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Jazleena PJ, Das A, Guiseppi A, Debard F, Sharma J, Yaikhomba M, Mignot T, Mauriello EMF, Gayathri P. Di-HAMP domains of a cytoplasmic chemoreceptor modulate nucleoid array formation and downstream signaling. mBio 2025; 16:e0005725. [PMID: 40249191 PMCID: PMC12077210 DOI: 10.1128/mbio.00057-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Accepted: 03/19/2025] [Indexed: 04/19/2025] Open
Abstract
In bacterial chemosensing, environmental cues are typically sensed by bacterial transmembrane receptors known as methyl-accepting chemotaxis proteins (MCPs). MCPs form highly organized arrays using the bacterial membrane as a scaffold. These arrays amplify the signals and transduce them into a cellular response. The FrzCD cytoplasmic receptor from Myxococcus xanthus is unique due to its ability to bind DNA and use the nucleoid as a scaffold to form arrays. In this study, we identified two HAMP (histidine kinase, adenylyl cyclase, MCP, and phosphatase) domains located between the DNA binding and signaling domains of FrzCD. In vitro experiments demonstrate that the di-HAMP domain restricts FrzCD to a dimeric form in solution and modulate FrzCD affinity for DNA, whereas the signaling domain stabilizes higher-order oligomeric assemblies upon DNA binding. Through fluorescence microscopy and analyses of M. xanthus social behavior, we demonstrate that the impact of the FrzCD HAMP domains on DNA binding and oligomerization significantly influences the formation of Frz clusters on the nucleoid as well as group motility and development. Our results suggest that the di-HAMP domain might have roles not only in signal transduction but also in the plasticity of chemosensory arrays. These observations illustrate mechanisms of regulation of a DNA-bound cytoplasmic array formed by a diffusible MCP.IMPORTANCEOur study identifies the presence of a di-HAMP domain in a cytoplasmic chemoreceptor, FrzCD, from Myxococcus xanthus, and highlights its role in dynamic receptor oligomerization on a DNA scaffold. By controlling receptor oligomerization and subsequently the array formation on the nucleoid, the di-HAMP domain imparts plasticity to receptor arrays. Such plasticity governs cellular responses to external signals and dictates bacterial social behaviors such as group motility and multicellular structure formation.
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Affiliation(s)
- P. J. Jazleena
- Biology, Indian Institute of Science Education and Research Pune, Pashan, Pune, India
| | - Apurba Das
- Biology, Indian Institute of Science Education and Research Pune, Pashan, Pune, India
| | - Annick Guiseppi
- Laboratoire de Chimie Bactérienne, CNRS, Aix-Marseille Univ, Marseille, Provence-Alpes-Côte d'Azur, France
| | - Fabian Debard
- Laboratoire de Chimie Bactérienne, CNRS, Aix-Marseille Univ, Marseille, Provence-Alpes-Côte d'Azur, France
| | - Jaya Sharma
- Biology, Indian Institute of Science Education and Research Pune, Pashan, Pune, India
| | - Mutum Yaikhomba
- Biology, Indian Institute of Science Education and Research Pune, Pashan, Pune, India
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, CNRS, Aix-Marseille Univ, Marseille, Provence-Alpes-Côte d'Azur, France
| | - Emilia M. F. Mauriello
- Laboratoire de Chimie Bactérienne, CNRS, Aix-Marseille Univ, Marseille, Provence-Alpes-Côte d'Azur, France
| | - Pananghat Gayathri
- Biology, Indian Institute of Science Education and Research Pune, Pashan, Pune, India
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Mo R, Zhu S, Chen Y, Li Y, Liu Y, Gao B. The evolutionary path of chemosensory and flagellar macromolecular machines in Campylobacterota. PLoS Genet 2022; 18:e1010316. [PMID: 35834583 PMCID: PMC9321776 DOI: 10.1371/journal.pgen.1010316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/26/2022] [Accepted: 06/27/2022] [Indexed: 01/06/2023] Open
Abstract
The evolution of macromolecular complex is a fundamental biological question, which is related to the origin of life and also guides our practice in synthetic biology. The chemosensory system is one of the complex structures that evolved very early in bacteria and displays enormous diversity and complexity in terms of composition and array structure in modern species. However, how the diversity and complexity of the chemosensory system evolved remains unclear. Here, using the Campylobacterota phylum with a robust “eco-evo” framework, we investigated the co-evolution of the chemosensory system and one of its important signaling outputs, flagellar machinery. Our analyses show that substantial flagellar gene alterations will lead to switch of its primary chemosensory class from one to another, or result in a hybrid of two classes. Unexpectedly, we discovered that the high-torque generating flagellar motor structure of Campylobacter jejuni and Helicobacter pylori likely evolved in the last common ancestor of the Campylobacterota phylum. Later lineages that experienced significant flagellar alterations lost some key components of complex scaffolding structures, thus derived simpler structures than their ancestor. Overall, this study revealed the co-evolutionary path of the chemosensory system and flagellar system, and highlights that the evolution of flagellar structural complexity requires more investigation in the Bacteria domain based on a resolved phylogenetic framework, with no assumptions on the evolutionary direction. Chemosensory system is the most complicated signal transduction system in bacteria with great diversity in both composition and structural organization across species. One of its important signaling output is flagellar motility driven by a propeller, which is made of dozens of proteins and shows considerable variation and complexity surrounding the core motor structure in different species. The evolution of both chemosensory system and flagellum are important biological questions but remain obscure. Here, we carefully examined the evolutionary paths of chemosensory system and flagellar structure in a bacterial phylum, providing detailed molecular evidences for their co-evolution. Our study provides a paradigm to study the evolution of macromolecular complexes based on robust bacterial phylogeny and co-evolved systems/components in genome context.
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Affiliation(s)
- Ran Mo
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Zhu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Chen
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuqian Li
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yugeng Liu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- * E-mail:
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Gumerov VM, Andrianova EP, Zhulin IB. Diversity of bacterial chemosensory systems. Curr Opin Microbiol 2021; 61:42-50. [PMID: 33684668 DOI: 10.1016/j.mib.2021.01.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/20/2022]
Abstract
Chemosensory system is the most complex, specialized mode of signal transduction in bacteria and archaea. It is composed of several core and auxiliary protein components that are highly organized in order to deliver a fast response to changing environmental conditions. Chemosensory pathways were studied in-depth in a handful of model organisms and experimentally characterized at least to some degree in approximately thirty other species. However, genome-wide analyses have revealed their presence in thousands of sequenced microbial genomes. Both experimental and computational studies uncovered substantial diversity in system design, functional regulation, cellular localization and phyletic distribution of chemosensory pathways. Here, we summarize advances and expose gaps in our current understanding of the diversity of chemosensory systems.
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Affiliation(s)
- Vadim M Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210 USA
| | | | - Igor B Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210 USA.
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How an unusual chemosensory system forms arrays on the bacterial nucleoid. Biochem Soc Trans 2021; 48:347-356. [PMID: 32129822 DOI: 10.1042/bst20180450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 11/17/2022]
Abstract
Chemosensory systems are signaling pathways elegantly organized in hexagonal arrays that confer unique functional features to these systems such as signal amplification. Chemosensory arrays adopt different subcellular localizations from one bacterial species to another, yet keeping their supramolecular organization unmodified. In the gliding bacterium Myxococcus xanthus, a cytoplasmic chemosensory system, Frz, forms multiple clusters on the nucleoid through the direct binding of the FrzCD receptor to DNA. A small CheW-like protein, FrzB, might be responsible for the formation of multiple (instead of just one) Frz arrays. In this review, we summarize what is known on Frz array formation on the bacterial chromosome and discuss hypotheses on how FrzB might contribute to the nucleation of multiple clusters. Finally, we will propose some possible biological explanations for this type of localization pattern.
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