Wherever we look
at life we can discover “organizational systems”, and elicit
principles of such organization.
I want to address
what genes may do, including the special requirements in multicellular
organisms.
Genes.
Genes are of course
the units of heredity.
Germ cells (ova
and spermatozoa) carry mostly the genes of ancestral lines, but as well
mutations, some of which are virally and environmentally induced
Genes are constituted
by sequences of bases called adenine (A) and guanine (G) (purines) and
cytosine (C) and thymine (T)(pyrimidines), which are linked to sugars
and phosphates as nucleotides.
A nucleoside consists
only of the base plus the sugar, and when the phosphate is added it
is called a nucleotide.
The genetic information
is coded in DNA (desoxyribonucleic acid).
The only way the
bases can pair is T-A and C-G (Watson and Crick) and the sequences form
the famous double helix, which these researchers described.
Most of the DNA
in our cells (eukaryotic cells) is in the nuclei, but some viruses have
DNA, which they are unable to use unless they are inside cells.
Viruses may have
between 20 and 200 genes, while prokaryotes (bacteria) have 1.000-3,
000 genes.
The nematode worm,
Caenorhabditis elegans has about 19,000 protein coding genes, while
human beings appear to have about 22,000 genes.
In the following
discussion about non-protein coding genetic material, I will attempt
to give insights into recent discoveries about “non-coding”
DNA and surprising new information about RNAs.
It is difficult
to explain viruses without seeing them as products of prokaryotic (and
perhaps later eukaryotic) cells.
The DNA carries
the master codes from which the body can synthesize proteins.
RNA (ribonucleic
acid) has the base uracil connected to the adenine rather than thymine,
U-A) and its sugar is ribose.
In eukaryotic cells
(cells with nuclei), messenger RNA (mRNA) is transcribed from DNA in
the nucleus, and travels through pores in the nuclear membrane in ribosomes
to the cytoplasm.
Some of the ribosomes
are then located on the rough endoplasmic reticulum, and the sequencing
of the bases on the messenger RNA, gives triplets which code for the
amino acid assembly into polypeptides and proteins.
This transcription
is a copy of the totality of the gene as an RNA transcript.
Then follows a process
called “splicing”, where intronic RNAs are removed leaving
the coding sequence we call messenger RNA.
Transfer RNA (tRNA)
molecules carry amino acids to ribosomes, which are the structures in
which proteins are assembled through the messenger RNA.
Ribosomes can also
migrate from nucleus to cytoplasm through the pores.
Ribosomal RNA (rRNA)
can vary in type from prokaryotes (cells without nuclei such as bacteria)
to eukaryotes and combine with proteins to form ribosomal subunits.
Prokaryotic ribosomal
subunits are called 50S (about 34 proteins) and 30S (about 21 proteins).
These will be mentioned when I describe certain antibiotic actions.
Eukaryotic (cells
with nuclei) ribosomal subunits are called 60S (about 50 proteins) and
40S (about 33 proteins)
In essence these
names or codings are the invention of scientists who discover ribosomal
structures and their functions.
Other RNAs are involved
in primers for DNA replication and other splicing and modification reactions
in RNA precursor assembly.
RNA also serves
as the genome for certain viruses (eg HIV)
In general the sequence
of information is from DNA to RNA, but in retroviruses like HIV, an
enzyme called reverse transcriptase uses the RNA genome to produce a
DNA copy.
The human genome
project, together with intricate details of the functional molecular
consequences, is truly revolutionizing biological knowledge.
We have paid much
attention to genes as carriers of codes for protein sequences, but so-called
coding DNA accounts for less than 1% of nuclear DNA in human beings.
Before we consider
so-called “non-coding DNA”, we can consider organizational
elements.
(1) CASCADES.
This describes
gene regulators which can switch on and off in appropriate time, situation
and coordination.
It can include
(a) Controlling
more than one gene.
(b) Participating
in a hierarchy of occurrences.
(c) Feedback
control.
(2) SIGNALLING
We might call
this “complex cell cross-talk”
A. Messengers
It must be apparent
that messengers or signalling substances (called ligands) can dock
onto specific receptor sites, thus initiating sequences of gene activations
and the production of proteins which trigger the next step.
B. Receptors
These have been
discovered in
(a) Cell membranes.
(Example: G coupled protein receptors. These have an extracellular
domain, a transmembrane domain and an intracellular domain.)
(b) Cytoplasm,
(c) Nucleus
C. Down-stream-events
This involves
intracellular switching (eg with G coupled protein receptors, GDP
is off and GTP is on, and the happening involves phosphorylation),
gene activations, transcriptions of DNA to RNA, assembly of proteins,
and often enzymes which trigger yet another step.
D. Cybernetical
happenings
involving feed
forward and feedback regulations. A product may turn off the activation.
(3) CELL POSITIONING.
With complex cell
arrangements, gene regulators are part of locating and orienting cells.
HOW IS THIS POSSIBLE?
Creatures have
a top or head end and a tail or bottom end.
They also have
lateral structures such as limbs or wings, and a front –back
axis.
Genes have been
discovered which make orienting proteins.
These are called
HOX genes and the HOX proteins code to the cell crucial information
about their position (eg top, middle or bottom)
They were discovered
in a fruit fly, and have been found in all animals.
Once such crucial
genes exist, they are highly conserved during evolution.
Human beings appear
to have at least 38 HOX genes.
PAX6 protein controls
the development of eyes in fruit fly and mammals.
So to reiterate,
signalling proteins give cells orientation.
Special cells
are organizers, and subtle gradients exist across groups of cells.
More will emerge
about these regulations.
(4) DIVIDING/RESTING.
During development
there is much more dividing, while in the adult state many adult cells
are resting from division. (Quiescent but functioning)
In a developing
embryo, cells are dividing rapidly and proteins move between inactive
and active forms.
Cyclins are very
unstable. They form rapidly and breakdown rapidly.
If a cyclin rises,
it will stick to the switch DNA of its own gene causing it to switch
off. Thus cyclin falls and the gene switches back on.
Cell surroundings
influence such events.
(5) FATES
Cells appear to
move passively, but there are “attractors”.
Spinal cells are
attracted to move along the spinal cord, and also to make a tube.
Eye cells can
arrange to make a cup.
Fingers cells
appear in paddle shapes, but apoptosis (programmed cell death allows
cells to die creating spaces between fingers.
We will see emerge
allowing of basic patterns, but there is enough variety to allow for
formation of unique individuals.
Consider, height,
build, proportion of muscle and muscle type, colour or skin, hair,
eyes, shape of face, nose, ears, as such physical variables!
While all of this
is happening, there are such other factors as prevailing environmental
conditions, nutrient intakes, state of hydration, temperature, presence
of microorganisms, and hormones.
What a journey
there is from the fertilized egg of human beings to the adult with
many 100 trillion cells!
Non-coding DNA
DNA sometimes codes
for RNA sequences that are not translated.
Names are given
to specific regions along chromosomes.
Exons are portions
of genes (DNA sequences) that are eventually spliced together to allow
formation of messenger RNA, and code for protein assembly.
Introns are segments
spliced from precursor RNAs during RNA processing located in spacing
between exons. They do not code for proteins.
Research has revealed
regulators of genes in at least three locations.
(1) Promoters,
which are upstream of transcription start sites,
(2) Inside introns
(3) Downstream,
in a polyadenylation tail region)
Most genes have
at least 15-20 discrete regulatory elements within 300 base pairs of
transcription start points.
Perhaps as many
as 35-50, 000 RNA only genes are located within non-coding DNA regions.
Some 1,194 sequences
are highly conserved, showing very little variation between rats, dogs,
cows and human beings. Of these about two- thirds were in introns, 244
in coding DNA and the rest in noncoding DNA.
The name “pseudogenes”
refers to non-protein making genes, which are complementary DNA sequences
on the other side of the DNA ladder.
In some cases the
alter-ego churns out antisense DNA.
If sense and antisense
RNAs meet, the gene cannot express the protein.
The example is Makorin1
p1, which is a pseudogene copy of makorin1, and cannot make the protein,
but when it is knocked out, makorin 1 shuts down.
It may well emerge
that as many plants and bacteria as well as >1,600 human genes can
express anti sense RNA, there is a big potential for the interplays
to bring about both defensive functions, but also pathogenic consequences.
By 2003, some 150
micro RNAs have been found in human beings. Many more will be found.
Nelson Lau and David
Bartel write of the discovery of RNA interference (RNA-i), which can
silence expression of threatening genes, by interrupting only the offender’s
messenger RNA without disturbing the messages of other genes.
Viruses on entering
cells may activate a blocking effect through RNA-i
Andrew Fire and
Craig Mello observed potent silencing effects on the unc-22 gene of
C elegans when the worms were inoculated with corresponding unc-22 double
stranded RNA, when neither the corresponding single-stranded RNAs, whether
sense or antisense, had any effect.
There are genes
to convert single-stranded RNA into double stranded RNA.
This was illustrated
by Douglas at Oregon State University, in the tobacco etch virus and
genetically engineered tobacco plants that contained copies of the coat
protein gene of the virus. Some plants proved to be resistant to this
virus.
This led to the
exploration of the nature and function of silencers.
Enzymes such as
PKR can block translations of all messenger RNAs (both normal and viral)
and RNAse-L indiscriminately destroys messenger RNAs.
How does RNAi
work?
Inside the cell,
the double stranded RNA encounters an enzyme dubbed Dicer, which cleaves
the long RNA into pieces.
These pieces are
22 nucleotides long and are known as short interfering RNAs (siRNAs)
Dicer cuts through
both strands of the long double-stranded RNA at slightly staggered positions,
so that each resulting siRNA has two overhanging nucleotides on one
strand at either end. The siRNA duplex is unwound and one strand is
loaded into an assembly of proteins to form the RNA-induced silencing
complex (RISC)
Positioned so that
messenger RNAs can contact it, the siRNA of RISC will adhere only to
a messenger RNA that closely complements its own nucleotide sequence.
Unlike the interferon
response, the silencing complex is highly selective in choosing its
target messenger RNAs.
When a matched messenger
RNA docks onto siRNA, an enzyme known as Slicer cuts the captured RNA
strand into two.
The RISC then releases
the 2 mRNA pieces (which are now incapable of directing protein synthesis)
and moves on, staying intact and free to find and find and cleave another
mRNA.
Tuschl and colleagues
put synthetic siRNAs into cultured mammalian cells and demonstrated
silencing of target genes with no interferon response.
This knowledge has
potential applications in cancer and viral infections.
In normal development
genes may be required to be active in embryonic cells and yet be readily
turned off later. Yet others need to be turned on later, so RNAi and
siRNAs are some among the microRNAs) of different origins) with specific
functions as described above.
With hindsight,
it seems obvious that cell mechanisms would run into chaos without systems
like this.
In summary, RNAs
have major roles in catalysing, signalling and switching in genetics.
Mitochondria in
cell cytoplasm also contains some DNA (see later)
This is entirely
from the maternal line (ova) as sperm mitochondrial DNA is lost in fertilisation.
The science of genetics
has advanced beyond our initial understandings.
Professor John Mattick,
writing in Scientific American in October 2004, writes that the credo
”one gene, one protein”, may be largely true for prokaryotes
(one celled organisms which lack a nucleus) but must be expanded in
eukaryotic organisms which possess nuclei.
He writes, “Proteins
do play a role in the regulation of eukaryotic gene expression, but
a parallel regulatory system consisting of RNA acting on DNA, RNAs and
proteins is also at work.”
This signalling
network is crucial to achieve the complexity seen in higher organisms.
It seems likely
that the introns are a later occurrence in the evolution of DNA sequences.
Self-splicing mobile
genetic pieces are termed group II introns, with properties that allow
insertion into genes and abilities to splice themselves out when expressed
as RNA.
Group II introns
are seldom found in bacteria, but with eukaryotic cells, transcription
occurs in the nucleus and translation in the cytoplasm. allowing time
for intron RNA to excise itself.
A further development
appears to be the emergence of “splice-somes” which are complexes
of small catalytic RNAs and many proteins, possessing a capacity to
snip intron RNA out of messenger RNA precursors.
In effect this allows
intronic RNAs to be involved in their own evolution.
This would explain
parallel regulatory systems which need coo-ordination.
RNAs can encode
short sequence specific signals doing such tasks as directing RNA molecules
to receptive targets in other RNAs and DNA.
The RNA-RNA and
RNA-DNA interactions could create structures that recruit proteins to
convert signals into actions.
Analogies arise
with the handling of bit information in computers.
Feedbacks and feed
forward mechanisms are the essence of cybernetics.
To follow development
of the fertilized egg to the 100 trillion cells of the adult human being
requires such an elegant cybernetic system. involving astonishing co-ordinations
of co-ordinations.
Two steps have been
studied.
(1) Modification
of chromatin
Recent studies
suggest that RNA signalling directs the tagging of chromatin determining
whether the genes in stretches of DNA will be accessible for translation
or stay dormant.
(2) Alternative
splicing.
This process generates
divergent repertoires of RNAs and proteins in the cells of different
tissues.
This is almost certainly
RNA controlled, partly by the tagging or grabbing of sequences and partly
by directing splice-some function.
Crucial elements
in higher living systems are highly conserved between species.
Something is needed
to guide these systems to complexity with minimum errors.
The word “cybernetic”
refers to “controlling systems”.
The more complex
the system, the more sophisticated is the control system.
Mattick points out
that if life began on Earth about 3.8 billion years ago, a leap in complexity
must have occurred about 1 billion years ago and more so in the Cambrian
“explosion” of invertebrates about 525 million years ago.
The genes, therefore,
do not sit as isolated pockets in a sea of junk DNA, but rather they
live in a regulatory environment, which is utterly crucial for our complexity.
Non-coding RNAs
have already been linked to B cell lymphomas, lung cancer, prostate
cancer, autism and schizophrenia.
In essence we now
understand that our genes, through gene products, and now non protein
coding genetic materials, shape the possibilities of our fundamental
functions, but as well shape a changing response to environmental influences
over varying time scales.
But there is more
to the complexity of life than this!
The divergence of
prehumans from chimpanzee ancestors about 6 million years ago, doesn’t
mean that certain genes that were conserved 100 million years ago, may
not still have polymorphisms that eventually give rise to special effects
in an altered biological terrain.
This is surely
more “grist for the mill” in terms of Professor Marcello Costa’s
descriptions about the complex loops which give rise to the emergence
of consciousness in the stages between those ancestors and us.
Add epigenetic discoveries
and we have elegant developments!
Recent research
is revealing amazing changes in gene expression and activity related
to environmental happenings, and this will form a basis for particular
protections for many diseases.
As mentioned earlier,
in specific circumstances genes are activated and cell chemistry changes.
Anyone who studies
genetic engineering knows that some viruses can be used to splice genes
from one species into another.
It is self evident
that scientists are exploiting a natural capability of some viruses.
It should be noted
that there are nonviral means for DNA to be transferred from cell to
cell.
Intra cellular organelles
called plasmids can be transferred between prokaryotes and also be carried
into eukaryotic cells by organisms which enter cells.
As long as life
exists, there is no possibility of there being no evolution.
Evolution involves
such gene insertions, and mutations as well as the direct inheritance
of parental or ancestral genes.
Now we can add other
mechanisms for inserting functional elements. (RNA editing) and transposons
(previously thought to be junk!)
Mattick mentions
the discovery of adenosine to inosine (A to I) editing discovered by
Erev Levanon and colleagues and announced in July 2004.
Again they arise
in non-coding RNA sequences called Alu elements.
A to I editing sequences
are very active in the brain and aberrant editing has been associated
with epilepsy and depression.
It is not hard to
suppose that the elegance of neural function demands huge programming
flexibility.
Now in 2009, Katherine
S Pollard has concentrated on genes that are distinctly concerned with
brain growth and such special functions as speech.
Pollard looked
at a region called human accelerated region 1 (HAR1).
HAR1 has been frozen
in time in the sense that it has been highly conserved through hundreds
of million of years.
HAR1 is highly active
in neurones which play a key role in the pattern and layout of developing
cerebral cortex.
Human beings and
chimps have evolved from similar ancestors from 6 million years ago,
and the HAR1 differs in humans and chimps by just 18 letters!
HAR1 does not encode
a protein, but does code for RNA, and a shared sequence between 2 genes,
gives rise to special forms of RNA.
The FOXP 2 gene
also contains crucial sequences which have to do with speech.
Other genes like
ASPM are being found which relate to brain size, better folding of the
cerebral cortex and specific brain functions.
Another gene regulatory
region, HAR2, has to do with wrist and thumb function leading to gains
in dexterity.
We do well to honour
the discovery of genes and we will do better as more details of patterns
of gene activation and transcription of codes reveal participation in
the web of life!
For the moment,
the message is that as long as we are biological beings, each of us
can decide to honour our own life, the life of others and the biological
economy, which is underpinning our present and future.
Does this make you
rethink what short term claims about drugs really mean in our whole
living patterns?
The concentrations
by business organizations and politicians on monetary policies, and
the so–called economic rationalisms will bring great disasters
unless we recognize, support and nurture the biological economy which
underpins all life.
Are the “John
Matticks’ of this world too rare in a climate of drug company directed
research?
We can be encouraged
that wonderful discoveries are being made in private genetic companies,
yet remain puzzled about an overall balance as to how to justly share
information.
We at last know
that signalling between living elements make the complexity workable!
The new thinking
paradigms are indeed cybernetic!
Let us love biology.
