Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors

Ortega, Davi R.; Zhulin, Igor B.

doi:10.1007/978-1-4939-7577-8_29

Cited by 3 publications

(5 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Protein domain architecture prediction. The domain architecture of the Ctermini of chemoreceptors are poorly conserved among members of this protein family 62 . Further, protein domains commonly appearing in this region, such as HAMP 63 and PAS 26 , are so diverse that in several instances predictive models have difficulty identifying them.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Repurposing a chemosensory macromolecular machine

et al. 2020

Self Cite

View full text Add to dashboard Cite

How complex, multi-component macromolecular machines evolved remains poorly understood. Here we reveal the evolutionary origins of the chemosensory machinery that controls flagellar motility in Escherichia coli. We first identify ancestral forms still present in Vibrio cholerae, Pseudomonas aeruginosa, Shewanella oneidensis and Methylomicrobium alcaliphilum, characterizing their structures by electron cryotomography and finding evidence that they function in a stress response pathway. Using bioinformatics, we trace the evolution of the system through γ-Proteobacteria, pinpointing key evolutionary events that led to the machine now seen in E. coli. Our results suggest that two ancient chemosensory systems with different inputs and outputs (F6 and F7) existed contemporaneously, with one (F7) ultimately taking over the inputs and outputs of the other (F6), which was subsequently lost.

show abstract

Section: Methodsmentioning

confidence: 99%

“…Chemoreceptor families and subfamilies are prone to have diverse Cterminal domain architectures so following the procedure in ref. 62 , we manually trimmed the sequences to only contain the regions common to all receptors. This final alignment was used to build a phylogenetic tree with RAxML.…”

Section: Methodsmentioning

confidence: 99%

Repurposing a chemosensory macromolecular machine

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…In addition to the MCP signal domain, most chemoreceptors contained one or more of the following domains: HAMP domains, acting as signal transmission from sensor domain to the signalling domain (Salah Ud‐Din & Roujeinikova, 2017); sensory domains, highly varied and including a variety of classes (e.g., Cache, PAS, protoglobin); transmembrane domains, typically present in a pair and surrounding the sensory domain, predicting that most sensory domains are located in the periplasm, with the remaining sensors being detached from the membrane and sensing in the cytoplasm (see Figure S3). All Rlv3841 chemoreceptors are class 36H (consisting of 36 heptads, with a structure highly conserved, see Figure S4A), except McrA, McrB and McrC (within the che2 cluster) which are class 34H (Alexander & Zhulin, 2007; Ortega & Zhulin, 2018). Most of the Rlv3841 chemoreceptors closely resemble the classic methylation sequences of E. coli Tsr (Figure S4B,D) (Rice & Dahlquist, 1991) with some alterations conserved within Rlv3841 (Figure S4C,E).…”

Section: Resultsmentioning

confidence: 99%

The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTS^Ntr regulation

Aroney,

Pini,

Kessler

et al. 2024

Environmental Microbiology

View full text Add to dashboard Cite

Motility and chemotaxis are crucial processes for soil bacteria and plant–microbe interactions. This applies to the symbiotic bacterium Rhizobium leguminosarum, where motility is driven by flagella rotation controlled by two chemotaxis systems, Che1 and Che2. The Che1 cluster is particularly important in free‐living motility prior to the establishment of the symbiosis, with a che1 mutant delayed in nodulation and reduced in nodulation competitiveness. The Che2 system alters bacteroid development and nodule maturation. In this work, we also identified 27 putative chemoreceptors encoded in the R. leguminosarum bv. viciae 3841 genome and characterized its motility in different growth conditions. We describe a metabolism‐based taxis system in rhizobia that acts at high concentrations of dicarboxylates to halt motility independent of chemotaxis. Finally, we show how PTSNtr influences cell motility, with PTSNtr mutants exhibiting reduced swimming in different media. Motility is restored by the active forms of the PTSNtr output regulatory proteins, unphosphorylated ManX and phosphorylated PtsN. Overall, this work shows how rhizobia typify soil bacteria by having a high number of chemoreceptors and highlights the importance of the motility and chemotaxis mechanisms in a free‐living cell in the rhizosphere, and at different stages of the symbiosis.

show abstract

“…PAS domains are well known to sense oxygen, redox potential and light, and they have been shown to be involved in taxis behavior, development, circadian rhythmicity, and regulation of metabolism [ 11 , 30 , 76 , 77 ]. Similarly, ‘MCPsignal’ [Pfam: PF00015] domains function as chemoreceptors for diverse signals [ 11 , 26 ]. Before identifying their distribution in our model organisms i.e.…”

Section: Resultsmentioning

confidence: 99%

“…CheY~P interacts with the motility system and regulates the motility apparatus via flagella or pili [ 8 – 10 ]. Reversible methylation and demethylation of MCPs via CheR and CheB, respectively, play an important role in chemotaxis adaptation or memory, by adjusting the MCP’s sensitivity for new signals [for reviews see [ 2 , 6 , 7 , 11 , 12 ]].…”

Section: Introductionmentioning

confidence: 99%

In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides

2018

View full text Add to dashboard Cite

BackgroundAn efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains. Myxobacteria are complex soil-dwelling social microbes that can perform a variety of physiologic and metabolic activities ranging from gliding motility, sporulation, biofilm formation, carotenoid and secondary metabolite biosynthesis, predation, and slime secretion. To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues.ResultsHere we report the in silico characterization of a putative energy taxis cluster, Cc-5, which is present in only one amongst 34 known and sequenced myxobacterial genomes, Corallococcus coralloides. In addition, we propose that this energy taxis cluster is involved in oxygen sensing, suggesting that C. coralloides can sense (either directly or indirectly) and then respond to changing concentrations of molecular oxygen.ConclusionsThis hypothesis is based on the presence of a unique MCP encoded in this gene cluster that contains two different oxygen-binding sensor domains, PAS and globin. In addition, the two monooxygenases encoded in this cluster may contribute to aerobic respiration via ubiquinone biosynthesis, which is part of the cytochrome bc1 complex. Finally, we suggest that this cluster was acquired from Actinobacteria, Gammaproteobacteria or Cyanobacteria. Overall, this in silico study has identified a potentially innovative and evolved mechanism of energy taxis in only one of the myxobacteria, C. coralloides.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5151-6) contains supplementary material, which is available to authorized users.

show abstract

Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors

Cited by 3 publications

References 21 publications

Repurposing a chemosensory macromolecular machine

Repurposing a chemosensory macromolecular machine

The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTS^Ntr regulation

In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides

Contact Info

Product

Resources

About

Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors

Cited by 3 publications

References 21 publications

Repurposing a chemosensory macromolecular machine

Repurposing a chemosensory macromolecular machine

The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTSNtr regulation

In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides

Contact Info

Product

Resources

About

The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTS^Ntr regulation