Mechanisms that control knox gene expression in the Arabidopsis shoot

Development ◽  
2000 ◽  
Vol 127 (24) ◽  
pp. 5523-5532 ◽  
Author(s):  
N. Ori ◽  
Y. Eshed ◽  
G. Chuck ◽  
J.L. Bowman ◽  
S. Hake
Keyword(s):  
Gene Expression ◽  
Knox Gene ◽  
Phenotypic Characteristics ◽  
Knox Genes ◽  
Meristem Maintenance ◽  
Leaf Differentiation ◽  
Shoot Meristems

Knotted1-like homeobox (knox) genes are expressed in specific patterns within shoot meristems and play an important role in meristem maintenance. Misexpression of the knox genes, KNAT1 or KNAT2, in Arabidopsis produces a variety of phenotypes, including lobed leaves and ectopic stipules and meristems in the sinus, the region between lobes. We sought to determine the mechanisms that control knox gene expression in the shoot by examining recessive mutants that share phenotypic characteristics with 35S::KNAT1 plants. Double mutants of serrate (se) with either asymmetric1 (as1) or asymmetric2 (as2) showed lobed leaves, ectopic stipules in the sinuses and defects in the timely elongation of sepals, petals and stamens, similar to 35S::KNAT1 plants. Ectopic stipules and in rare cases, ectopic meristems, were detected in the sinuses on plants that were mutant for pickle and either as1 or as2. KNAT1 and KNAT2 were misexpressed in the leaves and flowers of single as1 and as2 mutants and in the sinuses of leaves of the different double mutants, but not in se or pickle single mutants. These results suggest that AS1 and AS2 promote leaf differentiation through repression of knox expression in leaves, and that SE and PKL globally restrict the competence to respond to genes that promote morphogenesis.

The rough sheath2 gene negatively regulates homeobox gene expression during maize leaf development

Development ◽  
1998 ◽  
Vol 125 (15) ◽  
pp. 2857-2865 ◽  
Author(s):  
R. Schneeberger ◽  
M. Tsiantis ◽  
M. Freeling ◽  
J.A. Langdale
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Higher Plants ◽  
Leaf Shape ◽  
Ectopic Expression ◽  
Homeobox Gene ◽  
Current Evidence ◽  
Leaf Cell ◽  
Knox Gene ◽  
Knox Genes

Leaves of higher plants are produced in a sequential manner through the differentiation of cells that are derived from the shoot apical meristem. Current evidence suggests that this transition from meristematic to leaf cell fate requires the down-regulation of knotted1-like homeobox (knox) gene expression. If knox gene expression is not repressed, overall leaf shape and cellular differentiation within the leaf are perturbed. In order to identify genes that are required for the aquisition of leaf cell fates, we have genetically screened for recessive mutations that confer phenotypes similar to dominant mutations (e.g. Knotted1 and Rough sheath1) that result in the ectopic expression of class I knox genes. Independently derived mutations at the rough sheath2 (rs2) locus condition a range of pleiotropic leaf, node and internode phenotypes that are sensitive to genetic background and environment. Phenotypes include dwarfism, leaf twisting, disorganized differentiation of the blade-sheath boundary, aberrant vascular patterning and the generation of semi-bladeless leaves. knox genes are initially repressed in rs2 mutants as leaf founder cells are recruited in the meristem. However, this repression is often incomplete and is not maintained as the leaf progresses through developement. Expression studies indicate that three knox genes are ectopically or over-expressed in developing primordia and in mature leaves. We therefore propose that the rs2 gene product acts to repress knox gene expression (either directly or indirectly) and that rs2 gene action is essential for the elaboration of normal leaf morphology.

SEMAPHORE1 functions during the regulation of ancestrally duplicated knox genes and polar auxin transport in maize

Development ◽  
2002 ◽  
Vol 129 (11) ◽  
pp. 2663-2673 ◽  
Author(s):  
Michael J. Scanlon ◽  
David C. Henderson ◽  
Brad Bernstein
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Auxin Transport ◽  
Lateral Roots ◽  
Ectopic Expression ◽  
Polar Auxin Transport ◽  
Knox Gene ◽  
Endosperm Tissue ◽  
Knox Genes ◽  
Class 1

The expression of class 1 knotted1-like homeobox (knox) genes affects numerous plant developmental processes, including cell-fate acquisition, lateral organ initiation, and maintenance of shoot apical meristems. The SEMAPHORE1 gene product is required for the negative regulation of a subset of maize knox genes, the duplicated loci rough sheath 1 and gnarley1 (knox4). Recessive mutations in semaphore1 result in the ectopic expression of knox genes in leaf and endosperm tissue. Genetic analyses suggest that SEMAPHORE1 may regulate knox gene expression in a different developmental pathway than ROUGH SHEATH2, the first-identified regulator of knox gene expression in maize. Mutations at semaphore1 are pleiotropic, disrupting specific domains of the shoot. However, unlike previously described mutations that cause ectopic knox gene expression, semaphore1 mutations affect development of the embryo, endosperm, lateral roots, and pollen. Moreover, polar transport of the phytohormone auxin is significantly reduced in semaphore1 mutant shoots. The data suggest that many of the pleiotropic semaphore1 phenotypes result from defective polar auxin transport (PAT) in sem1 mutant shoots, and support models correlating down-regulated knox gene expression and PAT in maize shoots.

scholarly journals ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis

Development ◽  
2002 ◽  
Vol 129 (8) ◽  
pp. 1957-1965 ◽  
Author(s):  
Mary E. Byrne ◽  
Joseph Simorowski ◽  
Robert A. Martienssen
Keyword(s):  
Shoot Apical Meristem ◽  
Apical Meristem ◽  
Cell Function ◽  
The Novel ◽  
Knox Gene ◽  
Knox Genes ◽  
Lateral Organs ◽  
Gene Redundancy ◽  
Lateral Organ ◽  
Meristem Maintenance

The shoot apical meristem comprises undifferentiated stem cells and their derivatives, which include founder cells for lateral organs such as leaves. Meristem maintenance and lateral organ specification are regulated in part by negative interactions between the myb domain transcription factor ASYMMETRIC LEAVES1, which is expressed in lateral organ primordia, and homeobox transcription factors which are expressed in the shoot apical meristem (knox genes). The knox gene SHOOT MERISTEMLESS (STM) negatively regulates ASYMMETRIC LEAVES1 (AS1) which, in turn, negatively regulates other knox genes including KNAT1 and KNAT2, and positively regulates the novel gene LATERAL ORGAN BOUNDARIES (LOB). Genetic interactions with a second gene, ASYMMETRIC LEAVES2 (AS2), indicate it acts at the same position in this hierarchy as AS1. We have used a second-site suppressor screen to isolate mutations in KNAT1 and we show that KNAT1 is partially redundant with STM in regulating stem cell function. Mutations in KNAT2 show no such interaction. We discuss the regulation and evolution of redundancy among knox genes.

Phenotypic characteristics and gene expression profiles of human chondrocytes in tissuegene C

2021 ◽  
Vol 29 ◽  
pp. S211-S212
Author(s):  
I. Uzieliene ◽  
E. Bagdonas ◽  
J. Denkovskij ◽  
E. Bernotiene ◽  
H.-J. Yoon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Human Chondrocytes ◽  
Phenotypic Characteristics

Gene expression analysis in microdissected shoot meristems of Brassica napus microspore-derived embryos with altered SHOOTMERISTEMLESS levels

Planta ◽  
2012 ◽  
Vol 237 (4) ◽  
pp. 1065-1082 ◽  
Author(s):  
Mohamed Elhiti ◽  
Owen S. D. Wally ◽  
Mark F. Belmonte ◽  
Ainsley Chan ◽  
Yongguo Cao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Shoot Meristems

Class 1 KNOX Gene Expression Supports the Selaginella Rhizophore Concept

2010 ◽  
Vol 53 (4) ◽  
pp. 268-274 ◽  
Author(s):  
Junko Kawai ◽  
Yoichi Tanabe ◽  
Sumitomo Soma ◽  
Motomi Ito
Keyword(s):  
Gene Expression ◽  
Knox Gene ◽  
Class 1

scholarly journals An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors

2020 ◽  
Author(s):  
Lara Brian ◽  
Ben Warren ◽  
Peter McAtee ◽  
Jessica Rodrigues ◽  
Niels Nieuwenhuizen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Fruit Development ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Actinidia Chinensis ◽  
Knox Gene ◽  
Hub Genes ◽  
Flower And Fruit Development

Abstract BackgroundTranscriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. ResultsSixty-one samples covering diverse tissues at different developmental time points were selected for RNAseq analysis and an eFP browser was generated to visualise this dataset. 2,839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three “hub” genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF.ConclusionsThis study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The eFP browser is provided in an accessible format that allows researchers to download and work internally.

scholarly journals Predicting growth rate from gene expression

2018 ◽  
Vol 116 (2) ◽  
pp. 367-372 ◽  
Author(s):  
Thomas P. Wytock ◽  
Adilson E. Motter
Keyword(s):  
Gene Expression ◽  
Growth Rate ◽  
Population Level ◽  
Phenotypic Traits ◽  
Phenotypic Characteristics ◽  
K Nearest Neighbors ◽  
E Coli ◽  
Learning Technique ◽  
Genetic Level ◽  
Antibiotic Efficacy

Growth rate is one of the most important and most complex phenotypic characteristics of unicellular microorganisms, which determines the genetic mutations that dominate at the population level, and ultimately whether the population will survive. Translating changes at the genetic level to their growth-rate consequences remains a subject of intense interest, since such a mapping could rationally direct experiments to optimize antibiotic efficacy or bioreactor productivity. In this work, we directly map transcriptional profiles to growth rates by gathering published gene-expression data from Escherichia coli and Saccharomyces cerevisiae with corresponding growth-rate measurements. Using a machine-learning technique called k-nearest-neighbors regression, we build a model which predicts growth rate from gene expression. By exploiting the correlated nature of gene expression and sparsifying the model, we capture 81% of the variance in growth rate of the E. coli dataset, while reducing the number of features from >4,000 to 9. In S. cerevisiae, we account for 89% of the variance in growth rate, while reducing from >5,500 dimensions to 18. Such a model provides a basis for selecting successful strategies from among the combinatorial number of experimental possibilities when attempting to optimize complex phenotypic traits like growth rate.

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