Ecology; Biological Evolution; Genetics; Human Development; Molecular Biology; Developmental Biology; Arabidopsis
Yale Combined Program in the Biological and Biomedical Sciences (BBS): Plant Molecular Biology
Our lab is interested in pattern formation during plant development. The Arabidopsis petal is an ideal system for these studies, since it is dispensable for growth and reproduction, has a simple laminar structure, and is composed of only a few cell types. Using forward and reverse genetic approaches, as well as biochemical and genomic strategies, we are characterizing the transcriptional networks responsible for different aspects of petal development. We have also examined how cell-cell interactions regulate petal patterning. In order to understand how the developmental mechanisms responsible for floral patterning have evolved to give rise to the diversity of floral forms that we see today, we are characterizing these pathways in several other species. Using these approaches, we hope to elucidate how dividing cells acquire information about their position and differentiate accordingly, as well as how these processes have been modulated through evolution.
Specialized Terms: developmental genetics; Arabidopsis; evolution of development
Extensive Research Description
The Irish lab is interested in understanding plant growth and development. Our current research efforts are described below.
Stem cell proliferation and arrest in Citrus
In plants, cells of the shoot apical meristem (SAM) act as stem cells, giving rise to more stem cells as well as specialized cell types contributing to the leaves, branches and fruit. We are investigating the basis for thorn development in Citrus as a means to understand how the termination of stem cell proliferation is controlled. Thorns arise from SAM cells that fail to self-renew, and instead terminally differentiate, providing a unique opportunity to explore how SAM cell proliferation is controlled. We are using a combination of transcriptomics, molecular genetics and newly developed transgenic approaches to identify the genes and processes responsible for thorn development and how this unusual stem cell arrest process is controlled. Citrus plant growth, fruit yield and harvest costs are all affected by thorniness, and so understanding how to manipulate thorn production will also greatly impact the economics of this valuable fruit crop.
Control of petal organogenesis
Organ formation, whether in animals or plants, depends on several processes. These include delimitation of where an organ will form, growth of the organ, and its consequent differentiation. Using the Arabidopsis petal as a model organ system, we are investigating the genes and cellular processes that contribute to the development of this seemingly simple organ type. We are examining how a transcriptional repressor, RBE, coordinately regulates both organ boundary formation and organ growth. We have shown that RBE acts early in petal development to control the formation of organ boundaries, and recent results suggest that RBE also regulates a transcriptional cascade of events that act as a timing mechanism to control organ growth. We are currently investigating the cellular basis for growth control in petals, and how transcriptional changes are manifested as changes in cell proliferation.
Control of petal cell type differentiation
Petal conical epidermal cells are covered in radiate nanoridges that give these cells unique physical properties. The nanoridges are vital for pollinator attraction, iridescence, wettability, and can provide tactile cues. However, the molecular, cellular, and mechanical bases for how this unusual cell type is formed and functions is not well understood. We are using a combination of biochemical, molecular genetic, and modeling approaches to develop a mechanistic understanding of how conical epidermal cell morphology is achieved.
Gene networks controlling petal organogenesis
Huang T, Irish VF. 2015. Gene networks controlling petal organogenesis. J. Exp Bot. in press
Temporal Control of Plant Organ Growth by TCP Transcription Factors.
Huang T, Irish VF. 2015. Temporal Control of Plant Organ Growth by TCP Transcription Factors. Current Biology. 13:1765-1770
Natural variation identifies multiple loci controlling petal shape and size in Arabidopsis thaliana.
Abraham MC, Metheetrairut C, Irish VF. 2013. Natural variation identifies multiple loci controlling petal shape and size in Arabidopsis thaliana. PLoS One. 8:e56743
RBE controls microRNA164 expression to effect floral organogenesis.
Huang T, López-Giráldez F, Townsend JP, Irish VF. 2012. RBE controls microRNA164 expression to effect floral organogenesis. Development. 139:2161-9.
The flowering of Arabidopsis flower development
Irish VF. 2010. The flowering of Arabidopsis flower development. Plant Journal 61: 1014-1028
The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling
Mara CD, Huang T, Irish VF. 2010. The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling. The Plant Cell 22: 690-702.
An Arabidopsis F-box protein acts as a transcriptional cofactor to regulate floral development
Chae E, Tan Q. K-G, Hill TA, Irish VF. 2008. An Arabidopsis F-box protein acts as a transcriptional cofactor to regulate floral development. Development 135: 1235-1245
- DeMartino G, Pan I, Emmanuel E, Levy AA, Irish VF. 2006. Functional analyses of two tomato APETALA3 genes demonstrate diversification in their roles in regulating flowering. The Plant Cell 18: 1833-1845.
Functional divergence within the APETALA3/ PISTILLATA floral homeotic gene lineages.
Lamb RS. Irish VF. 2003. Functional divergence within the APETALA3/ PISTILLATA floral homeotic gene lineages. Proc. Nat. Acad. Sci. 100: 6558-6563.
Evolution of genetic mechanisms controlling petal development.
Kramer, E.M. and V.F. Irish. 1999. Evolution of genetic mechanisms controlling petal development. Nature, 399: 144-148.
Full List of PubMed Publications
- Saffer AM, Irish VF: Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux. Plant J. 2018 Mar 5; 2018 Mar 5. PMID: 29505161
- Jin D, Wu M, Li B, Bücker B, Keil P, Zhang S, Li J, Kang D, Liu J, Dong J, Deng XW, Irish V, Wei N: The COP9 Signalosome regulates seed germination by facilitating protein degradation of RGL2 and ABI5. PLoS Genet. 2018 Feb; 2018 Feb 20. PMID: 29462139
- LeBlanc C, Zhang F, Mendez J, Lozano Y, Chatpar K, Irish VF, Jacob Y: Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress. Plant J. 2018 Jan; 2017 Dec 22. PMID: 29161464
- Zhang F, LeBlanc C, Irish VF, Jacob Y: Rapid and efficient CRISPR/Cas9 gene editing in Citrus using the YAO promoter. Plant Cell Rep. 2017 Dec; 2017 Sep 1. PMID: 28864834
- Saffer AM, Irish VF: Isolation of mutants with abnormal petal epidermal cell morphology. Plant Signal Behav. 2017 Nov 2; 2017 Oct 26. PMID: 29072548
- Zhang F, May A, Irish VF: Type-B ARABIDOPSIS RESPONSE REGULATORs Directly Activate WUSCHEL. Trends Plant Sci. 2017 Oct; 2017 Sep 5. PMID: 28886911
- Irish V: The ABC model of floral development. Curr Biol. 2017 Sep 11. PMID: 28898659
- Saffer AM, Carpita NC, Irish VF: Rhamnose-Containing Cell Wall Polymers Suppress Helical Plant Growth Independently of Microtubule Orientation. Curr Biol. 2017 Aug 7; 2017 Jul 20. PMID: 28736166
- Reimegård J, Kundu S, Pendle A, Irish VF, Shaw P, Nakayama N, Sundström JF, Emanuelsson O: Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. Nucleic Acids Res. 2017 Apr 7. PMID: 28175342
- Li J, Wang Y, Zhang Y, Wang W, Irish VF, Huang T: RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis. J Exp Bot. 2016 Dec; 2016 Nov 12. PMID: 27838638
- Chitwood DH, Irish VF: A renaissance in plant development. Dev Biol. 2016 Nov 1; 2016 Sep 13. PMID: 27637462
- Huang T, Irish VF: Gene networks controlling petal organogenesis. J Exp Bot. 2016 Jan; 2015 Oct 1. PMID: 26428062
- Huang T, Irish VF: Temporal Control of Plant Organ Growth by TCP Transcription Factors. Curr Biol. 2015 Jun 29; 2015 Jun 11. PMID: 26073137
- Abraham MC, Metheetrairut C, Irish VF: Natural variation identifies multiple loci controlling petal shape and size in Arabidopsis thaliana. PLoS One. 2013; 2013 Feb 13. PMID: 23418598
- Huang T, López-Giráldez F, Townsend JP, Irish VF: RBE controls microRNA164 expression to effect floral organogenesis. Development. 2012 Jun; 2012 May 9. PMID: 22573623
- Lee HL, Irish VF: Gene duplication and loss in a MADS box gene transcription factor circuit. Mol Biol Evol. 2011 Dec; 2011 Jun 28. PMID: 21712469
- Geuten K, Irish V: Hidden variability of floral homeotic B genes in Solanaceae provides a molecular basis for the evolution of novel functions. Plant Cell. 2010 Aug; 2010 Aug 31. PMID: 20807882
- Pan IL, McQuinn R, Giovannoni JJ, Irish VF: Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development. J Exp Bot. 2010 Jun; 2010 Mar 24. PMID: 20335407
- Mara CD, Huang T, Irish VF: The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling. Plant Cell. 2010 Mar; 2010 Mar 19. PMID: 20305124
- Irish VF: The flowering of Arabidopsis flower development. Plant J. 2010 Mar. PMID: 20409275
- Irish VF: Evolution of petal identity. J Exp Bot. 2009; 2009 May 14. PMID: 19443615
- Irish VF: The Arabidopsis petal: a model for plant organogenesis. Trends Plant Sci. 2008 Aug; 2008 Jul 5. PMID: 18603466
- Mara CD, Irish VF: Two GATA transcription factors are downstream effectors of floral homeotic gene action in Arabidopsis. Plant Physiol. 2008 Jun; 2008 Apr 16. PMID: 18417639
- Chae E, Tan QK, Hill TA, Irish VF: An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development. Development. 2008 Apr; 2008 Feb 20. PMID: 18287201
- Drea S, Hileman LC, de Martino G, Irish VF: Functional analyses of genetic pathways controlling petal specification in poppy. Development. 2007 Dec; 2007 Oct 24. PMID: 17959716
- Hileman LC, Sundstrom JF, Litt A, Chen M, Shumba T, Irish VF: Molecular and phylogenetic analyses of the MADS-box gene family in tomato. Mol Biol Evol. 2006 Nov; 2006 Aug 22. PMID: 16926244
- de Martino G, Pan I, Emmanuel E, Levy A, Irish VF: Functional analyses of two tomato APETALA3 genes demonstrate diversification in their roles in regulating floral development. Plant Cell. 2006 Aug; 2006 Jul 14. PMID: 16844904
- Sundström JF, Nakayama N, Glimelius K, Irish VF: Direct regulation of the floral homeotic APETALA1 gene by APETALA3 and PISTILLATA in Arabidopsis. Plant J. 2006 May. PMID: 16640596
- Tan QK, Irish VF: The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development. Plant Physiol. 2006 Mar; 2006 Jan 20. PMID: 16428600
- Hileman LC, Drea S, Martino G, Litt A, Irish VF: Virus-induced gene silencing is an effective tool for assaying gene function in the basal eudicot species Papaver somniferum (opium poppy). Plant J. 2005 Oct. PMID: 16212610
- Nakayama N, Arroyo JM, Simorowski J, May B, Martienssen R, Irish VF: Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens. Plant Cell. 2005 Sep; 2005 Jul 29. PMID: 16055634
- Irish VF, Litt A: Flower development and evolution: gene duplication, diversification and redeployment. Curr Opin Genet Dev. 2005 Aug. PMID: 15964755
- Irish VF, Day CD: A weed for all reasons. Genome Biol. 2005; 2005 Sep 28. PMID: 16207368
- Irish VF, Benfey PN: Beyond Arabidopsis. Translational biology meets evolutionary developmental biology. Plant Physiol. 2004 Jun. PMID: 15208409
- Liu Y, Nakayama N, Schiff M, Litt A, Irish VF, Dinesh-Kumar SP: Virus induced gene silencing of a DEFICIENS ortholog in Nicotiana benthamiana. Plant Mol Biol. 2004 Mar. PMID: 15356389
- Litt A, Irish VF: Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development. Genetics. 2003 Oct. PMID: 14573491
- Irish VF: The evolution of floral homeotic gene function. Bioessays. 2003 Jul. PMID: 12815719
- Lamb RS, Irish VF: Functional divergence within the APETALA3/PISTILLATA floral homeotic gene lineages. Proc Natl Acad Sci U S A. 2003 May 27; 2003 May 13. PMID: 12746493
- Wang X, Feng S, Nakayama N, Crosby WL, Irish V, Deng XW, Wei N: The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development. Plant Cell. 2003 May. PMID: 12724534
- Zik M, Irish VF: Flower development: initiation, differentiation, and diversification. Annu Rev Cell Dev Biol. 2003. PMID: 14570566
- Zik M, Irish VF: Global identification of target genes regulated by APETALA3 and PISTILLATA floral homeotic gene action. Plant Cell. 2003 Jan. PMID: 12509532
- Lamb RS, Hill TA, Tan QK, Irish VF: Regulation of APETALA3 floral homeotic gene expression by meristem identity genes. Development. 2002 May. PMID: 11959818