International Journal of Advanced Bioinformatics

Research Article Open access

Comparison and analysis of XTX in coding frames of DNA sequences of

Escherichia coli k12 genome
C.Paruvathavarthini1*, H.Karthick1 and E.Rajasekaran2

1
Department of Bioinformatics, PRIST University, Thanjavur – 614 904
2
Department of Biotechnology, Periyar Maniyammai University, Thanjavur – 613 403

*
Corresponding author e-mail: ccmcvarthini@yahoo.com ;

Published: 00 ---- 2009 Received: 16 June 2009

Accepted: 04 August 2009

ABSTRACT

Computer based genome-wide screening of the DNA sequences of Escherichia coli strain K12 revealed that the importance of XTX
(where X = A, T, G or C) which codes for large hydrophobic groups in amino acids. We have analyzed nucleotide sequences of
Escherichia coli k12 and find that fraction of XTX in all six frames. Studies have demonstrated that frame 1, 3 and 5 (nucleotide)
has large amount of XTX compared to the frames 2, 4 and 6. We therefore performed an investigation and proved that the DNA
sequences have 30% of XTX in coding frames.

Keywords: frame analysis; hydrophobic residues.

INTRODUCTION genetic analyses and through bioinformatics studies are

The increasing genome sequence data of microorganisms has
provided the basis for comprehensive understanding of
organisms at the molecular level. Besides sequence data, a
large number of experimental and computational resources
are required for genome-scale analyses. Escherichia coli K-
12 has been one of the best characterized organisms in
molecular biology [1]. The field of genomics has been
expanding at a rapid pace since the annotated Escherichia
coli K-12 genome was published in 1997 [2], with the current
number of published genomes exceeding 66 and with another
364 on their way according to the Genomes OnLine Database
(GOLD) [3]. Deciphering the functions encoded by all gene
products of the genomes is the next big challenge in the field.
Function attributions through experimental, biochemical and
continuing, and microarray technology is shedding additional
light on the functions associated with the gene products of
the organism in question. The wealth of biological
information on E. coli is still increasing [4] and is
contributing to a better understanding of this organism as
well as of functions encoded in other organisms. The E. coli
K-12 chromosome is currently represented by 4,401 genes
encoding 116 RNAs and 4,285 proteins [5].
The aim of this study based on the analysis of the distribution
of nucleotide sequences of Escherichia coli K12. The coding
sequences (CDSs) are represented by modules that are
protein elements of at least 100 amino acids with biological
activity and independent evolutionary history [6]. The

Paruvathavarthini et al., International Journal Of Advanced Bioinformatics 0(0):00-00, (2009)

complete set of nucleotide sequences was collected from the
FTP site present in the NCBI (National Center for
Biotechnology Information) [7]. The sequences were saved
in the FASTA format. Then the sequences were analyzed by
means of home made C programs and the results saved in MS
Excel. In the worksheet, calculation of average, probable and
fraction of Thymine (T) was calculated and using those
values graph was done.
METHODOLOGY
Only the potential protein coding regions of genome
sequences (FASTA format) of the Escherichia coli k12
analyzed in this study were downloaded from the National
Centre for Biotechnology Information (NCBI) [7].
Trinucleotide analysis of all the nucleotide sequences of an
organism was performed using the ‘C’ program. This
program finds out the fraction of XTX in nucleotide
sequences of Escherichia coli k12 in all six frames.
Frequency of XTX occurrences, average and probable values
were calculated and the graph plotted using MS-Excel. All
those values are compared and discussed.
RESULTS AND DISCUSSION
Codon usage was defined as the number of times
(frequency) a codon is translated per unit time in the cell of
an organism. This is a definition for real-time codon usage.
But it is hard to be measured in vivo. Three different methods
to estimate the codon usage in E. coli and other organisms
in their studies including measuring the average frequencies
of codons in the sequenced protein coding genes in an
organism. All their methods gave approximately the same
results as regards the hierarchy for “most used’ and “least
used” codons within each synonymous codon family.
Therefore, it is reasonable to use averaged codon frequency
of the sequenced protein-coding reading frames of an
organism to roughly represent the real-time codon usage
although this may over-estimate the usages of infrequently or
rarely used codons and underestimate those of frequently
used codons because different reading frames are used and
translated for different number of times in the organism at a
given time [8]. Besides, this is what codon usage generally
means too many scientists in the past and at present.
The thymine in the second position of the codons is
considered as frame1. Nucleotides 1 and 3 of the codons are
considered as frames 3 and 2 respectively. The
complementary nucleotide of 1, 2 and 3 nucleotides of
codons are considered as frame 6, 4 and 5, respectively [11].
The frame 1, frame 2, frame 5 and frame 6 are looks like
normal distribution and the frame 3 is towards left and frame
4 is towards right when compared to other frames. The frame
1 is having very high fraction of XTX and the frame 4 is very
Paruvathavarthini et al.,
less fraction. The maximum percentage in frame 1, 2, 3, 4, 5
and 6 is 9% of 0.29, 9% of 0.26, 5% of 0.29, 11% of 0.21,
9% of 0.28 and 9% of 0.21 fraction of XTX (Figure 1).
The frame 1 and 2 is proportionally decreasing and the
average value of frame 4 is high when compared to frame 5
and frame 6. But frame 3 is very less average of XTX value
when compared to all frames (Figure 2).
The frame 2, frame 3, frame 5 and frame 6 is similar when
compared to frame 1 and frame 4. But frame 4 is very high
probable compared to all frames (Figure 3). It is
proportionally decreasing in frame 1, 2 and 3, but suddenly
increasing value in frame 4 and again decreased in frame 5
and frame 6.
The usage of codons and nucleotide combinations varies
along genes and systematic variation causes gradients in
usage. For triplets, changes in codon preference may occur
due to speed or accuracy. We find no relationship between
major/minor status of a codon and its gradient of usage. In a
comparison between values for translation speeds and
gradients of usage, 6 out of 9 codons with positive gradients
had a faster speed of translation than their synonyms. Due to
the limited translation speed data, no significance tests can be
made [9].
Genes can be classified as essential or nonessential based on
their indispensability for a living organism. . Analysis of
evolutionary conservation, protein length distribution and
amino acid usage between essential and nonessential genes in
Escherichia coli K12 demonstrated that essential genes are
relatively preserved throughout the bacterial kingdom when
compared to nonessential genes. Furthermore, results show
that essential genes, compared to nonessential genes, have a
significantly higher proportion of large (>534 amino acids)
and small proteins (<139 amino acids) relative to medium-
sized proteins. The pattern of amino acids usage shows a
similar trend for essential and nonessential genes, although
some notable exceptions are observed [10]. These findings
help to clarify our understanding of the evolutionary
mechanisms of essential and nonessential genes, relevant to
the study of mutagenesis and possibly allowing prediction of
gene properties in other poorly understood organisms. The
final conclusion is that the amount of thymine is reduced
during evolution that leads to production of diseased proteins
that unable to function normally [11].
CONCLUSION
The data presented in this paper strongly suggests that
machine learning theories, especially supervised methods,
International Journal Of Advanced Bioinformatics 0(0):00-00, (2009)
could provide the best initial approaches to characterizing and
assigning gene function in functional genomics. The overall
observation made and suggests that the thymine in DNA
plays an important role in producing stable and active
proteins. Particularly, the fraction of thymine in all 6 frames
of the nucleotide sequences is analyzed. In this study the
fraction of thymine in all 6 frames of the DNA sequences and
distribution of DNA sequences based on the fraction of
thymine is carried out on E.coli K12., It is observed that the
variation in the fraction of thymine in frames 1,2,5 & 6 are
similar compared to frame 3 and 4. The E.coli K12 show a
higher amount of sequences having the probable amount of
thymine in frame 4 is very high. The probable and average
fraction of thymine in frame 4 is higher and frame 3 is lesser
compared to other frames. From the overall observation
frame 3 is following the normal trend why because it is a
coding sequence. This study will help you to understand the
coding and non-coding DNA sequences. And also it leads to
play a major role in disease control. From the overall study
we found that the coding sequence must have the standard
ratio of 30% amount of XTX. It is observed in all cases that
frame3 is having least amount of thymine.
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Paruvathavarthini et al., International Journal Of Advanced Bioinformatics 0(0):00-00, (2009)

 0.35

0.3
FRACTION OF XTX

F1
0.25
F2
0.2 F3
0.15 F4
F5
0.1
F6
0.05

0
0 5 10 15 20 25
NO. OF. SEQUENCES XTX

Figure 1: Distribution of XTX in six frames

AVERAGE VALUE OF XTX IN ALL FRAMES

0.25

0.2
AVERAGE

0.15

0.1

0.05

0
0 1 2 3 4 5 6 7
FRAMES

Figure 2: This figure shows the average value of XTX in six frames

Paruvathavarthini et al., International Journal Of Advanced Bioinformatics 0(0):00-00, (2009)

 PROBABLE VALUE OF XTX IN ALL FRAMES

0.45
0.4
0.35
PROBABLE

0.3
0.25
0.2
0.15
0.1
0.05
0
0 1 2 3 4 5 6 7
FRAMES

Figure 3: This figure shows the probable value of XTX in six frames

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Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and sources are
credited.

Paruvathavarthini et al., International Journal Of Advanced Bioinformatics 0(0):00-00, (2009)