Differential transcriptional networks associated with key phases of ingrowth wall construction in trans-differentiating epidermal transfer cells of Vicia faba cotyledons

Abstract

BackgroundTransfer cells are characterized by intricate ingrowth walls, comprising an uniform wall upon which wall ingrowths are deposited. The ingrowth wall forms a scaffold to support an amplified plasma membrane surface area enriched in membrane transporters that collectively confers transfer cells with an enhanced capacity for membrane transport at bottlenecks for apo-/symplasmic exchange of nutrients. However, the underlying molecular mechanisms regulating polarized construction of the ingrowth wall and membrane transporter profile are poorly understood.ResultsAn RNAseq study of an inducible epidermal transfer cell system in cultured Vicia faba cotyledons identified transfer cell specific transcriptomes associated with uniform wall and wall ingrowth deposition. All functional groups of genes examined were expressed before and following transition to a transfer cell fate. What changed were the isoform profiles of expressed genes within functional groups. Genes encoding ethylene and Ca2+ signal generation and transduction pathways were enriched during uniform wall construction. Auxin-and reactive oxygen species-related genes dominated during wall ingrowth formation and ABA genes were evenly expressed across ingrowth wall construction. Expression of genes encoding kinesins, formins and villins was consistent with reorganization of cytoskeletal components. Uniform wall and wall ingrowth specific expression of exocyst complex components and SNAREs suggested specific patterns of exocytosis while dynamin mediated endocytotic activity was consistent with establishing wall ingrowth loci. Key regulatory genes of biosynthetic pathways for sphingolipids and sterols were expressed across ingrowth wall construction. Transfer cell specific expression of cellulose synthases was absent. Rather xyloglucan, xylan and pectin biosynthetic genes were selectively expressed during uniform wall construction. More striking was expression of genes encoding enzymes for re-modelling/degradation of cellulose, xyloglucans, pectins and callose. Extensins dominated the cohort of expressed wall structural proteins and particularly so across wall ingrowth development. Ion transporters were selectively expressed throughout ingrowth wall development along with organic nitrogen transporters and a large group of ABC transporters. Sugar transporters were less represented.ConclusionsPathways regulating signalling and intracellular organization were fine tuned whilst cell wall construction and membrane transporter profiles were altered substantially upon transiting to a transfer cell fate. Each phase of ingrowth wall construction was linked with unique cohorts of expressed genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0486-5) contains supplementary material, which is available to authorized users.

Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

“…Several transcriptome datasets have been previously generated for faba bean, from the cultivars Windsor [53], Icarus and Ascot [22], CDC Fatima, SSNS-1, and A01155 [39], Fiord [40,54], INRA-29H and Vf136 [42], BPL10 and Albus [29], and Wizard [43]. These datasets were generated from a selection of tissues including root, shoots, seedling, embryo, seed coat, leaves, or mixed tissues.…”

Identification of Candidate Transcriptional Regulators of Epidermal Transfer Cell Development in Vicia faba Cotyledons

“…Adaxial epidermal cells of cultured V. faba cotyledons trans -differentiate to become epidermal TCs but cells of the adjacent storage parenchyma tissue do not (Farley et al, 2000 ; Talbot et al, 2007 ; Dibley et al, 2009 ). Consequently, genes showing epidermal-specific change in expression upon cotyledon culture represent a pool of candidates likely to be involved in the trans -differentiation of epidermal TCs (Dibley et al, 2009 ; Zhang et al, 2015b ). To identify transcription factors showing epidermal-specific up-regulation, we performed RNA-Seq of epidermal cells and storage parenchyma isolated from cultured cotyledons.…”

“…Wall ingrowth formation in TCs represents a novel example of wall deposition in plant cells (McCurdy et al, 2008 ; McCurdy, 2015 ), presumably involving unique sets of genes to both initiate and then orchestrate the cellular events required for this highly localized wall deposition event. Indeed, transcript profiling in endosperm TCs of barley (Thiel et al, 2008 , 2012 ) and epidermal TCs of Vicia faba cotyledons (Dibley et al, 2009 ; Zhang et al, 2015b ) established that wall ingrowth deposition involves differential expression of many hundreds of genes, presumably organized within transcriptional cascades to coordinate expression of the biosynthetic machinery required for wall ingrowth deposition and TC function (Arun-Chinnappa et al, 2013 ). These studies identified a role for auxin and ethylene signaling in inducing TC development, and details of the involvement of epidermal-specific ethylene and reactive oxygen species signaling pathways in epidermal TC induction have been elucidated (Zhou et al, 2010 ; Andriunas et al, 2011 , 2012 ).…”

“…The development of RNA-Seq for transcriptional profiling in species without a sequenced genome, with its deep sequencing capabilities to detect changes in transcript abundance with high sensitivity (Simon et al, 2009 ; Martin et al, 2013 ; Weber, 2015 ), provides an opportunity to re-visit transcript profiling using the V. faba cotyledon culture system. Zhang et al ( 2015b ) used this approach to identify genes putatively involved in the inductive signaling of wall ingrowth deposition and the biosynthetic genes presumably involved in this process, but did not report the identities of transcription factors expected to switch on expression of biosynthetic genes in response to these signaling pathways. In this current study we used RNA-Seq to identify at least 43 transcription factors which show differential up-regulated expression in adaxial epidermal cells of V. faba cotyledons undergoing trans -differentiation to form epidermal TCs, and 10 which are similarly down-regulated.…”

Barley HISTIDINE KINASE 1 (HvHK1) coordinates transfer cell specification in the young endosperm

“…In contrast, specific metabolic and secondary transport processes (drug transport), amino acid methylation/alkylation and hydrolase activity are upregulated in RNAi lines. Activation of defense-related genes is emblematic for transfer cells in cereal grains but also in dicot (legume) seeds (Zhang et al, 2015). Concurrently, a suite of genes with structural similarity to defensins are Figure S4).…”