MOLECULAR BIOLOGY PAPER

ABOUT

“GENOME ORGANIZATION IN PROKARYOTES”

COMPILED

BY :

GITA TRI ANGGITA

4143342013

BILINGUAL BIOLOGY EDUCATION

MATHEMATIC AND NATURAL SCIENCE FACULTY

STATE UNIVERSITY OF MEDAN

2018

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 PREFACE

Praise and thanksgiving author thank to God Almighty, for His blessings
and His grace that we can finish term papers of Molecular Biology courses with
titles“Genome Organization in Prokaryotes”.

The author are grateful and espesially forlecture is Mam Fauziyah Harahap
who has given this task to perform analysis and learning the content of genetic
engineering, so that it can be used as a sources material addresses this semester.

The author is also aware that the task is still many short comings therefore
the author apologize if there are errors in the writing and in this case we also
expect criticism and constructive suggestions to the perfection of this task. In
conclusion the author thank may be useful and can add knowledge to the reader.

Medan, April 2018

Gita Tri Anggita

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 TABLE OF CONTENT

Preface ..................................................................................................................i

Table of Content...................................................................................................ii

CHAPTER I : INTRODUCTION

1.1 Background...................................................................................................1
1.2 Problem Formulation.....................................................................................1
1.3 Objective .......................................................................................................1
1.4 Benefit ..........................................................................................................2

CHAPTER II : DISCUSSION

2.1 Genome..........................................................................................................3
2.2 Genome Organization in Prokaryotes............................................................3
2.3 Variation in Genome Structure......................................................................9
2.4 DNA Packaging in Prokaryotic Cells..........................................................11
2.5 Genome Organization in Virus....................................................................13
CHAPTER III : CLOSING
3.1 Conclusion...................................................................................................17
3.2 Suggestion....................................................................................................17
REFERENCES......................................................................................................18

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 CHAPTER I
INTRODUCTION
1.1 Background
One of the fundamental differences between prokaryot and eukaryot bodies is
in the organization of its genetic material. In the eukaryot group, there is generally
only one major genetic material unit that carries all the genetic information
necessary for the survival of the body's growth. All units of genetic material are a
single genome that is the survival of living things. The simplest virus represents
the most efficient genomic organization compared to prokaryot and eukaryot
(Triwibowo, 2010).

The complexity of any genetic material possessed by prokaryotes, eukaryotes,

and viruses encourages us to better know the difference. Another very interesting
phenomenon in terms of genomic organization is the highly efficient system of
genetic material to every living organism. Although the size of the genetic
material is much longer than the size of the cell or its particle size, it can be
packed in such a way that it occupies only a fraction of the space inside the cell.
Therefore it is hoped that in this paper we can find the genome in prokaryot,
eukaryot, and virus.

1.2 Problem Formulation

1. What is definition of genome?
2. How is the genome organization of prokaryotes?
3. How is the structure of genome
4. How is the DNA packaging in prokaryotic cell?
5. How is the genome organization in virus?

1.3 Objective
Referring to the formulation of the above problems, the objectives to be achieved
in writing this paper are:

1. To know the definition of genome

2. To know the genome organization in prokaryotic
3. To know the variation of genome structure
4. To know DNA packaging in prokaryotic cell
5. To know the genome organization in virus

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1.4 Benefit
The expected benefits from the results of this paper are to improve the
understanding of the authors and fellow students about the genome in prokaryot,
eukaryot, virus.

CHAPTER II
DISCUSSION

2.1 Genome

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 Genome is a unity of gene that is naturally possessed by a single cell or
virus, or a unity of eukaryotic chromosomes in the haploid phase (Yuwono, 2005).
With this kind of limitation, it can be understood that a piece of DNA molecules
that do not carry the complete genetic information can not be referred to as gene
but only as fragments of DNA. Likewise, a chromosome of a body that has more
than one chromosome can not be called the genome of the body (Triwibowo,
2010).
A genital cell (gamet) contains half of the number of chromosomes present
in a somatic cell, therefore the number of chromosomes in a gamete is called
haploid(n). One haploid chromosome cell of a species is called the genome
(Suryo, 2005). The term genome refers to the haploid set of genetic information
contained in cells (in other words on chromosomes) of a particular species. The
number of chromosomes in each somatic cell is the same in all members of a
species. For example, human somatic cells contain 46 chromosomes, tobacco cells
containing 48, cows 60, pea 14, fruit flies 8, etc. So, genome is entire heredity
information of organism encoded either in DNA or RNA (in viruses). Genomic
organisation of an organism is this background layer of information which
unassumingly provides multiple layer of information to structure genome from the
array of nucleotide sequences.
The term genome was introduced by H. Wrinkler 1920 to denote the
complete set of chromosomal and extra-chromosomal genes present in an
organism, including a virus. The genome is the full complement of genetic
information in a cell, and contains the programme required for that cell to
function.

2.2 Genome Organization in Prokaryotes

Compared to eukaryotes, prokaryotes usually have much smaller genomes.
On average, a eukaryotic cell has 1000 times more DNA than a prokaryote. This
means that less DNA must be replicated with each division in prokaryotes.
Prokaryotes do not have a nucleus. However, they still must fit DNA that is 1000
times the length of the cell within the cell membrane (Fig. 2.1). The genome of
Escherichia coli, a bacterium widely used in molecular biology research, is 4700
kb in size and exists as one double-stranded circular DNA molecule, with no free

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5′ or 3′ ends. The chromosomal DNA is organized into a condensed ovoid
structure called a nucleoid. A considerable number of nonessential proteins, called
histone-like proteins or nucleoid-associated proteins, are thought to be involved in
DNA compaction and genome organization. These include HU (heat-unstable
protein), IHF (integration host factor), HNS (heat-stable nucleoid structuring), and
SMC (structural maintenance of chromosomes). HU and HNS are particularly
abundant. Further condensation packs the bacterial genome into supercoiled
domains of 20–100 kb. Approximately 50% of DNA supercoiling is unrestrained.
These domains are dynamic and unlikely to have sequence-specific domain
boundaries. Negative superhelicity is maintained by the action of topoisomerases,
in particular by the ability of gyrase to remove the positive supercoils generated
during replication and transcription.

Figure 2.1 The bacterial genome. Falsecolor transmission electron micrograph

(TEM) of a lysed bacterial cell (E. coli). The DNA is visible as the gold colored
fibrous mass lying around the bacterium. Magnification: ×15,700. (Credit: G.
Murti / Photo Researchers, Inc.)

Prokaryotes often have smaller rings of extrachromosomal DNA

termed plasmids. Most plasmids consist of only a few genes. Plasmids are not
required for survival in most environments because the prokaryotic chromosome
programs all of the cell’s essential functions. However, plasmids may contain
genes that provide resistance to antibiotics, metabolism of unusual nutrients, and

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other special functions. Plasmids replicate independently of the main
chromosome, and many can be readily transferred between prokaryotic cells.

2.2.1 Plasmid of Bacteria

Figure 2.2 Schematic representation of a bacterium containing plasmid DNA.

Plasmids are small, circular molecules of DNA that are extrachromosomal and
self-replicating within the host bacterium.

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  Origin of replication is The origin of replication (also called the replication
origin) is a particular sequence in a genome at which replication is
initiated.
 Genes are a unit of heredity that is transferred from a parent to offspring
and is held to determine some characteristic of the offspring and a
sequence of DNA or RNA which codes for a molecule that has a function.
 Intergenic regions are a stretch of DNA sequences located between genes.
Intergenic regions are a subset of noncoding DNA.
 Repetitive sequences are patterns of nucleic acids (DNA or RNA) that
occur in multiple copies throughout the genome.

Plasmids are small, double-stranded circular or linear DNA molecules carried

by bacteria, some fungi, and some higher plants. They are extrachromosomal
(meaning separate from the host cell chromosome), independent, and self-
replicating. At least one copy of a plasmid is passed on to each daughter cell
during cell division. Their relationship with their host cell could be considered as
either parasitic or symbiotic. They range in size from 2 to 100 kb (Fig. 3.7). The
majority of plasmids are circular; however, a variety of linear plasmids have been
isolated. A notable example is the linear plasmid pC1K1 carried by Claviceps
purpurea, a fungus found on rye. The fungus contains poisonous alkaloids that
cause ergotism – hallucinations and sometimes death – in humans who eat the
infected grain and was a likely contributor to the Salem Witch Trials.

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 Plasmids are important for our study for two main reasons: they are carriers of
resistance to antibiotics, and they provide convenient vehicles for recombinant
DNA technology.

2.2.2 Prokaryotes and Eukaryotes Genome

Prokaryotes Eukaryotes
Single cell multicellular
No nucleus Nucleus
One piece of DNA Chromosomes
Post-transcriptional not need mRNA Complex-contain Intron and Exon

Differences Between Prokaryotes and Eukaryotes Chromosome

Prokaryotic Chromosomes Eukaryotic Chromosomes
 Many prokaryotes contain a  Eukaryotes contain multiple linear
single circular chromosome chromosomes
 Prokaryotic chromosomes are  Eukaryotic chromosomes are
condensed in the nucleoid via condensed in a membrane-bound
DNA supercoiling and the nucleus via histones.
 In eukaryotes transcription occurs
binding of various architectural
in the nucleus and translation
proteins.
 Because prokaryotic DNA can occurs in the cytoplasm.
 Most eukaryotes contain two
interact with the cytoplasm,
copies of each gene (i.e., they are
transcription and translation
diploid)
occur silmutaneously.
 Some eukaryotic genomes are
 Most prokaryotes contain only
organized into operons but most
one copy of each gene (i.e., they
are not
are haploid)
 Extrachromosomal plasmids are
 Nonessential prokaryotic genes
not commonly in eukaryotes
are commonly encoded on
 Eukaryotes contain large amounts
extrachromosomal plasmids.
 Prokaryotic genomes are of noncoding and repetitive DNA.

efficient and compact,

containing little repetitive DNA.

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  Prokaryotes are usually much smaller than eukaryotic cells.
 Prokaryotes also differ from eukaryotes in that they contain only a single loop
of stable chromosomal DNA stored in an area named the nucleoid, while
eukaryote DNA is found on tightly bound and organised chromosomes.
Although some eukaryotes have satellite DNA structures called plasmids,
these are generally regarded as a prokaryote feature and many important
genes in prokaryotes are stored on plasmids.

Genes
 Prokaryotes also differ from eukaryotes in the structure, packing, density, and
arrangement of their genes on the chromosome. Prokaryotes have incredibly
compact genomes compared to eukaryotes, mostly because prokaryote genes
lack introns and large non-coding regions between each gene.
 Whereas nearly 95% of the human genome does not code for proteins
or RNA or includes a gene promoter, nearly all of the prokaryote genome
codes or controls something.

 Prokaryote genes are also expressed in groups, known as operons, instead of

individually, as in eukaryotes.

 In a prokaryote cell, all genes in an operon(three in the case of the famous lac
operon) are transcribed on the same piece of RNA and then made into separate
proteins, whereas if these genes were native to eukaryotes, they each would

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 have their own promoter and be transcribed on their own strand of mRNA.
This lesser degree of control over gene expression contributes to the simplicity
of the prokaryotes as compared to the eukaryotes.

2.3 Variations in Genome Structure

The size of prokaryotic genomes ranges from around 50 kb to more than 13
Mb (Schneiker et al. 2007; Ishii et al. 2013; Tatusova et al. 2015). These genomes
are also very compact, with gene density typically approaching 85% (Mira et al.
2001). There is, therefore, a direct proportionality between the size of the genome
and the number of encoded proteins. The smallest genomes (,500 kb) correspond
to obligatory endosymbionts that have arisen by reduction of larger genomes of
free-living bacteria. Some of these genomes have fewer genes than those strictly
required for autonomous life in E. Coli (McCutcheon and Moran 2012). Larger
genomes encode complex metabolic and genetic networks, some of them allowing
bacteria to differentiate or regroup into multicellular bodies (Guieysse and Wuertz
2012).
Variations in genome size affect cellular functions in different ways. The
gene repertoires associated with some housekeeping functions, like translation,
show little variation in the known range of genome size. Gene repertoires for other
functions are much more variable: smaller genomes are nearly depleted of sensory,
transport, communication, and regulatory functions, reflecting narrow
environmental ranges (Boussau et al. 2004; Konstantinidis and Tiedje 2004).
Importantly, larger genomes are thought to engage much more frequently in
horizontal gene transfer and encode more transposable elements. Genome size is
also positively correlated with the strength of purifying selection acting on protein
coding sequences. This suggests that natural selection is more efficient in larger
genomes, possibly as a result of larger effective population sizes. Very large gene
repertoires might in fact require efficient natural selection derived from large
effective population sizes, otherwise genes would be rapidly lost by genetic drift. It
is thus generally thought that larger genomes correspond to more versatile
prokaryotes that are less sexually isolated and in which selection is more efficient.

Table 1. Diversity of DNA-based genome organization.

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Genome Form Size (kb)

Eukaryote

2.4 DNA Packaging in Prokaryotic Cells

a. DNA Supercoiling

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The answer to this question lies in DNA packaging. Whereas eukaryotes wrap
their DNA around proteins called histones to help package the DNA into smaller
spaces, most prokaryotes do not have histones (with the exception of
those species in the domain Archaea). Thus, one way prokaryotes compress their
DNA into smaller spaces is through supercoiling. Imagine twisting a rubber band
so that it forms tiny coils. Now twist it even further, so that the original coils fold
over one another and form a condensed ball. When this type of twisting happens
to a bacterial genome, it is known as supercoiling. Genomes can be negatively
supercoiled, meaning that the DNA is twisted in the opposite direction of
the double helix, or positively supercoiled, meaning that the DNA is twisted in the
same direction as the double helix. Most bacterial genomes are negatively
supercoiled during normal growth.

b. Proteins Involved in Supercoiling

During the 1980s and 1990s, researchers discovered that multiple proteins
act together to fold and condense prokaryotic DNA. In particular, one protein
called HU, which is the most abundant protein in the nucleoid, works with
an enzyme called topoisomerase I to bind DNA and introduce sharp bends in the
chromosome, generating the tension necessary for negative supercoiling. Recent
studies have also shown that other proteins, including integration host factor
(IHF), can bind to specific sequences within the genome and introduce additional
bends (Rice et al., 1996). The folded DNA is then organized into a variety of
conformations (Sinden & Pettijohn, 1981) that are supercoiled and wound around
tetramers of the HU protein, much like eukaryotic chromosomes are wrapped
around histones (Murphy & Zimmerman, 1997).
Once the prokaryotic genome has been condensed, DNA topoisomerase
I, DNA gyrase, and other proteins help maintain the supercoils. One of these
maintenance proteins, H-NS, plays an active role in transcription by modulating
the expression of the genes involved in the response to environmental stimuli.
Another maintenance protein, factor for inversion stimulation (FIS), is abundant
during exponential growth and regulates the expression of more than 231 genes,
including DNA topoisomerase I (Bradley et al., 2007).

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c. Accessing Supercoiled Genes
Researchers have noted that the nucleoid usually appears as an irregularly
shaped mass within the prokaryotic cell, but it becomes spherical when the cell is
treated with chemicals to inhibit transcription or translation. Moreover, during
transcription, small regions of the chromosome can be seen to project from the
nucleoid into the cytoplasm (i.e., the interior of the cell), where they unwind and
associate with ribosomes, thus allowing easy access by various transcriptional
proteins (Dürrenberger et al., 1988). These projections are thought to explain the
mysterious shape of nucleoids during active growth. When transcription is
inhibited, however, the projections retreat into the nucleoid, forming the
aforementioned spherical shape.
Because there is no nuclear membrane to separate prokaryotic DNA from
the ribosomes within the cytoplasm, transcription and translation occur
simultaneously in these organisms. This is strikingly different from eukaryotic
chromosomes, which are confined to the membrane-bound nucleus during most of
the cell cycle. In eukaryotes, transcription must be completed in the nucleus
before the newly synthesized mRNA molecules can be transported to the
cytoplasm to undergo translation into proteins.

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2.4 Genome Organization in Virus
The viral genome is present in the capsid

Currently over 4000 viruses have been described. These are classified into
71 families. Although viruses are generally the smallest genomes, as a collection
of biological genomes they exhibit the greatest variation. The major difference is
that some of the genomes are DNA whereas others are RNA. In addition, both
DNA and RNA genomes can be either double- or single-stranded (ds or ss).
Finally, some ssRNA viruses use the RNA present in the genome to encode genes.
These are called positive-strand ssRNA genomes. Alternatively, negative strand
ssRNA genomes must be copied, and the copy (or negative strand) is used for
transcription.
DNA and RNA viral genomes have several distinguishing features. First
viral genomes can be monopartite or multipartite. If they are multipartite, they can
have several segments. All dsDNA genomes sequenced to date contain only a

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single nucleic acid molecule. A few of the ssDNA genomes have multiple
segments. In contrast, multipartite genomes are much more frequent for RNA
viruses. In particular, the negative strand ssRNA viral genomes are generally
multipartite.
DNA viruses tend to be larger in size than RNA viruses. It is hypothesized
that single-stranded virus are smaller because that type of molecule is more fragile
than the double stranded molecule. This is generally true for both ssDNA and
ssRNA viruses. Some ssDNA genomes can be as small as 1300 nt in length,
whereas the minimal genome size of a sequenced ssRNA virus is 2300 nt. Some
ssRNA viruses are as large as 31,000 nt, though. The fact that RNA viruses are
more susceptible to mutation is thought to have driven these to smaller genome
sizes. The largest viruses are the dsDNA viruses, which can be as large as 305,000
nt.

DNA VIRUSES
DNA viruses are typically classified as either ‘small’ or ‘large’ genomes.
As the term implies, the difference between these is the size of the genome.
Typical of all viruses, these genomes use nearly all of the sequences for genes that
encode proteins. The only difference is the actual number of proteins.
Another feature that distinguishes the ‘small’ and ‘large’ genomes is the
manner in which they are replicated. The ‘small’ genomes use a host DNA
polymerase for replication. The genome typically encodes proteins that prepare
the DNA for replication. In contrast, the ‘large’ genomes encode a DNA
polymerase that is responsible for the genomes’s replication. As the term implies,
‘large’ genome DNA viruses can also encode many more proteins.

RNA VIRUSES
In general, genomes of RNA viruses encode a limited number of proteins.
One protein that is very often encoded by these genomes is a RNA-dependent
RNA polymerase (RdRp). These polymerases are essential for the replication of
both positive and negative strand ssRNAs. as well as dsRNAs. This is true for
both monopartite and multipartite RNA viruses that show a range of 1-13 proteins.

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A major difference between + and – strand ssRNA viruses is that the polymersase
is contained within ss (-) virion whereas it is immediately translated from the
RNA of the ss(+) RNA.
As with DNA viruses, the genome is an example of maximizing it size.
For monopartite ssRNA viruses, the genome encodes a single polyprotein. This
protein is then processed into a number of small molecules, each of them critical
for the completion of the life cycle of the virus. In multipartite ssRNA genomes,
each segment normally contains a single gene.

A. DNA Viral Genomes

The Concept

DNA viruses are a major class of this biological entity. The viruses can be either
double- or single-stranded. In general, the single stranded genomes are smaller
than those that are double-stranded. Among the double-stranded genomes, these
can either have 'small' or 'large' genomes. One major difference between the two
genomes is the mechanism of DNA replication. Small genomes use host
polymerase activities, whereas large genomes encode a DNA polymerase.

B. RNA Viral Genomes

The Concept

RNA viral genomes can be either single- or double-stranded. In addition, these

can be multipartite, meaning they consist of several RNA molecules. The ssRNA
molecules are also classified as positive- or negative-strand or retrovirues. The +
and - strand ssRNA genomes are replicated by a RNA-dependent RNA
polymerase that is encoded by their genomes. Retroviruses are replicated as DNA
following the conversion of the RNA into DNA by a reverse transcriptase.

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Some viruses encode their own basic proteins, while others usurp the host cell
machinery. For example, papovavirus uses the host cell histones, H2A, H2B, H3,
and H4 to package its genome. Histone H1 is absent from the nucleosome-like
particles. Electron micrographs of SV40 show that the covalently closed, circular,
double-stranded DNA is organized in a chromatin-like structure called a
minichromosome.

Figure of Chromatin formation in simian virus 40 (SV40). (A) Electron

micrograph of SV40 viral particles. (Photograph courtesy of Norm Olson and
Timothy Baker, University of California, San Diego.) (B) SV40 DNA. (C) SV40
condensed minichromosome. (D) SV40 extended minichromosome associated
with host cell histones. (Parts B-D reproduced with permission from Singer, M.
and Berg, P. 1997. Exploring Genetic Mechanisms, University Science Books,
Sausalito, CA. Copyright © 1997 by University Science Books.)

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 CHAPTER III

CLOSING

3.1 Conclusion
The more simple a body, the more efficient the organization of its genome. The
virus which is the simplest bodies indicate the most efficient organization of the
genome, while the bodies of eukaryotic high level which is the most complex
living bodies have a genome organization of the most inefficient. The genomes of
most organisms are made of DNA; certain viruses and subviral pathogens have
RNA genomes. Bacterial chromosomal DNA exists as one double-stranded,
circular DNA molecule organized into a condensed structure called a nucleoid.
Plasmids are self-replicating small, double-stranded, circular or linear DNA
molecules carried by bacteria, some fungi, and some higher plants. Plasmids are
important tools for recombinant DNA technology. Bacteriophages and mammalian
DNA viruses have DNA genomes that occur in a variety of forms, ranging from
double-stranded to single-stranded DNA and linear to circular forms. Viruses
either package their genomes with their own basic proteins, or use host cell
histones.

3.2 Suggestion
With the existence of this paper is expected to the students in order to improve our
understanding of the genomes of prokaryotes, eukaryotes and viruses.

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Bradley, M. D., et al. Effects of Fis on Escherichia coli gene expression during
different growth stages. Microbiology 153, 2922–2940 (2007).

Guieysse B, Wuertz S. 2012. Metabolically versatile large genome prokaryotes.

Curr Opin Biotechnol 23: 467–473.

Lizabeth A. Allison. 2007. Fundamental Molecular Biology. USA: Blackwell

Publishing Ltd.

McCutcheon JP, Moran NA. 2012. Extreme genome reduction in symbiotic

bacteria. Nat Rev Microbiol 10: 13 26.

M. Touchon, Eduardo P.C. 2016. Coevolution of the Organization and Structure

of Prokaryotic Genomes. Cold Spring Harb Perspect Bio. doi: 10.1101.

Sinden, R. R., & Pettijohn, D. E. Chromosomes in living Escherichia coli cells are
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Academy of Sciences 78, 224–228 (1981).

Suryo. 2005. Genetika Strata 1.Gadjah Mada University Press. Yogyakarta.

Yuwono T. 2010. Biologi Molekuler . Penerbit Erlangga. Jakarta.

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