An evolutionary analysis identifies a conserved pentapeptide stretch containing the two essential lysine residues for rice L-myo-inositol 1-phosphate synthase catalytic activity

Basak, Papri; Maitra-Majee, Susmita; Das, Jayanta Kumar; Mukherjee, Avinandan; Dastidar, Shubhra Ghosh; Choudhury, Pabitra Pal; Majumder, Arun Lahiri

doi:10.1371/journal.pone.0185351

Cited by 25 publications

(32 citation statements)

References 40 publications

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“…Table 1 To understand the structural and chemical property of Amino Acid one need to understand the structural and chemical property of protein. It has been reported in a paper that molecular evolutionary analysis of conserved region based on chemical properties of the side chain of amino acids can determine the essential amino acids in the core catalytic region [8]. So here in this manuscript it is aimed to understand how the biochemical nature of each amino acid sequences figure out evolutionary conserved regions among glutamate genes of mammal and plant during the long process of evolution.…”

Section: A Classification Of Amino Acidsmentioning

confidence: 99%

“…now define the weight of each arc from V i to V j as 1, so that for every arc from V i to V j , total weight of the arcs of graph G m is, In this way the graphical representation of Amino Acid (aa) sequence can give us an idea about the distribution of chemical properties in them.Now the directed multi graph can be drawn through adjacency matrix. We can get its corresponding (8X8) adjacent matrix M for each pair of vertices as mentioned below in Table 10, which gives us 64 dimensional vectors in row order say R, where R=(w(1,1),w(1,2),.....w (1,8),....,w(8,1),…w (8,8)). Table 4.…”

Section: F Investigating Evolutionary Relationships Between Two Speciesmentioning

confidence: 99%

“…Analysis of DNA as well as amino acid sequences using underlying biological information hidden in them is an old approach, whereas Graphical representation of primary protein sequence give alignment free method which provides visual inspection of the sequence and instant provision of analyzing similarities with others. Numerous authors [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25] proposed several 2D and 3D graphical representations of DNA as well as amino acid sequences.. Some research papers are reported, where multiplet structure of amino acid sequences are the theme to investigate evolutionary relationship among the species [22].…”

Section: Introductionmentioning

confidence: 99%

“…Some research papers are reported, where multiplet structure of amino acid sequences are the theme to investigate evolutionary relationship among the species [22]. Attempt has also been made to find out invariant conservation of certain amino acids of various organism using biochemical properties of amino acid side chains [6][7][8].Several works have also been done with PPIs, where it is tried to find whether hub and the genes in network exhibit any kind of proximity with respect to the codons [27]. In this paper, the section of materials and methods has several sub sections.…”

Section: Introductionmentioning

confidence: 99%

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Sequence Characterization of Glutamate Receptor Genes of Rat a Vertebrate and Arabidopsis Thaliana a Plant

Sengupta¹,

Choudhury²

2018

Preprint

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iGluR gene family of a vertebrate, Rat and AtGLR gene family of a plant, Arabidopsis thaliana [4] perform some common functionalities in neuro-transmission, which have been compared quantitatively. Our attempt is based on the chemical properties of amino acids [6,7,8] comprising the primary protein sequences of the aforesaid genes. 19 AtGLR genes of length varying from 808 amino acid (aa) to 1039 aa and 16 iGluR genes length varying from 902aa to 1482 aa have been taken as data sets. Thus, we detected the commonalities (conserved elements) during the long evolution of plants and animals from a common ancestor [4]. Eight different conserved regions have been found based on individual amino acids. Two different conserved regions are also found, which are based on chemical groups of amino acids. We have tried too to find different possible patterns which are common throughout the data set taken. 9 such patterns have been found with size varying from 2 to 5 amino acids at different regions in each primary protein sequences. Phylogenetic trees of AtGLR and iGluR families have also been constructed. This approach is likely to shed light on the long course of evolution.

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Section: A Classification Of Amino Acidsmentioning

confidence: 99%

Section: F Investigating Evolutionary Relationships Between Two Speciesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Sequence Characterization of Glutamate Receptor Genes of Rat a Vertebrate and Arabidopsis Thaliana a Plant

Sengupta¹,

Choudhury²

2018

Preprint

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“…The chemical features of 20 amino acids have basically depended on eight chemical properties [7], [16], [17] All…”

Section: Bit Representation Of 64 Codons In Genetic Codementioning

confidence: 99%

Effective Variations of related Physicochemical Properties of Nucleotides Leading to Amino Acids for Characterizing Genes and Proteins

Sengupta¹,

Pp²

2018

Preprint

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The aim of this paper is to make quantitative analysis of the properties which is really being carried from DNA sequence and finally landing up to the properties of a protein structure through its primary protein sequence. Thus, the paper has a theory which is applicable for any arbitrary DNA sequence whether it is of various species or mutated data or a bunch of genes responsible for a function to be occurred. Irrespective to genes of any families, species, wild type or mutated, our paper here gives a standard model which defines a mapping between physicochemical properties of any arbitrary DNA sequence and physicochemical properties of its amino acid sequence. Experiments have been carried out with PPCA protein family and its four homologs PPC(B-E) which establishes that DNA sequence keeps its signature even after its translation into the corresponding amino acid sequence.

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Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis

Esposti

2023

FEBS Letters

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The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside‐out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.

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An evolutionary analysis identifies a conserved pentapeptide stretch containing the two essential lysine residues for rice L-myo-inositol 1-phosphate synthase catalytic activity

Cited by 25 publications

References 40 publications

Sequence Characterization of Glutamate Receptor Genes of Rat a Vertebrate and Arabidopsis Thaliana a Plant

Sequence Characterization of Glutamate Receptor Genes of Rat a Vertebrate and Arabidopsis Thaliana a Plant

Effective Variations of related Physicochemical Properties of Nucleotides Leading to Amino Acids for Characterizing Genes and Proteins

Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis

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