scholarly journals Bioinformatics and Experimental Analysis of Proteins of Two-Component Systems in Myxococcus xanthus

2007 ◽  
Vol 190 (2) ◽  
pp. 613-624 ◽  
Author(s):  
Xingqi Shi ◽  
Sigrun Wegener-Feldbrügge ◽  
Stuart Huntley ◽  
Nils Hamann ◽  
Reiner Hedderich ◽  
...  
Keyword(s):  
Protein Kinases ◽  
Fruiting Body ◽  
Gene Clusters ◽  
Response Regulators ◽  
Fruiting Body Formation ◽  
Orphan Genes ◽  
Body Formation ◽  
Component Systems ◽  
Genes Encoding ◽  
Two Component Systems

ABSTRACT Proteins of two-component systems (TCS) have essential functions in the sensing of external and self-generated signals in bacteria and in the generation of appropriate output responses. Accordingly, in Myxococcus xanthus, TCS are important for normal motility and fruiting body formation and sporulation. Here we analyzed the M. xanthus genome for the presence and genetic organization of genes encoding TCS. Two hundred seventy-two TCS genes were identified, 251 of which are not part of che gene clusters. We report that the TCS genes are unusually organized, with 55% being orphan and 16% in complex gene clusters whereas only 29% display the standard paired gene organization. Hybrid histidine protein kinases and histidine protein kinases predicted to be localized to the cytoplasm are overrepresented among proteins encoded by orphan genes or in complex gene clusters. Similarly, response regulators without output domains are overrepresented among proteins encoded by orphan genes or in complex gene clusters. The most frequently occurring output domains in response regulators are involved in DNA binding and cyclic-di-GMP metabolism. Our analyses suggest that TCS encoded by orphan genes and complex gene clusters are functionally distinct from TCS encoded by paired genes and that the connectivity of the pathways made up of TCS encoded by orphan genes and complex gene clusters is different from that of pathways involving TCS encoded by paired genes. Experimentally, we observed that orphan TCS genes are overrepresented among genes that display altered transcription during fruiting body formation. The systematic analysis of the 25 orphan genes encoding histidine protein kinases that are transcriptionally up-regulated during development showed that 2 such genes are likely essential for viability and identified 7 histidine protein kinases, including 4 not previously characterized that have important function in fruiting body formation or spore germination.

scholarly journals Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Noelle A. Held ◽  
Matthew R. McIlvin ◽  
Dawn M. Moran ◽  
Michael T. Laub ◽  
Mak A. Saito
Keyword(s):  
Marine Environment ◽  
Marine Bacteria ◽  
Response Regulator ◽  
Bacterial Species ◽  
South Pacific ◽  
Response Regulators ◽  
Orphan Genes ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems

ABSTRACTTwo-component sensory (TCS) systems link microbial physiology to the environment and thus may play key roles in biogeochemical cycles. In this study, we surveyed the TCS systems of 328 diverse marine bacterial species. We identified lifestyle traits such as copiotrophy and diazotrophy that are associated with larger numbers of TCS system genes within the genome. We compared marine bacterial species with 1,152 reference bacterial species from a variety of habitats and found evidence of extra response regulators in marine genomes. Examining the location of TCS genes along the circular bacterial genome, we also found that marine bacteria have a large number of “orphan” genes, as well as many hybrid histidine kinases. The prevalence of “extra” response regulators, orphan genes, and hybrid TCS systems suggests that marine bacteria break with traditional understanding of how TCS systems operate. These trends suggest prevalent regulatory networking, which may allow coordinated physiological responses to multiple environmental signals and may represent a specific adaptation to the marine environment. We examine phylogenetic and lifestyle traits that influence the number and structure of two-component systems in the genome, finding, for example, that a lack of two-component systems is a hallmark of oligotrophy. Finally, in an effort to demonstrate the importance of TCS systems to marine biogeochemistry, we examined the distribution ofProchlorococcus/Synechococcusresponse regulator PMT9312_0717 in metaproteomes of the tropical South Pacific. We found that this protein’s abundance is related to phosphate concentrations, consistent with a putative role in phosphate regulation.IMPORTANCEMarine microbes must manage variation in their chemical, physical, and biological surroundings. Because they directly link bacterial physiology to environmental changes, TCS systems are crucial to the bacterial cell. This study surveyed TCS systems in a large number of marine bacteria and identified key phylogenetic and lifestyle patterns in environmental sensing. We found evidence that, in comparison with bacteria as a whole, marine organisms have irregular TCS system constructs which might represent an adaptation specific to the marine environment. Additionally, we demonstrate the biogeochemical relevance of TCS systems by correlating the presence of the PMT9312_0717 response regulator protein to phosphate concentrations in the South Pacific. We highlight that despite their potential ecological and biogeochemical relevance, TCS systems have been understudied in the marine ecosystem. This report expands our understanding of the breadth of bacterial TCS systems and how marine bacteria have adapted to survive in their unique environment.

scholarly journals FibA and PilA act cooperatively during fruiting body formation of Myxococcus xanthus

2006 ◽  
Vol 61 (5) ◽  
pp. 1283-1293 ◽  
Author(s):  
Pamela J. Bonner ◽  
Wesley P. Black ◽  
Zhaomin Yang ◽  
Lawrence J. Shimkets
Keyword(s):  
Fruiting Body ◽  
Myxococcus Xanthus ◽  
Fruiting Body Formation ◽  
Body Formation

Fruiting-Body Formation of Tricholoma giganteum on Artificial Medium.

1995 ◽  
Vol 33 (3) ◽  
pp. 169-174 ◽  
Author(s):  
Kazunari INABA ◽  
Yoshinori TAKANO ◽  
Yoshikazu MAYUZUMI ◽  
Toshirou MITSUNAGA
Keyword(s):  
Fruiting Body ◽  
Fruiting Body Formation ◽  
Artificial Medium ◽  
Body Formation

Culmination in the slime mould Dictyostelium discoideum studied with a scanning electron microscope

Development ◽  
1976 ◽  
Vol 35 (2) ◽  
pp. 323-333
Author(s):  
D. J. Watts ◽  
T. E. Treffry
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Dictyostelium Discoideum ◽  
Fruiting Body ◽  
Maximum Height ◽  
Slow Process ◽  
Fruiting Body Formation ◽  
Basal Disc ◽  
Body Formation ◽  
Scanning Electron

Myxamoebae of Dictyostelium discoideum were allowed to develop on cellulose acetate filters, and specimens taken at various stages of fruiting body formation were prepared for study by scanning electron microscopy. In the immature fruiting body where the mass of pre-spore cells has just been lifted off the substratum by the developing stalk, the pre-spore cells are irregular in shape and are similar in appearance to cells in aggregates at earlier stages of development. As the stalk lengthens, the pre-spore cells gradually separate from one another and become rounded and elongate, but mature spores are not visible until the fruiting body reaches its maximum height. It is concluded that, contrary to previous reports, spore maturation is a slow process and is not completed until the sorus becomes pigmented. The mature stalk is surrounded by a smooth cellulose sheath but this does not envelop the cells of the basal disc, which remain discrete. The fruiting body is enclosed in a slime sheath and this may be important in holding together the mass of spores.

scholarly journals Multicellular Development in Myxococcus xanthus Is Stimulated by Predator-Prey Interactions

2007 ◽  
Vol 189 (15) ◽  
pp. 5675-5682 ◽  
Author(s):  
James E. Berleman ◽  
John R. Kirby
Keyword(s):  
Fruiting Body ◽  
Prey Availability ◽  
Process Analysis ◽  
Myxococcus Xanthus ◽  
Stringent Response ◽  
Fruiting Bodies ◽  
Fruiting Body Formation ◽  
Multicellular Development ◽  
Body Formation ◽  
Body Development

ABSTRACT Myxococcus xanthus is a predatory bacterium that exhibits complex social behavior. The most pronounced behavior is the aggregation of cells into raised fruiting body structures in which cells differentiate into stress-resistant spores. In the laboratory, monocultures of M. xanthus at a very high density will reproducibly induce hundreds of randomly localized fruiting bodies when exposed to low nutrient availability and a solid surface. In this report, we analyze how M. xanthus fruiting body development proceeds in a coculture with suitable prey. Our analysis indicates that when prey bacteria are provided as a nutrient source, fruiting body aggregation is more organized, such that fruiting bodies form specifically after a step-down or loss of prey availability, whereas a step-up in prey availability inhibits fruiting body formation. This localization of aggregates occurs independently of the basal nutrient levels tested, indicating that starvation is not required for this process. Analysis of early developmental signaling relA and asgD mutants indicates that they are capable of forming fruiting body aggregates in the presence of prey, demonstrating that the stringent response and A-signal production are surprisingly not required for the initiation of fruiting behavior. However, these strains are still defective in differentiating to spores. We conclude that fruiting body formation does not occur exclusively in response to starvation and propose an alternative model in which multicellular development is driven by the interactions between M. xanthus cells and their cognate prey.

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