Characterization of a Novel Nicotine Degradation Gene Cluster ndp in Sphingomonas melonis TY and Its Evolutionary Analysis

A multifunctional flavoprotein monooxygenase HspB for hydroxylation and C-C cleavage of 6-hydroxy-3-succinoyl-pyridine

Flavoprotein monooxygenases catalyze reactions, including hydroxylation and epoxidation, involved in the catabolism, detoxification, and biosynthesis of natural substrates and industrial contaminants. Among them, the 6-hydroxy-3-succinoyl-pyridine (HSP) monooxygenase (HspB) from Pseudomonas putida S16 facilitates the hydroxylation and C-C bond cleavage of the pyridine ring in nicotine. However, the mechanism for biodegradation remains elusive. Here, we refined the crystal structure of HspB and elucidated the detailed mechanism behind the oxidative hydroxylation and C-C cleavage processes. Leveraging structural information about domains for binding the cofactor flavin adenine dinucleotide (FAD) and HSP substrate, we used molecular dynamics simulations and quantum/molecular mechanics calculations to demonstrate that the transfer of an oxygen atom from the reactive FAD peroxide species (C4a-hydroperoxyflavin) to the C3 atom in the HSP substrate constitutes a rate-limiting step, with a calculated reaction barrier of about 20 kcal/mol. Subsequently, the hydrogen atom was rebounded to the FAD cofactor, forming C4a-hydroxyflavin. The residue Cys218 then catalyzed the subsequent hydrolytic process of C-C cleavage. Our findings contribute to a deeper understanding of the versatile functions of flavoproteins in the natural transformation of pyridine and HspB in nicotine degradation.IMPORTANCEPseudomonas putida S16 plays a pivotal role in degrading nicotine, a toxic pyridine derivative that poses significant environmental challenges. This study highlights a key enzyme, HspB (6-hydroxy-3-succinoyl-pyridine monooxygenase), in breaking down nicotine through the pyrrolidine pathway. Utilizing dioxygen and a flavin adenine dinucleotide cofactor, HspB hydroxylates and cleaves the substrate's side chain. Structural analysis of the refined HspB crystal structure, combined with state-of-the-art computations, reveals its distinctive mechanism. The crucial function of Cys218 was never discovered in its homologous enzymes. Our findings not only deepen our understanding of bacterial nicotine degradation but also open avenues for applications in both environmental cleanup and pharmaceutical development.

sRNA molecules participate in hyperosmotic stress response regulation in Sphingomonas melonis TY

Drought and salinity are ubiquitous environmental factors that pose hyperosmotic threats to microorganisms and impair their efficiency in performing environmental functions. However, bacteria have developed various responses and regulatory systems to cope with these abiotic challenges. Posttranscriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions can lead to the induction of specific small RNA molecules (sRNAs) that participate in stress response regulation. Here, we report a candidate functional sRNA landscape of Sphingomonas melonis TY under hyperosmotic stress, and 18 sRNAs were found with a clear response to hyperosmotic stress. These findings will help in the comprehensive analysis of sRNA regulation in Sphingomonas species. Weighted correlation network analysis revealed a 263 nucleotide sRNA, SNC251, which was transcribed from its own promoter and showed the most significant correlation with hyperosmotic response factors. Deletion of snc251 affected biofilm formation and multiple cellular processes, including ribosome-related pathways, aromatic compound degradation, and the nicotine degradation capacity of S. melonis TY, while overexpression of SNC251 facilitated biofilm formation by TY under hyperosmotic stress. Two genes involved in the TonB system were further verified to be activated by SNC251, which also indicated that SNC251 is a trans-acting sRNA. Briefly, this research reports a landscape of sRNAs participating in the hyperosmotic stress response in S. melonis and reveals a novel sRNA, SNC251, which contributes to the S. melonis TY biofilm formation and thus enhances its hyperosmotic stress response ability.IMPORTANCESphingomonas species play a vital role in plant defense and pollutant degradation and survive extensively under drought or salinity. Previous studies have focused on the transcriptional and translational responses of Sphingomonas under hyperosmotic stress, but the posttranscriptional regulation of small RNA molecules (sRNAs) is also crucial for quickly modulating cellular processes to adapt dynamically to osmotic environments. In addition, the current knowledge of sRNAs in Sphingomonas is extremely scarce. This research revealed a novel sRNA landscape of Sphingomonas melonis and will greatly enhance our understanding of sRNAs' acting mechanisms in the hyperosmotic stress response.

Insights into Pharmacological Activities of Nicotine and 6-Hydroxy-L-nicotine, a Bacterial Nicotine Derivative: A Systematic Review

The purported cognitive benefits associated with nicotine and its metabolites in the brain are a matter of debate. In this review, the impact of the pharmacologically active metabolite of a nicotine derivative produced by bacteria named 6-hydroxy-L-nicotine (6HLN) on memory, oxidative stress, and the activity of the cholinergic system in the brain was examined. A search in the PubMed, Science Direct, Web of Science, and Google Scholar databases, limiting entries to those published between 1992 and 2023, was conducted. The search focused specifically on articles about nicotine metabolites, memory, oxidative stress, and cholinergic system activity, as well as enzymes or pathways related to nicotine degradation in bacteria. The preliminary search resulted in 696 articles, and following the application of exclusion criteria, 212 articles were deemed eligible for inclusion. This review focuses on experimental studies supporting nicotine catabolism in bacteria, and the chemical and pharmacological activities of nicotine and its metabolite 6HLN.

Bacillus sp. YC7 from intestines of Lasioderma serricorne degrades nicotine due to nicotine dehydrogenase

A large number of nicotine-containing wastes produced during the tobacco manufacturing process are seriously harmful to the environment and human health. The degradation and transformation of nicotine-containing environmental contaminants to harmless substances has become an urgent requirement. Lasioderma serricorne can grow and reproduce in nicotine-rich sources, and their intestinal microbiota show promising potential to degrade and utilize nicotine. The purpose of this study is to screen and identify nicotine-degrading bacteria from the intestines of L. serricorne and explore their degradation characteristics. A dominant strain, YC7, with significant nicotine degradation capabilities was isolated from the intestines of L. serricorne. The strain was identified as Bacillus using a polyphasic approach. The test results showed it can produce multiple enzymes that include β-glucosidase, cellulase, proteases, and amylases. The nicotine-degrading bacteria were functionally annotated using databases. Nicotine dehydrogenase (NDH) was found by combining an activity tracking test and protein mass spectrometry analysis. The YC-7 NDH in the pathway was molecularly docked and functionally verified via the gene knockdown method. The binding ability of nicotine to nicotine-degrading enzymes was investigated using molecular docking. A high-efficiency nicotine-degrading bacteria, YC-7, was isolated and screened from tobacco, and the gene functions related to degradation were verified. This investigation provides a new hypothesis for screening nicotine-degrading bacteria and increases our knowledge of potential nicotine-degrading microbial sources.

Characterization of Hsp17, a Novel Small Heat Shock Protein, in Sphingomonas melonis TY under Heat Stress

Bacteria are constantly exposed to a variety of environmental stresses. Temperature is considered one of the most important environmental factors affecting microbial growth and survival. As ubiquitous environmental microorganisms, Sphingomonas species play essential roles in the biodegradation of organic contaminants, plant protection, and environmental remediation. Understanding the mechanism by which they respond to heat shock will help further improve cell resistance by applying synthetic biological strategies. Here, we assessed the transcriptomic and proteomic responses of Sphingomonas melonis TY to heat shock and found that stressful conditions caused significant changes in functional genes related to protein synthesis at the transcriptional level. The most notable changes observed were increases in the transcription (1,857-fold) and protein expression (11-fold) of Hsp17, which belongs to the small heat shock protein family, and the function of Hsp17 in heat stress was further investigated in this study. We found that the deletion of hsp17 reduced the capacity of the cells to tolerate high temperatures, whereas the overexpression of hsp17 significantly enhanced the ability of the cells to withstand high temperatures. Moreover, the heterologous expression of hsp17 in Escherichia coli DH5α conferred to the bacterium the ability to resist heat stress. Interestingly, its cells were elongated and formed connected cells following the increase in temperature, while hsp17 overexpression restored their normal morphology under high temperature. In general, these results indicate that the novel small heat shock protein Hsp17 greatly contributes to maintaining cell viability and morphology under stress conditions. IMPORTANCE Temperature is generally considered the most important factor affecting metabolic functions and the survival of microbes. As molecular chaperones, small heat shock proteins can prevent damaged protein aggregation during abiotic stress, especially heat stress. Sphingomonas species are widely distributed in nature, and they can frequently be found in various extreme environments. However, the role of small heat shock proteins in Sphingomonas under high-temperature stress has not been elucidated. This study greatly enhances our understanding of a novel identified protein, Hsp17, in S. melonis TY in terms of its ability to resist heat stress and maintain cell morphology under high temperature, leading to a broader understanding of how microbes adapt to environmental extremes. Furthermore, our study will provide potential heat resistance elements for further enhancing cellular resistance as well as the synthetic biological applications of Sphingomonas.

Regulation Mechanism of Nicotine Catabolism in Sphingomonas melonis TY by a Dual Role Transcriptional Regulator NdpR

A gene cluster ndp, responsible for nicotine degradation via a variant of the pyridine and pyrrolidine pathways, was previously identified in Sphingomonas melonis TY, but the regulation mechanism remains unknown. The gene ndpR within the cluster was predicted to encode a TetR family transcriptional regulator. Deletion of ndpR resulted in a notably shorter lag phase, higher maximum turbidity, and faster substrate degradation when cultivated in the presence of nicotine. Real-time quantitative PCR and promoter activity analysis in wild-type TY and TYΔndpR strains revealed that genes in the ndp cluster were negatively regulated by NdpR. However, complementation of ndpR to TYΔndpR did not restore transcription repression, but, instead, the complemented strain showed better growth than TYΔndpR. Promoter activity analysis indicates that NdpR also functions as an activator in the transcription regulation of ndpHFEGD. Further analysis through electrophoretic mobility shift assay and DNase I footprinting assay revealed that NdpR binds five DNA sequences within ndp and that NdpR has no autoregulation. These binding motifs overlap with the -35 or -10 box or are located distal upstream of the corresponding transcriptional start site. Multiple sequence alignment of these five NdpR-binding DNA sequences found a conserved motif, with two of the binding sequences being partially palindromic. 2,5-Dihydroxypyridine acted as a ligand of NdpR, preventing NdpR from binding to the promoter region of ndpASAL, ndpTB, and ndpHFEGD. This study revealed that NdpR binds to three promoters in the ndp cluster and is a dual-role transcriptional regulator in nicotine metabolism. IMPORTANCE Gene regulation is critical for microorganisms in the environment in which they may encounter various kinds of organic pollutants. Our study revealed that transcription of ndpASAL, ndpTB, and ndpHFEGD is negatively regulated by NdpR, and NdpR also exhibits a positive regulatory effect on PndpHFEGD. Furthermore, 2,5-dihydroxypyridine was identified as the effector molecular for NdpR and can both prevent the binding of free NdpR to the promoter and release NdpR from the promoters, which is different from previously reported NicR2. Additionally, NdpR was found to have both negative and positive transcription regulatory effects on the same target, PndpHFEGD, while only one binding site was identified, which is notably different from the previously reported TetR family regulators. Moreover, NdpR was revealed to be a global transcriptional regulator. This study provides new insight into the complex gene expression regulation of the TetR family.

Conjugation-Mediated Plasmid Transfer Enables Genetic Modification of Diverse Bacillus Species

Performing genetic manipulations in Bacillus strains is often hindered by difficulty in identifying conditions appropriate for DNA uptake. This shortcoming limits our understanding of the functional diversity within this genus and the practical application of new strains. We have developed a simple method for increasing the genetic tractability of Bacillus spp. through conjugation-mediated plasmid transfer via a diaminopimelic acid (DAP) auxotrophic Escherichia coli donor strain. We observe transfer into representatives of the Bacillus clades subtilis, cereus, galactosidilyticus, and Priestia megaterium and successfully applied this protocol to 9 out of 12 strains attempted. We utilized the BioBrick 2.0 plasmids pECE743 and pECE750, as well as the CRISPR plasmid pJOE9734.1, to generate a xylose-inducible green-fluorescent protein (GFP)-expressing conjugal vector, pEP011. The use of xylose-inducible GFP ensures ease of confirming transconjugants, which enables users to quickly rule out false positives. Additionally, our plasmid backbone offers the flexibility to be used in other contexts, including transcriptional fusions and overexpression, with only a few modifications. IMPORTANCE Bacillus species are widely used to produce proteins and to understand microbial differentiation. Unfortunately, outside a few lab strains, genetic manipulation is difficult and can prevent thorough dissection of useful phenotypes. We developed a protocol that utilizes conjugation (plasmids that initiate their own transfer) to introduce plasmids into a diverse range of Bacillus spp. This will facilitate a deeper study of wild isolates for both industrial and pure research uses.

Nutritional stress induced intraspecies competition revealed by transcriptome analysis in Sphingomonas melonis TY

Bacteria have developed various mechanisms by which they can compete or cooperate with other bacteria. This study showed that in the cocultures of wild-type Sphingomonas melonis TY and its isogenic mutant TYΔndpD grow with nicotine, the former can outcompete the latter. TYΔndpD undergoes growth arrest after four days when cocultured with wild-type TY, whereas the coculture has just entered a stationary phase and the substrate was nearly depleted, and the interaction between the two related strains was revealed by transcriptomic analysis. Analysis of the differential expression genes indicated that wild-type TY inhibited the growth of TYΔndpD mainly through toxin-antitoxin (TA) systems. The four upregulated antitoxin coding genes belong to type II TA systems in which the bactericidal effect of the cognate toxin was mainly through inhibition of translation or DNA replication, whereas wild-type TY with upregulated antitoxin genes can regenerate cognate immunity protein continuously and thus prevent the lethal action of toxin to itself. In addition, colicin-mediated antibacterial activity against closely related species may also be involved in the competition between wild-type TY and TYΔndpD under nutritional stress. Moreover, upregulation of carbon and nitrogen catabolism related-, stress response related-, DNA repair related-, and DNA replication-related genes in wild-type TY showed that it triggered a series of response mechanisms when facing dual stress of competition from isogenic mutant cells and nutritional limitation. Thus, we proposed that S. melonis TY employed the TA systems and colicin to compete with TYΔndpD under nutritional stress, thereby maximally acquiring and exploiting finite resources. KEY POINTS: • Cross-feeding between isogenic mutants and the wild-type strain. • Nutrition stress caused a shift from cooperation to competition. • TYΔndpD undergo growth arrest by exogenous and endogenous toxins.

Co-composting of fresh tobacco leaves and soil: an exploration on the utilization of fresh tobacco waste in farmland

A large amount of fresh tobacco waste with high water content are produced in farmland, and it may cause environmental pollution if it is not properly treated. The fresh tobacco waste is not easily collected and transported, resulting in its centralized treatment is expensive. This study is to clarify whether it is feasible to treat fresh tobacco wastes by co-composting of them and soil in farmland and applied the obtained compost product into the soil instead of a part of tobacco-specific fertilizer. The results showed that, compared with that in original soil, the relative abundance of Pseudomonas, Azotobacter, and Coprinus of the co-composted products increased by roughly 244%, 323%, and 675%, respectively, and effective nitrogen and available potassium increased by roughly 157% and 132%, respectively. In addition, the nicotine content in co-composted products decreased dramatically compared with the discarded tobacco leaves. The application of the co-composted products and 20% fertilizer amount (15 g/plant) (YD5) exhibited the highest relative abundance of beneficial microbial communities in the soil and the best growth of tobacco plants. The co-composting of fresh tobacco waste and soil in farmland is an effective measure to treat the fresh tobacco waste, and its products increased beneficial microorganisms and stimulate the growth of tobacco plants by replacing an amount of the fertilizer.

Bacterial seed endophyte shapes disease resistance in rice

Cereal crop production is severely affected by seed-borne bacterial diseases across the world. Locally occurring disease resistance in various crops remains elusive. Here, we have observed that rice plants of the same cultivar can be differentiated into disease-resistant and susceptible phenotypes under the same pathogen pressure. Following the identification of a seed-endophytic bacterium as the resistance-conferring agent, integration of high-throughput data, gene mutagenesis and molecular interaction assays facilitated the discovery of the underlying mode of action. Sphingomonas melonis that is accumulated and transmitted across generations in disease-resistant rice seeds confers resistance to disease-susceptible phenotypes by producing anthranilic acid. Without affecting cell growth, anthranilic acid interferes with the sigma factor RpoS of the seed-borne pathogen Burkholderia plantarii, probably leading to impairment of upstream cascades that are required for virulence factor biosynthesis. The overall findings highlight the hidden role of seed endophytes in the phytopathology paradigm of 'disease triangles', which encompass the plant, pathogens and environmental conditions. These insights are potentially exploitable for modern crop cultivation threatened by globally widespread bacterial diseases.

Physiology of a Hybrid Pathway for Nicotine Catabolism in Bacteria

Nicotine is a major N-heterocyclic aromatic alkaloid produced in tobacco plants and the main toxic chemical in tobacco waste. Due to its complex physiological effects and toxicity, it has become a concern both in terms of public health and the environment. A number of bacteria belonging to the genera Arthrobacter and Pseudomonas can degrade nicotine via the pyridine and pyrrollidine pathways. Recently, a novel hybrid of the pyridine and pyrrolidine pathways (also known as the VPP pathway) was found in the Rhizobiale group bacteria Agrobacterium tumefaciens S33, Shinella sp. HZN7 and Ochrobactrum sp. SJY1 as well as in other group bacteria. The special mosaic pathway has attracted much attention from microbiologists in terms of the study of their molecular and biochemical mechanisms. This will benefit the development of new biotechnologies in terms of the use of nicotine, the enzymes involved in its catabolism, and the microorganisms capable of degrading the alkaloid. In this pathway, some metabolites are hydroxylated in the pyridine ring or modified in the side chain with active groups, which can be used as precursors for the synthesis of some important compounds in the pharmaceutical and agricultural industries. Moreover, some enzymes may be used for industrial biocatalysis to transform pyridine derivatives into desired chemicals. Here, we review the molecular and biochemical basis of the hybrid nicotine-degrading pathway and discuss the electron transport in its oxidative degradation for energy conservation and bacterial growth.

3-Hydroxypyridine Dehydrogenase HpdA Is Encoded by a Novel Four-Component Gene Cluster and Catalyzes the First Step of 3-Hydroxypyridine Catabolism in Ensifer adhaerens HP1

3-Hydroxypyridine (3HP) is an important natural pyridine derivative. Ensifer adhaerens HP1 can utilize 3HP as its sole sources of carbon, nitrogen, and energy to grow, but the genes responsible for the degradation of 3HP remain unknown. In this study, we predicted that a gene cluster, designated 3hpd, might be responsible for the degradation of 3HP. The analysis showed that the initial hydroxylation of 3HP in E. adhaerens HP1 was catalyzed by a four-component dehydrogenase (HpdA1A2A3A4) and led to the formation of 2,5-dihydroxypyridine (2,5-DHP). In addition, the SRPBCC component in HpdA existed as a separate subunit, which is different from other SRPBCC-containing molybdohydroxylases acting on N-heterocyclic aromatic compounds. Moreover, the results demonstrated that the phosphoenolpyruvate (PEP)-utilizing protein and pyruvate-phosphate dikinase were involved in the HpdA activity, and the presence of the gene cluster 3hpd was discovered in the genomes of diverse microbial strains. Our findings provide a better understanding of the microbial degradation of pyridine derivatives in nature and indicated that further research on the origin of the discovered four-component dehydrogenase with a separate SRPBCC domain and the function of PEP-utilizing protein and pyruvate-phosphate dikinase might be of great significance.IMPORTANCE 3-Hydroxypyridine is an important building block for the synthesis of drugs, herbicides, and antibiotics. Although the microbial degradation of 3-hydroxypyridine has been studied for many years, the molecular mechanisms remain unclear. Here, we show that 3hpd is responsible for the catabolism of 3-hydroxypyridine. The 3hpd gene cluster was found to be widespread in Actinobacteria, Rubrobacteria, Thermoleophilia, and Alpha-, Beta-, and Gammaproteobacteria, and the genetic organization of the 3hpd gene clusters in these bacteria shows high diversity. Our findings provide new insight into the catabolism of 3-hydroxypyridine in bacteria.

ndpT encodes a new protein involved in nicotine catabolism by Sphingomonas melonis TY

Sphingomonas melonis TY utilizes nicotine as a sole source of carbon, nitrogen, and energy to grow. One of the genes in its ndp catabolic cluster, ndpT, encodes a hypothetical transporter. Since no transporter for nicotine has been identified in microorganisms, we investigated whether NdpT is responsible for nicotine transport. ndpT was induced by nicotine, and gene knockout and complementation studies clearly indicated that ndpT is essential for the catabolism of nicotine in strain TY. NdpT-GFP was located at the periphery of the cells, suggesting that NdpT is a membrane protein. Uptake assays with L-[¹⁴C] nicotine illustrated that nicotine uptake in strain TY is mediated by a constitutively synthesized permease with a K_m of 0.362 ± 0.07 μM and a V_max of 0.762 ± 0.068 μmol min^-1 (mg cell dry weight)^-1 and that ndpT may play a role in nicotine exclusion. Hence, we consider NdpT a nicotine catabolism-related protein.

The enzymes of microbial nicotine metabolism

Because of nicotine's toxicity and the high levels found in tobacco and in the waste from tobacco processing, there is a great deal of interest in identifying bacteria capable of degrading it. A number of microbial pathways have been identified for nicotine degradation. The first and best-understood is the pyridine pathway, best characterized for Arthrobacter nicotinovorans, in which the first reaction is hydroxylation of the pyridine ring. The pyrrolidine pathway, which begins with oxidation of a carbon-nitrogen bond in the pyrrolidine ring, was subsequently characterized in a number of pseudomonads. Most recently, a hybrid pathway has been described, which incorporates the early steps in the pyridine pathway and ends with steps in the pyrrolidine pathway. This review summarizes the present status of our understanding of these pathways, focusing on what is known about the individual enzymes involved.