The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Target verified. The UniProt accession Q88GC8 corresponds to pvdA / PP_3796 from Pseudomonas putida strain KT2440 and is functionally described as an L-ornithine N5-monooxygenase (ornithine hydroxylase), consistent with the pyoverdine (PVD) biosynthesis gene naming used across fluorescent pseudomonads. In the pyoverdine literature, pvdA is consistently used for the enzyme that produces N5-hydroxyornithine, a hydroxamate precursor required for the pyoverdine peptide backbone. (dell’anno2022novelinsightson pages 8-9, rice2010characterizationofan pages 24-27, barrientosmoreno2019argininebiosynthesismodulates pages 8-10)
Key terms.
- Pyoverdine (PVD): a high-affinity siderophore produced by many Pseudomonas spp. to chelate Fe(III) under iron limitation; pyoverdines are nonribosomal peptides with a conserved chromophore and strain-specific peptide backbone. (dell’anno2022novelinsightson pages 4-8)
- N-hydroxylating monooxygenase (NMO): a flavin-dependent enzyme subclass that hydroxylates amine nitrogens (here, L-ornithine N5), often in siderophore biosynthesis. (chocklett2009biochemicalcharacterizationof pages 20-25, rice2010characterizationofan pages 37-42)
pvdA encodes the enzyme catalyzing the N5-hydroxylation of L-ornithine to produce N5-hydroxyornithine, which is subsequently formylated by PvdF to yield N5-formyl-N5-hydroxyornithine (L-fOHOrn). This modified amino acid is incorporated by NRPS enzymes into the pyoverdine peptide backbone, contributing hydroxamate ligands used for iron binding. (schalk2025bacterialsiderophoresdiversity pages 4-7, dell’anno2022novelinsightson pages 8-9, rice2010characterizationofan pages 24-27)
PvdA belongs to the flavin-dependent N-hydroxylating monooxygenase / Class B flavin monooxygenase family. Mechanistic work on this enzyme family indicates:
- dependence on FAD as a flavin cofactor and molecular oxygen as the oxygen donor, proceeding through C4a-peroxy/hydroperoxyflavin intermediates that effect oxygen transfer to the substrate amine; (chocklett2009biochemicalcharacterizationof pages 20-25, rice2010characterizationofan pages 37-42)
- use of a reducing cofactor (typically NADPH) to reduce FAD during the reductive half reaction, consistent with Class B monooxygenase behavior; (rice2010characterizationofan pages 37-42)
- bacterial PvdA-family enzymes can be partially flavin-deficient after purification, with activity restored by adding exogenous FAD in assays (a practical point for biochemical reconstitution). (chocklett2009biochemicalcharacterizationof pages 20-25)
A kinetic/mechanistic observation for PvdA highlighted in recent syntheses is that substrate binding triggers O2 addition but not flavin reduction, consistent with gating of the oxidative half-reaction by L-ornithine binding (mechanistic specialization among NMOs). (manko2024pvdlorchestratesthe pages 13-14, schalk2025bacterialsiderophoresdiversity pages 23-27)
Evidence limitations for the exact KT2440 protein. In the retrieved corpus, direct kinetic constants (kcat, KM) for P. putida KT2440 PvdA (Q88GC8) were not found; mechanistic inferences rely chiefly on biochemical characterization of close homologs (notably P. aeruginosa PvdA) and broader NMO family evidence. (chocklett2009biochemicalcharacterizationof pages 20-25, schalk2025bacterialsiderophoresdiversity pages 23-27, rice2010characterizationofan pages 37-42)
Pyoverdine biosynthesis initiates in the cytoplasm with assembly of a precursor (often described in the literature as ferribactin-like intermediates) by large nonribosomal peptide synthetases (NRPSs) together with accessory tailoring enzymes; later steps include periplasmic maturation and secretion. Within this framework, PvdA supplies a specialized building block needed for NRPS assembly. (manko2024pvdlorchestratesthe pages 1-2, dell’anno2022novelinsightson pages 8-9, dell’anno2022novelinsightson pages 9-11)
A major recent conceptual development is the view that pyoverdine biosynthesis enzymes are organized in multi-enzyme assemblies. In P. aeruginosa (the best-studied system), in-cell interaction and microscopy approaches support that:
- PvdA physically interacts with all four pyoverdine NRPSs; and
- components can associate with membrane-linked supramolecular biosynthetic machineries (“siderosomes”), although complete in vitro reconstitution/isolation remains challenging. (manko2024pvdlorchestratesthe pages 1-2, schalk2025bacterialsiderophoresdiversity pages 4-7)
These spatial/organizational findings are important for functional annotation because they imply PvdA acts not as a freely diffusing enzyme only, but as a participant in a coordinated biosynthetic system with metabolite channeling or spatial coupling to downstream steps. (schalk2025bacterialsiderophoresdiversity pages 4-7, manko2024pvdlorchestratesthe pages 1-2)
The pyoverdine system is fundamentally an iron starvation response, often governed by Fur-mediated control and iron-responsive sigma-factor networks in pseudomonads (reviewed broadly for the pvd regulon). (rice2010characterizationofan pages 24-27)
In P. putida KT2440, genetic perturbations in arginine biosynthesis (ΔargG, ΔargH) demonstrated that pyoverdine production/secretion can be decoupled from structural gene transcription:
- pvdA and pvdD expression increased in these mutants, while pvdE (an inner-membrane transporter needed for immature pyoverdine handling) decreased, consistent with impaired maturation/export rather than simple failure to induce biosynthesis; (barrientosmoreno2019argininebiosynthesismodulates pages 8-10)
- figure-level evidence shows these transcriptional trends (qRT-PCR) and accompanying phenotypes, including altered pyoverdine distribution. (barrientosmoreno2019argininebiosynthesismodulates media 53ef4128)
These mutants showed reduced extracellular pyoverdine with intracellular retention and increased oxidative stress (CellROX readout), supporting a model in which iron capture, intracellular siderophore handling, and oxidative stress defenses are functionally intertwined. (barrientosmoreno2019argininebiosynthesismodulates pages 8-10, barrientosmoreno2019argininebiosynthesismodulates media 79b5b256, barrientosmoreno2019argininebiosynthesismodulates media 12115201)
A key KT2440-specific, recent implementation-level insight is that pyoverdine-mediated iron acquisition depends on a network of overlapping tripartite efflux systems.
Core secretion systems and ParXY as an additional contributor (Stein et al., 2023-12; Microbiology Spectrum). Pyoverdine in P. putida KT2440 is secreted primarily via PvdRT–OpmQ and MdtABC–OpmB, and Stein et al. showed the RND efflux system ParXY affects siderophore secretion and growth under iron limitation. (stein2023therndefflux pages 1-2, stein2023therndefflux pages 10-13)
Quantitative data from Stein et al. 2023 (selected):
- Under strong iron limitation, adding parX deletion to the double-secretion mutant background (ΔpvdRT-opmQ ΔmdtA; “Δpm”) produced a major additional growth defect: AUC of ΔpmΔparX ≈ 40% of Δpm, while a pyoverdine non-producer was ~2% of Δpm (indicating pyoverdine-dependent growth is severely compromised). (stein2023therndefflux pages 2-5)
- Rescue experiments supported iron-specific causality: 1 µM FeCl3 restored growth of ΔpmΔparX to Δpm levels, and 10 µM pyoverdine gave the best rescue; 1 µM CuSO4 did not rescue. (stein2023therndefflux pages 8-10)
- Regulatory readouts: a parXY promoter-lux fusion showed iron responsiveness—10 µM FeCl3 reduced luminescence ~7-fold, while 1 mM bipyridyl increased luminescence ~2-fold, indicating induction under iron limitation. (stein2023therndefflux pages 8-10)
- Deletion of parX caused approximately twofold reduced expression of both mdtABC-opmB and pvdL (a pyoverdine NRPS gene), consistent with coupling between efflux capacity and biosynthetic program. (stein2023therndefflux pages 10-13)
These data demonstrate that even though pvdA is a biosynthetic gene, its pathway output (pyoverdine availability for iron uptake) is strongly shaped by export/recycling capacity, which in turn impacts growth under iron scarcity—a key ecological and applied phenotype for KT2440 as an environmental bacterium. (stein2023therndefflux pages 2-5, stein2023therndefflux pages 8-10)
Single-molecule microscopy and interaction-focused approaches described in 2024 work on P. aeruginosa reinforce the emerging model of organized biosynthetic machineries and place PvdA among enzymes that interact with NRPSs in vivo. While not KT2440-specific, these studies are influential for the “current understanding” of how PvdA functions in cells beyond its catalytic activity. (manko2024pvdlorchestratesthe pages 1-2)
A 2024 study identified a two-component system (BfmRS) in P. aeruginosa that regulates siderophore gene clusters under osmotic stress and reported conservation and promoter binding by BfmR homologs from Pseudomonas species including P. putida KT2440, suggesting a conserved regulatory logic linking environmental stress to siderophore gene expression (including pvd clusters). ()
The 2023 KT2440 work emphasizes “overlapping activities” and partial functional redundancy among tripartite efflux systems for siderophore secretion—an important practical constraint when attempting to inhibit secretion (e.g., antimicrobial adjuvants) or engineer pyoverdine flux in biotechnology. (stein2023therndefflux pages 1-2, stein2023therndefflux pages 10-13)
Recent reviews highlight pyoverdines as multifunctional molecules beyond iron uptake, with relevance to biofilms, microbial interactions, and biotechnology. (schalk2025bacterialsiderophoresdiversity pages 23-27, dell’anno2022novelinsightson pages 8-9)
Biotechnological and translational relevance of the pvdA step. Because PvdA contributes to generating hydroxamate-containing residues critical for metal binding, it is a plausible control point for:
- metabolic/synthetic biology engineering of siderophore pathways (tuning iron acquisition, metal-binding specificity, or production yields); and
- anti-virulence strategies in pathogenic pseudomonads by blocking siderophore biosynthesis (PvdA-family NMOs are commonly cited as key enzymes in this logic). (schalk2025bacterialsiderophoresdiversity pages 23-27, chocklett2009biochemicalcharacterizationof pages 20-25, rice2010characterizationofan pages 24-27)
Expert perspective on system-level constraints. Authoritative synthesis emphasizes that siderophore function in vivo depends on not only biosynthesis but also membrane trafficking, periplasmic maturation, and secretion/recycling systems; thus, interpreting “pvdA function” in real-world settings (soil, host-associated environments, engineered bioprocesses) requires integrating catalysis with cellular organization and export networks. (schalk2025bacterialsiderophoresdiversity pages 4-7, dell’anno2022novelinsightson pages 9-11, stein2023therndefflux pages 8-10)
The following table consolidates the functional annotation, pathway placement, regulation, phenotypes, and recent developments for P. putida KT2440 pvdA (Q88GC8).
| Category | Key points | Best supporting sources (with year and DOI/URL where available) |
|---|---|---|
| Identity | Target verified: UniProt Q88GC8 in Pseudomonas putida KT2440 corresponds to pvdA / PP_3796, an L-ornithine N5-monooxygenase (ornithine hydroxylase) in pyoverdine biosynthesis; this matches the UniProt description and the broader Pseudomonas pyoverdine literature. P. putida studies treat pvdA as a pyoverdine structural gene, while foundational biochemical characterization is mainly from the close homolog in P. aeruginosa. (rice2010characterizationofan pages 24-27, barrientosmoreno2019argininebiosynthesismodulates pages 8-10) | Barrientos-Moreno et al., 2019, J Bacteriol; DOI: https://doi.org/10.1128/jb.00454-19. Rice, 2010 (primary characterization thesis/article excerpt). |
| Reaction | Primary function: catalyzes N5-hydroxylation of L-ornithine to make N5-hydroxyornithine, which is then formylated by PvdF to produce L-fOHOrn for incorporation into the pyoverdine peptide backbone. This is an early, committed tailoring step in pyoverdine assembly. (schalk2025bacterialsiderophoresdiversity pages 4-7, dell’anno2022novelinsightson pages 8-9, rice2010characterizationofan pages 24-27) | Dell’Anno et al., 2022, DOI: https://doi.org/10.3390/ijms231911507. Schalk, 2025, DOI: https://doi.org/10.1038/s41579-024-01090-6. |
| Cofactors & mechanism | PvdA belongs to the flavin-dependent N-hydroxylating monooxygenase / Class B FMO family. Mechanistic evidence from Pseudomonas and related homologs indicates use of FAD, molecular oxygen, and typically NADPH as reductant; catalysis proceeds through a C4a-hydroperoxyflavin intermediate. Purified bacterial NMOs can require exogenous FAD because recombinant proteins may be partially flavin-deficient. A kinetic study cited in recent reviews reports that in PvdA, substrate binding triggers O2 addition but not flavin reduction. (chocklett2009biochemicalcharacterizationof pages 20-25, manko2024pvdlorchestratesthe pages 13-14, schalk2025bacterialsiderophoresdiversity pages 23-27, rice2010characterizationofan pages 37-42) | Chocklett, 2009 (mechanistic NMO background). Rice, 2010 (PvdA characterization excerpt). Schalk, 2025, DOI: https://doi.org/10.1038/s41579-024-01090-6. |
| Pathway role | PvdA functions in the cytoplasmic phase of pyoverdine siderophore biosynthesis, supplying a modified amino acid building block needed by the NRPS assembly line. Pyoverdine is the major/specific siderophore used by fluorescent pseudomonads for high-affinity Fe(III) acquisition; the mature siderophore has extremely high ferric affinity (~10^-32 M^-1 reported in the pathway literature). (manko2024pvdlorchestratesthe pages 1-2, dell’anno2022novelinsightson pages 8-9, dell’anno2022novelinsightson pages 4-8, dell’anno2022novelinsightson pages 9-11, stein2023therndefflux pages 1-2) | Dell’Anno et al., 2022, DOI: https://doi.org/10.3390/ijms231911507. Manko et al., 2024, DOI: https://doi.org/10.3390/ijms25116013. Stein et al., 2023, DOI: https://doi.org/10.1128/spectrum.02300-23. |
| Cellular localization & complex context | Pyoverdine biosynthesis starts in the cytoplasm, with later periplasmic maturation and secretion. Recent cell-biological studies in P. aeruginosa indicate that PvdA can physically interact with all four pyoverdine NRPSs and is part of a membrane-associated multienzyme “siderosome” context; Schalk’s review also notes an N-terminal hydrophobic inner-membrane-anchoring region and varying interaction stoichiometries with NRPS partners. Direct isolation of the full complex remains incomplete. (schalk2025bacterialsiderophoresdiversity pages 4-7, manko2024pvdlorchestratesthe pages 1-2, dell’anno2022novelinsightson pages 8-9) | Manko et al., 2024, DOI: https://doi.org/10.3390/ijms25116013. Dell’Anno et al., 2022, DOI: https://doi.org/10.3390/ijms231911507. Schalk, 2025, DOI: https://doi.org/10.1038/s41579-024-01090-6. |
| Regulation & conditions | pvdA is embedded in the canonical iron-starvation-responsive pyoverdine regulon, typically controlled by Fur and pyoverdine sigma-factor circuitry in pseudomonads. In P. putida KT2440, arginine biosynthesis defects alter pyoverdine gene expression: pvdA and pvdD increase, but pvdE decreases, consistent with impaired maturation/export rather than simple biosynthetic shutdown. Recent 2024 work in P. aeruginosa identified BfmRS as a direct regulator of siderophore genes under osmotic stress; homologous BfmR from P. putida KT2440 could bind promoters of key siderophore genes, suggesting conservation of this regulatory logic across pseudomonads. Also, parXY expression is iron responsive: 10 µM FeCl3 reduced parXY promoter activity by ~7-fold, whereas 1 mM bipyridyl increased it ~2-fold. (rice2010characterizationofan pages 24-27, barrientosmoreno2019argininebiosynthesismodulates pages 8-10, stein2023therndefflux pages 10-13, stein2023therndefflux pages 8-10) | Barrientos-Moreno et al., 2019, DOI: https://doi.org/10.1128/jb.00454-19. Song et al., 2024, DOI: https://doi.org/10.1038/s42003-024-05995-z. Stein et al., 2023, DOI: https://doi.org/10.1128/spectrum.02300-23. |
| Phenotypes & quantitative data | In P. putida KT2440, pyoverdine homeostasis is tightly linked to secretion and stress adaptation. ΔargG/ΔargH mutants show higher pvdA/pvdD expression but reduced extracellular pyoverdine with intracellular retention, and higher ROS by CellROX assays; figure-based evidence shows increased intracellular vs extracellular pyoverdine and reduced pvdE expression. For secretion, Stein et al. found that in a ΔpvdRT-opmQ ΔmdtA background (Δpm), adding ΔparX caused the strongest extra defect under iron limitation: AUC ~40% of Δpm, while a pyoverdine-nonproducer was ~2% of Δpm. 1 µM FeCl3 rescued the triple-mutant growth defect to Δpm levels, and 10 µM pyoverdine gave the best rescue; 1 µM CuSO4 did not. parX deletion also caused ~2-fold lower mdtABC-opmB and pvdL expression in reporter assays. (barrientosmoreno2019argininebiosynthesismodulates pages 8-10, barrientosmoreno2019argininebiosynthesismodulates media bdcc705a, stein2023therndefflux pages 2-5, stein2023therndefflux pages 10-13, stein2023therndefflux pages 8-10) | Barrientos-Moreno et al., 2019, DOI: https://doi.org/10.1128/jb.00454-19. Stein et al., 2023, DOI: https://doi.org/10.1128/spectrum.02300-23. |
| Recent developments & applications | 2023–2024 work has shifted from simple gene-function assignment to pathway organization and export control: (i) ParXY was added to the network of overlapping pyoverdine secretion systems in P. putida KT2440; (ii) PvdL/NRPS spatial organization and PvdA interactions were visualized in live cells; (iii) BfmRS linked environmental stress to siderophore regulation. Reviews emphasize broader applications of pyoverdine biology in biotechnology, synthetic biology, antimicrobial targeting, and environmental metal acquisition, making PvdA relevant both as a biosynthetic engineering node and as a potential anti-virulence target by blocking siderophore production. (schalk2025bacterialsiderophoresdiversity pages 23-27, manko2024pvdlorchestratesthe pages 1-2, stein2023therndefflux pages 1-2) | Stein et al., 2023, DOI: https://doi.org/10.1128/spectrum.02300-23. Manko et al., 2024, DOI: https://doi.org/10.3390/ijms25116013. Dell’Anno et al., 2022, DOI: https://doi.org/10.3390/ijms231911507. Schalk, 2025, DOI: https://doi.org/10.1038/s41579-024-01090-6. |
Table: This table summarizes the best-supported functional annotation for Pseudomonas putida KT2440 pvdA (UniProt Q88GC8), integrating organism-specific evidence with mechanistic data from closely characterized homologs. It highlights reaction chemistry, pathway role, localization, regulation, phenotypes, and recent 2023–2024 developments.
For annotation of Q88GC8 in KT2440-like genomes, the strongest evidence-supported statements are:
1) Enzyme function: L-ornithine N5-hydroxylase producing N5-hydroxyornithine for pyoverdine biosynthesis (with PvdF yielding formylated product). (dell’anno2022novelinsightson pages 8-9, rice2010characterizationofan pages 24-27)
2) Pathway role: pyoverdine siderophore biosynthesis (iron acquisition) with downstream dependence on periplasmic processing and secretion. (dell’anno2022novelinsightson pages 9-11, stein2023therndefflux pages 8-10)
3) Cellular context: cytoplasmic biosynthetic stage; evidence from Pseudomonas indicates integration into multienzyme biosynthetic assemblies, likely membrane-associated. (manko2024pvdlorchestratesthe pages 1-2, schalk2025bacterialsiderophoresdiversity pages 4-7)
4) Physiology: critical for iron-limited growth and tied to oxidative stress balance through iron/siderophore homeostasis. (barrientosmoreno2019argininebiosynthesismodulates pages 8-10, barrientosmoreno2019argininebiosynthesismodulates media 12115201)
References
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(dell’anno2022novelinsightson pages 9-11): Filippo Dell’Anno, Giovanni Andrea Vitale, Carmine Buonocore, Laura Vitale, Fortunato Palma Esposito, Daniela Coppola, Gerardo Della Sala, Pietro Tedesco, and Donatella de Pascale. Novel insights on pyoverdine: from biosynthesis to biotechnological application. International Journal of Molecular Sciences, 23:11507, Sep 2022. URL: https://doi.org/10.3390/ijms231911507, doi:10.3390/ijms231911507. This article has 40 citations.
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(barrientosmoreno2019argininebiosynthesismodulates media 79b5b256): Laura Barrientos-Moreno, María Antonia Molina-Henares, Marta Pastor-García, María Isabel Ramos-González, and Manuel Espinosa-Urgel. Arginine biosynthesis modulates pyoverdine production and release in pseudomonas putida as part of the mechanism of adaptation to oxidative stress. Journal of Bacteriology, Nov 2019. URL: https://doi.org/10.1128/jb.00454-19, doi:10.1128/jb.00454-19. This article has 44 citations and is from a peer-reviewed journal.
(barrientosmoreno2019argininebiosynthesismodulates media 12115201): Laura Barrientos-Moreno, María Antonia Molina-Henares, Marta Pastor-García, María Isabel Ramos-González, and Manuel Espinosa-Urgel. Arginine biosynthesis modulates pyoverdine production and release in pseudomonas putida as part of the mechanism of adaptation to oxidative stress. Journal of Bacteriology, Nov 2019. URL: https://doi.org/10.1128/jb.00454-19, doi:10.1128/jb.00454-19. This article has 44 citations and is from a peer-reviewed journal.
(stein2023therndefflux pages 1-2): Nicola Victoria Stein, Michelle Eder, Fabienne Burr, Sarah Stoss, Lorenz Holzner, Hans-Henning Kunz, and Heinrich Jung. The rnd efflux system parxy affects siderophore secretion in pseudomonas putida kt2440. Dec 2023. URL: https://doi.org/10.1128/spectrum.02300-23, doi:10.1128/spectrum.02300-23. This article has 8 citations and is from a domain leading peer-reviewed journal.
(stein2023therndefflux pages 10-13): Nicola Victoria Stein, Michelle Eder, Fabienne Burr, Sarah Stoss, Lorenz Holzner, Hans-Henning Kunz, and Heinrich Jung. The rnd efflux system parxy affects siderophore secretion in pseudomonas putida kt2440. Dec 2023. URL: https://doi.org/10.1128/spectrum.02300-23, doi:10.1128/spectrum.02300-23. This article has 8 citations and is from a domain leading peer-reviewed journal.
(stein2023therndefflux pages 2-5): Nicola Victoria Stein, Michelle Eder, Fabienne Burr, Sarah Stoss, Lorenz Holzner, Hans-Henning Kunz, and Heinrich Jung. The rnd efflux system parxy affects siderophore secretion in pseudomonas putida kt2440. Dec 2023. URL: https://doi.org/10.1128/spectrum.02300-23, doi:10.1128/spectrum.02300-23. This article has 8 citations and is from a domain leading peer-reviewed journal.
(stein2023therndefflux pages 8-10): Nicola Victoria Stein, Michelle Eder, Fabienne Burr, Sarah Stoss, Lorenz Holzner, Hans-Henning Kunz, and Heinrich Jung. The rnd efflux system parxy affects siderophore secretion in pseudomonas putida kt2440. Dec 2023. URL: https://doi.org/10.1128/spectrum.02300-23, doi:10.1128/spectrum.02300-23. This article has 8 citations and is from a domain leading peer-reviewed journal.
(barrientosmoreno2019argininebiosynthesismodulates media bdcc705a): Laura Barrientos-Moreno, María Antonia Molina-Henares, Marta Pastor-García, María Isabel Ramos-González, and Manuel Espinosa-Urgel. Arginine biosynthesis modulates pyoverdine production and release in pseudomonas putida as part of the mechanism of adaptation to oxidative stress. Journal of Bacteriology, Nov 2019. URL: https://doi.org/10.1128/jb.00454-19, doi:10.1128/jb.00454-19. This article has 44 citations and is from a peer-reviewed journal.