Signal transduction and Gene expression

Signal transduction pathway

A series of molecular events and chemical reactions that lead to a cellular response to a signal.

Second messengers

Small molecules or ions that relay signals received from receptors to target molecules inside the cell.

Transcription factor (TF)

Proteins that bind to specific DNA sequences to regulate gene expression.

Receptor-like Kinases (RLKs)

Proteins that function as receptors and also transduce a signal by adding a phosphate from ATP.

Mitogen-activated protein kinase (MAPK)

A signaling pathway that amplifies signals to produce a rapid response to stimuli.

Phosphatases

Enzymes that remove phosphate groups from proteins, acting as 'off' switches for protein phosphorylation.

Epigenetic modifications

Chemical changes to DNA or histones that affect gene expression without altering the DNA sequence.

MicroRNAs (miRNAs)

Small non-coding RNA molecules that regulate gene expression by targeting mRNA for degradation or inhibition.

Auxin signaling pathway

A hormonal signaling pathway that employs negative regulation for gene expression in response to auxin levels.

Covalent modifications

Chemical alterations of proteins that can change their function, such as phosphorylation.

Cell autonomous response

A response that occurs within a single cell, independent of surrounding cells.

Non-cell autonomous response

A response that affects neighboring cells or tissues, often seen in plant signaling.

G-protein-coupled receptor

A large class of receptors that sense molecules outside the cell and activate internal signal transduction.

Transcriptional regulation

The control of the amount and timing of mRNA production from a gene.

RNA interference (RNAi)

A biological process in which RNA molecules inhibit gene expression or translation.

Promoter

A DNA sequence that initiates transcription of a particular gene.

Ubiquitin-26S proteasome pathway

A mechanism for protein degradation in cells involving ubiquitin tagging.

Hormonal responses

Responses initiated by plant hormones that affect growth and development.

PIF (phytochrome-interacting factor)

A transcription factor that mediates light-responsive gene expression in plants.

TIR1

An auxin receptor that binds auxin and facilitates the degradation of Aux/IAA proteins.

Cytokinin

A class of plant hormones that regulate cell division and growth.

Brassinosteroids

A class of plant hormones that promote growth and development.

Signal attenuation

The process of diminishing the strength of a signal during signal transduction.

Temporal- rapid response signaling (carnivorous or sensitive plants, young seeds responding to gravity)

release of ions that have been sequestered by energy dependent processes over time.

Temporal Slow response signaling (environmental stimuli, herbivores attack, pathogen)

rapid cytoplasmic influx of ionic second messengers, hormonal responses, gene expression and protien translation

Temporal Long term signaling (months/years)

environmental responses (mod. of plant architecture, root branching, sun/shade leaves, vernalization)

Spatial signaling

cell autonomous response (guard cells) and non cell autonomous (additional stomata when mature leaves are exposed to light intensity)

How do phosphates work in phosphorylation

they are the “off switch” of protein phosphorylation

Second Messengers

Ca, pH, and ROS are second messengers that amplifying signals and regulate activity of target signalings proteins to trigger physiological responsessuch as enzyme activation, gene expression changes, and cellular responses.

Ubiquitous second messenger

Ca is abundent

Regulation of transcription

done by distal regulatory promoter sequences, enhancers, and trans-acting factors. Trans-acting factors can work together with distal regulatory sequences by binding to activate transcription by making physical contact with the transcription initiation complex.

Monitoring Gene expresion

using Reporters: GUS reporter gene, LUC, and Fluorescent micrography showing regenerating vascular tissue, and GFPGen

Gene activity (transcription) measured by quantitative reverse transcription polymearse chain reaction and

high throughput transcriptomics , global gene expression profiling

regulation of gene expression at different levels

transcription (epigenetics), post transcriptional (mRNA lifetime), and post translational (covalent modification, degradation). ex: auxin signaling pathway

vernalization

can change epigenetic changes in gene expression. modifications include: cytosine methylation of DNA, and histone modifications.

Post transcriptional regulation

RNA interferences: miRNA in plants regulate and physiological events. encoded by specific MIR genes but act on other genes. known as trans-acting regulatory factors.

post translational regulation may involve what

protein modification and protein degradation. 26S proteasome pathway degradation

Auxin signaling pathways employs what

negative regulaiton.

low auxin conditions

auxin responsive transcription factors are complexed with Aux/IAA proteins, which repress their functions and prevent transcription of auxin-responsive genes.

high auxin conditions

When auxin levels rise, auxin binds to the TIR1 receptors.This promotes ubiquitination and proteasomal degradation of AUX/IAA proteins. Gene expression is then activated