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Article ; Online: A comprehensive review on methane's dual role: effects in climate change and potential as a carbon-neutral energy source.

Sobanaa, Murugesan / Prathiviraj, Ragothaman / Selvin, Joseph / Prathaban, Munisamy

Environmental science and pollution research international

2023 Volume 31, Issue 7, Page(s) 10379–10394

Abstract: The unprecedented population and anthropogenic activity rise have challenged the future look up for shifts in global temperature and climate patterns. Anthropogenic activities such as land fillings, building dams, wetlands converting to lands, combustion ...

Abstract	The unprecedented population and anthropogenic activity rise have challenged the future look up for shifts in global temperature and climate patterns. Anthropogenic activities such as land fillings, building dams, wetlands converting to lands, combustion of biomass, deforestation, mining, and the gas and coal industries have directly or indirectly increased catastrophic methane (CH
MeSH term(s)	Humans ; Climate Change ; Carbon Dioxide/metabolism ; Biodiversity ; Temperature ; Methane/metabolism
Chemical Substances	Carbon Dioxide (142M471B3J) ; Methane (OP0UW79H66)
Language	English
Publishing date	2023-10-26
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-023-30601-w
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Article ; Online: Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus ΔH.

Prathiviraj, R / Chellapandi, P

Anaerobe

2020 Volume 64, Page(s) 102216

Abstract: Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing ... ...

Abstract	Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO
MeSH term(s)	Comparative Genomic Hybridization ; DNA, Archaeal/genetics ; Genome, Archaeal ; Metabolic Networks and Pathways/genetics ; Methanobacteriaceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Stress, Physiological/genetics
Chemical Substances	DNA, Archaeal ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 23S
Language	English
Publishing date	2020-06-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1237621-8
ISSN	1095-8274 ; 1075-9964
ISSN (online)	1095-8274
ISSN	1075-9964
DOI	10.1016/j.anaerobe.2020.102216
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Article: Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus ΔH

Prathiviraj, R / Chellapandi, P

Anaerobe. 2020 Aug., v. 64

2020

Abstract: Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO₂ with H₂ to produce methane gas. It is the potential candidate in the biomethanation of CO₂ and CO in anaerobic reactors and ... ...

Abstract	Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO₂ with H₂ to produce methane gas. It is the potential candidate in the biomethanation of CO₂ and CO in anaerobic reactors and biogas upgrading process. However, systematic studies addressing its genome conservation and function remain scant in this genome. In this study, we have evaluated its evolutionary resemblance and metabolic discrepancy, particularly in starvation survival systems by comparing the genomic contexts with Methanothermobacter marburgensis str. Marburg (MMG) and Methanobacterium formicicum DSM 1535 (MFO). The phylogenomic analysis of this study indicated that there was a strong phylogenomic signal among MTH, MMG, and MFO in the whole-genome tree. DNA replication machinery was conserved in the MTH genome and might have evolved at different evolution rates. Genome synteny analysis observed collinearity of either gene orders or gene families has to be maintained with syntenic blocks located in the syntenic out-paralogs. A genome-wide metabolic analysis identified some unique putative metabolic subsystems in MTH, which are proposed to determine its growth characteristics in diverse environments. MTH genome comprised of 93 unique genes-coding for starvation survival and stress-response proteins. These proteins confer its adaptation to nutritional deprivation and other abiotic stresses. MTH has a typical system to withstand its growth and cell viability during stable operation and recovery after prolonged starvation. Thus, the present work will provide an insight to improve the genome refinement and metabolic reconstruction in parallel to other closely related species.
Keywords	DNA replication ; Methanobacterium formicicum ; abiotic stress ; anaerobic digesters ; biogas ; carbon dioxide ; carbon monoxide ; cell viability ; genes ; genomics ; germplasm conservation ; hydrogen ; methane ; methane production ; methanogens ; phylogeny ; proteins ; starvation ; stress response
Language	English
Dates of publication	2020-08
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1237621-8
ISSN	1075-9964
ISSN	1075-9964
DOI	10.1016/j.anaerobe.2020.102216
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Article ; Online: A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics.

Prathiviraj, R / Saranya, S / Bharathi, M / Chellapandi, P

Computers in biology and medicine

2021 Volume 132, Page(s) 104315

Abstract: Coronavirus disease (COVID-19) rapidly expands to a global pandemic and its impact on public health varies from country to country. It is caused by a new virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is imperative for relapsing ... ...

Abstract	Coronavirus disease (COVID-19) rapidly expands to a global pandemic and its impact on public health varies from country to country. It is caused by a new virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is imperative for relapsing current antiviral therapeutics owing to randomized genetic drift in global SARS-CoV-2 isolates. A molecular mechanism behind the emerging genomic variants is not yet understood for the prioritization of selective antivirals. The present computational study was aimed to repurpose existing antivirals for Indian SARS-CoV-2 isolates by uncovering a hijack mechanism based on structural and functional characteristics of protein variants. Forty-one protein mutations were identified in 12 Indian SARS-CoV-2 isolates by analysis of genome variations across 460 genome sequences obtained from 30 geographic sites in India. Two unique mutations such as W6152R and N5928H found in exonuclease of Surat (GBRC275b) and Gandhinagar (GBRC239) isolates. We report for the first time the impact of folding rate on stabilizing/retaining a sequence-structure-function-virulence link of emerging protein variants leading to accommodate hijack ability from current antivirals. Binding affinity analysis revealed the effect of point mutations on virus infectivity and the drug-escaping efficiency of Indian isolates. Emodin and artinemol suggested herein as repurposable antivirals for the treatment of COVID-19 patients infected with Indian isolates. Our study concludes that a protein folding rate is a key structural and evolutionary determinant to enhance the receptor-binding specificity and ensure hijack ability from the prevalent antiviral therapeutics.
MeSH term(s)	Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19 ; Humans ; Mutation ; Pandemics ; SARS-CoV-2
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2021-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2021.104315
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Article ; Online: Deciphering Molecular Virulence Mechanism of Mycobacterium tuberculosis Dop isopeptidase Based on Its Sequence-Structure-Function Linkage.

Prathiviraj, R / Chellapandi, P

The protein journal

2019 Volume 39, Issue 1, Page(s) 33–45

Abstract: The pupylation pathway marks proteins for prokaryotic ubiquitin-like protein (Pup)-proteasomal degradation and survival strategy of mycobacteria inside of the host macrophages. Deamidase of Pup (Dop) plays a central role in the pupylation pathway. It is ... ...

Abstract	The pupylation pathway marks proteins for prokaryotic ubiquitin-like protein (Pup)-proteasomal degradation and survival strategy of mycobacteria inside of the host macrophages. Deamidase of Pup (Dop) plays a central role in the pupylation pathway. It is still a matter of investigation to know the function of Dop in virulence of mycobacterial lineage. Hence, the present study was intended to describe the sequence-structure-function-virulence link of Dop for understanding the molecular virulence mechanism of Mycobacterium tuberculosis H37Rv (Mtb). Phylogenetic analysis of this study indicated that Dop has extensively diverged across the proteasome-harboring bacteria. The functional part of Dop was converged across the pathogenic mycobacterial lineage. The genome-wide analysis pointed out that the pupylation gene locus was identical to each other, but its genome neighborhood differed from species to species. Molecular modeling and dynamic studies proved that the predicted structure of Mtb Dop was energetically stable and low conformational freedom. Moreover, evolutionary constraints in Mtb Dop were intensively analyzed for inferring its sequence-structure-function relationships for the full virulence of Mtb. It indicated that evolutionary optimization was extensively required to stabilize its local structural environment at the side chains of mutable residues. The sequence-structure-function-virulence link of Dop might have retained in Mtb by reordering hydrophobic and hydrogen bonding patterns in the local structural environment. Thus, the results of our study provide a quest to understand the molecular virulence and pathogenesis mechanisms of Mtb during the infection process.
MeSH term(s)	Amidohydrolases/chemistry ; Amidohydrolases/classification ; Amino Acid Sequence ; Bacterial Proteins/chemistry ; Evolution, Molecular ; Molecular Dynamics Simulation ; Mycobacterium tuberculosis/metabolism ; Mycobacterium tuberculosis/pathogenicity ; Phylogeny ; Protein Conformation ; Protein Processing, Post-Translational ; Tuberculosis/microbiology ; Virulence ; Virulence Factors/chemistry ; Virulence Factors/classification
Chemical Substances	Bacterial Proteins ; Virulence Factors ; Amidohydrolases (EC 3.5.-) ; Dop protein, Mycobacterium tuberculosis (EC 3.5.-)
Language	English
Publishing date	2019-11-23
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-019-09876-x
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Article ; Online: Untargeted metabolomics-based network pharmacology reveals fermented brown rice towards anti-obesity efficacy.

Barathikannan, Kaliyan / Chelliah, Ramachandran / Vinothkanna, Annadurai / Prathiviraj, Ragothaman / Tyagi, Akanksha / Vijayalakshmi, Selvakumar / Lim, Min-Jin / Jia, Ai-Qun / Oh, Deog- Hwan

NPJ science of food

2024 Volume 8, Issue 1, Page(s) 20

Abstract: There is a substantial rise in the global incidence of obesity. Brown rice contains metabolic substances that can help minimize the prevalence of obesity. This study evaluated nine brown rice varieties using probiotic fermentation using Pediococcus ... ...

Abstract	There is a substantial rise in the global incidence of obesity. Brown rice contains metabolic substances that can help minimize the prevalence of obesity. This study evaluated nine brown rice varieties using probiotic fermentation using Pediococcus acidilacti MNL5 to enhance bioactive metabolites and their efficacy. Among the nine varieties, FBR-1741 had the highest pancreatic lipase inhibitory efficacy (87.6 ± 1.51%), DPPH assay (358.5 ± 2.80 mg Trolox equiv./100 g, DW), and ABTS assay (362.5 ± 2.32 mg Trolox equiv./100 g, DW). Compared to other fermented brown rice and FBR-1741 varieties, UHPLC-Q-TOF-MS/MS demonstrated significant untargeted metabolite alterations. The 17 most abundant polyphenolic metabolites in the FBR-1741 variety and 132 putative targets were assessed for obesity-related target proteins, and protein interaction networks were constructed using the Cystoscope software. Network pharmacology analysis validated FBR-1741 with active metabolites in the C. elegans obesity-induced model. Administration of FBR-1741 with ferulic acid improved lifespan decreased triglycerides, and suppressed the expression of fat-related genes. The enhanced anti-obesity properties of FBR-1741 suggest its implementation in obesity-functional food.
Language	English
Publishing date	2024-03-30
Publishing country	England
Document type	Journal Article
ISSN	2396-8370
ISSN (online)	2396-8370
DOI	10.1038/s41538-024-00258-x
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Article: Functional annotation of operome from Methanothermobacter thermautotrophicus ΔH: An insight to metabolic gap filling

Prathiviraj, R / P. Chellapandi

International journal of biological macromolecules. 2019 Feb. 15, v. 123

2019

Abstract: Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO2 with H2 for producing methane biofuel in thermophilic digesters. The genome of this organism contains ~50.5% conserved hypothetical proteins (HPs; operome) ... ...

Abstract	Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO2 with H2 for producing methane biofuel in thermophilic digesters. The genome of this organism contains ~50.5% conserved hypothetical proteins (HPs; operome) whose function is still not determined precisely. Here, we employed a combined bioinformatics approach to annotate a precise function to HPs and categorize them as enzymes, binding proteins, and transport proteins. Results of our study show that 315 (35.6%) HPs have exhibited well-defined functions contributing imperative roles in diverse cellular metabolism. Some of them are responsible for stress-response mechanisms and cell cycle, membrane transport, and regulatory processes. The genome-neighborhood analysis found five important gene clusters (dsr, ehb, kaiC, cmr, and gas) involving in the energetic metabolism and defense systems. MTH operome contains 223 enzymes with 15 metabolic subsystems, 15 cell cycle proteins, 17 transcriptional regulators and 33 binding proteins. Functional annotation of its operome is thus more fundamental to a profound understanding of the molecular and cellular machinery at systems-level.
Keywords	biofuels ; bioinformatics ; carbon dioxide ; cell cycle ; enzymes ; hydrogen ; metabolism ; methane ; methanogens ; multigene family ; physiological transport ; stress response ; transcription factors ; transport proteins
Language	English
Dates of publication	2019-0215
Size	p. 350-362.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2018.11.100
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Article ; Online: Functional annotation of operome from Methanothermobacter thermautotrophicus ΔH: An insight to metabolic gap filling.

Prathiviraj, R / Chellapandi, P

International journal of biological macromolecules

2018 Volume 123, Page(s) 350–362

Abstract: Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce ... ...

Abstract	Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Methanobacteriaceae/genetics ; Methanobacteriaceae/metabolism ; Molecular Sequence Annotation ; Multigene Family
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2018-11-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2018.11.100
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Article: Phylogenomic proximity and comparative proteomic analysis of SARS-CoV-2.

Prathiviraj, R / Kiran, George Seghal / Selvin, Joseph

Gene reports

2020 Volume 20, Page(s) 100777

Abstract: The coronavirus disease (COVID-19) belongs to the family Severe Acute Respiratory Syndrome (SARS-CoV). It can be more severe for some persons and can lead to pneumonia or breathing difficulties resulting in the death of immune-compromised patients. We ... ...

Abstract	The coronavirus disease (COVID-19) belongs to the family Severe Acute Respiratory Syndrome (SARS-CoV). It can be more severe for some persons and can lead to pneumonia or breathing difficulties resulting in the death of immune-compromised patients. We performed a phylogenomic and phylogeographic tree from the collected datasets. Phylogenomic analysis or sequence-based phylogeny showed an evolutionary relationship between the geographical strains. The phylogenomic tree grouped into two major clades consists of various isolates of SARS-CoV-2 and Bat SARS-like coronavirus, Bat coronavirus, and Pangolin coronavirus. The phylogenetic neighbor of newly sequenced Indian strains (Accession: MT012098.1, MT050493.1) was revealed to identify the variations between the nCoV-19 strains. The results showed keen evidence that SARS-CoV-2 has evolved from Bat SARS-like coronavirus. The evolutionary history and comparative proteomic analysis provide a new avenue for the current scientific research related to the coronavirus.
Keywords	covid19
Language	English
Publishing date	2020-07-08
Publishing country	United States
Document type	Journal Article
ISSN	2452-0144
ISSN	2452-0144
DOI	10.1016/j.genrep.2020.100777
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Article: Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates

Prathiviraj, Ragothaman / Chellapandi, Paulchamy / Begum, Ajima / Kiran, George Seghal / Selvin, Joseph

Virus research. 2022 Jan. 02, v. 307

2022

Abstract: The second wave of COVID-19 caused by severe acute respiratory syndrome virus (SARS-CoV-2) is rapidly spreading over the world. Mechanisms behind the flee from current antivirals are still unclear due to the continuous occurrence of SARS-CoV-2 genetic ... ...

Abstract	The second wave of COVID-19 caused by severe acute respiratory syndrome virus (SARS-CoV-2) is rapidly spreading over the world. Mechanisms behind the flee from current antivirals are still unclear due to the continuous occurrence of SARS-CoV-2 genetic variants. Brazil is the world's second-most COVID-19 affected country. In the present study, we identified the genomic and proteomic variants of Brazilian SARS-CoV-2 isolates. We identified 16 different genotypic variants were found among the 27 isolates. The genotypes of three isolates such as Bra/1236/2021 (G15), Bra/MASP2C844R2/2020 (G11), and Bra/RJ-DCVN5/2020 (G9) have a unique mutant in NSP4 (S184N), 2′O-Mutase (R216N), membrane protein (A2V) and Envelope protein (V5A). A mutation in RdRp of SARS-CoV-2, particularly the change of Pro-to Leu-at 323 resulted in the stabilization of the structure in BRA/CD1739-P4/2020. NSP4, NSP5 protein mutants are more virulent in genotype 15 and 16. A fast protein folding rate changes the structural stability and leads to escape for current antivirals. Thus, our findings help researchers to develop the best potent antivirals based on the new mutant of Brazilian isolates.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; antiviral agents ; genomics ; genotype ; membrane proteins ; mutants ; mutation ; proteomics ; research ; virulence ; viruses ; Brazil
Language	English
Dates of publication	2022-0102
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2021.198618
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