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Soria‐Píriz S, Corzo A, Jiménez‐Arias JL, González JM, Papaspyrou S. Niche selection in bacterioplankton: A study of taxonomic composition and single-cell characteristics in an acidic reservoir. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13255. [PMID: 38940640 PMCID: PMC11212339 DOI: 10.1111/1758-2229.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/14/2024] [Indexed: 06/29/2024]
Abstract
Niche selection and microbial dispersal are key factors that shape microbial communities. However, their relative significance varies across different environments and spatiotemporal scales. While most studies focus on the impact of these forces on community composition, few consider other structural levels such as the physiological stage of the microbial community and single-cell characteristics. To understand the relative influence of microbial dispersal and niche selection on various community structural levels, we concurrently examined the taxonomic composition, abundance and single-cell characteristics of bacterioplankton in an acidic reservoir (El Sancho, Spain) during stratification and mixing periods. A cluster analysis based on environmental variables identified five niches during stratification and one during mixing. Canonical correspondence analysis (CCA) revealed that communities within each niche differed in both, taxonomic and single-cell characteristics. The environmental variables that explained the variation in class-based ordination differed from those explaining the ordination based on single-cell characteristics. However, a Procrustes analysis indicated a high correlation between the CCA ordinations based on both structural levels, suggesting simultaneous changes in the microbial community at multiple structural levels. Our findings underscore the dominant role of environmental selection in occupying different microbial niches, given that microbial dispersal was not restricted.
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Affiliation(s)
- Sara Soria‐Píriz
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
| | - Alfonso Corzo
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
| | - Juan Luís Jiménez‐Arias
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
| | - Juan M. González
- Institute of Natural Resources and AgrobiologySpanish National Research Council, IRNAS‐CSICSevillaSpain
| | - Sokratis Papaspyrou
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
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2
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Ribeiro RF, da Mata VB, Tomaselli LDO, Simionato AA, Santos EDS, Faria ACL, Rodrigues RCS, do Nascimento C. Microbial Leakage through Three Different Implant-Abutment Interfaces on Morse Taper Implants In Vitro. Dent J (Basel) 2024; 12:226. [PMID: 39057013 PMCID: PMC11275855 DOI: 10.3390/dj12070226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/20/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The objective of this study was to evaluate microbial leakage by means of genome counts, through the implant-abutment interface in dental implants with different Morse taper abutments. Fifty-six samples were prepared and divided in four groups: CMC TB (14 Cylindrical Implants-14 TiBase Abutments), CMX TB (14 Conical Implants-14 TiBase Abutments), CMX PU (14 Conical Implants-14 Universal Abutment) and CMX U (14 Tapered Implants-14 UCLA Abutments). Assemblies had their interface submerged in saliva as the contaminant. Samples were subjected either to thermomechanical cycling (2 × 106 mechanical cycles with frequency of 5 Hz and load of 120 N simultaneously with thermal cycles of 5-55 °C) or thermal cycling (5-55 °C). After cycling, the contents from the inner parts of assemblies were collected and analyzed using the Checkerboard DNA-DNA hybridization technique. Significant differences in the total genome counts were found after both thermomechanical or thermal cycling: CMX U > CMX PU > CMX TB > CMC TB. There were also significant differences in individual bacterial counts in each of the groups (p < 0.05). Irrespective of mechanical cycling, the type of abutment seems to influence not only the total microbial leakage through the interface, but also seems to significantly reflect differences considering individual target species.
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Affiliation(s)
- Ricardo Faria Ribeiro
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-904, Brazil; (V.B.d.M.); (L.d.O.T.); (A.A.S.); (A.C.L.F.); (R.C.S.R.)
| | - Victor Barboza da Mata
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-904, Brazil; (V.B.d.M.); (L.d.O.T.); (A.A.S.); (A.C.L.F.); (R.C.S.R.)
| | - Lucas de Oliveira Tomaselli
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-904, Brazil; (V.B.d.M.); (L.d.O.T.); (A.A.S.); (A.C.L.F.); (R.C.S.R.)
| | - Anselmo Agostinho Simionato
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-904, Brazil; (V.B.d.M.); (L.d.O.T.); (A.A.S.); (A.C.L.F.); (R.C.S.R.)
| | - Emerson de Souza Santos
- Department of Clinical Analysis, Toxicology, and Food Science, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto 14040-903, Brazil;
| | - Adriana Cláudia Lapria Faria
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-904, Brazil; (V.B.d.M.); (L.d.O.T.); (A.A.S.); (A.C.L.F.); (R.C.S.R.)
| | - Renata Cristina Silveira Rodrigues
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-904, Brazil; (V.B.d.M.); (L.d.O.T.); (A.A.S.); (A.C.L.F.); (R.C.S.R.)
| | - Cássio do Nascimento
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-904, Brazil; (V.B.d.M.); (L.d.O.T.); (A.A.S.); (A.C.L.F.); (R.C.S.R.)
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3
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Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q. An evolutionary optimum amid moderate heritability in prokaryotic cell size. Cell Rep 2024; 43:114268. [PMID: 38776226 DOI: 10.1016/j.celrep.2024.114268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
We investigate the distribution and evolution of prokaryotic cell size based on a compilation of 5,380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita); however, most species congregate heavily around the mean. The distribution approximates but is distinct from log normality. Comparative phylogenetics suggests that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e., fractal). Evolutionary modeling indicates the presence of an optimal cell size to which most species gravitate. The size is equivalent to a coccus of 0.70 μm in diameter. Analyses of 1,361 species with sequenced genomes show that genomic traits contribute to size evolution moderately and synergistically. Given our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.
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Affiliation(s)
- Henry Secaira-Morocho
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abhinav Chede
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Luis Gonzalez-de-Salceda
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Qiyun Zhu
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
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4
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Abass S, Parveen R, Irfan M, Malik Z, Husain SA, Ahmad S. Mechanism of antibacterial phytoconstituents: an updated review. Arch Microbiol 2024; 206:325. [PMID: 38913205 DOI: 10.1007/s00203-024-04035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024]
Abstract
The increase of multiple drug resistance bacteria significantly diminishes the effectiveness of antibiotic armory and subsequently exaggerates the level of therapeutic failure. Phytoconstituents are exceptional substitutes for resistance-modifying vehicles. The plants appear to be a deep well for the discovery of novel antibacterial compounds. This is owing to the numerous enticing characteristics of plants, they are easily accessible and inexpensive, extracts or chemicals derived from plants typically have significant levels of action against infections, and they rarely cause serious adverse effects. The enormous selection of phytochemicals offers very distinct chemical structures that may provide both novel mechanisms of antimicrobial activity and deliver us with different targets in the interior of the bacterial cell. They can directly affect bacteria or act together with the crucial events of pathogenicity, in this manner decreasing the aptitude of bacteria to create resistance. Abundant phytoconstituents demonstrate various mechanisms of action toward multi drug resistance bacteria. Overall, this comprehensive review will provide insights into the potential of phytoconstituents as alternative treatments for bacterial infections, particularly those caused by multi drug resistance strains. By examining the current state of research in this area, the review will shed light on potential future directions for the development of new antimicrobial therapies.
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Affiliation(s)
- Sageer Abass
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Rabea Parveen
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mohammad Irfan
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Zoya Malik
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Syed Akhtar Husain
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sayeed Ahmad
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
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5
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Harlé O, Niay J, Parayre S, Nicolas A, Henry G, Maillard MB, Valence F, Thierry A, Guédon É, Falentin H, Deutsch SM. Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis. Appl Environ Microbiol 2024; 90:e0193623. [PMID: 38376234 PMCID: PMC10952386 DOI: 10.1128/aem.01936-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest. IMPORTANCE To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
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Affiliation(s)
- Olivier Harlé
- INRAE, Institut Agro, STLO, Rennes, France
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
| | - Jérôme Niay
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
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6
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Hansson A, Karlsen EA, Stensen W, Svendsen JSM, Berglin M, Lundgren A. Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy. ACS APPLIED MATERIALS & INTERFACES 2024; 16:6799-6812. [PMID: 38294883 PMCID: PMC10875647 DOI: 10.1021/acsami.3c16004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules' properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not function. It is particularly difficult to distinguish the influence of the AMP's molecular structure from other factors controlling the total exposure, including which type of bonds are formed between bacteria and the coating and how persistent these contacts are. Here, we combine label-free live-cell microscopy, microfluidics, and automated image analysis to study the response of surface-bound Escherichia coli challenged by the same small AMP either in solution or grafted to the surface through click chemistry. Initially after binding, the grafted AMPs inhibited bacterial growth more efficiently than did AMPs in solution. Yet, after 1 h, E. coli on the coated surfaces increased their expression of type-1 fimbriae, leading to a change in their binding mode, which diminished the coating's impact. The wealth of information obtained from continuously monitoring the growth, shape, and movements of single bacterial cells allowed us to elucidate and quantify the different factors determining the antibacterial efficacy of the grafted AMPs. We expect this approach to aid the design of elaborate antibacterial material coatings working by specific and selective actions, not limited to contact-killing. This technology is needed to support health care and food production in the postantibiotic era.
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Affiliation(s)
- Adam Hansson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Eskil André Karlsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Wenche Stensen
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - John S. M. Svendsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Mattias Berglin
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Anders Lundgren
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Centre
for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg 41346, Sweden
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7
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Guo T, Sperber AM, Krieger IV, Duan Y, Chemelewski VR, Sacchettini JC, Herman JK. Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization. J Bacteriol 2024; 206:e0020223. [PMID: 38047707 PMCID: PMC10810218 DOI: 10.1128/jb.00202-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023] Open
Abstract
YisK is an uncharacterized protein in Bacillus subtilis previously shown to interact genetically with the elongasome protein Mbl. YisK overexpression leads to cell widening and lysis, phenotypes that are dependent on mbl and suppressed by mbl mutations. In the present work, we characterize YisK's localization, structure, and enzymatic activity. We show that YisK localizes as puncta that depend on Mbl. YisK belongs to the fumarylacetoacetate hydrolase (FAH) superfamily, and crystal structures revealed close structural similarity to two oxaloacetate (OAA) decarboxylases: human mitochondrial FAHD1 and Corynebacterium glutamicum Cg1458. We demonstrate that YisK can also catalyze the decarboxylation of OAA (K m = 134 µM, K cat = 31 min-1). A catalytic dead variant (YisK E148A, E150A) retains wild-type localization and still widens cells following overexpression, indicating these activities are not dependent on YisK catalysis. Conversely, a non-localizing variant (YisK E30A) retains wild-type enzymatic activity in vitro but localizes diffusely and no longer widens cells following overexpression. Together, these results suggest that YisK may be subject to spatial regulation that depends on the cell envelope synthesis machinery. IMPORTANCE The elongasome is a multiprotein complex that guides lengthwise growth in some bacteria. We previously showed that, in B. subtilis, overexpression of an uncharacterized putative enzyme (YisK) perturbed function of the actin-like elongasome protein Mbl. Here, we show that YisK exhibits Mbl-dependent localization. Through biochemical and structural characterization, we demonstrate that, like its mitochondrial homolog FAHD1, YisK can catalyze the decarboxylation of the oxaloacetate to pyruvate and CO2. YisK is the first example of an enzyme implicated in central carbon metabolism with subcellular localization that depends on Mbl.
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Affiliation(s)
- Tingfeng Guo
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Anthony M. Sperber
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Inna V. Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Yi Duan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Veronica R. Chemelewski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Jennifer K. Herman
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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8
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Govers SK, Campos M, Tyagi B, Laloux G, Jacobs-Wagner C. Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle. Cell Syst 2024; 15:19-36.e5. [PMID: 38157847 DOI: 10.1016/j.cels.2023.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; de Duve Institute, UCLouvain, Brussels, Belgium; Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Toulouse, France
| | - Bhavyaa Tyagi
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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9
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Bohorquez LC, de Sousa J, Garcia-Garcia T, Dugar G, Wang B, Jonker MJ, Noirot-Gros MF, Lalk M, Hamoen LW. Metabolic and chromosomal changes in a Bacillus subtilis whiA mutant. Microbiol Spectr 2023; 11:e0179523. [PMID: 37916812 PMCID: PMC10714963 DOI: 10.1128/spectrum.01795-23] [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: 04/28/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE WhiA is a conserved DNA-binding protein that influences cell division in many Gram-positive bacteria and, in B. subtilis, also chromosome segregation. How WhiA works in Bacillus subtilis is unknown. Here, we tested three hypothetical mechanisms using metabolomics, fatty acid analysis, and chromosome confirmation capture experiments. This revealed that WhiA does not influence cell division and chromosome segregation by modulating either central carbon metabolism or fatty acid composition. However, the inactivation of WhiA reduces short-range chromosome interactions. These findings provide new avenues to study the molecular mechanism of WhiA in the future.
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Affiliation(s)
- Laura C. Bohorquez
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Joana de Sousa
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Transito Garcia-Garcia
- Laboratoire de Genetique Microbienne, Domaine de Vilvert, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Gaurav Dugar
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Martijs J. Jonker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Marie-Françoise Noirot-Gros
- Laboratoire de Genetique Microbienne, Domaine de Vilvert, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Leendert W. Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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10
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Som N, Reddy M. Cross-talk between phospholipid synthesis and peptidoglycan expansion by a cell wall hydrolase. Proc Natl Acad Sci U S A 2023; 120:e2300784120. [PMID: 37276399 PMCID: PMC10268279 DOI: 10.1073/pnas.2300784120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
The Gram-negative bacterial cell envelope is a complex multilayered structure comprising a bilayered phospholipid (PL) membrane that surrounds the cytoplasm (inner membrane or IM) and an asymmetric outer membrane (OM) with PLs in the inner leaflet and lipopolysaccharides in the outer leaflet. Between these two layers is the periplasmic space, which contains a highly cross-linked mesh-like glycan polymer, peptidoglycan (PG). During cell expansion, coordinated synthesis of each of these components is required to maintain the integrity of the cell envelope; however, it is currently not clear how such coordination is achieved. In this study, we show that a cross-link-specific PG hydrolase couples the expansion of PG sacculus with that of PL synthesis in the Gram-negative model bacterium, Escherichia coli. We find that unregulated activity of a PG hydrolytic enzyme, MepS is detrimental for growth of E. coli during fatty acid (FA)-limiting conditions. Further genetic and biochemical analyses revealed that cellular availability of FA or PL alters the post-translational stability of MepS by modulating the proteolytic activity of a periplasmic adaptor-protease complex, NlpI-Prc toward MepS. Our results indicate that loss of OM lipid asymmetry caused by alterations in PL abundance leads to the generation of a signal to the NlpI-Prc complex for the stabilization of MepS, which subsequently cleaves the cross-links to facilitate expansion of PG. In summary, our study shows the existence of a molecular cross-talk that enables coordinated expansion of the PG sacculus with that of membrane synthesis for balanced cell-envelope biogenesis.
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Affiliation(s)
- Nilanjan Som
- Centre for Cellular and Molecular Biology, Hyderabad, 500007Telangana, India
| | - Manjula Reddy
- Centre for Cellular and Molecular Biology, Hyderabad, 500007Telangana, India
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11
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Kifayat S, Yele V, Ashames A, Sigalapalli DK, Bhandare RR, Shaik AB, Nasipireddy V, Sanapalli BKR. Filamentous temperature sensitive mutant Z: a putative target to combat antibacterial resistance. RSC Adv 2023; 13:11368-11384. [PMID: 37057268 PMCID: PMC10089256 DOI: 10.1039/d3ra00013c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
In the pre-antibiotic era, common bacterial infections accounted for high mortality and morbidity. Moreover, the discovery of penicillin in 1928 marked the beginning of an antibiotic revolution, and this antibiotic era witnessed the discovery of many novel antibiotics, a golden era. However, the misuse or overuse of these antibiotics, natural resistance that existed even before the antibiotics were discovered, genetic variations in bacteria, natural selection, and acquisition of resistance from one species to another consistently increased the resistance to the existing antibacterial targets. Antibacterial resistance (ABR) is now becoming an ever-increasing concern jeopardizing global health. Henceforth, there is an urgent unmet need to discover novel compounds to combat ABR, which act through untapped pathways/mechanisms. Filamentous Temperature Sensitive mutant Z (FtsZ) is one such unique target, a tubulin homolog involved in developing a cytoskeletal framework for the cytokinetic ring. Additionally, its pivotal role in bacterial cell division and the lack of homologous structural protein in mammals makes it a potential antibacterial target for developing novel molecules. Approximately 2176 X-crystal structures of FtsZ were available, which initiated the research efforts to develop novel antibacterial agents. The literature has reported several natural, semisynthetic, peptides, and synthetic molecules as FtsZ inhibitors. This review provides valuable insights into the basic crystal structure of FtsZ, its inhibitors, and their inhibitory activities. This review also describes the available in vitro detection and quantification methods of FtsZ-drug complexes and the various approaches for determining drugs targeting FtsZ polymerization.
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Affiliation(s)
- Sumaiya Kifayat
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
| | - Vidyasrilekha Yele
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India
| | - Akram Ashames
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Dilep Kumar Sigalapalli
- Department of Pharmaceutical Chemistry, Vignan Pharmacy College, Jawaharlal Nehru Technological University Vadlamudi 522213 Andhra Pradesh India
| | - Richie R Bhandare
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada Chebrolu Guntur 522212 Andhra Pradesh India
| | | | - Bharat Kumar Reddy Sanapalli
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
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12
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Holland A, Pitoulias M, Soultanas P, Janniere L. The Replicative DnaE Polymerase of Bacillus subtilis Recruits the Glycolytic Pyruvate Kinase (PykA) When Bound to Primed DNA Templates. Life (Basel) 2023; 13:life13040965. [PMID: 37109494 PMCID: PMC10143966 DOI: 10.3390/life13040965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The glycolytic enzyme PykA has been reported to drive the metabolic control of replication through a mechanism involving PykA moonlighting functions on the essential DnaE polymerase, the DnaC helicase and regulatory determinants of PykA catalytic activity in Bacillus subtilis. The mutants of this control suffer from critical replication and cell cycle defects, showing that the metabolic control of replication plays important functions in the overall rate of replication. Using biochemical approaches, we demonstrate here that PykA interacts with DnaE for modulating its activity when the replication enzyme is bound to a primed DNA template. This interaction is mediated by the CAT domain of PykA and possibly allosterically regulated by its PEPut domain, which also operates as a potent regulator of PykA catalytic activity. Furthermore, using fluorescence microscopy we show that the CAT and PEPut domains are important for the spatial localization of origins and replication forks, independently of their function in PykA catalytic activity. Collectively, our data suggest that the metabolic control of replication depends on the recruitment of PykA by DnaE at sites of DNA synthesis. This recruitment is likely highly dynamic, as DnaE is frequently recruited to and released from replication machineries to extend the several thousand RNA primers generated from replication initiation to termination. This implies that PykA and DnaE continuously associate and dissociate at replication machineries for ensuring a highly dynamic coordination of the replication rate with metabolism.
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Affiliation(s)
- Alexandria Holland
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Matthaios Pitoulias
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, CEDEX, France
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13
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Zeng X, Huang M, Sun QX, Peng YJ, Xu X, Tang YB, Zhang JY, Yang Y, Zhang CC. A c-di-GMP binding effector controls cell size in a cyanobacterium. Proc Natl Acad Sci U S A 2023; 120:e2221874120. [PMID: 36947515 PMCID: PMC10068817 DOI: 10.1073/pnas.2221874120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial signaling molecule. It is also a critical player in the regulation of cell size and cell behaviors such as cell aggregation and phototaxis in cyanobacteria, which constitute an important group of prokaryotes for their roles in the ecology and evolution of the Earth. However, c-di-GMP receptors have never been revealed in cyanobacteria. Here, we report the identification of a c-di-GMP receptor, CdgR, from the filamentous cyanobacterium Anabaena PCC 7120. Crystal structural analysis and genetic studies demonstrate that CdgR binds c-di-GMP at the dimer interface and this binding is required for the control of cell size in a c-di-GMP-dependent manner. Different functions of CdgR, in ligand binding and signal transmission, could be separated genetically, allowing us to dissect its molecular signaling functions. The presence of the apo-form of CdgR triggers cell size reduction, consistent with the similar effects observed with a decrease of c-di-GMP levels in cells. Furthermore, we found that CdgR exerts its function by interacting with a global transcription factor DevH, and this interaction was inhibited by c-di-GMP. The lethal effect triggered by conditional depletion of DevH or by the production of several point-mutant proteins of CdgR in cells indicates that this signaling pathway plays critical functions in Anabaena. Our studies revealed a mechanism of c-di-GMP signaling in the control of cell size, an important and complex trait for bacteria. CdgR is highly conserved in cyanobacteria, which will greatly expand our understanding of the roles of c-di-GMP signaling in these organisms.
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Affiliation(s)
- Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Min Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Qing-Xue Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Ye-Jun Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Xiaomei Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yun-Bin Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Institut AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei430070, People’s Republic of China
- Innovation Academy for Seed Design Chinese Academy of Sciences, Beijing100049, People’s Republic of China
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14
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Rao NS, Ermann Lundberg L, Tomasson J, Tullberg C, Brink DP, Palmkron SB, van Niel EWJ, Håkansson S, Carlquist M. Non-inhibitory levels of oxygen during cultivation increase freeze-drying stress tolerance in Limosilactobacillus reuteri DSM 17938. Front Microbiol 2023; 14:1152389. [PMID: 37125176 PMCID: PMC10140318 DOI: 10.3389/fmicb.2023.1152389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/22/2023] [Indexed: 05/02/2023] Open
Abstract
The physiological effects of oxygen on Limosilactobacillus reuteri DSM 17938 during cultivation and the ensuing properties of the freeze-dried probiotic product was investigated. On-line flow cytometry and k-means clustering gating was used to follow growth and viability in real time during cultivation. The bacterium tolerated aeration at 500 mL/min, with a growth rate of 0.74 ± 0.13 h-1 which demonstrated that low levels of oxygen did not influence the growth kinetics of the bacterium. Modulation of the redox metabolism was, however, seen already at non-inhibitory oxygen levels by 1.5-fold higher production of acetate and 1.5-fold lower ethanol production. A significantly higher survival rate in the freeze-dried product was observed for cells cultivated in presence of oxygen compared to absence of oxygen (61.8% ± 2.4% vs. 11.5% ± 4.3%), coinciding with a higher degree of unsaturated fatty acids (UFA:SFA ratio of 10 for air sparged vs. 3.59 for N2 sparged conditions.). Oxygen also resulted in improved bile tolerance and boosted 5'nucleotidase activity (370 U/L vs. 240 U/L in N2 sparged conditions) but lower tolerance to acidic conditions compared bacteria grown under complete anaerobic conditions which survived up to 90 min of exposure at pH 2. Overall, our results indicate the controlled supply of oxygen during production may be used as means for probiotic activity optimization of L. reuteri DSM 17938.
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Affiliation(s)
- Nikhil Seshagiri Rao
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
- *Correspondence: Nikhil Seshagiri Rao,
| | - Ludwig Ermann Lundberg
- The Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- BioGaia, SE-103 64, Stockholm, Sweden
| | | | - Cecilia Tullberg
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Daniel P. Brink
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Shuai Bai Palmkron
- Department of Food Technology, Engineering and Nutrition, Department of Chemistry, Lund University, Lund, Sweden
| | - Ed W. J. van Niel
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Sebastian Håkansson
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
- BioGaia, SE-241 38, Eslöv, Sweden
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
- Magnus Carlquist,
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15
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MipZ caps the plus-end of FtsZ polymers to promote their rapid disassembly. Proc Natl Acad Sci U S A 2022; 119:e2208227119. [PMID: 36490318 PMCID: PMC9897490 DOI: 10.1073/pnas.2208227119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The spatiotemporal regulation of cell division is a fundamental issue in cell biology. Bacteria have evolved a variety of different systems to achieve proper division site placement. In many cases, the underlying molecular mechanisms are still incompletely understood. In this study, we investigate the function of the cell division regulator MipZ from Caulobacter crescentus, a P-loop ATPase that inhibits the polymerization of the treadmilling tubulin homolog FtsZ near the cell poles, thereby limiting the assembly of the cytokinetic Z ring to the midcell region. We show that MipZ interacts with FtsZ in both its monomeric and polymeric forms and induces the disassembly of FtsZ polymers in a manner that is not dependent but enhanced by the FtsZ GTPase activity. Using a combination of biochemical and genetic approaches, we then map the MipZ-FtsZ interaction interface. Our results reveal that MipZ employs a patch of surface-exposed hydrophobic residues to interact with the C-terminal region of the FtsZ core domain. In doing so, it sequesters FtsZ monomers and caps the (+)-end of FtsZ polymers, thereby promoting their rapid disassembly. We further show that MipZ influences the conformational dynamics of interacting FtsZ molecules, which could potentially contribute to modulating their assembly kinetics. Together, our findings show that MipZ uses a combination of mechanisms to control FtsZ polymerization, which may be required to robustly regulate the spatiotemporal dynamics of Z ring assembly within the cell.
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16
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Serbanescu D, Ojkic N, Banerjee S. Cellular resource allocation strategies for cell size and shape control in bacteria. FEBS J 2022; 289:7891-7906. [PMID: 34665933 PMCID: PMC9016100 DOI: 10.1111/febs.16234] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 01/14/2023]
Abstract
Bacteria are highly adaptive microorganisms that thrive in a wide range of growth conditions via changes in cell morphologies and macromolecular composition. How bacterial morphologies are regulated in diverse environmental conditions is a long-standing question. Regulation of cell size and shape implies control mechanisms that couple the growth and division of bacteria to their cellular environment and macromolecular composition. In the past decade, simple quantitative laws have emerged that connect cell growth to proteomic composition and the nutrient availability. However, the relationships between cell size, shape, and growth physiology remain challenging to disentangle and unifying models are lacking. In this review, we focus on regulatory models of cell size control that reveal the connections between bacterial cell morphology and growth physiology. In particular, we discuss how changes in nutrient conditions and translational perturbations regulate the cell size, growth rate, and proteome composition. Integrating quantitative models with experimental data, we identify the physiological principles of bacterial size regulation, and discuss the optimization strategies of cellular resource allocation for size control.
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Affiliation(s)
- Diana Serbanescu
- Department of Physics and Astronomy, University College London, UK
| | - Nikola Ojkic
- Department of Physics and Astronomy, University College London, UK
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17
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Lou J, Cai J, Hu X, Liang Y, Sun Y, Zhu Y, Meng Q, Zhu T, Gao H, Yu Z, Yin J. The stringent starvation protein SspA modulates peptidoglycan synthesis by regulating the expression of peptidoglycan synthases. Mol Microbiol 2022; 118:716-730. [PMID: 36308522 DOI: 10.1111/mmi.14996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 01/18/2023]
Abstract
The peptidoglycan (PG) layer of bacterial cells is essential for maintaining the cell shape and survival of cells; therefore, the synthesis of PG needs to be spatiotemporally controlled. While it is well established that PG synthesis is mediated posttranslationally through interactions between PG synthases and their cognate partners, much less is known about the transcriptional regulation of genes encoding these synthases. Based on a previous finding that the Gram-negative bacterium Shewanella oneidensis lacking the prominent PG synthase exhibits impaired cell wall integrity, we performed genetic selections to isolate the suppressors. We discovered that disrupting the sspA gene encoding stringent starvation protein A (SspA) is sufficient to suppress compromised PG. SspA serves as a transcriptional repressor that regulates the expression of the two types of PG synthases, class A penicillin-binding proteins and SEDS/bPBP protein complexes. SspA is an RNA polymerase-associated protein, and its regulation involves interactions with the σ70 -RNAP complex and an antagonistic effect of H-NS, a global nucleoid-associated protein. We also present evidence that the regulation of PG synthases by SspA is conserved in Escherichia coli, adding a new dimension to the current understanding of PG synthesis and its regulation.
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Affiliation(s)
- Jie Lou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jingxiao Cai
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiao Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yanqun Liang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yijuan Sun
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yiling Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiu Meng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Tingheng Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Haichun Gao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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18
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Sloan R, Surber J, Roy EJ, Hartig E, Morgenstein RM. Enzyme 1 of the phosphoenolpyruvate:sugar phosphotransferase system is involved in resistance to MreB disruption in wild-type and ∆envC cells. Mol Microbiol 2022; 118:588-600. [PMID: 36199205 PMCID: PMC9671846 DOI: 10.1111/mmi.14988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 01/12/2023]
Abstract
Cell wall synthesis in bacteria is determined by two protein complexes: the elongasome and divisome. The elongasome is coordinated by the actin homolog MreB while the divisome is organized by the tubulin homolog FtsZ. While these two systems must coordinate with each other to ensure that elongation and division are coregulated, this cross talk has been understudied. Using the MreB depolymerizing agent, A22, we found that multiple gene deletions result in cells exhibiting increased sensitivity to MreB depolymerization. One of those genes encodes for EnvC, a part of the divisome that is responsible for splitting daughter cells after the completion of cytokinesis through the activation of specific amidases. Here we show this increased sensitivity to A22 works through two known amidase targets of EnvC: AmiA and AmiB. In addition, suppressor analysis revealed that mutations in enzyme 1 of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) can suppress the effects of A22 in both wild-type and envC deletion cells. Together this work helps to link elongation, division, and metabolism.
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Affiliation(s)
- Ryan Sloan
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Jacob Surber
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Emma J. Roy
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Ethan Hartig
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Randy M. Morgenstein
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
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19
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Kellogg DR, Levin PA. Nutrient availability as an arbiter of cell size. Trends Cell Biol 2022; 32:908-919. [PMID: 35851491 PMCID: PMC9588502 DOI: 10.1016/j.tcb.2022.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023]
Abstract
Pioneering work carried out over 60 years ago discovered that bacterial cell size is proportional to the growth rate set by nutrient availability. This relationship is traditionally referred to as the 'growth law'. Subsequent studies revealed the growth law to hold across all orders of life, a remarkable degree of conservation. However, recent work suggests the relationship between growth rate, nutrients, and cell size is far more complicated and less deterministic than originally thought. Focusing on bacteria and yeast, here we review efforts to understand the molecular mechanisms underlying the relationship between growth rate and cell size.
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Affiliation(s)
- Douglas R Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St Louis, MO 63130, USA; Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St Louis, St Louis, MO 63130, USA.
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20
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Shinn MK, Cohan MC, Bullock JL, Ruff KM, Levin PA, Pappu RV. Connecting sequence features within the disordered C-terminal linker of Bacillus subtilis FtsZ to functions and bacterial cell division. Proc Natl Acad Sci U S A 2022; 119:e2211178119. [PMID: 36215496 PMCID: PMC9586301 DOI: 10.1073/pnas.2211178119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Intrinsically disordered regions (IDRs) can function as autoregulators of folded enzymes to which they are tethered. One example is the bacterial cell division protein FtsZ. This includes a folded core and a C-terminal tail (CTT) that encompasses a poorly conserved, disordered C-terminal linker (CTL) and a well-conserved 17-residue C-terminal peptide (CT17). Sites for GTPase activity of FtsZs are formed at the interface between GTP binding sites and T7 loops on cores of adjacent subunits within dimers. Here, we explore the basis of autoregulatory functions of the CTT in Bacillus subtilis FtsZ (Bs-FtsZ). Molecular simulations show that the CT17 of Bs-FtsZ makes statistically significant CTL-mediated contacts with the T7 loop. Statistical coupling analysis of more than 1,000 sequences from FtsZ orthologs reveals clear covariation of the T7 loop and the CT17 with most of the core domain, whereas the CTL is under independent selection. Despite this, we discover the conservation of nonrandom sequence patterns within CTLs across orthologs. To test how the nonrandom patterns of CTLs mediate CTT-core interactions and modulate FtsZ functionalities, we designed Bs-FtsZ variants by altering the patterning of oppositely charged residues within the CTL. Such alterations disrupt the core-CTT interactions, lead to anomalous assembly and inefficient GTP hydrolysis in vitro and protein degradation, aberrant assembly, and disruption of cell division in vivo. Our findings suggest that viable CTLs in FtsZs are likely to be IDRs that encompass nonrandom, functionally relevant sequence patterns that also preserve three-way covariation of the CT17, the T7 loop, and core domain.
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Affiliation(s)
- Min Kyung Shinn
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Megan C. Cohan
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Jessie L. Bullock
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kiersten M. Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Petra A. Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130
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21
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Dong M, Yang S, Yang X, Xu M, Hu W, Wang B, Huang Y, Xu J, Lu H, Yang Y, Chen X, Huang H, Sun G. Water quality drives the distribution of freshwater cable bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156468. [PMID: 35660596 DOI: 10.1016/j.scitotenv.2022.156468] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Cable bacteria are a group of recently found filamentous sulfide-oxidizing Desulfobulbaceae that significantly impact biogeochemical cycling. However, the limited understanding of cable bacteria distribution patterns and the driving force hindered our abilities to evaluate and maximize their contribution to environmental health. We evaluated cable bacteria assemblages from ten river sediments in the Pearl River Delta, China. The results revealed a clear biogeographic distribution pattern of cable bacteria, and their communities were deterministically assembled through water quality-driven selection. Cable bacteria are diverse in the river sediments with a few generalists and many specialists, and the water quality IV and V environments are the "hot spot." We then provided evidence on their morphology, function, and genome to demonstrate how water quality might shape the cable bacteria assemblages. Reduced cell width, inhibited function, and water quality-related adaptive genomic traits were detected in sulfide-limited water quality III and contaminant-stressed water quality VI environments. Specifically, those genomic traits were contributed to carbon and sulfur metabolism in the water quality III environment and stress resistance in the water quality VI environment. Overall, these findings provided a helpful baseline in evaluating the contribution of cable bacteria in the freshwater ecosystem and suggested that their high diversity and flexibility in phylogeny, morphology, and genome allowed them to adapt and contribute to various environmental conditions.
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Affiliation(s)
- Meijun Dong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Shan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Wenzhe Hu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Jiarou Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Huibin Lu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Haobin Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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22
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Ordek A, Gordesli-Duatepe FP. Impact of sodium nitroprusside concentration added to batch cultures of Escherichia coli biofilms on the c-di-GMP levels, morphologies and adhesion of biofilm-dispersed cells. BIOFOULING 2022; 38:796-813. [PMID: 36229918 DOI: 10.1080/08927014.2022.2131399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/19/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Biofilm dispersion can be triggered by the application of dispersing agents such as nitric oxide (NO)-donors, resulting in the release of biofilm-dispersed cells into the environment. In this work, biofilm-dispersed cells were obtained by adding different concentrations of NO-donor sodium nitroprusside (0.5, 5, 50 µM, and 2.5 mM of SNP) to batch cultures of pre-formed Escherichia coli biofilms. Except for those dispersed by 5 µM of SNP, biofilm-dispersed cells were found to be wider and longer than the planktonic cells and to have higher c-di-GMP levels and greater adhesion forces to silicon nitride surfaces in water as measured by atomic force microscope. Consequently, the optimum concentration of SNP to disperse E. coli biofilms was found to be 5 µM of SNP, whose addition to batch cultures resulted in a significant biofilm dispersion and the dispersed cells having c-di-GMP levels, morphologies and adhesion strengths similar to their planktonic counterparts.
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Affiliation(s)
- Ayse Ordek
- Bioengineering Graduate Program, Graduate School, Izmir University of Economics, Izmir, Turkey
| | - F Pinar Gordesli-Duatepe
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Izmir, Turkey
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23
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Lin N, Valiei A, McKay G, Nguyen D, Tufenkji N, Moraes C. Microfluidic Study of Bacterial Attachment on and Detachment from Zinc Oxide Nanopillars. ACS Biomater Sci Eng 2022; 8:3122-3131. [PMID: 35678761 DOI: 10.1021/acsbiomaterials.2c00233] [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: 11/28/2022]
Abstract
Nanopillars can influence how bacterial cells attach to a surface. Herein, we investigated whether self-assembled zinc oxide (ZnO) nanopillars synthesized on glass substrates via the conventional hydrothermal route possess anti-biofouling properties either by reducing the amount of initially attached cells or promoting the detachment of cells from the surface or both. To avoid complications associated with manual intervention methods of assessing bacterial attachment on nanopillar surfaces, we implemented a microfluidic approach. In our study, we synthesized two nanopillar topographies: a low surface density of ZnO nanopillars and a high surface density of ZnO nanopillars. Next, we mounted microfluidic channels to each of these substrates. This microfluidic approach allowed us to gently flow Pseudomonas aeruginosa, Staphylococcus aureus, or Bacillus subtilis cells onto the nanopillars for initial attachment before systematically increasing the flowrate to attempt to detach remaining attached cells without introducing air-liquid interface artefacts during the assay. Generally, initial bacterial attachment was similar across all substrates. However, cells consistently detached more readily from high-surface-density nanopillars compared to low-surface-density nanopillars. Electron microscopy revealed that cells that attached to high-surface-density nanopillars rested atop the nanopillars, fully exposed to microfluidic shear, whereas many cells became trapped in the void space between neighboring low-surface-density nanopillars, shielding these cells from detachment. Our findings indicate that self-assembled ZnO nanopillars can provide anti-biofouling properties under submerged flow but only if synthesized at high surface density.
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Affiliation(s)
- Nicholas Lin
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, Québec, Canada H3A 0C5
| | - Amin Valiei
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, Québec, Canada H3A 0C5
| | - Geoffrey McKay
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal, Québec, Canada H4A 3J1
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal, Québec, Canada H4A 3J1.,Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Québec, Canada H3A 2B4.,Department of Medicine, McGill University, 1001 Décarie Boulevard, Montréal, Québec, Canada H4A 3J1
| | - Nathalie Tufenkji
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, Québec, Canada H3A 0C5
| | - Christopher Moraes
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, Québec, Canada H3A 0C5.,Department of Biomedical Engineering, McGill University, 3775 University Street, Montréal, Québec, Canada H3A 2B4.,Rosalind and Morris Goodman Cancer Research Center, McGill University, 1160 Pine Avenue West, Montréal, Québec, Canada H3A 1A3.,Division of Experimental Medicine, McGill University, 1001 Décarie Boulevard, Montréal, Québec, Canada H4A 3J1
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24
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A High-Content Microscopy Screening Identifies New Genes Involved in Cell Width Control in Bacillus subtilis. mSystems 2021; 6:e0101721. [PMID: 34846166 PMCID: PMC8631317 DOI: 10.1128/msystems.01017-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
How cells control their shape and size is a fundamental question of biology. In most bacteria, cell shape is imposed by the peptidoglycan (PG) polymeric meshwork that surrounds the cell. Thus, bacterial cell morphogenesis results from the coordinated action of the proteins assembling and degrading the PG shell. Remarkably, during steady-state growth, most bacteria maintain a defined shape along generations, suggesting that error-proof mechanisms tightly control the process. In the rod-shaped model for the Gram-positive bacterium Bacillus subtilis, the average cell length varies as a function of the growth rate, but the cell diameter remains constant throughout the cell cycle and across growth conditions. Here, in an attempt to shed light on the cellular circuits controlling bacterial cell width, we developed a screen to identify genetic determinants of cell width in B. subtilis. Using high-content screening (HCS) fluorescence microscopy and semiautomated measurement of single-cell dimensions, we screened a library of ∼4,000 single knockout mutants. We identified 13 mutations significantly altering cell diameter, in genes that belong to several functional groups. In particular, our results indicate that metabolism plays a major role in cell width control in B. subtilis. IMPORTANCE Bacterial shape is primarily dictated by the external cell wall, a vital structure that, as such, is the target of countless antibiotics. Our understanding of how bacteria synthesize and maintain this structure is therefore a cardinal question for both basic and applied research. Bacteria usually multiply from generation to generation while maintaining their progenies with rigorously identical shapes. This implies that the bacterial cells constantly monitor and maintain a set of parameters to ensure this perpetuation. Here, our study uses a large-scale microscopy approach to identify at the whole-genome level, in a model bacterium, the genes involved in the control of one of the most tightly controlled cellular parameters, the cell width.
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25
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Karasz DC, Weaver AI, Buckley DH, Wilhelm RC. Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils. Environ Microbiol 2021; 24:1-17. [PMID: 34929753 DOI: 10.1111/1462-2920.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/30/2022]
Abstract
Bacteria can regulate cell morphology in response to environmental conditions, altering their physiological and metabolic characteristics to improve survival. Conditional filamentation, in which cells suspend division while continuing lateral growth, is a strategy with a range of adaptive benefits. Here, we review the causes and consequences of conditional filamentation with respect to bacterial physiology, ecology and evolution. We describe four major benefits from conditional filamentation: stress tolerance, surface colonization, gradient spanning and the facilitation of biotic interactions. Adopting a filamentous growth habit involves fitness trade-offs which are also examined. We focus on the role of conditional filamentation in soil habitats, where filamentous morphotypes are highly prevalent and where environmental heterogeneity can benefit a conditional response. To illustrate the use of information presented in our review, we tested the conditions regulating filamentation by the forest soil isolate Paraburkholderia elongata 5NT . Filamentation by P. elongata was induced at elevated phosphate concentrations, and was associated with the accumulation of intracellular polyphosphate, highlighting the role of filamentation in a phosphate-solubilizing bacterium. Conditional filamentation enables bacteria to optimize their growth and metabolism in environments that are highly variable, a trait that can impact succession, symbioses, and biogeochemistry in soil environments.
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Affiliation(s)
- David C Karasz
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Anna I Weaver
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, New York, 14853, USA.,Weill Institute for Cell and Molecular Biology, Weill Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
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26
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Flow cytometric analysis reveals culture condition dependent variations in phenotypic heterogeneity of Limosilactobacillus reuteri. Sci Rep 2021; 11:23567. [PMID: 34876641 PMCID: PMC8651721 DOI: 10.1038/s41598-021-02919-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/24/2021] [Indexed: 11/08/2022] Open
Abstract
Optimisation of cultivation conditions in the industrial production of probiotics is crucial to reach a high-quality product with retained probiotic functionality. Flow cytometry-based descriptors of bacterial morphology may be used as markers to estimate physiological fitness during cultivation, and can be applied for online monitoring to avoid suboptimal growth. In the current study, the effects of temperature, initial pH and oxygen levels on cell growth and cell size distributions of Limosilactobacillus reuteri DSM 17938 were measured using multivariate flow cytometry. A pleomorphic behaviour was evident from the measurements of light scatter and pulse width distributions. A pattern of high growth yielding smaller cells and less heterogeneous populations could be observed. Analysis of pulse width distributions revealed significant morphological heterogeneities within the bacterial cell population under non-optimal growth conditions, and pointed towards low temperature, high initial pH, and high oxygen levels all being triggers for changes in morphology towards cell chain formation. However, cell size did not correlate to survivability after freeze-thaw or freeze-drying stress, indicating that it is not a key determinant for physical stress tolerance. The fact that L. reuteri morphology varies depending on cultivation conditions suggests that it can be used as marker for estimating physiological fitness and responses to its environment.
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27
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Seef S, Herrou J, de Boissier P, My L, Brasseur G, Robert D, Jain R, Mercier R, Cascales E, Habermann BH, Mignot T. A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria. eLife 2021; 10:72409. [PMID: 34505573 PMCID: PMC8460266 DOI: 10.7554/elife.72409] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/09/2021] [Indexed: 12/21/2022] Open
Abstract
Myxococcus xanthus, a soil bacterium, predates collectively using motility to invade prey colonies. Prey lysis is mostly thought to rely on secreted factors, cocktails of antibiotics and enzymes, and direct contact with Myxococcus cells. In this study, we show that on surfaces the coupling of A-motility and contact-dependent killing is the central predatory mechanism driving effective prey colony invasion and consumption. At the molecular level, contact-dependent killing involves a newly discovered type IV filament-like machinery (Kil) that both promotes motility arrest and prey cell plasmolysis. In this process, Kil proteins assemble at the predator-prey contact site, suggesting that they allow tight contact with prey cells for their intoxication. Kil-like systems form a new class of Tad-like machineries in predatory bacteria, suggesting a conserved function in predator-prey interactions. This study further reveals a novel cell-cell interaction function for bacterial pili-like assemblages.
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Affiliation(s)
- Sofiene Seef
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Julien Herrou
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Paul de Boissier
- Aix-Marseille Université - CNRS UMR 7288, Institut de Biologie du Développement de Marseille and Turing Center for Living Systems, Marseille, France
| | - Laetitia My
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Gael Brasseur
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Donovan Robert
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Rikesh Jain
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France.,Aix-Marseille Université - CNRS UMR 7288, Institut de Biologie du Développement de Marseille and Turing Center for Living Systems, Marseille, France
| | - Romain Mercier
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Eric Cascales
- Aix-Marseille Université - CNRS UMR 7255, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Bianca H Habermann
- Aix-Marseille Université - CNRS UMR 7288, Institut de Biologie du Développement de Marseille and Turing Center for Living Systems, Marseille, France
| | - Tâm Mignot
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
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28
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Sun J, Shi H, Huang KC. Hyperosmotic Shock Transiently Accelerates Constriction Rate in Escherichia coli. Front Microbiol 2021; 12:718600. [PMID: 34489908 PMCID: PMC8418109 DOI: 10.3389/fmicb.2021.718600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial cells in their natural environments encounter rapid and large changes in external osmolality. For instance, enteric bacteria such as Escherichia coli experience a rapid decrease when they exit from host intestines. Changes in osmolality alter the mechanical load on the cell envelope, and previous studies have shown that large osmotic shocks can slow down bacterial growth and impact cytoplasmic diffusion. However, it remains unclear how cells maintain envelope integrity and regulate envelope synthesis in response to osmotic shocks. In this study, we developed an agarose pad-based protocol to assay envelope stiffness by measuring population-averaged cell length before and after a hyperosmotic shock. Pad-based measurements exhibited an apparently larger length change compared with single-cell dynamics in a microfluidic device, which we found was quantitatively explained by a transient increase in division rate after the shock. Inhibiting cell division led to consistent measurements between agarose pad-based and microfluidic measurements. Directly after hyperosmotic shock, FtsZ concentration and Z-ring intensity increased, and the rate of septum constriction increased. These findings establish an agarose pad-based protocol for quantifying cell envelope stiffness, and demonstrate that mechanical perturbations can have profound effects on bacterial physiology.
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Affiliation(s)
- Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
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29
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Power AL, Barber DG, Groenhof SRM, Wagley S, Liu P, Parker DA, Love J. The Application of Imaging Flow Cytometry for Characterisation and Quantification of Bacterial Phenotypes. Front Cell Infect Microbiol 2021; 11:716592. [PMID: 34368019 PMCID: PMC8335544 DOI: 10.3389/fcimb.2021.716592] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 12/25/2022] Open
Abstract
Bacteria modify their morphology in response to various factors including growth stage, nutrient availability, predation, motility and long-term survival strategies. Morphological changes may also be associated with specific physiological phenotypes such as the formation of dormant or persister cells in a “viable but non-culturable” (VBNC) state which frequently display different shapes and size compared to their active counterparts. Such dormancy phenotypes can display various degrees of tolerance to antibiotics and therefore a detailed understanding of these phenotypes is crucial for combatting chronic infections and associated diseases. Cell shape and size are therefore more than simple phenotypic characteristics; they are important physiological properties for understanding bacterial life-strategies and pathologies. However, quantitative studies on the changes to cell morphologies during bacterial growth, persister cell formation and the VBNC state are few and severely constrained by current limitations in the most used investigative techniques of flow cytometry (FC) and light or electron microscopy. In this study, we applied high-throughput Imaging Flow Cytometry (IFC) to characterise and quantify, at single-cell level and over time, the phenotypic heterogeneity and morphological changes in cultured populations of four bacterial species, Bacillus subtilis, Lactiplantibacillus plantarum, Pediococcus acidilactici and Escherichia coli. Morphologies in relation to growth stage and stress responses, cell integrity and metabolic activity were analysed. Additionally, we were able to identify and morphologically classify dormant cell phenotypes such as VBNC cells and monitor the resuscitation of persister cells in Escherichia coli following antibiotic treatment. We therefore demonstrate that IFC, with its high-throughput data collection and image capture capabilities, provides a platform by which a detailed understanding of changes in bacterial phenotypes and their physiological implications may be accurately monitored and quantified, leading to a better understanding of the role of phenotypic heterogeneity in the dynamic microbiome.
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Affiliation(s)
- Ann L Power
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniel G Barber
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Sophie R M Groenhof
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Sariqa Wagley
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ping Liu
- Shell International Exploration & Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - David A Parker
- Shell International Exploration & Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - John Love
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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30
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Abstract
Transcriptional regulators that integrate cellular and environmental signals to control cell division are well known in bacteria and eukaryotes, but their existence is poorly understood in archaea. We identified a conserved gene (cdrS) that encodes a small protein and is highly transcribed in the model archaeon Haloferax volcanii. The cdrS gene could not be deleted, but CRISPR interference (CRISPRi)-mediated repression of the cdrS gene caused slow growth and cell division defects and changed the expression of multiple genes and their products associated with cell division, protein degradation, and metabolism. Consistent with this complex regulatory network, overexpression of cdrS inhibited cell division, whereas overexpression of the operon encoding both CdrS and a tubulin-like cell division protein (FtsZ2) stimulated division. Chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) identified 18 DNA-binding sites of the CdrS protein, including one upstream of the promoter for a cell division gene, ftsZ1, and another upstream of the essential gene dacZ, encoding diadenylate cyclase involved in c-di-AMP signaling, which is implicated in the regulation of cell division. These findings suggest that CdrS is a transcription factor that plays a central role in a regulatory network coordinating metabolism and cell division. IMPORTANCE Cell division is a central mechanism of life and is essential for growth and development. Members of the Bacteria and Eukarya have different mechanisms for cell division, which have been studied in detail. In contrast, cell division in members of the Archaea is still understudied, and its regulation is poorly understood. Interestingly, different cell division machineries appear in members of the Archaea, with the Euryarchaeota using a cell division apparatus based on the tubulin-like cytoskeletal protein FtsZ, as in bacteria. Here, we identify the small protein CdrS as essential for survival and a central regulator of cell division in the euryarchaeon Haloferax volcanii. CdrS also appears to coordinate other cellular pathways, including synthesis of signaling molecules and protein degradation. Our results show that CdrS plays a sophisticated role in cell division, including regulation of numerous associated genes. These findings are expected to initiate investigations into conditional regulation of division in archaea.
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31
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Galinier A, Foulquier E, Pompeo F. Metabolic Control of Cell Elongation and Cell Division in Bacillus subtilis. Front Microbiol 2021; 12:697930. [PMID: 34248920 PMCID: PMC8270655 DOI: 10.3389/fmicb.2021.697930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/31/2021] [Indexed: 11/18/2022] Open
Abstract
To survive and adapt to changing nutritional conditions, bacteria must rapidly modulate cell cycle processes, such as doubling time or cell size. Recent data have revealed that cellular metabolism is a central regulator of bacterial cell cycle. Indeed, proteins that can sense precursors or metabolites or enzymes, in addition to their enzymatic activities involved in metabolism, were shown to directly control cell cycle processes in response to changes in nutrient levels. Here we focus on cell elongation and cell division in the Gram-positive rod-shaped bacterium Bacillus subtilis and we report evidences linking these two cellular processes to environmental nutritional availability and thus metabolic cellular status.
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Affiliation(s)
- Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Elodie Foulquier
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Marseille, France
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32
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Pradhan A, Mukkayyan N, Jakkala K, Ajitkumar P. Mycobacterial Populations Partly Change the Proportions of the Cells Undergoing Asymmetric/Symmetric Divisions in Response to Glycerol Levels in Growth Medium. Cells 2021; 10:1160. [PMID: 34064643 PMCID: PMC8151439 DOI: 10.3390/cells10051160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/25/2022] Open
Abstract
Twenty to thirty percent of the septating mycobacterial cells of the mid-log phase population showed highly deviated asymmetric constriction during division (ACD), while the remaining underwent symmetric constriction during division (SCD). The ACD produced short-sized cells (SCs) and normal/long-sized cells (NCs) as the sister-daughter cells, but with significant differential susceptibility to antibiotic/oxidative/nitrite stress. Here we report that, at 0.2% glycerol, formulated in the Middlebrook 7H9 medium, a significantly high proportion of the cells were divided by SCD. When the glycerol concentration decreased to 0.1% due to cell-growth/division, the ACD proportion gradually increased until the ACD:SCD ratio reached ~50:50. With further decrease in the glycerol levels, the SCD proportion increased with concomitant decrease in the ACD proportion. Maintenance of glycerol at 0.1%, through replenishment, held the ACD:SCD proportion at ~50:50. Transfer of the cells from one culture with a specific glycerol level to the supernatant from another culture, with a different glycerol level, made the cells change the ACD:SCD proportion to that of the culture from which the supernatant was taken. RT-qPCR data showed the possibility of diadenosine tetraphosphate phosphorylase (MSMEG_2932), phosphatidylinositol synthase (MSMEG_2933), and a Nudix family hydrolase (MSMEG_2936) involved in the ACD:SCD proportion-change in response to glycerol levels. We also discussed its physiological significance.
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Affiliation(s)
| | | | | | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India; (A.P.); (N.M.); (K.J.)
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Willdigg JR, Helmann JD. Mini Review: Bacterial Membrane Composition and Its Modulation in Response to Stress. Front Mol Biosci 2021; 8:634438. [PMID: 34046426 PMCID: PMC8144471 DOI: 10.3389/fmolb.2021.634438] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Antibiotics and other agents that perturb the synthesis or integrity of the bacterial cell envelope trigger compensatory stress responses. Focusing on Bacillus subtilis as a model system, this mini-review summarizes current views of membrane structure and insights into how cell envelope stress responses remodel and protect the membrane. Altering the composition and properties of the membrane and its associated proteome can protect cells against detergents, antimicrobial peptides, and pore-forming compounds while also, indirectly, contributing to resistance against compounds that affect cell wall synthesis. Many of these regulatory responses are broadly conserved, even where the details of regulation may differ, and can be important in the emergence of antibiotic resistance in clinical settings.
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Affiliation(s)
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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34
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Barton B, Grinnell A, Morgenstein RM. Disruption of the MreB Elongasome Is Overcome by Mutations in the Tricarboxylic Acid Cycle. Front Microbiol 2021; 12:664281. [PMID: 33968001 PMCID: PMC8102728 DOI: 10.3389/fmicb.2021.664281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/06/2021] [Indexed: 01/20/2023] Open
Abstract
The bacterial actin homolog, MreB, is highly conserved among rod-shaped bacteria and essential for growth under normal growth conditions. MreB directs the localization of cell wall synthesis and loss of MreB results in round cells and death. Using the MreB depolymerizing drug, A22, we show that changes to central metabolism through deletion of malate dehydrogenase from the tricarboxylic acid (TCA) cycle results in cells with an increased tolerance to A22. We hypothesize that deletion of malate dehydrogenase leads to the upregulation of gluconeogenesis resulting in an increase in cell wall precursors. Consistent with this idea, metabolite analysis revealed that malate dehydrogenase (mdh) deletion cells possess elevated levels of several glycolysis/gluconeogenesis compounds and the cell wall precursor, uridine diphosphate N-acetylglucosamine (UDP-NAG). In agreement with these results, the increased A22 resistance phenotype can be recapitulated through the addition of glucose to the media. Finally, we show that this increase in antibiotic tolerance is not specific to A22 but also applies to the cell wall-targeting antibiotic, mecillinam.
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Affiliation(s)
- Brody Barton
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Addison Grinnell
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Randy M Morgenstein
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
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35
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Ojkic N, Banerjee S. Bacterial cell shape control by nutrient-dependent synthesis of cell division inhibitors. Biophys J 2021; 120:2079-2084. [PMID: 33838134 DOI: 10.1016/j.bpj.2021.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 01/17/2023] Open
Abstract
By analyzing cell size and shapes of the bacterium Bacillus subtilis under nutrient perturbations, protein depletion, and antibiotic treatments, we find that cell geometry is extremely robust, reflected in a well-conserved scaling relation between surface area (S) and volume (V), S∼Vγ, with γ=0.85. We develop a molecular model supported by single-cell simulations to predict that the surface-to-volume scaling exponent γ is regulated by nutrient-dependent production of metabolic enzymes that act as cell division inhibitors in bacteria. Using theory that is supported by experimental data, we predict the modes of cell shape transformations in different bacterial species and propose a mechanism of cell shape adaptation to different nutrient perturbations. For organisms with high surface-to-volume scaling exponent γ, such as B. subtilis, cell width is not sensitive to growth-rate changes, whereas organisms with low γ, such as Acinetobacter baumannii, cell shape adapts readily to growth-rate changes.
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Affiliation(s)
- Nikola Ojkic
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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36
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Inactivation of GalU Leads to a Cell Wall-Associated Polysaccharide Defect That Reduces the Susceptibility of Enterococcus faecalis to Bacteriolytic Agents. Appl Environ Microbiol 2021; 87:AEM.02875-20. [PMID: 33483312 DOI: 10.1128/aem.02875-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Enterococcal plasmid-encoded bacteriolysin Bac41 is a selective antimicrobial system that is considered to provide a competitive advantage to Enterococcus faecalis cells that carry the Bac41-coding plasmid. The Bac41 effector consists of the secreted proteins BacL1 and BacA, which attack the cell wall of the target E. faecalis cell to induce bacteriolysis. Here, we demonstrated that galU, which encodes UTP-glucose-1-phosphate uridylyltransferase, is involved in susceptibility to the Bac41 system in E. faecalis Spontaneous mutants that developed resistance to the antimicrobial effects of BacL1 and BacA were revealed to carry a truncation deletion of the C-terminal amino acid (aa) region 288 to 298 of the translated GalU protein. This truncation resulted in the depletion of UDP-glucose, leading to a failure to utilize galactose and produce the enterococcal polysaccharide antigen (EPA), which is expressed abundantly on the cell surface of E. faecalis This cell surface composition defect that resulted from galU or EPA-specific genes caused an abnormal cell morphology, with impaired polarity during cell division and alterations of the limited localization of BacL1 Interestingly, these mutants had reduced susceptibility to beta-lactams besides Bac41, despite their increased susceptibility to other bacteriostatic antimicrobial agents and chemical detergents. These data suggest that a complex mechanism of action underlies lytic killing, as exogenous bacteriolysis induced by lytic bacteriocins or beta-lactams requires an intact cell physiology in E. faecalis IMPORTANCE Cell wall-associated polysaccharides of bacteria are involved in various physiological characteristics. Recent studies demonstrated that the cell wall-associated polysaccharide of Enterococcus faecalis is required for susceptibility to bactericidal antibiotic agents. Here, we demonstrated that a galU mutation resulted in resistance to the enterococcal lytic bacteriocin Bac41. The galU homologue is reported to be essential for the biosynthesis of species-specific cell wall-associated polysaccharides in other Firmicutes In E. faecalis, the galU mutant lost the E. faecalis-specific cell wall-associated polysaccharide EPA (enterococcal polysaccharide antigen). The mutant also displayed reduced susceptibility to antibacterial agents and an abnormal cell morphology. We demonstrated here that galU was essential for EPA biosynthesis in E. faecalis, and EPA production might underlie susceptibility to lytic bacteriocin and antibiotic agents by undefined mechanisms.
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37
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When the metabolism meets the cell cycle in bacteria. Curr Opin Microbiol 2021; 60:104-113. [PMID: 33677348 DOI: 10.1016/j.mib.2021.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022]
Abstract
Nutrients availability is the sinews of the war for single microbial cells, driving growth and cell cycle progression. Therefore, coordinating cellular processes with nutrients availability is crucial, not only to survive upon famine or fluctuating conditions but also to rapidly thrive and colonize plentiful environments. While metabolism is traditionally seen as a set of chemical reactions taking place in cells to extract energy and produce building blocks from available nutrients, numerous connections between metabolic pathways and cell cycle phases have been documented. The few regulatory systems described at the molecular levels show that regulation is mediated either by a second messenger molecule or by a metabolite and/or a metabolic enzyme. In the latter case, a secondary moonlighting regulatory function evolved independently of the primary catalytic function of the enzyme. In this review, we summarize our current understanding of the complex cross-talks between metabolism and cell cycle in bacteria.
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38
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The Ethanologenic Bacterium Zymomonas mobilis Divides Asymmetrically and Exhibits Heterogeneity in DNA Content. Appl Environ Microbiol 2021; 87:AEM.02441-20. [PMID: 33452021 DOI: 10.1128/aem.02441-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/23/2020] [Indexed: 02/04/2023] Open
Abstract
The alphaproteobacterium Zymomonas mobilis exhibits extreme ethanologenic physiology, making this species a promising biofuel producer. Numerous studies have investigated its biology relevant to industrial applications and mostly at the population level. However, the organization of single cells in this industrially important polyploid species has been largely uncharacterized. In the present study, we characterized basic cellular behavior of Z. mobilis strain Zm6 under anaerobic conditions at the single-cell level. We observed that growing Z. mobilis cells often divided at a nonmidcell position, which contributed to variant cell size at birth. However, the cell size variance was regulated by a modulation of cell cycle span, mediated by a correlation of bacterial tubulin homologue FtsZ ring accumulation with cell growth. The Z. mobilis culture also exhibited heterogeneous cellular DNA content among individual cells, which might have been caused by asynchronous replication of chromosome that was not coordinated with cell growth. Furthermore, slightly angled divisions might have resulted in temporary curvatures of attached Z. mobilis cells. Overall, the present study uncovers a novel bacterial cell organization in Z. mobilis IMPORTANCE With increasing environmental concerns about the use of fossil fuels, development of a sustainable biofuel production platform has been attracting significant public attention. Ethanologenic Z. mobilis species are endowed with an efficient ethanol fermentation capacity that surpasses, in several respects, that of baker's yeast (Saccharomyces cerevisiae), the most-used microorganism for ethanol production. For development of a Z. mobilis culture-based biorefinery, an investigation of its uncharacterized cell biology is important, because bacterial cellular organization and metabolism are closely associated with each other in a single cell compartment. In addition, the current work demonstrates that the polyploid bacterium Z. mobilis exhibits a distinctive mode of bacterial cell organization, likely reflecting its unique metabolism that does not prioritize incorporation of nutrients for cell growth. Thus, another significant result of this work is to advance our general understanding in the diversity of bacterial cell architecture.
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39
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Meunier A, Cornet F, Campos M. Bacterial cell proliferation: from molecules to cells. FEMS Microbiol Rev 2021; 45:fuaa046. [PMID: 32990752 PMCID: PMC7794046 DOI: 10.1093/femsre/fuaa046] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
Bacterial cell proliferation is highly efficient, both because bacteria grow fast and multiply with a low failure rate. This efficiency is underpinned by the robustness of the cell cycle and its synchronization with cell growth and cytokinesis. Recent advances in bacterial cell biology brought about by single-cell physiology in microfluidic chambers suggest a series of simple phenomenological models at the cellular scale, coupling cell size and growth with the cell cycle. We contrast the apparent simplicity of these mechanisms based on the addition of a constant size between cell cycle events (e.g. two consecutive initiation of DNA replication or cell division) with the complexity of the underlying regulatory networks. Beyond the paradigm of cell cycle checkpoints, the coordination between the DNA and division cycles and cell growth is largely mediated by a wealth of other mechanisms. We propose our perspective on these mechanisms, through the prism of the known crosstalk between DNA replication and segregation, cell division and cell growth or size. We argue that the precise knowledge of these molecular mechanisms is critical to integrate the diverse layers of controls at different time and space scales into synthetic and verifiable models.
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Affiliation(s)
- Alix Meunier
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, IBCG, 165 rue Marianne Grunberg-Manago, 31062 Toulouse, France
| | - François Cornet
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, IBCG, 165 rue Marianne Grunberg-Manago, 31062 Toulouse, France
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, IBCG, 165 rue Marianne Grunberg-Manago, 31062 Toulouse, France
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40
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Willdigg JR, Helmann JD. Mini Review: Bacterial Membrane Composition and Its Modulation in Response to Stress. Front Mol Biosci 2021. [PMID: 34046426 DOI: 10.3389/fmolb.2021.634438/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Antibiotics and other agents that perturb the synthesis or integrity of the bacterial cell envelope trigger compensatory stress responses. Focusing on Bacillus subtilis as a model system, this mini-review summarizes current views of membrane structure and insights into how cell envelope stress responses remodel and protect the membrane. Altering the composition and properties of the membrane and its associated proteome can protect cells against detergents, antimicrobial peptides, and pore-forming compounds while also, indirectly, contributing to resistance against compounds that affect cell wall synthesis. Many of these regulatory responses are broadly conserved, even where the details of regulation may differ, and can be important in the emergence of antibiotic resistance in clinical settings.
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Affiliation(s)
- Jessica R Willdigg
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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41
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Influence of Lactic Acid on Cell Cycle Progressions in Lactobacillus bulgaricus During Batch Culture. Appl Biochem Biotechnol 2020; 193:912-924. [PMID: 33206317 DOI: 10.1007/s12010-020-03459-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/08/2020] [Indexed: 02/02/2023]
Abstract
Lactic acid has been proved to inhibit the proliferation of lactic acid bacteria in the fermentation process. To shed light on the cell cycle alterations in acidic conditions, the cell division of Lactobacillus bulgaricus sp1.1 in batch culture was analyzed directly by implementing of the intracellular fluorescent tracking assay in different pH adjusted by lactic acid. Cell proliferation and cell division were investigated to be negatively controlled by the decrease of pH, and pH 4.1 was the critical condition of downregulating cell division but retains cell culturability. The cell area and cell length in pH 4.1 were examined by using fluorescent labeling, and they reduced to about 29.18-34.89% and 32.67-40% of cells cultured in the unacidified medium, respectively. The DNA replication initiation was undergoing prompted by the low extent of DNA condensation and higher expression of the dnaA gene in this critical pH. The results indicated that the cell cycle progressions of Lactobacillus bulgaricus sp1.1 in acidic conditions were arrested at intracellular biomass accumulation and cell division stage. These findings provide fundamental insight into cell cycle control of the acidic environment in Lactobacillus bulgaricus sp1.1.
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42
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Cell morphology maintenance in Bacillus subtilis through balanced peptidoglycan synthesis and hydrolysis. Sci Rep 2020; 10:17910. [PMID: 33087775 PMCID: PMC7578834 DOI: 10.1038/s41598-020-74609-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/28/2020] [Indexed: 01/12/2023] Open
Abstract
The peptidoglycan layer is responsible for maintaining bacterial cell shape and permitting cell division. Cell wall growth is facilitated by peptidoglycan synthases and hydrolases and is potentially modulated by components of the central carbon metabolism. In Bacillus subtilis, UgtP synthesises the glucolipid precursor for lipoteichoic acid and has been suggested to function as a metabolic sensor governing cell size. Here we show that ugtP mutant cells have increased levels of cell wall precursors and changes in their peptidoglycan that suggest elevated DL-endopeptidase activity. The additional deletion of lytE, encoding a DL-endopeptidase important for cell elongation, in the ugtP mutant background produced cells with severe shape defects. Interestingly, the ugtP lytE mutant recovered normal rod-shape by acquiring mutations that decreased the expression of the peptidoglycan synthase PBP1. Together our results suggest that cells lacking ugtP must re-adjust the balance between peptidoglycan synthesis and hydrolysis to maintain proper cell morphology.
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43
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Bandekar AC, Subedi S, Ioerger TR, Sassetti CM. Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria. Curr Biol 2020; 30:3961-3971.e6. [PMID: 32916109 PMCID: PMC7578119 DOI: 10.1016/j.cub.2020.07.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022]
Abstract
Although the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly growing bacteria, DNA replication and cell division are temporally resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine whether cell-cycle-dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations of Mycobacterium tuberculosis (Mtb). By enriching for genes that display a sinusoidal expression pattern, we discover 485 genes that oscillate with a period consistent with the cell cycle. During cytokinesis, the timing of gene induction could be used to predict the timing of gene function, as mRNA abundance was found to correlate with the order in which proteins were recruited to the developing septum. Similarly, the expression pattern of primary metabolic genes could be used to predict the relative importance of these pathways for different cell cycle processes. Pyrimidine synthetic genes peaked during DNA replication, and their depletion caused a filamentation phenotype that phenocopied defects in this process. In contrast, the inosine monophasphate dehydrogenase dedicated to guanosine synthesis, GuaB2, displayed the opposite expression pattern and its depletion perturbed septation. Together, these data imply obligate coordination between primary metabolism and cell division and identify periodically regulated genes that can be related to specific cell biological functions.
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Affiliation(s)
- Aditya C Bandekar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Sishir Subedi
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA.
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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44
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Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32894477 DOI: 10.1007/978-3-030-46886-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The internal spatial organization of prokaryotic organisms, including Escherichia coli, is essential for the proper functioning of processes such as cell division. One source of this organization in E. coli is the nucleoid, which causes the exclusion of macromolecules - e.g. protein aggregates and the chemotaxis network - from midcell. Similarly, following DNA replication, the nucleoid(s) assist in placing the Z-ring at midcell. These processes need to be efficient in optimal conditions and robust to suboptimal conditions. After reviewing recent findings on these topics, we make use of past data to study the efficiency of the spatial constraining of Z-rings, chemotaxis networks, and protein aggregates, as a function of the nucleoid(s) morphology. Also, we compare the robustness of these processes to nonoptimal temperatures. We show that Z-rings, Tsr clusters, and protein aggregates have temperature-dependent spatial distributions along the major cell axis that are consistent with the nucleoid(s) morphology and the volume-exclusion phenomenon. Surprisingly, the consequences of the changes in nucleoid size with temperature are most visible in the kurtosis of these spatial distributions, in that it has a statistically significant linear correlation with the mean nucleoid length and, in the case of Z-rings, with the distance between nucleoids prior to cell division. Interestingly, we also find a negative, statistically significant linear correlation between the efficiency of these processes at the optimal condition and their robustness to suboptimal conditions, suggesting a trade-off between these traits.
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45
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Han H, Wang Z, Li T, Teng D, Mao R, Hao Y, Yang N, Wang X, Wang J. Recent progress of bacterial FtsZ inhibitors with a focus on peptides. FEBS J 2020; 288:1091-1106. [PMID: 32681661 DOI: 10.1111/febs.15489] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/27/2020] [Accepted: 07/08/2020] [Indexed: 12/23/2022]
Abstract
In recent years, the rise of antibiotic resistance has become a primary health problem. With the emergence of bacterial resistance, the need to explore and develop novel antibacterial drugs has become increasingly urgent. Filamentous temperature-sensitive mutant Z (FtsZ), a crucial cell division protein of bacteria, has become a vital antibacterial target. FtsZ is a filamentous GTPase; it is highly conserved in bacteria and shares less than 20% sequence identity with the eukaryotic cytoskeleton protein tubulin, indicating that FtsZ-targeting antibacterial agents may have a low cytotoxicity toward eukaryotes. FtsZ can form a dynamic Z-ring in the center of the cell resulting in cell division. Furthermore, disturbance in the assembly of FtsZ may affect cellular dynamics and bacterial cell survival, making it a fascinating target for drug development. This review focuses on the recent discovery of FtsZ inhibitors, including peptides, natural products, and other synthetic small molecules, as well as their mechanism of action, which could facilitate the discovery of novel FtsZ-targeting clinical drugs in the future.
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Affiliation(s)
- Huihui Han
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zhenlong Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ting Li
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Da Teng
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ruoyu Mao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ya Hao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Na Yang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xiumin Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jianhua Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
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46
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Hesser AR, Matano LM, Vickery CR, Wood BM, Santiago AG, Morris HG, Do T, Losick R, Walker S. The length of lipoteichoic acid polymers controls Staphylococcus aureus cell size and envelope integrity. J Bacteriol 2020; 202:JB.00149-20. [PMID: 32482719 PMCID: PMC8404710 DOI: 10.1128/jb.00149-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/22/2020] [Indexed: 02/08/2023] Open
Abstract
The opportunistic pathogen Staphylococcus aureus is protected by a cell envelope that is crucial for viability. In addition to peptidoglycan, lipoteichoic acid (LTA) is an especially important component of the S. aureus cell envelope. LTA is an anionic polymer anchored to a glycolipid in the outer leaflet of the cell membrane. It was known that deleting the gene for UgtP, the enzyme that makes this glycolipid anchor, causes cell growth and division defects. In Bacillus subtilis, growth abnormalities from the loss of ugtP have been attributed to both the absence of the encoded protein and to the loss of its products. Here, we show that growth defects in S. aureus ugtP deletion mutants are due to the long, abnormal LTA polymer that is produced when the glycolipid anchor is missing from the outer leaflet of the membrane. Dysregulated cell growth leads to defective cell division, and these phenotypes are corrected by mutations in the LTA polymerase, ltaS, that reduce polymer length. We also show that S. aureus mutants with long LTA are sensitized to cell wall hydrolases, beta-lactam antibiotics, and compounds that target other cell envelope pathways. We conclude that control of LTA polymer length is important for S. aureus physiology and promotes survival under stressful conditions, including antibiotic stress.IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of community- and hospital-acquired infections and is responsible for a large fraction of deaths caused by antibiotic-resistant bacteria. S. aureus is surrounded by a complex cell envelope that protects it from antimicrobial compounds and other stresses. Here we show that controlling the length of an essential cell envelope polymer, lipoteichoic acid, is critical for controlling S. aureus cell size and cell envelope integrity. We also show that genes involved in LTA length regulation are required for resistance to beta-lactam antibiotics in MRSA. The proteins encoded by these genes may be targets for combination therapy with an appropriate beta-lactam.
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Affiliation(s)
- Anthony R Hesser
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Leigh M Matano
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - B McKay Wood
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ace George Santiago
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi G Morris
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Truc Do
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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47
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Gibhardt J, Heidemann JL, Bremenkamp R, Rosenberg J, Seifert R, Kaever V, Ficner R, Commichau FM. An extracytoplasmic protein and a moonlighting enzyme modulate synthesis of c-di-AMP in Listeria monocytogenes. Environ Microbiol 2020; 22:2771-2791. [PMID: 32250026 DOI: 10.1111/1462-2920.15008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023]
Abstract
The second messenger cyclic di-AMP (c-di-AMP) is essential for growth of many bacteria because it controls osmolyte homeostasis. c-di-AMP can regulate the synthesis of potassium uptake systems in some bacteria and it also directly inhibits and activates potassium import and export systems, respectively. Therefore, c-di-AMP production and degradation have to be tightly regulated depending on the environmental osmolarity. The Gram-positive pathogen Listeria monocytogenes relies on the membrane-bound diadenylate cyclase CdaA for c-di-AMP production and degrades the nucleotide with two phosphodiesterases. While the enzymes producing and degrading the dinucleotide have been reasonably well examined, the regulation of c-di-AMP production is not well understood yet. Here we demonstrate that the extracytoplasmic regulator CdaR interacts with CdaA via its transmembrane helix to modulate c-di-AMP production. Moreover, we show that the phosphoglucosamine mutase GlmM forms a complex with CdaA and inhibits the diadenylate cyclase activity in vitro. We also found that GlmM inhibits c-di-AMP production in L. monocytogenes when the bacteria encounter osmotic stress. Thus, GlmM is the major factor controlling the activity of CdaA in vivo. GlmM can be assigned to the class of moonlighting proteins because it is active in metabolism and adjusts the cellular turgor depending on environmental osmolarity.
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Affiliation(s)
- Johannes Gibhardt
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Jana L Heidemann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Rica Bremenkamp
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Roland Seifert
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Volkhard Kaever
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
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48
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Gray WT, Govers SK, Xiang Y, Parry BR, Campos M, Kim S, Jacobs-Wagner C. Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria. Cell 2020; 177:1632-1648.e20. [PMID: 31150626 DOI: 10.1016/j.cell.2019.05.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/01/2019] [Accepted: 05/08/2019] [Indexed: 01/10/2023]
Abstract
The scaling of organelles with cell size is thought to be exclusive to eukaryotes. Here, we demonstrate that similar scaling relationships hold for the bacterial nucleoid. Despite the absence of a nuclear membrane, nucleoid size strongly correlates with cell size, independent of changes in DNA amount and across various nutrient conditions. This correlation is observed in diverse bacteria, revealing a near-constant ratio between nucleoid and cell size for a given species. As in eukaryotes, the nucleocytoplasmic ratio in bacteria varies greatly among species. This spectrum of nucleocytoplasmic ratios is independent of genome size, and instead it appears linked to the average population cell size. Bacteria with different nucleocytoplasmic ratios have a cytoplasm with different biophysical properties, impacting ribosome mobility and localization. Together, our findings identify new organizational principles and biophysical features of bacterial cells, implicating the nucleocytoplasmic ratio and cell size as determinants of the intracellular organization of translation.
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Affiliation(s)
- William T Gray
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Yingjie Xiang
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT, USA
| | - Bradley R Parry
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Manuel Campos
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Sangjin Kim
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
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49
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pH-dependent activation of cytokinesis modulates Escherichia coli cell size. PLoS Genet 2020; 16:e1008685. [PMID: 32203516 PMCID: PMC7117782 DOI: 10.1371/journal.pgen.1008685] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/02/2020] [Accepted: 02/19/2020] [Indexed: 01/21/2023] Open
Abstract
Cell size is a complex trait, derived from both genetic and environmental factors. Environmental determinants of bacterial cell size identified to date primarily target assembly of cytosolic components of the cell division machinery. Whether certain environmental cues also impact cell size through changes in the assembly or activity of extracytoplasmic division proteins remains an open question. Here, we identify extracellular pH as a modulator of cell division and a significant determinant of cell size across evolutionarily distant bacterial species. In the Gram-negative model organism Escherichia coli, our data indicate environmental pH impacts the length at which cells divide by altering the ability of the terminal cell division protein FtsN to localize to the cytokinetic ring where it activates division. Acidic environments lead to enrichment of FtsN at the septum and activation of division at a reduced cell length. Alkaline pH inhibits FtsN localization and suppresses division activation. Altogether, our work reveals a previously unappreciated role for pH in bacterial cell size control. Bacteria are constantly under assault from endogenous and environmental stressors. To ensure viability and reproductive fitness, many bacteria alter their growth and replication in response to stressful conditions. Previous work from many groups has identified regulatory mechanisms linking cell division with nutrient availability and metabolic state. However, comparatively little is known about how the cell division machinery responds to physical and chemical cues in the environment. Here, we identify a fundamental property of the extracellular environment—environmental pH—as a significant contributor to bacterial cell size. Our genetic and cytological data indicate pH-dependent changes in E. coli cell size are in part due to differential localization of the cell division activator FtsN across pH environments. Increased abundance of FtsN at midcell in acidic environments promotes cell division at a reduced cell volume, while decreased abundance of FtsN at midcell in alkaline environments effectively delays cell division until a larger size is reached. Altogether, our work identifies pH as an environmental determinant of E. coli cell division and illuminates FtsN recruitment as a mediator of cell size.
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50
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Zhu C, Sun G, Wang X, Guo J, Li E, Yang Y, Xu M. Variable cell division time and asymmetric division site lead to filament-to-rod cell cycle of Lysinibacillus varians. FEMS Microbiol Lett 2020; 367:5810660. [PMID: 32196075 DOI: 10.1093/femsle/fnaa054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/19/2020] [Indexed: 12/27/2022] Open
Abstract
All well-established cell size homeostasis paradigms are based on the researches of rod bacteria like B. subtilis and E. coli, suggesting a constant division time (timer model), division size (sizer model) or added size (adder model) before division. However, Lysinibacillus varians, a new species with regular filament-to-rod cell cycle, is inconsistent with existing models. In this study, the cell size parameters of the type strain GY32, were investigated by combing multiple microscopy techniques and single-cell approach. Our results showed that the filaments of strain GY32 were unicellular cells with multiple nucleoids. The division time of GY32 cells was variable and their daughter cells produced by asymmetric binary fission had different birth sizes, which were proportional to their elongation rates, resulting in high heterogeneity among the sister cells. Furthermore, the added size from birth to division was significantly shorter than birth size (p < 0.01) and decreased along generations. The results above revealed that the asymmetric division site and varied cell size parameters resulted in filament-to-rod cell cycle of L. varians and cell size homeostasis could be a more complex and dynamic process than previously assumed. These findings would be helpful in elucidating the open questions in cell division and cell size heterogeneity.
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Affiliation(s)
- Chunjie Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,Guangdong Open Laboratory of Applied Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,Guangdong Open Laboratory of Applied Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China
| | - Xiaoming Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Panyu District, 510006, Guangzhou, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,Guangdong Open Laboratory of Applied Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China
| | - Enze Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,Guangdong Open Laboratory of Applied Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,Guangdong Open Laboratory of Applied Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China.,Guangdong Open Laboratory of Applied Microbiology, Central Xianlie 100, Yuexiu, 510070, Guangzhou, China
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