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Yang Y, Guo S, Hong CJ, Liang ZX, Ho CL. Initial cyclic-di-GMP upregulation triggers sporadic cellular expansion leading to improved cellular survival. Biotechnol J 2024; 19:e2300542. [PMID: 38403404 DOI: 10.1002/biot.202300542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/29/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Bacterial second messenger c-di-GMP upregulation is associated with the transition from planktonic to sessile microbial lifestyle, inhibiting cellular motility, and virulence. However, in-depth elucidation of the cellular processes resulting from c-di-GMP upregulation has not been fully explored. Here, we report the role of upregulated cellular c-di-GMP in promoting planktonic cell growth of Escherichia coli K12 and Pseudomonas aeruginosa PAO1. We found a rapid expansion of cellular growth during initial cellular c-di-GMP upregulation, resulting in a larger planktonic bacterial population. The initial increase in c-di-GMP levels promotes bacterial swarming motility during the growth phase, which is subsequently inhibited by the continuous increase of c-di-GMP, and ultimately facilitates the formation of biofilms. We demonstrated that c-di-GMP upregulation triggers key bacterial genes linked to bacterial growth, swarming motility, and biofilm formation. These genes are mainly controlled by the master regulatory genes csgD and csrA. This study provides us a glimpse of the bacterial behavior of evading potential threats through adapting lifestyle changes via c-di-GMP regulation.
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Affiliation(s)
- Yongshuai Yang
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Siyu Guo
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Can-Jian Hong
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Zhao-Xun Liang
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chun Loong Ho
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen, China
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2
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González Plaza JJ. Small RNAs as Fundamental Players in the Transference of Information During Bacterial Infectious Diseases. Front Mol Biosci 2020; 7:101. [PMID: 32613006 PMCID: PMC7308464 DOI: 10.3389/fmolb.2020.00101] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022] Open
Abstract
Communication shapes life on Earth. Transference of information has played a paramount role on the evolution of all living or extinct organisms since the appearance of life. Success or failure in this process will determine the prevalence or disappearance of a certain set of genes, the basis of Darwinian paradigm. Among different molecules used for transmission or reception of information, RNA plays a key role. For instance, the early precursors of life were information molecules based in primitive RNA forms. A growing field of research has focused on the contribution of small non-coding RNA forms due to its role on infectious diseases. These are short RNA species that carry out regulatory tasks in cis or trans. Small RNAs have shown their relevance in fine tuning the expression and activity of important regulators of essential genes for bacteria. Regulation of targets occurs through a plethora of mechanisms, including mRNA stabilization/destabilization, driving target mRNAs to degradation, or direct binding to regulatory proteins. Different studies have been conducted during the interplay of pathogenic bacteria with several hosts, including humans, animals, or plants. The sRNAs help the invader to quickly adapt to the change in environmental conditions when it enters in the host, or passes to a free state. The adaptation is achieved by direct targeting of the pathogen genes, or subversion of the host immune system. Pathogens trigger also an immune response in the host, which has been shown as well to be regulated by a wide range of sRNAs. This review focuses on the most recent host-pathogen interaction studies during bacterial infectious diseases, providing the perspective of the pathogen.
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Affiliation(s)
- Juan José González Plaza
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
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3
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Nishimura R, Abe A, Sakuma Y, Kuwae A. Bordetella bronchiseptica Bcr4 antagonizes the negative regulatory function of BspR via its role in type III secretion. Microbiol Immunol 2018; 62:743-754. [PMID: 30407657 DOI: 10.1111/1348-0421.12659] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022]
Abstract
Bordetella species, including B. pertussis, have a type III secretion system that is highly conserved among gram-negative pathogenic bacteria. Genes encoding the component proteins of the type III secretion system are localized at the bsc locus in the Bordetella genome. Here, the function of a hypothetical protein Bcr4 encoded at the bsc locus in the B. bronchiseptica genome was investigated. A Bcr4-deficient mutant was created and the amounts of type III secreted proteins (e.g., BopB, BopN and Bsp22) in both the supernatant fraction and whole-cell lysates of the Bcr4-deficient mutant were determined. It was found that the amounts of these proteins were significantly lower than in the wild-type strain. The amounts of type III secreted proteins in the supernatant fraction and whole-cell lysates were much greater in a Bcr4-overproducing strain than in the wild-type strain. The type III secreted protein BspR reportedly negatively regulates the type III secretion system. Here, it was observed that a Bcr4 + BspR double-knockout mutant did not secrete type III secreted proteins, whereas the amounts of these proteins in whole-cell lysates of this mutant were nearly equal to those in whole-cell lysates of the BspR-deficient mutant. Bcr4 thus appears to play an essential role in the extracellular secretion of type III secreted proteins. Our data also suggest that Bcr4 antagonizes the negative regulatory function of BspR.
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Affiliation(s)
- Ryutaro Nishimura
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato, Tokyo 108-8641, Japan
| | - Akio Abe
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato, Tokyo 108-8641, Japan
| | - Yusuke Sakuma
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato, Tokyo 108-8641, Japan
| | - Asaomi Kuwae
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato, Tokyo 108-8641, Japan
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4
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Hughes KT, Chevance FFV. "Lost in translation: Seeing the forest by focusing on the trees". RNA Biol 2018; 15:182-185. [PMID: 29130371 DOI: 10.1080/15476286.2017.1403717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
A complex process translates messenger RNA (mRNA) base sequence into protein amino acid sequence. Transfer RNAs must recognize 3-base codons in the mRNA to insert the correct amino acids into the growing protein. Codon degeneracy makes decoding complicated in that multiple (synonymous) triplets can encode a single amino acid and multiple tRNAs can have the same anticodon. Over the last twenty years, new developments in structural biology, genome sequencing and bioinformatics has elucidated the intricacies of the ribosome structure and the details of the translation process. High throughput analyses of sequence information support the idea that mRNA folding has a major effect on expression for codons at the 5'-end of mRNA (N-terminal region of a polypeptide). Despite a forest of sequence data, significant details of the complex translation process can escape detection. However, a sensitive translation assay has allowed a single tree in this forest to be revealing.
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Affiliation(s)
- Kelly T Hughes
- a Biology, University of Utah , Salt Lake City , UT , United States
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Ni B, Ghosh B, Paldy FS, Colin R, Heimerl T, Sourjik V. Evolutionary Remodeling of Bacterial Motility Checkpoint Control. Cell Rep 2017; 18:866-877. [PMID: 28122238 PMCID: PMC5289928 DOI: 10.1016/j.celrep.2016.12.088] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/16/2016] [Accepted: 12/27/2016] [Indexed: 11/21/2022] Open
Abstract
Regulatory networks play a central role in the relationship between genotype and phenotype in all organisms. However, the mechanisms that underpin the evolutionary plasticity of these networks remain poorly understood. Here, we used experimental selection for enhanced bacterial motility in a porous environment to explore the adaptability of one of the most complex networks known in bacteria. We found that the resulting phenotypic changes are mediated by adaptive mutations in several functionally different proteins, including multiple components of the flagellar motor. Nevertheless, this evolutionary adaptation could be explained by a single mechanism, namely remodeling of the checkpoint regulating flagellar gene expression. Supported by computer simulations, our findings suggest that the specific “bow-tie” topology of the checkpoint facilitates evolutionary tuning of the cost-benefit trade-off between motility and growth. We propose that bow-tie regulatory motifs, which are widespread in cellular networks, play a general role in evolutionary adaptation. Multiple mutations enhance swimming behavior under selection A universal trade-off relationship between motility and growth is observed Checkpoint remodeling provides a mechanism of evolutionary adaptation Bow-tie topology facilitates evolvability of the motility network
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Affiliation(s)
- Bin Ni
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Bhaswar Ghosh
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Ferencz S Paldy
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg 35043, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany.
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Abstract
The efficiency of codon translation in vivo is controlled by many factors, including codon context. At a site early in the Salmonella flgM gene, the effects on translation of replacing codons Thr6 and Pro8 of flgM with synonymous alternates produced a 600-fold range in FlgM activity. Synonymous changes at Thr6 and Leu9 resulted in a twofold range in FlgM activity. The level of FlgM activity produced by any codon arrangement was directly proportional to the degree of in vivo ribosome stalling at synonymous codons. Synonymous codon suppressors that corrected the effect of a translation-defective synonymous flgM allele were restricted to two codons flanking the translation-defective codon. The various codon arrangements had no apparent effects on flgM mRNA stability or predicted mRNA secondary structures. Our data suggest that efficient mRNA translation is determined by a triplet-of-triplet genetic code. That is, the efficiency of translating a particular codon is influenced by the nature of the immediately adjacent flanking codons. A model explains these codon-context effects by suggesting that codon recognition by elongation factor-bound aminoacyl-tRNA is initiated by hydrogen bond interactions between the first two nucleotides of the codon and anticodon and then is stabilized by base-stacking energy over three successive codons.
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The effects of codon context on in vivo translation speed. PLoS Genet 2014; 10:e1004392. [PMID: 24901308 PMCID: PMC4046918 DOI: 10.1371/journal.pgen.1004392] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
We developed a bacterial genetic system based on translation of the his operon leader peptide gene to determine the relative speed at which the ribosome reads single or multiple codons in vivo. Low frequency effects of so-called "silent" codon changes and codon neighbor (context) effects could be measured using this assay. An advantage of this system is that translation speed is unaffected by the primary sequence of the His leader peptide. We show that the apparent speed at which ribosomes translate synonymous codons can vary substantially even for synonymous codons read by the same tRNA species. Assaying translation through codon pairs for the 5'- and 3'- side positioning of the 64 codons relative to a specific codon revealed that the codon-pair orientation significantly affected in vivo translation speed. Codon pairs with rare arginine codons and successive proline codons were among the slowest codon pairs translated in vivo. This system allowed us to determine the effects of different factors on in vivo translation speed including Shine-Dalgarno sequence, rate of dipeptide bond formation, codon context, and charged tRNA levels.
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Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a major cause of urinary tract and nosocomial infections. Here, we propose and demonstrate proof-of-principle for a potential cell therapy approach against P. aeruginosa. Using principles of synthetic biology, we genetically modified E. coli to specifically detect wild type P. aeruginosa (PAO1) via its quorum sensing (QS) molecule, 3OC 12 HSL. Engineered E. coli sentinels respond to the presence of 3OC 12 HSL by secreting CoPy, a novel pathogen-specific engineered chimeric bacteriocin, into the extracellular medium using the flagellar secretion tag FlgM. Extracellular FlgM-CoPy is designed to kill PAO1 specifically. CoPy was constructed by replacing the receptor and translocase domain of Colicin E3 with that of Pyocin S3. We show that CoPy toxicity is PAO1 specific, not affecting sentinel E. coli or the other bacterial strains tested. In order to define the system's basic requirements and PAO1-killing capabilities, we further determined the growth rates of PAO1 under different conditions and concentrations of purified and secreted FlgM-CoPy. The integrated system was tested by co-culturing PAO1 cells, on semisolid agar plates, together with engineered sentinel E. coli, capable of secreting FlgM-CoPy when induced by 3OC 12 HSL. Optical microscopy results show that the engineered E. coli sentinels successfully inhibit PAO1 growth.
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Affiliation(s)
- Saurabh Gupta
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Eran E. Bram
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
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Mutations in flk, flgG, flhA, and flhE that affect the flagellar type III secretion specificity switch in Salmonella enterica. J Bacteriol 2009; 191:3938-49. [PMID: 19376867 DOI: 10.1128/jb.01811-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upon completion of the flagellar hook-basal body (HBB) structure, the flagellar type III secretion system switches from secreting rod/hook-type to filament-type substrates. The secretion specificity switch has been reported to occur prematurely (prior to HBB completion) in flk-null mutants (P. Aldridge, J. E. Karlinsey, E. Becker, F. F. Chevance, and K. T. Hughes, Mol. Microbiol. 60:630-643, 2006) and in distal rod gene gain-of-function mutants (flgG* mutants) that produce filamentous rod structures (F. F. Chevance, N. Takahashi, J. E. Karlinsey, J. Gnerer, T. Hirano, R. Samudrala, S. Aizawa, and K. T. Hughes, Genes Dev. 21:2326-2335, 2007). A fusion of beta-lactamase (Bla) to the C terminus of the filament-type secretion substrate FlgM was used to select for mutants that would secrete FlgM-Bla into the periplasmic space and show ampicillin resistance (Ap(r)). Ap(r) resulted from null mutations in the flhE gene, C-terminal truncation mutations in the flhA gene, null and dominant mutations in the flk gene, and flgG* mutations. All mutant classes required the hook length control protein (FliK) and the rod cap protein (FlgJ) for the secretion specificity switch to occur. However, neither the hook (FlgE) nor the hook cap (FlgD) protein was required for premature FlgM-Bla secretion in the flgG* and flk mutant strains, but it was in the flhE mutants. Unexpectedly, when deletions of either flgE or flgD were introduced into flgG* mutant strains, filaments were able to grow directly on the filamentous rod structures.
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Wang Q, Zhao Y, McClelland M, Harshey RM. The RcsCDB signaling system and swarming motility in Salmonella enterica serovar typhimurium: dual regulation of flagellar and SPI-2 virulence genes. J Bacteriol 2007; 189:8447-57. [PMID: 17905992 PMCID: PMC2168921 DOI: 10.1128/jb.01198-07] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Rcs phosphorelay is a multicomponent signaling system that positively regulates colanic acid synthesis and negatively regulates motility and virulence. We have exploited a spontaneously isolated mutant, IgaA(T191P), that is nearly maximally activated for the Rcs system to identify a vast set of genes that respond to the stimulation, and we report new regulatory properties of this signaling system in Salmonella enterica serovar Typhimurium. Microarray data show that the Rcs system normally functions as a positive regulator of SPI-2 and other genes important for the growth of Salmonella in macrophages, although when highly activated the system completely represses the SPI-1/SPI-2 virulence, flagellar, and fimbrial biogenesis pathways. The auxiliary protein RcsA, which works with RcsB to positively regulate colanic acid and other target genes, not only stimulates but also antagonizes the positive regulation of many genes in the igaA mutant. We show that RcsB represses motility through the RcsB box in the promoter region of the master operon flhDC and that RcsA is not required for this regulation. Curiously, RcsB selectively stimulates expression of the flagellar type 3 secretion genes fliPQR; an RcsAB box located downstream of fliR influences this regulation. We show that excess colanic acid impairs swimming and inhibits swarming motility, consistent with the inverse regulation of the two pathways by the Rcs system.
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Affiliation(s)
- Qingfeng Wang
- Section of Molecular Genetics and Microbiology & Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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Chevance FF, Takahashi N, Karlinsey JE, Gnerer J, Hirano T, Samudrala R, Aizawa SI, Hughes KT. The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution. Genes Dev 2007; 21:2326-35. [PMID: 17761814 PMCID: PMC1973146 DOI: 10.1101/gad.1571607] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The rod component of the bacterial flagellum polymerizes from the inner membrane across the periplasmic space and stops at a length of 25 nm at the outer membrane. Bushing structures, the P- and L-rings, polymerize around the distal rod and form a pore in the outer membrane. The flagellar hook structure is then added to the distal rod growing outside the cell. Hook polymerization stops after the rod-hook structure reaches approximately 80 nm in length. This study describes mutants in the distal rod protein FlgG that fail to terminate rod growth. The mutant FlgG subunits continue to polymerize close to the length of the normal rod-hook structure of 80 nm. These filamentous rod structures have multiple P-rings and fail to form the L-ring pore at the outer membrane. The flagella grow within the periplasm similar to spirochete flagella. This provides a simple method to evolve intracellular flagella as in spirochetes. The mechanism that couples rod growth termination to the ring assembly and outer membrane penetration exemplifies the importance of stopping points in the construction of a complex macromolecular machine that facilitate efficient coupling to the next step in the assembly pathway.
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Affiliation(s)
- Fabienne F.V. Chevance
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
- Corresponding author.E-MAIL ; FAX (801) 581-4668
| | - Noriko Takahashi
- Core Research for Evolutional Science and Technology (CREST), “Soft Nano-machine Project,” Kagamiyama Higashi-Hiroshima 739-0046, Japan
| | - Joyce E. Karlinsey
- Department of Microbiology, University of Washington Seattle, Washington 98195, USA
| | - Joshua Gnerer
- Department of Microbiology, University of Washington Seattle, Washington 98195, USA
| | - Takanori Hirano
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Ram Samudrala
- Department of Microbiology, University of Washington Seattle, Washington 98195, USA
| | - Shin-Ichi Aizawa
- Core Research for Evolutional Science and Technology (CREST), “Soft Nano-machine Project,” Kagamiyama Higashi-Hiroshima 739-0046, Japan
| | - Kelly T. Hughes
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
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