Transcriptome analyses of ragged seedling2 shoot apical meristem (SAM) vs non-mutant SAM
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE11325 | GEO | 2008/05/03
SECONDARY ACCESSION(S): PRJNA106645
REPOSITORIES: GEO
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Project description:The recessive mutation ragged seedling2-R (rgd2-R) conditions defective lateral development of maize leaves. Although dorsiventral patterning is established in rgd2-R mutant leaves, some swapping of adaxial/abaxial epidermal identity may occur. Molecular analyses indicate that RGD2 is required for the coordination of dorsiventral and lateral patterning during maize leaf development, yet the RGD2 gene product and the mechanisms of RGD2 function are unknown. In order to investigate the genetic mechanisms downstream of RGD2 gene function, SAM-specific transcriptional profiling of rgd2-R is compared to that of nonmutant using laser microdissection microarray. Whole SAMs were laser-microdissected from rgd2-R mutant and non-mutant seedlings grown under the same controlled conditions. Microarray profiles were generated for 28,671 maize cDNAs contained on gene chips SAM 1.1and SAM 3.0 (http://www.plantgenomics.iastate.edu/maizechip/). Two-condition experiment, rgd2 SAM vs non-mutant SAM cells. 6 Biological replicates with dye swap. One replicate per array.
2008-05-02 | E-GEOD-11325 | biostudies-arrayexpress
Project description:Loss of function mutations in the narrow sheath (ns) duplicate genes (ns1 and ns2) cause the deletion of a mediolateral domain from maize leaves. The ns genes encode duplicate WUSCHEL1-like homeobox (WOX) putative transcription factors that function redundantly and non-cell autonomously to direct recruitment of leaf founder cell-initials in a lateral domain of the shoot apex. In order to investigate the genetic mechanisms of NS1 gene function, SAM-specific transcriptional profiling of narrow sheath mutant1-R comparing to that of nonmutant using laser microdissection microarray. Whole SAMs were laser-microdissected from ns1-R mutant and non-mutant seedlings grown under the same controlled conditions. Microarray profiles were generated for 37,662 maize cDNAs contained on gene chips SAM 1.1, SAM 2.0 and SAM 3.0 (For details, see the the Iowa State University Center for Plant Genomics website). Keywords: Genetic modification
2007-03-14 | GSE7248 | GEO
Project description:The shoot apical meristem (SAM) of plants, a specialized stem cell niche at the growing shoot tip, integrates developmental and environmental signals to direct the initiation and patterning of new organs such as leaves. Its activity throughout the plant's lifetime is tightly controlled. To gain insight into gene regulatory networks behind stem cell maintenance and organogenesis, we generated a high-resolution gene expression atlas of distinct domains and cell types within the vegetative shoot apex of 14 day-old maize B73 seedlings using laser microdissection and RNA deep sequencing. Data for 9 domains was previously released under SRA: SRP101301. This release adds data for biological duplicate samples collected for the SAM central zone, and the adaxial and abaxial sides of leaf primordia.
2019-10-02 | GSE137715 | GEO
Project description:Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c were also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in which abBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. The observations provide first insights into the unique properties of abBS cells, cells previously considered to fulfill the same functions as other bundle sheath cells (BSCs), and a basis for understanding the C4 syndrome.
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Project description:Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c were also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in which abBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. The observations provide first insights into the unique properties of abBS cells, cells previously considered to fulfill the same functions as other bundle sheath cells (BSCs), and a basis for understanding the C4 syndrome.
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Project description:Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialised ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally-derived fringe. Recessive liguleless1 mutants lack ligules and auricles, and have upright leaves. We utilized laser-microdissection RNAseq to identify genes that are differentially expressed along discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation, and compared transcript accumulation in wild type and liguleless1 mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these ligule genes are also implicated to function during leaf initiation or lateral branching, and intersect multiple hormonal signalling pathways. We propose that genetic modules utilised in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia. In this study, we analysed the transcriptome associated with ligule formation using laser microdissection RNA-sequencing (LM-RNAseq). We quantified transcript accumulation in the PLB and adjacent pre-blade and pre-sheath regions of wild-type leaf primordia in order to identify candidate genes involved in proximal-distal patterning at the blade-sheath boundary. We also compared transcript accumulation in lg1-R mutants and wild-type siblings to identity genes acting downstream of LG1.
2014-09-12 | E-GEOD-61333 | biostudies-arrayexpress
Project description:Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialised ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally-derived fringe. Recessive liguleless1 mutants lack ligules and auricles, and have upright leaves. We utilized laser-microdissection RNAseq to identify genes that are differentially expressed along discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation, and compared transcript accumulation in wild type and liguleless1 mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these ligule genes are also implicated to function during leaf initiation or lateral branching, and intersect multiple hormonal signalling pathways. We propose that genetic modules utilised in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia.
2014-09-12 | GSE61333 | GEO
Project description:CRABS CLAW (CRC) encodes a transcription factor of the plant-specific YABBY class in the model plant Arabidopsis thaliana. This gene is highly expressed in the abaxial (external) domain of the gynoecium wall and contributes to the establishment of abaxial-adaxial (external-internal) polarity in that tissue. Here we derive a list of putative target genes of CRC, which include AUXIN RESPONSE FACTOR4 (ARF4) and ASSYMETRIC LEAVES1 (AS1), both of which are known to be involved in the establishment of abaxial-adaxial polarity in lateral organs. ETTIN (ETT), which is partially redundant with ARF4, was not identified as a direct target of CRC, and this observation led us to predict that crc/ett double mutants might resemble ett/arf4 double mutants, which show a very strong breakdown of abaxial-adaxial polarity in the gynoecium wall. We have confirmed this prediction by constructing double mutants using several available mutant alleles of crc, ett and arf4. Interestingly, AS1 plays a role in the establishment of adaxial tissue identity in lateral organs, though its expression is not restricted to the adaxial domain. The observed positive regulation of AS1 by CRC may thus occur very early in gynoecium development, before CRC expression becomes polarised, or at later stages of development, specifically in the abaxial domain.
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Project description:Scaffold proteins such as CNK1 are hubs for coordinating signalling pathways. Here, we demonstrate that CNK1 is a crucial transducer of growth factor-stimulated and oncogenic signalling. Activation of CNK1 depends on its dimerization executed by the N-terminal sterile motif alpha (SAM) domain. Accordingly, a CNK1 mutant lacking the SAM domain prevents CNK1-driven cell proliferation and matrix metalloproteinase 14 promoter activation. We identified phosphorylation of Ser22 by AKT as trigger for CNK1 dimerisation. Consistently, the mutant CNK1S22D mimicking constitutive phosphorylation stimulates CNK1 signalling, whereas the phosphoylation-dead mutant CNK1S22A does not. Searching the COSMIC database revealed Ser22 as target for oncogenic activation of CNK1. The mutant CNK1S22D and the oncogenic mutant CNK1S22F form clusters in serum-starved cells comparable to clusters of CNK1 in growth factor stimulated cells. Light-activatable CNK1, optoCNK1, based on the light-induced oligomerisation of cryptochrome 2 confirms that dimerization is the trigger for CNK1 activation. CNK1 dimers induced by activating Ser22 mutants or by light enhance cell invasion and ADP ribosylation factors 1 signalling associated with tumour formation. Positive and negative feedback mechanisms regulates CNK1 dimerisation and in this way its activity. Oncogenic mutants of CNK1 support the positive feedback while escape from negative feedback regulation.
2022-02-23 | PXD003831 | Pride