plant gene expression
DESCRIPTION
Genome Genes Expression. Plant Gene Expression. Same genome in somatic cells Different structures and functions. Differential gene expression Spatial: organs Temporal : time. Differential Gene Expression. Same proteins for Common processes - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/1.jpg)
Plant Gene Expression Genome Genes Expression
Differential gene expression Spatial: organs
Temporal : time
Same genome in somatic cells Different structures and functions
![Page 2: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/2.jpg)
Differential Gene Expression
Same proteins for Common processes
Some abundant proteins in certain cell types
Some minor proteins in certain cells at certain times
- 1 0 ,0 0 0 2 0 ,0 0 0 proteins in cells- - 1520% as tissue specific proteins
![Page 3: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/3.jpg)
Control of Gene Expression
Regulation at steps:
Transcription : which gene, when, howoften Post transcription : RNA processing and transport
Translation : which transcript and for howlong Post translation : activity and stability of proteins
![Page 4: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/4.jpg)
Control of Gene Expression
******
*
![Page 5: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/5.jpg)
Transcriptional Control
I Gene control regions & Regulatory protein components of genetic switch
Gene control regions 5 3’ Promoter and ’ Terminator 5’ Regulatory sequence
3(some inside or at ’)
![Page 6: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/6.jpg)
Proximal promoter
5’ promoter or proximal promoter
Common sequence: TATA / CAAT box
Binding site for transcription machinery
RNA Pol and general transcription factors
![Page 7: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/7.jpg)
Regulatory sequences or distal promoter
or cis element or responsive element
Specific and consensus for gene expression
Binding site for gene regulatory proteins
or trans acting element or trans element
or specific transcription factor
Distal promoter
![Page 8: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/8.jpg)
Transcriptional Control
Genetic switch: turning genes on / off
![Page 9: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/9.jpg)
Transcription Initiation
![Page 10: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/10.jpg)
Transcription Initiation
![Page 11: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/11.jpg)
Gene activating protein
DNA binding domain Gene activation domain
Specific binding at major groove of DNA Control rate of transcription initiation
except for general transcription factor TFIID: TATA binding protein that binds minor groove
![Page 12: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/12.jpg)
- Major Minor groove
![Page 13: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/13.jpg)
- DNA Protein interaction
Hydrogen bond Ionic bond
Hydrophobic interaction
Strong and Specific binding Compatible structure of DNAand Protein
- 2030 contacts per match
![Page 14: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/14.jpg)
Gene Activating Protein
DNA binding motif Helix Turn Helix
Zn fingerβ sheet
Leucine zipper Helix Loop Helix
![Page 15: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/15.jpg)
Helix Turn Helix
![Page 16: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/16.jpg)
Helix Turn Helix
![Page 17: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/17.jpg)
trp repressor dimer
Helix Turn Helix
![Page 18: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/18.jpg)
Zn Finger
![Page 19: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/19.jpg)
sheet
![Page 20: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/20.jpg)
Leucine Zipper
![Page 21: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/21.jpg)
Leucine zipper
![Page 22: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/22.jpg)
Helix Loop Helix
![Page 23: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/23.jpg)
Transcriptional control
II Chromatin structure
DNA packaging
Heterochromatin: condensed
Euchromatin: relaxed
![Page 24: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/24.jpg)
Chromatin structure
Most organisms have both types Except for
yeast: euchromatin some algae and maize B chromosome:
heterochromatin
![Page 25: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/25.jpg)
Chromatin structure
![Page 26: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/26.jpg)
Chromatin structureHeterochromatin
Genetically inactive Inaccessible for transcription machinery
Euchromatin Loose nucleosome / movable histones
Available for protein binding Genetically active
![Page 27: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/27.jpg)
Chromatin structure
![Page 28: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/28.jpg)
Chromatin structure
![Page 29: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/29.jpg)
Transcriptional control
III DNA methylation
Hypermethylation: Gene inactivation Methyl group on Base
Methylase
![Page 30: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/30.jpg)
Eukaryote: more often in CG dinucleotide Vertebrate: only in CG
DNA methylation
![Page 31: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/31.jpg)
Cytosine Methylation
Methyl group on position #5 of Cytosine ring 5meC
![Page 32: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/32.jpg)
Maintenance of methylation pattern
![Page 33: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/33.jpg)
- Methylation induced Mutation
Deamination of Cytosine / 5meCytosine Cytosine deamination (U)
Repair 5me Cytosine deamination (T)
Mutation
![Page 34: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/34.jpg)
- Methylation induced Mutation
![Page 35: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/35.jpg)
Methylation
Plants: - 34~ %of genome = CGAnimals: ~0.5-1 % of genome = CG
- Methylation found in 70 80% of CG
![Page 36: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/36.jpg)
Wheat Germ DNA
Highly methylated on CG or CNG 8 2 % of CG 19% of CA / CT
7 % of CC 80+ % of CAG / CTG
- 4 % of CAT
![Page 37: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/37.jpg)
- Post transcriptional Control I Attenuati
on Bacterial regulation of polycistronic RNA Complete/Incomplete RNAproduction
mRNA inhibit RNA polymerase incomplete transcription
mRNA interact with Regulatory protein complete transcription
![Page 38: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/38.jpg)
II Alternative splicing 1 primary transcript / many mature transcript 1 gene / diversed mRNA / many proteins
May function in different organs May function in different developmental stages May have opposite functions
- Post transcriptional Control
![Page 39: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/39.jpg)
Alternative Splicing
Exon skipping / Optional exon
Intron retention / Optional intron
Mutually exclusion exon
Alternative 5’ / 3’ splice site
Alternative selection of promoter / PolyAsite
![Page 40: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/40.jpg)
Alternative Splicing
![Page 41: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/41.jpg)
Alternative Splicing
![Page 42: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/42.jpg)
Alternative Splicing
![Page 43: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/43.jpg)
III Varied C terminus
- Post transcriptional Control
Polyadenylation at different sites Same proteins of Different lengths
w wwwww wwwwww wwwwwwwwwww w wwww wwww. /IV RNA transport
Half of primary transcripts: destroyed Parts of transcripts to be processed Most mature RNA: out to cytoplasm
![Page 44: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/44.jpg)
V RNA editing (modification) Addition or Deletion of U
Deamination of C to U (plant mt)
- Post transcriptional Control
VI Trans-Splicing Exons from 2 independent transcripts
![Page 45: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/45.jpg)
- Post transcriptional Gene Silencing
PTGS: transcription without translation
Found in plants and animals
Also in protozoa, insects and nematodes
Caused by transgene, virus or homologous dsRNA
![Page 46: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/46.jpg)
- Transgene induced PTGS
Cosuppression Silencing of Endogenous gene
Triggered by Transgene - Silencing occurs at post transcriptional level
Homologous transcripts made & exported Rapid degradation in cytoplasm
![Page 47: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/47.jpg)
Petunia - Transformed with pigment producing gene
Expected deep purple color Appeared variegated to white
- Transgene induced gene silencingwwww ww wwwwwwwwwwwww
- gene specific methylation
- Transgene induced PTGS
![Page 48: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/48.jpg)
- Viral induced PTGS
Introduction of certain viruses to host plants
dsRNA as trans- acting factor responsible for PTGS
w wwwwwwww w w w wwwwwwwwww for gene silencing
P T P T
![Page 49: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/49.jpg)
RNA interference
dsRNA to knock out gene expression so called RNA interference or RNAi by initiating Small Interfering RNA (siRNA)
to induce silencing of endogenous transcript
application
![Page 50: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/50.jpg)
RNAi
Much more efficient than using either strand as in cosuppression or antisense technology Good for Gene Knockout studies
wwwwww www wwwwwww wwwwww wwww-ww-wwwwwwww wwwwwwwwww Tool for Functional Genomics
wwwww ww wwwwwwwww w wwwwww ww w wwww w
![Page 51: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/51.jpg)
I mRNA stability - Bacterial RNA: 3 minute half life
Eukaryote: more stable esp. housekeeping mRNA except for tx of regulatory proteins
AU stretch at3’ UTR activates RNAdegradation by removing Poly A tail
Translational Control
![Page 52: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/52.jpg)
Translational Control
II Translational recoding / frameshifting mechanism found in virus
1 1mRNA for > proteinNNNNNNNNNNNNNNNNNN
![Page 53: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/53.jpg)
- Post translational Control I Protein activity
Folding: helix/ sheet Assembly: Subunits
Reversible phosphorylation
II Protein stability Degradation of unassemble, misfolded, or
damage protein
![Page 54: Plant Gene Expression](https://reader036.vdocuments.site/reader036/viewer/2022062518/56814467550346895db0fc54/html5/thumbnails/54.jpg)
Protein structure