PACLOBUTRAZOL-RESISTANCE Gene Family Regulates Floral Organ Growth with Unequal Genetic Redundancy in Arabidopsis thaliana

A PACLOBUTRAZOL-RESISTANCE (PRE) gene family, consisting of six genes in Arabidopsis thaliana, encodes a group of helix-loop-helix proteins that act in the growth-promoting transcriptional network. To delineate the specific role of each of the PRE genes in organ growth, we took a reverse genetic approach by constructing high order pre loss-of-function mutants of Arabidopsis thaliana. In addition to dwarf vegetative growth, some double or high order pre mutants exhibited defective floral development, resulting in reduced fertility. While pre2pre5 is normally fertile, both pre2pre6 and pre5pre6 showed reduced fertility. Further, the reduced fertility was exacerbated in the pre2pre5pre6 mutant, indicative of the redundant and critical roles of these PREs. Self-pollination assay and scanning electron microscopy analysis showed that the sterility of pre2pre5pre6 was mainly ascribed to the reduced cell elongation of anther filament, limiting access of pollens to stigma. We found that the expression of a subset of flower-development related genes including ARGOS, IAA19, ACS8, and MYB24 was downregulated in the pre2pre5pre6 flowers. Given these results, we propose that PREs, with unequal functional redundancy, take part in the coordinated growth of floral organs, contributing to successful autogamous reproduction in Arabidopsis thaliana.

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Abstract 13585: Up Regulation of Autophagy in Hsp60 Mutant Heart is an Adaptive Response to Increased Oxidative Stress and Causes Cardiomyopathy

Circulation ◽

10.1161/circ.130.suppl_2.13585 ◽

2014 ◽

Vol 130 (suppl_2) ◽

Author(s):

Hirokazu Enomoto ◽

Shinji Makino ◽

Nishant Mittal ◽

Akinori Kimura ◽

Takuro Arimura ◽

...

Keyword(s):

Oxidative Stress ◽

Stress Condition ◽

Heat Shock Protein 60 ◽

Loss Of Function ◽

Lower Survival Rate ◽

Protein Levels ◽

Fish Model ◽

Electron Microscopy Analysis ◽

Pericardial Edema ◽

Microscopy Analysis

Introduction: Despite the recent advance of genetic studies, genetic causes of hereditary dilated cardiomyopathy (DCM) are still unknown in most cases. Heat shock protein 60 (Hsp60) is a well-known chaperonin, responsible for correct folding and transportation of cytoplasmic protein to mitochondria. This study is aimed to investigate whether dysfunction of Hsp60 leads to cardiomyopathy in a fish model. Methods: We previously developed a zebrafish mutant, nbl, which has a missense mutation in hsp60, leading to the loss of function. To evaluate the phenotype of cardiomyopathy in nbl, we performed RT-PCR, western blot and immunohistochemistry of the hearts. Results: Homozygous nbl embryos showed lower survival rate (65%), compared to 81% in wild-type (WT) embryos, when subjected to 33°C (stress condition). We observed pericardial edema in 92% of nbl homozygous mutants. Also, nbl homozygotes showed sudden death at around 8 months post fertilization (mpf), when grown in non-stress condition. At 8 mpf, nbl mutants showed dilated heart and high expression of reactive oxygen species (ROS). Both mRNA and protein levels of Hsp60 were similar in nbl homozygotes and WT, at 3 mpf but, much higher expression of Hsp60 in nbl homozygotes was observed at 6 mpf, beginning of death of nbl homozygous mutants. Electron microscopy analysis showed dark mitochondria, disrupted sarcomeric structure and higher number of autophagosomes in nbl homozygote hearts at 8 mpf. We, then, analyzed autophagy related genes and found that atg5, atg3 and gabarap mRNAs were increased in nbl homozygotes, suggesting the increased autophagy might underlie the pathogenesis of DCM. Furthermore, analysis of genetically unrelated patients with familial DCM, who had no mutations in the known DCM-causing genes, identified an hsp60 mutation in one DCM family in which two of four mutation prone individuals died suddenly. Over expression of nbl mutation or DCM-associated hsp60 mutation, but not normal hsp60, increased autophagosomes in Hela cells carrying GFP-LC3. Conclusions: Functional loss of Hsp60 increased oxidative stress in the heart, which leads to increased autophagy and confer the susceptibility to cardiomyopathy.

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The early inflorescence of Arabidopsis thaliana demonstrates positional effects in floral organ growth and meristem patterning

Plant Reproduction ◽

10.1007/s00497-017-0320-3 ◽

2017 ◽

Vol 31 (2) ◽

pp. 171-191 ◽

Cited By ~ 6

Author(s):

Andrew R. G. Plackett ◽

Stephen J. Powers ◽

Andy L. Phillips ◽

Zoe A. Wilson ◽

Peter Hedden ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Floral Organ ◽

Organ Growth ◽

Positional Effects

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Genome-wide predictions of genetic redundancy in Arabidopsis thaliana

10.1101/2020.08.13.250225 ◽

2020 ◽

Author(s):

Siobhan A. Cusack ◽

Peipei Wang ◽

Bethany M. Moore ◽

Fanrui Meng ◽

Jeffrey K. Conner ◽

...

Keyword(s):

Machine Learning ◽

Arabidopsis Thaliana ◽

Model Building ◽

Expression Patterns ◽

Model Performance ◽

Machine Learning Algorithms ◽

Stress Conditions ◽

Loss Of Function ◽

Genetic Redundancy ◽

Gene Pairs

ABSTRACTGenetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features has not yet been established. In addition, the relative importance of these characteristics for genetic redundancy remains unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana. Benchmark gene pairs were classified based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including post-translational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used affected model performance significantly. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. Predictions were then tested using phenotype data withheld from model building and validated using well-characterized, redundant and nonredundant gene pairs. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs that are seemingly functionally redundant, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.

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Update on the Basic Helix-Loop-Helix Transcription Factor Gene Family in Arabidopsis thaliana

The Plant Cell ◽

10.1105/tpc.151140 ◽

2003 ◽

Vol 15 (11) ◽

pp. 2497-2502 ◽

Cited By ~ 146

Author(s):

Paul C. Bailey ◽

Cathie Martin ◽

Gabriela Toledo-Ortiz ◽

Peter H. Quail ◽

Enamul Huq ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factor ◽

Gene Family ◽

Transcription Factor Gene ◽

Factor Gene ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Transcription Factor Gene Family

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Regulation of floral organ abscission in Arabidopsis thaliana

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0805539105 ◽

2008 ◽

Vol 105 (40) ◽

pp. 15629-15634 ◽

Cited By ~ 176

Author(s):

Sung Ki Cho ◽

Clayton T. Larue ◽

David Chevalier ◽

Huachun Wang ◽

Tsung-Luo Jinn ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Protein Kinase ◽

Map Kinase ◽

Floral Organ ◽

Dominant Negative ◽

Mitogen Activated Protein Kinase ◽

Loss Of Function ◽

Dominant Negative Form ◽

Mitogen Activated Protein ◽

Kinase Cascade

Abscission is a developmental program that results in the active shedding of infected or nonfunctional organs from a plant body. Here, we establish a signaling pathway that controls abscission in Arabidopsis thaliana from ligand, to receptors, to downstream effectors. Loss of function mutations in Inflorescence Deficient in Abscission (IDA), which encodes a predicted secreted small protein, the receptor-like protein kinases HAESA (HAE) and HAESA-like 2 (HSL2), the Mitogen-Activated Protein Kinase Kinase 4 (MKK4) and MKK5, and a dominant-negative form of Mitogen-Activated Protein Kinase 6 (MPK6) in a mpk3 mutant background all have abscission-defective phenotypes. Conversely, expression of constitutively active MKKs rescues the abscission-defective phenotype of hae hsl2 and ida plants. Additionally, in hae hsl2 and ida plants, MAP kinase activity is reduced in the receptacle, the part of the stem that holds the floral organs. Plants overexpressing IDA in a hae hsl2 background have abscission defects, indicating HAE and HSL2 are epistatic to IDA. Taken together, these results suggest that the sequential action of IDA, HAE and HSL2, and a MAP kinase cascade regulates the programmed separation of cells in the abscission zone.

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Predictive models of genetic redundancy in Arabidopsis thaliana

Molecular Biology and Evolution ◽

10.1093/molbev/msab111 ◽

2021 ◽

Author(s):

Siobhan A Cusack ◽

Peipei Wang ◽

Serena G Lotreck ◽

Bethany M Moore ◽

Fanrui Meng ◽

...

Keyword(s):

Machine Learning ◽

Arabidopsis Thaliana ◽

Expression Patterns ◽

Model Performance ◽

Machine Learning Algorithms ◽

Stress Conditions ◽

Loss Of Function ◽

Genetic Redundancy ◽

Gene Pairs ◽

Phenotype Data

Abstract Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features derived from accumulating omics and mutant phenotype data is yet to be established. In addition, the relative importance of these features for genetic redundancy remains largely unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including post-translational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used significantly affected model performance based on hold-out, testing phenotype data. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. We also explored the potential reasons underlying mispredictions and limitations of our studies. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.

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The Streptomyces volatile 3-octanone alters auxin/cytokinin and growth in Arabidopsis thaliana via the gene family KISS ME DEADLY

10.1101/2020.02.15.949685 ◽

2020 ◽

Cited By ~ 1

Author(s):

Bradley R. Dotson ◽

Vasiliki Verschut ◽

Klas Flärdh ◽

Paul G. Becher ◽

Allan G. Rasmusson

Keyword(s):

Arabidopsis Thaliana ◽

Plant Growth ◽

Gene Family ◽

Growth Promotion ◽

Lateral Roots ◽

Primary Root ◽

Growth Hormones ◽

Loss Of Function ◽

Growth Responses ◽

Cytokinin Signaling

AbstractPlants enhance their growth in the presence of particular soil bacteria due to volatile compounds affecting the homeostasis of plant growth hormones. However, the mechanisms of volatile compound signaling and plant perception has been unclear. This study identifies the bioactive volatile 3-octanone as a plant growth stimulating volatile, constitutively emitted by the soil bacterium Streptomyces coelicolor grown on a rich medium. When 3-octanone is applied to developing Arabidopsis thaliana seedlings, a family-wide induction of the Kelch-repeat F-box genes known as KISS ME DEADLY (KMD) subsequently alters auxin/cytokinin homeostasis to promote the growth of lateral roots and inhibit the primary root. Loss of function of the KMD family or other alterations of auxin/cytokinin homeostasis suppresses the volatile-induced growth response. This reveals a function of KMDs in the pathway of microbial volatile perception and plant growth responses.Significance StatementVolatiles from soil microbes are profound stimulators of plant growth. This work identifies for the first time a plant hormone signaling regulator, the gene family KISS ME DEADLY (KMD), to be an early essential step in plant growth promotion by a soil bacterial volatile, 3-octanone. The KMD-regulated gene network alters the tissue sensitivity balance for the growth hormones auxin and cytokinin, modifying root growth rate and architecture. Previously, the Kelch repeat F-box gene family of KMDs have been shown to be important down-regulators of both positive cytokinin signaling and phenylpropanoid biosynthesis, but upstream cues were unknown. This report places the KMD family regulation of plant growth and defense into its biotic context.

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Material analysis techniques using the ion mill

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100167639 ◽

1996 ◽

Vol 54 ◽

pp. 1034-1035

Author(s):

J. P. Benedict ◽

R. M. Anderson ◽

S. J. Klepeis

Keyword(s):

Polished Surface ◽

Surface Material ◽

Analysis Techniques ◽

Material Analysis ◽

Optical Inspection ◽

Electron Microscopy Analysis ◽

Microscopy Analysis ◽

Argon Ions ◽

The Impact ◽

Scanning Electron

Ion mills equipped with flood guns can perform two important functions in material analysis; they can either remove material or deposit material. The ion mill holder shown in Fig. 1 is used to remove material from the polished surface of a sample for further optical inspection or SEM ( Scanning Electron Microscopy ) analysis. The sample is attached to a pohshing stud type SEM mount and placed in the ion mill holder with the polished surface of the sample pointing straight up, as shown in Fig 2. As the holder is rotating in the ion mill, Argon ions from the flood gun are directed down at the top of the sample. The impact of Argon ions against the surface of the sample causes some of the surface material to leave the sample at a material dependent, nonuniform rate. As a result, the polished surface will begin to develop topography during milling as fast sputtering materials leave behind depressions in the polished surface.

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