CHELLAPANDI Paulchamy

• PhD Biotechnology
• Professor and Head at Bharathidasan University

Anaerobic digestion (AD) systems generate biogas from protein-rich waste, with certain anaerobes modulating gene regulatory networks (GRNs) to manage ammonia toxicity. This study reconstructs GRN models for five key anaerobes—a hyper-ammonia-producing anaerobe Acetoanaerobium sticklandii H1, an anaerobic sulfur-reducing bacterium Desulfovibrio vulg...

DNA replication origins play a crucial role in cellular division and are evolutionarily conserved across domains. This study investigated the evolutionary transitions of replication origins between archaea and bacteria by analyzing 2733 bacterial and 257 archaeal genomes. Our findings revealed that certain methanogens and bacteria share phylogeneti...

Space exploration and research are uncovering the potential for terrestrial life to survive in outer space, as well as the environmental factors that affect life during interplanetary transfer. The presence of methane in the Martian atmosphere suggests the possibility of methanogens, either extant or extinct, on Mars. Understanding how methanogens...

Cyclotides are small disulfide-rich peptides (28–37 amino acids) with a wide range of biological activities. The Rubiaceae family is a good source for cyclotide production, but the quantity produced is not sufficient. Therefore, we aimed to enhance cyclotide production in Oldenlandia umbellata (Rubiaceae family) cell cultures using a fungal elicita...

The oil and gas industry produces significant amounts of waste including petroleum wastewater, waste drilling fluid, and oil sludge. Bioremediation uses microorganisms and plants to degrade toxic substances. This offers a cost-effective and less labor-intensive solution for managing waste and recovering contaminated areas. Methanogens play a key ro...

Our study focused on enhancing the production of anthraquinone derivatives in Oldenlandia umbellata using fungal elicitors. Aspergillus niger, Mucor prayagensis, and Trichoderma viride were used to elicit the anthraquinone derivatives in root cultures. The elicitation process led to an increase in the production of phytochemicals and secondary meta...

“In silico organisms” are computational genome-scale metabolic models used in systems and synthetic biology developed by constraint-based metabolic simulations using multi-omics and phenotypic data. The quality of these models is hidden because of the limited availability of genomic information and genome-scale metabolic reconstruction methods. In...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease (COVID-19) pandemic and has infected more than 561M people worldwide. The World Health Organization (WHO) has declared it an international public health concern. Approximately 80% of subclinical COVID-19 cases continue to rapidly spread in...

Snake venom metalloproteinases (SVMPs) are enzymatic proteins found in snake venom and are known for their diverse biological activities, including induction of hemorrhage and degradation of fibrinogen. This study aimed to design and characterize anticancer peptides (ACPs) derived from an SVMP library based on their physicochemical properties. A co...

An aquaculture automation system (AcAS) is a user-friendly single-window unit. This allows end users to monitor and control the entire system easily through a built-in, customizable graphical user interface. AcAS was designed for simplicity, making it easy to configure and use. This system was integrated with highly efficient industrial-grade envir...

Traditional commercial media are costly and not ideal for large-scale probiotic production in aquaculture. Choosing the right carbon source for probiotic growth and understanding how biomass production works can offer valuable insights for potential use in aquaculture. In this study, we tested 12 starchy extracts as potential cost-effective alterna...

The aquaculture automation system (AcAS) is a user-friendly single-window unit. This allows end users to easily monitor and control the entire system through a built-in, customizable graphical user interface. AcAS was designed for simplicity, making it easy to configure and use. This system was integrated with highly efficient industrial-grade envi...

Ophiocordyceps sinensis is widely used in traditional Asian medicine and grows at high altitudes (3,000–4,000 meters) on the Qinghai-Tibet Plateau. This fungus is an expensive and rare species that is difficult to cultivate. Increasing global demand, limited commercial trade, and precious resources drive an urgent need for the development of artifi...

Marvels of Artificial and Computational Intelligence in Life Sciences is a primer for scholars and students who are interested in the applications of artificial intelligence (AI) and computational intelligence (CI) in life sciences and other industries. The book consists of 16 chapters (9 of which focus on AI and 7 of which showcase the benefits of...

Marvels of Artificial and Computational Intelligence in Life Sciences is a primer for scholars and students who are interested in the applications of artificial intelligence (AI) and computational intelligence (CI) in life sciences and other industries. The book consists of 16 chapters (9 of which focus on AI and 7 of which showcase the benefits of...

Biogas reactors operating with protein-based biomass have a high methane potential and industrial value. Protein-rich materials, including gelatin processing and ossein factory waste, are suitable feedstocks for use in ammonia-tolerant biogas digesters. However, the anaerobic digestion of these materials is limited by the accumulation of ammonia, h...

Objective: Clostridium botulinum type A is a neurotoxin-producing, spore-forming anaerobic bacterium that causes botulism in humans. The evolutionary genomic context of this organism is not yet known to understand its molecular virulence mechanisms in the human intestinal tract. Hence, this study aimed to investigate the mechanisms underlying viru...

Clostridium botulinum type A3 str. Loch Maree is a clinically important strain that produces botulinum neurotoxin type A3 and causes foodborne, infant, and wound botulism worldwide. Studying the mechanism underlying the virulence of this organism is imperative to understand its antibacterial resistance and discovering new drugs or inhibitors. The b...

Coronavirus disease (COVID-19) has rapidly expanded into a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Genetic drift in global SARS-CoV-2 isolates and protein evolution have an impact on their ability to escape from current antiviral therapeutics. Hence, our study aimed to reveal how mutations in the...

The identification of goatfish has been commonly performed morphologically. Although traditional patterns of identification are available, there are still difficulties in differentiating species because of their similar appearances. The present study attempted to differentiate the two species Upeneus vittatus and U. tragula based on their mtCOI gen...

Archaea are a primary domain of the living kingdom, and they play an important role in biogeochemical cycles. Since the inclusion of new archaeal phylogenetic lineages in the universal tree, the origin and evolution history of this domain has been debated. To address this issue, we planned to examine the growth-associated maintenance energy and the...

The ability to design efficient enzymes for a broad class of different reactions would be of tremendous practical interest in both science and industry. Computer-assisted designing is a novel approach to generating industrial enzymes for biotechnological applications. Objectives: The main aim of this study was to design an enzyme construct with div...

Cervical cancer is one of the most common gynecological cancers in women and its molecular pathogenesis and disease progression are yet fully understood. Finding new biomarkers is important to detect early diagnosis of cervical cancer to reduce its incidence and mortality rates among women. We have selected 3 microarray gene expression datasets (GS...

Global regulatory network modeling is a great concern of addressing metabolic complexity especially of a non-model organism to prioritize novel drug and vaccine targets. In this study, a knowledge-based bottom-up approach was used to reconstruct a transcriptional regulatory network of Methanobrevibacter ruminantium M1, one of the predominant hydrog...

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 id...

Acetoanaerobium sticklandii DSM519 (CST) is a hype-ammonia producing non-pathogenic anaerobe that can use amino acids as important carbon and energy sources through the Stickland reactions. Biochemical aspects of this organism have been extensively studied, but systematic studies addressing its metabolic discrepancy remain scant. In this perspectiv...

Coronavirus disease (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new coronavirus isolated from Wuhan, China. It is a global health emergency, and there is no effective antiviral therapeutics available to date. Continuous structural genomic insights of SARS-CoV-2 proteins provide a warranty for the...

The second wave of COVID-19, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is rapidly spreading over the world. The mechanism behind the escaping from current antivirals is still not clear, due to the occurrence of continuous variants in SARS-CoV-2 genomes. Brazil is the world’s second most COVID-19-affected c...

Globally, the shrimp farming industry faces increasing challenges and pressure to reduce the broken shrimps and maintain a healthier pond environment. Shrimps lack an adaptive immune system to combat invading pathogens due to an imbalance in beneficial gut microbiota. The use of top-dressing agents like probiotics and pond optimizes is an alternati...

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...

Methanobrevibacter ruminantium M1 (MRU) is a rod-shaped rumen methanogen with the ability to use H2 and CO2, and formate as substrates for methane formation in the ruminants. Enteric methane emitted from this organism can also be influential to the loss of dietary energy in ruminants and humans. To date, there is no successful technology to reduce...

Genome-scale regulatory networks are a great concern in studying the crucial problems in bacterial genome biology. Methanothermobacter thermautotrophicus ΔH (MTH) is a model organism of thermophilic methanogenic archaea contributing to a large environmental impact in global carbon cycling and strain used in the biofuel industry. Nonetheless, system...

Coronavirus disease (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is a global health emergency and no clinically approved vaccines or antiviral drugs available to date. Intensive research on SARS-CoV-2 is urgently warranted to understand its pathogenesis and virulence mechanisms and to disco...

Acetoanaerobium sticklandii DSM 519 is a hyperammonia-producing anaerobe that catabolizes proteins and amino acids into organic solvents and volatile acids via the Stickland reactions. However, the specific growth rate and metabolic capability of this organism on proteins and amino acids are not yet known. Therefore, the present study was intended...

Uronate dehydrogenase (EC:1.1.1.203) belongs to the NAD-dependent epimerase/dehydratase (NDE/D) subfamily, which converts D-galacturonic acid and D-glucuronic acid into D-galactaric acid and D-glucaric acid, respectively. Uronate dehydrogenase-catalyzed reaction is reversible and no substrate-specific activity in nature. Therefore, evolution-guided...

Peptidase clan is the largest group of proteases with common ancestry as identified by structural homology. A peptidase with unknown catalytic type is referred to as an unassigned peptidase clan, which can be classified into 8 peptidase families (U32, U40, U49, U56, U57, U62, U69, and U72). The members of this clan are widely dispersed in diverse m...

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 func...

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 lineag...

Abstract Purpose Biomethane is an environment-friendly, economic, and alternative energy resource for a clean and green future. In the present study, we have evaluated the biomethanation potential of acetate-utilizing methanogenic culture (AUMC) and gelatin-enriched mixed culture (GEMC) with Clostridium acetobutylicum NCIM 2841 (GEMC-CA.) on gelati...

A proteome-wide protein-protein interaction (PPI) network of Methanobrevibacter ruminantium M1 (MRU), a predominant rumen methanogen, was constructed from its metabolic genes using a gene neighborhood algorithm and then compared with closely related rumen methanogens Using proteome-wide PPI approach, we constructed network encompassed 2194 edges an...

Acetoanaerobium sticklandii DSM 519 is a hyper-ammonia-producing anaerobe. It has the ability to produce organic solvents and acids from protein catabolism through Stickland reactions and specialized pathways. Nevertheless, its protein catabolism-directed biofuel production has not yet been understood. The present study aimed to decipher such growt...

The proteins perform their functions independently and control all biological systems through protein–protein interaction (PPI) networks. The majority of proteins interact with others for proper biological activity in complex cellular and metabolic processes. A proteome-scale study affords the importance to reveal the function of molecular complexe...

C2 toxin produced from Clostridium botulinum serotypes C and D has a potential role in many pathophysiological mechanisms in birds and animals. It has encompassed an ADP ribosyltransferase subunit (C2I) and a translocation/binding subunit (C2II). In the present study, we intended to produce C2I mutant proteins as recombinant subunit vaccines by usi...

Acetoanaerobium sticklandii DSM 519 is a hyper-ammonia producing anaerobic bacterium that can be able utilizes amino acids as sole carbon and energy sources for its growth and energetic metabolism. A lack of knowledge on its molecular machinery and 30.5% conserved hypothetical proteins (HPs; operome) hinders the successful utility in biofuel applic...

Studying amino acid catabolism-coupled methanogenesis is the important standpoints to decipher the metabolic behavior of a methanogenic culture. l-Glycine and l-alanine are acted as sole carbon and nitrogen sources for acidogenic bacteria. One amino acid is oxidized and another one is reduced for acetate production via pyruvate by oxidative deamina...

Malaria is a life-threatening mosquito-borne blood disease caused by infection with Plasmodium parasites. Anti-malarial drug resistance is a global threat to control and eliminate malaria and therefore, it is very important to discover and evaluate new drug targets. The 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase (IspD) homolog is a se...

In the present work, we addressed the impact of a human–food web–animal interface on the prevalence of food-borne pathogens in mixed farms of Tamil Nadu, India. We have isolated and identified six strains of Clostridium sp. and five strains of Enterococcus sp. from food and animal sources disposed near to the veterinary and poultry farms. Phylogene...

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 approa...

Clostridium botulinum is a strictly anaerobic spore forming bacterium found in soil and sediments, producing botulinum neurotoxins. Group III strains of this organism are only able to produce neurotoxin types C, mosaic C/D, D/C, and D, which are associated with bird botulism. The threats and outbreak cycle of bird botulism are enhanced in the aquat...

Methanobacterium formicicum (Methanobacteriaceae family) is an endosymbiotic methanogenic Archaean found in the digestive tracts of ruminants and elsewhere. It has been significantly implicated in global CH4 emission during enteric fermentation processes. In this review, we discuss current genomic and metabolic aspects of this microorganism for the...

Clostridium botulinum is a foodborne bacterium capable of producing a potent botulinum neurotoxin with seven serotypes (A–G). Type A strains are being a great concern for causing foodborne, infant and wound botulism in worldwide. Antibacterial resistance is a not a big problem for treating diseases caused by this organism, but antitoxin treatment a...

Model-driven systems engineering has been more fascinating process for the microbial production of biofuel and bio-refineries in chemical and pharmaceutical industries. Genome-scale modeling and simulations have been guided for metabolic engineering of Clostridium species for the production of organic solvents and organic acids. Among them, Clostri...

Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence stat...

Methanosarcina mazei Go1 is a heterotrophic methanogenic archaean contributing a significant role in global methane cycling and biomethanation process. Phylogenomic relatedness and metabolic discrepancy of this genome were described herein by comparing its whole genome sequence, intergenomic distance, genome function, synteny homologs and origin of...

Clostridium botulinum group III strains are able to produce cytotoxins, C2 toxin and C3 exotoxin, along with botulinum neurotoxin types C and D. C2 toxin and C3 exotoxin produced from this organism are the most important members of bacterial ADP-ribosyltransferase superfamily. Both toxins have distinct pathophysiological functions in the avian and...

Methanogens have major environmental and economic importance since they serve as a key component of the carbon cycle by degrading low carbon molecules in anaerobic environments to generate CH4. Genome-scale metabolic modeling is a proficient computational tool for integrative analysis of their cellular and metabolic processes. Methods: We explored...

Clustered regularly interspaced short palindromic repeats (CRISPRs) are direct features of the prokaryotic genomes involved in resistance to their bacterial viruses and phages. Herein, we have identified CRISPR loci together with CRISPR-associated sequences (CAS) genes to reveal their immunity against genome invaders in the thermophilic archaea and...

Clostridium botulinum is anaerobic pathogenic bacterium causing food-born botulism in human and animals by producing botulinum neurotoxins A-H, C2 and C3 cytotoxins. Physiological group III strains (type C and D) of this bacterium are capable of producing C2 and C3 toxins in cattle and avian. Herein, we have revealed the structure-function disparit...

A computational systems biology representation was utilized for understanding the molecular and metabolic behaviors of heavy metal assimilation system in the genome Methanosarcina barkeri str. Fusaro. A known functional protein of this system was identified by text mining. A combined functional annotation approach was employed to discover the missi...

Twenty bacterial strains, which are capable of degrading monocrotophos, were isolated from five soil samples collected from agriculture soils in India. The ability of the strains to mineralize monocrotophos was investigated under different culture conditions. A potential strain degrading monocrotophos was selected and named KPA-1. The strain was id...

Snake venoms are rich sources of metalloproteinases that are of biological interest due to their diverse molecular diversity and selective therapeutic applications. Snake venoms metalloproteinases (SVMPs) belong to the MEROPS peptidase family M12B or reprolysin subfamily, which are consisted of four major domains include a reprolysin catalytic doma...

In the present study, we have evaluated the impacts of point mutations on structural and functional evolution of hypothetical proteins identical to bacterial ADP-ribosylation superfamily members using bioinformatics approaches. A combined approach of molecular modelling and dynamics was employed to generate energetically stable structures from hypo...

Objective: The objective was to design an enzyme construct with diverse function from urease sequences of haloarchaean, Haloarcula marismortui ATCC 43049 based on its conserved domain consisting metal-binding region and active sites. Methods: Complete urease sequences of haloarchaea were retrieved from National Center for Biotechnology Information...

In the present work, a combined approach of molecular modeling and systems biology was used to reveal how structural dynamics of enzymes involving in methanogenesis contributed to do reverse methanogenic reactions in methanotrophic archaea. The binding energies and molecular interaction distances of homology models and crystallographic structures o...

The conserved domain of sequences revealed in methanogens is considered for designing enzymes among which the attention has been focused on the metalloenzymes showing evolutionary significances. Methods. Molecular evolution, molecular modelling and molecular docking methods. Results. Molecular evolutionary hypothesis has been applied for designing...

The objective of the present work was to evaluate the ossein factory wastes, which include primary clarified bone waste (PCBW) and sinews for methane production, by monitoring methanogenic activity of predigested biogas plant slurry. A specific methanogenic activity of biogas plant slurry (anaerobic seed) was measured at 38 degrees C using differen...

Methanogens are a diverse group of organisms that can live in a wide range of environments. Herein, cobalt and tungsten assimilation pathways have proposed to be established in the genomes of Methanococcus maripaludies C5 and Methanosarcina mazei Go1, respectively. All of the proteins involved in the proposed pathways were identified from public do...

The information provided by completely sequenced genomes of methanogens can yield insights into a deeper molecular understanding of evolutionary mechanisms. This review describes the advantages of using metabolic pathways to clarify evolutionary correlation of methanogens with archaea and prokaryotes. Metabolic trees can be used to highlight simila...

The metalloenzymes are proteins with enzymatic activity which contain metals tightly bound in their active sites to display a chemical action. This review describes the recent developments and success of using computational methods and algorithms for designing industrial enzymes. A recent approach based on functional amino acids or peptides as char...

Using 16S rDNA gene sequencing technique, three different species of non-symbiotic bacteria of entomopatho-genic nematodes (EPNs) (Steinernema sp. and Heterorhabditis sp.) were isolated and identified from infected insect cadavers {Galleria mellonella larvae) after 48-hour post infections. Sequence similarity analysis revealed that the strains SRK3...

In the present scenario the antimicrobial peptides of animal sources are being considered as suitable alternatives to the classical antibiotics for preventing pathogenic microorganisms without allowing them to develop resistance. Cathelicidins are one of the major classes of antimicrobial peptides widely distributed in mammalian neutrophils and epi...

Since a metabolic pathway with similar function has similar evolutionary relationship, the operation of metabolic pathways is essential to the survival of organisms, and metabolism related genes usually constitute only 10-20% of the total number of genes, metabolic pathway-based analysis can minimize the effect of the gene number, and thus allow mo...

Objective: The objective was to design a biocatalyst formyltetrahydrofolate ligase from the sequences of archaea bacteria based on the evolutionary conservation at metal- and substrate-binding regions. Methods: Complete formyltetrahydrofolate ligase sequences of archaea were retrieved from Gen- Pept of National Center for Biotechnology Information...