Overview and Key Functions of XylR OpenAI o3-deep-research-2025-06-26 71 citations 2026-03-21T00:01:37.574511

Overview and Key Functions of XylR

XylR (UniProt P06519) is a 67-kDa transcriptional regulatory protein in Pseudomonas putida that controls the breakdown of aromatic hydrocarbons. It belongs to the NtrC family of σ^54-dependent enhancer-binding proteins (EBPs), meaning it uses an ATP-driven mechanism to activate transcription from specific promoters (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). XylR is the master regulator of the TOL plasmid pWW0 upper pathway, which governs the initial oxidative catabolism of toluene and xylenes (pmc.ncbi.nlm.nih.gov). In the presence of its effector molecules (toluene, m-xylene, p-xylene, or related aromatic analogues), XylR binds the target promoter (called Pu) and triggers expression of enzymes that convert those aromatics into benzoate derivatives (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This allows P. putida to grow on toluene and xylenes as carbon sources, making XylR a pivotal factor in the bacterium’s ability to degrade environmental pollutants (pmc.ncbi.nlm.nih.gov). Notably, XylR requires both the protein and the inducer to be present for activation – effectively implementing an AND-gate logic for pathway induction (pmc.ncbi.nlm.nih.gov). This tight control prevents unnecessary expression of catabolic genes in the absence of substrate. XylR also positively regulates the xylS gene (from the Pu-related promoter Ps1) when aromatics are present, linking the “upper” pathway to the “meta” pathway for complete mineralization of the compounds (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). In summary, XylR’s primary biological role is to sense aromatic solvents and activate a transcriptional program for their metabolism, a function central to P. putida’s biodegradation and environmental adaptability (pmc.ncbi.nlm.nih.gov).

Mechanism and Structure of XylR

Domain Architecture: XylR is a multi-domain protein with a modular design common to σ^54 EBPs. It contains: (1) an N-terminal regulatory domain (also called the A domain) that serves as an effector-binding sensor, (2) a central AAA+ ATPase domain responsible for oligomerization and energy coupling, and (3) a C-terminal DNA-binding domain with a helix-turn-helix motif for binding upstream activation sequences on DNA (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). The N-terminal sensor of XylR belongs to the “V4R” (vinyl-4-reductase) family of ligand-binding domains and specifically recognizes small aromatic compounds (pmc.ncbi.nlm.nih.gov). Binding of toluene or m-/p-xylene at this domain induces a conformational change that relieves an intramolecular repression* on the central ATPase domain (pubmed.ncbi.nlm.nih.gov). In the absence of effectors, the A-domain maintains XylR in an inactive state by contacting and occluding surfaces of the catalytic domain (pubmed.ncbi.nlm.nih.gov). Once an aromatic effector is bound, the N-terminal domain releases its “brake” on the central domain (pubmed.ncbi.nlm.nih.gov), allowing XylR subunits to assemble into an active oligomer.

Activator Complex and σ^54 Interaction: Active XylR functions as a hexameric ring (typical of AAA+ EBPs) that binds to enhancer sites on the DNA and stimulates transcription initiation (pmc.ncbi.nlm.nih.gov). XylR binds specific upstream activation sequences (UAS) located ~150 bp upstream of the σ^54-dependent Pu promoter (pubmed.ncbi.nlm.nih.gov). There are two such UAS sites (proximal and distal), and XylR often binds as dimers to these sites. Upon effector activation, multiple DNA-bound XylR dimers oligomerize into a hexamer, forming a DNA-looped complex (often facilitated by the DNA-bending protein IHF in P. putida) (pubmed.ncbi.nlm.nih.gov). The XylR hexamer then uses energy from ATP hydrolysis to interact with the σ^54–RNA polymerase holoenzyme positioned at the Pu promoter (pmc.ncbi.nlm.nih.gov). A conserved amino acid motif (e.g. GAFTGA loop in the AAA+ domain) makes contact with σ^54, helping to remodel the closed promoter complex into an open transcriptionally active complex (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Through this ATP-dependent mechanism, XylR effectively unlocks the promoter, enabling RNA polymerase to initiate transcription of the downstream catabolic genes.

Experimental evidence: Mutational studies strongly support this mechanism. For example, deletion of XylR’s N-terminal domain produces a constitutively active protein that can activate Pu even without any aromatic inducer (pubmed.ncbi.nlm.nih.gov). Point mutations in the inter-domain linker (e.g. introducing a proline kink) also yield “semi-constitutive” XylR variants, mimicking the effect of inducer binding by destabilizing the repressive interaction between domains (pubmed.ncbi.nlm.nih.gov) (pubmed.ncbi.nlm.nih.gov). Conversely, mutations in the ATP-binding motifs of the AAA+ domain (e.g. Walker motifs) abolish XylR’s ability to hydrolyze ATP and activate transcription (pmc.ncbi.nlm.nih.gov). These findings confirm that (1) the N-terminal domain normally imposes autoinhibition, and (2) ATP-driven hexamerization is essential for XylR’s transcriptional activation function.

Subcellular localization: XylR carries out its function in the bacterial cytoplasm, specifically associated with the nucleoid DNA where its target promoters reside. As a DNA-binding transcription factor, XylR is not membrane-bound or secreted; it diffuses in the cytosol and binds to the TOL plasmid’s Pu promoter region when activated. Recent single-cell studies of P. putida revealed that after XylR activates transcription, the resulting xyl mRNAs form distinct foci in the cytoplasm, co-localizing with ribosome-rich regions away from the nucleoid (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This suggests that transcription of XylR-regulated genes occurs at the nucleoid, but the transcripts quickly relocate to translation zones in the cell. Such spatial organization may enhance efficient translation of the catabolic enzymes, although XylR itself remains DNA-bound only transiently during activation cycles (pubmed.ncbi.nlm.nih.gov). In sum, XylR operates within the cell’s interior, bridging the genomic DNA (plasmid promoter) and the transcriptional machinery in an ATP-dependent manner, with tightly controlled timing and localization.

Regulation of XylR Expression and Activity

Autoregulation: The xylR gene is part of a divergently transcribed regulatory region together with xylS. XylR regulates its own expression by negative feedback. It binds to its own promoter region to repress transcription of xylR, maintaining relatively constant XylR protein levels whether inducer is present or not (pmc.ncbi.nlm.nih.gov). This autoregulatory loop prevents excessive accumulation of XylR. Interestingly, studies have shown that XylR levels change very little upon addition of m-xylene (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). By keeping itself at a steady concentration, XylR ensures a swift and proportionate response to inducers without runaway expression. At the same time, XylR’s divergent neighbor xylS has a σ^54-dependent promoter (Ps1) that XylR activates in the presence of aromatic effectors (pmc.ncbi.nlm.nih.gov). Thus, when XylR is induced by toluene/xylenes, it not only turns on the catabolic enzymes but also boosts xylS output (which in turn will activate the downstream meta-cleavage enzymes). This forms a feed-forward cascade: XylR → xylS → meta-operon, tightly coordinating the two stages of toluene/xylene degradation (pmc.ncbi.nlm.nih.gov). Notably, XylR’s binding sites for self-repression and for xylS activation overlap in the intergenic region, and XylR can simultaneously repress its own promoter while activating xylS under inducing conditions (pmc.ncbi.nlm.nih.gov). This elegant arrangement guarantees that XylR is present in sufficient amount but not overproduced, and that xylS (and thus the lower pathway) is induced only when the upper pathway has been triggered.

Global and physiological regulation: Beyond its own promoter, XylR activity is modulated by global carbon availability and other host factors. P. putida employs a catabolite repression-like mechanism involving the Crc protein, which post-transcriptionally inhibits XylR production when preferred carbon sources are abundant (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Specifically, Crc (together with a small RNA) can bind the xylR mRNA, blocking its translation under nutrient-rich conditions (pmc.ncbi.nlm.nih.gov). This means that if easily metabolizable substrates (e.g. succinate or glucose) are present, the cell suppresses XylR synthesis, thereby preventing unwarranted expression of toluene/xylene degradation genes. Once the preferred carbon is depleted and an aromatic pollutant is the main carbon source, Crc-mediated repression lifts and XylR protein accumulates to activate the Pu pathway. In addition to Crc, several other global regulators and environmental signals feed into the XylR/Pu system. For example, the DNA-bending protein IHF (Integration Host Factor) binds near the Pu promoter and can affect XylR’s ability to initiate transcription, especially in stationary phase cells (pubmed.ncbi.nlm.nih.gov). Alternative sigma factors (σ^70, σ^38 for stationary phase, etc.) and alarmone signaling (ppGpp) also indirectly influence the Pu promoter’s responsiveness (pmc.ncbi.nlm.nih.gov). However, under standard inducing conditions (e.g. minimal media with m-xylene as sole carbon), these host factors are tuned such that XylR-Pu operates at optimal capacity (pmc.ncbi.nlm.nih.gov). Experimental evidence underscores some of these controls: for instance, by growing cells in defined medium without amino acids (removing catabolite repression), one can derepress xylR translation and observe a stronger Pu induction response (pmc.ncbi.nlm.nih.gov). In summary, P. putida tightly regulates XylR at multiple levels – DNA (autogenous repression), RNA (Crc-mediated translational control), and protein activity (effector binding requirement and possibly protein–protein interactions) – to integrate the presence of aromatic compounds with the cell’s nutritional status and stress conditions.

Biotechnological Applications and Recent Developments

Biodegradation and environmental impact: XylR plays a crucial role in bioremediation of toxic aromatic pollutants. The TOL plasmid systems endowed with XylR allow Pseudomonas putida to consume compounds like toluene, xylenes, and benzene (collectively part of BTEX contaminants) in soil and water environments (pmc.ncbi.nlm.nih.gov). Because XylR ensures that catabolic enzymes are produced only in the presence of the target pollutants, it makes P. putida an efficient and safe biodegradation agent – energy is not wasted expressing these pathways unless the pollutant is present. The significance of XylR is highlighted by the fact that it has become a model system for aromatic hydrocarbon sensing in bacteria (pmc.ncbi.nlm.nih.gov). Assinder and Williams (1990) noted that mutants lacking functional XylR cannot grow on toluene or m-xylene, underscoring that XylR is essential for activating the upstream pathways that funnel these compounds into central metabolism (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). In natural settings, XylR-regulated pathways contribute to the natural attenuation of oil-derived pollutants.

Synthetic biology and biosensors: The highly specific yet inducible nature of XylR has been leveraged to create biosensors for environmental monitoring. Researchers have used XylR and the Pu promoter as a basis for detecting aromatic compounds (the presence of an analyte triggers reporter gene expression via XylR). Notably, XylR’s innate ligand range is quite broad – it responds not only to toluene and xylenes but also to a “surprising variety of structural analogs,” including other alkylbenzenes (pmc.ncbi.nlm.nih.gov). This versatility was exploited to construct biosensors for BTEX compounds (benzene, toluene, ethylbenzene, xylene), which are common groundwater contaminants from petroleum (pmc.ncbi.nlm.nih.gov). Biosensor strains or devices using XylR can thus light up (for example, produce fluorescence) in the presence of these pollutants, enabling detection of contamination in situ (pmc.ncbi.nlm.nih.gov). Moreover, P. putida harboring the XylR circuit has been tested in field settings to report on soil pollutant levels (pmc.ncbi.nlm.nih.gov).

Researchers have also engineered XylR for expanded or altered specificity. For instance, de Lorenzo’s group created XylR mutants that can sense nitroaromatic compounds (such as 2,4-dinitrotoluene, a component of TNT) which are not natural effectors of wild-type XylR (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). One exciting application of this was the development of bacterial sensors for landmines: an XylR variant was designed to detect trace nitrotoluene leaching from buried explosives, triggering a visible reporter as a “landmine detector” (pmc.ncbi.nlm.nih.gov). This showcases the adaptability of XylR’s sensing domain – a few amino acid changes can retarget it to new chemicals. Additionally, synthetic circuit design has combined XylR with logic gates to create more complex regulatory behaviors. By rewiring XylR production or coupling it with other signals, researchers achieved Boolean logic operations in Pseudomonas: for example, XylR-based circuits that require two conditions to be met (multi-input AND gates) or that display enhanced specificity to one aromatic over similar compounds (pmc.ncbi.nlm.nih.gov). One study generated XylR mutants with reduced promiscuity, so that the sensor would respond to a specific pollutant without cross-reacting to others, thereby “overcoming the natural promiscuity of XylR” (pmc.ncbi.nlm.nih.gov). These advances, including rational protein engineering and domain shuffling, have made XylR a versatile platform for biosensor development (pmc.ncbi.nlm.nih.gov). As of 2023, XylR remains of interest not only for its classic role in biodegradation but also as a template for designing custom microbial regulators in environmental biotechnology.

Current research directions: The XylR/Pu regulatory module continues to be studied as a paradigm of complex gene regulation. Modern systems biology approaches have modeled the TOL network as a metabolic amplifier circuit, describing how XylR and XylS create a robust two-tier response that optimizes m-xylene degradation (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Advanced microscopy has provided new insight into the spatial dynamics of XylR-regulated gene expression, revealing that transcripts from XylR-activated operons are not randomly distributed but rather concentrate at specific cytoplasmic foci for efficient translation (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). There is also interest in structural biology of XylR: while no full crystal structure is available yet (due to the difficulty of such large, flexible proteins), computational modeling of XylR’s N-terminal domain has been performed to understand how aromatic effectors bind and cause allosteric changes (pmc.ncbi.nlm.nih.gov). Comparisons with its close homolog DmpR (which shares ~65% identity) are helping to pinpoint the amino acid differences that determine ligand specificity (pmc.ncbi.nlm.nih.gov). Together, these efforts contribute to a current understanding of XylR as not just a singular protein, but as part of an integrated network that senses the environment, regulates a catabolic pathway, and interfaces with the cell’s physiology. Given its importance in pollution degradation and its amenability to engineering, XylR is likely to remain a focus of both fundamental and applied research, bridging microbiology, ecology, and synthetic biology.

References:

Citations

  1. AnnotationURLCitation(end_index=482, start_index=362, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=XylR%20%20,76%20%2C%20%2064%2C%20162')
  2. AnnotationURLCitation(end_index=661, start_index=483, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=Summary%3A%20Bacterial%20enhancer%20binding%20proteins,of%20the%20central%20catalytic%20domain')
  3. AnnotationURLCitation(end_index=927, start_index=807, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=XylR%20%20,76%20%2C%20%2064%2C%20162')
  4. AnnotationURLCitation(end_index=1341, start_index=1174, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=expression%20of%20the%20dmp%20operon%2C,on%20toluene%20and%20related%20hydrocarbons')
  5. AnnotationURLCitation(end_index=1481, start_index=1342, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=substrate%20is%20available%20,This%20factor%20has%20the')
  6. AnnotationURLCitation(end_index=1820, start_index=1653, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=expression%20of%20the%20dmp%20operon%2C,on%20toluene%20and%20related%20hydrocarbons')
  7. AnnotationURLCitation(end_index=2133, start_index=1980, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=As%20shown%20in%20Figure%201,Unlike%20Pu%2C%20however%2C%20a%20second')
  8. AnnotationURLCitation(end_index=2592, start_index=2439, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=As%20shown%20in%20Figure%201,Unlike%20Pu%2C%20however%2C%20a%20second')
  9. AnnotationURLCitation(end_index=2737, start_index=2593, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=two%20series%20of%20biotransformations,or%20in%20combination')
  10. AnnotationURLCitation(end_index=3095, start_index=2959, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=Several%20NtrC,was%20also%20engineered%20to%20detect')
  11. AnnotationURLCitation(end_index=3702, start_index=3582, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=XylR%20%20,76%20%2C%20%2064%2C%20162')
  12. AnnotationURLCitation(end_index=3818, start_index=3703, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=XylR%20%20,76%2C%20161%2C%20162')
  13. AnnotationURLCitation(end_index=4114, start_index=3977, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=Other%20%CF%83,XylR%20and%20DmpR%20proteins%20confirm')
  14. AnnotationURLCitation(end_index=4425, start_index=4276, title='Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/7565083/#:~:text=in%20a%20hybrid%20protein%20still,located%20at%20the%20central%20domain')
  15. AnnotationURLCitation(end_index=4694, start_index=4566, title='Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/7565083/#:~:text=the%20signal,located%20at%20the%20central%20domain')
  16. AnnotationURLCitation(end_index=4946, start_index=4797, title='Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/7565083/#:~:text=in%20a%20hybrid%20protein%20still,located%20at%20the%20central%20domain')
  17. AnnotationURLCitation(end_index=5387, start_index=5209, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=Summary%3A%20Bacterial%20enhancer%20binding%20proteins,of%20the%20central%20catalytic%20domain')
  18. AnnotationURLCitation(end_index=5678, start_index=5508, title='Transient XylR binding to the UAS of the Pseudomonas putida sigma54 promoter Pu revealed with high intensity UV footprinting in vivo - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/14627825/#:~:text=The%20binding%20of%20the%20transcriptional,vivo%20genomic%20footprinting%20procedure%20that')
  19. AnnotationURLCitation(end_index=6082, start_index=5959, title='Transient XylR binding to the UAS of the Pseudomonas putida sigma54 promoter Pu revealed with high intensity UV footprinting in vivo - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/14627825/#:~:text=XylR%20protein%20is%20not%20permanently,Only')
  20. AnnotationURLCitation(end_index=6398, start_index=6220, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=Summary%3A%20Bacterial%20enhancer%20binding%20proteins,of%20the%20central%20catalytic%20domain')
  21. AnnotationURLCitation(end_index=6754, start_index=6600, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=activators%20that%20assemble%20as%20hexameric,54%7D%20for%20remodeling')
  22. AnnotationURLCitation(end_index=6922, start_index=6755, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=expression%20of%20the%20dmp%20operon%2C,on%20toluene%20and%20related%20hydrocarbons')
  23. AnnotationURLCitation(end_index=7440, start_index=7316, title='Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/7565083/#:~:text=inducers,the%20release%20of%20the%20repression')
  24. AnnotationURLCitation(end_index=7822, start_index=7665, title='Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/7565083/#:~:text=regulatory%20protein%20XylR%2C%20of%20the,of%20the%20protein%20stimulated%20the')
  25. AnnotationURLCitation(end_index=7949, start_index=7823, title='Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/7565083/#:~:text=between%20the%20N,extent%20in%20vivo%20as%20XylR')
  26. AnnotationURLCitation(end_index=8275, start_index=8117, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=match%20at%20L473%20XylR%2C%20the,mutagenesis%20of%20the%20key%20aspartate')
  27. AnnotationURLCitation(end_index=9177, start_index=9026, title='Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC8545136/#:~:text=flow%20remains%20unknown,based%20system%2C%20which%20likewise%20led')
  28. AnnotationURLCitation(end_index=9342, start_index=9178, title='Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC8545136/#:~:text=signals%20stemming%20from%20xylUW%20or,were%20separately%20recorded%20with%20the')
  29. AnnotationURLCitation(end_index=9786, start_index=9663, title='Transient XylR binding to the UAS of the Pseudomonas putida sigma54 promoter Pu revealed with high intensity UV footprinting in vivo - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/14627825/#:~:text=XylR%20protein%20is%20not%20permanently,Only')
  30. AnnotationURLCitation(end_index=10502, start_index=10372, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=the%20mechanism%20for%20regulation%20of,xylene')
  31. AnnotationURLCitation(end_index=10774, start_index=10666, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=the%20XylR%20auto,xylene')
  32. AnnotationURLCitation(end_index=10905, start_index=10775, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=the%20mechanism%20for%20regulation%20of,xylene')
  33. AnnotationURLCitation(end_index=11337, start_index=11185, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=inputs%20are%20strictly%20necessary%20to,XylS%20bound%20to%203%20MBz')
  34. AnnotationURLCitation(end_index=11805, start_index=11661, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=two%20series%20of%20biotransformations,or%20in%20combination')
  35. AnnotationURLCitation(end_index=12150, start_index=12020, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=the%20mechanism%20for%20regulation%20of,xylene')
  36. AnnotationURLCitation(end_index=12811, start_index=12691, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=global%20regulators%20,27%20%2C%2036')
  37. AnnotationURLCitation(end_index=12965, start_index=12812, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=physiological%20conditions%2C%20these%20default%20connections,35%2C28')
  38. AnnotationURLCitation(end_index=13248, start_index=13095, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=physiological%20conditions%2C%20these%20default%20connections,35%2C28')
  39. AnnotationURLCitation(end_index=14058, start_index=13935, title='Transient XylR binding to the UAS of the Pseudomonas putida sigma54 promoter Pu revealed with high intensity UV footprinting in vivo - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/14627825/#:~:text=XylR%20protein%20is%20not%20permanently,Only')
  40. AnnotationURLCitation(end_index=14346, start_index=14216, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=,acids%20and%20other%20repressive%20substrates')
  41. AnnotationURLCitation(end_index=14672, start_index=14519, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=physiological%20conditions%2C%20these%20default%20connections,35%2C28')
  42. AnnotationURLCitation(end_index=15070, start_index=14917, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=physiological%20conditions%2C%20these%20default%20connections,35%2C28')
  43. AnnotationURLCitation(end_index=15924, start_index=15788, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=Several%20NtrC,was%20also%20engineered%20to%20detect')
  44. AnnotationURLCitation(end_index=16447, start_index=16311, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=Several%20NtrC,was%20also%20engineered%20to%20detect')
  45. AnnotationURLCitation(end_index=16824, start_index=16684, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=by%20this%20bacterium%20as%20a,This%20factor%20has%20the')
  46. AnnotationURLCitation(end_index=16992, start_index=16825, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=expression%20of%20the%20dmp%20operon%2C,on%20toluene%20and%20related%20hydrocarbons')
  47. AnnotationURLCitation(end_index=17752, start_index=17616, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=Several%20NtrC,was%20also%20engineered%20to%20detect')
  48. AnnotationURLCitation(end_index=18070, start_index=17931, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=toluene%20and%20m,Heras%20and%20de%20Lorenzo%2C%202011a')
  49. AnnotationURLCitation(end_index=18386, start_index=18247, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=toluene%20and%20m,Heras%20and%20de%20Lorenzo%2C%202011a')
  50. AnnotationURLCitation(end_index=18645, start_index=18506, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=toluene%20and%20m,Heras%20and%20de%20Lorenzo%2C%202011a')
  51. AnnotationURLCitation(end_index=19050, start_index=18921, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=,the%20implementation%20of%20simple%20Boolean')
  52. AnnotationURLCitation(end_index=19183, start_index=19051, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=,attractive%20TF%20for%20biosensor%20development')
  53. AnnotationURLCitation(end_index=19550, start_index=19420, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=oil%20industry,turned%20XylR%20into%20a%20most')
  54. AnnotationURLCitation(end_index=20229, start_index=20097, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=,attractive%20TF%20for%20biosensor%20development')
  55. AnnotationURLCitation(end_index=20588, start_index=20434, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=%28Garmendia%20et%20al,attractive%20TF%20for%20biosensor%20development')
  56. AnnotationURLCitation(end_index=20865, start_index=20733, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=,attractive%20TF%20for%20biosensor%20development')
  57. AnnotationURLCitation(end_index=21515, start_index=21383, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=metabolic%20amplifier%20motif%20%28MAM%29,xylene')
  58. AnnotationURLCitation(end_index=21663, start_index=21516, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=As%20shown%20in%20Figure%201,low%20amount%20of%20XylS%20protein')
  59. AnnotationURLCitation(end_index=22084, start_index=21933, title='Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC8545136/#:~:text=flow%20remains%20unknown,based%20system%2C%20which%20likewise%20led')
  60. AnnotationURLCitation(end_index=22249, start_index=22085, title='Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC8545136/#:~:text=signals%20stemming%20from%20xylUW%20or,were%20separately%20recorded%20with%20the')
  61. AnnotationURLCitation(end_index=22747, start_index=22557, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=action%20of%20aromatic%20effectors%20on,2920.2002.00265.x%20%5BDOI%5D%20%5BPubMed%5D%20%5BGoogle%20Scholar')
  62. AnnotationURLCitation(end_index=23006, start_index=22903, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=Another%20NtrC,2000')
  63. AnnotationURLCitation(end_index=23714, start_index=23591, title='Transient XylR binding to the UAS of the Pseudomonas putida sigma54 promoter Pu revealed with high intensity UV footprinting in vivo - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/14627825/#:~:text=XylR%20protein%20is%20not%20permanently,Only')
  64. AnnotationURLCitation(end_index=23978, start_index=23850, title='Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/7565083/#:~:text=the%20signal,located%20at%20the%20central%20domain')
  65. AnnotationURLCitation(end_index=24229, start_index=24076, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=As%20shown%20in%20Figure%201,Unlike%20Pu%2C%20however%2C%20a%20second')
  66. AnnotationURLCitation(end_index=24380, start_index=24230, title='The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3253710/#:~:text=substrate%20is%20available%20,promoter%20Pm%20either%20by%20itself')
  67. AnnotationURLCitation(end_index=24617, start_index=24497, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=XylR%20%20,76%20%2C%20%2064%2C%20162')
  68. AnnotationURLCitation(end_index=24785, start_index=24618, title='The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC3429621/#:~:text=expression%20of%20the%20dmp%20operon%2C,on%20toluene%20and%20related%20hydrocarbons')
  69. AnnotationURLCitation(end_index=25025, start_index=24874, title='Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC8545136/#:~:text=flow%20remains%20unknown,based%20system%2C%20which%20likewise%20led')
  70. AnnotationURLCitation(end_index=25266, start_index=25130, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=Several%20NtrC,was%20also%20engineered%20to%20detect')
  71. AnnotationURLCitation(end_index=25399, start_index=25267, title='Transcription factor-based biosensors enlightened by the analyte - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC4486848/#:~:text=,attractive%20TF%20for%20biosensor%20development')