Transcript Regulation of Gene Expression

CHAPTER 28
Regulation of Gene Expression
Lehninger Principles of Biochemistry
6th Ed
28.1 Principles of Gene Regulation
28.2 Regulation of Gene Expression in Bacteria
28.3 Regulation of Gene Expression in Eukaryotes
Lehninger Principles of Biochemistry
6th Ed
28.1 Principles of Gene Regulation
-RNA polymerase binds to DNA at promoters
-Transcription initiation is regulated by proteins that bind
to or near promoters
-Many bacterial genes are clustered and regulated in
operons
-The lac Operon is subject to negative regulation
-Regulatory proteins have discrete DNA-binding domains
-Regulatory proteins also have protein-protein interaction
domains
Lehninger Principles of Biochemistry
6th Ed
Seven Processes that Affect the Steady-State Concentration
of a Protein
How to Control Protein’s Activity in
the Cell !!!
-How much primary RNA transcript to make
-How to process this RNA into mRNA
-How rapidly to degrade the mRNA
-How much protein to make from this mRNA
-How efficiently to target the protein to its
location
-How to alter the intrinsic activity of this
protein
-How rapidly to degrade the protein
FIGURE 28–1 Seven processes that affect
the steady-state concentration of a protein.
Each process has several potential points of
regulation.
Lehninger Principles of Biochemistry 6th Ed
Trends in Understanding Gene Regulation
• Past focus has been on understanding
transcription initiation
• There is increasing elucidation of posttranscriptional and translational regulation
• Mechanisms can be elaborate and
interdependent, especially in development
• Regulation relies on precise protein-DNA and
protein-protein contacts
Lehninger Principles of Biochemistry
6th Ed
28.1 Principles of Gene Regulation
Terminology-Gene Regulation
 Housekeeping gene
 Under constitutive expression
 Constantly expressed in ~ all cells
 Regulated gene
 Levels of the gene product rise and fall with the needs of
the organism
 Such genes are inducible
 able to be turned on
 and repressible
 able to be turned off
Lehninger Principles of Biochemistry
6th Ed
RNA polymerase binding to promoters is a
major target of regulation
• RNA polymerases bind to promoter sequences near
starting point of transcription initiation (Fig. 28-2)
• The RNA pol-promoter interaction greatly influences the
rate of transcription initiation
• Regulatory proteins (transcription factors) work to enhance
or inhibit this interaction between RNA pol and the
promoter DNA
Lehninger Principles of Biochemistry 6th
Ed
Consensus Sequence of Many E. coli Promoters
FIGURE 28–2 Consensus sequence for many E. coli promoters. Most base
substitutions in the–10 and –35 regions have a negative effect on promoter
function. Some promoters also include the UP (upstream promoter) element (see
Fig. 26–5).
Lehninger Principles of Biochemistry
6th Ed
Transcription initiation is regulated by
proteins that bind to or near promoters
 Specificity factors
 Alter the specificity of RNA pol. For a given promoter or set of promoters ex)
 subunit of the E. coli RNA pol-> mediates promoter recognition and binding
(Fig 28-3)
 Repressors (Fig 28-4)
 Impede access of RNA polymerase to the promoter
ex) repressors bind to specific sites on the DNA (operator in bacteria)
 Effectors
 bind to repressor and induce a conformational change
 may increase or decrease repressor’s affinity for the operator and thus
may increase or decrease transcription
 Activators (Fig 28-4)
 Enhance the RNA polymerase-promoter interaction
Ex) many eukaryotic activators bind to DNA sites “enhancer”
 Architectural regulators (Fig 28-5)
Lehninger Principles of Biochemistry 6th Ed
Many E. coli promoters have a sequence close to a
consensus sequence
• Most bacterial promoters include the conserved –10
and –35 regions that interact with the  factor of
RNA polymerase
– Substitutions in this –10 to –35 region usually reduce the
affinity of RNA Pol for the promoter
• Some promoters also include the upstream element
that interacts with the  subunit of RNA polymerase
Lehninger Principles of Biochemistry
6th Ed
FIGURE 28-3 Consensus sequence for promoters that regulate
expression of the E. coli heat shock genes. This system responds to
temperature increases as well as some other environmental stresses,
resulting in the induction of a set of proteins. Binding of RNA polymerase
to heat shock promoters is mediated by a specialized  subunit of the
polymerase,  32, which replaces  70 in the RNA polymerase initiation
complex.
Lehninger Principles of Biochemistry
6th Ed
FIGURE 28-5 The interaction between
activators/repressors and RNA
polymerase in eukaryotes
The looping is facilitated in some cases by
proteins called architectural regulators that
bind to intervening sites and facilitate the
looping of the DNA. Most of the eukaryotic
systems involve protein activators. The
actual interaction between the activators and
the RNA polymerase at the promoter is often
mediated by intermediary proteins called
coactivators. In some instances, protein
repressors may take the place of coactivators,
binding to the activators and preventing the
activating interaction
6th ed only
Lehninger Principles of Biochemistry
6th Ed
Many bacterial genes are transcribed and regulated
together in an operon
• An operon is a cluster of genes sharing a promoter and regulatory
sequences
– Genes are transcribed together so mRNAs are―several genes represented
on one mRNA
• First example: the lac operon
FIGURE 28–6 Representative bacterial operon. Genes A, B, and C are transcribed
on one polycistronic mRNA. Typical regulatory sequences include binding sites for
proteins that either activate or repress transcription from the promoter.
Lehninger Principles of Biochemistry 6th Ed
The lac operon reveals many principles of gene
regulation
• Work of Jacob and Monod
• Shows how three genes for metabolism of lactose:
– -galactosidase (lacZ)
• Cleaves lactose to yield glucose and galactose
– Lactose permease (galactoside permease; lacY)
• Transports lactose into cell
– Thiogalactoside transacetylase (lacA)-unknown
• are regulated together as an operon
• rely on negative regulation via a repressor
Lehninger Principles of Biochemistry
6th Ed
Lactose Metabolism in E. coli
• Allolactose (an inducer) binds to
repressor, causes it to dissociate
from operator
– -galactosidase not only hydrolyzes
lactose; it can also isomerize lactose
into allolactose.
– [Allolactose]  when [Lactose] 
FIGURE 28–7 Lactose metabolism in E. coli. Uptake and
metabolism of lactose require the activities of galactoside
(lactose) permease and β-galactosidase. Conversion of lactose
to allolactose by transglycosylation is a minor reaction also
catalyzed by β-galactosidase.
Lehninger Principles of Biochemistry 6th Ed
Lactose metabolism in E. coli
 When glucose is abundant and lactose is lacking, cells
make only very low levels of enzymes for lactose
metabolism
 Transcription is repressed
 If glucose is scarce and cells are fed lactose, the cells
can use it as their energy source
 The cells suddenly express the genes for the enzymes
for lactose metabolism
 Transcription is no longer repressed
Lehninger Principles of Biochemistry
6th Ed
The lac Operon is subject to negative regulation
• A gene called lacI encodes a repressor called the Lac repressor
– Has its own promoter PI
• So transcription of the repressor is independent of transcription of the
enzymes the repressor regulates.
– Repressor can bind to three operator sites (O1–O3)
• Lac repressor binds primarily to operator O1
– O1 is adjacent to promoter
– Binding of repressor helps prevent RNA polymerase from binding to
promoter
• Repressor also binds to one of two secondary operators, with the
DNA looped between this secondary operator and O1 (see Fig. 288b)
– Reduces transcription, but transcription occurs at a low, basal rate even
with the repressor bound
Lehninger Principles of Biochemistry
6th Ed
FIGURE 28–8a The lac operon. (a) The lac operon. The lacI gene encodes the Lac repressor. The lac Z, Y, an
A genes encode β-galactosidase, galactoside permease, and thiogalactoside transacetylase, respectively. P is the
promoter for the lac genes, and PI is the promoter for the I gene. O1 is the main operator for the lac operon; O2
and O3 are secondary operator sites of lesser affinity for the Lac repressor. The inverted repeat to which the Lac
repressor binds in O1 is shown in the inset. (b) The Lac repressor binds to the main operator and O2 or O3,
apparently forming a loop in the DNA.
Lehninger Principles of Biochemistry
6th Ed
Regulatory Proteins have discrete DNA-binding
domains
Binding of proteins to DNA often involves hydrogen bonding
•
•
•
•
Gln/Asn can form specific H-bond with Adenine’s N-6 and H-7 H’s
Arg can form specific H-bonds with Cytosine-Guanine base pair
See Fig. 28-10
Major groove is right size for -helix and has exposed H-bonding
groups
Asn, Gln/ Glu/
Protein
Lys, Arg
FIGURE 28–10 Specific amino acid
residue–base pair interactions.
The two examples shown have been
observed in DNA-protein binding.
DNA
Lehninger Principles of Biochemistry
6th Ed
Protein-DNA Binding Motifs
• A few protein arrangements are used in thousands of
different regulatory proteins and are hence called motifs
– Helix-turn-helix
• Used by Lac repressor
–
–
–
–
Zinc finger
Homeodomain
Leucine zipper
Basic helix-loop-helix
Lehninger Principles of Biochemistry
6th Ed
The helix-turn-helix motif is common in
DNA-binding proteins
• ~ 20 aa
– One -helix for recognition
for DNA (red in the next
slide), then -turn, then
another -helix
– Sequence-specific binding
due to specific contacts
between the recognition
helix and the major groove
• Four DNA-binding helix-turnhelix motifs (gray) in the Lac
repressor
FIGURE 28–11 Helix-turn-helix.
Lehninger Principles of Biochemistry
6th Ed
The zinc finger motif is common in eukaryotic
transcription factors
• ~30 aa
• “Finger” portion is a peptide
loop cross-linked by Zn2+
– Zn2+ usually coordinated by 4 Cys,
or 2 Cys, 2 His
• Interact with DNA or RNA
– Binding is weak, so several zinc
fingers often act in tandem
• Binding can range from
sequence-specific to random
FIGURE 28–12 Zinc fingers. (PDB ID
1ZAA) Three zinc fingers (shades of red)
of the regulatory protein Zif268,
complexed with DNA (blue). Each Zn2+
coordinates with two His and two Cys
residues.
Lehninger Principles of Biochemistry
6th Ed
The Homeodomain motif
- Identified in some proteins that
function as transcriptional
regulators, especially during
eukaryotic development.
- Related to the helix-tern-helix
motif.
- The DNA sequence that encodes
this domain is known as the
homeobox
Lehninger Principles of Biochemistry
6th Ed
Regulatory Proteins also have protein-protein
interaction domains
• Regulatory proteins contain domains not only for DNA binding
but also for protein-protein interactions-with RNA polymerase,
other regulatory proteins, or other subunits of the same
regulatory protein
• motif
– Helix-turn-helix
• Used by Lac repressor
–
–
–
–
Zinc finger
Homeodomain
Leucine zipper
Basic helix-loop-helix
Lehninger Principles of Biochemistry
6th Ed
FIGURE 28–14b Leucine zippers.
(b) (PDB ID 1YSA) Leucine zipper from
the yeast activator protein GCN4. Only
the “zippered” α helices (gray), derived
from different subunits of the dimeric
protein, are shown. The two helices wrap
around each other in a gently coiled coil.
The interacting Leu side chains and the
conserved residues in the DNA-binding
region are colored to correspond to the
sequence in (a).
FIGURE 28–15 Helix-loop-helix
Lehninger Principles of Biochemistry
6th Ed
The Leucine Zipper Motif
•
•
•
•
•
Dimer of two amphipathic -helices plus a DNA-binding domain
Each helix is hydrophobic on one side and hydrophilic on the other
– Hydrophobic side is contact between the two monomers
~Every seventh residue in helices is Leu
Helices form a coiled coil
DNA-binding domain has basic residues (Lys, Arg) to interact with polyanionic
DNA
FIGURE 28–14a Leucine zippers. (a) Comparison of amino acid sequences of several leucine
zipper proteins. Note the Leu (L) residues (red) at every seventh position in the zipper region, and
the number of Lys (K) and Arg (R)Lehninger
residues
in the DNA-binding
Principles
of Biochemistry region (yellow).
6th Ed
Eukaryotic gene regulation relies on combinatorial control
• In yeast, only 300 transcription factors for thousands of
genes
• Transcription factors mix and match
• Different combinations regulate different genes
• Relies on protein-protein interactions
Lehninger Principles of Biochemistry
6th Ed
28.3 Regulation of Gene Expression in Eukaryotes
-Transcriptionally activate chromatin is structurally distinct from inactive
chromatin
-Most eukaryotic promoters are positively regulated
-DNA-binding activators and coactivators facilitate assemble of the general
transcription factors
-The genes of galactose metabolism in yeast are subject to both positive
and negative regulation
-Transcription activators have a modulator structure
-Eukaryotic gene expression can be regulated by intercellular and
intercellular signals
-Regulation can result from phosphorylation of nuclear transcription factors
-Many eukaryotic mRNAs are subject to translational repression
-Posttranscriptoinial gene silencing is mediated by RNA interference
-RNA-mediated regulation of gene expression takes many forms in
Eukaryotes
-Development is controlled by cascades of regulatory proteins
Summary 28.3 Regulation of Gene expression in Eukaryotes
 In eukaryotes, positive regulation is more common than negative regulation,
and transcription is accompanied by large changes in chromatin structure
 Promoters for Pol II typically have a TATA box and Inr sequence, as well as
multiple binding sites for transcription activators. The latter sites, sometimes
located hundreds or thousands of base pairs away from the TATA box, are
called upstream activator sequences in yeast and enhancers in higher eukaryotes.
 Large complexes of proteins are generally required to regulated transcriptional
activity. The effects of transcription activators on Pol II are mediated by
coactivator protein complexes such as Mediator. The modular structures of the
activators have distinct activation and DNA-binding domains. Other protein
complexes, including histone acetyltransferases and ATP-dependent complexes
such as SWI/SNF and NURF, reversibly remodel and modify chromatin
structure.
Lehninger Principles of Biochemistry
6th Ed
Summary 28.3 Regulation of Gene expression in Eukaryotes
 Hormones affect the regulation of gene expression in one of two ways. Steroid
hormones interact directly with intracellular receptors that are DNA-binding
regulatory proteins; binding of the hormone has either positive or negative
effects on the transcription of genes targeted by the hormone. Nonsteroidal
hormones bind to cell surface receptors, triggering as signaling pathway that
can lead to phosphorylation of a regulatory protein, affecting its activity
 RNA-mediated regulation plays an important role in eukaryotic gene expression,
with the range of known mechanisms expanding
 Development of a multicellular organism presents the most complex regulatory
challenge. The fate of cells in the early embryo is determined by establishment
of anterior-posterior and dorsal-ventral gradients of proteins that act as
transcription activators or translational repressors, regulating the genes required
for the development of structures appropriate to a particular part of the
organism. Sets of regulatory genes operate in temporal and spatial succession,
transforming given areas of an egg cell into predictable
 The differentiation of stem cells into functional tissues can be controlled by
extracellular signals and conditions
Transcriptionally activate chromatin is
structurally distinct from inactive chromatin
Key Features of Eukaryotic Gene Regulation!
1. Access of eukaryotic promoters to RNA polymerase is
hindered by chromatin structure
– thus requires remodeling chromatin
2. Positive regulation mechanisms predominate and are
required for even a basal level of gene expression
3. Eukaryotic gene expression requires a complicated set of
proteins!!!
Lehninger Principles of Biochemistry
6th Ed
• Euchromatin = less-condensed chromatin, distinguished
from transcriptionally inactive heterochromatin (~10%)
• Transcriptionally active genes have:
– Nucleosomes repositioned
– Histone variants
– Covalent modifications to nucleosomes
– These transcription-associated structural changes in
chromatin are collectively called “Chromatin remodeling”
– The remodeling involves enzymes that promote these
changes (Table 28-2)
Lehninger Principles of Biochemistry
6th Ed
Nucleosomes can be restructured by specific protein
complexes
• SWI/SNF (SWItch/Sucrose NonFermentable) Complex
– Works with proteins of ISWI (imitation switch) family
– ATP-dependent alteration of spacing between nucleosomes, etc.
– Stimulate transcription factor binding
• NURF: a member of ISW1 family, remodels chromatin in ways that complement and
overlap the activity of SWI/SNF.
• SWR1 Family
– Change histone content(lose H1, replace H2 and H3 with variants H3.3 and
H2AZ.
(Table 28-2)
Lehninger Principles of Biochemistry 6th
Ed
Covalent Modification of Histones
•
Methylation
•
Phosphorylation
•
Acetylation
•
Ubiquitination
•
Sumoylation
•
Occur mostly in the N-terminal domain of the histones found near the
exterior of the nucleosome particle
Central domain (involved in histone-histone
interaction) +Lysine rich N-terminal domain
Covalent modification of histones allows recruitment of
enzymes and transcription factors
• Methylation of Lys-4 and Lys-36 at Histone3
(H3) and Arg of H3 and H4
– Results in transcriptional activation
– Recruits histone acetyltransferases (HATs)
that then acetylate a particular Lys
DNA(-)
– Acetylation of Lys results in decreased
affinity of histone for DNA
– Reversed by histone deacetylases
(HDACs) that make chromatin inactive
Lehninger Principles of Biochemistry 6th Ed
Idea of a “Nucleosome Code” or “Histone Code”
• Some speculate that genomes encode directions for
nucleosome organization
– Nucleosomes seem to occur at specific sequences
– Covalent modifications seem to occur at specific
regions/sequences
• A nucleosome positioning code or histone
modification code explains these observations
Lehninger Principles of Biochemistry
6th Ed
Most eukaryotic promoters are positively regulated
• Eukaryotic RNA pol have little or not intrinsic affinity for their promotes;
initiation of transcription is almost always dependent on the action of
multiple activator proteins.
Fig 28-27 The advantages of combinatorial control
Lehninger Principles of Biochemistry
6th Ed
DNA-binding activators and coactivators facilitate
assemble of the general transcription factors
In addition to TATA box and Inr (initiator) sequences, PoI II
promoters vary greatly in both no. and location of additional
sequences required for the regulation of transcription.
Additional regulatory sequences:
•Enhancer in higher eukaryotes
•Upstream activator sequences (UASs) in yeast
Lehninger Principles of Biochemistry
6th Ed
RNA polymerase II binding to eukaryotic genes requires
five types of proteins
• Transcription activators
– Proteins that bind to Upstream Activator Sequences (UASs),
Enhancers
• Architectural regulators to facilitate DNA looping
• Chromatin modification/remodeling proteins
• Coactivators
– Act indirectly (with other proteins, not with DNA)
• Basal transcription factors (fig 26-9, table 26-2)
Lehninger Principles of Biochemistry
6th Ed
FIGURE 28–5 The interaction between
activators/repressors and RNA polymerase
in eukaryotes. Eukaryotic activators and
repressors often bind sites thousands of base
pairs from the promoters they regulate. DNA
looping, often facilitated by architectural
regulators, brings the sites together. The
interaction between activators and RNA
polymerase is often mediated by coactivators,
as shown. Repression is sometimes mediated
by repressors (described later) that bind to
activators, thereby preventing the activating
interaction with RNA polymerase.
Lehninger Principles of Biochemistry
6th Ed
Enhancer proteins are diverse
• Can bind thousands of
nucleotides away from the
TATA box of the promoter
• Can have DNA-binding,
protein-binding, and/or signal
molecule-binding domains
– Can bind with multiple proteins
• Some regulate a few genes;
some regulate many
hundreds of genes
Lehninger Principles of Biochemistry
6th Ed
Architectural regulators regulate looping
• Looping of DNA allows distant enhancers to
modulate assembly at promoters
– Example: High Mobility Group (HMG) proteins
• Have multiple functions, including architectural regulation
Lehninger Principles of Biochemistry
6th Ed
Coactivators such as mediator and TATA-binding
protein (TBP) assist RNA polymerase
• Mediator complex binds to
carboxyl-terminal domain(CTD) of
RNA Pol II
– Required for both basal and
regulated transcription at many
promoters
– Later provides assembly surface
for other complexes
• TATA-Binding Protein is first
component of preinitiation complex
(PIC) at the typical TATA box of a
promoter
Lehninger Principles of Biochemistry
6th Ed
Details of Eukaryotic Regulation that Are Emerging
• Binding of activators triggers many promoters to bind
RNA Pol II
– Binding one activator seems to enable binding of additional
activators
– Often components bind in a regular order
– Histones are displaced as activators bind
– Process coordinates with chromatin remodeling
(Fig. 28-29)
Lehninger Principles of Biochemistry
6th Ed
Reversible Transcriptional Activation
- Although rarer, some eukaryotic regulatory proteins that bind to PoL II
promoters or that interact with transcriptional activators can act as repressors,
inhibiting the formation of active PICs
Lehninger Principles of Biochemistry
6th Ed
The genes of galactose metabolism in yeast are
subject to both positive and negative regulation
The regulation of genes for importing and metabolizing
galactose in yeast illustrates important principles
• Genes for galactose metabolism (GAL) are spread over
several chromosomes
• But all have similar promoters
– TATA box, Inr sequences, Upstream Activator Sequence (UASG)
recognized by Gal4 protein (Gal4p)
Lehninger Principles of Biochemistry
6th Ed
All GAL genes are regulated by a
common set of proteins
• Galactose binds Gal3p, then
forms a complex with Gal4p and
Gal80p(inhibitor for Gal4p)
• Allows Gal4p to be activator
• Gal4 also recruits the SWI/NSF
and mediator complexes for
opening the chromatin
Lehninger Principles of Biochemistry
6th Ed
Transcription activators have a modulator
structure
• Three types of structural domains used in activation by
transcription activators
 Gal4p has separate activation domain with many acidic amino
acid residues. “acidic activation domain of Gal4p” (acidic
nature is critical to its function)
 Sp1’s DNA binding sites=GCbox (GGGCGG) near TATA box
In addition to DNA binding domain with zinc finger, two other
domains in Sp1 function in activation are notable in that 25%
of their AA residues are Gln (glutamine-rich domain)
 CTF1 bind CCAAT site. DNA-binding domain of CTF1
contains many basic AA residues, and the binding region is
probably arranged as an a helix. This protein has neither a
hlix-turn-helix nor a zinc finger motif. It has proline-rich
activation domain (proline >20%)
Lehninger Principles of Biochemistry
6th Ed
Eukaryotic gene expression can be regulated by
intercellular and intercellular signals
• Steroid hormone: two types of steroid-binding nuclear
receptor
- The hormone-receptor complex acts by binding to highly
specific DNA sequences called hormone response elements
(HRE).
• Hormone receptors have DNAbinding domain with zinc fingers
• Hormone receptors also have
ligand-binding region at Cterminus that is highly variable
between different receptors
Lehninger Principles of Biochemistry 6th Ed
Hormones bind to one of two types of receptors
Fig. 28-32
• Monomeric Type 1 (NR)―receptors for sex hormones and
glucocorticoids
– Found in cytoplasm in complex w/Hsp70
– When hormone binds, Hsp70 dissociates
• Receptor dimerizes
• Exposes nuclear localization region
– So hormone-receptor complex travels to nucleus to be transcriptional
activator
• Type II (includes thyroid hormone receptor; TR)
– Found in nucleus bound to DNA and corepressor Retinoid X
receptor (RXR)
– Hormone binds, corepressor dissociates
– Receptor-hormone complex then activates transcription
• SRA, an unusual coactivator for some HR(like AR), act as part of a
ribonucleoprotin complex.
Lehninger Principles of Biochemistry 6th Ed
Fig. 28-32 Mechanisms of steroid hormone receptor function
Lehninger Principles of Biochemistry 6th Ed
Regulation can result from phosphorylation of
nuclear transcription factors
Eukaryotic gene expression is also regulated by
peptide hormones
• 2 messengers lead to activation of transcription factors
• Example: -adrenergic pathway (ex.epinephrine)
– cAMP activates protein kinase A (PKA)
– PKA enters nucleus, phosphorylates cAMP response elementbinding protein (CREB)
– CREB is a transcription activator of genes leading to fuel use rather
than fuel storage
Lehninger Principles of Biochemistry
6th Ed
Many eukaryotic mRNAs are subject to translational
repression
Eukaryotes have at least four main mechanisms of translational regulation
1. Translation initiation factors are subject to phosphorylation by
protein kinases. The phosphorylated forms are often less active and
cause a general depression of translation in the cells.
Ex) when reticulocytes become deficient in iron or heme, the translation of
globin mRNA is repressed. HCR(hemin-controlled repressor) protein kinase
is activated, catalyzing the phosphorylation of eIF2.
2. Some proteines bind directly to mRNA and act as translational
repressors. At 3’UTR (Fig 28-34)
3. Binding proteins, present in eukaryotes
From yeast to mammals, disrupt the interaction
Between dIF4E and eIF4G (fig. 27-28)
The mammalian versions are known as 4E-BPs
(eIF4E binding proteins)
4. RNA-mediated regulation of gene expression,
Lehninger Principles of Biochemistry
6th Ed
Posttranscriptoinial gene
silencing is mediated by RNA
interference
Micro-RNAs prevent translation of
mRNA
• Micro-RNAs (miRNAs) silence
genes by binding to mRNAs
– Can prevent transcription of the mRNA
by cleaving it (via endonucleases
Drosha or Dicer) or by blocking it
• Some miRNAs are made briefly
during development, called small
temporal RNAs (stRNAs)
Lehninger Principles of Biochemistry
6th Ed
Researchers can shut down genes
artificially via RNA interference
• Any dsRNA that corresponds to
an mRNA and is introduced
into a cell will be cleaved by
Dicer into short segments
called small interfering RNAs
(siRNAs)
• These will bind to the mRNA to
silence its translation
• Process is called RNA
interference
Lehninger Principles of Biochemistry
6th Ed
RNA-mediated regulation of gene
expression takes many forms in Eukaryotes
• ncRNA (noncoding RNAs) DO NOT encode proteins,
including rRNAs and tRNAs
Ex) the special-function RNAs in eukarytoes include miRNAs,
snRNA (RNA slicing), snoRNAs (rRNA modification)
SRA (coactivator)
Lehninger Principles of Biochemistry
6th Ed
Stem cells have developmental potential that can be
controlled
Development is controlled by cascades of regulatory
proteins
The life cycle of the fruit fly includes complete metamorphosis during its progression from
an embryo to an adult (Fig 28-36).
Among the most important characteristics of the embryo are its polarity (the anteritor and
posterior parts of the animal are readily distinguished, as are its dorsal and ventral parts)
and its metamerism (the embryo body is made up of serially repeating segments, each with
characteristic features)
During the development, these segments become organized into a head, thorax, and
abdomen. Each segment of the adult thorax has a different set of appendages (Fig. 28-26).
Development of this complex pattern is under genetic control, and a variety of patternregulating genes have been discovered that dramatically affect the organization of the body.
Lehninger Principles of Biochemistry
6th Ed
Figure 28-26. Life cycle of the fruit fly Drosophila m
Lehninger Principles of Biochemistry
6th Ed
Proteins that, through changes in local concentration or activity, cause the
surrounding tissue to take up a particular shape or structure are sometimes
referred to as morphogen; they are the products of pattern-regulating
genes.
3 major classes of pattern-regulating genes
1.maternal, 2.segmentation, 3.homeotic genes
-function in successive stages of development to specify the basic features
of the Drosophila embryo body.
1.Maternal genes are expressed in the unfertilized egg, and the resulting maternal
mRNAs remain dormant until fertilization. These provide most of the proteins needed
in very early development, until the cellular blastoderm is formed. Some of the
proteins encoded by maternal mRNAs direct the spatial organization of the
developing embryo at early stages, establishing its polarity.
2.Segmentation genes, transcribed after fertilization, direct the formation of the
proper number of body segments. Gap genes(divide the developing embryo into
several broad regions, pair-rule gene together with segment polarity genes define
14 strips that become the 14 sements of normal embryo.
3.Homeotic genes are expressed still later, they specify which organs and
appendages will develop in particular
body segemtns.
Lehninger Principles
of Biochemistry
6th Ed
The key to tissue regeneration lied in stem cells-cells
that have retained the capacity to differentiate into
various tissues.
-In human, after an egg is fertilized, the first few cell
divisions create a ball of totipotent cells (the morula),
cells that have the capacity to differentiate individually
into any tissue or even into a complete organism (Fig
28-43)
The inner layers form the germ layers of the developing
fetus-the ectoderm, mesoderm, endoderm. These cells
are pluripotent: They can give rise to cells of all three
germ layers and can differentiate into may types of
tissues. However, they can’t differentiated into a
complete organism. Some of these cell are unipotent:
they can develop into only one type of cell and/or tissue.
It is the pluripotent cells of the blastocyst, the
embryonic stem cells.
In adult organism, adult stem cells, as products of
additional differentiation, have a more limited potential
for further development than do embryonic stem cells.
Ex. hematopoietic stem cells of bone marrow. They are
referred to as multipotent.