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Article: A Molecular Interaction Map of

Saha, Deeya / Kundu, Sudip

2021 Volume 12, Page(s) 613067

Abstract: Klebsiella ... ...

Abstract	Klebsiella pneumoniae
Language	English
Publishing date	2021-02-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.613067
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Article: The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses.

Saha, Deeya / Iannuccelli, Marta / Brun, Christine / Zanzoni, Andreas / Licata, Luana

Frontiers in microbiology

2022 Volume 13, Page(s) 849781

Abstract: Viral infections are one of the major causes of human diseases that cause yearly millions of deaths and seriously threaten global health, as we have experienced with the COVID-19 pandemic. Numerous approaches have been adopted to understand viral ... ...

Abstract	Viral infections are one of the major causes of human diseases that cause yearly millions of deaths and seriously threaten global health, as we have experienced with the COVID-19 pandemic. Numerous approaches have been adopted to understand viral diseases and develop pharmacological treatments. Among them, the study of virus-host protein-protein interactions is a powerful strategy to comprehend the molecular mechanisms employed by the virus to infect the host cells and to interact with their components. Experimental protein-protein interactions described in the scientific literature have been systematically captured into several molecular interaction databases. These data are organized in structured formats and can be easily downloaded by users to perform further bioinformatic and network studies. Network analysis of available virus-host interactomes allow us to understand how the host interactome is perturbed upon viral infection and what are the key host proteins targeted by the virus and the main cellular pathways that are subverted. In this review, we give an overview of publicly available viral-human protein-protein interactions resources and the community standards, curation rules and adopted ontologies. A description of the main virus-human interactome available is provided, together with the main network analyses that have been performed. We finally discuss the main limitations and future challenges to assess the quality and reliability of protein-protein interaction datasets and resources.
Language	English
Publishing date	2022-04-21
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.849781
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Article: Interplay between gene expression and gene architecture as a consequence of gene and genome duplications: evidence from metabolic genes of

Mukherjee, Dola / Saha, Deeya / Acharya, Debarun / Mukherjee, Ashutosh / Ghosh, Tapash Chandra

Physiology and molecular biology of plants : an international journal of functional plant biology

2022 Volume 28, Issue 5, Page(s) 1091–1108

Abstract: Gene and genome duplications have been widespread during the evolution of flowering plant which resulted in the increment of biological complexity as well as creation of plasticity of a genome helping the species to adapt to changing environments. ... ...

Abstract	Gene and genome duplications have been widespread during the evolution of flowering plant which resulted in the increment of biological complexity as well as creation of plasticity of a genome helping the species to adapt to changing environments. Duplicated genes with higher evolutionary rates can act as a mechanism of generating novel functions in secondary metabolism. In this study, we explored duplication as a potential factor governing the expression heterogeneity and gene architecture of Primary Metabolic Genes (PMGs) and Secondary Metabolic Genes (SMGs) of Supplementary information: The online version contains supplementary material available at 10.1007/s12298-022-01188-2.
Language	English
Publishing date	2022-06-02
Publishing country	India
Document type	Journal Article
ZDB-ID	2487126-6
ISSN	0974-0430 ; 0971-5894
ISSN (online)	0974-0430
ISSN	0971-5894
DOI	10.1007/s12298-022-01188-2
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Article ; Online: Social experience and pheromone receptor activity reprogram gene expression in sensory neurons.

Deanhardt, Bryson / Duan, Qichen / Du, Chengcheng / Soeder, Charles / Morlote, Alec / Garg, Deeya / Saha, Aishani / Jones, Corbin D / Volkan, Pelin Cayirlioglu

G3 (Bethesda, Md.)

2023 Volume 13, Issue 6

Abstract: Social experience and pheromone signaling in olfactory neurons affect neuronal responses and male courtship behaviors in Drosophila. We previously showed that social experience and pheromone signaling modulate chromatin around behavioral switch gene ... ...

Abstract	Social experience and pheromone signaling in olfactory neurons affect neuronal responses and male courtship behaviors in Drosophila. We previously showed that social experience and pheromone signaling modulate chromatin around behavioral switch gene fruitless, which encodes a transcription factor necessary and sufficient for male sexual behaviors. Fruitless drives social experience-dependent modulation of courtship behaviors and physiological sensory neuron responses to pheromone; however, the molecular mechanisms underlying this modulation of neural responses remain less clear. To identify the molecular mechanisms driving social experience-dependent changes in neuronal responses, we performed RNA-seq from antennal samples of mutants in pheromone receptors and fruitless, as well as grouped or isolated wild-type males. Genes affecting neuronal physiology and function, such as neurotransmitter receptors, ion channels, ion and membrane transporters, and odorant binding proteins are differentially regulated by social context and pheromone signaling. While we found that loss of pheromone detection only has small effects on differential promoter and exon usage within fruitless gene, many of the differentially regulated genes have Fruitless-binding sites or are bound by Fruitless in the nervous system. Recent studies showed that social experience and juvenile hormone signaling co-regulate fruitless chromatin to modify pheromone responses in olfactory neurons. Interestingly, genes involved in juvenile hormone metabolism are also misregulated in different social contexts and mutant backgrounds. Our results suggest that modulation of neuronal activity and behaviors in response to social experience and pheromone signaling likely arise due to large-scale changes in transcriptional programs for neuronal function downstream of behavioral switch gene function.
MeSH term(s)	Animals ; Male ; Drosophila Proteins/metabolism ; Sexual Behavior, Animal/physiology ; Drosophila/genetics ; Pheromones/metabolism ; Sensory Receptor Cells/metabolism ; Gene Expression ; Drosophila melanogaster/genetics
Chemical Substances	Drosophila Proteins ; Pheromones
Language	English
Publishing date	2023-03-27
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkad072
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Article: Interplay between gene expression and gene architecture as a consequence of gene and genome duplications: evidence from metabolic genes of Arabidopsis thaliana

Mukherjee, Dola / Saha, Deeya / Acharya, Debarun / Mukherjee, Ashutosh / Ghosh, Tapash Chandra

Physiology and molecular biology of plants. 2022 May, v. 28, no. 5

2022

Abstract	Gene and genome duplications have been widespread during the evolution of flowering plant which resulted in the increment of biological complexity as well as creation of plasticity of a genome helping the species to adapt to changing environments. Duplicated genes with higher evolutionary rates can act as a mechanism of generating novel functions in secondary metabolism. In this study, we explored duplication as a potential factor governing the expression heterogeneity and gene architecture of Primary Metabolic Genes (PMGs) and Secondary Metabolic Genes (SMGs) of Arabidopsis thaliana. It is remarkable that different types of duplication processes controlled gene expression and tissue specificity differently in PMGs and SMGs. A complex relationship exists between gene architecture and expression patterns of primary and secondary metabolic genes. Our study reflects, expression heterogeneity and gene structure variation of primary and secondary metabolism in Arabidopsis thaliana are partly results of duplication events of different origins. Our study suggests that duplication has differential effect on PMGs and SMGs regarding expression pattern by controlling gene structure, epigenetic modifications, multifunctionality and subcellular compartmentalization. This study provides an insight into the evolution of metabolism in plants in the light of gene and genome scale duplication.
Keywords	Arabidopsis thaliana ; epigenetics ; evolution ; gene expression ; genes ; metabolism ; molecular biology ; plasticity
Language	English
Dates of publication	2022-05
Size	p. 1091-1108.
Publishing place	Springer India
Document type	Article
ZDB-ID	2487126-6
ISSN	0974-0430 ; 0971-5894
ISSN (online)	0974-0430
ISSN	0971-5894
DOI	10.1007/s12298-022-01188-2
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Article ; Online: Deciphering the intrinsic properties of fungal proteases in optimizing phytopathogenic interaction.

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

Gene

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
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: The role of introns in the conservation of the metabolic genes of Arabidopsis thaliana

Mukherjee, Dola / Ashutosh Mukherjee / Debarun Acharya / Deeya Saha / Sandip Chakraborty / Tapash Chandra Ghosh

Genomics. 2018 Sept., v. 110, no. 5

2018

Abstract: In Arabidopsis thaliana, primary metabolic genes (PMGs) are more evolutionarily conserved and intron-rich than secondary metabolic genes. We observed that PMGs are more primitive and pan-taxonomically persistent as compared to secondary (SMGs) and non- ... ...

Abstract	In Arabidopsis thaliana, primary metabolic genes (PMGs) are more evolutionarily conserved and intron-rich than secondary metabolic genes. We observed that PMGs are more primitive and pan-taxonomically persistent as compared to secondary (SMGs) and non-metabolic genes (NMGs). This difference in primitiveness and persistence is primarily correlated with intron number and is independent of gene expression level. We propose a twofold explanation behind higher intron enrichment in PMGs. Firstly, introns might increase protein versatility amongst PMGs through alternative splicing, providing selective advantage of PMGs and making them more persistent across diverse plant taxa. Also, multifunctional PMGs may acquire functional domains by increasing the intronic burden. Additionally, single nucleotide polymorphisms (SNPs) accumulate at a higher rate in introns as compared to exons. Moreover, a strong negative correlation between cumulative exonic SNPs density and intron number indicates that introns may protect the exonic regions against the deleterious effect of these mutations, making them more conserved.
Keywords	alternative splicing ; Arabidopsis thaliana ; exons ; introns ; single nucleotide polymorphism
Language	English
Dates of publication	2018-09
Size	p. 310-317.
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.2017.12.003
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Article ; Online: Overlapping genes: A significant genomic correlate of prokaryotic growth rates.

Saha, Deeya / Podder, Soumita / Panda, Arup / Ghosh, Tapash Chandra

Gene

2016 Volume 582, Issue 2, Page(s) 143–147

Abstract: Elucidating the genomic features influencing prokaryotic growth rates has always been a study of interest. Previously, it was observed that overlapping genes (OGs) play a crucial role in the prokaryotic genome size reduction. This study is focused to ... ...

Abstract	Elucidating the genomic features influencing prokaryotic growth rates has always been a study of interest. Previously, it was observed that overlapping genes (OGs) play a crucial role in the prokaryotic genome size reduction. This study is focused to explore whether OGs act as a potential correlate of prokaryotic growth rates. For this purpose, we compiled a dataset of 25 archaeal and 117 eubacterial genomes and analyzed the inter-correlation between the proportion of overlapping regions in these genomes with their growth rates. Here, we observed that the proportion of overlapping region holds a significant negative correlation with generation time in archaeal domain, whereas no correlation was observed in the eubacterial domain. However, after masking the effect of tRNA, rRNA multiplicity and environmental diversity, OGs show an independent effect over growth rates in the eubacterial domain as well as in the archaeal domain. Moreover, the influence of OGs on prokaryotic growth rates provides different delineations in archaeal and eubacterial domains. In archaea, both long overlap frequency (LOF) and short overlap frequency (SOF) influence the growth rates by increasing the degree of operonization. On the contrary, in the case of bacteria, neither SOF nor LOF plays any significant role in achieving faster growth rates.
MeSH term(s)	Archaea/genetics ; Archaea/growth & development ; Bacteria/genetics ; Bacteria/growth & development ; Genes, Overlapping ; Genome, Archaeal ; Genome, Bacterial ; Time Factors
Language	English
Publishing date	2016-05-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2016.02.002
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