Essays, Posts & Presentations

The distribution of amino acid changes in different species

Zhamilya Bilyalova

Author

Zhamilya Bilyalova

Title

The distribution of amino acid changes in different species

Description

Analysis and comparison of A=to-I RNA editing in cephalopod species (squids and octopuses) and humans.

The distribution of amino acid changes in different species

Analysis and comparison of A=to-I RNA editing in cephalopod species (squids and octopuses) and humans.

Zhamilya Bilyalova, Jun. 24, 2018

Introduction: What is RNA editing?

RNA editing is a process that changes a RNA transcript such that it would no longer correspond to a sequence of DNA in a genome. There are many types of changes. A-to-I RNA editing is widespread in animals and results in the modification of a adenosine to inosine which will be read as a guanine. Nucleotides are being changed by enzymes that catalyze the editing.

Nucleobases that participate in A-to-I editing in mRNA:

In[]:=

Grid[{Map[Labeled[ChemicalData[#],#,Left]&,{"Inosine","Adenine","Guanine"}]},Spacings2]

Out[]=

Inosine

Adenine

Guanine

A-to-I editing in messenger RNA (mRNA) can cause changes in the amino acid sequence of a protein (amino acid recoding). Codons, 64 combinations in total, are codes for specific amino acids (one amino acid can relate to more than one codon).

To find what codons correspond to a specific amino acid, we can implement this code: An example is given for amino acid glycine:

In[]:=

glycine

CHEMICAL

[EntityProperty["Chemical","Codons"]]

Out[]=

{GGU,GGC,GGA,GGG}

Properties of a specific amino acid:

In[]:=

glycine

CHEMICAL

["Properties"];

And this is a table of amino acids and their corresponding codons: header

In[]:=

Grid[Map[{#,#[EntityProperty["Chemical","Codons"]]}&,Interpreter["Chemical"][{"Ser","Gly","Cys","Phe","Leu","Tyr","tryptophan","Arg","histidine","Gln","Pro","Ile","Met","Val","Ala","Asn","Lys","Asp","Glu"}]],FrameAll]

Out[]=

L-serine	{UCU,UCC,UCA,UCG,AGU,AGC}
glycine	{GGU,GGC,GGA,GGG}
L-cysteine	{UGU,UGC}
L-phenylalanine	{UUU,UUC}
L-leucine	{UUA,UUG,CUU,CUC,CUA,CUG}
L-tyrosine	{UAU,UAC}
L-tryptophan	{UGG}
L-arginine	{CGU,CGC,CGA,CGG,AGA,AGG}
L-histidine	{CAU,CAC}
L-glutamine	{CAA,CAG}
L-proline	{CCU,CCC,CCA,CCG}
L-isoleucine	{AUU,AUC,AUA}
L-methionine	{AUG}
L-valine	{GUU,GUC,GUA,GUG}
L-alanine	{GCU,GCC,GCA,GCG}
L-asparagine	{AAU,AAC}
L-lysine	{AAA,AAG}
L-aspartic acid	{GAU,GAC}
L-glutamic acid	{GAA,GAG}

Goal of this essay and description of the data

It was recently discovered that RNA editing and amino acid changes are widespread in cephalopods. In this essay, I attempt to analyse and compare the distribution of amino acid changes in cephalopod species (Squid, Sepia, Octopus vulgaris, Octopus bimaculoides) and human.

The data set consists of calculated expected distribution ("Expected amount", "Expected frequency") and observed distribution ("Edits", "Frequency") of amino acid changes in humans, four cephalopod species, and conserved edits from those species. KR represents a change from amino acid K to amino acid R. "syn" means synonymous, does not make any changes to amino acid and is likely to not have an effect. "stop_W" means stop to w and causes a significant change in a protein sequence.

Data

In[]:=

data=SemanticImport@URLDownload["https://github.com/ZhamilyaB/Summer2018Starter/raw/master/Computational%20Essay/editingcodonsimplifieddata.csv"];

Out[]=

	Change	Expected_amount	Expected_frequency	Edits	Frequency	Difference	Fold_difference	Species
human	KR	2	0.0606061	220	0.142487	-0.081881	2.35104	human
	SG	2	0.0606061	151	0.0977979	-0.0371919	1.61367	human
	IM	1	0.030303	38	0.0246114	0.00569163	0.812176	human
	TA	4	0.121212	148	0.0958549	0.0253572	0.790803	human
	17 total ›
specific_sepia	KR	2	0.0416667	14503	0.136295	-0.0946282	3.27108	specific_sepia
	SG	2	0.0416667	6856	0.0644306	-0.022764	1.54634	specific_sepia
	NS	2	0.0416667	5836	0.054845	-0.0131783	1.31628	specific_sepia
	KE	2	0.0416667	5552	0.052176	-0.0105094	1.25222	specific_sepia
	17 total ›
conserved_cephalopods	KR	2	0.0416667	243	0.212042	-0.170375	5.08901	conserved_cephalopods
	SG	2	0.0416667	106	0.0924956	-0.050829	2.2199	conserved_cephalopods
	YC	2	0.0416667	66	0.0575916	-0.015925	1.3822	conserved_cephalopods
	RG	2	0.0416667	64	0.0558464	-0.0141798	1.34031	conserved_cephalopods
	17 total ›
specific_oct_bim	KR	2	0.042	8304	0.133	-0.091	3.18491	specific_oct_bim
	SG	2	0.042	4503	0.072	-0.03	1.72708	specific_oct_bim
	NS	2	0.042	3484	0.056	-0.014	1.33625	specific_oct_bim
	IM	1	0.021	1543	0.025	-0.004	1.1836	specific_oct_bim
	17 total ›
specific_squid	KR	2	0.0416667	8647	0.133439	-0.0917726	3.20254	specific_squid
	SG	2	0.0416667	4518	0.0697211	-0.0280545	1.67331	specific_squid
	NS	2	0.0416667	3451	0.0532554	-0.0115887	1.27813	specific_squid
	syn	15	0.3125	22614	0.348976	-0.0364761	1.11672	specific_squid
	17 total ›
showing 1–5 of 6

All types of amino acids changes are categorized as either radical or conserved. Radical changes are those that change the physicochemical property of the amino acid while conservative changes do not. The ratio of radical to conservative changes indicates how many changes are likely to have a negative effect.

Out[]=

Change	A	B	C
YC	R	R	R
TA	C	C	C
syn
SG	C	C	C
RG	R	R	R
QR	C	R	R
pW
NS	C	R	C
ND	R	C	R
MV	C	C	C
KR	C	C	C
KE	R	R	R
IV	C	C	C
IM	C	C	C
HR	C	C	C
EG	R	R	R
DG	R	R	R

Assumptions

Amino acid changes also can be random or non-random: Random edits are likely to be slightly bad and don’t make an animal better, Non-random edits are likely to be good, be actively preserved in the population and seen more in conserved. In humans most changes are random, therefore, they are most likely to have a negative effect. In Individual cephalopod species, amino acid changes are a lot less random and they are less likely to have a negative effect. In conserved, changes are least random and most likely to have a positive effect.

Visualisation and Exploration

Expected frequency vs. actual frequency

Out[]=

human

specific_sepia

conserved_cephalopods

specific_oct_bim

specific_squid

specific_oct_vul

Frequency

Aminoacids changes

	KR
	SG
	IM
	TA
	IV
	syn
	MV
	HR
	NS
	ND

	QR
	KE
	EG
	RG
	YC
	DG
	stop-W

Expected Frequency

For importing images I was using Wolfram|Alpha Query, which is a very helpful tool to find correct images and more information on a subject right inside Mathematica.



In[]:=

Squid image

Assuming Squid is referring to a species specification. Use "Squid" as

a food

. Use "Squid" as

an amusement park ride

a measurement device

referring to English words

. Use "Squid" as

a measurement device

referring to English words

. Use "the input" as

referring to English words

Assuming squids. Use

longfin inshore squid

instead

Input interpretation:

squids

image

Result:

In[]:=

squids

SPECIES SPECIFICATION



image



Out[]=

The comparison of frequencies of changes in all species

With this plot we are trying to explore the amino acid changes that are

1) the most different and the most similar in all of the species.

2) how and why are they different or similar?

3) and what is the general pattern?

Out[]=

Changes

Species

	human
	specific_oct_bim
	conserved_cephalopods
	specific_sepia
	specific_squid
	specific_oct_vul

Frequency

First observation:
Humans have a different pattern from each one of cephalopod species, but cephalopod species together have a similar pattern which means that this amino acid preference is connected to cephalopod species being special.

Out[]=

Changes

Species

	human
	specific_oct_bim
	conserved_cephalopods
	specific_sepia
	specific_squid
	specific_oct_vul

Frequency

Second observation:
EG, TA, KE changes in human are most different and therefore are more likely to have a negative effect. As well contributed to cephalopod species being special.
If we check these three changes, it turns out: EG, KE are radical changes and TA is conserved which doesn’t disprove our assumptions.

The comparison of amount of changes in cephalopod species

Out[]=

Changes

Species

	human
	specific_oct_bim
	conserved_cephalopods
	specific_sepia
	specific_squid
	specific_oct_vul

Edits

Observation:
Squid and sepia have more similar number of edits compared to oct_bim and oct_vul because they are just different kinds of octopus.

Out[]=

Changes
	Edits

By applying Logarithmic function we can clearly see the pattern of amino acid changes in each species is very similar and different from human

Out[]=

Changes
	Edits

Frequencies in different species

How are the distribution different/similar between different species?

Out[]=

Species

Aminoacids changes

	KR
	SG
	IM
	TA
	IV
	syn
	MV
	HR
	NS
	ND

	QR
	KE
	EG
	RG
	YC
	DG
	stop-W

Frequency

First, we notice that KR and synonymous are conserved. We can observe that they have higher frequency in cephalopod species which means that the ratio of radical to conserved in cephalopod species is less than this ratio in humans and conserved_cephalopods. Which is exactly the difference in ratios of radical to conserved in all the species from the research.

Ratio of radical to conserved:

Out[]=

Average	R/C
squid	0.57
sepia	0.59
oct_bim	0.55
oct_vul	0.56
conserved	0.53
human	0.78

Further explorations

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods, Cell 169, 191–202 (2017).

Author contact information

zhamilya.bilyalova@prismsus.org

Cite this as: Zhamilya Bilyalova, "The distribution of amino acid changes in different species" from the Notebook Archive (2018), https://notebookarchive.org/2019-02-b3xrfr7

The distribution of amino acid changes in different species

Introduction: What is RNA editing?

Goal of this essay and description of the data

Data

Assumptions

Visualisation and Exploration

Expected frequency vs. actual frequency​

​​The comparison of frequencies of changes in all species

The comparison of amount of changes in cephalopod species

Frequencies in different species

Further explorations

Author contact information

Expected frequency vs. actual frequency

The comparison of frequencies of changes in all species