Skip to main content

arif uddin

Follower

1

Following

2

Public Views

Interests

Uploads

Papers by arif uddin

Synonymous codon usage and context analysis of genes associated with pancreatic cancer

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2020

Pancreatic cancer is a fatal disorder which originates in pancreas. Its mortality rate is increas... more Pancreatic cancer is a fatal disorder which originates in pancreas. Its mortality rate is increasing with time. Some studies also reported that pancreatic cancer would be ranked 2nd by the year 2030. Codon usage bias (CUB) arises when synonymous codons for each amino acid are not used randomly in the coding sequences of genes. We used bioinformatic methods to analyze the compositional properties, codon context and codon usage trend of the genes associated with pancreatic cancer as no work was reported yet. From the base composition analysis, the pancreatic cancer genes were found to be GC-rich and at the 3rd codon position the G/C ending codons were more preferred to A/T ending ones. The CUB was low in genes associated with pancreatic cancer. Correspondence analysis proposed that other than base constraints, CUB might also be affected by some other factors such as natural selection. Moreover, results of correlation analysis indicated that CUB and various GC contents i.e. GC, GC1, GC2, GC3 played important role in the release of free energy by transcripts of the genes associated with pancreatic cancer. The low compAI values of coding sequences suggested a low translation rate of the genes.

Codon Usage in Human Mitochondrial Genes in the Context of Cancer

International Journal of Pharmacy and Pharmaceutical Sciences, 2016

Objective: Mitochondria are the powerhouse of the cell . Mitochondrial DNA is more susceptible to... more Objective: Mitochondria are the powerhouse of the cell . Mitochondrial DNA is more susceptible to oxidative damage due to the lack of histone protein and chromatin structure. The alteration in the level of gene expression in cytochrome c oxidase gene is associated with cancer. The expression of coxiii gene was found to be lower in human colonic carcinoma. However, a systematic analysis of codon usage in human mitochondrial protein-coding genes has not been reported yet. This study gives an insight into the understanding of the pattern of codon usage and expression in human mitochondrial genes. Methods: We used a bioinformatics approach to analyse the codon usage parameters by using bioinformatics tools like an effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU) etc. Results: The comparison of codon usage pattern among different mitochondrial genes suggests that mitochondrial genes have a lower level of codon usage bias and high expr...

Mutation Pressure Dictates Codon Usage Pattern in Mitochondrial Atpase8 in Some Mammalian Species

Background: Codon usage bias is the phenomenon of unequal use of synonymous codons in a gene; som... more Background: Codon usage bias is the phenomenon of unequal use of synonymous codons in a gene; some codons are more preferred than others. However codon usage pattern is different in different genes and organisms and is mainly caused by mutation and selection pressure. Codon usage bias is mostly found in highly expressed genes. Mammals are the highly evolved organisms in animal kingdom. Study of codon usage bias helps in better understanding of molecular biology, genetics and evolution of genes. Methods and Result: We used bioinformatics approach to understand the pattern of codon usage bias of mitochondrial atpase8 gene in ten species of mammals. We have found that GC content varies from 27.5 to 46.4% with a mean of 37.49±5.12 and GC content at 3 rd codon position varies from 16.2 to 47.8% with a mean of 34.11±9.76. ENC values are much higher and range from 42 to 60 with a mean of 54.1±5.93. A highly positive correlation was found between ENC and GC (r=0.9333, p<0.001), ENC and G...

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Biology, 2021

The protein-coding gene FoxP2 (fork head box protein P2) plays a major role in communication and ... more The protein-coding gene FoxP2 (fork head box protein P2) plays a major role in communication and evolutionary changes. The present study carried out a comprehensive codon usage bias analysis in the FoxP2 gene among a diverse group of animals including fishes, birds, reptiles, and mammals. We observed that in the genome of fishes for the FoxP2 gene, codons ending with C or G were most frequently used, while in birds, reptiles, and mammals, codons ending with T or A were most frequently used. A higher ENC value was observed for the FoxP2 gene indicating a lower CUB. Parity role two-bias plots suggested that apart from mutation pressure, other factors such as natural selection might have influenced the CUB. The frequency distribution of the ENC observed and ENC expected ratio revealed that mutation pressure plays a key role in the patterns of codon usage of FoxP2. Besides, correspondence analysis exposed the composition of the nucleobase under mutation bias affects the codon usage of t...

Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia

Journal of Cellular Physiology, 2020

In this study, we used a bioinformatics approach to analyze the nucleotide composition and patter... more In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.

Morphological markers associated with pericarp colour and its inheritance pattern in black scented rice of Manipur

Tropical Plant Research, 2020

Rice (Oryza sativa) is the most widely consumed staple food for a large section of world's popula... more Rice (Oryza sativa) is the most widely consumed staple food for a large section of world's population. Biotechnological developments have led plant breeders to develop for more efficient selection strategies instead of the traditional phenotype-based plant selection method. Rice varieties other than white are usually called red or black rice. Black scented rice is in great demand and mostly grown in Asian countries. The intensity of pericarp in black rice ranges from dark purple to light purple, and the genetic mechanism underlying this colour variation is yet to be identified. Therefore, the inheritance patterns of black rice cultivars and the phenotypic markers associated with black pericarp colour have been studied in this study. Phenotypic investigation of the black scented rice may aid in the breeding of anthocyanin-rich rice varieties and may provide insights into the potential enhancement of this valuable antioxidant in a variety of foodstuffs. The experiments were conducted on F 1 and F 2 individuals developed from the crosses between indigenous black scented rice (Chakhao) cultivars of Manipur and the local white landrace cultivars. The segregation ratio of F 2 individuals was analyzed with the chi-square formula. The F 2 population showed some of the morphological markers like purple coleoptiles, purplish-black colour at leaf tip and stalks and the formation of black rings (auricles) were associated with pericarp colours. This, in fact, revealed the inheritance pattern of pericarp colour in black scented rice. The present study provides useful information on the inheritance of pericarp colour in black scented rice of Manipur and possesses the potential for their further genetic improvement.

Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae

Archives of Virology, 2021

The present study was carried out on 62 genome sequences of members of the family Anelloviridae, ... more The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.

format_quoteENC values for Anelloviridae genomes ranged from 36.65 to 57.40, indicating low codon usage bias yet significant variation among genomes.format_quote

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Archives of Virology, 2020

Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid... more Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.

Preference of A/T ending codons in mitochondrial ATP6 gene under phylum Platyhelminthes

Molecular and Biochemical Parasitology, 2018

Unequal usage of synonymous codons in the gene transcript for an amino acid is known as codon usa... more Unequal usage of synonymous codons in the gene transcript for an amino acid is known as codon usage bias (CUB). It is a unique property of gene as well as genome. Mutation and natural selection are known to be the major factors that influence CUB. Other factors encompass gene expression level, GC content, codon position, recombination rate, RNA stability and gene length. CUB analysis helps in in-depth understanding of the molecular biology, genetics and genome evolution in a species. We used bioinformatic methods to explore the pattern of CUB in MT-ATP6 gene in different classes of platyhelminthes. The analysis is based on genetic code of translational table 14 of National Center of Biotechnology Information (NCBI) where the codon AAA codes for asparagine and TAA for tyrosine amino acid. The synonymous codon usage order (SCUO), an index of CUB, values in different classes namely cestoda, monogenea, rabditophora, trematoda and turbellaria of platyhelminths were found to be 0.43, 0.32, 0.49, 0.40 and 0.36, respectively which suggest that the codon usage bias of ATP6 gene was low (SCUO < 0.50). Highly significant correlation (p < 0.001) was found between SCUO and various GC contents indicating that GC composition had an influence on CUB. From the relative synonymous codon usage (RSCU) analysis on codons, we found most of the over-represented codons in all the classes were A/ T ending types, which suggested that the preferred codons were influenced by compositional constraints. The PR2 plot revealed asymmetric usage of AT and GC bases among the four fold degenerate codon families with greater usage of G and T over A and C. Highly significant correlation (p < 0.001) was found between overall nucleotide composition and its 3rd codon position suggesting that both natural selection and mutation pressure might have influenced the CUB among different classes. Neutrality analysis revealed that natural selection might play a major role. Mutational responsive index (MRI) and translational selection (P2) values elucidated that selection for translational efficiency moderately affected the codon usage bias in MT-ATP6 gene.

Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta

Journal of Integrative Agriculture, 2019

Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensi... more

format_quoteNatural selection strongly influences CUB in cp genes of tea species, with significant correlation (P<0.01) between expressed gene levels and codon usage order.format_quote

Compositional dynamics and codon usage pattern of BRCA1 gene across nine mammalian species

Genomics, Jan 27, 2018

The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological... more The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological processes. The aminoacyl-tRNA synthetases (AARS) are a family of heterogenous enzymes responsible protein synthesis and whose secondary functions include a role in autoimmune myositis. Our findings reveal that the compositional constraint and the preference of more A/T -ending codons determine the codon usage patterns in BRCA1 gene while more G/C-ending codons influence the codon usage pattern of AARS gene among mammals. The codon usage bias in BRCA1 and AARS genes is low. The codon CGC encoding arginine amino acid and the codon TTA encoding leucine were uniformly distributed in BRCA1 and AARS genes, respectively in mammals including human. Natural selection might have played a major role while mutation pressure might have played a minor role in shaping the codon usage pattern of BRCA1 and AARS genes.

Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents

Mitochondrion, Sep 28, 2017

The study of codon usage coupled with phylogenetic analysis is an important tool to understand th... more The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes. The codon usage bias was low as revealed from high ENC value. Correlation between codon usage and GC3 suggested that all the codons ending with G/C were positively correlated with GC3 but vice versa for A/T ending codons with the exception of ND4L and ND5 genes. Neutrality plot revealed that for the genes ATP6, COI, COIII, CYB, ND4 and ND4L, natural selection might have played a major role while mutation pressure might h...

format_quotePhylogenetic analysis reveals variable evolutionary relationships of mitochondrial genes across six continents, highlighting geography's influence on gene evolution.format_quote

Codon usage pattern of complex III gene of respiratory chain among platyhelminthes

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, Jan 21, 2017

Codon usage bias refers to the phenomenon where synonymous codons are used with unequal frequenci... more Codon usage bias refers to the phenomenon where synonymous codons are used with unequal frequencies. To understand the patterns of codon usage in mitochondrial cytochrome B (MT-CYB) gene of phylum platyhelminth we used bioinformatic approaches to analyze the protein coding sequences of five different classes - cestoda, monogenea, rabditophora, trematoda and turbellaria. It was found from nucleotide composition analysis that in all the classes, A/T-ended codons were preferred over G/C-ended codons. From box plot analysis GC1 found to have highest response to codon usage bias. Correspondence analysis indicated that besides mutation other factors such as natural selection might also affect the codon usage pattern. Neutrality plot reveals that both mutation and natural selection played role in codon usage pattern in five classes of MT-CYB gene. Various factors namely nucleotide composition, natural selection and mutation pressure affected the codon usage pattern.

format_quoteFourteen codons in Cestoda and 11 in Monogenea exhibited RSCU values >1.6, indicating significant codon usage bias towards A/T-ended codons.format_quote

Factors affecting the codon usage bias of SRY gene across mammals

Gene, Jan 30, 2017

Codon usage bias (CUB) is extensively found in a wide variety genomes and it is mostly affected b... more Codon usage bias (CUB) is extensively found in a wide variety genomes and it is mostly affected by mutation pressure and natural selection. Analysis of CUB helps in studying the evolutionary features of a genome. The SRY gene plays an important role in male reproductive organ and a good candidate to study the evolutionary forces, since little work was reported earlier on this gene. We used bioinformatic methods to analyze the protein-coding sequences of SRY gene in 172 different mammalian species to understand the patterns of codon usage and the evolutionary forces acting on it. We found that the codon bias of SRY gene varies widely across mammals. Relative synonymous codon usage (RSCU) value revealed that the codons such as TCG, CCG, CAT, ATT, ACT, GCT, GTT, GCG, GGG and GGT were over-represented. Correspondence analysis indicated that the distribution of codons was more close to the axes indicating that compositional constraints might correlate to codon bias. Z-score analysis on R...

format_quoteNatural selection is dominant over mutation pressure in determining codon usage bias of the SRY gene across 172 mammals.format_quote

Codon usage bias and its influencing factors for Y-linked genes in human

Computational biology and chemistry, Jan 27, 2017

The non-uniform usage of synonymous codons during translation of a protein is the codon usage bia... more The non-uniform usage of synonymous codons during translation of a protein is the codon usage bias and is mainly influenced by natural selection and mutation pressure. We have used bioinformatic approaches to analyze codon usage bias of human Y-linked genes. Effective number of codon (ENC) suggested that the overall extent of codon usage bias of genes was low. The relative synonymous codon usage (RSCU) analysis revealed that AGA and CTG codons were over-represented in Y-linked genes. Compositional constraint under mutation pressure influenced the codon usage pattern as revealed by the correspondence analysis (COA). Parity plot suggests that both natural selection and mutation pressure might have influenced the codon usage bias of Y-linked genes.

Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome

Genetica, Jan 18, 2017

Analysis of codon usage pattern is important to understand the genetic and evolutionary character... more Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position. The codon usage pattern was different in different genes as revealed from correspondence analysis (COA). A significant correlation between effective number of codons (ENC) and various GC contents suggests that both mutation pressure and natural selection affect the codon usage pattern of genes located in human Y chromosome. In addition, Y-linked genes have significant difference in GC contents at the second and third codon positions, expression level, and codon us...

Codon usage bias and phylogenetic analysis of mitochondrial ND1 gene in pisces, aves, and mammals

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, Jan 24, 2016

The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subu... more The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subunit of the respiratory chain complex I and involved in the first step of the electron transport chain of oxidative phosphorylation (OXPHOS). To understand the pattern of compositional properties, codon usage and expression level of mitochondrial ND1 genes in pisces, aves, and mammals, we used bioinformatic approaches as no work was reported earlier. In this study, a perl script was used for calculating nucleotide contents and different codon usage bias parameters. The codon usage bias of MT-ND1 was low but the expression level was high as revealed from high ENC and CAI value. Correspondence analysis (COA) suggests that the pattern of codon usage for MT-ND1 gene is not same across species and that compositional constraint played an important role in codon usage pattern of this gene among pisces, aves, and mammals. From the regression equation of GC12 on GC3, it can be inferred that the na...

Codon usage trend in mitochondrial CYB gene

Gene, 2016

Here we reported the pattern of codon usage and the factors which influenced the codon usage patt... more Here we reported the pattern of codon usage and the factors which influenced the codon usage pattern in mitochondrial cytochrome B (MT-CYB) gene among pisces, aves and mammals. The F1 axis of correspondence analysis showed highly significant positive correlation with nucleobases A3, C and C3 and significant negative correlation with T and T3 while F2 of correspondence analysis showed significant positive correlation with C and C3 and significant negative correlation with A and A3. From the neutrality plot, it was evident that the GC12 was influenced by mutation pressure and natural selection with a ratio of 0.10/0.90 = 0.11 in pisces, 0.024/0.976 = 0.0245 in aves and in mammals 0.215/0.785 = 0.273, which indicated that the role of natural selection was more than mutation pressure on structuring the bases at the first and second codon positions. Natural selection played the major role; but compositional constraint and mutation pressure also played a significant role in codon usage pattern. Analysis of codon usage pattern has contributed to the better understanding of the mechanism of distribution of codons and the evolution of MT-CYB gene.

Transcription factor gene GATA2: Association of leukemia and nonsynonymous to the synonymous substitution rate across five mammals

Genomics, Jan 2, 2016

GATA2 gene encodes a member of the GATA family of zinc-finger transcription factors that play a p... more GATA2 gene encodes a member of the GATA family of zinc-finger transcription factors that play a pivotal role during the transition of primitive blood forming cells into white blood cells. Mutation in GATA2 results in the loss of function or even gain of function, including abnormal proliferation of white blood cells that may predispose to acute myeloid leukemia. Our results showed that the codon usage in GATA2 has been influenced by GC mutation bias where nature has highly favored fourteen most over represented codons but disfavored the ATA codon across five mammals. Purifying natural selection has affected GATA2 gene in human and other mammals to maintain its protein function during the period of evolution. Our findings report an insight into the codon usage patterns in gaining the clues for codon optimization to alter the translational efficiency as well as for the functional conservation of gene expression and the significance of nucleotide composition in GATA2 gene within mammals.

Codon bias and gene expression of mitochondrial ND2 gene in chordates

Bioinformation, 2015

Background: Mitochondrial ND gene, which encodes NADH dehydrogenase, is the first enzyme of the m... more Background: Mitochondrial ND gene, which encodes NADH dehydrogenase, is the first enzyme of the mitochondrial electron transport chain. Leigh syndrome, a neurodegenerative disease caused by mutation in the ND2 gene (T4681C), is associated with bilateral symmetric lesions in basal ganglia and subcortical brain regions. Therefore, it is of interest to analyze mitochondrial DNA to glean information for evolutionary relationship. This study highlights on the analysis of compositional dynamics and selection pressure in shaping the codon usage patterns in the coding sequence of MT-ND2 gene across pisces, aves and mammals by using bioinformatics tools like effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU) etc. Results: We observed a low codon usage bias as reflected by high ENC values in MT-ND2 gene among pisces, aves and mammals. The most frequently used codons were ending with A/C at the 3 rd position of codon and the gene was AT rich in all the three classes. The codons TCA, CTA, CGA and TGA were over represented in all three classes. The F1 correspondence showed significant positive correlation with G, T3 and CAI while the F2 axis showed significant negative correlation with A and T but significant positive correlation with G, C, G3, C3, ENC, GC, GC1, GC2 and GC3. Conclusions: The codon usage bias in MT-ND2 gene is not associated with expression level. Mutation pressure and natural selection affect the codon usage pattern in MT-ND 2 gene.