My research seeks to understand from a molecular perspective, how plants despite being sessile and immobile, can efficiently perceive environmental (biotic and abiotic) signals and launch short- and long-term biological responses that enable them to survive in environments considered hostile to plants. In particular, I study the signaling pathways of nitric oxide, cyclic nucleotides (e.g. cAMP and cGMP) and ABA. The broader aim of my research is to apply this knowledge for potential biotechnological innovations that can generate stress- and disease-tolerant crops. My current research can be divided into three main areas: 1) Plant cell signaling, 2) Probiotics and antibiotic resistance and, 3) Sustainable and indoor horticulture. Address: Wenzhou-Kean University 88 Daxue Road, Ouhai Wenzhou Zhejiang Province 325060 China
International Journal of Molecular Sciences, Sep 2, 2024
Increasing numbers of reports have revealed novel catalytically active cryptic guanylate cyclases... more Increasing numbers of reports have revealed novel catalytically active cryptic guanylate cyclases (GCs) and adenylate cyclases (ACs) operating within complex proteins in prokaryotes and eukaryotes. Here we review the structural and functional aspects of some of these cyclases and provide examples that illustrate their roles in the regulation of the intramolecular functions of complex proteins, such as the phytosulfokine receptor (PSKR), and reassess their contribution to signal generation and tuning. Another multidomain protein, Arabidopsis thaliana K+ uptake permease (AtKUP5), also harbors multiple catalytically active sites including an N-terminal AC and C-terminal phosphodiesterase (PDE) with an abscisic acid-binding site. We argue that this architecture may enable the fine-tuning and/or sensing of K+ flux and integrate hormone responses to cAMP homeostasis. We also discuss how searches with motifs based on conserved amino acids in catalytic centers led to the discovery of GCs and ACs and propose how this approach can be applied to discover hitherto masked active sites in bacterial, fungal, and animal proteomes. Finally, we show that motif searches are a promising approach to discover ancient biological functions such as hormone or gas binding.
Background
Schaalia species are primarily found among the oral microbiota of humans and other ani... more Background Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences. Results Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24. Conclusions Based on these findings, strain NCTC 9931 T (= ATCC 17982 T = DSM 43331 T = CIP 104728 T = CCUG 18309 T = NCTC 14978 T = CGMCC 1.90328 T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24 T (= NCTC 14980 T = CGMCC 1.90329 T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health.
Metabolic processes in prokaryotic and eukaryotic organisms are often modulated by kinases which ... more Metabolic processes in prokaryotic and eukaryotic organisms are often modulated by kinases which are in turn, dependent on Ca2+ and the cyclic mononucleotides cAMP and cGMP. It has been established that some proteins have both kinase and cyclase activities and that active cyclases can be embedded within the kinase domains. Here, we identified phosphodiesterase (PDE) sites, enzymes that hydrolyse cAMP and cGMP, to AMP and GMP, respectively, in some of these proteins in addition to their kinase/cyclase twin-architecture. As an example, we tested the Arabidopsis thaliana KINγ, a subunit of the SnRK2 kinase, to demonstrate that all three enzymatic centres, adenylate cyclase (AC), guanylate cyclase (GC) and PDE, are catalytically active, capable of generating and hydrolysing cAMP and cGMP. These data imply that the signal output of the KINγ subunit modulates SnRK2, consequently affecting the downstream kinome. Finally, we propose a model where a single protein subunit, KINγ, is capable of regulating cyclic mononucleotide homeostasis, thereby tuning stimulus specific signal output.
Numerous green-synthesized nanoparticles are being evaluated for their potential application in s... more Numerous green-synthesized nanoparticles are being evaluated for their potential application in soil, yet understanding their influence on plant performance and their rhizocompartments associated microbes is a gap that needs to be addressed. In this study, we investigated how applying iron oxide nanoparticles (control 0, low 25 and high 50 mg/kg) impacted the rhizocompartments associated microbial communities and plant secondary metabolites grown in natural soil microcosm. The transcriptional analysis showed that the majority of artemisinin and flavonoid biosynthetic pathway genes were significantly upregulated in plants with the application of low concentration of green-synthesized iron oxide nanoparticles (FeO.NPs) when compared with control plants, suggesting a fine collaboration between these metabolites’ pathways, as indicated by a remarkable increase in artemisinin content (2-fold), ferulic acid (7.6-fold), luteolin (4.3-fold) and syringic acid (6.2-fold). The response of rhizocompartments microbial communities and associated soil enzymes was investigated using high-throughput sequencing and profiler test kits, respectively. The soil microbial community structure was altered upon FeO.NPs exposure in both low and high treated soils as indicated by multivariate analysis. For instance, bacterial phyla Bacteroidetes and Gemmatimonadetes and fungal phyla Ascomycota demonstrated a significant rise in relative abundance in both the rhizosphere and rhizoplane in low and high treatments relative to the control. Moreover, genera level analysis revealed that Cupriavidus, Vibrionimonas, and Burkholderia displayed higher relative abundance (p < 0.05) in low FeO.NPs concentration while Giaella and Nonomuraea didn't show any noticeable response to FeO.NPs. In terms of fungal genera, Oidiodendron and Cryptococcus showed high relative abundance under low treatment. The altered microbiome profile is possibly associated with soil enzymes, for instance, urease and catalase activities were increased by 1.76 and 1.71-fold, respectively in low FeO.NPs. Thus, this study demonstrates the effects of FeO.NPs gradients on plant secondary metabolites and soil enzyme activities, while contributing new insights into their specific impacts on the microbial community composition in the rhizocompartments of plant root system.
Cyclic nucleotides 3',5'-cAMP and 3',5'-cGMP are now established signaling components of the plan... more Cyclic nucleotides 3',5'-cAMP and 3',5'-cGMP are now established signaling components of the plant cell while their 2',3' positional isomers are increasingly recognized as such. 3',5'-cAMP/cGMP is generated by adenylate cyclases (ACs) or guanylate cyclases (GCs) from ATP or GTP, respectively, whereas 2',3'-cAMP/cGMP is produced through the hydrolysis of double-stranded DNA or RNA by synthetases. Recent evidence suggests that the cyclic nucleotide generating and inactivating enzymes moonlight in proteins with diverse domain architecture operating as molecular tuners to enable dynamic and compartmentalized regulation of cellular signals. Further characterization of such moonlighting enzymes and extending the studies to noncanonical cyclic nucleotides promises new insights into the complex regulatory networks that underlie plant development and responses, thus offering exciting opportunities for crop improvement.
Probiotics have long been associated with a myriad of health benefits, so much so that their adve... more Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.
The rise in antibiotic-resistant bacteria caused by the excessive use of antibiotics has led to t... more The rise in antibiotic-resistant bacteria caused by the excessive use of antibiotics has led to the urgent exploration of alternative antimicrobial solutions. Among these alternatives, antimicrobial proteins, and peptides (Apps) have garnered attention due to their wide-ranging antimicrobial effects. This study focuses on evaluating the antimicrobial properties of Solanum lycopersicum heme-binding protein 2 (SlHBP2), an apoplastic protein extracted from tomato plants treated with 1-Methyl tryptophan (1-MT), against Pseudomonas syringae pv. tomato DC3000 (Pst). Computational studies indicate that SlHBP2 is annotated as a SOUL heme-binding family protein. Remarkably, recombinant SlHBP2 demonstrated significant efficacy in inhibiting the growth of Pst within a concentration range of 3-25 μg/mL. Moreover, SlHBP2 exhibited potent antimicrobial effects against other microorganisms, including Xanthomonas vesicatoria (Xv), Clavibacter michiganensis subsp. michiganensis (Cmm), and Botrytis cinerea. To understand the mechanism of action employed by SlHBP2 against Pst, various techniques such as microscopy and fluorescence assays were employed. The results revealed that SlHBP2 disrupts the bacterial cell wall and causes leakage of intracellular contents. To summarize, the findings suggest that SlHBP2 has significant antimicrobial properties, making it a potential antimicrobial agent against a wide range of pathogens. Although further studies are warranted to explore the full potential of SlHBP2 and its suitability in various applications.
In bacteria, fungi and animals, 3′-5′-cyclic adenosine monophosphate (cAMP) and adenylate cyclase... more In bacteria, fungi and animals, 3′-5′-cyclic adenosine monophosphate (cAMP) and adenylate cyclases (ACs), enzymes that catalyse the formation of 3′,5′-cAMP from ATP, are recognized as key signalling components. In contrast, the presence of cAMP and its biological roles in higher plants have long been a matter of controversy due to the generally lower amounts in plant tissues compared with that in animal and bacterial cells, and a lack of clarity on the molecular nature of the generating and degrading enzymes, as well as downstream effectors. While treatment with 3′,5′-cAMP elicited many plant responses, ACs were, however, somewhat elusive. This changed when systematic searches with amino acid motifs deduced from the conserved catalytic centres of annotated ACs from animals and bacteria identified candidate proteins in higher plants that were subsequently shown to have AC activities in vitro and in vivo. The identification of active ACs moonlighting within complex multifunctional proteins is consistent with their roles as molecular tuners and regulators of cellular and physiological functions. Furthermore, the increasing number of ACs identified as part of proteins with different domain architectures suggests that there are many more hidden ACs in plant proteomes and they may affect a multitude of mechanisms and processes at the molecular and systems levels.
International Journal of Molecular Sciences, Jun 20, 2023
Melanoma is a highly malignant skin cancer that is known for its resistance to treatments. In rec... more Melanoma is a highly malignant skin cancer that is known for its resistance to treatments. In recent years, there has been significant progress in the study of non-apoptotic cell death, such as pyroptosis, ferroptosis, necroptosis, and cuproptosis. This review provides an overview of the mechanisms and signaling pathways involved in non-apoptotic cell death in melanoma. This article explores the interplay between various forms of cell death, including pyroptosis, necroptosis, ferroptosis, and cuproptosis, as well as apoptosis and autophagy. Importantly, we discuss how these non-apoptotic cell deaths could be targeted as a promising therapeutic strategy for the treatment of drug-resistant melanoma. This review provides a comprehensive overview of non-apoptotic processes and gathers recent experimental evidence that will guide future research and eventually the creation of treatment strategies to combat drug resistance in melanoma.
Computational and Structural Biotechnology Journal, Jan 1, 2023
Biological systems consist of multiple components of different physical and chemical properties t... more Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.
International Journal of Molecular Sciences, Nov 25, 2022
Melanoma is the most aggressive form of skin cancer, characterized by life-threatening and rapidl... more Melanoma is the most aggressive form of skin cancer, characterized by life-threatening and rapidly spreading progression. Traditional targeted therapy can alleviate tumors by inactivating hyperactive kinases such as BRAF or MEK but inevitably encounters drug resistance. The advent of immunotherapy has revolutionized melanoma treatment and significantly improved the prognosis of melanoma patients. MicroRNAs (miRNAs) are intricately involved in innate and adaptive immunity and are implicated in melanoma immunotherapy. This systematic review describes the roles of miRNAs in regulating the functions of immune cells in skin and melanoma, as well as the involvement of miRNAs in pharmacology including the effect, resistance and immune-related adverse events of checkpoint inhibitors such as PD-1 and CTLA-4 inhibitors, which are used for treating cutaneous, uveal and mucosal melanoma. The expressions and functions of miRNAs in immunotherapy employing tumor-infiltrating lymphocytes and Toll-like receptor 9 agonists are also discussed. The prospect of innovative therapeutic strategies such as the combined administration of miRNAs and immune checkpoint inhibitors and the nanotechnology-based delivery of miRNAs are also provided. A comprehensive understanding of the interplay between miRNAs and immunotherapy is crucial for the discovery of reliable biomarkers and for the development of novel miRNA-based therapeutics against melanoma.
The phytohormone auxin is essential for plant growth and development as well as cellular and syst... more The phytohormone auxin is essential for plant growth and development as well as cellular and systemic responses to environmental cues. The auxin receptor TRANSPORT INHIBITOR RESPONSE 1/AUXIN-SIGNALING F-BOX (TIR1/AFB) lies within an E3 ubiquitin ligase complex (SCFTIR1/AFB) consisting of Skp, Cullin, and F-box proteins. Auxin brings together TIR1/AFB and the transcriptional repressor Auxin/INDOLE-3-ACETIC ACID (Aux/IAA), which allows the SCFTIR1/AFB complex to transfer activated ubiquitin to Aux/IAA, thereby targeting it for proteasomal degradation. This liberates the transcription factors AUXIN-RESPONSE FACTORs (ARFs) for auxin-dependent transcription. Just when we thought that the major components in the auxin signaling pathway had been identified, an adenylate cyclase (AC), embedded in the TIR1/AFB receptors, has emerged as an essential component of auxin signaling in gravitropism and root growth inhibition.
The majority of proteins in both prokaryote and eukaryote proteomes consist of two or more functi... more The majority of proteins in both prokaryote and eukaryote proteomes consist of two or more functional centers, which allows for intramolecular tuning of protein functions. Such architecture, as opposed to animal orthologs, applies to the plant cyclases (CNC) and phosphodiesterases (PDEs), the vast majority of which are part of larger multifunctional proteins. In plants, until recently, only two cases of combinations of CNC-PDE in one protein were reported. Here we propose that in plants, multifunctional proteins in which the PDE motif has been identified, the presence of the additional CNC center is common. Searching the Arabidopsis thaliana proteome with a combined PDE-CNC motif allowed the creation of a database of proteins with both activities. One such example is methylenetetrahydrofolate dehydrogenase, in which we determined the activities of adenylate cyclase (AC) and PDE. Based on biochemical and mutagenesis analyses we assessed the impact of the AC and PDE catalytic centers on the dehydrogenase activity. This allowed us to propose additional regulatory mechanism that govern folate metabolism by cAMP. It is therefore conceivable that the combined CNC-PDE architecture is a common regulatory configuration, where control of the level of cyclic nucleotides (cNMP) influences other catalytic activities of the protein.
HNOXPred is a webserver for the prediction of gas sensing H-NOX proteins from amino acid sequence... more HNOXPred is a webserver for the prediction of gas sensing H-NOX proteins from amino acid sequence. Heme-Nitric oxide/Oxygen (H-NOX) proteins are gas sensing hemoproteins found in diverse organisms ranging from bacteria to eukaryotes. Recently, gas sensing complex multi-functional proteins containing only the conserved amino acids at the heme centers of H-NOX proteins, have been identified through a motif-based approach. Based on experimental data and H-NOX candidates reported in literature, HNOXPred is created to automate and facilitate the identification of similar H-NOX centers across systems. The server features HNOXSCORES scaled from 0 to 1 that consider in its calculation, the physicochemical properties of amino acids constituting the heme center in H-NOX in addition to the conserved amino acids within the center. From user input amino acid sequence, the server returns positive hits and their calculated HNOXSCORES ordered from high to low confidence which are accompanied by interpretation guides and recommendations. The utility of this server is demonstrated using the human proteome as an example. The HNOXPred server is available at https://www.hnoxpred.com.
Drug resistance remains a global threat, and the rising trend of consuming probiotic-containing f... more Drug resistance remains a global threat, and the rising trend of consuming probiotic-containing foods, many of which harbor antibiotic resistant determinants, has raised serious health concerns. Currently, the lack of accessibility to location-, drug-and species-specific information of drugresistant probiotics has hampered efforts to combat the global spread of drug resistance. Here, we describe the development of ProbResist, which is a manually curated online database that catalogs reports of probiotic bacteria that have been experimentally proven to be resistant to antibiotics. ProbResist allows users to search for information of drug resistance in probiotics by querying with the names of the bacteria, antibiotic or location. Retrieved results are presented in a downloadable table format containing the names of the antibiotic, probiotic species, resistant determinants, region where the study was conducted and digital article identifiers (PubMed Identifier and Digital Object Identifier) hyperlinked to the original sources. The webserver also presents a simple analysis of information stored in the database. Given the increasing reports of drug-resistant probiotics, an exclusive database is necessary to catalog them in one platform. It will enable medical practitioners and experts involved in policy making to access this information quickly and conveniently, thus contributing toward the broader goal of combating drug resistance. Database URL: https://probresist.com.
International Journal of Molecular Sciences, May 23, 2022
Responding to environmental stimuli with appropriate molecular mechanisms is essential to all lif... more Responding to environmental stimuli with appropriate molecular mechanisms is essential to all life forms and particularly so in sessile organisms such as plants. To this end, plants have evolved both rapid early mechanisms such as the activation of channels and kinases directly or indirectly through protein sensors, as well as the slower systemic adaptive responses that include changes in their transcriptomes and proteomes. To enable these processes and concomitantly tune their responses to the environment, complex cellular-signaling mechanisms have evolved, some of which have no homologues in animals. This Special Issue aims to broaden the current understanding of plant cell signaling, specifically highlighting recent and exciting discoveries such as the identification of novel signaling molecules and mechanisms that participate across all stages of plant growth and development, and in cellular and biological processes triggered by abiotic and biotic stresses.
The sesquiterpene abscisic acid (ABA) is an ancient stress response molecule. In plants, many ABA... more The sesquiterpene abscisic acid (ABA) is an ancient stress response molecule. In plants, many ABA-dependent processes operate via PYR/PYL/RCAR receptor complexes, but results from several studies have suggested that not all plant responses function through this mechanism. Since the ABA-dependent processes of animals and humans also operate in the absence of such receptors, we hypothesize that plant and animal proteomes harbour proteins with undiscovered ABA-binding sites. We propose that carefully curated amino acid search motifs deduced from the binding sites of experimentally confirmed ABA-binding proteins can identify many more candidates in plant and animal proteomes. Some of these candidates show structural folds that are compatible with ABA-binding. This approach identifies plant candidates including annotated ABA downstream signaling components SnRK2.2 and SnRK2.6, and proteins involved in protein folding and RNA polyadenylation. The identified ABA-binding candidates in the human proteome affect among other processes, immune responses and tumor progression. If these candidates are eventually validated experimentally, it will imply that the regulation and tuning of ABA-dependent processes is considerably more complex than hitherto suspected. It will also help to clarify the role of this conserved signaling molecule in mammals.
Antimicrobial resistance (AR) is considered a “silent pandemic” that is responsible for more than... more Antimicrobial resistance (AR) is considered a “silent pandemic” that is responsible for more than 700,000 deaths per year; a figure that could rise to 10 million by 2050 if no action is taken. The use or rather misuse of antimicrobial drugs in hospitals has long been recognized as the main cause for the spread of antimicrobial resistant genes (ARGs) and this has become even more apparent during the SARS-CoV-2 pandemic where antimicrobial drugs were often prescribed unnecessarily to treat secondary infections. In recent years, food production and agriculture among other anthropogenic activities, have exacerbated this problem. While the impact of clinical antimicrobial use and resistance has been well-documented, the contributions from other sources and how they fit into the overall prevalence of AR is less understood. The underlying problem of AR is further complicated by the dynamic transmission of AR leading to the establishment of ARG reservoirs across various stages along the food chain. This Research Topic aims to offer a balanced overview of this global threat by gathering research focusing on AR along the food chain, from farm to fork.
We are an international group of biological scientists, conservationists, and environmentalists w... more We are an international group of biological scientists, conservationists, and environmentalists who have been closely following the plight and conservation of pangolins over a number of years. Pangolins comprise the mammalian Order Pholidota, which contains eight living species found in diverse habitats in Africa (4 species) and Asia (4 species), which provide important ecosystem services, including providing “pest” control and improving soil quality. They remain the most threatened and trafficked mammal species in the world. For over a century, there have been numerous attempts to rescue and maintain these animals in captivity, but with very few examples of success, chiefly because they usually die of infection. In 2016, the genomes of the Critically Endangered Chinese and Malayan pangolins were sequenced and revealed two important findings. First, to the best of our knowledge, pangolins are the only mammals known to lack the IFNE (Interferon epsilon) gene (important for mucosal immunity), suggesting that their resistance to pathogens may be reduced. Moreover, we found that pangolins have a reduced number of the heat shock protein (HSP) gene family members, suggesting stress susceptibility inducing immunosuppression, more so than other mammalian lineages. These findings may help explain why captive pangolins frequently succumb to infection.
Background: Probiotic lozenges have been developed to harvest the benefits of probiotics for oral... more Background: Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria. Aim: To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro. Results: Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128 µg/mL) and chloramphenicol (> 512 µg/mL) for all probiotics but only one was resistant to piperacillin (MIC = 32 µg/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments. Conclusion: Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.
International Journal of Molecular Sciences, Sep 2, 2024
Increasing numbers of reports have revealed novel catalytically active cryptic guanylate cyclases... more Increasing numbers of reports have revealed novel catalytically active cryptic guanylate cyclases (GCs) and adenylate cyclases (ACs) operating within complex proteins in prokaryotes and eukaryotes. Here we review the structural and functional aspects of some of these cyclases and provide examples that illustrate their roles in the regulation of the intramolecular functions of complex proteins, such as the phytosulfokine receptor (PSKR), and reassess their contribution to signal generation and tuning. Another multidomain protein, Arabidopsis thaliana K+ uptake permease (AtKUP5), also harbors multiple catalytically active sites including an N-terminal AC and C-terminal phosphodiesterase (PDE) with an abscisic acid-binding site. We argue that this architecture may enable the fine-tuning and/or sensing of K+ flux and integrate hormone responses to cAMP homeostasis. We also discuss how searches with motifs based on conserved amino acids in catalytic centers led to the discovery of GCs and ACs and propose how this approach can be applied to discover hitherto masked active sites in bacterial, fungal, and animal proteomes. Finally, we show that motif searches are a promising approach to discover ancient biological functions such as hormone or gas binding.
Background
Schaalia species are primarily found among the oral microbiota of humans and other ani... more Background Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences. Results Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24. Conclusions Based on these findings, strain NCTC 9931 T (= ATCC 17982 T = DSM 43331 T = CIP 104728 T = CCUG 18309 T = NCTC 14978 T = CGMCC 1.90328 T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24 T (= NCTC 14980 T = CGMCC 1.90329 T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health.
Metabolic processes in prokaryotic and eukaryotic organisms are often modulated by kinases which ... more Metabolic processes in prokaryotic and eukaryotic organisms are often modulated by kinases which are in turn, dependent on Ca2+ and the cyclic mononucleotides cAMP and cGMP. It has been established that some proteins have both kinase and cyclase activities and that active cyclases can be embedded within the kinase domains. Here, we identified phosphodiesterase (PDE) sites, enzymes that hydrolyse cAMP and cGMP, to AMP and GMP, respectively, in some of these proteins in addition to their kinase/cyclase twin-architecture. As an example, we tested the Arabidopsis thaliana KINγ, a subunit of the SnRK2 kinase, to demonstrate that all three enzymatic centres, adenylate cyclase (AC), guanylate cyclase (GC) and PDE, are catalytically active, capable of generating and hydrolysing cAMP and cGMP. These data imply that the signal output of the KINγ subunit modulates SnRK2, consequently affecting the downstream kinome. Finally, we propose a model where a single protein subunit, KINγ, is capable of regulating cyclic mononucleotide homeostasis, thereby tuning stimulus specific signal output.
Numerous green-synthesized nanoparticles are being evaluated for their potential application in s... more Numerous green-synthesized nanoparticles are being evaluated for their potential application in soil, yet understanding their influence on plant performance and their rhizocompartments associated microbes is a gap that needs to be addressed. In this study, we investigated how applying iron oxide nanoparticles (control 0, low 25 and high 50 mg/kg) impacted the rhizocompartments associated microbial communities and plant secondary metabolites grown in natural soil microcosm. The transcriptional analysis showed that the majority of artemisinin and flavonoid biosynthetic pathway genes were significantly upregulated in plants with the application of low concentration of green-synthesized iron oxide nanoparticles (FeO.NPs) when compared with control plants, suggesting a fine collaboration between these metabolites’ pathways, as indicated by a remarkable increase in artemisinin content (2-fold), ferulic acid (7.6-fold), luteolin (4.3-fold) and syringic acid (6.2-fold). The response of rhizocompartments microbial communities and associated soil enzymes was investigated using high-throughput sequencing and profiler test kits, respectively. The soil microbial community structure was altered upon FeO.NPs exposure in both low and high treated soils as indicated by multivariate analysis. For instance, bacterial phyla Bacteroidetes and Gemmatimonadetes and fungal phyla Ascomycota demonstrated a significant rise in relative abundance in both the rhizosphere and rhizoplane in low and high treatments relative to the control. Moreover, genera level analysis revealed that Cupriavidus, Vibrionimonas, and Burkholderia displayed higher relative abundance (p < 0.05) in low FeO.NPs concentration while Giaella and Nonomuraea didn't show any noticeable response to FeO.NPs. In terms of fungal genera, Oidiodendron and Cryptococcus showed high relative abundance under low treatment. The altered microbiome profile is possibly associated with soil enzymes, for instance, urease and catalase activities were increased by 1.76 and 1.71-fold, respectively in low FeO.NPs. Thus, this study demonstrates the effects of FeO.NPs gradients on plant secondary metabolites and soil enzyme activities, while contributing new insights into their specific impacts on the microbial community composition in the rhizocompartments of plant root system.
Cyclic nucleotides 3',5'-cAMP and 3',5'-cGMP are now established signaling components of the plan... more Cyclic nucleotides 3',5'-cAMP and 3',5'-cGMP are now established signaling components of the plant cell while their 2',3' positional isomers are increasingly recognized as such. 3',5'-cAMP/cGMP is generated by adenylate cyclases (ACs) or guanylate cyclases (GCs) from ATP or GTP, respectively, whereas 2',3'-cAMP/cGMP is produced through the hydrolysis of double-stranded DNA or RNA by synthetases. Recent evidence suggests that the cyclic nucleotide generating and inactivating enzymes moonlight in proteins with diverse domain architecture operating as molecular tuners to enable dynamic and compartmentalized regulation of cellular signals. Further characterization of such moonlighting enzymes and extending the studies to noncanonical cyclic nucleotides promises new insights into the complex regulatory networks that underlie plant development and responses, thus offering exciting opportunities for crop improvement.
Probiotics have long been associated with a myriad of health benefits, so much so that their adve... more Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.
The rise in antibiotic-resistant bacteria caused by the excessive use of antibiotics has led to t... more The rise in antibiotic-resistant bacteria caused by the excessive use of antibiotics has led to the urgent exploration of alternative antimicrobial solutions. Among these alternatives, antimicrobial proteins, and peptides (Apps) have garnered attention due to their wide-ranging antimicrobial effects. This study focuses on evaluating the antimicrobial properties of Solanum lycopersicum heme-binding protein 2 (SlHBP2), an apoplastic protein extracted from tomato plants treated with 1-Methyl tryptophan (1-MT), against Pseudomonas syringae pv. tomato DC3000 (Pst). Computational studies indicate that SlHBP2 is annotated as a SOUL heme-binding family protein. Remarkably, recombinant SlHBP2 demonstrated significant efficacy in inhibiting the growth of Pst within a concentration range of 3-25 μg/mL. Moreover, SlHBP2 exhibited potent antimicrobial effects against other microorganisms, including Xanthomonas vesicatoria (Xv), Clavibacter michiganensis subsp. michiganensis (Cmm), and Botrytis cinerea. To understand the mechanism of action employed by SlHBP2 against Pst, various techniques such as microscopy and fluorescence assays were employed. The results revealed that SlHBP2 disrupts the bacterial cell wall and causes leakage of intracellular contents. To summarize, the findings suggest that SlHBP2 has significant antimicrobial properties, making it a potential antimicrobial agent against a wide range of pathogens. Although further studies are warranted to explore the full potential of SlHBP2 and its suitability in various applications.
In bacteria, fungi and animals, 3′-5′-cyclic adenosine monophosphate (cAMP) and adenylate cyclase... more In bacteria, fungi and animals, 3′-5′-cyclic adenosine monophosphate (cAMP) and adenylate cyclases (ACs), enzymes that catalyse the formation of 3′,5′-cAMP from ATP, are recognized as key signalling components. In contrast, the presence of cAMP and its biological roles in higher plants have long been a matter of controversy due to the generally lower amounts in plant tissues compared with that in animal and bacterial cells, and a lack of clarity on the molecular nature of the generating and degrading enzymes, as well as downstream effectors. While treatment with 3′,5′-cAMP elicited many plant responses, ACs were, however, somewhat elusive. This changed when systematic searches with amino acid motifs deduced from the conserved catalytic centres of annotated ACs from animals and bacteria identified candidate proteins in higher plants that were subsequently shown to have AC activities in vitro and in vivo. The identification of active ACs moonlighting within complex multifunctional proteins is consistent with their roles as molecular tuners and regulators of cellular and physiological functions. Furthermore, the increasing number of ACs identified as part of proteins with different domain architectures suggests that there are many more hidden ACs in plant proteomes and they may affect a multitude of mechanisms and processes at the molecular and systems levels.
International Journal of Molecular Sciences, Jun 20, 2023
Melanoma is a highly malignant skin cancer that is known for its resistance to treatments. In rec... more Melanoma is a highly malignant skin cancer that is known for its resistance to treatments. In recent years, there has been significant progress in the study of non-apoptotic cell death, such as pyroptosis, ferroptosis, necroptosis, and cuproptosis. This review provides an overview of the mechanisms and signaling pathways involved in non-apoptotic cell death in melanoma. This article explores the interplay between various forms of cell death, including pyroptosis, necroptosis, ferroptosis, and cuproptosis, as well as apoptosis and autophagy. Importantly, we discuss how these non-apoptotic cell deaths could be targeted as a promising therapeutic strategy for the treatment of drug-resistant melanoma. This review provides a comprehensive overview of non-apoptotic processes and gathers recent experimental evidence that will guide future research and eventually the creation of treatment strategies to combat drug resistance in melanoma.
Computational and Structural Biotechnology Journal, Jan 1, 2023
Biological systems consist of multiple components of different physical and chemical properties t... more Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.
International Journal of Molecular Sciences, Nov 25, 2022
Melanoma is the most aggressive form of skin cancer, characterized by life-threatening and rapidl... more Melanoma is the most aggressive form of skin cancer, characterized by life-threatening and rapidly spreading progression. Traditional targeted therapy can alleviate tumors by inactivating hyperactive kinases such as BRAF or MEK but inevitably encounters drug resistance. The advent of immunotherapy has revolutionized melanoma treatment and significantly improved the prognosis of melanoma patients. MicroRNAs (miRNAs) are intricately involved in innate and adaptive immunity and are implicated in melanoma immunotherapy. This systematic review describes the roles of miRNAs in regulating the functions of immune cells in skin and melanoma, as well as the involvement of miRNAs in pharmacology including the effect, resistance and immune-related adverse events of checkpoint inhibitors such as PD-1 and CTLA-4 inhibitors, which are used for treating cutaneous, uveal and mucosal melanoma. The expressions and functions of miRNAs in immunotherapy employing tumor-infiltrating lymphocytes and Toll-like receptor 9 agonists are also discussed. The prospect of innovative therapeutic strategies such as the combined administration of miRNAs and immune checkpoint inhibitors and the nanotechnology-based delivery of miRNAs are also provided. A comprehensive understanding of the interplay between miRNAs and immunotherapy is crucial for the discovery of reliable biomarkers and for the development of novel miRNA-based therapeutics against melanoma.
The phytohormone auxin is essential for plant growth and development as well as cellular and syst... more The phytohormone auxin is essential for plant growth and development as well as cellular and systemic responses to environmental cues. The auxin receptor TRANSPORT INHIBITOR RESPONSE 1/AUXIN-SIGNALING F-BOX (TIR1/AFB) lies within an E3 ubiquitin ligase complex (SCFTIR1/AFB) consisting of Skp, Cullin, and F-box proteins. Auxin brings together TIR1/AFB and the transcriptional repressor Auxin/INDOLE-3-ACETIC ACID (Aux/IAA), which allows the SCFTIR1/AFB complex to transfer activated ubiquitin to Aux/IAA, thereby targeting it for proteasomal degradation. This liberates the transcription factors AUXIN-RESPONSE FACTORs (ARFs) for auxin-dependent transcription. Just when we thought that the major components in the auxin signaling pathway had been identified, an adenylate cyclase (AC), embedded in the TIR1/AFB receptors, has emerged as an essential component of auxin signaling in gravitropism and root growth inhibition.
The majority of proteins in both prokaryote and eukaryote proteomes consist of two or more functi... more The majority of proteins in both prokaryote and eukaryote proteomes consist of two or more functional centers, which allows for intramolecular tuning of protein functions. Such architecture, as opposed to animal orthologs, applies to the plant cyclases (CNC) and phosphodiesterases (PDEs), the vast majority of which are part of larger multifunctional proteins. In plants, until recently, only two cases of combinations of CNC-PDE in one protein were reported. Here we propose that in plants, multifunctional proteins in which the PDE motif has been identified, the presence of the additional CNC center is common. Searching the Arabidopsis thaliana proteome with a combined PDE-CNC motif allowed the creation of a database of proteins with both activities. One such example is methylenetetrahydrofolate dehydrogenase, in which we determined the activities of adenylate cyclase (AC) and PDE. Based on biochemical and mutagenesis analyses we assessed the impact of the AC and PDE catalytic centers on the dehydrogenase activity. This allowed us to propose additional regulatory mechanism that govern folate metabolism by cAMP. It is therefore conceivable that the combined CNC-PDE architecture is a common regulatory configuration, where control of the level of cyclic nucleotides (cNMP) influences other catalytic activities of the protein.
HNOXPred is a webserver for the prediction of gas sensing H-NOX proteins from amino acid sequence... more HNOXPred is a webserver for the prediction of gas sensing H-NOX proteins from amino acid sequence. Heme-Nitric oxide/Oxygen (H-NOX) proteins are gas sensing hemoproteins found in diverse organisms ranging from bacteria to eukaryotes. Recently, gas sensing complex multi-functional proteins containing only the conserved amino acids at the heme centers of H-NOX proteins, have been identified through a motif-based approach. Based on experimental data and H-NOX candidates reported in literature, HNOXPred is created to automate and facilitate the identification of similar H-NOX centers across systems. The server features HNOXSCORES scaled from 0 to 1 that consider in its calculation, the physicochemical properties of amino acids constituting the heme center in H-NOX in addition to the conserved amino acids within the center. From user input amino acid sequence, the server returns positive hits and their calculated HNOXSCORES ordered from high to low confidence which are accompanied by interpretation guides and recommendations. The utility of this server is demonstrated using the human proteome as an example. The HNOXPred server is available at https://www.hnoxpred.com.
Drug resistance remains a global threat, and the rising trend of consuming probiotic-containing f... more Drug resistance remains a global threat, and the rising trend of consuming probiotic-containing foods, many of which harbor antibiotic resistant determinants, has raised serious health concerns. Currently, the lack of accessibility to location-, drug-and species-specific information of drugresistant probiotics has hampered efforts to combat the global spread of drug resistance. Here, we describe the development of ProbResist, which is a manually curated online database that catalogs reports of probiotic bacteria that have been experimentally proven to be resistant to antibiotics. ProbResist allows users to search for information of drug resistance in probiotics by querying with the names of the bacteria, antibiotic or location. Retrieved results are presented in a downloadable table format containing the names of the antibiotic, probiotic species, resistant determinants, region where the study was conducted and digital article identifiers (PubMed Identifier and Digital Object Identifier) hyperlinked to the original sources. The webserver also presents a simple analysis of information stored in the database. Given the increasing reports of drug-resistant probiotics, an exclusive database is necessary to catalog them in one platform. It will enable medical practitioners and experts involved in policy making to access this information quickly and conveniently, thus contributing toward the broader goal of combating drug resistance. Database URL: https://probresist.com.
International Journal of Molecular Sciences, May 23, 2022
Responding to environmental stimuli with appropriate molecular mechanisms is essential to all lif... more Responding to environmental stimuli with appropriate molecular mechanisms is essential to all life forms and particularly so in sessile organisms such as plants. To this end, plants have evolved both rapid early mechanisms such as the activation of channels and kinases directly or indirectly through protein sensors, as well as the slower systemic adaptive responses that include changes in their transcriptomes and proteomes. To enable these processes and concomitantly tune their responses to the environment, complex cellular-signaling mechanisms have evolved, some of which have no homologues in animals. This Special Issue aims to broaden the current understanding of plant cell signaling, specifically highlighting recent and exciting discoveries such as the identification of novel signaling molecules and mechanisms that participate across all stages of plant growth and development, and in cellular and biological processes triggered by abiotic and biotic stresses.
The sesquiterpene abscisic acid (ABA) is an ancient stress response molecule. In plants, many ABA... more The sesquiterpene abscisic acid (ABA) is an ancient stress response molecule. In plants, many ABA-dependent processes operate via PYR/PYL/RCAR receptor complexes, but results from several studies have suggested that not all plant responses function through this mechanism. Since the ABA-dependent processes of animals and humans also operate in the absence of such receptors, we hypothesize that plant and animal proteomes harbour proteins with undiscovered ABA-binding sites. We propose that carefully curated amino acid search motifs deduced from the binding sites of experimentally confirmed ABA-binding proteins can identify many more candidates in plant and animal proteomes. Some of these candidates show structural folds that are compatible with ABA-binding. This approach identifies plant candidates including annotated ABA downstream signaling components SnRK2.2 and SnRK2.6, and proteins involved in protein folding and RNA polyadenylation. The identified ABA-binding candidates in the human proteome affect among other processes, immune responses and tumor progression. If these candidates are eventually validated experimentally, it will imply that the regulation and tuning of ABA-dependent processes is considerably more complex than hitherto suspected. It will also help to clarify the role of this conserved signaling molecule in mammals.
Antimicrobial resistance (AR) is considered a “silent pandemic” that is responsible for more than... more Antimicrobial resistance (AR) is considered a “silent pandemic” that is responsible for more than 700,000 deaths per year; a figure that could rise to 10 million by 2050 if no action is taken. The use or rather misuse of antimicrobial drugs in hospitals has long been recognized as the main cause for the spread of antimicrobial resistant genes (ARGs) and this has become even more apparent during the SARS-CoV-2 pandemic where antimicrobial drugs were often prescribed unnecessarily to treat secondary infections. In recent years, food production and agriculture among other anthropogenic activities, have exacerbated this problem. While the impact of clinical antimicrobial use and resistance has been well-documented, the contributions from other sources and how they fit into the overall prevalence of AR is less understood. The underlying problem of AR is further complicated by the dynamic transmission of AR leading to the establishment of ARG reservoirs across various stages along the food chain. This Research Topic aims to offer a balanced overview of this global threat by gathering research focusing on AR along the food chain, from farm to fork.
We are an international group of biological scientists, conservationists, and environmentalists w... more We are an international group of biological scientists, conservationists, and environmentalists who have been closely following the plight and conservation of pangolins over a number of years. Pangolins comprise the mammalian Order Pholidota, which contains eight living species found in diverse habitats in Africa (4 species) and Asia (4 species), which provide important ecosystem services, including providing “pest” control and improving soil quality. They remain the most threatened and trafficked mammal species in the world. For over a century, there have been numerous attempts to rescue and maintain these animals in captivity, but with very few examples of success, chiefly because they usually die of infection. In 2016, the genomes of the Critically Endangered Chinese and Malayan pangolins were sequenced and revealed two important findings. First, to the best of our knowledge, pangolins are the only mammals known to lack the IFNE (Interferon epsilon) gene (important for mucosal immunity), suggesting that their resistance to pathogens may be reduced. Moreover, we found that pangolins have a reduced number of the heat shock protein (HSP) gene family members, suggesting stress susceptibility inducing immunosuppression, more so than other mammalian lineages. These findings may help explain why captive pangolins frequently succumb to infection.
Background: Probiotic lozenges have been developed to harvest the benefits of probiotics for oral... more Background: Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria. Aim: To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro. Results: Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128 µg/mL) and chloramphenicol (> 512 µg/mL) for all probiotics but only one was resistant to piperacillin (MIC = 32 µg/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments. Conclusion: Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.
Nitric oxide (NO) is an important signaling molecule in plants. In the pollen of Arabidopsis thal... more Nitric oxide (NO) is an important signaling molecule in plants. In the pollen of Arabidopsis thaliana, NO causes re-orientation of the growing tube and this response is mediated by 3′,5′-cyclic guanosine monophosphate (cGMP). However, in plants, NO-sensors have remained somewhat elusive. Here, we present work on an NO-binding candidate, Arabidopsis thaliana DIACYLGLYCEROL KINASE 4 (ATDGK4; AT5G57690). In addition to the annotated diacylglycerol kinase domain, this molecule also harbors a predicted heme-NO/oxygen (H-NOX) binding site and a guanylyl cyclase (GC) catalytic domain which we have identified based on the alignment of functionally conserved amino acid residues across species. We have constructed a 3D model of the molecule, from which we have estimated the locations of the kinase catalytic center, the ATP-binding site, the GC and H-NOX domains. We have also modeled docking of ATP to the kinase catalytic center. The recombinant ATDGK4 demonstrated kinase activity in vitro, catalyzing the ATP-dependent conversion of sn-1,2-diacylglycerol (DAG) to phosphatidic acid (PA). This activity is inhibited by the mammalian DAG kinase inhibitor R59949 and importantly also by the NO donors diethylamine NONOate (DEA NONOate) and sodium nitroprusside (SNP). Recombinant ATDGK4 also has GC activity in vitro, catalyzing the conversion of guanosine-5'-triphosphate (GTP) to cGMP. The catalytic domains of ATDGK4 kinase and GC may be independently regulated since the kinase but not the GC, is inhibited by NO while Ca2+ only stimulates the GC. It is likely that the DAG kinase product, PA, causes the release of Ca2+ from the intracellular stores and Ca2+ in turn activates the GC domain of ATDGK4 through a feedback mechanism. Analysis of publicly available microarray data has revealed that ATDGK4 is highly expressed in the pollen. Here, the pollen tubes of overexpressing atdgk4 recorded slower growth rates than the wild-type (Col-0) and importantly, they showed altered NO responses. Specifically, the overexpressing atdgk4 pollen tubes have growth rates that were less affected by NO and showed reduced bending angles when challenged by an NO source. Further works on atdgk4 knockout/knockdown mutants will reveal the biological functions of ATDGK4 in NO and/or cGMP signaling in the pollen, and in the broader fertilization process.
Postharvest Ripening Physiology of Crops, Feb 22, 2016
Comparative proteomics has emerged as a powerful tool to study complex biological processes in fr... more Comparative proteomics has emerged as a powerful tool to study complex biological processes in fruits throughout their development and ripening. This is greatly aided by the rapid growth of genomics, transcriptomics and expressed sequence tags (ESTs) databases, which allows for protein identification and paves way for systems analyses and inference of molecular data. Fruit development and ripening are complex developmental processes that involve well-coordinated biological programs; the knowledge of which has valuable economic ramifications centered on the agricultural industry. Besides, fruit ripening is accompanied by numerous phenotypic and physiological changes, such as skin and hypanthium color and increase in sugar levels, which are regulated by environmental factors like light and temperature and/or internal factors such as hormonal and gene regulation. The latter is key in the classification of fruit species into their respective climacteric and non-climacteric categories. Comparative proteomics is therefore a useful tool to gain information on the molecular events taking place during fruit maturation in addition to finding biotechnological strategies to improve horticultural traits such as fruit quality, shelf-life and yield. In this chapter, an overview of methods utilized in fruit proteomics as well as a global proteome and systems biology analysis of fruits during ripening is presented.
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Papers by Aloysius Wong
Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences.
Results
Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24.
Conclusions
Based on these findings, strain NCTC 9931 T (= ATCC 17982 T = DSM 43331 T = CIP 104728 T = CCUG 18309 T = NCTC 14978 T = CGMCC 1.90328 T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24 T (= NCTC 14980 T = CGMCC 1.90329 T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health.
immunotherapy has revolutionized melanoma treatment and significantly improved the prognosis of melanoma patients. MicroRNAs (miRNAs) are intricately involved in innate and adaptive immunity and are implicated in melanoma immunotherapy. This systematic review describes the roles of miRNAs in regulating the functions of immune cells in skin and melanoma, as well as the involvement of miRNAs in pharmacology including the effect, resistance and immune-related adverse events of
checkpoint inhibitors such as PD-1 and CTLA-4 inhibitors, which are used for treating cutaneous, uveal and mucosal melanoma. The expressions and functions of miRNAs in immunotherapy employing tumor-infiltrating lymphocytes and Toll-like receptor 9 agonists are also discussed. The
prospect of innovative therapeutic strategies such as the combined administration of miRNAs and immune checkpoint inhibitors and the nanotechnology-based delivery of miRNAs are also provided. A comprehensive understanding of the interplay between miRNAs and immunotherapy is crucial for the discovery of reliable biomarkers and for the development of novel miRNA-based therapeutics against melanoma.
Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences.
Results
Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24.
Conclusions
Based on these findings, strain NCTC 9931 T (= ATCC 17982 T = DSM 43331 T = CIP 104728 T = CCUG 18309 T = NCTC 14978 T = CGMCC 1.90328 T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24 T (= NCTC 14980 T = CGMCC 1.90329 T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health.
immunotherapy has revolutionized melanoma treatment and significantly improved the prognosis of melanoma patients. MicroRNAs (miRNAs) are intricately involved in innate and adaptive immunity and are implicated in melanoma immunotherapy. This systematic review describes the roles of miRNAs in regulating the functions of immune cells in skin and melanoma, as well as the involvement of miRNAs in pharmacology including the effect, resistance and immune-related adverse events of
checkpoint inhibitors such as PD-1 and CTLA-4 inhibitors, which are used for treating cutaneous, uveal and mucosal melanoma. The expressions and functions of miRNAs in immunotherapy employing tumor-infiltrating lymphocytes and Toll-like receptor 9 agonists are also discussed. The
prospect of innovative therapeutic strategies such as the combined administration of miRNAs and immune checkpoint inhibitors and the nanotechnology-based delivery of miRNAs are also provided. A comprehensive understanding of the interplay between miRNAs and immunotherapy is crucial for the discovery of reliable biomarkers and for the development of novel miRNA-based therapeutics against melanoma.