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Article ; Online: Deciphering the intrinsic properties of fungal proteases in optimizing phytopathogenic interaction.

Podder, Soumita / Saha, Deeya / Ghosh, Tapash C

2019 Volume 711, Page(s) 143934

Abstract: Phytopathogenic fungi secrete a wide range of enzymes to penetrate and colonize host tissues. Of them protease activity is reported to increase disease aggressiveness in the plant. With the aim to explore the reason of the higher infection potential of ... ...

Abstract	Phytopathogenic fungi secrete a wide range of enzymes to penetrate and colonize host tissues. Of them protease activity is reported to increase disease aggressiveness in the plant. With the aim to explore the reason of the higher infection potential of proteases, we have compared several genomic and proteomic attributes among different hydrolytic enzymes coded by five pathogenic fungal species which are the potent infectious agents of plant. Categorizing the enzymes into four major groups, namely protease, lipase, amylase and cell-wall degraders, we observed that proteases are evolutionary more conserved, have higher expression levels, contain more hydrophobic buried residues, short linear motifs and post-translational modified (PTM) sites than the other three groups of enzymes. Again, comparing these features of protease between pathogenic and non-pathogenic Aspergillus sps, we have hypothesized that protein structural properties could play significant roles in imposing infection potency to the fungal proteases.
MeSH term(s)	Aspergillus/classification ; Aspergillus/genetics ; Aspergillus/pathogenicity ; Computational Biology/methods ; Computer Simulation ; Conserved Sequence ; Fungal Proteins/chemistry ; Fungal Proteins/genetics ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Hydrophobic and Hydrophilic Interactions ; Peptide Hydrolases/chemistry ; Peptide Hydrolases/genetics ; Phylogeny ; Protein Conformation ; Protein Processing, Post-Translational ; Proteomics/methods
Chemical Substances	Fungal Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2019-06-19
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2019.06.024
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Article: Deciphering the intrinsic properties of fungal proteases in optimizing phytopathogenic interaction

Podder, Soumita / Saha, Deeya / Ghosh, Tapash C

Gene. 2019 Aug. 30, v. 711

2019

Abstract	Phytopathogenic fungi secrete a wide range of enzymes to penetrate and colonize host tissues. Of them protease activity is reported to increase disease aggressiveness in the plant. With the aim to explore the reason of the higher infection potential of proteases, we have compared several genomic and proteomic attributes among different hydrolytic enzymes coded by five pathogenic fungal species which are the potent infectious agents of plant. Categorizing the enzymes into four major groups, namely protease, lipase, amylase and cell-wall degraders, we observed that proteases are evolutionary more conserved, have higher expression levels, contain more hydrophobic buried residues, short linear motifs and post-translational modified (PTM) sites than the other three groups of enzymes. Again, comparing these features of protease between pathogenic and non-pathogenic Aspergillus sps, we have hypothesized that protein structural properties could play significant roles in imposing infection potency to the fungal proteases.
Keywords	Aspergillus ; amylases ; carboxylic ester hydrolases ; cell walls ; enzyme activity ; genomics ; hydrophobicity ; pathogenesis ; plant pathogenic fungi ; proteinases ; proteomics ; tissues
Language	English
Dates of publication	2019-0830
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2019.06.024
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Article ; Online: The combined influence of codon composition and tRNA copy number regulates translational efficiency by influencing synonymous nucleotide substitution.

Victor, Manish P / Acharya, Debarun / Chakraborty, Sandip / Ghosh, Tapash C

Gene

2020 Volume 745, Page(s) 144640

Abstract: Codon usage bias is an important genomic phenomenon, where highly expressed genes use optimal codons for smoother translation with high yield, facilitated by the cognate tRNAs. Here, we presented the tRNA co-adaptation index (co-AI) by correlating tRNA ... ...

Abstract	Codon usage bias is an important genomic phenomenon, where highly expressed genes use optimal codons for smoother translation with high yield, facilitated by the cognate tRNAs. Here, we presented the tRNA co-adaptation index (co-AI) by correlating tRNA gene copy number and codon composition in Saccharomyces cerevisiae. We observed that this co-AI is positively correlated with protein abundance and translation rate. Considering nucleotide substitutions, co-AI influences synonymous substitutions more than gene expression and protein abundance, the most important determinants of evolutionary rate. Co-AI correlates positively with mRNA secondary structure stability and mRNA half-life, which may lead to protein accumulation under high co-AI. However, the highly expressed proteins encoded by high co-AI genes are assisted by molecular chaperones to attain their proper functional conformation and prevent accumulation.
MeSH term(s)	Codon Usage ; Gene Dosage ; Nucleic Acid Conformation ; Protein Biosynthesis/genetics ; RNA Stability ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribosomes/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Silent Mutation
Chemical Substances	RNA, Messenger ; Saccharomyces cerevisiae Proteins ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2020-04-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2020.144640
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Article ; Online: Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution.

Acharya, Debarun / Ghosh, Tapash C

BMC genomics

2016 Volume 17, Page(s) 71

Abstract: Background: Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from ... ...

Abstract	Background: Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from small-scale duplication (SSD) to whole genome duplication (WGD). Studies with yeast revealed ample differences between these duplicates: Yeast WGD pairs were functionally more similar, less divergent in subcellular localization and contained a lesser proportion of essential genes. In this study, we explored the differences in evolutionary genomic properties of human SSD and WGD genes, with the identifiable human duplicates coming from the two rounds of whole genome duplication occurred early in vertebrate evolution. Results: We observed that these two groups of duplicates were also dissimilar in terms of their evolutionary and genomic properties. But interestingly, this is not like the same observed in yeast. The human WGDs were found to be functionally less similar, diverge more in subcellular level and contain a higher proportion of essential genes than the SSDs, all of which are opposite from yeast. Additionally, we explored that human WGDs were more divergent in their gene expression profile, have higher multifunctionality and are more often associated with disease, and are evolutionarily more conserved than human SSDs. Conclusions: Our study suggests that human WGD duplicates are more divergent and entails the adaptation of WGDs to novel and important functions that consequently lead to their evolutionary conservation in the course of evolution.
MeSH term(s)	Animals ; Biological Evolution ; Evolution, Molecular ; Gene Duplication/genetics ; Humans ; Vertebrates/genetics
Language	English
Publishing date	2016-01-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-016-2392-0
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Article: The combined influence of codon composition and tRNA copy number regulates translational efficiency by influencing synonymous nucleotide substitution

Victor, Manish P / Acharya, Debarun / Chakraborty, Sandip / Ghosh, Tapash C

Gene. 2020 June 30, v. 745

2020

Abstract	Codon usage bias is an important genomic phenomenon, where highly expressed genes use optimal codons for smoother translation with high yield, facilitated by the cognate tRNAs. Here, we presented the tRNA co-adaptation index (co-AI) by correlating tRNA gene copy number and codon composition in Saccharomyces cerevisiae. We observed that this co-AI is positively correlated with protein abundance and translation rate. Considering nucleotide substitutions, co-AI influences synonymous substitutions more than gene expression and protein abundance, the most important determinants of evolutionary rate. Co-AI correlates positively with mRNA secondary structure stability and mRNA half-life, which may lead to protein accumulation under high co-AI. However, the highly expressed proteins encoded by high co-AI genes are assisted by molecular chaperones to attain their proper functional conformation and prevent accumulation.
Keywords	Saccharomyces cerevisiae ; codon usage ; correlation ; gene dosage ; gene expression ; genomics ; half life ; lead ; molecular chaperones ; protein synthesis
Language	English
Dates of publication	2020-0630
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-light
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2020.144640
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The optimization of mRNA expression level by its intrinsic properties-Insights from codon usage pattern and structural stability of mRNA.

Victor, Manish P / Acharya, Debarun / Begum, Tina / Ghosh, Tapash C

Genomics

2018 Volume 111, Issue 6, Page(s) 1292–1297

Abstract: Codon usage bias (CUB) and mRNA structural stability are important intrinsic features of mRNA that correlate positively with mRNA expression level. However, it remains unclear whether the mRNA expression level can be regulated by adjusting these two ... ...

Abstract	Codon usage bias (CUB) and mRNA structural stability are important intrinsic features of mRNA that correlate positively with mRNA expression level. However, it remains unclear whether the mRNA expression level can be regulated by adjusting these two parameters, influencing the mRNAs' structure. Here we explored the influence of CUB and mRNA structural stability on mRNA expression levels in Saccharomyces cerevisiae, using both wild type and computationally mutated mRNAs. Although in wild type, both CUB and mRNA stability positively regulate the mRNA expression level, any deviation from natural situation breaks such equilibrium. The naturally occurring codon composition is responsible for optimizing the mRNA expression, and under such composition, the mRNA structure having highest stability is selected by nature.
MeSH term(s)	Codon ; Codon Usage ; RNA Stability ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Codon ; RNA, Messenger
Language	English
Publishing date	2018-09-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2018.08.009
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Article: The optimization of mRNA expression level by its intrinsic properties—Insights from codon usage pattern and structural stability of mRNA

Victor, Manish P / Acharya, Debarun / Begum, Tina / Ghosh, Tapash C

Genomics. 2019 Dec., v. 111, no. 6

2019

Abstract	Codon usage bias (CUB) and mRNA structural stability are important intrinsic features of mRNA that correlate positively with mRNA expression level. However, it remains unclear whether the mRNA expression level can be regulated by adjusting these two parameters, influencing the mRNAs' structure. Here we explored the influence of CUB and mRNA structural stability on mRNA expression levels in Saccharomyces cerevisiae, using both wild type and computationally mutated mRNAs. Although in wild type, both CUB and mRNA stability positively regulate the mRNA expression level, any deviation from natural situation breaks such equilibrium. The naturally occurring codon composition is responsible for optimizing the mRNA expression, and under such composition, the mRNA structure having highest stability is selected by nature.
Keywords	gene expression ; messenger RNA ; Saccharomyces cerevisiae
Language	English
Dates of publication	2019-12
Size	p. 1292-1297.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2018.08.009
Database	NAL-Catalogue (AGRICOLA)

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Article: Overlapping Regions in HIV-1 Genome Act as Potential Sites for Host-Virus Interaction.

Saha, Deeya / Podder, Soumita / Ghosh, Tapash C

Frontiers in microbiology

2016 Volume 7, Page(s) 1735

Abstract: More than a decade, overlapping genes in RNA viruses became a subject of research which has explored various effect of gene overlapping on the evolution and function of viral genomes like genome size compaction. Additionally, overlapping regions (OVRs) ... ...

Abstract	More than a decade, overlapping genes in RNA viruses became a subject of research which has explored various effect of gene overlapping on the evolution and function of viral genomes like genome size compaction. Additionally, overlapping regions (OVRs) are also reported to encode elevated degree of protein intrinsic disorder (PID) in unspliced RNA viruses. With the aim to explore the roles of OVRs in HIV-1 pathogenesis, we have carried out an in-depth analysis on the association of gene overlapping with PID in 35 HIV1- M subtypes. Our study reveals an over representation of PID in OVR of HIV-1 genomes. These disordered residues endure several vital, structural features like short linear motifs (SLiMs) and protein phosphorylation (PP) sites which are previously shown to be involved in massive host-virus interaction. Moreover, SLiMs in OVRs are noticed to be more functionally potential as compared to that of non-overlapping region. Although, density of experimentally verified SLiMs, resided in 9 HIV-1 genes, involved in host-virus interaction do not show any bias toward clustering into OVR,
Language	English
Publishing date	2016-11-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.01735
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Article ; Online: Exploring the differences in evolutionary rates between monogenic and polygenic disease genes in human.

Podder, Soumita / Ghosh, Tapash C

Molecular biology and evolution

2010 Volume 27, Issue 4, Page(s) 934–941

Abstract: Comparative analyses on disease and nondisease (ND) genes have greatly facilitated the understanding of human diseases. However, most studies have grouped all the disease genes together and have performed comparative analyses with other ND genes. Thus, ... ...

Abstract	Comparative analyses on disease and nondisease (ND) genes have greatly facilitated the understanding of human diseases. However, most studies have grouped all the disease genes together and have performed comparative analyses with other ND genes. Thus, the molecular mechanism of disease on which disease genes can be separated into monogenic and polygenic diseases (MDs and PDs) has been ignored in earlier studies. Here, we report a comprehensive study of PD and MD genes with respect to ND genes. Our work shows that MD genes are more conserved than PD genes and that ND genes are themselves more conserved than both classes of disease genes. By separating the ND genes into housekeeping and other genes, it was found that housekeeping genes are the most conserved among all categories of genes, whereas other ND genes show an evolutionary rate intermediate between MD and PD genes. Although PD genes have a higher number of interacting partners than MD and ND genes, the reasons for their higher evolutionary rate require explanation. We provide evidences that the faster evolutionary rate of PD genes is influenced by 1) the predominance of date hubs in protein-protein interaction network, 2) the higher number of disorder residues, 3) the lower expression level, and 4) the involvement with more regulatory processes. Logistic regression analysis suggests that the relative importance of the four individual factors in determining the evolutionary rate variation among the four classes of proteins is in the order of mRNA expression level > presence of party/date hubs > disorder > involvement of proteins in core/regulatory processes.
MeSH term(s)	Disease/genetics ; Evolution, Molecular ; Gene Expression ; Humans ; Proteins/genetics ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2010-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msp297
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Article ; Online: Investigating different duplication pattern of essential genes in mouse and human.

Acharya, Debarun / Mukherjee, Dola / Podder, Soumita / Ghosh, Tapash C

PloS one

2015 Volume 10, Issue 3, Page(s) e0120784

Abstract: Gene duplication is one of the major driving forces shaping genome and organism evolution and thought to be itself regulated by some intrinsic properties of the gene. Comparing the essential genes among mouse and human, we observed that the essential ... ...

Abstract	Gene duplication is one of the major driving forces shaping genome and organism evolution and thought to be itself regulated by some intrinsic properties of the gene. Comparing the essential genes among mouse and human, we observed that the essential genes avoid duplication in mouse while prefer to remain duplicated in humans. In this study, we wanted to explore the reasons behind such differences in gene essentiality by cross-species comparison of human and mouse. Moreover, we examined essential genes that are duplicated in humans are functionally more redundant than that in mouse. The proportion of paralog pseudogenization of essential genes is higher in mouse than that of humans. These duplicates of essential genes are under stringent dosage regulation in human than in mouse. We also observed slower evolutionary rate in the paralogs of human essential genes than the mouse counterpart. Together, these results clearly indicate that human essential genes are retained as duplicates to serve as backed up copies that may shield themselves from harmful mutations.
MeSH term(s)	Animals ; Evolution, Molecular ; Gene Duplication ; Genes, Developmental ; Genes, Essential ; Humans ; Mice ; Models, Genetic ; Pseudogenes
Language	English
Publishing date	2015-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0120784
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