiquitin proteolytic pathway.
van Nocker S, Vierstra RD.
J Biol Chem. 1993 Nov 25;268(33):24766- PMID: 8227036 Free Article

Homologs of the essential ubiquitin conjugating enzymes UBC1, 4, and 5 in yeast are encoded by a multigene family in Arabidopsis thaliana.
Girod PA, Carpenter TB, van Nocker S, Sullivan ML, Vierstra RD.
Plant J. 1993 Apr;3(4):545- PMID: 8220461 Free Article

Two cDNAs from Arabidopsis thaliana encode putative RNA binding proteins containing glycine-rich domains.
van Nocker S, Vierstra RD.
Plant Mol Biol. 1993 Feb;21(4):695- PMID: 8448367

Cloning and characterization of a 20-kDa ubiquitin carrier protein from wheat that catalyzes multiubiquitin chain formation in vitro.
Van Nocker S, Vierstra RD.
Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10297- PMID: 1658801
Similar articles

 

Michigan State University Michigan State University Close Menu button Menu and Search button Open Close