Robert Franks - Academia.edu (original) (raw)

Papers by Robert Franks

13 14 • Divergence of developmental mechanisms within populations may lead to hybrid 15 developme... more 13 14 • Divergence of developmental mechanisms within populations may lead to hybrid 15 developmental failure, and may be a factor driving speciation in angiosperms. 16 • We investigate patterns of endosperm and embryo development in Mimulus guttatus and the 17 closely related, serpentine endemic M. nudatus, and compare them to those of reciprocal 18 hybrid seed. We address whether disruption in hybrid seed development is the primary 19 source of reproductive isolation between these sympatric taxa. 20 • M. guttatus and M. nudatus differ in the pattern and timing of endosperm and embryo 21 development. Some hybrid seed exhibit early disruption of endosperm development and are 22 completely inviable, while others develop relatively normally at first, but later exhibit 23 impaired endosperm proliferation and low germination success. These developmental 24 patterns are reflected in mature hybrid seed, which are either small and flat (indicating little 25 to no endosperm), or shriveled (...

Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in ... more Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in Arabidopsis thaliana

Wiley interdisciplinary reviews. Developmental biology

The gynoecium is the female reproductive structure of flowering plants, and is the site of ovule ... more The gynoecium is the female reproductive structure of flowering plants, and is the site of ovule and seed development. The gynoecium is critical for reproductive competence and for agricultural productivity in many crop plants. In this review we focus on molecular aspects of the development of the Arabidopsis thaliana gynoecium. We briefly introduce gynoecium structure and development and then focus on important research advances published within the last year. We highlight what has been learned recently with respect to: (1) the role of auxin in the differential development of the medial and lateral domains of the Arabidopsis gynoecium; (2) the interaction between cytokinin and auxin during gynoecial development; (3) the role of auxin in the termination of the floral meristem and in the transition of floral meristem to gynoecium; and (4) recent studies that suggest a degree of evolutionary conservation of auxin mechanisms during gynoecial development in other eudicots.

Methods in molecular biology (Clifton, N.J.), 2016

The use of chloral hydrate optical clearing paired with differential interference contrast micros... more The use of chloral hydrate optical clearing paired with differential interference contrast microscopy allows the analysis of internal structures of developing plant organs without the need for paraffin embedding and sectioning. This approach is appropriate for the analysis of the developing gynoecium or seedpod of the flowering plant Arabidopsis thaliana and many other types of fixed plant material. Early stages of ovule development are observable with this approach.

Background Plant meristems are analogous to animal stem cell niches as they maintain a pool of un... more Background Plant meristems are analogous to animal stem cell niches as they maintain a pool of undifferentiated cells that divide and differentiate to give rise to organs. The carpel margin meristem is a vital, multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Results Using a floral synchronization system and a SHATTERPROOF2 domain-specific reporter, paired with fluorescence-activated cell sorting and RNA sequencing, we assayed the transcriptome of the gynoecial medial domai...

Development (Cambridge, England), 2002

Proper regulation of homeotic gene expression is critical for pattern formation during both anima... more Proper regulation of homeotic gene expression is critical for pattern formation during both animal and plant development. A negative regulatory mechanism ensures that the floral homeotic gene AGAMOUS is only expressed in the center of an Arabidopsis floral meristem to specify stamen and carpel identity and to repress further proliferation of the floral meristem. We report the genetic identification and characterization of a novel gene, SEUSS, that is required in the negative regulation of AGAMOUS. Mutations in SEUSS cause ectopic and precocious expression of AGAMOUS mRNA, leading to partial homeotic transformation of floral organs in the outer two whorls. The effects of seuss mutations are most striking when combined with mutations in LEUNIG, a previously identified repressor of AGAMOUS. More complete homeotic transformation of floral organs and a greater extent of organ loss in all floral whorls were observed in the seuss leunig double mutants. By in situ hybridization and double a...

Journal of Experimental Zoology, 1992

Our goal is to understand the molecular mechanisms that govern the formation of the central nervo... more Our goal is to understand the molecular mechanisms that govern the formation of the central nervous system. In particular, we have focused on the development of a small group of neurons and glia that lie along the midline of the Drosophila CNS. These midline cells possess a number of unique attributes which make them particularly amenable to molecular, cellular, and genetic examinations of nervous system formation and function. In addition, the midline cells exhibit distinctive ontogeny, morphology, anatomical position, and patterns of gene expression which suggest that they may provide unique functions to the developing CNS. The single-minded gene encodes a nuclear protein which is specifically expressed in the midline cells and has been shown to play a crucial role in midline cell development and CNS formation. Genetic experiments reveal that sim is required for the expression of many CNS midline genes which are thought to be involved in the proper differentiation of these cells. In order to identify additional genes which are expressed in some or all of the midline cells a t different developmental stages, a technique known as enhancer trap screening was employed. This screen led to the identification of a large number of potential genes which exhibit various midline expression patterns and may be involved in discrete aspects of midline cell development. Further molecular, genetic, and biochemical analyses of sim and several of the enhancer trap lines are being pursued. This should permit elucidation of the genetic hierarchy which acts in the specification, differentiation, and function of these CNS midline cells.

Annals of botany, 2013

LFY homologues encode transcription factors that regulate the transition from vegetative to repro... more LFY homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inﬂorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.). The study sought to determine whether LFY homologues in Cornus species are expressed during floral and inflorescence development and if the pattern of expression is consistent with a function in regulating floral development and inflorescence architectures in the genus. Total RNAs were extracted using the CTAB method and the first-strand cDNA was synthesized using the SuperScript III first-strand synthesis system kit (Invitrogen). Expression of CorLFY was investigated by RT-PCR and RNA in situ hybridization. Phylogenetic analyses were conducted usi...

Frontiers in Plant Science, 2015

Janick/Horticultural Reviews, Volume 27, 2001

Plant physiology, 2014

Although it is generally accepted that auxin is important for the patterning of the female reprod... more Although it is generally accepted that auxin is important for the patterning of the female reproductive organ, the gynoecium, the flow as well as the temporal and spatial actions of auxin have been difficult to show during early gynoecial development. The primordium of the Arabidopsis (Arabidopsis thaliana) gynoecium is composed of two congenitally fused, laterally positioned carpel primordia bisected by two medially positioned meristematic regions that give rise to apical and internal tissues, including the ovules. This organization makes the gynoecium one of the most complex plant structures, and as such, the regulation of its development has remained largely elusive. By determining the spatiotemporal expression of auxin response reporters and localization of PINFORMED (PIN) auxin efflux carriers, we have been able to create a map of the auxin flow during the earliest stages of gynoecial primordium initiation and outgrowth. We show that transient disruption of polar auxin transpor...

Frontiers in Plant Science, 2014

Methods in molecular biology (Clifton, N.J.), 2014

Almost three decades of genetic and molecular analyses have resulted in detailed insights into ma... more Almost three decades of genetic and molecular analyses have resulted in detailed insights into many of the processes that take place during flower development and in the identification of a large number of key regulatory genes that control these processes. Despite this impressive progress, many questions about how flower development is controlled in different angiosperm species remain unanswered. In this chapter, we discuss some of these open questions and the experimental strategies with which they could be addressed. Specifically, we focus on the areas of floral meristem development and patterning, floral organ specification and differentiation, as well as on the molecular mechanisms underlying the evolutionary changes that have led to the astounding variations in flower size and architecture among extant and extinct angiosperms.

The Plant Cell, 2000

The carpel is the female reproductive organ of flowering plants. In Arabidopsis, congenital fusio... more The carpel is the female reproductive organ of flowering plants. In Arabidopsis, congenital fusion of two carpels leads to the formation of an enclosed gynoecium. The margins of the two fused carpels are meristematic in nature and give rise to placentas, ovules, septa, abaxial repla, and the majority of the stylar and stigmatic tissues. Thus, understanding how the marginal tissues are specified and identifying genes that direct their development may provide important insight into higher plant reproductive development. In this study, we show that LEUNIG and AINTEGUMENTA are two critical regulators of marginal tissue development. Double mutants of leunig aintegumenta fail to develop placentas, ovules, septa, stigma, and style. This effect is specific to the leunig aintegumenta double mutant and is not found in other double mutant combinations such as leunig apetala2 or aintegumenta apetala2. Additional analyses indicate that the absence of marginal tissues in leunig aintegumenta double mutants is not mediated by ectopic AGAMOUS. We propose that LEUNIG and AINTEGUMENTA act together to control the expression of common target genes that regulate cell proliferation associated with marginal tissue development.

THE PLANT CELL ONLINE, 2004

A common aspect of gene regulation in all developmental systems is the sustained repression of ke... more A common aspect of gene regulation in all developmental systems is the sustained repression of key regulatory genes in inappropriate spatial or temporal domains. To understand the mechanism of transcriptional repression of the floral homeotic gene AGAMOUS (AG), we identified two mutations in the BELLRINGER (BLR) gene based on a striking floral phenotype, in which homeotic transformations from sepals to carpels are found in flowers derived from old terminating shoots. Furthermore, this phenotype is drastically enhanced by growth at a high temperature and by combining blr with mutants of LEUNIG and SEUSS, two putative transcriptional corepressors of AG. We showed that the floral phenotype of blr mutants is caused by derepression of AG, suggesting that BLR functions as a transcription repressor. Because BLR encodes a BELL1-like (BELL) homeobox protein, direct binding of BLR to AG cis-regulatory elements was tested by gel-shift assays, and putative BLR binding motifs were identified. In addition, these putative BLR binding motifs were shown to be conserved in 17 of the 29 Brassicaceae species by phylogenetic footprinting. Because BELL homeobox proteins are a family of plant-specific transcription factors with 12 members in Arabidopsis thaliana, our findings will facilitate the identification of regulatory targets of other BELL proteins and help determine their biological functions. The age-dependent and high temperature-enhanced derepression of AG in blr mutants led us to propose that AG expression might be regulated by a thermal time-dependent molecular mechanism.

PLoS ONE, 2011

In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thaliana o... more In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thaliana ovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using the ATH1 transcriptomics platform we identified transcripts that were differentially expressed in seu ant double mutant relative to wild type and single mutant gynoecia. In particular we sought to identify transcripts whose expression was dependent on the coordinated activities of the SEU and ANT gene products. Our analysis identifies a diverse set of transcripts that display altered expression in the seu ant double mutant tissues. The analysis of overrepresented Gene Ontology classifications suggests a preponderance of transcriptional regulators including multiple members of the REPRODUCTIVE MERISTEMS (REM) and GROWTH-REGULATING FACTOR (GRF) families are mis-regulated in the seu ant gynoecia. Our in situ hybridization analyses indicate that many of these genes are preferentially expressed within the developing CMM. This study is the first step toward a detailed description of the transcriptional regulatory hierarchies that control the development of the CMM and ovule initiation. Understanding the regulatory hierarchy controlled by SEU and ANT will clarify the molecular mechanism of the functional redundancy of these two genes and illuminate the developmental and molecular events required for CMM development and ovule initiation.

Planta, 2006

Unlike in animals where cell migrations and programmed cell death play key roles in organ shape d... more Unlike in animals where cell migrations and programmed cell death play key roles in organ shape determination, in plants organ shape is largely a result of coordinated cellular growth (cell divisions and cell elongations). We have investigated the role of the SEUSS and LEUNIG genes in Arabidopsis thaliana (L.) Heynh. petal development to better understand the molecular mechanisms through which cellular growth and organ shape are coordinated in plants. SEUSS and LEUNIG encode components of a putative transcriptional regulatory complex that controls organ identity speciWcation through the repression of the Xoral organ identity gene AGAMOUS. SEUSS and LEUNIG also regulate petal shape through AGAMOUS-independent mechanisms; however, the molecular and cellular actions of SEUSS and LEUNIG during petal development are unknown. Here we show that SEUSS and LEUNIG control blade cell number and vasculature development within the petal. Furthermore, SEUSS and LEUNIG regulate petal polarity along the adaxial/abaxial axis. We present a model where SEUSS and LEUNIG are required to potentiate the key polarity genes PHABULOSA and FILAMENTOUS FLOWER/YABBY1 and thus inXuence cellular growth within the developing petal blade.

PLANT PHYSIOLOGY, 2010

Multimeric protein complexes are required during development to regulate transcription and orches... more Multimeric protein complexes are required during development to regulate transcription and orchestrate cellular proliferation and differentiation. The Arabidopsis (Arabidopsis thaliana) SEUSS (SEU) gene encodes a transcriptional adaptor that shares sequence similarity with metazoan Lim domain-binding transcriptional adaptors. In Arabidopsis, SEU forms a physical complex with the LEUNIG transcriptional coregulator. This complex regulates a number of diverse developmental events, including proper specification of floral organ identity and number and the development of female reproductive tissues derived from the carpel margin meristem. In addition to SEU, there are three Arabidopsis SEUSS-LIKE (SLK) genes that encode putative transcriptional adaptors. To determine the functions of the SLK genes and to investigate the degree of functional redundancy between SEU and SLK genes, we characterized available slk mutant lines in Arabidopsis. Here, we show that mutations in any single SLK gene...

New Phytologist, 2012

Despite increasing interest in the molecular mechanisms of floral diversity, few studies have inv... more Despite increasing interest in the molecular mechanisms of floral diversity, few studies have investigated the developmental and genetic bases of petaloid bracts. This study examined morphological patterns of bract initiation and expression patterns of B-class MADS-box genes in bracts of several Cornus species. We suggest that petaloid bracts in this genus may not share a single evolutionary origin. Developmental pathways of bracts and spatiotemporal expression of B-class genes in bracts and flowers were examined for four closely related dogwood species. Divergent morphological progressions and gene expression patterns were found in the two sister lineages with petaloid bracts, represented by Cornus florida and Cornus canadensis. Phylogeny-based analysis identified developmental and gene expression changes that are correlated with the evolution of petaloid bracts in C. florida and C. canadensis. Our data support the existence of independent evolutionary origins of petaloid bracts in C. canadensis and C. florida. Additionally, we suggest that functional transference within B-class gene families may have contributed to the origin of bract petaloidy in C. florida. However, the underlying mechanisms of petaloid bract development likely differ between C. florida and C. canadensis. In the future this hypothesis can be tested by functional analyses of Cornus B-class genes.

Integrative and Comparative Biology, 2010