This document summarizes research on B-box proteins. It begins by describing the structure of zinc finger domains and their ability to bind DNA, RNA, or proteins. It then discusses B-box (BBX) proteins, which contain zinc finger domains and are involved in plant protein-protein interactions and transcription factor activity. The document reviews studies of BBX proteins in animals and plants, describing their roles in processes like photomorphogenesis, flowering time regulation, and shade avoidance responses. Case studies are presented on specific BBX proteins in Arabidopsis and crops like rice and soybean.
Transcription factors are modular in structure means constructed with standardized units or dimension allowing flexibility and variety in use. It contain 3 domains as ;
1. DNA binding domain – This domain binds to responsive elements present in target DNA. It is conserved region of structure.
2. Trans-activation domain – This domain contain binding site for another proteins ( repressor , activator) . This domains do not generate identifiable electron density in the crystallography analysis , which indicates that thay do not form discreate structures and acts as induced fit model
3. Signal sensing domain - Sense external signals and transmits these to rest of transcription complex
Transcription factors are modular in structure means constructed with standardized units or dimension allowing flexibility and variety in use. It contain 3 domains as ;
1. DNA binding domain – This domain binds to responsive elements present in target DNA. It is conserved region of structure.
2. Trans-activation domain – This domain contain binding site for another proteins ( repressor , activator) . This domains do not generate identifiable electron density in the crystallography analysis , which indicates that thay do not form discreate structures and acts as induced fit model
3. Signal sensing domain - Sense external signals and transmits these to rest of transcription complex
Fine Structure of Gene- Biotechnology, Microbiology PPT DownloadEducation Bhaskar
Fine Structure of Gene- Biotechnology, Microbiology PPT, PDF
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SYNOPSIS
Introduction
History of gene
Definition of gene
Gene structure
Prokaryote gene
Eukaryote gene
Significance of introns.
References
Fine Structure of Gene- Biotechnology, Microbiology PPT DownloadEducation Bhaskar
Fine Structure of Gene- Biotechnology, Microbiology PPT, PDF
Download the presentation
SYNOPSIS
Introduction
History of gene
Definition of gene
Gene structure
Prokaryote gene
Eukaryote gene
Significance of introns.
References
photoperiodism its discovery,significance,classifications,mechanism,critical day length,quality of light, night break phenomenon,phytochrome.florigen,floering genes, circadian rhythm
Majority of agronomic traits are quantitative and are controlled polygenetically.Instead of producing transgenic plants through single gene transfer many researchers are attempting on multigene engineering. The simultaneous transfer of multiple genes in to plants will enable us to produce plants with more desirable characters. Engineering of genes coding for complete metabolic pathways, bacterial operons or biopharmaceuticals that require an assembly of complex multisubunit proteins etc are some of the successful examples of multigene engineering.
Gene for gene system in plant fungus interactionVinod Upadhyay
MOLECULAR CHARACTERIZATION OF GENE FOR GENE SYSTEMS IN PLANT- FUNGUS INTERACTION AND THE APPLICATIONS OF AVIRULENCE GENES IN CONTROL OF PLANT PATHOGENS
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Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
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As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
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2. 2
Om Prakash Patidar
University of agricultural
sciences , dharwad, karnataka
Date of seminar 31 oct 2014
3. Introduction
B-box proteins in animals
B-box proteins in plants
Conclusion
3
Structural classification
Functions and related Case studies
4. Zinc finger proteins
• Zinc finger protein contain Zinc finger domains that are stabilized by metal
ions including zinc.
Characterized by 2 anti parallel b sheets and 1 a helix
Structure stabilized by binding of Zinc ion
Zinc binding mediated by specific cysteine (b sheets) and histidine (a
helix) residues
4
2 b sheets
1 a helix
Zn
5. zinc finger domains
• Zinc finger domains make multiple contacts on target molecule
• Can bind to DNA, RNA or protein.
• Versatility in binding results in specialized functions including gene
transcription, translation, mRNA trafficking, cytoskeletal organization and
chromatin remodeling.
• There are several classes in zinc finger protein. One of them is BBX
proteins.
5
6. B-Box (BBX) Proteins-
are a class of zinc-finger transcription factors.
Involved in protein-protein interactions.
contain a B-box domain with one or two B-box
motifs, and
6
A-box B-box
RING B-1 B-2
COILED COIL
7. B-Box proteins in Animals
• Here BBX often associated with other domains
like RING and coiled coil domains.
7
R B CC
(TRIM)
18. Distribution of the BBX genes on the rice chromosomes.
The segmental duplicated genes are indicated in a different color and are connected by lines 18
21. Summary of roles of B-box proteins in
plants
• In seedling photomorphogenesis.
• In flowering.
• In shade avoidance Responses.
• In abiotic and biotic stresses.
21
25. Case study
LZF1, a HY5-regulated transcriptional factor, functions in
Arabidopsis de-etiolation (photomorphogenesis)
25
Chang et al., 2008
26. Mechanism of regulation of photomorphogenesis
26
Phytochrome
HY5
LZF1 (light regulated zinc
finger protein, BBX)
MYB75/PAP1
(Anthocyanin
accumulation)
Ferredoxin-thioredoxin
cascade for
chloroplast
biogenesis
Inhibition of
Hypocotyl
growth rate
sun
Photomorphogenesis
27. LZF1 acts synergistically with HY5 in the light-regulated inhibition of hypocotyl
elongation
Wild genotypes (normal Hy5 and LZF1)
Over expression of LZF1
27
1
23
45
6
7
(Double mutants)
1 2 3 4 5 6 7 1 2 3 4 5 6 7
DARK LIGHT
Less hypcotyl length
28. RT-PCR analyses of Lzf1 and MYB75 in Col (wild) and
LZF1-ox plants ( at 5 day old stage)
(Anthocyanin promoting
factor)
28
(Control)
(Wild) (overexpressing)
29. LZF1(B-box protein) regulates anthocyanin and chlorophyll accumulation in
seedlings during photomorphogenesis.
29
overexp
ressing
overexpr
essing
mutant
mutant
30. Shade Avoidance Response(SAR)
Shade Avoidance:
Morphological changes like Hypocotyl and stem elongation, Acceleration of flowering
to avoid shade and to compete for light in high density plantings.
30
31. 31
Mechanism of shade avoidance response
More far red in
shade
BBX
(red) (Far red)
Jiao et al., Nature review genetics, 2007
33. BBX in Shade Avoidance Response(SAR)
• Inhibitors of SAR- BBX 19, BBX 21, BBX22
• Promoters of SAR-BBX18,BB24,BBX25
• BBX21- act as component of negative
feedback to avoid exaggerated response of
SAR genes(PAR1, HFR1,ATHB2 etc.)
33
34. SAR inhibition by BBX21
34
Mutants of BBX
No inhibition of
hypocotyl growth
in shade
Mutant gene
36. case study
Hd1, A Major Photoperiod Sensitivity QTL in Rice, is Closely Related to the
Arabidopsis Flowering Time Gene CONSTANS (Atbbx1)
- Yano et al., 2000 36
37. mapping population & created genetic map of photo sensitive gene loci
37
(hd1) mutant
Late flowering
(Hd1) wild
Early flowering
Major QTL for flowering in rice:
a B-box protein.
38. 38
Fine mapping of Hd1 region using markers on chromosome 6 of rice
RFLP
YAC
PAC
4 CAPS markers co-segregated with Hd1
P0038c5
39. Comparison Of rice Hd1, Arabidopsis CO, and Brassica
napus BnCOA1 B-boxes
39
40. hd1 NILs(mutant, late flowering) are transformed with Hd1(wild, early flowering) candidate
40
gene segment (apal 7.1 kb) isolated from Nipponbare
8
6
4
2
0
52 53 54 55 73 74 75 76
Hd1 Transformed NILs
hd1 NILs.
Days to heading
No. of plants
Hd1(wild)
Transformation of hd1 containing
NILs, late flowering lines
Those lines transformed shown early flowering due to presesnce of Hd1
41. Case study
Expression of the Arabidopsis thaliana BBX32 Gene in
Soybean Increases Grain Yield
- Preuss et al.,2012
(Monsanto Company, USA & Mendel Biotechnology inc., USA)
41
42. Micro array to detected that there is higher alteration of gene expression near dawn(6 am)
42
Arabidopsis
Atbbx32 Soybean 8 transgenic lines
Multilocation multiseason trial for yield
Out of 8, 4 yielded more than 5% over control
2 lines selected of it & grown in field and in controlled chamber
Observation taken at different stages and Similar results found as earlier in multilocation trials
Studied circadian clock components and found the cause of phenotypic changes
and higher yield
Search for Atbbx32 homolog in soybean by phylogeny
study
Gmbbx52 & Gmbbx53 found homolog,
There over expression gave same results as by Atbbx32
44. To understand physiological impacts two representative lines
(line1&2) grown in both controlled and field conditions
44
45. AtBBX32 extends the reproductive period between R3
and R7developmental stages in soybean resulting in a
delay in final maturity compared to control
Developmental stages
R1(Initiation of
flowering.)
R3 (Onset of pod
development)
R7 (Beginning of
maturation)
R8 Stage where
95% of the pods are
physiologically
mature.
Control 38.1 57.8 112.5 120.4
Event1 39.3 57.7 115.8* 122.8*
Event2 39 57.2 116.7* 123.6*
45
47. Microarray data from field grown lines
(line1 and line 2)
(3 am) (6 am) (9 am) (12 pm) (3pm)
Total 219 genes show 2–8 fold changes in abundance in both transgenic events relative to the control.
Dark bar- Genes increased in abundance
light bar- Genes decreased in abundance.
47
Incr
eas
ed
D
e
cr
e
a
s
e
d
84% of total
genes changes
at 6 am (dark to
light transition)
48. Expression of AtBBX32 in soybean affects the transcript
abundance of central clock components near 6 am(ZT 0)
Gm LCL2
GmTOC1
48
(5 am) (2 pm) (2 am)
(5 am) (7 am) (5 pm) (2 am)
51. Labs working on B-box proteins
51
Postal Address:
Mendel Biotechnology lab, Inc.
3935 Point Eden Way
Hayward, California ,
USA
St. Louis --World Headquarters
Monsanto Company lab
800 North Lindbergh Blvd.
St. Louis, Missouri, USA 63167
Signal Transduction lab
National Institute of technology
Durgapur, West Bengal, India
National Institute of Plant
Genome Research
Aruna Asaf Ali Marg,
New Delhi - 110 067
Dr. holm’s laboratory
Box 100, SE-405 30
Gothenburg, SWEDEN
52. Future line of work
• understanding the molecular mechanisms of
each individual BBX protein.
• the complexity and modularity of the system
is to be understand and simplified
• Bringing this knowledge from lab to farmers
field at commercial level in order to increase
food production.
52
