MUHAMMAD AHSAN RAFI

0039-BH-BIO-T-19

ASSIGNMENT SUBMITTED TO : DR. UZMA

MICROBIAL GENETICS

ASSIGNMENT TOPIC: DNA thermodynamics and kinetics applications in microbial genomics

and latest trends
DNA thermodynamics and kinetics applications in microbial genomics and latest
trends

Introduction:

There’s been a rapid expansion and growth in the field of microbial genomics throughout the
past years. The sequencing of two dozen of microbial genomes has been accomplished and
many more sequencings is expected to accomplish in the coming years. The genomic sequence
of different strains of the same species has also been processed for example Mycobacterium
tuberculosis AND Helicobacter pylori. (1)

Historical aspect:

According to the RNA world hypothesis, the modern organism is considered to be the
decedents of RNA. It is believed that the primitive RNA molecule had a random sequence which
emerged the first genome which was coded was an enzyme called polymerase ribozyme.

The Quasispecies theory proposed by Eigen gives an idea that the occurrence of an error causes
such transitions and leading to the genomic stability.

This leads to a recent theoretical approach were we will apply the quasispecie theory by
combining it with the thermodynamic and kinetic description in replication process of RNA. In
this way, it will be easier for us to analyses the overall behavior of RNA replicators which will be
based upon the kinetic data known by us. (2)

Thermodynamic energetics and the whole genome doubling in cancer:

One of the major causes of

most of the cancers is concluded to be the genomic instability. In this unfortunate situation, the
change in the copy number of chromosomes and genes takes place during some important
cellular process including genome replication. This leads to the genomic instability which
happens to be strong biomarker used for poor prognosis.
In a research on human tumor, the analysis of DNA copy number in tumor cells revealed an
genomic instability in term of energetics of the cell. The distribution energy of genes in every
tumor cell was found out to be increasing fractionally which related the genomic instability with
the physiochemical stability. It was also observed that genome doubling is way more favorable
from genome which was not already fragmented.

Future studies suggested that the genomic instability had a major contribution toward
tumorigeneses which was proved by insertion and deletion of cancer causing genes.

The copy number of DNA which is leading to the formation of tumor provided us a
thermodynamic analysis of each and every profile in case of tumor. This interdependence
occurs at universal level in most of the cancer types. Further analysis made two classifications
on the basis of either or not the tumor under study has gone through the whole genomic
duplication (WGD). This analysis revealed that the copy numbers which has a comparatively
narrower distribution are proved to be more favorable towards WGD transition comparative to
others. This analysis also provided us with the deviation from a completely stable distribution.

The result of this observation was obvious that the change in copy number is tend to be more
common in high ploidy tumors and in results it provide support to the altered selection
pressure upon whole genomic distribution.

Tumorigenesis is a complicated process involving multiple alterations which are combined

together in order to rewire the circuitry of cell towards survival and unrestrained growth.

Genomic instability at the sub chromosomal and chromosomal level is a reason of lethal and
aggressive cancer growth. Some of the classic examples of copy number alterations of the DNA
which is contributing towards the tumor phenotype is the deletion of tumor suppressor gene
and amplification of Oncogene.

Most advanced studies of tumor genes has revealed the presence of high CNAs across the
entire genome which includes both normal and tumor containing specific patterns. (3)
Many a process such as replication stress, DNA damage repair, telomere attribution, breakage
fusion bridge cycle, lagging chromosomes and defective mitoses etc. can be a cause of CNAs. (4)

The surprisal analysis:

The data is always provided in the form of CN of the gene to the average
CN which is supposed to be the ploidy of the tumor. The CN which is required in actual is
obtained by the equation

CN =⟨p⟩CAN

This equation is used to determine the ploidy for example the imbalancement of alleles of SNPs
in the genome.(5)

For a tumor under study, most of the genes have approximately two or three CNs. If the value
rises to four it will show that there’s been a WGD in the tumor’s history.

The purpose of surprisal analysis is the qualitative representation of CN for every locus of a
gene. If we represent this locus with the Xi(n)Xi(n) in a tested tumor, the tumor index used to
label it is n. in this analysis, the gene loci will be used as a representation of the DNA loci
spanning the whole genome. We start the process with the minimal amount of free energy
which is being subjected to constraint. This is considered as the standard approach in case
of statistical thermodynamics which will ultimately leads to the generic expression given
below:

Xi (n) =X0i (n)exp((μi(n) −μ 0i(n))/kT)

Here Xi (n) represents the value of CN of specific gene under study I is the CN of
tumor and n is in stable state. The exponential part represents its derivatiation
From the stable state. μi(n) factor represents the chemical potential posseses by the
locus.

The units used to describe the thermodynamic potential is the same as unit of energy so we can
assume that it is scaled by thermal energy given here which is kT which will allow the folds to
change there dimensions by infinite number of times. K here presents the Boltzmann constant.

So according to the equation, if the condition of cell is such that

μi(n) > μoi(n)

that will mean that the CN of the locus is higher comparative to the one in stable state which
means the instability of genomic leading to cancer. (6)

The genome of Syntrophus aciditrophicus and thermodynamic limit:

Biochemically speaking, the

syntrophic bacteria shows the weird behavior in our understanding towards anaerobic flow of
carbon compounds in the biosphere. The complete genomic sequence of this bacteria provides
us with an overview of energy transformation and electron transport chain, the genome is
known to contain 3179300 base pairs containing 3169 genes. Out of these total genes, 1618
genes were only assigned for putative functions. Metabolic study suggested that the metabolic
pathways of most of the gram-negative bacteria’s were present in this one. But in addition to
that, it also requires a need for a reverse electron transport chain, which is accomplished by the
presence of ion translocating Rnf-type electron transfer complex along with a membrane
bounded Fe-S protein and menaquinone. (7)

Syntrophus aciditrphicus has a rod-shaped structure and is classified as Gram negative bacteria.
They survive by degrading fatty acids, cyclohexane carboxylate and benzoate etc.
phylogenetically, they are considered as the subdivision of a type of bacteria called
Proteobacteria. They have some qualities of Geobacter and sulfate reducers. They have a vital
role of recycling the organic matter into carbon dioxide and methane. There pure strains are
not easily available so only a little is known about their metabolism but their energy yielding
pathway is well understood. They perform slow reproduction yield low energy because they
always require a symbiotic partner for there growth. They degrade a number of compounds
under the anaerobic conditions. These compounds include alcohols, lactates, organic acids and
fatty acid. There degradation is syntrophic (thermodynamic interaction between different
microbial species) the syntrophic interactions between microbial species is such as these is very
necessary for the complete degradation of organic matter. in most of the syntrophic
interactions, the partners act as a strong multicellular organism performing their function while
in close physical contact. (8)

In all these optimal growth mechanisms, the equilibrium change is still known to be zero and
the free energy that is just available must be used by some other organism present in the
system. So, we can say that the syntropy shows us one of the extreme evolution of life.

The basic step in syntrophic type of metabolism is the need of electron transport chain which is
backbone of this whole process. Normally, the oxidation reduction reactions provide us with a
negative energy which we can say that a thermodynamically favorable reaction. This will
proceed by the formation of formate or hydrogen from the electroN which was generated by
the oxidation process of acetyle co enzyme A from there intermediate version i.e. enoyl-CoA .
this transformation represents an incredible energy barrier of -10mV. Thus, we can say that the
key feature towards the syntrophic type of metabolism is the components of the membrane
which are involved in usage and generation of ion gradients.

The genome sequence of this bacterium when studies, it provided us the first minnow glimpse
of mechanism followed by genetic program that is directing reverse electron transport chain
and energy conservation. So this bacteria is considered to be the specialist in syntrophic life
having limited respiratory and fermentative metabolism.
Functional Genetic Instructions (FGI):

Life was impossible without functional genetic instructions.

The life is stabilized only because of FGI is maintaining it in stable ordered with the minimal
entropy changes. The transmembrane potential is allowing cell to perform a specific cellular
function including metabolism. This is done by exporting waste products and importing new
nutrients inside cell body. Even though cells are membrane bounded semi permeable but they
still considered as the open system. So, they must be able to identify and obtain different type
of molecules so they can avoid any type of genetic mistakes. As the matter of fact, we can see
regulated transcription and translation, DNA replication as a pathway for communication which
is allowing FGI to make an organism with the ultimate goal f reproduction. To understand this,
we can consider bacteria as thermodynamic efficiency, researchers estimated the
thermodynamic efficiency of bacterium named Pseudomonas oxalates under the C-limited
hemostatic conditions and claimed that there are some bacteria that are optimized in a way to show us
the thermodynamic efficiency of 23-24 %. (10)

The thermodynamic efficiency is obtained by the extent of reduction of given carbon substrate. So
optimal values of thermodynamic efficiency would be different for both autotrophs and heterotrophs.

While talking about functional genetic instructions, the understanding of the sematic separation of
different functional genetic messages from biochemical molecules is important. These genetic messages
are embedded inside the biochemical structure of RNA and DNA. The information which is stored inside
DNA molecule in the form of genetic code has nothing to do with the element which is comprising the
biochemical structure of DNA molecule. The genetic code is determined by the sequence of basic
condones not the nature of codons.

The process to synthesize a cell from the surrounding always requires energy as input which means loss
of entropy. During the death of the cell, the energy never dies, it is transformed back to the system.
Since the laws of thermodynamic is always followed even in the most complicated systems of life.
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